Methods of inhibiting m6a reader ythdf1 for treating neurodegenerative disease

Abstract

The present disclosure provides methods related to treating neurodegeneration and neuroinflammation. In particular, the present disclosure identifies YTH domain-containing family protein 1 (YTHDF1) as a novel therapeutic target for Alzheimer's disease. Embodiments of the present disclosure provide methods of therapy for neurodegenerative disease that involve inhibiting YTHDF1 to induce attenuation of chronic neuroinflammation.

Description

[0001]Docket No.: 11001-216WO1 METHODS OF INHIBITING M6A READER YTHDF1 FOR TREATING NEURODEGENERATIVE DISEASE CROSS REFERENCE TO RELATED APPLICATIONS This application claims the benefit of U.S. Provisional Patent Application 63 / 560,001, filed March 1, 2024, the disclosure of which is hereby incorporated by reference in its entirety. GOVERNMENT SUPPORT CLAUSE This invention was made with government support under Grant Nos. AG077610, AG079141, and AG056061 awarded by the National Institutes of Health. The government has certain rights in the invention. FIELD OF THE INVENTION The present disclosure provides methods for treating or preventing neurodegeneration and neuroinflammation, including but not limited to a subject at risk for or having Alzheimer’s disease, comprising inhibiting YTH domain-containing family protein 1 (YTHDF1). INCORPORATION BY REFERENCE The contents of the xml file named “10110-216WO1_ST26” which was created on March 3, 2025, and is 11,261 bytes in size, are hereby incorporated by reference in their entirety. BACKGROUND OF THE INVENTION N6-methyladenosine (m6A) is the most abundant epigenetic transcriptional modification in eukaryotic mRNA and non-coding RNA. The dynamic and reversible m6A modification adds a new dimension to the control of gene expression and has been documented to play essential roles in regulating alternative splicing, RNA stability, and translation. Elucidating the significance of epitranscriptomic regulation of gene expression in memory and brain diseases is a nascent field of study. Emerging studies predict that mRNA methylation could be potentially involved in neuronal mechanisms involved in Alzheimer's disease (AD). Nevertheless, very little is experimentally known about the impact of RNA m6A modification on AD pathophysiology. The m6A RNA modification is initiated by methylases, removed by RNA demethylases, and recognized by m6A- binding proteins, namely so-called m6A writers, erasers, and readers. ^ Docket No.: 11001-216WO1 The misfolding of tau protein oligomers and the resulting aggregation of misfolded tau in neuronal tangles is a pathological hallmark of AD. A recent study linked tau oligomers with stress granules, which recruit RNA-binding proteins and the m6A transcripts and contribute to tau oligomer toxicity in the cytoplasm. The assembly of such complexes, which is increased in the brain tissue of individuals with and mouse models of AD, is part of a stress response that includes the formation of stress granules and reduced protein synthesis. Nevertheless, very little is experimentally known about the impact of m6A RNA- YTHDF1 regulation of gene expression on AD pathophysiology. There is an urgent need for new therapeutics for the treatment of Alzheimer's disease and other neurodegenerative disorders. SUMMARY OF THE INVENTION It has been surprisingly and unexpectedly discovered that YTH domain-containing family protein 1 (YTHDF1) promotes neuroinflammation and tau aggregation in Alzheimer’s disease, and inhibition of YTHDF1 is a novel therapeutic target for the treatment of Alzheimer’s disease. Alterations in the levels of several m6A regulators in human AD and m6A RNA methylation in mouse AD models have previously been reported. Emerging evidence implicates essential functions for YTHDF1, the classical reader protein that binds to m6A- modified transcripts to promote their translation, in gene expression relevant to AD pathophysiology and neuroinflammatory responses. Notably, there is a significant increase in YTHDF1 expression in AD. To study the role of m6A methylation as it relates to tau pathogenesis, a Ythdf1 (a cytoplasmic m6A reader gene) a new mouse line (PS19:Ythdf1- / -) was generated using a previously described knockout and PS19 tauopathy mice as described herein (see, e.g., FIGs. 9-10, 11A-11B, 12 of Example 5). Compared with PS19 mice, the 9-month-old PS19:Ythdf1- / - mice showed higher soluble phosphorylated Tau in high-salt RAB buffer and lower insoluble phosphorylated Tau extracted in 70% formic acid (see FIG. 15-16 of Example 8). Loss of YTHDF1 reduced the hyperactivity in the PS19 tauopathy mouse model and ameliorated the working memory deficits in PS19 mice in the novel object recognition test (see, e.g., FIG.17A- 17C of Example 9). From bulk RNAseq results, the deletion of YTHDF1 in the PS19 tauopathy mouse model was found to suppress the inflammatory responses as evidenced by gene ontology representation of the downregulated differentially expressed genes (e.g., Ccl6, Cst7, Itgax, ^ Docket No.: 11001-216WO1 Ccl4, and Clec7a) (see, e.g., FIG. 13A-13E of Example 6). Next, enhanced crosslinking and immunoprecipitation (eCLIP) approaches were employed to identify YTHDF1 targets. This analysis identified Nceh1, Timp2, and Egr1 among the 382 methylated mRNA regions recognized by YTHDF1 (see, e.g., FIG.18-25, 26A-26B of Example 10), which could regulate the Tau-mediated neuroinflammatory response. While not wishing to be bound by any one theory, these findings indicate that YTHDF1, an m6A reader protein, plays an essential role in promoting tau pathology-related immune response in the brain. The improved methods of treatment as described herein provide a significant advance in the state of the art of treating Alzheimer’s disease and other neurodegenerative diseases. A summary of embodiments of the invention is described in further detail below. BRIEF DESCRIPTION OF THE FIGURES The accompanying drawings, which are incorporated in and constitute a part of this specification, illustrate certain examples of the present disclosure and, together with the description, serve to explain, without limitation, the principles of the disclosure. Like numbers represent the same elements throughout the figures. FIG. 1 shows components of the m6A system and their roles. The m6A RNA modification is dynamically regulated by RNA methyltransferase and demethylases and recognized by m6A-binding proteins, namely, m6A writers, erasers, and readers. FIG.2 shows YTHDF1 expression in the human brain. Immunostaining of control (left) shows predominant neuronal YTHDF1 immunostaining (green). Higher magnification images of AD brains (right), co-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ blue) reveal glial expression of YTHDF1 in addition to neurons. FIG. 3 shows Microglia express YTHDF1 in APPSAAbrain. Microglia near amyloid deposits. Staining with mAb 3D6 (^-amyloid^^^^ ^^^^!"#^^^ (green), and Iba1 in APPSAAmouse model of Alzheimer’s amyloidosis. FIG. 4 shows YTHDF1 in microglia surrounding A^ deposits in the brain of 5XFAD mouse model of Alzheimer’s amyloidosis. FIG.5A-5B show microglial YTHDF1 expression in the PS19 tauopathy mouse model. FIG. 5A shows immunostaining of PS19 mice revealed YTHDF1 (green) and p-tau staining (blue) in AT8+ neurons. FIG.5B shows YTHDF1 expression is observed in Iba1+ microglia. FIG.6 shows the staging of preclinical AD tauopathy mouse model PS19. FIG.7 shows neuronal expression of YTHDF1 in non-transgenic mice. ^ Docket No.: 11001-216WO1 FIG.8 shows neuronal expression of YTHDF1 in PS19 mice. FIG.9 shows experimental designs using the PS19:Ythdf1- / - mice as described herein. FIG. 10 shows a qPCR analysis of Ythdf1 and human MAPT expression in cohorts of mice. n=4 males and 4 females for each genotype. FIG.11A-11B show the selectivity of a newly generated YTHDF1 mAb. FIG. 11A shows YTHDF1 protein expression was visualized using specific mAb by immunoblot. FIG. 11B shows YTHDF1 protein expression was visualized using specific mAb by immunoprecipitation. FIG. 12 shows YTHDF1 protein expression was visualized using specific mAb by immunostaining. FIG. 13A-13E show YTHDF1 regulates proinflammatory genes. Pilot RNAseq data from Wt, Ythdf1- / -, PS19, and PS19:Ythdf1- / - mice. FIG.13A shows the Principal Component Analysis of the variance in the dataset. FIG.13B shows a Volcano plot analysis of differential gene expression. FIG.13C shows K-means clustering of differentially expressed genes (DEGs). FIG.13D shows GO analysis of DEG clusters by mapping them on objectively defined AD-associated domains highlighted several biological pathways, notably inflammatory response. The loss of YTHDF1 attenuates immune responses. FIG.13E shows that PS19 males show more immune-related DEGs than female mice. Deletion of YTHDF1 in PS19 suppressed the inflammatory response for both genders. The loss of YTHDF1 attenuates tau pathology-related immune response in PS19 transgenic mice at 9 months of age. FIG. 14A-14B show that YTHDF1 regulates lipopolysaccharide (LPS)-induced neuroinflammation. FIG. 14A shows YTHDF1 limits the induction of acute inflammatory response to peripheral LPS administration as visualized by the heatmap and box plots.8-month-old Wt and Ythdf1- / - mice were peripherally administered with 0.75 mg / kg LPS once. RNA was isolated 6 h after LPS administration (acute). Neuroinflammation activation was quantified by performing qPCRs against 75 representative targets selected from different gene categories: pro-inflammatory, anti-inflammatory, immune checkpoint, IFN^ response, IFN^ response, shared interferon response, LPS super-responder astrocyte, homeostatic microglia, DAM1 microglia, DAM2 microglia, CC Chemokines, CXC chemokines, and complement genes. The results are represented as a heatmap corresponding to Log2-FC (blue / white / red color scheme). ^ Docket No.: 11001-216WO1 The data were analyzed by 2-way ANOVA, and the LPS, Genotype, and LPS / Genotype interaction significance values in -Log10 are represented on the right (green shading). FIG. 14B shows YTHDF1 attenuates chronic inflammation in response to peripheral LPS administration as visualized by the heatmap and box plots.8-month-old Wt and Ythdf1- / - mice were peripherally administered with 0.75 mg / kg LPS for four consecutive days. RNA was isolated after day 4 (chronic). Neuroinflammation activation was quantified by performing qPCRs against 75 representative targets selected from different gene categories: pro- inflammatory, anti-inflammatory, immune checkpoint, IFN^ response, IFN^ response, shared interferon response, LPS super-responder astrocyte, homeostatic microglia, DAM1 microglia, DAM2 microglia, CC Chemokines, CXC chemokines, and complement genes. The results are represented as a heatmap corresponding to Log2-FC (blue / white / red color scheme). The data were analyzed by 2-way ANOVA, and the LPS, Genotype, and LPS / Genotype interaction significance values in -Log10 are represented on the right (green shading). FIG. 15 shows total tau species in RAB- and RIPA-soluble fractions and formic-acid extracts were quantified using MSD assays. n=9-11 mice per sex per genotype. FIG. 16 shows a decrease of insoluble p-tau in female Ythdf1- / - mice. P-Tau (pThr- 231) species in RAB- and RIPA-soluble fractions and formic-acid extracts were quantified using MSD assays. n=9-11 mice per sex per genotype. FIG. 17A shows that loss of YTHDF1 reduced the hyperactivity in PS19 mice. PS19:Ythdf1- / - mice behave like wild type animals rather than PS19 transgenic mice with behavioral deficits. FIG. 17B shows that 8 months of age, male mice (n=10 Wt, 9 KO, 10 PS19, 9 PS19 Ythdf1- / -) were characterized by novel object recognition test. The loss of YTHDF1 rescued working memory, which is worsened due to tau pathology in PS19 mice. FIG.17C shows that at 8 months of age, male mice (n=10 Wt, 9 KO, 10 PS19, 9 PS19 Ythdf1- / -) were characterized by elevated plus maze [left] and clasping score [right]. PS19 mice displayed hyperactivity and frequent entry into open arms of the elevated plus maze and exhibited motor deficits. The loss of YTHDF1 rescued these deficits. FIG. 18 shows the eCLIP-seq workflow. After UV-crosslinking, fractionation, and immunoisolation, the m6A-RNA fragment- YTHDF1 complexes were fractionated through NuPAGE gels. RNA fragments were used for library prep and sequencing. FIG.19 shows the Metagene plot profiles of the distribution of the modified m6A sites along the 5$UTR, coding sequence, and 3$UTR. The density mean ± SEM for each genotype ^ Docket No.: 11001-216WO1 (n=4 / genotype) is shown as a ribbon. The metagene plot shows where m6A sites preferentially occur in the transcript, highlighting the typical stop codon-proximal peak. FIG. 20 shows a sequence logo representing the top 10 consensus sequence motifs by clustering all enriched m6A peaks in all the eCLIP-seq samples in this study. FIG.21 shows an Upset plot of differentially recognized peaks in YTHDF1 eCLIP-seq between Wt and PS19 mice, called by three conventional methods.382 peaks were recognized by all three methods. FIG. 22 shows eCLIP-seq identified the YTHDF1-dependent epitranscriptomic signature induced by tau pathology in mice. For example, Nceh1, one of the anti-inflammatory DAM genes, shows significantly less binding to YTHDF1. Egr1, an essential microglial transcription factor, is upregulated in AD brains and mouse models and downregulated in the YTHDF1 recognition. FIG. 23 shows a Gene-set overlap graph of gene sets enriched in the PS19 tauopathy model. Nodes represent individual gene sets, and edges represent overlaps based on the adjusted rand index (ARI). Nodes are colored based on the significance of enrichment: darker nodes represent gene-sets enriched with more statistical significance. The sizes of the circles represent the number of genes that belong to the gene-set. Nine gene-set clusters representing biological themes are identified, containing 66, 42, 14, 27, 11, 28, 26, 13, and 102 gene-sets, respectively. FIG.24 shows Cluster annotations generated by text-mining analysis of the nine gene- sets. The font sizes in the word cloud are proportional to the frequency of each word’s appearance in the cluster. FIG. 25 shows loadings, also known as weights: The log2FC of genes belonging to gene sets in the cluster are plotted against the number of gene sets in the cluster to which the gene belongs. FIG.26A shows the exploration of m6A-YTHDF1 regulation of gene expression. The top 15 transcriptional regulators of DEG from our RNAseq dataset were queried using the TRRUST database (Transcriptional Regulatory Relationships Unraveled by Sentence-based Text mining), and the results were plotted as a Circos plot. DEGs are indicated on the left and shaded by log2 FC [Wt vs. PS19 outer annulus and PS19 vs. PS19: Ythdf1- / - inner annulus], and the TFs (red) are indicated on the right. FIG.26B shows a table listing all 17 TFs that regulate > 4 bulk RNAseq DEGs and are recognized by YTHDF1 in our eCLIP-seq dataset. FIG.27A shows the experimental design of Examples 11-13 as described herein. ^ Docket No.: 11001-216WO1 FIG.27B shows the experimental design of Example 14 as described herein. FIG.27C shows the experimental design of Example 14 as described herein. FIGs.28A-28B shows feasibility proteomics data. FIG. 28A shows the proteome coverage of YTHDF1 detected in the mouse brain by DIA proteomics. FIG. 28B shows the relative expression of YTHDF1 detected in the mouse brain by DIA proteomics. DETAILED DESCRIPTION The following description of the disclosure is provided as an enabling teaching of the disclosure in its best, currently known embodiment(s). To this end, those skilled in the relevant art will recognize and appreciate that many changes can be made to the various embodiments of the invention described herein, while still obtaining the beneficial results of the present disclosure. It will also be apparent that some of the desired benefits of the present disclosure can be obtained by selecting some of the features of the present disclosure without utilizing other features. Accordingly, those who work in the art will recognize that many modifications and adaptations to the present disclosure are possible and can even be desirable in certain circumstances and are a part of the present disclosure. Thus, the following description is provided as illustrative of the principles of the present disclosure and not in limitation thereof. Reference will now be made in detail to the embodiments of the invention, examples of which are illustrated in the drawings and the examples. This invention may, however, be embodied in many different forms and should not be construed as limited to the embodiments set forth herein. Definitions In this specification and in the claims that follow, reference will be made to many terms, which shall be defined to have the following meanings: Throughout the specification and claims, the word "comprise" and other forms of the word, such as "comprising" and "comprises," means including but not limited to, and is not intended to exclude, for example, other additives, components, integers, or steps. As used in the description and the appended claims, the singular forms "a," "an," and "the" include plural referents unless the context dictates otherwise. Thus, for