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Ji M, Yu D, Liu X, Wang L, Zhang D, Yang Z, Huang W, Fan H, Wang L, Sun H. Glutathione-dependent degradation of SMARCA2/4 for targeted lung cancer therapy with improved selectivity. Eur J Med Chem 2024; 277:116751. [PMID: 39128328 DOI: 10.1016/j.ejmech.2024.116751] [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: 06/03/2024] [Revised: 07/20/2024] [Accepted: 08/03/2024] [Indexed: 08/13/2024]
Abstract
SMARCA2 and SMARCA4 are the mutually exclusive catalytic subunits of the mammalian Switch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex, and have recently been considered as attractive synthetic lethal targets for PROTAC-based cancer therapy. However, the potential off-tissue toxicity towards normal tissues remains a concern. Here, we optimize a GSH-inducible SMARCA2/4-based PROTAC precursor with selective antitumor activity towards lung cancer cells and negligible cytotoxicity towards normal cells in both in vitro and in vivo studies. The precursor is not bioactive or cytotoxic, but preferentially responds to endogenous GSH in GSH-rich lung cancer cells, releasing active PROTAC to degrade SMARCA2/4 via PROTAC-mediated proteasome pathway. Subsequent xenograft model study reveals that selective SMARCA2/4 degradation in lung tumors triggers DNA damage and apoptosis, which significantly inhibits lung cancer cell proliferation without obvious adverse events towards normal tissues. This study exemplifies the targeted degradation of SMARCA2/4 in lung cancer cells by the GSH-responsive PROTAC precursor, highlighting its potential as an encouraging cancer therapeutic strategy.
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Affiliation(s)
- Ming Ji
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Chemical Biology, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Dehao Yu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Chemical Biology, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Xinmin Liu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Chemical Biology, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Luo Wang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Chemical Biology, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Dongli Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Chemical Biology, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Zhengduo Yang
- Department of Pathology, Tianjin Union Medical Center, Tianjin, 300121, China
| | - Wanqiao Huang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Chemical Biology, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Heli Fan
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Chemical Biology, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Lulu Wang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Chemical Biology, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China.
| | - Huabing Sun
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Chemical Biology, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China.
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2
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Trejo-Villegas OA, Heijink IH, Ávila-Moreno F. Preclinical evidence in the assembly of mammalian SWI/SNF complexes: Epigenetic insights and clinical perspectives in human lung disease therapy. Mol Ther 2024; 32:2470-2488. [PMID: 38910326 DOI: 10.1016/j.ymthe.2024.06.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 04/18/2024] [Accepted: 06/20/2024] [Indexed: 06/25/2024] Open
Abstract
The SWI/SNF complex, also known as the BRG1/BRM-associated factor (BAF) complex, represents a critical regulator of chromatin remodeling mechanisms in mammals. It is alternatively referred to as mSWI/SNF and has been suggested to be imbalanced in human disease compared with human health. Three types of BAF assemblies associated with it have been described, including (1) canonical BAF (cBAF), (2) polybromo-associated BAF (PBAF), and (3) non-canonical BAF (ncBAF) complexes. Each of these BAF assemblies plays a role, either functional or dysfunctional, in governing gene expression patterns, cellular processes, epigenetic mechanisms, and biological processes. Recent evidence increasingly links the dysregulation of mSWI/SNF complexes to various human non-malignant lung chronic disorders and lung malignant diseases. This review aims to provide a comprehensive general state-of-the-art and a profound examination of the current understanding of mSWI/SNF assembly processes, as well as the structural and functional organization of mSWI/SNF complexes and their subunits. In addition, it explores their intricate functional connections with potentially dysregulated transcription factors, placing particular emphasis on molecular and cellular pathogenic processes in lung diseases. These processes are reflected in human epigenome aberrations that impact clinical and therapeutic levels, suggesting novel perspectives on the diagnosis and molecular therapies for human respiratory diseases.
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Affiliation(s)
- Octavio A Trejo-Villegas
- Lung Diseases and Functional Epigenomics Laboratory (LUDIFE), Biomedicine Research Unit (UBIMED), Facultad de Estudios Superiores-Iztacala (FES-Iztacala), Universidad Nacional Autónoma de México (UNAM), Avenida de los Barrios #1, Colonia Los Reyes Iztacala, Tlalnepantla de Baz, 54090, Estado de México, México
| | - Irene H Heijink
- Departments of Pathology & Medical Biology and Pulmonology, GRIAC Research Institute, University Medical Center Groningen, University of Groningen, 9713 Groningen, the Netherlands
| | - Federico Ávila-Moreno
- Lung Diseases and Functional Epigenomics Laboratory (LUDIFE), Biomedicine Research Unit (UBIMED), Facultad de Estudios Superiores-Iztacala (FES-Iztacala), Universidad Nacional Autónoma de México (UNAM), Avenida de los Barrios #1, Colonia Los Reyes Iztacala, Tlalnepantla de Baz, 54090, Estado de México, México; Research Unit, Instituto Nacional de Enfermedades Respiratorias (INER), Ismael Cosío Villegas, 14080, Ciudad de México, México; Research Tower, Subdirección de Investigación Básica, Instituto Nacional de Cancerología (INCan), 14080, Ciudad de México, México.
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3
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Morris M, Ararat K, Cutshall H, Gokden M, Rodriguez A, Rooper L, Lindberg M, Nix JS. SMARCA4-deficient central nervous system metastases: A case series and systematic review. J Neuropathol Exp Neurol 2024; 83:638-654. [PMID: 38687619 DOI: 10.1093/jnen/nlae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024] Open
Abstract
SMARCA4 alterations can be encountered in a variety of human neoplasms, and metastases to the central nervous system (CNS) are rare, offering a challenge to neuropathologists despite not representing a distinct diagnostic entity. To better understand the clinical and histologic presentation of such neoplasms, we report an observational case series and systematic review of 178 unique articles that yielded 15 published cases and 7 cases from institutional files. In the systematic review, the median age was 58 years, the male-to-female ratio was 2:1, and the most common diagnosis was lung adenocarcinoma; all CNS metastases were discovered within 1 year of presentation. In the case series, the median age was 58 years, the male-to-female ratio was 6:1, and all known metastases originated from the lung. Most patients had a smoking history and died of disease. GATA-3 positivity was seen in most case series examples. Concurrent TP53 mutations (83.3%) and a high tumor mutation rate (60%) were common. To our knowledge, this is the only case series and systematic review in the English literature aimed at assessing SMARCA4-altered metastases in the CNS and vertebral column. We highlight the challenges of neuropathologic evaluation of such tumors and provide observational evidence of early metastases, histologic appearances, and immunohistochemical findings, including previously unreported GATA-3 positivity.
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Affiliation(s)
- Meaghan Morris
- Department of Pathology, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Kerime Ararat
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Hannah Cutshall
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Murat Gokden
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Analiz Rodriguez
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Lisa Rooper
- Department of Pathology, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Matthew Lindberg
- Department of Pathology, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - James Stephen Nix
- Department of Pathology, The Johns Hopkins Hospital, Baltimore, Maryland, USA
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4
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Shiba-Ishii A, Isagawa T, Shiozawa T, Mato N, Nakagawa T, Takada Y, Hirai K, Hong J, Saitoh A, Takeda N, Niki T, Murakami Y, Matsubara D. Novel therapeutic strategies targeting bypass pathways and mitochondrial dysfunction to combat resistance to RET inhibitors in NSCLC. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167249. [PMID: 38768929 DOI: 10.1016/j.bbadis.2024.167249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 05/11/2024] [Accepted: 05/15/2024] [Indexed: 05/22/2024]
Abstract
RET fusion is an oncogenic driver in 1-2 % of patients with non-small cell lung cancer (NSCLC). Although RET-positive tumors have been treated with multikinase inhibitors such as vandetanib or RET-selective inhibitors, ultimately resistance to them develops. Here we established vandetanib resistance (VR) clones from LC-2/ad cells harboring CCDC6-RET fusion and explored the molecular mechanism of the resistance. Each VR clone had a distinct phenotype, implying they had acquired resistance via different mechanisms. Consistently, whole exome-seq and RNA-seq revealed that the VR clones had unique mutational signatures and expression profiles, and shared only a few common remarkable events. AXL and IGF-1R were activated as bypass pathway in different VR clones, and sensitive to a combination of RET and AXL inhibitors or IGF-1R inhibitors, respectively. SMARCA4 loss was also found in a particular VR clone and 55 % of post-TKI lung tumor tissues, being correlated with higher sensitivity to SMARCA4/SMARCA2 dual inhibition and shorter PFS after subsequent treatments. Finally, we detected an increased number of damaged mitochondria in one VR clone, which conferred sensitivity to mitochondrial electron transfer chain inhibitors. Increased mitochondria were also observed in post-TKI biopsy specimens in 13/20 cases of NSCLC, suggesting a potential strategy targeting mitochondria to treat resistant tumors. Our data propose new promising therapeutic options to combat resistance to RET inhibitors in NSCLC.
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MESH Headings
- Humans
- Carcinoma, Non-Small-Cell Lung/drug therapy
- Carcinoma, Non-Small-Cell Lung/pathology
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/metabolism
- Proto-Oncogene Proteins c-ret/antagonists & inhibitors
- Proto-Oncogene Proteins c-ret/genetics
- Proto-Oncogene Proteins c-ret/metabolism
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Lung Neoplasms/drug therapy
- Lung Neoplasms/pathology
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Mitochondria/metabolism
- Mitochondria/drug effects
- Piperidines/pharmacology
- Piperidines/therapeutic use
- Protein Kinase Inhibitors/therapeutic use
- Protein Kinase Inhibitors/pharmacology
- Cell Line, Tumor
- Quinazolines/pharmacology
- Quinazolines/therapeutic use
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcription Factors/antagonists & inhibitors
- Signal Transduction/drug effects
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Oncogene Proteins, Fusion/antagonists & inhibitors
- DNA Helicases/genetics
- DNA Helicases/metabolism
- DNA Helicases/antagonists & inhibitors
- Cytoskeletal Proteins
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Affiliation(s)
- Aya Shiba-Ishii
- Department of Diagnostic Pathology, Institute of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Takayuki Isagawa
- Center for Data Science, Jichi Medical University, Tochigi, Japan
| | - Toshihiro Shiozawa
- Department of Respiratory Medicine, Institute of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Naoko Mato
- Division of Pulmonary Medicine, Department of Medicine, Jichi Medical University, Ibaraki, Japan
| | - Tomoki Nakagawa
- Department of Pathology, University of Tsukuba Hospital, Ibaraki, Japan
| | - Yurika Takada
- Department of Diagnostic Pathology, Institute of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Kanon Hirai
- Department of Diagnostic Pathology, Institute of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Jeongmin Hong
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Anri Saitoh
- Division of Molecular Pathology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Norihiko Takeda
- Division of Cardiology and Metabolism, Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | - Toshiro Niki
- Department of Pathology, Jichi Medical University, Tochigi, Japan
| | - Yoshinori Murakami
- Division of Molecular Pathology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Daisuke Matsubara
- Department of Diagnostic Pathology, Institute of Medicine, University of Tsukuba, Ibaraki, Japan.
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5
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Redin E, Sridhar H, Zhan YA, Pereira Mello B, Zhong H, Durani V, Sabet A, Manoj P, Linkov I, Qiu J, Koche RP, de Stanchina E, Astorkia M, Betel D, Quintanal-Villalonga Á, Rudin CM. SMARCA4 controls state plasticity in small cell lung cancer through regulation of neuroendocrine transcription factors and REST splicing. J Hematol Oncol 2024; 17:58. [PMID: 39080761 PMCID: PMC11290012 DOI: 10.1186/s13045-024-01572-3] [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: 04/28/2024] [Accepted: 07/03/2024] [Indexed: 08/02/2024] Open
Abstract
INTRODUCTION Small Cell Lung Cancer (SCLC) can be classified into transcriptional subtypes with distinct degrees of neuroendocrine (NE) differentiation. Recent evidence supports plasticity among subtypes with a bias toward adoption of low-NE states during disease progression or upon acquired chemotherapy resistance. Here, we identify a role for SMARCA4, the catalytic subunit of the SWI/SNF complex, as a regulator of subtype shift in SCLC. METHODS ATACseq and RNAseq experiments were performed in SCLC cells after pharmacological inhibition of SMARCA4. DNA binding of SMARCA4 was characterized by ChIPseq in high-NE SCLC patient derived xenografts (PDXs). Enrichment analyses were applied to transcriptomic data. Combination of FHD-286 and afatinib was tested in vitro and in a set of chemo-resistant SCLC PDXs in vivo. RESULTS SMARCA4 expression positively correlates with that of NE genes in both SCLC cell lines and patient tumors. Pharmacological inhibition of SMARCA4 with FHD-286 induces the loss of NE features and downregulates neuroendocrine and neuronal signaling pathways while activating non-NE factors. SMARCA4 binds to gene loci encoding NE-lineage transcription factors ASCL1 and NEUROD1 and alters chromatin accessibility, enhancing NE programs. Enrichment analysis applied to high-confidence SMARCA4 targets confirmed neuron related pathways as the top GO Biological processes regulated by SMARCA4 in SCLC. In parallel, SMARCA4 also controls REST, a known suppressor of the NE phenotype, by regulating SRRM4-dependent REST transcript splicing. Furthermore, SMARCA4 inhibition drives ERBB pathway activation in SCLC, rendering SCLC tumors sensitive to afatinib. CONCLUSIONS This study nominates SMARCA4 as a key regulator of the NE state plasticity and defines a novel therapeutic strategy for SCLC.
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Affiliation(s)
- Esther Redin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Harsha Sridhar
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yingqian A Zhan
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Hong Zhong
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Vidushi Durani
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine Graduate School of Medical Sciences, New York, NY, USA
| | - Amin Sabet
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Parvathy Manoj
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Irina Linkov
- Precision Pathology Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Juan Qiu
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elisa de Stanchina
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maider Astorkia
- Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Doron Betel
- Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, 10065, USA
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
- Department of Physiology, Biophysics and Systems Biology, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | | | - Charles M Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Weill Cornell Medicine Graduate School of Medical Sciences, New York, NY, USA.
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6
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Xie Y, Zhou Z, Deng D, Liu Y. Malignant melanoma arising from giant congenital melanocytic nevus with SMARCA2 gene mutation. Asian J Surg 2024; 47:3320-3321. [PMID: 38604858 DOI: 10.1016/j.asjsur.2024.03.171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 03/22/2024] [Indexed: 04/13/2024] Open
Affiliation(s)
- Yongyi Xie
- Department of Pathology, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Zhiyu Zhou
- Department of Pathology, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Dan Deng
- Department of Dermatology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Yeqiang Liu
- Department of Pathology, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China.
