Compositions and Methods for Modulating NCOA4-mediated Autophagic Targeting of Ferritin

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. Provisional Patent Application Serial No. 61/971,419, filed March 27, 2014, and U.S. Provisional Patent Application Serial No. 61/990,544, filed May 8, 2014; the entire contents of which are herein incorporated by reference.

TECHNICAL FIELD

This invention relates to the field of molecular and cellular biology, and more particularly to nuclear receptor coactivator 4 (NCOA4)-mediated autophagic targeting of ferritin. BACKGROUND

Autophagy, the process by which proteins and organelles are sequestered in double-membrane structures called autophagosomes and delivered to lysosomes for degradation, is critical in diseases such as cancer and neurodegeneration. Much of the present understanding of this process has emerged from analysis of bulk cytoplasmic autophagy, but the present understanding of how specific cargo including organelles, proteins, or intracellular pathogens are targeted for selective autophagy is limited.

SUMMARY

In some aspects, provided herein is a method of modulating autophagic targeting of ferritin in a cell. In some aspects, the method can include modulating the level and/or activity of nuclear receptor coactivator 4 (NCOA4) in the cell.

In some aspects, provided herein is a method of modulating the bioavailability of iron in a cell. In some aspects, the method includes modulating the level and/or activity of NCOA4 in the cell.

In some aspects, provided herein is a method of modulating an interaction between NCOA4 and ferritin in a cell. In some aspects, the method includes delivering to the interior of a cell comprising NCOA4 and ferritin an agent that modulates the interaction between NCOA4 and ferritin. In some aspects, this method is in vitro or ex vivo and the method includes culturing the cell with the agent.

In certain aspects of the above methods, the cell can be in a subject and the method can comprise administering the agent to the subject. In some aspects, the subject is administered a cell that expresses NCOA4 or a fragment thereof that can be secreted from the cell and internalized by another cell in the subject. In some aspects, the subject is administered a cell that expresses an inhibitor or antagonist of NCOA4, as described herein (e.g., a polypeptide, peptide fragment, small molecule, antisense oligonucleotide, etc.). In other aspects, the subject is administered a cell that expresses an agonist of NCOA4 (e.g., HERC2 or active fragment thereof, agonistic antibody or intrabody, etc.) including of the activity of NCOA4 (e.g., an active fragment or full length NCOA4). The cell is preferably (but not necessarily) a cell derived from the subject, or the progeny of a cell derived from the subject.

In certain aspects, provided herein is a method of protecting a cell from reactive oxygen species (ROS)-induced cell death. In some aspects, the method includes decreasing the level and/or activity of NCOA4 in a cell comprising an increased level of ROS.

In certain of the above methods, modulating the level and/or activity of NCOA4 is decreasing the level and/or activity of NCOA4. In some aspects, decreasing the level and/or activity of NCOA4 comprises decreasing the interaction between ferritin and NCOA4. In some aspects of the above methods, modulating the interaction between NCOA4 and ferritin is decreasing the interaction between NCOA4 and ferritin. In some aspects, the interaction between ferritin and NCOA4 is decreased by delivering to the interior of the cell an inhibitor comprising a peptide fragment of NCOA4 or of ferritin. In some aspects, the peptide fragment is a peptide fragment of NCOA4 comprising: SEQ ID NO: 1 (SRIADSFQVIKNSPLSEWLIRPPYKEGSPK), or the peptide comprising SEQ ID NO: 1 with no more than 10 conservative amino acid substitutions; or SEQ ID NO: 11 (SFQVIKNSPLSEWLIRPPYKEGSPK) or the peptide comprising SEQ ID NO: 11 with no more than 10 conservative amino acid substitutions, or an amino acid sequence having at least 85% identity with SEQ ID NO: 1 or SEQ ID NO: 11. In some aspects, the peptide fragment is a peptide fragment of NC0A4 comprising SEQ ID NO: 2 (KAMTPSRIADSFQVIKNSPLSEWLIRPPYKEGSPKEVPGTEDRAGKQK), or the peptide comprising SEQ ID NO: 2 with no more than 10 conservative amino acid substitutions, or an amino acid sequence having at least 85% sequence identity with SEQ ID NO: 2. In some aspects, the peptide fragment is a peptide fragment of FTH1 comprising or consisting of: amino acids 16 -34 of SEQ ID NO: 6 or amino acids 16-34 of SEQ ID NO: 6 with no more than 10 conservative substitutions; amino acids 103-125 of SEQ ID NO: 6 or amino acids 103-125 of SEQ ID NO: 6 with no more than 10 conservative substitutions; amino acids 78-88 of SEQ ID NO: 6 or amino acids 78-88 of SEQ ID NO: 6 with no more than 5 conservative substitutions; or an amino acid sequence having at least 85% identity with amino acids 16-34 of SEQ ID NO: 6, amino acids 103- 125 of SEQ ID NO: 6, or amino acids 78-88 of SEQ ID NO: 6.

In some aspects, decreasing the level and/or activity of NCOA4 and/or decreasing the interaction between ferritin and NCOA4 includes delivering to the interior of the cell an inhibitory agent, e.g., an inhibitory antibody or intrabody, a dominant negative form of a target polypeptide (e.g., NCOA4, HERC2, ferritin (FTH1 and/or FTL), an ATG8 paralog), a peptide fragment that binds to NCOA4 (e.g., a ferritin fragment, a HERC2 fragment, a ATG8 paralog fragment, a NCOA4 fragment, wherein the fragments are not functionally active), a small molecule (e.g., aptamer), an antisense oligonucleotide (e.g. shRNA, siRNA, etc.) that targets NCOA4, HERC2, ferritin or an ATG8 paralog described herein. In some aspects, decreasing the level and/or activity of NCOA4 comprises delivering to the interior of the cell a peptide comprising SEQ ID NO: 3 (SMVTEDWLVQNHQDPCKVEEVCRANEPCTSFAECVCDENCEKEALYKWL LKKEG), or the peptide comprising SEQ ID NO: 3 with no more than 10 conservative amino acid substitutions, or an amino acid sequence having at least 85% sequence identity with SEQ ID NO: 3. In some aspects, decreasing the level and/or activity of NCOA4 comprises delivering to the interior of the cell a ferritin FTH1 peptide comprising or consisting of: amino acids 16 -34 of SEQ ID NO: 6 or amino acids 16-34 of SEQ ID NO: 6 with no more than 10 conservative substitutions; amino acids 103-125 of SEQ ID NO: 6 or amino acids 103-125 of SEQ ID NO: 6 with no more than 10 conservative substitutions; amino acids 78-88 of SEQ ID NO: 6 or amino acids 78-88 of SEQ ID NO: 6 with no more than 5 conservative substitutions; or an amino acid sequence having at least 85% identity with amino acids 16-34 of SEQ ID NO: 6, amino acids 103- 125 of SEQ ID NO: 6, or amino acids 78-88 of SEQ ID NO: 6. Non-limiting examples of antisense oligonucleotides that can be used according to the methods disclosed herein include, e.g., siRNA against NCOA4,e.g., shNCOA4-l : 5'

CCCAGGAAGTATTACTTAATT 3' (TRCN0000019724) (SEQ ID NO: 12), shNCOA4-2: 5' GCTGGCAAACAGAAGTTTAAA 3' (TRCN0000019726) (SEQ ID NO: 13), siNCOA4-l : 5' ACAAAGAUCUAGCCAAUCA 3' (SEQ ID NO: 15) and siNCOA4-2: 5' GACCUUAUUUAUCAGCUUA 3' (SEQ ID NO: 16), and siRNA against HERC2 (Gene ID: 8924, NM 004667.5), e.g., siHERC2-l : 5'

GCACAGAGUAUCACAGGUA 3' (SEQ ID NO: 17) and siHERC2-2: 5'

CGAUGAAGGUUUGGUAUUU 3' (SEQ ID NO: 18). Methods for designing suitable antisense oligonucleotides based on the known sequence of the target nucleic acid are well known in the art.

In some aspects of the above methods for decreasing autophagic targeting of ferritin in a cell and for decreasing the bioavailability of iron in a cell, the method can include decreasing the recruitment of NCOA4/ferritin complexes to autophagosomes. In some aspects, the recruitment is decreased by delivering to the interior of the cell an inhibitor of the interaction between NCOA4 and an ATG8 paralog. In some aspects, the ATG8 paralog is GABA(A) receptor-associated protein-like 2 (GABARAPL2) or microtubule-associated proteins 1 A/IB light chain 3A (LC3).

In other aspects of the above methods for modulating the level and/or activity of NCOA4 and/or for modulating the interaction between NCOA4 and ferritin, the modulating is increasing. In some aspects, increasing the level and/or activity of NCOA4 or increasing the interaction between NCOA4 and ferritin comprises delivering to the interior of the cell an NCOA4 polypeptide or functionally active fragment thereof. In some aspects, the NCOA4 polypeptide or functionally active fragment thereof binds to the ferritin heavy chain (FTH1) and/or to ferritin light chain (FLT) and/or to an ATG8 paralog (e.g., GABARAPL2 and/or LC3). In some aspects, the NCOA4 polypeptide or functionally active fragment thereof comprises SEQ ID NO: 1

(SRIADSFQVIKNSPLSEWLIRPPYKEGSPK), or the peptide comprising SEQ ID NO: 1 with no more than 10 conservative amino acid substitutions, or an amino acid sequence having at least 85% sequence identity with SEQ ID NO: 1. In some aspects, the NCOA4 polypeptide or functionally active fragment thereof comprises SEQ ID NO: 11, or the peptide comprising SEQ ID NO: 11 with no more than 10 conservative amino acid substitutions, or an amino acid sequence having at least 85% sequence identity with SEQ ID NO: 11. In some aspects, the NCOA4 polypeptide or functionally active fragment thereof comprises SEQ ID NO: 2 (KAMTPSRIADSFQVIKNSPLSEWLIRPPYKEGSPK EVPGTEDRAGKQK), or the peptide comprising SEQ ID NO: 2 with no more than 10 conservative amino acid substitutions, or an amino acid sequence having at least 85% sequence identity with SEQ ID NO: 2. In some aspects, increasing the level and/or activity of NCOA4 or increasing the interaction between NCOA4 and ferritin comprises delivering to the interior of the cell an agent that increases the expression of NCOA4 in the cell. In some aspects, increasing the level and/or activity of NCOA4 or increasing the interaction between NCOA4 and ferritin comprises increasing the level and/or activity of HERC2 in the cell. In some aspects, the method comprises delivering to the interior of the cell an agent that increases the expression and/or activity of HERC2. In some aspects, the method comprises delivering to the interior of the cell a HERC2 polypeptide or a functionally active fragment thereof. In some aspects, the HERC2 polypeptide or functionally active fragment thereof binds to a domain of NCOA4 which comprises SEQ ID NO: 3

(SMVTEDWLVQNHQDPCKVEEVCRANEPCTSFAECVCDENCEKEALYKWLLK EG).

In some aspects, also provided herein are methods of treating a cancer. The methods can include administering to a subject in need thereof a composition comprising an inhibitor that decreases the level and/or activity of NCOA4 in a cancer cell in the subject, and wherein the cancer is reliant on selective autophagy for growth. In some aspects, the cancer is pancreatic cancer, lung cancer, melanoma, breast cancer, glioblastoma, colorectal cancer, prostate cancer, multiple myeloma, renal cell carcinoma, chronic lymphocytic leukemia, lymphoma, or chronic myelogenous leukemia. In some aspects, the inhibitor decreases selective autophagy in the cancer cell. In some aspects, also provided herein is a method of treating a condition or disorder associated with iron overload. The method can include administering to a subject in need thereof a composition comprising an inhibitor that decreases the level and/or activity of NCOA4 in a cell of the subject. In some aspects, the condition or disorder is hemochromatosis. In some aspects, the condition or disorder is iron overload due to transfusion. In some aspects, decreasing the level and/or activity of NCOA4 comprises decreasing the interaction between ferritin and NCOA4 in the cell of the subject.

In some aspects of the above methods of treatment, the level and/or activity of NCOA4 in a cell of the subject can be decreased by administering to the subject a composition comprising a peptide fragment of NCOA4 or of ferritin, wherein the fragment is not a functionally active fragment (i.e., the fragment does not have at least one of the functional activities of the wild-type protein that is involved in the process of NCOA4-mediated autophagic targeting of ferritin, as described herein). In some aspects, the peptide fragment is a peptide fragment of NCOA4 comprising SEQ ID NO: 1

(SRIADSFQVIKNSPLSEWLIRPPYKEGSPK), or the peptide comprising SEQ ID NO: 1 with no more than 10 conservative amino acid substitutions; or SEQ ID NO: 11 (SFQVIKNSPLSEWLIRPPYKEGSPK), or the peptide comprising SEQ ID NO: 11 with no more than 10 conservative amino acid substitutions, or an amino acid sequence having at least 85% identity with SEQ ID NO: 1 or SEQ ID NO: 11. In some aspects, the peptide fragment is a peptide fragment of NCOA4 comprising SEQ ID NO: 2

(KAMTPSRIADSFQVIKNSPLSEWLIRPPYKEGSPKEVPGTEDRAGKQK) or the peptide comprising SEQ ID NO: 2 with no more than 10 conservative amino acid substitutions, or an amino acid sequence having at least 85% identity with SEQ ID NO: 2. In some aspects, the ferritin fragment is a fragment of FTH1 comprising or consisting of: amino acids 16 -34 of SEQ ID NO: 6 or amino acids 16-34 of SEQ ID NO: 6 with no more than 10 conservative substitutions; amino acids 103-125 of SEQ ID NO: 6 or amino acids 103-125 of SEQ ID NO: 6 with no more than 10 conservative substitutions; amino acids 78-88 of SEQ ID NO: 6 or amino acids 78-88 of SEQ ID NO: 6 with no more than 5 conservative substitutions; or an amino acid sequence having at least 85% identity with amino acids 16-34 of SEQ ID NO: 6, amino acids 103-125 of SEQ ID NO: 6, or amino acids 78-88 of SEQ ID NO: 6.

In some aspects of the above methods, decreasing the level and/or activity of NCOA4 includes administering to the subject a composition comprising an inhibitory agent, e.g., an inhibitory antibody or intrabody, a dominant negative form of a target polypeptide (e.g., NCOA4, HERC2, ferritin (FTHl and/or FTL), an ATG8 paralog), a peptide fragment that binds to NCOA4 (e.g., a ferritin fragment, a HERC2 fragment, a ATG8 paralog fragment, a NCOA4 fragment, wherein the fragments are not functionally active), a small molecule (e.g., aptamer), an antisense oligonucleotide (e.g. shRNA, siRNA, etc.) that targets NCOA4, HERC2, ferritin or an ATG8 paralog described herein. In some aspects of these methods, the ferritin fragment is a fragment of FTHl comprising or consisting of: amino acids 16 -34 of SEQ ID NO: 6 or amino acids 16-34 of SEQ ID NO: 6 with no more than 10 conservative substitutions; amino acids 103-125 of SEQ ID NO: 6 or amino acids 103-125 of SEQ ID NO: 6 with no more than 10 conservative substitutions; amino acids 78-88 of SEQ ID NO: 6 or amino acids 78-88 of SEQ ID NO: 6 with no more than 5 conservative substitutions; or an amino acid sequence having at least 85% identity with amino acids 16-34 of SEQ ID NO: 6, amino acids 103-125 of SEQ ID NO: 6, or amino acids 78-88 of SEQ ID NO: 6. Non-limiting examples of antisense oligonucleotides that can be used according to the methods disclosed herein include, e.g., siRNA against NCOA4,e.g., shNCOA4-l : 5'

CCCAGGAAGTATTACTTAATT 3' (TRCN0000019724) (SEQ ID NO: 12), shNCOA4-2: 5' GCTGGCAAACAGAAGTTTAAA 3' (TRCN0000019726) (SEQ ID NO: 13), siNCOA4-l : 5' ACAAAGAUCUAGCCAAUCA 3' (SEQ ID NO: 15) and siNCOA4-2: 5' GACCUUAUUUAUCAGCUUA 3' (SEQ ID NO: 16), and siRNA against HERC2 (Gene ID: 8924, NM 004667.5), e.g., siHERC2-l : 5'

GCACAGAGUAUCACAGGUA 3' (SEQ ID NO: 17) and siHERC2-2: 5'

CGAUGAAGGUUUGGUAUUU 3' (SEQ ID NO: 18). Methods for designing suitable antisense oligonucleotides based on the known sequence of the target nucleic acid are well known in the art. In some aspects, decreasing the level and/or activity of NCOA4 comprises delivering to the interior of the cell a peptide comprising SEQ ID NO: 3

(SMVTEDWLVQNHQDPCKVEEVCRANEPCTSFAECVCDENCEKEALYKWLLK EG), or the peptide comprising SEQ ID NO: 3 with no more than 10 conservative amino acid substitutions, or an amino acid sequence having at least 85% identity with SEQ ID NO: 3. In some aspects, the method includes decreasing the recruitment of

NCOA4/ferritin complexes to autophagosomes in the cell of the subject. In some aspects, the recruitment is decreased by administering to the subject a composition comprising an inhibitor of the interaction of NCOA4 with an ATG8 paralog (e.g., GABARAPL2 or LC3).

In some aspects, also provided herein is a method of treating iron deficiency anemia. The methods can include administering to a subject with anemia a composition comprising an agent that increases the level and/or activity of NCOA4 in a cell of the subject. In other aspects, also provided herein is a method of increasing erythropoiesis. The method can include administering to a subject in need of increased erythropoiesis a composition comprising an agent that increases the level and/or activity of NCOA4 in a cell of the subject. In some aspects, increasing the level and/or activity of NCOA4 includes administering to the subject an NCOA4 polypeptide or functionally active fragment thereof. In some aspects, the NCOA4 polypeptide or functionally active fragment thereof binds to FTH1 and/or FTL in the cell of the subject. In some aspects, the NCOA4 polypeptide or functionally active fragment thereof interacts with an ATG8 paralog (e.g., GABARAPL2 or LC3) in the cell of the subject. In some aspects, the NCOA4 polypeptide or functionally active fragment thereof comprises SEQ ID NO: 1 (SRIADSFQVIKNSPLSEWLIRPPYKEGSPK), or the peptide comprising SEQ ID NO: 1 with no more than 10 conservative amino acid substitutions; or SEQ ID NO: 11 (SFQVIKNSPLSEWLIRPPYKEGSPK), or the peptide comprising SEQ ID NO: 11 with no more than 10 conservative amino acid substitutions; or an amino acid sequence having at least 85% identity with SEQ ID NO: 1 or SEQ ID NO: 11. In some aspects, the

NCOA4 polypeptide or functionally active fragment thereof comprises SEQ ID NO: 2 (KAMTPSRIADSFQVIKNSPLSEWLIRPPYKEGSPKEVPGTEDRAGKQK), or the NCOA4 polypeptide or fragment comprising SEQ ID NO: 2 with no more than 10 conservative amino acid substitutions, or an amino acid sequence having at least 85% identity with SEQ ID NO: 2. In some aspects, increasing the level and/or activity of NCOA4 comprises increasing the interaction between NCOA4 and ferritin. In some aspects, increasing the level and/or activity of NCOA4 comprises administering to the subject an agent that increases the expression of NCOA4 in the subject. In some aspects, increasing the level and/or activity of NCOA4 includes increasing the level and/or activity of HERC2 in the cell. In some aspects, increasing the level and/or activity of HERC2 in the cell includes administering to the subject a composition comprising an agent that increases the expression and/or activity of HERC2. In some aspects, the method comprises administering to the subject a composition comprising a HERC2 polypeptide or a functionally active fragment thereof. In some aspects, the HERC2 polypeptide or functionally active fragment thereof binds to a domain of NCOA4 which comprises SEQ ID NO: 3

(SMVTEDWLVQNHQDPCKVEEVCRANEPCTSFAECVCDENCEKEALYKWLLK EG).

In some aspects, also described herein is a method of identifying a compound that modulates the expression level of NCOA4. In some aspects, the method includes contacting a cell with a candidate compound, and determining the expression level of NCOA4. In some aspects, the modulating is increasing or decreasing the expression level. In some aspects, the expression level is the mRNA expression level. In some aspects, the expression level is the protein expression level.

In some aspects, also described herein is a method of identifying a compound that modulates the activity of NCOA4. The method can include:

(a) contacting a cell with a candidate compound;

(b) determining the level in the cell of one or more of the following:

(i) bioavailable iron relative to a control cell;

(ii) ferritin in autophagosomes and/or lysosomes;

(iii) NCOA4 present in autophagosomes and/or lysosomes;

(iv) NCOA4/ferritin complexes;

(v) NCOA4/HERC2 complexes;

(vi) NCOA4/ ATG8 paralog complexes; and

(vii) degradation of ferritin via autophagy; and

(c) if the candidate compound modulates the level of one or more of (b)(i)-

(b)(vii), identifying the candidate compound as a compound that modulates the activity of NCOA4. In some aspects, the method further includes selecting the identified compound for further testing and/or for formulation as a drug product (e.g.,

pharmaceutical formulation). In some aspects, the modulating is increasing or decreasing.

In some aspects, also provided herein is a method of identifying a compound that modulates the binding of NCOA4 to ferritin. The method can include: contacting a NCOA4 reagent with a ferritin reagent in the presence of a candidate compound; and determining whether the candidate compound modulates binding of the NCOA4 reagent to the ferritin reagent. In some aspects, the modulating is decreasing the binding. In some aspects, the modulating is increasing the binding. In some aspects, the NCOA4 reagent comprises a full-length NCOA4 polypeptide. In some aspects, the NCOA4 reagent comprises a peptide comprising or consisting of SEQ ID NO: 11, SEQ ID NO: 1 or SEQ ID NO: 2. In some aspects the ferritin reagent is purified apo-ferritin from human liver or equine spleen or produced recombinantly in E. coli as either FTH1, FTL, or a combination of FTH1 and FTL.

In some aspects, also provided herein is a method of identifying a compound that modulates the binding of NCOA4 to an ATG8 paralog. The method can include:

contacting a NCOA4 reagent with an ATG8 paralog reagent in the presence of a candidate compound; and determining whether the candidate compound modulates binding of the NCOA4 reagent to the ATG8 paralog reagent. In some aspects, the modulating is decreasing the binding. In some aspects, the modulating is increasing the binding. In some aspects, the NCOA4 reagent comprises a full-length NCOA4 polypeptide or a fragment thereof which retains binding to the ATG8 paralog reagent (e,g, a GABARAPL2 reagent or LC3 reagent). In some aspects, one or more of the reagents for use in the methods of identifying compounds ("screening assays") are recombinantly expressed protein from E. coli.

In some aspects, also provided herein is a method of identifying a compound that modulates the binding of NCOA4 to HERC2. The method can include: contacting a NCOA4 reagent with a HERC2 reagent in the presence of a candidate compound; and determining whether the candidate compound modulates binding of the NCOA4 reagent to the HERC2 reagent. In some aspects, the modulating is decreasing the binding. In some aspects, the modulating is increasing the binding. In some aspects, the NCOA4 reagent comprises a full-length NCOA4 polypeptide or a fragment thereof which retains binding to HERC2 (e.g., a fragment comprising or consisting of SEQ ID NO: 3). In some aspects, one or more of the reagents for use in the methods of identifying compounds ("screening assays") are recombinantly expressed protein from E. coli.

In some aspects, also described herein is a method of diagnosing anemia in a subject, the method comprising identifying one or more of the following conditions in the subject: (a) a mutation in NCOA4; (b) a decreased level and/or activity of NCOA4; (c) a decreased level of NCOA4/ferritin complexes; and (d) a decreased level of

NCOA4/ATG8 paralog complexes.

In any of the above described methods, the NCOA4 can be human NCOA4 or a fragment thereof. In any of the above aspects, the ferritin can be human ferritin (FTH1 or FTL). In any of the above aspects, the ATG8 paralog can be a human ATG8 paralog. In any of the above aspects, HERC2 can be human HERC2. Alternatively, any or all of these proteins can be mammalian, non-human (e.g., non-human primate) proteins.

In some aspects, also described herein is a composition comprising a small molecule antagonist that targets SEQ ID NO: 11, 1, 2, or 3. In other aspects, the small molecule targets a sequence in a protein that binds to SEQ ID NO: 11, 1, 2, or 3 (e.g., the corresponding sequence in the region of ferritin that binds to SEQ ID NO: 11, 1 and 2, and the corresponding sequence in HERC2 that binds to SEQ ID NO: 3 (e.g., a region in HERC2 within residues 1700-2700 of SEQ ID NO: 8).

In some aspects, also described herein is a binding molecule that binds to a sequence within SEQ ID NO: 11, 1, 2, or 3. In some aspects, the binding molecule is an antibody or intrabody.

In some aspects, also described herein is a peptide fragment of NCOA4 comprising: SEQ ID NO: 1 (SRIADSFQVIKNSPLSEWLIRPPYKEGSPK), or the peptide comprising SEQ ID NO: 1 with no more than 10 conservative amino acid substitutions; or SEQ ID NO: 11 (SFQVIKNSPLSEWLIRPPYKEGSPK), or the peptide comprising SEQ ID NO: 11 with no more than 10 conservative amino acid substitutions; or an amino acid sequence having at least 85% sequence identity with SEQ ID NO: 1 or SEQ ID NO: 11. Also described herein is a peptide fragment of NCOA4 comprising SEQ ID NO: 2 or the peptide fragment comprising SEQ ID NO: 2 with no more than 10 conservative amino acid substitutions. Also described herein is a peptide fragment of NCOA4 consisting of: SEQ ID NO: 1 or the peptide fragment consisting of SEQ ID NO: 1 with no more than 10 conservative amino acid substitutions; or SEQ ID NO: 11 or the peptide fragment consisting of SEQ ID NO: 11 with no more than 10 conservative amino acid substitutions. Also described herein is a peptide fragment of NCOA4 consisting of SEQ ID NO: 2 or the peptide fragment consisting of SEQ ID NO: 2 with no more than 10 conservative amino acid substitutions, or an amino acid sequence having at least 85% sequence identity with SEQ ID NO: 2. Also described herein is a peptide fragment of NCOA4 comprising SEQ ID NO: 3, or the peptide fragment comprising SEQ ID NO: 3 with no more than 10 conservative amino acid substitutions, an amino acid sequence having at least 85% sequence identity with SEQ ID NO: 3. Also described herein is a peptide fragment of NCOA4 consisting of SEQ ID NO: 3 or the peptide fragment consisting of SEQ ID NO: 3 with no more than 10 conservative amino acid substitutions, or an amino acid sequence having at least 85% sequence identity with SEQ ID NO: 3.