example, reference to "a composition" includes mixtures of two or more such compositions, reference to "an agonist" includes mixtures of two or more such agonists and the like. ^ Docket No.: 11001-216WO1 "Optional" or "optionally" means that the subsequently described event or circumstance can or cannot occur and that the description includes instances where the event or circumstance occurs and instances where it does not. An "agonist" is a molecule that interacts with a target to cause or promote increased activation of the target. An "antagonist" is a molecule that opposes the action of an agonist. Antagonists prevent, reduce, inhibit or neutralize the activity of agonists, and antagonists also prevent, inhibit constitutive activity of a target, e.g., a target receptor, even in the absence of an identified agonist, can be reduced or reduced. Antisense, Sense, and Antigene: Double-stranded DNA (dsDNA) has two strands, a 5'— >3' strand, referred to as the plus strand, and a 3'— 5' strand (the reverse compliment), referred to as the minus strand. Because RNA polymerase adds nucleic acids in a 5'— 3' direction, the minus strand of the DNA serves as the template for the RNA during transcription. Thus, the RNA formed will have a sequence complementary to the minus strand and identical to the plus strand (except that U is substituted for T). Antisense molecules are molecules that are specifically hybridizable or specifically complementary to either RNA or the plus strand of DNA. Sense molecules are molecules that are specifically hybridizable or specifically complementary to the minus strand of DNA. Antigene molecules are either antisense or sense molecules directed to a dsDNA target. Antisense oligonucleotide: A sequence of at least about 8 nucleotides, such as about at least 10, 12, 15, 20, 30 or 50 nucleotides, wherein the sequence is from a gene sequence (such as all or a portion of a cDNA or gene sequence, or the reverse complement thereof), arranged in reverse orientation relative to the promoter sequence in a transformation vector. By "reduce" or other forms of the word, such as "reducing" or "reduction," it is meant lowering of an event or characteristic e.g., tumor growth). It is understood that this is typically in relation to some standard or expected value. In other words, it is relative, but it is not always necessary for the standard or relative value to be referred to. For example, "reduces tumor growth" means decreasing the number of tumor cells relative to a standard or a control. By "prevent" or other forms of the word, such as "preventing" or "prevention," is meant to stop a particular event or characteristic, to stabilize or delay the development or progression of a particular event or characteristic, or to minimize the chances that a particular event or characteristic will occur. Prevent does not require comparison to a control as it is typically more absolute than, for example, reduce. As used herein, something could be reduced but not prevented, but something that is reduced could also be prevented. Likewise, something could be prevented but not reduced, but something that is prevented could also be reduced. It is ^ Docket No.: 11001-216WO1 understood that where reduce or prevent are used, unless specifically indicated otherwise, the use of the other word is also expressly disclosed. As used herein, "treatment" refers to obtaining beneficial or desired clinical results. Beneficial or desired clinical results include, but are not limited to, any one or more of alleviation of one or more symptoms (such as tumor growth), diminishment of the extent of tumor growth, stabilized (i.e., not worsening) state of cell proliferation, preventing or delaying spread of tumors, delaying occurrence or recurrence of tumors, delay or slowing of tumor progression, and remission (whether partial or total). "Increase" can refer to any change that results in a higher level of gene expression, protein expression, amount of a symptom, disease, composition, condition, or activity. A substance is also understood to increase the level of the gene, the protein, the composition, or the amount of the condition when the level of the gene, the protein, the composition, or the amount of the condition is more / higher relative to the output of the level of the gene, the protein, the composition, or the amount of the condition without the substance. Also, for example, an increase can be a change in the symptoms of a disorder such that the symptoms are less than previously observed. An increase can be any individual, median, or average increase in a condition, symptom, activity, composition in a statistically significant amount. Thus, the increase can be a 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100% increase so long as the increase is statistically significant. "Decrease" can refer to any change that results in a lower level of gene expression, protein expression, amount of a symptom, disease, composition, condition, or activity. A substance is also understood to decrease the level of the gene, the protein, the composition, or the amount of the condition when the level of the gene, the protein, the composition, or the amount of the condition is less / lower relative to the output of the level of the gene, the protein, the composition, or the amount of the condition without the substance. A decrease can be any individual, median, or average decrease in a condition, symptom, activity, composition in a statistically significant amount. Thus, the decrease can be a 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100% decrease so long as the decrease is statistically significant. The term "gene" or "gene sequence" refers to the coding sequence or control sequence, or fragments thereof. A gene may include any combination of coding sequence and control sequence, or fragments thereof. Thus, a "gene" as referred to herein may be all or part of a native gene. A polynucleotide sequence as referred to herein may be used interchangeably with the term "gene”, or may include any coding sequence, non-coding sequence or control ^ Docket No.: 11001-216WO1 sequence, fragments thereof, and combinations thereof. The term "gene" or "gene sequence" includes, for example, control sequences upstream of the coding sequence (for example, the ribosome binding site). "Inhibit", "inhibiting," and "inhibition" mean to decrease an activity, response, condition, disease, or other biological parameter. This can include but is not limited to the complete ablation of the activity, response, condition, or disease. This may also include, for example, a 10% reduction in the activity, response, condition, or disease as compared to the native or control level. Thus, the reduction can be a 1, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100%, or any amount of reduction in between as compared to native or control levels. “Inhibitors” and “activators” of expression or of activity are used to refer to inhibitory or activating molecules, respectively, identified using in vitro and in vivo assays for expression or activity of a described target protein, e.g., ligands, agonists, antagonists, and their homologs and mimetics. Inhibitors are agents that, e.g., inhibit expression or bind to, partially or totally block stimulation or protease activity, decrease, prevent, delay activation, inactivate, desensitize, or down regulate the activity of the described target protein. Activators are agents that, e.g., induce or activate the expression of a described target protein or bind to, stimulate, increase, open, activate, facilitate, enhance activation or protease inhibitor activity, sensitize or up regulate the activity of described target protein (or encoding polynucleotide). Inhibition of a described target protein is achieved when the activity value relative to the control is about 80%, optionally 50% or 25, 10%, 5% or 1%. Activation of the described target protein is achieved when the activity value relative to the control is 110%, optionally 150%, optionally 200, 300%, 400%, 500%, or 1000- 3000% or more. The term "patient" refers to a human needing treatment for a neurodegenerative disease for example including but not limited to a human needing a treatment for Alzheimer’s disease. However, the term "patient" can also refer to non-human animals, preferably mammals such as dogs, cats, horses, cows, pigs, sheep, and non-human primates, among others, that need treatment. A "pharmaceutically acceptable" component is suitable for use with humans and / or animals without undue adverse side effects (such as toxicity, irritation, and allergic response) commensurate with a reasonable benefit / risk ratio. "Pharmaceutically acceptable salt" refers to a salt that is pharmaceutically acceptable and has the desired pharmacological properties. Such salts include those that may 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 alkali metals, e.g., sodium, ^ Docket No.: 11001-216WO1 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). When two acidic groups are present, a pharmaceutically acceptable salt may be a mono-acid-mono-salt or a di-^^^^^^^^^^^^^^%^^^^^^^^ there are more than two acidic groups present, some or all of such groups can be converted into salts. "Pharmaceutically acceptable excipient" refers to an excipient that is conventionally 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. A "pharmaceutically acceptable carrier" is a carrier, such as a solvent, suspending agent, or vehicle, for delivering the disclosed compounds to the patient. The carrier can be liquid or solid and is selected with the planned manner of administration in mind. Liposomes are also a type of pharmaceutical carrier. As used herein, "carrier" includes any and all solvents, dispersion media, vehicles, coatings, diluents, antibacterial and antifungal agents, isotonic and absorption delaying agents, buffers, carrier solutions, suspensions, colloids, and the like. The use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active ingredient, its use in the therapeutic compositions is contemplated. The term "therapeutically effective amount" means the amount of active compound or pharmaceutical agent that elicits the biological or medicinal response in a tissue, system, animal, or human being sought by a researcher, veterinarian, medical doctor, or other clinician. In reference to Alzheimer’s disease or another neurodegenerative, an effective amount comprises an amount sufficient to cause prevention and / or to decrease the growth rate of one or more pathological hallmarks (including but not limited to amyloid beta aggregates, oligomeric tau formation, tau aggregates, hyperphosphorylated tau species, neuroinflammation) or to prevent or delay cognitive and / or behavioral phenotypes associated with disease. In some embodiments, an effective amount is an amount sufficient to delay development of one or more pathological hallmarks or one or more cognitive and / or behavioral phenotypes. In some embodiments, an effective amount is an amount sufficient to prevent or ^ Docket No.: 11001-216WO1 delay occurrence and / or recurrence. An effective amount can be administered in one or more doses. Effective amounts of a compound or composition described herein for treating a mammalian subject can include about 0.1 to about 1000 mg / kg of body weight of the subject / day, such as from about 1 to about 100 mg / Kg / day, especially from about 10 to about 100 mg / Kg / day. The doses can be acute or chronic. A broad range of disclosed composition dosages is believed to be safe and effective. The terms “identical” or percent “identity,” in the context of two or more nucleic acids or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same (i.e., about 60% identity, preferably 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or higher identity over a specified region when compared and aligned for maximum correspondence over a comparison window or designated region) as measured using a BLAST or BLAST 2.0 sequence comparison algorithms with default parameters described below, or by manual alignment and visual inspection (see, e.g., NCBI web site or the like). Such sequences are then said to be “substantially identical.” This definition also refers to, or may be applied to, the compliment of a test sequence. The definition also includes sequences that have deletions and / or additions, as well as those that have substitutions. As described below, the preferred algorithms can account for gaps and the like. Preferably, identity exists over a region that is at least about 10 amino acids or 20 nucleotides in length, or more preferably over a region that is 10-50 amino acids or 20-50 nucleotides in length. As used herein, percent (%) nucleotide sequence identity is defined as the percentage of amino acids in a candidate sequence that are identical to the nucleotides in a reference sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity. Alignment for purposes of determining percent sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST, BLAST-2, ALIGN, ALIGN-2 or Megalign (DNASTAR) software. Appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full-length of the sequences being compared can be determined by known methods. For sequence comparisons, typically one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated, if ^ Docket No.: 11001-216WO1 necessary, and sequence algorithm program parameters are designated. Preferably, default program parameters can be used, or alternative parameters can be designated. The sequence comparison algorithm then calculates the percent sequence identities for the test sequences relative to the reference sequence, based on the program parameters. One example of an algorithm that is suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al. (1977) Nuc. Acids Res. 25:3389-3402, and Altschul et al. (1990) J. Mol. Biol. 215:403-410, respectively. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information. This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al. (1990) J. Mol. Biol. 215:403-410). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using,&^^^ ^ '^^^^^^^^ ^^( ^^'^^^^ ^^^^ )^^^^^^^^^^*^ ^^^^^^^^ ^'^^^^ &^^^ ^^)^^^^ ^&^^^^'^^^^^ ^^^^^ ^^^^^^^^%^^ +,^^ ^^^^ -^ ^)^^^^^%^ ^'^^^^ &^^^ ^^^^^^'^^^^^ ^^^^^ ^^^^ ^^^^%^^ .,^ / ^ ^^^^ amino acidsequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity 0^&^^^^^^^^^^1^^ ^^^'^^^2^^^2^^ ^^^^^^^' ^ ^^^^2^^^'^^^^^^^^^^^^3^^^^^^^^^^^^^^^ ^^^^^^^^^accumulation of one or more negative- ^'^^^^^^ ^^^^^ ^^ ^^^^^^^^^^^^ ^^^ ^^^^ ^^^^ ^&^ ^^^^^^^sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) or 10, M=5, N=-4 and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength of 3, and expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff and Henikoff (1989) Proc. Natl. Acad. Sci. USA 89:10915) alignments (B) of 50, expectation (E) of 10, M=5, N=- 4, and a comparison of both strands. The BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90:5873-5787). