RELATED APPLICATIONS

[0001] This patent application claims the benefit of, and priority to, U.S. Provisional Patent Application No. 62/216,976 filed on September 10, 2015. The entire content of the foregoing application is incorporated herein by reference, including all text, tables and drawings.

SEQUENCE LISTING

[0002] The instant application contains a Sequence Listing which has been submitted in ASCII format via EFS-Web and is hereby incorporated by reference in its entirety. Said ASCII copy, created on September 9, 2016, is named LIAI0448513_ST25.txt and is 15 KB (15,022 bytes) in size.

GOVERNMENT SUPPORT

[0003] This invention was made, in part, with government support under grant number ROl HL134236 awarded by NIH. The government has certain rights in the invention.

INTRODUCTION

[0004] Monocytes are the main immune cell type that infiltrate atherosclerotic plaques, and a substantial body of evidence implicates monocytes as key players in the early stages of atherosclerosis. Mice have two major monocyte populations that can be found in the bone marrow (BM) and circulating in the blood. Both of these populations express the myeloid- defining markers CDllb and Csflr (CD115), which can be used to identify these cells by flow cytometry. The two major monocyte populations can be separated based on the expression of the cell surface antigen Ly6C.

[0005 ] Ly 6C ^hi monocytes are the short-lived precursors of inflammatory macrophages and are key drivers of atherosclerosis ¹ . Ly6C ^hl monocytes are recruited to atherosclerotic lesions in a Ccr2 and Ccr5-dependent manner, and preventing recruitment almost completely abrogates atherosclerosis in mice fed a high diet ² . Less in known about Ly6C ^low monocyte function however they do infiltrate atherosclerotic lesions ² , and circumstantial evidence suggests that they protect against atherosclerosis, and generally act in wound repair ³ ' ⁴ .

Ly6C ^low monocytes display a characteristic patrolling behaviour on the vascular endothelium ⁵ and help to remove damaged endothelial cells ⁶ .

[0006] Ly6C ^low monocyte development requires the transcription factor Nr4al (Nur77; Nuclear Receptor Subfamily 4 Group A Member 1; e.g., UniProtKB: P22736) as Nr4al ^'A mice completely lack Ly6C ^low monocytes ⁷ . Nr4al is highly expressed and its effects are cell- intrinsic. Hence Nr4al is a lineage-determining transcription factor for Ly6C ^low monocytes. In two independent models of atherosclerosis (Apoe ' ^~ and Ldlf' ^~ ), Ντ4αΓ' ^~ mice develop worse disease ³ indicating a restorative function for Ly6C ^low monocytes in atherosclerosis. This interpretation is confounded by the fact that Nr4aV' ^~ macrophages are more

inflammatory, a processes that adversely affects atherosclerosis ³ .

[0007] Evidence suggests that the human CD14 ⁺ CD16 ^" monocytes are equivalent to the mouse Ly6C ^hl population and that CD14 ^dim CD16 ⁺ monocytes are similar to Ly6C ^low monocytes ⁸ ' ⁹ . CD14 ^dim CD16 ⁺ monocytes also have high Nr4al expression suggesting conserved function and raising the possibility that modulating Nr4al may allow manipulation of this subset in humans.

SUMMARY

[0008] Disclosed herein is the identification of transcription factors that regulate Nr4al during Ly6C ^low or CD14 ^dim CD16 ⁺ monocyte development. Modulation of such transcription factors allows for treatment of diseases as set forth herein.

[0009] In a first aspect, there is provided a method of treating an autoimmune disease in a subject in need thereof, the method including administering to the subject an effective amount of a PTPRA (Protein Tyrosine Phosphatase, Receptor Type A) antagonist.

[0010] In another aspect, there is provided a method of decreasing inflammation in a synovium of a subject in need thereof, the method including administering to the subject an effective amount of a PTPRA antagonist.

[0011] In another aspect, there is provided a method of decreasing expression of PTPRA in a fibroblast-like synoviocyte, the method including contacting said fibroblast-like synoviocyte with an effective amount of a PTPRA antagonist.

[0012] In another aspect, there is provided a method of decreasing TNF activity, IL-1 activity and/or PDGF activity in a fibroblast-like synoviocyte, the method including contacting the fibroblast-like synoviocyte with an effective amount of a PTPRA antagonist.

[0013] In another aspect, there is provided a method of decreasing invasiveness or migration of a fibroblast-like synoviocyte, the method including contacting the fibroblast-like synoviocyte with an effective amount of a PTPRA antagonist.

[0014] In another aspect, there is provided a pharmaceutical composition including a PTPRA antagonist and a pharmaceutically acceptable excipient.

[0015] In some aspects, there is provided a method of modulating CD14 ^dim CD16 ⁺ (CD115 ⁺ CD1 lb ⁺ GRl ^~ (Ly6C ^~ )) monocytes or macrophages. In some embodiments, methods of modulating CD14 ^dim CD16 ⁺ (CD115 ⁺ CDllb ⁺ GRr (Ly6C ^" )) monocytes or macrophages comprises increasing or decreasing the amounts of CD14 ^dim CD16 ⁺

(CD115 ⁺ CDl lb ⁺ GRl ^~ (Ly6C ^~ )) monocytes or macrophages in a subject (e.g., mammal or human). As described herein, the expression or activity of Nr4al (Nur77) can directly effect the activity and/or amounts of CD14dimCD16+ (CD115+CDllb+GRl- (Ly6C-)) monocyte/macrophage populations in a subject. Thus, in certain embodiments, a method of modulating CD14 ^dim CD16 ⁺ (CD115 ⁺ CDllb ⁺ GRr (Ly6C ^" )) monocytes or macrophages comprises modulating expression or activity of a transcription factor that regulates expression of Nr4al (Nur77). In certain aspects, a method of stimulating, promoting, increasing or inducing CD14 ^dim CD16 ⁺ (CD115 ⁺ CDllb ⁺ GRr (Ly6C ^" )) monocyte or macrophage cell production, development, survival, proliferation, differentiation or activity, comprises modulating expression or activity of a transcription factor that regulates expression of Nr4al (Nur77).

[0016] Certain transcription factors are disclosed herein that bind to a 5' upstream regulatory DNA sequence in the 5' untranslated region (UTR) of the Nr4al gene, the cis- regulatory promoter region of the Nr4al gene, or in any other trans-acting Nr4al -associated enhancer sequence, such as those identified herein, where such transcription factors can modulate Nr4al gene expression. Accordingly, disclosed herein, in certain embodiments, are transcription factors that bind to specific regulatory DNA sequences located in the 5 ' UTR of the Nr4al gene, such as enhancer region 2 (Nr4alse_2) in Ly6C- monocyte or upstream progenitor cell types thereof, or a homologous region in CD14 ^dim CD16 ⁺

(CD115 ⁺ CD1 lb ⁺ GRl ^~ (Ly6C ^~ )) monocytes or upstream progenitor cell types thereof. In some embodiments, the transcription factors are Klf2 and Klf4.

[0017] In some aspects, there are provided methods of inhibiting growth of a

hyperproliferative cell, tumor cell, cancer cell, neoplastic cell, metastatic cell or tumor, wherein the method comprises administering an agonist or antagonist to a subject. In certain embodiments, an agonist or antagonist is an agonist or antagonist of a transcription factor identified herein. In certain embodiments, an agonist or antagonist is an agonist or antagonist of a Nur77 transcription or expression. In certain embodiments, an agonist or antagonist is an antibody, a small molecule, a peptide, an inhibitory nucleic acid, an allosteric inhibitor or a ligand mimetic. In some embodiments, an antagonist or antagonist is an antibody, or binding fragment thereof, that specifically binds to a Klf2 or Klf4 polypeptide. In some

embodiments, an antagonist is an inhibitory nucleic acid that targets or binds to an mRNA directing the expression of a Klf2 or Klf4 polypeptide.

[0018] In some aspects, a method comprises decreasing, reducing, inhibiting, suppressing, limiting or controlling an undesirable or aberrant immune response, immune disorder, inflammatory response, inflammation autoimmune response, autoimmune disease, adverse cardiovascular event or cardiovascular disease in the subject. In certain

embodiments, the method comprises administering an agent, agonist, or antagonist to a subject to treat or prevent an undesirable or aberrant immune response, immune disorder, inflammatory response, inflammation autoimmune response, autoimmune disease, adverse cardiovascular event or cardiovascular disease. In some embodiments, the method comprises treating cancer in a subject.

[0019] In certain aspects, there is provided a pharmaceutical composition comprising an agonist or antagonist of a transcription factor that regulates expression of Nr4al (Nur77) for treatment of an aberrant immune response, immune disorder, inflammatory response, inflammation, an autoimmune response, disorder or disease, cancer or an adverse

cardiovascular event or cardiovascular disease in a subject. In some embodiments, the transcription factor binds to the DNA sequence in the region Nr4alse_2 in Ly6C- monocyte or upstream progenitor cell types thereof or a homologous region in CD14 ^dim CD16 ⁺

(CD115 ⁺ CD1 lb ⁺ GRl ^~ (Ly6C ^~ )) monocytes or upstream progenitor cell types thereof. In certain embodiments, the transcription factor is Klf2 or Klf4. In certain embodiments, the agonist or antagonist is an antibody, a small molecule, a peptide, an inhibitory nucleic acid, an allosteric inhibitor or a ligand mimetic.

[0020] In some aspects, provided herein are methods of identifying an agent that modulates, increases or decreases CD14 ^dim CD16 ⁺ (CD115 ⁺ CDllb ⁺ GRr (Ly6C ^" )) monocyte or macrophage amounts or activity. A representative method comprises: (a) contacting an experimental agent with an Nr4al promoter region in the presence of Klf2, Klf4 and/or Nf- KB, wherein the Nr4al promoter region is operably linked to a reporter nucleic acid; (b) determining an amount of the reporter nucleic acid, or a transcribed or translated product thereof; (c) comparing the amount determined in (b) to a control amount of reporter nucleic acid, or a transcribed or translated product thereof, wherein a difference between the amount determined in (b) and the control amount indicates the experimental agent is an agent that modulates, increases or decreases CD14 ^dim CD16 ⁺ (CD115 ⁺ CDllb ⁺ GRr (Ly6C ^" )) monocyte or macrophage amounts or activity. In some embodiments, a experimental agent is an antibody or inhibitory nucleic acid. In some embodiments, a experimental agent is an antibody that specifically binds to Klf2 or Klf4.

[0021] In some embodiments, presented herein is a vertebrate, (e.g., a mammal, e.g., a rodent; e.g., a rat, e.g., a mouse, or the like) comprising deficient, disrupted or modified Nr4alse_2 sequence. A vertebrate deficient in an Nr4alse_2 sequence can be homozygous or heterozygous for a deleted, modified or disrupted Nr4alse_2A sequence. In some embodiments, presented herein is method of using a vertebrate, (e.g., a mammal, e.g., a rodent; e.g., a rat, e.g., a mouse, or the like) comprising a deficient, disrupted or modified Nr4alse_2 sequence to identify CD14dimCD16+ (CD115+CDl lb+GRl- (Ly6C-)) monocyte functions.

BRIEF DESCRIPTION OF THE DRAWINGS

[0022] Fig. 1. shows a UCSC genome browser screenshot showing, from top to bottom, PU.l peaks in Ly6C ^low monocytes, overlays of H3K27ac and H3K4me2 respectively with Ly6C ^hl monocytes in Red and Ly6C ^low monocytes in blue. The lower tracks show our enhancer candidate predictions and the Nr4al gene model.

[0023] Fig. 2. shows a graph of luciferase activity (y-axis) in RAW264.7 cells of 12 candidate enhancer sub-domains within Nr4alse (x-axis). SEM shown, ** P<0.01, **** P<0.0001.

[0024] Fig. 3. shows a UCSC genome browser track showing the positions of designed sgRNAs and how they relate to the Nr4alse sub-domains.

[0025] Fig. 4(a) shows representative flow cytometry plots showing blood monocyte frequencies in Nr4alse_e2 ^_/" , e6 ^_/~ and e9 ^_/~ mice obtained from homozygous null founder mice (wild type (WT)). Gated Lin (CD3, CD19, Ly6G) ^~ , CD115 ⁺ cells are shown stained for Ly6C (y-axis) and MHCII (x-axis). Fig. 4(b) shows a bar chart showing the reduction of Ly6C ^low monocytes in Nr4alse_e2 mice.

[0026] Fig. 5 shows over-represented TFBS in Nr4alse candidate enhancer elements. Shown is a UCSC genome browser screenshot showing E02 from Nr4alse illustrating the positions of motifs for Klf, AR and PU.l (Spfil) transcription factors.

[0027] Fig. 6 shows a graph of enhancer activity at Nr4alse_2 as measured by luciferase assay. Data are plotted as the relative reporter activity of the (gene: enhancer / gene:promoter only) pair and are normalized with respect to the pEntry (no cDNA) control.

[0028] Fig. 7 shows a graph of cDNA overexpression of various Klf transcription factors in RAW264.7 cells in the presence of Nr4al-TSS (promoter), Nr4al-E2 (promoter + E2) and Neg (no promoter or E2) demonstrating increased E2-dependent transcription in the presence of Klf transcription factors.

[0029] Fig. 8 shows a graph of LPS-dependent activity of the Nr4al-E2 reporter, and interaction effect with Klf2 transcription factor.

[0030] Fig. 9. Epigenomic profiling of Mo subsets and progenitors supports the model of Ly6C ^ht to Ly6C ^low Mo conversion. Fig. 9(a) shows a gating strategy used to sort monocytes and upstream progenitors. Cells were previously gated on live singlets (using a FSC-W/FSC- A gate). Fig. 9(b) shows UCSC genome browser screenshots showing H3K27ac and H3K4me2 tag distributions at key lineage genes. Fig. 9(c) shows distribution of H3K4me2 and H3K27ac tags +lkb from PU.l peak centers in DE enhancers.

[0031] Fig. 10. Ly6C ^low Mo possess a cell-specific SE at the Nr4al locus. Fig. 10(a) shows a UCSC genome browser screenshot of the Nr4al locus depicting Ly6C ^ow Mo PU.1 and C/ΕΒΡβ binding and H3K4me2 and H3K27ac in both Ly6C ^hi and Ly6C ^low Mo. Fig. 10(b) and Fig. 10(c) show graphs of H3K4me2 and H3K27ac tag counts (y-axis) at Nr4alse in MDP, cMoP, Ly6C ^hi and Ly6C ^low Mo as labelled on the x-axis. Fig. 10(d) shows a graphical illustration of mRNA-Seq expression levels of Nr4al in various tissue macrophage subsets taken from Lavin et al (2014), labelled 'Lavin', and from data disclosed herein, labelled 'Thomas'. Fig. 10(e) shows H3K27ac levels at Nr4alse for the same MP populations as in Fig. 10(d).

[0032] Fig. 11 - Identification of a conserved SE sub-domain essential for Ly6C ^low Mo development. Fig. 11(a) shows relative luciferase activity in RAW264.7 cells of candidate enhancer regions cloned into pGlA.Nr4al vector. Results shown are averaged over 2 independent experiments. Error bars represent SD, P- values calculated by 2-way anova * P<0.05, **P<0.01, ****P<0.0001. Fig. 11(b) shows a UCSC genome browser screenshot of the human Nr4al locus. H3K27ac tracks for CD14 ⁺ CD16 ^dim (classical) and CD14 ^dim CD16 ⁺ (non-classical) Mo are shown alongside BLAT alignments of nucleosome-free DNA sequence obtained from mouse E2, E6 and E9. Mo DNase-Seq data were taken from (Boyle et al, 2008); nucleotide sequence conservation is indicated using the GERP track. Fig. 11(c) shows PCR Genotyping of Nr4alse_2, Nr4alse_6 and Nr4alse_9 mice. Fig. 11(d) and Fig. 11(e) shows enumeration of peripheral blood Mo in Nr4alse_2 (E2), Nr4alse_6 (E6) and Nr4alse_9 (E9) mice. Parametric t-tests performed relative to WT, ** p< 0.01 *** p<0.001. f) FACS gating and representative flow plot for each genotype in Fig. 11(d) and Fig. 11(e).

[0033] Fig. 12 - Nr4alse_2 does not regulate Nr4al mRNA expression in response to inflammatory stimuli. Fig. 12(a) shows Nr4al mRNA expression levels in thioglycollate- elicited macrophages obtained from Nr4al ^flox/flox mice crossed to Lys2-Cre and Csflr-Cre, WT (Cre- littermates) are shown as control. Fig. 12(b) shows a Kaplan-Mayer curve showing survival of WT, Nr4alse_2 ^/ and Nr4al ^'A mice in response to a single dose of 2.5mg/kg LPS LP. Mantel-Cox (Log rank) test results: WT vs. Nr4al ^~ ' ^~ p<0.01, Nr4alse_2 ^~/~ vs. Nr4ar p<0.05, Nr4alse_2 ^~/~ vs. WT p>0.05. Fig. 12(c) shows an RT-PCR time course of Nr4al mRNA in primary thioglycollate-elicited macrophages following LPS stimulation

(lOOng/ml). Fig. 12(d) shows a Western blot showing Nr4al levels lh post LPS stimulation (lOOng/ml). Fig. 12(e) shows Nr4al mRNA expression in dose escalation at lh post LPS stimulation. Fig. 12(f) shows inflammatory cytokine mRNA expression in primary peritoneal macrophages (PM) lh post injection of lug LPS LP. Fig. 12(g) shows nitric oxide in PM culture supernatant 96h after LPS stimulation.

[0034] Fig. 13 - Identification of motifs associated with Ly6C ^low Mo development. Fig. 13(a) shows normalized PU.l ChlP-Seq signal in Ly6C ^hi and Ly6C ^low Mo of Ly6C ^low Mo- specific PU.l sites ±400 bases from PU.l peak center. Fig. 13(b) shows H3K27ac ±500 bases of Ly6C ^low Mo-specific PU.l peaks. Fig. 13(c) shows relative expression of genes proximal to Ly6C ^low Mo-specific PU.l peaks. Fig. 13(d) shows overrepresented motifs in Ly6C ^low Mo specific PU.l peaks identified by de novo enrichment analysis. Fig. 13(e) shows RNA-Seq expression levels of TFs predicted to bind motifs in Fig. 13(d).

