TREATMENT OF NEUORODEGENERATIVE DISEASES THROUGH THE INHIBITION OF ATAXIN-2 CROSS REFERENCE TO OTHER APPLICATIONS [0001] This application claims the benefit of U.S. Provisional Application No.63/286,436, filed December 6, 2021, and U.S. Provisional Application No.63/388,086, filed July 11, 2022 the contents of which are hereby incorporated by reference in its entirety. INCORPORATION BY REFERENCE OF SEQUENCE LISTING PROVIDED AS A TEXT FILE [0002] A sequence listing is provided herewith as a sequence listing xml, “S21-420_STAN- 1920WO_Seqlist” created on December 5, 2022, and having a size of 4 KB. The contents of the sequence listing xml are incorporated by reference herein in their entirety. GOVERNMENT RIGHTS [0003] This invention was made with Government support under contract R35 NS097263-05 and F32 NS116208-02 awarded by the National Institutes of Health. The Government has certain rights in the invention. INTRODUCTION [0004] Many neurodegenerative diseases are associated with accumulation of misfolded proteins, and strategies to rid of these proteins are emerging as a promising therapeutic approach. A hyper-phosphorylated, ubiquitinated and cleaved form of TDP-43, known as pathologic TDP43, is a major disease-associated protein in nearly all cases of amyotrophic lateral sclerosis (ALS), and is also present in numerous other neurodegenerative disorders such as behavioral variant frontotemporal dementia (bvFTD), primary progressive aphasia (PPA), and limbic-predominant age-related TDP-43 encephalopathy (LATE). Despite the prominent presence of TDP-43 aggregates in multiple neurodegenerative diseases, targeting TDP-43 directly presents many challenges, in that it is tightly regulated and essential, and reducing its levels results in numerous deleterious effects, for example embryonic lethality during development, or motor phenotypes in adult mice. [0005] Other approaches have been used to target a modifier of TDP-43 aggregation and toxicity. Ataxin-2, a polyglutamine (polyQ) protein for which long (>34) polyQ expansions cause spinocerebellar ataxia 2 (SCA2) and intermediate-length (22-34) repeats are a risk factor for ALS, is a potent modifier of TDP-43 aggregation and toxicity in multiple model systems including yeast, Drosophila, primary neurons, and mice. The polyQ expansions lead to increased ataxin-2 protein levels, and antisense oligonucleotides (ASOs) targeting ataxin- 2 in vivo show marked protection against motor deficits and extend lifespan in TDP-43 overexpressing mice and in SCA2 mice. These results have motivated recent administration of ataxin-2 targeting ASOs to human ALS patients with or without long polyQ expansions in clinical trials. Gene-based therapies, like ASOs, hold great promise to provide disease- modifying treatments for these devastating neurodegenerative diseases but they are unfortunately inaccessible to many patients worldwide. [0006] Defective RNA processing contributes to ALS. Ataxin-2 harbors a PAM2-domain, binds to poly(A)-binding protein, and contains an Lsm-domain commonly found in splicing factors. These domains likely promote ataxin-2 localization to mRNP granules and direct its role as a translational regulator. Ataxin-2 functions in multiple types of mRNP granules such as P-bodies and stress granules, and its association with mRNP granules in Drosophila neurons is linked to translation-dependent long-term memory. Knockdown of ataxin-2 reduces recruitment of TDP-43 to stress granules. [0007] There is a critical need for alternative therapies to treat neurogenerative diseases associated with Ataxin-2, and comprising long and intermediate polyQ expansions. Described herein are methods and compositions for treating ATXN2 associated neurodegenerative diseases. SUMMARY [0008] Compositions and methods are provided for treating a mammalian subject for a neurodegeneration disease, including, without limitation, amyotrophic lateral sclerosis (ALS), spinocerebellar ataxia 2 (SCA2), etc., by inhibition of Ataxin-2 (ATXN-2). An ATXN2 inhibitor is delivered to the subject is a dose effective to reduce ATXN2 protein levels or function, thereby reducing the symptoms of the neurodegenerative disease. [0009] In some embodiments, an ATXN2 inhibitor, which may be referred to as an anti-ATXN2 agent, is a bisphosphonate. In some embodiments, an anti-ATXN2 bisphosphonate is an inhibitor of v-ATPase. Other inhibitors of v-ATPase are also useful as anti-ALXN2 agents, e.g. thonzonium, alexidine, and the like. In other embodiments, an anti-ATXN2 agent inhibits the NOGO receptor, NgR1 (also referred to as RTN4R). An NgR1 inhibitor may be a genetic agent that inhibits NgR1 expression, or may interfere with NgR1 signaling, e.g. by competitive inhibition or blocking of the interaction between NgR1 and NOGO, neutralization of NOGO, NEP1-40 inhibitor, and the like. [0010] In some embodiments, a pharmaceutical formulation is provided, comprising an anti- ATXN2 agent as identified herein, and a pharmaceutically acceptable excipient. The formulation may be provided in a unit dose. The formulation may be suitable for parenteral or oral delivery. The formulation may be suitable for direct delivery to the brain. [0011] In the methods of the disclosure, an effective dose of an anti-ATXN-2 agent is administered to an individual having, or at risk of having, a neurogenerative disease, in a dose effective to stabilize, reduce or prevent clinical symptoms of the disease. A variety of neurogenerative diseases may be treated by practicing the methods, including ALS, SCA2, Parkinson’s disease, spinocerebellar ataxia type 1, Machado-Joseph Disease also known as spinocerebellar ataxia type 3, tauopathies, or other neurodegenerative diseases. In some embodiments the neurodegenerative disease is ALS. In some embodiments the neurodegenerative disease is SCA. In some embodiments the anti-ATXN2 agent is a bisphosphonate, including without limitation etidronate and alendronate. In some embodiments the anti-ATXN2 agent is an inhibitor of NgR1. The individual may be human. The individual may be monitored, e.g. before, during and/or after treatment, for inhibition of ATXN2. The individual may be monitored for inhibition of NgR1. The individual may be monitored for inhibition of vATPase. The individual may be monitored for clinical indicia of disease. [0012] In some embodiments, a method is provided for treatment of a human subject for ALS, the method comprising administering an effective dose of etidronate or alendronate. A method is provided for treatment of a human subject for SCA2, the method comprising administering an effective dose of etidronate or alendronate. A method is provided for treatment of a human subject for ALS, the method comprising administering to the brain an effective dose of an NgR1 inhibitor. A method is provided for treatment of a human subject for SCA2, the method comprising administering to the brain an effective dose of an NgR1 inhibitor. [0013] The effects of anti-ATXN2 agents on neurogenerative diseases may comprise a range of outcomes, which are optionally monitored following treatment. For instance, outcomes may include a reduction in symptoms associated with ALS, such as reduced muscle weakness, muscle atrophy, fasciculations, emotional lability, or respiratory muscle weakness relative to no treatment. Methods of treatment disclosed herein may provide for a reduction in symptoms associated with ALS or SCA2 such as reduced ataxia, speech and swallowing difficulties, muscle wasting, or slow eye movement. [0014] In various aspects and embodiments, the methods may include administering to an individual suffering from a neurodegenerative disease such as ALS or SCA2 an effective dose of an anti-ATXN2 agent, where the treatment reduces or stabilizes clinical symptoms of the disease. In one embodiment, the individual is a human. In some embodiments the anti-ATXN2 agent is combined with a secondary therapeutic agent, including without limitation riluzole, baclofen, quinine, phenytoin, glycopyrrolate, amitriptyline, benztropine, trihexyphenidyl, transdermal hyoscine, atropine, fluvoxamine, dextromethorphan, quinidine, gabapentin, etc. In some embodiments, more than one anti-ATXN2 agent may be administered to an individual. [0015] The effective dose of each drug in a combination therapy may be lower than the effective dose of the same drug in a monotherapy. In some embodiments the combined therapies are administered concurrently. In some embodiments the two therapies are phased, for example where one compound is initially provided as a single agent, e.g. as maintenance, and where the second compound is administered during a relapse, for example at or following the initiation of a relapse, at the peak of relapse, etc. BRIEF DESCRIPTION OF THE DRAWINGS [0016] The invention is best understood from the following detailed description when read in conjunction with the accompanying drawings. The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee. It is emphasized that, according to common practice, the various features of the drawings are not to-scale. On the contrary, the dimensions of the various features are arbitrarily expanded or reduced for clarity. Included in the drawings are the following figures. [0017] FIGs. 1A-1D: Genome-wide CRISPR–Cas9 KO screens in human cells identify regulators of ataxin-2 protein levels. (A) Pooled CRISPR–Cas9 screening paradigm. After transducing HeLa cells expressing Cas9 with a lentiviral sgRNA library, we fixed and co- immunostained the cells for ataxin-2 and a control protein (β-actin or GAPDH). We then used FACS to sort top and bottom 20% ataxin-2 expressors relative to control protein levels (duplicate sorts per each control). After isolating genomic DNA from these populations, as well as the unsorted control population, we performed NGS to read sgRNA barcodes. (B) Volcano plots based on effect and confidence scores summarizing genes that modify ataxin-2 protein levels relative to β-actin (left) or GAPDH (right) levels when knocked out (FDR < 0.05). Highlighted in blue and red are hits that overlap across all screens. (C) Validation of numerous top hit genes overlapping across all screens. We transfected HeLa-Cas9 cells with non- targeting (NT) siRNAs or with siRNAs targeting mRNA transcripts encoded by hit genes, then performed immunoblotting on lysates. Quantifications are normalized to the NT siRNA condition (mean±SD; analyzed using 2-way ANOVA; ****: p<0.0001, ***: p<0.001, **: p<0.01, *: p<0.05, ns: not significant). (D) Representative immunoblot of ataxin-2 and □-actin protein levels upon treatment with NT, PNISR, PAXBP1, or ATXN2 siRNAs in HeLa cells. [0018] FIG. 2. Schematic of proteins encoded by selected hits (5% FDR), categorized by function and subcellular localization. [0019] FIGs.3A-3F: Inhibiting lysosomal v-ATPase leads to decreased ataxin-2 protein levels in vitro. (A) Left, volcano plot shows confidence score on y-axis and effect score on x-axis, with gene hits encoding subunits of lysosomal v-ATPases highlighted in red. Right, a representation of the lysosomal v-ATPase, with its V0 and V1 domains, as well as individual subunits. (B) Immunoblot and (C) Quantification of ataxin-2 protein levels after HeLa cells were transfected with siRNAs against various v-ATPase subunits. (D) RT-qPCR quantification of ATXN2 RNA levels after siRNA knockdown of v-ATPase subunits in HeLa cells. Values normalized to β-actin RNA levels. Quantifications for c and d are normalized to the NT siRNA condition (mean ± SD; analyzed using one-way ANOVA with post-hoc Dunnett’s multiple comparisons tests; ****: p<0.0001, ***: p<0.001, **: p<0.01, *: p<0.05, ns: not significant). (E) Immunoblot on lysates from WT or ATP6V1A KO HeLa cell lines. (F) Representative microscopy images of WT or ATP6V1A KO cells, stained for ataxin-2 or β-actin (scale bar = 20 µm). Ataxin-2 fluorescence quantifications are shown on the right (lines denote mean ± SD; analyzed using unpaired t- test; ****: p<0.0001). [0020] FIGs.4A-4K: Small molecule drug Etidronate lowers ataxin-2 protein levels in human iPSC-derived neurons, mouse primary neurons, and in vivo in mice. (A) Timeline of induced neuron differentiation in a human iPSC line with NGN2 stably integrated and drug treatment. (B) Immunoblot on lysates from human iPSC-derived neurons treated with various doses of Etidronate. (C) Quantification of Figure 3B, with ataxin-2 protein levels normalized to H2O- treated condition (mean ± SD; analyzed using one-way ANOVA with post-hoc Dunnett’s multiple comparisons tests; *: p<0.05). (D) Timeline of primary neuron plating from embryonic mouse cortex and drug treatment. (E) Immunoblot on lysates from mouse primary neurons treated with various doses of Etidronate. (F) Quantification of the dose-dependent effect of Etidronate on ataxin-2 (normalized to control condition). (G) Representative microscopy images of mouse cortical neurons treated with sham (H2O) or 10 µM Etidronate for 24 hours, stained for MAP2, ataxin-2, and DAPI (scale bar = 10 µm). (H) Representative microscopy images of mouse cortical neurons treated with H2O or 10 µM Etidronate for 24 hours, with 0.5 mM sodium arsenite treatment for the final hour. The neurons were stained for PABP, MAP2, and DAPI (scale bar = 10 µm). (I) Quantifications of cells containing PABP-positive stress granules (SGs) (mean ± SEM; analyzed using unpaired t-test; ****: p<0.0001, **: p<0.01). (J) Example immunoblot of cortex lysates from mice given normal or drug- infused water and MediGel ^. (K) Quantification of immunoblots (e.g., Figure 3J) probing for ataxin-2 (normalized t _{o H2O-treated condition)} using lysates from cortices of mice that received water or drug treatment (mean ± SEM; analyzed using Welch’s t-test; **: p<0.01). We performed the experiment two independent times, for a total of n=15 in each treatment group. [0021] FIGs. 5A-5H: Calibration steps prior to conducting genome-wide screens. (A) Overview of screen optimization strategy. Briefly, HeLa cells expressing Cas9 were infected with a lentiviral sgRNA targeting ataxin-2, and puromycin was used to select for cells that received a guide. Cells were kept pooled to retain a mosaic population. These cells were then fixed in methanol, immunostained, and sorted using FACS for the top and bottom 25% of ataxin-2 expressors relative to a control protein (GAPDH or β-actin). The sorted and unsorted populations were Sanger sequenced and analyzed for insertions or deletions (indels) at the ATXN2 locus. (B) Immunoblot of the WT and ATXN2 mosaic KO populations, as generated in panel a. (C) Gating strategy for FACS. Left, FACS plot for WT population around which a gate is drawn; Right, mosaic population relative to the WT population. The green and orange gates represent the bottom and top 25% of ATXN2 expressors relative to GAPDH, respectively. (D) Indel (insertion and deletion) analysis of the unsorted mosaic population (i.e. FACS plot in panel c, Right) when Sanger sequenced at the ATXN2 locus, showing a mixture of cells containing various indels. (E) Indel analysis at ATXN2 locus for the sorted populations. Left, overrepresentation of ATXN2 WT cells in the top 25% population (orange gate in panel c); Right, underrepresentation of WT cells / mostly various indels in the bottom 25% sorted population (green gate in panel c). (F) Same as in panel C, except using β-actin as control. (G) Same as in panel D, except using β-actin as control. (H) Same as in panel E, except using β-actin as control. [0022] FIGs.6A-6B. Validation of screen results in neuroblastoma cell line SH-SY5Y, related to Figure 1. (A) Validation of numerous top hit genes in SH-SY5Y cells using siRNA transfections and immunoblot analyses as in Fig.1 C and D. Quantifications are normalized to the NT siRNA condition (mean ± SD; analyzed using 2-way ANOVA; ****: p<0.0001, ***: p<0.001, **: p<0.01, *: p<0.05, ns: not significant). (B) Representative immunoblot of ataxin-2 and β-actin protein levels upon application of NT, LUC7L3, SNRPA, LSM12, and ATXN2 siRNAs to SH-SY5Y cells. [0023] FIGs. 7A-7D: Other polyQ protein levels are unaltered and TDP-43 is slightly decreased in ATP6V1A KO cells. (A) Immunoblot on lysates from ATP6V1A KO HeLa cells probed for huntingtin, ataxin-2, ataxin-1, and GAPDH. (B) Quantification of immunoblot in panel (A), normalized to GAPDH (loading control) levels and to the WT cell line (mean ± SD). (C) Immunoblot on same lysates as (A) reveals a moderate decrease in TDP-43 protein levels, as quantified in (D) (mean ± SD). For both (B) and (D), the data was analyzed using 2-way ANOVA with post-hoc Šídák's multiple comparisons tests (****: p<0.001, **: p<0.01, ns: not significant). [0024] FIG.8: MA plot 72 hours after treatment with NT vs. ATP6V1A siRNAs in HeLa cells. To determine whether there are broad transcriptional changes after knocking down a v- ATPase subunit, we performed RNA-seq after HeLa cells were treated with NT or ATP6V1A siRNAs. Few noteworthy transcriptional changes are seen (apart from ATP6V1A itself) upon knockdown of ATP6V1A (FDR<0.01). Importantly, ATXN2 mRNA levels were not altered by ATP6V1A knockdown (yellow circle). [0025] FIGs.9A-9D: Treating human SH-SY5Y cells or mouse cortical neurons with another bisphosphonate leads to decreased ataxin-2 protein levels. (A) Immunoblot on lysates from human SH-SY5Y cells with various doses of Alendronate. (B) Quantification of the immunoblot in (B) reveals a dose-dependent effect of Alendronate on ataxin-2 protein levels (mean ± SD, normalized to control condition). (C) Immunoblot on lysates from mouse primary neurons treated with various doses of Alendronate. (D) Quantification of the dose-dependent effect of Alendronate on ataxin-2 (mean ± SD, normalized to control condition). [0026] FIGs. 10A-10D. Treating human SH-SY5Y or mouse cortical neurons with Thonzonium, another small molecule drug, leads to decreased ataxin-2 protein levels. (A) Immunoblot on lysates from human SH-SY5Y cells with various doses of Thonzonium. (B) Quantification of the immunoblot in (A) reveals a dose-dependent effect of Thonzonium on ataxin-2 protein levels (mean ± SD, normalized to control condition). (C) Immunoblot on lysates from mouse primary neurons treated with various doses of Thonzonium. (D) Quantification of the dose-dependent effect of Thonzonium on ataxin-2 (mean ± SD, normalized to control condition). [0027] FIGs.11A-11D: Treating mouse cortical neurons with Etidronate does not affect TDP- 43 localization. (A) Representative microscopy images of mouse primary neurons treated with sham (H2O) or 10 µM Etidronate for 24 hours then stained for TDP-43, MAP2, and DAPI (scale bar = 10 µm). Quantifications of TDP-43 fluorescence in the nucleus and cytoplasm (normalized to sham condition) are shown in (B) and (C), respectively (lines denote mean ± SD; analyzed using unpaired t-test; *: p<0.05, ****: p<0.0001). (D) While TDP-43 fluorescence is very moderately decreased in both the nucleus and cytoplasm, the TDP-43 nucleus-to- cytoplasmic ratio is not affected (mean ± SEM; ns = not significant). [0028] FIGs.12A-12L: Generation of the ataxin-2-HiBiT cell line and overview of the whole- genome siRNA screen. (A) We engineered an endogenous C-terminal HiBiT fusion on ataxin- 2 using CRISPR-Cas9 genome editing in HEK293T cells. LgBiT compliments the HiBiT protein tag to form NanoBiT. As a control, we stably incorporated firefly luciferase (FFLuc) into this line. (B) Antibody-based immunoblotting and HiBiT substrate-based detection on ataxin- 2-HiBiT cell lysates transfected with siRNA. Quantified in (C) and (D). (E) HiBiT signal measured via luciferase assay on cells transfected with increasing doses of siRNA. (F) Schematic of the whole- genome siRNA screen for regulators of ataxin-2 levels. (G) Plot showing results of HiBiT replicates after filtering for changes in FFLuc. Datapoints in blue are primary screen hits that decrease ataxin-2. ATXN2 siRNA (red) was the strongest hit. (H) GO- Slim Biological Process analysis of the hits from the primary screen. (I) Summary of the major steps in pre-mRNA splicing, illustrating the involvement of the PRP19-associated complex (PRP19C) and the U1, U2, U4, U5, and U6 snRNP RNA-protein complexes. (J) A list of the siRNAs that reduce ataxin-2 validated in the secondary screen. (K) Ataxin-2-HiBiT cells treated with siRNAs against several splicing components followed by a luciferase assay to measure HiBiT activity. Each splicing factor knockdown significantly reduces HiBiT signal relative to non-targeting. Two-way ANOVA with multiple comparisons: WBP11, SRSF3, and LSM5, p ≤ 0.001. ATXN2, SNRPB, SNRPC, SNRPD2, SNRPD3, SNRP70, PRPF8, ICE1, and AQR, p ≤ 0.0001. (L) Immunoblot of unedited HEK293T cell lysates after siRNA treatment. C and D, Student’s t-test. E, One-way ANOVA with multiple comparisons. **p ≤ 0.01. Error bars represent ± SEM. [0029] FIGs. 13A-13I: Targeting RTN4R lowers levels of ataxin-2. (A) High confidence hits ranked by average HiBiT Z-score, then filtered for essentiality (gene effect, DepMap) and CNS expression (GTEx). (B) HiBiT signal measured by luciferase assay in ataxin-2-HiBiT cells transfected with designated siRNA. (C) Immunoblot for ataxin-2 and GAPDH on lysates derived from unedited HEK293T cells treated with designated siRNA. Ataxin-2 levels are quantified in (D). We performed RT-qPCR on RNA from cells treated as in (C). We probed for RTN4R transcript (E) or ATXN2 transcript (F) along with ACTB for normalization. (G) We treated ataxin-2-HiBiT cells with siRNA then treated cells for 8hr with proteasome inhibitor MG- 132 or DMSO and performed a luciferase assay to measure HiBiT activity. (H) The NEP1-40 peptide, a shared extracellular