Protein-RNA Networks Regulated by Normal and ALS-Associated Mutant HNRNPA2B1 in the Nervous System

Fernando J Martinez; Gabriel A Pratt; Eric L Van Nostrand; Ranjan Batra; Stephanie C Huelga; Katannya Kapeli; Peter Freese; Seung J Chun; Karen Ling; Chelsea Gelboin-Burkhart; Layla Fijany; Harrison C Wang; Julia K Nussbacher; Sara M Broski; Hong Joo Kim; Rea Lardelli; Balaji Sundararaman; John P Donohue; Ashkan Javaherian; Jens Lykke-Andersen; Steven Finkbeiner; C Frank Bennett; Manuel Ares Jr; Christopher B Burge; J Paul Taylor; Frank Rigo; Gene W Yeo

doi:10.1016/j.neuron.2016.09.050

Protein-RNA Networks Regulated by Normal and ALS-Associated Mutant HNRNPA2B1 in the Nervous System

Neuron. 2016 Nov 23;92(4):780-795. doi: 10.1016/j.neuron.2016.09.050. Epub 2016 Oct 20.

Authors

Fernando J Martinez¹, Gabriel A Pratt², Eric L Van Nostrand¹, Ranjan Batra¹, Stephanie C Huelga¹, Katannya Kapeli³, Peter Freese⁴, Seung J Chun⁵, Karen Ling⁵, Chelsea Gelboin-Burkhart¹, Layla Fijany¹, Harrison C Wang¹, Julia K Nussbacher¹, Sara M Broski⁶, Hong Joo Kim⁷, Rea Lardelli⁸, Balaji Sundararaman¹, John P Donohue⁹, Ashkan Javaherian⁶, Jens Lykke-Andersen⁸, Steven Finkbeiner¹⁰, C Frank Bennett⁵, Manuel Ares Jr⁹, Christopher B Burge⁴, J Paul Taylor⁷, Frank Rigo⁵, Gene W Yeo¹¹

Affiliations

¹ Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Stem Cell Program and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
² Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Stem Cell Program and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioinformatics and Systems Biology, University of California, San Diego, La Jolla, CA 92093, USA.
³ Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Stem Cell Program and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.
⁴ Department of Biology, MIT, Cambridge, MA 02139, USA.
⁵ Ionis Pharmaceuticals, Carlsbad, CA 92010, USA.
⁶ Taube/Koret Center for Neurodegenerative Disease Research, Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA.
⁷ Howard Hughes Medical Institute, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
⁸ Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
⁹ Department of Molecular, Cell, and Developmental Biology, Sinsheimer Labs, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
¹⁰ Taube/Koret Center for Neurodegenerative Disease Research, Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Departments of Neurology and Physiology, University of California, San Francisco, San Francisco, CA 94107, USA.
¹¹ Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Stem Cell Program and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioinformatics and Systems Biology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore; Molecular Engineering Laboratory, A(∗)STAR, Singapore 138673, Singapore. Electronic address: geneyeo@ucsd.edu.

Abstract

HnRNPA2B1 encodes an RNA binding protein associated with neurodegeneration. However, its function in the nervous system is unclear. Transcriptome-wide crosslinking and immunoprecipitation in mouse spinal cord discover UAGG motifs enriched within ∼2,500 hnRNP A2/B1 binding sites and an unexpected role for hnRNP A2/B1 in alternative polyadenylation. HnRNP A2/B1 loss results in alternative splicing (AS), including skipping of an exon in amyotrophic lateral sclerosis (ALS)-associated D-amino acid oxidase (DAO) that reduces D-serine metabolism. ALS-associated hnRNP A2/B1 D290V mutant patient fibroblasts and motor neurons differentiated from induced pluripotent stem cells (iPSC-MNs) demonstrate abnormal splicing changes, likely due to increased nuclear-insoluble hnRNP A2/B1. Mutant iPSC-MNs display decreased survival in long-term culture and exhibit hnRNP A2/B1 localization to cytoplasmic granules as well as exacerbated changes in gene expression and splicing upon cellular stress. Our findings provide a cellular resource and reveal RNA networks relevant to neurodegeneration, regulated by normal and mutant hnRNP A2/B1. VIDEO ABSTRACT.

Publication types

Video-Audio Media

MeSH terms

Alternative Splicing / genetics*
Amyotrophic Lateral Sclerosis / genetics*
Amyotrophic Lateral Sclerosis / metabolism
Animals
Case-Control Studies
Cell Survival / genetics*
D-Amino-Acid Oxidase / genetics
D-Amino-Acid Oxidase / metabolism
Fibroblasts / metabolism*
Fluorescent Antibody Technique
Gene Expression
Gene Expression Profiling
Heterogeneous-Nuclear Ribonucleoprotein Group A-B / genetics*
Heterogeneous-Nuclear Ribonucleoprotein Group A-B / metabolism
Humans
Induced Pluripotent Stem Cells
Mice
Motor Neurons / metabolism*
Mutation
Polyadenylation
Protein Transport / genetics*

Substances

Heterogeneous-Nuclear Ribonucleoprotein Group A-B
D-Amino-Acid Oxidase

Abstract

Publication types

MeSH terms

Substances

Grants and funding