Also described herein is a peptide fragment of FTH1 comprising: amino acids 16 -34 of SEQ ID NO: 6 or amino acids 16-34 of SEQ ID NO: 6 with no more than 10 conservative substitutions; amino acids 103-125 of SEQ ID NO: 6 or amino acids 103-125 of SEQ ID NO: 6 with no more than 10 conservative substitutions; amino acids 78-88 of SEQ ID NO: 6 or amino acids 78-88 of SEQ ID NO: 6 with no more than 5 conservative substitutions; or an amino acid sequence having at least 85% identity with amino acids 16-34 of SEQ ID NO: 6, amino acids 103-125 of SEQ ID NO: 6, or amino acids 78-88 of SEQ ID NO: 6. Also described herein is a peptide fragment of FTH1 consisting of: amino acids 16 -34 of SEQ ID NO: 6 or amino acids 16-34 of SEQ ID NO: 6 with no more than 10 conservative substitutions; amino acids 103-125 of SEQ ID NO: 6 or amino acids 103-125 of SEQ ID NO: 6 with no more than 10 conservative substitutions; amino acids 78-88 of SEQ ID NO: 6 or amino acids 78-88 of SEQ ID NO: 6 with no more than 5 conservative substitutions; or an amino acid sequence having at least 85% identity with amino acids 16-34 of SEQ ID NO: 6, amino acids 103-125 of SEQ ID NO: 6, or amino acids 78-88 of SEQ ID NO: 6.

In certain above aspects, the peptide fragment is a synthetic peptide fragment. Also provided herein are isolated nucleic acids. An isolated nucleic acid encompassed herein includes a nucleotide sequence that:

(a) encodes a peptide fragment described herein, such as:

a peptide fragment of NCOA4 comprising: SEQ ID NO: 1

(SRIADSFQVIKNSPLSEWLIRPPYKEGSPK), or the peptide comprising SEQ ID NO: 1 with no more than 10 conservative amino acid substitutions; or SEQ ID NO: 11 (SFQVIKNSPLSEWLIPvPPYKEGSPK), or the peptide comprising SEQ ID NO: 11 with no more than 10 conservative amino acid substitutions; or an amino acid sequence having at least 85% sequence identity with SEQ ID NO: 1 or SEQ ID NO: 11; or a peptide fragment of NCOA4 comprising SEQ ID NO: 2, or the peptide fragment comprising SEQ ID NO: 2 with no more than 10

conservative amino acid substitutions; or a peptide fragment of NCOA4 consisting of: SEQ ID NO: 1 or the peptide fragment consisting of SEQ ID NO: 1 with no more than 10 conservative amino acid substitutions; or the peptide fragment consisting of SEQ ID NO: 11, or the peptide fragment consisting of SEQ ID NO: 11 with no more than 10 conservative amino acid substitutions; or a peptide fragment of NCOA4 consisting of SEQ ID NO: 2, or the peptide fragment consisting of SEQ ID NO: 2 with no more than 10 conservative amino acid substitutions, or an amino acid sequence having at least 85% sequence identity with SEQ ID NO: 2; or a peptide fragment of NCOA4 comprising SEQ ID NO: 3, or the peptide fragment comprising SEQ ID NO: 3 with no more than 10 conservative amino acid substitutions, or an amino acid sequence having at least 85%) sequence identity with SEQ ID NO: 3; or a peptide fragment of NCOA4 consisting of SEQ ID NO: 3, or the peptide fragment consisting of SEQ ID NO: 3 with no more than 10 conservative amino acid substitutions, or an amino acid sequence having at least 85% sequence identity with SEQ ID NO: 3; or a peptide fragment of FTH1 comprising amino acids 16 -34 of SEQ ID NO: 6 or amino acids 16-34 of SEQ ID NO: 6 with no more than 10 conservative substitutions; or a peptide fragment of FTH1 comprising amino acids 103-125 of SEQ ID NO: 6 or amino acids 103-125 of SEQ ID NO: 6 with no more than 10 conservative substitutions; or a peptide fragment of FTH1 comprising amino acids 78-88 of SEQ ID NO: 6 or amino acids 78-88 of SEQ ID NO: 6 with no more than 5 conservative substitutions; or a peptide fragment of FTH1 comprising an amino acid sequence having at least 85% identity with amino acids 16-34 of SEQ ID NO: 6, amino acids 103-125 of SEQ ID NO: 6, or amino acids 78-88 of SEQ ID NO: 6; or a peptide fragment of FTH1 consisting of amino acids 16 -34 of SEQ ID NO: 6 or amino acids 16-34 of SEQ ID NO: 6 with no more than 10 conservative substitutions; or a peptide fragment of FTH1 consisting of amino acids 103-125 of SEQ ID NO: 6 or amino acids 103-125 of SEQ ID NO: 6 with no more than 10 conservative substitutions; or a peptide fragment of FTH1 consisting of amino acids 78-88 of SEQ ID NO: 6 or amino acids 78-88 of SEQ ID NO: 6 with no more than 5 conservative substitutions; or a peptide fragment of FTH1 consisting of an amino acid sequence having at least 85% identity with amino acids 16-34 of SEQ ID NO: 6, amino acids 103-125 of SEQ ID NO: 6, or amino acids 78-88 of SEQ ID NO: 6.

(b) hybridizes under stringent conditions to the complement of the polynucleotide that encodes the peptide fragment described in (a); or

(c) is the complement of (a).

In some aspects, the isolated nucleic acid described above is cDNA.

In some aspects, the isolated nucleic acid is derived from SEQ ID NO: 5, e.g., portion thereof.

In some aspects, also provided herein is an expression vector comprising any one or more of the nucleic acids (a) and (b) described above. Also provided herein is a host cell comprising an expression vector comprising any one or more of the nucleic acids (a) and (b) described above.

Also provided herein is a method of making a peptide fragment. The method can include culturing a host cell describe herein, e.g. a host cell comprising an expression vector comprising any one or more of the nucleic acids (a) and (b) described above, under conditions suitable for expressing the peptide fragment.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention pertains. In case of conflict, the present document, including definitions, will control.

All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. The materials, methods, and examples disclosed herein are illustrative only and not intended to be limiting.

The details of one or more embodiments of the invention are set forth in the accompanying drawings and the description below. Preferred methods and materials are described below, although methods and materials similar or equivalent to those described herein can also be used in the practice or testing of the present invention. Other features, objects, and advantages of the invention will be apparent from the description and drawings, and from the claims.

DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.

Figure 1 (a) contains a diagram illustrating autophagosome enrichment workflow using PANC1, PATU-8988T, or MCF7 cells cultured in light media ((K0) lysine (50 μg/mL) and light (R0) arginine (85 μg/mL)) or heavy media (light lysine was replaced with K8-lysine, and light arginine replaced with RIO-arginine at the same concentrations). The cells were mixed and autophagosomes were purified, followed by peptide identification and quantification.

Figure 1 (b) is graph quantifying the Log2(H:L) for autophagosome proteins from PANC1 cells (Ex. 3), overlaid with a scheme for identification of candidate autophagosome proteins.

Figure 1 (c) contains Venn diagrams showing autophagosome candidate overlap from biologic replicate experiments for PANC1 and MCF7 cells, as well as overlap between PANC1 and MCF7 datasets.

Figure 1 (d) is a Pearson correlation plot for overlapping candidates from PANC1 experiments (86 proteins, comparing Ex. 2 vs. Ex. 3 in Fig. 1 (c)). Figure 1 (e) is a Log2(H:L) heat map of Class 1A candidates from PANC1 and MCF7 cells.

Figure 2 (a) contains fluorescent images of U20S and 8988T cells untreated (CTRL) or treated with chloroquine (CQ). GFP-NCOA4 co-localizes with endogenous LC3 in CQ-treated cells. Scale bar, 20 μιη.

Figure 2 (b) contains images of HA immunob lot results for NCOA4-HA-FLAG in a GST-pull-down assay of NCOA4-HA-FLAG from stable 293T cells using the indicated GST-ATG8 proteins.

Figure 2 (c) contains photographs of immunoblot results for lysates of 8988T cells treated with chloroquine (CQ) or BAF (8 hours) or DMSO, and immunoblotted for NCOA4, LC3B, and ACTB as a loading control; *, cross-reactive band (for discussion, see description of Fig. 19(d)-(e), below).

Figure 2 (d) photographs of immunoblot results for purified 8988T

autophagosome fractions analyzed using antibodies to NCOA4 and LC3B. TAX1BP1, a newly identified autophagy receptor, was included as a positive control. LD is gradient load, Al is autophagosome fraction, A2 is the autophagolysosome fraction, L is the lysosome fraction, M is the mitochondrial fraction.

Figure 2 (e) is a schematic diagram of the NCOA4 interaction network from cells expressing NCOA4-HA-FLAG or FTH1-HA-FLAG. Black lines (this study) depict directionality of interaction observed with line thickness weighted by WDN-score (293T dataset); dotted lines, indicate STRING database. Numbers in parentheses indicate log2(H:L) ratio of NCOA4, FTH1, and FTL from MCF7 Ex. 1 dataset.

Figures 2 (f), (g) contain immunoblot results from extracts from 293T cells stably expressing the indicated proteins and immunoprecipitated with an anti-FLAG antibody, and immunoblotted with the indicated antibodies. An anti-ACTB antibody was used as a loading control. The upper three blots indicate FLAG-IP results, and the lower four panels represent the input.

Figure 2 (h) contains representative fluorescent confocal images of GFP-NCOA4 and ferritin after no treatment or FAC (ferric ammonium citrate) treatment (24 h) inU20S and 8988T cells; scale bar, 10 μιη. Figure 3 (a), upper panel, contains photographs of immunoblot results for lysates of 8988T cells following incubation with FAC (ferric ammonium citrate), NCOA4 depletion using shR A, and 9 hour iron chelation with the indicated chelators (DFO (deferoxamine mesylate), BPS (bathophenanthroline disulfonate), DFP (deferiprone)). Relative FTHl levels (n=3, biologic triplicate) for each chelator are quantified using an anti-FTH-1 antibody; an anti-ACTB antibody was used as a loading control. shGFP was a negative control for NCOA4 depletion. For each treatment groups (FAC (no iron chelation), DFO, BPS and DFP), the relative FTHl levels in the control group (shGFP) and NCOA4-depleted groups (shNCOA4-l and shNCOA4-2) are quantified in the graph in the lower panel; bars and error bars represent mean values and standard deviation (s.d.), respectively: ** (p<0.01) and * (p<0.02) comparing FTHl levels between 8988T shGFP versus 8988T shNCOA4-l or versus shNCOA4-2 (one-sided t-test). NCOA4 depletion rescued ferritin degradation.

Figure 3 (b) contains photographs of immunoblot results for lysates of U202 cells following incubation with FAC, in a DFO chelation time course (times are indicated "hr": hours). DFO was added at time 0; two NCOA4 antibodies were used for immunob lotting (top panel Sigma antibody, 2 ^nd panel Bethyl antibody). An anti-FTHl antibody was used in the third panel and an anti-ACTB antibody was used in the fourth panel (loading control).

Figure 3 (c) contains fluorescent confocal images of U20S cells subjected to DFO chelation in the presence of lysosomal protease inhibitors for 6 hours. GFP-NCOA4 co-localizes with endogenous LC3 and endogenous ferritin; scale bar, 20 μιη. Higher magnification views of the boxed areas are shown in the insets.

Figure 3 (d), left panel, contains fluorescent confocal images of immunostained 8988T cells incubated with control shRNA (GFP) or depleted of NCOA4 by incubation with one of two different shRNAs (shRNANCOA4-l and -2), and subjected to DFO chelation in the presence of lysosomal protease inhibitors for 9 hours. Cells were fixed and immunostained using antibodies to ferritin and LAMP2. Scale bar, 10 μιη. The right panel contains a bar graph quantifying punctate ferritin fraction from >100 cells per cell line from 2 independent experiments (biologic duplicate); bars and error bars represent mean values and s.d., respectively: *** denotes p<0.001 using a one-sided t-test. Figure 3 (e), left panel, contains photographs of immunoblot results from lysates from 8988T cells treated as in Figure 3 (a); the lysates were analyzed using the indicated antibodies (NCOA-4, IRP2, TFRC, and ACTB (loading control)); lanes 1-3 were untreated groups (no FAC or DFO)), lanes 4-9 were treated as indicated. The right panel contains a bar graph quantifying the relative protein level of the indicated proteins (IRP2, TFRC) based on at least 3 independent experiments (biologic triplicate); bars and error bars represent mean values and s.d., respectively: * (p<0.05) using a one-sided t-test.

Figure 3 (f) is a bar graph quantifying cell viability measured at 72 h in 8988T cells stably expressing shGFP or shNCOA4-l and treated with H2O2; bars and error bars represent mean values and s.d., respectively of technical triplicates: *** (p<0.001) using a two-sided t-test.

Figure 4 is a schematic diagram of the N and C-terminal regions of NCOA4, based on secondary structure predictions. Overlapping N-terminal and C-terminal fragments were designed as follows: NCOA4 N-terminal fragment, amino acids 1-245, and NCOA4 C-terminal fragment, amino acids 235-614.

Figure 5 contains photographs of immunoblot results. MYC-tagged versions of the full-length, N-terminal NCOA4 (amino acids (aa) 1-245) and C-terminal NCOA4 (aa235-614 of SEQ ID NO:4) as well as a transcript variant, NCOA4B (consisting of amino acids 1-238 and 555-614 of full-length NCOA4 (SEQ ID NO: 4)), were incubated with ferritin purified from horse spleen (consisting of a mixture of FTH1 and FTL subunits). An anti-MYC antibody immunoprecipitation was performed followed by immunoblotting with the indicated antibodies. Full-length NCOA4 and C-terminal NCOA4 bind to ferritin.

Figure 6 is a diagram showing the design of C-terminal fragments of NCOA4, based on secondary structure predictions. Overlapping C-terminal fragments were designed as follows: NCOA4 C-terminal, amino acids 235-560, 235-401, 383-560, and 545-614.

Figure 7 contains photographs of immunoblot results from a GST pull-down assay of ferritin using GST-NCOA4 proteins, GST alone as control. FTH1 immunoblot for ferritin. Ponceau stain for loading of GST-NCOA4 fragments (there are multiple break-down products of the GST-NCOA4 fragments). Figure 8 contains photographs of immunoblot results (upper two images) from a GST pull-down assay of ferritin using GST-NCOA4 proteins (as labeled), and GST alone as control. The upper two images show anti-FTHl immunoblot antibody results for ferritin. Coomassie stain for loading of GST-NCOA4 fragments (there are multiple break-down products of the GST-NCOA4 fragments) and anti-GST immunoblot show a band at the appropriate size for the predicted size of the various GST-NCOA4 fragments, as well as breakdown products (lowermost image). Fragments with amino acids 383-522 and fragments with amino acids 475-522 bind to ferritin.

Figure 9 contains photographs of immunoblot results from a GST pull-down assay of ferritin using GST-NCOA4 proteins (produced using an in vitro translation system). Lane B is an in vitro translation reaction with a GST-NCOA4 construct, negative control. The upper image shows the results of an anti-FTHl antibody immunoblot for ferritin and the lower image shows the results of anti-GST antibody immunoblot for GST-NCOA4 fragments.

Figure 10A contains an image of an immunoblot result of a GST pull-down assay of FTH1 using GST-NCOA4 proteins (as labeled), and GST alone as control. An anti- FTHl antibody immunoblot was performed. GST-NCOA4 fragment binds to FTH1. Load lane is 20% of FTH1 input.

Figure 10B contains an image of an immunoblot result of a GST pull-down assay of FTL using GST-NCOA4 proteins (as labeled), and GST alone as control. An anti-FTL antibody immunoblot was performed for FTL. GST-NCOA4 fragment binds minimally to FTL. Load lane is 20% of FTL input.

Figure 11 contains photographs of immunoblot results (upper two images) from a GST pull-down assay of ferritin using GST-NCOA4 fragments, or GST alone as control, and of Coomassie staining. An anti-FTHl antibody immunoblot was performed for ferritin. Coomassie stain for loading of GST-NCOA4 fragments was used (lowermost image). The following NCOA4 fragments (coupled to GST) were tested: amino acid residues (aa)475-572 (as indicated); #15: aa475-500; #16: aa 480-500; #17: aa 480-504; #18: aa 485-509; #19: aa490-514; #20: aa495-522.

Figure 12 contains photographs of immunoblot results from a GST pull-down assay of HERC2-FLAG Fragment 3 using GST-NCOA4 protein fragments (as labeled), or GST alone as control. An anti-FLAG immunoblot for HERC2-FLAG was performed. Coomassie stain for loading of GST-NCOA4 fragments is shown in lowermost image. The following NCOA4 fragments were tested, as indicated in the figure: aa383-522; aa510-560; aa383-436; aa436-485; and aa475-522.

Figure 13 (a) is an area-proportional Venn diagram showing the overlap of proteins identified in three prior autophagosome proteomics studies [Overbye, A., et al., Autophagy 3, 300-322 (2007); Gao, W., et al. The Journal of Biological Chemistry 285, 1371-1383, (2010); Dengjel, J., et al. Molecular & Cellular Proteomics: MCP 11, Mi l l 014035 (2012)]. Proteins overlapping between datasets are noted (MAP1LC3B:

microtubule-associated protein 1 light chain 3 beta; PCBP1 : poly(rC) binding protein 1; PSMC6: proteasome (prosome, macropain) 26S subunit, CMPK1 : cytidine

monophosphate (UMP-CMP) kinase 1 , cytosolic; HSPA5 : heat shock 70kDa protein 5 (glucose-regulated protein); PRDX6: peroxiredoxin 6; ASS1 : argininosuccinate synthase 1; ENOl : enolase 1; FBPl : fructose- 1,6-bisphosphatase 1; MDHl : malate dehydrogenase 1, NAD; PEBPl : phosphatidylethanolamme binding protein 1; PRDXl : peroxiredoxin 1; PRDX2: peroxiredoxin 2.

Figure 13 (b) contains fluorescence microscopy images of PANC1 cells stably expressing GFP-MAP1LC3B and treated with Wormannin (1 hour ("h") or Chloroquine (4 hours ("h"), or untreated, as indicated (DAPI stain).

Figure 13 (c) contains photographs of centrifuge tubes filled with lysed 8988T cells mixed with Nycodenz and placed at the bottom of a discontinuous density gradient with Nycodenz layers at the indicated concentrations (left image). After 3 hours ("hr") centrifugation at the indicated speed, 4 bands appeared at the indicated interfaces with enrichment of the indicated organelles (Al, A2, L and M) in each interface (right image).

Figure 13 (d) contains photographs of centrifuge tubes containing lysates of 8988T cells treated with either Wortmannin (lhour ("h"), 200 iiM) or chloroquine (4h, 25 μΜ) subjected to gradient centrifugation. A decreased amount of material is recovered from the Al (autophagosome) interface (boxed) due to the effect of Wortmannin on autophagosome formation. Figure 13 (e) contains fluorescence microscopy images of gradient load (LD) and autophagosome fraction (Al) from 8988T cells stably expressing GFP-MAP1LC3B after either chloroquine or Wortmannin treatment.

Figure 13 (f) contains fluorescence microscopy images of the indicated fractions from density gradient of 8988T cells stably expressing GFP-MAP1LC3B treated with chloroquine (Al fraction image is also presented in panel e and gradient picture is also presented in panel c).

Figure 13 (g) contains photographs of immunoblot results for lysates PANC1 autophagosome fractions analyzed by immunoblotting using antibodies to LAMP2, VDACl, and LC3B. LD is gradient load, Al is autophagosome fraction from 15-20% Nycodenz interface, A2 is the autophagolysosome fraction from the 20-24% Nycodenz interface, L is the lysosome fraction from the 24-26% Nycodenz interface, M is the mitochondrial fraction from the 26%-50% nycodenz interface.

Figure 13 (h) contains photographs of immunoblot results for lysates of 8988T autophagosome fractions analyzed as in Figure 13 (g).

Figure 13 (i) contains photographs of immunoblot results using antibodies to p62 and LC3B-II on lysates of 8988T autophagosomes (Al fraction) incubated at 37°C for 1 hour -/+ Triton X-100 and centrifuged at high speed.

Fig. 13 j) is a Pearson correlation plot for overlapping candidates from MCF7 experiments (102 proteins, comparing Log2 ratio of Heavy Lys (H)/16 hour chloroquine treatment (CQ) to Light Lys ("L")/no treatment in Ex. 1 versus Ex. 2.

Figure 13 (k) contains photographs of electron micrographs of 8988T gradient load (LD, left panel) and 8988T autophagosome fraction (Al, right panel) at 6800x magnification, scale bar 500 nm.

Figure 13 (1) contains photographs of electron micrographs of 8988T gradient load (LD, left panel) and 8988T autophagosome fraction (Al, right panel) at 18500x magnification, scale bar 500 nm.

Figure 13 (m) contains photographs of electron micrographs of 8988T autophagosome fraction (Al) at 23000x magnification, scale bar 100 nm. Arrowhead: double-membrane autophagosome; arrow: fused autophagolysosome. Figure 14 (a) is an autophagosome proteomics class 1 A candidate list, with enriched proteins, "not enriched" proteins, and "not identified" proteins in each group indicated (MCF7, 8988T SILAC, and 8988T LC3-IP).

Figure 14 (b) is a Venn diagram showing the overlap between Class 1 candidates (MCF7 and PANC1) and candidates from 4 hr chloroquine (CQ) SILAC 8988T gradient autophagosome purification experiment.

Figure 14 (c) lists the protein expression data from 8988T SILAC gradient autophagosome for Class 1A candidates (and FTH1), with enriched proteins, "not enriched" proteins, and "not identified" proteins identified in each group. Number of peptides identified for each protein is noted (8988T peptide #) and the Log2(Heavy:Light ratio) of each quantified protein is noted (8988T Log2(H:L).

Figure 14 (d) is a heat map of Class 1A candidates (and FTH1) comparing PANC1 and 8988T cells treated for 4 hours (h) with chloroquine (CQ).

Figure 15 contains representative confocal images of candidates from

autophagosome proteomics, prepared to determine which candidates co localize in autophagosomes after chloroquine (CQ) treatment in 8988T and U20S cells expressing HA-tagged candidates. Autophagosomes were identified by immunostaining of endogenous LC3B). Representative colocalization is marked by white arrows. Scale bar, 10 μιη. MGRN1 is included as an example of one of the candidates that did not show colocalization.

Figure 16 (a) is a schematic diagram illustrating GFP-immunoisolation of GFP- LC3B labeled autophagosomes from 8988T cells, and Figure 16 (b) contains a table of the data from GFP-immunoisolation for Class 1 A candidates, with enriched proteins, "not enriched" proteins, and "not identified" proteins identified in each group.

Log2(CQ_peptide#:WOPvT_peptide#) represents the log ₂ ratios of peptide numbers of proteins identified in autophagosomes purified from chloroquine versus wortmannin- treated cells and Log2(CQ_peptide#:WCL_peptide#) represents the log ₂ ratios of peptide numbers of proteins identified in autophagosomes purified from chloroquine-treated cells versus peptide numbers from a whole-cell lysate sample. Zero value denominators were systematically replaced with a value of 0.5 to generate a log ₂ ratio. Candidates were qualified as enriched if both log ₂ ratios were greater than 0.5. Figure 17 (a) is a schematic diagram depicting the analysis and comparison of Dengjel et al. data and candidate list with data derived from MCF7 autophagosome proteomics experiments as detailed in methods section. Shading of gene symbols denotes proteins identified as MCF7 candidates.

Figures 17 (b)-(e) contain schematic diagrams depicting the analysis and comparison of Dengjel et al. data and candidate list with data derived from both MCF7 and PANCl autophagosome proteomics experiments (Class 1 and 2 proteins) as detailed in the methods section (Example 1). The key for Figs. 17 (b)-(e) appears in Fig. 17 (e). Orange shading of gene symbols denotes proteins identified as Class 1 or 2 candidates.

Figure 18 (a) contains fluorescent images of U20S and 898T cells, untreated

("CTRL"), or treated with chloroquine (+CQ). GFP-NCOA4 co-localizes with mCherry- LC3B in CQ-treated cells. Scale bar, 20 μιη.

Figure 18 (b) contains fluorescent images of U20S cells, untreated, or treated with chloroquine (+CQ). GFP-NCOA4 co-localizes with mCherry-GABARAPL2 in CQ-treated cells. Scale bar, 20 μιη.

Figure 18 (c) contains fluorescent images of U20S and 898T cells, untreated ("CTRL"), or treated with chloroquine (+CQ). GFP-NCOA4 co-localizes with endogenous GABARAPL2 in CQ-treated cells. Scale bar, 20 μιη.

Figure 18 (d) contains fluorescent images of 898T cells treated with chloroquine (+CQ). GFP-NCOA4 does not colocalize with endogenous Mannose 6-Phosphate Receptor (M6PR) in CQ-treated cells. Scale bar, 20 μιη.

Figure 18 (e) contains fluorescent images of U20S, untreated ("CTRL"), or treated with choloroquine (+CQ). HERC2 does not co-localize in autophagosomes. Immunostaining of U20S cells subjected to CQ treatment, endogenous LC3B and endogenous HERC2, scale bar, 20 μιη.

Figure 19 (a) contains photographs of immunoblots of lysates from 8988T cells cultured with FAC for 24 hours, washed, followed by chelation with the indicated combinations of chelators (DFO, BPS, DFP) -/+ lysosomal protease inhibitors (E-64d and PepstatinA) or proteasomal inhibitor, Bortezomib (BTZ), (lane 5) for 8 hours. Blots were probed with antibodies to ACTB or FTH1. Figure 19 (b) contains photographs of immunoblots of lysates from U20S cells cultured with FAC for 24 hours, washed, followed by chelation with 2 chelators (DFO, DFX) -/+ lysosomal protease inhibitors (E-64d and PepstatinA (E-64d+PepA)). Blots were probed with antibodies to ACTB or FTH1.

Figure 19 (c) contains photographs of immunoblots of lysates from 8988T cells transfected with luciferase control siR A or validated siRNA to ATG5. The cells were cultured with FAC, washed, and subjected to DFO chelation for 9 hours. Lysates were immunob lotted using antibodies to FTH1, ATG5, and ACTB.

Figure 19 (d) contains photographs of immunoblots of lysates from 8988T cells following RNAi-mediated knockdown of NCOA4. 8988T cells stably expressing a control shRNA (shGFP) and two independent shRNAs to NCOA4 (shNCOA4-l and shNCOA4-2) were lysed and analyzed by immunoblotting with two different antibodies to NCOA4 and ACTB as a loading control. Middle panel shows immunoblot probed with NCOA4 antibody from Bethyl Laboratories (#A302-272A). A non-specific band migrates just below the NCOA4 specific band. Top panel shows immunoblot probed with NCOA4 antibody from Sigma (SAB 1404569).

Figure 19 (e) contains photographs of immunoblot results for lysates from U20S cells stably expressing shGFP, shNCOA4-l, or shNCOA4-2. Lysates were analyzed by immunoblotting with two different antibodies to NCOA4 and ACTB as a loading control. Middle panel shows immunoblot probed with NCOA4 antibody from Bethyl Laboratories (#A302-272A).

Figure 19 (f), left panel, contains photographs of immunoblot results for lysates of U20S cells following NCOA4 depletion and iron chelation. The right panel is a bar graph quantifying the relative FTH1 levels (n=3) for each indicated chelator. Bars and error bars represent mean values and s.d., respectively: ** (p<0.01) and * (p<0.02) comparing FTH1 levels between different cell lines to shGFP control (one-sided t-test).