region of the NoGo proteins, binds to RTN4/NoGo-Receptor and prevents further signaling through the receptor. (I) We treated ataxin-2-HiBiT cells for 48hr with increasing doses of NEP1- 40 and performed a luciferase assay to measure HiBiT activity. B and I, One-way ANOVA with multiple comparisons. G, Two-way ANOVA with multiple comparisons. D, E, and F, Student’s t- test. *p ≤ 0.05, **p ≤ 0.01, ***p ≤ 0.001, ****p ≤ 0.0001. Error bars represent ± SEM. [0030] FIGs. 14A-14N: RTN4R knockdown or inhibition of RTN4/NoGo-Receptor in mouse and human neurons and in mouse brain reduces ataxin-2 levels. (A) Primary neurons isolated from embryonic mouse cortex. Treatment timeline for shRNA lentivirus or RTN4/NoGo- Receptor peptide inhibitor NEP1-40 in primary mouse neurons. DIV=days in vitro. (B) Induced neuron differentiation in a human iPSC line with NGN2 stably integrated, as verified by Tuj1 (green) and NeuN (red) immunostaining, scale bar 20μm. Treatment timeline for shRNA lentivirus or NEP1- 40 in human induced neurons (iNeurons). DPI=days post induction. (C) Immunoblot on lysates from mouse neurons treated with shRNA. (D) Quantification of ataxin- 2 and RTN4/NoGo- Receptor levels. (E) Immunoblot on lysates from iNeurons treated with shRNA. (F) Quantification of ataxin-2 and RTN4/NoGo-Receptor. (G) Immunoblot on lysates from primary mouse neurons treated with increasing doses of NEP1-40. Quantification is shown in (H). (I) Immunocytochemistry and fluorescence microscopy on mouse neurons treated with 50 μM NEP1-40. MAP2 labels neurons, DAPI labels nuclei. Scale bar=20μm. (J) Quantification of neuronal ataxin-2 fluorescence. (K) Immunoblot on lysates from iNeurons treated for 48 hours with increasing doses of NEP1-40. Quantification is shown in (L). (M) Immunoblot on whole cortex lysates from RTNR +/+, +/-, and -/- mice. Quantification in (N). D, F, and J, Student’s t-test. H, L, and N, One-way ANOVA with multiple comparisons. *p ≤ 0.05, **p ≤ 0.01, ***p ≤ 0.001, ****p ≤ 0.0001. Error bars represent ± SEM. [0031] FIGs. 15A-15E: Reduction of ataxin-2 increases axonal regrowth after axotomy. (A) Timeline for axotomy and regeneration experiment using mouse primary neurons grown in microfluidics chambers. (B) Immunoblot on lysates from mouse neurons treated with Atxn2 shRNA. (C) Brightfield images of an inner chamber of the axonal compartment of a microfluidics chamber before and after vacuum-assisted axotomy. Scale bar=50μm. (D) Immunocytochemistry and fluorescence microscopy on the axonal compartment after 48 hours of regrowth after axotomy. Tuj1 labels axons. Scale bar=50μm. (E) Quantification of the length of regenerating neurites (identified by the morphological presence of a growth cone) from three separate chambers per condition. One-way ANOVA with multiple comparisons. ****p ≤ 0.0001. Error bars represent ± SEM. [0032] FIGs.16A-16C: Ataxin-2 screen results and filters. Plots of the primary screen HiBiT data (A) and FFLuc data (B) for both replicates. R ² = 0.688 and 0.7645, respectively. (C) Filters applied to screen results to determine the highest confidence ataxin-2 regulators. [0033] FIGs. 17A-17B: Shared protein domain between ataxin-2 and its regulators. (A) InterPro domain enrichment of primary screen hits. (B) Bottom: representation of ataxin-2 protein domains including the poly-glutamine stretch (polyQ), the LSm and LSm-associated (LSm AD) domains, and the PABP-interacting motif (PAM). Top: graph of the IUPred2 score, a prediction of protein disorder, for the amino acid sequence of ataxin-2. [0034] FIGs. 18A-18B: Further validation of screen results. (A) Immunoblot of ataxin-2 and GAPDH levels after siRNA treatment in unedited HEK293T cell lysates. (B) RT-qPCR on RNA from cells treated with non-targeting siRNA or siRNA targeting various splicing factors. We probed for ATXN2 transcript along with ACTB for normalization. Two-way ANOVA with multiple comparisons: WBP11 and AQR, p ≤ 0.05. LSM5 and SNRPB, p ≤ 0.01. ATXN2 and SNRPD2, p ≤ 0.001. SFRS3, p ≤ 0.0001. Error bars represent ± SEM. [0035] FIGs.19A-19D: Further validation of RTN4R as a regulator of ataxin-2. (A) Immunoblot on SH- SY5Y cell lysates after RTN4R siRNA treatment. Ataxin-2 levels are quantified in (B). (C) Immunoblot on HEK293T cell lysates after ATXN2 siRNA treatment. RTN4/NoGo- Receptor levels are quantified in (D). Student’s t-test. *p ≤ 0.05. Error bars represent ± SEM. [0036] FIGs. 20A-20B: Knockdown of RTN4R does not alter the expression of other polyQ proteins or ATXN2L. (A) Immunoblot of ATXN2L (Ataxin-2 paralog) and polyQ disease proteins ataxin-2, huntingtin, and ataxin-3 after RTN4R siRNA treatment in unedited HEK293T cell lysates. Quantified in (B). Student’s t-test. *p ≤ 0.05. Error bars represent ± SEM. [0037] FIGs.21A-21B: Knockdown of RTN4R reduces TDP-43 localization to stress granules. (A) We treated HEK293T cells with siRNA, and subsequently treated for 30 minutes with 0.5mM sodium arsenite to induce stress granules. We probed for TDP-43 and the stress granule marker G3BP via immunocytochemistry. Scale bar=10μm. The average fluorescence of TDP-43 in stress granules is quantified in (B). One-way ANOVA, *p ≤ 0.05, ***p ≤ 0.001. Error bars represent ± SEM. [0038] FIGs.22A-22B: Knockdown of RTN4R does not decrease ataxin-2 through autophagy pathways and does not increase general proteasome activity. (A) We treated ataxin-2-HiBiT cells with siRNA, then treated for 24hr with autophagy inhibitor Bafilomycin A1 or DMSO. We performed a luciferase assay to measure HiBiT activity. (B) Proteasome activity assay (utilizing Suc-LLVY- AMC as a substrate) in HEK293T cell lysates after RTN4R siRNA treatment. Two- way ANOVA with multiple comparisons. **p ≤ 0.01, ****p ≤ 0.0001. Error bars represent ± SEM. [0039] FIGs. 23A-23E: Full immunoblot on neuron lysates treated with two different shRNA constructs targeting RTN4R and RT-qPCR on shRNA-treated primary neurons. (A) Immunoblot of ataxin-2 and RTN4/NoGo-Receptor levels after 12 days of shRNA treatment in cortical neuron cultures. We used two shRNA constructs targeting different regions of RTN4R, along with a non- targeting shRNA construct. Quantification of ataxin-2 (B) and RTN4/NoGo- Receptor (C) levels. (D), (E), We performed RT-qPCR on RNA from shRNA-treated mouse neurons. We probed for RTN4R transcript (D) and ATXN2 transcript (E) along with GAPDH as a housekeeping gene for normalization. Student’s t-test. **p ≤ 0.01, ***p ≤ 0.001, ****p ≤ 0.0001. Error bars represent ± SEM. [0040] FIGs.24A-24B: RNA sequencing of RTN4R knockdown iNeurons. (A) MA plot of RNA sequencing results following shRNA treatment. (B) GO Slim Biological Process analysis was performed on transcripts with a Log2 fold change greater than 1 (up) or less than -1 (down) with a p-value greater than 0.01. The top results are shown here. [0041] FIGs. 25A-25C: RTN4R knockdown effects in neurons. (A) Immunoblot of the Sm- containing SNRPB and actin after designated shRNA treatment in iNeuron cultures. Quantification of SNRPB levels in (B). (C) Mouse cortical neurons were treated for 12 days with non-targeting or RTN4R shRNA, and subsequently treated for 3 or 5 days with lentivirus expressing GFP or TDP-43. Caspase-3/7 activity was measured in 4 biological replicates per condition, values normalized to GFP control in each condition. B, Student’s t- test. C, One-way ANOVA with multiple comparisons, *p ≤ 0.05 and ****p ≤ 0.0001. Error bars represent ± SEM. DETAILED DESCRIPTION OF THE EMBODIMENTS [0042] As described in the present disclosure, fluorescence activated cell sorting (FACS)- based CRISPR, and small interfering RNA(siRNA) based screening, was used to identify novel Ataxin-2 (ATXN2)-associated genes based on their ability to modulate ATXN2 protein levels. Anti-ATXN2 agents include, for example, bisphosphonates, such as etidronate, alendronate, etc., other vATPase inhibitors, e.g. thonzonium, and inhibitors of Nogo-66 receptor 1 (NgR1), which are identified herein based on an ability to inhibit the function or activity of ATXN-2 associated gene products in a dose dependent manner. As examples, anti-ATXN2 agents were found to achieve ATXN2 protein reduction through lysosomal v-ATPase inhibition, in the case of etidronate or thonzonium, or through competitive inhibition in the case of NEP1-40. [0043] Improvement in the use of disease-modifying therapies in neurological diseases is of great clinical interest. In certain aspects and embodiments the present methods and compositions address this need. [0044] Before the present methods are described, it is to be understood that this invention is not limited to particular methods described, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting, since the scope of the present invention will be limited only by the appended claims. [0045] Where a range of values is provided, it is understood that each intervening value, to the tenth of the unit of the lower limit unless the context clearly dictates otherwise, between the upper and lower limit of that range and any other stated or intervening value in that stated range is encompassed within the invention. The upper and lower limits of these smaller ranges may independently be included in the smaller ranges, subject to any specifically excluded limit in the stated range. As used herein and in the appended claims, the singular forms "a", "and", and "the" include plural referents unless the context clearly dictates otherwise. [0046] Unless defined otherwise, 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 any methods and materials similar or equivalent to those described herein can also be used in the practice or testing of the present invention, the preferred methods and materials are now described. All publications mentioned herein are incorporated herein by reference to disclose and describe the methods and/or materials in connection with which the publications are cited. [0047] The publications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the present invention is not entitled to antedate such publication by virtue of prior invention. Further, the dates of publication provided may be different from the actual publication dates, which may need to be independently confirmed. [0048] General methods in molecular and cellular biochemistry can be found in such standard textbooks as Molecular Cloning: A Laboratory Manual, 3rd Ed. (Sambrook et al., Harbor Laboratory Press 2001); Short Protocols in Molecular Biology, 4th Ed. (Ausubel et al. eds., John Wiley & Sons 1999); Protein Methods (Bollag et al., John Wiley & Sons 1996); Nonviral Vectors for Gene Therapy (Wagner et al. eds., Academic Press 1999); Viral Vectors (Kaplift & Loewy eds., Academic Press 1995); Immunology Methods Manual (I. Lefkovits ed., Academic Press 1997); and Cell and Tissue Culture: Laboratory Procedures in Biotechnology (Doyle & Griffiths, John Wiley & Sons 1998). Reagents, cloning vectors, and kits for genetic manipulation referred to in this disclosure are available from commercial vendors such as BioRad, Stratagene, Invitrogen, Sigma-Aldrich, and ClonTech. [0049] The present inventions have been described in terms of particular embodiments found or proposed by the present inventor to comprise preferred modes for the practice of the invention. It will be appreciated by those of skill in the art that, in light of the present disclosure, numerous modifications and changes can be made in the particular embodiments exemplified without departing from the intended scope of the invention. All such modifications are intended to be included within the scope of the appended claims. [0050] The subject methods may be used for prophylactic or therapeutic purposes. As used herein, the term "treating" is used to refer to both prevention of relapses, and treatment of pre- existing conditions. For example, the prevention of neurodegenerative disease may be accomplished by administration of the agent prior to development of a relapse, after an initial diagnosis. "Treatment" as used herein covers any treatment of a disease in a mammal, particularly a human, and includes: inhibiting the disease symptom, i.e., arresting its development; or relieving the disease symptom, i.e., causing regression of the disease or symptom. The treatment of ongoing disease, where the treatment stabilizes or improves the clinical symptoms of the patient, is of particular interest. [0051] "Inhibiting" the onset of a disorder shall mean either lessening the likelihood of the disorder's onset, or preventing the onset of the disorder entirely. Reducing the severity of a relapse shall mean that the clinical indicia associated with a relapse are less severe in the presence of the therapy than in an untreated disease. As used herein, onset may refer to a relapse in a patient that has ongoing relapsing remitting disease. The methods of the invention are specifically applied to patients that have been diagnosed with a neurodegenerative disease. Treatment is aimed at the treatment or reducing severity of relapses, which are an exacerbation of a pre-existing condition. [0052] "Diagnosis" as used herein generally includes determination of a subject's susceptibility to a disease or disorder, determination as to whether a subject is presently affected by a disease or disorder, prognosis of a subject affected by a disease or disorder (e.g., identification of disease states, stages of ALS or SCA, or responsiveness of ALS or SCA to therapy), and use of therametrics (e.g., monitoring a subject's condition to provide information as to the effect or efficacy of therapy). [0053] The term "biological sample" encompasses a variety of sample types obtained from an organism and can be used in a diagnostic or monitoring assay. The term encompasses blood, cerebral spinal fluid, and other liquid samples of biological origin, solid tissue samples, such as a biopsy specimen or tissue cultures or cells derived therefrom and the progeny thereof. The term encompasses samples that have been manipulated in any way after their procurement, such as by treatment with reagents, solubilization, or enrichment for certain components. The term encompasses a clinical sample, and also includes cells in cell culture, cell supernatants, cell lysates, serum, plasma, biological fluids, and tissue samples. [0054] The terms "individual," "subject," "host," and "patient," used interchangeably herein and refer to any mammalian subject for whom diagnosis, treatment, or therapy is desired, for example humans, non-human primate, mouse, rat, guinea pig, rabbit, etc. [0055] "Inhibiting" the expression of a gene in a cell shall mean either lessening the degree to which the gene is expressed, or preventing such expression entirely. [0056] Ataxin-2 is a member of the Like-Sm (LSm) family of RNA-binding proteins and contains a polyglutamine (polyQ) repeat of ∼22–23 amino acids in healthy individuals, whereas significant expansion of the polyQ repeat to over 34 amino acids is the genetic cause of SCA2. Ataxin-2 intermediate-length polyQ repeat expansions (27–33 amino acids) are associated with increased risk of ALS, a neurodegeneration with abnormal cytoplasmic aggregation of TDP-43 called TDP-43 proteinopathy. Ataxin-2 contains PAM2 in its C-terminal region along with the N-terminal LSm domain which directly binds to a 3′-UTR of specific mRNAs and promotes its stability and protein production. [0057] ATXN2-associated genes may be any gene that has an influence on the ATXN2 gene or gene product. For instance, ATXN2-associated genes may include ALG1, DPAGT1, RFT1, CFAP20, CLASRP, LUC7L3, PNISR, SNRPA, PAXBP, ATXN7L3, ENY2, USP22, CMTR2, CMTR2, ATP6V0C, ATP6V1A, ATP6V1B2, ATP6V1C1, ATP6V1D, LSM12, RP11-894J14.5, TSC1, TSC2, UBA3, RTN4R, EFHD2, TRAPPC1, MAP3K11, MFAP1, UNC84A, ZNF32, or ASB8. For example, the screenings disclosed herein have identified v-ATPases and RTN4R (NgR1) as suitable targets for inhibition to reduce ATXN2. [0058] The V-ATPases are large multi-subunit complexes composed of two domains: a membrane integral V0 sector involved in proton translocation and a peripheral V1 domain catalyzing ATP hydrolysis. The integral V0 domain is a 260 kDa complex containing six different subunits (a, c, c’, c”, d, and e) whereas the V1 domain is a 640 kDa complex including eight different subunits (A, B, C, D, E, F, G, and H). In higher eukaryotes, several different H ⁺ - ATPase subunits have multiple isoforms encoded by separate genes that are located throughout the genome with differing tissue expression patterns. For example, there are two isoforms for the B, E, d, and e subunits; three for the C and G subunits; and four for the A subunit. Some of the isoforms have different expression patterns in various tissues. For example, the d1 subunit is ubiquitously expressed while the d2 homolog is expressed only in the kidney, osteoclast and lung. Similarly, the G1 isoform is expressed ubiquitously while G2 and G3 isoforms are found mainly in neuronal tissue and kidney. [0059] Some subunits are encoded through splice variants, such as the a, d, e, C, G and H subunits. This complexity leads to different possible permutations of subunit structure in individual proton pumps and unique subunit identities of pumps at different locations, which may allow the regulation of V-ATPase in a cell type and subcellular compartment specific manner. The peripheral domain and the integral domain are assembled separately and brought together into a functional proton pump at the required organelles. [0060] In neuronal and neuroendocrine cells, the V-ATPase is equipped with the accessory subunits ATP6AP1 and ATP6AP2. ATP6AP1, also known as Ac45, was first identified as the accessory subunit of V-ATPase in chromaffin granules. ATP6AP1 functions to guide the V- ATPase to certain subcellular compartments such as neuroendocrine regulated secretory vesicles and regulates their activity, the intragranular pH and Ca ²⁺ -dependent exocytotic membrane fusion. ATP6AP2 was first identified as the C-terminal fragment of the (pro) renin receptor (PRR) for renin and prorenin. Ablation of PRR in cardiomyocytes reveals that PRR is an integral component for the stability and assembly of V0 subunits. ATP6AP2 is a key accessory protein for V-ATPase functions in the CNS and essential for stem cell self-renewal and neuronal survival. [0061] In the presynaptic bouton, V-ATPase is responsible for generating the H ⁺ - electrochemical gradient in synaptic vesicles, which drives the refilling of newly formed synaptic vesicles with neurotransmitter. Synaptic vesicle V-ATPase also participates in the step of fusion. Relying on its H ⁺ -pumping ability, V-ATPase modulates multiple cellular activities including endosome maturation and trafficking, protein processing and degradation via different autophagic pathways in multiple vesicle organelles such as lysosome and endosome. The acidic environment of the lysosomes is critical for not only the function of lysosomes but also many cellular processes related to lysosomes. V-ATPase is also involved in pH sensing, nutrient signalling, and scaffold for protein-protein interactions. [0062] Nogo-66 receptor 1 (NgR1, alternatively referred to as RTN4R) is a glycosylphosphatidyl inositol-linked protein that belong to the leucine-rich repeat superfamily. Through binding to myelin-associated inhibitors, NgR1 contributes to the inhibition of axonal regeneration after spinal cord injury. NgR1 has been shown to limit axonal sprouting, plasticity, and regeneration in the adult CNS after binding to myelin-associated inhibitors, such as Nogo, MAG, and OMgp. Furthermore, NgR1 binds with high affinity to the glycosaminoglycan moiety of proteoglycans and participate in chondroitin sulfate proteoglycan-mediated inhibition of axon growth from cultured neurons. NgRs lack a transmembrane domain, and require the formation of complexes with coreceptors to trigger downstream signaling pathways. A large number of cis-interacting proteins have been reported to bind to NgR1: adaptors, such as LINGO-1 or AMIGO3; and signaling coreceptors, such as TROY and/or P75NTR. After ligand binding to NgR1, a trimeric complex is formed, thereby activating the RhoA/ROCK cascade, which can lead to growth cone collapse and neurite growth inhibition. [0063] The Nogo receptor (NgR) family and their ligands have been implicated in regulating forms of experience- dependent plasticity in the adult brain. Nogo receptor 1 (NgR1) has been shown to regulate structural plasticity in the adult system. Knockout of NgR1 extends the critical period for experience-dependent plasticity in the ocular dominance paradigm in visual cortex, as well as extending critical period plasticity for acoustic preference. In addition, various forms of neuronal activity induction have been demonstrated to rapidly downregulate NgR1 expression in mice, as seen with wheel running, kainic acid, electroconvulsive seizures and amphetamine. [0064] Regulation of the Nogo receptor homologs NgR2 and NgR3 by neuronal activity have also been reported. In support of this role in activity-dependent plasticity, NgR1 has been demonstrated to regulate synaptic plasticity. Ablation or blocking of NgR1 enhances hippocampal long-term potentiation (LTP) in slice preparations, and appears to be mediated by the binding of NgR1 to selected ligands such as Nogo-A, and fibroblast growth factor-2 (FGF2). The extension of the critical period plasticity into adulthood is also reflected in an increase in spine turnover in the cortex of adult NgR1 ^−/− mice, and a shift toward immature spine subtypes in the hippocampus of NgR1 ^−/− mice. At a behavioral level, modulation of NgR1 has resulted in mild memory phenotypes. Forebrain NgR1 overexpression impairs long-term