Association Study of Exon Variants in the NF-κB and TGFβ Pathways Identifies CD40 as a Modifier of Duchenne Muscular Dystrophy

Luca Bello, Jaya Punetha, Heather Gordish-Dressman, Mamta Giri, Eric P. Hoffman, Luca Bello, Andrea Barp, Sara Vianello, Elena Pegoraro, Kevin M. Flanigan, Kevin M. Flanigan, Kevin M. Flanigan, Robert B. Weiss, Pietro Spitali, Annemieke Aartsma-Rus, Annemieke Aartsma-Rus, Volker Straub, Hanns Lochmüller, Francesco Muntoni, Irina ZaharievaAlessandra Ferlini, Eugenio Mercuri, Sylvie Tuffery-Giraud, Mireille Claustres, Craig M. McDonald, Diane M. Dunn, Kathryn J. Swoboda, Eduard Gappmaier, Michael T. Howard, Jacinda B. Sampson, Mark B. Bromberg, Russell Butterfield, Lynne Kerr, Alan Pestronk, Julaine M. Florence, Anne Connolly, Glenn Lopate, Paul Golumbek, Jeanine Schierbecker, Betsy Malkus, Renee Renna, Catherine Siener, Richard S. Finkel, Carsten G. Bonnemann, Livija Medne, Allan M. Glanzman, Jean Flickinger, Jerry R. Mendell, Wendy M. King, Linda Lowes, Lindsay Alfano, Katherine D. Mathews, Carrie Stephan, Karla Laubenthal, Kris Baldwin, Brenda Wong, Paula Morehart, Amy Meyer, John W. Day, Cameron E. Naughton, Marcia Margolis, Avital Cnaan, Richard T. Abresch, Erik K. Henricson, Lauren P. Morgenroth, Tina Duong, V. Viswanathan Chidambaranathan, W. Douglas Biggar, Laura C. McAdam, Jean Mah, Mar Tulinius, Robert Leshner, Carolina Tesi Rocha, Mathula Thangarajh, Andrew Kornberg, Monique Ryan, Yoram Nevo, Alberto Dubrovsky, Paula R. Clemens, Hoda Abdel-Hamid, Anne M. Connolly, Alan Pestronk, Jean Teasley, Tulio E. Bertorini, Kathryn North, Richard Webster, Hanna Kolski, Nancy Kuntz, Sherilyn Driscoll, Jose Carlo, Ksenija Gorni, Timothy Lotze, John W. Day, Peter Karachunski, John B. Bodensteiner

Research output: Contribution to journalArticlepeer-review

27 Scopus citations

Abstract

The expressivity of Mendelian diseases can be influenced by factors independent from the pathogenic mutation: in Duchenne muscular dystrophy (DMD), for instance, age at loss of ambulation (LoA) varies between individuals whose DMD mutations all abolish dystrophin expression. This suggests the existence of trans-acting variants in modifier genes. Common single nucleotide polymorphisms (SNPs) in candidate genes (SPP1, encoding osteopontin, and LTBP4, encoding latent transforming growth factor β [TGFβ]-binding protein 4) have been established as DMD modifiers. We performed a genome-wide association study of age at LoA in a sub-cohort of European or European American ancestry (n = 109) from the Cooperative International Research Group Duchenne Natural History Study (CINRG-DNHS). We focused on protein-altering variants (Exome Chip) and included glucocorticoid treatment as a covariate. As expected, due to the small population size, no SNPs displayed an exome-wide significant p value (< 1.8 × 10−6). Subsequently, we prioritized 438 SNPs in the vicinities of 384 genes implicated in DMD-related pathways, i.e., the nuclear-factor-κB and TGFβ pathways. The minor allele at rs1883832, in the 5′-untranslated region of CD40, was associated with earlier LoA (p = 3.5 × 10−5). This allele diminishes the expression of CD40, a co-stimulatory molecule for T cell polarization. We validated this association in multiple independent DMD cohorts (United Dystrophinopathy Project, Bio-NMD, and Padova, total n = 660), establishing this locus as a DMD modifier. This finding points to cell-mediated immunity as a relevant pathogenetic mechanism and potential therapeutic target in DMD.

Original languageEnglish (US)
Pages (from-to)1163-1171
Number of pages9
JournalAmerican Journal of Human Genetics
Volume99
Issue number5
DOIs
StatePublished - Nov 3 2016

Bibliographical note

Funding Information:
We would like to thank all participants and their families. We gratefully acknowledge Stanley F. Nelson and Richard T. Wang (UCLA) for generating Exome Chip data, Akanchha Kesari (Children’s National Medical Center) for help with genotyping, Bruno F. Gavassini (University of Padova) for technical help with immunoblot experiments, Michela Guglieri and Kate Bushby (Newcastle University) for providing clinical data, and biobank staff Dan Cox and Mojgan Reza (Newcastle University) for processing samples. L.B. was supported by an Italian Ministry of Education PhD grant for the Doctorate School of Medical, Clinical, and Experimental Science at the University of Padova. We acknowledge funding from Association Française contre les Myopathies (support to Bio-NMD, grants 15092 and 17724 ); Dutch Duchenne Parent Project (support to P.S.); the European Union (support to Bio-NMD grant 241665 , Neuromics grant 305121 , RD-Connect grant 305444 ); the Italian Duchenne Parent Project (support to A.F.); the Medical Research council Centre for Neuromuscular Diseases Biobanks (support to London and Newcastle Biobanks), part of Eurobiobank ; National Institute for Health Research Biomedical Research Centre at Great Ormond Street Hospital for Children, NHS Foundation Trust, and University College London; Telethon Italy Foundation (support to Nemo Centers and Padova Neuromuscular Biobank, grant GTB12001D ); the U.S. Department of Defense (support to CINRG, grant # W81XWH-12-1-0417 ); the U.S. Department of Education / NIDRR (support to CINRG, grants H133B031118 and H133B090001 ); the National Institutes of Health / NINDS (support to K.M.F. and R.B.W.; grant R01 NS085238 ); and the U.S. National Institutes of Health / NIAMS (support to CINRG, grant R01AR061875 ).

Funding Information:
K.M.F. has served on clinical or scientific advisory boards for Sarepta Therapeutics, PTC Therapeutics, Audentes Therapeutics, Marathon Therapeutics, and Italafarmaco and has also served as a trial site investigator for PTC Therapeutics, BioMarin, Akashi Therapeutics, and Sarepta Therapeutics. A.A.-R. reports being employed by LUMC, which has patents on exon-skipping technology, and as a co-inventor on some of these patents, stands to gain from a share of potential royalties; furthermore, she reports being SAB member for Philae Pharmaceutical and ProQR, ad hoc consultant for GLC consulting, Deerfield, Global Guidepoint, BioClinica, PTC Therapeutics, BioMarin, Summit Plc, Bristol-Meier-Squibb, and a speaker at symposia organized by PTC Therapeutics and BioMarin (remuneration for consulting, SAB, and speaker activities go to LUMC). F.M. has received consulting fees from PTC Therapeutics, Sarepta Therapeutics, BioMarin, Roche, Biogen, Italfarmaco, Avexis, Pfizer, Trivorsan, and Catabasis and is supported by the National Institute of Health Research Biomedical Research Centre at Great Ormond Street Hospital for Children's NHS Foundation Trust and University College London. H.G.-D. is a founder and shareholder of TRiNDS LLC, and a consulting statistician for AGADA BioSciences. E.P.H. is an employee and shareholder of ReveraGen BioPharma and is a founder and shareholder of AGADA BioSciences and TRiNDS LLC.

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