[0035] Fig. 14 - Klf2 drives Ly6C ^hi to Ly6C ^low Mo conversion via Nr4alse_2. Fig. 14(a) shows overexpression of candidate TFs in the presence of pGL4.Nr4al_e2 and pGL4.Nr4al reporter vectors in RAW264.7 cells. The enhancer index is calculated as described in the methods. Fig. 14(b) shows blood Mo frequencies in Lys2-Cre Kifif ^ox/flox and Lys2-Cre _Kl j fiox/flox _{mice Fig 14(} ^ _shows N _r 4 _a ] _m RNA expression levels in primary Ly6C ^hl Mo d) Klf2 mRNA correlated against Nr4al in Ly6C ^low Mo. Fig. 14(e) shows the same data as Fig. 14(d) for Klf4 mRNA. Fig. 14(f) Klj2 mRNA expression levels in primary human Mo subsets as measured by microarray.

[0036] Fig. 15 - Nr4alse_2 is a monocyte-specific enhancer. Fig. 15(a) shows a gating scheme for tissue macrophage sorting. All cells were previously gated on live singlets. The side scatter high profile of lung CDllc ⁺ macrophages is shown in the right panel (blue). Fig. 15(b) and Fig. 15(c) shows relative Nr4al mRNA expression in tissue macrophages and blood Ly6C ^hi and Ly6Cl ^ow Mo. Statistics for Fig. 15(b) and Fig. 15(c) were measured by students t-test * p<0.05, ** p<0.01. Fig. 15(d) shows representative sections of B16F10 tumors in WT, Nr4al ^' and E2 ^' mice. Fig. 15(e) and Fig. 15(f) show quantification of cancer metastasis area. Error bars represent SD statistics were analyzed by ANOVA * p<0.05.

[0037] Fig. 16(a) shows differentially bound H3K4me2 peaks (P,l*10 ^~5 ). A total of 640 enhancer regions were found to be differentially regulated between all conditions. Fig. 16(b) shows differentially bound H3K27ac peaks (P,l*10 ^~5 ). A total of 9,879 enhancer regions were found to be differentially regulated between all conditions. Fig. 16(c) shows hierarchical clustering of DE enhancer regions. Bands on the left show clusters used to define groups in Fig. 9(c). Fig. 16(d) shows the presence/absence of de novo motif instances in clusters associated with MDP, MDP/cMoP, Ly6C ^hi /Ly6C ^low Mo, or Ly6C ^low Mo only, as defined in Fig. 9(c) and Fig. 16(c). Only motif instances with a significance p-value 10 ^"40 are shown, alongside the representative motif identified by HOMER.

[0038] Fig. 17 shows gene expression profiles Differential gene expression pairwise comparisons in mRNA-Seq data.

[0039] Fig. 18 shows a UCSC genome browser screenshot of Nr4al and surrounding region. The Nr4al -associated super-enhancer (Nr4alse) is highlighted by a vertical grey band. Super-enhancer predictions for Ly6C ^low monocytes are shown in black directly above the gene prediction track.

[0040] Fig. 19(a) shows a UCSC genome browser screenshot showing positions of CRISPR sgRNA sites for E2, E6 and E9 KO mice. The TFs track shows superimposed PU.l and CEBPb transcription factor binding profiles in Ly6C ^low Mo. Fig. 19(b) shows a schematic of pGL4.10 luciferase reporter vector containing Nr4al 300bp of Nr4al promoter upstream of the TSS and the 5' UTR sequence. Fig. 19(c) shows sgRNA design.

[0041] Fig. 20(a) shows mRNA expression levels of transcription factors belonging to family of over-represented motifs present in Ly6C ^low monocyte enhancer regions based on RNA-Seq data. Fig. 20(b) shows Klf motifs (identified using HOMER) present in the Nr4al E2 enhancer sub-sequence.

[0042] Fig. 21(a) shows flow cytometric analysis of Mo subset frequencies in the bone marrow of Mac-Klf2 and Mac-Klf4 mice. Fig. 21(b) shows frequencies of GFP+ cells transduced with GFP and shRNA expressing retrovirus targeting Klf2, Klf4, or non-targeting control (NTC) sequence. Fig. 21(c) and Fig. 21(d) show Klf2 (c) and Klf 4 (d) mRNA expression in blood monocyte subsets sorted from Mac-Klf2 and Mac-Klf4 mice. Fig. 21(e) Fig. 21(f ) show Klf2 (e) and Klf4 (f) mRNA expression levels correlated against Nr4al mRNA expression in Ly6C ^hl Mo.

[0043] Fig. 22(a) shows tissue macrophage subset frequencies in WT and Nr4alse_2 ^~ ' ^~ mice as measured by FACS. Fig. 22(b) shows blood monocyte subset frequencies in WT, Nr4al ^_/~ and Nr4alse_2 ^~/~ mice 18 days after injection with 300,000 B16F10 melanoma cells. Fig. 22(c) shows quantification of histological sections for B16F10 tumors. Fig. 22(d) shows size distribution of individual tumors within lungs of mice relating to Fig. 15(d). Statistics for Fig. 22(c) and Fig. 22(d) were performed using students t-test, p values are shown.

DETAILED DESCRIPTION

[0044] Enhancers regulate cell-specific patterns of gene expression and can be quantitated genome-wide using ChlP-Seq directed against the histone modification

H3K4me2. Active enhancers can be further identified based on H3K27ac ^{10 11} . Lineage- determining transcription factors (LDTFs) establish and maintain cell-specific enhancer repertoires. The major myeloid LDTF is PU.l ¹¹ . Differential PU.l binding occurs between different macrophage populations and these cell-specific PU.l peaks co-localize with motifs associated with transcription factors that maintain the identity of these distinct populations ¹² .

[0045] Disclosed herein are profiled enhancer landscapes of primary Ly6C ^hl and Ly6C ^low monocytes to identify factors regulating Ly6C ^low monocyte development. The strategy integrated a molecular analysis of Nr4al -associated enhancers with regulatory information inferred from genome-wide ChlP-Seq analysis to define high priority targets.

[0046] Disclosed herein are H3K4me2, H3K27ac and PU.1 ChlP-Seq data for primary mouse Ly6C ^hl and Ly6C ^low monocytes. Large enhancer region upstream of Nr4al that shows greatly increased activity in Ly6C ^low monocytes were identified (Fig. 1). This region, termed Nr4alse, displays the characteristics of a super-enhancer. Super-enhancers typically span >10kb and are found nearby, and control the expression of, genes important for cell-type specification ¹³ ' ¹⁴ . Thus it was found that Nr4alse regulates Nr4al in Ly6C ^low monocytes.

[0047] To characterize the regions of Nr4alse that are functionally relevant for transcriptional regulation 12 regions defined on the basis of nucleosome depletion and PU.l occupancy, two measures of active transcription factor binding ¹¹ , were cloned. Luciferase reporters consisting of the Nr4al promoter and each of these 12 candidate loci (Figures 1 and 2) were tested for enhancer activity using the macrophage like RAW264.7 cell line. Regions E02, E06 and E09 were found to display basal enhancer activity (Fig. 2). A large fold- change induction of these enhancers in RAW264.7 cells was not expected as the requisite transcription factors are expected to be specific to the Ly6C ^low monocyte subset.

[0048] Enhancer landscapes of both human CD14 ⁺ CD16 ^" and CD14 ^dim CD16 ⁺ monocytes have been reported ¹⁵ . Although not wishing to be bound to or limited by any theory, if the human CD14 ^im CD16 monocyte population is truly orthologous to the mouse Ly6C ^ow monocyte subset then the transcriptional regulation of lineage-determining transcription factors would be subject to conservation by natural selection. Using a comparative genomics approach it was found that orthologous human DNA sequence to mouse regions E02, E06 and E09 contain elevated H3K27ac in the CD14 ^dim CD16 ⁺ Ly6C ^low monocyte equivalent.

[0049] As disclosed herein, it was discovered that E02, E06 and E09 are functional, evolutionarily conserved, sequences relevant for Nr4al gene expression in Ly6C ^low monocytes. Using the CRISPR-Cas9 system ¹⁶ ' ¹⁷ mice were made containing deletions of each of these regions to test their role in Ly6C ^low monocyte development. CRISPR-Cas9 is a nuclease complex that uses an RNA oligonucleotide (sgRNA) to direct the Cas9 nuclease to the site of genomic DNA cleavage with high precision. Administration of two sgRNA molecules alongside Cas9 results in pairs of DNA double-stranded breaks that are fused by the non-homologous end-joining DNA repair pathway ¹⁸ . As outlined in Fig. 3 this approach has been used to make Nr4alse_2, 6 and 9 ^_/" mice respectively.

[0050] As disclosed herein, it was discovered by sequencing that the desired deletions are present, and multiple instances of germline transmission have been observed for each strain.

[0051] Global Ντ4αΓ' ^~ mice lack Ly6C ^low monocytes, and therefore blood monocyte population frequencies in Nr4alse_2, e6 and e9 ^~ ' ^~ founder mice were assessed. Excitingly it was found that a single region, Nr4alse_2, is required for the Ly6C ^low monocyte subset in vivo (Fig. 4a, b). These findings are consistent with the hypothesis that a single, or small number, of transcription factors regulate Ly6C ^low monocyte commitment by converging at a single genomic locus.

[0052] Without being bound to or limited by any particular theory, the transcription factors driving Nr4al expression in Ly6C ^low monocytes may impart a global transcriptional signature within Ly6C ^low monocyte-specific enhancers. De novo motif analysis of Ly6C ^low monocyte-associated enhancers identified several motifs including those for PU.l and Nur77.

[0053] As also disclosed herein, motifs for CEBP, RUNX, KLF, MEF2, AP-1, AR/E2F and SMAD4 transcription factors were identified. These de novo motifs were mapped to Nr4alse_2 sequence to identify candidate motifs driving transcriptional activity at this region. Instances of KLF, AR and PU.l motifs were identified in this region (Fig. 5). In addition, a lower confidence Nf-κΒ motif associated with Ly6C ^ow monocytes that was present in the E2 region has been identified.

[0054] As disclosed herein, it was determined that transcription factors that bind to motifs identified in Fig. 5 regulate Nr4al transcription in Ly6C ^low monocytes. RNA-Seq gene expression data was interrogated to find transcription factors that are both expressed in Ly6C ^low monocytes and up-regulated in Ly6C ^low relative to Ly6C ^hl monocytes. Both monocyte subsets express multiple transcription factors that can bind to these motifs

Specifically these transcription factors are Spil (PU.l), Etsl (PU.l), Spib (PU.l), Nr4al (AR-halfsite), Klf2 (KLF), Klf4 (KLF), Klf6 (KLF) , KlflO (KLF) , Klfl3 (KLF).

[0055] An in vitro approach was taken to identify transcription factors that act via Nr4alse_2 enhancer element. cDNA clones (TrueORF, Origene) for each of the transcription factors defined above were transfected into macrophage-like RAW264.7 cells alongside the Nr4alse_2 reporter vector. RAW264.7 cells are a well established workhorse for macrophage transcriptional regulation assays. As background controls the Nr4al -TSS region without E2 enhancer sequence was used, and a vector containing neither the Nr4al -TSS promoter or enhancer region. Figs. 6 and 7 show the results from the study and cDNA overexpression of each of the transcription factors in the presence of the E2 enhancer sequence. These data clearly show that Klf family transcription factors, and klf2 and Klf 4 in particular drive the expression of Nr4al-luciferase activity.

[0056] As disclosed herein, also identified was an Nf-κΒ site within the E2 region and tested if this region is responsive to Nf-κΒ signalling. For this study the E2 reporter (and TSS-only, and negative control plasmid) was treated with the Tlr4 ligand LPS, a potent regulator of Nf-κΒ activity. The results from this study (Fig. 8) show that the E2 region is also LPS responsive, and that there is a synergistic effect between Klf2 and Nf-κΒ at the E2 locus.

[0057] As disclosed herein, mechanisms that regulate the expression of Nr4al in Ly6C ^low monocytes (via the Nr4alse_2 region) represent a druggable target. Agonising this pathway increases Ly6C ^low monocyte numbers, antagonising the pathway blocks the production of these cells. Without being be bound to or limited by to any particular theory, Klf

transcription factors and Nf-κΒ may play crucial roles in this process.

[0058] Thus in one embodiment, there is provided a novel approach to affect (promote/inhibit) non-classical (Ly6C ^ow in mouse and CD14 ^im CD16 in human) monocyte development. By modulating the activity of transcription factors that bind to the DNA sequence in the region Nr4alse_2 in Ly6C ^low monocytes, or upstream progenitor cell types (classical monocyte, cMoP, MDP), the transcription activity of Nr4al can be modulated. In turn this affects the activity of this cell type, which is of therapeutic importance, including in inflammation and wound healing. In certain embodiments of the provided methods,

CD14 ^dira CD16 ⁺ (CD115 ⁺ CD1 lb ⁺ GRl ^~ (Ly6C-)) monocytes or macrophages are modulated by modulating Nf-κΒ. In particular embodiments of the invention methods, Nf-κΒ is modulated in combination with modulating transcription factors.

[0059] In some embodiments, disclosed herein is a method of modulating the activity of CD14 ^dim CD16 ⁺ monocyte or macrophage cell production development, survival, proliferation differentiation or activity. Methods of modulating monocytes or macrophage can be in vitro methods or in vivo methods. In vitro methods often comprise contacting one or more cells, or portions thereof, with an agonist or antagonist. In vivo methods often comprise providing or administering an agonist or antagonist to a subject (e.g., a mammal, a human).

[0060] In certain embodiments, an agonist or antagonist is an antibody, or binding fragment thereof. In some embodiments an antibody, or binding fragments thereof, binds specifically to KLf2, Klf4 or Nf-κΒ. Accordingly, an antagonist antibody, or binding fragment thereof can bind specifically to Klf2, Klf4 or Nf-κΒ, which binding can inhibit or block the transcriptional regulatory activity of Klf2, Klf4 or Nf-κΒ. For example, specific binding of an antagonist antibody to Klf2 can inhibit or block binding of Klf2 to its DNA binding site or inhibit or block the transcriptional regulatory activity of Klf2. Alternatively, an agonist antibody, or binding fragment thereof can bind specifically to Klf2, Klf4 or Nf-κΒ, which binding can promote, increase, stimulate or induce the transcriptional activity of Klf2, Klf4 or Nf-κΒ. For example, specific binding of an agonist antibody to Klf2 can promote, increase, stimulate or induce binding of Klf2 to its DNA binding site or promote, increase, stimulate or induce the transcriptional regulatory activity of Klf2. Methods of identifying, selecting and/or assaying the agonist or antagonist activity of an antibody that specifically binds to Klf2, Klf4 or Nf-κΒ are disclosed herein.

[0061] In some embodiments, an agonist or antagonist antibody is administered to a subject. In certain embodiments, a subject having a disease or disorder (e.g.,

lymphoproliferative disorder (e.g., a cancer)) is treated for said disorder by administering to the subject an agonist or antagonist antibody. In certain embodiments, a subject having an autoimmune disorder or disease is treated for said disorder by administering to the subject an agonist or antagonist antibody.

[0062] The terms "antagonist" and the like refer to an agent which reduces the level of activity of a transcription factor or the level of expression of a transcription factor, e.g., Klf2 or Klf4. An antagonist can be a binding agent, a small molecule inhibitor, an allosteric inhibitor, an antibody, an inhibitory nucleic acid, an RNAi molecule, or a ligand mimetic.

[0063] The terms "subject," "patient," "individual," etc. are not intended to be limiting and can be generally interchanged. That is, an individual described as a "patient" does not necessarily have a given disease, but may be merely seeking medical advice.

[0064] As used herein, the terms "treat" and "prevent" may refer to any delay in onset, reduction in the frequency or severity of symptoms, amelioration of symptoms, improvement in patient comfort or function (e.g. nt function), decrease in severity of the disease state, etc. The effect of treatment can be compared to an individual or pool of individuals not receiving a given treatment, or to the same patient prior to, or after cessation of, treatment. The term "prevent" generally refers to a decrease in the occurrence of a given disease (e.g. an autoimmune, inflammatory autoimmune, cancer, infectious, immune, or other disease) or disease symptoms in a patient. As indicated above, the prevention may be complete (no detectable symptoms) or partial, such that fewer symptoms are observed than would likely occur absent treatment.

[0065] "Nucleic acid" or "oligonucleotide" or "polynucleotide" or grammatical equivalents used herein means at least two nucleotides covalently linked together. The term "nucleic acid" includes single-, double-, or multiple- stranded DNA, RNA and analogs (derivatives) thereof. Oligonucleotides are typically from about 5, 6, 7, 8, 9, 10, 12, 15, 25, 30, 40, 50 or more nucleotides in length, up to about 100 nucleotides in length. Nucleic acids and polynucleotides are a polymers of any length, including longer lengths, e.g. , 200, 300, 500, 1000, 2000, 3000, 5000, 7000, 10,000, or even longer. Nucleic acids containing one or more carbocyclic sugars are also included within one definition of nucleic acids.

Modifications of the ribose-phosphate backbone may be done for a variety of reasons, e.g. , to increase the stability and half-life of such molecules in physiological environments or as probes on a biochip. Mixtures of naturally occurring nucleic acids and analogs can be made; alternatively, mixtures of different nucleic acid analogs, and mixtures of naturally occurring nucleic acids and analogs may be made.

[0066] A particular nucleic acid sequence also encompasses "splice variants." Similarly, a particular protein encoded by a nucleic acid encompasses any protein encoded by a splice variant of that nucleic acid. "Splice variants," as the name suggests, are products of alternative splicing of a gene. After transcription, an initial nucleic acid transcript may be spliced such that different (alternate) nucleic acid splice products encode different polypeptides. Mechanisms for the production of splice variants vary, but include alternate splicing of exons. Alternate polypeptides derived from the same nucleic acid by read-through transcription are also encompassed by this definition. Any products of a splicing reaction, including recombinant forms of the splice products, are included in this definition. An example of potassium channel splice variants is discussed in Leicher, et al., J. Biol. Chem. 273(52):35095-35101 (1998).