memory, without affecting short-term memory, whilst constitutive knockout of NgR1 impairs working memory without affecting spatial memory. Additionally, NgR1 ^−/− mice also exhibit improved extinction learning in cued conditioned fear. This suggests that NgR1-mediated structural plasticity may underlie some forms of behavioral plasticity, but highlight the potential functional redundancy of these receptors. [0065] As used herein, an "antagonist," or “inhibitor” agent refers to a molecule which, when interacting with (e.g., binding to) a target protein, decreases the amount or the duration of the effect of the biological activity of the target protein (e.g., interaction between leukocyte and endothelial cell in recruitment and trafficking). Antagonists may include proteins, nucleic acids, carbohydrates, antibodies, or any other molecules that decrease the effect of a protein. Unless otherwise specified, the term “antagonist” can be used interchangeably with “inhibitor” or “blocker”. [0066] The term "agent" as used herein includes any substance, molecule, element, compound, entity, or a combination thereof. It includes, but is not limited to, e.g., protein, oligopeptide, small organic molecule, polysaccharide, polynucleotide, and the like. It can be a natural product, a synthetic compound, or a chemical compound, or a combination of two or more substances. Unless otherwise specified, the terms “agent”, “substance”, and “compound” can be used interchangeably. [0067] The term "analog" is used herein to refer to a molecule that structurally resembles a molecule of interest, but which has been modified in a targeted and controlled manner, by replacing a specific substituent of the reference molecule with an alternate substituent. Compared to the starting molecule, an analog may exhibit the same, similar, or improved utility. Synthesis and screening of analogs, to identify variants of known compounds having improved traits (such as higher potency at a specific receptor type, or higher selectivity at a targeted receptor type and lower activity levels at other receptor types) is an approach that is well known in pharmaceutical chemistry. [0068] Anti-ATXN2 agent. As used herein, an anti-ATXN2 agent blocks the activity or function of an ATXN2 or an ATXN2-associated gene or gene product, such that ATXN2 protein levels are reduced, or ATXN2 protein function and/or activity is reduced, particularly with respect to human AXTN2. [0069] In some embodiments, an ATXN2 inhibitor, which may be referred to as an anti-ATXN2 agent, is a bisphosphonate. In some embodiments, an anti-ATXN2 bisphosphonate is an inhibitor of v-ATPase. Other inhibitors of v-ATPase are also useful as anti-ALXN2 agents, e.g. thonzonium, alexidine, and the like. In other embodiments, an anti-ATXN2 agent inhibits the NOGO receptor, NgR1 (also referred to as RTN4R). An NgR1 inhibitor may be a genetic agent that inhibits NgR1 expression, or may interfere with NgR1 signaling, e.g. by competitive inhibition or blocking of the interaction between NgR1 and NOGO, neutralization of NOGO, NEP1-40 inhibitor, and the like. [0070] Bisphosphonates. In some embodiments, an anti-ataxin-2 agent is a bisphosphonate. Without being limited by the theory, bisphosphonates may inhibit ataxin-2 by inhibition of v- ATPase through incorporation into molecules of newly formed adenosine triphosphate (ATP). In some embodiments the bisphosphonate is etodronate. In some embodiments the bisphosphonate is alendronate. In some embodiments the bisphosphonate is tiludronate. In some embodiments, suitability of a bisphosphonate may be determined by assessing its effect on the inhibition of vATPase. [0071] Bisphosphonates are chemically stable derivatives of inorganic pyrophosphate (PPi), a naturally occurring compound in which 2 phosphate groups are linked by esterification. Like their natural analogue PPi, bisphosphonates have a very high affinity for bone mineral because they bind to hydroxyapatite crystals. In addition to their ability to inhibit calcification, bisphosphonates inhibit hydroxyapatite breakdown, thereby effectively suppressing bone resorption. The core structure of bisphosphonates differs from PPi in that bisphosphonates contain a central nonhydrolyzable carbon; the phosphate groups flanking this central carbon are maintained. Nearly all bisphosphonates in current clinical use also have a hydroxyl group attached to the central carbon (termed the R ¹ position). The flanking phosphate groups provide bisphosphonates with a strong affinity for hydroxyapatite crystals in bone, whereas the hydroxyl motif further increases a bisphosphonate’s ability to bind calcium. Collectively, the phosphate and hydroxyl groups create a tertiary rather than a binary interaction between the bisphosphonate and the bone matrix, giving bisphosphonates their remarkable specificity for bone. [0072] Non–nitrogen-containing bisphosphonates, e.g. etidronate, clodronate, and tiludronate, may be categorized as first-generation bisphosphonates. Because of their close structural similarity to PPi, non–nitrogen-containing bisphosphonates become incorporated into molecules of newly formed adenosine triphosphate (ATP) by the class II aminoacyl– transfer RNA synthetases after osteoclast-mediated uptake from the bone mineral surface. Intracellular accumulation of these nonhydrolyzable ATP analogues is believed to be cytotoxic to osteoclasts because they inhibit multiple ATP-dependent cellular processes. [0073] Second- and third-generation bisphosphonates include, for example, alendronate, risedronate, ibandronate, pamidronate, and zoledronic acid, and have nitrogen-containing R ² side chains. It is believed that nitrogen-containing bisphosphonates bind to and inhibit the activity of farnesyl pyrophosphate synthase, a key regulatory enzyme in the mevalonic acid pathway critical to the production of cholesterol, other sterols, and isoprenoid lipids. [0074] Currently available formulations of bisphosphonates include once-weekly, e.g. alendronate or risedronate; and monthly, e.g. ibandronate or risedronate, oral formulations. IV formulation are also available, e.g. for pamidronate, ibandronate, and zoledronic acid, which for most clinical conditions require even less frequent dosing, and have eliminated the gastrointestinal adverse effects incurred by some patients managed with oral bisphosphonates. Such formulations are believed to have pharmacodynamic equivalence to daily dosing of each drug. Daily dose formulations are also available. [0075] The dose of bisphosphonate will depend on the periodicity of administration, as well as the specific drug that is chosen. The dose may be, for example, equivalent to that conventionally used for treating bone diseases. For alendronate, the conventional dose may be from about 5, about 10 mg, about 20 mg up to about 40 mg daily for an adult, or an equivalent dosage administered weekly, e.g.70 milligrams (mg) once a week. For etidronate, for example, the conventional dose may be from about 5 mg/kg, up to about 20 mg/kg. For tiludronate, for example, 200-400 mg tiludronic acid is administered every 3 months. Such dosages may be adjusted based on response of the neurologic disease, e.g. about 1.5X the conventional dosing for bone disease, about 2X, about 2.5X or more, up to the maximum tolerated dose. [0076] Additional inhibitors of a lysosomal v-ATPase include, without limitation, thonzonium, alexidine, YM-175, bafilomycin, concanamycin, archazolid, lobatamide, apicularen, oximidine, cruentaren etc. The dose will depend on the periodicity of administration, as well as the specific drug that is chosen. The dosage of, for example, bafilomycin A1 may be administered to achieve less than the maximum inhibition level of 0.5 μM. [0077] In other embodiments an anti-ATXN2 agent is antibody or a fragment thereof that specifically binds to a lysosomal v-ATPase subunit, such as a ATP6V0C, ATP6V1A, ATP6V1B2, ATP6V1C1, or ATP6V1D gene product. [0078] When inhibition of NgR1 is desired, any NgR1 inhibitor may be used. These include, without limitation, NgR1 antagonist peptide (NAP2) or variants thereof, etc. NEP1-40 and NAP2 are described in GrandPre et al (Nature.2002 May 30;417(6888):547-51.) and Sun et al. (Mol Cell Neurosci.2016 Mar;71:80-91), respectively, herein specifically incorporated by reference. The polypeptide sequence of human NEP1-40 is RIYKGVIQAIQKSDEGHPFRAYLESEVAISEELVQKYSNS. Alternative inhibitors include RTN4/NoGo-Receptor decoy, for example AXER-204 is a human fusion protein that acts as a soluble decoy/trap for Nogo-A (see, for example, clinical NCT03989440, herein specifically incorporated by reference). Brain-specific angiogenesis inhibitors (BAIs) are adhesion-GPCRs whose extracellular sequences are composed of an N-terminal domain, 4–5 thrombospondin type-1 repeats (TSRs), a hormone-binding domain (HBD), and a GAIN domain, which have been shown to be inhibitors of NgR1 (see, for example, Wang et al. (2021) Cell Nov 24;184(24):5869-5885.e25, herein specifically incorporated by reference). Alternatively, antibodies or a fragment thereof that is specific for Nogo or for NgR1 can be administered. Alternatively, genetic constructs are useful to knockout NgR1, e.g. using CRISPR or other genome editing modalities. The dose will depend on the periodicity of administration, as well as the specific drug that is chosen. [0079] Antagonists of interest include antibodies or fragments thereof, soluble receptors, receptor or ligand fragments, conjugates of receptors and Fc regions, and the like. Generally, as the term is utilized in the specification, “antibody” or “antibody moiety” is intended to include any polypeptide chain-containing molecular structure that has a specific shape which fits to and recognizes an epitope, where one or more non-covalent binding interactions stabilize the complex between the molecular structure and the epitope. The archetypal antibody molecule is the immunoglobulin, and all types of immunoglobulins (IgG, IgM, IgA, IgE, IgD, etc.), from all sources (e.g., human, rodent, rabbit, cow, sheep, pig, dog, other mammal, chicken, turkey, emu, other avians, etc.) are considered to be “antibodies.” Antibodies utilized in the present invention may be polyclonal antibodies, although monoclonal antibodies are preferred because they may be reproduced by cell culture or recombinantly, and may be modified to reduce their antigenicity. [0080] Antibody fusion proteins may include one or more constant region domains, e.g. a soluble receptor-immunoglobulin chimera, refers to a chimeric molecule that combines a portion of the soluble adhesion molecule counterreceptor with an immunoglobulin sequence. The immunoglobulin sequence preferably, but not necessarily, is an immunoglobulin constant domain. The immunoglobulin moiety may be obtained from IgG1, IgG2, IgG3 or IgG4 subtypes, IgA, IgE, IgD or IgM, but preferably IgG1 or IgG3. [0081] A straightforward immunoadhesin combines the binding region(s) of the "adhesin" protein with the hinge and Fc regions of an immunoglobulin heavy chain. Ordinarily nucleic acid encoding the soluble adhesion molecule will be fused C-terminally to nucleic acid encoding the N-terminus of an immunoglobulin constant domain sequence, however N- terminal fusions are also possible. Typically, in such fusions the encoded chimeric polypeptide will retain at least functionally active hinge, CH2 and CH3 domains of the constant region of an immunoglobulin heavy chain. Fusions are also made to the C-terminus of the Fc portion of a constant domain, or immediately N-terminal to the CH1 of the heavy chain or the corresponding region of the light chain. The precise site at which the fusion is made is not critical; particular sites are well known and may be selected in order to optimize the biological activity, secretion or binding characteristics. [0082] Antibodies that have a reduced propensity to induce a violent or detrimental immune response in humans (such as anaphylactic shock), and which also exhibit a reduced propensity for priming an immune response which would prevent repeated dosage with the antibody therapeutic are preferred for use in the invention. These antibodies are preferred for all administrative routes, including intrathecal administration. Thus, humanized, chimeric, or xenogenic human antibodies, which produce less of an immune response when administered to humans, are preferred for use in the present invention. [0083] Chimeric antibodies may be made by recombinant means by combining the murine variable light and heavy chain regions (VK and VH), obtained from a murine (or other animal- derived) hybridoma clone, with the human constant light and heavy chain regions, in order to produce an antibody with predominantly human domains. The production of such chimeric antibodies is well known in the art, and may be achieved by standard means (as described, e.g., in U.S. Patent No. 5,624,659, incorporated fully herein by reference). Humanized antibodies are engineered to contain even more human-like immunoglobulin domains, and incorporate only the complementarity-determining regions of the animal-derived antibody. This is accomplished by carefully examining the sequence of the hyper-variable loops of the variable regions of the monoclonal antibody, and fitting them to the structure of the human antibody chains. Alternatively, polyclonal or monoclonal antibodies may be produced from animals which have been genetically altered to produce human immunoglobulins, such as the Abgenix XenoMouse or the Medarex HuMAb ^ technology. Alternatively, single chain antibodies (Fv, as described below) can be produced from phage libraries containing human variable regions. [0084] In addition to entire immunoglobulins (or their recombinant counterparts) that comprise Fc regions, immunoglobulin fragments comprising the epitope binding site (e.g., Fab’, F(ab’)2, or other fragments) are useful as antibody moieties in the present invention. Such antibody fragments may be generated from whole immunoglobulins by ficin, pepsin, papain, or other protease cleavage. “Fragment” or minimal immunoglobulins may be designed utilizing recombinant immunoglobulin techniques. For instance “Fv” immunoglobulins for use in the present invention may be produced by linking a variable light chain region to a variable heavy chain region via a peptide linker (e.g., poly-glycine or another sequence which does not form an alpha helix or beta sheet motif). [0085] Small molecule agents that inhibit, for example, vATPase or NgR1, encompass numerous chemical classes, though typically they are organic molecules, e.g. small organic compounds having a molecular weight of more than 50 and less than about 2,500 daltons. Candidate agents comprise functional groups necessary for structural interaction with proteins, particularly hydrogen bonding, and typically include at least an amine, carbonyl, hydroxyl or carboxyl group, preferably at least two of the functional chemical groups. The candidate agents often comprise cyclical carbon or heterocyclic structures and/or aromatic or polyaromatic structures substituted with one or more of the above functional groups. Candidate agents are also found among biomolecules including peptides, saccharides, fatty acids, steroids, purines, pyrimidines, derivatives, structural analogs or combinations thereof. [0086] Candidate agents are obtained from a wide variety of sources including libraries of synthetic or natural compounds. For example, numerous means are available for random and directed synthesis of a wide variety of organic compounds and biomolecules, including expression of randomized oligonucleotides and oligopeptides. Alternatively, libraries of natural compounds in the form of bacterial, fungal, plant and animal extracts are available or readily produced. Additionally, natural or synthetically produced libraries and compounds are readily modified through conventional chemical, physical and biochemical means, and may be used to produce combinatorial libraries. Known pharmacological agents may be subjected to directed or random chemical modifications, such as acylation, alkylation, esterification, amidification, etc. to produce structural analogs. Test agents can be obtained from libraries, such as natural product libraries or combinatorial libraries, for example. [0087] Libraries of candidate compounds can also be prepared by rational design. (See generally, Cho et al., Pac. Symp. Biocompat.305-16, 1998); Sun et al., J. Comput. Aided Mol. Des.12:597-604, 1998); each incorporated herein by reference in their entirety). For example, libraries of GABA _A inhibitors can be prepared by syntheses of combinatorial chemical libraries (see generally DeWitt et al., Proc. Nat. Acad. Sci. USA 90:6909-13, 1993; International Patent Publication WO 94/08051; Baum, Chem. & Eng. News, 72:20-25, 1994; Burbaum et al., Proc. Nat. Acad. Sci. USA 92:6027-31, 1995; Baldwin et al., J. Am. Chem. Soc.117:5588-89, 1995; Nestler et al., J. Org. Chem.59:4723-24, 1994; Borehardt et al., J. Am. Chem. Soc.116:373- 74, 1994; Ohlmeyer et al., Proc. Nat. Acad. Sci. USA 90:10922-26, all of which are incorporated by reference herein in their entirety.) [0088] Candidate antagonists can be tested for activity by any suitable standard means. As a first screen, the antibodies may be tested for binding against the adhesion molecule of interest. As a second screen, antibody candidates may be tested for binding to an appropriate cell line, e.g. leukocytes or endothelial cells, or to primary tumor tissue samples. For these screens, the candidate antibody may be labeled for detection (e.g., with fluorescein or another fluorescent moiety, or with an enzyme such as horseradish peroxidase). After selective binding to the target is established, the candidate antibody, or an antibody conjugate produced as described below, may be tested for appropriate activity, including the ability to block leukocyte recruitment to the central nervous system in an in vivo model, such as an appropriate mouse or rat epilepsy model, as described herein. [0089] "Suitable conditions" shall have a meaning dependent on the context in which this term is used. That is, when used in connection with an antibody, the term shall mean conditions that permit an antibody to bind to its corresponding antigen. When used in connection with contacting an agent to a cell, this term shall mean conditions that permit an agent capable of doing so to enter a cell and perform its intended function. In one embodiment, the term "suitable conditions" as used herein means physiological conditions. [0090] A “subject” or “patient” in the context of the present teachings is generally a mammal, for example a human. Mammals other than humans can be advantageously used as subjects that represent animal models of inflammation. A subject can be male or female. [0091] To “analyze” includes determining a set of values associated with a sample by measurement of a marker (such as, e.g., presence or absence of a marker or constituent expression levels) in the sample and comparing the measurement against measurement in a sample or set of samples from the same subject or other control subject(s). The markers of the present teachings can be analyzed by any of various conventional methods known in the art. To “analyze” can include performing a statistical analysis to, e.g., determine whether a subject is a responder or a non-responder to a therapy (e.g., an anti- ATXN2 treatment as described herein). [0092] A "pharmaceutically acceptable excipient," "pharmaceutically acceptable diluent," "pharmaceutically acceptable carrier," and "pharmaceutically acceptable adjuvant" means an excipient, diluent, carrier, and adjuvant that are useful in preparing a pharmaceutical composition that are generally safe, non-toxic and neither biologically nor otherwise undesirable, and include an excipient, diluent, carrier, and adjuvant that are acceptable for veterinary use as well as human pharmaceutical use. "A pharmaceutically acceptable excipient, diluent, carrier and adjuvant" as used in the specification and claims includes both one and more than one such excipient, diluent, carrier, and adjuvant. [0093] As used herein, a "pharmaceutical composition" is meant to encompass a composition suitable for administration to a subject, such as a mammal, especially a human. In general a “pharmaceutical composition” is sterile, and preferably free of contaminants that are capable of eliciting an undesirable response within the subject (e.g., the compound(s) in the pharmaceutical composition is pharmaceutical grade). Pharmaceutical compositions can be designed for administration to subjects or patients in need thereof via a number of different routes of administration including oral, buccal, rectal, parenteral, intraperitoneal, intradermal, intracheal, intramuscular, subcutaneous, and the like. In some embodiments, it may be desirable to administer an anti ATXN2 agent into the brain region, e.g. ventricles, CSF, etc. A continuous delivery device includes, for example, an implanted device that releases a metered amount of an anti- ATXN2 agent continuously over a period of time. Convection-enhanced delivery (CED) is a technique that generates a pressure gradient at the tip of an infusion catheter to deliver therapeutics directly through the interstitial spaces of the central nervous system. [0094] "Dosage unit" refers to physically discrete units suited as unitary dosages for the particular individual to be treated. Each unit can contain a predetermined quantity of active compound(s) calculated to produce the desired therapeutic effect(s) in association with the required pharmaceutical carrier. The specification