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Udine E, DeJesus-Hernandez M, Tian S, das Neves SP, Crook R, Finch NA, Baker MC, Pottier C, Graff-Radford NR, Boeve BF, Petersen RC, Knopman DS, Josephs KA, Oskarsson B, Da Mesquita S, Petrucelli L, Gendron TF, Dickson DW, Rademakers R, van Blitterswijk M. Abundant transcriptomic alterations in the human cerebellum of patients with a C9orf72 repeat expansion. Acta Neuropathol 2024; 147:73. [PMID: 38641715 PMCID: PMC11031479 DOI: 10.1007/s00401-024-02720-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 02/28/2024] [Accepted: 03/18/2024] [Indexed: 04/21/2024]
Abstract
The most prominent genetic cause of both amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) is a repeat expansion in the gene C9orf72. Importantly, the transcriptomic consequences of the C9orf72 repeat expansion remain largely unclear. Here, we used short-read RNA sequencing (RNAseq) to profile the cerebellar transcriptome, detecting alterations in patients with a C9orf72 repeat expansion. We focused on the cerebellum, since key C9orf72-related pathologies are abundant in this neuroanatomical region, yet TDP-43 pathology and neuronal loss are minimal. Consistent with previous work, we showed a reduction in the expression of the C9orf72 gene and an elevation in homeobox genes, when comparing patients with the expansion to both patients without the C9orf72 repeat expansion and control subjects. Interestingly, we identified more than 1000 alternative splicing events, including 4 in genes previously associated with ALS and/or FTLD. We also found an increase of cryptic splicing in C9orf72 patients compared to patients without the expansion and controls. Furthermore, we demonstrated that the expression level of select RNA-binding proteins is associated with cryptic splice junction inclusion. Overall, this study explores the presence of widespread transcriptomic changes in the cerebellum, a region not confounded by severe neurodegeneration, in post-mortem tissue from C9orf72 patients.
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Affiliation(s)
- Evan Udine
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
- Neuroscience Ph.D. Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA
| | | | - Shulan Tian
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, 55905, USA
| | | | - Richard Crook
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
| | - NiCole A Finch
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
| | - Matthew C Baker
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
| | - Cyril Pottier
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
| | | | | | | | | | | | - Björn Oskarsson
- Department of Neurology, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Sandro Da Mesquita
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
- Neuroscience Ph.D. Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
- Neuroscience Ph.D. Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Tania F Gendron
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
- Neuroscience Ph.D. Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
- Neuroscience Ph.D. Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA
- VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Marka van Blitterswijk
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd S, Jacksonville, FL, 32224, USA.
- Neuroscience Ph.D. Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA.
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Chung M, Carter EK, Veire AM, Dammer EB, Chang J, Duong DM, Raj N, Bassell GJ, Glass JD, Gendron TF, Nelson PT, Levey AI, Seyfried NT, McEachin ZT. Cryptic exon inclusion is a molecular signature of LATE-NC in aging brains. Acta Neuropathol 2024; 147:29. [PMID: 38308693 PMCID: PMC10838224 DOI: 10.1007/s00401-023-02671-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/30/2023] [Accepted: 12/17/2023] [Indexed: 02/05/2024]
Abstract
The aggregation, mislocalization, and phosphorylation of TDP-43 are pathologic hallmarks of several neurodegenerative diseases and provide a defining criterion for the neuropathologic diagnosis of Limbic-predominant Age-related TDP-43 Encephalopathy (LATE). LATE neuropathologic changes (LATE-NC) are often comorbid with other neurodegenerative pathologies including Alzheimer's disease neuropathologic changes (ADNC). We examined whether TDP-43 regulated cryptic exons accumulate in the hippocampus of neuropathologically confirmed LATE-NC cases. We found that several cryptic RNAs are robustly expressed in LATE-NC cases with or without comorbid ADNC and correlate with pTDP-43 abundance; however, the accumulation of cryptic RNAs is more robust in LATE-NC with comorbid ADNC. Additionally, cryptic RNAs can robustly distinguish LATE-NC from healthy controls and AD cases. These findings expand our current understanding and provide novel potential biomarkers for LATE pathogenesis.