[0067] An "inhibitory nucleic acid" is a nucleic acid (e.g. DNA, RNA, polymer of nucleotide analogs) that is capable of binding to a target nucleic acid (e.g. an mRNA translatable into a transcription factor) and reducing transcription of the target nucleic acid (e.g. mRNA from DNA) or reducing the translation of the target nucleic acid (e.g. , mRNA) or altering transcript splicing (e.g. single stranded morpholino oligo). In certain embodiments, the "inhibitory nucleic acid" is a nucleic acid that is capable of binding (e.g. hybridizing) to a target nucleic acid (e.g. an mRNA translatable into a transcription factor) and reducing translation of the target nucleic acid. The target nucleic acid is or includes one or more target nucleic acid sequences to which the inhibitory nucleic acid binds (e.g. hybridizes). Thus, an inhibitory nucleic acid typically is or includes a sequence (also referred to herein as an "antisense nucleic acid sequence") that is capable of hybridizing to at least a portion of a target nucleic acid at a target nucleic acid sequence. An example of an inhibitory nucleic acid is an antisense nucleic acid. Another example of an inhibitory nucleic acid is siRNA or RNAi (including their derivatives or pre-cursors, such as nucleotide analogs). Further examples include shRNA, miRNA, shmiRNA, or certain of their derivatives or pre-cursors. In some embodiments, the inhibitory nucleic acid is single stranded. In some embodiments, the inhibitory nucleic acid is double stranded.

[0068] An "antisense nucleic acid" is a nucleic acid (e.g. DNA, RNA or analogs thereof) that is at least partially complementary to at least a portion of a specific target nucleic acid (e.g. a target nucleic acid sequence), such as an mRNA molecule (e.g. a target mRNA molecule) (see, e.g. , Weintraub, Scientific American, 262:40 (1990)), for example antisense, siRNA, shRNA, shmiRNA, miRNA (microRNA). Thus, antisense nucleic acids are capable of hybridizing to (e.g. selectively hybridizing to) a target nucleic acid (e.g. target mRNA). In some embodiments, the antisense nucleic acid hybridizes to the target nucleic acid sequence (e.g. mRNA) under stringent hybridization conditions. In some embodiments, the antisense nucleic acid hybridizes to the target nucleic acid (e.g. mRNA) under moderately stringent hybridization conditions. Antisense nucleic acids may comprise naturally occurring nucleotides or modified nucleotides such as, e.g. , phosphorothioate, methylphosphonate, and -anomeric sugar-phosphate, backbone-modified nucleotides.

[0069] In some embodiments, an antagonist is an inhibitory nucleic acid. In certain embodiments, an inhibitory nucleic acid is an inhibitory RNA (iRNA), non-limiting examples of which include siRNA, RNAi, shRNA, miRNA, shmiRNA, morpholino oligos, the like, including derivatives and pre-cursors thereof, such as those comprising nucleotide analogs, and combinations thereof. An iRNA can mediate the targeted cleavage of an RNA transcript via an RNA-induced silencing complex (RISC) pathway. An iRNA can direct the sequence- specific degradation of mRNA through a process known as RNA interference (RNAi). In some embodiments, an iRNA modulates (e.g., inhibits, suppresses, blocks) the expression of a Klf2, Klf4 or Nf-κΒ polypeptide in a cell (e.g., a cell within a subject).

[0070] In some embodiments an iRNA includes a single stranded RNA that interacts with a target RNA sequence (e.g., Klf2, Klf4 or Nf-κΒ target mRNA sequence), which interaction directs cleavage or degradation of the target RNA. In another embodiment, an iRNA is a single-stranded siRNA that is introduced into a cell or organism to inhibit a target mRNA. Single- stranded siRNAs are generally 15-100 or 15-30 nucleotides in length and are sometimes chemically modified. The design and testing of single- stranded siRNAs are described in U.S. Pat. No. 8,101,348 and in Lima et al., (2012) Cell 150: 883-894.

[0071] In some embodiments, an iRNA is a single-stranded antisense RNA molecule that inhibits a target via an antisense inhibition mechanism. A single-stranded antisense RNA molecule is often complementary to a sequence within a target mRNA. Antisense RNA can inhibit translation in a stoichiometric manner by base pairing to a target mRNA and physically obstructing the translation machinery, see Dias, N. et al., (2002) Mol Cancer Ther 1:347-355. Alternatively, a single-stranded antisense RNA molecule can inhibit a target mRNA by hydridizing to a target mRNA and cleaving the target through an RNaseH cleavage event. A single-stranded antisense RNA molecule may be of any suitable length. In some embodiments, an antisense RNA is about 15 to about 30 nucleotides, or 30 nucleotides or more, in length and has a sequence that is completely or partially complementary to a target mRNA sequence.

[0072] In some embodiments, an iRNA is a double- stranded RNA and is referred to herein as a dsRNAi agent. A dsRNAi agent is often a complex of ribonucleic acid molecules, having a duplex structure comprising two anti-parallel and substantially complementary nucleic acid strands, referred to as having "sense" and "antisense" orientations with respect to a target RNA. In some embodiments of the invention, a dsRNAi agent triggers the degradation of a target RNA, e.g., an mRNA, through a post-transcriptional gene-silencing mechanism referred to herein as RNA interference or RNAi.

[0073] An iRNA generally can comprise one or two strands. In some embodiments, an iRNA comprises one strand of iRNA. In certain embodiments, an iRNA comprises two substantially complementary strands. In some embodiments, two strands of an iRNA are each separate RNA molecules. In some embodiments, two strands of an iRNA are covalently connected by a linker.

[0074] In certain embodiments, an iRNA comprises a morpholino oligo. In some embodiments, an antisense nucleic acid is a morpholino oligo. In some embodiments, a morpholino oligo is a single stranded antisense nucleic acid, as is know in the art. In some embodiments, a morpholino oligo decreases protein expression of a target, reduces translation of the target mRNA, reduces translation initiation of the target mRNA, or modifies transcript splicing. In some embodiments, the morpholino oligo is conjugated to a cell permeable moiety (e.g. peptide). Antisense nucleic acids may be single or double stranded nucleic acids.

[0075] In the cell, the antisense nucleic acids may hybridize to the target mRNA, forming a double-stranded molecule. The antisense nucleic acids interfere with the translation of the mRNA, since the cell will not translate a mRNA that is double-stranded. The use of antisense methods to inhibit the in vitro translation of genes is well known in the art (Marcus- Sakura, Anal. Biochem., 172:289, (1988)). Antisense molecules which bind directly to the DNA may be used. [0076] Inhibitory nucleic acids can be delivered to the subject using any appropriate means known in the art, including by injection, inhalation, or oral ingestion. Another suitable delivery system is a colloidal dispersion system such as, for example, macromolecule complexes, nanocapsules, microspheres, beads, and lipid-based systems including oil-in- water emulsions, micelles, mixed micelles, and liposomes. An example of a colloidal system is a liposome. Liposomes are artificial membrane vesicles which are useful as delivery vehicles in vitro and in vivo. Nucleic acids, including RNA and DNA within liposomes and be delivered to cells in a biologically active form (Fraley, et al, Trends Biochem. Sci. , 6:77, 1981). Liposomes can be targeted to specific cell types or tissues using any means known in the art. Inhibitory nucleic acids (e.g. antisense nucleic acids, morpholino oligos) may be delivered to a cell using cell permeable delivery systems (e.g. cell permeable peptides). In some embodiments, inhibitory nucleic acids are delivered to specific cells or tissues using viral vectors or viruses.

[0077] An "siRNA" refers to a nucleic acid that forms a double stranded RNA, which double stranded RNA has the ability to reduce or inhibit expression of a gene or target gene when the siRNA is present (e.g. expressed) in the same cell as the gene or target gene. The siRNA is typically about 5 to about 100 nucleotides in length, more typically about 10 to about 50 nucleotides in length, more typically about 15 to about 30 nucleotides in length, most typically about 20-30 base nucleotides, or about 20-25 or about 24-29 nucleotides in length, e.g., 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length. siRNA molecules and methods of generating them are described in, e.g. , Bass, 2001, Nature, 411, 428-429; Elbashir et al, 2001, Nature, 411, 494-498; WO 00/44895; WO 01/36646; WO 99/32619; WO 00/01846; WO 01/29058; WO 99/07409; and WO 00/44914. A DNA molecule that transcribes dsRNA or siRNA (for instance, as a hairpin duplex) also provides RNAi. DNA molecules for transcribing dsRNA are disclosed in U.S. Patent No. 6,573,099, and in U.S. Patent Application Publication Nos. 2002/0160393 and 2003/0027783, and Tuschl and Borkhardt, Molecular Interventions, 2: 158 (2002).

[0078] The siRNA can be administered directly or siRNA expression vectors can be used to induce RNAi that have different design criteria. A vector can have inserted two inverted repeats separated by a short spacer sequence and ending with a string of T's which serve to terminate transcription.

[0079] Construction of suitable vectors containing the desired therapeutic gene coding and control sequences employs standard ligation and restriction techniques, which are well understood in the art (see Maniatis et al., in Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, New York (1982)). Isolated plasmids, DNA sequences, or synthesized oligonucleotides are cleaved, tailored, and re-ligated in the form desired.

[0080] The terms "polypeptide," "peptide" and "protein" are used interchangeably herein to refer to a polymer of amino acid residues. The terms apply to amino acid polymers in which one or more amino acid residue is an artificial chemical mimetic of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers and non-naturally occurring amino acid polymer.

[0081] The term "amino acid" refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function in a manner similar to the naturally occurring amino acids. Naturally occurring amino acids are those encoded by the genetic code, as well as those amino acids that are later modified, e.g., hydroxyproline, γ- carboxyglutamate, and O-phosphoserine. Amino acid analogs refers to compounds that have the same basic chemical structure as a naturally occurring amino acid, i.e., an a carbon that is bound to a hydrogen, a carboxyl group, an amino group, and an R group, e.g., homoserine, norleucine, methionine sulfoxide, methionine methyl sulfonium. Such analogs have modified R groups (e.g., norleucine) or modified peptide backbones, but retain the same basic chemical structure as a naturally occurring amino acid. Amino acid mimetics refers to chemical compounds that have a structure that is different from the general chemical structure of an amino acid, but that functions in a manner similar to a naturally occurring amino acid.

[0082] Amino acids may be referred to herein by either their commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission. Nucleotides, likewise, may be referred to by their commonly accepted single-letter codes.

[0083] "Conservatively modified variants" applies to both amino acid and nucleic acid sequences. With respect to particular nucleic acid sequences, conservatively modified variants refers to those nucleic acids which encode identical or essentially identical amino acid sequences, or where the nucleic acid does not encode an amino acid sequence, to essentially identical sequences. Because of the degeneracy of the genetic code, a large number of functionally identical nucleic acids encode any given protein. For instance, the codons GCA, GCC, GCG and GCU all encode the amino acid alanine. Thus, at every position where an alanine is specified by a codon, the codon can be altered to any of the corresponding codons described without altering the encoded polypeptide. Such nucleic acid variations are "silent variations," which are one species of conservatively modified variations. Every nucleic acid sequence herein which encodes a polypeptide also describes every possible silent variation of the nucleic acid. One of skill will recognize that each codon in a nucleic acid (except AUG, which is ordinarily the only codon for methionine, and TGG, which is ordinarily the only codon for tryptophan) can be modified to yield a functionally identical molecule. Accordingly, each silent variation of a nucleic acid which encodes a polypeptide is implicit in each described sequence with respect to the expression product, but not with respect to actual probe sequences.

[0084] As to amino acid sequences, one of skill will recognize that individual substitutions, deletions or additions to a nucleic acid, peptide, polypeptide, or protein sequence which alters, adds or deletes a single amino acid or a small percentage of amino acids in the encoded sequence is a "conservatively modified variant" where the alteration results in the substitution of an amino acid with a chemically similar amino acid.

Conservative substitution tables providing functionally similar amino acids are well known in the art. Such conservatively modified variants are in addition to and do not exclude polymorphic variants, interspecies homologs, and alleles disclosed herein.

[0085] The following eight groups each contain amino acids that are conservative substitutions for one another: 1) Alanine (A), Glycine (G); 2) Aspartic acid (D), Glutamic acid (E); 3) Asparagine (N), Glutamine (Q); 4) Arginine (R), Lysine (K); 5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V); 6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W); 7) Serine (S), Threonine (T); and 8) Cysteine (C), Methionine (M) (see, e.g. , Creighton, Proteins (1984)).

[0086] The term "recombinant" when used with reference, e.g., to a cell, or nucleic acid, protein, or vector, indicates that the cell, nucleic acid, protein or vector, has been modified by the introduction of a heterologous nucleic acid or protein or the alteration of a native nucleic acid or protein, or that the cell is derived from a cell so modified. Thus, for example, recombinant cells express genes that are not found within the native (non-recombinant) form of the cell or express native genes that are otherwise abnormally expressed, under expressed or not expressed at all. [0087] The term "heterologous" when used with reference to portions of a nucleic acid indicates that the nucleic acid comprises two or more subsequences that are not found in the same relationship to each other in nature. For instance, the nucleic acid is typically recombinantly produced, having two or more sequences from unrelated genes arranged to make a new functional nucleic acid, e.g., a promoter from one source and a coding region from another source. Similarly, a heterologous protein indicates that the protein comprises two or more subsequences that are not found in the same relationship to each other in nature (e.g., a fusion protein).

[0088] "Antibody" refers to a polypeptide comprising a framework region from an immunoglobulin gene or fragments thereof that specifically binds and recognizes an antigen. The recognized immunoglobulin genes include the kappa, lambda, alpha, gamma, delta, epsilon, and mu constant region genes, as well as the myriad immunoglobulin variable region genes. Light chains are classified as either kappa or lambda. Heavy chains are classified as gamma, mu, alpha, delta, or epsilon, which in turn define the immunoglobulin classes, IgG, IgM, IgA, IgD and IgE, respectively. Typically, the antigen-binding region of an antibody will be most critical in specificity and affinity of binding. In some embodiments, antibodies or fragments of antibodies may be derived from different organisms, including humans, mice, rats, hamsters, camels, etc. Antibodies disclosed herein may include antibodies that have been modified or mutated at one or more amino acid positions to improve or modulate a desired function of the antibody (e.g. glycosylation, expression, antigen recognition, effector functions, antigen binding, specificity, etc.).

[0089] An exemplary immunoglobulin (antibody) structural unit comprises a tetramer. Each tetramer is composed of two identical pairs of polypeptide chains, each pair having one "light" (about 25 kD) and one "heavy" chain (about 50-70 kD). The N-terminus of each chain defines a variable region of about 100 to 1 10 or more amino acids primarily responsible for antigen recognition. The terms variable light chain (VL) and variable heavy chain (VH) refer to these light and heavy chains respectively.

[0090] Antibodies exist, e.g., as intact immunoglobulins or as a number of well- characterized fragments produced by digestion with various peptidases. Thus, for example, pepsin digests an antibody below the disulfide linkages in the hinge region to produce F(ab)' _2, a dimer of Fab which itself is a light chain joined to VH-CH1 by a disulfide bond. The F(ab)' 2 may be reduced under mild conditions to break the disulfide linkage in the hinge region, thereby converting the F(ab) ' 2 dimer into an Fab' monomer. The Fab' monomer is essentially Fab with part of the hinge region (see Fundamental Immunology (Paul ed., 3d ed. 1993). While various antibody fragments are defined in terms of the digestion of an intact antibody, one of skill will appreciate that such fragments may be synthesized de novo either chemically or by using recombinant DNA methodology. Thus, the term antibody, as used herein, also includes antibody fragments either produced by the modification of whole antibodies, or those synthesized de novo using recombinant DNA methodologies (e.g., single chain Fv) or those identified using phage display libraries (see, e.g. , McCafferty et al. , Nature 348:552-554 (1990)).

[0091] For preparation of suitable antibodies as disclosed herein and for use according to the methods disclosed herein, e.g., recombinant, monoclonal, or polyclonal antibodies, many techniques known in the art can be used (see, e.g., Kohler & Milstein, Nature 256:495-497 (1975); Kozbor et al., Immunology Today 4: 72 (1983); Cole et al. , pp. 77-96 in Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc. (1985); Coligan, Current Protocols in Immunology (1991); Harlow & Lane, Antibodies, A Laboratory Manual (1988); and Goding, Monoclonal Antibodies: Principles and Practice (2d ed. 1986)). The genes encoding the heavy and light chains of an antibody of interest can be cloned from a cell, e.g., the genes encoding a monoclonal antibody can be cloned from a hybridoma and used to produce a recombinant monoclonal antibody. Gene libraries encoding heavy and light chains of monoclonal antibodies can also be made from hybridoma or plasma cells. Random combinations of the heavy and light chain gene products generate a large pool of antibodies with different antigenic specificity (see, e.g., Kuby, Immunology (3 ed. 1997)). Techniques for the production of single chain antibodies or recombinant antibodies (U.S. Patent

4,946,778, U.S. Patent No. 4,816,567) can be adapted to produce antibodies to polypeptides as disclosed herein. Also, transgenic mice, or other organisms such as other mammals, may be used to express humanized or human antibodies (see, e.g. , U.S. Patent Nos. 5,545,807; 5,545,806; 5,569,825; 5,625,126; 5,633,425; 5,661,016, Marks et al., Bio/Technology 10:779- 783 (1992); Lonberg et al., Nature 368:856-859 (1994); Morrison, Nature 368:812-13

(1994) ; Fishwild et al., Nature Biotechnology 14:845-51 (1996); Neuberger, Nature

Biotechnology 14:826 (1996); and Lonberg & Huszar, Intern. Rev. Immunol. 13:65-93

(1995) ). Alternatively, phage display technology can be used to identify antibodies and heteromeric Fab fragments that specifically bind to selected antigens (see, e.g. , McCafferty et al. , Nature 348:552-554 (1990); Marks et al. , Biotechnology 10:779-783 (1992)). Antibodies can also be made bispecific, i.e., able to recognize two different antigens (see, e.g., WO 93/08829, Traunecker et al, EMBO J. 10:3655-3659 (1991); and Suresh et al, Methods in Enzymology 121 :210 (1986)). Antibodies can also be heteroconjugates, e.g., two covalently joined antibodies, or immunotoxins (see, e.g., U.S. Patent No. 4,676,980, WO 91/00360; WO 92/200373 ; and EP 03089).