Figure 19 (g) contains photographs of immunoblot results of lysates of U20S cells stably expressing shGFP, shNCOA4-l, or shNCOA4-2 and cultured with FAC for 24 hours, washed, and subjected to DFO chelation -/+ lysosomal protease inhibitors (E- 64d and PepstatinA (E-64d+PepA)). Lysates were immunoblotted using antibodies to NCOA4, FTH1, and ACTB. Figure 20 (a) contains fluorescent microscopy images of 8988T cells, and Fig. 20 (b) contains fluorescent microscopy images of U20S cells, cultured in the presence or absence of FAC for 24 hours, washed, and subjected to DFO chelation -/+ lysosomal protease inhibitors (E-64d and PepstatinA). Cells were fixed and immunostained using antibodies to ferritin and LAMP2. Higher magnification views of the boxed areas are shown in the insets. Scale bar, 10 μιη.

Figure 20 (c) contains fluorescent images of U20S cells, Fig. 20 (d) contains fluorescent images ofIMR90 cells, and Figure 20 (e) contains fluorescent images of HPDE cells, expressing a control shRNA (shGFP) and two independent shRNAs to NCOA4 (shNCOA4-l and shNCOA4-2) subjected to DFO chelation in the presence of lysosomal protease inhibitors for 9 hours and immunostained for ferritin, and LAMP2 (left panel in each figure). Scale bar, 10 μιη. The right panel in Figures 20 (c), (d) contain a bar graph quantifying the punctate ferritin fraction, in Fig. 20 (c) from >75 cells per cell line from 2 independent experiments (number of U20S cells quantitated is as follows: shGFP: 133 cells, shNCOA4-l : 103 cells, shNCOA4-2: 79 cells); and in Fig. 20

(d) , from >25 cells per cell line in two independent experiments and from more than 10 microscopy fields (number of IMR90 cells quantified is as follows: shGFP: 29 cells, shNCOA4-l : 26 cells, shNCOA4-2: 31 cells). Quantitation was not possible in Fig. 20

(e) due to the high background signal in shGFP control cells. Bars and error bars represent mean values and s.d., respectively: *** denotes p<0.001 using a one-sided t-test.

Figure 21 (a) contains fluorescent images of 8988T cells stably expressing either a control MSCV empty vector or the murine homolog of NCOA4 (selected with blasticidin) as well as stably expressing shRNAs (shGFP, shNCOA4-l, shNCOA4-2, selected with puromycin) and cultured in the presence or absence of FAC for 24 hours, washed, and subjected to DFO chelation in the presence of lysosomal protease inhibitors (E-64d and PepstatinA). Cells were fixed and immunostained using antibodies to ferritin and LAMP2. Scale bar, 10 μιη (left panel). The right panel contains graphs quantifying the punctate ferritin fraction from >100 cells per cell line (number of 8988T cells quantified is as follows: 8988T-control MSCV-shGFP: 100 cells, 8988T-control-MSCV- shNCOA4-l : 125 cells, 8988T-control-MSCV-shNCOA4-2: 132 cells, 8988T-mouse- NCOA4-shGFP: 151 cells, 8988T-mouse-NCOA4-shNCOA4-l : 153 cells, 8988T- mouse-NCOA4-shNCOA4-2: 172 cells). Bars and error bars represent mean values and s.d., respectively: *** denotes p<0.001 using a one-sided t-test.

Figure 21 (b) contains photographs of immunoblots of lysates of 8988T cells stably expressing either a control MSCV empty vector or the murine homo log of NCOA4 (selected with blasticidin), as well as stably expressing a control shRNA (shGFP) and two independent shRNAs to NCOA4 (shNCOA4-l and shNCOA4-2). The cells were lysed and analyzed by immunoblotting with an antibody to NCOA4 and to ACTB as a loading control. Light and dark exposures are shown. A non-specific band migrates just below the NCOA4 specific band.

Figure 21 (c) contains photographs of immunoblots of lysates of 8988T cells expressing murine HA-NCOA4 protein or control (empty vector). Cell lysates were probed with an anti-HA antibody, or an anti-ACTB antibody as a loading control.

Figure 22 (a) contains fluorescent images of 8988T cells transfected with luciferase control siRNA or two independent siRNAs to NCOA4 and subjected to DFO chelation in the presence of lysosomal protease inhibitors for 9 hours. Scale bar, 20 um. Cells were immunostained for ferritin and LAMP2.

Figure 22 (b) contains fluorescent images of 8988T cells transfected with luciferase control siRNA or two independent siRNAs to HERC2 and subjected to DFO chelation in the presence of lysosomal protease inhibitors for 9 hours. Scale bar, 20 um. Cells were immunostained for ferritin and LAMP2.

Figure 22 (c) contains photographs of immunoblot results for lysates of 8988T cells transfected with luciferase control siRNA or two independent siRNAs to HERC2. Lysates were immunoblotted using antibodies to HERC2 and ACTB (loading control).

Figure 22 (d) contains photographs of immunoblot results for lysates of U20S, IMR90, and 8988T cells. Cells were transfected with luciferase control siRNA or two independent siRNAs to NCOA4. Lysates were immunoblotted using antibodies to NCOA4, IRP2, TFRC, FTH1, and ACTB. Light and dark exposures are shown for TFRC.

Figure 22 (e) contains photographs of immunoblot results for lysates of 8988T cells stably expressing either a control MSCV empty vector or mouse NCOA4 and cultured in the presence of FAC for the indicated times. Cells were lysed and analyzed by immunob lotting with antibodies to NCOA4, FTH1 and ACTB as a loading control. A non-specific band migrates just below the NCOA4 specific band.

Figures 23 (A) - (D) are photogaphs of a SDS-PAGE gel of a GST pull-down assay of wild type (WT) FTH1 and point mutants of FTH1 using NCOA4 (amino acids383-522)-GST protein. Point mutants of FTH1 tested were H14A, Q15A, R23A, D90A (Figure 23A); C91A, D92A, D93A, E95A (Figure 23B); E102A, H106A, Nl 10A, K120A (Figure 23 C): and T123A, D124A, N126A, and R157A (Figure 23D). NCOA4- GST and FTH1 bands were stained with InstantBlue Stain (Expedeon).

DETAILED DESCRIPTION

Provided herein are methods and compositions for modulating (e.g., increasing or reducing) NCOA4-mediated autophagic targeting of ferritin. These methods and compositions are also useful for, e.g., treating diseases and disorders such as cancer, anemia, and iron overload.

As described in the Examples, below, quantitative proteomics was employed to identify a cohort of novel and known autophagosome-enriched proteins, including cargo receptors. One of the novel cargo receptors identified was NOCA4. Like known cargo receptors, NCOA4 was highly enriched in autophagosomes, and associated with ATG8 proteins that recruit cargo-receptor complexes into autophagosomes. Unbiased identification of NCOA4-associated proteins revealed ferritin heavy and light chains, components of an iron-filled cage structure that protects cells from reactive iron species but is degraded via autophagy to release iron through an unknown mechanism. It was found that delivery of ferritin to lysosomes required NCOA4, and an inability of

NCOA4-deficient cells to degrade ferritin led to decreased bioavailable intracellular iron. The Examples thus identify NCOA4 as a selective cargo receptor for autophagic turnover of ferritin (ferritinophagy) critical for iron homeostasis and provides a resource for further dissection of autophagosomal cargo-receptor connectivity.

As used herein, "NCOA4" is interchangeable with the term "nuclear receptor coactivator 4." "NCOA4" encompasses mammalian NCOA4, including, e.g., human NCOA4, including various genetic variants and isoforms of NCOA4. Non-human NCOA4 can be from any of species listed below for a "subject". Nucleic acid and amino acid sequences for NCOA4 are known in the art. By way of non-limiting example, a protein sequence for human NCOA4 has GenBank Accession No. NP 001138735.1 :

1 mntfqdqsgs ssnrepllrc sdarrdlela iggvlraeqq ikdnlrevka qihscisrhl 61 eclrsrevwl yeqvdliyql keetlqqqaq qlysllgqfn clthqlectq nkdlanqvsv 121 clerlgsltl kpedstvllf eadtitlrqt ittfgslkti qipehlmaha ssanigpfle 181 krgcismpeq ksasgivavp fsewllgskp asgyqapyip stdpqdwltq kqtlensqts 241 sracnffnnv ggnlkglenw llksekssyq kcnshsttss fsiemekvgd qelpdqdemd 301 lsdwlvtpqe shklrkpeng sretsekfkl lfqsynvndw lvktdsctnc qgnqpkgvei 361 enlgnlkcln dhleakkpls tpsmvtedwl vqnhqdpckv eevcranepc tsfaecvcde 421 ncekealykw llkkegkdkn gmpvepkpep ekhkdslnmw lcprkevieq tkapkamtps 481 riadsfqvik nsplsewlir ppykegspke vpgtedragk qkfkspmnts wcsfntadwv 541 lpgkkmgnls qlssgedkwl lrkkaqevll nsplqeehnf ppdhyglpav cdlfacmqlk 601 vdkekwlyrt plqm (SEQ ID NO: 4).

The mRNA reference sequence for the above human amino acid sequence has GenBank® Accession No. NM_001145263 (SEQ ID NO: 5).

As used herein, the term "autophagic targeting of ferritin" means the transport of ferritin to an autophagosome by NCOA4 in a cell. The cell can be in vitro/ex vivo or in a subject (e.g. a mammal).

As used herein, the term "selective autophagy" means the selective elimination by autophagy in a cell of unwanted components such as but not limited to aberrant protein aggregates, lipid droplets, dysfunctional organelles, and invading pathogens.

As used herein, the term "modulating the level of NCOA4" means causing any increase or decrease in the mRNA and/or protein level of NCOA4 (e.g., in a cell or a subject (e.g. a mammal)).

As used herein, the term "modulating the activity of NCOA4" means causing any increase or decrease in one or more functions of NCOA4 involved in autophagic targeting of ferritin. Functions involved in autophagic targeting of ferritin include, e.g., interaction of NCOA4 with one or more of ferritin (e.g., the heavy chain of ferritin, FTH1 and/or the light chain of ferritin (FTL)), E3 ubiquitin-protein ligase HERC2 (HERC2), and an ATG8 paralog (e.g., GABARAPL2, LC3). As used herein, the term "modulating the level of HERC2" means causing any increase or decrease in in the mRNA and/or protein level of HERC2 (e.g., in a cell or a subject (e.g. a mammal)).

As used herein, the term "modulating the activity of HERC2" means causing any increase or decrease in one or more functions of HERC2 involved in regulating expression and/or activity of NCOA4 (e.g., in a cell and/or subject (e.g., a mammal)).

The level or activity of a target gene or polypeptide (e.g., NCOA4, HERC2) is modulated (decreased or increased), if the change in the level or activity of the target gene relative to a control is at least 1.5-fold, at least 2-fold, at least 3-fold, at least 4-fold, at least 5-fold, at least 10-fold, at least 50-fold, at least 100-fold, or more, relative to a starting level of activity (e.g., control or no treatment).

Typically, when an agonist (e.g., small molecule, polypeptide, antibody, intrabody, peptide fragment, allosteric binding of an agent, etc.) is administered as a therapy (e.g., for treating anemia, and increasing red blood cell production (erythropoiesis)), the therapy is deemed effective if the level and/or activity of the target gene or polypeptide is increased by at least 1.5-fold, at least 2-fold, at least 3-fold, at least 4-fold, at least 5-fold, at least 10-fold, at least 50-fold, at least 100-fold, or more, relative to the level of the target gene or polypeptide at the beginning of or before commencement of the therapy.

As used herein, an NCOA4 peptide or NCOA4 polypeptide fragment that is an inhibitor of NCOA4, e.g., an inhibitor of the expression of NCOA4 and/or activity of

NCOA4, an inhibitor of the interaction between NCOA4 and ferritin, or between NOCA4 and an ATG8 paralog or HERC2, is not a functionally active fragment of NCOA4.

Typically, when an antagonist/inhibitor (e.g., small molecule, antibody, intrabody, polypeptide, peptide fragment, etc.) is administered as a therapy (e.g., for treating cancer, treating iron overload (e.g. iron overload due to transfusion, hemochromatosis), inhibiting the interaction of NCOA4 with ferritin, inhibiting the interaction of NCOA4 with HERC2 or an ATG8 paralog (e.g., GABARAPL2 or LC3), etc.), the therapy is deemed effective if the level or activity of the target gene or polypeptide is increased by at least 1.5 -fold, at least 2-fold, at least 3 -fold, at least 4-fold, at least 5 -fold, at least 10-fold, at least 50-fold, at least 100-fold, or more, relative to the level of the target gene or polypeptide at the beginning of or before commencement of the therapy. As used herein, "decreasing the interaction between ferritin and NCOA4" means causing any decrease in the amount of NCOA4 bound to ferritin or the amount of ferritin bound to NCOA4, e.g., a decrease of at least 1.5-fold, at least 2-fold, at least 3-fold, at least 4-fold, at least 5 -fold, at least 10-fold, at least 50-fold, at least 100-fold, or more, relative to a starting level (e.g., control or no treatment) of interaction.

Also provided herein are "peptide fragments of NCOA4." Such fragments do not encompass full-length NCOA4. In some embodiments, the peptide fragment has a length of less than 614 amino acids (e.g., 613, 612, 611, 610, etc., e.g., 600, 590, 580, 570, 560. 550, 540, 530, 520, 510, 500, 480, 460, 440, 420, 400, 380, 360, 340, 320, 300, 280, 260, 240, 220, 200, 180, 160, 140, 120, 100, 80, 60, 50, 40, 35, 30, 25 amino residues in length). In some embodiments, a peptide fragment comprises or consists of SEQ ID NO: 11 or the peptide fragment of SEQ ID NO: 11 with no more than 10 conservative amino acid substitutions. In some embodiments, a peptide fragment comprises SEQ ID NO: 1 or the peptide fragment comprising SEQ ID NO: 1 with no more than 10 conservative amino acid substitutions. In some embodiments, a peptide fragment of NCOA4 comprises SEQ ID NO: 2 or the peptide fragment comprises SEQ ID NO: 2 with no more than 10 conservative amino acid substitutions. In some embodiments, a peptide fragment of NCOA4 consists of SEQ ID NO: 1 or the peptide fragment consists of SEQ ID NO: 1 with no more than 10 conservative amino acid substitutions. In some embodiments, a peptide fragment of NCOA4 consists of SEQ ID NO: 2 or the peptide fragment consists of SEQ ID NO: 2 with no more than 10 conservative amino acid substitutions.

Also provided herein are "peptide fragments of ferritin." An exemplary human ferritin heavy chain (FTH1) sequence has GenBank® Accession No. NP 002023 (SEQ ID NO: 6) (183 amino acids). An exemplary mRNA reference sequence for human FTH1 is GenBank® Accession No. NM 002032.2 (SEQ ID NO: 21). An exemplary human ferritin light chain sequence (FTL) has GenBank Accession No. NP 000137 (SEQ ID NO: 7) (175 amino acids). An exemplary mRNA reference sequence for human FTL is GenBank® Accession No. NM 000146.3 (SEQ ID NO: 22). Such fragments do not encompass full-length ferritin (i.e., full length FTL and/or full length FTH1). In some embodiments, an FTH1 peptide fragment has, or an FTH1 nucleic acid encodes a peptide fragment that has, a length of less than 183 amino acids, e.g., 182, 181, 180, 170, 160, 150, 140, 130, 120, 110, 100, 90, 80, 70, 60, 50, 40, 35, 30, 25, 20, 19, 18, 17, 16, 15, 14, 13 12, 11, 10, 9, 8, 7, 6, or 5 amino acid residues in length). In some embodiments, a peptide fragment of FTHl comprises or consists of amino acids 16-34 of SEQ ID NO: 6 or the peptide fragment of FTHl comprises or consists if amino acids 16-34 of SEQ ID NO: 6 with no more than 10 conservative amino acid substitutions. Moreover, the peptide fragment of FTHl can comprise or consist of a segment of amino acids 16-34 of SEQ ID NO: 6, the segment being 18 or fewer amino acids in length (e.g., 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, or 5 amino acids in length) and will preferably include Arg at a position corresponding to residue 23 of SEQ ID NO: 6. In some embodiments, a peptide fragment of FTHl comprises or consists of amino acids 103-125 of SEQ ID NO: 6 or the peptide fragment of FTHl comprises or consists if amino acids 103-125 of SEQ ID NO: 6 with no more than 10 conservative amino acid substitutions. Moreover, the peptide fragment of FTHl can comprise or consist of a segment of amino acids 103-125 of SEQ ID NO: 6, the segment being 22 or fewer amino acids in length (e.g., 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, or 5 amino acids in length). In some embodiments, a peptide fragment of FTHl comprises or consists of amino acids 78-88 of SEQ ID NO: 6 or the peptide fragment of FTHl comprises or consists if amino acids 78-88 of SEQ ID NO: 6 with no more than 5 conservative amino acid substitutions. Moreover, the peptide fragment of FTHl can comprise or consist of a segment of amino acids 78-88 of SEQ ID NO: 6, the segment being 10 or fewer amino acids in length (e.g., 9, 8, 7, 6, or 5 amino acids in length). In some embodiments, an FTL peptide fragment has, or an FTL nucleic acid encodes a peptide fragment that has, a length of less than 175 amino acids, e.g., 174, 173, 172, 171, 170, 160, 150, 140, 130, 120, 110, 100, 90, 80, 70, 60, 50, 40, 35, 30, 25, 20, 15, 10, etc. amino residues in length. A peptide fragment of ferritin can include a fragment of one or both of FTHl and FTL. Such ferritin fragments can also include 20 or fewer (e.g., 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1) conservative amino acid substitutions.

Similar fragments of ATG8 paralogs and HERC2 are also encompassed by the present disclosure. Such fragments also do not encompass the full length, wild-type sequences. An exemplary amino acid sequence for human HERC2 has GenBank® Accession No. NP_004658 (SEQ ID NO: 8) (4834 amino acids). An exemplary mRNA reference sequence for human HERC2 is GenBank® Accession No. NM 004667.5 (SEQ ID NO: 23). In some embodiments, a fragment of HERC2 has, or a HERC2 nucleic acid encodes a peptide fragment of HERC2 that has, a length of less than 4834 amino acids (e.g., 4833, 4832, 4800, 4700, 4600, 4500, 4400, 4300, 4200, 4100, 4000, 3500, 3000, 2500, 2000, 1500. 1000, 500, 400, 300, 200, 100, 50, 25, 20, 15, etc.). HERC2 peptide fragments can also include 20 or fewer (e.g., 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1) conservative amino acid substitutions. In a specific embodiment, a HERC2 fragment consists of or comprises amino acid residues 1700-2700 of SEQ ID NO: 8. In certain embodiments, a HERC2 fragment has an amino acid sequence that has at least 85% sequence identity with SEQ ID NO: 8.

An exemplary amino acid sequence for the ATG8 paralog GABARAPLR2 (gamma-aminobutyric acid receptor-associated protein-like 2) has GenBank Accession No. CAG47013 (also NP 009216) (SEQ ID NO: 9) (117 amino acids). An exemplary mRNA reference sequence for human GABARAPLR2 is GenBank® Accession No. NM 007285.6 (SEQ ID NO: 24). Peptide fragments of GABARAPLR2 have, or GABARAPLR2 nucleic acids encode peptide fragments of GABARAPLR2 that have, a length that is less than the length of the full-length wild-type sequence. Thus, in some embodiments, a peptide fragment of GABARAPLR2 has a length of less than 117 amino acids (e.g., 116, 115, 114, 113, 112, 111, 110, 105, 100, 75, 50, 25, 20, 15, etc.).

GABARAPLR2 peptide fragments can also include 20 or fewer (e.g., 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1) conservative amino acid substitutions. In certain embodiments, a GABARAPLR2 fragment has an amino acid sequence that has at least 85% sequence identity with SEQ ID NO: 9.

An exemplary amino acid sequence for the ATG8 paralog LC3 (microtubule- associated protein 1 light chain 3 alpha (MAP1LC3A)) has GenBank Accession No. NP 852610 (SEQ ID NO: 10) (125 amino acids). An exemplary mRNA reference sequence for human LC3 is GenBank® Accession No. NM_181509.2 (SEQ ID NO: 25). Peptide fragments of LC3 have, or LC3 nucleic acid sequences encoding peptide fragments of LC3 have, a length that is less than the length of the full-length, wild-type sequence. Thus, in some embodiments, a peptide fragment of LC3 has a length of less than 125 amino acids (e.g., 124, 123, 122, 121, 120, 115, 110, 105, 100, 75, 50, 25, 20, 15, etc.). LC3 peptide fragments can also include 20 or fewer (e.g., 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1) conservative amino acid substitutions. In certain embodiments, a LC3 fragment has an amino acid sequence that has at least 85% sequence identity with SEQ ID NO: 10.

Also encompassed herein are peptide fragments that have at least 85% sequence identity to a peptide fragment described herein, e.g., a peptide fragment having at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%o, at least 99%> or greater sequence identity to: SEQ ID NO: 1,2, 3, 11, a fragment of SEQ ID NO: 4, 6, 7, or 8, e.g., amino acids 16-34 of SEQ ID NO: 6, amino acids 103-125 of SEQ ID NO: 6, or amino acids 78-88 of SEQ ID NO: 6.

As used herein, "sequence identity" or "identity" in the context of two nucleic acid or polypeptide sequences makes reference to a specified percentage of residues in the two sequences that are identical when aligned for maximum correspondence over a specified comparison window, as measured by sequence comparison algorithms or by visual inspection. When percentage of sequence identity is used in reference to polypeptides it is recognized that residue positions which are not identical often differ by conservative amino acid substitutions, where amino acid residues are substituted for other amino acid residues with similar chemical properties (e.g., charge or hydrophobicity) and therefore do not change the functional properties of the molecule. When sequences differ in conservative substitutions, the percent sequence identity may be adjusted upwards to correct for the conservative nature of the substitution. Sequences that differ by such conservative substitutions are said to have "sequence similarity" or "similarity." Means for making this adjustment are well known to those of skill in the art. Typically this involves scoring a conservative substitution as a partial rather than a full mismatch, thereby increasing the percentage sequence identity. Thus, for example, where an identical amino acid is given a score of 1 and a non-conservative substitution is given a score of zero, a conservative substitution is given a score between zero and 1. The scoring of conservative substitutions is calculated, e.g., as implemented in the program PC/GENE (Intelligenetics, Mountain View, California). Polypeptides with substitutions will generally have not more than 50 (e.g., not more than one, two, three, four, five, six, seven, eight, nine, ten, 12, 15, 20, 25, 30, 35, 40, or 50) conservative amino acid substitutions, although more are possible. A conservative substitution is the substitution of one amino acid for another with similar characteristics. Conservative substitutions include substitutions within the following groups: valine, alanine and glycine; leucine, valine, and isoleucine; aspartic acid and glutamic acid; asparagine and glutamine; serine, cysteine, and threonine; lysine and arginine; and phenylalanine and tyrosine. The non- polar hydrophobic amino acids include alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan and methionine. The polar neutral amino acids include glycine, serine, threonine, cysteine, tyrosine, asparagine and glutamine. The positively charged (basic) amino acids include arginine, lysine and histidine. The negatively charged (acidic) amino acids include aspartic acid and glutamic acid. Any substitution of one member of the above-mentioned polar, basic or acidic groups by another member of the same group can be deemed a conservative substitution. By contrast, a non- conservative substitution is a substitution of one amino acid for another with dissimilar characteristics.

As used herein, "percentage of sequence identity" means the value determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison, and multiplying the result by 100 to yield the percentage of sequence identity.

In certain embodiments, a peptide fragment of a polypeptide disclosed herein has "substantial identity" with a reference sequence (e.g., a wild-type sequence of the polypeptide, e.g., of NCOA4, ferritin (FTL or FTH1), HERC2, GABARAPL2, or LC3)). The term "substantial identity" in the context of a peptide indicates that a peptide comprises a sequence with at least 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, or 79%, preferably 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, or 89%, more preferably at least 90%, 91%, 92%, 93%, or 94%, or even more preferably, 95%, 96%, 97%), 98%o or 99%, sequence identity to the reference sequence over a specified comparison window. Preferably, optimal alignment is conducted using the homology alignment algorithm of Needleman and Wunsch, J. Mol. Biol. 48:443 (1970). An indication that two peptide sequences are substantially identical is that one peptide is immunologically reactive with antibodies raised against the second peptide. Thus, a peptide is substantially identical to a second peptide, for example, where the two peptides differ only by a conservative substitution. One of skill in the art will recognize that these values can be appropriately adjusted to determine corresponding identity of proteins encoded by two nucleotide sequences by taking into account codon degeneracy, amino acid similarity, reading frame positioning, and the like. Substantial identity of amino acid sequences for these purposes normally means sequence identity of at least 70%>, more preferably at least 80%>, 90%>, and most preferably at least 95%.

Methods for alignment of sequences for comparison are well known in the art. For example, the determination of percent identity between any two sequences can be accomplished using a mathematical algorithm. Non-limiting examples of such mathematical algorithms are the algorithm of Myers and Miller, CABIOS, 4: 11 (1988); the local homology algorithm of Smith et al, Adv. Appl. Math., 2:482 (1981); the homology alignment algorithm of Needleman and Wunsch, JMB, 48:443 (1970); the search-for-similarity-method of Pearson and Lipman, Proc. Natl. Acad. Sci. USA, 85:2444 (1988); the algorithm of Karlin and Altschul, Proc. Natl. Acad. Sci. USA, 87:2264 (1990), modified as in Karlin and Altschul, Proc. Natl. Acad. Sci. USA, 90:5873 (1993).

Computer implementations of these mathematical algorithms can be utilized for comparison of sequences to determine sequence identity. Such implementations include, but are not limited to: CLUSTAL in the PC/Gene program (available from Intelligenetics, Mountain View, California); the ALIGN program (Version 2.0) and GAP, BESTFIT, BLAST, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Version 8 (available from Genetics Computer Group (GCG), 575 Science Drive, Madison, Wisconsin, USA). Alignments using these programs can be performed using the default parameters. The CLUSTAL program is well described by Higgins et al, Gene, 73:237 (1988); Higgins et al, CABIOS, 5: 151 (1989); Corpet et al, Nucl. Acids Res,, 16: 10881 (1988); Huang et al, CABIOS, 8: 155 (1992); and Pearson et al, Meth. Mol. Biol, 24:307 (1994). The ALIGN program is based on the algorithm of Myers and Miller, supra. The BLAST programs of Altschul et al, JMB, 215:403 (1990); Nucl Acids Res., 25:3389 (1990), are based on the algorithm of Karlin and Altschul supra.

Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/). This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold. These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always > 0) and N (penalty score for mismatching residues; always < 0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when the cumulative alignment score falls off by the quantity X from its maximum achieved value, the cumulative score goes to zero or below due to the accumulation of one or more negative-scoring residue alignments, or the end of either sequence is reached.

In addition to calculating percent sequence identity, the BLAST algorithm also performs a statistical analysis of the similarity between two sequences. One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a test nucleic acid sequence is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid sequence to the reference nucleic acid sequence is less than about 0.1, more preferably less than about 0.01, and most preferably less than about 0.001.

