Lupus Susceptibility Region Containing CDKN1B rs34330 Mechanistically Influences Expression and Function of Multiple Target Genes, Also Linked to Proliferation and Apoptosis

Singh B 1 , Maiti GP 1 , Zhou X 2 , Fazel-Najafabadi M 1 , Bae SC 3 , Sun C 1 Show all authors , Terao C 4 , Okada Y 5 , Heng Chua K 6 , Kochi Y 7 , Guthridge JM 1 , Zhang H 2 , Weirauch M 8 , James JA 1 , Harley JB 8 , Varshney GK 1 , Looger LL 9 , Nath SK 1

Affiliations 

  • 1 Oklahoma Medical Research Foundation, Oklahoma City
  • 2 Peking University First Hospital, Peking University, Ministry of Health of China, Beijing, China
  • 3 Hanyang University Hospital for Rheumatic Diseases, Seoul, Republic of Korea
  • 4 RIKEN Center for Integrative Medical Sciences, RIKEN Yokohama Campus, Yokohama, Japan, and University of Shizuoka, Shizuoka, Japan
  • 5 Osaka University, Osaka, Japan
  • 6 University of Malaya, Kuala Lumpur, Malaysia
  • 7 Tokyo Medical and Dental University, RIKEN Center for Integrative Medical Sciences, RIKEN Yokohama Campus, Yokohama, Japan
  • 8 Cincinnati Children's Hospital Medical Center, University of Cincinnati, and Cincinnati VA Medical Center, Cincinnati, Ohio, USA
  • 9 Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia, USA
Arthritis Rheumatol, 2021 Dec;73(12):2303-2313.
PMID: 33982894 DOI: 10.1002/art.41799

Abstract

OBJECTIVE: In a recent genome-wide association study, a significant genetic association between rs34330 of CDKN1B and risk of systemic lupus erythematosus (SLE) in Han Chinese was identified. This study was undertaken to validate the reported association and elucidate the biochemical mechanisms underlying the effect of the variant.

METHODS: We performed an allelic association analysis in patients with SLE, followed by a meta-analysis assessing genome-wide association data across 11 independent cohorts (n = 28,872). In silico bioinformatics analysis and experimental validation in SLE-relevant cell lines were applied to determine the functional consequences of rs34330.

RESULTS: We replicated a genetic association between SLE and rs34330 (meta-analysis P = 5.29 × 10-22 , odds ratio 0.84 [95% confidence interval 0.81-0.87]). Follow-up bioinformatics and expression quantitative trait locus analysis suggested that rs34330 is located in active chromatin and potentially regulates several target genes. Using luciferase and chromatin immunoprecipitation-real-time quantitative polymerase chain reaction, we demonstrated substantial allele-specific promoter and enhancer activity, and allele-specific binding of 3 histone marks (H3K27ac, H3K4me3, and H3K4me1), RNA polymerase II (Pol II), CCCTC-binding factor, and a critical immune transcription factor (interferon regulatory factor 1 [IRF-1]). Chromosome conformation capture revealed long-range chromatin interactions between rs34330 and the promoters of neighboring genes APOLD1 and DDX47, and effects on CDKN1B and the other target genes were directly validated by clustered regularly interspaced short palindromic repeat (CRISPR)-based genome editing. Finally, CRISPR/dead CRISPR-associated protein 9-based epigenetic activation/silencing confirmed these results. Gene-edited cell lines also showed higher levels of proliferation and apoptosis.

CONCLUSION: Collectively, these findings suggest a mechanism whereby the rs34330 risk allele (C) influences the presence of histone marks, RNA Pol II, and IRF-1 transcription factor to regulate expression of several target genes linked to proliferation and apoptosis. This process could potentially underlie the association of rs34330 with SLE.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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