for the dosage unit forms can be dictated by (a) the unique characteristics of the active compound(s) and the particular therapeutic effect(s) to be achieved, and (b) the limitations inherent in the art of compounding such active compound(s). [0095] "Pharmaceutically acceptable excipient” means an excipient that is useful in preparing a pharmaceutical composition that is generally safe, non-toxic, and desirable, and includes excipients that are acceptable for veterinary use as well as for human pharmaceutical use. Such excipients can be solid, liquid, semisolid, or, in the case of an aerosol composition, gaseous. [0096] "Pharmaceutically acceptable salts and esters" means salts and esters that are pharmaceutically acceptable and have the desired pharmacological properties. Such salts include salts that can be formed where acidic protons present in the compounds are capable of reacting with inorganic or organic bases. Suitable inorganic salts include those formed with the alkali metals, e.g. sodium and potassium, magnesium, calcium, and aluminum. Suitable organic salts include those formed with organic bases such as the amine bases, e.g., ethanolamine, diethanolamine, triethanolamine, tromethamine, N methylglucamine, and the like. Such salts also include acid addition salts formed with inorganic acids (e.g., hydrochloric and hydrobromic acids) and organic acids (e.g., acetic acid, citric acid, maleic acid, and the alkane- and arene-sulfonic acids such as methanesulfonic acid and benzenesulfonic acid). Pharmaceutically acceptable esters include esters formed from carboxy, sulfonyloxy, and phosphonoxy groups present in the compounds, e.g., C1-6 alkyl esters. When there are two acidic groups present, a pharmaceutically acceptable salt or ester can be a mono-acid-mono- salt or ester or a di-salt or ester; and similarly where there are more than two acidic groups present, some or all of such groups can be salified or esterified. Compounds named in this invention can be present in unsalified or unesterified form, or in salified and/or esterified form, and the naming of such compounds is intended to include both the original (unsalified and unesterified) compound and its pharmaceutically acceptable salts and esters. Also, certain compounds named in this invention may be present in more than one stereoisomeric form, and the naming of such compounds is intended to include all single stereoisomers and all mixtures (whether racemic or otherwise) of such stereoisomers. [0097] The terms "pharmaceutically acceptable", "physiologically tolerable" and grammatical variations thereof, as they refer to compositions, carriers, diluents and reagents, are used interchangeably and represent that the materials are capable of administration to or upon a human without the production of undesirable physiological effects to a degree that would prohibit administration of the composition. [0098] A "therapeutically effective amount" means the amount that, when administered to a subject for treating a disease, is sufficient to effect treatment for that disease. [0099] The invention has been described in terms of particular embodiments found or proposed by the present inventor to comprise preferred modes for the practice of the invention. It will be appreciated by those of skill in the art that, in light of the present disclosure, numerous modifications and changes can be made in the particular embodiments exemplified without departing from the intended scope of the invention. Due to biological functional equivalency considerations, changes can be made in protein structure without affecting the biological action in kind or amount. All such modifications are intended to be included within the scope of the appended claims. Conditions for treatment [00100] Neurodegenerative diseases. The term "Neurogenerative disease" refers to diseases and conditions that are characterized by progressive degeneration of the structure and function of the central nervous system or the peripheral nervous system. For instance, neurodegenerative disease may include Alexander's disease, Alper's disease, Alzheimer's disease, Amyotrophic lateral sclerosis, Ataxia telangiectasia, Batten disease, Canavan disease, Cerebral palsy, Cockayne syndrome, Corticobasal degeneration, Creutzfeldt- Jakob disease, Diabetic neuropathy, Frontotemporal lobar degeneration, Glaucoma, Guillain- Barre syndrome, Hereditary spastic paraplegia, Huntington's disease, HIV associated dementia, Kennedy's disease, Krabbe's disease, Lewy body dementia, Motor neuron disease, Multiple System Atrophy, Multiple sclerosis, Narcolepsy, Neuroborreliosis, Niemann Pick disease, Parkinson's disease, Pelizaeus- Merzbacher Disease, Peripheral neuropathy, Pick's disease, Primary lateral sclerosis, Prion diseases, Progressive Supranuclear Palsy, Refsum's disease, Sandhoff's disease, Schilder's disease, Spinocerebellar ataxia, Spinal cord injury, Spinal muscular atrophy, Steele- Richardson-Olszewski disease, stroke and other ischaemic disorders, Tabes dorsalis or traumatic brain injury. Neurodegenerative diseases of particular interest are amyotrophic lateral sclerosis and spinocerebellar ataxia type 2. [00101] Amyotrophic lateral sclerosis is a group of rare neurological diseases that mainly involve the nerve cells (neurons) responsible for controlling voluntary muscle movement. It is characterized by steady, relentless, progressive degeneration of corticospinal tracts, anterior horn cells, bulbar motor nuclei, or a combination. Symptoms vary in severity and may include muscle weakness and atrophy, fasciculations, emotional lability, and respiratory muscle weakness. Diagnosis involves nerve conduction studies, electromyography, and exclusion of other disorders via MRI and laboratory tests. Current treatment is supportive. The majority of ALS cases (90 percent or more) are considered sporadic. [00102] Most patients with ALS present with random, asymmetric symptoms, consisting of cramps, weakness, and muscle atrophy of the hands (most commonly) or feet. Weakness progresses to the forearms, shoulders, and lower limbs. Fasciculations, spasticity, hyperactive deep tendon reflexes, extensor plantar reflexes, clumsiness, stiffness of movement, weight loss, fatigue, and difficulty controlling facial expression and tongue movements soon follow. Other symptoms include hoarseness, dysphagia, and slurred speech; because swallowing is difficult, salivation appears to increase, and patients tend to choke on liquids. Late in the disorder, a pseudobulbar affect occurs, with inappropriate, involuntary, and uncontrollable excesses of laughter or crying. Sensory systems, consciousness, cognition, voluntary eye movements, sexual function, and urinary and anal sphincters are usually spared. Death is usually caused by failure of the respiratory muscles; 50% of patients die within 3 yr of onset, 20% live 5 yr, and 10% live 10 yr. Survival for > 30 yr is rare. [00103] The drugs riluzole (Rilutek) and edaravone (Radicava) have been approved to treat certain forms of ALS. Riluzole is believed to reduce damage to motor neurons by decreasing levels of glutamate, which transports messages between nerve cells and motor neurons. Clinical trials in people with ALS showed that riluzole prolongs survival by a few months, particularly in the bulbar form of the disease, but does not reverse the damage already done to motor neurons. Edaravone has been shown to slow the decline in clinical assessment of daily functioning in persons with ALS. [00104] Animal models for ALS include mutations in the SOD1 gene. Missense mutations in the SOD1 gene on chromosome 21 were the first identified causes of autosomal dominant FALS. SOD1 is a ubiquitous cytoplasmic and mitochondrial enzyme which functions in a dimeric state to catalyse the breakdown of harmful reactive oxygen species (ROS), thereby preventing oxidative stress. Sod1 ^−/− mice do not have any motor neuron loss, but they have a significant distal motor axonopathy, demonstrating the important role of SOD1 in normal neuronal function. The significant loss of motor neurons in transgenic mice expressing mutant SOD1 is likely to result from a toxic gain-of-function. [00105] The spinocerebellar ataxia type 2 (SCA2) is one of the most common polyglutamine (polyQ) disorders. Caused by a dominant expansion of a CAG repeat tract (CAGexp) at ATXN2, SCA2 is related to a polyQ with more than 32–33 glutamines in ataxin-2. Disease usually starts in adulthood and clinical picture is not homogeneous. Main symptoms are related to cerebellar dysfunction, and include ataxic gait, cerebellar dysarthria as well as dysmetria. Other symptoms include uncoordinated movement (ataxia), speech and swallowing difficulties, muscle wasting, slow eye movement, and sometimes dementia . Severe saccade slowing and peripheral neuropathy are very frequent and affect more than 50% of case series . Besides, several other manifestations might appear, such as pyramidal findings, extrapyramidal syndromes (including dystonic movements and parkinsonism), lower motor neuron findings, cognitive deterioration, and others. ATXN2 expansion explains most but not all variability in age at onset (AO) of symptoms, and it was related to presence of some neurological findings such as dystonic movements and parkinsonism. Mean (SD) age at onset was around 30 to 33 (14) years and median survival was 68 [95% CI: 65–70] years, usually after a wheelchair period. [00106] Multiple mouse models of SCA2 exist. In the first SCA2 mouse model was a transgenic line SCA2-58Q. In these mice, a full-length human ATXN2 gene with 58 CAG repeats was expressed under Purkinje cell protein 2 (Pcp2) promoter specifically in the cerebellar PCs of the mice. These mice are characterized by a progressive general motor coordination impairment and the age at onset is 32 weeks of age, as scored by the beam walk and rotarod tests, that showed longer latencies to cross the beam and an increased number of foot slips compared with wild-type (WT) mice. At 24 weeks of age, significant loss of the cerebellar PCs was observed in these mice together with a progressive loss of calbindin-28k that represents a marker for neuronal dysfunction. [00107] The most recent transgenic mouse model of SCA2, the BAC-72Q line, was created with a bacterial artificial chromosome (BAC), including the entire ATXN2 gene in which an exon 1 was edited to include an expanded CAG repeat under the endogenous human promoter. The BAC-SCA2-72Q mice were characterized by weight loss, progressive impairment in the accelerating rotarod performance starting at 16 week of age, and also by thinning of the PC dendritic trees and the reduction of the calbindin and the Pcp2 expression levels in the cerebellum. Other mouse models exist and are further described in Karam et al. (Adv Exp Med Biol.2018;1049:197-218.), herein specifically incorporated by reference. Methods [00108] The present disclosure provides methods for treating neurodegenerative diseases, including ALS and SCA2. The methods comprise administering to the subject an effective amount of an agent that is an anti-ATXN2 agent as a single agent or combined with an additional one or more agent(s). Methods of treatment may include determining the effectiveness of therapy by monitoring clinical indicia for stabilization or reduction of adverse disease symptoms. [00109] In some embodiments, including without limitation administration of bisphosphonates, administration may be oral. In some embodiments, including without limitation administration of polypeptides, such as NEP1-40, antibodies, etc. administration may be localized to the brain. [00110] Numerous localized drug delivery strategies have been developed to circumvent the blood brain barrier. For example, the insertion of polymeric implants that release drugs slowly into the surrounding tissue has been reported to be successful in treating tissues locally. Treatment may be enhanced by alternative delivery methods that increase the penetration distance of the drug into tissue and eliminate the rapid decay in concentration with distance that is characteristic of diffusion mediated transport. Convection-enhanced drug delivery (CED) uses direct infusion of a drug-containing liquid into tissue so that transport is dominated by convection. By increasing the rate of infusion, the convection rate can be made large compared with the elimination rate in a region of tissue about the infusion point. Thus, CED has the potential of increasing the drug penetration distance and mitigating the decay in concentration with distance from the release point. [00111] Nanoparticles as drug or gene carriers may be used, e.g. in combination with CED. Transport of particles through the extracellular space of tissues is hindered by the large size of nanoparticles (10-100 nm), which are much larger than small molecule drugs or therapeutic proteins that more easily penetrate the brain extracellular matrix (ECM). However, nanoparticles may be able to penetrate brain tissue provided that particles are less than 100 nm in diameter, are neutral or negatively charged, and are not subject to rapid elimination mechanisms. [00112] In some embodiments the agent is delivered as continuous intraventricular CNS administration. In some embodiments, intraventricular administration is combined with systemic administration, for example utilizing an implantable device to deliver the agent. In some embodiments the implantable device is an osmotic pump. The device may be implanted intraventricularly, for example, with a conventional stereotaxic apparatus. [00113] A continuous delivery device includes, for example, an implanted device that releases a metered amount of an agent continuously over a period of time. The device may be implanted so as to release the anti-ATXN2 agent into the cerebrospinal fluid (CSF). An example of such devices is an osmotic pump, which operates because of an osmotic pressure difference between a compartment within the pump, called the salt sleeve, and the tissue environment in which the pump is implanted. The high osmolality of the salt sleeve causes water to flux into the pump through a semipermeable membrane which forms the outer surface of the pump. As the water enters the salt sleeve, it compresses the flexible reservoir, displacing the test solution from the pump at a controlled, predetermined rate. The rate of delivery is controlled by the water permeability of the pump’s outer membrane. Thus, the delivery profile of the pump is independent of the drug formulation dispensed. Drugs of various molecular configurations, including ionized drugs and macromolecules, can be dispensed continuously in a variety of compatible vehicles at controlled rates. [00114] In certain embodiments the anti-ATXN2 agent is combined with a therapeutic dose of a drug used to treat ALS or SCA2 such as riluzole, baclofen, quinine, phenytoin, glycopyrrolate, amitriptyline, benztropine, trihexyphenidyl, transdermal hyoscine, atropine, fluvoxamine, dextromethorphan, quinidine, or gabapentin. The active agents may be administered in separate formulations, or may be combined, e.g. in a unit dose. The formulation may be for oral administration, for local intraventricular or CED administration, etc. [00115] In some embodiments the combined therapies are administered concurrently, where the administered dose of any one of the compounds may be a conventional dose, or less than a conventional dose. In some embodiments the two therapies are phased, for example where one compound is initially provided as a single agent, e.g. as maintenance, and where the second compound is administered during a relapse, for example at or following the initiation of a relapse, at the peak of relapse, etc. [00116] In various aspects and embodiments of the methods and compositions described herein, administering the therapeutic compositions can be effected or performed using any of the various methods and delivery systems known to those skilled in the art. The administering can be performed, for example, intravenously, orally, via implant, transmucosally, transdermally, intramuscularly, intrathecally, and subcutaneously. The delivery systems employ a number of routinely used pharmaceutical carriers. [00117] In methods of use, an effective dose of an anti-ATXN2 agent of the invention is administered alone, or combined with additional active agents for the treatment of a condition as listed above. The effective dose may be from about 1 ng/kg weight, 10 ng/kg weight, 100 ng/kg weight, 1 µg/kg weight, 10 µg/kg weight, 25 µg/kg weight, 50 µg/kg weight, 100 µg/kg weight, 250 µg/kg weight, 500 µg/kg weight, 750 µg/kg weight, 1 mg/kg weight, 5 mg/kg weight, 10 mg/kg weight, 25 mg/kg weight, 50 mg/kg weight, 75 mg/kg weight, 100 mg/kg weight, 250 mg/kg weight, 500 mg/kg weight, 750 mg/kg weight, for example up to about 500 mg/kg weight, and the like. The dosage may be administered multiple times as needed, e.g. every 4 hours, every 6 hours, every 8 hours, every 12 hours, every 18 hours, daily, every 2 days, every 3 days, weekly, and the like. The dosage may be administered orally. [00118] Examples of doses for polypeptide drugs, e.g. peptides, antibodies, etc. may include, but are not necessarily limited to a range from about 0.05 mg/kg to about 10 mg/kg (e.g., from about 0.1 mg/kg to about 10 mg/kg, from about 0.1 mg/kg to about 7.5 mg/kg, from about 0.1 mg/kg to about 5 mg/kg, from about 0.1 mg/kg to about 4 mg/kg, from about 0.1 mg/kg to about 3 mg/kg, from about 0.5 mg/kg to about 10 mg/kg, from about 0.5 mg/kg to about 7.5 mg/kg, from about 0.5 mg/kg to about 5 mg/kg, from about 0.5 mg/kg to about 4 mg/kg, from about 0.5 mg/kg to about 3 mg/kg, from about 1 mg/kg to about 10 mg/kg, from about 1 mg/kg to about 7.5 mg/kg,from about 1 mg/kg to about 5 mg/kg, from about 1 mg/kg to about 4 mg/kg, from about 1 mg/kg to about 3 mg/kg, about 1 mg/kg, about 2 mg/kg, about 3 mg/kg, about 4 mg/kg, about 5 mg/kg, about 7.5 mg/kg, or about 10 mg/kg). [00119] Examples of doses for small molecules, e.g. bisphosphonates, can vary widely, but may be 0.05 µg/kg to about 20 mg/kg (e.g., from about 0.1 µg/kg to about 10 mg/kg, from about 0.1 µg/kg to about 7.5 mg/kg, from about 0.1 µg/kg to about 5 mg/kg, from about 0.1 µg/kg to about 4 mg/kg, from about 0.1 µg/kg to about 3 mg/kg, from about 0.5 µg/kg to about 10 mg/kg, from about 0.5 µg/kg to about 7.5 µg/kg, from about 0.5 µg/kg to about 5 mg/kg, from about 0.5 µg/kg to about 4 mg/kg, from about 0.5 µg/kg to about 3 mg/kg, from about 1 µg/kg to about 10 mg/kg, from about 1 µg/kg to about 7.5 mg/kg, from about 1 µg/kg to about 5 mg/kg, from about 1 µg/kg to about 4 mg/kg, from about 1 µg/kg to about 3 mg/kg, about 1 µg/kg, about 2 mg/kg, about 3 mg/kg, about 4 mg/kg, about 5 mg/kg, about 7.5 mg/kg, or about 10 mg/kg). [00120] The compositions can be administered in a single dose, or in multiple doses, usually multiple doses over a period of time, e.g. daily, every-other day, weekly, semi-weekly, monthly etc. for a period of time sufficient to reduce severity of the inflammatory disease, which can comprise 1, 2, 3, 4, 6, 10, or more doses. [00121] Determining a therapeutically or prophylactically effective amount of an agent according to the present methods can be done based on animal data using routine computational methods. The effective dose will depend at least in part on the route of administration. Pharmaceutical Compositions [00122] The above-discussed compounds can be formulated using any convenient excipients, reagents and methods. Compositions are provided in formulation with a pharmaceutically acceptable excipient(s). A wide variety of pharmaceutically acceptable excipients are known in the art and need not be discussed in detail herein. Pharmaceutically acceptable excipients have been amply described in a variety of publications, including, for example, A. Gennaro (2000) “Remington: The Science and Practice of Pharmacy,” 20th edition, Lippincott, Williams, & Wilkins; Pharmaceutical Dosage Forms and Drug Delivery Systems (1999) H.C. Ansel et al., eds., 7 ^th ed., Lippincott, Williams, & Wilkins; and Handbook of Pharmaceutical Excipients (2000) A.H. Kibbe et al., eds., 3 ^rd ed. Amer. Pharmaceutical Assoc. [00123] The pharmaceutically acceptable excipients, such as vehicles, adjuvants, carriers or diluents, are readily available to the public. Moreover, pharmaceutically acceptable auxiliary substances, such as pH adjusting and buffering agents, tonicity adjusting agents, stabilizers, wetting agents and the like, are readily available to the public. [00124] In some embodiments, the subject compound is formulated in an aqueous buffer. Suitable aqueous buffers include, but are not limited to, acetate, succinate, citrate, and phosphate buffers varying in strengths from 5mM to 100mM. In some embodiments, the aqueous buffer includes reagents that provide for an isotonic solution. Such reagents include, but are not limited to, sodium chloride; and sugars e.g., mannitol, dextrose, sucrose, and the like. In some embodiments, the aqueous buffer further includes a non-ionic surfactant such as polysorbate 20 or 80. Optionally the formulations may further include a preservative. Suitable preservatives include, but are not limited to, a benzyl alcohol, phenol, chlorobutanol, benzalkonium chloride, and the like. In many cases, the formulation is stored at about 4ºC. Formulations may also be lyophilized, in which case they generally include cryoprotectants such as sucrose, trehalose, lactose, maltose, mannitol, and the like. Lyophilized formulations can be stored over extended periods of time, even at ambient temperatures. In some embodiments, the subject compound is