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7
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Manolakos P, Boccuto L, Ivankovic DS. A Critical Review of the Impact of SMARCA4 Mutations on Survival Outcomes in Non-Small Cell Lung Cancer. J Pers Med 2024; 14:684. [PMID: 39063938 PMCID: PMC11278206 DOI: 10.3390/jpm14070684] [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: 05/14/2024] [Revised: 06/11/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
This critical review investigates the impact of SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 4 (SMARCA4) mutations on survival outcomes in non-small cell lung cancer (NSCLC) through an analysis of 21 peer-reviewed articles. Survival analyses across this review demonstrated consistently worse outcomes for SMARCA4-mutated vs. SMARCA4 wild-type NSCLC patients, specifically emphasizing class 1 truncating mutations as an independent factor for poor overall survival. In addition, this review explores the clinicopathologic characteristics of SMARCA4 mutations and their impact on various treatment modalities, including immune checkpoint inhibitors (ICIs) both with and without Kirsten rat sarcoma viral oncogene homolog (KRAS) co-mutations. The potential ineffectiveness of ICI treatment in NSCLC is explored through the impact of SMARCA4/KRAS co-mutations on the tumor microenvironment. Moreover, this NSCLC review consistently reported statistically worse overall survival outcomes for SMARCA4/KRAS co-mutations than SMARCA4 wild-type/KRAS-mutated cohorts, extending across ICIs, chemo-immunotherapy (CIT), and KRAS G12C inhibitors. Designing prospective clinical SMARCA4-mutated or SMARCA4/KRAS co-mutated NSCLC trials to evaluate targeted therapies and immunotherapy may lead to a better understanding of how to improve cancer patients' outcomes and survival rates.
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Affiliation(s)
- Peter Manolakos
- Healthcare Genetics and Genomics PhD Program, Clemson University, Clemson, SC 29634, USA; (L.B.); (D.S.I.)
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8
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Bhat KP, Vijay J, Vilas CK, Asundi J, Zou J, Lau T, Cai X, Ahmed M, Kabza M, Weng J, Fortin JP, Lun A, Durinck S, Hafner M, Costa MR, Ye X. CRISPR activation screens identify the SWI/SNF ATPases as suppressors of ferroptosis. Cell Rep 2024; 43:114345. [PMID: 38870012 DOI: 10.1016/j.celrep.2024.114345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 04/22/2024] [Accepted: 05/24/2024] [Indexed: 06/15/2024] Open
Abstract
Ferroptosis is an iron-dependent cell death mechanism characterized by the accumulation of toxic lipid peroxides and cell membrane rupture. GPX4 (glutathione peroxidase 4) prevents ferroptosis by reducing these lipid peroxides into lipid alcohols. Ferroptosis induction by GPX4 inhibition has emerged as a vulnerability of cancer cells, highlighting the need to identify ferroptosis regulators that may be exploited therapeutically. Through genome-wide CRISPR activation screens, we identify the SWI/SNF (switch/sucrose non-fermentable) ATPases BRM (SMARCA2) and BRG1 (SMARCA4) as ferroptosis suppressors. Mechanistically, they bind to and increase chromatin accessibility at NRF2 target loci, thus boosting NRF2 transcriptional output to counter lipid peroxidation and confer resistance to GPX4 inhibition. We further demonstrate that the BRM/BRG1 ferroptosis connection can be leveraged to enhance the paralog dependency of BRG1 mutant cancer cells on BRM. Our data reveal ferroptosis induction as a potential avenue for broadening the efficacy of BRM degraders/inhibitors and define a specific genetic context for exploiting GPX4 dependency.
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Affiliation(s)
- Kamakoti P Bhat
- Department of Discovery Oncology, Genentech, South San Francisco, CA 94080, USA
| | - Jinchu Vijay
- Roche Canada, Mississauga, Ontario L5N 5M8, Canada
| | - Caroline K Vilas
- Oncology Bioinformatics, Genentech, South San Francisco, CA 94080, USA
| | - Jyoti Asundi
- Department of Discovery Oncology, Genentech, South San Francisco, CA 94080, USA
| | - Jun Zou
- Department of Discovery Oncology, Genentech, South San Francisco, CA 94080, USA
| | - Ted Lau
- Department of Discovery Oncology, Genentech, South San Francisco, CA 94080, USA
| | - Xiaoyu Cai
- Regenerative Medicine, Genentech, South San Francisco, CA 94080, USA
| | | | - Michal Kabza
- 7N Sp. Z O. O. by order of Roche Polska, 02-670 Warsaw, Poland
| | - Julie Weng
- Department of Discovery Oncology, Genentech, South San Francisco, CA 94080, USA
| | - Jean-Philippe Fortin
- Data Science and Statistical Computing, Genentech, South San Francisco, CA 94080, USA
| | - Aaron Lun
- Data Science and Statistical Computing, Genentech, South San Francisco, CA 94080, USA
| | - Steffen Durinck
- Oncology Bioinformatics, Genentech, South San Francisco, CA 94080, USA
| | - Marc Hafner
- Department of Discovery Oncology, Genentech, South San Francisco, CA 94080, USA; Oncology Bioinformatics, Genentech, South San Francisco, CA 94080, USA
| | - Michael R Costa
- Department of Discovery Oncology, Genentech, South San Francisco, CA 94080, USA
| | - Xin Ye
- Department of Discovery Oncology, Genentech, South San Francisco, CA 94080, USA.
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9
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Wang Y, Meraz IM, Qudratullah M, Kotagiri S, Han Y, Xi Y, Wang J, Lissanu Y. SMARCA4 mutation induces tumor cell-intrinsic defects in enhancer landscape and resistance to immunotherapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.18.599431. [PMID: 38948751 PMCID: PMC11212967 DOI: 10.1101/2024.06.18.599431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Cancer genomic studies have identified frequent alterations in components of the SWI/SNF (SWItch/Sucrose Non- Fermenting) chromatin remodeling complex including SMARCA4 and ARID1A . Importantly, clinical reports indicate that SMARCA4 -mutant lung cancers respond poorly to immunotherapy and have dismal prognosis. However, the mechanistic basis of immunotherapy resistance is unknown. Here, we corroborated the clinical findings by using immune-humanized, syngeneic, and genetically engineered mouse models of lung cancer harboring SMARCA4 deficiency. Specifically, we show that SMARCA4 loss caused decreased response to anti-PD1 immunotherapy associated with significantly reduced infiltration of dendritic cells (DCs) and CD4+ T cells into the tumor microenvironment (TME). Mechanistically, we show that SMARCA4 loss in tumor cells led to profound downregulation of STING, IL1β and other components of the innate immune system as well as inflammatory cytokines that are required for efficient recruitment and activity of immune cells. We establish that this deregulation of gene expression is caused by cancer cell-intrinsic reprogramming of the enhancer landscape with marked loss of chromatin accessibility at enhancers of genes involved in innate immune response such as STING, IL1β, type I IFN and inflammatory cytokines. Interestingly, we observed that transcription factor NF-κB binding motif was highly enriched in enhancers that lose accessibility upon SMARCA4 deficiency. Finally, we confirmed that SMARCA4 and NF-κB co-occupy the same genomic loci on enhancers associated with STING and IL1β, indicating a functional interplay between SMARCA4 and NF-κB. Taken together, our findings provide the mechanistic basis for the poor response of SMARCA4 -mutant tumors to anti-PD1 immunotherapy and establish a functional link between SMARCA4 and NF-κB on innate immune and inflammatory gene expression regulation.
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10
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Wankhede D, Grover S, Hofman P. SMARCA4 alterations in non-small cell lung cancer: a systematic review and meta-analysis. J Clin Pathol 2024; 77:457-463. [PMID: 38702192 DOI: 10.1136/jcp-2024-209394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 04/22/2024] [Indexed: 05/06/2024]
Abstract
AIMS A mutation in the SMARCA4 gene which encodes BRG1, a common catalytic subunit of switch/sucrose non-fermentable chromatin-remodelling complexes, plays a vital role in carcinogenesis. SMARCA4 mutations are present in approximately 10% of non-small cell lung cancers (NSCLC), making it a crucial gene in NSCLC, but with varying prognostic associations. To explore this, we conducted a systematic review and meta-analysis on the prognostic significance of SMARCA4 mutations in NSCLC. METHODS Electronic database search was performed from inception to December 2022. Study characteristics and prognostic data were extracted from each eligible study. Depending on heterogeneity, pooled HR and 95% CI were derived using the random-effects or fixed-effects models. RESULTS 8 studies (11 cohorts) enrolling 8371 patients were eligible for inclusion. Data on overall survival (OS) and progression-free survival (PFS) were available from 8 (10 cohorts) and 1 (3 cohorts) studies, respectively. Comparing SMARCA4-mutated NSCLC patients with SMARCA4-wild-type NSCLC patients, the summary HRs for OS and PFS were 1.49 (95% CI 1.18 to 1.87; I2=84%) and 3.97 (95% CI 1.32 to 11.92; I2=79%), respectively. The results from the trim-and-fill method for publication bias and sensitivity analysis were inconsistent with the primary analyses. Three studies reported NSCLC prognosis for category I and II mutations separately; category I was significantly associated with OS. CONCLUSION Our findings suggest that SMARCA4 mutation negatively affects NSCLC OS and PFS. The prognostic effects of SMARCA4-co-occurring mutations and the predictive role of SMARCA4 mutation status in immunotherapy require further exploration.
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Affiliation(s)
- Durgesh Wankhede
- German Cancer Research Center, Heidelberg, Germany
- Faculty of Medicine, Univeristy of Heidelberg, Heidelberg, Germany
| | - Sandeep Grover
- Center for Human Genetics, Universitatsklinikum Giessen und Marburg - Standort Marburg, Marburg, Germany
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, University Côte d'Azur, Nice, France
- Hospital-Integrated Biobank BB-0033-00025, Pasteur Hospital, Nice, France
- University Hospital Federation OncoAge, CHU de Nice, University Côte d'Azur, Nice, France
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11
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Pang LL, Zhou HQ, Zhang YX, Zhuang WT, Pang F, Chen LJ, Liao J, Huang YH, Mao TQ, Mai ZH, Zhang L, Fang WF. SWI/SNF family mutations in advanced NSCLC: genetic characteristics and immune checkpoint inhibitors' therapeutic implication. ESMO Open 2024; 9:103472. [PMID: 38833972 PMCID: PMC11179082 DOI: 10.1016/j.esmoop.2024.103472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 03/21/2024] [Accepted: 04/21/2024] [Indexed: 06/06/2024] Open
Abstract
BACKGROUND SWItch/Sucrose NonFermentable (SWI/SNF) mutations have garnered increasing attention because of their association with unfavorable prognosis. However, the genetic landscape of SWI/SNF family mutations in Chinese non-small-cell lung cancer (NSCLC) is poorly understood. In addition, the optimal treatment strategy has not yet been determined. PATIENTS AND METHODS We collected sequencing data on 2027 lung tumor samples from multiple centers in China to comprehensively analyze the genomic characteristics of the SWI/SNF family within the Chinese NSCLC population. Meanwhile, 519 patients with NSCLC from Sun Yat-sen University Cancer Center were enrolled to investigate the potential implications of immunotherapy on patients with SWI/SNF mutations and to identify beneficial subpopulations. We also validated our findings in multiple publicly available cohorts. RESULTS Approximately 15% of Chinese patients with lung cancer harbored mutations in the SWI/SNF chromatin remodeling complex, which were mutually exclusive to the EGFR mutations. Patients with SWI/SNFmut NSCLC who received first-line chemoimmunotherapy had better survival outcomes than those who received chemotherapy alone (median progression-free survival: 8.70 versus 6.93 months; P = 0.028). This finding was also confirmed by external validation using the POPLAR/OAK cohort. SWI/SNFmut NSCLC is frequently characterized by high tumor mutational burden and concurrent TP53 or STK11/KEAP mutations. Further analysis indicated that TP53 and STK11/KEAP1 mutations could be stratifying factors in facilitating personalized immunotherapy and guiding patient selection. CONCLUSIONS This study provides a step forward in understanding the genetic and immunological characterization of SWI/SNF genetic alterations. Moreover, our study reveals substantial benefits of immunotherapy over chemotherapy for SWI/SNF-mutant patients, especially the SWI/SNFmut and TP53mut subgroups.
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Affiliation(s)
- L-L Pang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou
| | - H-Q Zhou
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou
| | - Y-X Zhang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou
| | - W-T Zhuang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou
| | - F Pang
- Shanghai OrigiMed Co., Ltd, Shanghai
| | - L-J Chen
- Shanghai OrigiMed Co., Ltd, Shanghai
| | - J Liao
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou
| | - Y-H Huang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou
| | - T-Q Mao
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou
| | - Z-H Mai
- Department of Thoracic Surgery, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - L Zhang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou.
| | - W-F Fang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou.
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12
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Zhang D, Ma B, Dragovich PS, Ma L, Chen S, Chen EC, Ye X, Liu J, Pizzano J, Bortolon E, Chan E, Zhang X, Chen YC, Levy ES, Yauch RL, Khojasteh SC, Hop CECA. Tissue distribution and retention drives efficacy of rapidly clearing VHL-based PROTACs. COMMUNICATIONS MEDICINE 2024; 4:87. [PMID: 38755248 PMCID: PMC11099041 DOI: 10.1038/s43856-024-00505-y] [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: 05/24/2023] [Accepted: 04/19/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Proteolysis-targeting chimeras (PROTACs) are being developed for therapeutic use. However, they have poor pharmacokinetic profiles and their tissue distribution kinetics are not known. METHODS A typical von Hippel-Lindau tumor suppressor (VHL)-PROTAC 14C-A947 (BRM degrader)-was synthesized and its tissue distribution kinetics was studied by quantitative whole-body autoradiography (QWBA) and tissue excision in rats following IV dosing. Bile duct-cannulated (BDC) rats allowed the elucidation of in vivo clearance pathways. Distribution kinetics was evaluated in the tissues and tumors of mice to support PK-PD correlation. In vitro studies enabled the evaluation of cell uptake mechanisms and cell retention properties. RESULTS Here, we show that A947 quickly distributes into rat tissues after IV dosing, where it accumulates and is retained in tissues such as the lung and liver although it undergoes fast clearance from circulation. Similar uptake/retention kinetics enable tumor growth inhibition over 2-3 weeks in a lung cancer model. A947 quickly excretes in the bile of rats. Solute carrier (SLC) transporters are involved in hepatocyte uptake of PROTACs. Sustained BRM protein degradation is seen after extensive washout that supports prolonged cell retention of A947 in NCI-H1944 cells. A947 tissue exposure and pharmacodynamics are inversely correlated in tumors. CONCLUSIONS Plasma sampling for VHL-PROTAC does not represent the tissue concentrations necessary for efficacy. Understanding of tissue uptake and retention could enable less frequent IV administration to be used for therapeutic dosing.
