Human Molecular Genetics Advance Access first published online on October 28, 2009
This version [Corrected Proof] published online on November 13, 2009
Human Molecular Genetics, doi:10.1093/hmg/ddp498
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Sporadic ALS has compartment-specific aberrant exon splicing and altered cell–matrix adhesion biology
1 Translational Research Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA, 2 Center for Neurogenetics & Neurotherapeutics, University of Washington, Seattle, WA 98195, USA and 3 Section of Neurology, Virginia Mason Medical Center, Seattle, WA 98101, USA
* To whom correspondence should be addressed at: Translational Research Program, Benaroya Research Institute at Virginia Mason, 1201 Ninth Avenue, Seattle, WA 98101, USA. Tel: +1 2063411944; Fax: +1 2062237543; Email: jravits{at}benaroyaresearch.org
Received August 7, 2009; Revised October 9, 2009; Accepted October 26, 2009
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by progressive weakness from loss of motor neurons. The fundamental pathogenic mechanisms are unknown and recent evidence is implicating a significant role for abnormal exon splicing and RNA processing. Using new comprehensive genomic technologies, we studied exon splicing directly in 12 sporadic ALS and 10 control lumbar spinal cords acquired by a rapid autopsy system that processed nervous systems specifically for genomic studies. ALS patients had rostral onset and caudally advancing disease and abundant residual motor neurons in this region. We created two RNA pools, one from motor neurons collected by laser capture microdissection and one from the surrounding anterior horns. From each, we isolated RNA, amplified mRNA, profiled whole-genome exon splicing, and applied advanced bioinformatics. We employed rigorous quality control measures at all steps and validated findings by qPCR. In the motor neuron enriched mRNA pool, we found two distinct cohorts of mRNA signals, most of which were up-regulated: 148 differentially expressed genes (P 
10–3) and 411 aberrantly spliced genes (P 10–5). The aberrantly spliced genes were highly enriched in cell adhesion (P 10–57), especially cell–matrix as opposed to cell–cell adhesion. Most of the enriching genes encode transmembrane or secreted as opposed to nuclear or cytoplasmic proteins. The differentially expressed genes were not biologically enriched. In the anterior horn enriched mRNA pool, we could not clearly identify mRNA signals or biological enrichment. These findings, perturbed and up-regulated cell–matrix adhesion, suggest possible mechanisms for the contiguously progressive nature of motor neuron degeneration. Data deposition: GeneChip raw data (CEL-files) have been deposited for public access in the Gene Expression Omnibus (GEO), www.ncbi.nlm.nih.gov/geo, accession number GSE18920
[NCBI GEO]
.
Present address: Programs in Biomedical and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
Present address: John Welsh Cardiovascular Diagnostic Laboratory, Department of Pediatrics (Cardiology), Texas Children's Hospital, Baylor College of Medicine, Houston, TX 77030, USA.
¶ Present address: Departments of Pediatrics and Cellular & Molecular Medicine, Rady's Children Hospital, University of California, San Diego 2123, USA.