A Genome-Wide Association Study implicates NR2F2 in Lymphangioleiomyomatosis Pathogenesis
- Wonji Kim1,2,*,
- Krinio Giannikou3,*,
- John R. Dreier3,
- Sanghun Lee4,
- Magdalena E. Tyburczy3,
- Edwin K. Silverman2,3,
- Elżbieta Radzikowska5,
- Shulin Wu6,
- Chin-Lee Wu6,
- Elizabeth P. Henske3,
- Gary Hunninghake3,
- Havi Carel7,
- Antonio Roman8,
- Miquel Angel Pujana9,
- Joel Moss10,
- Sungho Won11,12⇑ and
- David J. Kwiatkowski3
- 1Interdisciplinary Program of Bioinformatics, Seoul National University, Seoul, Korea
- 2Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- 3Division of Pulmonary and Critical Care Medicine and of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- 4Department of Medical Consilience, Graduate School, Dankook University, Seoul, Korea
- 5National Tuberculosis and Lung Diseases Research Institute, Warsaw, Poland
- 6Urology Research Laboratory, Massachusetts General Hospital, Boston, MA, USA
- 7Department of Philosophy, University of Bristol, UK
- 8Vall d'Hebron University Hospital, CIBERES, Barcelona, Spain
- 9ProCURE, Catalan Institute of Oncology, Oncobell, Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain
- 10Cardiovascular and Pulmonary Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MDGTEx
- 11Department of Public Health Sciences, Seoul National University, Seoul, Korea
- 12Institute of Health and Environment, Seoul National University, Seoul, Korea
- Dr Sungho Won, 1 Kwanak-ro Kwanak-gu, Department of Public Health Sciences, Seoul National University, Seoul 151-742, Korea. E-mail: sunghow{at}gmail; Prof. David J. Kwiatkowski, 20 Shattuck Street, Division of Pulmonary Medicine, Brigham and Women's Hospital, Boston, MA 02115. E-mail: dk{at}rics.bwh.harvard.edu
* Equal contribution
Abstract
Rationale Lymphangioleiomyomatosis occurs either associated with Tuberous Sclerosis Complex or as sporadic disease (S-LAM). Risk factors for development of S-LAM are unknown.
Objectives We hypothesised that DNA sequence variants outside of TSC2/TSC1 might be associated with susceptibility for S-LAM, and performed a Genome Wide Association Study (GWAS).
Methods Genotyped and imputed data on 5 426 936 SNPs in 426 S-LAM subjects were compared, using conditional logistic regression, to similar data from 852 females from COPDGene in a matched case-control design. For replication studies, genotypes for 196 non-Hispanic white (NHW) female S-LAM subjects were compared with three different sets of controls. RNA-seq and immunohistochemistry analyses were also performed.
Results Two non-coding genotyped SNPs met genome-wide significance; rs4544201 and rs2006950 (p-value=4.2×10−8, 6.1×10−9, respectively) which are in the same 35 kb linkage disequilibrium block on chr15q26.2. This association was replicated in an independent cohort. NR2F2, a nuclear receptor and transcription factor, was the only nearby protein-coding gene. NR2F2 expression was higher by RNA-seq in one abdominal LAM tumour and four kidney angiomyolipomas, a LAM-related tumour, compared to all TCGA cancers. Immunohistochemistry showed strong nuclear expression in both LAM and angiomyolipoma tumours.
Conclusions SNPs on chr15q26.2 are associated with S-LAM, and chromatin and expression data suggest that this association may occur through effects on NR2F2 expression, which potentially plays an important role in S-LAM development.
Footnotes
This manuscript has recently been accepted for publication in the European Respiratory Journal. It is published here in its accepted form prior to copyediting and typesetting by our production team. After these production processes are complete and the authors have approved the resulting proofs, the article will move to the latest issue of the ERJ online. Please open or download the PDF to view this article.
Conflict of interest: Dr Kim has nothing to disclose.
Conflict of interest: Dr Giannikou has no conflict of interest.
Conflict of interest: Mr Dreier has no conflict of interest.
Conflict of interest: Dr Lee has nothing to disclose.
Conflict of interest: Dr Tyburczy has no conflict of interest.
Conflict of interest: Dr Silverman reports grants from NIH, during the conduct of the study; personal fees from Novartis; and grant and travel support from GlaxoSmithKline, outside the submitted work.
Conflict of interest: Dr Radzikowska have no conflict of interest.
Conflict of interest: Dr Wu has nothing to disclose.
Conflict of interest: Dr Wu has nothing to disclosure.
Conflict of interest: Dr Henske has no conflict of interest
Conflict of interest: Dr Hunninghake reports personal fees from Genentech, personal fees from Boehringer-Ingelheim, personal fees from Gerson Lehrman Group, personal fees from Mitsubishi Chemical, outside the submitted work.
Conflict of interest: Dr Carel has nothing to disclose.
Conflict of interest: Dr Pujana reports grants from Roche Pharma outside the submitted work.
Conflict of interest: Dr Moss has nothing to disclose.
Conflict of interest: Dr Kwiatkowski has nothing to disclose.
Conflict of interest: Dr Won has nothing to disclose.
Conflict of interest: Dr Roman has nothing to disclose.
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