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Affiliation(s)
- Mingee Chung
- Department of Cell Biology, Emory University, Atlanta, GA, 30322, USA
- Laboratory for Translational Cell Biology, Emory University, Atlanta, GA, 30322, USA
| | - E Kathleen Carter
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA
| | - Austin M Veire
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Eric B Dammer
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA
| | - Jianjun Chang
- Department of Cell Biology, Emory University, Atlanta, GA, 30322, USA
| | - Duc M Duong
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA
| | - Nisha Raj
- Department of Cell Biology, Emory University, Atlanta, GA, 30322, USA
- Laboratory for Translational Cell Biology, Emory University, Atlanta, GA, 30322, USA
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Gary J Bassell
- Department of Cell Biology, Emory University, Atlanta, GA, 30322, USA
- Laboratory for Translational Cell Biology, Emory University, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
| | - Jonathan D Glass
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA
| | - Tania F Gendron
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Peter T Nelson
- Department of Pathology and Sanders-Brown Center On Aging, University of Kentucky, Lexington, KY, 40536, USA
| | - Allan I Levey
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA.
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA.
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA.
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA.
| | - Zachary T McEachin
- Department of Cell Biology, Emory University, Atlanta, GA, 30322, USA.
- Laboratory for Translational Cell Biology, Emory University, Atlanta, GA, 30322, USA.
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA.
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA.
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3
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Agra Almeida Quadros AR, Li Z, Wang X, Ndayambaje IS, Aryal S, Ramesh N, Nolan M, Jayakumar R, Han Y, Stillman H, Aguilar C, Wheeler HJ, Connors T, Lopez-Erauskin J, Baughn MW, Melamed Z, Beccari MS, Olmedo Martínez L, Canori M, Lee CZ, Moran L, Draper I, Kopin AS, Oakley DH, Dickson DW, Cleveland DW, Hyman BT, Das S, Ertekin-Taner N, Lagier-Tourenne C. Cryptic splicing of stathmin-2 and UNC13A mRNAs is a pathological hallmark of TDP-43-associated Alzheimer's disease. Acta Neuropathol 2024; 147:9. [PMID: 38175301 PMCID: PMC10766724 DOI: 10.1007/s00401-023-02655-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024]
Abstract
Nuclear clearance and cytoplasmic accumulations of the RNA-binding protein TDP-43 are pathological hallmarks in almost all patients with amyotrophic lateral sclerosis (ALS) and up to 50% of patients with frontotemporal dementia (FTD) and Alzheimer's disease. In Alzheimer's disease, TDP-43 pathology is predominantly observed in the limbic system and correlates with cognitive decline and reduced hippocampal volume. Disruption of nuclear TDP-43 function leads to abnormal RNA splicing and incorporation of erroneous cryptic exons in numerous transcripts including Stathmin-2 (STMN2, also known as SCG10) and UNC13A, recently reported in tissues from patients with ALS and FTD. Here, we identify both STMN2 and UNC13A cryptic exons in Alzheimer's disease patients, that correlate with TDP-43 pathology burden, but not with amyloid-β or tau deposits. We also demonstrate that processing of the STMN2 pre-mRNA is more sensitive to TDP-43 loss of function than UNC13A. In addition, full-length RNAs encoding STMN2 and UNC13A are suppressed in large RNA-seq datasets generated from Alzheimer's disease post-mortem brain tissue. Collectively, these results open exciting new avenues to use STMN2 and UNC13A as potential therapeutic targets in a broad range of neurodegenerative conditions with TDP-43 proteinopathy including Alzheimer's disease.
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Affiliation(s)
- Ana Rita Agra Almeida Quadros
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Zhaozhi Li
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Xue Wang
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - I Sandra Ndayambaje
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sandeep Aryal
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Nandini Ramesh
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Matthew Nolan
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Rojashree Jayakumar
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Yi Han
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hannah Stillman
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Corey Aguilar
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hayden J Wheeler
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Theresa Connors
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jone Lopez-Erauskin
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Michael W Baughn
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Ze'ev Melamed
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Melinda S Beccari
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Laura Olmedo Martínez
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael Canori
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Chao-Zong Lee
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Laura Moran
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Derek H Oakley
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Don W Cleveland
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Bradley T Hyman
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sudeshna Das
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.
- Department of Neurology, Mayo Clinic, Jacksonville, FL, USA.
| | - Clotilde Lagier-Tourenne
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA.
