Genome-wide Analysis Identifies Nuclear Factor 1C as a Novel Transcription Factor and Potential Therapeutic Target in Small Cell Lung Cancer

Vivek Shukla; Haitao Wang; Lyuba Varticovski; Songjoon Baek; Ruihong Wang; Xinwei Wu; Frank Echtenkamp; Frank Villa Hernandez; Katherine P Prothro; Sudheer K Gara; Mary R Zhang; Stephanie Shiffka; Razi Raziuddin; Leonard M Neckers; W Marston Linehan; Haobin Chen; Gordon L Hager; David S Schrump

doi:10.1016/j.jtho.2024.03.023

Genome-wide Analysis Identifies Nuclear Factor 1C as a Novel Transcription Factor and Potential Therapeutic Target in Small Cell Lung Cancer

J Thorac Oncol. 2024 Apr 5:S1556-0864(24)00131-X. doi: 10.1016/j.jtho.2024.03.023. Online ahead of print.

Authors

Vivek Shukla¹, Haitao Wang¹, Lyuba Varticovski², Songjoon Baek², Ruihong Wang¹, Xinwei Wu¹, Frank Echtenkamp³, Frank Villa Hernandez¹, Katherine P Prothro¹, Sudheer K Gara¹, Mary R Zhang¹, Stephanie Shiffka¹, Razi Raziuddin², Leonard M Neckers³, W Marston Linehan³, Haobin Chen¹, Gordon L Hager², David S Schrump⁴

Affiliations

¹ Thoracic Epigenetics Section, Thoracic Surgery Branch.
² Laboratory of Receptor Biology and Gene Expression.
³ Urologic Oncology Branch.
⁴ Thoracic Epigenetics Section, Thoracic Surgery Branch. Electronic address: David_Schrump@nih.gov.

PMID: 38583771
DOI: 10.1016/j.jtho.2024.03.023

Abstract

Background: Recent insights regarding mechanisms mediating stemness, heterogeneity, and metastatic potential of lung cancers have yet to be fully translated to effective regimens for the treatment of these malignancies. This study sought to identify novel targets for lung cancer therapy.

Methods: Transcriptomes and DNA methylomes of 14 SCLC and 10 NSCLC lines were compared to normal human small airway epithelial cells (SAEC) and induced pluripotent stem cell (iPSC) clones derived from SAEC. SCLC lines, lung iPSC (Lu-iPSC), and SAEC were further evaluated by DNase I hypersensitivity (DHS-seq). Changes in chromatin accessibility and depths of transcription factor (TF) footprints were quantified using Bivariate analysis of Genomic Footprint. Standard techniques were used to examine growth and tumorigenencity as well as changes in transcriptomes and glucose metabolism of SCLC cells following Nuclear Factor 1C (NFIC) knockdown, and to examine NFIC expression in SCLC cells following exposure to BET inhibitors.

Results: Significant commonality of transcriptomes and DNA methylomes was observed between Lu-iPSC and SCLC; however, this analysis was uninformative regarding pathways unique to lung cancer. Linking results of DNase-seq to RNA-seq enabled identification of networks not previously associated with SCLC. When combined with footprint depth, NFIC, a transcription factor not previously associated with SCLC, had the highest score of occupancy at open chromatin sites. Knockdown of NFIC impaired glucose metabolism, decreased stemness, and inhibited growth of SCLC cells in-vitro and in-vivo. ChIP-seq analysis identified numerous sites occupied by Bromodomain-containing protein 4 (BRD4) in the NFIC promoter region. Knock-down of BRD4 or treatment with Bromodomain and extra-terminal domain (BET) inhibitors (BETi) markedly reduced NFIC expression in SCLC cells and SCLC PDX models. Approximately 8% of genes downregulated by BETi treatment were repressed by NFIC knockdown in SCLC, while 34% of genes repressed following NFIC knockdown were also downregulated in SCLC cells following BETi treatment.

Conclusions: NFIC is a key TF and possible mediator of transcriptional regulation by BET family proteins in SCLC. Our findings highlight the potential of genome-wide chromatin accessibility analysis for elucidating mechanisms of pulmonary carcinogenesis and identifying novel targets for lung cancer therapy.

Keywords: DNA footprint; NFIC; bromodomain inhibitors; chromatin landscape; enhancers; lung cancer; transcriptional regulation.