TY - JOUR
T1 - Integrative transcriptomic analysis of the amyotrophic lateral sclerosis spinal cord implicates glial activation and suggests new risk genes
AU - NYGC ALS Consortium
AU - Humphrey, Jack
AU - Venkatesh, Sanan
AU - Hasan, Rahat
AU - Herb, Jake T.
AU - de Paiva Lopes, Katia
AU - Küçükali, Fahri
AU - Byrska-Bishop, Marta
AU - Evani, Uday S.
AU - Narzisi, Giuseppe
AU - Fagegaltier, Delphine
AU - Sleegers, Kristel
AU - Phatnani, Hemali
AU - Knowles, David A.
AU - Fratta, Pietro
AU - Raj, Towfique
N1 - Funding Information:
We thank all members of the Raj laboratory for their feedback on the manuscript. This work was supported by National Institutes of Health (NIH) National Institute on Aging grants R56-AG055824 and U01-AG068880 (J.H. and T.R.), NIH National Institute of Neurological Disorders and Stroke grant U54NS123743 (J.H., T.R. and P.F.) and NIH Medical Scientist Training Program grant T3GM007280 (J.T.H.). P.F. is supported by a UK Medical Research Council Senior Clinical Fellowship and the Lady Edith Wolfson Fellowship (MR/M008606/1 and MR/S006508/1). F.K. is supported by a BOF DOCPRO fellowship from the University of Antwerp Research Fund. P.F. is supported by the UK Motor Neurone Disease Association, the Rosetrees Trust and the UCLH NIHR Biomedical Research Centre. This work was supported, in part, through the computational resources and staff expertise provided by Scientific Computing at the Icahn School of Medicine at Mount Sinai. Research reported in this paper was supported by the Office of Research Infrastructure of the NIH under award numbers S10OD018522 and S10OD026880. All NYGC ALS Consortium activities are supported by the ALS Association (19-SI-459) and the Tow Foundation. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.
Funding Information:
We thank all members of the Raj laboratory for their feedback on the manuscript. This work was supported by National Institutes of Health (NIH) National Institute on Aging grants R56-AG055824 and U01-AG068880 (J.H. and T.R.), NIH National Institute of Neurological Disorders and Stroke grant U54NS123743 (J.H., T.R. and P.F.) and NIH Medical Scientist Training Program grant T3GM007280 (J.T.H.). P.F. is supported by a UK Medical Research Council Senior Clinical Fellowship and the Lady Edith Wolfson Fellowship (MR/M008606/1 and MR/S006508/1). F.K. is supported by a BOF DOCPRO fellowship from the University of Antwerp Research Fund. P.F. is supported by the UK Motor Neurone Disease Association, the Rosetrees Trust and the UCLH NIHR Biomedical Research Centre. This work was supported, in part, through the computational resources and staff expertise provided by Scientific Computing at the Icahn School of Medicine at Mount Sinai. Research reported in this paper was supported by the Office of Research Infrastructure of the NIH under award numbers S10OD018522 and S10OD026880. All NYGC ALS Consortium activities are supported by the ALS Association (19-SI-459) and the Tow Foundation. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.
Publisher Copyright:
© 2022, The Author(s), under exclusive licence to Springer Nature America, Inc.
PY - 2023/1
Y1 - 2023/1
N2 - Amyotrophic lateral sclerosis (ALS) is a progressively fatal neurodegenerative disease affecting motor neurons in the brain and spinal cord. In this study, we investigated gene expression changes in ALS via RNA sequencing in 380 postmortem samples from cervical, thoracic and lumbar spinal cord segments from 154 individuals with ALS and 49 control individuals. We observed an increase in microglia and astrocyte gene expression, accompanied by a decrease in oligodendrocyte gene expression. By creating a gene co-expression network in the ALS samples, we identified several activated microglia modules that negatively correlate with retrospective disease duration. We mapped molecular quantitative trait loci and found several potential ALS risk loci that may act through gene expression or splicing in the spinal cord and assign putative cell types for FNBP1, ACSL5, SH3RF1 and NFASC. Finally, we outline how common genetic variants associated with splicing of C9orf72 act as proxies for the well-known repeat expansion, and we use the same mechanism to suggest ATXN3 as a putative risk gene.
AB - Amyotrophic lateral sclerosis (ALS) is a progressively fatal neurodegenerative disease affecting motor neurons in the brain and spinal cord. In this study, we investigated gene expression changes in ALS via RNA sequencing in 380 postmortem samples from cervical, thoracic and lumbar spinal cord segments from 154 individuals with ALS and 49 control individuals. We observed an increase in microglia and astrocyte gene expression, accompanied by a decrease in oligodendrocyte gene expression. By creating a gene co-expression network in the ALS samples, we identified several activated microglia modules that negatively correlate with retrospective disease duration. We mapped molecular quantitative trait loci and found several potential ALS risk loci that may act through gene expression or splicing in the spinal cord and assign putative cell types for FNBP1, ACSL5, SH3RF1 and NFASC. Finally, we outline how common genetic variants associated with splicing of C9orf72 act as proxies for the well-known repeat expansion, and we use the same mechanism to suggest ATXN3 as a putative risk gene.
UR - http://www.scopus.com/inward/record.url?scp=85143624022&partnerID=8YFLogxK
U2 - 10.1038/s41593-022-01205-3
DO - 10.1038/s41593-022-01205-3
M3 - Article
C2 - 36482247
AN - SCOPUS:85143624022
SN - 1097-6256
VL - 26
SP - 150
EP - 162
JO - Nature Neuroscience
JF - Nature Neuroscience
IS - 1
ER -