formulated for sustained release. [00125] In some embodiments, the anti-ATXN2 agent is formulated with a second agent in a pharmaceutically acceptable excipient(s). [00126] The subject formulations can be administered orally, subcutaneously, intramuscularly, parenterally, or other route, including, but not limited to, for example, oral, rectal, nasal, topical (including transdermal, aerosol, buccal and sublingual), vaginal, parenteral (including subcutaneous, intramuscular, intravenous and intradermal), intravesical or injection into an affected organ. [00127] Each of the active agents can be provided in a unit dose of from about 0.1 µg, 0.5 µg, 1 µg, 5 µg, 10 µg, 50 µg, 100 µg, 500 µg, 1 mg, 5 mg, 10 mg, 50, mg, 100 mg, 250 mg, 500 mg, 750 mg or more. [00128] The anti-ATXN2 agent may be administered in a unit dosage form and may be prepared by any methods well known in the art. Such methods include combining the subject compound with a pharmaceutically acceptable carrier or diluent which constitutes one or more accessory ingredients. A pharmaceutically acceptable carrier is selected on the basis of the chosen route of administration and standard pharmaceutical practice. Each carrier must be "pharmaceutically acceptable" in the sense of being compatible with the other ingredients of the formulation and not injurious to the subject. This carrier can be a solid or liquid and the type is generally chosen based on the type of administration being used. [00129] Examples of suitable solid carriers include lactose, sucrose, gelatin, agar and bulk powders. Examples of suitable liquid carriers include water, pharmaceutically acceptable fats and oils, alcohols or other organic solvents, including esters, emulsions, syrups or elixirs, suspensions, solutions and/or suspensions, and solution and or suspensions reconstituted from non-effervescent granules and effervescent preparations reconstituted from effervescent granules. Such liquid carriers may contain, for example, suitable solvents, preservatives, emulsifying agents, suspending agents, diluents, sweeteners, thickeners, and melting agents. Preferred carriers are edible oils, for example, corn or canola oils. Polyethylene glycols, e.g. PEG, are also good carriers. [00130] Any drug delivery device or system that provides for the dosing regimen of the instant disclosure can be used. A wide variety of delivery devices and systems are known to those skilled in the art. Example 1 Genome-wide CRISPR screen reveals v-ATPase as a drug target to lower levels of ALS protein ataxin-2 [00131] Antisense oligonucleotide therapy targeting ATXN2—a gene in which mutations cause neurodegenerative diseases spinocerebellar ataxia type 2 and amyotrophic lateral sclerosis— has entered clinical trials in humans. Additional methods to lower ataxin-2 levels would be beneficial not only in uncovering potentially cheaper or less invasive therapies, but also in defining how ataxin-2 is normally regulated. Here we report a genome-wide fluorescence activated cell sorting (FACS)-based CRISPR screen in human cells for regulators of ataxin-2 protein levels, from which we identified several subunits of the lysosomal vacuolar ATPase (v- ATPase). We demonstrate that multiple Food and Drug Administration (FDA)- approved small molecule v-ATPase inhibitors can lower ataxin-2 protein levels in mouse and human neurons, and that oral administration of at least one of these drugs—Etidronate—is sufficient to lower ataxin-2 levels in the brains of mice. Together, we uncover Etidronate as a safe and inexpensive compound for lowering ataxin-2 levels and demonstrate the value of FACS-based screens in identifying novel genetic and/or druggable modifiers of human disease proteins. [00132] We developed a fluorescence activated cell sorting (FACS)-based screening method using pooled CRISPR/Cas9-mediated genome-wide deletion libraries in conjunction with antibody staining to detect endogenous protein levels. The screen revealed numerous novel genetic modifiers of ataxin-2 protein levels, including multiple subunits of the lysosomal vacuolar ATPase (v-ATPase). We demonstrate that inhibiting the lysosomal v-ATPase with small molecule drugs (FDA-approved) results in decreased ataxin-2 protein levels in human and mouse neurons, as well as in vivo in the brains of mice upon oral administration of one of the drugs—Etidronate. These results signify the value and ease (screen from start to finish in one week) of a FACS-based screening approach to define novel regulators of normal and/or disease proteins, and the potential to repurpose readily available small molecule drugs for diseases impacted by protein levels. Results [00133] FACS-based genome-wide CRISPR-Cas9 KO screens in human cells reveal modifiers of ataxin-2 protein levels. To find additional ways (e.g., new targets or pathways) to lower ataxin-2 levels, we developed a fluorescence-activated cell sorting (FACS)-based genome- wide CRISPR knockout (KO) screen for modifiers of endogenous ataxin-2 protein levels (i.e., without protein tags like Flag or GFP or overexpression) (Figure 1A). We optimized conditions to sensitively detect changes in ataxin-2 protein levels in human cells by antibody staining and FACS (Figure S1) and engineered HeLa cells to stably express Cas9 along with either a blasticidin-resistance cassette (HeLa-Cas9-Blast) or blue fluorescent protein (BFP) (HeLa- Cas9-BFP). To create genome-wide KO cell lines, we transduced HeLa-Cas9-Blast and HeLa- Cas9-BFP cells (as biological replicates) with a lentiviral sgRNA library comprising 10 sgRNAs per gene—targeting ~21,000 human genes—and ~10,000 safe-targeting sgRNAs (Morgens et al., 2017) (Figure 1A). After fixing the cells in methanol and immunostaining them with antibodies targeting endogenous ataxin-2 and a control protein (GAPDH or β-actin), we used FACS to sort the highest and lowest 20% levels of endogenous ataxin-2 expressors relative to levels of the control protein (Figure 1A). We performed the screen four times, twice each with β-actin and GAPDH as the control proteins. We used two different control proteins instead of one to minimize the possibility of selecting hits that were simply global regulators of transcription, translation, or cell size, or otherwise idiosyncratic to the biology of a given control protein. [00134] After sorting cells based on ataxin-2 expression levels, we extracted genomic DNA and performed next generation sequencing (NGS) of the barcoded sgRNAs. Using the Cas9 high-throughput maximum- likelihood estimator (casTLE) algorithm (Morgens et al., 2016), we isolated genes that when knocked out increased or decreased ataxin-2 protein levels (Figure 1B). A false discovery rate (FDR) cutoff of 5% revealed an overlapping set of 52 gene knockouts that decreased—and 36 that increased—ataxin-2 levels across the four screens. As expected, the strongest hit that lowered ataxin-2 levels was ATXN2 itself, demonstrating the effectiveness of this screening approach (Figure 1B). [00135] We individually validated screen hits by treating HeLa cells with siRNAs targeting those gene products followed by immunoblotting. We selected genes for follow-up based on a combination of significance (casTLE) score and effect size (Morgens et al., 2016), as well as known and predicted direct (physical) and indirect (functional) associations with ataxin-2 or between hits. The list of hits included genes known to have a direct association with ataxin-2, such as LSM12, as well as many novel and potent genetic modifiers of ataxin-2 protein levels, such as CFAP20, CLASRP, CMTR2, LUC7L3, PAXBP1, PNISR, ATP6V1A, and ATP6V1C1, and others (Figure 1C, 1D, and 2). Strikingly, some of the hits (e.g., PNISR and PAXBP1) lowered ataxin-2 levels as much as targeting ataxin-2 itself (Figure 1D). We further validated hits in the human neuroblastoma cell line SH-SY5Y, where many— but not all—had a significant effect on ataxin-2 protein levels (Figure S2A and S2B). In addition to identifying numerous previously unknown regulators of ataxin-2, the high rate of validation of hits from the initial screen and its relative ease (a genome-wide screen can be completed in < 1 week from fixation to NGS analysis) suggests these FACS/antibody-staining based screens—using fixed cells to uncover regulators of endogenous protein levels—may be useful in many other contexts. [00136] Inhibiting lysosomal v-ATPase via genetic or pharmacologic perturbation lowers ataxin-2 protein levels and stress granule number in vitro. We observed a striking number of genes encoding subunits of lysosomal vacuolar ATPases (v-ATPases) that decreased ataxin- 2 levels when knocked out (Figure 3A). Lysosomal v-ATPases help to maintain an acidic pH (~4.5) in the lysosome, by pumping protons from the cytosol to the lumen via consumption of ATP (Maxson and Grinstein, 2014). We used siRNAs and immunoblotting to confirm that knocking down numerous v-ATPase subunits leads to decreased ataxin-2 protein levels (Figure 3B and 3C). We also generated a constitutive knockout of the v-ATPase subunit ATP6V1A—a central subunit in v-ATPase function (Maxson and Grinstein, 2014)—using CRISPR-Cas9 in HeLa cells, which resulted in a marked decrease in ataxin-2 protein levels (Figure 3E and 3F). Levels of other polyQ disease proteins huntingtin and ataxin-1 were unaltered in these cells (Figure S3A and S3B), while TDP-43 was modestly decreased (Figure S3C and S3D). To determine whether the mechanism of regulation was at the protein or RNA level, we performed RT-qPCR after applying siRNAs to knock down numerous v-ATPase subunits and observed no change in steady state ATXN2 mRNA levels (Figure 3D). RNA- sequencing confirmed that knocking down a v-ATPase subunit using siRNAs did not lead to changes in ATXN2 mRNA levels or other noteworthy transcriptional changes (Figure S4). These results provide evidence that the mechanism of v-ATPase regulation of ataxin-2 is at the protein level. [00137] In addition to being enriched as screen hits, the v-ATPases stood out for another reason: the availability of small molecule inhibitors. One of these small molecule v-ATPase inhibitors is Etidronate (~206 Daltons), which was FDA-approved in 1977 as a drug to treat Paget disease of bone (Altman et al., 1973). Interestingly, Paget disease of bone has been connected to TDP-43 proteinopathy (Gitcho et al., 2009; Neumann et al., 2007; Watts et al., 2004). Etidronate is a bisphosphonate whose chemical structure and high affinity for bone minerals very selectively induces apoptosis in osteoclasts, popularizing their use in skeletal disorders like osteoporosis over multiple decades (Drake et al., 2008). Despite their apoptosis- inducing role in osteoclasts, bisphosphonates have also been suggested to limit apoptosis in other cell types, and their structural similarity to inorganic pyrophosphate led to the discovery that bisphosphonates inhibit the v-ATPase (David et al., 1996; Drake et al., 2008). Etidronate has a 0.8901 predicted probability of crossing the blood brain barrier (BBB) according to ADMET in silico modeling (Cheng et al., 2012), and also a wide therapeutic index. Given these encouraging properties, especially its safety in humans, we tested whether Etidronate treatment could lower ataxin-2 levels in human and mouse neurons. We also tested whether two other FDA-approved drugs—Alendronate and Thonzonium—would decrease ataxin-2 protein levels. Alendronate (~249 Daltons) is a second-generation bisphosphonate (also known as Fosamax®), whereas Thonzonium (~511 Daltons) inhibits the v-ATPase through a different mechanism (uncoupling the proton transport and ATPase activity of the v-ATPase proton pumps). [00138] Treating human neurons (iPSC-derived or neuroblastoma SH-SY5Y cells) for 24 hours with Etidronate, Alendronate, or Thonzonium resulted in dose-dependent decreases in ataxin- 2 protein levels (Figure 4A- C, S5A, S5B, S6A, and S6B). We also tested all three drugs in mouse cortical neurons in vitro and observed similar dose-dependent ataxin-2 decreases (Figure 4D-G, S5C, S5D, S6C, and S6D). Although Thonzonium and Alendronate decreased ataxin-2 protein levels across a wide range of doses (Figure S5C, S5D, S6C and S6D), they became toxic to mouse neurons at concentrations greater than 10 µM. This toxic dose has been previously reported for Thonzonium (Chan et al., 2012). Etidronate, however, was not toxic even at doses up to 100 µM (highest concentration tested) (Figure 4E and 4F). ^The differences in toxic doses align with their known differences in IC ₅₀ (the concentration of drug t ^{hat is} needed to inhibit a biological process by half) (David et al., 1996). Given Etidronate’s well-known safety, small size, and predicted ability to cross the BBB, we chose to focus on Etidronate for the following experiments. Still, it is noteworthy that three different v-ATPase inhibitors—working through distinct mechanisms—potently decrease ataxin-2 protein levels in neurons without causing the type of toxicity seen in osteoclasts. [00139] We next tested Etidronate’s effects on TDP-43 levels and/or localization, since TDP-43 nuclear depletion and cytoplasmic aggregation are pathologic hallmarks of ALS (Neumann et al., 2006). When we treated mouse cortical neurons with 10 µM Etidronate, we saw a slight (~10%) decrease in TDP-43 levels in the nucleus and cytoplasm (Figure S7A-C), similar to our observation of a moderate TDP-43 decrease in ATP6V1A KO HeLa cells (Figure S3C and S3D). Etidronate treatment did not, however, affect the nuclear-to-cytoplasmic TDP-43 ratio (Figure S7D). Given the protective role of ataxin-2 in formation of stress granules (cytoplasmic foci that form in response to various forms of stress) (Becker et al., 2017; Zhang et al., 2018), we also tested the effect of Etidronate treatment on stress granule formation. Specifically, we treated mouse primary neurons with 10 µM Etidronate for 23 hours prior to adding 0.5 mM sodium arsenite for one hour to induce stress granule formation. Compared to non-drug treated cells, Etidronate-treated neurons had fewer stress granules (Figure 4H and 4I). Since stress granule formation increases the likelihood of subsequent conversion into pathologic insoluble aggregates (Li et al., 2013), we hypothesize that inhibiting the v-ATPase using Etidronate may reduce the propensity for pathologic aggregate formation. [00140] Oral administration of Etidronate lowers ataxin-2 protein levels in vivo. Given our in vitro findings that these v-ATPase inhibitors can lower ataxin-2 levels, we next tested if peripheral administration of Etidronate in vivo could decrease ataxin-2 levels in the brains of mice. Because oral administration of the drug mimics the most common mode of drug intake for humans and given the wide range of doses that lowered ataxin-2 protein levels in vitro ( _{Figure 4C and 4D), we} dissolved Etidronate into drinking water (~2 µg/mL concentration) and M ^{ediGel ^ (ClearH} 2 ^{O) (~20} mg/kg/day concentration) and allowed voluntary consumption by wild type adult mice (~3-4 months old) over one week (Figure 4J). We performed immunoblotting on cortical extracts from mice that drank and ate either normal or drug-infused water and MediGel ^, respectively. After a one-week treatment period, we observed a ~20% decrease in ataxin-2 protein levels in the brains of mice that consumed Etidronate compared to the control group (n=15 in each group) (Figure 4J and 4K). These findings suggest that Etidronate administration in the water supply and MediGel ^ is sufficient to lower levels of ataxin-2 in the brains of mice. [00141] Here we used a highly efficient and robust FACS-based CRISPR screen to uncover numerous regulators of ataxin-2 levels—a validated target for ALS and SCA2 based on human genetics—including genes encoding several subunits of lysosomal v-ATPases for which small molecule drugs are available. We demonstrate that multiple small molecule v-ATPase inhibitors can safely and effectively decrease ataxin-2 levels in mouse and human neurons across a wide range of doses in vitro, and that Etidronate can lower ataxin-2 levels in the brain in vivo when orally administered to mice. We also determine that Alendronate—a structural analog of Etidronate—is similarly effective in decreasing ataxin-2 levels in neurons in vitro, indicating the potential to further develop and/or test structural analogs of bisphosphonates that can most effectively cross the BBB and decrease ataxin-2 levels in the brain. Given Etidronate’s known safety profile and our demonstration of its ability to lower ataxin-2 levels in the brain in vivo, we postulate that Etidronate could serve as a starting compound for future optimization to decrease ataxin-2 levels in the brain. While we did not test the efficacy of Etidronate in lowering polyQ-expanded forms of ataxin-2, we speculate that v- ATPase inhibition may also be effective against longer polyQ expansions because previous studies have reported that longer repeat lengths enhance ataxin-2 stability thereby increasing its levels (Elden et al., 2010; Hart and Gitler, 2012). Clinical trials in humans will be required to determine Etidronate or other bisphosphonates’ safety and efficacy as a treatment for ALS or SCA2. ASO and gene therapy approaches show promise for neurodegenerative disease but are currently prohibitively expensive (hundreds of thousands of US dollars per year for ASOs or several million US dollars for a one-time gene therapy treatment). We purchased 1g of Etidronate for $50. If effective as a therapeutic, the affordability of these compounds could be especially useful in developing countries, like Cuba, where SCA2 is relatively common. [00142] In Example 2 we present a complementary screen for regulators of ataxin-2 using a distinct approach: a whole-genome arrayed siRNA-based screen in a HEK293T cell line containing an 11-amino acid HiBit tag in frame with ataxin-2. Perhaps due to one screen being conducted in HeLa cells versus the other in HEK293T cells—or one being a CRISPR-Cas9- based knockout screen versus the other being a siRNA HiBit screen—the screens led to very distinct hits (only one gene in common – LSM12). However, both sets of screens did reveal several converging themes of ataxin-2 regulation, such as the presence of many spliceosome components and LSm domain-containing proteins. Moreover, in both studies we took special care to validate many hit genes individually in the cell lines in which the screens were conducted, to ensure the robustness and validity of each respective screen. Given the high rates of hit validation for each screen, we speculate that the lack of hit overlap is largely due to differences in the cell types (i.e., different genes expressed) and screening systems (CRISPR knockout vs. HiBit knockdown). Another contributor to differences between the two screens could stem from one screen being pooled (all cells mixed together and competing against one another) while the other is arrayed (analyzed one by one). Importantly, we followed up on hits of interest to confirm that their regulation of ataxin-2 was conserved in more disease-relevant neuronal cell lines, such as SH-SY5Y neuroblastoma cells, human iPSC-derived neurons, and mouse cortical neurons. The differences in hits between the different screening platforms and cell lines underscores the importance of validating hits in disease-relevant cell lines. New CRISPR-based gene perturbation libraries will empower arrayed genome-wide screens (Yin et al., 2022). Since many human diseases are caused by moderate increases or decreases in a gene product, we suspect that the protein levels-based screening approach presented here, in the accompanying manuscript by Rodriguez et al., and in screens by others (Lu et al., 2013; Park et al., 2013; Rousseaux et al., 2018; Yin et al., 2022), could be broadly applicable to different human disease situations, including haploinsufficiency. Methods [00143] Pooled FACS Screen. Generating HeLa-Cas9 cells. To generate cells that stably express Cas9, lentivirus containing Cas9 with blasticidin resistance cassette (Cas9-Blast) or blue fluorescent protein (Cas9-BFP) were generated using standard protocols. Low-passage HeLa cells were transfected at 40-50% confluency in a 100 mm dish with lentiviral concentrations such that the infection rate was ~20%, to reduce the chance that a single cell will incorporate multiple lentiviral particles. 