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Affiliation(s)
- Donglu Zhang
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA.
| | - Bin Ma
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | | | - Li Ma
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Shu Chen
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Eugene C Chen
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Xiaofen Ye
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Joyce Liu
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Jennifer Pizzano
- Arvinas; 5 Science Park, 395 Winchester Ave, New Haven, CT, 06511, USA
| | | | - Emily Chan
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Xing Zhang
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Yi-Chen Chen
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | | | - Robert L Yauch
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
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13
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Göbel C, Schoof M, Holdhof D, Spohn M, Schüller U. SMARCA4 Loss and Mutated β-Catenin Induce Proliferative Lesions in the Murine Embryonic Cerebellum. J Neurosci 2024; 44:e1605232024. [PMID: 38383496 PMCID: PMC11007475 DOI: 10.1523/jneurosci.1605-23.2024] [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: 08/24/2023] [Revised: 01/26/2024] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
Almost all medulloblastomas (MB) of the Wingless/Int-1 (WNT) type are characterized by hotspot mutations in CTNNB1, and mouse models have convincingly demonstrated the tumor-initiating role of these mutations. Additional alterations in SMARCA4 are detected in ∼20% of WNT MB, but their functional role is mostly unknown. We, therefore, amended previously described brain lipid binding protein (Blbp)-cre::Ctnnb1(ex3)fl/wt mice by the introduction of floxed Smarca4 alleles. Unexpectedly, mutated and thereby stabilized β-catenin on its own induced severe developmental phenotypes in male and female Blbp-cre::Ctnnb1(ex3)fl/wt mice in our hands, including a thinned cerebral cortex, hydrocephalus, missing cerebellar layering, and cell accumulations in the brainstem and cerebellum. An additional loss of SMARCA4 even resulted in prenatal death for most mice. Respective Blbp-cre::Ctnnb1(ex3)fl/wt::Smarca4fl/rec mutants (male and female) developed large proliferative lesions in the cerebellum evolving from E13.5 to E16.5. Histological and molecular analysis of these lesions by DNA methylation profiling and single-cell RNA sequencing suggested an origin in early undifferentiated SOX2-positive cerebellar progenitors. Furthermore, upregulated WNT signaling, altered actin/cytoskeleton organization, and reduced neuronal differentiation were evident in mutant cells. In vitro, cells harboring alterations in both Ctnnb1 and Smarca4 were negatively selected and did not show tumorigenic potential after transplantation in adult female recipient mice. However, in cerebellar explant cultures, mutant cells displayed significantly increased proliferation, suggesting an important role of the embryonic microenvironment in the development of lesions. Altogether, these results represent an important first step toward the unraveling of tumorigenic mechanisms induced by aberrant WNT signaling and SMARCA4 deficiency.
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Affiliation(s)
- Carolin Göbel
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg D-20251, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg D-20251, Germany
| | - Melanie Schoof
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg D-20251, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg D-20251, Germany
| | - Dörthe Holdhof
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg D-20251, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg D-20251, Germany
| | - Michael Spohn
- Research Institute Children's Cancer Center Hamburg, Hamburg D-20251, Germany
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg D-20251, Germany
| | - Ulrich Schüller
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg D-20251, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg D-20251, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg D-20251, Germany
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14
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Deng Q, Lakra P, Gou P, Yang H, Meydan C, Teater M, Chin C, Zhang W, Dinh T, Hussein U, Li X, Rojas E, Liu W, Reville PK, Kizhakeyil A, Barisic D, Parsons S, Wilson A, Henderson J, Scull B, Gurumurthy C, Vega F, Chadburn A, Cuglievan B, El-Mallawany NK, Allen C, Mason C, Melnick A, Green MR. SMARCA4 is a haploinsufficient B cell lymphoma tumor suppressor that fine-tunes centrocyte cell fate decisions. Cancer Cell 2024; 42:605-622.e11. [PMID: 38458188 PMCID: PMC11003852 DOI: 10.1016/j.ccell.2024.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 12/30/2023] [Accepted: 02/14/2024] [Indexed: 03/10/2024]
Abstract
SMARCA4 encodes one of two mutually exclusive ATPase subunits in the BRG/BRM associated factor (BAF) complex that is recruited by transcription factors (TFs) to drive chromatin accessibility and transcriptional activation. SMARCA4 is among the most recurrently mutated genes in human cancer, including ∼30% of germinal center (GC)-derived Burkitt lymphomas. In mice, GC-specific Smarca4 haploinsufficiency cooperated with MYC over-expression to drive lymphomagenesis. Furthermore, monoallelic Smarca4 deletion drove GC hyperplasia with centroblast polarization via significantly increased rates of centrocyte recycling to the dark zone. Mechanistically, Smarca4 loss reduced the activity of TFs that are activated in centrocytes to drive GC-exit, including SPI1 (PU.1), IRF family, and NF-κB. Loss of activity for these factors phenocopied aberrant BCL6 activity within murine centrocytes and human Burkitt lymphoma cells. SMARCA4 therefore facilitates chromatin accessibility for TFs that shape centrocyte trajectories, and loss of fine-control of these programs biases toward centroblast cell-fate, GC hyperplasia and lymphoma.
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Affiliation(s)
- Qing Deng
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Priya Lakra
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Panhong Gou
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Haopeng Yang
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cem Meydan
- Department of Medicine and Weill Cornell Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Matthew Teater
- Department of Medicine and Weill Cornell Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Christopher Chin
- Department of Medicine and Weill Cornell Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Wenchao Zhang
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tommy Dinh
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Usama Hussein
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xubin Li
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Estela Rojas
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Weiguang Liu
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Patrick K Reville
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Atish Kizhakeyil
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Darko Barisic
- Department of Medicine and Weill Cornell Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Sydney Parsons
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ashley Wilson
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jared Henderson
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Brooks Scull
- Department of Pediatrics, Baylor College of Medicine, Texas Children's Cancer Center, Houston, TX, USA
| | | | - Francisco Vega
- Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Branko Cuglievan
- Department of Pediatrics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nader Kim El-Mallawany
- Department of Pediatrics, Baylor College of Medicine, Texas Children's Cancer Center, Houston, TX, USA
| | - Carl Allen
- Department of Pediatrics, Baylor College of Medicine, Texas Children's Cancer Center, Houston, TX, USA
| | - Christopher Mason
- Department of Medicine and Weill Cornell Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Ari Melnick
- Department of Medicine and Weill Cornell Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Michael R Green
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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15
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Yamashita K, Sewastjanow-Silva M, Yoshimura K, Rogers JE, Rosa Vicentini E, Pool Pizzi M, Fan Y, Zou G, Li JJ, Blum Murphy M, Gan Q, Waters RE, Wang L, Ajani JA. SMARCA4 Mutations in Gastroesophageal Adenocarcinoma: An Observational Study via a Next-Generation Sequencing Panel. Cancers (Basel) 2024; 16:1300. [PMID: 38610978 PMCID: PMC11010836 DOI: 10.3390/cancers16071300] [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: 02/14/2024] [Revised: 03/19/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND The clinical impact of SMARCA4 mutations (SMARCA4ms) in gastroesophageal adenocarcinoma (GEA) remains underexplored. This study aimed to examine the association of SMARCA4ms with clinical outcomes and co-occurrence with other gene mutations identified through a next-generation sequencing (NGS) panel in GEA patients. METHODS A total of 256 patients with metastatic or recurrent GEA who underwent NGS panel profiling at the MD Anderson Cancer Center between 2016 and 2022 were included. Comparative analyses were performed to assess clinical outcomes related to SMARCA4ms. The frequency and types of SMARCA4ms and their co-occurrence with other gene mutations were also examined. RESULTS SMARCA4ms were identified in 19 patients (7.4%). These SMARCA4ms were significantly associated with non-signet ring cell subtype (p = 0.044) and PD-L1 positive expression (p = 0.046). No difference in survival between the SMARCA4m and SMARCA4-normal group was observed (p = 0.84). There were significant associations between SMARCA4ms and FANCA, IGF1R, KRAS, FANCL, and PTEN alterations. Notably, 15 of the 19 SMARCA4m cases involved SNV missense mutations, with frequent co-occurrences noted with TP53, KRAS, ARID1A, and ERBB2 mutations. CONCLUSIONS These results serve as the first comprehensive examination of the relationship between SMARCA4ms and clinical outcomes in GEA.
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Affiliation(s)
- Kohei Yamashita
- Departments of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (K.Y.); (M.S.-S.); (K.Y.); (E.R.V.); (M.P.P.); (Y.F.); (G.Z.); (J.J.L.); (M.B.M.)
| | - Matheus Sewastjanow-Silva
- Departments of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (K.Y.); (M.S.-S.); (K.Y.); (E.R.V.); (M.P.P.); (Y.F.); (G.Z.); (J.J.L.); (M.B.M.)
| | - Katsuhiro Yoshimura
- Departments of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (K.Y.); (M.S.-S.); (K.Y.); (E.R.V.); (M.P.P.); (Y.F.); (G.Z.); (J.J.L.); (M.B.M.)
| | - Jane E. Rogers
- Department of Pharmacy Clinical Programs, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Ernesto Rosa Vicentini
- Departments of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (K.Y.); (M.S.-S.); (K.Y.); (E.R.V.); (M.P.P.); (Y.F.); (G.Z.); (J.J.L.); (M.B.M.)
| | - Melissa Pool Pizzi
- Departments of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (K.Y.); (M.S.-S.); (K.Y.); (E.R.V.); (M.P.P.); (Y.F.); (G.Z.); (J.J.L.); (M.B.M.)
| | - Yibo Fan
- Departments of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (K.Y.); (M.S.-S.); (K.Y.); (E.R.V.); (M.P.P.); (Y.F.); (G.Z.); (J.J.L.); (M.B.M.)
| | - Gengyi Zou
- Departments of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (K.Y.); (M.S.-S.); (K.Y.); (E.R.V.); (M.P.P.); (Y.F.); (G.Z.); (J.J.L.); (M.B.M.)
| | - Jenny J. Li
- Departments of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (K.Y.); (M.S.-S.); (K.Y.); (E.R.V.); (M.P.P.); (Y.F.); (G.Z.); (J.J.L.); (M.B.M.)
| | - Mariela Blum Murphy
- Departments of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (K.Y.); (M.S.-S.); (K.Y.); (E.R.V.); (M.P.P.); (Y.F.); (G.Z.); (J.J.L.); (M.B.M.)
| | - Qiong Gan
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Q.G.); (R.E.W.)
| | - Rebecca E. Waters
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Q.G.); (R.E.W.)
| | - Linghua Wang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Jaffer A. Ajani
- Departments of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (K.Y.); (M.S.-S.); (K.Y.); (E.R.V.); (M.P.P.); (Y.F.); (G.Z.); (J.J.L.); (M.B.M.)
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16
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Shinno Y, Ohe Y. Thoracic SMARCA4-deficient undifferentiated tumor: current knowledge and future perspectives. Jpn J Clin Oncol 2024; 54:265-270. [PMID: 38117955 DOI: 10.1093/jjco/hyad175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 11/28/2023] [Indexed: 12/22/2023] Open
Abstract
Thoracic SMARCA4-deficient undifferentiated tumor is a newly recognized disease entity characterized as a high-grade malignant neoplasm with an undifferentiated or rhabdoid phenotype. The tumor was initially identified as a subtype of thoracic sarcoma with SMARCA4 loss, but further investigation resulted in its classification as a subtype of epithelial malignancies in the current World Health Organization classification. SMARCA4-deficient undifferentiated tumor is highly aggressive and has a poor prognosis. Because of its rarity, an optimal treatment strategy has not yet been identified. In this review, we summarize the literature on SMARCA4-deficient undifferentiated tumor in terms of its clinical characteristics, diagnosis, treatment strategy and future perspectives.
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Affiliation(s)
- Yuki Shinno
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Yuichiro Ohe
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo, Japan
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17
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Le MK, Oishi N, Mochizuki K, Kondo T. Immunohistochemical detection of cancer genetic abnormalities. Pathol Res Pract 2024; 255:155109. [PMID: 38340581 DOI: 10.1016/j.prp.2024.155109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/07/2024] [Indexed: 02/12/2024]
Abstract
New applications of immunohistochemistry (IHC) expand rapidly due to the development of molecular analyses and an increased understanding of molecular biology. IHC becomes much more important as a screening or even a confirmatory test for molecular changes in cancer. The past decades have witnessed the release of many immunohistochemical markers of the new generation. The novel markers have extensively high specificity and sensitivity for the detection of genetic abnormalities. In addition to diagnostic utility, IHC has been validated to be a practical tool in terms of treatments, especially molecular targeted therapy. In this review, we first describe the common alterations of protein IHC staining in human cancer: overexpression, underexpression, or loss of expression and altered staining pattern. Next, we examine the relationship between staining patterns and genetic aberrations regarding both conventional and novel IHC markers. We also mention current mutant-specific and fusion-specific antibodies and their concordance with molecular techniques. We then describe the basic molecular mechanisms from genetic events to corresponding protein expression patterns (membranous, cytoplasmic, or nuclear patterns). Finally, we shortly discuss the applications of immunohistochemistry in molecular targeted therapy. IHC markers can serve as a complementary or companion diagnostic test to provide valuable information for targeted therapy. Moreover, immunohistochemistry is also crucial as a companion diagnostic test in immunotherapy. The increased number of IHC novel antibodies is broadening its application in anti-cancer therapies.
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Affiliation(s)
- Minh-Khang Le
- Department of Pathology, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Naoki Oishi
- Department of Pathology, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Kunio Mochizuki
- Department of Pathology, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Tetsuo Kondo
- Department of Pathology, University of Yamanashi, Yamanashi 409-3898, Japan.
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Zhang X, Zhang Y, Zhang Q, Lu M, Chen Y, Zhang X, Zhang P. Role of AT-rich interaction domain 1A in gastric cancer immunotherapy: Preclinical and clinical perspectives. J Cell Mol Med 2024; 28:e18063. [PMID: 38041544 PMCID: PMC10902580 DOI: 10.1111/jcmm.18063] [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: 09/13/2023] [Revised: 10/31/2023] [Accepted: 11/14/2023] [Indexed: 12/03/2023] Open
Abstract
The application of immune checkpoint inhibitor (ICI) using monoclonal antibodies has brought about a profound transformation in the clinical outcomes for patients grappling with advanced gastric cancer (GC). Nonetheless, despite these achievements, the quest for effective functional biomarkers for ICI therapy remains constrained. Recent research endeavours have shed light on the critical involvement of modified epigenetic regulators in the pathogenesis of gastric tumorigenesis, thus providing a glimpse into potential biomarkers. Among these regulatory factors, AT-rich interaction domain 1A (ARID1A), a pivotal constituent of the switch/sucrose non-fermentable (SWI/SNF) complex, has emerged as a promising candidate. Investigations have unveiled the pivotal role of ARID1A in bridging the gap between genome instability and the reconfiguration of the tumour immune microenvironment, culminating in an enhanced response to ICI within the landscape of gastric cancer treatment. This all-encompassing review aims to dissect the potential of ARID1A as a valuable biomarker for immunotherapeutic approaches in gastric cancer, drawing from insights garnered from both preclinical experimentation and clinical observations.
