Yi Zeng

All Publications

• An emergent disease-associated motor neuron state precedes cell death in ALS. Cell Gautier, O., Blum, J. A., Nguyen, T. P., Cao, S., Klemm, S., Yamakawa, M., Huh, D., Hurt, J. A., Sinnott-Armstrong, N., Zeng, Y., Davis, C. O., Bombosch, J., Liu, C., Encarnacion, L. N., Guttenplan, K. A., Chen, D., Kathiria, A., Zhao, L., Moore, S., Meng, A., Ong, K., Cleveland, D. W., Ravits, J., Rexach, J. E., Greenleaf, W. J., Gitler, A. D. 2026

  Abstract

  To define molecular determinants of motor neuron degeneration in amyotrophic lateral sclerosis (ALS), we generated longitudinal single-nucleus transcriptomes and chromatin accessibility profiles of spinal motor neurons together with spatial transcriptomics from the SOD1-G93A mouse model. Vulnerable alpha motor neurons showed thousands of molecular changes, marking a transition into a distinct cell state we named "disease-associated motor neurons" (DMs). We identified transcription factor networks that govern how healthy cells transition into DMs and those associated with motor neuron subtype-selective vulnerability. Upregulation of DM-associated transcription factors in human motor neurons induced key features of DMs, demonstrating an active regulatory component. Human ALS spinal cord single-nucleus RNA sequencing data demonstrated conservation of the DM signature in alpha motor neurons, and human orthologs of regions differentially accessible in SOD1-G93A mouse motor neurons were enriched for ALS genetic risk variants. Together, these findings establish a conserved, genetically linked motor neuron signature in ALS.

  View details for DOI 10.1016/j.cell.2026.05.047

  View details for PubMedID 42335888

• Cryptic splicing in synaptic and membrane excitability genes links TDP-43 loss to neuronal dysfunction. Science translational medicine Guo, C., Chen, K., Vatsavayai, S., Akiyama, T., Liu, C., Zeng, Y., Sianto, O., Yang, E., Bombosch, J., Powell, R., Zhen, S., Mekhoubad, S., Morrie, R. D., Miller, G., Ilic, D., Boll, M., Parnell, E., Penzes, P., Lipstein, N., Green, E. M., Petrucelli, L., Seeley, W. W., Gitler, A. D. 2026; 18 (852): eaeb8517

  Abstract

  TAR DNA binding protein 43 (TDP-43) pathology is a defining pathological hallmark of multiple neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). A major feature of TDP-43 pathology is its nuclear depletion, leading to the aberrant inclusion of cryptic exons during RNA splicing. STMN2 and UNC13A have emerged as prominent TDP-43 splicing targets, but the broader impact of TDP-43-dependent cryptic splicing on neuronal function remains unclear. Here, we report previously unidentified TDP-43 splicing targets critical for membrane excitability and synaptic function, including KALRN, RAP1GAP, SYT7, and KCNQ2. Using human stem cell-derived neurons, we showed that TDP-43 reduction induces cryptic splicing and down-regulation of these genes, resulting in impaired excitability and synaptic transmission. In postmortem brains from patients with FTD, these cryptic splicing events occurred selectively in neurons with TDP-43 pathology. Suppressing individual cryptic splicing events using antisense oligonucleotides partially restored neuronal function, and combined targeting almost fully rescued the synaptic deficit caused by TDP-43 loss. Together, our findings provide evidence that cryptic splicing in these synaptic and membrane excitability genes is not only a downstream marker but instead a direct driver of neuronal dysfunction, establishing a mechanistic link between TDP-43 pathology and neurodegeneration in ALS and FTD.

  View details for DOI 10.1126/scitranslmed.aeb8517

  View details for PubMedID 42234776

• Granulin loss and TMEM106B risk converge on lysosomal C-terminal fragment pathology in frontotemporal dementia. bioRxiv : the preprint server for biology Zeng, Y., Xiong, J., Lovchykova, A., Nguyen, T. P., Song, A., Gitler, S. W., Abu-Remaileh, M., Gitler, A. D. 2026