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Chang K, Ling JP, Redding-Ochoa J, An Y, Li L, Dean SA, Blanchard TG, Pylyukh T, Barrett A, Irwin KE, Moghekar A, Resnick SM, Wong PC, Troncoso JC. Loss of TDP-43 splicing repression occurs early in the aging population and is associated with Alzheimer's disease neuropathologic changes and cognitive decline. Acta Neuropathol 2023; 147:4. [PMID: 38133681 DOI: 10.1007/s00401-023-02653-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 12/23/2023]
Abstract
LATE-NC, the neuropathologic changes of limbic-predominant age-related TAR DNA-binding protein 43 kDa (TDP-43) encephalopathy are frequently associated with Alzheimer's disease (AD) and cognitive impairment in older adults. The association of TDP-43 proteinopathy with AD neuropathologic changes (ADNC) and its impact on specific cognitive domains are not fully understood and whether loss of TDP-43 function occurs early in the aging brain remains unknown. Here, using a large set of autopsies from the Baltimore Longitudinal Study of Aging (BLSA) and another younger cohort, we were able to study brains from subjects 21-109 years of age. Examination of these brains show that loss of TDP-43 splicing repression, as judged by TDP-43 nuclear clearance and expression of a cryptic exon in HDGFL2, first occurs during the 6th decade, preceding by a decade the appearance of TDP-43+ neuronal cytoplasmic inclusions (NCIs). We corroborated this observation using a monoclonal antibody to demonstrate a cryptic exon-encoded neoepitope within HDGFL2 in neurons exhibiting nuclear clearance of TDP-43. TDP-43 nuclear clearance is associated with increased burden of tau pathology. Age at death, female sex, high CERAD neuritic plaque score, and high Braak neurofibrillary stage significantly increase the odds of LATE-NC. Faster rates of cognitive decline on verbal memory (California Verbal Learning Test immediate recall), visuospatial ability (Card Rotations Test), mental status (MMSE) and semantic fluency (Category Fluency Test) were associated with LATE-NC. Notably, the effects of LATE-NC on verbal memory and visuospatial ability are independent of ADNC. However, the effects of TDP-43 nuclear clearance in absence of NCI on the longitudinal trajectories and levels of cognitive measures are not significant. These results establish that loss of TDP-43 splicing repression is an early event occurring in the aging population during the development of TDP-43 proteinopathy and is associated with increased tau pathology. Furthermore, LATE-NC correlates with high levels of ADNC but also has an impact on specific memory and visuospatial functions in aging that is independent of AD.
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Affiliation(s)
- Koping Chang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department and Graduate Institute of Pathology, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, 100225, Taiwan
| | - Jonathan P Ling
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Javier Redding-Ochoa
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Yang An
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Ling Li
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Office of the Chief Medical Examiner, State of Maryland, Baltimore, MD, 21223, USA
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Stephanie A Dean
- Office of the Chief Medical Examiner, State of Maryland, Baltimore, MD, 21223, USA
| | - Thomas G Blanchard
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Tatiana Pylyukh
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Alexander Barrett
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Katherine E Irwin
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Abhay Moghekar
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Susan M Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Philip C Wong
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Juan C Troncoso
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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Mehta PR, Brown AL, Ward ME, Fratta P. The era of cryptic exons: implications for ALS-FTD. Mol Neurodegener 2023; 18:16. [PMID: 36922834 PMCID: PMC10018954 DOI: 10.1186/s13024-023-00608-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/17/2023] [Indexed: 03/18/2023] Open
Abstract
TDP-43 is an RNA-binding protein with a crucial nuclear role in splicing, and mislocalises from the nucleus to the cytoplasm in a range of neurodegenerative disorders. TDP-43 proteinopathy spans a spectrum of incurable, heterogeneous, and increasingly prevalent neurodegenerative diseases, including the amyotrophic lateral sclerosis and frontotemporal dementia disease spectrum and a significant fraction of Alzheimer's disease. There are currently no directed disease-modifying therapies for TDP-43 proteinopathies, and no way to distinguish who is affected before death. It is now clear that TDP-43 proteinopathy leads to a number of molecular changes, including the de-repression and inclusion of cryptic exons. Importantly, some of these cryptic exons lead to the loss of crucial neuronal proteins and have been shown to be key pathogenic players in disease pathogenesis (e.g., STMN2), as well as being able to modify disease progression (e.g., UNC13A). Thus, these aberrant splicing events make promising novel therapeutic targets to restore functional gene expression. Moreover, presence of these cryptic exons is highly specific to patients and areas of the brain affected by TDP-43 proteinopathy, offering the potential to develop biomarkers for early detection and stratification of patients. In summary, the discovery of cryptic exons gives hope for novel diagnostics and therapeutics on the horizon for TDP-43 proteinopathies.
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Affiliation(s)
- Puja R Mehta
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL Queen Square Motor Neuron Disease Centre, London, WC1N 3BG, UK
| | - Anna-Leigh Brown
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL Queen Square Motor Neuron Disease Centre, London, WC1N 3BG, UK
| | - Michael E Ward
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Pietro Fratta
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL Queen Square Motor Neuron Disease Centre, London, WC1N 3BG, UK.