4 days after adding the lentivirus, the culturing media was changed to blasticidin (10 µg/mL)-containing DMEM, high glucose, GlutaMAX™, HEPES media media (Gibco) to select for cells that incorporated Cas9-Blast. The blasticidin- containing DMEM media was replaced every 24 hours until a control plate in parallel of the same quantity of non-Cas9-infected HeLa cells exhibited complete cell death. Cas9-BFP cells were clonally isolated using FACS. [00144] Genome-wide deletion library production and titering. All gRNA oligonucleotides were constructed on a microfluidic array, then lentivirus was generated using standard protocols. Briefly, all guides were pooled together at roughly the same concentration (10 sgRNAs per gene targeting ~21,000 human genes and ~10,000 safe-targeting sgRNAs), which were cloned into a lentiviral backbone. This pool was used to transfect low-passage HEK293T cells at 70-80% confluency in 150 mm dishes, from which the resulting supernatant contained all 25,000 sgRNAs, with each sgRNA represented ~1000 times. [00145] Generating genome-wide knockout cell line. HeLa-Cas9 cells were cultured in DMEM, high glucose, GlutaMAX™, HEPES media (Gibco) containing 10% FBS (Omega) and 1% penicillin-streptomycin (P/S) (Gibco) in 150 mm plates. The viral media generated above— containing 1000x representation of each sgRNA—was used to infect the HeLa-Cas9 cells. The virus titering was performed such that 5-10% of cells were mCherry-positive, to reduce the chance that a single cell will incorporate multiple gRNAs.24 hours after infection, media was changed to DMEM media containing puromycin (1 µg/mL) to select for infected cells. The puromycin-containing media was replaced every 24 hours until >90% of cells were mCherry- positive, and an uninfected control plate containing HeLa-Cas9 cells exhibited complete cell death when subjected to puromycin selection. The cells were grown for an additional five days to give Cas9 ample time to cut. [00146] Fixation and IF. After trypsinization, approximately 400 million cells of the genome- wide deletion cell line were fixed in 100% methanol for 10 minutes at -20°C. The number of cells to fix was chosen based on ensuring 1000x coverage of the whole genome (250,000 guide elements) while accounting for cells lost during fixation/staining/FACS. After placing in blocking solution (0.4% PBS-Triton containing 5% normal donkey serum and 0.5% BSA) for one hour, primary antibodies against ataxin-2 (1:100; Rabbit; ProteinTech 21776-1-AP) and house-keeping protein GAPDH (1:500; Mouse; Sigma-Aldrich G8795) or β-actin (1:100; Mouse; ThermoFisher Scientific MA1-744) were added to the sample and left overnight at 4°C on a shaker. After rinsing one time in PBS-Triton (0.4%), fluorescent secondary antibodies were added (1:500) for two hours. The cells were then rinsed in PBS, resuspended in PBS containing 2 mM EDTA, and taken directly to the FACS facility for sorting. [00147] Fluorescence activated cell sorting. To identify genetic modifiers of ataxin-2 protein levels, the cell suspension was sorted using a BD FACSAria II cell sorter with a 70 µm nozzle (BD Biosciences). Cell populations containing the lowest and highest 20% of ataxin-2 levels— relative to β-actin or GAPDH— were sorted, respectively. Each sorted population, as well as the unsorted (starting) population, were spun down at 600g for 20 minutes at room temperature before extracting genomic DNA. [00148] Genomic DNA extraction, PCR amplification, and next-generation sequencing. Genomic DNA was extracted immediately after pelleting using the Blood and Tissue DNeasy Maxi Kit (QIAGEN, 51194). The DNA was isolated according to the manufacturer’s instructions, with the exception of eluting with buffer EB, rather than buffer AE. After PCR amplification using Agilent Herculase II Fusion DNA Polymerase Kit, deep sequencing was performed on an Illumina NextSeq 550 platform to determine library composition. Guide composition between the sorted top 20% and the unsorted (starting) populations were compared using Cas9 high Throughput maximum Likelihood Estimator (casTLE) (Morgens et al., 2016) to determine genes that, when knocked out, increased or decreased ataxin-2 protein levels. Briefly, enrichment of individual guides was calculated as median normalized log ratios of counts between the various conditions. Gene-level effects were then calculated from ten guides targeting each gene, and an effect size estimate was derived for each gene with an associated-likelihood ratio to describe the significance of the gene-level effects. By randomly permutating the targeting elements, the distribution of the log-likelihood ratio was estimated and P values derived (Morgens et al., 2016). All data is available under Gene Expression Omnibus accession no. GSE189417. [00149] Validation & Drug Treatments. Cell culture and siRNA transfection. HeLa cells (ATCC ^® ) were cultured in DMEM, high glucose, GlutaMAX™, HEPES media (Gibco) containing 10% f _{etal-bovine serum (FBS) (Omega) and 1%} ^{penicillin-streptomycin (P/S) (Gibco) in a controlled humidified incubator at 37°C with 5% CO} ₂ ^{. For} _{knockdown experiments, cells were reverse} transfected with SMARTPool ON-TARGETplus siRNAs (GE Dharmacon) targeting a control siRNA pool (D001810-10) or a gene of interest at a final concentration of 200 nM for 72 hours in 12-well plates, after complexing with DharmafectI (GE Dharmacon) in Opti-MEM (Gibco) for 30 minutes. [00150] SH-SY5Y cells (ATCC ^® ) were cultured in DMEM/F12, GlutaMAX™-supplemented m _{edia (Gibco)} containing 10% FBS (Omega) and 1% P/S (Gibco) at 37°C with 5% CO ₂ . s ^{iRNA reverse transfection} experiments were conducted similarly as for HeLa, except for performing knockdown for 96 hours in two doses (a second dose given after 24 hours with a full media change) and complexing with Lipofectamine RNAiMAX (Invitrogen) in Opti-MEM (Gibco) for 20 minutes prior to addition of cells. Cells were cultured in 24-well plates. [00151] Generating ATXN2 mosaic knockout cell line. To generate mosaic ATXN2 KO HeLa- Cas9 cells, a sgRNA oligonucleotide targeting the first shared exon in ATXN2 (sequence GATGGCATGGAGCCCGATCC) was cloned into a lentiviral backbone that contains mCherry and a puromycin resistance cassette. This construct was used to transfect low-passage HEK293T cells at 70-80% confluency in 100 mm plates. HeLa-Cas9 cells (cultured in DMEM, high glucose, GlutaMAX™, HEPES media containing 10% FBS and 1% penicillin- streptomycin in 100 mm plates) were then infected with the lentiviral media generated above, such that ~50% of cells were mCherry-positive. 24 hours after infection, the media was changed to puromycin-containing media (1 µg/mL) to select for cells that received a sgRNA. The puromycin- containing media was replaced every 24 hours until >90% of cells were mCherry-positive, and an uninfected control plate containing HeLa-Cas9 cells exhibited complete cell death upon subjection to puromycin selection. The cells were grown for an additional week to give Cas9 ample time to cut prior to use in flow cytometry. [00152] Western Blots. Ice-cold RIPA buffer (Sigma-Aldrich R0278) containing protease inhibitor cocktail (Thermo Fisher 78429) and phosphatase inhibitor (Thermo Fisher 78426) were placed on cells for lysis. After 1-2 minutes, the lysates were moved to Protein LoBind tubes (Eppendorf 02243108), vortexed, and placed on ice. The lysates were vortexed two more times after 10 minute intervals then pelleted at maximum speed on a table-top centrifuge for 15 minutes at 4°C. After moving the supernatant to new Protein LoBind tubes, protein concentrations were determined using bicinchoninic acid (Invitrogen 23225) assays. Samples were denatured at 70°C in LDS sample buffer (Invitrogen NP0008) containing 2.5% 2- mercaptoethanol (Sigma-Aldrich) for 10 minutes. Samples were run on 4–12% Bis–Tris gels (Thermo Fisher) using gel electrophoresis, then wet-transferred (Bio-Rad Mini Trans- Blot Electrophoretic Cell 170-3930) onto 0.45 µm nitrocellulose membranes (Bio-Rad 162- 0115) at 100V for 90 minutes. Odyssey Blocking Buffer (LiCOr 927-40010) was applied to membranes for one hour then replaced with Odyssey Blocking Buffer containing antibodies against ataxin-2 (1:1000, ProteinTech 21776-1-AP) and β-actin (1:2000, Thermo Fisher Scientific MA1-744) and placed on a shaker overnight at room temperature. After rinsing three times in PBS-Tween (0.1%) for 10 minutes each, membranes were incubated in Odyssey Blocking Buffer containing HRP-conjugated anti-rabbit IgG (H+L) (1:2000, Life Technologies 31462) or anti-mouse IgG (H+L) (1:2000, Fisher 62-6520) secondary antibodies for one hour. After rinsing the blots three additional times in PBS-Tween (0.1%), the membranes were developed using ECL Prime kit (Invitrogen) and imaged using ChemiDoc XRS+ System and Image Lab software (Bio-Rad Laboratories). [00153] RT-qPCR and RNA Quantification. After reverse transfection with siRNAs in 12-well plates as described in the ‘Cell culture and siRNA transfection’ section, the PureLink® RNA Mini Kit was used to isolate RNA with DNase digestion (Thermo Fisher Scientific 12183025). To convert RNA to cDNA, we used the Applied Biosystems High-Capacity cDNA Reverse Transcription kit (Thermo Fisher Scientific 4368813). Each sample had biological triplicates, and technical quadruplicates for each of the replicates. qPCR was performed using TaqMan™ Universal Master Mix II (Thermo Fisher Scientific4440040), using 1 µL of 20X TaqMan gene- specific expression assay to the reaction and our probes of interest (Thermo Fisher Scientific; human ATXN2: Hs00268077_m1, human ACTB: Hs01060665_g1). The Delta-Delta Ct method was run on the thermocycler and visualized on Thermo Fisher Connect™, from which relative expression values were averaged across all biological/technical replicates per condition. [00154] RNA-sequencing. To determine whether there are broad transcriptional changes after knocking down a v- ATPase subunit, we performed RNA-seq after HeLa cells were treated with NT or ATP6V1A siRNAs for 72 hours, as described in the 'Cell culture and siRNA transfection' section. Briefly, we isolated RNA using the PureLink® RNA Mini Kit with DNase digestion (Thermo Fisher Scientific 12183025), then determined RNA quantity and purity by optical density measurements of OD260/280 and OD230/260 using a NanoDrop spectrophotometer. We assessed structural integrity of the total RNA using a 2200 TapeStation Instrument with RNA ScreenTapes (Agilent Technologies), then prepared mRNA libraries using SureSelect Strand-Specific RNA Library Preparation kit for Illumina (G9691B) on an Agilent Bravo Automated Liquid Handling Platform, following the manufacturer’s protocol. Libraries were sequenced on an Illumina Nova-Seq 6000 machine. Once the data was retrieved, alignment of RNA-sequencing reads to the human hg38 transcriptome was performed using STAR v2.7.3a(Dobin et al., 2013) following ENCODE standard options, read counts were generated using RSEM v1.3.1, and differential expression analysis was performed in R v4.0.2 using the DESeq2 package v1.28.1 (Love et al., 2014). All data is available under Gene Expression Omnibus accession no. GSE189417. [00155] In vitro drug treatments. Mouse primary neurons were obtained from timed-pregnant, C57BL/6 mice at E16.5 (Charles River). The cortices were dissected out and dissociated into single-cell suspensions with a papain dissociation system (Worthington Biochemical Corporation) and plated onto poly-L-lysine (Sigma Aldrich)-coated plates (0.1% (wt/vol)) at a density of 350,000 cells per well in 24-well plates. The neurons were grown in Neurobasal medium (Gibco) supplemented with P/S (Gibco), GlutaMAX (Invitrogen), and ^{B-27 serum-free} supplements (Gibco) at 37°C with 5% CO ₂ . After 4 days in vitro (DIV), a full media _change was performed containing various concentrations of Etidronate (ranging from 1 nM to 100 µM) or water (control), or Thonzonium (ranging from 1 nM to 10 µM) or DMSO (control), and cells were lysed 24 hours later to collect protein. All mouse experiments were approved by the Stanford University Administrative Panel on Animal Care (APLAC). [00156] Human iPSCs-derived neurons (iNeurons) were induced utilizing a Tet-On induction system to express the transcription factor Ngn2. Briefly, iPSCs were maintained in mTeSR1 medium (Stemcell Technologies) on Matrigel-coated plates (Fisher Scientific CB-40230). The following day, doxycycline (2 µg/mL) was added to the media to induce Ngn2 expression, followed by puromycin (2 µg/mL) treatment to rapidly and efficiently induce iNeurons. Three days following induction, the differentiating iNeurons were dissociated using Accutase (STEMCELL Technologies) and resuspended in a culture medium consisting of Neurobasal media (Thermo Fisher), N2 (Thermo Fisher), B-27 (Thermo Fisher), BDNF/GDNF (R&D Systems) on Matrigel-coated assay plates. This resuspension mixture was then plated onto Matrigel-coated 24-well plates. Half-media changes were performed every 2-3 days.6-7 days after Ngn2 induction, the cells were treated with various doses of Etidronate (dissolved in media) or water (control, all to equal volumes) and lysed 24 hours later for protein collection. [00157] For SH-SY5Y cells, they were seeded at a density of 5x10 ⁵ cells per well in 24-well plates. One day after plating, the cells were treated with various doses of Alendronate or Thonzonium (dissolved in media, all to equal volumes) and lysed 24 hours later for protein collection. [00158] Immunocytochemistry, microscopy, and image quantification. WT or ATP6V1A KO HeLa cells were grown on poly-L-lysine-coated glass coverslips [0.1% (wt/vol)] in 24-well plates (four wells per condition), then fixed with 4% paraformaldehyde for 30 minutes. Next, the cells were rinsed 3 times with PBS then blocked with 1% BSA containing 0.4% Triton X- 100 for one hour. After overnight primary antibody incubation (1:1000 ataxin-2, ProteinTech 21776-1-AP; 1:1000 β-actin, Thermo Fisher Scientific MA1-744), cells were rinsed 3 times with PBS prior to incubating with fluorescent secondary antibodies (1:500) for one hour. After rinsing with PBS 3 times, coverslips were mounted using Prolong Diamond Antifade mount containing DAPI (Thermo Fisher Scientific). All steps were carried out at room temperature. Images were acquired using a Zeiss LSM 710 confocal microscope (three fields-of-view per coverslip, four coverslips per condition). Images were processed and analyzed using ImageJ (version 2.1.0). Quantification of fluorescence intensities was conducted on >270 cells per condition. [00159] To determine whether Etidronate treatment led to changes in TDP-43 protein levels and localization via immunocytochemistry, we followed the same protocol as above, except that we plated primary neurons from mouse embryos (E16.5) in 24-well plates on glass coverslips at 350,000 cells/well density. In brief, after treating these neurons with H2O or 10 µ ^{M Etidronate for 24 hours (four wells per condition), we} _{immunostained the cells using} antibodies against TDP-43 (1:1000, ProteinTech 10782-2-AP) and MAP2 (1:1000, Synaptic Systems 188004), then mounted coverslips onto slides using Prolong Diamond Antifade mount containing DAPI (Thermo Fisher Scientific). We also immunostained cells with the same treatment conditions for ataxin-2 (1:1000, Novus NBP1-90063) and MAP2. For the stress granule assay, we added 0.5 mM sodium arsenite to the cells for the final hour prior to the 4% paraformaldehyde fixation step and utilized antibodies against PABP (1:1000, Abcam ab21060) and MAP2, followed by Prolong Diamond Antifade mount containing DAPI (Thermo Fisher Scientific). Images were acquired using a Zeiss LSM 710 confocal microscope (20~30 images taken per condition over four coverslips) then processed and analyzed using ImageJ (version 2.1.0). We analyzed 250 or more cells per condition. For stress granule quantification, the numbers of cells containing PABP-positive stress granules—as well as total number of cells—were counted for each image. We calculated the proportion of SG-containing cells / total cells for each image, which would each count as a single data point. All image quantifications were conducted by a person blind to the treatment condition. [00160] In vivo drug treatments. 3-4-month-old WT C57/BL6 mice were given normal ( _{control group) or} Etidronate-infused water (~2 µg/mL) and MediGel ^ Sucralose (ClearH ₂ O) ( ^{~20 mg/kg/day concentration)} _{(treatment group) for voluntary consumption, with 15 animals} in each group. After one week, the animals perfused with PBS before dissecting out their brains for flash-freezing. Olfactory bulbs were removed, the hemispheres were separated, and each hemisphere was divided into cortex and cerebellum chunks. Left cortices were then Dounce homogenized and treated for protein extraction in a conventional manner, as described above in the Western Blots section. [00161] Statistical Methods. Analyses were performed using RStudio (version 1.3.959) or Prism 9.0 (GraphPad), and graphs were generated using Prism 9.0. Data represent mean ± SD. Specific tests (e.g., unpaired t-test, one-way ANOVA, two-way ANOVA, post-hoc tests) and significance are indicated in figure legends. [00162] Data and code availability. The data supporting the findings of this study are available from the corresponding author upon reasonable request. All sequencing data is available under Gene Expression Omnibus accession no. GSE189417. Source code for analyzing CRISPR screen data using casTLE method (Morgens et al., 2016) are available. Example 2 Targeting RTN4/NoGo-Receptor reduces levels of ALS protein ataxin-2 [00163] Gene-based therapeutic strategies to lower ataxin-2 levels are emerging for neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and spinocerebellar ataxia type 2 (SCA2). To identify additional ways of reducing ataxin-2 levels, we performed an arrayed genome-wide screen in human cells for regulators of ataxin-2 and identified RTN4R, the gene encoding the RTN4/NoGo-Receptor, as a top hit. RTN4R knockdown, or treatment with a peptide inhibitor, was sufficient to lower ataxin-2 protein levels in mouse and human neurons in vitro and Rtn4r knockout mice have reduced ataxin-2 levels in vivo. Remarkably, we observed that ataxin-2 shares a role with the RTN4/NoGo-Receptor in limiting axonal regeneration. Reduction of either protein increases axonal regrowth following axotomy. These data define the RTN4/NoGo-Receptor as a novel therapeutic target for ALS and SCA2 and implicate the targeting of ataxin-2 as a potential treatment following nerve injury. [00164] To discover targets and pathways to lower ataxin-2 levels, we developed an arrayed whole-genome siRNA screen to specifically measure ataxin-2 levels. siRNA targets that decrease ataxin-2 were highly enriched for components of the spliceosome. Targeting one of the strongest hits, RTN4R, or peptide inhibition of RTN4R (also known as RTN4/NoGo- receptor), a regulator of neurite development, reduced ataxin-2 levels in vitro and in vivo. Moreover, knockdown of ataxin-2 promoted axonal regeneration in primary cortical neurons following injury. These results leverage the robust effect of ataxin-2 as a disease modifier to define novel therapeutic targets. Results [00165] Whole-genome siRNA screen identifies genes and cellular pathways that regulate ataxin-2 levels We made a quantitative and highly sensitive reporter of endogenous ataxin-2 protein levels by inserting the HiBiT tag on the C-terminus of ataxin-2 in HEK293T cells using CRISPR-Cas9 genome editing (Figure 12A). HiBiT is an 11-amino acid peptide subunit of the NanoBiT luciferase enzyme that is inert on its own but binds with high affinity to LgBiT, reconstituting NanoBiT. This allows for easy and specific detection of ataxin-2 using an antibody-free blotting method (Figure 12B-D). An in-well reaction of ataxin-2-HiBiT cell lysate with the exogenous addition of LgBiT and the furimazine substrate generates quantifiable bioluminescence as a direct measure of ataxin-2 abundance (Figure 12E). In parallel, we stably incorporated firefly luciferase (FFluc) into the ataxin-2-HiBiT line to normalize for protein abundance. [00166] We used the ataxin-2-HiBiT cell line to perform a genome-wide screen using arrayed siRNA pools targeting 21,121 mRNA transcripts (Figure 12F, 12G, and 16). We performed the screen in duplicate for both ataxin-2-HiBiT levels and FFluc levels, a control for ruling out siRNAs with nonspecific effects on gene expression. We classified an siRNA as a primary screen hit if it had an average HiBiT Z-score less than -1.65, indicating a significant negative impact on ataxin-2 levels, and an average FFluc Z-score greater than -1. We excluded siRNAs that significantly impacted expression levels of the FFluc control in the same direction as ataxin-2 levels—resulting in 348 primary screen hits (Data Table 2). We selected primary screen hits for validation based on function in shared pathways (e.g., splicing) or known roles in the nervous system. We performed a secondary validation screen using 102 siRNA pools, of which 77 validated and we classified these as “high confidence hits” (Figure 16C, Table 2). [00167] Gene ontology analysis of the primary screen hits revealed an enrichment in constituents of the pre-mRNA splicing pathway (Figure 12H and 12I), and 36 of the 77 high confidence hits have roles in the major spliceosome complexes (Figure 12J). These proteins are enriched for the like-Sm or LSm domain (Figure 17), a protein domain critical for complex formation and splicing activity (He and Parker, 2000). Ataxin-2 has an LSm domain that is one of the few predicted structured regions of this largely disordered protein. We independently validated several high confidence hits using siRNAs in unedited HEK293T cells and immunoblotting for ataxin-2 (Figure 12K, 1L, and 18A). We also performed RT-qPCR and found that some of these hits affected steady-state ATXN2 mRNA levels (Figure 18B). The presence of a shared LSm domain combined with the regulation revealed by this screen suggests a potential functional connection between ataxin-2 and the spliceosome. [00168] Knockdown or inhibition of the RTN4/NoGo-Receptor lowers ataxin-2 levels. Because splicing is an essential cellular process and splicing defects contribute to ALS (Lagier- Tourenne et al., 2010), we sought to identify the optimal target with therapeutic potential by first filtering high confidence hits for essentiality (using the Dependency Map (DepMap) database, average gene effect>-1). DepMap is a resource of essential genes across a range of cell types (Meyers et al., 2017, McFarland et al., 2018), usually used to identify cancer vulnerabilities that can be exploited. However, for neurodegeneration targets, we sought to avoid essential genes, thus filtered these out of our hit list. We also filtered hits for central nervous system expression (GTEx database, cortical pTPM>15) (2013) (Figure 