To obtain gapped alignments for comparison purposes, Gapped BLAST (in BLAST 2.0) can be utilized as described in Altschul et al, Nucleic Acids Res. 25 :3389 (1997). Alternatively, PSI-BLAST (in BLAST 2.0) can be used to perform an iterated search that detects distant relationships between molecules. See Altschul et al, supra. When utilizing BLAST, Gapped BLAST, PSI-BLAST, the default parameters of the respective programs (e.g. BLASTN for nucleotide sequences, BLASTX for proteins) can be used. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, a cutoff of 100, M=5, N=-4, and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix. See the Worldwide Web at ncbi.nlm.nih.gov. Alignment may also be performed manually by inspection.

Peptide fragments of ferritin (FTH1 and FTL), ATG8 paralogs, and HERC2 that are functionally active fragments retain the ability to bind to NCOA4. Determining binding to NCOA4 is routine in the art, and can be determined by any suitable method, such as, but not limited to, immunoprecipitation/immunoblot (as described herein), using instruments such as Biacore (see the Worldwide Web at

biacore.com/lifesciences/index.html) and Octet Red (see the WoldWideWeb at fortebio.com/interactions/April_2008/), and/or co-crystalliation studies.

As used herein, a "peptide fragment of NCOA4" that is an inhibitor of the interaction between NCOA4 and ferritin, is capable of reducing the binding of NCOA4 to one or both of the heavy and light chains of ferritin (FTH1 and FTL, respectively), e.g., by at least 1.5-fold, at least 2-fold, at least 3-fold, at least 4-fold, at least 5-fold, at least 10-fold, at least 50-fold, at least 100-fold, or more, relative to a starting level of binding (e.g., control or no treatment). In a preferred embodiment, a peptide fragment of NCOA4 inhibits the interaction between NCOA4 and FTH1. In some embodiments, a peptide fragment of NCOA4 inhibits the interaction between NCOA4 and FTH1, e.g., by at least 1.5-fold, at least 2-fold, at least 3-fold, at least 4-fold, at least 5-fold, at least 10-fold, at least 50-fold, at least 100-fold, or more, relative to a starting level of interaction (e.g., control or no treatment).

As used herein, a "peptide fragment of ferritin" that is an inhibitor of the interaction between NCOA4 and ferritin, is capable of reducing the binding of NCOA4 to one or both of the heavy and light chains of ferritin (FTH1 and FTL, respectively), e.g., by at least 1.5-fold, at least 2-fold, at least 3-fold, at least 4-fold, at least 5-fold, at least 10-fold, at least 50-fold, at least 100-fold, or more, relative to a starting level of interaction (e.g., control or no treatment).

Each of the above-disclosed peptide fragments is contemplated for use herein as a composition or formulation.

A "decreased recruitment of NCOA4/ferritin complexes to autophagosomes" can be detected in vitro techniques known in the art, e.g., by Western blot, using antibodies specific for NCOA4 and/or ferritin.

As discussed above, "conservative amino acid substitutions" are well-known in the art and may be made generally without altering the biological activity of the resulting polypeptide (e.g., a peptide fragment of NCOA4, e.g., SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, or SEQ ID NO: 11; or a peptide fragment of FTH1, e.g., amino acids 16- 34 of SEQ ID NO: 6, amino acids 103-125 of SEQ ID NO: 6; or amino acids 78-88 of SEQ ID NO: 6). For example, such substitutions are generally made by interchanging within the groups of polar residues, charged residues, hydrophobic residues, small residues, and the like. Conservative substitutions are described above. If necessary, such substitutions may be determined empirically merely by testing the resulting modified protein for the ability to bind to and/or interact with the appropriate ligand (e.g., ferritin and/or a ATG8 paralog and/or HERC2) in in vitro biological assays (e.g., immunoassays, such as immunoprecipitation and Western blot). In some embodiments, a peptide disclosed herein (e.g., a peptide comprising SEQ ID NO:l, 2 or 3) has no more than than 30, no more than 25, no more than 20, no more than 15, no more than 10, no more than 9, no more than 8, no more than 7, no more than 6, no more than 5, no more than 4, no more than 3, no more than 2, or no more than 1 conservative amino acid substitutions. All that is required is that: (i) such variants of NCOA4 or fragments thereof have at least 25% (e.g., at least: 30%; 40%; 50%; 60%; 70%; 75%; 80%; 85%; 90%; 95%; 97%; 98%; 99%; 99.5%, or 100% or even greater) of the ability of wild-type, full-length, NCOA4 to bind to ferritin; (ii) such variants of NCOA4 or fragments thereof have at least 25% (e.g., at least: 30%; 40%; 50%; 60%; 70%; 75%; 80%; 85%; 90%; 95%; 97%; 98%; 99%; 99.5%, or 100% or even greater) of the ability of wild-type, full- length, NCOA4 to bind to bind to wild-type HERC2; and/or (iii) such variants of NCOA4 have at least 25% (e.g., at least: 30%; 40%; 50%; 60%; 70%; 75%; 80%; 85%; 90%; 95%; 97%; 98%; 99%; 99.5%, or 100% or even greater) of the ability of the relevant wild-type, full-length NCOA4 protein to bind to wild-type GABARAPL2 or

microtubule-associated proteins 1 A/IB light chain 3A (LC3). Moreover, all that is required is that such variants of FTH1 or fragments thereof have at least 25% (e.g., at least: 30%; 40%; 50%; 60%; 70%; 75%; 80%; 85%; 90%; 95%; 97%; 98%; 99%; 99.5%, or 100% or even greater) of the ability of wild-type, full-length, FTH1 to bind to

NCOA4.

As used herein, the term "delivering to the interior of the cell", e.g., of an agent, means causing an agent (e.g., antibody, intrabody, peptide fragment, polypeptide, small molecule, antisense oligonucleotide, etc.) to pass through and/or be transported through the outer cell membrane into at least the cytosol of the cell.

As used herein, a "NCOA4 reagent" contains, comprises or is: (a) full-length, wild-type NCOA4; (b) a functional fragment of NCOA4; or (c) (a) or (b) but with not more than 20 conservative substitutions (see above). In addition, "NCOA4 reagents" can include with (a), (b), or (c), internal or terminal (C or N) irrelevant amino acid sequences (e.g., sequences derived from other proteins or synthetic sequences not corresponding to any naturally occurring protein). The sequences can be, for example, an antigenic tag (e.g., FLAG, polyhistidine, hemagluttanin (HA), glutathione-S-transferase (GST), or maltose-binding protein (MBP)). Heterologous sequences can also be proteins useful as diagnostic or detectable markers, for example, luciferase, green fluorescent protein (GFP), or chloramphenicol acetyl transferase (CAT). Heterologous sequences can be of varying length and, in some cases, can be a longer sequence than the NCOA4 polypeptide. Generally, the heterologous sequences are about 1- 50 (e.g., two, four, eight, ten, 15, 20, 25, 30, 35, 40, or 45) amino acids in length. NCOA4 reagents, other than full-length, wild-type NCOA4, have at least 25% (e.g., at least 30%, at least 35%, at least 40%, at least 50%, at least 55%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, at least 99%, at least 99.5%, or 100% or more) of the ability of the full-length, wild-type, NCOA4 to bind to either or both of the heavy and light chain of ferritin and/or to an ATG8 paralog reagent (described below) and/or to a HERC2 reagent (described below).

As used herein, a "ferritin reagent", e.g., for the screening assays disclosed herein, include, e.g., (a) full-length, wild-type ferritin; (b) a functional fragment of ferritin; or (c) (a) or (b) but with not more than 20 conservative substitutions, apo-ferritin from human liver or equine spleen or produced recombinantly in E. coli as FTH1, FTL, or a combination of FTH1 and FTL. In functional fragments of ferritin, there can be, for example, a full length FTH1 and a fragment of FTL, a fragment of FTH1 and full length FTL, a fragment of full length of either FTH1 or FTL, or a fragment of both FTH1 and FTL. Ferritin reagents, other than full-length, wild-type, ferritin, have at least 25% (e.g., at least 30%, at least 35%, at least 40%, at least 50%, at least 55%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, at least 99%, at least 99.5%, or 100% or more) of the ability of the full-length wild-type ferritin to bind to NCOA4 (e.g., to SEQ ID NO: 11, SEQ ID NO: 1, or SEQ ID NO:2 in NCOA4). In addition, "ferritin reagents" can also include internal or terminal (C or N) irrelevant amino acid sequences (e.g., sequences derived from other proteins or synthetic sequences not corresponding to any naturally occurring protein) as described above for NCOA4 polypeptides.

As used herein, a "ATG8 paralog reagent," e.g., for the screening assays disclosed herein, include, e.g., (a) full-length, wild-type ATG8 paralog (e.g., GABARAPL2 or LC3); (b) a functional fragment of an ATG8 paralog; or (c) (a) or (b) but with not more than 10 conservative substitutions. The ATG8 paralog can be a recombinantly expressed protein from E .coli. ATG8 paralog reagents, other than a full-length, wild-type ATG8 paralog, have at least 25% (e.g., at least 30%>, at least 35%, at least 40%>, at least 50%>, at least 55%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, at least 99%, at least 99.5%, or 100% or more) of the ability of the full-length wild- type ATG8 paralog to bind to NCOA4. In addition, "ATG8 paralog reagents" can also include internal or terminal (C or N) irrelevant amino acid sequences (e.g., sequences derived from other proteins or synthetic sequences not corresponding to any naturally occurring protein) as described above for NCOA4 polypeptides.

As used herein, a "HERC2 reagent," e.g., for the screening assays disclosed herein, include, e.g., (a) full-length, wild-type HERC2; (b) a functional fragment of HERC2; or (c) (a) or (b) but with not more than 10 conservative substitutions. The

HERC2 can be a recombinantly expressed protein from E .coli. HERC2 reagents, other than a full-length, wild-type HERC2 (e.g., human HERC2), have at least 25% (e.g., at least 30%, at least 35%, at least 40%, at least 50%, at least 55%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, at least 99%, at least 99.5%, or 100% or more) of the ability of the full-length wild-type HERC2 to bind to NCO A4. HERC2 reagents have the ability to bind to SEQ ID NO: 3 in NCOA4. In addition, "HERC2 reagents" can also include internal or terminal (C or N) irrelevant amino acid sequences (e.g., sequences derived from other proteins or synthetic sequences not corresponding to any naturally occurring protein) as described above for NCOA4 polypeptides.

As used herein, the term "subject" means any animal, including any vertebrate, including any mammal, and, in particular, a human, and can also be referred to, e.g., as an individual or patient. Anon-human mammal can be, for example, without limitation a non-human primate (such as a monkey, baboon, gorilla, or orangutan), a bovine animal, a horse, a whale, a dolphin, a sheep, a goat, a pig, a dog, a feline animal (such as a cat), a rabbit, a guinea pig, a hamster, a gerbil, a rat, or a mouse. Non-mammalian vertebrates include without limitation, a bird, a reptile, or a fish.

As used herein, "reducing" means any level of reduction up to and including full inhibition.

As used herein, a "subject in need of increased erythropoiesis" can be, for example and without limitation, a subject who has a low red blood cell count, anemia, and/or excessive blood loss.

The term "nucleic acid hybridization" refers to the pairing of complementary strands of nucleic acids. The mechanism of pairing involves hydrogen bonding, which may be Watson-Crick, Hoogsteen or reversed Hoogsteen hydrogen bonding, between complementary nucleoside or nucleotide bases (nucleobases) of the strands of nucleic acids. For example, adenine and thymine are complementary nucleobases that pair through the formation of hydrogen bonds. Hybridization can occur under varying circumstances. Nucleic acid molecules are "hybridizable" to each other when at least one strand of one nucleic acid molecule can form hydrogen bonds with the complementary bases of another nucleic acid molecule under defined stringency conditions. Stringency of hybridization is determined, e.g., by (i) the temperature at which hybridization and/or washing is performed, and (ii) the ionic strength and (iii) concentration of denaturants such as formamide of the hybridization and washing solutions, as well as other parameters. Hybridization requires that the two strands contain substantially

complementary sequences. Depending on the stringency of hybridization, however, some degree of mismatches may be tolerated. Under "low stringency" conditions, a greater percentage of mismatches are tolerable (i.e., will not prevent formation of an anti-parallel hybrid). See Molecular Biology of the Cell, Alberts et al., 3rd ed., New York and London: Garland Publ, 1994, Ch. 7.

Typically, hybridization of two strands at high stringency requires that the sequences exhibit a high degree of complementarity over an extended portion of their length. Examples of high stringency conditions include: hybridization to filter-bound DNA in 0.5 M NaHP04, 7% SDS, 1 mM EDTA at 65°C, followed by washing in O.lx SSC/0.1% SDS (where lx SSC is 0.15 M NaCl, 0.15 M Na citrate) at 68°C or for oligonucleotide (oligo) inhibitors washing in 6xSSC/0.5% sodium pyrophosphate at about 37°C (for 14 nucleotide-long oligos), at about 48°C (for about 17 nucleotide-long oligos), at about 55°C (for 20 nucleotide-long oligos), and at about 60°C (for 23 nucleotide-long oligos).

Conditions of intermediate or moderate stringency (such as, for example, an aqueous solution of 2xSSC at 65°C; alternatively, for example, hybridization to filter- bound DNA in 0.5 M NaHP04, 7% SDS, 1 mM EDTA at 65°C followed by washing in 0.2 x SSC/0.1% SDS at 42°C) and low stringency (such as, for example, an aqueous solution of 2xSSC at 55°C), require correspondingly less overall complementarity for hybridization to occur between two sequences. Specific temperature and salt conditions for any given stringency hybridization reaction depend on the concentration of the target DNA or RNA molecule and length and base composition of the probe, and are normally determined empirically in preliminary experiments, which are routine (see Southern, J. Mol. Biol. 1975;98:503; Sambrook et al, Molecular Cloning: A Laboratory Manual, 2nd ed., vol. 2, ch. 9.50, CSH Laboratory Press, 1989; Ausubel et al. (eds.), 1989, Current Protocols in Molecular Biology, Vol. I, Green Publishing Associates, Inc., and John Wiley & Sons, Inc., New York, at p. 2.10.3). An extensive guide to the hybridization of nucleic acids is found in, e.g., Tijssen (1993) Laboratory Techniques in Biochemistry and Molecular Biology—Hybridization with Nucleic Acid Probes part I, chapt 2, "Overview of principles of hybridization and the strategy of nucleic acid probe assays," Elsevier, N.Y. ("Tijssen").

As used herein, the term "standard hybridization conditions" refers to

hybridization conditions that allow hybridization of two nucleotide molecules having at least 50% sequence identity. According to a specific embodiment, hybridization conditions of higher stringency may be used to allow hybridization of only sequences having at least 75% sequence identity, at least 80%> sequence identity, at least 85%> sequence identity, at least 90%> sequence identity, at least 95% sequence identity, or at least 99%) sequence identity.

As used herein, the phrase "under hybridization conditions" means under conditions that facilitate specific hybridization of a nucleic acid sequence to a complementary sequence. The terms "hybridizing specifically to" and "specific hybridization" and "selectively hybridize to," as used herein refer to the binding, duplexing, or hybridizing of a nucleic acid molecule preferentially to a particular nucleotide sequence under at least moderately stringent conditions, and preferably, highly stringent conditions, as discussed above.

"Polypeptide" and "protein" are used interchangeably and mean any peptide- linked chain of amino acids, regardless of length or post-translational modification.

As used herein, the term "nucleic acid" or "oligonucleotide" refers to a deoxyribonucleotide or ribonucleotide in either single- or double-stranded form. The term also encompasses nucleic-acid- like structures with synthetic backbones. DNA backbone analogues provided by the invention include phosphodiester, phosphorothioate, phosphorodithioate, methylphosphonate, phosphoramidate, alkyl phosphotriester, sulfamate, 3'-thioacetal, methylene(methylimino), 3'-N-carbamate, morpholino carbamate, and peptide nucleic acids (PNAs); see Oligonucleotides and Analogues, a Practical Approach, edited by F. Eckstein, IRL Press at Oxford University Press (1991); Antisense Strategies, Annals of the New York Academy of Sciences, Volume 600, Eds. Baserga and Denhardt (NYAS 1992); Milligan (1993) J. Med. Chem. 36: 1923-1937; Antisense Research and Applications (1993, CRC Press). PNAs contain non-ionic backbones, such as N-(2-aminoethyl) glycine units. Phosphorothioate linkages are described in WO 97/03211; WO 96/39154; Mata (1997) Toxicol. Appl. Pharmacol. 144: 189-197. Other synthetic backbones encompassed by the term include methyl- phosphonate linkages or alternating methylphosphonate and phosphodiester linkages (Strauss-Soukup (1997) Biochemistry 36:8692-8698), and benzylphosphonate linkages (Samstag (1996) Antisense Nucleic Acid Drug Dev 6: 153-156). The term nucleic acid is used interchangeably with cDNA, cRNA, mRNA, oligonucleotide, probe and amplification product.

In certain embodiments, it is desirable to determine (e.g., assay, measure, approximate) the level (e.g., expression or activity), e.g., one of the above-identified markers. The expression level of such markers may be determined according to any suitable method known in the art. A non-limiting example of such a method includes real-time PCR (RT-PCR), e.g., quantitative RT-PCR (QPCR), which measures the expression level of the mRNA encoding the polypeptide. Real-time PCR evaluates the level of PCR product accumulation during amplification. RNA (or total genomic DNA for detection of germline mutations) is isolated from a sample. RT-PCR can be performed, for example, using a Perkin Elmer/ Applied Biosystems (Foster City, Calif.) 7700 Prism instrument. Matching primers and fluorescent probes can be designed for genes of interest using, based on the genes' nucleic acid sequences (e.g., as described above), for example, the primer express program provided by Perkin Elmer/ Applied Biosystems (Foster City, Calif). Optimal concentrations of primers and probes can be initially determined by those of ordinary skill in the art, and control (for example, beta- actin) primers and probes may be obtained commercially from, for example, Perkin Elmer/ Applied Biosystems (Foster City, Calif).

To quantitate the amount of the specific nucleic acid of interest in a sample, a standard curve is generated using a control. Standard curves may be generated using the Ct values determined in the real-time PCR, which are related to the initial concentration of the nucleic acid of interest used in the assay. Standard dilutions ranging from 10-10 ⁶ copies of the gene of interest are generally sufficient. In addition, a standard curve is generated for the control sequence. This permits standardization of initial content of the nucleic acid of interest in a tissue sample to the amount of control for comparison purposes. Methods of QPCR using TaqMan probes are well known in the art. Detailed protocols for QPCR are provided, for example, for RNA in: Gibson et al, 1996, Genome Res., 10:995-1001; and for DNA in: Heid et al, 1996, Genome Res., 10:986-994; and in Innis et al. (1990) Academic Press, Inc. N.Y.

Expression of mRNA, as well as expression of peptides and other biological factors can also be determined using microarray, methods for which are well known in the art [see, e.g., Watson et al. Curr Opin Biotechnol (1998) 9: 609-14; "DNA microarray technology: Devices, Systems, and Applications" Annual Review of Biomedical

Engineering; Vol. 4: 129-153 (2002); Chehab et al. (1989) "Detection of specific DNA sequences by fluorescence amplification: a color complementation assay" Proc. Natl. Acad. Sci. USA, 86: 9178-9182; Lockhart et al. (1996) "Expression monitoring by hybridization to high-density oligonucleotide arrays" Nature Biotechnology, 14: 1675- 1680; and M. Schena et al. (1996) "Parallel human genome analysis: Microarray-based expression monitoring of 1000 genes" Proc. Natl. Acad. Sci. USA, 93: 10614-10619; Peptide Microarrays Methods and Protocols; Methods in Molecular Biology; Volume 570, 2009, Humana Press; and Small Molecule Microarrays Methods and Protocols; Series: Methods in Molecular Biology, Vol. 669, Uttamchandani, Mahesh; Yao, Shao Q. (Eds.) 2010, 2010, Humana Press]. For example, mRNA expression profiling can be performed to identify differentially expressed genes, wherein the raw intensities determined by microarray are log2-transformed and quantile normalized and gene set enrichment analysis (GSEA) is performed according, e.g., to Subramanian et al. (2005) Proc Natl Acad Sci USA 102:15545-15550).

Other suitable amplification methods include, but are not limited to ligase chain reaction (LCR) (see Wu and Wallace (1989) Genomics 4:560, Landegren et al. (1988) Science 241 : 1077, and Barringer et al. (1990) Gene 89: 117), transcription amplification (Kwoh et al. (1989) Proc. Natl. Acad. Sci. USA 86: 1173), self-sustained sequence replication (Guatelli et al. (1990) Proc. Nat. Acad. Sci. USA 87: 1874), dot PCR, and linker adapter PCR, etc. In another embodiment, DNA sequencing may be used to determine the presence of ER in a genome. Methods for DNA sequencing are known to those of skill in the art.

Other methods for detecting gene expression (e.g., mRNA levels) include Serial Analysis of Gene Expression applied to high-throughput sequencing (SAGEseq), as described in Wu ZJ et al. Genome Res. 2010 Dec;20(12): 1730-9. 2.

Methods for detecting the expression levels of polypeptides are also known in the art. Non-limiting examples of suitable methods for detecting expression levels of gene products (i.e., polypeptides) described herein include, e.g., flow cytometry,

immunoprecipitation, Western blot (see, e.g., Battle TE, Arbiser J, & Frank DA (2005) The natural product honokiol induces caspase-dependent apoptosis in B-cell chronic lymphocytic leukemia (B-CLL) cells. Blood 106(2):690-697), ELISA (enzyme-linked immunosorbent assay) and/or immunohistochemistry.

Antisense Nucleic Acids

Antisense oligonucleotides can be used to inhibit the expression of a target polypeptide of the invention (e.g., NCOA4, HERC2, an ATG8 paralog, etc). Antisense oligonucleotides typically are about 5 nucleotides to about 30 nucleotides in length, about 10 to about 25 nucleotides in length, or about 20 to about 25 nucleotides in length. For a general discussion of antisense technology, see, e.g., Antisense DNA and RNA, (Cold Spring Harbor Laboratory, D. Melton, ed., 1988).

Appropriate chemical modifications of the inhibitors are made to ensure stability of the antisense oligonucleotide, as described below. Changes in the nucleotide sequence and/or in the length of the antisense oligonucleotide can be made to ensure maximum efficiency and thermodynamic stability of the inhibitor. Such sequence and/or length modifications are readily determined by one of ordinary skill in the art.

The antisense oligonucleotides can be DNA or RNA or chimeric mixtures, or derivatives or modified versions thereof, and can be single-stranded or double-stranded. Thus, for example, in the antisense oligonucleotides set forth in herein, when a sequence includes thymidine residues, one or more of the thymidine residues may be replaced by uracil residues and, conversely, when a sequence includes uracil residues, one or more of the uracil residues may be replaced by thymidine residues.

Antisense oligonucleotides comprise sequences complementary to at least a portion of the corresponding target polypeptide. However, 100% sequence

complementarity is not required so long as formation of a stable duplex (for single stranded antisense oligonucleotides) or triplex (for double stranded antisense

oligonucleotides) can be achieved. The ability to hybridize will depend on both the degree of complementarity and the length of the antisense oligonucleotides. Generally, the longer the antisense oligonucleotide, the more base mismatches with the

corresponding nucleic acid target can be tolerated. One skilled in the art can ascertain a tolerable degree of mismatch by use of standard procedures to determine the melting point of the hybridized complex.

Antisense nucleic acid molecules can be encoded by a recombinant gene for expression in a cell (see, e.g., U.S. Patent Nos. 5,814,500 and 5,811,234), or alternatively they can be prepared synthetically (see, e.g., U.S. Patent No. 5,780,607).

The antisense oligonucleotides can be modified at the base moiety, sugar moiety, or phosphate backbone, or a combination thereof. In one embodiment, the antisense oligonucleotide comprises at least one modified sugar moiety, e.g., a sugar moiety such as arabinose, 2-fluoroarabinose, xylulose, and hexose.

In another embodiment, the antisense oligonucleotide comprises at least one modified phosphate backbone such as a phosphorothioate, a phosphorodithioate, a phosphoramidothioate, a phosphoramidate, a phosphordiamidate, a methylphosphonate, an alkyl phosphotriester, and a formacetal or analog thereof. Examples include, without limitation, phosphorothioate antisense oligonucleotides (e.g., an antisense oligonucleotide phosphothioate modified at 3' and 5' ends to increase its stability) and chimeras between methylphosphonate and phosphodiester oligonucleotides. These oligonucleotides provide good in vivo activity due to solubility, nuclease resistance, good cellular uptake, ability to activate RNase H, and high sequence selectivity.

Other examples of synthetic antisense oligonucleotides include oligonucleotides that contain phosphorothioates, phosphotriesters, methyl phosphonates, short chain alkyl, or cycloalkyl intersugar linkages or short chain heteroatomic or heterocyclic intersugar linkages. Most preferred are those with CH2-NH-0-CH2, CH2-N(CH3)-0-CH2, CH2-0- N(CH3)-CH2, CH2-N(CH3)-N(CH3)-CH2 and 0-N(CH3)-CH2-CH2 backbones (where phosphodiester is 0-P02-0-CH2). U.S. Patent No. 5,677,437 describes heteroaromatic oligonucleoside linkages. Nitrogen linkers or groups containing nitrogen can also be used to prepare oligonucleotide mimics (U.S. Patent Nos. 5,792,844 and 5,783,682). U.S.

Patent No. 5,637,684 describes phosphoramidate and phosphorothioamidate oligomeric compounds.

In other embodiments, such as the peptide-nucleic acid (PNA) backbone, the phosphodiester backbone of the oligonucleotide may be replaced with a polyamide backbone, the bases being bound directly or indirectly to the aza nitrogen atoms of the polyamide backbone (Nielsen et al., Science 1991;254: 1497). Other synthetic

oligonucleotides may contain substituted sugar moieties comprising one of the following at the 2' position: OH, SH, SCH3, F, OCN, 0(CH2)nNH2 or 0(CH2)nCH3 where n is from 1 to about 10; CI to CIO lower alkyl, substituted lower alkyl, alkaryl or aralkyl; CI; Br; CN; CF3; OCF3; 0-; S-, or N-alkyl; 0-, S-, or N-alkenyl; SOCH3; S02CH3; ON02; N02; N3; NH2; heterocycloalkyl; heterocycloalkaryl; aminoalkylamino; polyalkylamino; substituted sialyl; a fluorescein moiety; an RNA cleaving group; a reporter group; an intercalator; a group for improving the pharmacokinetic properties of an oligonucleotide; or a group for improving the pharmacodynamic properties of an oligonucleotide, and other substituents having similar properties.