  Abstract

  Frontotemporal dementia (FTD) is the second most common cause of dementia after Alzheimer disease. Mutations in GRN, which encodes progranulin, are a major cause of FTD. Common genetic variants in the TMEM106B gene modify risk of FTD and the effect is especially strong in GRN mutation carriers. Intriguingly, in GRN mutation carriers, being homozygous for the protective TMEM106B haplotype seems to confer near lifetime protection against FTD. Despite the strong genetic link between GRN and TMEM106B, how these two genes interact mechanistically has remained unresolved. Recent studies have revealed that a C-terminal fragment of TMEM106B forms amyloid fibrils and accumulates in the brains of older individuals and patients with neurodegenerative disorders, including FTD. How the production of this fragment connects to granulin deficiency is also unknown. Using lysosome immunoprecipitation, we show that granulin deficiency drives the accumulation of the TMEM106B C-terminal fragment within lysosomes in Grn-knockout mice and GRN-null human iPSC-derived neurons. Recombinant progranulin supplementation reduced TMEM106B C-terminal fragment accumulation. Isogenic neurons carrying the TMEM106B risk allele displayed allele-dose-dependent fragment accumulation that was reversible by progranulin. Structural and genetic analyses demonstrated that TMEM106B dimerization stabilizes the protein and limits C-terminal fragment formation. These findings define a lysosomal pathway linking granulin deficiency to TMEM106B C-terminal fragment accumulation and explain how protective TMEM106B alleles can confer resistance to FTD, even for GRN mutation carriers.

  View details for DOI 10.64898/2026.03.25.713523

  View details for PubMedID 41929021

  View details for PubMedCentralID PMC13042028

• KIF5A downregulation in spinal muscular atrophy links axonal regeneration defects with ALS. JCI insight Akiyama, T., Zeng, Y., Guo, C., Gautier, O., Koepke, L., Lyons, H., Molotsky, E., Bombosch, J. S., Sianto, O., Ross, J. P., Hoang, P., Zhao, L., Spencer, C., Sumner, C. J., Monje, M., Day, J. W., Gitler, A. D. 2026

  Abstract

  Spinal muscular atrophy (SMA) is a devastating neuromuscular disorder caused by mutations in the survival motor neuron 1 (SMN1) gene leading to decreased SMN protein levels and motor neuron dysfunction. SMN-restoring therapies offer clinical benefit, but the downstream molecular consequences of SMN reduction remain incompletely understood. SMN deficiency resulted in downregulation of kinesin heavy chain isoform 5A (KIF5A) in human neurons and in a mouse model of SMA. SMN associated with KIF5A mRNA and contributed to its stability. Reduced SMN levels impaired axon regeneration, which was rescued by KIF5A overexpression. Because KIF5A has also been connected to ALS, these findings provide evidence of a molecular link between SMA and ALS pathophysiology, highlighting KIF5A as an SMN regulated factor. Our findings suggest SMN-independent interventions targeting KIF5A could represent a complementary therapeutic approach for SMA and other motor neuron diseases.

  View details for DOI 10.1172/jci.insight.197941

  View details for PubMedID 41885937

• Defects in intron recycling suppress the antiviral response via a mechanism of intronic endogenous dsRNA JOURNAL OF EXPERIMENTAL MEDICINE Duan, C., Buerer, L., Bowers, C., Taggart, A. J., O'brien, M. H., Gunasekera, S., Lin, C., Wang, J., Zeng, Y., Staley, J. P., Fredericks, A. M., Monaghan, S. F., Welch, A., Clark, N. E., Gao, D., Marr, N., Zhang, S., Casanova, J., Fairbrother, W. G. 2026; 223 (4)

  Abstract

  Loss of the lariat debranching enzyme DBR1 causes cytoplasmic accumulation of intron lariats, but why this reduces cell-intrinsic immunity is unclear. Here, we show that intronic inverted repeats Alu (IR Alus), normally degraded after splicing, form long double-stranded RNA (dsRNA) structures when lariats escape recycling. Viral introns evolve under pressure to avoid dsRNA, whereas human introns are enriched for them. Using computational, immunostaining, and genomic approaches, we demonstrate that DBR1 deficiency elevates cytoplasmic dsRNA and attenuates RNase L and PKR signaling. Our data suggest high levels of IR Alu dsRNA titrate PKR, potentially providing a mechanistic explanation for viral susceptibility in DBR1-deficient cells. Cytoplasmic RIP-seq against dsRNA finds introns to be a more abundant source of IR Alus than 3' UTRs in WT cells. Our findings suggest the high load of IR Alus in introns creates a situation where the efficiency of lariat recycling is a powerful modulator of endogenous dsRNA levels in human cells.

