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Shukla V, Wang H, Varticovski L, Baek S, Wang R, Wu X, Echtenkamp F, Villa-Hernandez F, Prothro KP, Gara SK, Zhang MR, Shiffka S, Raziuddin R, Neckers LM, Linehan WM, Chen H, Hager GL, Schrump DS. Genome-Wide Analysis Identifies Nuclear Factor 1C as a Novel Transcription Factor and Potential Therapeutic Target in SCLC. J Thorac Oncol 2024:S1556-0864(24)00131-X. [PMID: 38583771 DOI: 10.1016/j.jtho.2024.03.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 03/14/2024] [Accepted: 03/30/2024] [Indexed: 04/09/2024]
Abstract
INTRODUCTION 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 with normal human small airway epithelial cells (SAECs) and induced pluripotent stem cell (iPSC) clones derived from SAEC. SCLC lines, lung iPSC (Lu-iPSC), and SAEC were further evaluated by DNase I hypersensitive site sequencing (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 evaluate growth, tumorigenicity, and changes in transcriptomes and glucose metabolism of SCLC cells after NFIC knockdown and to evaluate NFIC expression in SCLC cells after exposure to BET inhibitors. RESULTS Considerable 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 DHS-seq to RNA sequencing 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 BRD4 in the NFIC promoter region. Knockdown of BRD4 or treatment with Bromodomain and extra-terminal domain (BET) inhibitors (BETis) markedly reduced NFIC expression in SCLC cells and SCLC PDX models. Approximately 8% of genes down-regulated by BETi treatment were repressed by NFIC knockdown in SCLC, whereas 34% of genes repressed after NFIC knockdown were also down-regulated in SCLC cells after 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.
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Affiliation(s)
- Vivek Shukla
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland; Present Address: Division of Nonclinical Sciences (DNCS), FDA, Silver Spring, Maryland
| | - Haitao Wang
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Lyuba Varticovski
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Ruihong Wang
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Xinwei Wu
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Frank Echtenkamp
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Frank Villa-Hernandez
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Katherine P Prothro
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Sudheer K Gara
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Mary R Zhang
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Stephanie Shiffka
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Razi Raziuddin
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Leonard M Neckers
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Haobin Chen
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland; Present Address: Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - David S Schrump
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
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Chen X, Deng M, Wang Z, Huang C. MMP3C: an in-silico framework to depict cancer metabolic plasticity using gene expression profiles. Brief Bioinform 2023; 25:bbad471. [PMID: 38145946 PMCID: PMC10749788 DOI: 10.1093/bib/bbad471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/08/2023] [Accepted: 11/30/2023] [Indexed: 12/27/2023] Open
Abstract
Metabolic plasticity enables cancer cells to meet divergent demands for tumorigenesis, metastasis and drug resistance. Landscape analysis of tumor metabolic plasticity spanning different cancer types, in particular, metabolic crosstalk within cell subpopulations, remains scarce. Therefore, we proposed a new in-silico framework, termed as MMP3C (Modeling Metabolic Plasticity by Pathway Pairwise Comparison), to depict tumor metabolic plasticity based on transcriptome data. Next, we performed an extensive metabo-plastic analysis of over 6000 tumors comprising 13 cancer types. The metabolic plasticity within distinct cell subpopulations, particularly interplay with tumor microenvironment, were explored at single-cell resolution. Ultimately, the metabo-plastic events were screened out for multiple clinical applications via machine learning methods. The pilot research indicated that 6 out of 13 cancer types exhibited signs of the Warburg effect, implying its high reliability and robustness. Across 13 cancer types, high metabolic organized heterogeneity was found, and four metabo-plastic subtypes were determined, which link to distinct immune and metabolism patterns impacting prognosis. Moreover, MMP3C analysis of approximately 60 000 single cells of eight breast cancer patients unveiled several metabo-plastic events correlated to tumorigenesis, metastasis and immunosuppression. Notably, the metabolic features screened out by MMP3C are potential biomarkers for diagnosis, tumor classification and prognosis. MMP3C is a practical cross-platform tool to capture tumor metabolic plasticity, and our study unveiled a core set of metabo-plastic pairs among diverse cancer types, which provides bases toward improving response and overcoming resistance in cancer therapy.
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Affiliation(s)
- Xingyu Chen
- Dr. Neher’s Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR 999078, China
| | - Min Deng
- CRDA, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR 999078, China
| | - Zihan Wang
- Dr. Neher’s Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR 999078, China
| | - Chen Huang
- Dr. Neher’s Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR 999078, China
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Melnikova L, Golovnin A. Multiple Roles of dXNP and dADD1- Drosophila Orthologs of ATRX Chromatin Remodeler. Int J Mol Sci 2023; 24:16486. [PMID: 38003676 PMCID: PMC10671109 DOI: 10.3390/ijms242216486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/11/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023] Open
Abstract
The Drosophila melanogaster dADD1 and dXNP proteins are orthologues of the ADD and SNF2 domains of the vertebrate ATRX (Alpha-Thalassemia with mental Retardation X-related) protein. ATRX plays a role in general molecular processes, such as regulating chromatin status and gene expression, while dADD1 and dXNP have similar functions in the Drosophila genome. Both ATRX and dADD1/dXNP interact with various protein partners and participate in various regulatory complexes. Disruption of ATRX expression in humans leads to the development of α-thalassemia and cancer, especially glioma. However, the mechanisms that allow ATRX to regulate various cellular processes are poorly understood. Studying the functioning of dADD1/dXNP in the Drosophila model may contribute to understanding the mechanisms underlying the multifunctional action of ATRX and its connection with various cellular processes. This review provides a brief overview of the currently available information in mammals and Drosophila regarding the roles of ATRX, dXNP, and dADD1. It discusses possible mechanisms of action of complexes involving these proteins.
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Affiliation(s)
- Larisa Melnikova
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
| | - Anton Golovnin
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
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