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is ^ Docket No.: 11001-216WO1 considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.2, more preferably less than about 0.01. Methods In some aspects, this disclosure relates to treating a subject having a neurodegenerative disease by administering to the subject a therapeutically effective amount of an inhibitor of YTH domain family member 1 (YTHDF1). In some embodiments, the neurodegenerative disease comprises Alzheimer's disease. In some embodiments, this disclosure relates to use of molecules for treating or preventing neurodegenerative diseases, including but not limited to Alzheimer’s disease. In some embodiments, provided herein are molecules (e.g., small molecule inhibitors, antisense nucleic acids, peptides, recombinant vectors, CRISPR- sgRNAs, small hairpin RNAs (shRNAs), microRNAs (miRNAs), small interfering RNAs (siRNAs), or combinations thereof) that inhibit YTHDF1. “Alzheimer's disease” or “AD” as used herein refers to all forms of dementia, identified as a degenerative and terminal cognitive disorder. The disease may be static, the result of a unique global brain injury, or progressive, resulting in a long-term decline in cognitive function due to damage or disease in the body beyond what might be expected from normal aging. Particularly, it has been identified that Alzheimer’s disease is caused by the accumulation of the beta-amyloid protein, or A^, and it has been known that the induction of the degeneration and death of nerve cells caused by the amyloid protein is involved in the mechanism of Alzheimer’s disease. The beta-amyloid protein involved in Alzheimer's has several different molecular forms that collect between neurons. One form, beta-amyloid 42, is thought to be especially toxic. As noted herein, YTHDF1 levels are increased in the brains of Alzheimer’s disease subjects. It should be understood that a treatment of Alzheimer’s disease may be a treatment of one or more of memory loss, poor judgment leading to bad decisions, loss of spontaneity and sense of initiative, repeating questions, having difficulties to organize thoughts, mood and personality changes, and / or increased anxiety and / or aggression. Methods for diagnosing or assessing a subject at risk for or having cognitive function impairment or a related condition are well-known in the art and are routinely conducted by a physician or other medical professional. For example, a variety of tests known to those skilled in the art can be used to demonstrate cognitive impairment, or the lack thereof, in a human. ^ Docket No.: 11001-216WO1 These tests include, but are not limited to, the Alzheimer's Disease Assessment Scale- cognitive subscale (ADAS-cog), the clinical global impression of change scale (CIBlC-phis scale), the Alzheimer's Disease Cooperative Study Activities of Daily Living Scale (ADCS- ADL), the*^^^^ *^^^^^^ 4^^^^^ 51^^^ ^**45^^^ ^^^^ -^ ^^)^%'^^^^^^'^ ^^2^^^^^%^ ^-^^^^^ ^^^^ 6^^^^'^^^Dementia Rating Scale (CDR), the Cambridge Neuropsychological Test Automated Battery (CANTAB), and the Sandoz Clinical Assessment-Geriatric (SC AG). In addition, cognitive function may be measured using imaging techniques such as Positron Emission Tomography (PET), functional magnetic resonance imaging (fMRI), or Single Photon Emission Computed Tomography (SPECT) to measure brain activity. In animal model systems, cognitive impairment can be measured in any number of ways known in the art, including using the Morris Water Maze or Object Recognition Task. Treatment can be indicated by one or more of mental status and neuropsychological testing indicating improvement in memory, mitigation of memory loss, and / or improvement in other thinking skills, and / or brain imaging (e.g., using magnetic resonance imaging (MRI), computerized tomography (CT), or positron emission tomography (PET)) indicating mitigation of brain shrinkage, amyloid deposits, or neurofibrillary tangles, improvement in nutrient metabolism in brain, inhibition of an increase of a YTHDF1 level in a biological sample, and / or decreasing a YTHDF1 level in a biological sample as compared with prior to treatment of the subject or as compared with the incidence of such symptom in a study population. As used herein, "alleviating a symptom" of a neurodegenerative disease is ameliorating any condition or symptom associated with the neurodegenerative disease. As compared with an equivalent untreated control, such reduction is by at least 5%, 10%, 20%, 40%, 50%, 60%, 80%, 90%, 95%, 99% or more as measured by any standard technique. In one aspect, provided herein is a method for treating a subject at risk for or having neurodegenerative disease, comprising administering a therapeutically effective amount of an inhibitor of YTH domain-containing family protein 1 (YTHDF1). In some embodiments, the neurodegenerative disease is selected from Alzheimer’s disease, amyotrophic lateral sclerosis (ALS), spinocerebellar ataxia 2 (SCA2), Parkinson’s disease, chronic traumatic encephalopathy (CTE), multiple sclerosis, depression, epilepsy, spinocerebellar ataxia type 1, Machado-Joseph Disease, Down's syndrome, Dementia puglistica, Pick's disease, progressive supranuclear palsy (PSP), Guam parkinsonism dementia complex, Fronto-temporal dementia (FTD), Cortico-Basal Degeneration (CBD), Pallido- Pontal-Nigral Degeneration, Progressive Nuclear Palsy (PNP), Parkinsonism of Chromosome 17 (FTDP-17), Dementia with Lewy bodies, Huntington's disease, Multiple System Atrophy, ^ Docket No.: 11001-216WO1 fatty liver disease (liver steatosis), al-anti-trypsin deficiency, muscle diseases, sporadic inclusion body myositis, limb girdle muscular dystrophy type 2B, prion disease, Creutzfeldt- Jakob disease, and Miyoshi myopathy. In some embodiments, the neurodegenerative disease is Alzheimer’s disease. In another aspect, provided herein is a method for treating a subject at risk for or having Alzheimer's disease, comprising administering a therapeutically effective amount of an inhibitor of YTHDF1. In another aspect, provided herein is a method for treating a subject at risk for or having a neurodegenerative disease, comprising: ^^^^^^^^^^^^^^^^^^^)^^^&^^^^^^^^^ ^7^'^^^^^^^^^^^^'^^^^^ whether one or more transcripts comprising or polypeptides involved in Disease-Associated Astrocyte (DAA) / Disease- Associated Microglia (DAM), are differentially expressed in the^^^)^^^ '^^)^^^^^^^^^^ ^^ '^^^^^^^ ^^^)^^^^ ^^^^ ^^^^^^ if one or more transcripts comprising orpolypeptides encoded by the genes in step ii) are differentially expressed, then administering a therapeutically effective amount of an inhibitor of YTHDF1. The term “disease-associated astrocyte (DAA)” as used herein refers to differentially expressed transcripts or polypeptides in astrocytes having GFAP high expression. Transcripts and / or polypeptides within this category are highlighted, for example, in Habib, N. et al. Disease-associated astrocytes in Alzheimer's disease and aging. Nat Neurosci. 2020 8 ^^9^^^^:;,^-706, incorporated herein by reference. The term “Disease- Associated Microglia (DAM)” as used herein refers to differentially expressed transcripts or polypeptides in immune cells expressing typical microglial markers, including but not limited to IBA1. Transcripts and / or polypeptides within this category are highlighted, for example, in Rangaraju, S. Identification and therapeutic modulation of a pro- inflammatory subset of disease-associated-microglia in Alzheimer's disease. Mol -^ ^^^^^^^^^ / ^9,^<^*^%^9^^^^^^^:9=, incorporated herein by reference. In another aspect, provided herein is a method for treating a subject at risk for or having a neurodegenerative disease, comprising: ^^^^^^^^^^^^^^^^^^^)^^^&^^^^^^^^^ ^7^'^^^^^^^^^^^^'^^^^^ whether one or more transcripts comprising or polypeptides encoded by a human homolog of Muc1, Adamts1, Loxl1, Eln, Lox, Thsd4, Serpine1, Il33, Ptger4, Epha6, Rtn4rl2, Prkcg, Kcnip2, Cpne6, Grm2, Rgs14, Ptk2b, Atp2b4, Icam5, Tamalin, Slc30a3, Nptx2, Actn2, Ablim3, Baiap2, Epha3, Auts2, Iqgap2, Myo5b, Ctsh, Hexa, Npc2, Ctss, Ctsc, Ctsd, Unc93b1, Cryab, Ctsz, Grn, Ctsl, Cst7, Gfap, Laptm5, Rab6b, Cd68, Man2b1, Hexb, Ifi30, Cd74, Ptprc, Cd22, Csf2rb, Lag3, St14, Fcer1g, Csf3r, Ly9, Cd9, Prnp, Cd86, B2m, Cd64, Osmr, Cd33, Itgax, Il21r, Plau, Abca1, Fas, Cd274, Icam1, Slamf9, Adgre1, Tgfbr2, Csf2rb, Itgb2, Gsdmd, Fcgr2b, C4b, ^ Docket No.: 11001-216WO1 Cscl10, Cd14, Aif1, Pld4, Axl, Tlr2, Cnr2, Cela1, Clec7a, Csf1r, Cd180, C3, Cyba, Csf1, Cybb, C4a, Tnfrsf1a, Ticam2, Cxcl5, Siglec1, Ly86, Tlr1, Ptaf4, Nrros, S1pr3, Lgals9, Casp4, Cd44, Havcr2, Tgfb1, Pycard, C3ar1, Il1b, Slc11a1, F11r, Tlr7, Hgk, F11r, Irf5, Mpeg1, Gm9442, Mid1-Ps1, Mid1, A2m, Cdk1a, Neat1, Ly86, Lyz2, Erdr1, Gm47283, Gm21860, Lox, Lgals3, Neurod6, Lct, Gm37459, Rasl10a, Pcdh20, Dsp, Gm19963, Ccl6, Cst7, Itgax, Ccl4, or Clec7a, or a combination thereof, are differentially expressed in the sample compared with a control ^^^)^^^^^^^^^^^^^^if one or more transcripts comprising or polypeptides encoded by the genes in step ii) are differentially expressed, then administering a therapeutically effective amount of an inhibitor of YTHDF1. Methods of sequencing transcript levels or polypeptide / protein levels are known throughout the art. As used herein, the term “RNA-seq” otherwise known as “RNA sequencing”, refers to a next-generation sequencing technology which reveals the presence and quantity of RNA in a sample which can be used to analyze the cellular transcriptome. In some embodiments, the one or more transcripts comprising or polypeptides encoded by a human homolog of Ccl6, Cst7, Itgax, Ccl4, or Clec7a, or a combination thereof. In some embodiments, detecting step (ii) is carried out using RNA-seq. In some embodiments, detecting step (ii) is carried out using mass spectrometry. In some embodiments, detecting step (ii) is carried out using data-independent acquisition (DIA) and / or parallel reaction monitoring (PRM) mass spectrometry. In some embodiments, detecting step (ii) is carried out using data-independent acquisition (DIA) and / or selective reaction monitoring (SRM) mass spectrometry. In some embodiments, the sample comprises blood. In some embodiments, the sample comprises cerebrospinal fluid. In another aspect, provided herein is a method for treating a subject at risk for or having a neurodegenerative disease, comprising: ^^^^^^^^^^^^^^>-^^&^^^^^^^^^)^^^&^^^^^^^^^ ^7^'^^^ (ii) detecting whether N6-methyladenosine (m6A) methylation pattern of an RNA transcript comprising a human homolog of Pik3r1, Map2k4, Pak3, Pak1, Map2k1, Camk2g, Grm5, Gria3, Gria2, Grm1, Reep1, Kcnc2, Kcnc1, Kcnd2, Kcnd3, Camsap2, Gda, Mapt, Map1b, Pak1, Ank2, Ppp3cb, Atp2b4, Slc8a1, Pak1, Dnm3, Atl1, Myh10, Scn2a, Scn1a, Prkce, Sybu, Vsnl1, Ppp3cb, Atp2b2, Foxp2, Psap, Rora, Hcn1, Kcnd2, Scn2b, Kcnd3, Scn1a, Nceh1, Timp2, Nrf1, Ets2, Smad4, Crebbp, E2f1, Egr1, Ets1, Ep300, Cebpb, Nfe2l2, Stat1, Stat3, Sp3, Rela, Jun, Nfkb1, or Sp1^^^^^^^'^^^^^^^^^^^^^^^^^&^^^^^^^^^^^^)^^^'^^)^^^^^^^^^^^^'^^^^^^^^^^)^^^^ and (iii) if one or more transcripts of the genes in step ii) have differentially methylated regions ^ Docket No.: 11001-216WO1 in the sample compared with the control sample, then administering a therapeutically effective amount of an inhibitor of YTHDF1. Methods of sequencing m6A methylation are known in the art, for example, Zhu, L. et al. Comprehensive Analysis of Blood-Based m6A Methylation in Human Ischemic Stroke. Mol Neurobiol 60, 431–446 (2023), incorporated herein by reference. Briefly, total RNA is extracted from peripheral blood and / or cerebrospinal fluid and / or tissue samples. Following this, mRNA is fragmented, for example in the presence of metal ions, and incubated with an anti-m6a antibody. Subsequently, m6A-modified mRNA is immunoprecipitated and prepared for RNA-seq (e.g., Illumina sequencer). Raw reads can be filtered using FASTP software and clean reads aligned to a reference genome. Aligned reads can also be used for peak calling of methylated regions with, for example, exomePeak2 software. In some embodiments, m6A peaks that are differentially methylated between groups are identified using, for example exomePeak2 software, with the following criteria: fold change ^^6^?@?9^^^^^^?.?, / ,A / ^In some embodiments, genes that are differentially expressed between groups are identified from the RNA-seq data (e.g., the corresponding MeRIP-seq input library ^^^^^^^^^^^^^^^&^^^^^^^^^'^^^^^^^:^^6?@?9^^^^^^?.?, / ,A / In some embodiments, blood cells may be cultured ex vivo and alternative methylation sequencing methods may be performed, including but not limited to deamination of adenosines, RNA Targeting and sequencing (DART-seq). DART-seq is reviewed in Meyer, K.D. DART- seq: an antibody-free method for global m6A detection. Nat Methods 16, 1275–1280 (2019), incorporated herein by reference. In some embodiments, m6A methylation may be assayed using chemical labeling, e.g., m6A-selective chemical labeling (m6A-SEAL), which employs chemical probes to tag m6A sites within RNA. m6A-SEAL is reviewed in, for example, Clyde, Dorothy. "New tools for transcriptome-wide mapping of m6A." Nature reviews Genetics 21.7 (2020): 387-387, incorporated herein by reference. In some embodiments, miCLIP (m6A individual-nucleotide resolution UV crosslinking and immunoprecipitation) is used to assay methylation status / patterns in a sample isolated from a subject as described herein, which involves UV crosslinking, immunoprecipitation, and chemical modification to yield high-resolution mapping of m6A sites. miCLIP is reviewed in Grozhik, A.V. et al. Mapping m6A at Individual- Nucleotide Resolution Using Crosslinking and Immunoprecipitation (miCLIP). Methods Mol ^^^^ / ^9,^;^^A^9:AA-78, incorporated herein by reference. In alternative embodiments, Nanopore RNA sequencing may be used for assaying RNA m6A methylation status and / or patterns as described herein. Nanopore RNA sequencing is ^ Docket No.: 11001-216WO1 reviewed in Hendra, C. et al. Detection of m6A from direct RNA sequencing using a multiple instance learning framework. Nat Methods 19, 1590–1598 (2022), incorporated herein by reference. In yet a further alternative embodiment, mass-spectrometry-based methods may be used to detect RNA m6A methylation status and / or patterns as described herein. In some embodiments, the mass-spectrometry based method to assay the m6A epitranscriptome in a sample isolated from a subject as described herein comprises m6A-LAIC-seq. m6A-LAIC-seq is described in Molinie, B. et al. m6A-LAIC-seq reveals the census and complexity of the m6A epitranscriptome. Nat Methods 13, 692–698 (2016), incorporated herein by reference. In an alternative aspect, provided herein is a method for preventing or treating neuroinflammation in a subject at risk for or having a neurodegenerative disease, comprising administering a therapeutically effective amount of an inhibitor of YTHDF1. In some embodiments, the neuroinflammation comprises chronic neuroinflammation. In another aspect, provided herein is a method for preventing or treating neuroinflammation in a subject at risk for or having a neurodegenerative disease, comprising:^^^^ ^^^^^^^^^^ ^^ ^^^)^^^ &^^^^ ^^^^ ^ ^7^'^^^ ^^^^^ ^^^^'^^^^^ ^^^^^^^^ ^^^^ ^^^ ^^^^^ ^^^^^'^^)^^^comprising or polypeptides encoded by a human homolog of Ccl6, Cst7, Itgax, Ccl4, Clec7a, Il10, Tnfa, Ccl22, Irf1, Ifitm3, Spp1, Timp1, Gfap, Tgfb1, Arg1, Bst2, Spp1, or Vim are ^^&&^^^^^^^^^%^^1)^^^^^^^^^^^^^^^^^)^^^'^^)^^^^^^^^^^^^'^^^^^^^^^^)^^^^^^^^^^^^^^if one or more transcripts comprising or polypeptides encoded by the genes in step ii) are differentially expressed, then administering a therapeutically effective amount of an inhibitor of YTHDF1. In some embodiments, detecting step (ii) is carried out using RNA-seq. In some embodiments, detecting step (ii) is carried out using mass spectrometry. In some embodiments, detecting step (ii) is carried out using data-independent acquisition (DIA) and / or parallel reaction monitoring (PRM) mass spectrometry. In some embodiments, detecting step (ii) is carried out using data-independent acquisition (DIA) and / or selective reaction monitoring (SRM) mass spectrometry. PRM is a targeted mass spectrometry technique that allows for highly-sensitive and quantitative assay of pre-selected peptides in a sample. PRM is typically used as a validation step following a discovery-based proteomics experiment, i.e., wherein differentially expressed genes / peptides / proteins are discovered in an experimental condition compared to a control (e.g., PS19:Ythdf1- / - versus PS19, as described herein). SRM is a method for detecting and quantifying specific, predetermined analytes (e.g., metabolites, drugs, peptides, and the like) with known fragmentation properties. SRM is ^ Docket No.: 11001-216WO1 reviewed in Hasin, Yehudit, Marcus Seldin, and Aldons Lusis. "Multi-omics approaches to disease." Genome biology 18 (2017): 1-15, incorporated herein by reference. The SRM step comprises a targeted liquid chromatography-tandem mass spectrometry method. In some of the methods provided herein, a known concentration of isotopically labeled peptide standards are added, or spiked, into the peptide solution and used for relative quantification of the one or more targeted peptides. The ratio of internal standard (e.g., isotopically labeled peptides) to the one or more target peptides is determined by comparing the SRM results of the target peptides with a standard curve generated from the SRM analysis. This ratio can be further used to determine the amount of peptide in the sample. PRM and SRM rely on data-independent acquisition (DIA), which allows for sampling of one or more peptides in a given m / z range in a sample, allowing for an unbiased acquisition of proteomics data. DIA offers enhanced quantitative accuracy, precision, and reproducibility compared to traditional LC / MS methods. DIA is reviewed in Fröhlich, Klemens, et al. "Data- independent acquisition: A milestone and prospect in clinical mass spectrometry-based proteomics." Molecular & Cellular Proteomics (2024): 100800, incorporated herein by reference. In some embodiments, the sample comprises blood. In some embodiments, the sample comprises cerebrospinal fluid. In some embodiments, the neuroinflammation comprises chronic neuroinflammation. In another aspect, provided herein is a method for preventing or treating chronic neuroinflammation in a subject at risk for or having a neurodegenerative disease, comprising administering a therapeutically effective amount of an inhibitor of YTHDF1. In the methods provided herein, a mass spectrometry peak volume derived from a certain peptide can be calculated by detecting and determining peak shape for a given mass during elution from an LC-MS system. Since isotopically labeled peptides have known masses and one or more target peptides have known masses, the intensity of the peaks corresponding to these masses can be tracked during the elution period. Numerous software programs are available for detecting and determining the intensity of these peaks, for example, Skyline-daily software available from Aitis TSQ. Based on the results of the assay method, the amounts of the selected peptides can be used to identify YTHDF1 dysregulation, or lack thereof, in subject or reference sample. In some embodiments, the inhibitor of YTHDF1 is selected from an antibody or a derivative thereof, an antibody-drug conjugate, a fusion protein, a small molecule, a dsRNA, ^ Docket No.: 11001-216WO1 an siRNA, an anti-sense technology, an aptamer, a gene editing technology, or a combination thereof. In some embodiments, the inhibitor of YTHDF1 is a small molecule. In some embodiments, the small molecule comprises 