  View details for DOI 10.1084/jem.20250344

  View details for Web of Science ID 001712248700001

  View details for PubMedID 41817448

• TDP-43-mediated alternative polyadenylation is associated with a reduction in VPS35 and VPS29 expression in frontotemporal dementia. PLoS biology Maheswari Jawahar, V., Zeng, Y., Armour, E. M., Yue, M., Citrano, K., Lovchykova, A., Reeves, M. M., Rawlinson, B., DeTure, M., Dunmore, J. A., Song, Y., Ball, S. K., Wszolek, Z. K., Graff-Radford, N. R., Boeve, B. F., Knopman, D. S., Day, G. S., Small, S. A., Dickson, D. W., Ward, M. E., Gendron, T. F., Zhang, Y., Prudencio, M., Gitler, A. D., Petrucelli, L. 2026; 24 (1): e3003573

  Abstract

  TAR DNA-binding protein 43 (TDP-43) dysfunction is a hallmark of several neurodegenerative diseases, including frontotemporal dementia, amyotrophic lateral sclerosis, and Alzheimer's disease. Although cryptic exon inclusion is a well-characterized consequence of TDP-43 loss of function, emerging evidence reveals broader roles in RNA metabolism, notably in the regulation of alternative polyadenylation (APA) of disease-relevant transcripts. In the present study, we examined 3' untranslated region lengthening events in the brains of individuals with frontotemporal lobar degeneration with TDP-43 pathology (FTLD-TDP), focusing on the functional impact of APA dysregulation. To investigate whether TDP-43-mediated APA events occur in the postmortem brain, we measured the 3' untranslated region length of the retromer component vacuolar protein sorting 35 (VPS35) and the ETS transcription factor (ELK1) in the frontal cortex of a large cohort of FTLD-TDP patients and of healthy controls, and evaluated if these APA events are associated with FTLD-TDP clinical characteristic, markers of TDP-43 pathology [e.g., hyperphosphorylated TDP-43 and cryptic stathmin-2 RNA], or the expression of VPS35 and VPS29 proteins, the latter being essential to the retromer complex. We identified robust 3' untranslated region lengthening of VPS35 and ELK1 in FTLD-TDP, which strongly associated with markers of TDP-43 pathology, and ELK1 APA also associated with an earlier age of disease onset. Functionally, VPS35 APA was associated with reduced VPS35 and VPS29 protein expression, and lower VPS35 levels were associated with increased hyperphosphorylated TDP-43 and cryptic stathmin-2 RNA. Together, these data implicate APA dysregulation as a critical downstream consequence of TDP-43 dysfunction and suggest that TDP-43 loss may contribute to retromer impairment through APA-mediated repression of retromer subunits.

  View details for DOI 10.1371/journal.pbio.3003573

  View details for PubMedID 41490046

• TDP-43 nuclear loss in FTD/ALS causes widespread alternative polyadenylation changes. Nature neuroscience Zeng, Y., Lovchykova, A., Akiyama, T., Rayner, S. L., Maheswari Jawahar, V., Liu, C., Sianto, O., Guo, C., Calliari, A., Prudencio, M., Dickson, D. W., Petrucelli, L., Gitler, A. D. 2025

  Abstract

  In frontotemporal dementia and amyotrophic lateral sclerosis, the RNA-binding protein TDP-43 is depleted from the nucleus of neurons in the brain and spinal cord. A key function of TDP-43 has emerged as a repressor of cryptic exon inclusion during pre-mRNA splicing, but a role for TDP-43 in other RNA-processing events remains unresolved. Here we show that loss of TDP-43 from neuronal nuclei of human brain and disease-causing mutations in TDP-43 are associated with widespread changes in alternative polyadenylation (APA). Using high-resolution polyadenylation site mapping, we comprehensively defined TDP-43-regulated APA events in human stem cell-derived neurons and found that both the strength and position of TDP-43 binding influence polyA site usage. APA events caused by loss of TDP-43 impact expression of disease-relevant genes (for example, SFPQ, NEFL and TMEM106B). These findings provide evidence that, in addition to cryptic exon inclusion, APA changes are a new facet of TDP-43 pathology.

  View details for DOI 10.1038/s41593-025-02049-3

  View details for PubMedID 41120750

  View details for PubMedCentralID 3108889

• Cryptic splicing in synaptic and membrane excitability genes links TDP-43 loss to neuronal dysfunction. bioRxiv : the preprint server for biology Guo, C., Chen, K., Vatsavayai, S. C., Akiyama, T., Zeng, Y., Liu, C., Sianto, O., Yang, E., Bombosch, J., Powell, R., Zhen, S., Mekhoubad, S., Morrie, R. D., Miller, G., Green, E. M., Petrucelli, L., Seeley, W. W., Gitler, A. D. 2025

