Tau-Mediated Disruption of the Spliceosome Triggers Cryptic RNA Splicing and Neurodegeneration in Alzheimer’s Disease

SUMMARY In Alzheimer’s disease (AD), spliceosomal proteins with critical roles in RNA processing aberrantly aggregate and mislocalize to Tau neurofibrillary tangles. We test the hypothesis that Tau-spliceosome interactions disrupt pre-mRNA splicing in AD. In human postmortem brain with AD pathology, Tau coimmunoprecipitates with spliceosomal components. In Drosophila, pan-neuronal Tau expression triggers reductions in multiple core and U1-specific spliceosomal proteins, and genetic disruption of these factors, including SmB, U1–70K, and U1A, enhances Tau-mediated neurodegeneration. We further show that loss of function in SmB, encoding a core spliceosomal protein, causes decreased survival, progressive locomotor impairment, and neuronal loss, independent of Tau toxicity. Lastly, RNA sequencing reveals a similar profile of mRNA splicing errors in SmB mutant and Tau transgenic flies, including intron retention and non-annotated cryptic splice junctions. In human brains, we confirm cryptic splicing errors in association with neurofibrillary tangle burden. Our results implicate spliceosome disruption and the resulting transcriptome perturbation in Tau-mediated neurodegeneration in AD.

[1]  M. Folstein,et al.  Clinical diagnosis of Alzheimer's disease , 1984, Neurology.

[2]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[3]  V. Plagnol,et al.  Quantitative analysis of cryptic splicing associated with TDP-43 depletion , 2016, BMC Medical Genomics.

[4]  Sean J. Miller,et al.  Tau Protein Disrupts Nucleocytoplasmic Transport in Alzheimer’s Disease , 2018, Neuron.

[5]  S. Gygi,et al.  Evidence that C9ORF72 Dipeptide Repeat Proteins Associate with U2 snRNP to Cause Mis-splicing in ALS/FTD Patients. , 2017, Cell reports.

[6]  Bradley T. Hyman,et al.  Neurofibrillary tangles but not senile plaques parallel duration and severity of Alzheimer's disease , 1992, Neurology.

[7]  Michael Benatar,et al.  Prion-like domain mutations in hnRNPs cause multisystem proteinopathy and ALS , 2013, Nature.

[8]  D. Dias-Santagata,et al.  Oxidative stress mediates tau-induced neurodegeneration in Drosophila. , 2007, The Journal of clinical investigation.

[9]  A. Levey,et al.  Quantitative Analysis of the Brain Ubiquitylome in Alzheimer's Disease , 2018, Proteomics.

[10]  W. Boelens,et al.  The human U1A snRNP protein regulates polyadenylation via a direct interaction with poly(A) polymerase , 1994, Cell.

[11]  S. Sugano,et al.  Frequent pathway mutations of splicing machinery in myelodysplasia , 2011, Nature.

[12]  S. Amara,et al.  Tissue-specific expression and cDNA cloning of small nuclear ribonucleoprotein-associated polypeptide N. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[13]  Jeffrey Wilusz,et al.  The highways and byways of mRNA decay , 2007, Nature Reviews Molecular Cell Biology.

[14]  Tomaž Curk,et al.  Analysis of alternative splicing associated with aging and neurodegeneration in the human brain. , 2011, Genome research.

[15]  Chadwick M. Hales,et al.  U1 small nuclear ribonucleoprotein complex and RNA splicing alterations in Alzheimer’s disease , 2013, Proceedings of the National Academy of Sciences.

[16]  P. Wong,et al.  TDP-43 repression of nonconserved cryptic exons is compromised in ALS-FTD , 2015, Science.

[17]  Brad T. Sherman,et al.  Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists , 2008, Nucleic acids research.

[18]  Daniel J. Muller,et al.  Tau protein liquid–liquid phase separation can initiate tau aggregation , 2018, The EMBO journal.

[19]  Hu Li,et al.  RNA binding proteins co-localize with small tau inclusions in tauopathy , 2018, Acta neuropathologica communications.

[20]  M. Mann,et al.  Quantitative proteomics reveals subset-specific viral recognition in dendritic cells. , 2010, Immunity.

[21]  J. Shulman,et al.  Functional screening of Alzheimer pathology genome-wide association signals in Drosophila. , 2011, American journal of human genetics.

[22]  J. Weissenbach,et al.  Identification and characterization of a spinal muscular atrophy-determining gene , 1995, Cell.

[23]  M. Feany,et al.  Lysosomal Dysfunction Promotes Cleavage and Neurotoxicity of Tau In Vivo , 2010, PLoS genetics.