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Affiliation(s)
- Xuemei Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Youzhi Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- School of PharmacyHubei University of Science and TechnologyXianningChina
| | - Qiaoyun Zhang
- School of PharmacyHubei University of Science and TechnologyXianningChina
| | - Mengyao Lu
- Department of Oncology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Yuan Chen
- Department of Oncology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Xiaoyu Zhang
- Division of Gastrointestinal Surgery, Department of General Surgery, Huai'an Second People's Hospitalthe Affiliated Huai'an Hospital of Xuzhou Medical UniversityHuaianChina
| | - Peng Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
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19
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Zhou P, Fu Y, Tang Y, Jiang L, Wang W. Thoracic SMARCA4-deficient undifferentiated tumor: A clinicopathological and prognostic analysis of 35 cases and immunotherapy efficacy. Lung Cancer 2024; 189:107471. [PMID: 38306886 DOI: 10.1016/j.lungcan.2024.107471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 02/04/2024]
Abstract
BACKGROUND Thoracic SMARCA4-deficient undifferentiated tumor (SMARCA4-UT) is a recently recognized distinct clinicopathological entity according to the fifth edition of the 2021 World Health Organization Classification (WHO) for thoracic tumors. Thoracic SMARCA4-UTs are diagnostically challenging to diagnose, especially on small biopsies. METHODS We identified 35 thoracic SMARCA4-UTs from the Department of Pathology of West China Hospital, Sichuan University, between January 2017 and December 2022. In the present study, we summarized the clinicopathological features, prognostic significance and immunotherapy efficacy of thoracic SMARCA4-UTs. RESULTS All 35 patients were male, and 88.6 % were smokers. The left upper lobe (25.7 %) and mediastinum (20.0 %) were the most affected sites. 17.1 % of the patients received surgical treatment. 30.4 % of the patients were stage III, and 69.6 % were stage IV. Solid architecture (100 %), rhabdoid morphology (51.4 %) and necrosis (42.9 %) were the common histological features. Immunohistochemical staining revealed CD34 and synaptophysin positivity in most patients (76.9 % and 65.2 %, respectively). Patients had unfavorable outcomes. Patients who received immunotherapy had better OS and PFS than those who did not (p = 0.007 and p = 0.02, respectively). Five patients were evaluated for immunotherapy efficacy, and four of those patients were negative expression of PD-L1. Cases 1-4 presented TIL counts ranging from 20 to 1000/HPF. Case 5 presented TIL counts of 5-10/HPF. Mutations in SMARCA4 were confirmed in cases 4 and 5, and the TMB was 5.98 and 5.03 mutations/Mb, respectively. Case 1 achieved a CR, cases 2-4 achieved a PR, and case 5 had a PD. Five patients who received immunotherapy were all alive, with OS ranging from 10.7 to 33.6 months. CONCLUSIONS Thoracic SMARCA4-UTs exhibited an aggressive clinical course, presented solid architecture with or without necrosis and/or rhabdoid morphology, and frequently expressed CD34 and synaptophysin. Some thoracic SMARCA4-UTs appear to be associated with responsiveness to immunotherapy, suggesting the need for validation in larger series.
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Affiliation(s)
- Ping Zhou
- Department of Pathology, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, Sichuan 610041, China
| | - Yiyun Fu
- Department of Pathology, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, Sichuan 610041, China
| | - Yuan Tang
- Department of Pathology, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, Sichuan 610041, China
| | - Lili Jiang
- Department of Pathology, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, Sichuan 610041, China
| | - Weiya Wang
- Department of Pathology, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, Sichuan 610041, China.
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20
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Di Maggio F, Boccia G, Nunziato M, Filotico M, Montesarchio V, D'Armiento M, Corcione F, Salvatore F. A Novel DNA Variant in SMARCA4 Gene Found in a Patient Affected by Early Onset Colon Cancer. Int J Mol Sci 2024; 25:2716. [PMID: 38473962 DOI: 10.3390/ijms25052716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 02/21/2024] [Accepted: 02/24/2024] [Indexed: 03/14/2024] Open
Abstract
Colorectal cancer is the third leading cause of death from neoplasia worldwide. Thanks to new screening programs, we are now seeing an increase in Early Onset of ColoRectal Cancer (EOCRC) in patients below the age of 50. Herein, we report a clinical case of a woman affected by EOCRC. This case illustrates the importance of genetic predisposition testing also in tumor patients. Indeed, for our patient, we used a combined approach of multiple molecular and cellular biology technologies that revealed the presence of an interesting novel variant in the SMARCA4 gene. The latter gene is implicated in damage repair processes and related, if mutated, to the onset of various tumor types. In addition, we stabilized Patient-Derived Organoids from the tumor tissue of the same patient and the result confirmed the presence of this novel pathogenic variant that has never been found before even in early onset cancer. In conclusion, with this clinical case, we want to underscore the importance of including patients even those below the age of 50 years in appropriate screening programs which should also include genetic tests for predisposition to early onset cancers.
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Affiliation(s)
- Federica Di Maggio
- CEINGE-Biotecnologie Avanzate Franco Salvatore, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", 80131 Naples, Italy
| | - Giuseppe Boccia
- Department of Public Health, University of Naples "Federico II", 80131 Naples, Italy
| | - Marcella Nunziato
- CEINGE-Biotecnologie Avanzate Franco Salvatore, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", 80131 Naples, Italy
| | - Marcello Filotico
- Department of Public Health, University of Naples "Federico II", 80131 Naples, Italy
| | | | - Maria D'Armiento
- Pathology Unit, Department of Public Health, University of Naples "Federico II", 80131 Naples, Italy
| | - Francesco Corcione
- Department of Public Health, University of Naples "Federico II", 80131 Naples, Italy
| | - Francesco Salvatore
- CEINGE-Biotecnologie Avanzate Franco Salvatore, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", 80131 Naples, Italy
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21
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Lee B, Hwang S, Bae H, Choi KH, Suh YL. Diagnostic utility of genetic alterations in distinguishing IDH-wildtype glioblastoma from lower-grade gliomas: Insight from next-generation sequencing analysis of 479 cases. Brain Pathol 2024:e13234. [PMID: 38217295 DOI: 10.1111/bpa.13234] [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: 08/08/2023] [Accepted: 12/20/2023] [Indexed: 01/15/2024] Open
Abstract
The accurate diagnosis and classification of gliomas are essential for appropriate treatment planning and prognosis prediction. This study aimed to investigate the molecular diagnostics of IDH-wildtype diffuse astrocytic gliomas and identify potential genetic variants that could differentiate glioblastoma (GBM) from lower-grade gliomas when DNA methylation analysis is not feasible. In total, 479 H3-and IDH-wildtype diffuse astrocytic gliomas were included in this study. All the cases were diagnosed according to the 2021 World Health Organization (WHO) classification of central nervous system (CNS) tumors. Panel sequencing data were collected, and clinicopathological information was retrieved from medical records. Genetic alterations and histological findings were analyzed to determine their diagnostic utility and prognostic implications. Out of 479 cases, 439 (91.6%) were diagnosed with GBM, including 28 cases that were molecularly diagnosed as GBM. However, 40 (8.4%) cases could not be classified according to the 2021 WHO classification and were diagnosed as lower-grade diffuse astrocytic glioma, IDH-wildtype, not elsewhere classified (LGNEC). In addition to the three genetic alterations included in the diagnostic criteria of GBM, PTEN and EGFR mutations were found to be enriched in GBM. Patients harboring mTOR pathway mutations demonstrated a more favorable prognosis and often exhibited morphology resembling subependymal giant cell astrocytoma, along with a high tumor mutational burden. Among patients with mTOR pathway mutations, those lacking molecular diagnostic features of GBM exhibited outstanding survival outcomes, even in the presence of grade 4 histology. Integration of molecular features enhanced the diagnostic accuracy of IDH-wildtype gliomas. Some molecular alterations enriched in GBM offer valuable insights for molecular diagnosis and glioma classification. Furthermore, high-grade diffuse astrocytic gliomas featuring mTOR pathway mutations in the absence of molecular diagnostic features of GBM could represent more favorable tumor types distinct from GBM.
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Affiliation(s)
- Boram Lee
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Soohyun Hwang
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hyunsik Bae
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Pathology center, Seegene Medical Foundation, Seoul 04805, Republic of Korea
| | - Kyue-Hee Choi
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Yeon-Lim Suh
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
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22
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Sun L, Fu Q, Chen L, Di M, Cao J. SMARCA4‑deficient non‑small cell lung cancer with an EGFR mutation: A case report. Oncol Lett 2023; 26:513. [PMID: 37927421 PMCID: PMC10623088 DOI: 10.3892/ol.2023.14100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/20/2023] [Indexed: 11/07/2023] Open
Abstract
SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily a, member 4 (SMARCA4)-deficient non-small cell lung cancer (dNSCLC) is a rare malignant tumor that originates in the lungs. It occurs more frequently in male smokers, and the epidermal growth factor receptor (EGFR) gene is often mutation-free. In the present study, the case of a 60-year-old, non-smoking female patient diagnosed with SMARCA4-dNSCLC is reported. Biopsy of the tumor showed solid flaky, nest-like infiltrating growth. Immunohistochemistry revealed the following: SMARCA4/BRG1(-), SMARCB1/INI-1(+), cytokeratin7 (+), cytokeratin 5.2 (+), CK5/6(+) and calretinin(+). The Ki-67 positivity index was 75%, and the thyroid transcription factor-1, NapsinA, p40, nuclear protein in testis, CD34, Sal-like protein 4, SRY-box transcription factor 2 and synaptophysin were negative. Molecular analysis showed mutations in both EGFR and TP53. The pathological diagnosis was SMARCA4-dNSCLC with an EGFR gene mutation. The present case report could be used for broadening the pathological diagnosis of SMARCA4-dNSCLC and for selecting appropriate treatment approaches.
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Affiliation(s)
- Lijun Sun
- Department of Pathology, Xiaoshan Affiliated Hospital of Wenzhou Medical University, Hangzhou, Zhejiang 311200, P.R. China
| | - Qiong Fu
- Department of Pathology, Xiaoshan Affiliated Hospital of Wenzhou Medical University, Hangzhou, Zhejiang 311200, P.R. China
| | - Lijiang Chen
- Department of Pathology, Xiaoshan Affiliated Hospital of Wenzhou Medical University, Hangzhou, Zhejiang 311200, P.R. China
| | - Meijuan Di
- Department of Pathology, Xiaoshan Affiliated Hospital of Wenzhou Medical University, Hangzhou, Zhejiang 311200, P.R. China
| | - Jianhua Cao
- Department of Respiratory Medicine, Xiaoshan Affiliated Hospital of Wenzhou Medical University, Hangzhou, Zhejiang 311200, P.R. China
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23
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Wagner SK, Moon AS, Howitt BE, Renz M. SMARCA4 loss irrelevant for ARID1A mutated ovarian clear cell carcinoma: A case report. Gynecol Oncol Rep 2023; 50:101305. [PMID: 38033359 PMCID: PMC10685047 DOI: 10.1016/j.gore.2023.101305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 11/08/2023] [Accepted: 11/12/2023] [Indexed: 12/02/2023] Open
Abstract
Clear cell carcinomas are rare and relatively chemo-insensitive ovarian cancers with a characteristic molecular pathogenesis. Alterations in ARID1A, a component of the multiprotein chromatin remodeling complex SWI/SNF, are likely early events in the development of ovarian clear cancers arising from atypical endometriosis. Insight into additional driver events and particularly mutations in the same chromatin remodeling complex is limited. Isolated loss of SMARCA4, encoding the ATPase of the SWI/SNF complex, characterizes other aggressive gynecologic cancers including small cell carcinomas of the ovary hypercalcemic type (SCCOHT), undifferentiated endometrial carcinomas (UDEC), and uterine sarcomas (SDUS). The ovarian clear cell carcinoma of a 48-year-old showed in the initial surgical specimen a subclonal loss of SMARCA4 in addition to an ARID1A mutation, i.e., two alterations in the SWI/SNF heterochromatin remodeling complex. We anticipated that the SMARCA4 loss would worsen the disease course in analogy to SCCOHT, UDEC, and SDUS. However, the disease did not accelerate. Instead, the recurrent disease showed restored SMARCA4 expression while retaining the ARID1A mutation. Combinatorial redundancy, diversity and sequence in the SWI/SNF complex assembly as well as DNA- and tissue-specificity may explain the observed irrelevance of SMARCA4 loss in the presented ARID1A mutated ovarian clear cell carcinoma.
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Affiliation(s)
- Samantha Kay Wagner
- Department of Obstetrics & Gynecology, Stanford University, Stanford, CA, USA
| | - Ashley S. Moon
- Gynecologic Oncology Division, Department of Obstetrics & Gynecology, Stanford University, Stanford, CA, USA
| | - Brooke E. Howitt
- Department of Clinical Pathology, Stanford University, Stanford, CA, USA
| | - Malte Renz
- Gynecologic Oncology Division, Department of Obstetrics & Gynecology, Stanford University, Stanford, CA, USA
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24
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Affiliation(s)
- Kangjing Chen
- MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, P.R. China,School of Life Sciences, Tsinghua University, Beijing, P.R. China
| | - Junjie Yuan
- MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, P.R. China,School of Life Sciences, Tsinghua University, Beijing, P.R. China,Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing, Beijing, China
| | - Youyang Sia
- MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, P.R. China,School of Life Sciences, Tsinghua University, Beijing, P.R. China
| | - Zhucheng Chen
- MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, P.R. China,School of Life Sciences, Tsinghua University, Beijing, P.R. China,Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing, Beijing, China,CONTACT Zhucheng Chen MOE Key Laboratory of Protein Science, Tsinghua University, Beijing100084, P.R. China
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25
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Göbel C, Godbole S, Schoof M, Holdhof D, Kresbach C, Loose C, Neumann J, Schüller U. MYC overexpression and SMARCA4 loss cooperate to drive medulloblastoma formation in mice. Acta Neuropathol Commun 2023; 11:174. [PMID: 37919824 PMCID: PMC10621315 DOI: 10.1186/s40478-023-01654-2] [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: 07/12/2023] [Accepted: 09/17/2023] [Indexed: 11/04/2023] Open
Abstract
Group 3 medulloblastoma is one of the most aggressive types of childhood brain tumors. Roughly 30% of cases carry genetic alterations in MYC, SMARCA4, or both genes combined. While overexpression of MYC has previously been shown to drive medulloblastoma formation in mice, the functional significance of SMARCA4 mutations and their suitability as a therapeutic target remain largely unclear. To address this issue, we combined overexpression of MYC with a loss of SMARCA4 in granule cell precursors. Both alterations did not increase proliferation of granule cell precursors in vitro. However, combined MYC overexpression and SMARCA4 loss successfully induced tumor formation in vivo after orthotopic transplantation in recipient mice. Resulting tumors displayed anaplastic histology and exclusively consisted of SMARCA4-negative cells although a mixture of recombined and non-recombined cells was injected. These observations provide first evidence for a tumor-promoting role of a SMARCA4 deficiency in the development of medulloblastoma. In comparing the transcriptome of tumors to the cells of origin and an established Sonic Hedgehog medulloblastoma model, we gathered first hints on deregulated gene expression that could be specifically involved in SMARCA4/MYC driven tumorigenesis. Finally, an integration of RNA sequencing and DNA methylation data of murine tumors with human samples revealed a high resemblance to human Group 3 medulloblastoma on the molecular level. Altogether, the development of SMARCA4-deficient medulloblastomas in mice paves the way to deciphering the role of frequently occurring SMARCA4 alterations in Group 3 medulloblastoma with the perspective to explore targeted therapeutic options.