  Abstract

  TDP-43 pathology is a defining pathological hallmark of multiple neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). A major feature of TDP-43 pathology is its nuclear depletion, leading to the aberrant inclusion of cryptic exons during RNA splicing. STMN2 and UNC13A have emerged as prominent TDP-43 splicing targets, but the broader impact of TDP-43-dependent cryptic splicing on neuronal function remains unclear. Here, we report new TDP-43 splicing targets critical for membrane excitability and synaptic function, including KALRN, RAP1GAP, SYT7 and KCNQ2. Using human stem cell-derived neurons, we show that TDP-43 reduction induces cryptic splicing and downregulation of these genes, resulting in impaired excitability and synaptic transmission. In postmortem brains from patients with FTD, these cryptic splicing events occur selectively in neurons with TDP-43 pathology. Importantly, suppressing individual cryptic splicing events using antisense oligonucleotides partially restores neuronal function, and combined targeting almost fully rescues the synaptic deficit caused by TDP-43 loss. Together, our findings provide evidence that cryptic splicing in these synaptic and membrane excitability genes is not only a downstream marker but instead a direct driver of neuronal dysfunction, establishing a mechanistic link between TDP-43 pathology and neurodegeneration in ALS and FTD.

  View details for DOI 10.1101/2025.08.28.672801

  View details for PubMedID 40949955

  View details for PubMedCentralID PMC12424808

• An emergent disease-associated motor neuron state precedes cell death in a mouse model of ALS. bioRxiv : the preprint server for biology Gautier, O., Blum, J. A., Nguyen, T. P., Klemm, S., Yamakawa, M., Sinnott-Armstrong, N., Zeng, Y., Davis, C. O., Bombosch, J., Nakayama, L., Guttenplan, K. A., Chen, D., Kathira, A., Zhao, L., Rexach, J. E., Greenleaf, W. J., Gitler, A. D. 2025

  Abstract

  To uncover molecular determinants of motor neuron degeneration and selective vulnerability in amyotrophic lateral sclerosis (ALS), we generated longitudinal single-nucleus transcriptomes and chromatin accessibility profiles of spinal motor neurons from the SOD1-G93A ALS mouse model. Vulnerable alpha motor neurons showed thousands of molecular changes, marking a transition into a novel cell state we named 'disease-associated motor neurons' (DAMNs). We identified transcription factor regulatory networks that govern how healthy cells transition into DAMNs as well as those linked to vulnerable and resistant motor neuron subtypes. Using spatial transcriptomics, we found reactive glia located near motor neurons early in disease, suggesting early signaling events between motor neurons and glia. Finally, we found that the human orthologs of genomic regions with differential accessibility in SOD1-G93A alpha motor neurons are enriched for single nucleotide polymorphisms associated with human ALS, providing evidence that the genetic underpinnings of motor neuron vulnerability are conserved.

  View details for DOI 10.1101/2025.08.21.671404

  View details for PubMedID 40909710

  View details for PubMedCentralID PMC12407787

• KIF5A downregulation in spinal muscular atrophy links axonal regeneration defects with ALS. bioRxiv : the preprint server for biology Akiyama, T., Zeng, Y., Guo, C., Gautier, O., Koepke, L. S., Bombosch, J., Sianto, O., Ross, J. P., Hoang, P. T., Zhao, L. Y., Spencer, C., Monje, M., Day, J. W., Gitler, A. D. 2025

  Abstract

  Spinal muscular atrophy (SMA) is a devastating neuromuscular disorder caused by mutations in the Survival Motor Neuron 1 (SMN1) gene, leading to decreased SMN levels and motor neuron dysfunction. SMN-restoring therapies offer clinical benefit, but the downstream molecular consequences of SMN reduction remain incompletely understood. Here, we demonstrate that SMN deficiency results in downregulation of KIF5A in human neurons and in a mouse model of SMA. We provide evidence that reduced SMN levels impair axon regeneration, which is rescued by KIF5A overexpression and that the RNA-binding protein SMN functions to stabilize KIF5A mRNA. These findings provide evidence of a molecular link between SMA and ALS pathophysiology, highlighting KIF5A as a new SMN target. Our findings suggest SMN-independent interventions targeting KIF5A could represent a complementary therapeutic approach for SMA and other motor neuron diseases.

  View details for DOI 10.1101/2025.07.11.664426

  View details for PubMedID 40672150

  View details for PubMedCentralID PMC12265700

• Nonsense-mediated decay masks cryptic splicing events caused by TDP-43 loss. bioRxiv : the preprint server for biology Zeng, Y., Sianto, O., Lovchykova, A., Liu, C., Akiyama, T., Petrucelli, L., Gitler, A. D. 2025

  Abstract

  In frontotemporal dementia and amyotrophic lateral sclerosis, the RNA-binding protein TDP-43 is lost from the nucleus, leading to cryptic exon inclusion events in dozens of neuronal genes. Here, we show that many cryptic splicing events have been missed by standard RNA-sequencing analyses because they are substrates for nonsense-mediated decay. By inhibiting nonsense-mediated decay in neurons we unmask hundreds of novel cryptic splicing events caused by TDP-43 depletion, providing a new picture to TDP-43 loss of function in neurons.

