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Kong R, Patel AS, Sato T, Jiang F, Yoo S, Bao L, Sinha A, Tian Y, Fridrikh M, Liu S, Feng J, He X, Jiang J, Ma Y, Grullon K, Yang D, Powell CA, Beasley MB, Zhu J, Snyder EL, Li S, Watanabe H. Transcriptional Circuitry of NKX2-1 and SOX1 Defines an Unrecognized Lineage Subtype of Small-Cell Lung Cancer. Am J Respir Crit Care Med 2022; 206:1480-1494. [PMID: 35848993 PMCID: PMC9757094 DOI: 10.1164/rccm.202110-2358oc] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 07/18/2022] [Indexed: 12/24/2022] Open
Abstract
Rationale: The current molecular classification of small-cell lung cancer (SCLC) on the basis of the expression of four lineage transcription factors still leaves its major subtype SCLC-A as a heterogeneous group, necessitating more precise characterization of lineage subclasses. Objectives: To refine the current SCLC classification with epigenomic profiles and to identify features of the redefined SCLC subtypes. Methods: We performed unsupervised clustering of epigenomic profiles on 25 SCLC cell lines. Functional significance of NKX2-1 (NK2 homeobox 1) was evaluated by cell growth, apoptosis, and xenograft using clustered regularly interspaced short palindromic repeats-Cas9 (CRISPR-associated protein 9)-mediated deletion. NKX2-1-specific cistromic profiles were determined using chromatin immunoprecipitation followed by sequencing, and its functional transcriptional partners were determined using coimmunoprecipitation followed by mass spectrometry. Rb1flox/flox; Trp53flox/flox and Rb1flox/flox; Trp53flox/flox; Nkx2-1flox/flox mouse models were engineered to explore the function of Nkx2-1 in SCLC tumorigenesis. Epigenomic landscapes of six human SCLC specimens and 20 tumors from two mouse models were characterized. Measurements and Main Results: We identified two epigenomic subclusters of the major SCLC-A subtype: SCLC-Aα and SCLC-Aσ. SCLC-Aα was characterized by the presence of a super-enhancer at the NKX2-1 locus, which was observed in human SCLC specimens and a murine SCLC model. We found that NKX2-1, a dual lung and neural lineage factor, is uniquely relevant in SCLC-Aα. In addition, we found that maintenance of this neural identity in SCLC-Aα is mediated by collaborative transcriptional activity with another neuronal transcriptional factor, SOX1 (SRY-box transcription factor 1). Conclusions: We comprehensively describe additional epigenomic heterogeneity of the major SCLC-A subtype and define the SCLC-Aα subtype by the core regulatory circuitry of NKX2-1 and SOX1 super-enhancers and their functional collaborations to maintain neuronal linage state.
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Affiliation(s)
- Ranran Kong
- Department of Thoracic Surgery and
- Division of Pulmonary, Critical Care and Sleep Medicine
- Tisch Cancer Institute
| | - Ayushi S. Patel
- Division of Pulmonary, Critical Care and Sleep Medicine
- Tisch Cancer Institute
- Division of Hematology and Medical Oncology, Laura and Isaac Perlmutter Cancer Center, Langone Medical Center, New York University, New York, New York
| | - Takashi Sato
- Division of Pulmonary, Critical Care and Sleep Medicine
- Tisch Cancer Institute
- Department of Respiratory Medicine, School of Medicine, Kitasato University, Sagamihara, Japan
- Division of Pulmonary Medicine, Department of Medicine, School of Medicine, Keio University, Tokyo, Japan
| | - Feng Jiang
- Division of Pulmonary, Critical Care and Sleep Medicine
- Tisch Cancer Institute
| | - Seungyeul Yoo
- Department of Genetics and Genomic Sciences, and
- Sema4, Stamford, Connecticut
| | - Li Bao
- People’s Hospital of Ningxia Hui Autonomous Region, Yinchuan, China
| | - Abhilasha Sinha
- Division of Pulmonary, Critical Care and Sleep Medicine
- Tisch Cancer Institute
| | - Yang Tian
- Division of Pulmonary, Critical Care and Sleep Medicine
- Tisch Cancer Institute
| | - Maya Fridrikh
- Division of Pulmonary, Critical Care and Sleep Medicine
- Tisch Cancer Institute
| | - Shuhui Liu
- Division of Infectious Diseases, Department of Medicine
| | - Jie Feng
- Department of Nephrology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Xijing He
- Department of Orthopedics, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Xi’an International Medical Center, Xi’an, China
| | | | | | - Karina Grullon
- Division of Pulmonary, Critical Care and Sleep Medicine
- Tisch Cancer Institute
| | - Dawei Yang
- Division of Pulmonary, Critical Care and Sleep Medicine
- Tisch Cancer Institute
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital Fudan University, Shanghai, China; and
| | - Charles A. Powell
- Division of Pulmonary, Critical Care and Sleep Medicine
- Tisch Cancer Institute
| | - Mary Beth Beasley
- Department of Pathology and Laboratory Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jun Zhu
- Tisch Cancer Institute
- Department of Genetics and Genomic Sciences, and
- Sema4, Stamford, Connecticut
| | - Eric L. Snyder
- Department of Pathology
- Department of Oncological Sciences, and
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | | | - Hideo Watanabe
- Division of Pulmonary, Critical Care and Sleep Medicine
- Tisch Cancer Institute
- Department of Genetics and Genomic Sciences, and
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