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Affiliation(s)
- Carolin Göbel
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, 20251, Germany
- Research Institute Children's Cancer Center Hamburg, Martinistrasse 52, Building N63 (LIV), Hamburg, D-20251, Germany
| | - Shweta Godbole
- Center for Molecular Neurobiology, Falkenried 94, Hamburg, 20251, Germany
| | - Melanie Schoof
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, 20251, Germany
- Research Institute Children's Cancer Center Hamburg, Martinistrasse 52, Building N63 (LIV), Hamburg, D-20251, Germany
| | - Dörthe Holdhof
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, 20251, Germany
- Research Institute Children's Cancer Center Hamburg, Martinistrasse 52, Building N63 (LIV), Hamburg, D-20251, Germany
| | - Catena Kresbach
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, 20251, Germany
- Research Institute Children's Cancer Center Hamburg, Martinistrasse 52, Building N63 (LIV), Hamburg, D-20251, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, 20251, Germany
| | - Carolin Loose
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, 20251, Germany
- Research Institute Children's Cancer Center Hamburg, Martinistrasse 52, Building N63 (LIV), Hamburg, D-20251, Germany
| | - Julia Neumann
- Center for Molecular Neurobiology, Falkenried 94, Hamburg, 20251, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, 20251, Germany
| | - Ulrich Schüller
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, 20251, Germany.
- Research Institute Children's Cancer Center Hamburg, Martinistrasse 52, Building N63 (LIV), Hamburg, D-20251, Germany.
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, 20251, Germany.
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26
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Maher J, Stagg N, Cain G, Andaya R, Katavolos P, Gallardo-Chang F, Pham A, Ye X, Januario T, Alcantar T, Caothien R, Roose-Girma M, Zhang D, Li R, Chen S, Yauch RL. Smarca2 genetic ablation is phenotypically benign in a safety assessment of tamoxifen-inducible conditional knockout rats. Toxicol Appl Pharmacol 2023; 475:116627. [PMID: 37453479 DOI: 10.1016/j.taap.2023.116627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/19/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
SMARCA2 and SMARCA4 are the ATPases of the SWI/SNF chromatin remodeling complex, which play a significant role in regulating transcriptional activity and DNA repair in cells. SMARCA2 has become an appealing synthetic-lethal, therapeutic target in oncology, as mutational loss of SMARCA4 in many cancers leads to a functional dependency on residual SMARCA2 activity. Thus, for therapeutic development, an important step is understanding any potential safety target-associated liabilities of SMARCA2 inhibition. To best mimic a SMARCA2 therapeutic, a tamoxifen-inducible (TAMi) conditional knockout (cKO) rat was developed using CRISPR technology to understand the safety profile of Smarca2 genetic ablation in a model system that avoids potential juvenile and developmental phenotypes. As the rat is the prototypical rodent species utilized in toxicology studies, a comprehensive toxicological and pathological assessment was conducted in both heterozygote and homozygous knockout rats at timepoints up to 28 days, alongside relevant corresponding controls. To our knowledge, this represents the first TAMi cKO rat model utilized for safety assessment evaluations. No significant target-associated phenotypes were observed when Smarca2 was ablated in mature (11- to 15-week-old) rats; however subsequent induction of SMARCA4 was evident that could indicate potential compensatory activity. Similar to mouse models, rat CreERT2-transgene and TAMi toxicities were characterized to avoid confounding study interpretation. In summary, a lack of significant safety findings in Smarca2 cKO rats highlights the potential for therapeutics targeting selective SMARCA2 ATPase activity; such therapies are predicted to be tolerated in patients without eliciting significant on-target toxicities.
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Affiliation(s)
- Jonathan Maher
- Genentech, Inc., South San Francisco, CA 94080, USA; Pliant Therapeutics, Inc., South San Francisco, CA 94080, USA
| | - Nicola Stagg
- Genentech, Inc., South San Francisco, CA 94080, USA; Turning Point Therapeutics, Inc., San Diego, CA 92121, USA
| | - Gary Cain
- Genentech, Inc., South San Francisco, CA 94080, USA
| | | | - Paula Katavolos
- Genentech, Inc., South San Francisco, CA 94080, USA; Bristol Myers Squibb, New Brunswick, NJ 08901, USA; 23&Me, Inc., South San Francisco, CA 94080, USA
| | | | - Anna Pham
- Genentech, Inc., South San Francisco, CA 94080, USA
| | - Xiaofen Ye
- Genentech, Inc., South San Francisco, CA 94080, USA
| | - Tom Januario
- Genentech, Inc., South San Francisco, CA 94080, USA
| | | | | | | | - Donglu Zhang
- Genentech, Inc., South San Francisco, CA 94080, USA
| | - Ruina Li
- Genentech, Inc., South San Francisco, CA 94080, USA
| | - Shu Chen
- Genentech, Inc., South San Francisco, CA 94080, USA
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27
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de Miguel FJ, Gentile C, Feng WW, Silva SJ, Sankar A, Exposito F, Cai WL, Melnick MA, Robles-Oteiza C, Hinkley MM, Tsai JA, Hartley AV, Wei J, Wurtz A, Li F, Toki MI, Rimm DL, Homer R, Wilen CB, Xiao AZ, Qi J, Yan Q, Nguyen DX, Jänne PA, Kadoch C, Politi KA. Mammalian SWI/SNF chromatin remodeling complexes promote tyrosine kinase inhibitor resistance in EGFR-mutant lung cancer. Cancer Cell 2023; 41:1516-1534.e9. [PMID: 37541244 PMCID: PMC10957226 DOI: 10.1016/j.ccell.2023.07.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 05/10/2023] [Accepted: 07/11/2023] [Indexed: 08/06/2023]
Abstract
Acquired resistance to tyrosine kinase inhibitors (TKI), such as osimertinib used to treat EGFR-mutant lung adenocarcinomas, limits long-term efficacy and is frequently caused by non-genetic mechanisms. Here, we define the chromatin accessibility and gene regulatory signatures of osimertinib sensitive and resistant EGFR-mutant cell and patient-derived models and uncover a role for mammalian SWI/SNF chromatin remodeling complexes in TKI resistance. By profiling mSWI/SNF genome-wide localization, we identify both shared and cancer cell line-specific gene targets underlying the resistant state. Importantly, genetic and pharmacologic disruption of the SMARCA4/SMARCA2 mSWI/SNF ATPases re-sensitizes a subset of resistant models to osimertinib via inhibition of mSWI/SNF-mediated regulation of cellular programs governing cell proliferation, epithelial-to-mesenchymal transition, epithelial cell differentiation, and NRF2 signaling. These data highlight the role of mSWI/SNF complexes in supporting TKI resistance and suggest potential utility of mSWI/SNF inhibitors in TKI-resistant lung cancers.
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Affiliation(s)
| | - Claudia Gentile
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - William W Feng
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Shannon J Silva
- Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Akshay Sankar
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Wesley L Cai
- Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT 06510, USA
| | | | - Camila Robles-Oteiza
- Department of Immunobiology, Yale School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Madeline M Hinkley
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jeanelle A Tsai
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Antja-Voy Hartley
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Jin Wei
- Department of Immunobiology, Yale School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Laboratory Medicine, Yale School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Anna Wurtz
- Yale Cancer Center, New Haven, CT 06520, USA
| | - Fangyong Li
- Yale Center for Analytical Sciences, Yale School of Public Health, Laboratory of Epidemiology and Public Health, 60 College St, New Haven, CT 06510, USA
| | - Maria I Toki
- Yale Cancer Center, New Haven, CT 06520, USA; Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT 06510, USA
| | - David L Rimm
- Yale Cancer Center, New Haven, CT 06520, USA; Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Medicine (Section of Medical Oncology), Yale School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Robert Homer
- Yale Cancer Center, New Haven, CT 06520, USA; Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Craig B Wilen
- Department of Immunobiology, Yale School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Laboratory Medicine, Yale School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Andrew Z Xiao
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT 06510, USA; Yale Stem Cell Center, Yale School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Qin Yan
- Yale Cancer Center, New Haven, CT 06520, USA; Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT 06510, USA; Yale Stem Cell Center, Yale School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Don X Nguyen
- Yale Cancer Center, New Haven, CT 06520, USA; Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Medicine (Section of Medical Oncology), Yale School of Medicine, Yale University, New Haven, CT 06510, USA; Yale Stem Cell Center, Yale School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Pasi A Jänne
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - Katerina A Politi
- Yale Cancer Center, New Haven, CT 06520, USA; Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Medicine (Section of Medical Oncology), Yale School of Medicine, Yale University, New Haven, CT 06510, USA; Yale Stem Cell Center, Yale School of Medicine, Yale University, New Haven, CT 06510, USA.
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Navickas SM, Giles KA, Brettingham-Moore KH, Taberlay PC. The role of chromatin remodeler SMARCA4/BRG1 in brain cancers: a potential therapeutic target. Oncogene 2023:10.1038/s41388-023-02773-9. [PMID: 37433987 PMCID: PMC10374441 DOI: 10.1038/s41388-023-02773-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 06/16/2023] [Accepted: 06/29/2023] [Indexed: 07/13/2023]
Abstract
The chromatin remodeler SMARCA4/BRG1 is a key epigenetic regulator with diverse roles in coordinating the molecular programs that underlie brain tumour development. BRG1 function in brain cancer is largely specific to the tumour type and varies further between tumour subtypes, highlighting its complexity. Altered SMARCA4 expression has been linked to medulloblastoma, low-grade gliomas such as oligodendroglioma, high-grade gliomas such as glioblastoma and atypical/teratoid rhabdoid tumours. SMARCA4 mutations in brain cancer predominantly occur in the crucial catalytic ATPase domain, which is associated with tumour suppressor activity. However, SMARCA4 is opposingly seen to promote tumourigenesis in the absence of mutation and through overexpression in other brain tumours. This review explores the multifaceted interaction between SMARCA4 and various brain cancer types, highlighting its roles in tumour pathogenesis, the pathways it regulates, and the advances that have been made in understanding the functional relevance of mutations. We discuss developments made in targeting SMARCA4 and the potential to translate these to adjuvant therapies able to enhance current methods of brain cancer treatment.
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Affiliation(s)
- Sophie M Navickas
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Katherine A Giles
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
- Children's Medical Research Institute, 214 Hawkesbury Road, Westmead, NSW, 2145, Australia
| | - Kate H Brettingham-Moore
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Phillippa C Taberlay
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia.
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29
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Negrao MV, Araujo HA, Lamberti G, Cooper AJ, Akhave NS, Zhou T, Delasos L, Hicks JK, Aldea M, Minuti G, Hines J, Aredo JV, Dennis MJ, Chakrabarti T, Scott SC, Bironzo P, Scheffler M, Christopoulos P, Stenzinger A, Riess JW, Kim SY, Goldberg SB, Li M, Wang Q, Qing Y, Ni Y, Do MT, Lee R, Ricciuti B, Alessi JV, Wang J, Resuli B, Landi L, Tseng SC, Nishino M, Digumarthy SR, Rinsurongkawong W, kawong VR, Vaporciyan AA, Blumenschein GR, Zhang J, Owen DH, Blakely CM, Mountzios G, Shu CA, Bestvina CM, Garassino MC, Marrone KA, Gray JE, Patel SP, Cummings AL, Wakelee HA, Wolf J, Scagliotti GV, Cappuzzo F, Barlesi F, Patil PD, Drusbosky L, Gibbons DL, Meric-Bernstam F, Lee JJ, Heymach JV, Hong DS, Heist RS, Awad MM, Skoulidis F. Comutations and KRASG12C Inhibitor Efficacy in Advanced NSCLC. Cancer Discov 2023; 13:1556-1571. [PMID: 37068173 PMCID: PMC11024958 DOI: 10.1158/2159-8290.cd-22-1420] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/08/2023] [Accepted: 03/29/2023] [Indexed: 04/19/2023]
Abstract
Molecular modifiers of KRASG12C inhibitor (KRASG12Ci) efficacy in advanced KRASG12C-mutant NSCLC are poorly defined. In a large unbiased clinicogenomic analysis of 424 patients with non-small cell lung cancer (NSCLC), we identified and validated coalterations in KEAP1, SMARCA4, and CDKN2A as major independent determinants of inferior clinical outcomes with KRASG12Ci monotherapy. Collectively, comutations in these three tumor suppressor genes segregated patients into distinct prognostic subgroups and captured ∼50% of those with early disease progression (progression-free survival ≤3 months) with KRASG12Ci. Pathway-level integration of less prevalent coalterations in functionally related genes nominated PI3K/AKT/MTOR pathway and additional baseline RAS gene alterations, including amplifications, as candidate drivers of inferior outcomes with KRASG12Ci, and revealed a possible association between defective DNA damage response/repair and improved KRASG12Ci efficacy. Our findings propose a framework for patient stratification and clinical outcome prediction in KRASG12C-mutant NSCLC that can inform rational selection and appropriate tailoring of emerging combination therapies. SIGNIFICANCE In this work, we identify co-occurring genomic alterations in KEAP1, SMARCA4, and CDKN2A as independent determinants of poor clinical outcomes with KRASG12Ci monotherapy in advanced NSCLC, and we propose a framework for patient stratification and treatment personalization based on the comutational status of individual tumors. See related commentary by Heng et al., p. 1513. This article is highlighted in the In This Issue feature, p. 1501.