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Bampton A, Gatt A, Humphrey J, Cappelli S, Bhattacharya D, Foti S, Brown AL, Asi Y, Low YH, Foiani M, Raj T, Buratti E, Fratta P, Lashley T. HnRNP K mislocalisation is a novel protein pathology of frontotemporal lobar degeneration and ageing and leads to cryptic splicing. Acta Neuropathol 2021; 142:609-27. [PMID: 34274995 DOI: 10.1007/s00401-021-02340-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 02/08/2023]
Abstract
Heterogeneous nuclear ribonucleoproteins (HnRNPs) are a group of ubiquitously expressed RNA-binding proteins implicated in the regulation of all aspects of nucleic acid metabolism. HnRNP K is a member of this highly versatile hnRNP family. Pathological redistribution of hnRNP K to the cytoplasm has been linked to the pathogenesis of several malignancies but, until now, has been underexplored in the context of neurodegenerative disease. Here we show hnRNP K mislocalisation in pyramidal neurons of the frontal cortex to be a novel neuropathological feature that is associated with both frontotemporal lobar degeneration and ageing. HnRNP K mislocalisation is mutually exclusive to TDP-43 and tau pathological inclusions in neurons and was not observed to colocalise with mitochondrial, autophagosomal or stress granule markers. De-repression of cryptic exons in RNA targets following TDP-43 nuclear depletion is an emerging mechanism of potential neurotoxicity in frontotemporal lobar degeneration and the mechanistically overlapping disorder amyotrophic lateral sclerosis. We silenced hnRNP K in neuronal cells to identify the transcriptomic consequences of hnRNP K nuclear depletion. Intriguingly, by performing RNA-seq analysis we find that depletion of hnRNP K induces 101 novel cryptic exon events. We validated cryptic exon inclusion in an SH-SY5Y hnRNP K knockdown and in FTLD brain exhibiting hnRNP K nuclear depletion. We, therefore, present evidence for hnRNP K mislocalisation to be associated with FTLD and for this to induce widespread changes in splicing.
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Humphrey J, Emmett W, Fratta P, Isaacs AM, Plagnol V. Quantitative analysis of cryptic splicing associated with TDP-43 depletion. BMC Med Genomics 2017; 10:38. [PMID: 28549443 PMCID: PMC5446763 DOI: 10.1186/s12920-017-0274-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 05/17/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Reliable exon recognition is key to the splicing of pre-mRNAs into mature mRNAs. TDP-43 is an RNA-binding protein whose nuclear loss and cytoplasmic aggregation are a hallmark pathology in amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). TDP-43 depletion causes the aberrant inclusion of cryptic exons into a range of transcripts, but their extent, relevance to disease pathogenesis and whether they are caused by other RNA-binding proteins implicated in ALS/FTD are unknown. METHODS We developed an analysis pipeline to discover and quantify cryptic exon inclusion and applied it to publicly available human and murine RNA-sequencing data. RESULTS We detected widespread cryptic splicing in TDP-43 depletion datasets but almost none in another ALS/FTD-linked protein FUS. Sequence motif and iCLIP analysis of cryptic exons demonstrated that they are bound by TDP-43. Unlike the cryptic exons seen in hnRNP C depletion, those repressed by TDP-43 cannot be linked to transposable elements. Cryptic exons are poorly conserved and inclusion overwhelmingly leads to nonsense-mediated decay of the host transcript, with reduced transcript levels observed in differential expression analysis. RNA-protein interaction data on 73 different RNA-binding proteins showed that, in addition to TDP-43, 7 specifically bind TDP-43 linked cryptic exons. This suggests that TDP-43 competes with other splicing factors for binding to cryptic exons and can repress cryptic exon inclusion. CONCLUSIONS Our quantitative analysis pipeline confirms the presence of cryptic exons during the depletion of TDP-43 but not FUS providing new insight into to RNA-processing dysfunction as a cause or consequence in ALS/FTD.
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Affiliation(s)
- Jack Humphrey
- University College London Genetics Institute, Gower Street, London, UK.
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, UK.
| | - Warren Emmett
- University College London Genetics Institute, Gower Street, London, UK
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, UK
- The Francis Crick Institute, Midland Road, London, UK
| | - Pietro Fratta
- Department of Motor Neuroscience and Movement Disorders, UCL Institute of Neurology, Queen Square, London, UK
| | - Adrian M Isaacs
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, UK
| | - Vincent Plagnol
- University College London Genetics Institute, Gower Street, London, UK
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