6-mercaptopurine hydrate, or a pharmaceutically acceptable salt thereof. In some embodiments, the small molecule is selected from 2-[9-[3,3- Bis(hydroxymethyl) cyclobutyl]purin-6-yl]-2,7-diazaspiro[4,4]nonan-8-one (N-7), 5- aminolevulinic acid, 5-fluorouracil, 6-mercaptopurine hydrate, adenine, allopurinol, aminophylline, benzyl alcohol, diflunisal, ebselen, flucytosine, glycine, guaifenesin, histamine (phosphate), hydroxyurea, isocarboxazid, methimazole, N,3-Dimethyl-2H-pyrazolo[4,3- d]pyrimidin-7-amine, N-Methyl-1H-indazole-3-carboxamide, niclosamide (NIC), pindolol, salvianolic acid C (SAC), tegaserod, theophylline, tiopronin, uracil, or a pharmaceutically acceptable salt thereof. In some embodiments, the inhibitor of YTHDF1 is derived from a molecule disclosed in International Patent Publication No. WO2022007890A1, incorporated herein by reference. In some embodiments, the inhibitor of YTHDF1 is derived from a small molecule selected from 2-[9-[3,3-Bis(hydroxymethyl) cyclobutyl]purin-6-yl]-2,7-diazaspiro[4,4]nonan- 8-one (N-7), H-14, D-20, D-15, B-16, H-15, N-12, H-9, L-8, L-4, I-20, E-14, or K-18 as disclosed in Wang, C. & Zhou, H. Discovery of a new inhibitor for YTH domain-containing m6A RNA readers. RSC Chem. Biol., 2024, 5, 914-923, incorporated herein by reference, or a pharmaceutically acceptable salt thereof. In some embodiments, the small molecule comprises ebselen, or a pharmaceutically acceptable salt thereof. In some embodiments, the small molecule comprises niclosamide (NIC), or a pharmaceutically acceptable salt thereof. In some embodiments, the small molecule comprises salvianolic acid C (SAC), or a pharmaceutically acceptable salt thereof. In some embodiments, the small molecule comprises tegaserod, or a pharmaceutically acceptable salt thereof. In some embodiments, the small molecule blocks the binding of YTHDF1 to m6a- modified mRNAs. In some embodiments, the inhibitor of YTHDF1 is an antibody or a derivative thereof. In some embodiments, the antibody or a derivative thereof comprises a monoclonal antibody. In some embodiments, the antibody or a derivative thereof comprises a humanized antibody. In some embodiments, the inhibitor of YTHDF1 is an antibody that specifically binds an epitope on a YTHDF1 protein, or a fragment thereof. ^ Docket No.: 11001-216WO1 Anti-YTHDF1 antibodies suitable for the present invention are known in the prior art. Suitable anti-YTHDF1 antibodies are for instance also commercially available from Santa Cruz Biotechnology Inc. (Dallas, TX, USA), Cell Signaling Technology, ThermoFisher, or Abcam (Cambridge, UK). For example, an antibody specific to human YTHDF1 can be selected or derived from an anti-YTHDF1 antibody (Abcam, Cat # ab230330), an anti-YTHDF1 antibody (Abcam, Cat # ab157542), an anti-YTHDF1 antibody (Abcam, Cat # ab264409), or EPR22349-41 (Abcam, Cat # ab220162). For example, an antibody specific to human YTHDF1 can be selected or derived from 3A2H12 (ThermoFisher, Cat # 66745-1-IG), an anti-YTHDF1 polyclonal antibody (ThermoFisher, Cat # 17479-1-AP), PSH0-23 (ThermoFisher, Cat # MA5-50793), an anti- YTHDF1 polyclonal antibody (ThermoFisher, Cat # 26787-1-AP), an anti-YTHDF1 polyclonal antibody (ThermoFisher, Cat # PA5-141053), an anti-YTHDF1 polyclonal antibody (ThermoFisher, Cat # PA5-144638), an anti-YTHDF1 polyclonal antibody (ThermoFisher, Cat # PA5-89122), an anti-YTHDF1 polyclonal antibody (ThermoFisher, Cat # PA5-104503), an anti-YTHDF1 polyclonal antibody (ThermoFisher, Cat # PA5-110587), an anti-YTHDF1 polyclonal antibody (ThermoFisher, Cat # PA5-101252), an anti-YTHDF1 polyclonal antibody (ThermoFisher, Cat # PA5-68445), an anti-YTHDF1 polyclonal antibody (ThermoFisher, Cat # 65736ACTMOTIF), an anti-YTHDF1 polyclonal antibody (ThermoFisher, Cat # XXX), an anti-YTHDF1 polyclonal antibody (ThermoFisher, Cat # A305-849A-T), an anti-YTHDF1 polyclonal antibody (ThermoFisher, Cat # CL48817479100UL), an anti-YTHDF1 polyclonal antibody (ThermoFisher, Cat # CL59417479100UL), an anti-YTHDF1 polyclonal antibody (ThermoFisher, Cat # PA5-49875), or an anti-YTHDF1 polyclonal antibody (ThermoFisher, Cat # A305-849A). In some embodiments, antibody specific to human YTHDF1 can be selected or derived from an anti-YTHDF1 antibody (Cell Signaling Technology, Catalog # 86463). In some embodiments, the anti-YTHDF1 antibody is a monoclonal antibody. The monoclonal anti-YTHDF1 antibody is preferably humanized. Methods to obtain humanized antibodies are well known in the art. In some embodiments, the inhibitor of YTHDF1 is an antibody-drug conjugate. In some embodiments, the inhibitor of YTHDF1 comprises siRNA, shRNA, or anti- sense oligonucleotides. In some embodiments, the inhibitor of YTHDF1 is an siRNA. Methods of down-regulating or silencing genes are known in the art. For example, expressed protein activity can be down-regulated or eliminated using antisense ^ Docket No.: 11001-216WO1 oligonucleotides (ASOs), protein aptamers, nucleotide aptamers, and RNA interference (RNAi) (e.g., small interfering RNAs (siRNA), short hairpin RNA (shRNA), and micro RNAs (miRNA) (see e.g., Rinaldi and Wood (2017) Nature Reviews Neurology 14, describing ASO ^^^^^)^^^^^^^^^^^^^^^^^4%^^^^^^^9,,^^^#^^^^^51)^^^^^^^'^^ / ^^;^^^9<B-303G, describing^^^^^^^^^^^^^^^3%^^^^^^^^^^^^^^^^^^)^^^>-^^^#^^^^^^^^^^^^ / ^ ^^BB9^^^^^ / ^- / ! / ^^'^^ / ^4'^ / ^660, 27-^^^^*^^^^^^^BB9^^^^^^^^^%^^^=^^9^:^<,;-15, describing targeting deoxyribonucleotide ^^( ^^'^^^^C^^^^^^^^ / ^^9,,^^^6 ^^^D)^^^6^^^^^^^^ / ^^,^^^-<^^^^^'^^^^^^^^)^^^^^^^^>^%^^^^^^^^^ al. (2004) Nature Biotechnology 22(3), 326 - ^^,^^^^^'^^^^^^^>-^^^^^ ^^)araj and Melendez (2006) Clinical and Experimental Pharmacology and Physiology 33(5-6), 504-510, describing>-^^^^ ^^^^^^^ ^^^ ^^ / ^ ^9,,A^^^^^ ^^^ >^2^^^^ ^&^ ^^%^^^^^^%^ ^;^^ ^=;-^;^^^ ^^^'^^^^^^^ >-^^^^Dykxhoom and Lieberman (2005) Annual Review of Medicine 56, 401-423, describing RNAi). RNAi molecules are commercially available from a variety of sources (e.g., Ambion, "0^^4^^^^^^^^^^'^^^*D^^^^2^^^^^^^^ / ^4^2^^^^^^^>-^^^^^^' ^^^^^^^^^^)^^^^^^^^ ^^^^^^^2^^^^^%^ ^&^^^^^^^^^^^^^^^^E^^^^^^^^^^^^^^^^^^^^^^ / ^ / ^^6'^^1^^^^^^^^^^^^^^^^^^^^^CD6F-iT™ RNAi^^^^^^^^^^ ^^2^^^^^^^^^ ^^>-^^G^^^^^^^^^ ^^^^^^ ^^^^^^^^^^"^^^^^^^^^^^&^^^^^^'^^H^>^^^^^'^^Computing). Traits influential in defining optimal siRNA sequences include G / C content at the termini of tire siRNAs, Tm of specific internal domains of the siRNA, siRNA length, position of the target sequence within the CDS (coding region), and nucleotide content of the 3' overhangs. Methods of RNA interference comprising administering YTHDF1 siRNA are disclosed in, for example, Fu Y, Zhuang X. m6A-binding YTHDF proteins promote stress granule&^^^^^^^^ / ^ -^^ ^^^ 6^^^^'^^^ ^^^^^^% / ^ 9,9,^^^^B^:BAA-63. doi: 10.1038 / s41589-020-0524-y,incorporated herein by reference. In some embodiments, the inhibitor of YTHDF1 is an interfering shRNA or vector encoding thereof that targets YTHDF1 mRNA. Anti-YTHDF1 siRNA suitable for the present invention are known in the prior art. Suitable anti-YTHDF1 siRNA are for instance also commercially available from ThermoFisher, Santa Cruz Biotechnology, and Qiagen. In some embodiments, the anti-YTHDF1 siRNA is derived or selected from one or ^^^^^^&^"^^^^^^^^^^^^^^^^%^^^^^9B;=^^^6^^^^^^^I^=^B9=9,^^"^^^^^^^^^^^^^^^^%^^^^^9B;=A^^ 6^^^^^^^I^=^B9=9,^^^^^"^^^^^^^^^^^^^^^^%^^^^^9B;==^^6^^^^^^^I^=^B9=9, / In some embodiments, the anti-YTHDF1 siRNA is derived or selected from one or more of YTHDF1 siRNA (Santa Cruz, Cat # sc-155423), YTHDF1 shRNA Plasmid (Santa ^ Docket No.: 11001-216WO1 Cruz, Catalog # sc-155423-SH), or YTHDF1 shRNA Lentiviral Particles (Santa Cruz, Catalog # sc-155423-V). In some embodiments, the anti-YTHDF1 siRNA is derived from or comprises YTHDF1 siRNA (Qiagen, Catalog # SI00764715). In some embodiments, the anti-YTHDF1 siRNA is derived from or comprises GCACTGACTGGTGTCCTTT (SEQ ID NO: 3), or a nucleic acid sequence at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical thereto. In some embodiments, the anti-YTHDF1 siRNA is derived from or comprises GATACAGTTCATGACAATGA (SEQ ID NO: 4), or a nucleic acid sequence at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical thereto. In some embodiments, the anti-YTHDF1 siRNA is derived from or comprises CAGGCTGGAGAATAACGACAA (SEQ ID NO: 5), or a nucleic acid sequence at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical thereto. In some embodiments, the inhibitor of YTHDF1 comprises a gene editing technology. In some embodiments, the gene editing technology comprises CRISPR-based methods. CRISPR based gene editing methods are known to those of skill in the art and are reviewed in, e.g., Wang, Joy Y., and Jennifer A. Doudna. CRISPR technology: A decade of genome editing is only the beginning. Science 379.6629 (2023):eadd8643, incorporated herein by reference. In some embodiments, the CRISPR-based gene editing methods comprise using the gRNA AGCAGCCACTTCAACCCCGCTGG (SEQ ID NO: 6), or a nucleic acid sequence at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical thereto. In some embodiments, the CRISPR-based gene editing methods comprise using the gRNA GGACCATGGTGCCTCGCTGAGGG (SEQ ID NO: 7), or a nucleic acid sequence at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical thereto. In some embodiments, the inhibitor of YTHDF1 is formulated in lipid nanoparticles (LNPs). In some embodiments, the inhibitor of YTHDF1 is formulated in exosomes. In some embodiments, the subject is a human. In some embodiments, the composition described herein may be in a dosage form. The dosage forms can be adapted for administration by any appropriate route. Appropriate routes include, but are not limited to, oral (including buccal or sublingual), rectal, epidural, ^ Docket No.: 11001-216WO1 intracranial, intraocular, inhaled, intranasal, topical (including buccal, sublingual, or transdermal), vaginal, intraurethral, parenteral, intracranial, subcutaneous, intramuscular, intravenous, intraperitoneal, intradermal, intraosseous, intracardiac, intraarticular, intracavemous, intrathecal, intravitreal, intracerebral, gingival, subgingival, intracerebroventricular, and intradermal. Such formulations may be prepared by any method known in the art. The disclosed methods can be performed any time prior to the onset of a neurological disorder. In one aspect, the disclosed methods can be employed 60, 59, 58, 57, 56, 55, 54, 53, 52, 51, 50, 49, 48, 47, 46, 45, 44, 43, 42, 41, 40, 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 %^^^^^^^9^^^^^ ^,^^B^^<^^;^^^^^A^^=^^^^^9^^^^^^^^^^^^^^^^,^^9B^^9<^^9;^^9^^^9A^^9=^^9^^^99^^9^^^9,^^ 19, 18, 17, 16, 15, ^=^^^^^^^9^^^^^^^,^^B^^<^^;^^^^^A^^=^^^^^^^^^%^^^^,^^=<^^^^^^^,^^9=^^^<^^^A^^^9^^ ^,^^B^^<^^;^^^^^A^^=^^^^^^^^9^^^ ^^^)^^^^^^^^^^^^^^^^^^^&^^^^^ ^^^^^^'^^^^^^^^^^^^^^^^^^^9^^^^^=^^A^^^^^ 7, 8, 9, 10, 11, 12, 15, 18, 9=^^^,^^^^^^=<^^^,^^^ ^^^^^^^=^^A^^^^^;^^<^^B^^^,^^^^^^^9^^^^^^^=^^^A^^^^^^ 17, 18, 19, 20, 21, 22, 23, 24, 9A^^9^^^9;^^9<^^9B^^^,^^=A^^^,^^B,^^^^^^^^^^^%^^^=^^A^^^^^;^^<^^B^^ ^,^^^^^^^9^^^^^^^^^^^^^^^^^^^^9^^^^^=^^A^^^^^;^^<^^B^^^,^^^^^^^9^^^^^^^=^^^A^^^^^^^;^^^<^^^B^^9,^^9^^^ 22, 23, 24, 25, 26, 27, 28, 29, 30, 45, or 60 years after the onset of a neurological disorder. Dosing frequency for the composition of any preceding aspects, includes, but is not limited to, at least once every year, once every two years, once every three years, once every four years, once every five years, once every six years, once every seven years, once every eight years, once every nine years, once every ten year, at least once every two months, once every three months, once every four months, once every five months, once every six months, once every seven months, once every eight months, once every nine months, once every ten months, once every eleven months, at least once every month, once every three weeks, once every two weeks, once a week, twice a week, three times a week, four times a week, five times a week, six times a week, daily, two times per day, three times per day, four times per day, five times per day, six times per day, eight times per day, nine times per day, ten times per day, eleven times per day, twelve times per day, once every 12 hours, once every 10 hours, once every 8 hours, once every 6 hours, once every 5 hours, once every 4 hours, once every 3 hours, once every 2 hours, once every hour, once every 40 min, once every 30 min, once every 20 min, or once every 10 min. Administration can also be continuous and adjusted to maintaining a level of the compound within any desired and specified range. Dosages are typically modified according to the characteristics of the subject (weight, gender, age, etc.), severity of disease (e.g., degree of cognitive deficits, levels of disease- ^ Docket No.: 11001-216WO1 associated biomarkers), specifics and purity of the active agent to be administered, route of administration, nature of the formulation, and numerous other factors. Generally, the active agent (i.e., an inhibitor of YTHDF1 as described herein, or a derivative thereof) is administered to the subject at a dosage ranging from 0.1 pg / kg body weight to 100 g / kg body weight. In some embodiments, the active agent is administered to the subject at a dosage of from 1 pg / kg to 10 g / kg, from 10 pg / kg to 1 g / kg, from 10 pg / kg to 500 mg / kg, from 10 pg / kg to 100 mg / kg, from 10 pg / kg to 10 mg / kg, from 10 pg / kg to 1 mg / kg, from 10 pg / kg to 500 pg / kg, or from 10 pg / kg to 100 pg / kg body weight. The dosage of administration for the active agent disclosed herein can be from about 0.01 mg / kg body weight to about 100 mg / kg body weight. In some examples, the dosage is about 0.01 mg / kg body weight, about 0.05mg / kg body weight, about 0.1 mg / kg body weight, about 0.5 mg / kg body weight, about Img / kg body weight, about 1.5 mg / kg body weight, about 2mg / kg body weight, about 2.5 mg / kg body weight, about 3 mg / kg body weight, about 3.5 mg / kg body weight, about 4 mg / kg body weight, about 4.5 mg / kg body weight, about 5 mg / kg body weight, about 5.5 mg / kg body weight, about 6 mg / kg body weight, about 6.5 mg / kg body weight, about 7 mg / kg body weight, about 7.5 mg / kg body weight, about 8mg / kg body weight, about 8.5 mg / kg body weight, about 9 mg / kg body weight, about 9.5 mg / kg body weight, about 10 mg / kg body weight, about 11 mg / kg body weight, about 12 mg / kg body weight, about 13 mg / kg body weight, about 14 mg / kg body weight, about 15 mg / kg body weight, about 20 mg / kg body weight, about 25 mg / kg body weight, about 30 mg / kg body weight, about 35 mg / kg body weight, about 40 mg / kg body weight, about 45 mg / kg body weight, about 50 mg / kg body weight, about 55 mg / kg body weight, about 60 mg / kg body weight, about 65 mg / kg body weight, about 70 mg / kg body weight, about 75 mg / kg body weight, about 80 mg / kg body weight, about 85 mg / kg body weight, about 90 mg / kg body weight, about 95 mg / kg body weight, or about 100 mg / kg body weight. Dosages above or below the range cited above may be administered to the individual patient if desired. EXAMPLES The following examples are set forth below to illustrate the compositions, devices, methods, and results according to the disclosed subject matter. These examples are not intended to be inclusive of all aspects of the subject matter disclosed herein, but rather to illustrate representative methods and results. These examples are not intended to exclude equivalents and variations of the present invention which are apparent to one skilled in the art. ^ Docket No.: 11001-216WO1 Example 1. YTHDF1 and m6A RNA methylation in neurodegenerative disease Elucidating the significance of epitranscriptomic regulation of gene expression in memory and brain diseases is a nascent field of study. Emerging studies predict that mRNA methylation could be potentially involved in neuronal mechanisms underlying brain development, learning and memory, memory formation and consolidation, and pathogenesis in Alzheimer's disease (AD), Parkinson’s disease, multiple sclerosis, depression, and epilepsy. N6-methyladenosine (m6A) RNA methylation is the most abundant methylation modification in eukaryotic RNAs. This dynamic and reversible m6A modification adds a new dimension to the control of gene expression, splicing, RNA editing, and RNA lifespan, and its dysfunction has been associated with different diseases, including neurodevelopment, aging, and neurological diseases. Dysfunction of m6A is also associated with fundamental disease- associated hallmarks such as oxidative stress, mitochondrial dysfunction, stress granule formation, and inflammatory response. Notably, m6A is a novel and essential regulator of anti- and pro-inflammatory responses in cultured primary rat microglia. The m6A RNA modification is initiated by methylases, removed by RNA demethylases, and recognized by m6A-binding proteins, namely so-called m6A writers, erasers, and readers (FIG. 1). In the cytosol, m6A-modified RNA is bound by the cytoplasmic “readers” YTH domain-containing family protein 1 (YTHDF1) YTHDF2, YTHDF3, and eukaryotic initiation Factor 3 (eIF3) to modulate stability, translational efficiency or the degradation of RNA. As a classical m6A reader, YTHDF1 binds to m6A-modified transcripts to promote their translation. In addition, YTHDF1 interacts with eIF1 to