[24]  E. Zackai,et al.  Mutations within the spliceosomal gene SNRPB affect its auto‐regulation and are causative for classic cerebro‐costo‐mandibular syndrome , 2015, Clinical genetics.

[25]  D. J. Driscoll,et al.  Prader-Willi syndrome. , 1984, Current problems in pediatrics.

[26]  C. Cowan,et al.  Are Tau Aggregates Toxic or Protective in Tauopathies? , 2013, Front. Neurol..

[27]  Benjamin J. Blencowe,et al.  Alternative Splicing in the Mammalian Nervous System: Recent Insights into Mechanisms and Functional Roles , 2015, Neuron.

[28]  Zhandong Liu,et al.  Data Analysis Pipeline for RNA‐seq Experiments: From Differential Expression to Cryptic Splicing , 2017, Current protocols in bioinformatics.

[29]  Sarah J. Kurley,et al.  The spliceosome is a therapeutic vulnerability in MYC-driven cancer , 2015, Nature.

[30]  Xun Hu,et al.  TDP-43 Mutations in Familial and Sporadic Amyotrophic Lateral Sclerosis , 2008, Science.

[31]  Miguel Beato,et al.  bwtool: a tool for bigWig files , 2014, Bioinform..

[32]  N. Bonini,et al.  Maintaining the brain: insight into human neurodegeneration from Drosophila melanogaster mutants , 2009, Nature Reviews Genetics.

[33]  David A. Bennett,et al.  Neuropathologic intermediate phenotypes enhance association to Alzheimer susceptibility alleles , 2009, Neurology.

[34]  Marco Y. Hein,et al.  The Perseus computational platform for comprehensive analysis of (prote)omics data , 2016, Nature Methods.

[35]  B. Prusty,et al.  Impaired spliceosomal UsnRNP assembly leads to Sm mRNA down-regulation and Sm protein degradation , 2017, The Journal of cell biology.

[36]  W. Boelens,et al.  A complex secondary structure in U1A pre‐mRNA that binds two molecules of U1A protein is required for regulation of polyadenylation. , 1993, The EMBO journal.

[37]  Kim Schneider,et al.  Coping with Protein Quality Control Failure. , 2017, Annual review of cell and developmental biology.

[38]  A. Hyman,et al.  Liquid-liquid phase separation in biology. , 2014, Annual review of cell and developmental biology.

[39]  Stephen M. Mount,et al.  The Drosophila U1-70K Protein Is Required for Viability, but Its Arginine-Rich Domain Is Dispensable , 2004, Genetics.

[40]  Graydon B. Gonsalvez,et al.  The Sm-Protein Methyltransferase, Dart5, Is Essential for Germ-Cell Specification and Maintenance , 2006, Current Biology.

[41]  H. Braak,et al.  Neuropathological stageing of Alzheimer-related changes , 2004, Acta Neuropathologica.

[42]  Joshua J. White,et al.  Extensive cryptic splicing upon loss of RBM17 and TDP43 in neurodegeneration models. , 2016, Human molecular genetics.

[43]  Timothy D. Craggs,et al.  Phase Transition of a Disordered Nuage Protein Generates Environmentally Responsive Membraneless Organelles , 2015, Molecular cell.

[44]  L. Tora,et al.  A fraction of the transcription factor TAF15 participates in interactions with a subset of the spliceosomal U1 snRNP complex. , 2011, Biochimica et biophysica acta.

[45]  Joshua M. Shulman,et al.  Tauopathy in Drosophila: Neurodegeneration Without Neurofibrillary Tangles , 2001, Science.

[46]  Scott Waddell,et al.  Olfactory learning skews mushroom body output pathways to steer behavioral choice in Drosophila , 2015, Current Opinion in Neurobiology.

[47]  Burkhard Becher,et al.  Immune attack: the role of inflammation in Alzheimer disease , 2015, Nature Reviews Neuroscience.

[48]  Fidel Ramírez,et al.  deepTools: a flexible platform for exploring deep-sequencing data , 2014, Nucleic Acids Res..

[49]  Bradley T. Hyman,et al.  The Intersection of Amyloid Beta and Tau at Synapses in Alzheimer’s Disease , 2014, Neuron.

[50]  R. Zhai,et al.  NMNAT suppresses tau-induced neurodegeneration by promoting clearance of hyperphosphorylated tau oligomers in a Drosophila model of tauopathy. , 2012, Human molecular genetics.

[51]  Bin Zhang,et al.  Integrative transcriptome analyses of the aging brain implicate altered splicing in Alzheimer’s disease susceptibility , 2018, Nature Genetics.

[52]  A. Levey,et al.  Deep proteomic network analysis of Alzheimer’s disease brain reveals alterations in RNA binding proteins and RNA splicing associated with disease , 2018, Molecular Neurodegeneration.