  View details for DOI 10.1101/2025.07.09.664014

  View details for PubMedID 40672339

  View details for PubMedCentralID PMC12265704

• Regulators, mount up. Science (New York, N.Y.) Zeng, Y., Gitler, A. D. 2024; 386 (6717): 24-25

  Abstract

  Cryptic exons enable delivery of therapies only to sick neurons in a motor neuron disease.

  View details for DOI 10.1126/science.ads5951

  View details for PubMedID 39361768

• A developmental mechanism to regulate alternative polyadenylation in an adult stem cell lineage. Genes & development Gallicchio, L., Matias, N. R., Morales-Polanco, F., Nava, I., Stern, S., Zeng, Y., Fuller, M. T. 2024

  Abstract

  Alternative cleavage and polyadenylation (APA) often results in production of mRNA isoforms with either longer or shorter 3' UTRs from the same genetic locus, potentially impacting mRNA translation, localization, and stability. Developmentally regulated APA can thus make major contributions to cell type-specific gene expression programs as cells differentiate. During Drosophila spermatogenesis, ∼500 genes undergo APA when proliferating spermatogonia differentiate into spermatocytes, producing transcripts with shortened 3' UTRs, leading to profound stage-specific changes in the proteins expressed. The molecular mechanisms that specify usage of upstream polyadenylation sites in spermatocytes are thus key to understanding the changes in cell state. Here, we show that upregulation of PCF11 and Cbc, the two components of cleavage factor II (CFII), orchestrates APA during Drosophila spermatogenesis. Knockdown of PCF11 or cbc in spermatocytes caused dysregulation of APA, with many transcripts normally cleaved at a proximal site in spermatocytes now cleaved at their distal site, as in spermatogonia. Forced overexpression of CFII components in spermatogonia switched cleavage of some transcripts to the proximal site normally used in spermatocytes. Our findings reveal a developmental mechanism where changes in expression of specific cleavage factors can direct cell type-specific APA at selected genes.

  View details for DOI 10.1101/gad.351649.124

  View details for PubMedID 39111825

• Frontotemporal lobar degeneration targets brain regions linked to expression of recently evolved genes. Brain : a journal of neurology Pasquini, L., Pereira, F. L., Seddighi, S., Zeng, Y., Wei, Y., Illán-Gala, I., Vatsavayai, S. C., Friedberg, A., Lee, A. J., Brown, J. A., Spina, S., Grinberg, L. T., Sirkis, D. W., Bonham, L. W., Yokoyama, J. S., Boxer, A. L., Kramer, J. H., Rosen, H. J., Humphrey, J., Gitler, A. D., Miller, B. L., Pollard, K. S., Ward, M. E., Seeley, W. W. 2024

  Abstract

  In frontotemporal lobar degeneration (FTLD), pathological protein aggregation in specific brain regions is associated with declines in human-specialized social-emotional and language functions. In most patients, disease protein aggregates contain either TDP-43 (FTLD-TDP) or tau (FTLD-tau). Here, we explored whether FTLD-associated regional degeneration patterns relate to regional gene expression of human accelerated regions (HARs), conserved sequences that have undergone positive selection during recent human evolution. To this end, we used structural neuroimaging from patients with FTLD and human brain regional transcriptomic data from controls to identify genes expressed in FTLD-targeted brain regions. We then integrated primate comparative genomic data to test our hypothesis that FTLD targets brain regions linked to expression levels of recently evolved genes. In addition, we asked whether genes whose expression correlates with FTLD atrophy are enriched for genes that undergo cryptic splicing when TDP-43 function is impaired. We found that FTLD-TDP and FTLD-tau subtypes target brain regions with overlapping and distinct gene expression correlates, highlighting many genes linked to neuromodulatory functions. FTLD atrophy-correlated genes were strongly enriched for HARs. Atrophy-correlated genes in FTLD-TDP showed greater overlap with TDP-43 cryptic splicing genes and genes with more numerous TDP-43 binding sites compared with atrophy-correlated genes in FTLD-tau. Cryptic splicing genes were enriched for HAR genes, and vice versa, but this effect was due to the confounding influence of gene length. Analyses performed at the individual-patient level revealed that the expression of HAR genes and cryptically spliced genes within putative regions of disease onset differed across FTLD-TDP subtypes.