facilitate cap-dependent translation of m6A-modified RNA. On the other hand, YTHDF2 recognizes m6A and reduces the stability of target transcripts. YTHDF3 promotes m6A-modified transcript translation in synergy with YTHDF1 and affects methylated mRNA decay mediated through YTHDF2. The role of YTHDF1 in the nervous system has gained interest with the observation that YTHDF1 binds to over 1000 transcripts in the hippocampus and facilitates translation of m6A-modified transcripts in response to neuronal stimulation, and this process contributes to hippocampus- dependent learning and memory. Potential neurodegenerative disease-associated pathways implicated by m6A include mitochondrial function, inflammatory response, and oxidative stress. A recent study linked tau oligomers with stress granules, which are commonly seen in Alzheimer’s disease (AD) and other neurodegenerative diseases, which recruit RNA-binding proteins and m6A-RNA transcripts. ^ Docket No.: 11001-216WO1 Thus, emerging evidence implicates important functions for YTHDF1 in neuronal and microglial gene expression relevant to AD pathophysiology. Example 2. YTHDF1 in Alzheimer's disease To address the significant knowledge gap in the role of m6A in neurodegenerative disease pathophysiology, it was questioned whether YTHDF1, a key m6A reader, has a role in tau pathogenesis and neuroinflammation in AD. AD is a devastating age-associated neurodegenerative disorder with no treatment or means that would prevent it, cure it, or even slow its progression. The hallmarks of AD include ^-amyloid (A^) plaques and hyper-phosphorylated tau (p-tau) in neurofibrillary tangles, accompanied by neuroinflammation and synaptic / neuronal loss. A recent study linked tau oligomers with stress granules, which recruit RNA-binding proteins and m6A RNA transcripts. Moreover, m6A serves as a novel and essential regulator of microglia's anti-inflammatory and proinflammatory responses. Thus, there is a solid rationale for investigating how m6A modulates AD-associated tau pathology and inflammatory responses. Moreover, YTHDF1 has been shown to increase Activity-Regulated Cytoskeleton- associated protein (ARC) levels in cells exposed to A^ peptides by promoting translation of m6A-modified ARC transcripts. YTHDF1-mediated translation of DNMT3A in monocyte- derived macrophages with Mettl3 deficiency attenuated ^-tubulin acetylation, thus enhancing the migration of monocyte-derived macrophages to the brain and accelerating A^ clearance. YTHDF1-mediated translation of tau and calmodulin transcripts facilitates cortical neuronal migration and DRG axon elongation. YTHDF1-mediated m6A-RNA translation also influences a variety of neuronal functions, monocyte-mediated A^ clearance, tau oligomer-related stress granule formation, and TRAF6, TLR9, and NLRP3 levels. YTHDF1 further affects inflammatory-related factors, such as IL-1^, IL-6, TNF-J and NF-KB, by regulating the expression of TRAF6. Moreover, YTHDF1 enhances TLR9 mRNA translation in an m6A-dependent manner and facilitates inflammation by promoting NLRP3 translation and subsequent IL-1^ production. Furthermore, 5XFAD mouse brain microglia have an overall increase in m6A and an upregulation of Ythdf1 expression. Finally, microarray data from 624 fresh-frozen post-mortem brain tissue showed a significant increase in YTHDF1 expression in AD. Notably, m6A serves as a novel and essential regulator of the anti-inflammatory and proinflammatory responses of microglia, which have profound influence on cerebral amyloid ^ Docket No.: 11001-216WO1 burden and tau pathology. Moreover, the brain utilizes different cellular pathways to modulate inflammatory responses in AD. Finally, altered expression of m6A regulators have been found in individuals with cognitive impairment. Thus, emerging evidence implicates essential functions for YTHDF1 in gene expression relevant to AD pathophysiology and neuroinflammatory responses. Immunohistochemical staining was performed to assess whether and where YTHDF1 is expressed in human brain. YTHDF1 expression was confirmed in the human brain, with immunostaining of control brain shown predominant neuronal YTHDF1 immunostaining (FIG. 2). High magnification images of AD brains that were co-stained with GFAP (a marker of astrocytes) or IBA1 (a marker of microglial cells) or mAb 3D6, which labels A^ deposits in amyloid plaques. The immunostained brain section samples revealed glial expression of YTHDF1 in addition to neurons, in some cases co-localizing with pathological A^ plaques (FIG.2). Example 3. YTHDF1 in Alzheimer’s disease preclinical models Following confirmation of neuronal and glial cell expression of YTHDF1 in control and AD brain, confirmatory studies were performed in preclinical animal models of AD. Following immunostaining, slides were scanned using VS200 Whole Slide Scanner, and 7-9 sections per mouse were analyzed by QuPath and ImageJ / Fiji software. Higher magnification images were acquired on an automated Nikon Ti2 microscope fitted with the Yokogawa spinning- disk field scanning confocal system. At least 5 sections / mice were analyzed using ImageJ / Fiji and QuPath software. Unbiased stereology were applied when appropriate. YTHDF1 staining was observed in neurons and microglia in APPSAA(FIG.3), 5XFAD (FIG.4), and PS19 (FIG.5A-5B) models of AD amyloid and tau pathology. In addition to this, microglial YTHDF1 was observed surrounding amyloid deposits in 5XFAD mice (FIG. 4), suggesting that YTHDF1 could play a role in inflammation-mediated amyloid neuropathology. Although microglial YTHDF1 expression is observed in preclinical AD mouse models, the involvement of YTHDF1 function in AD pathophysiology in an AD amyloid model has yet to be assessed. Example 4. Generation of a Ythdf1 knockout mouse model of Alzheimer's Whole-mount staining of non-transgenic mice shows that YTHDF1 is robustly expressed in neurons throughout the hippocampus and the cortex (FIG.7). ^ Docket No.: 11001-216WO1 Next, the expression pattern of YTHDF1 was analyzed in PS19 model mice. The PS19 mouse line is a prominent transgenic mouse model of AD, wherein mutant human MAPT comprising mutation encoding a P301S substitution is inserted, with expression driven by the mouse prion protein (Prnp) promoter (FIG.6). Mild neuropathological evidence in PS19 mice, including gliosis and synaptic loss, is seen at approximately 3 months (FIG. 6). At 6 months, moderate neuropathological hallmarks are exhibited, including tau tangles (FIG. 6). Further, behavioral deficits can be observed, including changes of long-term potentiation / long-term depression of neuronal synapses, as well as noticeable cognitive impairment. Finally, at around 9 months, neuronal loss can be observed and around this stage, some PS19 mice begin to die (FIG.6). YTHDF1 staining in PS19 mice showed prominent neuronal and glial (as seen by co- localization with microglial marker Iba1) expression (FIG.8). To address this significance of YTHDF1 in AD pathophysiology, a Ythdf1 knockout mice were generated in a transgenic tau background (PS19:Ythdf1- / -) (FIG.9). Both male and female mice were used in the following Examples, and sex was considered as a biological variable. Based on previously published work and a priori power analysis (>0.80 statistical power to detect significant differences, p<0.05), 15 animals of each sex / genotype were to be used in behavior studies and 10 animals of each sex / genotype / age were to be used for neuropathology and biochemical experiments (FIG. 9). FACS for surface staining, RNAseq, e-CLIP, and proteomics will be performed with n@6 animals (sex / genotype / age) (FIG. 9). Behavior and neuropathology assessments will be conducted in a blinded manner without identifying genotypes. Multiple well-characterized pathology and cellular marker antibodies were employed to characterize neuropathology and are to be complemented with RT-qPCR, quantitative immunoblots (LiCOR), and MSD / Luminex assays to ensure unambiguous results. Statistical significance was assessed using significance level p<0.05 by unpaired Student’s t-test, linear mixed-effects models, one-way ANOVA, two-way ANOVA, or repeated-measures ANOVA with Tukey’s post hoc test, as appropriate comparisons. GraphPad Prism v.10, SPSS v.26, and R software will be used. Details on data analysis and statistical testing of transcriptomics and proteomics data are detailed under each Aim. Example 5. Generation of YTHDF1-specific molecular tools ^ Docket No.: 11001-216WO1 RT-qPCR analysis was performed to verify human MAPT expression and Ythdf1 expression in the various mice groups. While Ythdf1 expression was seen in Wt (non- transgenic) and PS19 mice, both the Ythdf1- / - knockout mouse and the PS19:Ythdf1- / - showed little to no expression thereof (FIG.10). Human MAPT expression was only observed in PS19 and PS19:Ythdf1- / - mice (FIG.10). To target YTHDF1 specifically among other YTH domain containing family members, new antibodies were generated. YTHDF1 shares 65% sequence identity with its homologs YTHDF2 and YTHDF3. Since many commercial YTHDF1 antibodies cross-react with the homologs, mAbs unique to YTHDF1 were generated. The specificity of these antibodies were validated by Western blots (FIG. 11A), immunoprecipitation (FIG.11B), and immunostaining on Wt and Ythdf1- / - mouse brain (FIG. 12). Using the newly developed mAb, prominent neuronal expression of YTHDF1 was observed throughout the brain in wild type mice. In contrast, YTHDF1 staining was not observed in Ythdf1- / - mice (FIG.12) Example 6. RNA-seq Analysis of PS19:Ythdf1- / - mice As an unbiased approach to gain molecular insights, RNAseq analysis was performed of transcriptome changes in the brains of PS19 and PS19:Ythdf1- / - mice. As described above, without YTHDF1 function, m6A RNA will not be preferentially chosen for protein translation, and is expected to reveal transcriptomic changes and biological pathways that depend on m6A. As an unbiased approach to gaining molecular insights into biological pathways that depend on m6A RNA / YTHDF1-mediated translation, RNAseq analysis of transcriptome changes in the brains of PS19 and PS19:Ythdf1- / - mice was performed. Principal component analysis (PCA) showed distinct sex-^^)^^^^^^^^^^^^^1)^^^^^^^^^^^^^^4^B^^&&^'^^^^^^^^^)^^^^^ by the loss of YTHDF1 expression (FIG.13A). This pilot study, performed using a limited number of mice, showed 15 differentially ^1)^^^^^^^^^^^^^^^5^^^^) / ^^7^., / ,^^^C^^9^6^+, / A^^^^^!^^^&^- / - compared to Wt and 143 DEG in PS19:Ythdf1- / - compared to PS19 controls (FIG. 13B). The downregulation of several key neuroinflammatory genes (such as Cst7, Itgax, Clec7a, Ccl4, and Ccl6^^FIG. 13B) indicates that YTHDF1 is essential in promoting tau pathology-related immune response in 9-month-old animals. K-means clustering of DEG revealed four distinct patterns of regulation by tau pathogenesis and YTHDF1 expression (FIG.13C), which were mapped to biological domains that correspond to recently described AD-associated endophenotypes (FIG. 13D). Cluster 1, ^ Docket No.: 11001-216WO1 positively regulated by YTHDF1 under both normal and tauopathy conditions, was enriched in genes related to extracellular matrix and positive regulation of inflammatory response. Cluster 2 genes were downregulated by tau pathology and negatively regulated by YTHDF1. Cluster 2 genes included genes involved in glutamatergic synaptic function and regulating the actin cytoskeleton. Cluster 3 genes were upregulated by tau pathology in a YTHDF1-dependent manner and included canonical inflammatory response genes and genes involved in lysosomal function. In summary, this pilot study performed using a limited number of mice demonstrated that the loss of YTHDF1 in the PS19 tauopathy model suppressed inflammatory responses in both sexes (FIG.13A-13E). Example 7. YTHDF1 differentially regulates LPS-induced neuroinflammation during the acute and chronic phases Following the demonstration that YTHDF1 regulated AD-related expression changes in PS19 mice, the role of YTHDF1 in neuroinflammation was assessed. Peripheral administration of LPS over four consecutive days (chronic) or even a single injection (acute) can reliably induce neuroinflammation by activating TLR4-signaling, resulting in an altered gene signature and cytokine release. The involvement of YTHDF1 function in inflammatory response was examined by LPS administration and RT-qPCR analysis of well-defined pro- and anti-inflammatory genes, type- I interferon-activated genes, and DAM and DAA genes (FIG. 14A-14B). The results show a robust activation of acute (single) and chronic (four) neuroinflammatory response in WT animals. Interestingly, the acute response was significantly exacerbated in Ythdf1- / - mice as evidenced by robust induction of pro-inflammatory markers including Tnfa, Stat1, Stat2, Igtp, Cst7, and Spp1 (FIG.14A). In contrast, activation of chronic neuroinflammation was attenuated in Ythdf1- / - mice as evidenced by expression levels of inflammatory markers including but not limited to Il10, Tnfa, Ccl22, Irf1, Ifitm3, Cst7, Ccl6, Spp1, Timp1, and Gfap (FIG.14B). These intriguing findings indicate that YTHDF1 limits neuroinflammatory activation during the acute phase but is required to sustain the chronic phase. This observation is extremely relevant because it is becoming evident that failure of immune resolution underlies chronic inflammation and subsequent neurodegeneration in AD. Example 8. Examination of YTHDF1 modulation of cerebral tau burden ^ Docket No.: 11001-216WO1 The exciting RNAseq results of Example 6 warranted a detailed investigation that explores the role of m6A in the progression of tau pathology by Ythdf1 deletion in the PS19 tau transgenic model and elucidation of the mechanisms thereof. Neuropathology characterization was performed on brains harvested at 9 months. Forebrain tissue was sequentially extracted into high-salt RAB and RIPA soluble and insoluble fractions, and total and phospho-tau (pThr-231) were quantified by MSD assays. Significant increases were found in the levels of total tau in the RAB-soluble fractions in both male and female PS19:Ythdf1- / - mice compared to PS19 (FIG.15). Moreover, insoluble (70% formic acid-extracted) total and p-tau levels were significantly lower in female PS19:Ythdf1- / - mice (FIG.16). These results demonstrate that YTHDF1 is involved in tau aggregation and that YTHDF1 could be targeted in AD to limit this highly relevant pathological hallmark. Example 9. Behavioral characterization of PS19:Ythdf1- / - mice To investigate the in vivo function of YTHDF1 in the tauopathy model PS19 mice, behavior tests were performed in PS19:Ythdf1- / - mice. In a pilot cohort of 9-month-old mice, the loss of YTHDF1 was found to reduce the hyperactivity, which exhibits as longer travel distances and higher movement velocity of PS19 mice in the open field test (FIG.17A). In the novel object recognition test, PS19 mice showed no preference for the novel^^7^'^^ ^^'^^^^^^^^^ '^^)^^^^^ ^^^G^^ L^^^^^^=^M9^ / ^A^^)., / ,,,^N^^!"