Oligonucleotides may also have sugar mimetics such as cyclobutyls or other carbocyclics in place of the pentofuranosyl group. Nucleotide units having nucleosides other than adenosine, cytidine, guanosine, thymidine and uridine may be used, such as inosine. In other embodiments, locked nucleic acids (LNA) can be used (reviewed in, e.g., Jepsen and Wengel, Curr. Opin. Drug Discov. Devel. 2004; 7: 188-194; Crinelli et al, Curr. Drug Targets 2004; 5:745-752). LNA are nucleic acid analog(s) with a 2'-0, 4'-C methylene bridge. This bridge restricts the flexibility of the ribofuranose ring and locks the structure into a rigid C3-endo conformation, conferring enhanced hybridization performance and exceptional biostability. LNA allows the use of very short

oligonucleotides (less than 10 bp) for efficient hybridization in vivo. In one embodiment, an antisense oligonucleotide can comprise at least one modified base moiety such as a group including but not limited to 5-fluorouracil, 5- bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xantine, 4-acetylcytosine, 5- (carboxyhydroxylmethyl) uracil, 5-carboxymethylaminomethyl-2-thiouridine, 5- carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylqueosine, inosine, N6-isopentenyladenine, 1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2- methyladenine, 2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-adenine, 7- methylguanine, 5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil, beta- D-mannosylqueosine, 5-methoxycarboxymethyluracil, 5-methoxyuracil, 2-methylthio- N6-isopentenyladenine, uracil-5-oxyacetic acid (v), pseudouracil, queosine, 2- thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil, uracil-5- oxyacetic acid methylester, uracil-5-oxyacetic acid (v), 5-methyl-2-thiouracil, 3-(3- amino-3-N-2-carboxypropyl) uracil, (acp3)w, and 2,6-diaminopurine.

In another embodiment, the antisense oligonucleotide can include a-anomeric oligonucleotides. An a-anomeric oligonucleotide forms specific double-stranded hybrids with complementary RNA in which, contrary to the usual β-units, the strands run parallel to each other (Gautier et al, Nucl. Acids Res. 1987; 15:6625-6641).

Oligonucleotides may have morpholino backbone structures (U.S. Pat. No.

5,034,506). Thus, in yet another embodiment, the antisense oligonucleotide can be a morpholino antisense oligonucleotide (i.e., an oligonucleotide in which the bases are linked to 6-membered morpholine rings, which are connected to other morpholine-linked bases via non-ionic phosphorodiamidate intersubunit linkages). Morpholino

oligonucleotides are highly resistant to nucleases and have good targeting predictability, high in-cell efficacy and high sequence specificity (U.S. Patent No. 5,034,506;

Summerton, Biochim. Biophys. Acta 1999; 1489: 141-158; Summerton and Weller, Antisense Nucleic Acid Drug Dev. 1997; 7: 187-195; Arora et al, J. Pharmacol. Exp. Ther. 2000;292:921-928; Qin et al, Antisense Nucleic Acid Drug Dev. 2000; 10: 11-16; Heasman et al, Dev. Biol. 2000; 222: 124-134; Nasevicius and Ekker, Nat. Genet. 2000; 26:216-220).

Antisense oligonucleotides may be chemically synthesized, for example using appropriately protected ribonucleoside phosphoramidites and a conventional DNA/RNA synthesizer. Antisense nucleic acid oligonucleotides can also be produced intracellularly by transcription from an exogenous sequence. For example, a vector can be introduced in vivo such that it is taken up by a cell within which the vector or a portion thereof is transcribed to produce an antisense RNA. Such a vector can remain episomal or become chromosomally integrated, so long as it can be transcribed to produce the desired antisense RNA. Such vectors can be constructed by recombinant DNA technology methods standard in the art. Vectors can be plasmid, viral, or others known in the art, used for replication and expression in mammalian cells. In another embodiment, "naked" antisense nucleic acids can be delivered to adherent cells via "scrape delivery", whereby the antisense oligonucleotide is added to a culture of adherent cells in a culture vessel, the cells are scraped from the walls of the culture vessel, and the scraped cells are transferred to another plate where they are allowed to re-adhere. Scraping the cells from the culture vessel walls serves to pull adhesion plaques from the cell membrane, generating small holes that allow the antisense oligonucleotides to enter the cytosol.

RNAi

Reversible short inhibition of a target polypeptide (e.g., NCOA4, HERC2, or an ATG8 paralog) of the invention may also be useful. Such inhibition can be achieved by use of siRNAs. RNA interference (RNAi) technology prevents the expression of genes by using small RNA molecules such as small interfering RNAs (siRNAs). This technology in turn takes advantage of the fact that RNAi is a natural biological mechanism for silencing genes in most cells of many living organisms, from plants to insects to mammals (McManus et al, Nature Reviews Genetics, 2002, 3(10) p. 737). RNAi prevents a gene from producing a functional protein by ensuring that the molecule intermediate, the messenger RNA copy of the gene is destroyed siRNAs can be used in a naked form and incorporated in a vector, as described below.

RNA interference (RNAi) is a process of sequence-specific post-transcriptional gene silencing by which double stranded RNA (dsRNA) homologous to a target locus can specifically inactivate gene function in plants, fungi, invertebrates, and vertebrates, including mammals (Hammond et al. , Nature Genet. 2001 ;2 : 110- 119; Sharp, Genes Dev. 1999;13: 139-141). This dsRNA-induced gene silencing is mediated by short double-

so stranded small interfering RNAs (siRNAs) generated from longer dsRNAs by

ribonuclease III cleavage (Bernstein et al, Nature 2001; 409:363-366 and Elbashir et al., Genes Dev. 2001; 15: 188-200). RNAi-mediated gene silencing is thought to occur via sequence-specific RNA degradation, where sequence specificity is determined by the interaction of an siRNA with its complementary sequence within a target RNA (see, e.g., Tuschl, Chem. Biochem. 2001; 2:239-245).

For mammalian systems, RNAi commonly involves the use of dsRNAs that are greater than 500 bp; however, it can also be activated by introduction of either siRNAs (Elbashir, et al, Nature 2001; 411 : 494-498) or short hairpin RNAs (shRNAs) bearing a fold back stem-loop structure (Paddison et al, Genes Dev. 2002; 16: 948-958; Sui et al, Proc. Natl. Acad. Sci. USA 2002; 99:5515-5520; Brummelkamp et al, Science 2002; 296:550-553; Paul et al, Nature Biotechnol. 2002; 20:505-508).

The siRNAs are preferably short double stranded nucleic acid duplexes comprising annealed complementary single stranded nucleic acid molecules. Preferably, the siRNAs are short dsRNAs comprising annealed complementary single strand RNAs. siRNAs may also comprise an annealed RNA:DNA duplex, wherein the sense strand of the duplex is a DNA molecule and the antisense strand of the duplex is a RNA molecule.

Preferably, each single stranded nucleic acid molecule of the siRNA duplex is of from about 19 nucleotides to about 27 nucleotides in length. In preferred embodiments, duplexed siRNAs have a 2 or 3 nucleotide 3' overhang on each strand of the duplex. In preferred embodiments, siRNAs have 5 '-phosphate and 3'-hydroxyl groups.

RNAi molecules may include one or more modifications, either to the phosphate- sugar backbone or to the nucleoside. For example, the phosphodiester linkages of natural RNA may be modified to include at least one heteroatom other than oxygen, such as nitrogen or sulfur. In this case, for example, the phosphodiester linkage may be replaced by a phosphothioester linkage. Similarly, bases may be modified to block the activity of adenosine deaminase. Where the RNAi molecule is produced synthetically, or by in vitro transcription, a modified ribonucleoside may be introduced during synthesis or transcription. The skilled artisan will understand that many of the modifications described above for antisense oligonucleotides may also be made to RNAi molecules. Such modifications are well known in the art. siRNAs may be introduced to a target cell as an annealed duplex siRNA, or as single stranded sense and antisense nucleic acid sequences that, once within the target cell, anneal to form the siRNA duplex. Alternatively, the sense and antisense strands of the siRNA may be encoded on an expression construct that is introduced to the target cell. Upon expression within the target cell, the transcribed sense and antisense strands may anneal to reconstitute the siRNA.

shRNAs typically comprise a single stranded "loop" region connecting

complementary inverted repeat sequences that anneal to form a double stranded "stem" region. Structural considerations for shRNA design are discussed, for example, in

McManus et al, RNA 2002;8:842-850. In certain embodiments the shRNA may be a portion of a larger RNA molecule, e.g., as part of a larger RNA that also contains U6 RNA sequences (Paul et al, supra).

In preferred embodiments, the loop of the shRNA is from about 1 to about 9 nucleotides in length. In preferred embodiments the double stranded stem of the shRNA is from about 19 to about 33 base pairs in length. In preferred embodiments, the 3' end of the shRNA stem has a 3' overhang. In particularly preferred embodiments, the 3' overhang of the shRNA stem is from 1 to about 4 nucleotides in length. In preferred embodiments, shRNAs have 5 '-phosphate and 3'-hydroxyl groups.

Non- limiting examples of shRNA molecules that can be used according to the methods disclosed herein include, e.g., siRNA against NCOA4,e.g., shNCOA4-l : 5'

CCCAGGAAGTATTACTTAATT 3' (TRCNOOOOO 19724) (SEQ ID NO: 12), shNCOA4- 2: 5' GCTGGCAAAC AGAAGTTTAAA 3 ' (TRCNOOOOO 19726) (SEQ ID NO: 13), siNCOA4-l : 5' ACAAAGAUCUAGCCAAUCA 3' (SEQ ID NO: 15) and siNCOA4-2: 5' GACCUUAUUUAUCAGCUUA 3' (SEQ ID NO: 16), and siRNA against HERC2 (Gene ID: 8924, NM 004667.5), e.g., siHERC2-l : 5' GCACAGAGUAUCACAGGUA 3' (SEQ ID NO: 17) and siHERC2-2: 5' CGAUGAAGGUUUGGUAUUU 3' (SEQ ID NO: 18).

Although RNAi molecules preferably contain nucleotide sequences that are fully complementary to a portion of the target nucleic acid, 100% sequence complementarity between the RNAi probe and the target nucleic acid is not required. Similar to the above-described antisense oligonucleotides, RNAi molecules can be synthesized by standard methods known in the art, e.g., by use of an automated synthesizer. RNAs produced by such methodologies tend to be highly pure and to anneal efficiently to form siRNA duplexes or shRNA hairpin stem- loop structures. Following chemical synthesis, single stranded RNA molecules are deprotected, annealed to form siRNAs or shRNAs, and purified (e.g., by gel electrophoresis or HPLC). Alternatively, standard procedures may be used for in vitro transcription of RNA from DNA templates carrying RNA polymerase promoter sequences (e.g., T7 or SP6 RNA polymerase promoter sequences). Efficient in vitro protocols for preparation of siRNAs using T7 RNA polymerase have been described (Donze and Picard, Nucleic Acids Res. 2002; 30:e46; and Yu et al, Proc. Natl. Acad. Sci. USA 2002; 99:6047-6052). Similarly, an efficient in vitro protocol for preparation of shRNAs using T7 RNA polymerase has been described (Yu et al, supra). The sense and antisense transcripts may be synthesized in two independent reactions and annealed later, or may be synthesized simultaneously in a single reaction.

RNAi molecules may be formed within a cell by transcription of RNA from an expression construct introduced into the cell. For example, both a protocol and an expression construct for in vivo expression of siRNAs are described in Yu et al, supra. The delivery of siRNA to tumors can potentially be achieved via any of several gene delivery "vehicles" that are currently available. These include viral vectors, such as adenovirus, lentivirus, herpes simplex virus, vaccinia virus, and retrovirus, as well as chemical-mediated gene delivery systems (for example, liposomes), or mechanical DNA delivery systems (DNA guns). The oligonucleotides to be expressed for such siRNA- mediated inhibition of gene expression would be between 18 and 28 nucleotides in length. Protocols and expression constructs for in vivo expression of shRNAs have been described (Brummelkamp et al, Science 2002; 296:550-553; Sui et al, supra; Yu et al, supra; McManus et al, supra; Paul et al, supra).

The expression constructs for in vivo production of RNAi molecules comprise RNAi encoding sequences operably linked to elements necessary for the proper transcription of the RNAi encoding sequence(s), including promoter elements and transcription termination signals. Preferred promoters for use in such expression constructs include the polymerase-III HI -RNA promoter (see, e.g., Brummelkamp et al., supra) and the U6 polymerase-III promoter (see, e.g., Sui et al, supra; Paul, et al. supra; and Yu et al., supra). The RNAi expression constructs can further comprise vector sequences that facilitate the cloning of the expression constructs. Standard vectors are known in the art (e.g., pSilencer 2.0-U6 vector, Ambion Inc., Austin, TX).

Ribozyme Inhibition

The level of expression of a target polypeptide of the invention can also be inhibited by ribozymes designed based on the nucleotide sequence thereof.

Ribozymes are enzymatic RNA molecules capable of catalyzing the sequence- specific cleavage of RNA (for a review, see Rossi, Current Biology 1994;4:469-471). The mechanism of ribozyme action involves sequence-specific hybridization of the ribozyme molecule to complementary target RNA, followed by an endonucleolytic cleavage event. The composition of ribozyme molecules must include: (i) one or more sequences complementary to the target RNA; and (ii) a catalytic sequence responsible for RNA cleavage (see, e.g., U.S. Patent No. 5,093,246).

The use of hammerhead ribozymes is preferred. Hammerhead ribozymes cleave RNAs at locations dictated by flanking regions that form complementary base pairs with the target RNA. The sole requirement is that the target RNA has the following sequence of two bases: 5'-UG-3'. The construction of hammerhead ribozymes is known in the art, and described more fully in Myers, Molecular Biology and Biotechnology: A

Comprehensive Desk Reference, VCH Publishers, New York, 1995 (see especially Figure 4, page 833) and in Haseloff and Gerlach, Nature 1988; 334:585-591.

As in the case of antisense oligonucleotides, ribozymes can be composed of modified oligonucleotides (e.g., for improved stability, targeting, etc.). These can be delivered to cells which express the target polypeptide in vivo. A preferred method of delivery involves using a DNA construct "encoding" the ribozyme under the control of a strong constitutive pol III or pol II promoter, so that transfected cells will produce sufficient quantities of the ribozyme to catalyze cleavage of the target mRNA encoding the target polypeptide. However, because ribozymes, unlike antisense molecules, are catalytic, a lower intracellular concentration may be required to achieve an adequate level of efficacy.

Ribozymes can be prepared by any method known in the art for the synthesis of DNA and RNA molecules, as discussed above. Ribozyme technology is described further in Intracellular Ribozyme Applications: Principals and Protocols, Rossi and Couture eds., Horizon Scientific Press, 1999.

Triple Helix Forming Oligonucleotides (TFOs)

Nucleic acid molecules useful to inhibit expression level of a target polypeptide of the invention via triple helix formation are preferably composed of deoxynucleotides. The base composition of these oligonucleotides is typically designed to promote triple helix formation via Hoogsteen base pairing rules, which generally require sizeable stretches of either purines or pyrimidines to be present on one strand of a duplex.

Nucleotide sequences may be pyrimidine -based, resulting in TAT and CGC triplets across the three associated strands of the resulting triple helix. The pyrimidine-rich molecules provide base complementarity to a purine-rich region of a single strand of the duplex in a parallel orientation to that strand. In addition, nucleic acid molecules may be chosen that are purine-rich, e.g., those containing a stretch of G residues. These molecules will form a triple helix with a DNA duplex that is rich in GC pairs, in which the majority of the purine residues are located on a single strand of the targeted duplex, resulting in GGC triplets across the three strands in the triplex.

Alternatively, sequences can be targeted for triple helix formation by creating a so-called "switchback" nucleic acid molecule. Switchback molecules are synthesized in an alternating 5'-3', 3'-5' manner, such that they base pair with first one strand of a duplex and then the other, eliminating the necessity for a sizeable stretch of either purines or pyrimidines to be present on one strand of a duplex.

Similarly to RNAi molecules, antisense oligonucleotides, and ribozymes, described above, triple helix molecules can be prepared by any method known in the art. These include techniques for chemically synthesizing oligodeoxyribonucleotides and oligoribonucleotides such as, e.g., solid phase phosphoramidite chemical synthesis.

Alternatively, RNA molecules can be generated by in vitro or in vivo transcription of DNA sequences "encoding" the particular RNA molecule. Such DNA sequences can be incorporated into a wide variety of vectors that incorporate suitable RNA polymerase promoters such as the T7 or SP6 polymerase promoters. See, Nielsen, RE. "Triple Helix: Designing a New Molecule of Life", Scientific American, December, 2008; Egholm, M., et al. "PNA Hybridizes to Complementary Oligonucleotides Obeying the Watson-Crick Hydrogen Bonding Rules." (1993) Nature, 365, 566-568; Nielsen, RE. ^* PNA Technology ^* . Mol Biotechnol. 2004;26:233-48.

Antibodies and Aptamers

The polypeptide targets described herein, e.g., NCOA4, HERC2, an ATG8 paralog, etc.) can be inhibited (e.g., the level can be reduced) by the administration to or expression in a subject or a cell or tissue thereof, of blocking antibodies or aptamers against the polypeptide.

Antibodies, or their equivalents and derivatives, e.g., intrabodies, or other antagonists of the polypeptide, may be used in accordance with the present methods. Methods for engineering intrabodies (intracellular single chain antibodies) are well known. Intrabodies are specifically targeted to a particular compartment within the cell, providing control over where the inhibitory activity of the treatment is focused. This technology has been successfully applied in the art (for review, see Richardson and Marasco, 1995, TIBTECH vol. 13; Lo et al. (2009) Handb Exp Pharmacol.181 :343-73; Maraasco, W.A. (1997) Gene Therapy 4: 11-15; see also, U.S. Pat. Appln. Pub. No.

2001/0024831 by Der Maur et al. and U.S. Pat. No. 6,004,940 by Marasco et al).

Administration of a suitable dose of the antibody or the antagonist (e.g., aptamer) may serve to block the level (expression or activity) of the polypeptide in order to treat or prevent a disease or condition disclosed herein (e.g., a cancer that uses selective autophagy for growth, anemia, iron overload, etc.).

In addition to using antibodies and aptamers to inhibit the levels and/or activity of a target polypeptide, it may also be possible to use other forms of inhibitors. For example, it may be possible to identify antagonists that functionally inhibit the target polypeptide (e.g., NCOA4, HERC2, an ATG8 paralog, etc.). In addition, it may also be possible to interfere with the interaction of the polypeptide with its substrate. Other suitable inhibitors will be apparent to the skilled person.

The antibody (or other inhibitors and antagonists) can be administered by a number of methods. For example, for the administration of intrabodies, one method is set forth by Marasco and Haseltine in PCT WO 94/02610. This method discloses the intracellular delivery of a gene encoding the intrabody. In one embodiment, a gene encoding a single chain antibody is used. In another embodiment, the antibody would contain a nuclear localization sequence. By this method, one can intracellularly express an antibody, which can block activity of the target polypeptide in desired cells.

Aptamers are oligonucleic acid or peptide molecules that bind to a specific target molecule. Aptamers can be used to inhibit gene expression and to interfere with protein interactions and activity. Nucleic acid aptamers are nucleic acid species that have been engineered through repeated rounds of in vitro selection (e.g., by SELEX (systematic evolution of ligands by exponential enrichment)) to bind to various molecular targets such as small molecules, proteins, nucleic acids, and even cells, tissues and organisms. Peptide aptamers consist of a variable peptide loop attached at both ends to a

protamersein scaffold. Aptamers are useful in biotechnological and therapeutic applications as they offer molecular recognition properties that rival that of antibodies. Aptamers can be engineered completely in a test tube, are readily produced by chemical synthesis, possess desirable storage properties, and elicit little or no immunogenicity in therapeutic application. Aptamers can be produced using the methodology disclosed in a U.S. Pat. No. 5,270,163 and WO 91/19813.

Small Molecules

Chemical agents, referred to in the art as "small molecule" compounds are typically organic, non-peptide molecules, having a molecular weight less than 10,000 Da, preferably less than 5,000 Da, more preferably less than 1,000 Da, and most preferably less than 500 Da. This class of modulators includes chemically synthesized molecules, for instance, compounds from combinatorial chemical libraries. Synthetic compounds may be rationally designed or identified utilizing the screening methods described below. Methods for generating and obtaining small molecules are well known in the art (Schreiber, Science 2000; 151 : 1964-1969; Radmann et al, Science 2000; 151 : 1947- 1948).

In certain embodiments, the above described inhibitors and agonists can be directly targeted to a specific cell type (e.g., a cancer cell, or a red blood cell) or to a site of erythropoiesis (e.g., bone marrow). The skilled artisan will appreciate that methods for specific cell targeting are well known in the art. By way of non-limiting example, antibodies, e.g., an anti-tumor antigen antibody, may be conjugated to an inhibitor or agonist described herein, in order to target the inhibitor or agonist to, for example and without limitation, a cancer cell. Further the site of administration (e.g., direct injection into a tumor) can further increase the specificity of cell targeting.

In some embodiments, the methods can comprise recording the results (e.g., diagnostic) in a database or medical history (e.g., medical records) of the subject, selecting the subject for increased monitoring or periodically monitoring the health of the subject (e.g., for development or changes in the signs or symptoms of the cancer (e.g. pancreatic cancer, lung cancer, melanoma, breast cancer, glioblastoma, colorectal cancer, prostate cancer, multiple myeloma, renal cell carcinoma, chronic lymphocytic leukemia, lymphoma, chronic myelogenous leukemia, etc.), e.g., tumor development and/or changes in tumor size (e.g., increased or decreased size), such as e.g., clinical breast exam, mammography, MRI, or other suitable imaging or other diagnostic method(s) known in the art.

Administration and Treatment

Compositions and formulations comprising an inhibitor/antagonist or agonist (i.e., an "agent") disclosed herein (e.g., an inhibitor/antagonist or agonist of a gene or polypeptide involved in NCOA4-mediated autophagic targeting of ferritin, e.g., NCOA4, an ATG8 paralog, HERC2), can be administered topically, parenterally, orally, by inhalation, as a suppository, or by other methods known in the art. The term "parenteral" includes injection (for example, intravenous, intraperitoneal, epidural, intrathecal, intramuscular, intraluminal, intratracheal or subcutaneous). Exemplary routes of administration include, e.g., intravenous, intraductal, and intratumoral. Other exemplary routes of administration include, e.g., an implantable delivery device (e.g., subcutaneously implanted devices, intrathecal pumps, intrauterine devices,

biodegradable material such as poly(lactic-co-glycolic acid) or PLGA, etc.).

While it is possible to use an agent of the invention for therapy as is, it may be preferable to administer an inhibitor or agonist as a pharmaceutical formulation, e.g., in admixture with a suitable pharmaceutical excipient, diluent, or carrier selected with regard to the intended route of administration and standard pharmaceutical practice. Pharmaceutical formulations comprise at least one active compound, or a

pharmaceutically acceptable derivative thereof, in association with a pharmaceutically acceptable excipient, diluent, and/or carrier. The excipient, diluent and/or carrier must be "pharmaceutically acceptable." As used herein, the phrase "pharmaceutically acceptable" refers to molecular entities and compositions that are generally believed to be

physiologically tolerable and do not typically produce an allergic or similar untoward reaction, such as gastric upset, dizziness and the like, when administered to a human..

Administration of a composition or formulation can be once a day, twice a day, or more often. Frequency may be decreased during a treatment maintenance phase of the disease or disorder, e.g., once every second or third day instead of every day or twice a day. The dose and the administration frequency will depend on the clinical signs, which confirm maintenance of the remission phase, with the reduction or absence of at least one or more preferably more than one clinical signs of the acute phase known to the person skilled in the art. More generally, dose and frequency will depend in part on recession of pathological signs and clinical and subclinical symptoms of a disease condition or disorder contemplated for treatment with the present compounds.

It will be appreciated that the amount of an inhibitor required for use in treatment will vary with the route of administration, the nature of the condition for which treatment is required, and the age, body weight and condition of the patient, and will be ultimately at the discretion of the attendant physician or veterinarian. Compositions will typically contain an effective amount of the active agent(s), alone or in combination. Preliminary doses can be determined according to animal tests, and the scaling of dosages for human administration can be performed according to art-accepted practices.

Length of treatment, i.e., number of days, will be readily determined by a physician treating the subject; however the number of days of treatment may range from 1 day to about 20 days. As provided by the present methods, and discussed below, the efficacy of treatment can be monitored during the course of treatment to determine whether the treatment has been successful, or whether additional (or modified) treatment is necessary.

As used herein, "treating" or "treatment" of a state, disorder or condition includes:

(1) preventing or delaying the appearance of clinical or sub-clinical symptoms of the state, disorder or condition developing in a mammal that may be afflicted with or predisposed to the state, disorder or condition but does not yet experience or display clinical or subclinical symptoms of the state, disorder or condition; and/or (2) inhibiting the state, disorder or condition, i.e., arresting, reducing or delaying the development of the disease or a relapse thereof (in case of maintenance treatment) or at least one clinical or sub-clinical symptom thereof; and/or (3) relieving the disease, i.e., causing regression of the state, disorder or condition or at least one of its clinical or sub-clinical symptoms; and/or (4) causing a decrease in the severity of one or more symptoms of the disease. The benefit to a subject to be treated is either statistically significant or at least perceptible to the patient or to the physician.

As used herein, the term "treating cancer" (e.g., a cancer that is reliant on selective autophagy for growth (such as but not limited to pancreatic cancer, lung cancer, melanoma, breast cancer, glioblastoma, colorectal cancer, prostate cancer, multiple myeloma, renal cell carcinoma, chronic lymphocytic leukemia, lymphoma, and chronic myelogenous leukemia) means causing a partial or complete decrease in the rate of growth of a tumor, and/or in the size of the tumor and/or in the rate of local or distant tumor metastasis in the presence of an inhibitor of the invention, and/or any decrease in tumor survival.

As used herein, the term "preventing a disease" (e.g., a cancer that is reliant on selective autophagy for growth, anemia, iron overload, etc., as disclosed herein) in a subject means for example, to stop the development of one or more symptoms of a disease in a subject before they occur or are detectable, e.g., by the patient or the patient's doctor. Preferably, the disease (e.g., cancer) does not develop at all, i.e., no symptoms of the disease are detectable. However, it can also result in delaying or slowing of the development of one or more symptoms of the disease. Alternatively, or in addition, it can result in the decreasing of the severity of one or more subsequently developed symptoms.

As used herein "combination therapy" means the treatment of a subject in need of treatment with a certain composition or drug in which the subject is treated or given one or more other compositions or drugs for the disease in conjunction with the first and/or in conjunction with one or more other therapies, such as, e.g., a cancer therapy such as chemotherapy, radiation therapy, and/or surgery. Such combination therapy can be sequential therapy wherein the patient is treated first with one treatment modality (e.g., drug or therapy), and then the other (e.g., drug or therapy), and so on, or all drugs and/or therapies can be administered simultaneously. In either case, these drugs and/or therapies are said to be "coadministered." It is to be understood that "coadministered" does not necessarily mean that the drugs and/or therapies are administered in a combined form (i.e., they may be administered separately or together to the same or different sites at the same or different times).