  View details for DOI 10.1093/brain/awae205

  View details for PubMedID 38940350

• The debranching enzyme Dbr1 regulates lariat turnover and intron splicing. Nature communications Buerer, L., Clark, N. E., Welch, A., Duan, C., Taggart, A. J., Townley, B. A., Wang, J., Soemedi, R., Rong, S., Lin, C. L., Zeng, Y., Katolik, A., Staley, J. P., Damha, M. J., Mosammaparast, N., Fairbrother, W. G. 2024; 15 (1): 4617

  Abstract

  The majority of genic transcription is intronic. Introns are removed by splicing as branched lariat RNAs which require rapid recycling. The branch site is recognized during splicing catalysis and later debranched by Dbr1 in the rate-limiting step of lariat turnover. Through generation of a viable DBR1 knockout cell line, we find the predominantly nuclear Dbr1 enzyme to encode the sole debranching activity in human cells. Dbr1 preferentially debranches substrates that contain canonical U2 binding motifs, suggesting that branchsites discovered through sequencing do not necessarily represent those favored by the spliceosome. We find that Dbr1 also exhibits specificity for particular 5' splice site sequences. We identify Dbr1 interactors through co-immunoprecipitation mass spectrometry. We present a mechanistic model for Dbr1 recruitment to the branchpoint through the intron-binding protein AQR. In addition to a 20-fold increase in lariats, Dbr1 depletion increases exon skipping. Using ADAR fusions to timestamp lariats, we demonstrate a defect in spliceosome recycling. In the absence of Dbr1, spliceosomal components remain associated with the lariat for a longer period of time. As splicing is co-transcriptional, slower recycling increases the likelihood that downstream exons will be available for exon skipping.

  View details for DOI 10.1038/s41467-024-48696-1

  View details for PubMedID 38816363

  View details for PubMedCentralID PMC11139901

• Developmental Regulation of Alternative Polyadenylation in an Adult Stem Cell Lineage. bioRxiv : the preprint server for biology Gallicchio, L., R Matias, N., Morales-Polanco, F., Nava, I., Stern, S., Zeng, Y., Fuller, M. T. 2024

  Abstract

  Co-transcriptional alternate processing of nascent mRNA molecules can make major contributions to cell type specific gene expression programs as proliferating precursor cells initiate terminal differentiation. Alternative Cleavage and Polyadenylation (APA) can result in the production of mRNA isoforms from the same gene locus with either longer or shorter 3'UTRs. In Drosophila spermatogenesis, approximately 500 genes undergo APA as proliferating spermatogonia differentiate into spermatocytes, producing transcript isoforms with shortened 3'UTRs, and resulting in profound stage specific changes in the proteins expressed. The molecular mechanisms that specify usage of upstream polyadenylation sites in spermatocytes are thus key to understanding the changes in cell state. Here, we show that PCF11 and Cbc, the two components of Cleavage factor II (CFII), orchestrate APA switching during Drosophila spermatogenesis. Knockdown of PCF11 or cbc in spermatocytes caused dysregulation of APA, with many transcripts normally cleaved at a proximal site in spermatocytes now cleaved at their distal site, as in spermatogonia. Although PCF11 is widely expressed, cbc is strongly upregulated in spermatocytes. Our findings reveal a developmental mechanism where changes in activity of specific cleavage factors can direct cell type specific APA at selected genes, presenting CFII as a key developmental regulator of APA during spermatogenesis.

  View details for DOI 10.1101/2024.03.18.585561

  View details for PubMedID 38562704

• A 3'UTR Insertion Is a Candidate Causal Variant at the TMEM106B Locus Associated With Increased Risk for FTLD-TDP. Neurology. Genetics Chemparathy, A., Le Guen, Y., Zeng, Y., Gorzynski, J., Jensen, T. D., Yang, C., Kasireddy, N., Talozzi, L., Belloy, M., Stewart, I., Gitler, A. D., Wagner, A. D., Mormino, E., Henderson, V. W., Wyss-Coray, T., Ashley, E., Cruchaga, C., Greicius, M. D. 2024; 10 (1): e200124