13A). We reasoned that selecting targets with high nervous system specificity may eliminate potential negative off-target effects in non-diseased tissues. Following these filtering steps, the top hit was RTN4R, the gene that encodes RTN4/NoGo- Receptor. RTN4/NoGo-Receptor has been implicated in axon regeneration, sprouting, and plasticity (Fournier et al., 2001, McGee et al., 2005, Wang et al., 2020, Wang et al., 2011, Akbik et al., 2013, Bhagat et al., 2016, Kim et al., 2004, Fink et al., 2015), and targeting its ligand NoGo- A modulates mutant SOD1 mouse models of ALS (Jokic et al., 2006, Bros-Facer et al., 2014, Fournier et al., 2001, Yang et al., 2009). RTN4/NoGo-Receptor has several glia- and neuron- derived ligands including the three gene products of the RTN4 gene—NoGo-A, B, and C—as well as oligodendrocyte myelin glycoprotein (OMgp) and myelin-associated glycoprotein (MAG) (Schwab, 2010, Domeniconi et al., 2002, Wang et al., 2002). Other high-affinity ligands include BAI adhesion-GPCRs (Wang et al., Chong et al., 2018), LGI1 (Thomas et al., 2010), BLyS (Zhang et al., 2009), and LOTUS (Sato et al., 2011). RTN4R knockdown reduced ataxin-2 levels by HiBiT assay and immunoblot (Figure 13B-D). We confirmed this in SH-SY5Y neuroblastoma cells (Figure 19A and 19B). Conversely, knockdown of ataxin-2 had no effect on RTN4/NoGo- Receptor levels (Figure 19C and 19D). This effect seems specific to ataxin-2 and not polyQ proteins in general because knocking down RTN4R did not affect expression levels of polyQ disease proteins huntingtin and ataxin-3 nor the ataxin-2 paralog ATXN2L (Figure 20). As another functional readout of decreased ataxin-2 function (Becker et al., 2017), RTN4R knockdown reduced recruitment of TDP-43 to stress granules (Figure 21). These data provide evidence that RTN4/NoGo-Receptor is required to maintain ataxin-2 levels. [00169] Regulation of ataxin-2 by RTN4/NoGo-Receptor occurs at the protein level because RTN4R knockdown did not affect ATXN2 mRNA levels (Figure 13E and 13F). The HiBiT system allows for monitoring protein degradation (Riching et al., 2018). We used the ataxin-2- HiBiT line to test if RTN4R knockdown leads to ataxin-2 protein degradation by the proteasome or autophagy. Following siRNA knockdown of RTN4R, treatment of cells with a proteasome inhibitor (Figure 13G), but not an autophagy inhibitor (Figure 22A), resulted in an increase in ataxin-2 to levels comparable to the non-targeting control, indicating that ataxin- 2 is degraded by the proteasome. RTN4R knockdown did not increase 20S proteasome activity (Figure S7B), suggesting a specific effect on ataxin-2 proteasomal degradation caused by RTN4R knockdown. [00170] NEP1-40 is a peptide that acts as a competitive RTN4/NoGo-Receptor antagonist. It is a fragment of the luminal region of NoGo-A, B and C that binds to RTN4/NoGo-Receptor to prevent ligand signaling (Figure 13H) (GrandPré et al., 2002). NEP1-40 treatment decreased ataxin-2 levels in the ataxin-2-HiBiT cells (Figure 13I). Thus, targeting RTN4R by either genetic knockdown or with a peptide inhibitor leads to decreased levels of ataxin-2. [00171] Knockdown or inhibition of the RTN4/NoGo-Receptor lowers ataxin-2 levels in mouse and human neurons. To extend our findings to neurons, we tested this interaction in mouse cortical neurons and human iPSC-derived neurons (iNeurons) (Figure 14A and 14B) (Bieri et al., 2019). Treatment of mouse cortical neurons and human iNeurons with lentiviruses expressing shRNA targeting mouse or human RTN4R respectively resulted in about a 50% reduction of ataxin-2 (Figure 14C-F), without affecting levels of ATXN2 mRNA (Figure 23). Application of the NEP1-40 inhibitor peptide caused a dose-dependent reduction of ataxin-2 in both mouse cortical neurons and human iNeurons (Figure 14G-L). Longer incubation times after the addition of shRNA expressing lentivirus were needed to see a significant knockdown of the RTN4/NoGo-Receptor whereas NEP1-40 addition binds and blocks the receptor effectively within hours of application (GrandPré et al., 2002). To test the specificity of RTN4R knockdown, we performed RNA sequencing of iNeurons following RTN4R shRNA treatment. We found several transcript level alterations (Figure 24A, Table 3), but none of these connected to pathways highlighted by our ataxin-2 screen, suggesting a specific effect of RTN4R knockdown on ataxin-2 levels (Figure 24B). Together, these results suggest that targeting RTN4/NoGo-Receptor, either genetically or with a peptide inhibitor, is sufficient to markedly decrease levels of ataxin-2 in neurons. [00172] Since Sm-containing SNRP genes were among the strongest modifiers of ataxin-2 levels in our screen, we tested if knockdown of RTN4/NoGo-Receptor impacted SNRP gene expression. However, knocking down RTN4R did not affect SNRPB expression levels (Figure S25A-B). This suggests that RTN4R’s effect on ataxin-2 levels is independent of splicing pathways, however a more systematic approach is needed to rule out every splicing factor yielded by our screen. Because ataxin-2 is a modifier of TDP-43 toxicity (Elden et al., 2010, Becker et al., 2017), we tested the effect of RTN4R knockdown on TDP-43-induced toxicity. We upregulated TDP-43 to induce degeneration and cell death in primary neurons (Maor-Nof et al., 2021), then measured caspase activation as a readout of cell death. Knockdown of RTN4R for 12 days prior to TDP-43 upregulation, prevented TDP-43-induced caspase activation (Figure S10C). These data extend our findings in HEK293T cells where reduction of RTN4R decreased TDP-43 transport into stress granules, to further show that RTN4R knockdown can mitigateTDP-43-induced cellular toxicity. [00173] Finally, we tested the effects of RTN4/NoGo-Receptor on ataxin-2 levels in vivo. We analyzed heterozygous and homozygous Rtn4r knockout mice. These mice are fertile and viable with no apparent deficits in the nervous system (Kim et al., 2004). We observed a dose- dependent reduction in ataxin-2 in lysates from mouse cortex from the Rtn4r heterozygous and homozygous knockout mice compared to wild-type mice (Figure 14M and 14N), providing evidence that reduction of RTN4/NoGo-Receptor is sufficient to lower levels of ataxin-2 in the nervous system. [00174] Knockdown of ataxin-2 improves axon regrowth after injury. RTN4/NoGo-Receptor signaling destabilizes the actin cytoskeleton leading to growth cone collapse, limiting neurite outgrowth (Chivatakarn et al., 2007, Schwab, 2010, Montani et al., 2009). Reduction or inhibition of RTN4/NoGo-Receptor or its ligands has been shown to limit axonal regeneration following injury (Wang et al., 2020, Wang et al., 2011, Kim et al., 2004, Fink et al., 2015, Fournier et al., 2001, Schwab and Strittmatter, 2014). Importantly, our RNA sequencing results in iNeurons showed an increase in abundance of transcripts involved in axonal extension and neuronal development following RTN4R knockdown (Figure 24B). Since we have demonstrated that knocking down or inhibiting RTN4/NoGo-Receptor lowers ataxin-2, we tested if reducing ataxin-2 levels is sufficient to promote axon regeneration, perhaps functioning downstream of RTN4/NoGo-Receptor. We plated primary mouse neurons in the soma compartment of microfluidics chambers (Figure 15A), treated with lentivirus expressing shRNA targeting either Atxn2 or Rtn4r at DIV5 (Figure 15B), and allowed neurons to mature and project axons through the microchannels and into the inner chamber of the axonal compartment. At DIV17, we performed vacuum-assisted axotomy to fully sever axons projecting into the inner chamber (Figure 15C) and permitted neurons to regenerate axons for 48hr. We analyzed Tuj1- stained axons and found that the average length of regrown axons was markedly increased in either the Rtn4r or Atxn2 knockdown conditions relative to the non- targeting control; non-targeting- 148.9µm, Rtn4r-188.8µm, and Atxn2-184.8µm (Figure 15D and 15E). These results provide evidence of a role for ataxin-2 in limiting regeneration after nerve injury and present ataxin-2 as a potential therapeutic target following nerve injury. Additionally, this finding provides further evidence that RNA-binding proteins that drive RNA granule formation following stress can limit axon regeneration - as has been reported for TIAR- 2 (Andrusiak et al., 2019, Becker et al., 2017, Liu-Yesucevitz et al., 2011, Boeynaems and Gitler, 2019). [00175] Here we performed an unbiased genome-wide screen and discovered RTN4/NoGo- Receptor as a novel regulator of ataxin-2 levels. We provide evidence that RTN4R functions upstream of ataxin-2. Since ataxin-2 has been implicated in two neurodegenerative diseases - ALS and SCA2 - efforts are underway to target it therapeutically including the use of ASOs targeting ATXN2 (Becker et al., 2017, Scoles et al., 2017). In Example 1 we identified v- ATPase as a target to lower ataxin-2 levels and Etidronate and other bisphosphonates as potent small molecule inhibitors of ataxin-2 levels. We now present an additional way to reduce ataxin-2 levels. It is notable that we provide extensive validation of the lead hits from each screen. [00176] RTN4/NoGo-Receptor is an optimal target for therapeutic reduction of ataxin-2 because in addition to gene-based strategies there are several ways in which it may be targeted including receptor inhibition, demonstrated here, as well as neutralization of its ligands (Schwab, 2010). A RTN4/NoGo-Receptor Decoy (Wang et al., 2011, Wang et al., 2020) is being investigated in a clinical trial for chronic spinal cord injury (ClinicalTrials.gov identifier: NCT03989440). With additional targets and strategies to lower ataxin-2 levels in hand, combination therapies can be used to have maximum therapeutic benefit and to mitigate potential negative effects of relying on a single strategy. Methods _{[00177] Cell culture and transfection.} ^{HEK293T cells were maintained in a 37°C incubator with 5% CO} ₂ ^{in DMEM with Glutamax and} _{HEPES (Thermo Fisher Scientific, cat# 10564-029), 10%} fetal bovine serum (vol/vol; Invitrogen, cat# 16000-044), and 1% Pen/Strep (vol/vol; Invitrogen, cat# 15140-122). Cells were reverse transfected on 96-well plates for luciferase assays.25µL of Opti-MEM (Life Technologies, cat# 31985-062) with 0.12µL of Dharmafect 1 (Horizon Discovery, cat# T-2001-03) and 200nM (unless specified in figure) of ON-TARGETplus siRNA (Horizon Discovery) or non-targeting (Horizon Discovery, cat# D-001810-10) was added to an individual well and incubated at room temperature for 30 minutes.1.0x10 ⁴ cells/well in 100µL of medium (without Pen/Strep) was added to the wells, and the plate was placed in the incubator for 72hr. To interrogate proteasome or autophagy regulation by HiBiT assay, 72hr after reverse transfection cells were treated for 6hr with 10µM MG-132 (Millipore Sigma, cat# M7449) or 24hr with 100µM Bafilomycin A (Sigma Aldrich, cat# B1793) or DMSO prior to lysing. [00178] For immunoblotting, unedited HEK293T cells were maintained as above. Unedited cells were used to reduce cell line-specific effects. Cells were reverse transfected on 12-well plates. 200µL of Opti- MEM with 4µL of Dharmafect 1 and 200nM of ON-TARGETplus siRNA or non- targeting control was added to an individual well and incubated at room temperature for 30 minutes.2.0x10 ⁵ cells/well were plated in 1mL of medium without Pen/Strep and placed in the incubator for 72hr prior to lysing for experimentation. [00179] Small-scale Luciferase Assays. Ataxin-2-HiBiT cells were lysed in-well with 125µL of Nano-Glo® HiBiT Lytic Buffer, and lysate from one well was split and used for detection of both HiBiT- and FFLuc-generated luminescence. 25µL of lysate was placed in two wells of an opaque white, flat bottom 96-well assay plate (Sigma Aldrich, cat# CLS3990). For HiBiT detection, 25µL of HiBiT lytic reagent (1:25 substrate, 1:50 LgBiT) was added to the lysate (Promega, cat# N3050). For FFluc detection, 25µL of ONE-Glo Assay Buffer (Promega, cat# E6120) was added to the lysate. Plates were incubated in the dark with gentle rotation for 10 minutes, then luminescence was measured on a Tecan Spark plate reader (Tecan). For all assays, HiBiT signal was normalized to the FFluc signal for each individual well of the original transfected plate then normalized to the non-targeting/untreated control, this value is represented in bar graphs. [00180] Genome Editing. HEK293T cells (ATCC) were transfected using Lipofectamine™ CRISPRMAX™ Cas9 Transfection Reagent (Thermo Fisher Scientific, cat# cmax00003), TrueCut Cas9 Protein V2 (Thermo Fisher Technology, cat# A36497), purified sgRNA and ssDNA (IDT).72 hr later, cells were lifted and re-plated at a density of <1 cell/well in a 96-well plate. Wells were grown to confluency and split onto an additional plate. A HiBiT assay was performed on the additional plate as a preliminary screen for successful knock-in. The wells with HiBiT signal above the negative control (unedited cells) were maintained and confirmed for knock-in by Sanger sequencing. For firefly luciferase integration, the successful clone was transduced with lentivirus using pLenti CMV V5-LUC Blast (Addgene, cat# w567-1), followed by blasticidin selection. Transduced cells were pooled and saved for future experimentation. [00181] Immunoblotting. Cells were lysed in RIPA buffer (Sigma Aldrich, cat# R0278) supplemented with Complete mini protease inhibitor tablet (EMD Millipore, cat# 11836170001) and clarified by centrifugation at 21,000 x g for 15 minutes. Protein concentration was measured by BCA protein assay (Thermo Fisher Scientific, cat# 23225). Lysates were diluted to equal protein concentration in 1X NuPAGE® LDS Sample Buffer (Life Technologies, cat# NP0008). Lysates were boiled at 70°C for 10 minutes, then loaded on a NuPAGE® Novex® 4-12% Bis-Tris Protein gel (Life Technologies, cat# NP0321). Protein was transferred onto a nitrocellulose membrane (Bio-Rad, cat# 162-0115) at 4°C for 1hr and 45 minutes in 1X NuPAGE® Transfer Buffer (Life Technologies, cat# NP0006-1). Blocking and antibody incubation was performed in 2% BSA (Sigma Aldrich, cat# A7906) in PBS + 0.1% tween-20 (PBST). Washes were performed in PSBT. Primary antibodies were used at 1:1000, this includes: ataxin-2 antibody (Novus, cat# NBP1- 90063), Tuj1 antibody (BioLegend, cat# 802001), actin antibody (EMD Millipore, cat# MAB1501), RTN4/NoGo-Receptor antibody (Abcam, ab184556), and GAPDH antibody (Sigma Aldrich, cat# G8795). Goat anti-Rabbit HRP (Life Technologies, cat# 31462) or goat anti-mouse HRP (Thermo Fisher Scientific, cat# 62-6520) secondary antibodies were used at 1:5000. Membranes were developed in ECL Prime (Sigma Aldrich, cat# GERPN2232), and imaged on a Bio-Rad ChemiDoc XRS+ imager (BioRad). HiBiT-based immunoblotting was performed according to the Nano-Glo® HiBiT Blotting System protocol (Promega, cat# n2410). [00182] For mouse cortex, male and female mice at P20 were sacrificed for tissue harvesting. Ice cold RIPA buffer with protease inhibitor was added and tissue was homogenized using a motorized pestle. Crude lysates were rocked at 4°C for 30 minutes, passed through a homogenization column (Qiagen, cat# 79656), and centrifuged at 21,000 x g for 15 minutes. Protein was quantified in the clarified supernatant and prepared for immunoblotting as above. [00183] Whole-genome siRNA screen. The whole-genome siRNA screen was performed in the High-Throughput Bioscience Center (HTBC) at Stanford University. Briefly, we used the Dharmacon Human Genome siARRAY library (cat# G-005000-025) to target 21,121 genes individually in a single well of a 384-well plate with 4 pooled siRNAs. All siRNA pools were tested in duplicate for both FFluc and HiBiT on 4 separate plates. Each plate had three controls: siTOX control siRNA, nontargeting control siRNA, and ATXN2 siRNA (Horizon Discovery, cat# L-011772-00) as a toxicity, negative, and positive control, respectively. All siRNAs were reverse transfected using 10µL of Opti-MEM, 0.075µL/well of Dharmafect 1, and 10µL siRNA (final concentration of 50nM). Cells were seeded at 1000 cells/well in 30µL of media (as above without Pen/Strep) in solid white 384-well plates, ^{then placed in a 37°C} incubator with 5% CO ² . After 3 days, plates were removed from the _{incubator. HiBiT lytic} reagent was made by diluting Nano-Glo® HiBiT Lytic Substrate (1:50) and LgBiT Protein (1:100) in Nano-Glo® HiBiT Lytic Buffer. For HiBiT detection, 10 µL of HiBiT lytic reagent was dispensed into wells with a Multidrop Reagent Dispenser (Thermo Scientific), and rapidly shook for 15 seconds. For FFluc detection, 10µL of ONE-Glo Assay Buffer was dispensed into wells and rapidly shook for 15 seconds. Luminescence was read on a Tecan Infinite M1000 Pro (Tecan). [00184] Z-scores were calculated for each siRNA replicate using the in-plate standard deviation, then averaged for both HiBiT and FFluc conditions respectively. The average Z- scores were used to filter for primary screen hits. siRNAs were only considered if they had an average FFluc Z-score greater than -1, this cutoff removed any siRNA treatment that resulted in FFluc levels decreased more than one standard deviation from the mean. Since directionality of effect matters specifically when searching for a treatment that decreases ataxin-2, we implemented this cutoff for FFluc to ensure that our negative control was not similarly affected indicating a global and non-specific effect on the treated cells. siRNAs were categorized as negative regulators of ataxin-2 expression if they had an average HiBiT Z-score less than - 1.65.102 of these were retested in a secondary screen by reselecting siRNAs from the original library stock. The same experimental parameters applied, except for the performance of a single replicate for FFluc detection. High confidence hits were chosen if they had a greater than 30% decrease in average HiBiT levels relative to the non- targeting siRNA control run in parallel on the same plate. High confidence hits were ranked by average HiBiT Z-score, then were filtered further to determine the most optimal therapeutic target. [00185] These were filtered out if they had an average gene effect less than or equal to -1 as determined by DEMETR2 or CERES (depmap.org). Either measure shows the essentiality of a given gene across all cell lines tested for RNAi or CRISPR/Cas9 knockout respectively, where -1 is the median score for all essential genes and a score of 0 suggests the gene has no effect on survival in the cell lines tested. While such measures were developed to test genetic dependencies in cancer cell lines, we reasoned that implementing a cutoff of -1, indicating a “common essential” gene—would remove genes with the potential to cause toxicity in neural tissues or off-target toxicity elsewhere, making it an undesirable therapeutic target. The resulting hits were further filtered if they had a corresponding GTEx cortical pTPM less than 15. [00186] Lentivirus production. HEK293T cells were grown on 10cm culture dishes to 80-90% confluency. Cells were transfected using Lipofectamine 3000. Briefly, 10µg of shRNA vector (Mission® shRNA, Sigma Aldrich), 2.9µg pRSV-REV, 5.8µg pMDLg/pRRE, 3.5µg pMD2.G, and 40µL of P3000 was added to 1mL of Opti-MEM. This was combined with another 1mL of Opti-MEM with 40µL of Lipofectamine 3000. This mixture was incubated at room temperature for 10 minutes then added to cells in media without antibiotics.48hr after transfection, media was removed from cells, passed through a 0.45µm PES filter, and combined with Lenti-X concentrator (Takara, cat# 631232). The mixture was incubated over night at 4°C. This was centrifuged at 1,500 x g for 45 minutes at 4°C. The pellet was resuspended in 1mL Neurobasal Medium (Life Technologies, cat # 21103-049), 50µL was added directly to cells for transduction. [00187] Primary neuron culture. Animals were bred, cared for, and experimented on as approved by the Administrative Panel of Laboratory Animal Care (APLAC) of Stanford University. Time-pregnant C57BL/6 mice were procured from Charles River Labs. Mouse embryos were removed at E16.5, and cortices were isolated and placed in ice cold Dissociation Media (DM; PBS without Mg ²⁺ or Ca ²⁺ , supplemented with 0.6% glucose, 10mM HEPES, and Pen/Strep). Neurons were dissociated with the Papain Dissociation System (Worthington Biochemical Corporation, cat# LK003153). Cells were seeded on Poly-L-lysine (Sigma Aldrich, cat# P4832) coated 24-well plates at a density of 350,000cells/well. They were grown in Neurobasal media supplemented with B-27 at 1:50 (Life Technologies, cat# 17504-044), Glutamax at 1:100 (Invitrogen, cat# 35050-061) and Pen/Strep. ^{Neurons were maintained in} a 37°C incubator with 5% CO2 with half media changes every 4 to 5 _days. [00188] At DIV 5, neurons were transduced with virus as above (Mission® shRNA, mouse RTN4R: TRCN0000436683).24hr later, a half media change was performed. Neurons were maintained for 12 days after transduction prior to harvesting for experimentation. For caspase activity assays, this was followed by re-treatment with lentivirus expressing GFP or TDP-43 (Maor-Nof et al., 2021). Three or five days later, cells were lysed and the Caspase-Glo 3/7 assay (Promega, cat# G8090) was performed according to manufacturer protocol. For NEP1- 40 (Tocris, cat# 1984) treatment, 1mg of NEP1-40 was diluted in 21.62µL of DMSO and 843.2µL of nuclease-free water (Thermo Fisher Scientific, cat# AM9937) to a working concentration of 250µM. The peptide was added to the final concentration specified along with vehicle (0µM). Cells were maintained for 48hr prior to experimentation. [00189] For microfluidics chamber experiments, primary neurons were isolated