Promoter-Specific Variants in NeuroD1 and H3K4me3 Coincident Regions and Clinical Outcomes of Small Cell Lung Cancer

Seung Soo Yoo, Sunwoong Lee, Jin Eun Choi, Mi Jeong Hong, Sook Kyung Do, Jang Hyuck Lee, Won Kee Lee, Ji Eun Park, Yong Hoon Lee, Sun Ha Choi, Hyewon Seo, Jaehee Lee, Shin Yup Lee, Seung Ick Cha, Chang Ho Kim, Hyo Gyoung Kang, Jae Yong Park

Research output: Contribution to journalArticlepeer-review

Abstract

BACKGROUND: Neurogenic differentiation 1 (NeuroD1) is a representative small cell lung cancer (SCLC) transcription regulator involved in the carcinogenesis and behavior of SCLC. Histone modifications play an important role in transcription, and H3 lysine 4 trimethylation (H3K4me3) is primarily associated with promoter regions. METHODS: We investigated the association between single nucleotide polymorphisms (SNPs) in NeuroD1 and H3K4me3 coincident regions, selected using ChIP sequencing (ChIP-seq), and the clinical outcomes of 261 patients with SCLC. RESULTS: Among 230 SNPs, two were significantly associated with both the chemotherapy response and overall survival (OS) of patients with SCLC. RNF145 rs2043268A>G was associated with worse chemotherapy response and OS (under a recessive model, adjusted odds ratio [aOR], 0.50, 95% confidence interval [CI], 0.26-0.94, P = 0.031, and adjusted hazard ratio [aHR], 1.88, 95% CI, 1.38-2.57, P < 0.001). CINP rs762105A>G was also associated with worse chemotherapy response and OS (under a dominant model, aOR, 0.47, 95% CI, 0.23-0.99, P = 0.046, and aHR, 2.03, 95% CI, 1.47-2.82, P < 0.001). ChIP-quantitative polymerase chain reaction and luciferase assay confirmed that the two SNPs were located in the active promoter regions and influenced the promoter activity of each gene. CONCLUSION: To summarize, among SNPs selected using ChIP-seq in promoter regions with high peaks in both NeuroD1 and H3K4me3, RNF145 rs2043268A>G and CINP rs762105A>G were associated with clinical outcomes in patients with SCLC and also affected the promoter activity of each gene.

Original languageEnglish
Pages (from-to)e381
JournalJournal of Korean Medical Science
Volume38
Issue number45
DOIs
StatePublished - 20 Nov 2023

Keywords

  • ChIP-seq
  • H3K4me3
  • NeuroD1
  • Small Cell Lung Cancer
  • Variant

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