[0092] Methods for humanizing or primatizing non-human antibodies are well known in the art (e.g. , U.S. Patent Nos. 4,816,567; 5,530, 101 ; 5,859,205; 5,585,089; 5,693,761 ;

5,693,762; 5,777,085 ; 6, 180,370; 6,210,671 ; and 6,329,511 ; WO 87/02671 ; EP Patent Application 0173494; Jones et al. (1986) Nature 321 :522; and Verhoyen et al. (1988) Science 239: 1534). Humanized antibodies are further described in, e.g. , Winter and Milstein (1991) Nature 349:293. Generally, a humanized antibody has one or more amino acid residues introduced into it from a source which is non-human. These non-human amino acid residues are often referred to as import residues, which are typically taken from an import variable domain. Humanization can be essentially performed following the method of Winter and coworkers (see, e.g. , Morrison et al. , PNAS USA, 81 :6851-6855 (1984), Jones et al, Nature 321 :522-525 (1986); Riechmann et al, Nature 332:323-327 (1988); Morrison and Oi, Adv. Immunol , 44:65-92 (1988), Verhoeyen et al, Science 239: 1534-1536 (1988) and Presta, Curr. Op. Struct. Biol. 2:593-596 (1992), Padlan, Molec. Immun. , 28:489-498 (1991); Padlan, Molec. Immun., 31(3): 169-217 (1994)), by substituting rodent CDRs or CDR sequences for the corresponding sequences of a human antibody. Accordingly, such humanized antibodies are chimeric antibodies (U.S. Patent No. 4,816,567), wherein substantially less than an intact human variable domain has been substituted by the corresponding sequence from a non- human species. In practice, humanized antibodies are typically human antibodies in which some CDR residues and possibly some FR residues are substituted by residues from analogous sites in rodent antibodies. For example, polynucleotides comprising a first sequence coding for humanized immunoglobulin framework regions and a second sequence set coding for the desired immunoglobulin complementarity determining regions can be produced synthetically or by combining appropriate cDNA and genomic DNA segments. Human constant region DNA sequences can be isolated in accordance with well known procedures from a variety of human cells.

[0093] A "chimeric antibody" is an antibody molecule in which (a) the constant region, or a portion thereof, is altered, replaced or exchanged so that the antigen binding site (variable region) is linked to a constant region of a different or altered class, effector function and/or species, or an entirely different molecule which confers new properties to the chimeric antibody, e.g., an enzyme, toxin, hormone, growth factor, drug, etc.; or (b) the variable region, or a portion thereof, is altered, replaced or exchanged with a variable region having a different or altered antigen specificity. Typical antibodies of, and for use according to the invention include humanized and/or chimeric monoclonal antibodies.

[0094] In some embodiments, the antibody is conjugated to an "effector" moiety. The effector moiety can be any number of molecules, including labeling moieties such as radioactive labels or fluorescent labels, or can be a therapeutic moiety. In one aspect the antibody modulates the activity of the protein. Such effector moieties include, but are not limited to, an anti-tumor drug, a toxin, a radioactive agent, a cytokine, a second antibody or an enzyme.

[0095] The immunoconjugate can be used for targeting the effector moiety to a cell, e.g. CD14dimCD16+ monocytes, assay of which can be readily apparent when viewing the bands of gels with approximately similarly loaded with test and controls samples. Examples of cytotoxic agents include, but are not limited to ricin, doxorubicin, daunorubicin, taxol, ethidium bromide, mitomycin, etoposide, tenoposide, vincristine, vinblastine, colchicine, dihydroxy anthracin dione, actinomycin D, diphteria toxin, Pseudomonas exotoxin (PE) A, PE40, abrin, and glucocorticoid and other chemotherapeutic agents, as well as radioisotopes. Suitable detectable markers include, but are not limited to, a radioisotope, a fluorescent compound, a bioluminescent compound, chemiluminescent compound, a metal chelator or an enzyme.

[0096] Additionally, the recombinant proteins disclosed herein including the antigen- binding region of any of the antibodies disclosed herein can be used to treat inflammation. In such a situation, the antigen-binding region of the recombinant protein is joined to at least a drug having therapeutic activity. The second drug can include, but is not limited to, a nonsteroidal anti-inflammatory drug. Suitable nonsteroidal anti-inflammatory drugs include aspirin, celecoxib (Celebrex), diclofenac (Voltaren), diflunisal (Dolobid), etodolac (Lodine), ibuprofen (Motrin), indomethacin (Indocin), ketoprofen (Orudis), ketorolac (Toradol), nabumetone (Relafen), naproxen (Aleve, Naprosyn), oxaprozin (Daypro), piroxicam

(Feldene), salsalate (Amigesic), sulindac (Clinoril), tolmetin (Tolectin). [0097] Techniques for conjugating therapeutic agents to antibodies are well known (see, e.g., Arnon et al., "Monoclonal Antibodies For Immunotargeting Of Drugs In Cancer Therapy", in MONOCLONAL ANTIBODIES AND CANCER THERAPY, Reisfeld et al. (eds.), pp. 243-56 (Alan R. Liss, Inc. 1985); Hellstrom et al., ANTIBODIES FOR DRUG DELIVERY IN CONTROLLED DRUG DELIVERY (2nd Ed.), Robinson et al. (eds.), pp. 623-53 (Marcel Dekker, Inc. 1987); Thorpe, "Antibody Carriers Of Cytotoxic Agents In Cancer Therapy: A Review" in Monoclonal Antibodies '84: Biological And Clinical Applications, Pinchera et al. (eds.), pp. 475-506 (1985); and Thorpe et al., "The Preparation And Cytotoxic Properties Of Antibody-Toxin Conjugates", Immunol. Rev., 62: 119-58 (1982)).

[0098] The phrase "specifically (or selectively) binds" to an antibody or "specifically (or selectively) immunoreactive with," when referring to a protein or peptide, refers to a binding reaction that is determinative of the presence of the protein, often in a heterogeneous population of proteins and other biologies. Thus, under designated immunoassay conditions, the specified antibodies bind to a particular protein at least two times the background and more typically more than 10 to 100 times background. Specific binding to an antibody under such conditions requires an antibody that is selected for its specificity for a particular protein. For example, polyclonal antibodies can be selected to obtain only those polyclonal antibodies that are specifically immunoreactive with the selected antigen and not with other proteins. This selection may be achieved by subtracting out antibodies that cross-react with other molecules. A variety of immunoassay formats may be used to select antibodies specifically immunoreactive with a particular protein. For example, solid-phase ELISA immunoassays are routinely used to select antibodies specifically immunoreactive with a protein (see, e.g. , Harlow & Lane, Using Antibodies, A Laboratory Manual (1998) for a description of immunoassay formats and conditions that can be used to determine specific

immunoreactivity) .

[0099] An "RNAi molecule" is an siRNA, shRNA, miRNA, shmiRNA, or other nucleic acid, as well known in the art, that is capable of inducing RNAi and hybridizing to an RNA that is translatable to a transcription factor. The RNAi molecule is typically capable of decreasing the amount of transcription factor that is translated in a cell.

[00100] A "ligand mimetic" is a binding agent that is designed to mimic, in structure or in binding mode, a known ligand or is capable of inhibiting the binding of a natural or physiological ligand to a transcription factor. In some embodiments, a ligand mimetic is a synthetic chemical compound, peptide, protein, fusion protein, peptidomimetic, or modified natural ligand. For example, a ligand mimetic may bind the same amino acids or a subset of the same amino acids on a transcription factor that a natural ligand of the transcription factor binds during the physiological functioning of the transcription factor. Ligand mimetics include biopolymers (e.g. proteins, nucleic acids, or sugars), lipids, chemical molecules with molecular weights less than five hundred (500) Daltons, one thousand (1000) Daltons, five thousand (5000) Daltons, less than ten thousand (10,000) Daltons, less than twenty five thousand (25,000) Daltons, less than fifty thousand (50,000) Daltons, less than seventy five thousand (75,000), less than one hundred thousand (100,000), or less than two hundred fifty thousand (250,000) Daltons. In some embodiments, the synthetic chemical compound is greater than two hundred fifty thousand (250,000) Daltons. In certain embodiments, the binding agent is less than five hundred (500) Daltons. In some embodiments, a ligand mimetic is a protein.

[00101] In some embodiments, a ligand mimetic is a small chemical molecule. The term "small chemical molecule" and the like, as used herein, refers to a molecule that has a molecular weight of less than two thousand (2000) Daltons. In some embodiments, a small chemical molecule is a molecule that has a molecular weight of less than one thousand (1000) Daltons. In other embodiments, a small chemical molecule is a molecule that has a molecular weight of less than five hundred (500) Daltons. In other embodiments, a small chemical molecule is a molecule that has a molecular weight of less than five hundred (500) Daltons. In other embodiments, a small chemical molecule is a molecule that has a molecular weight of less than one hundred (100) Daltons.

[00102] In some embodiments, a transcription factor inhibitor is a small molecule. In other embodiments the inhibitor is an allosteric inhibitor of a transcription factor.

[00103] In some embodiments, there is provided herein a method of modulating

CD14 ^dim CD16 ⁺ (CD115 ⁺ CDl lb ⁺ GRr (Ly6C ^" )) monocytes or macrophages, the method comprising modulating expression or activity of Nr4al (Nur77). In some embodiments, there is provided herein a method of modulating an amount of CD14 ^dim CD16 ⁺

(CD115 ⁺ CDl lb ⁺ GRl ^~ (Ly6C ^~ )) monocytes or macrophages in a subject. In some embodiments, provided herein is a method of increasing or decreasing an amount of

CD14 ^dim CD16 ⁺ (CD115 ⁺ CDl lb ⁺ GRr (Ly6C ^" )) monocytes or macrophages in a subject, the method comprising administering an agonist or antagonist described herein. An amount of monocytes or macrophages can be increased or decreased from about 2-fold to 10,000 fold or more relative to an amount of monocytes or macrophages existing in a subject prior to administering an agent (e.g., an agonist or antagonist) described herein. In certain embodiments, disclosed herein is a method of stimulating, promoting, increasing or inducing CD14 ^dim CD16 ⁺ monocyte or macrophage cell production, development, survival, proliferation, differentiation or activity, comprising modulating expression or activity of a transcription factor that regulates expression of Nr4al (Nur77).

[00104] In certain embodiments, provided herein is a method of identifying an agent that modulates CD14 ^dim CD16 ⁺ (CD115 ⁺ CDllb ⁺ GRr (Ly6C ^" )) monocytes or macrophages. In certain embodiments, disclosed herein is a method of identifying an agent that modulates the amount of CD14 ^dim CD16 ⁺ (CD115 ⁺ CDllb ⁺ GRr (Ly6C ^" )) monocytes or macrophages in a subject. In certain embodiments, disclosed herein is a method of identifying an agent that increases or decreases an amount of CD14 ^dim CD16 ⁺ (CD115 ⁺ CD1 lb ⁺ GRl ^" (Ly6C ^" )) monocytes or macrophages in a subject. An agent can be an antibody, a small molecule, a peptide, a polypeptide or protein, an inhibitory nucleic acid, an allosteric inhibitor or a ligand mimetic. In certain embodiments, an agent is an agonist or antagonist of Nr4al activity or expression. In certain embodiments, an agent is an agonist or antagonist of Klf2 or Klf4 activity or expression.

[00105] In some embodiments, a method of identifying an agent that modulates, increases or decreases CD14 ^dim CD16 ⁺ (CD115 ⁺ CDllb ⁺ GRr (Ly6C ^" )) monocyte or macrophage amounts or activity comprises identifying an agent that modulates, increases, or decreases Nr4alexpression. In some embodiments, a method of identifying an agent that modulates, increases or decreases CD14 ^dim CD16 ⁺ (CD115 ⁺ CDllb ⁺ GRr (Ly6C ^" )) monocyte or macrophage amounts or activity comprises identifying an agent that modulates, increases or decreases activity or expression of a transcription factor that regulates expression of Nr4al (Nur77). In some embodiments, a method of identifying an agent that modulates, increases or decreases CD14 ^dim CD16 ⁺ (CD115 ⁺ CDllb ⁺ GRr (Ly6C ^" )) monocyte or macrophage amounts or activity comprises identifying an agent that modulates, increases or decreases activity or expression of Klf2, Klf4 and/or Nf-κΒ. In certain embodiments, agents that modulate, increase or decrease expression Nr4al can be identified by monitoring the activity of a transcriptional regulatory region of Nr4al, which can be operably linked to a reporter sequence. In one non-limiting example, an experimental agent can be contacted with Klf2, Klf4 and/or Nf-κΒ in the presence of an Nr4al transcriptional regulatory region (e.g., any one or more of Enhancer_01 to Enhancer_12, e.g., see Fig. 19) operably linked to a suitable reporter. Expression or activity of the reporter can be monitored to determine if the experimental agent decreases or increases reporter activity. In some embodiments, a method of identifying an agent that modulates, increases or decreases

CD14 ^dim CD16 ⁺ (CD115 ⁺ CDllb ⁺ GRr (Ly6C ^" )) monocyte or macrophage amounts or activity comprises identifying an agent that modulates, increases, or decreases

Nr4alexpression in the presence of Klf2, Klf4 and/or Nf-κΒ.

[00106] In some embodiments, a method of identifying an agent that modulates, increases or decreases CD14 ^dim CD16 ⁺ (CD115 ⁺ CDllb ⁺ GRr (Ly6C ^" )) monocyte or macrophage amounts or activity comprises contacting an experimental agent with an Nr4al promoter region. An Nr4al promoter region can be a nucleic acid region 20 base pairs (bp) to 1500 bp in length located within the 5' untranslated region (UTR) the Nr4al gene (HGNC: 7980, Entrez Gene: 3164, Ensembl: ENSG00000123358). In some embodiments, an Nr4al promoter region is 20 bp to 1000 bp, 20 bp to 750 bp, 20 bp to 500 bp, 20 bp to 250 bp or 20 bp to 100 bp in length. In certain embodiments, an Nr4al promoter region comprises about 20-1500 base pairs 5' of the Nr4al transcriptional start site, or a subsequence thereof. In certain embodiments, an Nr4al promoter region comprises an enhancer region (e.g., enhancer_01 (Nr4alse_l), 02 (Nr4alse_2), 03 (Nr4alse_3), 04 (Nr4alse_4), 05 (Nr4alse_5), 06 (Nr4alse_6), 07 (Nr4alse_7), 08 (Nr4alse_8), 09 (Nr4alse_9), 10 (Nr4alse_10), 11 (Nr4alse_l l), 12 (Nr4alse_12), or a combination thereof, e.g., see Fig. 19). In certain embodiments an Nr4al promoter region comprises an enhancer region isolated by a set of primer sequences shown in Table 1 , or an Nr4al promoter region isolated as described herein (e.g., see section entitled "Enhancer Cloning"). In certain embodiments, an Nr4al promoter region comprises or consists of enhancer site E2 (Nr4alse_2), E6 (Nr4alse_6) or E9

(Nr4alse_9) as disclosed herein.

[00107] Any suitable methods of detecting enhancer/promoter activity can be used to detect enhancer/promoter activity or transcription factor activity. In certain embodiments, an Nr4al promoter region, enhancer region, subsequence or combination thereof is operably linked to a suitable reporter nucleic acid. Reporter nucleic acids can be detected directly upon transcription, or indirectly upon translation of a suitable reporter sequence. A multitude of suitable reporter nucleic acids and suitable reporter polypeptides are known, any of which can be used for a method herein. In some embodiments, a reporter nucleic acid is a nucleic acid encoding Nr4al. In some embodiments, a reporter nucleic acid is a nucleic acid encoding a luciferase. Expression of a reporter nucleic acid can be determined indirectly by measuring the amount or activity of a polypeptide encoded by a reporter nucleic acid (e.g., a reporter polypeptide).

[00108] In some embodiments, a method of identifying an agent that modulates, increases or decreases CD14 ^dim CD16 ⁺ (CD115 ⁺ CDllb ⁺ GRr (Ly6C ^" )) monocyte or macrophage amounts or activity comprises contacting an experimental agent with an Nr4al promoter region operably linked to a reporter nucleic acid, in the presence of a transcription factor, non-limiting examples of which include Klf2, Klf4, and Nf-κΒ. Any suitable control can be used for a method herein. In certain embodiments a control assay is an experimental method performed in the absence of an experimental agent. Non-limiting examples of experimental agents include antibodies, inhibitory nucleic acids, small molecules, peptide, polypeptides, proteins, allosteric inhibitors, ligand mimetics, the like or combinations thereof. In certain embodiments an experimental agent binds specifically to Klf2, Klf4 or an Nf-κΒ polypeptide. In certain embodiments an experimental agent binds specifically to a nucleic acid encoding an Klf2, Klf4 or an Nf-κΒ polypeptide.

[00109] In certain embodiments, an agent that modulates, increases or decreases CD14 ^dim CD16 ⁺ (CD115 ⁺ CDllb ⁺ GRr (Ly6C ^" )) monocyte or macrophage amounts or activity can be identified by comparing the expression, amount or activity of a reporter nucleic acid or reporter polypeptide produced in the presence of an experimental agent to an amount or activity of a reporter nucleic acid or reporter polypeptide produced in the absence of an experimental agent (e.g., a control). In certain embodiments, an experimental agent that increases the amount or activity of a reporter nucleic acid or reporter polypeptide relative to a control amount produced in the absence of an experimental agent is an agent that modulates or increases CD14 ^dim CD16+ (CD115+CDllb+GRr (Ly6C ^" )) monocyte or macrophage amounts or activity. In certain embodiments, an experimental agent that decreases the amount or activity of a reporter nucleic acid or reporter polypeptide relative to a control amount produced in the absence of an experimental agent is an agent that modulates or decreases CD14 ^dim CD16 ⁺ (CD115 ⁺ CDllb ⁺ GRr (Ly6C ^" )) monocyte or macrophage amounts or activity.