#^^^^ ^^^^ rescued thisdeficit [p<0.0001], indicating amelioration of working memory as expected for 9 month-old mice (FIG.17B). PS19 mice exhibited hyperactivity and frequent entry into open arms of the elevated plus maze [F(1, 34)=11.46, p<0.01], which was reversed by the loss of YTHDF1 [post hoc Tukey’s test - PS19 vs. PS19:Ythdf1- / -, p<0.01] (FIG.17C, left). As expected, PS19 mice exhibited motor deficits [F(1, 34)=34.49, p<0.0001]. The loss of YTHDF1 rescued this deficit in PS19:Ythdf1- / - mice [p<0.0001] (FIG.17C, right). Thus, it appears that YTHDF1 function is necessary for tau-related behavioral deficits in the PS19 model. Example 10. Characterization of m6A-YHDF1 function in tauopathy through eCLIP- sequencing ^ Docket No.: 11001-216WO1 To test the hypothesis that YTHDF1-dependent m6A function is altered during AD progression, we characterized YTHDF1-specific epitranscriptomic signature in the tauopathy model by enhanced CrossLinking and ImmunoPrecipitation (eCLIP)-seq analysis (FIG.18). Enhanced eCLIP-seq was performed on Wt and PS19 brains (n=4 per genotype) to map YTHDF1 binding sites. This analysis identified 13,133 to 23,789 m6A peaks from each sample library. In accordance with previous reports, m6A peaks were enriched near the stop codon and 3’UTR (FIG.19). Significantly enriched binding motifs of YTHDF1 were identified by eCLIP analysis (FIG.20). Three methods were ^^^^^^^'^^^^^^&&^^^^^^^^^%^^^^^%^^^^^^^^^^^^^^^^*>^^^^ 382 YTHDF1-dependent DMRs were identified with all three methods (FIG. 21). Gene ontology analysis clustered the 382 high-confidence regions into 9 gene-set clusters (FIG. 23- 25). The largest groups were related to “muscle and ataxia,” “microtubule de- or polymerization,” and “peptide release functions.” Two DAM markers, Nceh1 and Timp2, were among the transcripts in m6A-YTHDF1 complexes represented at lower levels in the PS19 brain. Several transcripts encoding transcription factors were represented in our high- confidence YTHDF1 eCLIP dataset. To bridge the Ythdf1- / - RNAseq study (FIG. 13A-13E) and YTHDF1 eCLIP-seq results (FIG.21-25), the RNAseq DEGs were queried from male Wt versus PS19 (437 DEGs) and PS19 versus PS19:Ythdf1- / - (143 DEGs) against the manually- curated TRRUST database to predict regulatory interactions. This analysis identified the top-ranked regulatory interactions of transcriptional factors that could potentially drive the transcriptomic changes in response to tau pathology or the loss of YTHDF1 expression (FIG. 26A-26B). This analysis revealed that SPI, JUN, and NF-KB potentially regulate transcriptional upregulation of several genes that function in inflammation ^^^^'%^^E^^^^^^^^^^^^^^^^^^4^B^^^^^^^^^1)^^^^^^^^^&^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^4^B:Ythdf1- / - mouse brain. In ongoing studies, the protein abundance and activities of these transcriptional regulators is being examined. Conclusion Precisely how YTHDF1 function influences AD pathophysiology has never been tested. Significant progress in this regard has been made herein by examining the involvement of YTHDF1 in tau pathophysiology in PS19 tauopathy model mice. The preliminary studies in PS19:Ythdf1- / - mice as described herein yielded interesting findings, including but not limited to attenuated behavioral deficits and molecular analyses ^ Docket No.: 11001-216WO1 which are consistent with an essential role for YTHDF1 in disease-associated neuroinflammatory response (FIG.13A-13E, 15-16, 17A-17C, 26A-26B), indicating YTHDF1 modulates the glial response to tauopathy. The requirement for YTHDF1 to elicit an appropriate inflammatory response to systemic LPS challenge in vivo independently validated YTHDF1’s function in acute and chronic neuroinflammation (FIG.14A-14B). These results nominate YTHDF1 as a prominent therapeutic target in Alzheimer's disease and tauopathies. Example 11. Generation of APPSAAYthdf1- / - mice to analyze how YTHDF1 function modifies cerebral A^ burden and neuroinflammatory response. Differential m6A mRNA methylation occurs in AD mouse models. YTHDF1 is found mostly in neurons, but its expression in astrocytes and microglia surrounding amyloid deposits becomes apparent in human APP knock-in mice (APPSAA) (FIG.3) and human AD brains (FIG. 2). Moreover, elevated YTHDF1 expression has been observed in individuals with cognitive impairment and AD. Preliminary studies described herein demonstrated that YTHDF1 loss attenuates neuroinflammatory responses in tauopathy (FIG. 13A-13E) and LPS-induced inflammation models (FIG.14B). The goal of this Example is to generate APPSAA:Ythdf1- / - mice to elucidate the involvement of YTHDF1 function in amyloid pathophysiology using detailed neuropathology and comprehensive molecular characterization. APPSAAmice develop mild behavior deficits, manifested as robust hyperactivity, habituation deficits, and disinhibition alterations. Regardless, behavioral tests will be performed in Wt, Ythdf1- / -, APPSAA, and APPSAA:Ythdf1- / - mice [n=15 / sex / genotype] to evaluate hippocampus-dependent learning / memory between 6-7 months of age using the open field, novel object recognition, Y-maze, the Morris water maze, contextual fear conditioning tests, and locomotor functions using a composite phenotype scoring 50 (schematics in FIG. 27A). We will follow standard procedures and have experience with all mentioned behavior assays. A Ythdf1- / - mice in the physiological humanized A^ [with familial AD-linked mutations] knock-in model of cerebral amyloidosis (APPSAAF^OF^^^^^&^^^^^^^^^^^^^^^SAAfor simplicity) will be generated to investigate YTHDF1’s involvement in the pathophysiological sequelae of cerebral amyloid burden, and neuroinflammation. APPSAAis an excellent model for testing this hypothesis because this human APP KI line avoids APP overexpression artifacts ^ Docket No.: 11001-216WO1 and phenocopies key pathogenic features, including robust microglial response to A^ deposition. Colonies of APPSAA:Ythdf1- / - mice will be bred in C57BL / 6J genetic background to generate the cohorts needed for this investigation: Wt, Ythdf1- / -, APPSAA, and APPSAA:Ythdf1- / -. Comparative analyses using PS19 and PS19:Ythdf1- / - mice will be performed. In preliminary studies, it was found that the loss of YTHDF1 expression does not result in adverse effects in the PS19 background or the 5XFAD background. Generation of Ythdf1- / - mice in the APPSAAKI / KI background will be insightful into other AD because the APPSAAmodel is more physiologically reflective of human AD without confounding APP overexpression artifacts. Through an integrated analysis of eCLIP- and RNAseq data, several transcription factors were further identified among the ~400 YTHDF1 targets that could account for key pathways regulated by differentially expressed genes. The goal of this aim will be to generate the YTHDF1-dependent epitranscriptomic signature of the APPSAAmouse brain and perform parallel reaction monitoring (PRM) validation. Furthermore, the findings will be corroborated in post- mortem AD brains using YTHDF1-RNA immunoprecipitation qPCR (RIP-qPCR). Example 12. Amyloid pathogenesis in mice lacking YTHDF1 alleles To test the hypothesis that YTHDF1 function modifies cerebral A^ burden and neuroinflammatory response, the APPSAA:Ythdf1- / - mouse will be examined for A^ pathology. The novel APPSAAmodel has been extensively characterized to have no change in APP expression levels, altered APP processing resulting in elevated A^42 / 40 ratio (by 4 month), progressive amyloid deposition (by 4 month), and neuroinflammation. Assays will be performed to compare the extent of neuropathology in cohorts of APPSAAand APPSAA:Ythdf1- / - mice at 3, 6, and 9-months of age to quantify pathology between sexes and genotypes as they age and deposit increasing amounts of A^. To characterize amyloid pathogenesis, APP metabolism will be analyzed by immunoblots of brain extracts (the levels of full-length APP, APPs^, APPsJ, ^-CTFs), quantify the levels of A^ 38 / 40 / 42 species in brain homogenates by MSD multiplex assay (n=10 / genotype / sex) and perform IHC / IF analysis (n=10 / genotype / sex) of amyloid deposition (ThioS, mAb 3D6, mAb Ab9, and pAb M78 immunostaining). Astrocyte (GFAP) and microglia (IBA1 and CD68) activation will be assessed at the gross level by IF. To quantify synaptic and neuronal loss, WB and IF analysis of synaptophysin and PSD95 levels will be performed and the results will be overlapped and assessed by PSD95 / C1q co-localization. PSD95, an excitatory post-synaptic protein marker, ^ Docket No.: 11001-216WO1 and C1q, a complement system immune protein, co-localize in synapses far in advance of A^ plaque deposition and mediate early synapse loss. By comparing the results from APPSAAand APPSAA:Ythdf1- / - mice, it will be determined whether the loss of YTHDF1 expression modifies cerebral amyloid burden (FIG. 27A). Example 13. Testing whether YTHDF1 function regulates neuroinflammation in response to amyloid deposition The scope of this Example is to perform a detailed molecular characterization of gene expression and microglial activation status in APPSAAmice with and without Ythdf1 expression. First, FACS analysis will be performed on mononuclear cells isolated from the cortex and hippocampus of 3-, 6-, and 9-month old APPSAAand APPSAA:Ythdf1- / - mice (n=6 / genotype / sex) to measure the surface expression of CD11b, CD45, CD11c, and Ly6c (FIG. 27A). The three time points represent mice with a mild, moderate, and severe amyloid burden. This experiment will allow the quantification of the proportion of DAM microglia (surface CD11c expression) and correlate to the extent of amyloid burden in APPSAAmice with or without YTHDF1 expression. The ex vivo studies will be complemented by immunostaining brain sections using select homeostatic and DAM phenotype markers, including IBA1, P2RY12, TMEM119, TYROBP, TREM2, CD11c, CST7, CLEC7a, and IFITM3 along with ThioS and A^ antibodies (mAb 3D6 and pAb M78 to stain all A^ and fibrillar A^, respectively) (n>6 / genotype / sex). Finally, RT-qPCR analyses will also be performed on total RNA isolated from whole brain and sorted microglia to quantify the expression of genes representing pro-inflammatory, anti-inflammatory, immune checkpoint, IFN^ response, IFN^ response, shared interferon response, LPS super-responder astrocyte, homeostatic microglia, DAM1 microglia, DAM2 microglia, CC Chemokines, CXC chemokines, and complement genes (FIG.27A). Second, in vivo labeling of A^-containing microglia will be performed in 3-, 6-, and 9- month-old mice by administering methoxy-X04 (10 mg / kg, i.p.) and FACS-isolate CD11b+CD45int microglia the following day (n=6 / genotype / sex), essentially as described previously. Methoxy-X04+ (A^-containing) and negative microglia will be collected for bulk RNAseq analysis. Transcriptomics data will be analyzed using a combination of differential expression and network analytic (Weighted Gene Co-expression Network Analysis) approaches. One-way ANOVA will be used to identify group-wise differences in the RNAseq ^ Docket No.: 11001-216WO1 data, followed by post-hoc pairwise comparisons (Tukey’s HSD) with Benjamini-Hochberg correction (FDR<5%) for multiple-pairwise comparisons using R software and statistical analyses in GraphPad Prism v.10 or SPSS v.26. PCA, K-means clustering of DEGs, and MAGMA will be performed as in preliminary results described herein (FIG.13A-13E). Gene Ontology (GO) functional annotation of modules with traits will be performed to identify molecular processes and biological functions regulated by DEG groups, indicating key cellular processes over- or under-represented in the different groups. Finally, APPSAA:Ythdf1- / - mouse networks will be compared to the networks identified in human brain data from ROS- MAP, AMP-AD, and other published transcriptomic datasets in AD models, such as the enrichment of homeostatic versus DAM genes. Overall, insights into cellular pathways and signaling mediators will identify key drivers linking YTHDF1 expression to its role in modulating amyloid neuropathology. Expected results and interpretation. Based on preliminary data from PS19 and LPS models, it is expected that the loss of YTHDF1 will attenuate inflammatory response in the brain, regardless of discernable differences in cerebral amyloid burden. Based on YTHDF1’s positive regulation of DAM genes during the LPS response and in tauopathy mice, one could expect the loss of YTHDF1 might impair the microglial degradation or compaction of A^. A detailed characterization of microglial phenotype and their proximity to A^ deposits in mice, complemented by transcriptional profiling of X04+ and X04- microglia, will help interpret the pathological findings appropriately. Based on preliminary findings, it is expected that the loss of YTHDF1 will significantly decrease the proportion of CD11c+ microglia amongst CD11b+CD45int microglia. If this is the case, it is an indication that the YTHDF1 function is critical for microglial transition to the DAM state. An RNAseq analyses will corroborate the FACS data and provide additional insights into m6A-YTHDF1-mediated disease pathways. Since the APP KI mice will be employed, confounding issues arising from APP overexpression will be avoided. As depicted in FIG. 3, A^ deposits are readily observed and microglial activation near the deposits in 8-month-old APPSAAmice. There is growing consensus that APPSAAand APPNL-G-F KI mice are excellent experimental models to dissect pivotal disease mechanisms related to A^ deposition. On the other hand, the 5XFAD line has been successfully used to study microglial activation states and their responses to amyloidosis following the manipulation of LOAD risk factors TREM2 and CD33, as well as neuroinflammation signaling. 5XFAD:Ythdf1- / - mice will be considered as an alternate model. As this investigation proceeds, conducting single-cell ^ Docket No.: 11001-216WO1 RNAseq studies might become necessary for a more detailed characterization of the microglial transition states. Example 14. Testing whether YTHDF1-dependent m6A function is altered during AD progression There is sufficient data to implicate m6A RNA regulation in biological processes associated with cognitive impairment and AD progression. Consistent with post-transcriptional gene regulation in AD, large-scale multi-omics analysis of the AD brain revealed strong proteomic changes related to the disease not observed at the RNA level. YTHDF1 transcript abundance is significantly higher in the brains of patients with AD and in microglia isolated from 5XFAD brains. In preliminary studies, it was observed YTHDF1 expression in microglia and astrocytes in the human brain and AD models (FIG. 2, 3, 4, 5A-5B). Furthermore, characterization of PS19:Ythdf1- / - mice revealed an essential YTHDF1 function in the activation of inflammatory gene expression in response to tauopathy (FIG. 13A-13E, 14A- 14B). YTHDF1-mediated m6A RNA translation will be characterized in the context of AD amyloid pathogenesis to gain molecular insights. There is only scant information on the cellular expression of YTHDF1 in the human brain, and nothing is known about the m6A-YTHDF1 modality of gene expression in individuals with AD. To elucidate the precise role of YTHDF1 in AD, it is imperative to identify YTHDF1 bound m6A transcripts in the context of AD pathogenesis. To address this issue, eCLIP-seq of APPSAAmice will be performed, using the approach described herein used to study PS19 mice (FIG. 18-25, 26A-26B). A comparison of eCLIP-seq data from non-transgenic, PS19, and APPSAAmice will reveal novel insights and elucidate how m6A-YTHDF1 modality for translation influences AD pathophysiology. The enhanced CrossLinking ImmunoPrecipitation (eCLIP) workflow will be applied to crosslink m6A RNA-YTHDF1 complexes and selectively identify the transcripts bound by YTHDF1 in Wt (no pathology), APPSAA, and APPSAA:Ythdf1- / - (negative control) mouse brains (n=6 / genotype / sex, at 3-, 6-, and 9-months of age). For the eCLIP-seq assay, frozen mouse hippocampus and cortex tissue will be ground into fine powder by cryo-grinder and exposed to 400 mJ / cm2 254 nm ultraviolet radiation to stabilize protein-RNA interaction by UV- crosslinking. Complexes will be subject to optimized sonication, and m6A RNA-YTHDF1 complexes will be immuno-isolated using YTHDF1 mAb-coupled to Dynabeads. Specific mAb against YTHDF1 is a crucial reagent which has been generated (FIG. 11A-11B). Bound m6A RNA fragment-YTHDF1 complexes above 75 kDa protein size will be ^ Docket No.: 11001-216WO1 isolated by gel fractionation (FIG. 18^^^^^)^9^^^^^^^^^^^^^^^^^^^)^^^^^^^^^^F^^^^^^^^^^^^>-^^ fragments bound to YTHDF1. Subsequently, the RNA fragments will be used to prepare libraries for NextGen sequencing 33 (FIG. 18). Finally, size-matched input control (SMInput) libraries will be generated using 2% fragmented samples at the pre-IP stage to serve as critical non-specific background signals. The libraries will be sequenced using standard SE75 conditions on the Illumina NextSeq 2000 platform (USF Genomics Core). Two approaches will be used, incorporating negative controls to improve the reliability of our eCLIP data. First, eCLIP libraries will be produced from an IgG isotype-only control, which should capture non-specifically immunoprecipitated RNA fragments at a much lower abundance than YTHDF1 mAb. Second, eCLIP libraries will be generated from APPSAAand APPSAA:Ythdf1- / -mice and compared, with the expectation that libraries made from KO mouse brain tissue using YTHDF1 mAb will only have non-specifically captured RNA fragments. Moreover, SMInput normalization will help us filter out experimental artifacts from the dataset. Since YTHDF1 is an abundant RNA-binding protein, 25 million reads per eCLIP-seq dataset will provide enough coverage for a comprehensive analysis. Raw reads will be processed using Eclipsebio’s analysis pipeline (Lunar, v1). Unique molecular identifiers (UMIs) will be pruned using umi_tools (v1.1.1). Adapter sequences will be trimmed using cutadapt (v3.2), and reads will be mapped to a custom database of repetitive elements and rRNA sequences. Non-repeat reads will be mapped to the mm10 genome using STAR (v2.7.7a), and PCR duplicates will be removed with umi_tools. RBP-eCLIP peaks will be identified using CLIPper (YeoLab / clipper) and validated with exomePeak2 (ZW- xjtlu / exomePeak2) and MeTDiff (compgenomics / MeTDiff). For each peak, IP versus input fold enrichments and p-values will be calculated, and significant peaks will be filtered by stringent cutoff: log2 (FC) > 3 and -log10 (p value) > 3. Peaks will be annotated using GENCODE M25, and metagene analysis will be performed using the Guitar package (ver 2.20.0). Gene set enrichment analysis and visualization will be conducted using clusterProfiler (YuLab-SMU / clusterProfiler) and vissE (DavisLaboratory / vissE). The data will be visualized as heatmap and volcano plots, and YTHDF1-bound differentially abundant target transcripts (Y-DATs) will be summarized as GO pathways and protein interaction networks to gain novel insights. The YTHDF1-mediated translational regulation of select Y-DATs will be validated. Specifically, a set of eCLIP-identified transcripts will be chosen from the above analysis and ask if the encoded protein abundance differs in Ythdf1- / - mice. To accomplish this goal, global and targeted proteomic approaches will be performed using data- independent acquisition ^ Docket No.: 11001-216WO1 (DIA) and parallel reaction monitoring (PRM) analyses to quantify the steady-state levels of Y-DAT-encoded proteins in brain lysates prepared