[53]  Bruce L. Miller,et al.  Ubiquitinated TDP-43 in Frontotemporal Lobar Degeneration and Amyotrophic Lateral Sclerosis , 2006, Science.

[54]  Marco Y. Hein,et al.  Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ * , 2014, Molecular & Cellular Proteomics.

[55]  P. Park,et al.  p53 prevents neurodegeneration by regulating synaptic genes , 2014, Proceedings of the National Academy of Sciences.

[56]  A. Levey,et al.  RNA-binding proteins with basic-acidic dipeptide (BAD) domains self-assemble and aggregate in Alzheimer's disease , 2018, The Journal of Biological Chemistry.

[57]  Gene W. Yeo,et al.  ALS-causative mutations in FUS/TLS confer gain- and loss-of-function by altered association with SMN and U1-snRNP , 2015, Nature Communications.

[58]  Xun Hu,et al.  Mutations in FUS, an RNA Processing Protein, Cause Familial Amyotrophic Lateral Sclerosis Type 6 , 2009, Science.

[59]  Larry N. Singh,et al.  U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation , 2010, Nature.

[60]  Richard Hollister,et al.  Neuronal loss correlates with but exceeds neurofibrillary tangles in Alzheimer's disease , 1997, Annals of neurology.

[61]  J. Shulman,et al.  Genetic modifiers of tauopathy in Drosophila. , 2003, Genetics.

[62]  Nele A. Haelterman,et al.  MiMIC: a highly versatile transposon insertion resource for engineering Drosophila melanogaster genes , 2011, Nature Methods.

[63]  S. Armstrong,et al.  Modulation of splicing catalysis for therapeutic targeting of leukemias with spliceosomal mutations , 2016, Nature Medicine.

[64]  H. Salz,et al.  The Drosophila sex determination gene snf encodes a nuclear protein with sequence and functional similarity to the mammalian U1A snRNP protein. , 1994, Genes & development.

[65]  T. Montine,et al.  Aggregates of Small Nuclear Ribonucleic Acids (snRNAs) in Alzheimer's Disease , 2014, Brain pathology.

[66]  Christopher B. Burge,et al.  Maximum Entropy Modeling of Short Sequence Motifs with Applications to RNA Splicing Signals , 2004, J. Comput. Biol..

[67]  R. Chitta,et al.  Global analysis of TDP-43 interacting proteins reveals strong association with RNA splicing and translation machinery. , 2010, Journal of proteome research.

[68]  Roy Parker,et al.  Formation and Maturation of Phase-Separated Liquid Droplets by RNA-Binding Proteins. , 2015, Molecular cell.

[69]  Yi Tang,et al.  Therapeutic approaches to treat human spliceosomal diseases. , 2019, Current opinion in biotechnology.

[70]  S. Ackerman,et al.  Mutation of a U2 snRNA Gene Causes Global Disruption of Alternative Splicing and Neurodegeneration , 2012, Cell.

[71]  Hans-Ulrich Klein,et al.  A multi-omic atlas of the human frontal cortex for aging and Alzheimer’s disease research , 2018, Scientific Data.

[72]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[73]  A. Kanagaraj,et al.  Phase Separation by Low Complexity Domains Promotes Stress Granule Assembly and Drives Pathological Fibrillization , 2015, Cell.

[74]  Madhav Thambisetty,et al.  A Multi-network Approach Identifies Protein-Specific Co-expression in Asymptomatic and Symptomatic Alzheimer's Disease. , 2017, Cell systems.

[75]  Lili Wan,et al.  RNA and Disease , 2009, Cell.

[76]  Gene W. Yeo,et al.  Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43 , 2011, Nature Neuroscience.

[77]  H. Levine,et al.  Pathological Tau Promotes Neuronal Damage by Impairing Ribosomal Function and Decreasing Protein Synthesis , 2016, The Journal of Neuroscience.

[78]  Douglas L. Black,et al.  Neuronal regulation of alternative pre-mRNA splicing , 2007, Nature Reviews Neuroscience.

[79]  Marco Y. Hein,et al.  A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation , 2015, Cell.

[80]  David A Bennett,et al.  Religious Orders Study and Rush Memory and Aging Project. , 2018, Journal of Alzheimer's disease : JAD.

[81]  Hu Li,et al.  Interaction of tau with the RNA-Binding Protein TIA1 Regulates tau Pathophysiology and Toxicity. , 2016, Cell reports.

[82]  J. Power,et al.  Alzheimer’s Disease and Cancer: When Two Monsters Cannot Be Together , 2019, Front. Neurosci..

[83]  Diana M. Mitrea,et al.  C9orf72 Dipeptide Repeats Impair the Assembly, Dynamics, and Function of Membrane-Less Organelles , 2016, Cell.