[00110] In some embodiments, a vertebrate, (e.g., a mammal, e.g., a rodent; e.g., a rat, e.g., a mouse, or the like) deficient in an Nr4alse_2 sequence is generated. A vertebrate deficient in an Nr4alse_2 sequence can be homozygous or heterozygous for a deleted, modified or disrupted Nr4alse_2A sequence. A vertebrate deficient in an Nr4alse_2 sequence can be used, in certain embodiments, for identifying

CD14dimCD16+ (CD115+CDl lb+GRl- (Ly6C-)) monocyte functions. Monocyte functions identified can be classical or non-classical monocyte functions.

[00111] In embodiments, an immune disorder, inflammatory response, inflammation, autoimmune response, disorder or diseases is rheumatoid arthritis, juvenile rheumatoid arthritis, osteoarthritis, psoriatic arthritis, multiple sclerosis (MS), encephalomyelitis, myasthenia gravis, systemic lupus erythematosus (SLE), asthma, allergic asthma, autoimmune thyroiditis, atopic dermatitis, eczematous dermatitis, psoriasis, Sjogren's Syndrome, Crohn's disease, aphthous ulcer, iritis, conjunctivitis, keratoconjunctivitis, ulcerative colitis (UC), inflammatory bowel disease (IBD), cutaneous lupus erythematosus, scleroderma, vaginitis, proctitis, erythema nodosum leprosum, autoimmune uveitis, allergic encephalomyelitis, acute necrotizing hemorrhagic encephalopathy, idiopathic bilateral progressive sensorineural hearing loss, aplastic anemia, pure red cell anemia, idiopathic thrombocytopenia, polychondritis, Wegener's granulomatosis, chronic active hepatitis, Stevens-Johnson syndrome, idiopathic sprue, lichen planus, Graves' disease, sarcoidosis, primary biliary cirrhosis, uveitis posterior, interstitial lung fibrosis, Hashimoto's thyroiditis, autoimmune polyglandular syndrome, insulin-dependent diabetes mellitus, insulin-resistant diabetes mellitus, immune-mediated infertility, autoimmune Addison's disease, pemphigus vulgaris, pemphigus foliaceus, dermatitis herpetiformis, autoimmune alopecia, vitiligo, autoimmune hemolytic anemia, autoimmune thrombocytopenic purpura, pernicious anemia, Guillain-Barre syndrome, stiff-man syndrome, acute rheumatic fever, sympathetic ophthalmia, Goodpasture's syndrome, systemic necrotizing vasculitis, antiphospholipid syndrome or an allergy, Behcet's disease, severe combined immunodeficiency (SCID), recombinase activating gene (RAG 1/2) deficiency, adenosine deaminase (ADA) deficiency, interleukin receptor common γ chain (yc) deficiency, Janus-associated kinase 3 (JAK3) deficiency and reticular dysgenesis; primary T cell immunodeficiency such as DiGeorge syndrome, Nude syndrome, T cell receptor deficiency, MHC class II deficiency, TAP-2 deficiency (MHC class I deficiency), ZAP70 tyrosine kinase deficiency and purine nucleotide phosphorylase (PNP) deficiency, antibody deficiencies, X-linked agammaglobulinemia (Bruton's tyrosine kinase deficiency), autosomal recessive agammaglobulinemia, Mu heavy chain deficiency, surrogate light chain (γ5/14.1) deficiency, Hyper-IgM syndrome: X-linked (CD40 ligand deficiency) or non-X-linked, Ig heavy chain gene deletion, IgA deficiency, deficiency of IgG subclasses (with or without IgA deficiency), common variable

immunodeficiency (CVID), antibody deficiency with normal immunoglobulins; transient hypogammaglobulinemia of infancy, interferon γ receptor (IFNGR1, IFNGR2) deficiency, interleukin 12 or interleukin 12 receptor deficiency, immunodeficiency with thymoma, Wiskott-Aldrich syndrome (WAS protein deficiency), ataxia telangiectasia (ATM

deficiency), X-linked lymphoproliferative syndrome (SH2D1A/SAP deficiency), and hyper IgE syndrome.

[00112] In another aspect, there is provided a pharmaceutical composition comprising an agonist or antagonist of a transcription factor that regulates expression of Nr4al (Nur77) for treatment of an aberrant immune response, immune disorder, inflammatory response, inflammation, an autoimmune response, disorder or disease, cancer or an adverse

cardiovascular event or cardiovascular disease in a subject. In certain embodiments, the transcription factor is Klf2 or Klf4. In some embodiments, a pharmaceutical composition comprises an agonist or antagonist of Klf2 or Klf4.

[00113] In certain embodiments, a pharmaceutical composition described herein is used to regulate expression of Nr4al (Nur77) for treatment of an aberrant immune response, immune disorder, inflammatory response, inflammation, an autoimmune response, disorder or disease, lymphoproliferative disorder, cancer or an adverse cardiovascular event or cardiovascular disease in a subject. In certain embodiments, a pharmaceutical composition described herein is used for the treatment of an autoimmune disease or a lymphoproliferative disease.

[00114] In embodiments, the pharmaceutical composition is for treating an individual who has a disease by administering to the individual a pharmaceutical composition including a therapeutically effective amount of a transcription factor that regulates expression of Nr4al (Nur77) and a pharmaceutically acceptable excipient.

[00115] The compositions disclosed herein can be administered by any means known in the art. For example, compositions may include administration to a subject intravenously, intradermally, intraarterially, intraperitoneally, intralesionally, intracranially, intraarticularly, intraprostaticaly, intrapleurally, intratracheally, intranasally, intravitreally, intravaginally, intrarectally, topically, intratumorally, intramuscularly, intrathecally, subcutaneously, subconjunctival, intravesicularlly, mucosally, intrapericardially, intraumbilically, intraocularly, orally, locally, by inhalation, by injection, by infusion, by continuous infusion, by localized perfusion, via a catheter, via a lavage, in a creme, or in a lipid composition. Administration can be local or systemic.

[00116] Solutions of the active compounds as free base or pharmacologically acceptable salt can be prepared in water suitably mixed with a surfactant, such as

hydroxypropylcellulose. Dispersions can also be prepared in glycerol, liquid polyethylene glycols, and mixtures thereof and in oils. Under ordinary conditions of storage and use, these preparations can contain a preservative to prevent the growth of microorganisms.

[00117] Pharmaceutical compositions can be delivered via intranasal or inhalable solutions or sprays, aerosols or inhalants. Nasal solutions can be aqueous solutions designed to be administered to the nasal passages in drops or sprays. Nasal solutions can be prepared so that they are similar in many respects to nasal secretions. Thus, the aqueous nasal solutions usually are isotonic and slightly buffered to maintain a pH of 5.5 to 6.5. In addition, antimicrobial preservatives, similar to those used in ophthalmic preparations, and appropriate drug stabilizers, if required, may be included in the formulation. Various commercial nasal preparations are known and can include, for example, antibiotics and antihistamines.

[00118] Oral formulations can include excipients as, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate and the like. These compositions take the form of solutions, suspensions, tablets, pills, capsules, sustained release formulations or powders. In some embodiments, oral pharmaceutical compositions will comprise an inert diluent or assimilable edible carrier, or they may be enclosed in hard or soft shell gelatin capsule, or they may be compressed into tablets, or they may be incorporated directly with the food of the diet. For oral therapeutic administration, the active compounds may be incorporated with excipients and used in the form of ingestible tablets, buccal tablets, troches, capsules, elixirs, suspensions, syrups, wafers, and the like. The percentage of the compositions and preparations may, of course, be varied and may conveniently be between about 2 to about 75% of the weight of the unit, or typically between 25-60%. The amount of active compounds in such compositions is such that a suitable dosage can be obtained.

[00119] For parenteral administration in an aqueous solution, for example, the solution should be suitably buffered and the liquid diluent first rendered isotonic with sufficient saline or glucose. Aqueous solutions, in particular, sterile aqueous media, are especially suitable for intravenous, intramuscular, subcutaneous and intraperitoneal administration. For example, one dosage could be dissolved in 1 ml of isotonic NaCl solution and either added to 1000 ml of hypodermoclysis fluid or injected at the proposed site of infusion.

[00120] Sterile injectable solutions can be prepared by incorporating the active compounds or constructs in the required amount in the appropriate solvent followed by filtered sterilization. Generally, dispersions are prepared by incorporating the various sterilized active ingredients into a sterile vehicle which contains the basic dispersion medium.

Vacuum-drying and freeze-drying techniques, which yield a powder of the active ingredient plus any additional desired ingredients, can be used to prepare sterile powders for reconstitution of sterile injectable solutions. The preparation of more, or highly, concentrated solutions for direct injection is also contemplated. DMSO can be used as solvent for extremely rapid penetration, delivering high concentrations of the active agents to a small area.

[00121] 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 belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the invention, suitable methods and materials are described herein.

[00122] All patents, patent applications, publications, and other references, GenBank citations and ATCC citations cited herein are incorporated by reference in their entirety. In case of conflict, the specification, including definitions, will control.

[00123] All of the features disclosed herein may be combined in any combination. Each feature disclosed in the specification may be replaced by an alternative feature serving a same, equivalent, or similar purpose.

[00124] Any appropriate element disclosed in one aspect or embodiment of a method or composition disclosed herein is equally applicable to any other aspect or embodiment of a method or composition. For example, the therapeutic agents set forth in the description of the pharmaceutical compositions provided herein are equally applicable to the methods of treatment and vice versa. [00125] As used herein, the singular forms "a", "and," and "the" include plural referents unless the context clearly indicates otherwise. Thus, for example, reference to "an agonist" "an antagonist" includes a plurality of such agonists and antagonists.

[00126] As used herein, all numerical values or numerical ranges include integers within such ranges and fractions of the values or the integers within ranges unless the context clearly indicates otherwise. Thus, to illustrate, reference to 80% or more identity, includes 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94% etc., as well as 81.1%, 81.2%, 81.3%, 81.4%, 81.5%, etc., 82.1%, 82.2%, 82.3%, 82.4%, 82.5%, etc., and so forth.

[00127] Reference to an integer with more (greater) or less than includes any number greater or less than the reference number, respectively. Thus, for example, a reference to less than 100, includes 99, 98, 97, etc. all the way down to the number one (1); and less than 10, includes 9, 8, 7, etc. all the way down to the number one (1).

[00128] As used herein, all numerical values or ranges include fractions of the values and integers within such ranges and fractions of the integers within such ranges unless the context clearly indicates otherwise. Thus, to illustrate, reference to a numerical range, such as 1-10 includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, as well as 1.1, 1.2, 1.3, 1.4, 1.5, etc., and so forth.

Reference to a range of 1-50 therefore includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, etc., up to and including 50, as well as 1.1, 1.2, 1.3, 1.4, 1.5, etc., 2.1, 2.2, 2.3, 2.4, 2.5, etc., and so forth.

[00129] Reference to a series of ranges includes ranges which combine the values of the boundaries of different ranges within the series. Thus, to illustrate reference to a series of ranges, for example, of 1-10, 10-20, 20-30, 30-40, 40-50, 50-60, 60-75, 75-100, 100-150, 150-200, 200-250, 250-300, 300-400, 400-500, 500-750, 750-850, includes ranges of 1-20, 1- 30, 1-40, 1-50, 1-60, 10-30, 10-40, 10-50, 10-60, 10-70, 10-80, 20-40, 20-50, 20-60, 20-70, 20-80, 20-90, 50-75, 50-100, 50-150, 50-200, 50-250, 100-200, 100-250, 100-300, 100-350, 100-400, 100-500, 150-250, 150-300, 150-350, 150-400, 150-450, 150-500, etc.

[00130] The invention is generally disclosed herein using affirmative language to describe the numerous embodiments and aspects. The invention also specifically includes embodiments in which particular subject matter is excluded, in full or in part, such as substances or materials, method steps and conditions, protocols, or procedures. For example, in certain embodiments or aspects of the invention, materials and/or method steps are excluded. Thus, even though the invention is generally not expressed herein in terms of what the invention does not include aspects that are not expressly excluded in the invention are nevertheless disclosed herein.

[00131] A number of embodiments of the invention have been described. Nevertheless, one skilled in the art, without departing from the spirit and scope of the invention, can make various changes and modifications of the invention to adapt it to various usages and conditions. Accordingly, the following examples are intended to illustrate but not limit the scope of the invention claimed in any way.

Examples

Example 1

Deleting an Nr4al super-enhancer subdomain ablates Ly6C ^low monocytes while preserving macrophage gene function

Summary

[00132] Mononuclear phagocytes are a heterogeneous family that occupy all tissues and assume numerous roles to support tissue function and systemic homeostasis. Our ability to dissect the roles of individual subsets is limited by a lack of technologies that ablate gene function within specific mononuclear phagocyte sub-populations. Using Nr4al -dependent Ly6C ^low monocytes a proof-of-principle approach that addresses these limitations is disclosed. Combining ChlP-Seq and molecular approaches we identify a single, conserved, sub-domain within the Nr4al enhancer that is essential for Ly6C ^low monocyte development. Mice lacking this enhancer lack Ly6C ^low monocytes but retain Nr4al gene expression in macrophages during steady state and in response to LPS. As Nr4al regulates inflammatory gene expression and Ly6C ^low monocytes, decoupling these processes allows Ly6C ^low monocytes to be studied without confounding influences.

Introduction

[00133] Mononuclear phagocytes (MP) are an ontologically diverse family of cells comprised of macrophages and monocytes (Mo) (Perdiguero and Geissmann, 2016). From a traditional standpoint the primary functions of MP involve recognition and clearance of invading pathogens, maintaining tissue integrity and resolving inflammation (Sica and Mantovani, 2012). To perform these diverse functions MP occupy all bodily tissues and display a tremendous degree of phenotypic plasticity. In recent years transcriptomic profiling efforts have revealed the full extent of this heterogeneity, and functional studies have unveiled diverse, specialized and often unexpected roles for individual MP subsets (Amit et al., 2016). In this context, tissue macrophages and blood Mo may be considered accessory cells that allow optimal performance of the host tissue (Okabe and Medzhitov, 2016). In complement to their roles in immunity and host defense, tissue MP are now also recognized as major regulators of higher-order physiological processes including systemic energy balance (Odegaard and Chawla, 2011), intestinal peristalsis (Muller et al., 2014) and cognitive function (Parkhurst et al., 2013). Delineating the full extent of MP functions in health and disease represents a largely unexplored frontier in both immunology and physiology.

[00134] Mo constitute the blood-borne phase of the MP system and are composed of at least two subsets in both mouse and human that are believed to be conserved (Cros et al., 2010). Mouse Mo subsets can be discriminated using the Ly6C surface antigen (Geissmann et al., 2010), Ly6C ^hl Mo are progenitors of inflammatory, and some tissue-resident

macrophages. Ly6C ^low Mo exhibit a patrolling behavior on the vascular endothelium and contribute to vascular homeostasis by maintaining the endothelial layer (Carlin et al., 2013). In addition, Ly6C ^low Mo have recently been shown to play a crucial role protecting against the seeding of tumor metastases in the lung (Hanna et al., 2015).

[00135] An indispensable approach to understand cellular behavior is through loss-of- function. The identification of lineage defining transcription factors (LDTFs) for MP subsets has led to new insights into the functions of these cells. For example, the transcription factor Nr4al is the master regulator of the Ly6C ^low Mo subset (Hanna et al., 2011). Nr4al is uniquely highly expressed in Ly6C ^low Mo, and is required in a cell-intrinsic fashion.

Accordingly Nr4al ^'A mice were instrumental in revealing a role for Ly6C ^low Mo in tumor metastasis (Hanna et al., 2015). In another example, loss of the transcription factor Spic selectively ablates splenic red pulp macrophages revealing a role for this population in iron homeostasis (Kohyama et al., 2009). Similarly macrophage-specific deletion of Gata6 impairs the maturation of peritoneal macrophages leading to the discovery that these cells modulate B-l cell IgA production (Okabe and Medzhitov, 2014). [00136] Pleiotropy, exemplified by the differential action of a single gene in multiple cell types, is a major obstacle to understanding cell-specific gene function. To overcome this problem the Cre recombinase-loxP (Cre-Lox) system is routinely used to ablate genes containing loxP-flanked exons by controlling Cre enzyme expression with cell-specific promoters. The ability of the Cre-Lox system to excise gene expression in a cell-specific manner is limited by the cell-specificity of Cre transgenes and the time taken for

recombination to occur (Yona et al., 2012). These considerations present problems when using the Cre-Lox system to study gene function within populations of closely related cells. A prime example of this problem is Nr4al. Nr4al ^{~ '} mice lack Ly6C ^low Mo, macrophage Nr4al is also induced by LPS and represses inflammatory gene expression (Hanna et al., 2012). These confounding influences limit the utility of Nr4al ^~ ' ^~ to study Ly6C ^low Mo.

Furthermore, the current MP Cre transgenes (Lys2-Cre, Csflr-Cre, Cx3crl-Cre) cannot delete Ly6C ^low Mo Nr4al without also disrupting Nr4al across MP subsets. These pan- myeloid effects of the current myeloid Cre transgenes limit the ability of conditional deletion approaches to determine gene- and cell-type function within the diverse MP compartment.

[00137] Enhancers are critical determinants of gene expression (Andersson et al., 2014) and are identified by chromatin immunoprecipitation sequencing (ChlP-Seq) on the basis of high levels of histone H3 lysine 4 monomethylation (H3K4mel) and dimethylation

(H3K4me2) (Heintzman et al., 2007; Heinz et al., 2010). MP enhancers are enriched for the LDTFs PU.l and C/ΕΒΡβ, which instruct enhancer selection (Heinz et al., 2010). Enhancers are subject to additional regulation leading to their further classification as 'poised' or 'active'. Enhancers are activated upon binding of signal dependent transcription factors (SDTFs), leading to acetylation at H3 lysine 27 (H3K27ac) and the increased expression of associated genes (Creyghton et al., 2010; Heinz et al., 2013). The enhancer landscapes between MP subsets show considerable diversity (Gosselin et al., 2014; Lavin et al., 2014) and result from the myriad environmental niches these populations are exposed to. As Nr4al shows unique expression characteristics in Ly6C ^low Mo, we hypothesize a SDTF acting at a cell-specific enhancer regulates transcription of the Ly6C ^low Mo LDTF Nr4al .