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Affiliation(s)
- Marcelo V. Negrao
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Haniel A. Araujo
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Giuseppe Lamberti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Neal S. Akhave
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Teng Zhou
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Lukas Delasos
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - J. Kevin Hicks
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center, Tampa, Florida, USA
| | - Mihaela Aldea
- Institut Gustave Roussy, Villejuif, France
- Paris-Saclay University, Paris, France
| | | | - Jacobi Hines
- University of Chicago Medical Center, Chicago, Illinois, USA
| | | | - Michael J. Dennis
- Moores Cancer Center, University of California San Diego, San Diego, California, USA
| | - Turja Chakrabarti
- Department of Medicine, Division of Hematology and Oncology, University of California San Francisco, San Francisco, California, USA
| | - Susan C. Scott
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Paolo Bironzo
- Department of Oncology, University of Turin, Turin, Italy
| | - Matthias Scheffler
- Department for Internal Medicine, Center for Integrated Oncology Köln-Bonn, University Hospital Cologne, Germany
| | - Petros Christopoulos
- Department of Thoracic Oncology, Thoraxklinik and National Center for Tumor Diseases at Heidelberg University Hospital
| | | | - Jonathan W. Riess
- University of California Davis Comprehensive Cancer Center, Sacramento, California, USA
| | - So Yeon Kim
- Yale School of Medicine, New Haven, Connecticut, USA
| | | | - Mingjia Li
- Division of Medical Oncology, The Ohio State University - James Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Qi Wang
- Bioinformatics & Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yun Qing
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ying Ni
- Center for Immunotherapy & Precision Immuno-Oncology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Minh Truong Do
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Richard Lee
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Biagio Ricciuti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Joao Victor Alessi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jing Wang
- Bioinformatics & Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Blerina Resuli
- Istituto Nazionale Tumori IRCCS “Regina Elena”, Rome, Italy
| | - Lorenza Landi
- Istituto Nazionale Tumori IRCCS “Regina Elena”, Rome, Italy
| | - Shu-Chi Tseng
- Department of Radiology, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Mizuki Nishino
- Department of Radiology, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Subba R. Digumarthy
- Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Waree Rinsurongkawong
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Vadeerat Rinsurong kawong
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Ara A. Vaporciyan
- Department Thoracic & Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - George R. Blumenschein
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Jianjun Zhang
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Dwight H. Owen
- Division of Medical Oncology, The Ohio State University - James Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Collin M. Blakely
- Department of Medicine, Division of Hematology and Oncology, University of California San Francisco, San Francisco, California, USA
| | - Giannis Mountzios
- Fourth Department of Medical Oncology and Clinical Trials Unit, Henry Dunant Hospital Center, Greece
| | - Catherine A. Shu
- Department of Medicine, Columbia University, New York, New York, USA
| | | | | | - Kristen A. Marrone
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jhanelle E. Gray
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center, Tampa, Florida, USA
| | - Sandip Pravin Patel
- Moores Cancer Center, University of California San Diego, San Diego, California, USA
| | - Amy L. Cummings
- University of California Los Angeles, Los Angeles, California, USA
| | | | - Juergen Wolf
- Department for Internal Medicine, Center for Integrated Oncology Köln-Bonn, University Hospital Cologne, Germany
| | | | | | - Fabrice Barlesi
- Institut Gustave Roussy, Villejuif, France
- Paris-Saclay University, Paris, France
| | | | | | - Don L. Gibbons
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - J. Jack Lee
- Bioinformatics & Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - John V. Heymach
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - David S. Hong
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Mark M. Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ferdinandos Skoulidis
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
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Neil AJ, Zhao L, Isidro RA, Srivastava A, Cleary JM, Dong F. SMARCA4 Mutations in Carcinomas of the Esophagus, Esophagogastric Junction, and Stomach. Mod Pathol 2023; 36:100183. [PMID: 37054973 DOI: 10.1016/j.modpat.2023.100183] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 03/08/2023] [Accepted: 03/29/2023] [Indexed: 04/15/2023]
Abstract
Deficiency of SMARCA4, a member of the SWI/SNF chromatin remodeling complex, has been described in a subset of undifferentiated gastroesophageal carcinomas with an aggressive clinical course. The full spectrum and frequency of SMARCA4 mutations in gastroesophageal cancer are unknown. We interrogated our institutional database and identified patients with gastroesophageal carcinomas who underwent cancer next-generation sequencing. We classified SMARCA4 mutations, assessed histologic features, and correlated SMARCA4 mutations with SMARCA4 protein expression by immunohistochemistry. SMARCA4 mutations were identified in gastroesophageal carcinomas from 107 (9.1%) of 1174 patients. Forty-nine SMARCA4 mutations, including 26 missense variants and 23 protein-truncating variants, were interpreted as pathogenic in 42 (3.6%) of 1174 patients. Thirty (71%) of 42 cancers with pathogenic SMARCA4 mutations were located in the esophagus or esophagogastric junction, and 12 cancers (29%) were located in the stomach. Sixty-four percent of carcinomas with pathogenic truncating SMARCA4 variants were poorly differentiated or undifferentiated compared with 25% of carcinomas with pathogenic missense variants. Eight of 12 carcinomas with truncating SMARCA4 variants and none of the 7 carcinomas with pathogenic SMARCA4 missense variants showed loss of SMARCA4 expression by immunohistochemistry. Four carcinomas with pathogenic truncating SMARCA4 variants were associated with Barrett esophagus. SMARCA4-mutated gastroesophageal cancers were enriched for APC (31%) and CTNNB1 (14%) mutations and exhibited similar frequency of TP53 (76%) and ARID1A (31%) mutations compared with gastroesophageal cancers without pathogenic SMARCA4 mutations. The median overall survival was 13.6 months for patients who presented with metastasis at diagnosis and 22.7 months for patients without metastasis. Overall, SMARCA4-mutated gastroesophageal cancers exhibit a spectrum of histologic grade, an association with Barrett esophagus, and a concurrent mutational pattern similar to SMARCA4-wild-type gastroesophageal adenocarcinomas. Although SMARCA4-deficient gastroesophageal carcinomas are associated with poorly differentiated and undifferentiated histology, the spectrum of histologic and molecular features suggests overlapping pathogenic pathways with conventional gastroesophageal adenocarcinomas.
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Affiliation(s)
- Alexander J Neil
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Lei Zhao
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Raymond A Isidro
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Amitabh Srivastava
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts; Now with Department of Pathology, Memorial Sloan Kettering Cancer Center, New York
| | - James M Cleary
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Fei Dong
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts.
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Zhu X, Fu Z, Chen SY, Ong D, Aceto G, Ho R, Steinberger J, Monast A, Pilon V, Li E, Ta M, Ching K, Adams BN, Negri GL, Choiniere L, Fu L, Pavlakis K, Pirrotte P, Avizonis DZ, Trent J, Weissman BE, Klein Geltink RI, Morin GB, Park M, Huntsman DG, Foulkes WD, Wang Y, Huang S. Alanine supplementation exploits glutamine dependency induced by SMARCA4/2-loss. Nat Commun 2023; 14:2894. [PMID: 37210563 DOI: 10.1038/s41467-023-38594-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/09/2023] [Indexed: 05/22/2023] Open
Abstract
SMARCA4 (BRG1) and SMARCA2 (BRM) are the two paralogous ATPases of the SWI/SNF chromatin remodeling complexes frequently inactivated in cancers. Cells deficient in either ATPase have been shown to depend on the remaining counterpart for survival. Contrary to this paralog synthetic lethality, concomitant loss of SMARCA4/2 occurs in a subset of cancers associated with very poor outcomes. Here, we uncover that SMARCA4/2-loss represses expression of the glucose transporter GLUT1, causing reduced glucose uptake and glycolysis accompanied with increased dependency on oxidative phosphorylation (OXPHOS); adapting to this, these SMARCA4/2-deficient cells rely on elevated SLC38A2, an amino acid transporter, to increase glutamine import for fueling OXPHOS. Consequently, SMARCA4/2-deficient cells and tumors are highly sensitive to inhibitors targeting OXPHOS or glutamine metabolism. Furthermore, supplementation of alanine, also imported by SLC38A2, restricts glutamine uptake through competition and selectively induces death in SMARCA4/2-deficient cancer cells. At a clinically relevant dose, alanine supplementation synergizes with OXPHOS inhibition or conventional chemotherapy eliciting marked antitumor activity in patient-derived xenografts. Our findings reveal multiple druggable vulnerabilities of SMARCA4/2-loss exploiting a GLUT1/SLC38A2-mediated metabolic shift. Particularly, unlike dietary deprivation approaches, alanine supplementation can be readily applied to current regimens for better treatment of these aggressive cancers.
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Affiliation(s)
- Xianbing Zhu
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
| | - Zheng Fu
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
| | - Shary Y Chen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - Dionzie Ong
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Giulio Aceto
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
| | - Rebecca Ho
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - Jutta Steinberger
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
| | - Anie Monast
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
| | - Virginie Pilon
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
| | - Eunice Li
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Monica Ta
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Kyle Ching
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Bianca N Adams
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
| | - Gian L Negri
- Canada's Michael Smith Genome Science Centre, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - Luc Choiniere
- Rosalind & Morris Goodman Cancer Institute, Metabolomics Innovation Resource, McGill University, Montreal, QC, Canada
| | - Lili Fu
- Department of Pathology, McGill University Health Centre, Montreal, QC, Canada
| | - Kitty Pavlakis
- Department of Pathology, IASO women's hospital, Athens, Greece
| | - Patrick Pirrotte
- Cancer & Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA
- Integrated Mass Spectrometry Shared Resource, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Daina Z Avizonis
- Rosalind & Morris Goodman Cancer Institute, Metabolomics Innovation Resource, McGill University, Montreal, QC, Canada
| | - Jeffrey Trent
- Translational Genomics Research Institute, Division of Integrated Cancer Genomics, Phoenix, AZ, USA
| | - Bernard E Weissman
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Ramon I Klein Geltink
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Gregg B Morin
- Canada's Michael Smith Genome Science Centre, British Columbia Cancer Research Institute, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Morag Park
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
| | - David G Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, BC, Canada
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC, Canada
| | - William D Foulkes
- Departments of Human Genetics, Medicine and Oncology McGill University, Montreal, QC, Canada
- Division of Medical Genetics, Department of Specialized Medicine and Cancer Research Program, McGill University Health Centre, Montreal, QC, Canada
- Division of Medical Genetics, Department of Specialized Medicine and Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Yemin Wang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
- Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, BC, Canada.
| | - Sidong Huang
- Department of Biochemistry, McGill University, Montreal, QC, Canada.
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada.
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Pan M, Jiang C, Zhang Z, Achacoso N, Solorzano-Pinto AV, Tse P, Chung E, Suga JM, Thomas S, Habel LA. Sex- and Co-Mutation-Dependent Prognosis in Patients with SMARCA4-Mutated Malignancies. Cancers (Basel) 2023; 15:2665. [PMID: 37345003 DOI: 10.3390/cancers15102665] [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: 03/07/2023] [Revised: 04/12/2023] [Accepted: 05/03/2023] [Indexed: 06/23/2023] Open
Abstract
BACKGROUND Whether sex and co-mutations impact prognosis of patients with SMARCA4-mutated (mutSMARCA4) malignancies is not clear. METHODS This cohort included patients from Northern California Kaiser Permanente with next-generation sequencing (NGS) performed from August 2020 to October 2022. We used Cox regression modeling to examine the association between sex and overall survival (OS), adjusting for demographics, performance status, Charlson comorbidity index, receipt of treatment, tumor mutation burden (TMB), and TP53, KRAS, CDKN2A, STK11, and Keap1 co-mutations. RESULTS Out of 9221 cases with NGS performed, 125 cases (1.4%) had a mutSMARCA4. The most common malignancies with a mutSMARCA4 were non-small cell lung cancer (NSCLC, 35.2%), esophageal and stomach adenocarcinoma (12.8%), and cancer of unknown primary (11.2%). The most common co-mutations were p53 (mutp53, 59.2%), KRAS (mutKRAS, 28.8%), CDKN2A (mutCDKN2A, 31.2%), STK11 (mutSTK11, 12.8%), and Keap1 (mutKeap1, 8.8%) mutations. Male patients had substantially worse OS than female patients both among the entire mutSMARCA4 cohort (HR = 1.71, [95% CI 0.92-3.18]) with a median OS of 3.0 versus 43.3 months (p < 0.001), and among the NSCLC subgroup (HR = 14.2, [95% CI 2.76-73.4]) with a median OS of 2.75 months versus un-estimable (p = 0.02). Among all patients with mutSMARCA4, mutp53 versus wtp53 (HR = 2.12, [95% CI 1.04-4.29]) and mutSTK11 versus wtSTK11 (HR = 2.59, [95% CI 0.87-7.73]) were associated with worse OS. Among the NSCLC subgroup, mutp53 versus wtp53 (HR = 0.35, [0.06-1.97]) and mutKRAS versus wtKRAS (HR = 0.04, [0.003-.45]) were associated with better OS, while mutCDKN2A versus wtCDKN2A (HR = 5.04, [1.12-22.32]), mutSTK11 versus wtSTK11 (HR = 13.10, [95% CI 1.16-148.26]), and mutKeap1 versus wtKeap1 (HR = 5.06, [95% CI 0.89-26.61}) were associated with worse OS. CONCLUSION In our cohort of patients with mutSMARCA4, males had substantially worse prognosis than females, while mutTP53, mutKRAS, mutCDKN2A, mutSTK11 and mutKeap1were differentially associated with prognosis among all patients and among the NSCLC subgroup. Our results, if confirmed, could suggest potentially unidentified mechanisms that underly this sex and co-mutation-dependent prognostic disparity among patients whose tumor bears a mutSMARCA4.
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Affiliation(s)
- Minggui Pan
- Department of Oncology and Hematology, Kaiser Permanente, Santa Clara, CA 94051, USA
- Division of Research, Kaiser Permanente, Oakland, CA 94612, USA
- Division of Oncology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Chen Jiang
- Division of Research, Kaiser Permanente, Oakland, CA 94612, USA
| | - Zheyang Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, and National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen 361102, China
| | - Ninah Achacoso
- Division of Research, Kaiser Permanente, Oakland, CA 94612, USA
| | | | - Pam Tse
- Division of Research, Kaiser Permanente, Oakland, CA 94612, USA
| | - Elaine Chung
- Division of Research, Kaiser Permanente, Oakland, CA 94612, USA
| | - Jennifer Marie Suga
- Department of Oncology and Hematology, Kaiser Permanente, Vallejo, CA 94589, USA
| | - Sachdev Thomas
- Department of Oncology and Hematology, Kaiser Permanente, Vallejo, CA 94589, USA
| | - Laurel A Habel
- Division of Research, Kaiser Permanente, Oakland, CA 94612, USA
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Lengel HB, Mastrogiacomo B, Connolly JG, Tan KS, Liu Y, Fick CN, Dunne EG, He D, Lankadasari MB, Satravada BA, Sun Y, Kundra R, Fong C, Smith S, Riely GJ, Rudin CM, Gomez DR, Solit DB, Berger MF, Li BT, Mayo MW, Matei I, Lyden DC, Adusumilli PS, Schultz N, Sanchez-Vega F, Jones DR. Genomic mapping of metastatic organotropism in lung adenocarcinoma. Cancer Cell 2023; 41:970-985.e3. [PMID: 37084736 PMCID: PMC10391526 DOI: 10.1016/j.ccell.2023.03.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 02/02/2023] [Accepted: 03/22/2023] [Indexed: 04/23/2023]
Abstract
We analyzed 2,532 lung adenocarcinomas (LUAD) to identify the clinicopathological and genomic features associated with metastasis, metastatic burden, organotropism, and metastasis-free survival. Patients who develop metastasis are younger and male, with primary tumors enriched in micropapillary or solid histological subtypes and with a higher mutational burden, chromosomal instability, and fraction of genome doublings. Inactivation of TP53, SMARCA4, and CDKN2A are correlated with a site-specific shorter time to metastasis. The APOBEC mutational signature is more prevalent among metastases, particularly liver lesions. Analyses of matched specimens show that oncogenic and actionable alterations are frequently shared between primary tumors and metastases, whereas copy number alterations of unknown significance are more often private to metastases. Only 4% of metastases harbor therapeutically actionable alterations undetected in their matched primaries. Key clinicopathological and genomic alterations in our cohort were externally validated. In summary, our analysis highlights the complexity of clinicopathological features and tumor genomics in LUAD organotropism.