[84]  C. Lorson,et al.  A single nucleotide in the SMN gene regulates splicing and is responsible for spinal muscular atrophy. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[85]  John Q. Trojanowski,et al.  Consensus Recommendations for the Postmortem Diagnosis of Alzheimer’s Disease , 1997, Neurobiology of Aging.

[86]  Charles C. White,et al.  A molecular network of the aging human brain provides insights into the pathology and cognitive decline of Alzheimer’s disease , 2018, Nature Neuroscience.

[87]  Lili Wan,et al.  SMN Deficiency Causes Tissue-Specific Perturbations in the Repertoire of snRNAs and Widespread Defects in Splicing , 2008, Cell.

[88]  S. Lovestone,et al.  GSK-3β inhibition reverses axonal transport defects and behavioural phenotypes in Drosophila , 2004, Molecular Psychiatry.

[89]  D L Price,et al.  Alzheimer's disease: a disorder of cortical cholinergic innervation. , 1983, Science.

[90]  D. Ito,et al.  RNA binding proteins and the pathological cascade in ALS/FTD neurodegeneration , 2017, Science Translational Medicine.

[91]  Qun Pan,et al.  Regulation of alternative splicing by the core spliceosomal machinery. , 2011, Genes & development.

[92]  Bing Zhang,et al.  WebGestalt: an integrated system for exploring gene sets in various biological contexts , 2005, Nucleic Acids Res..

[93]  C. Will,et al.  Spliceosome structure and function. , 2011, Cold Spring Harbor perspectives in biology.

[94]  Lan Lin,et al.  rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data , 2014, Proceedings of the National Academy of Sciences.

[95]  J. Anne Arginine methylation of SmB is required for Drosophila germ cell development , 2010, Development.

[96]  A. Spradling,et al.  A genetic toolkit for tagging intronic MiMIC containing genes , 2015, eLife.

[97]  Christopher B. Burge,et al.  Protein-RNA Networks Regulated by Normal and ALS-Associated Mutant HNRNPA2B1 in the Nervous System , 2016, Neuron.

[98]  R. Lührmann,et al.  The C-terminal RG Dipeptide Repeats of the Spliceosomal Sm Proteins D1 and D3 Contain Symmetrical Dimethylarginines, Which Form a Major B-cell Epitope for Anti-Sm Autoantibodies* , 2000, The Journal of Biological Chemistry.

[99]  Benjamin W Booth,et al.  A library of MiMICs allows tagging of genes and reversible, spatial and temporal knockdown of proteins in Drosophila , 2015, eLife.

[100]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[101]  J. Shulman,et al.  Uncoupling neuronal death and dysfunction in Drosophila models of neurodegenerative disease , 2016, Acta neuropathologica communications.

[102]  N. Perrimon,et al.  Functional screening in Drosophila identifies Alzheimer's disease susceptibility genes and implicates Tau-mediated mechanisms. , 2014, Human molecular genetics.

[103]  J. Valcárcel,et al.  The splicing regulator TIA‐1 interacts with U1‐C to promote U1 snRNP recruitment to 5′ splice sites , 2002, The EMBO journal.

[104]  M. Feany,et al.  Comparison of pathways controlling toxicity in the eye and brain in Drosophila models of human neurodegenerative diseases. , 2004, Human molecular genetics.

[105]  Dietmar Riedel,et al.  Liquid–liquid phase separation of the microtubule-binding repeats of the Alzheimer-related protein Tau , 2017, Nature Communications.

[106]  David Shepherd,et al.  Soluble hyper-phosphorylated tau causes microtubule breakdown and functionally compromises normal tau in vivo , 2010, Acta Neuropathologica.

[107]  Yanhui Hu,et al.  FlyBase at 25: looking to the future , 2016, Nucleic Acids Res..

[108]  H. Dvinge,et al.  Widespread intron retention diversifies most cancer transcriptomes , 2015, Genome Medicine.

[109]  B. Snel,et al.  STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. , 2000, Nucleic acids research.

[110]  J. Schneider,et al.  The effect of social networks on the relation between Alzheimer's disease pathology and level of cognitive function in old people: a longitudinal cohort study , 2006, The Lancet Neurology.

[111]  M. Feany,et al.  Glial Fibrillary Tangles and JAK/STAT-Mediated Glial and Neuronal Cell Death in a Drosophila Model of Glial Tauopathy , 2010, The Journal of Neuroscience.

[112]  M. Feany,et al.  A Conserved Cytoskeletal Signaling Cascade Mediates Neurotoxicity of FTDP-17 Tau Mutations In Vivo , 2017, The Journal of Neuroscience.