[00138] Here we explore this hypothesis by mapping the Nr4al enhancer locus in Ly6C ^low Mo. We identify a single sub-domain 4kb upstream of the Nr4al transcription start site that is essential for Ly6C ^low Mo development. Dissection of this element provides insight into the transcriptional processes driving Ly6C ^low Mo development. Furthermore, using mice that lack this enhancer we show that macrophage Nr4al gene expression is unaffected both in response to inflammatory signaling and during steady state.

Results

Ly6C ^low Mo are ontological neighbors to Ly6C ^hi Mo

[00139] Lineage tracing and BrdU pulse-chase studies have established a consensus that Ly6C ^hi Mo give rise to Ly6C ^low Mo (Yona et al., 2012). Yet it remains possible that Ly6C ^low Mo arise independent of the Ly6C ^hl population. The Mo dendritic cell precursor (MDP) that expresses Flt3 (CD135), Cx3crl and Kit (CD117) gives rise to all mouse Mo (Hettinger et al., 2013). MDPs undergo further restriction towards the Mo lineage upon their differentiation into the common Mo progenitor (cMoP), at which point expression of FLT3 is lost and Ly6C expression is gained (Hettinger et al., 2013).

[00140] We reasoned that if Ly6C ^low Mo arise independently of the Ly6C ^hl population that we would observe a signature that was common to the Ly6C ^low Mo and their progenitor, but not the Ly6C ^hi Mo. To test this hypothesis we performed ChlP-Seq on MDP, cMoP, Ly6C ^hi and Ly6C ^low Mo (Fig. 9a) using H3K4me2 to define enhancers, and activity with H3K27ac. To assess data quality we visually inspected loci associated with prototypical marker genes for the profiled cell types (Fig. 9b). As expected MDPs showed enrichment for H3K27ac at the Flt3 locus whereas both MDPs and cMoPs showed H3K27ac at the Kit locus, both used to sort these populations. In contrast to Ly6C ^low Mo, Ly6C ^hl Mo and cMoPs show enhancer activity at the Ly6C2 locus encoding for the Ly6C surface antigen. Surprisingly MDPs also showed activity at the Ly6C2 locus in spite of low mRNA and cell-surface protein levels (Fig. 9a,b), perhaps indicating a priming of this locus prior to transcription. Finally, in Ly6C ^low Mo Cx3crl shows marked H3K27ac reflecting the robust Cx3crl expression in this population (Carlin et al., 2013).

[00141] To gain a global overview of enhancer dynamics during Mo development H3K4me2 and H3K27ac were quantitated at all 99,462 enhancers defined as H3K4me2 enriched regions greater than 2.5kb from the nearest transcription start site. Differential enrichment (DE) of histone marks was then computed between all pairwise comparisons identifying a total of 620 DE H3K4me2 regions (0.62% of total, Fig. 16(a)) and 9,879 H3K27ac regions (9.93% of total, Fig. 16(b)). Unbiased hierarchical clustering of DE enhancers (Fig. 1(c), Fig. 16(c)) showed that significant changes in H3K27ac are mirrored by more subtle shifts in H3K4me2. De novo motif analysis within these defined clusters identifies transcriptional processes driving Mo differentiation (Fig. 16(d)). All enhancer clusters were enriched for ETS (PU.l) motifs. Progenitor-associated enhancers showed restricted over-representation of Myb motifs, which were lost upon Ly6C ^hi Mo

differentiation, concomitant with the acquisition of CEBP, and KLF motifs. At the global acetylation level Ly6C ^low Mo enhancers were uniquely characterized by over-represented NR4A and Mef2a motifs. Importantly we did not observe a signature of enhancer or motif usage that was shared between Ly6C ^low Mo and either progenitor but not the Ly6C ^hl Mo, nor did such a pattern emerge at the transcriptomic level (Fig. 17). Instead, the patterns of differential enhancer usage are consistent with a continuous transition between the MDP and Ly6C ^low Mo with both the cMoP and Ly6C ^hl Mo falling as intermediaries in this cascade. Collectively, these data strongly support the consensus model of Mo development in which Ly6C ^low Mo derive directly from the Ly6C ^hl Mo population.

Ly6C ^low Mo possess a cell-specific super-enhancer at the Nr4al locus.

[00142] Super-enhancers (SE) are a recently defined class of highly cell-type specific enhancer (Whyte et al., 2013) that selectively mark genes involved in lineage specification and function. The defining features of SEs include their extended size, adornment with LDTFs and genomic correlates of high gene expression (Hnisz et al., 2013). As Ly6C ^low Mo highly express Nr4al and require it for their development (Hanna et al., 2011) we postulated that it is a SE regulated gene. We used H3K27ac levels to define SEs in Ly6C ^low Mo, confirming that Nr4al does overlap a SE (Nr4alse; Fig. 10(a) and 17). Validating the SE characteristics of Nr4alse, we also observed a high density of the MP LDTFs PU.l and CEBP (Fig. 18). Enumeration of H3K4me2 and H3K27ac tag counts at Nr4alse in MDP, cMoP, Ly6C ^hi and Ly6C ^low Mo shows a selective and robust (5-fold) acquisition of H3K27ac in Ly6C ^low Mo, demonstrating that Nr4alse is a Ly6C ^low Mo-specific SE region (Fig. 10b, c).

[00143] Formation of SEs represents a confluence of developmental and environmental cues (Hnisz et al., 2015). We leveraged the phenotypic heterogeneity of the diverse MP family to address whether steady-state Nr4al expression may be regulated by distinct mechanisms. First we assessed Nr4al expression in MP populations taken from Lavin et al (2014) and our own Mo subset data. We observe steady-state levels of Nr4al spanning three orders of magnitude (Fig. lOd). Importantly Nr4al expression in Ly6C ^hl Mo from both datasets (Ly6C ¹ and Mono) are consistent, facilitating the comparison between datasets. Consistent with previous observations we also observe by far the highest Nr4al expression in Ly6C ^low Mo (Hanna et al., 2011).

[00144] Next we questioned whether the range of Nr4al mRNA expression is associated with the continuous acquisition of a fixed enhancer signature at Nr4alse, or if Ly6C ^low Mo possesses a unique H3K27ac profile. We visualized H3K27ac at Nr4alse in MP populations corresponding those in Fig. lOd (Fig. lOe). We observed comparable H3K27ac tag distributions between Ly6C ^hl Mo populations, facilitating a qualitative comparison between datasets. Each population was found to differ in both the absolute level of histone acetylation observed and, to varying degrees, also in the histone acetylation 'fingerprint' at Nr4alse (Fig. 10(e)). Notably, the most intense H3K27ac signature at Nr4alse was observed in Ly6C ^low Mo (Fig. 10(d) & Fig. 10(e)). Taken together, these findings imply that distinct mechanisms may regulate steady-state Nr4al expression between MP populations.

Nr4alse_2 is a conserved SE sub-domain essential for Ly6C ^lo Mo development

[00145] We sought to identify regions of Nr4alse that regulate Nr4al gene expression in Ly6C ^low Mo. Based on PU.l and C/ΕΒΡβ binding in Ly6C ^low Mo (Fig. 19(a)) we cloned 12 candidate sequences into luciferase reporters containing a minimal Nr4al promoter (Fig. 19(b). E2, E6, E8 and E9 induced modest but consistent luciferase activity in the myeloid RAW264.7 cell line indicating that these regions may regulate Nr4al in Ly6C ^low Mo (Fig. 11a). It has been suggested that human CD14 ^dim CD16 ^hl Mo are homologous to mouse Ly6C ^low Mo. This notion is based on global gene expression profiling and observation of the characteristic patrolling behavior in CD14 ^dim CD16 ^hl Mo (Cros et al., 2010). We reasoned that if CD14 ^dim CD16 ^hi and Ly6C ^low Mo are truly orthologous that Nr4al should be regulated by a conserved mechanism. To test this hypothesis we assessed the genetic regulatory state of human DNA sequences orthologous to mouse E2, E6, E8 and E9 in human Mo using publicly available datasets (Boyle et al., 2008; Schmidl et al., 2014). Human Mo DNase-Seq clearly shows open chromatin at orthologous regions to mouse E2, E6 and E9 (Fig. l ib), however no orthologue for E8 was identified using BLAT. Human E2, E6 and E9 also possessed

H3K27ac, and H3K27ac levels were higher at E2 and E6 in CD14 ^dim CD16 ^hi Mo than CD14 ^hl CD16 ^neg Mo, consistent with the pattern observed between mouse Mo subsets (Fig. lib). This provides evidence that E2, E6 and E9 are functionally conserved enhancer elements between species, supporting the notion that these regions are important regulators of MP Nr4al gene expression.

[00146] To test the in vivo functions of E2, E6 and E9 we used the CRISPR-Cas9 system to generate three mouse strains, each containing a deletion of enhancer sequence to give Nr4alse_2 ^'A , Nr4alse_6 ^'A and Nr4alse_9 ^~ ' ^~ mice respectively (Fig. 11c, Fig. 19(c)). FACS analysis of peripheral Mo revealed a reduction in Mo frequencies in Nr4alse_2 ^/ , no difference in Nr4alse_9 ^'A , and a modest increase in Nr4alse_6 ^'A mice (Fig. lid). WT-like Mo subset ratios were preserved in both Nr4alse_6 ^'A and Nr4alse_9 ^'A mice, however a striking deficit in Ly6C ^low Mo phenocopying the Nr4al ^'A strain was present in Nr4alse_2 ^'A mice (Fig. lle,f) (Hanna et al., 2011). Therefore the conserved super-enhancer sub-domain Nr4alse_2 is indispensable for Ly6C ^low Mo development.

Nr4alse_2 deletion decouples inflammation-associated Nr4al gene expression from Ly6C ^low Mo-associated Nr4al expression.

[00147] Current genetic models to study MP Nr4al are based on global Nr4al ^'A mice or Cre recombinase mediated deletion of Nr4al ^flox/flox alleles using myeloid specific Cre transgenes, which include, but are not restricted to Csflr, Lys2 (LysM) and Cx3crl. While these tools ablate MP Nr4al they are non-specific with respect to individual MP subsets (Chow et al., 2011; Yona et al., 2012). Consequently, in models that lack Ly6C ^low Mo, Nr4al is also disrupted in macrophages (Fig. 12a). As Ly6C ^low Mo are absent in Nr4alse_2 ^A mice and Nr4al is a key suppressor of macrophage inflammatory gene expression we questioned whether Nr4al se_2 ^_/~ macrophages possess wild type-like responses to inflammatory stimuli.

[00148] During endotoxic shock macrophage mediated production of inflammatory cytokines ultimately precipitates organ failure and mortality (Jacob et al., 2007). As Nr4aV ^A mice are more sensitive to LPS-induced organ failure (Li et al., 2015) we decided to test the role of Nr4alse_2 in this setting. We administered a single high dose of LPS (2.5 mg/kg) to Nr4alse_2 ^'A , Nr4al ^'A , and WT mice by IP injection. All three groups displayed disheveled fur and shivering within the first 72 hours however Nr4al ^'A mice showed a significantly higher mortality than both WT and Nr4alse_2 ^A groups, whose symptoms resolved in the 72- 120-hour time window (Fig. 12b). To understand the role of Nr4alse_2 in the regulation of Nr4al gene expression we measured Nr4al responses to LPS stimulation in thioglycollate- elicited macrophages. WT, Nr4alse_2 ^+A and Nr4alse_2 ^'A macrophages all show the well- characterized peak of Nr4al mRNA at lh followed by a return to baseline by 3h (Fig. 12c, Pei et al., 2005). Western blot analysis also confirmed protein induction in WT and

Nr4alse_2 ^' macrophages at lh following stimulation (Fig. 12d). Furthermore, in a dose- response setting (Fig. 12e) we observed no differences in Nr4al mRNA levels between WT, Nr4alse_2 ^+I~ and Nr4alse_2 ^A macrophages. Finally, following LPS challenge we detected higher levels of 1112, Mb and Nos2 mRNA and iNOS activity in Nr4al ^'A mice relative to Nr4alse_2 ^' mice, which expressed levels comparable to wild type controls (Fig. 12(f) & Fig. 12(g)). These studies confirm that the Nr4alse_2 region does not regulate Nr4al expression in response to TLR4 stimulation.

Differential PU.l binding reveals candidate regulators ofLy6C ^low Mo gene expression.

[00149] We sought to determine the molecular mechanisms regulating Nr4al expression in Ly6C ^low Mo. Cooperative interactions between PU.l and secondary co-factors establish and maintain macrophage enhancer repertoires (Heinz et al., 2010, 2013). Furthermore, differences in SDTF activity elicited within tissue microenvironments are responsible for the diverse range of MP enhancers observed in vivo (Gosselin et al., 2014; Lavin et al., 2014). One mechanism for enhancer acquisition involves SDTF driving the formation of latent enhancers associated with de novo H3K4me2 and PU.l binding (Kaikkonen et al., 2013; Ostuni et al., 2013). Thus the subset of de novo PU.l binding events provides valuable information concerning secondary SDTF identity by virtue of motif enrichment (Gosselin et al., 2014).

[00150] To define motifs associated with Ly6C ^low Mo we determined PU.1 binding profiles in Ly6C ^hi and Ly6C ^low Mo, identifying a total of 65,070 PU.l peaks. Strict criteria for differential binding led to the identification of 345 Ly6C ^low Mo specific PU.l peaks (Fig. 13 a) that possess the hallmarks of a latent enhancer repertoire. These include increased H3K4me2 and nucleosome phasing at regions immediately surrounding the PU.l peaks (Fig. 20(a)); elevated H3K27ac (Fig. 13b); and, increased expression of proximal mRNA transcripts (Fig. 13c) in Ly6C ^low Mo relative to upstream progenitors. Thus, the Ly6C ^low Mo PU.l-specific peak profile is associated with enhancers that regulate the Ly6C ^low Mo gene expression program. Motifs implicated in Ly6C ^low Mo gene expression were identified using de novo motif enrichment analysis on this PU.1 peak set. In strong agreement with our earlier analysis (Fig. 16(c)) we recovered ETS, C/EBP and NR4A motifs (Fig. 13d)as expected, alongside IRF, KLF, RUNX and MEF2 motifs. Using our RNA-Seq dataset we identified transcription factors that are expressed in Ly6C ^low Mo and can bind to these motifs (Fig. 13(e)), considering the most abundant as our primary candidate. This approach defined Cebpb, Ι , Klf2, Mef2a, Nr4al, Sfpil (PU.l) and Runx2 as principal regulators of Ly6C ^low Mo gene expression.

Klfl regulates Ly6C ^low Mo conversion via Nr4alse_2.

[00151] To identify transcription factors that regulate Nr4al expression via Nr4alse_2 we overexpressed each candidate with the Nr4alse_2 reporter. Cebpb, Irf5, Klfl, Mefla, Nr4al and Runx2 were co-transfected into RAW264.7 macrophages alongside either the Nr4al-TSS or Nr4alse_2-TSS luciferase reporter plasmids. To account for promoter dependent effects of the cDNA and the intrinsic activity of the E2 sequence, an enhancer index was calculated that denotes the difference in the ratio of induced luciferase activity between Nr4al-E2-TSS and Nr4al-TSS. We found that only Klfl drives E2-dependent luciferase expression (Fig. 14a). Supporting this finding a motif search for the enriched IRF, KLF, RUNX and MEF2 motifs within the E2 region identified a cluster of 3 KLF motifs but failed to find any instances of the other motif classes (Fig. 20(b)).

[00152] We chose to investigate the role of KLF factors in Ly6C ^low Mo development. KLFs are broadly expressed in Ly6C ^low Mo with Klfl and Klf4 being the most abundant (Fig. 13e). Owing to the perinatal and embryonic lethality of Klf2 ^_/" and Klf4 ^_/" mice we assessed Mo frequencies in myeloid- specific Lyz2-Cre Klf ^os/flox and Lyz2-Cre Klf^ ^ox/flox mice (denoted Mac-Klf2 and Mac-Klf4 respectively, Liao et al., 2011; Mahabeleshwar et al., 2011) . Flow cytometric analysis of Mac-Klf4 blood Mo showed a decrease in both populations (Fig. 14b), consistent with previous reports (Alder et al., 2008). In Mac-Klf2 mice Ly6C ^hi Mo were unaffected however Ly6C ^low Mo were partially reduced (Fig. 14b). Similar results were also observed in the bone marrow of Mac-Klf2 and Mac-Klf4 mice and in bone marrow chimeric mice retro virally transduced with shRNA targeting Klfl and Klf4 (Fig. 21 (a) & (b)).

[00153] We have previously observed incomplete deletion of loxP-flanked genes in blood Mo using the Lys2-Cre system (Hanna et al., 2015). Therefore the differences in Mo frequencies between Mac-Klf2 and Mac-Klf4 mice may either reflect intrinsic differences in the ability of each gene to regulate Mo development, or simply the abundance of each TF in each subset. To address this we measured Klfl and Klf4 mRNA in Ly6C ^hi and Ly6C ^low Mo sorted from Mac-Klf2 and Mac-Klf4 mice using primers that span the loxP-flanked exon to determine recombination efficiency. In Mac-Klf2 mice 72% and 91% loss of Klf2 mRNA was observed for Ly6C ^hl and Ly6C ^low Mo respectively (Fig. 21(c)). Thus the selective loss of Ly6C ^low Mo in Mac-Klf2 mice is not consistent with the incomplete deletion of Klf2 in Ly6C ^hl Mo. A role for Klf2 in Ly6C ^hl to Ly6C ^low Mo conversion is also consistent with the induction of Klf2 gene expression in the transition between subsets (Fig. 13e). In Mac-Klf4 mice Klf4 mRNA was reduced by 63% and 69% in Ly6C ^hi and Ly6C ^low Mo respectively (Fig. 21(d)). Although Mac-Klf4 mice possess fewer Ly6C ^low Mo it is not clear whether this results from fewer precursor Ly6C ^hi Mo, a decrease in Ly6C ^hi to Ly6C ^low Mo conversion, or both. We reasoned that if Klf2 or Klf4 regulate Ly6C ^hl to Ly6C ^low Mo conversion via Nr4al that Kl 2/4 gene expression would predict Mo Nr4al expression. Indeed, Nr4al mRNA expression levels were lower in Ly6C ^hl Mo derived from Mac-Klf2 mice, but not Mac-Klf4 mice (Fig. 14c). Subsequent investigation revealed a significant positive correlation between Klf2 and Nr4al transcript levels in both Mo subsets, however no such relationship was found between Klf4 and Nr4al gene expression (Fig. 14(d) & (e) and Fig. 21 (e) & (f)).