The term "pharmaceutically acceptable derivative" as used herein means any pharmaceutically acceptable salt, solvate or prodrug, e.g., ester, of a compound of the invention, which upon administration to the recipient is capable of providing (directly or indirectly) a compound of the invention, or an active metabolite or residue thereof. Such derivatives are recognizable to those skilled in the art, without undue experimentation. Nevertheless, reference is made to the teaching of Burger's Medicinal Chemistry and Drug Discovery, 5th Edition, Vol. 1 : Principles and Practice, which is incorporated herein by reference to the extent of teaching such derivatives. Pharmaceutically acceptable derivatives include salts, solvates, esters, carbamates, and/or phosphate esters.

As used herein the terms "therapeutically effective" and "effective amount", used interchangeably, applied to a dose or amount refer to a quantity of a composition, compound or pharmaceutical formulation that is sufficient to result in a desired activity upon administration to an animal in need thereof. Within the context of the present invention, the term "therapeutically effective" refers to that quantity of a composition, compound or pharmaceutical formulation that is sufficient to reduce or eliminate at least one symptom of a disease or condition specified herein, e.g., cancer, anemia, iron overload, etc. When a combination of active ingredients is administered, the effective amount of the combination may or may not include amounts of each ingredient that would have been effective if administered individually. The dosage of the therapeutic formulation will vary, depending upon the nature of the disease or condition, the patient's medical history, the frequency of administration, the manner of administration, the clearance of the agent from the host, and the like. The initial dose may be larger, followed by smaller maintenance doses. The dose may be administered, e.g., weekly, biweekly, daily, semi-weekly, etc., to maintain an effective dosage level.

Therapeutically effective dosages can be determined stepwise by combinations of approaches such as (i) characterization of effective doses of the composition or compound in in vitro cell culture assays using tumor cell growth and/or survival as a readout followed by (ii) characterization in animal studies using tumor growth inhibition and/or animal survival as a readout, followed by (iii) characterization in human trials using enhanced tumor growth inhibition and/or enhanced cancer survival rates as a readout.

In some embodiments, the methods and compositions disclosed herein can be used for the treatment of cancer, either as initial therapy or as a second-line option if resistance to another therapy develops.

Chemotherapeutic agents, which can be administered in a combination therapy with a method and/or composition disclosed herein, include for example: taxanes such as taxol, taxotere or their analogues; alkylating agents such as cyclophosphamide, isosfamide, melphalan, hexamethylmelamine, thiotepa or dacarbazine; antimetabolites such as pyrimidine analogues, for instance 5-fluorouracil, cytarabine, capecitabine, and gemcitabine or its analogues such as 2-fluorodeoxycytidine; folic acid analogues such as methotrexate, idatrexate or trimetrexate; spindle poisons including vinca alkaloids such as vinblastine, vincristine, vinorelbine and vindesine, or their synthetic analogues such as navelbine, or estramustine and a taxoid; platinum compounds such as cisplatin;

epipodophyllotoxins such as etoposide or teniposide; antibiotics such as daunorubicin, doxorubicin, bleomycin or mitomycin, enzymes such as L-asparaginase, topoisomerase inhibitors such as topotecan or pyridobenzoindole derivatives; and various agents such as procarbazine, mitoxantrone, and biological response modifiers or growth factor inhibitors such as interferons or interleukins. Other chemotherapeutic agents include, though are not limited to, a p38/JAK kinase inhibitor, e.g., SB203580; a phospatidyl inositol-3 kinase (PI3K) inhibitor, e.g., LY294002; a MAPK inhibitor, e.g. PD98059; a JAK inhibitor, e.g., AG490; preferred chemotherapeutics such as UCN-01, NCS, mitomycin C (MMC), NCS, and anisomycin; taxoids in addition to those describe above (e.g., as disclosed in U.S. Pat. Nos. 4,857,653; 4,814,470; 4,924,011, 5,290,957; 5,292,921; 5,438,072; 5,587,493; European Patent No. 0 253 738; and PCT Publication Nos. WO 91/17976, WO 93/00928, WO 93/00929, and WO 96/01815. In other embodiments, a cancer therapy can include but is not limited to immunotherapy such as the administration of cytokines and growth factors such as interferon (IFN)-gamma, tumor necrosis factor (TNF)-alpha, TNF-beta, and/or similar cytokines, or an antagonist of a tumor growth factor (e.g., TGF- and IL- 10). Antiangiogenic agents that can be used in the therapy of cancer, include, e.g., endostatin, angiostatin, TNP-470, Caplostatin (Stachi-Fainaro et al., Cancer Cell 7(3), 251 (2005)). Drugs that interfere with intracellular protein synthesis can also be used in the methods of the present invention; such drugs are known to those skilled in the art and include puromycin, cycloheximide, and ribonuclease.

For radiation therapy, common sources of radiation used for cancer treatment include, but are not limited to, high-energy photons that come from radioactive sources such as cobalt, cesium, iodine, palladium, or a linear accelerator, proton beams; neutron beams (often used for cancers of the head, neck, and prostate and for inoperable tumors), x or gamma radiation, electron beams, etc.

It is well known that radioisotopes, drugs, and toxins can be conjugated to antibodies or antigen-binding antibody fragments which specifically bind to markers which are produced by or associated with cancer cells, and that such antibody conjugates can be used to target the radioisotopes, drugs or toxins to tumor sites to enhance their therapeutic efficacy and minimize side effects. Examples of these agents and methods are reviewed in Wawrzynczak and Thorpe (in Introduction to the Cellular and Molecular Biology of Cancer, L. M. Franks and N. M. Teich, eds, Chapter 18, pp. 378-410, Oxford University Press. Oxford, 1986), in Immunoconjugates: Antibody Conjugates in

Radioimaging and Therapy of Cancer (C. W. Vogel, ed., 3-300, Oxford University Press, N.Y., 1987), in Dillman, R. O. (CRC Critical Reviews in Oncology/Hematology 1 :357, CRC Press, Inc., 1984), in Pastan et al. (Cell 47:641, 1986) in Vitetta et al. (Science 238: 1098-1104, 1987) and in Brady et al. (Int. J. Rad. Oncol. Biol. Phys. 13: 1535-1544, 1987). Other examples of the use of immunoconjugates for cancer and other forms of therapy have been disclosed, inter alia, in U.S. Pat. Nos. 4,331,647, 4,348,376, 4,361,544, 4,468,457, 4,444,744, 4,460,459, 4,460,561 4,624,846, 4,818,709, 4,046,722, 4,671,958, 4,046,784, 5,332,567, 5,443,953, 5,541,297, 5,601,825, 5,637,288, 5,677,427, 5,686,578, 5,698,178, 5,789,554, 5,922,302, 6,187,287, and 6,319,500. In addition, unconjugated antibodies (e.g., antibodies to epidermal growth factor receptors such a HER2/neu) can be used for the treatment of cancer. Exemplary cancer-cell specific antibodies that can be used in the combination therapies disclosed herein are described, for example, in the review by Scott et al. (Nature Reviews Cancer 12, 278-287 (April 2012)). See also, Weiner, L. M., et al. Monoclonal antibodies: versatile platforms for cancer

immunotherapy. Nature Rev. Immunol.10, 317-327 (2010); Beatty, G. L. et al. CD40 agonists alter tumor stroma and show efficacy against pancreatic carcinoma in mice and humans. Science331, 1612-1616 (2011); Musolino, A. et al. Immunoglobulin G fragment C receptor polymorphisms and clinical efficacy of trastuzumab-based therapy in patients with HER-2/neu-positive metastatic breast cancer. J. Clin. Oncol.26, 1789-1796 (2008); Ferris, R. L., et al. Tumor antigen-targeted, monoclonal antibody-based immunotherapy: clinical response, cellular immunity, and immunoescape. J. Clin. Oncol.28, 4390-4399 (2010); and Scott, A. M. et al. A Phase I clinical trial with monoclonal antibody ch806 targeting transitional state and mutant epidermal growth factor receptor. Proc. Natl Acad. Sci. USA104, 4071-4076 (2007).

Other therapies include, e.g., hematopoietic stem cell transplant (HSCT), e.g., for treatment of acute myeloid leukemia (AML) patients and many other cancers. Peptide Preparation

The polypeptides (including peptide fragments described herein (e.g., peptide fragments of NCOA4, ferritin (FTH1 and/or FTL), ATG8 paralogs (e.g., GABARAPLR2, LC3), and HERC2) can be manufactured by standard in vitro recombinant DNA techniques and in vivo transgenesis using nucleotide sequences encoding the appropriate polypeptides, such as those nucleotide sequences described above (e.g., SEQ ID NOs: 5, 21-25 and sequences at least 85% sequence identity thereto, or that encode a peptide that has at least 85% sequence identity to a peptide having a sequence set forth in SEQ ID NO: 1, 2, 3, 4, 6, 7, 8, 9 or 10). Methods well-known to those skilled in the art can be used to introduce mutations and construct expression vectors containing relevant coding sequences and appropriate transcriptional/translational regulatory elements. See, for example, the techniques described in Sambrook et al, Molecular Cloning: A Laboratory Manual (2nd Ed.) [Cold Spring Harbor Laboratory, N.Y., 1989], and Ausubel et al, Current Protocols in Molecular Biology [Green Publishing Associates and Wiley

Interscience, N.Y., 1989].

The transcriptional/translational regulatory elements referred to above include but are not limited to inducible and non-inducible promoters, enhancers, operators and other elements that are known to those skilled in the art and that drive or otherwise regulate gene expression. Such regulatory elements include but are not limited to the

cytomegalovirus hCMV immediate early gene, the early or late promoters of SV40 adenovirus, the lac system, the trp system, the TAC system, the TRC system, the major operator and promoter regions of phage A, the control regions of fd coat protein, the promoter for 3 phosphoglycerate kinase, the promoters of acid phosphatase, and the promoters of the yeast a mating factors.

The expression systems that may be used for purposes of the invention include but are not limited to microorganisms such as bacteria (for example, E. coli and B.

subtilis) transformed with recombinant bacteriophage DNA, plasmid DNA, or cosmid

DNA expression vectors containing nucleic acid molecules encoding enhancing agents or immunogenic stimuli; yeast (for example, Saccharomyces and Pichia) transformed with recombinant yeast expression vectors containing a nucleic acid encoding enhancing agents or immunogenic stimuli; insect cell systems infected with recombinant virus expression vectors (for example, baculovirus) containing a nucleic acid encoding enhancing agents or immunogenic stimuli; plant cell systems infected with recombinant virus expression vectors (for example, cauliflower mosaic virus (CaMV) or tobacco mosaic virus (TMV)) or transformed with recombinant plasmid expression vectors (for example, Ti plasmid) containing a nucleotide sequence encoding; or mammalian cell systems (for example, COS, CHO, BHK, 293, VERO, HeLa, MDCK, WI38, NIH 3T3, MCF7, 8988T, PANC1, PATU-8988T, and U20S cells) harboring recombinant expression constructs containing promoters derived from the genome of mammalian cells (for example, the metallothionein promoter) or from mammalian viruses (for example, the adenovirus late promoter and the vaccinia virus 7.5K promoter). Also useful as host cells are primary or secondary cells obtained directly from a mammal and transfected with a plasmid vector or infected with a viral vector.

Cells transfected or transduced with the expression vectors described herein can then be used, for example, for large or small scale in vitro manufacture of polypeptides (e.g., peptide fragments) by methods known in the art. Such methods typically involve culturing the cells under conditions that maximize production of the polypeptide and isolating the polypeptide from the culture, i.e., the cells and/or the culture medium.

Methods for purifying biological macromolecules (e.g., proteins) are known in the art. For example, polypeptides, including peptide fragments, described herein can be purified by combinations of ethanol precipitation and isoelectric focusing from culture fluids of clones containing the mutated genes. See, Blomster-Hautamaa and Schlievert, Methods Enzymol 165:37-43 (11) (1988). The degree of purity of the macromolecules can be measured by any appropriate method, e.g., column chromatography, polyacrylamide gel electrophoresis, or HPLC analysis.

In other embodiments, polypeptides, peptides, as well as salts thereof may be synthesized, e.g., using solid-phase or liquid-phase synthesis, according to any known suitable method of peptide synthesis {see, e.g., Chemistry of Peptide Synthesis; N. L. Benoiton; CRC Press, 2006, 290 pages).

Kits

In certain embodiments, kits are provided for diagnosing anemia in a subject.

The above kits can comprise means (e.g., reagents, dishes, solid substrates (e.g., microarray slides, ELISA plates, multiplex beads), solutions, media, buffers, etc.) for determining the level of expression or activity of one or more of the genes or proteins described herein (e.g., NCOA4, HERC2, ATG8 paralogs, ferritin, etc). Such kits can further comprise instructions for use, e.g., guidelines for determining diagnosing anemia in a subject, based on the level of expression or activity of the one or more genes detected using the kit. Also provided are kits for the treatment of a disease or disorder described herein (e.g., cancer, anemia, iron overload, etc.). Such kits can comprise, e.g., one or more of the agents described herein, e.g., a peptide fragment (functionally active or inhibitory) of one or more of NCOA4, an ATG8 paralog (GABARAPL2 or LC3), and HERC2). In some embodiments, the kits comprise full-length sequences of the NCOA4, ATG8 paralog, ferritin (FTH1 and/or FTL), and/or HERC2. In certain embodiments, the kits can comprise an inhibitor of NCOA4 (e.g., an inhibitor of the interaction of NCOA4 with ferritin (e.g., with FTH1 and/or FTL), an inhibitor of the interaction of NCOA4 with an ATG8 paralog, an inhibitor of the interaction of NCOA4 with HERC2). Such inhibitors are described in detail herein, and include, e.g., small molecules, antisense

oligonucleotides, antibodies, intrabodies, etc. In certain embodiments, the kits can comprise an agonist of NCOA4 (e.g., an agonist of the interaction of NCOA4 with ferritin (e.g., with FTH1 and/or FTL), an agonist of the interaction of NCOA4 with an ATG8 paralog, an agonist of the interaction of NCOA4 with HERC2). An agonist includes, e.g., an agonistic antibody, a recombinant polypeptide or functional fragment thereof (e.g., SEQ ID NO: 11, SEQ ID NO: 1, SEQ ID NO: 2, amino acids 16-34 of SEQ ID NO: 6, amino acids 103-125 of SEQ ID NO: 6; amino acids 78-88 of SEQ ID NO: 6, and sequences having at least 85% sequence identity thereto).

In some embodiments, the kits can comprise one or more of a peptide fragment comprising or consisting of SEQ ID NO: 11 , SEQ ID NO: 1 , SEQ ID NO: 2, or SEQ ID NO: 3, amino acids 16-34 of SEQ ID NO: 6, amino acids 103-125 of SEQ ID NO: 6; amino acids 78-88 of SEQ ID NO: 6, and sequences having at least 85% sequence identity thereto.

In some embodiments, the kits can comprise one or more of an NCOA4 reagent, a ferritin reagent, an ATG8 paralog reagent, a HERC2 reagent, as described above, for screening assays.

The kits, regardless of type, will generally comprise one or more containers into which the biological agents (e.g. inhibitors) are placed and, preferably, suitably aliquotted. The components of the kits may be packaged either in aqueous media or in lyophilized form. The kits can also comprise one or more pharmaceutically acceptable excipients, diluents, and/or carriers. In accordance with the present invention, there may be employed conventional molecular biology, microbiology, recombinant DNA, immunology, cell biology and other related techniques within the skill of the art. See, e.g., Sambrook et al., (2001) Molecular Cloning: A Laboratory Manual. 3rd ed. Cold Spring Harbor Laboratory Press: Cold Spring Harbor, N.Y.; Sambrook et al., (1989) Molecular Cloning: A Laboratory Manual. 2nd ed. Cold Spring Harbor Laboratory Press: Cold Spring Harbor, N.Y.; Ausubel et al, eds. (2005) Current Protocols in Molecular Biology. John Wiley and Sons, Inc.:

Hoboken, N.J.; Bonifacino et al, eds. (2005) Current Protocols in Cell Biology. John Wiley and Sons, Inc.: Hoboken, N.J.; Coligan et al, eds. (2005) Current Protocols in Immunology, John Wiley and Sons, Inc.: Hoboken, N.J.; Coico et al, eds. (2005) Current Protocols in Microbiology, John Wiley and Sons, Inc.: Hoboken, N.J.; Coligan et al, eds. (2005) Current Protocols in Protein Science, John Wiley and Sons, Inc.: Hoboken, N.J.; Enna et al., eds. (2005) Current Protocols in Pharmacology John Wiley and Sons, Inc.: Hoboken, N.J.; Hames et al, eds. (1999) Protein Expression: A Practical Approach. Oxford University Press: Oxford; Freshney (2000) Culture of Animal Cells: A Manual of Basic Technique. 4th ed. Wiley-Liss; among others. The Current Protocols listed above are updated several times every year.

EXAMPLES

Example 1: Materials and Methods

Methods Summary

Cells were grown in Lys(K)-free and Arg(R)-free DMEM/dialyzed fetal bovine serum, with light (K0, R0) or heavy (K8/R0 or K8/R10) Lys/Arg, and treated with CQ (25 μΜ) for 4 or 16 hours. Mixed cells were lysed and autophagosomes were purified as described [see, Marzella, L., et al. The Journal of Cell Biology; 93, 144-154 (1982); and Koga, H., et al. FASEB Journal: official publication of the Federation of American Societies for Experimental Biology 24, 3052-3065 (2010)], prior to SDS-PAGE and in- gel digestion with trypsin or Lys-C, and LC-MS/MS (see detailed methods below).

Candidate autophagosomal proteins were identified by employing a multi-step filtering process including a log2(heavy:light) ratio cut-off and enrichment in autophagosomes versus whole proteome. Interaction proteomics employed 293T, 8988T, or PANC1 cells stably expressing NCOA4 or FTH1 HA-FL AG-tagged constructs and CompPASS to identify HCIPs [Sowa, M. E., et al. Cell 138, 389-403, (2009)]. Chelation assays were performed similarly to those previously described with slight modifications [Asano, T. et al. Molecular and Cellular Biology 31, 2040-2052, (2011)]. Cells stably expressing shRNAs to NCOA4 were cultured for 24 hours in iron-enriched media (supplemental Ferric Ammonium Citrate added) and subsequently subjected to iron chelation with multiple different chelators prior to immunoblotting or immunofluorescence.

Cell culture and reagents

PANC1, PATU-8988T (8988T), MCF7, U20S, IMR90, and 293T cell lines were obtained from the American Type Culture Collection or the German Collection of Microorganisms and Cell Cultures. HPDE cells were cultured as previously described [Yang, S. et al. Genes & Development 25, 717-729, (2011)]. All cell lines were tested routinely for mycoplasma contamination.

Antibodies

The following antibodies were used in these studies. Lamp 2 (Abeam Ab25631; Western 1 : 1000; IF 1 : 100); HA (Covance MMS 101P; Western blot ("Western") 1 :2000; immunofluorescence ("IF"): 1 : 100); MAP1LC3B (LC3B) (Cell Signaling 2775; Western 1 :2000); MAP1LC3B (LC3B) (Cell Signaling 3868; IF 1 :200); MAP1LC3B (LC3B) (nanoTools 0231-100/LC3-5F10; IF 1 : 100); VDAC1 (Abeam Ab28777; Western

1 : 1000); ferritin (Rockland 200-401-090-0100; IF 1 :400); FTH1 (Cell Signaling 3998; Western 1 : 1000); NCOA4 (ARA70) (Bethyl Laboratories A302-272A; Western 1 : 1000); NCOA4 (Sigma SAB1404569; Western 1 : 1000); SQSTM1 (Abnova H00008878-M01; Western 1 :5000); TAX1BP1 (Cell Signaling 8182; Western 1 : 1000); ATG5 (Cell Signaling 2630; Western 1 : 1000); HERC2 (BD Transduction Laboratories 612366;

Western 1 : 1000); FTL (Abnova Ab69090; Western 1 : 1000); ACTB (Sigma A2066;

Western 1 :5000); MYC (Santa Cruz Sc-40; Western 1 : 1000); IRP2 (Santa Cruz Sc- 33682; Western 1 :500); TFRC (BD Transduction Laboratories 612124; Western 1 :2000); Mannose 6-Phosphate Receptor (Abeam ab2733; IF 1 : 100); GABARAPL2 (gift from Millennium Pharmaceuticals, IF 1 : 100). The following secondary antibodies were used: Anti-Rabbit IgG (H+L) HRP Conjugate (Western Secondary 1 :7500); Anti-Mouse IgG (H+L) HRP Conjugate (Western Secondary 1 :7500); Alexa Fluor ^® 488 anti-Mouse IgG (H+L) (IF Secondary 1 : 1000); Alexa Fluor ^® 594 anti-Rabbit IgG (H+L) (IF Secondary

1 : 1000), Alexa Flour ^® 633 anti-Rabbit IgG (H+L) (IF Secondary 1 : 1000). "Western" and "Western blot" are used interchangeabley throughout with the term "immunoblot."

RNAi ATG5 siRNA (Gene ID: 9474, NM 004849.3) was purchased from Invitrogen as previously published [Yang, S. et ah, supra]. siRNAs were transfected using a reverse transfection protocol and RNAiMax (Invitrogen). siControl was a siRNA designed against luciferase. Lentiviral shRNA plasmid clones (pLKO. l) were obtained from the RNAi Consortium collection: shNCOA4-l : 5' CCCAGGAAGTATTACTTAATT 3' (TRCN0000019724) (SEQ ID NO : 12), shNCO A4-2 : 5 '

GCTGGCAAACAGAAGTTTAAA 3' (TRCN0000019726) (SEQ ID NO: 13) and shGFP: 5 ^* GCAAGCTGACCCTGAAGTTCAT 3 ^* (Addgene plasmid #30323) (SEQ ID NO: 14). NCOA4 Gene ID: 8031, NM_001145263.1. Lentivirus was produced as described previously [Yang, S. et ah, supra]. Additional siRNAs used in this work were purchased from Invitrogen against NCO A4 (Gene ID : 8031 , NM_001145263.1), siNCOA4-l : 5' ACAAAGAUCUAGCCAAUCA 3' (SEQ ID NO: 15) and siNCOA4-2: 5' GACCUUAUUUAUCAGCUUA 3' (SEQ ID NO: 16) and against HERC2 (Gene ID: 8924, NM 004667.5), siHERC2-l : 5' GCACAGAGUAUCACAGGUA 3' (SEQ ID NO: 17) and siHERC2-2: 5' C G AUG AAGGUUUGGUAUUU 3' (SEQ ID NO: 18).

Chemicals

Ferric ammonium citrate (FAC; Fisher Scientific, 36 to 180 μΜ titrated for each cell line based on level of FTHl translation at 24h post-addition of FAC), deferoxamine mesylate (DFO; Bio Vision; 100 μΜ), bathophenanthroline disulfonate (BPS; Sigma; 300 μΜ), Deferiprone (DFP, Sigma, 100 μΜ), Deferasirox (DFX; Selleckchem; 30 μΜ), E64-d (Sigma; 10 μg/mL), PepstatinA (CalBiochem; 10 μg/mL), Bortezomib (BTZ; gift from Millenium Pharmaceuticals; 1 μΜ), Chloroquine (CQ; Sigma; 10 or 25 μΜ), Bafilomycin Al (BAF; Sigma; 50 nM), hydrogen peroxide (H2O2; Sigma), CellTiter- Glo ^® (Promega).

SILAC -based Density Gradient Centrifugation Autophagosome Enrichment

PANC1, 8988T, and MCF7 cells were grown in lysine and arginine free DMEM supplemented with 10% dialyzed FBS (Gibco), 2 mM L-glutamine, penicillin- streptomycin, and light (K0) lysine (50 μg/mL) and light (R0) arginine (85 μg/mL). Heavy media was the same except the light lysine was replaced with K8-lysine

(Cambridge Isotopes) and the light arginine was replaced with RIO-arginine at the same concentrations (PANC1 and 8988T cell lines were also grown in K8-only heavy media (K8, R0)). Where indicated, cells (10 ⁸ ) were treated with Wortmannin (200 nM) or CQ (25 μΜ) for the times indicated. After the indicated treatments, heavy and light cells were mixed 1 : 1 by cell number. Autophagosome purification was performed as described previously [Marzella, L., et al., supra; Koga et al., supra] with slight modifications. All steps were carried out at 4°C. Briefly, cells were washed three times with PBS and resuspended in Buffer A (250 mM Sucrose, 10 mM HEPES, pH 7.4, 1 mM EDTA, protease inhibitors (EDTA-free, Roche)). Cells were lysed by nitrogen cavitation and homogenized using a potter-elvehjem homogenizer with a teflon pestle. Lysates were centrifuged at 2000 x g, the supernatant was centrifuged at 17,000 x g and resuspended in 0.95 mL Buffer A. Lysate was diluted with 1.45 mL 85.6% Nycodenz (Sigma- Aldrich) solution. A discontinuous Nycodenz gradient (26%>, 24%>, 20%>, 15%>) was layered on top of the lysate and spun at 24,700 rpm in a SW41 rotor (Beckman). Fractions were collected as indicated, pelleted at 24,000 x g, and used for downstream applications (immunob lotting, electron microscopy, mass spectrometry).

Autophagosome Immunoisolation

8988T cells stably expressing GFP-LC3B were treated as above. Lysis and clarification centrifugation steps are as described above. GFP-based immunoisolation was performed as previously described [Gao, W. et al, supra]. Briefly, lysates were incubated with μMACS™ microbeads (magnetic beads coated with anti-GFP, MACS Miltenyi Biotec) for 1 hour at 4°C with mixing. Lysate-bead mixture was applied to a LS Column in a MidiMACS™ Separator, washed, eluted, pelleted and prepared for downstream analysis (mass spectrometry).

Mass spectrometry analysis of Autophagosomes

Enriched autophagosomes were prepared for mass spectrometry analysis as described [Shevchenko, A. et al. Nature Protocols 1, 2856-2860, (2006)]. Briefly, pelleted autophagosomes were resuspended in 2% SDS, 50 mM Tris, pH 7.5, 2 mM EDTA, boiled for 10 minutes, and centrifuged at 16,100xg for 5 minutes at room temperature. Supernatants were subjected to SDS-PAGE followed by in-gel digestion with trypsin (K8, R10 heavy samples and 8988T K8 sample) or Lys-C (PANCl K8 heavy samples). For generation of comparison whole cell lysate datasets, untreated heavy and light labeled cells were mixed in a 1 : 1 ratio, lysed as described above, and subjected to SDS-PAGE followed by in-gel digestion. Approximately 10 μg of total whole cell lysate was used for this analysis, however, multiple dilutions of whole cell lysate extract were separated by SDS-PAGE and a lane with equal intensity of overall coommassie staining to the autophagosome separations was chosen for processing.

Peptides were subjected to the CI 8 stage-tip method and resuspended in 5% formic acid, 5% acetonitrile prior to mass spec analysis.