  Abstract

  Single-nucleotide variants near TMEM106B associate with the risk of frontotemporal lobar dementia with TDP-43 inclusions (FTLD-TDP) and Alzheimer disease (AD) in genome-wide association studies (GWASs), but the causal variant at this locus remains unclear. Here, we asked whether a novel structural variant on TMEM106B is the causal variant.An exploratory analysis identified structural variants on neurodegeneration-related genes. Subsequent analyses focused on an Alu element insertion on the 3'UTR of TMEM106B. This study included data from longitudinal aging and neurogenerative disease cohorts at Stanford University, case-control cohorts in the Alzheimer Disease Sequencing Project (ADSP), and expression and proteomics data from Washington University in St. Louis (WUSTL). Four hundred thirty-two individuals from 2 Stanford aging cohorts were whole-genome long-read and short-read sequenced. A total of 16,906 samples from ADSP were short-read sequenced. Genotypes, transcriptomics, and proteomics data were available in 1,979 participants from an aging and dementia cohort at WUSTL. Selection criteria were specific to each cohort. In primary analyses, the linkage disequilibrium between the TMEM106B locus variants in the FTLD-TDP GWAS and the 3'UTR insertion was estimated. We then estimated linkage by ancestry in the ADSP and evaluated the effect of the TMEM106B lead variant on mRNA and protein levels.The primary analysis included 432 participants (52.5% female, age range 45-92 years). We identified a 316 bp Alu insertion overlapping the TMEM106B 3'UTR tightly linked with top GWAS variants rs3173615(C) and rs1990622(A). In ADSP European ancestry participants, this insertion is in equivalent linkage with rs1990622(A) (R2 = 0.962, D' = 0.998) and rs3173615(C) (R2 = 0.960, D' = 0.996). In African ancestry participants, the insertion is in stronger linkage with rs1990622(A) (R2 = 0.992, D' = 0.998) than with rs3173615(C) (R2 = 0.811, D' = 0.994). In public data sets, rs1990622 was consistently associated with TMEM106B protein levels but not with mRNA expression. In the WUSTL data set, rs1990622 is associated with TMEM106B protein levels in plasma and CSF, but not with TMEM106B mRNA expression.We identified a novel Alu element insertion in the 3'UTR of TMEM106B in tight linkage with the lead FTLD-TDP risk variant. The lead variant is associated with TMEM106B protein levels, but not expression. The 3'UTR insertion is a lead candidate for the causal variant at this complex locus, pending confirmation with functional studies.

  View details for DOI 10.1212/NXG.0000000000200124

  View details for PubMedID 39911968

  View details for PubMedCentralID PMC10848896

• TDP-43 nuclear loss in FTD/ALS causes widespread alternative polyadenylation changes. bioRxiv : the preprint server for biology Zeng, Y., Lovchykova, A., Akiyama, T., Liu, C., Guo, C., Jawahar, V. M., Sianto, O., Calliari, A., Prudencio, M., Dickson, D. W., Petrucelli, L., Gitler, A. D. 2024

  Abstract

  In frontotemporal dementia and amyotrophic lateral sclerosis, the RNA-binding protein TDP-43 is depleted from the nucleus. TDP-43 loss leads to cryptic exon inclusion but a role in other RNA processing events remains unresolved. Here, we show that loss of TDP-43 causes widespread changes in alternative polyadenylation, impacting expression of disease-relevant genes (e.g., ELP1, NEFL, and TMEM106B) and providing evidence that alternative polyadenylation is a new facet of TDP-43 pathology.

  View details for DOI 10.1101/2024.01.22.575730

  View details for PubMedID 38328059

  View details for PubMedCentralID PMC10849503

• FTLD targets brain regions expressing recently evolved genes. medRxiv : the preprint server for health sciences Pasquini, L., Pereira, F. L., Seddighi, S., Zeng, Y., Wei, Y., Illán-Gala, I., Vatsavayai, S. C., Friedberg, A., Lee, A. J., Brown, J. A., Spina, S., Grinberg, L. T., Sirkis, D. W., Bonham, L. W., Yokoyama, J. S., Boxer, A. L., Kramer, J. H., Rosen, H. J., Humphrey, J., Gitler, A. D., Miller, B. L., Pollard, K. S., Ward, M. E., Seeley, W. W. 2023

  Abstract

  In frontotemporal lobar degeneration (FTLD), pathological protein aggregation is associated with a decline in human-specialized social-emotional and language functions. Most disease protein aggregates contain either TDP-43 (FTLD-TDP) or tau (FTLD-tau). Here, we explored whether FTLD targets brain regions that express genes containing human accelerated regions (HARs), conserved sequences that have undergone positive selection during recent human evolution. To this end, we used structural neuroimaging from patients with FTLD and normative human regional transcriptomic data to identify genes expressed in FTLD-targeted brain regions. We then integrated primate comparative genomic data to test our hypothesis that FTLD targets brain regions expressing recently evolved genes. In addition, we asked whether genes expressed in FTLD-targeted brain regions are enriched for genes that undergo cryptic splicing when TDP-43 function is impaired. We found that FTLD-TDP and FTLD-tau subtypes target brain regions that express overlapping and distinct genes, including many linked to neuromodulatory functions. Genes whose normative brain regional expression pattern correlated with FTLD cortical atrophy were strongly associated with HARs. Atrophy-correlated genes in FTLD-TDP showed greater overlap with TDP-43 cryptic splicing genes compared with atrophy-correlated genes in FTLD-tau. Cryptic splicing genes were enriched for HAR genes, and vice versa, but this effect was due to the confounding influence of gene length. Analyses performed at the individual-patient level revealed that the expression of HAR genes and cryptically spliced genes within putative regions of disease onset differed across FTLD-TDP subtypes. Overall, our findings suggest that FTLD targets brain regions that have undergone recent evolutionary specialization and provide intriguing potential leads regarding the transcriptomic basis for selective vulnerability in distinct FTLD molecular-anatomical subtypes.