as above and plated on one side of a Poly-D-lysine coated microfluidics chamber (Xona Microfluidics, cat# XC450) with a microchannel length of 450µm at a density of 200,000cells/chamber. Media was changed the next day, then half-changed every 3 days following. Lentivirus was added to the somatic compartment as above, then maintained for 12 days prior to axotomy. Vacuum- assisted axotomy was achieved by complete aspiration of media from the axonal compartment/inner chamber, allowing for an air bubble to dislodge and shear axons(Tong et al., 2015). Media was replaced and completely aspirated a second time. Media was replaced carefully to prevent the inclusion of any air bubbles in the inner chamber. A half media change was performed the next day. Neurons were allowed to regrow axons for a total of 48hr prior to fixation. [00190] iNeuron culture. We induced neuron differentiation in human iPSC-derived neurons (iNeurons) using a previously established protocol with a Tet-On induction system that allows expression of the transcription factor NGN2(Bieri et al., 2019). Briefly, iPS cells were maintained with mTeSR1 medium (Stemcell Technologies, cat# 85850) on Matrigel (Fisher Scientific, cat# CB-40230). On the next day of passage, NGN2 was expressed by adding doxycycline (2µg/ml) and selection with puromycin (2µg/ml) for rapid and highly efficient iNeuron induction. Three days after induction, iNeurons were dissociated and grown in Neurobasal medium containing N-2 supplement (Gibco, cat# 17502048), B-27 supplement, BDNF (R&D Systems) and GDNF (R&D Systems) on Matrigel-coated plates. [00191] At 7 days post neural induction, iNeurons were transduced with virus as above (Mission® shRNA, human RTN4R: TRCN0000061558).24hr later, a half media change was performed. iNeurons were maintained for 3 days before being re-transduced with a half dose of virus, then maintained for another 5 days prior to harvesting for experimentation. For NEP1- 40 treatment, 1mg of NEP1- 40 was diluted as above. The peptide was added at 7 days post induction to the final concentration specified along with vehicle (0µM). Cells were maintained for 48hr prior to lysis. [00192] Immunocytochemistry and fluorescence microscopy. Cells were fixed for 10 minutes in a solution of 4% paraformaldehyde/4% sucrose in PBS-MC (PBS with 1mM MgCl ₂ and 0.1 mM CaCl ₂ ). Then cells were washed in PBS-MC, and permeabilized for 10 minutes in 0.1% Triton-X in PBS-MC. Cells were blocked in 2% BSA for an hour, then incubated in primary antibody for at least 2 hours at room temperature [ataxin-2 (Novus), MAP2 (Synaptic Systems, cat# 188004), Tuj1 (BioLegend, cat# 802001), NeuN (EMD Millipore, cat# MAB377)]. Cells were washed 3 times with PBS-MC, followed by incubation in species-specific Alexa Fluor®- labeled secondary antibody (Thermo Fisher Scientific) for 1 hour at 1:1000. Cells were subsequently washed and placed in ProLong Gold Antifade with DAPI (Thermo Fisher Scientific, cat# P36931), and imaged using a Leica DMI6000B fluorescent microscope. [00193] Images were processed in ImageJ. For neuronal expression, individual MAP2 labeled soma were selected as regions of interest (ROIs), in which ataxin-2 fluorescence was measured and averaged within each frame. This was performed for 4 frames per biological replicate (4 replicates for the NEP1-40 treatment and 3 for the vehicle), totaling 16 frames for the NEP1-40 condition and 12 for the vehicle. For stress granule analysis, stress granules were automatically determined based on shape and size using the Analyze Particles function in ImageJ in the G3BP channel. Each stress granule was made into an ROI in which TDP-43 fluorescence was measured and averaged for every stress granule in the frame. This was performed for 6 frames per biological duplicate, totaling 12 frames per condition. For axonal regrowth after axotomy, entire axonal compartments were imaged for three microfluidics chambers per shRNA condition (9 total). A grid was superimposed onto each image with demarcations every 15µm after the end of the microchannels. Regenerating neurites were surveyed beginning 75µm from the end of the microchannel before which individual neurites are difficult to parse and there is a build-up of sheared neurites without the presence of growth cones. The length of every Tuj1-labeled neurite with a growth cone was determined by their crossing point on the grid and binned into lengths. Neurites with punctate Tuj1 staining were excluded from analysis, as these neurites were likely undergoing degeneration. The average of all neurites from each condition was taken. [00194] RNA Quantification and Sequencing. Cells were reverse transfected with siRNA in 12- well plates as described above. RNA was isolated using the PureLink® RNA Mini Kit according to the kit protocol with DNase digestion (Thermo Fisher Scientific, cat# 12183025).500ng of RNA was used to make cDNA using the Applied Biosystems High-Capacity cDNA Reverse Transcription kit (Thermo Fisher Scientific, cat# 4368813). For RNA sequencing, polyA- selected libraries were prepared in biological duplicate for each shRNA condition using the TruSeq Stranded mRNA kit from Illumina and sequenced on a HiSeq 4000 (Illumina) with paired end, 75 nucleotide-long reads. GEO accession number GSE200530. qPCR was performed in a 20µL reaction using TaqMan™ Universal Master Mix II (Thermo Fisher Scientific, cat# 4440040) and 25ng of RNA. 1µL of 20X TaqMan gene-specific expression assay was added to the reaction (Thermo Fisher Scientific; human ATXN2: Hs00268077_m1, human ACTB: Hs01060665_g1, human RTN4R: Hs00368533_m1, mouse ATXN2:Mm00485932_m1, mouse GAPDH:Mm99999915_g1, mouse RTN4R: Mm00452228_m1). All conditions were run in technical triplicates that were averaged to account for each of the biological triplicates. Thermocycler was programmed according to the suggested protocol. Relative expression was calculated using the ΔΔCt method. [00195] Statistical analyses. Statistical analyses were performed in GraphPad Prism v.9, except the screen data calculations, which was performed in MATLAB (MathWorks). An unpaired Student’s t-test (two tailed) with a 95% confidence interval (CI) was performed for all assays comparing two experimental groups. A two-way analysis of variance (ANOVA) with a 95% CI was performed for the HiBiT assays with multiple siRNA conditions compared to respective non-targeting controls run in parallel and siRNA/drug treatment. A one-way ANOVA with multiple comparisons was performed for all other experiments with more than two experimental conditions. A Fisher’s LSD test was performed for the NEP1-40 treated HiBiT assay. A Dunnett’s multiple comparisons test was performed for all others. All bar graphs show the mean ± SEM. All samples were randomly assigned to experimental groups. No statistical methods were used to predetermine sample sizes.

List of High Confidence Hits. % HiBiT signal relative to control was calculated from data collected in the secondary screen. Two biological replicates were performed for HiBiT signal and averaged and then normalized to the average signal from the non-targeting control wells run in parallel. Table 2: [00196] 2013. The Genotype-Tissue Expression (GTEx) project. Nat Genet, 45, 580-5. [00197] AKBIK, F. V., BHAGAT, S. M., PATEL, P. R., CAFFERTY, W. B. & STRITTMATTER, S. M.2013. Anatomical plasticity of adult brain is titrated by Nogo Receptor 1. Neuron, 77, 859- 66. [00198] ANDREEV, D. E., O'CONNOR, P. B., FAHEY, C., KENNY, E. M., TERENIN, I. M., DMITRIEV, S. E., CORMICAN, P., MORRIS, D. W., SHATSKY, I. N. & BARANOV, P. V.2015. Translation of 5' leaders is pervasive in genes resistant to eIF2 repression. Elife, 4, e03971. [00199] ANDRUSIAK, M. G., SHARIFNIA, P., LYU, X., WANG, Z., DICKEY, A. M., WU, Z., CHISHOLM, A. D. & JIN, Y. 2019. Inhibition of Axon Regeneration by Liquid-like TIAR-2 Granules. Neuron, 104, 290-304.e8. [00200] BAKTHAVACHALU, B., HUELSMEIER, J., SUDHAKARAN, I. P., HILLEBRAND, J., SINGH, A., PETRAUSKAS, A., THIAGARAJAN, D., SANKARANARAYANAN, M., MIZOUE, L., ANDERSON, E. N., PANDEY, U. B., ROSS, E., VIJAYRAGHAVAN, K., PARKER, R. & RAMASWAMI, M.2018. RNP-Granule Assembly via Ataxin-2 Disordered Domains Is Required for Long- Term Memory and Neurodegeneration. Neuron, 98, 754-766 e4. [00201] BECKER, L. A., HUANG, B., BIERI, G., MA, R., KNOWLES, D. A., JAFAR-NEJAD, P., MESSING, J., KIM, H. J., SORIANO, A., AUBURGER, G., PULST, S. M., TAYLOR, J. P., RIGO, F. & GITLER, A. D. 2017. Therapeutic reduction of ataxin-2 extends lifespan and reduces pathology in TDP-43 mice. Nature, 544, 367-371. [00202] BHAGAT, S. M., BUTLER, S. S., TAYLOR, J. R., MCEWEN, B. S. & STRITTMATTER, S. M. 2016. Erasure of fear memories is prevented by Nogo Receptor 1 in adulthood. Mol Psychiatry, 21, 1281-9. [00203] BIERI, G., BRAHIC, M., BOUSSET, L., COUTHOUIS, J., KRAMER, N. J., MA, R., NAKAYAMA, L., MONBUREAU, M., DEFENSOR, E., SCHÜLE, B., SHAMLOO, M., MELKI, R. & GITLER, A. D. 2019. LRRK2 modifies α-syn pathology and spread in mouse models and human neurons. Acta Neuropathol, 137, 961-980. [00204] BOEYNAEMS, S. & GITLER, A. D.2019. Axons Gonna Ride 'til They Can't No More. Neuron, 104, 179-181. [00205] BROS-FACER, V., KRULL, D., TAYLOR, A., DICK, J. R., BATES, S. A., CLEVELAND, M. S., PRINJHA, R. K. & GREENSMITH, L.2014. Treatment with an antibody directed against Nogo-A delays disease progression in the SOD1G93A mouse model of Amyotrophic lateral sclerosis. Hum Mol Genet, 23, 4187-200. [00206] BROWN, A. L., WILKINS, O. G., KEUSS, M. J., HILL, S. E., ZANOVELLO, M., LEE, W. C., BAMPTON, A., LEE, F. C. Y., MASINO, L., QI, Y. A., BRYCE-SMITH, S., GATT, A., HALLEGGER, M., FAGEGALTIER, D., PHATNANI, H., NEWCOMBE, J., GUSTAVSSON, E. K., SEDDIGHI, S., REYES, J. F., COON, S. L., RAMOS, D., SCHIAVO, G., FISHER, E. M. C., RAJ, T., SECRIER, M., LASHLEY, T., ULE, J., BURATTI, E., HUMPHREY, J., WARD, M. E. & FRATTA, P. 2022. TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A. Nature, 603, 131- 137. [00207] CHIVATAKARN, O., KANEKO, S., HE, Z., TESSIER-LAVIGNE, M. & GIGER, R. J. 2007. The Nogo-66 receptor NgR1 is required only for the acute growth cone-collapsing but not the chronic growth-inhibitory actions of myelin inhibitors. J Neurosci, 27, 7117-24. [00208] CHONG, Z. S., OHNISHI, S., YUSA, K. & WRIGHT, G. J.2018. Pooled extracellular receptor-ligand interaction screening using CRISPR activation. Genome Biol, 19, 205. [00209] DIXON, A. S., SCHWINN, M. K., HALL, M. P., ZIMMERMAN, K., OTTO, P., LUBBEN, T. H., BUTLER, B. L., BINKOWSKI, B. F., MACHLEIDT, T., KIRKLAND, T. A., WOOD, M. G., EGGERS, C. T., ENCELL, L. P. & WOOD, K. V.2016. NanoLuc Complementation Reporter Optimized for Accurate Measurement of Protein Interactions in Cells. ACS Chem Biol, 11, 400- 8. [00210] DOMENICONI, M., CAO, Z., SPENCER, T., SIVASANKARAN, R., WANG, K., NIKULINA, E., KIMURA, N., CAI, H., DENG, K., GAO, Y., HE, Z. & FILBIN, M.2002. Myelin- associated glycoprotein interacts with the Nogo66 receptor to inhibit neurite outgrowth. Neuron, 35, 283-90. [00211] ELDEN, A. C., KIM, H. J., HART, M. P., CHEN-PLOTKIN, A. S., JOHNSON, B. S., FANG, X., ARMAKOLA, M., GESER, F., GREENE, R., LU, M. M., PADMANABHAN, A., CLAY- FALCONE, D., MCCLUSKEY, L., ELMAN, L., JUHR, D., GRUBER, P. J., RÜB, U., AUBURGER, G., TROJANOWSKI, J. Q., LEE, V. M., VAN DEERLIN, V. M., BONINI, N. M. & GITLER, A. D. 2010. Ataxin-2 intermediate-length polyglutamine expansions are associated with increased risk for ALS. Nature, 466, 1069-75. [00212] FINK, K. L., STRITTMATTER, S. M. & CAFFERTY, W. B. 2015. Comprehensive Corticospinal Labeling with mu-crystallin Transgene Reveals Axon Regeneration after Spinal Cord Trauma in ngr1-/- Mice. J Neurosci, 35, 15403-18. [00213] FITTSCHEN, M., LASTRES-BECKER, I., HALBACH, M. V., DAMRATH, E., GISPERT, S., AZIZOV, M., WALTER, M., MULLER, S. & AUBURGER, G. 2015. Genetic ablation of ataxin-2 increases several global translation factors in their transcript abundance but decreases translation rate. Neurogenetics, 16, 181-92. [00214] FOURNIER, A. E., GRANDPRE, T. & STRITTMATTER, S. M.2001. Identification of a receptor mediating Nogo-66 inhibition of axonal regeneration. Nature, 409, 341-6. [00215] GRANDPRÉ, T., LI, S. & STRITTMATTER, S. M.2002. Nogo-66 receptor antagonist peptide promotes axonal regeneration. Nature, 417, 547-51. [00216] HE, W. & PARKER, R. 2000. Functions of Lsm proteins in mRNA degradation and splicing. Curr Opin Cell Biol, 12, 346-50. [00217] JOKIC, N., GONZALEZ DE AGUILAR, J. L., DIMOU, L., LIN, S., FERGANI, A., RUEGG, M. A., SCHWAB, M. E., DUPUIS, L. & LOEFFLER, J. P.2006. The neurite outgrowth inhibitor Nogo-A promotes denervation in an amyotrophic lateral sclerosis model. EMBO Rep, 7, 1162-7. [00218] KIM, G., GAUTIER, O., TASSONI-TSUCHIDA, E., MA, X. R. & GITLER, A. D.2020. ALS Genetics: Gains, Losses, and Implications for Future Therapies. Neuron, 108, 822-842. [00219] KIM, G., NAKAYAMA, L., BLUM, J. A., AKIYAMA, T., BOEYNAEMS, S., CHAKRABORTY, M., COUTHOUIS, J., TASSONI-TSUCHIDA, E., RODRIGUEZ, C. M., BASSIK, M. C. & GITLER, A. D.2021. Small molecule v-ATPase inhibitor Etidronate lowers levels of ALS protein ataxin-2. bioRxiv, 2021.12.20.473567. [00220] KIM, J. E., LIU, B. P., PARK, J. H. & STRITTMATTER, S. M.2004. Nogo-66 receptor prevents raphespinal and rubrospinal axon regeneration and limits functional recovery from spinal cord injury. Neuron, 44, 439-51. [00221] KOZLOV, G., TREMPE, J. F., KHALEGHPOUR, K., KAHVEJIAN, A., EKIEL, I. & GEHRING, K.2001. Structure and function of the C-terminal PABC domain of human poly(A)- binding protein. Proc Natl Acad Sci U S A, 98, 4409-13. [00222] LAGIER-TOURENNE, C., POLYMENIDOU, M. & CLEVELAND, D. W.2010. TDP-43 and FUS/TLS: emerging roles in RNA processing and neurodegeneration. Hum Mol Genet, 19, R46-64. [00223] LASTRES-BECKER, I., NONIS, D., EICH, F., KLINKENBERG, M., GOROSPE, M., KOTTER, P., KLEIN, F. A., KEDERSHA, N. & AUBURGER, G. 2016. Mammalian ataxin-2 modulates translation control at the pre-initiation complex via PI3K/mTOR and is induced by starvation. Biochim Biophys Acta, 1862, 1558-69. [00224] LIM, C. & ALLADA, R. 2013. ATAXIN-2 activates PERIOD translation to sustain circadian rhythms in Drosophila. Science, 340, 875-9. [00225] LIU-YESUCEVITZ, L., BASSELL, G. J., GITLER, A. D., HART, A. C., KLANN, E., RICHTER, J. D., WARREN, S. T. & WOLOZIN, B.2011. Local RNA translation at the synapse and in disease. J Neurosci, 31, 16086-93. [00226] MA, X. R., PRUDENCIO, M., KOIKE, Y., VATSAVAYAI, S. C., KIM, G., HARBINSKI, F., BRINER, A., RODRIGUEZ, C. M., GUO, C., AKIYAMA, T., SCHMIDT, H. B., CUMMINGS, B. B., WYATT, D. W., KURYLO, K., MILLER, G., MEKHOUBAD, S., SALLEE, N., MEKONNEN, G., GANSER, L., RUBIEN, J. D., JANSEN-WEST, K., COOK, C. N., PICKLES, S., OSKARSSON, B., GRAFF- RADFORD, N. R., BOEVE, B. F., KNOPMAN, D. S., PETERSEN, R. C., DICKSON, D. W., SHORTER, J., MYONG, S., GREEN, E. M., SEELEY, W. W., PETRUCELLI, L. & GITLER, A. D.2022. TDP-43 represses cryptic exon inclusion in the FTD-ALS gene UNC13A. Nature, 603, 124-130. [00227] MANGUS, D. A., AMRANI, N. & JACOBSON, A.1998. Pbp1p, a factor interacting with Saccharomyces cerevisiae poly(A)-binding protein, regulates polyadenylation. Mol Cell Biol, 18, 7383-96. [00228] MAOR-NOF, M., SHIPONY, Z., LOPEZ-GONZALEZ, R., NAKAYAMA, L., ZHANG, Y. J., COUTHOUIS, J., BLUM, J. A., CASTRUITA, P. A., LINARES, G. R., RUAN, K., RAMASWAMI, G., SIMON, D. J., NOF, A., SANTANA, M., HAN, K., SINNOTT-ARMSTRONG, N., BASSIK, M. C., GESCHWIND, D. H., TESSIER-LAVIGNE, M., ATTARDI, L. D., LLOYD, T. E., ICHIDA, J. K., GAO, F. B., GREENLEAF, W. J., YOKOYAMA, J. S., PETRUCELLI, L. & GITLER, A. D.2021. p53 is a central regulator driving neurodegeneration caused by C9orf72 poly(PR). Cell, 184, 689-708.e20. [00229] MCFARLAND, J. M., HO, Z. V., KUGENER, G., DEMPSTER, J. M., MONTGOMERY, P. G., BRYAN, J. G., KRILL-BURGER, J. M., GREEN, T. M., VAZQUEZ, F., BOEHM, J. S., GOLUB, T. R., HAHN, W. C., ROOT, D. E. & TSHERNIAK, A.2018. Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration. Nature Communications, 9, 4610. [00230] MCGEE, A. W., YANG, Y., FISCHER, Q. S., DAW, N. W. & STRITTMATTER, S. M. 2005. Experience-driven plasticity of visual cortex limited by myelin and Nogo receptor. Science, 309, 2222-6. [00231] MEYERS, R. M., BRYAN, J. G., MCFARLAND, J. M., WEIR, B. A., SIZEMORE, A. E., XU, H., DHARIA, N. V., MONTGOMERY, P. G., COWLEY, G. S., PANTEL, S., GOODALE, A., LEE, Y., ALI, L. D., JIANG, G., LUBONJA, R., HARRINGTON, W. F., STRICKLAND, M., WU, T., HAWES, D. C., ZHIVICH, V. A., WYATT, M. R., KALANI, Z., CHANG, J. J., OKAMOTO, M., STEGMAIER, K., GOLUB, T. R., BOEHM, J. S., VAZQUEZ, F., ROOT, D. E., HAHN, W. C. & TSHERNIAK, A. 2017. Computational correction of copy number effect improves specificity of CRISPR– Cas9 essentiality screens in cancer cells. Nature Genetics, 49, 1779- 1784. [00232] MONTANI, L., GERRITS, B., GEHRIG, P., KEMPF, A., DIMOU, L., WOLLSCHEID, B. & SCHWAB, M. E. 2009. Neuronal Nogo-A modulates growth cone motility via Rho- GTP/LIMK1/cofilin in the unlesioned adult nervous system. J Biol Chem, 284, 10793-807. [00233] NEUWALD, A. F. & KOONIN, E. V.1998. Ataxin-2, global regulators of bacterial gene expression, and spliceosomal snRNP proteins share a conserved domain. J Mol Med (Berl), 76, 3-5. [00234] NONHOFF, U., RALSER, M., WELZEL, F., PICCINI, I., BALZEREIT, D., YASPO, M. L., LEHRACH, H. & KROBITSCH, S.2007. Ataxin-2 interacts with the DEAD/H-box RNA helicase DDX6 and interferes with P-bodies and stress granules. Mol Biol Cell, 18, 1385-96. [00235] NUSSBACHER, J. K., TABET, R., YEO, G. W. & LAGIER-TOURENNE, C. 2019. Disruption of RNA Metabolism in Neurological Diseases and Emerging Therapeutic Interventions. Neuron, 102, 294-320. [00236] PAUL, S., DANSITHONG, W., FIGUEROA, K. P., SCOLES, D. R. & PULST, S. M. 2018. Staufen1 links RNA stress granules and autophagy in a model of neurodegeneration. Nat Commun, 9, 3648. [00237] PAULSON, H. L., SHAKKOTTAI, V. G., CLARK, H. B. & ORR, H. T. 2017. Polyglutamine spinocerebellar ataxias - from genes to potential treatments. Nat Rev Neurosci, 18, 613- 626. [00238] RICHING, K. M., MAHAN, S., CORONA, C. R., MCDOUGALL, M., VASTA, J. D., ROBERS, M. B., URH, M. & DANIELS, D. L.2018. Quantitative Live-Cell Kinetic Degradation and Mechanistic Profiling of PROTAC Mode of Action. ACS Chem Biol, 13, 2758-2770. [00239] SATO, Y., IKETANI, M., KURIHARA, Y., YAMAGUCHI, M., YAMASHITA, N., NAKAMURA, F., ARIE, Y., KAWASAKI, T., HIRATA, T., ABE, T., KIYONARI, H., STRITTMATTER, S. M., GOSHIMA, Y. & TAKEI, K. 2011. Cartilage acidic protein-1B (LOTUS), an endogenous Nogo receptor antagonist for axon tract formation. Science, 333, 769-73. [00240] SCHWAB, M. E.2010. Functions of Nogo proteins and their receptors in the nervous system. Nat Rev Neurosci, 11, 799-811. [00241] SCHWAB, M. E. & STRITTMATTER, S. M. 2014. Nogo limits neural plasticity and recovery from injury. Curr Opin Neurobiol, 27, 53-60. [00242] SCOLES, D. R., MEERA, P., SCHNEIDER, M. D., PAUL, S., DANSITHONG, W., FIGUEROA, K. P., HUNG, G., RIGO, F., BENNETT, C. F., OTIS, T. S. & PULST, S. M.2017. Antisense oligonucleotide therapy for spinocerebellar ataxia type 2. Nature, 544, 362-366. [00243] SCOLES, D. R. & PULST, S. M.2018. Spinocerebellar Ataxia Type 2. Adv Exp Med Biol, 1049, 175- 195. [00244] TAYLOR, J. P., BROWN, R. H., JR. & CLEVELAND, D. W.2016. Decoding ALS: from genes to mechanism. Nature, 539, 197-206. [00245] THOMAS, R., FAVELL, K., MORANTE-REDOLAT, J., POOL, M., KENT, C., WRIGHT, M., DAIGNAULT, K., FERRARO, G. B., MONTCALM, S., DUROCHER, Y., FOURNIER, A., PEREZ-TUR, J. & BARKER, P. A.2010. LGI1 is a Nogo receptor 1 ligand that antagonizes myelin-based growth inhibition. J Neurosci, 30, 6607-12. [00246] TONG, Z., SEGURA-FELIU, M., SEIRA, O., HOMS CORBERA, A., ANTONIO, J., RÍO, J., ADE, J. & SAMITIER, J. 2015. A microfluidic neuronal platform for neuron axotomy and controlled regenerative studies. RSC Advances, 5, 0-1. [00247] WANG, J., MIAO, Y., WICKLEIN, R., SUN, Z., WANG, J., JUDE, K. M., FERNANDES, R. A., MERRILL, S. A., WERNIG, M., GARCIA, K. C. & SÜDHOF, T. C. RTN4/NoGo-receptor binding to BAI adhesion-GPCRs regulates neuronal development. Cell. [00248] WANG, K. C., KIM, J. A., SIVASANKARAN, R., SEGAL, R. & HE, Z.2002. P75 interacts with the Nogo receptor as a co-receptor for Nogo, MAG and OMgp. Nature, 420, 74-8. [00249] WANG, X., DUFFY, P., MCGEE, A. W., HASAN, O., GOULD, G., TU, N., HAREL, N. Y., HUANG, Y., CARSON, R. E., WEINZIMMER, D., ROPCHAN, J., BENOWITZ, L. I., CAFFERTY, W. B. & STRITTMATTER, S. M. 2011. Recovery from chronic spinal cord contusion after Nogo receptor intervention. Ann Neurol, 70, 805-21. [00250] WANG, X., ZHOU, T., MAYNARD, G. D., TERSE, P. S., CAFFERTY, W. B., KOCSIS, J. D. & [00251] STRITTMATTER, S. M. 2020. Nogo receptor decoy promotes recovery and corticospinal growth in non-human primate spinal cord injury. Brain, 143, 1697-1713. [00252] YANG, Y. S., HAREL, N. Y. & STRITTMATTER, S. M.2009. Reticulon-4A (Nogo-A) redistributes protein disulfide isomerase to protect mice from SOD1-dependent amyotrophic lateral sclerosis. J Neurosci, 29, 13850-9. [00253] YOKOSHI, M., LI, Q., YAMAMOTO, M., OKADA, H., SUZUKI, Y. & KAWAHARA, Y. 2014. Direct binding of Ataxin-2 to distinct elements in 3' UTRs promotes mRNA stability and protein expression. Mol Cell, 55, 186-98. [00254] ZHANG, L., ZHENG, S., WU, H., WU, Y., LIU, S., FAN, M. & ZHANG, J. 2009. Identification of BLyS (B lymphocyte stimulator), a non-myelin-associated protein, as a functional ligand for Nogo-66 receptor. J Neurosci, 29, 6348-52. [00255] ZHANG, Y., LING, J., YUAN, C., DUBRUILLE, R. & EMERY, P. 2013. A role for Drosophila ATX2 in activation of PER translation and circadian behavior. Science, 340, 879- 82.