Peptides were separated on 100 μιη x 25 cm CI 8 reversed phase (Maccel CI 8 3μιη 200A, The Nest Group, Inc.) with a 90 min gradient of 6% to 27% acetonitrile in 0.125% formic acid. The twenty-two most intense peaks from each full MS scan acquired in the Orbitrap Velos Pro (Thermo) were selected for MS/MS (RAW files available upon request). Sequest-based identification using a Human UNIPROT database followed by a target decoy-based linear discriminant analysis was used for peptide and protein identification as described [Huttlin, E. L. et al. Cell 143, 1174-1189 (2010)]. Several experiments were processed in tandem using a protein sieve and protein assembler in-house processing tool, including PANCl CQ 4 hr with PANCl Ex. 1 and PANC1 Ex. 2, PANC1 Ex. 3 and PANC1 WCL together. "WCL" = Whole cell lysate. MCF7 Ex. 1, MCF7 Ex. 2, and MCF7 WCL were processed together. However, all datasets were processed independently for calculation of Pearson correlation of log2(H:L) ratios between datasets for Fig. Id and Fig. 13 j). Other parameters used for database searching include: 50 ppm precursor mass tolerance; 1.0 Da product ion mass tolerance; tryptic or Lys-C digestion with up to three missed cleavages; and variable oxidation of Met (+15.994946). A protein level false-discovery rate of <1% was used as a threshold for protein identifications using the target decoy strategy. Quantification of each protein was determined using the peak heights for light and heavy forms for that protein. The criterion for protein quantification was a summed signal-to-noise ratio of >10.

Quantification of protein level was by calculating the median value of the ratios of light to heavy. Of note, contaminants including Keratin, Lys-C, or Trypsin were removed from the data in order to avoid interference with data filtering as below. In addition, peptides identified for MAP1LC3B (Gene ID: 81631, NP 073729.1) are shared with a protein from an additional gene coding region with a gene symbol MAP1LC3B2 (Gene ID

643246, NP 001078950.1). The protein assembler program reported MAP1LC3B2 as the protein identified. However there were no peptides to discriminate the two proteins. There is one amino acid difference between MAP1LC3B and MAP1LC3B2 (CI 13Y). But no peptides were identified within the region of CI 13Y (identified peptides are as follows: ³¹ IPVIIER ³⁷ (SEQ ID NO: 19) and ⁵² FLVPDHVNMSELIK ⁶⁵ (SEQ ID NO: 20)). The log2(H:L) ratios for MAP1LC3B is thus reported in the present figures, and the protein identifier is left as MAP1LC3B2.

Bioinformatic analysis Candidate autophagosomal proteins were identified by employing a multi-step filtering process beginning with an enrichment cut-off including proteins with

log2(heavy:light) ratios greater than 1.0 for MCF7 datasets, 1.5 for PANC1 16 h datasets and 0.5 for PANC1 and 8988T 4 h CQ datasets (0.5 was used as a cut-off in the 4 h CQ datasets given the overall relatively lower level of maximum log2(heavy:light) ratios). To be included, proteins had to be represented by 2 or more peptides. At this point in the analysis, approximately 600 proteins remained per dataset as potential candidates. In order to remove abundant proteins that may be non-specifically captured by bulk autophagy, candidates were filtered against the relative abundance of the proteome measured independently by LC-MS by directly comparing number of peptides identified per protein.

Of note, a whole cell lysate proteome dataset was prepared from MCF7, PANCl, and 8988T cells as detailed above and was used for comparison within cell lines. In the datasets not processed together (PANCl 4h CQ and PANCl Ex. 1 versus PANCl WCL (whole cell lysate) comparisons were done based on pairing of gene symbols that did not distinguish between isoforms within the same gene symbol. Finally, a two-sided Student's t-test was used as a measure of statistical confidence of the observed log2(heavy:light) ratio taking into account the standard deviation of the log2(heavy:light) ratio and number of peptides measured per protein. A p-value of less that 0.05 was used for inclusion as a candidate (except for the PANCl Ex. 1 dataset that used Lys-C for digestion where a p-value of less than 0.1 was used). For each dataset, this typically left approximately 150 candidates. Subsequently, the overlap between the three PANCl 16 h CQ biological replicate datasets was determined, and 86 proteins were identified in common. The overlap between two MCF7 datasets consisted of 102 proteins. Finally, the overlap between the PANCl and MCF7 datasets was determined (33 proteins in common, 122 proteins specific to either PANCl or MCF7 datasets). This set of 155 proteins is referred to as Class 1 candidate autophagosomal proteins. A subset of the top 50 candidate proteins, termed Class 1 A candidates, was developed based on presence in typically 3 or more independent experiments and those with known or potential links with autophagy. Finally, non-Class 1 proteins with a log2(H:L)>2.0 in any 2 of the 5 independent PANCl (PANCl Ex. 1-3) or MCF7 (Ex. 1-2) profiling experiments (16 h in CQ) were also identified, and this dataset is referred to as Class 2 autophagosome- enriched proteins.

For analysis of the semi-quantitative 8988T GFP immunoisolation experiment, data was sorted by comparing log2 ratios of peptide numbers of proteins identified in autophago somes purified from chloroquine versus wortmannin treated cells and log2 ratios of peptide numbers of proteins identified in autophagosomes purified from chloroquine treated cells versus peptide numbers from a whole cell lysate sample. Zero value denominators were systematically replaced with a value of 0.5 in order to generate a log2 ratio. Candidates were qualified as enriched if both log2 ratios were greater than 0.5.

For preparation of the data shown in Figure 17, the overlap between the MCF7 candidate proteins identified in this work and the stimulus independent autophagosomal candidates identified in Dengjel et al. [supra] was determined (Table 1 in Dengjel et al., supra). Only two proteins overlapped, namely p62/SQSTMl and GABARAPL2. To understand the lack of overlap between the datasets, the proteins from the Dengjel et al. list were analyzed using the data from the MCF7 experiments described herein. Of note, the Dengjel et al. experiments also used the MCF7 cell line. The Dengjel datasets were curated to ensure the gene symbols published in the Dengjel et al. study matched the updated version of the database used in the present proteomics analyses. For the 96 Dengjel et al. candidate proteins, the log2(H:L) ratio observed in both MCF7 Ex. 1 and 2 autophagosome enrichments was first determined. A majority of the proteins had a log2(H:L) ratio greater than 1.0 (77 out of 96). However, of the 77 proteins with a log2(H:L) ratio greater than 1.0, only 2 proteins passed the whole proteome abundance filter used in the present analysis to remove abundant proteins that may be non- specifically captured by bulk autophagy (Fig. 17(a). The 4 hour and 16 hour PANC1 autophagosome proteomics datasets used to create the final Class 1 and 2 list was subsequently included in order to obtain as much coverage and comparison of the proteins identified in the Dengjel et al. datasets as possible.

The overlap with the Dengjel et al. dataset is not significantly improved even when the data was expanded to include the PANC1 datasets (Fig. 17(b), Fig. 20) now with an overlap of 4 proteins (SQSTM1, GABARAPL2, VPS35, MAP1LC3B). Three experiments that Dengjel et al. described were analyzed independently using the same approach as above. Similarly, while a large proportion of the 'Cluster A' proteins from each experiment were enriched by log2(H:L) ratio in the present datasets, only a small number of these proteins passed the whole proteome abundance filter and were found in the present Class 1 and 2 dataset (Fig. 17(c)-(e)). By relaxing the log2(H:L) ratio cutoff and redundancy stringency (Fig. 17(b)-(e)) to include non-class 1 and 2 proteins in the analysis, the additional overlap only ranges from 5-15% depending on the individual dataset.

Of note, the Class 1-2 candidates that were also identified in the Dengjel et al. Concanamycin A 'Cluster A' proteins included NCOA4. The likely reason for the large number of proteins with a log2(H:L) ratio greater than 1.0 but that did not pass the whole proteome abundance filter stems from the protein correlation profiling methodology used by Dengjel et al. Specifically, the authors of Dengjel et al. relied on an

'autophagosomal' enrichment profile that required identification and quantification of candidate proteins in all 6 iodixanol fractions for creation of an evaluable profile. This likely biased their identification towards proteins with a high abundance in the whole proteome that would be more likely to be identified in all 6 fractions. As above, abundant proteins are more likely to be captured by non-selective bulk autophagy.

Finally, by using the overlap of the 3 different experiments, they further biased their candidate list towards abundant proteins captured by autophagy under all 3 conditions tested such as proteasome subunits and heat-shock proteins. It is noted that Dengjel et al. clustered all of the identified proteins from their proteomics experiments into three clusters: A, B, and C. Cluster A was defined as "autophagosome-associated proteins"; however, they did not specify these proteins as autophagic cargo receptors. The broad category of "autophagosome-associated proteins" could mean any number of things, and does not imply autophagic cargo receptor.

Electron Microscopy

Pelleted autophagosome fractions (Al) were fixed in 2.5% Glutaraldehyde, 1.25% Paraformaldehyde, and 0.03% picric acid in 0.1 M sodium cacodylate buffer (pH 7.4) for 1 hour at room temperature, washed in 0.1 M Sodium Cacodylate buffer (pH 7.4), and postfixed for 30 minutes in 1% Osmium tetroxide (Os04)/1.5% Potassiumferrocyanide (KFeCN ₆ ). Autophagosome pellets were washed in water 3 times and incubated in 1% aqueous uranyl acetate for 30 minutes followed by 2 washes in water and subsequent dehydration in grades of alcohol (5 minutes each; 50%, 70%, 95%, 2 times 100%).

Autophagosome pellets were infiltrated overnight in a 1 : 1 mixture of propyleneoxide and TAAB Epon (Marivac Canada Inc. St. Laurent, Canada). The samples were subsequently embedded in TAAB Epon and polymerized at 60°C for 48 hours. Ultrathin sections (about 60 nm) were cut on a Reichert Ultracut-S microtome, picked up on to copper grids stained with lead citrate and examined in a TecnaiG ² Spirit BioTWIN transmission electron microscope and images were recorded with an AMT 2k CCD camera.

Interaction Proteomics

Interaction proteomics was performed essentially as described previously, but with small modifications [Sowa, M. E., et al. supra]. Briefly, 293T, PANC1, or 8988T cells were transduced with a lentiviral vector expressing NCOA4-HA-FLAG (NCOA4 amino acid sequence: NP 001138735.1) (SEQ ID NO: 4) or FTH 1 -HA-FLAG (293T only, NP 002023.2 (SEQ ID NO: 6)) and stable cell lines were selected in puromycin. Cells from 4 x 15 cm dishes at 80% confluence were harvested and lysed in 3 ml of 50 mM Tris-HCl (pH 7.4), 150 mM NaCl, 0.5% Nonidet P40, 2 mM DTT and protease inhibitors. Cleared lysates were filtered through 0.45 μιη spin filters (Millipore Ultrafree- CL) and immunoprecipitated with 30 μΐ anti-HA resin (Sigma). Complexes were washed 4 times with lysis buffer, exchanged into PBS for a further 3 washes, eluted with HA peptide and precipitated with 10%> TCA. TCA-precipitated proteins were trypsinized, purified with Empore C18 extraction media (3 M), and analyzed via LC-MS/MS with a LTQ-Velos linear ion trap mass spectrometer (Thermo) with an 18 cm ³ 125 μιη (ID) C18 column and a 50 minute 8%-26% acetonitrile gradient. All AP-MS experiments in 293T cells were performed in biological duplicate and for each biological experiment, complexes were analyzed twice by LC-MS/MS to generate technical duplicates. AP-MS experiments in 8988T and PANC1 cells were performed on a single AP but with technical duplicates. Spectra were searched with Sequest against a target-decoy human tryptic UNIPROT-based peptide database, and these results were loaded into the

Comparative Proteomics Analysis Software Suite (CompPASS) to identify high confidence candidate interacting proteins (HCIPs) [Sowa, M.E. et al, supra]. Here, a statistics table, derived from analogous AP-MS data for 172 unrelated proteins in 293T cells was employed to determine weighted and normalized D-scores (WDN-score) as well as Z-scores based on spectral counts. The PANC1 data was analyzed using a PANC1 specific statistics table with 12 unrelated AP-MS PANC1 experiments and the 8988T AP-MS experiment was analyzed using the 293T statistics table given no statistics table was available for the 8988T cell line. The D-score measures the reproducibility, abundance, and frequency of individual proteins detected in each individual analysis. To identify NCOA4 associated proteins, proteins were filtered at a 2% false discovery rate for those with a WDN-score > 1.0, Z and average assembled peptide spectral matches (APSMs) > 2 in both biological duplicates. Data presented in Fig. 2 (e) are derived from the 293T AP-MS experiments and the figure was made using Cytoscape [Lopes, C. T. et al. Bioinformatics 26, 2347-2348 (2010)]. STRING database data are represented as previously [Sowa, M.E., et al, supra]. FTH1 and FTL interactors were confirmed in both PANC1 and 8988T AP-MS experiments and HERC2 in the 8988T AP-MS.

NEURL4 was included in the interaction network given identification in the 293T AP- MS experiment and previously published data revealing a HERC2-NEURL4 interaction [Martinez-Noel, G., et al. Molecular and Cellular Biology 32, 3095-3106 (2012)].

Immunological Methods and Microscopy

To assess enrichment of autophagosome associated proteins in autophagosome purifications, the gradient load and autophagosome fractions were extracted in 50 mM Tris-HCl (pH 7.4), 150 mM NaCl, 1% Nonidet P40, 0.1% SDS, 2 mM EDTA, 2 mM

DTT, protease inhibitors and subjected to immunob lotting with the indicated antibodies. To assess autophagosome integrity, purified autophagosome fractions (Al) were incubated in buffer A for 1 hour at 37°C plus or minus 0.5% Triton X-100, centrifuged at 16,000xg for 10 minutes, and the supernatant and pellet were subjected to

immunoblotting with the indicated antibodies. To validate interactions between NCOA4 and candidate interacting proteins, 293T cells stably expressing NCOA4-HA-FLAG were harvested at 80% confluency. Extracts (50 mM Tris-HCl (pH 7.4), 150 mM NaCl, 0.5% Nonidet P40, 2 mM DTT, and protease inhibitors) from cells were subjected to immunoprecipitation with anti-FLAG resin (M2 agarose; Sigma), and washed complexes subjected to immunoblotting with the indicated antibodies. Likewise, 293T cells stably expressing FTH1-HA-FLAG with transient expression of MYC-NCOA4 were harvested at 80% confluency, lysed as above, subjected to immunoprecipitation as above, and immunoblotted with the indicated antibodies.

To examine localization of high-priority candidate proteins, full-length clones of the indicated candidate proteins were stably expressed as HA-FLAG fusions in 8988T and U20S cells. Cells were plated on glass coverslips, treated with vehicle or CQ (10 μΜ, 4 hours (h)), and fixed with 4% paraformaldehyde prior to immunofluorescence using anti-FJA to detect candidate proteins and anti-LC3B to detect autophagosomes. All images were collected with a Yokogawa CSU-X1 spinning disk confocal with Borealis modification on a Nikon Ti-E inverted microscope equipped with lOOx Plan Apo NA 1.4 objective lens. HA-candidate protein fluorescence was excited with the 488nm line (selected with an AOTF) from Spectral Applied Precision LMM-7 solid state laser launch. Emission was collected with a quad band pass polychroic mirror (Semrock) and a Chroma ET525/50m emissions filter. LC3B fluorescence was excited with the 561 nm line from the LMM-7 launch, and emission collected with the Semrock polychroic and a Chroma ET620/60m emission filter. For triple colocalization (Fig. 3c), ferritin fluorescence was excited with the 642 nm line from the LMM-7 launch, and emission collected with the Semrock polychroic and a Chroma ET700/75m emission filter. Images were acquired with a Hamamatsu ORCA-AG cooled CCD camera controlled with MetaMorph 7 software. Z-series optical sections were collected with a step size of 0.2 microns, using the internal Nikon Ti-E focus motor. Co-localization was determined based on examination of single z slices using MetaMorph 7 software (results are tabulated in Fig. 14 (a)).

To examine NCOA4 protein levels while blocking autophagic flux, 8988T cells were treated with vehicle (PBS or DMSO), CQ (10 μΜ, 8 hours), or Bafilomycin Al (50 nM, 8 hours), extracted in 50 mM Tris-HCl (pH 7.4), 150 mM NaCl, 1% Nonidet P40, 0.1% SDS, 2 mM EDTA, 2 mM DTT, protease inhibitors and subjected to

immunoblotting with the indicated antibodies.

To examine co-localization of NCOA4 with LC3B and ferritin, a N-terminal GFP fusion of NCOA4 was used. U20S and 8988T cells stably expressing GFP-NCOA4 were treated with vehicle (PBS or DMSO), CQ (10 μΜ, 4 hours), Bafilomycin Al (50 nM, 4 hours), or FAC (ferric ammonium citrate, 36 μΜ or 180 μΜ, 24 hours) and fixed with 4% paraformaldehyde prior to immunofluorescence using anti-LC3B to label autophagosomes or anti-ferritin in FAC loaded cells. Images were collected as described above with 6-10 z-series optical sections collected with a step size of 0.2 microns, using the internal Nikon Ti-E focus motor. Z-series are displayed as maximum z-projections.

GST Pull-down

The six human paralog ATG8 proteins were produced as N-terminal GST fusions (GST-ATG8) and transformed in E. coli BL21 (DE3) cells. Protein expression was induced with 1 mM IPTG for 3 hours at 37°C. Cells were collected by centrifugation, re- suspended in 25 mM Tris-HCl (pH 7.4), 10% (w/v) sucrose and lysed with a single freeze-thaw cycle followed by sonication. After centrifugation, lysates were incubated with 10 μΐ of a 50%> (v/v) slurry of glutathione Sepharose 4B beads for 30 minutes at 4°C. Beads were washed thoroughly with 150 mM NaCl, 20 mM Tris (pH 7.4), 2 mM DTT, 0.5%) (w/v) Nonidet P-40, leaving 50-100 μg of GST-fusion protein bound to the beads. Beads were then mixed with 300 μg of lysate from a NCOA4-HA-FLAG stably expressing 293T cell line. The assay mix was incubated for 30 minutes at 4°C, and beads were washed four times with 1 ml wash buffer. Proteins were eluted with SDS sample buffer and analyzed by 4-20% gradient SDS-PAGE and immunoblotting with HA antibody. Pounceau stain was used to visualize GST-ATG8 bands.

Chelation assays

Chelation assays were performed similarly to those previously described with slight modifications [Asano et ah, supra]. Briefly, U20S and 8988T cells stably expressing shRNAs as described above (shGFP, shNCOA4-l, shNCOA4-2, selected with puromycin) were plated (2xl0 ⁵ cells/well) and cultured for 24 hours in FAC (36 μΜ or 180 μΜ). Cells were washed three times with PBS and subjected to iron chelation with the described chelators minus or plus lysosomal protease inhibitors (E-64d and

PepstatinA) or the proteasomal inhibitor, Bortezomib. Cells were harvested at the indicated time points, washed with PBS, and lysed in 50 mM Tris-HCl (pH 7.4), 150 mM NaCl, 1% Nonidet P40, 0.1% SDS, 2 mM EDTA, 2 mM DTT, protease inhibitors and analyzed by 4-20% gradient SDS-PAGE followed by immunoblotting with the indicated antibodies. Experiments were performed at a minimum in biological triplicate.

Quantitation of Western blots was performed using ImageJ [Schneider, C. A., et al. Nature Methods 9, 671-675 (2012)]. Cells were treated similarly for

immunofluorescence experiments (including IMR90 and HPDE cells). Cells plated on glass coverslips were treated as described and fixed with 4% paraformaldehyde prior to immunofluorescence using anti-ferritin and anti-LAMP2. Data were collected as described above.

For quantitation of ferritin localization, at least 5, 40x fields were collected for biological replicate experiments. The fraction of punctate ferritin was quantitated by measuring the percentage of punctate ferritin immunofluorescence divided by total cellular ferritin immunofluorescence using MetaMorph software. At least 5 fields were quantitated from biological duplicate experiments. For Fig. 3 (d), the number of 8988T cells quantitated expressing shGFP was 155, for 8988T cells expressing shNCOA4-l : 113, and shNCOA4-2: 138. For Fig. 20(c), the number of U20S cells quantitated is as follows: shGFP: 133 cells, shNCOA4-l : 103 cells, shNCOA4-2: 79 cells. For

Fig. 20 (d), the number of IMR90 cells quantified is as follows: shGFP: 29 cells, shNCOA4-l : 26 cells, shNCOA4-2: 31 cells. For Fig. 21 (a), the number of 8988T cells quantified is as follows: 8988T-control MSCV-shGFP: 100 cells, 8988T-control-MSCV- shNCOA4-l : 125 cells, 8988T-control-MSCV-shNCOA4-2: 132 cells, 8988T-mouse- NCOA4-shGFP: 151 cells, 8988T-mouse-NCOA4-shNCOA4-l : 153 cells, 8988T- mouse-NCOA4-shNCOA4-2: 172 cells. Exposure times were held constant between experiments. Rescue experiments were performed using retroviral (MSCV blasticidin) based expression of the murine homolog of NCOA4 (NP 001029160.1) with a N- terminal HA tag.

H2O2 assay

Experiments were performed as described previously with slight modifications [Kurz, T., et al. The FEBS Journal; 273, 3106-3117, (2006)]. 8988T cells stably expressing shGFP or shNCOA4-l were plated on a 96-well plate and treated with increasing concentrations of H2O2 as indicated for 30 minutes followed by 72 hours of culturing in complete media. Relative cell viability was measured using CellTiter-Glo ^® . Experiments were performed at least three times, each time in technical triplicate.

Methods for Defining NCOA4-Ferritin and NCOA4-HERC2 Interaction

NCOA-4-Ferritin Interaction Mapping

To probe the interaction between ferritin and NCOA4, initial binding assays using MYC-tagged NCOA4 full-length and truncation constructs produced using an in vitro translation ("IVT") system were conducted. MYC-NCOA4 fragments were cloned using PCR into a modified T7 cell-free expression vector (pT7CFEl-NMyc, #88863, Thermo Scientific). 1-Step Human Coupled IVT Kit - DNA from Thermo Scientific (product #88881) was used to produce MYC-tagged NCOA4 constructs as described in the product manual. Apoferritin (Sigma, A3641-100mg) was added in a pull-down assay using anti-c-Myc Agarose Affinity Gel antibody produced in rabbit (Sigma, A7470- 1ML). Affinity purification reactions were washed thoroughly with 150 mM NaCl, 20 mM Tris (pH 7.4), and 2 mM dithiothreitol. Proteins were eluted with SDS sample buffer and analyzed by 4-20% gradient SDS-PAGE and immunob lotting with anti-FTHl antibody (Cell Signaling 3998; Western blot 1 : 1,000) or anti-MYC antibody (Santa Cruz Sc-40; western blot 1 : 1 ,000).

The full-length, N-terminal (amino acids (aa) 1-245 of SEQ ID NO: 4) and C- terminal (aa235-614 of SEQ ID NO:4) MYC-NCOA4 were incubated with ferritin purified from horse spleen (Apoferritin (Sigma, A3641-100mg), consisting of a mixture of FTHl and FTL subunits) and anti-MYC immunoprecipitation was performed followed by immunoblotting as described above.

GST-tagged NCOA4 constructs were also made to probe the interactions of C- terminal portions of NCOA4 with ferritin. NCOA4-truncation constructs were produced using Gateway cloning (Invitrogen, Life Technologies, catalog # 11789-013 and 11791 - 019) into a pDEST60 N-terminal GST fusion plasmid (GST-NCOA4) from EMD Millipore (Gateway Nova pET-60-DEST, product #71851-3) and transformed in E. coli BL21 (DE3) cells (New England Biosciences, C2527I).

NCOA4 truncation constructs were designed based on NCBI reference sequence: NP 001138735.1 (SEQ ID NO: 4). In particular, fragments of SEQ ID NO: 4 consisting of amino acids (aa) 1-245, aa235-614, aa235-560, aa235-401, aa383-560, aa545-614, aa383-522, aa510-560, aa383-436, aa436-485, aa475-522, aa475-500, aa480-500, aa480- 504, aa485-509, aa490-514, aa495-522 were designed. Protein expression in the DE3 cells was induced with 1 mM isopropyl-beta-D-thiogalactopyranoside (IPTG) (Sigma, I6758-10G) for 3 hours at 37°C. Cells were collected by centrifugation, re-suspended in 25 mM Tris-HCl (pH 7.4), 10% (w/v) sucrose and lysed with a single freeze-thaw cycle followed by sonication. After centrifugation, a GST pull-down assay was performed.

In the GST pull-down assay, lysates were incubated with 10 μΐ of a 50% (v/v) slurry of glutathione Sepharose 4B beads (GE Healthcare Lifesciences, 17-0756-01) for 30 minutes at 4°C. Beads were washed thoroughly with 150 mM NaCl, 20 mM Tris (pH 7.4), 2 mM dithiothreitol (DTT), 0.5% (w/v) Nonidet P-40, leaving 50-100 μg of GST- fusion protein bound to the beads. Beads were then mixed with 0.5-2 μg of apo-ferritin purified from equine spleen (Sigma F4503) or recombinant human FTH1 or FTL produced in Rosetta E. coli (EMD Millipore, 70953-3). The assay mix was incubated for 2 hours at 4°C, and beads were washed four times with 1 ml wash buffer. Proteins were eluted with SDS sample buffer and analyzed by 4-20% gradient SDS-PAGE and immunob lotting with anti-FTHl antibody (as above) or anti-FLAG antibody (Sigma, F1804-200UG). Pounceau stain was used to visualize GST-NCOA4 bands. (Pounceau, Sigma, P7170-1L, protocol as per product manual).

NCOA-4-HERC2 Interaction Mapping

To map the interaction of NCOA-4 with HERC2, the GST-NCOA4 truncation constructs described above were also tested in a GST pull-down assay with HERC2- FLAG expressing 293T cell line. HERC2-FLAG fragment (F3, HERC2 amino acids 1700-2700) was produced as described in Bekker- Jensen et al., Nature Cell Biology (2010) 12; 80-86. The HERC2-FLAG F3 was transiently transfected into 293T cells using standard transfection procedures using PEI (Polysciences, #23966-2).

Lysates were obtained, as above, and incubated with 10 μΐ of a 50% (v/v) slurry of glutathione Sepharose 4B beads for 30 minutes at 4°C. Beads were washed thoroughly with 150 mM NaCl, 20 mM Tris (pH 7.4), 2 mM DTT, 0.5% (w/v) Nonidet P-40, leaving 50-100 μg of GST-fusion protein bound to the beads. Beads were then mixed with 300 μg of lysate from a HERC2-FLAG expressing 293T cell line, as above. The assay mix was incubated for 2 hours at 4°C, and beads were washed four times with 1 ml wash buffer. Proteins were eluted with SDS sample buffer and analyzed by 4-20% gradient SDS-PAGE and immunoblotting with anti-HERC2 antibody or anti-FLAG antibody, as above. Coomassie stain was used to visualize GST-NCOA4 bands as above.