  View details for DOI 10.1101/2023.10.27.23297687

  View details for PubMedID 37961381

  View details for PubMedCentralID PMC10635220

• A 3' UTR Deletion Is a Leading Candidate Causal Variant at the TMEM106B Locus Reducing Risk for FTLD-TDP. medRxiv : the preprint server for health sciences Chemparathy, A., Le Guen, Y., Zeng, Y., Gorzynski, J., Jensen, T., Kasireddy, N., Talozzi, L., Belloy, M. E., Stewart, I., Gitler, A. D., Wagner, A. D., Mormino, E., Henderson, V. W., Wyss-Coray, T., Ashley, E., Greicius, M. D. 2023

  Abstract

  Single nucleotide variants (SNVs) near TMEM106B have been associated with risk of frontotemporal lobar dementia with TDP pathology (FTLD-TDP) but the causal variant at this locus has not yet been isolated. The initial leading FTLD-TDP genome-wide association study (GWAS) hit at this locus, rs1990622, is intergenic and is in linkage disequilibrium (LD) with a TMEM106B coding SNV, rs3173615. We developed a long-read sequencing (LRS) dataset of 407 individuals in order to identify structural variants associated with neurodegenerative disorders. We identified a prevalent 322 base pair deletion on the TMEM106B 3' untranslated region (UTR) that was in perfect linkage with rs1990622 and near-perfect linkage with rs3173615 (genotype discordance in two of 274 individuals who had LRS and short-read next-generation sequencing). In Alzheimer's Disease Sequencing Project (ADSP) participants, this deletion was in greater LD with rs1990622 (R2=0.920916, D'=0.963472) than with rs3173615 (R2=0.883776, D'=0.963575). rs1990622 and rs3173615 are less closely linked (R2=0.7403, D'=0.9915) in African populations. Among African ancestry individuals in the ADSP, the deletion is in even greater LD with rs1990622 (R2=0.936841, D'=0.976782) than with rs3173615 (R2=0.764242, D'=0.974406). Querying publicly available genetic datasets with associated mRNA expression and protein levels, we confirmed that rs1990622 is consistently a protein quantitative trait locus but not an expression quantitative trait locus, consistent with a causal variant present on the TMEM106B 3'UTR. In summary, the TMEM106B 3' UTR deletion is a large genetic variant on the TMEM106B transcript that is in higher LD with the leading GWAS hit rs1990622 than rs3173615 and may mediate the protective effect of this locus in neurodegenerative disease.

  View details for DOI 10.1101/2023.07.06.23292312

  View details for PubMedID 37461476

  View details for PubMedCentralID PMC10350161

• Profiling lariat intermediates reveals genetic determinants of early and late co-transcriptional splicing MOLECULAR CELL Zeng, Y., Fair, B. J., Zeng, H., Krishnamohan, A., Hou, Y., Hall, J. M., Ruthenburg, A. J., Li, Y., Staley, J. P. 2022; 82 (24): 4681-+

  Abstract

  Long introns with short exons in vertebrate genes are thought to require spliceosome assembly across exons (exon definition), rather than introns, thereby requiring transcription of an exon to splice an upstream intron. Here, we developed CoLa-seq (co-transcriptional lariat sequencing) to investigate the timing and determinants of co-transcriptional splicing genome wide. Unexpectedly, 90% of all introns, including long introns, can splice before transcription of a downstream exon, indicating that exon definition is not obligatory for most human introns. Still, splicing timing varies dramatically across introns, and various genetic elements determine this variation. Strong U2AF2 binding to the polypyrimidine tract predicts early splicing, explaining exon definition-independent splicing. Together, our findings question the essentiality of exon definition and reveal features beyond intron and exon length that are determinative for splicing timing.

  View details for DOI 10.1016/j.molcel.2022.11.004

  View details for Web of Science ID 000919688000008

  View details for PubMedID 36435176