from Wt and Ythdf1- / -, APPSAA, and APPSAA:Ythdf1- / - mice (n=6 / genotype / sex, at 3-, 6- and 9-months of age) (FIG.27B). Cortical and hippocampal tissues will be processed using the iST sample preparation kit (PreOmics, GMBH) and an optimized protocol. Digested peptides will then be analyzed by dia-PASEF using a timsTOF Pro instrument with a nanoElute 2 UHPLC system. A spectral library will be generated through data-dependent acquisition (DDA) of fractionated (offline high pH reversed-phase HPLC) trypsin-digested lysate of pooled Wt, Ythdf1- / -, APPSAA, and brains. MSFragger (v. 4.10) will be used to search dda-PASEF raw data against the Uniprot mouse proteome database, filtering at a 1.0% FDR for both peptides and proteins. Search results will be utilized to build a spectral library (using EasyPQP) for subsequent dia-PASEF analysis of the mouse brain tissue obtained from our experimental groups (e.g., Wt, Ythdf1- / -, APPSAA, and APPSAA:Ythdf1- / - mice). Library-free DIA searching will also be employed to refine our results and ensure the most comprehensive proteome coverage. DIA searching and label-free quantitation (LFQ) of selected targets will be performed by DIA-NN (v.1.8.1). PRM will then be utilized to validate DIA results and improve detection and precision for quantifying lower abundance proteins. The timsTOF Pro will be operated in prm-PASEF mode using the same LC method as the DIA analysis to cover selected targets based on m6A RNA-YTHDF1-mediated translational regulation (see above). PRM acquisition parameters for each target will be extracted from the DIA data using an in-house script 73 to optimize peptide selection and scheduling for peak quantitative precision. PRM data will be compared against empirical libraries using Skyline v. 23.1 to ensure high-quality library matching (dotp > 0.9). For PRM statistical analysis, the total area for each peptide target will be utilized to quantitatively compare selected targets between the genotype groups using the MSstats tool installed within Skyline. MSstats results will be filtered based on a p.adj < 0.05. To date, YTHDF1 localization in the human brain was examined in a single study that used brain tissue from 4 controls and 5 individuals with mild cognitive impairment. Moreover, this study did not examine advanced AD cases. Thus, the results from this study are inadequate for making unambiguous conclusions regarding disease-associated changes in the cell-type expression pattern of YTHDF1. To this end, mAbs were generated that uniquely react with YTHDF1 (no immunoreactivity in Ythdf1- / - ^^^^^^^FIG. 11A-11B) and YTHDF1 expression has been characterized in mouse models and human brain (FIG.2, 3, 4, 5A-5B, 7-8, 12). ^ Docket No.: 11001-216WO1 The cellular expression of YTHDF1 in AD cases relative to age-matched controls will be examined ^^M9A^)^^^^^^ )^^^^^^^^^1^^^^'^^' ^^^^^^^%^^^)^^^^^^)^^^^^^^^^%^^^^ / ^Staining of control and AD samples has been initiated and the sample size will be adjusted based on the pilot data. RNA-Binding Protein Immunoprecipitation-qPCR analysis (RIP- qPCR) of post- mortem frozen tissue (prefrontal cortex) from AD cases and age-matched controls will be performed ^^M9A^)^^^^^^ )^^^^^^^^^1^^^, with the goal of validating findings from AD mouse models in human brain tissue (FIG.27B). Specifically, a list of Y-DATs from the APPSAAcohort and PS19 cohort has been generated. It will be assessed whether Y-DAT's abundance will differ between control and AD brains. RIP-qPCR workflow utilizes the initial steps of eCLIP, but after crosslinking, the samples are used for immunoprecipitation using YTHDF1 mAb without fragmentation. RNA will be then isolated and used for qPCR analysis of Y-DATs. Through YTHDF1 RIP-qPCR, we will quantify the abundance of Y-DATs in AD brains relative to age- matched controls. By combining the outcome of this investigation (APPSAA) and available data from the PS19 model, it is expected to identify YTHDF1-bound m6A RNA targets under AD pathogenic conditions to generate important insights. Specifically, identifying microglial transcripts in the eCLIP-seq data will advance the field by elucidating how the m6A reader YTHDF1 functions in mRNA translation regulation by influencing AD pathogenesis and neuroinflammation. Integrating unbiased large-scale datasets (RNAseq and eCLIP-seq) from 3-, 6-, and 9-month- old APPSAAand PS19 mice will also provide tremendous power to make significant discoveries that will be both novel and highly significant. Concordance between eCLIP-seq and PRM quantification of proteins is expected in APPSAAvs. APPSAA:Ythdf1- / - comparison. It is also expected that RIP-qPCR analysis will reveal significant differences between control and AD cases and indicate congruency with the eCLIP-seq from AD mouse models. The combined data from cellular YTHDF1 expression in the human brain and RIP-qPCR analysis will establish a cell-type specific function for YTHDF1 in AD pathogenesis. There is growing interest in understanding the regulation of gene expression by dynamic m6A RNA modification. m6A-RNA-mediated signaling has been described in multiple neuronal functions and brain dysfunction. Although alterations in m6A modifications have been implicated in brain disorders, the functional consequences of such global m6A have not been experimentally linked to biological mechanisms relevant to AD pathophysiology. Rationale: Preliminary data suggest that YTHDF1 function dynamically modulates microglial gene expression in response to acute and chronic inflammatory challenges (FIG. ^ Docket No.: 11001-216WO1 14A-14B). The studies using the in vivo LPS model as described herein are highly relevant because a meta-analysis of microglial / myeloid cell expression profiles from mouse models and human neurodegenerative diseases identified the induction of IFN-related and LPS-related transcripts in 5XFAD microglia in a TREM2-dependent manner. The goal of this Example is to characterize how YTHDF1 participates in the regulation of inflammatory responses, through a combination of unbiased and hypothesis-driven approaches, including transcriptomics, proteomics, and analysis de novo protein synthesis in Ythdf1- / - mice. This comprehensive experimental design will allow the definition of how YTHDF1-mediated translation of m6A RNA dynamically facilitates neuroimmune signaling. To perform RNAseq analysis of YTHDF1’s function in adaptive response to acute versus chronic LPS challenges. Studies will perform RNAseq analysis on forebrain tissue from Wt and Ythdf1- / - mice (n=6 / genotype / sex) administered 0.75 mg / kg LPS to elicit a ^^ ^^^^&^^^^^^^^%^^^^)^^^^^^'^^^^^^^^^^^^^^^^^^^^^^'^^2^^^^^^^^ / ^>-^^^^^^^^^^^^^^^^^^^^^^^^&^^^^ the single LPS (acute) or after four consecutive days of LPS administration (chronic) (FIG. 14A-14B). Preliminary studies using RNA isolated from 8- month-old Wt and Ythdf1- / - mice after acute and chronic LPS challenge have been performed (FIG.14A-14B). Preliminary RT-qPCR analysis will be extended using an unbiased RNAseq approach and generate important insights into YTHDF1 function in LPS-mediated inflammatory activation. Transcriptomics data will be analyzed using a combination of differential expression and WGCNA approaches. Briefly, the data will be examined by PCA, identify LPS-induced ^5^^^^) / ^^7^., / ,^^^C^^9^6^+, / A^^^^^Ythdf1- / - compared to Wt controls, and perform K- means clustering of DEGs to elucidate gene clusters and biological pathways regulated by YTHDF1 function under acute and chronic neuroinflammatory challenge. To perform proteomic characterization of YTHDF1’s function in adaptive response to acute versus chronic LPS challenges, deep discovery proteomics will be performed of Wt and Ythdf1- / - mice acutely or chronically challenged with LPS. Cortical and hippocampal tissue samples from saline- or LPS-administered animals (n=6 / genotype / sex) will be processed for peptide isolation and analyzed by diaPASEF using a timsTOF Pro instrument with a nanoElute 2 UHPLC system as described above. DIA library matching (using libraries generated as previously described) and quantitation will be performed by DIA-NN (v.1.8.1). Perseus (v.2.0) will be utilized for statistical analysis and filtering of DIA-NN output following statistical rationale / analysis below. Sample sizes are estimated based on power analysis with expected variability from label-free quantitation (LFQ) of brain tissue proteome datasets obtained in our labs. ^ Docket No.: 11001-216WO1 Considering LFQ-based method and depth of coverage in terms of quantifiable proteins, an average CV of 10-15% was obtained at a depth of proteome coverage of >8,000 proteins in a standard data-independent acquisition approach (FIG.28A-28B). Considering this average CV and alpha=0.05, n=5 is sufficient to achieve 0.90 power at >1.5 fold-change (effect size cutoff is 2.61 for the two-tailed difference between two independent means using G*Power 3.1). This^^^^^^^^'^^^ '^^' ^^^^^^^ ^^^ ^^^^^^ ^^^ ^^^ ^2^^^^^^ 6P^ &^^^ ^^^^ ^^^^^^^ ^^^^^^^^^ ^^^^2^^^^ C^Q^measurement error tends to increase with decreasing LFQ intensity and unique peptide coverage (lower abundance proteins). Therefore, n=6 / genotype / sex will be utilized. A conventional FDR correction approach (e.g., Benjamini-Hochberg) is not sufficiently sensitive to determine differentially expressed proteins in two-group comparisons. However, a combined filtering approach that considers variance and t-test difference will be used (Welch’s t-test and z-score), which has been shown to adequately control FDR (<10% typically) while maintaining sensitivity. ANOVA with permutation-based FDR (<0.05) will be employed for multiple group comparisons. All dataset quality assessment, filtering, imputation, and statistical analyses will be performed in Perseus (v.2.0). Differentially expressed proteins will be uploaded into Ingenuity Pathway Analysis to determine enriched canonical pathways, upstream regulators, and biological / disease processes as determined by Fisher’s exact test with Benjamini-Hochberg correction (corrected p value < 0.05). Bioinformatic prediction of activation / inhibition of these regulators and pathways will be based on z-score value (> 2 or <-2 for predicted activation or inhibition, respectively). Additional bioinformatic analysis will be performed with MetaNetwork, which implements the WGCNA approach for proteomics data. Unsupervised generation of protein clusters (modules) will be performed, followed by pair-wise comparison of experimental groups based on mean module eigenprotein expression values. G:Profiler will be used to determine functional roles of the significantly changed module eigenproteins and STRING to verify protein-protein interaction networks within these modules. Validation of Proteomics: The strongest novel candidate hits and pathways will be validated by orthogonal assays (e.g., IHC and immunoblotting). Furthermore, proteomics studies will be complemented by measuring signaling events in MAPK (ERK, JNK, and p38 MAPK), Akt / mTOR / PI3K, and NF-KB signaling pathways using Luminex assays of specific phospho-proteins. To characterize m6A RNA-YTHDF1 mediated de novo protein synthesis, YTHDF1- m6A-dependent translational profiles will be measured in brain slices. De novo protein synthesis will be examined using an established BONCAT method. L-azidohomoalanine ^ Docket No.: 11001-216WO1 (AHA) is an amino acid analog of methionine that contains an azido moiety, which can be detected later by Click-chemistry. Coronal slices of cortex and hippocampus (250 R^^^^^'E^^^^ per brain) from saline or LPS-administered (acute or chronic) Wt and Ythdf1- / - mice (n=6 / genotype / sex) will be incubated with ACSF containing 1 mM AHA for 3h. Protein synthesis will be inhibited with cycloheximide (negative control) or stimulated with forskolin (positive control) by adding them 15 minutes before adding AHA. Aliquots of homogenates will be subject to a Click-chemistry reaction to tag AHA with biotin-alkyne, and nascent proteins will be captured on streptavidin beads. Nascent protein synthesis will be quantified, and the samples will be processed for DIA proteomics and analyzed as discussed above. Proteins translated in a YTHDF1-dependent manner will be determined by comparing LFQ measurements from Wt and Ythdf1- / - mice. Additional comparisons will identify YTHDF1- dependent proteins differentially translated during acute and chronic inflammatory conditions. Bioinformatic analysis (as described above) will be performed to elucidate biological pathways regulated by YTHDF1-dependent de novo protein synthesis under acute and chronic neuroinflammatory challenges. The transcriptomic and proteomic landscape in the mouse brain will be defined in the context of LPS-induced acute and chronic neuroinflammation. These efforts will determine YTHDF1-dependent functional changes at the transcript and protein levels and reveal YTHDF1-dependent biological pathways involved in brain neuroinflammatory responses. The results are expected to indicate that the YTHDF1 function limits activation of the acute response but is required to sustain the chronic inflammatory response (see, e.g., FIG.14A-14B herein). The results from YTHDF1-m6A-mediated de novo protein synthesis studies will provide novel insights into the temporal window of YTHDF1 function during the inflammatory response. Sn overlap in YTHDF1-dependent functional changes between the data from the LPS model and APPSAAmice is also expected. Characterization of dynamic translational control and behavioral adaptations by m6A mRNA methylation and YTHDF1 in the striatum is ongoing. ^ Docket No.: 11001-216WO1 REFERENCES References cited herein are not an admission of prior art. 1. Wardowska A. m6A RNA Methylation in Systemic Autoimmune Diseases-A New Target for Epigenetic- ^^^^^^"^^^^)%S^^^^^^^'^ ^^'^^^^^^^^^^^ / ^9,9^^^=^^^ / ^5) ^^9,9^,^,A / ^ ^^^:^^, / ^^B,O)^^=,^,9^< / ^^ ^*^^^^*^^:^^^<,;;^9^^^*6^^:^^*6<,,^A9B / 2. Li J, Yang X, Qi Z, Sang Y, Liu Y, Xu B, Liu W, Xu Z, Deng Y. The role of mRNA m6A ^^^^%^^^^^^^^^^^^^^^^^2^ ^^^%^^^^ / ^6^^^^H^^^^^'^^^'^ / ^9,^B^B^^^ / ^^^^:^^, / ^^<^O^^^A;<-019- 0330-y. 3. Fu Y, Dominissini D, Rechavi G, He C. Gene expression regulation mediated through ^^2^^^^^^^^^^^^^^>-^^^^^^%^^^^^^ / ^-^^^>^2^^^^^^ / ^9,^=^^A^A^:9B^-306. Epub 2014 / 03 / 26. doi: 10.1038 / nrg3724. PubMed PMID: 24662220. 4. Jiang X, Liu B, Nie Z, Duan L, Xiong Q, Jin Z, Yang C, Chen Y. 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Biol., 2024, 5, 914-923 ^ Docket No.: 11001-216WO1 SEQUENCES SEQ ID NO: 1 – YTHDF1 nucleic acid sequence (DNA) atgtcggccaccagcgtggacacccagagaacaaaaggacaagataataaagtacaaaatggttcgttacatcagaaggatacagtt catgacaatgactttgagccctaccttactggacagtcaaatcagagtaacagttacccctcaatgagcgacccctacctgtccagctatt acccgccgtccattggatttccttactccctcaatgaggctccgtggtctactgcaggggaccctccgattccatacctcaccacctacg gacagctcagtaacggagaccatcattttatgcacgatgctgtttttgggcagcctgggggcctggggaacaacatctatcagcacag gttcaattttttccctgaaaaccctgcgttctcagcatgggggacaagtgggtctcaaggtcagcagacccagagctccgcgtatggga gcagctacacctaccccccgagctccctgggtggcacggtggttgatgggcagccaggctttcacagcgacaccctcagcaaggcc cccgggatgaacagcctggagcagggcatggttggcctgaagattggggacgtcagctcctccgccgtcaagacggtgggctctgt cgtcagcagcgtggcactgactggtgtcctttctggcaacggtgggacaaatgtgaacatgccagtttcaaagccgacctcgtgggct gccattgccagcaagcctgcaaaaccacagcctaaaatgaaaacaaagagcgggcctgtcatggggggtgggctgccccctccac ccataaagcataacatggacattggcacctgggataacaaggggcctgtgccgaaggccccagtcccccagcaggcaccctctcca caggctgccccacagccccagcaggtggctcagcctctcccagcacagcccccagctttggctcaaccgcagtatcagagccctca gcagccaccccagacccgctgggttgccccacgcaacagaaacgcggcgtttgggcagagcggaggggctggcagcgatagca actctcctggaaacgtccagcctaattctgcccccagcgtcgaatcccaccccgtccttgaaaaactgaaggctgctcacagctacaac ccgaaagagtttgagtggaatctgaaaagcgggcgtgtgttcatcatcaagagctactctgaggacgacatccaccgctccattaagta ctccatctggtgtagcacagagcacggcaacaagcgcctggacagcgccttccgctgcatgagcagcaaggggcccgtctacctgc tcttcagcgtcaatgggagtgggcatttttgtggggtggccgagatgaagtcccccgtggactacggcaccagtgccggggtctggtc tcaggacaagtggaaggggaagtttgatgtccagtggatttttgttaaggatgtacccaataaccagctccggcacatcaggctggaga ataacgacaacaaaccggtcacaaactcccgggacacccaggaggtgcccttagaaaaagccaagcaagtgctgaaaattatcagtt cctacaagcacacaacctccatcttcgacgactttgctcactacgagaagcgccaggaggaggaggaggtggtgcgcaaggaacg gcagagtcgaaacaaacaatga SEQ ID NO: 2 – YTHDF1 amino acid sequence (AA) MSATSVDTQRTKGQDNKVQNGSLHQKDTVHDNDFEPYLTGQSNQSNSYPSMSDPYL SSYYPPSIGFPYSLNEAPWSTAGDPPIPYLTTYGQLSNGDHHFMHDAVFGQPGGLGNN IYQHRFNFFPENPAFSAWGTSGSQGQQTQSSAYGSSYTYPPSSLGGTVVDGQPGFHSD TLSKAPGMNSLEQGMVGLKIGDVSSSAVKTVGSVVSSVALTGVLSGNGGTNVNMPV SKPTSWAAIASKPAKPQPKMKTKSGPVMGGGLPPPPIKHNMDIGTWDNKGPVPKAP VPQQAPSPQAAPQPQQVAQPLPAQPPALAQPQYQSPQQPPQTRWVAPRNRNAAFGQS GGAGSDSNSPGNVQPNSAPSVESHPVLEKLKAAHSYNPKEFEWNLKSGRVFIIKSYSE DDIHRSIKYSIWCSTEHGNKRLDSAFRCMSSKGPVYLLFSVNGSGHFCGVAEMKSPV DYGTSAGVWSQDKWKGKFDVQWIFVKDVPNNQLRHIRLENNDNKPVTNSRDTQEV PLEKAKQVLKIISSYKHTTSIFDDFAHYEKRQEEEEVVRKERQSRNKQ SEQ ID NO: 3 – YTHDF1 siRNA (RNA) ^ Docket No.: 11001-216WO1 GCACTGACTGGTGTCCTTT SEQ ID NO: 4 – shYTHDF1 (RNA) GATACAGTTCATGACAATGA SEQ ID NO: 5 – shYTHDF1 (RNA) CAGGCTGGAGAATAACGACAA SEQ ID NO: 6 – YTHDF1 guide RNA (RNA) AGCAGCCACTTCAACCCCGCTGG SEQ ID NO: 7 – YTHDF1 guide RNA (RNA) GGACCATGGTGCCTCGCTGAGGG SEQ ID NO: 8 – YTHDF1 forward primer (DNA) GGCAGAAGGGTGGTTTGACTG SEQ ID NO: 9 - YTHDF1 reverse primer (DNA) GAGCGGTGGATGTCGTCCTC ^