Example 2: NCOA4 Modulates Autophagic Targeting of Ferritin

Autophagosomes are decorated by a family of ubiquitin-like adaptor ATG8 proteins that are conjugated to phosphatidylethanolamine through the action of an autophagy-specific E1-E2-E3 cascade. While ATG8 proteins are known to recruit a small number of cargo receptors to insipient autophagosomes, the full repertoire of selective autophagic cargo and their cognate receptor proteins remain poorly defined [Kirkin, V., et al. Molecular Cell 34, 259-269, (2009)]. Selective autophagy may be particularly important for the survival or growth of particular cancer cell types [Yang, S. et al. supra; Sandilands, E. et al. Nature Cell Biology 14, 51-60 (2012)] but in other contexts may act as a tumor suppressor to maintain normal cellular homeostasis and constrain tumor initiation [Kimmelman, A. C. Genes & Development 25, 1999-2010

(2011) ; White, E. Nature reviews. Cancer 12, 401-410, (2012)]. Thus, a more comprehensive understanding of autophagy cargo-receptor pairs is required for understanding autophagic mechanisms that contribute to proteo stasis.

Three previous studies [Overbye, A., et al. Autophagy; 3, 300-322 (2007); Gao, W. et al, supra; Dengjel, J. et al, supra] described the use of mass spectrometry to identify proteins in autophagosomal preparations, but since there was a low overlap in the proteins identified between these studies (Fig. 13a), and limitations of the approaches used, it was decided to catalog resident autophagosomal proteins using quantitative proteomics. Stable isotopic labeling by amino acids in cell culture (SILAC) was combined with an established density gradient separation protocol [Marzella et al, suprap; Koga et al, supra] to quantitatively identify proteins enriched in autophagosome preparations. This analysis was performed using two pancreatic cancer cell lines (PANC1 and 8988T) that require autophagy for growth, as well as the MCF7 breast cancer cell line, which is less reliant on autophagy for growth [Yang, S., et al, supra]. Given the high basal autophagy of PANC1 and 8898T cells, light cells were briefly treated with the PI3 kinase inhibitor Wortmannin (1 hour ("h") to suppress

autophagosome formation, while heavy cells were treated with the lysosomal inhibitor Chloroquine (CQ) for 4 hours, to maximize the number of autophagosomes (Fig. la, Fig. 13(b)). As shown in Fig. 13(b), PANC1 cells have a high level of basal autophagy (left panel), and lh Wortmannin (200 nM) treatment blocked autophagosome formation (middle panel), and 4h chloroquine treatment (25 μΜ) caused accumulation of autophagosomes (right panel). This approach allows for robust identification of proteins intimately associated with autophagosome-enriched samples as opposed to proteins that simply co-migrate with these vesicles during gradient centrifugation.

To test for autophagosome-associated proteins, 8988T cells were lysed, mixed with Nycodenz, and placed at the bottom of a discontinuous density gradient with Nycodenz layers at the following concentrations: 15%, 20%, 24%>, 26%> and 85.6%>. As shown in Fig. 13c, the resulting fractions Al, A2, L and M, contained the autophagosome fraction (15-20% interface), autophagolysosome fraction (20-24% interface), lysosome fraction (24-26% interface), and mitochondria fraction (26-50% interface), respectively.

As expected, the autophagosome-enriched fraction was enriched for the ATG8 protein MAP1LC3B (LC3B) as assayed by immunob lotting (Fig. 13 (e), (g), (h)) or immunofluorescence (Figs. 13 (e), (f)), and contained characteristic double-membrane vesicles by electron microscopy (Figs. 13 (k)-(m)). To determine if the autophagosomes were intact, LC3B and p62/SQSTMl release upon detergent treatment was tested. 8988T autophagosomes (Al fraction) were incubated at 37°C for 1 hour -/+ Triton X-100 and centrifuged at high speed. The resulting pellet was resuspended in equal volume to supernatant and assayed by immunoblotting with antibodies to p62 and LC3B. The autophagosomes were determined to be intact (Fig. 13(i)). Autophagosomes and autophagolysosomes are heterogeneous in nature, as they form via a dynamic interplay between other membrane-rich organelles, each containing their own specific complement of proteins.

Single-label (heavy Lys) profiling of the autophagosomal fraction from PANC1 after 4 or 16 h of CQ treatment, as well as double-label (heavy Lys and Arg) profiling of PANC1 and MCF7 derived autophagosomal preparations at 16 hours of CQ treatment resulted in the quantification of >2000 proteins. Proteins were selected based on significantly increased log2 (heavy:light) ratios and the presence of 2 or more peptides, and subsequently filtered against the relative abundance of the proteome measured independently by LC-MS (Fig. lb), thereby removing abundant proteins that may be non- specifically captured by bulk autophagy. 86 proteins with log2(H:L)>l .5 were identified in all 3 PANC1 replicates (Pearson correlation of 0.92 for a representative pair), and 102 proteins with log2(H:L)>1.0 in both MCF7 replicates (Pearson correlation of 0.89) (Fig. 1 (c), (d), Fig. 13(j)). The union of these two high stringency datasets are referred to as Class 1 autophagosome-enriched proteins, and a high priority subset of these proteins based on their presence in >3 data sets or known involvement in autophagy as Class 1 A (Fig. le, Fig. 14 (a)). Non-Class 1 proteins with a log2(H:L)>2.0 in any 2 of the 5 PANC1 or MCF7 experiments (16 h in CQ) were also identified, and this lower stringency dataset is referred to as Class 2 autophagosome-enriched proteins. As expected, PANC1 cells treated with CQ for 16 h showed a greater accumulation of candidate proteins than PANC1 or 8988T cells treated for 4 h (Fig. 1 (e), Fig. 14).

Within the Class 1 A proteins, 2 ATG8 paralogs (GABARAPL2, LC3B), 4 known autophagy cargo receptors (SQSTMl/p62, CALCOC02/NDP52, OPTN, NBR1), and 4 proteins that were previously reported to associate with ATG8 family members and/or cargo receptors, or to be involved in autophagosomal membrane fusion (KEAP1, TMEM59, FYCOl, STX17) were identified (Fig. 1 (e), Fig. 14(a)). Moreover, 2 proteins reported as selective autophagy cargo (APP, NRP1), and 7 proteins identified as high- confidence interacting proteins in the previously published Autophagy Interaction Network [Behrends, C, et al. Nature; 466, 68-76, (2010)] were identified (Fig. 1 (e), Fig. 14 (a)). Furthermore, the autophagy pathway proteins RB1CC1, ATG9A, TBC1D15, and the OPTN-binding protein TBKl were identified in the Class 2 dataset. The presence of several plasma membrane and endocytosis-related proteins (Fig. 1 (e), Fig. 14 (a)) is consistent with intermixing of these membrane sources during autophagosome maturation or lysosomal fusion. Co-localization with LC3B-positive puncta was observed for 7 of 11 Class 1A proteins tested (Fig. 14 (a), Fig. 15).

As further validation, 8988T pancreatic cancer cells were subjected to both SILAC -based autophagosomal profiling using density gradient purification and a semiquantitative proteomic approach using an immunopurification-based autophagosome enrichment scheme by immunoprecipitation of tagged GFP-LC3B (Fig. 14 (b)-(d) and Fig. 16). In total, 40 proteins were identified in common between the 50 Class 1A autophagosomal proteins and those identified as enriched in autophagosomes purified from 8988T cells. Comparative analysis of the MCF7 candidate proteins with a previously reported autophagosomal quantitative proteomics analysis [Marzella et al., supra] that used the same cell line revealed 2 overlapping proteins from their final combined data set (SQSTM1 and GABARAPL2) (Fig. 17).

Expanding the analysis to also include the PANC 1 datasets only increased the overlap to a total of 4 proteins from the Class 1 and 2 lists. This low rate of overlap appears to reflect the fact that a large fraction of proteins previously reported to reside in autophagosomes would have been removed upon filtering at high stringency for abundance in the total proteome (see Methods (Example 1), Fig. 17), indicating that these likely are present in autophagosomes due to non-selective bulk degradation of cytosolic contents, or are co-purifying contaminants. Likewise there was minimal overlap between the Class 1 and 2 proteins described here with two additional proteomics efforts

[Overbye, A., et al., supra; Gao, W., et al., supra]. While it is understandable that there would be variation between datasets depending on cell type, autophagy stimulus, and purification technique, the present dataset represents the most robust autophagosome proteomics effort to date given the number of bona fide autophagy related proteins identified among the Class 1 and 2 candidates.

Among the most highly and consistently enriched autophagosomal proteins was NCOA4 (nuclear receptor coactivator 4) (Fig. 1 (e)), which was also enriched in an independent autophagosome proteomics study, although not included in their final list of autophagosomal proteins due to the method of analysis [Dengjel et al., supra] (see, Fig. 17 and Example 1). NCOA4 was originally identified as a protein that interacts with the androgen receptor (AR), and its overexpression was reported to activate transcription of AR-regulated genes [Yeh, S. & Chang, C. Proceedings of the National Academy of Sciences of the United States of America 93, 5517-5521 (1996)]. However, not all studies have supported a role for NCOA4 in AR function [Gao, T., et al. Molecular Endocrinology 13, 1645-1656 (1999)], and the data described below reveals a previously unrecognized role for NCOA4 as an autophagy cargo receptor.

Initially, the localization of NCOA4 was examined. GFP-NCOA4 was diffusely localized in the cytoplasm in U20S cells that have a low level of basal autophagy but accumulated in cytoplasmic puncta that are largely co-incident with LC3B-positive puncta in response to CQ in U20S cells as well as 8988T cells, consistent with localization of GFP-NCOA4 in autophagosomes (Fig. 2 (a), Fig. 18 (a)). In addition, NCOA4 showed significant co-localization with GAB ARAPL2 -positive puncta

(Fig. 18 (b)-(c)), which is consistent with it being amongst the strongest interactors in a GST-ATG8 binding assays performed in vitro using cell extracts (Fig. 2 (b)). Consistent with the proteomic data, NCOA4 was enriched in purified autophagosomes by immunoblotting, and its levels were markedly increased in response to blockade of autophagosome degradation by CQ or Bafilomycin Al (BAF) (Figs. 2 (c)-(d)).

Moreover, NCOA4 did not co-localize with the late endosome marker Mannose 6- Phosphate Receptor (Fig. 18 (d)). Together this data supports the predominantly autophagosomal localization of NCOA4 puncta. A canonical LIR (LC 3 -interacting region) motif was not identified in NCOA4, although the existence of non-canonical ATG8 binding motifs [von Muhlinen, N. et al. Molecular Cell 48, 329-342 (2012)] may suggest that NCOA4 employs such an alternative motif for interaction.

To begin to understand potential roles for NCOA4 in autophagy, affinity purification-mass spectrometry (AP-MS) of stably expressed NCOA4-HA-FLAG was performed, and the Comparative Proteomics Software Analysis Suite (CompPASS) was used to identify high confidence candidate interacting proteins (HCIPs). AP-MS of

NCOA4-HA-FLAG from PANC1, 8988T, and 293T cells revealed a number of HCIPs including both the ferritin heavy chain (FTH1) and ferritin light chain (FTL), as well as HERC2 and NEURL4, which are known to associate with each other (Fig. 2 (e))

[Martinez-Noel, G. et al. Molecular and Cellular Biology 32, 3095-3106 (2012)].

Interaction of NCOA4-HA-FLAG with selected endogenous HCIPs was verified by anti- FLAG immunoprecipitation followed by immunob lotting (Fig. 2f). FTH1-HA-FLAG reciprocally associated with endogenous NCOA4 as determined by AP-MS (Fig. 2 (e)) and also associated with co-expressed MYC-NCOA4 (Fig. 2 (g)). The absence of HERC2-NEURL4 in ferritin immune complexes suggested that NCOA4 makes distinct complexes with ferritin and HERC2-NEURL4. Consistent with this, neither HERC2 nor NEURL4 were enriched in autophagosomal fractionsand HERC2 does not co localize with autophagosomes (Fig. 18 (e)).

FTH1 and FTL form a 24-subunit macromolecular iron-storage complex critical for iron homeostasis [Pantopoulos, K., et al., supra]. Early electron microscopy studies identified iron-laden ferritin in lysosomes and more recently, it was shown that in cells subjected to iron chelation, ferritin is delivered to the lysosome for degradation via autophagy, presumably to promote iron availability [Asano, T. et al. supra; Kidane, T. Z., et al. American Journal of Physiology. Cell Physiology 291, (2006); Trump, B. F., et al. The American Journal of Pathology 72, 295-336 (1973)]. Interestingly, FTH1 and FTL were enriched in autophagosomal fractions from MCF7 and 8988T cells based on mass spectrometry (Fig. 2 (e), Fig. 14). Furthermore, ferritin and NCOA4 demonstrated extensive co-localization in puncta in several cell lines upon stimulation of ferritin expression with ferric ammonium citrate (FAC), reflecting the high level of ferritin undergoing autophagic targeting and lysosomal degradation (Fig. 2 (h)). This process is referred to as "ferritinophagy."

Given the interaction between NCOA4 and ferritin, and their localization in autophagosomes, the hypothesis that NCOA4 acts as an autophagy receptor for ferritinophagy was tested. In response to low intracellular iron levels, ferritin is degraded to release its iron stores. This can be stimulated experimentally by chelation of iron

[Asano, T. et al., supra]. While some reports have suggested that ferritin is degraded via the proteasome [De Domenico, I., et al. The EMBO Journal 25, 5396-5404, (2006)], it was validated that in the cell lines examined in the studies described herein, ferritin is primarily degraded by the lysosome in response to multiple distinct chelators (Fig. 19(a)- (b)), as observed previously (Asano et al., supra). In addition, genetic inhibition of autophagy using R Ai against ATG5 reduced ferritin degradation in response to iron chelation (Fig. 19 (c)). Importantly, suppression of NCOA4 expression with multiple shRNAs followed by iron chelation abrogated ferritin degradation in multiple cell lines and with chemically distinct chelators (Fig. 3a-b, Fig. 19 (d)-(g)). Consistent with the above results, ferritin localized to lysosomes and accumulated to a significant degree upon lysosomal protease inhibition (Fig. 20 (a)-(b)). Furthermore, ferritin simultaneously colocalizes with NCOA4 and LC3B positive puncta representing autophagosomes (Fig. 3 (c)). If NCOA4 functions as an essential receptor for ferritinophagy, depletion of NCOA4 would be predicted to block ferritin localization with lysosomes. Indeed, depletion of NCOA4 blocked ferritin co-localization with lysosomes and led to a diffuse localization pattern (Fig. 3 (d), Fig. 20 (c)). NCOA4 is also critical in mediating the targeting of ferritin to autophagosomes in non-transformed IMR90 and HPDE cells, indicating that this is a general cellular mechanism for the degradation of ferritin by autophagy (Fig. 20 (d)-(e)). As a control for the specificity of the shRNAs, a non- degradable murine NCOA4 cDNA was able to significantly rescue the ferritin lysosomal localization (Fig. 21 (a)-(c)). These results were confirmed with two additional siRNAs against NCOA4 (Fig. 22 (a)). Again, consistent with a distinct role for the

HERC2/NCOA4 complex, HERC2 knockdown had no effect on lysosomal delivery of ferritin (Fig. 22 (b)-(c)).

Iron plays an essential role in multiple cellular processes and as such iron metabolism is a tightly regulated process controlled by a network of iron-dependent proteins [Pantopoulos et al., supra]. Ferritin forms an intracellular iron storage protein complex capable of chelating up to 4500 atoms of iron, thus protecting the cell from free iron participating in the generation of free radicals via Fenton-like reactions [Kurz, T., et al., supra]. Iron stored in ferritin is utilized during periods of low iron levels and recent evidence suggests that iron can be liberated from ferritin upon degradation of ferritin in the lysosome [Asano et al, supra]. As the present evidence suggested that NCOA4 mediates the transport of ferritin to the lysosome via the autophagosome, it was next determined how NCOA4 knockdown affects the network of iron regulatory proteins. First, NCOA4 depletion increased basal ferritin levels relative to control cells (Fig. 3 (a), lane 1 versus lanes 6 and 11, Fig. 19 (f), lane 1 versus lanes 5 and 9). This suggested that NCOA4-deficient cells would display reduced iron bioavailability. Therefore, the levels of the iron-response protein 2 (IRP2), an RNA-binding protein that binds to iron response elements (IRE) on a set of iron-regulated mRNAs to control their translation

[Pantopoulos, K.et al. Biochemistry 51, 5705-5724, (2012)] were examined. Cellular iron levels control IRE -binding activity of IRP2, with high and low iron levels promoting IRP2 turnover and stabilization, respectively [Pantopoulos, K.et al., supra]. It was found that NCOA4 depletion increased IRP2 abundance to an extent comparable to control cells subjected to iron chelation (Fig. 3 (e), lane 7 versus lane 6). A higher IRP2 level in

NCOA4-depleted cells would be anticipated to stabilize transferrin receptor mRNA and increase translation of the transferrin receptor to increase intracellular iron. Indeed, the abundance of the transferrin receptor is increased in NCOA4-depleted 8988T cells (Fig. 3 (e), lane 1 versus lanes 2-3). These results were confirmed with two independent siRNAs to NCOA4 in 8988T, U20S, and IMR90 cell lines (Fig. 22 (d)). Overall, siRNA-mediated knockdown of NCOA4 in U20S, IMR90 and, 8988T cells led to increases in IRP2, FTH1, and TFRC levels. Conversely, ectopic expression of NCOA4 in 8988T cells attenuated the increase of ferritin seen in FAC treated control cells implying that the increased NCOA4 is promoting ferritin turnover (Fig. 22 (e)). The abundance of NCOA4 was altered by iron loading or chelation, although no canonical iron response element [Pantopoulos, K.et al., supra] was identified (Fig. 3 (b),

Fig. 22 (e)).

Next, the biological consequences of reduced iron availability and lysosomal ferritin degradation in response to NCOA4 depletion were examined. Lysosomal iron has been shown to react with reactive oxygen species (ROS) leading to free radical formation via Fenton-like reactions, which results in lysosomal bursting and cell death [Kurz et al., supra]. Therefore, NCOA4 knockdown should provide protection from cell death after ROS challenge. As shown in Fig. 3 (f), control cells were more sensitive to hydrogen peroxide challenge than NCOA4-depleted cells.

Selective autophagy is increasingly recognized as a regulated process through which specific cellular proteins, complexes, and organelles are degraded in the lysosome in response to diverse stimuli. Previous work suggested that delivery of the ferritin complex to lysosomes occurs via autophagy and regulates iron bioavailability [Asano et al., supra; Kidane et al, supra]. The present identification of NCOA4 as a specific cargo receptor for ferritin provides the first mechanistic understanding of how the ferritin complex is selectively delivered to autophagosomes. Flux through the pathway is regulated by iron availability, and in turn, disruption of the pathway through modulation of NCOA4 levels leads to alterations in the activity of IRP2, and altered sensitivity of cells to ROS. Moreover, NCOA4 mRNA is induced in red blood cells during

erythropoiesis, and its expression correlates with genes involved in heme -biosynthesis [Nilsson, R. et al. Cell Metabolism 10, 119-130, (2009)], raising the possibility that

NCOA4 function is important for both cellular remodeling and iron availability during differentiation [Griffiths, R. E. et al. Autophagy; 8, 1150-1151, (2012)]. While the present data provide compelling evidence for the role of NCOA4 as a ferritinophagy cargo receptor, it does not rule out that it may have other roles in specific cellular contexts. However, given the present findings in normal and tumor cells of diverse tissue origin, this work demonstrates that the targeting of ferritin to autophagosomes by NCOA4 is a general cellular mechanism for regulating bioavailable iron. This work also reveals the potential of quantitative autophagy proteomics to uncover receptor-cargo relationships and to further elucidate the mechanisms underlying both macro and selective autophagy.

Example 3: Mapping the Interaction between NCOA-4 and Ferritin

To probe the interaction between ferritin and NCOA4, initial binding assays using MYC-tagged NCOA4 full-length and truncation constructs produced using an in vitro translation system were conducted according to the methods described, above. The fragments were designed based on secondary structure prediction: coiled coil domain at N-terminus and no known structure/homology with any other proteins in C-terminus. See, Figure 4. As shown in Figure 5, full-length (aal-614 of SEQ ID NO: 4) and C- terminal MYC-NCOA4 (aa235-614 and aa555-614) associated with ferritin but N- terminal MYC-NCOA4 did not associate with ferritin. Further, NCOAB, a naturally occurring transcript variant of NCOA4 that consists of amino acids 1-238 and 555-614 (a single construct), did not bind ferritin. The bottom two panels in Fig. 5 show the input to the immunoprecipitation assay ("IP"), i.e., there was FTH1 already in the IVT lysate (without adding the equine apoferritin) and these are the GST-NCOA4 fragments added to the IP. (Apoferritin was added to the binding reactions for which the data is shown in the upper two images in Fig. 5).

In another set of experiments, to further probe the interaction between ferritin and NCOA4, binding assays using GST-tagged NCOA4 truncation constructs were as described, above. Briefly, portions of the C-terminal domain of NCOA4 fused to the C- terminus of GST were expressed, and then the fusion proteins were immobilized on glutathione Sepharose beads. Fragments (aa235-614, aa235-560, aa383-560, aa235-401, and aa545-614 of SEQ ID NO: 4) were designed based on secondary structure prediction in C-terminus (see the schematic diagram in Fig. 6).

The GST pull-down assay was performed and bands were visualized with anti- FTH1 antibody or Ponceau staining, as described above. As shown in Fig. 7, C-terminal NCOA4, aa235-560, and aa383-560 bound to ferritin. The minimal region of NCOA4 that recapitulated binding to ferritin in this experiment was amino acid residues 383-560. Furthermore, an anti-GST antibody immunoblot showed a band at the appropriate size for the predicted size of the various GST-NCOA4 fragments, as well as breakdown products.

Additional experiments were conducted to determine the minimal amino acid sequence of NCOA4 that was required for NCOA4 interaction with ferritin. Additional GST-tagged fragments of NCOA4 were tested (produced as described in Example 1), including aa383-522, aa511-560, aa383-436, aa401-436, aa436-485, and aa475-522 of SEQ ID NO:4. As shown in Figure 8, the minimal NCOA sequence that interacted with ferritin in this experiment was aa475-522 (corresponding to

KAMTPSRIADSFQVIKNSPLSEWLIRPPYKEGSPKEVPGTEDRAGKQK (SEQ ID NO: 2)).

A further experiment was conducted which was an IVT -based interaction experiment using C-terminal His-GST-HA tagged NCOA4 constructs and GST pulldown (note 436-485 did not express). Data are shown in Fig. 9, and the results show that that the load for fragments of aa383-522 and aa475-522 were equal, and those fragments equally pulled down (bound to) FTH1. Further experiments were conducted to determine the minimal binding fragment of NCOA4 that can bind to ferritin. A GST pull-down assay of ferritin using GST- NCOA4 proteins fragments, and GST alone as control, was performed. An anti-FTHl immunoblot was performed for ferritin. The following NCOA4 fragments (coupled to GST) were tested: amino acid residues (aa)475-572; aa475-500; aa480-500; aa480-504; aa485-509; aa490-514; and aa495-522. As shown in Figure 11, anti-GST immunoblot showed a band at the appropriate size for the predicted size of the various GST-NCOA4 fragments, as well as breakdown products, and aa475-522 and aa485-509 bound to ferritin. Thus, the minimal fragment of NCOA4 that binds to ferritin was aa485-509, which corresponds to amino acids SFQVIKNSPLSEWLIRPPYKEGSPK (SEQ ID NO : 11).

Example 4: NCOA4 Binds Preferentially and Directly to FTH1

To understand if there was subunit specificity for NCOA4 binding to ferritin, the NCOA4 C-terminus (aa235-614) fusion protein was immobilized on glutathione

Sepharose beads, as described in Example 1. Recombinant purified FTH1 or FTL produced in E. coli was added at concentrations of 0.2 μg and 1 μg, and binding was determined using the GST pull-down assay described in Example 1, above. As shown in Figs. 10A and 10B, FTH1 but not FTL interacted with the NCOA4 C-terminus, suggesting that NCOA4 interacts with specificity in vivo for FTH1. These results also suggest that certain cells may use ferritinophagy more than others (e.g., cells that produce more FTH1 as opposed to FTL).

Example 5: Mapping the Interaction between NCOA4 and HERC2

To map the interaction between NCOA4 and HERC2, it was first determined that

NCOA4 (383-560) binds to HERC2 fragment "3" (amino acid residues 1700-2700 of SEQ ID NO: 8 (NP 004658)). A flag-tagged HERC2 fragment was expressed in 293T cells and cell lysates were tested in a GST-NCOA4 binding assay, using various GST- NCOA4 fragments. Anti-FLAG immunoblot for HERC2-FLAG was performed.

Coomassie stain for loading of GST-NCOA4 fragments (note there are multiple breakdown products of the GST-NCOA4 fragments) was also performed. The following NCOA4 fragments were tested, amino acid residues (aa)383-522; aa510-560; aa383-436; aa436-485; and aa475-522. Anti-GST immunoblot showed a band at the appropriate size for the predicted size of the various GST-NCOA4 fragments as well as breakdown products. As shown in Figure 12, aa383-522 and aa383-436 bound to HERC2-FLAG. The minimal region of NCOA4 required for binding to HERC2 was thus determined to be aa383-436, corresponding to SEQ ID NO: 3 (SMVTEDWLVQNHQDPCKVEEVCRA NEPCTSFAECVCDENCEKEALYKWLLKKEG).

Example 6: Mapping the Interaction between NCOA4 and FTHl

Wild-type (WT) and point mutants of FTHl were produced recombinantly in E. coli and purified by chromatographic techniques including size exclusion

chromatography to confirm oligomeric ferritin cage assembly (elution at 440 kDa size on Superose 6 column). In a GST pull-down assay, NCOA4(aa383-522)-GST or GST alone was incubated with 10 μΐ of a 50% (v/v) slurry of glutathione Sepharose 4B beads (GE Healthcare Lifesciences, 17-0756-01) for 30 minutes at 4°C. Beads were washed thoroughly with 150 mM NaCl, 20 mM Tris (pH 7.4), 2 mM dithiothreitol (DTT), 0.5% (w/v) Nonidet P-40, leaving 50-100 μg of GST-fusion protein bound to the beads. Beads were then mixed with 40 μg of recombinant human WT or point mutant FTHl produced in Pvosetta E. coli (EMD Millipore, 70953-3). The assay mix was incubated for 30 minutes at 4°C, and beads were washed three times with 1 ml wash buffer. Proteins were eluted with SDS sample buffer and analyzed by 4-20% gradient SDS-PAGE. InstantBlue Stain (Expedeon: catalog # ISB1L) was used to visualize GST-NCOA4 bands and FTHl bands. As shown in Figures 23A-D, the NCOA4(383-522)-GST fragment bound only very weakly to the FTHl R23A point mutant but bound to FTHl WT and other point mutants of FTHl strongly. Based on this result and the known 3 -dimensional structure of FTHl (PDB: 3AJO), it is predicted that all or part of the two alpha helices of FTHl would be involved in the interaction with NCOA4; the alpha helices include amino acids D16-V34 and C103-K125 (numbering starts from methionine encoded by start codon) of FTHl . The interaction would very likely also involve the loop structure (G78-K88) adj acent to the R23 site of FTH 1. A number of embodiments of the invention have been described. Nevertheless, it will be understood that various modifications may be made without departing from the spirit and scope of the invention. Accordingly, other embodiments are within the scope of the following claims.