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Affiliation(s)
- Harry B Lengel
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brooke Mastrogiacomo
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - James G Connolly
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kay See Tan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yuan Liu
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Cameron N Fick
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elizabeth G Dunne
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Di He
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Manendra B Lankadasari
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Baby Anusha Satravada
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yichao Sun
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ritika Kundra
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chris Fong
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shaleigh Smith
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gregory J Riely
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charles M Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel R Gomez
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David B Solit
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael F Berger
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bob T Li
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marty W Mayo
- Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Irina Matei
- Department of Pediatrics, Meyer Cancer Center, Weill Cornell Medicine of Cornell University, New York, NY, USA
| | - David C Lyden
- Department of Pediatrics, Meyer Cancer Center, Weill Cornell Medicine of Cornell University, New York, NY, USA
| | - Prasad S Adusumilli
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nikolaus Schultz
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Francisco Sanchez-Vega
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - David R Jones
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Strickland AL, Maniar KP, Tanner E, Shanes E, Jennings L, Wei JJ. Borderline With Bad Behavior: An Unusual Low-grade Serous Carcinoma With Dedifferentiation From a Serous Borderline Tumor. Int J Gynecol Pathol 2023; 42:241-246. [PMID: 36867463 DOI: 10.1097/pgp.0000000000000885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
The pathogenesis of serous ovarian tumors has been extensively investigated, with a dualistic model dividing these cancers into 2 groups. Type I tumors, including low-grade serous carcinoma, is characteristic for concurrent presence of borderline tumors, less atypical cytology, relatively indolent biologic behavior, and molecular aberrations related to the MAPK pathway with chromosomal stability. Meanwhile, type II tumors, such as high-grade serous carcinoma, are notable for no significant association with borderline tumors, higher grade cytology, more aggressive biologic behavior, and TP53 mutations along with chromosomal instability. We describe a case of morphologic low-grade serous carcinoma with focally increased cytologic atypia arising in serous borderline tumors involving both ovaries, which demonstrated highly aggressive behavior despite several years of surgical and chemotherapeutic management. Each recurrent specimen contained more uniform higher grade morphology than what was seen in the original specimen. Immunohistochemical and molecular studies in both the original tumor and the most recent recurrence demonstrate identical mutations in the MAPK genes, but with additional mutations in the latter, notably an acquisition of a variant of possible clinical significance in the SMARCA4 gene, which is associated with dedifferentiation and aggressive biologic behavior. This case challenges our current and still evolving understanding of the pathogenesis, biologic behavior, and expected clinical outcome of low-grade serous ovarian carcinomas. It also underscores the need for further investigation into this complicated tumor.
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Affiliation(s)
- Amanda L Strickland
- Department of Pathology (A.L.S., K.P.M., E.S., L.J., J.J.W.); and Division of Gynecologic Oncology, Department of Obstetrics and Gynecology (E.T., J.J.), Northwestern University Feinberg School of Medicine, Chicago, Illinois
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Jiang J, Chen Z, Gong J, Han N, Lu H. Thoracic SMARCA4-deficient undifferentiated tumor. Discov Oncol 2023; 14:51. [PMID: 37115343 PMCID: PMC10147882 DOI: 10.1007/s12672-023-00639-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 03/20/2023] [Indexed: 04/29/2023] Open
Abstract
Thoracic SMARCA4-deficient undifferentiated tumor (SMARCA4-UT) is a recently described smoking-related malignancy. The pathogenesis of SMARCA4-UT is the mutational inactivation and loss of expression of a subunit encoding the mammalian switch/sucrose nonfermenting ATPase-dependent chromatin remodeling complex (which can be mobilized using adenosine triphosphate hydrolysis nucleosomes and regulate other cellular processes including development, differentiation, proliferation, and apoptosis), in particular SMARCA4 and SMARCA2. The dynamic activity of this complex plays an important role in regulating the activation and repression of gene expression programs. SMARCA4-UT exhibits morphological features similar to the malignant rhabdoid tumor (MRT), small cell carcinoma of the ovary of the hypercalcemic type (SCCOHT), and INI1-deficient tumor, but SMARCA4-UT differs from SCCOHT and MRT from a genomic perspective. SMARCA4-UT mainly involves the mediastinum and lung parenchyma, and appears as a large infiltrative mass that easily compresses surrounding tissues. At present, chemotherapy is a common treatment, but its efficacy is not clear. Moreover, the inhibitor of the enhancer of zeste homolog 2 showed promising efficacy in some patients with SMARCA4-UT. This study aimed to review the clinical characteristics, diagnosis, treatment, and prognosis of SMARCA4-UT.
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Affiliation(s)
- Jiapeng Jiang
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310053, People's Republic of China
- Zhejiang Key Laboratory of Diagnosis & Treatment Technology on Thoracic Oncology (Lung and Esophagus), Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
- Department of Thoracic Medical Oncology, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Zhixin Chen
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310053, People's Republic of China
- Zhejiang Key Laboratory of Diagnosis & Treatment Technology on Thoracic Oncology (Lung and Esophagus), Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
- Department of Thoracic Medical Oncology, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Jiali Gong
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310053, People's Republic of China
- Zhejiang Key Laboratory of Diagnosis & Treatment Technology on Thoracic Oncology (Lung and Esophagus), Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
- Department of Thoracic Medical Oncology, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Na Han
- Zhejiang Key Laboratory of Diagnosis & Treatment Technology on Thoracic Oncology (Lung and Esophagus), Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
- Department of Thoracic Medical Oncology, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Hongyang Lu
- Zhejiang Key Laboratory of Diagnosis & Treatment Technology on Thoracic Oncology (Lung and Esophagus), Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China.
- Department of Thoracic Medical Oncology, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China.
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Andrades A, Peinado P, Alvarez-Perez JC, Sanjuan-Hidalgo J, García DJ, Arenas AM, Matia-González AM, Medina PP. SWI/SNF complexes in hematological malignancies: biological implications and therapeutic opportunities. Mol Cancer 2023; 22:39. [PMID: 36810086 PMCID: PMC9942420 DOI: 10.1186/s12943-023-01736-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/30/2023] [Indexed: 02/23/2023] Open
Abstract
Hematological malignancies are a highly heterogeneous group of diseases with varied molecular and phenotypical characteristics. SWI/SNF (SWItch/Sucrose Non-Fermentable) chromatin remodeling complexes play significant roles in the regulation of gene expression, being essential for processes such as cell maintenance and differentiation in hematopoietic stem cells. Furthermore, alterations in SWI/SNF complex subunits, especially in ARID1A/1B/2, SMARCA2/4, and BCL7A, are highly recurrent across a wide variety of lymphoid and myeloid malignancies. Most genetic alterations cause a loss of function of the subunit, suggesting a tumor suppressor role. However, SWI/SNF subunits can also be required for tumor maintenance or even play an oncogenic role in certain disease contexts. The recurrent alterations of SWI/SNF subunits highlight not only the biological relevance of SWI/SNF complexes in hematological malignancies but also their clinical potential. In particular, increasing evidence has shown that mutations in SWI/SNF complex subunits confer resistance to several antineoplastic agents routinely used for the treatment of hematological malignancies. Furthermore, mutations in SWI/SNF subunits often create synthetic lethality relationships with other SWI/SNF or non-SWI/SNF proteins that could be exploited therapeutically. In conclusion, SWI/SNF complexes are recurrently altered in hematological malignancies and some SWI/SNF subunits may be essential for tumor maintenance. These alterations, as well as their synthetic lethal relationships with SWI/SNF and non-SWI/SNF proteins, may be pharmacologically exploited for the treatment of diverse hematological cancers.
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Affiliation(s)
- Alvaro Andrades
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
| | - Paola Peinado
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain ,grid.451388.30000 0004 1795 1830Present Address: The Francis Crick Institute, London, UK
| | - Juan Carlos Alvarez-Perez
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
| | - Juan Sanjuan-Hidalgo
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain
| | - Daniel J. García
- grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.4489.10000000121678994Department of Biochemistry and Molecular Biology III and Immunology, University of Granada, Granada, Spain
| | - Alberto M. Arenas
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
| | - Ana M. Matia-González
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
| | - Pedro P. Medina
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
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37
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SMARCA4: Current status and future perspectives in non-small-cell lung cancer. Cancer Lett 2023; 554:216022. [PMID: 36450331 DOI: 10.1016/j.canlet.2022.216022] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/07/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022]
Abstract
SMARCA4, also known as transcription activator, is an ATP-dependent catalytic subunit of SWI/SNF (SWItch/Sucrose NonFermentable) chromatin-remodeling complexes that participates in the regulation of chromatin structure and gene expression by supplying energy. As a tumor suppressor that has aberrant expression in ∼10% of non-small-cell lung cancers (NSCLCs), SMARCA4 possesses many biological functions, including regulating gene expression, differentiation and transcription. Furthermore, NSCLC patients with SMARCA4 alterations have a weak response to conventional chemotherapy and poor prognosis. Therefore, the mechanisms of SMARCA4 in NSCLC development urgently need to be explored to identify novel biomarkers and precise therapeutic strategies for this subtype. This review systematically describes the biological functions of SMARCA4 and its role in NSCLC development, metastasis, functional epigenetics and potential therapeutic approaches for NSCLCs with SMARCA4 alterations. Additionally, this paper explores the relationship and regulatory mechanisms shared by SMARCA4 and its mutually exclusive catalytic subunit SMARCA2. We aim to provide innovative treatment strategies and improve clinical outcomes for NSCLC patients with SMARCA4 alterations.
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38
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Kirk NA, Kim KB, Park KS. Effect of chromatin modifiers on the plasticity and immunogenicity of small-cell lung cancer. Exp Mol Med 2022; 54:2118-2127. [PMID: 36509828 PMCID: PMC9794818 DOI: 10.1038/s12276-022-00905-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 12/14/2022] Open
Abstract
Tumor suppressor genes (TSGs) are often involved in maintaining homeostasis. Loss of tumor suppressor functions causes cellular plasticity that drives numerous types of cancer, including small-cell lung cancer (SCLC), an aggressive type of lung cancer. SCLC is largely driven by numerous loss-of-function mutations in TSGs, often in those encoding chromatin modifiers. These mutations present a therapeutic challenge because they are not directly actionable. Alternatively, understanding the resulting molecular changes may provide insight into tumor intervention strategies. We hypothesize that despite the heterogeneous genomic landscape in SCLC, the impacts of mutations in patient tumors are related to a few important pathways causing malignancy. Specifically, alterations in chromatin modifiers result in transcriptional dysregulation, driving mutant cells toward a highly plastic state that renders them immune evasive and highly metastatic. This review will highlight studies in which imbalance of chromatin modifiers with opposing functions led to loss of immune recognition markers, effectively masking tumor cells from the immune system. This review also discusses the role of chromatin modifiers in maintaining neuroendocrine characteristics and the role of aberrant transcriptional control in promoting epithelial-to-mesenchymal transition during tumor development and progression. While these pathways are thought to be disparate, we highlight that the pathways often share molecular drivers and mediators. Understanding the relationships among frequently altered chromatin modifiers will provide valuable insights into the molecular mechanisms of SCLC development and progression and therefore may reveal preventive and therapeutic vulnerabilities of SCLC and other cancers with similar mutations.
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Affiliation(s)
- Nicole A. Kirk
- grid.27755.320000 0000 9136 933XDepartment of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908 USA
| | - Kee-Beom Kim
- grid.258803.40000 0001 0661 1556BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu, 41566 Republic of Korea
| | - Kwon-Sik Park
- grid.27755.320000 0000 9136 933XDepartment of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908 USA
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Cantley J, Ye X, Rousseau E, Januario T, Hamman BD, Rose CM, Cheung TK, Hinkle T, Soto L, Quinn C, Harbin A, Bortolon E, Chen X, Haskell R, Lin E, Yu SF, Del Rosario G, Chan E, Dunlap D, Koeppen H, Martin S, Merchant M, Grimmer M, Broccatelli F, Wang J, Pizzano J, Dragovich PS, Berlin M, Yauch RL. Selective PROTAC-mediated degradation of SMARCA2 is efficacious in SMARCA4 mutant cancers. Nat Commun 2022; 13:6814. [PMID: 36357397 PMCID: PMC9649729 DOI: 10.1038/s41467-022-34562-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 10/28/2022] [Indexed: 11/12/2022] Open
Abstract
The mammalian SWItch/Sucrose Non-Fermentable (SWI/SNF) helicase SMARCA4 is frequently mutated in cancer and inactivation results in a cellular dependence on its paralog, SMARCA2, thus making SMARCA2 an attractive synthetic lethal target. However, published data indicates that achieving a high degree of selective SMARCA2 inhibition is likely essential to afford an acceptable therapeutic index, and realizing this objective is challenging due to the homology with the SMARCA4 paralog. Herein we report the discovery of a potent and selective SMARCA2 proteolysis-targeting chimera molecule (PROTAC), A947. Selective SMARCA2 degradation is achieved in the absence of selective SMARCA2/4 PROTAC binding and translates to potent in vitro growth inhibition and in vivo efficacy in SMARCA4 mutant models, compared to wild type models. Global ubiquitin mapping and proteome profiling reveal no unexpected off-target degradation related to A947 treatment. Our study thus highlights the ability to transform a non-selective SMARCA2/4-binding ligand into a selective and efficacious in vivo SMARCA2-targeting PROTAC, and thereby provides a potential new therapeutic opportunity for patients whose tumors contain SMARCA4 mutations.
