Abstract

Increasing evidence suggests that defective RNA processing contributes to the development of amyotrophic lateral sclerosis (ALS). This may be especially true for ALS caused by a repeat expansion in C9orf72 (c9ALS), in which the accumulation of RNA foci and dipeptide-repeat proteins are expected to modify RNA metabolism. We report extensive alternative splicing (AS) and alternative polyadenylation (APA) defects in the cerebellum of c9ALS subjects (8,224 AS and 1,437 APA), including changes in ALS-associated genes (for example, ATXN2 and FUS), and in subjects with sporadic ALS (sALS; 2,229 AS and 716 APA). Furthermore, heterogeneous nuclear ribonucleoprotein H (hnRNPH) and other RNA-binding proteins are predicted to be potential regulators of cassette exon AS events in both c9ALS and sALS. Co-expression and gene-association network analyses of gene expression and AS data revealed divergent pathways associated with c9ALS and sALS.

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Acknowledgements

We are extremely grateful to all individuals who agreed to donate their brains to research. This work was supported by the National Institutes of Health/National Institute on Aging (R01AG026251 and P50AG016574 to L.P.), the National Institutes of Health/National Institute of Neurological Disorders and Stroke (R21NS089979 to T.F.G. and K.B.B.; R21NS084528, R01NS088689 and R01NS077402 to L.P.; R01NS063964 to L.P. and C.D.L.; P01NS084974 to L.P., D.W.D., R.R. and K.B.B.), the National Institute of Environmental Health Sciences (R01ES20395 to L.P.), the Department of Defense (ALSRP AL130125 to L.P.), the Mayo Clinic Foundation (L.P.), the Mayo Clinic Center for Individualized Medicine (L.P. and K.B.B.), the ALS Association (K.B.B., L.P., M.P. and T.F.G.), the Robert Packard Center for ALS Research at Johns Hopkins (L.P.), Target ALS (L.P.), the ALS Association (Milton Safenowitz postdoctoral fellowships to V.V.B. and M.P.), the Canadian Institutes of Health Research (postdoctoral fellowship to V.V.B.), the Siragusa Foundation (Career Development Award for Young Investigators to V.V.B.), and the Robert and Clarice Smith & Abigail Van Buren Alzheimer's Disease Research Foundation (postdoctoral fellowship to V.V.B.). H.L. and M.E.M. are supported by the Mayo Clinic Center for Individualized Medicine and the Donors Cure Foundation.

Author information

Author notes

    • Mercedes Prudencio
    • , Veronique V Belzil
    • , Ranjan Batra
    •  & Christian A Ross

    These authors contributed equally to this work.

Affiliations

  1. Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA.

    • Mercedes Prudencio
    • , Veronique V Belzil
    • , Ranjan Batra
    • , Tania F Gendron
    • , Luc J Pregent
    • , Melissa E Murray
    • , Kevin F Bieniek
    • , Michael DeTure
    • , Wing C Lee
    • , Mary D Davis
    • , Matthew C Baker
    • , Ralph B Perkerson
    • , Marka van Blitterswijk
    • , Caroline T Stetler
    • , Rosa Rademakers
    • , Dennis W Dickson
    •  & Leonard Petrucelli
  2. Information Technology, Mayo Clinic, Rochester, Minnesota, USA.

    • Christian A Ross
  3. Department of Neurology, Mayo Clinic, Jacksonville, Florida, USA.

    • Karen K Overstreet
    • , Amelia E Piazza-Johnston
    • , Pamela Desaro
    •  & Kevin B Boylan
  4. Mayo Graduate School, Mayo Clinic College of Medicine, Rochester, Minnesota, USA.

    • Kevin F Bieniek
  5. Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA.

    • Sherri M Biendarra
    •  & Hu Li
  6. Integrative Physiology, Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado, USA.

    • Christopher D Link

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Contributions

M.P., V.V.B., R.B. and C.A.R. contributed equally to this work. M.P., V.V.B. and L.P. contributed to the conception and design of the study. M.P., V.V.B., L.J.P., M.E.M., K.K.O., A.E.P.-J., P.D., M.D., M.D.D., M.C.B., R.B.P., K.B.B. and D.W.D. contributed to tissue selection and collection. M.P., L.J.P. and M.D.D. performed RNA extractions. M.P., V.V.B. and M.D.D. made cDNA. M.P. ran qRT-PCRs for expression and AS validation. R.B., C.A.R. and H.L. performed expression and WGCNA bioinformatics analyses. R.B. conducted AS, APA and system network analyses. M.P. and R.B. carried out GO analyses. H.L. supervised the bioinformatics analyses. T.F.G. and K.B. performed histological analyses. M.P., V.V.B., R.B., C.A.R., T.F.G., C.D.L., H.L. and L.P. interpreted the data and prepared the manuscript. All authors contributed to critical revision of the manuscript for important intellectual content and approved the final version for publication.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Hu Li or Leonard Petrucelli.

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https://doi.org/10.1038/nn.4065

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