[00154] While of a preliminary nature, these correlative findings suggest that KIJ2 regulates Ly6C ^low Mo development via Nr4alse_2. Given our evidence for a conserved mechanism of Nr4al gene expression between (Fig. 1 lb) we predict that KLF2 expression follows a similar pattern in human Mo subsets. Interrogation of microarray data for KLF2 in human Mo subsets confirmed this hypothesis, showing significantly higher KLF2 levels in human CD14 ^dim CD16 ^hi Mo (Fig. 14f).

Nr4alse_2 is a Mo-specific enhancer.

[00155] Nr4alse_2 regulates Nr4al expression in Ly6C ^low Mo but not in response to LPS stimulation. Furthermore, at steady state, macrophage Nr4al expression spans three orders of magnitude. To determine the extent to which Nr4alse 2 is Ly6C ^low Mo specific we measured Nr4al levels in various MP populations from Nr4alse_2 ^{~ ~} mice. Blood Mo, F4/80 ^hi large, F4/80 ^mt small peritoneal macrophages (LPM and SPM respectively), CDl lc ⁺ lung alveolar macrophages, and F4/80 ⁺ splenic red pulp macrophages were selected (Fig. 15a). In line with previous observations (Tacke et al., 2015) macrophage frequencies were largely unchanged in Nr4al ^'A mice, except for moderately fewer F4/80 ^hi LPM (Fig. 22(a)). RT-PCR analysis captured the expected range of Nr4al levels between macrophage populations (Fig. 15b). Strikingly however no differences in Nr4al mRNA expression were detected between tissue macrophages, except for moderately lower levels in Nr4alse_2 ^'A splenic macrophages. In contrast to this a substantial reduction in steady state Nr4al mRNA expression levels was observed in both Ly6C ^hl and Ly6C ^low Mo (Fig. 15c) showing that Nr4alse_2 is a Mo-specific enhancer.

[00156] We recently reported that Ly6C ^low Mo prevent cancer metastasis to the lung (Hanna et al., 2015). To demonstrate the utility of the Nr4alse_2 ^A model to study Ly6C ^low Mo we assessed tumor burden in mice using a well-established model of metastasis. B16F10 melanoma cells were intravenously injected into WT, Nr4al ^'A and Nr4alse_2 ^'A mice. 18 days after challenge mice were sacrificed and tumor burden was measured by histology. Both Nr4al ^'A and Nr4alse_2 ^~ mice showed a loss of Ly6C ^low Mo (Fig. 22(b)) and significantly higher tumor burden than WT (Fig. 15d,e) however no difference was observed between Nr4al ^'A and Nr4alse_2 ^A mice. Consistent with a critical role for Ly6C ^low Mo in controlling metastasis, the differences are explained by fewer tumor regions rather than tumor size (Fig. 22(c) & (d)). Therefore the Nr4alse_2 ^~ ' ^~ model effectively decouples Nr4al -dependent inflammatory phenotypes from Ly6C ^low Mo function, providing a new and improved tool to study the function of these cells. In contrast to conditional deletion strategies using the Cre- Lox system, enhancer targeting confers an unprecedented degree of specificity, enabling the causal inference of individual MP subsets in disease.

Discussion

A single super-enhancer sub-domain regulates Ly6C ^lo Mo development

[00157] During our investigation into the transcriptional regulatory pathways of Ly6C ^low Mo development we identified Nr4alse_2 as a single domain that is absolutely required for Ly6C ^low Mo development. We also observed distinct, cell-subset specific, patterns of H3K27ac at the Nr4alse locus leading us to investigate whether Nr4al gene expression is controlled by distinct mechanisms between MP subsets. Nr4alse_2 ^A mice lack Ly6C ^low Mo, yet macrophage Nr4al expression is largely unaffected during steady state and during inflammation. This implies a modular structure for the Nr4al locus control region Nr4alse and is consistent with a recent analysis of several SEs showing that these regions consist of multiple sub-domains (Hnisz et al., 2015). Disrupting these sub-domains differentially affected target gene expression depending upon the locus. For example at SIK1, additive effects between sub-domains contribute towards the stable induction of gene expression, whereas at Prdml4, mRNA expression was regulated almost entirely by one of five sub- domains (Hnisz et al., 2015). Our study has identified three active and conserved MP enhancers upstream of Nr4al; Nr4alse_2, Nr4alse_6 and Nr4alse_9, yet only Nr4alse_2 regulates Ly6C ^low Mo development. This highlights the importance of detailed molecular analyses to establish the relevance of individual enhancer elements, and TF binding motifs within these elements. Whether Nr4alse_6 and Nr4alse_9 regulate MP Nr4al gene expression in response to other stimuli is a line of future enquiry.

Enhancer targeting as a strategy to identify regulators of tissue MP development.

[00158] Our studies suggest that KLF transcription factors regulate Nr4al gene expression via Nr4alse_2. Ly6C ^low Mo enhancers are enriched for KLF motifs, and these motifs are present in Nr4alse_2. Multiple KLF family members are expressed in Ly6C ^low Mo, which may act redundantly at Nr4alse_2. In Ly6C ^low Mo Klf2 and Klf4 are the most abundant family members, thus we investigated the roles of these genes. Both Klf2 and Klf4 regulate macrophage inflammatory gene expression by inhibiting p300 and PCAF recruitment to Nf- KB (Das et al., 2006; Liao et al., 2011). The different roles ascribed to each factor may arise from the different contexts in which they are expressed. Klf4 is induced during Ly6C ^hl Mo differentiation, and is further up-regulated in macrophages by IL-4. In this context Klf4 regulates Ly6C ^hl Mo development and facilitates the M2 program of macrophage activation (Feinberg et al., 2007; Liao et al., 2011). Klf2 however is expressed in circulating Mo, and strongly reduced by hypoxia leading to increased Nf-KB/HiF- 1 activity (Mahabeleshwar et al., 2011).

[00159] Our findings suggest non-redundant roles for Klf2 and Klf4 in in Mo development. Klf4 expression is high in both Mo subsets and Mac-Klf4 mice have fewer Mo. However, the ratio of Ly6C ^hi to Ly6C ^low Mo, and Ly6C ^low Mo Nr4al expression are not affected in Mac- Klf4 mice (Fig. 14c). However, depletion of Klf2 facilitated a selective loss of Ly6C ^low Mo and Klf2 mRNA levels were predictive of Nr4al levels, implying a causal relationship between Klf2 and Nr4al . Despite repeated attempts we were not able to obtain successful immunoprecipitation of KLF2 at the Nr4alse locus due to an absence of high-quality commercial antibodies, neither was overexpression of Klf2 sufficient to up-regulate Nr4al mRNA in vitro (data not shown). These preliminary findings suggest that Klf2 acts via Nr4alse_2 locus and is necessary but not sufficient for Ly6C ^ow Mo development. The identification of additional critical co-factors acting via Nr4alse_2, the Nr4al promoter or elsewhere will pave the way for a more detailed mechanistic understanding of how

Nr4alse_2 regulates Nr4al gene expression in Ly6C ^low Mo development.

Enhancer targeting as an approach to overcome pleiotropic effects in closely related cell types.

[00160] MP occupy all tissues of the body where these cells perform specialized functions to facilitate homeostasis. For example, Ly6C ^low Mo maintain vascular integrity by facilitating removal of damaged endothelium (Carlin et al., 2013), alveolar macrophages maintain lung function by clearing surfactants (Nakamura et al., 2013), red pulp macrophages contribute to iron homeostasis by recycling erythrocytes (Kohyama et al., 2009), whereas the microglia's dedicated functions include supporting brain function by synaptic pruning (Paolicelli et al., 2011). These specialized functions are imparted by tissue-specific LTDFs; Ly6C ^low Mo require Nr4al (Hanna et al., 2011); alveolar macrophages rely upon PPARy (Schneider et al., 2014); splenic red pulp-macrophages macrophages need Spic (Kohyama et al., 2009); while resident peritoneal macrophages depend upon the transcription factor GATA6 (Okabe and Medzhitov, 2014).

[00161] In some cases, such as for Gata6 and Spic, LDTF expression within the MP system is cell-specific such that macrophage-specific deletion of the factor is sufficient to study the function of the associated subset. However, for the most part both the expression and requirement of key MP TFs are not cell- specific. Epigenetic analyses of MP subsets reveals shared motif usage and co-expression of cognate TFs over multiple subsets (Lavin et al., 2014). For example PPAR motifs are enriched in alveolar and renal macrophage enhancers and PPARy regulates both alveolar macrophage and osteoclast differentiation (Schneider et al., 2014; Wan et al., 2007). Disease processes complicate matters further by invoking dynamic transcription factor expression and altering requirements, in this context PPARy is up-regulated by IL-4 and controls alternative macrophage activation (Odegaard et al., 2007). Similarly, Nr4al is required for Ly6C ^low Mo development and is also induced by LPS (Hanna et al., 2011; Pei et al., 2005). These pleiotropic effects limit our ability to study individual MP subsets and the lack of specificity provided by current myeloid Cre transgenes presents a significant problem when attempting to target individual subsets. [00162] We have shown that enhancer targeting can overcome these limitations. Our approach leverages the unique enhancer repertoires resulting from the exclusive environment each MP subset occupies. While the concept of cell specific enhancers controlling LDTF expression is not new (Zheng et al., 2010), to our knowledge this application and degree of specificity is. We show that targeting cell-specific SE sub-domains within key LDTFs functionally decouples cell-specific aspects of gene expression while retaining physiological characteristics of gene function relevant to neighboring cell subsets. In our case, targeting the Nr4alse_2 sub-domain has led to the generation of a new loss-of-function tool to study Ly6C ^low Mo that preserves both Nr4al expression in other MP populations and the rapid kinetics of Nr4al expression in response to LPS signaling. Conceptually this strategy can be applied to any scenario in which gene expression is regulated by distinct enhancer sequences providing a new approach to study gene function amongst closely related cell types.

Experimental procedures

Mice

Mice were maintained in-house or purchased from the Jackson laboratory. All experiments followed guidelines of the La Jolla Institute for Allergy and Immunology (LIAI) Animal Care and Use Committee, and approval for use of rodents was obtained from LIAI according to criteria outlined in the Guide for the Care and Use of Laboratory Animals from the National Institutes of Health. Mice were euthanized by C02 inhalation

Cell sorting

Mice were sacrificed by CO ₂ inhalation and bone marrow or blood extracted into DPBS + 2mM ETDA. Following RBC lysis cells were blocked and stained for surface antigens and purified by flow cytometry as described herein.

Thioglycollate elicited macrophages

Thioglycollate elicited macrophages were elicited by intraperitoneal injection of 1ml 4% Brewer's Thioglycollate Medium. 5 days after injection macrophages were harvested and cultured as described in the extended experimental procedures

RNA isolation and RNA-Seq Sorted cells were immediately spun down and stored in Trizol. RNA was extracted using DirectZol columns (Zymo Research). RNA was prepared for sequencing using the TruSeq v2 kit (Illumina).

ChlP-Seq

Histone ChIP was performed using the protocol described in (Gilfillan et al., 2012) and transcription factor ChIP performed essentially as described in (Gosselin et al., 2014), with modifications described in the extended methods. ChlP-Seq libraries were prepared using the ThruPlex-FD kit (Rubicon Genomics).

Molecular cloning and overexpression studies

Enhancers were cloned into the Sail and BamHl sites of a pGL4.10 series vector described in (Heinz et al, 2013) modified to contain an Nr4al minimal promoter (300 bp) and 5'UTR . Transfection assays were performed in murine RAW264.7 macrophages using Lipofectamine LTX. cDNA expression vectors were obtained from Origene. Full details are in the extended experimental procedures.

CRISPR mouse generation

Mouse genome editing was performed essentially as described with minor modifications (Concepcion et al., 2015; Wang et al., 2013). Four sgRNA (two pairs targeting each enhancer flanking region) were injected into embryos of superovulated C57BL/6 mice along with Cas9 mRNA (Life Technologies) at the UCSD transgenic core facility. Knockout mice were mated with C57BL/6 and offspring thereafter maintained via sibling mating.

Bone marrow chimeras

Bone marrow was shipped on ice as described in the extended experimental methods.

Recipient mice were lethally irradiated and bone marrow transplanted by retroorbital injection. Mice were allowed to recover for at least 6 weeks before performing experiments.

Cancer study

300,000 B16F10 melanoma cells were injected via tail vein into recipient mice. Lungs were harvested in zinc buffered formalin and mounted into paraffin blocks. Sections were stained with H&E and slides were scanned with an AxioScan Zl (Zeiss), see extended experimental procedures. Endotoxin sensitivity assay

Ultrapure LPS-EB (Invivogen) was made up in PBS and injected IP. Mice were monitored three times daily for the first 72 hours and twice daily thereafter.

Bioinformatics data analysis

FASTQ files were mapped to the mouse mmlO reference genome using RNA-STAR for RNA-Seq experiments, or Bowtie for ChlP-Seq studies. RNA-Seq expression levels were quantitated using featureCounts and differential expression analyzed using edgeR. ChlP-Seq analysis was performed using HOMER. For full details see extended experimental procedures.

Accession Numbers

Illumina sequencing for this project has been deposited at NCBI's Gene Expression Omnibus (GEO) as a SuperSeries under the accession number GSE80040.

Acknowledgements

Funding sources: R01HLxll8765, R01CA202987 and R01HL112039 to CCH;

R01DK091183, R01CA17390 and R01HL088093 to CKG; R00HL123485 to CER;

R01GM086912 to BAH; R01HL086548 and R01075427 to MKJ. AHA Fellowships 16POST27630002 to GDT and 12DG 12070005 to RNH. KDR was supported in part by a Ruth L. Kirschstein National Research Service Award (NRSA) Institutional Predoctoral Training Grant, T32 GM008666, from the National Institute of General Medical Sciences.

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Example 2

Supplemental Materials and Methods Cell preparation and isolation

Bone marrow monocytes were harvested from femurs, tibias and hip bones of 8-12 week old male C57BL/6 mice (strain 006664) obtained from the Jackson laboratory (Bar Harbor, ME). Prior to FACS staining cells were subject to a brief (3 minute) red blood cell lysis (RBC lysis buffer, EBiosciences) at room temperature. All FACS staining was performed in FACS buffer (DPBS + 10% FCS + 2mM EDTA). Prior to surface staining FC receptors were blocked with anti-CD16/32 (clone 93) for 30 minutes. Surface staining was performed for 30 minutes in a final volume of 500μ1 for FACS sorts and ΙΟΟμΙ for regular flow cytometry. Surface staining was performed using Live/Dead Yellow (Thermo Fisher) and antibody combinations in accordance with the gating schemes in the figures. Lineage positive cells were identified using pooled APC conjugated anti-CD3, CD19, Ly6G and NK1.1 (clonesl45- 2C11, 1D3, 1A8 and PK136 respectively). Additional cell surface markers used were CD117-PE-Cy7 (ACK2), CD115 PE or BV421 (clone AFS98), Ly6C APC-Cy7 or PerCP- Cy5.5 (clone HK1.4), CD135-PE (clone A2F10.1), CDllc-FITC (clone N418), F4/80 PE- Cy7 (clone BM8), CDl lb FITC (clone Ml/70) and MHCII-BV605 (clone Ml/70). All antibodies were obtained from Biolegend (San Diego, CA). Samples were washed twice in at least 200μ1 FACS buffer before acquisition. Cells were sorted using a FACS Aria II (BD biosciences) and conventional flow cytometry using an LSRII (BD biosciences). All flow cytometry was performed on live cells.

ChIP and sequencing library preparation

ChIP assays for histone modifications were performed as previously described (Gilfillan et al., 2012). To obtain sufficient numbers of MDPs bone marrow from 10 mice were pooled and sorted. For each ChIP assay 500,000 FACS isolated cells were immediately washed with PBS and resuspended in MNase digestion buffer (50mM Tris pH 8.0, ImM CaC12, 0.2% Triton X-100). Cells were then digested in to mononucleosomal fragments using

micrococcal nuclease (MNase, Affymetrix, CA). Enzymatic digestion was quenched by addition of 1/10 volume stop buffer (HOmM Tris pH 8.0, 55mM EDTA), samples briefly sonicated using a Bioruptor (Diagenode, Belgium) and then adjusted to RIPA buffer conditions by adding an equal volume of 2x RIPA buffer (280mM NaCl, 1.8% Triton lOO, 0.2% SDS, 0.2% Sodium Deoxycholate, 5mM EGTA). Immunoprecipitations were performed in a final volume of 100 μΐ. 2 μg of anti-H3K4me2 (Millipore 07-030) or 2μg of anti-H3K27ac (Diagenode C15410196) were added and incubated overnight with rotation at 4 °C. Antibody-antigen-DNA complexes were recovered by incubating for 2 hours with 10 μΐ Protein A Dynabeads previously washed in RIPA buffer (lOmM Tris pH 8.0, 140mM NaCl, ImM EDTA, 1% Triton X-100, 0.2% SDS, 0.2% Sodium Deoxycholate). Complexes were then washed 5x in ice cold RIPA buffer and lx in LiCl wash buffer (lOmM Tris pH 8.0, 250mM LiCl, ImM EDTA, 0.5% Igepal CA-630, 0.5% Sodium deoxycholate), each wash was performed in 200 μΐ at 4 °C for 5 minutes with rotation. All above buffers were supplemented with lx Protease inhibitor Cocktail, ImM PMSF and 5mM Sodium Butyrate (Sigma). Beads were subject to a final wash in 200 μΐ ice cold TE buffer (Invitrogen) without protease inhibitors and eluted in 100 μΐ 1% SDS-TE buffer at 37 °C for 20 minutes. Finally, protein was treated with 2 μΐ proteinase K (Ambion) for lh at 55 °C and DNA purified using a ChIP Clean & Concentrate column (Zymo, Irvine, CA) eluting in 30 μΐ final volume.