Claims

Docket No.: 11001-216WO1 CLAIMS What is claimed is:

1. A method for treating a subject at risk for or having neurodegenerative disease, comprising administering a therapeutically effective amount of an inhibitor of YTH domain-containing family protein 1 (YTHDF1).

2. The method of claim 1, wherein the neurodegenerative disease is selected from Alzheimer’s disease, amyotrophic lateral sclerosis (ALS), spinocerebellar ataxia 2 (SCA2), Parkinson’s disease, chronic traumatic encephalopathy (CTE), multiple sclerosis, depression, epilepsy, spinocerebellar ataxia type 1, Machado-Joseph Disease, Down's syndrome, Dementia puglistica, Pick's disease, progressive supranuclear palsy (PSP), Guam parkinsonism dementia complex, Fronto-temporal dementia (FTD), Cortico-Basal Degeneration (CBD), Pallido-Pontal-Nigral Degeneration, Progressive Nuclear Palsy (PNP), Parkinsonism of Chromosome 17 (FTDP-17), Dementia with Lewy bodies, Huntington's disease, Multiple System Atrophy, fatty liver disease (liver steatosis), al-anti-trypsin deficiency, muscle diseases, sporadic inclusion body myositis, limb girdle muscular dystrophy type 2B, prion disease, Creutzfeldt-Jakob disease, or Miyoshi myopathy.

3. The method of claim 1 or 2, wherein the neurodegenerative disease is Alzheimer’s disease.

4. A method for treating a subject at risk for or having Alzheimer's disease, comprising administering a therapeutically effective amount of an inhibitor of YTHDF1.

5. A method for treating a subject at risk for or having a neurodegenerative disease, comprising: (i) ^^^^^^^^^^^^^^^)^^^&^^^^^^^^^ ^7^'^^ (ii) detecting whether one or more transcripts comprising or polypeptides encoded by a human homolog of Muc1, Adamts1, Loxl1, Eln, Lox, Thsd4, Serpine1, Il33, Ptger4, Epha6, Rtn4rl2, Prkcg, Kcnip2, Cpne6, Grm2, Rgs14, Ptk2b, Atp2b4, Icam5, Tamalin, Slc30a3, Nptx2, Actn2, Ablim3, Baiap2, Epha3, Auts2, Iqgap2, Myo5b, Ctsh, Hexa, Npc2, Ctss, Ctsc, Ctsd, Unc93b1, Cryab, Ctsz, Grn, Ctsl, Cst7, Gfap, Laptm5, Rab6b, Cd68, Man2b1, Hexb, Ifi30, Cd74, Ptprc, Cd22, Csf2rb, Lag3, St14, Fcer1g, Csf3r, Ly9, Cd9, Prnp, Cd86, B2m, Cd64, Osmr, Cd33, Itgax, Il21r, Plau, Abca1, Fas, Cd274, Icam1, Slamf9, Adgre1, Tgfbr2, Csf2rb, Itgb2, Gsdmd, Fcgr2b, C4b, Cscl10, Cd14, Aif1, Pld4, Axl, Tlr2, Cnr2, Cela1, Clec7a, Csf1r, Cd180, C3, Cyba, Csf1, Cybb, C4a, Tnfrsf1a, Ticam2, ^Docket No.: 11001-216WO1 Cxcl5, Siglec1, Ly86, Tlr1, Ptaf4, Nrros, S1pr3, Lgals9, Casp4, Cd44, Havcr2, Tgfb1, Pycard, C3ar1, Il1b, Slc11a1, F11r, Tlr7, Hgk, F11r, Irf5, Mpeg1, Gm9442, Mid1-Ps1, Mid1, A2m, Cdk1a, Neat1, Ly86, Lyz2, Erdr1, Gm47283, Gm21860, Lox, Lgals3, Neurod6, Lct, Gm37459, Rasl10a, Pcdh20, Dsp, Gm19963, Ccl6, Cst7, Itgax, Ccl4, or Clec7a, or a combination thereof, are ^^&&^^^^^^^^^%^^1)^^^^^^^^^^^^^^^^^)^^^'^^)^^^^^^^^^^^^'^^^^^^^^^^)^^^^^^^ (iii) if one or more transcripts comprising or polypeptides encoded by the genes in step ii) are differentially expressed, then administering a therapeutically effective amount of an inhibitor of YTHDF1.

6. The method of claim 5, wherein the one or more transcripts comprising or polypeptides encoded by a human homolog of Ccl6, Cst7, Itgax, Ccl4, or Clec7a, or a combination thereof.

7. The method of claim 5 or 6, wherein detecting step (ii) is carried out using RNA-seq.

8. The method of claim 5 or 6, wherein detecting step (ii) is carried out using mass spectrometry.

9. The method of claim 8, wherein detecting step (ii) is carried out using data-independent acquisition (DIA) and / or selective reaction monitoring (SRM) mass spectrometry.

10. The method of any one of claims 5-9, wherein the sample comprises blood.

11. The method of any one of claims 5-9, wherein the sample comprises cerebrospinal fluid.

12. The method of any one of claims 5-11, wherein the neurodegenerative disease is selected from Alzheimer’s disease, amyotrophic lateral sclerosis (ALS), spinocerebellar ataxia 2 (SCA2), Parkinson’s disease, chronic traumatic encephalopathy (CTE), multiple sclerosis, depression, epilepsy, spinocerebellar ataxia type 1, Machado-Joseph Disease, Down's syndrome, Dementia puglistica, Pick's disease, progressive supranuclear palsy (PSP), Guam parkinsonism dementia complex, Fronto-temporal dementia (FTD), Cortico-Basal Degeneration (CBD), Pallido-Pontal-Nigral Degeneration, Progressive Nuclear Palsy (PNP), Parkinsonism of Chromosome 17 (FTDP-17), Dementia with Lewy bodies, Huntington's disease, Multiple System Atrophy, fatty liver disease (liver steatosis), al-anti-trypsin deficiency, muscle diseases, sporadic inclusion body myositis, limb girdle muscular dystrophy type 2B, prion disease, Creutzfeldt-Jakob disease, or Miyoshi myopathy.

13. The method of any one of claims 5-12, wherein the neurodegenerative disease is Alzheimer's disease. ^Docket No.: 11001-216WO1 14. A method for treating a subject at risk for or having a neurodegenerative disease, comprising: (i) ^^^^^^^^^^>-^^&^^^^^^^^^)^^^&^^^^^^^^^ ^7^'^^ (ii) detecting whether N6-methyladenosine (m6A) methylation pattern of an RNA transcript comprising a human homolog of Pik3r1, Map2k4, Pak3, Pak1, Map2k1, Camk2g, Grm5, Gria3, Gria2, Grm1, Reep1, Kcnc2, Kcnc1, Kcnd2, Kcnd3, Camsap2, Gda, Mapt, Map1b, Pak1, Ank2, Ppp3cb, Atp2b4, Slc8a1, Pak1, Dnm3, Atl1, Myh10, Scn2a, Scn1a, Prkce, Sybu, Vsnl1, Ppp3cb, Atp2b2, Foxp2, Psap, Rora, Hcn1, Kcnd2, Scn2b, Kcnd3, Scn1a, Nceh1, Timp2, Nrf1, Ets2, Smad4, Crebbp, E2f1, Egr1, Ets1, Ep300, Cebpb, Nfe2l2, Stat1, Stat3, Sp3, Rela, Jun, Nfkb1, or Sp1, or a combination thereof, in the sample compared ^^^^^^^'^^^^^^^^^^)^^^^^^^ (iii) if one or more transcripts of the genes in step ii) have differentially methylated regions in the sample compared with the control sample, then administering a therapeutically effective amount of an inhibitor of YTHDF1.

15. The method of claim 14, wherein detecting step (ii) is carried out using RNA-seq.

16. The method of claim 14 or 15, wherein the sample comprises blood.

17. The method of claim 14 or 15, wherein the sample comprises cerebrospinal fluid.

18. The method of any one of claims 14-17, wherein the neurodegenerative disease is selected from Alzheimer’s disease, amyotrophic lateral sclerosis (ALS), spinocerebellar ataxia 2 (SCA2), Parkinson’s disease, chronic traumatic encephalopathy (CTE), multiple sclerosis, depression, epilepsy, spinocerebellar ataxia type 1, Machado-Joseph Disease, Down's syndrome, Dementia puglistica, Pick's disease, progressive supranuclear palsy (PSP), Guam parkinsonism dementia complex, Fronto-temporal dementia (FTD), Cortico-Basal Degeneration (CBD), Pallido-Pontal-Nigral Degeneration, Progressive Nuclear Palsy (PNP), Parkinsonism of Chromosome 17 (FTDP-17), Dementia with Lewy bodies, Huntington's disease, Multiple System Atrophy, fatty liver disease (liver steatosis), al-anti-trypsin deficiency, muscle diseases, sporadic inclusion body myositis, limb girdle muscular dystrophy type 2B, prion disease, Creutzfeldt-Jakob disease, or Miyoshi myopathy.

19. The method of any one of claims 14-18, wherein the neurodegenerative disease is Alzheimer's disease.

20. The method of any one of claims 1-19, wherein the inhibitor of YTHDF1 is selected from an antibody or a derivative thereof, an antibody-drug conjugate, a fusion protein, ^Docket No.: 11001-216WO1 a small molecule, a dsRNA, an siRNA, an anti-sense technology, an aptamer, a gene editing technology, or a combination thereof.

21. The method of claim 20, wherein the inhibitor of YTHDF1 is an antibody or a derivative thereof.

22. The method of claim 21, wherein the antibody or a derivative thereof comprises a monoclonal antibody.

23. The method of claim 21 or 22, wherein the antibody or a derivative thereof comprises a humanized antibody.

24. The method of claim 20, wherein the inhibitor of YTHDF1 is an antibody-drug conjugate.

25. The method of claim 20, wherein the inhibitor of YTHDF1 is a small molecule.

26. The method of claim 25, wherein the small molecule comprises 6-mercaptopurine hydrate, or a pharmaceutically acceptable salt thereof.

27. The method of claim 25, wherein the small molecule comprises ebselen, or a pharmaceutically acceptable salt thereof.

28. The method of claim 25, wherein the small molecule comprises niclosamide (NIC), or a pharmaceutically acceptable salt thereof.

29. The method of claim 25, wherein the small molecule comprises salvianolic acid C (SAC), or a pharmaceutically acceptable salt thereof.

30. The method of claim 25, wherein the small molecule comprises tegaserod, or a pharmaceutically acceptable salt thereof.

31. The method of any one of claims 25-30, wherein the small molecule blocks the binding of YTHDF1 to m6a-modified mRNAs.

32. The method of claim 20, wherein the inhibitor of YTHDF1 is an siRNA.

33. The method of claim 20, wherein the gene editing technology comprises CRISPR-based methods.

34. The method of any one of claims 1-33, wherein the inhibitor of YTHDF1 is formulated in lipid nanoparticles (LNPs).

35. The method of any one of claims 1-33, wherein the inhibitor of YTHDF1 is formulated in exosomes.

36. A method for preventing or treating neuroinflammation in a subject at risk for or having a neurodegenerative disease, comprising administering a therapeutically effective amount of an inhibitor of YTHDF1. ^Docket No.: 11001-216WO1 37. The method of claim 36, wherein the neuroinflammation comprises chronic neuroinflammation.

38. A method for preventing or treating neuroinflammation in a subject at risk for or having a neurodegenerative disease, comprising: (i) ^^^^^^^^^^^^^^^)^^^&^^^^^^^^^ ^7^'^^ (ii) detecting whether one or more transcripts comprising or polypeptides encoded by a human homolog of Ccl6, Cst7, Itgax, Ccl4, Clec7a, Il10, Tnfa, Ccl22, Irf1, Ifitm3, Spp1, Timp1, Gfap, Tgfb1, Arg1, Bst2, Spp1, or Vim are differentially ^1)^^^^^^^^^^^^^^^^^)^^^'^^)^^^^^^^^^^^^'^^^^^^^^^^)^^^^^^^ (iii) if one or more transcripts comprising or polypeptides encoded by the genes in step ii) are differentially expressed, then administering a therapeutically effective amount of an inhibitor of YTHDF1.

39. The method of claim 38, wherein detecting step (ii) is carried out using RNA-seq.

40. The method of claim 38, wherein detecting step (ii) is carried out using mass spectrometry.

41. The method of claim 40, wherein detecting step (ii) is carried out using data- independent acquisition (DIA) and / or selective reaction monitoring (SRM) mass spectrometry.

42. The method of any one of claims 38-41, wherein the sample comprises blood.

43. The method of any one of claims 38-41, wherein the sample comprises cerebrospinal fluid.

44. The method of any one of claims 36-43, wherein the neuroinflammation comprises chronic neuroinflammation.

45. A method for preventing or treating chronic neuroinflammation in a subject at risk for or having a neurodegenerative disease, comprising administering a therapeutically effective amount of an inhibitor of YTHDF1.

46. The method of any one of claims 36-45, wherein the neurodegenerative disease is selected from Alzheimer’s disease, amyotrophic lateral sclerosis (ALS), spinocerebellar ataxia 2 (SCA2), Parkinson’s disease, chronic traumatic encephalopathy (CTE), multiple sclerosis, depression, epilepsy, spinocerebellar ataxia type 1, Machado-Joseph Disease, Down's syndrome, Dementia puglistica, Pick's disease, progressive supranuclear palsy (PSP), Guam parkinsonism dementia complex, Fronto-temporal dementia (FTD), Cortico-Basal Degeneration (CBD), Pallido-Pontal-Nigral Degeneration, Progressive Nuclear Palsy (PNP), Parkinsonism of Chromosome 17 ^Docket No.: 11001-216WO1 (FTDP-17), Dementia with Lewy bodies, Huntington's disease, Multiple System Atrophy, fatty liver disease (liver steatosis), al-anti-trypsin deficiency, muscle diseases, sporadic inclusion body myositis, limb girdle muscular dystrophy type 2B, prion disease, Creutzfeldt-Jakob disease, or Miyoshi myopathy.

47. The method of any one of claims 36-46, wherein the neurodegenerative disease is Alzheimer's disease.

48. The method of any one of claims 36-47, wherein the inhibitor of YTHDF1 is selected from an antibody or a derivative thereof, an antibody-drug conjugate, a fusion protein, a small molecule, a dsRNA, an siRNA, an anti-sense technology, an aptamer, a gene editing technology, or a combination thereof.

49. The method of claim 48, wherein the inhibitor of YTHDF1 is an antibody or a derivative thereof.

50. The method of claim 49, wherein the antibody or a derivative thereof comprises a monoclonal antibody.

51. The method of claim 49 or 50, wherein the antibody or a derivative thereof comprises a humanized antibody.

52. The method of claim 48, wherein the inhibitor of YTHDF1 is an antibody-drug conjugate.

53. The method of claim 48, wherein the inhibitor of YTHDF1 is a small molecule.

54. The method of claim 53, wherein the small molecule comprises 6-mercaptopurine hydrate, or a pharmaceutically acceptable salt thereof.

55. The method of claim 53, wherein the small molecule comprises ebselen, or a pharmaceutically acceptable salt thereof.

56. The method of claim 53, wherein the small molecule comprises niclosamide (NIC), or a pharmaceutically acceptable salt thereof.

57. The method of claim 53, wherein the small molecule comprises salvianolic acid C (SAC), or a pharmaceutically acceptable salt thereof.

58. The method of claim 53, wherein the small molecule comprises tegaserod, or a pharmaceutically acceptable salt thereof.

59. The method of any one of claims 53-58, wherein the small molecule blocks the binding of YTHDF1 to m6a-modified mRNAs.

60. The method of claim 48, wherein the inhibitor of YTHDF1 is an siRNA.

61. The method of claim 48, wherein the gene editing technology comprises CRISPR-based methods. ^Docket No.: 11001-216WO1 62. The method of any one of claims 36-61, wherein the inhibitor of YTHDF1 is formulated in lipid nanoparticles (LNPs).

63. The method of any one of claims 36-61, wherein the inhibitor of YTHDF1 is formulated in exosomes.

64. The method of any one of claims 1-63, wherein the subject is a human. ^

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