ChIP for PU.l and C/EBPb were performed as previously described (Gosselin et al., 2014). 500,000 sorted cells were washed in PBS and immediately fixated for 9 minutes at room temperature in 1% methanol free formaldehyde in PBS (ThermoFisher Scientific). Fixation was quenched by addition of 1/20 volume 2.625M glycine solution and cells were washed twice with PBS. Cell pellets were then snap frozen in a dry ice/methanol bath and stored at - 80oC until needed. Nuclei were enriched by resuspending cell pellets in lOmM HEPES pH 7.9, 85mM KC1, lmM EDTA, 0.5% Igepal CA-630 and incubating on ice for 10 minutes. Nuclei were harvested by spinning at 3000 g for 10 minutes, and lysed in 130 μΐ lysis buffer (lOmM Tris pH 8.0, lOOmM NaCl, lmM EDTA, 0.5mM EGTA, 0.1% Sodium

Deoxycholate, 0.5% N-lauroylsarcosine). DNA was transferred in to Covaris micro tubes (Covaris, MA) sheared into 150-600bp fragments using a Covaris E220 (14 mins, duty cycle 3%, 100 cycles per burst). Final volume was adjusted to 200 μΐ and 22 μΐ 10% Triton X-100 added, cell debris was then cleared by spinning at maximum speed for 5 minutes. 20 μΐ of protein A dynabeads pre-conjugated to 3ug anti PU.l or C/EBPb (sc-352x and sc-150x respectively, Santa Cruz Biotechnology, CA) were added to each chromatin preparation and incubated with rotation for 2h at 4 °C. Antibody-antigen-DNA complexes were then washed in 3x WBI (20mM Tris pH 7.4, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2mM EDTA, ), 3x LiCl WB (lOmM Tris pH 7.4, 250mM LiCl,, 1% Triton X-100, 0.7% Sodium

Deoxycholate, 1% Igepal CA-630) and lx TET (TE, 0.2% Tween-20) buffer. All wash volumes were 200 μΐ. DNA was eluted in 1% SDS-TE for 30 minutes at 37 °C, NaCl was added to a final concentration of 300mM and crosslinking reversed overnight at 65 °C.

Finally, protein was treated with 2 μΐ proteinase K (Ambion) for lh at 55 °C and DNA purified using a ChIP Clean & Concentrate column (Zymo, Irvine, CA) eluting in 30 μΐ final volume.

ChlP-Seq libraries were prepared using an initial 0.3 - 5 ng DNA using the ThruPlex-FD kit (Rubicon Genomics, MI) in accordance with the manufacturer's guidelines. RNA-Seq libraries were prepared using the Tru-Seq v2 library preparation kit (Illumina, La Jolla, CA) in accordance with the manufacturer's instructions. RNA-Seq differential expression analysis

Sequencing libraries were sequenced using an Illumina HiSeq at the LIAI sequencing core facility. RNA-Seq libraries were sequenced as paired-end 50 base reads, and ChlP-Seq libraries were sequenced as single-end 50 base reads. Illumina BCL files were converted into FASTQ format using bcl2fastq (vl.8.4, Illumina).

Paired end RNA-Seq reads were mapped to the mouse mmlO reference genome using RNA- STAR v2.3.0 (Dobin et al., 2013) compiled with gene models derived from the Ensembl v73 genome annotation set. Gene counts were quantitated with the same annotation set using featureCounts (Liao et al., 2013). Differential expression analysis was performed using edgeR v3.4.2 (Robinson et al., 2010). Variance calculations were computed using the common dispersion method and sequencing depth differences adjusted using the 'relative log expression' method. Differential expression was computed against all pairwise comparisons and an FDR (Benjamini-Hochberg) corrected P-value threshold of le-5 applied for calling statistical significance. RPKM calculations were computed in edgeR using gene lengths derived from featureCounts. Publicly available RNA-Seq data from Levin et al were obtained from GEO GSE63340 (Levin et al, 2014) and processed as above.

ChlP-Seq peak calling, differential binding and UCSC genome browser visualization

ChlP-Seq reads were mapped to the mmlO reference genome using Bowtie (v , Langmead et al., 2009). Homer (v4.4, Heinz et al., 2010) was used for ChlP-Seq peak calling.

Enhancer regions were defined by merging biological replicates for H3K4me2 libraries and running the findPeaks algorithm with 'style -histone' against the MNase-treated DNA input control. H3K4me2 profiles defined by each cell type were then aggregated using mergePeaks to give the final H3K4me2 peak set. These peaks were assigned to target genes using HOMER, and enhancers defined as H3K4me2 peaks whose centers were >2.5kb from the nearest annotated transcription start site. Enhancer activity was measured by quantitating H3K4me2 and H3K27ac within these defined enhancer regions. Differences in sequencing depth were accounted for by normalizing to an effective library size of lxl 0 ⁷ reads per lane. Transcription factor ChlP-Seq peaks were called using HOMER by running the findPeaks algorithm with the 'style -factor' flag using CH20 treated input DNA control as background sequence. Transcription factor peaks were called independently for each lane and merged using mergePeaks prior to quantification of tags within peaks using the annotatePeaks command in HOMER. Visualization was performed at the UCSC genome browser using big Wig files generated in HOMER.

ChlP-Seq data for Lavin et al (2014) were obtained using GEO accession GSE63339 and processed as above. Human ChlP-Seq data were accessed from GEO accession SRP015328 and mapped to the human hgl9 reference genome using the protocols outlined above. The big Wig file of human monocyte DNase-Seq was downloaded from the ENCODE project at <URL:

https://www.encodeproject.Org/files/ENCFF000TAU/@ @download/ENCFF000TAU.bigWig > accessed September 10, 2015, and visualized directly in the UCSC genome browser.

Microarray data

Human monocyte Klf2 expression was obtained from NCBI GEO Profiles under accession GDS4219, data shown are for probe ID 219371_s_at, which is representative of the three probes available for Klf2 on this array type in this experiment.

Differential enhancer profiling, hierarchical clustering and ChlP-Seq visualization

Differential histone and transcription factor binding were determined using edgeR. To identify patterns of enhancer usage between MDP, cMoP, Ly6C ^hl and Ly6C ^low monocytes we employed a very permissive threshold for differential expression, this was to identify any weak signals in the data arising from these closely related cell types. Statistical significance was computed between all pairwise comparisons of cell types using an FDR corrected (Benjamini-Hochberg) p value threshold of 0.01 without the application of a fold-change cutoff. Variance was estimated using the common dispersion estimate by treating all conditions as pseudoreplicates of a single group. The final set of differentially enriched (DE) enhancers represents the union of all differentially bound enhancers determined by H3K4me2 or H3K27ac in any pairwise comparison.

In order to perform hierarchical clustering, matrices of tag counts for H3K4me2 and

H3K27ac for the set of DE enhancers were obtained. Each matrix was independently mean centered and variance stabilized (with respect enhancers, row mean / row SD). The normalized matrices were then concatenated and subject to hierarchical clustering using a Euclidean distance and complete linkage clustering approach using the base functions in R. Based upon visual inspection, the results the tree was cut into nine clusters, the ordering of these clusters was used to order the final histogram figure (Fig. 9c). Within each cluster enhancers were then ranked according to their 'peak score' as determined by HOMER, this ranking was used to order rows within clusters in Fig. 9c. All PU.l peaks overlapping each DE enhancer were extracted and H3K4me2/H3K27ac tag counts calculated +/-lkb from each PU.l peak center using HOMER's annotatePeaks with option '-ghist'. The final results were plotted using the R package gplots.

UCSC genome browser tracks were visualized using track hubs generated with the HOMER program makeBigWigHub.pl.

Differential PU.l peak calling between Ly6C ^hi and Lv6C ^low Mo

A complete monocyte PU.1 peak set was obtained by concatenating the PU.1 peaks defined in both Ly6C ^hl and Ly6C ^low Mo as described in 'ChlP-Seq peak calling, differential binding and UCSC genome browser visualization'. Tag counts for PU.l libraries were counted within this peak set for both monocyte populations and differential binding an analysis was performed in edgeR using the same procedures as for differential histone binding. For PU.l peaks an FDR corrected (Benjamini-Hochberg) p-value cutoff of le-5 and log2 fold change cutoff of 3 were applied.

Enhancer cloning

All specific cloning details for individual sequences are in Table 1. The Nr4al 5'UTR and 650 bases of promoter sequence were cloned into the Kpnl and Sail sites of a minimal pGL4.10 luc2 reporter vector. This vector, termed pGL4.10-TSS was used as the host vector for all enhancer clones. All enhancer sequences were isolated from genomic DNA by PCR using the primers detailed in Table 1. For PCR using Phusion High-fidelity polymerase (NEB, MA) ΙΟμΙ 5x HF buffer, Ιμΐ lOmM dNTP, 2.5μ1 F primer (lOuM), 2.5μ1 R primer (lOuM) 2μ1 mouse genomic DNA (250ng), 1.5μ1 DMSO, 30μ1 H20 and 0.5μ1 Phusion polymerase were used per reaction. PCR was performed using the following protocol at the indicated annealing temperature: - lx 98oC 30s; 30x 98oC 10s, anneal 30s, 72oC 30s; 72oC lOmin. For PCR using LA Taq GC buffer (Clontech, Mountain View, CA) 25μ1 GC buffer I, 8μ1 dNTP, 2.5μ1 F primer (lOuM), 2.5μ1 R primer (lOuM), 2μ1 DNA (250ng), 9.5μ1 H20 and 0.5 μΐ LA-Taq were used per reaction. PCR was performed as per the manufacturer's instructions using the annealing temperatures in Table 1 and 1 -minute extension time. PCR products were purified by gel extraction using Zymoclean Gen DNA recovery columns (Zymo, Irvine, CA). All cloning was performed at 1:4 vector: insert molar ratio using NEB reagents (Ipswich, MA) and clones were validated by PCR sequencing. PCR was performed using a MyCycler (BioRad, Irvine, CA)

Transfection and overexpression experiments

RAW264.7 macrophages were obtained from ATCC and maintained at low passage (<15) in DMEM +(10%FCS, 1% Pen/Strep, 1% L-glut). Transfection studies were performed using 0.3ug pGL4.10 luciferase reporter and 0.2ug cDNA or 0.5ug pGL4.10 luciferase reporter only, in addition 0.04ug pmaxGFP (Lonza, Basel) and O.Olug pTK Renilla (ThermoFisher, Waltham, MA) luciferase control were added. 0.55ug of plasmid DNA was complexed at 8: 1 ratio with lipofectamine LTX as per manufacturer's guidelines and ΙΟΟμΙ per well given to RAW.264.7 cells at -70% confluency and activity measured typically 12-16 hours later using the Dual Luciferase Reporter Assay (Promega, Madison, WI) on Sirius luminometer (Titerkek-Berthold, Pforzheim, Germany). shRNA virus BMT experiments

PLAT-E packaging cells were grown to 60-70% confluency in DMEM (Gibco, +10%FCS, 1% L-glut, 1 μg/ml puromycin, 10 μg/ml blasticidin) in 10 cm dishes at 37°C in 10% C02. Pools of three UltramiR (TRANSomiC technologies, Huntsville, AL) retroviral vectors (LMN) for Klf2 (ULTRA-3224750, ULTRA-3224748, ULTRA-3224747), Klf4 (ULTRA- 3224770, ULTRA-3224769, ULTRA-3224768) and Non-targeting shRNA control were transfected into PLAT-E cells using JetPrime transfection in accordance with the

manufacture's guidelines. 7 μg total DNA was transfected per 10 cm plate. 1 hour prior to transfection media was replaced with antibiotic free media, cells were incubated overnight. The following were replaced with fresh 10 ml DMEM, without antibiotics. The following morning the retroviral supernatant was harvested and used for transduction of bone marrow stem cells (below). 8 ml fresh DMEM was added to the cells and the last step repeated the following day.

Murine stem cells were isolated from bone marrow by negative selection using the EasySep Mouse Hematopoietic Progenitor Isolation Kit (StemCell technologies, Vancouver, BC) in accordance with manufacturer's guidelines. Cells were resuspended in 2.5ml of STEMSPAN SFEM media (StemCell Technologies, Vancouver) containing 200 ng/ml rmSCF, 40 ng/ml rhIL-6 and 20 ng/ml rmIL-3 in 6 well plates previously coated for 2 hours with 2ml of 25 μg/ml human fibronectin and washed once with PBS. Bone marrow stem cells from one mouse were split between 2 wells and an equal volume (1.25ml) retroviral supernatant was added to each well. Cells were then spun at 850g for lh at 37°C and incubated for 22h at 37°C in 10% CO ₂ . A second batch of retrovirus was added the following day and spin transduction repeated. Following the second transduction cells were harvested and transferred via retroorbital injection into lethally irradiated C57BL/6 host mice (2x 600 Rads, 2-3 hours apart). Bone marrow was allowed to reconstitute for 6 weeks prior to analysis.

CRISPR mouse generation

sgRNA sequences were designed using the CRISPR Design web tool online at <URL:

http://crispr.mit.edu>. To minimize off-target effects we only considered sgRNAs with a score >70. For each enhancer deletion two pairs of sgRNAs flanking the target region were designed that were at least 50 base pairs apart. sgRNA templates were ordered as Ultramers from IDT (Coralville, IA) as a chimeric T7 promoter sequence, variable crRNA (see Table 2 for individual sequence information) and invariable tracrRNA. In order to promote robust transcription from the T7 promoter the first two bases of each sgRNA sequence were substituted for guanines. dsDNA templates for each sgRNA were generated by PCR using the Pfu Ultra II polymerase (Agilent Technologies, Santa Clara, CA). PCR reactions were cleaned using ChIP Clean & Concentrate columns (Zymo, Irvine, CA) and used as input for in vitro transcription using the MEGAscript T7 kit (Thermo Fisher, Waltham, MA) in accordance with the manufacturer's instructions. RNA was cleaned using the MEGAclear kit (Thermo Fisher) in accordance with the manufacturer's guidelines.

For embryo injections 0.5 day fertilized embryos were collected from 3-4 week-old superovulated C57BL/6 females (Harlan, WI) by injecting 5.0 I.U each of PMSG (Sigma Aldrich) and hCG (Sigma Aldrich). Embryos were transferred into M2 medium (Millipore) and injected into the cytoplasm with sgRNA mixed at 25¾/μ1 each along with SOng/μΙ Cas9 mRNA (GeneArt CRISPR Nuclease mRNA, Thermo Fisher) to give a final lSOng/μΙ RNA in IDTE buffer. These injected embryos were cultured in an incubator in KSOMaa medium (Zenith) in a humidified atmosphere of 5% C02 at 37C over night. The embryos were implanted at 2-cell stage into recipient pseudo pregnant ICR female mice. Embryo injections were performed at the University of California, San Diego transgenic core facility.

CRISPR mouse breeding and genotyping Founder mice were screened for the presence of one or two altered alleles using a PCR strategy that flanks the expected mutation. PCRs were designed such that the wild type product is 2 - 3kb and the respective deletion allele around lkb shorter. Primer sequences and PCR details are in Table 3. PCRs were carried out using the specified kits in accordance with the manufacturer's guidelines, with primer extension and annealing temperatures stated in the table. Founder animals were crossed with C57BL/6 mice obtained from the Jackson laboratory (strain 000664) to obtain heterozygous Fl animals that were interbred via sibling mating to generate Nr4alse_2 ^'/~ , Nr4alse_6 ^'/~ , and Nr4alse_9 ^'/~ mice. Observed phenotypes were present in homozygous null mice derived from at least three independent founder mice for each strain. For the Nr4alse_2-I- strain we also confirmed by Sanger sequencing that the downstream DNA sequence from the deletion into the Nr4al first intron was not modified

LPS challenge

Male mice aged 8-15 weeks old were intraperitoneally injected with 2.5* 10 ⁶ EU/kg

(equivalent to 2.5mg/kg) Ultrapure LP-EB (Invivogen) in PBS. Mice were age and sex matched in all experiments. Prior to injection LPS was sonicated for 5 minutes at room temperature in a bath sonicator (FS20H, Fisher Scientific). Mice were monitored three times daily for the first 72 hours and twice daily thereafter.

B16F10, histology and microscopy quantification

300,000 B16F10 melanoma cells were intravenously injected by tail vein injection into recipient mice as previously described (Hanna et al 2015). 18 days following injection mice were sacrificed, lungs were filled with zinc buffered formalin and stored in the same buffer before embedding into paraffin blocks. Sections were cut at 4 μιη, adhered to positively charged slides and dried over night. Sections were dewaxed with Slide Brite, rehydrated and stained with hematoxylin (Thermofisher), differentiated with acid alcohol, blued with Scott's water and stained with eosin (Thermofisher). Slides were scanned with ZEISS AxioScan Zl slide scanner using 10x/0.3NA or 20x/0.8NA objective.

Klf mice

For Lys2 ^Cre Klf ^ox/flox and Lys2 ^Cre Klf ^loxfflox studies bone marrow (femur, tibia and hip bone) and Cre negative littermate controls were harvested, cleaned and shipped overnight on wet ice in BMM (RPMI, 1% Hepes, 1% Anti/Anti (Gibco), 1% BME (Gibco), 1% NEAA (Gibco), 1% Sodium Pyruvate (Gibco), 10% FCS). Bone marrow was harvested by scraping bones clean and immersing in 70% ethanol for 10 seconds before extracting marrow by centrifugation at 5,900g for 15 seconds in a 1.5ml Eppendorf tube. Bone marrow was immediately resuspended in room temperature sterile PBS and injected into lethally irradiated recipient mice (2 x 600 rads) by retroorbital injection at a ratio of 3:1 (recipient to donor). Mice were allowed to reconstitute for at least 6 weeks prior to sacrifice and analysis.

Table 2. crRNA design and sequences.

sgRNAs were ordered as ultramers composed of an upstream T7 promoter (underlined), crR A (lower case) and invariant downstream tracrRNA sequence (boxed) as shown:

fTAATACGACTCACTATAG btgaa ctga a ctcccca ccgGTTTTAG AG CTAG AA ATAG CAAGTTAA AATAAG

GCTAGTCCGTTATC AACTTG AAA AAGTG G CACCG AGTCGGTG CTTTT ( SE Q. ID. NO.: 59)

Table 3. PCR details for enhancer knockout mouse genotyping.