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Affiliation(s)
- Jennifer Cantley
- grid.504169.f0000 0004 7667 0983Arvinas, LLC, 5 Science Park, New Haven, CT 06511 USA
| | - Xiaofen Ye
- grid.418158.10000 0004 0534 4718Genentech, 1 DNA Way, South San Francisco, 94080 USA
| | - Emma Rousseau
- grid.504169.f0000 0004 7667 0983Arvinas, LLC, 5 Science Park, New Haven, CT 06511 USA
| | - Tom Januario
- grid.418158.10000 0004 0534 4718Genentech, 1 DNA Way, South San Francisco, 94080 USA
| | - Brian D. Hamman
- HotSpot Therapeutics, Inc. 1 Deerpark Dr., Ste C, Monmouth Junction, NJ 08852 USA
| | - Christopher M. Rose
- grid.418158.10000 0004 0534 4718Genentech, 1 DNA Way, South San Francisco, 94080 USA
| | - Tommy K. Cheung
- grid.418158.10000 0004 0534 4718Genentech, 1 DNA Way, South San Francisco, 94080 USA
| | - Trent Hinkle
- grid.418158.10000 0004 0534 4718Genentech, 1 DNA Way, South San Francisco, 94080 USA
| | - Leofal Soto
- grid.504169.f0000 0004 7667 0983Arvinas, LLC, 5 Science Park, New Haven, CT 06511 USA
| | - Connor Quinn
- grid.504169.f0000 0004 7667 0983Arvinas, LLC, 5 Science Park, New Haven, CT 06511 USA
| | - Alicia Harbin
- grid.504169.f0000 0004 7667 0983Arvinas, LLC, 5 Science Park, New Haven, CT 06511 USA
| | - Elizabeth Bortolon
- grid.504169.f0000 0004 7667 0983Arvinas, LLC, 5 Science Park, New Haven, CT 06511 USA
| | - Xin Chen
- grid.504169.f0000 0004 7667 0983Arvinas, LLC, 5 Science Park, New Haven, CT 06511 USA
| | - Roy Haskell
- grid.504169.f0000 0004 7667 0983Arvinas, LLC, 5 Science Park, New Haven, CT 06511 USA
| | - Eva Lin
- grid.418158.10000 0004 0534 4718Genentech, 1 DNA Way, South San Francisco, 94080 USA
| | - Shang-Fan Yu
- grid.418158.10000 0004 0534 4718Genentech, 1 DNA Way, South San Francisco, 94080 USA
| | - Geoff Del Rosario
- grid.418158.10000 0004 0534 4718Genentech, 1 DNA Way, South San Francisco, 94080 USA
| | - Emily Chan
- grid.418158.10000 0004 0534 4718Genentech, 1 DNA Way, South San Francisco, 94080 USA
| | - Debra Dunlap
- grid.418158.10000 0004 0534 4718Genentech, 1 DNA Way, South San Francisco, 94080 USA
| | - Hartmut Koeppen
- grid.418158.10000 0004 0534 4718Genentech, 1 DNA Way, South San Francisco, 94080 USA
| | - Scott Martin
- grid.418158.10000 0004 0534 4718Genentech, 1 DNA Way, South San Francisco, 94080 USA
| | - Mark Merchant
- grid.418158.10000 0004 0534 4718Genentech, 1 DNA Way, South San Francisco, 94080 USA
| | - Matt Grimmer
- grid.418158.10000 0004 0534 4718Genentech, 1 DNA Way, South San Francisco, 94080 USA
| | - Fabio Broccatelli
- grid.418158.10000 0004 0534 4718Genentech, 1 DNA Way, South San Francisco, 94080 USA
| | - Jing Wang
- grid.504169.f0000 0004 7667 0983Arvinas, LLC, 5 Science Park, New Haven, CT 06511 USA
| | - Jennifer Pizzano
- grid.504169.f0000 0004 7667 0983Arvinas, LLC, 5 Science Park, New Haven, CT 06511 USA
| | - Peter S. Dragovich
- grid.418158.10000 0004 0534 4718Genentech, 1 DNA Way, South San Francisco, 94080 USA
| | - Michael Berlin
- grid.504169.f0000 0004 7667 0983Arvinas, LLC, 5 Science Park, New Haven, CT 06511 USA
| | - Robert L. Yauch
- grid.418158.10000 0004 0534 4718Genentech, 1 DNA Way, South San Francisco, 94080 USA
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40
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Chang G, Li W, Bai H, Duan J, Wang Z, Du X, Yu R, Wang Y, Wang M, Zhu Y, Zhang X, Li L, Wan R, Wang J. Correlations of switch/sucrose nonfermentable complex mutations with clinical outcomes in advanced non-small cell lung cancer. Thorac Cancer 2022; 13:2951-2959. [PMID: 36126963 PMCID: PMC9626335 DOI: 10.1111/1759-7714.14635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The switch/sucrose nonfermentable complex mutations (SWI/SNF-mut) are common in non-small cell lung cancer (NSCLC). However, the association of SWI/SNF-mut with the clinical outcomes of immune checkpoint inhibitors (ICIs), particularly of epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs), has not been established. METHODS We retrospectively collected data of patients at Cancer Hospital Chinese Academy of Medical Sciences. Patients with advanced NSCLC who received programmed cell death protein-1 or programmed cell death ligand 1 (PD-[L]1) inhibitors were included in cohort 1 and those with EGFR mutations (EGFR-mutant) received EGFR-TKIs monotherapy were included in cohort 2. Two reported Memorial Sloan-Kettering Cancer Center (MSKCC) cohorts received immunotherapy alone used as the validation for cohort 1. We analyzed the relationship between SWI/SNF alterations and clinical outcomes in each cohort. RESULTS In total, 1162 patients were included, of which 230 patients (19.8%) were identified as SWI/SNF-mut with the most common genetic alterations being ARID1A (33.4%) and SMARCA4 (28.3%). In cohort 1 (n = 146), patients with co-mutations of SWI/SNF and Kirsten rat sarcoma oncogene (KRAS) (SWI/SNFmutKRASmut, n = 18) had significantly prolonged progression-free survival (PFS) (8.6 m vs. 1.9 m; hazard ratio [HR], 0.31; 95% confidence intervals [CI], 0.11-0.83; p = 0.032) to PD-(L)1 inhibitors monotherapy, which was consistent with the MSKCC cohorts (not reach [NR] vs. 6.3 m; HR, 0.36, 95% CI, 0.15-0.82; p = 0.016). In cohort 2 (n = 205), ARID1A-mut (n = 16) was associated with improved PFS after EGFR-TKIs (20.6 m vs. 11.2 m; HR, 0.47, 95% CI, 0.27-0.94; p = 0.023). CONCLUSIONS In advanced NSCLC, patients with SWI/SNFmutKRASmut seem to benefit more from ICIs. Furthermore, ARID1A-mut may provide a protective effect to EGFR-TKIs in EGFR-mutant patients. However, this is a retrospective single-institution analysis that requires further validation by large prospective studies.
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Affiliation(s)
- Geyun Chang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Weihua Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Hua Bai
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Jianchun Duan
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Zhijie Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Xinyang Du
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Ruofei Yu
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Yaxi Wang
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Minghao Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Yixiang Zhu
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Xue Zhang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Li Li
- Department of Medical Records, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Rui Wan
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Jie Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
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Suresh S, Dix D, Wang L, Blydt-Hansen TD. High urinary CXCL10/Cr with onset of Burkitt lymphoma in a pediatric kidney transplant recipient. Pediatr Transplant 2022; 26:e14354. [PMID: 35869900 DOI: 10.1111/petr.14354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 05/08/2022] [Accepted: 06/07/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND Urinary CXCL10/Cr is a promising diagnostic tool for early detection of TCMR in pediatric transplant recipients, and most studies focus on its utility in the context of localized allograft inflammation thus far. Other sources of inflammation that may be detected by CXCL10 are less clear. METHODS We present a case review of a patient with BL, who was enrolled in a prospective trial of urinary CXCL10 monitoring. To evaluate the potential confounding, we tested for association of CXCL10/Cr and EBV viral load in a prospective cohort of pediatric transplant recipients with serial testing for urinary CXCL10/Cr. RESULTS This report describes a 15-year-old boy, 3.5 years post-transplant with chronic EBV viremia, stable kidney function and no history of rejection. Urinary CXCL10/Cr level increased acutely to 79.43 ng/mmol, 0.8 months prior to onset of BL, identified by a surge in EBV viral load. In a national cohort of 97 pediatric kidney transplant recipients, there was no association between urinary CXCL10/Cr with EBV viral loads when comparing periods of pre-viremia (5.8 ± 9.2 ng/mmol) to active viremia (4.0 ± 5.3 ng/mmol) and periods of active viremia (7.1 ± 8.9 ng/mmol) to post-viremia (4.4 ± 9.8 ng/mmol). CONCLUSIONS Acute rise in urinary CXCL10/Cr was associated with onset of graft-associated BL. We were not able to confirm a general association of EBV viral load and urinary CXCL10. As non-invasive monitoring is implemented using biomarkers like CXCL10 in the clinic, attention will be needed to identify other uncommon, potential sources of CXCL10 elevation.
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Affiliation(s)
- Shwetha Suresh
- The University of British Columbia Faculty of Medicine, Vancouver, British Columbia, Canada
| | - David Dix
- Oncology, BC Children's Hospital, Vancouver, British Columbia, Canada
| | - Li Wang
- Pathology & Laboratory Medicine, BC Children's Hospital, Vancouver, British Columbia, Canada
| | - Tom D Blydt-Hansen
- Department of Nephrology, BC Children's Hospital, Vancouver, British Columbia, Canada
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Talvitie EM, Liljeroos L, Vilhonen H, Orte K, Leivo I, Kallajoki M, Taimen P. Comprehensive genomic profiling of Finnish lung adenocarcinoma cohort reveals high clinical actionability and SMARCA4 altered tumors with variable histology and poor prognosis. Neoplasia 2022; 32:100832. [PMID: 35964518 PMCID: PMC9391575 DOI: 10.1016/j.neo.2022.100832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 07/31/2022] [Accepted: 08/01/2022] [Indexed: 10/30/2022]
Abstract
INTRODUCTION Lung adenocarcinoma is the most common type of lung cancer and typically carries a high number of mutations. However, the genetic background of the tumors varies according to patients' ethnic background and smoking status. Little data is available on the mutational landscape and the frequency of actionable genomic alterations in lung adenocarcinoma in the Finnish population. MATERIALS AND METHODS We evaluated the gene alteration frequencies of 135 stage I-IV lung adenocarcinomas operated at Turku University Hospital between 2004 and 2017 with a large commercial comprehensive genomic profiling panel. Additionally, we correlated the alterations in selected genes with disease outcomes in 115 stage I-III patients with comprehensive follow-up data. The genomic alterations in a sub-cohort of 30 never-smokers were assessed separately. RESULTS Seventy percent of patients in the overall cohort and 77% in the never-smoker sub-cohort harbored an alteration or a genomic signature targetable by FDA and/or EMA approved drug for non-small cell carcinoma, respectively. In multivariable analysis for disease-specific survival, any alteration in SMARCA4 (DSS; HR 3.911, 95%CI 1.561-9.795, P=0.004) exhibited independent prognostic significance along with stage, tumor mutation burden, and predominant histological subtypes. CONCLUSIONS Over two thirds of our overall cohort, and especially never-smokers had an actionable genomic alteration or signature. SMARCA4 alterations, detected in 7.4% of the tumors, independently predicted a shortened overall and disease-specific survival regardless of the alteration type. Most SMARCA4 alterations in our cohort were missense mutations associated with differentiated predominant histological subtypes and immunohistochemical SMARCA4/BRG1 and TTF-1 positive status.
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Affiliation(s)
- Eva-Maria Talvitie
- Department of Genomics, Turku University Hospital, Kiinamyllynkatu 10, 20520 Turku, Finland.
| | | | - Heikki Vilhonen
- University of Turku, Department of Pulmonary Diseases and Clinical Allergology and Division of Medicine, Department of Pulmonary Diseases, Turku University Hospital, Hämeentie 11, 20521 Turku, Finland
| | - Katri Orte
- Department of Pathology, Turku University Hospital, Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Ilmo Leivo
- Department of Pathology, Turku University Hospital, Kiinamyllynkatu 10, 20520 Turku, Finland; Institute of Biomedicine and FICAN West Cancer Centre, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Markku Kallajoki
- Department of Pathology, Turku University Hospital, Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Pekka Taimen
- Department of Pathology, Turku University Hospital, Kiinamyllynkatu 10, 20520 Turku, Finland; Institute of Biomedicine and FICAN West Cancer Centre, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland
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Kitamura H, Takeda H, Motohashi H. Genetic, Metabolic and Immunological Features of Cancers with NRF2 Addiction. FEBS Lett 2022; 596:1981-1993. [PMID: 35899372 DOI: 10.1002/1873-3468.14458] [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: 05/08/2022] [Accepted: 07/18/2022] [Indexed: 11/10/2022]
Abstract
Nuclear factor erythroid-derived 2-like 2 (NRF2) is a master transcription factor that coordinately regulates the expression of many cytoprotective genes and plays a central role in defense mechanisms against oxidative and electrophilic insults. Although increased NRF2 activity is principally beneficial for our health, NRF2 activation in cancer cells is detrimental. Many human cancers exhibit persistent NRF2 activation and such cancer cells rely on NRF2 for most of their malignant characteristics, such as therapeutic resistance and aggressive tumorigenesis, and thus fall into NRF2 addiction. The persistent activation of NRF2 confers great advantages on cancer cells, whereas it is not tolerated by normal cells, suggesting that certain requirements are necessary for a cell to exploit NRF2 and evolve into malignant a cancer cell. In this review, recent reports and data on the genetic, metabolic and immunological features of NRF2-activated cancer cells are summarized, and prerequisites for NRF2 addiction in cancer cells and their therapeutic applications are discussed.
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Affiliation(s)
- Hiroshi Kitamura
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan
| | - Haruna Takeda
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan
| | - Hozumi Motohashi
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan
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Genomic landscape of Epstein-Barr virus-positive extranodal marginal zone lymphomas of mucosa-associated lymphoid tissue. Mod Pathol 2022; 35:938-945. [PMID: 34952945 DOI: 10.1038/s41379-021-01002-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 11/08/2022]
Abstract
Epstein-Barr virus (EBV)-positive extranodal marginal zone lymphomas of mucosa-associated lymphoid tissue (MALT lymphomas) were initially described in solid organ transplant recipients, and, more recently, in other immunodeficiency settings. The overall prevalence of EBV-positive MALT lymphomas has not been established, and little is known with respect to their genomic characteristics. Eight EBV-positive MALT lymphomas were identified, including 1 case found after screening a series of 88 consecutive MALT lymphomas with EBER in situ hybridization (1%). The genomic landscape was assessed in 7 of the 8 cases with a targeted high throughput sequencing panel and array comparative genomic hybridization. Results were compared to published data for MALT lymphomas. Of the 8 cases, 6 occurred post-transplant, 1 in the setting of primary immunodeficiency, and 1 case was age-related. Single pathogenic/likely pathogenic mutations were identified in 4 of 7 cases, including mutations in IRF8, BRAF, TNFAIP3, and SMARCA4. Other than TNFAIP3, these genes are mutated in <3% of EBV-negative MALT lymphomas. Copy number abnormalities were identified in 6 of 7 cases with a median of 6 gains and 2 losses per case, including 4 cases with gains in regions encompassing several IRF family or interacting genes (IRF2BP2, IRF2, and IRF4). There was no evidence of trisomies of chromosomes 3 or 18. In summary, EBV-positive MALT lymphomas are rare and, like other MALT lymphomas, are usually genetically non-complex. Conversely, while EBV-negative MALT lymphomas typically show mutational abnormalities in the NF-κB pathway, other than the 1 TNFAIP3-mutated case, no other NF-κB pathway mutations were identified in the EBV-positive cases. EBV-positive MALT lymphomas often have either mutations or copy number abnormalities in IRF family or interacting genes, suggesting that this pathway may play a role in these lymphomas.
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Ogunbona OB, Lin X, Hornick JL, Lubin DJ, Wang Q, Reid MD, Schneider F, Li D, Shin DM, Shi Q. Cytomorphologic and immunophenotypical analysis of SMARCA4 (BRG1)-deficient non-small cell lung carcinoma. J Am Soc Cytopathol 2022; 11:183-193. [PMID: 35491322 DOI: 10.1016/j.jasc.2022.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 03/31/2022] [Accepted: 04/02/2022] [Indexed: 06/14/2023]
Abstract
INTRODUCTION Inactivation of SMARCA4/BRG1 (Brahma-related gene 1), a member of the switch/sucrose nonfermentable subfamily of adenosine triphosphate-dependent chromatin remodeling complexes, has been demonstrated in a subset of non-small cell lung carcinomas (NSCLCs). However, the cytomorphologic features of SMARCA4-deficient NSCLCs (SMARCA4-dNSCLC) have only rarely been reported. MATERIALS AND METHODS Eight cytology cases of SMARCA4-dNSCLC and eight SMARCA4-retained NSCLC (SMARCA4-rNSCLC) cases were retrieved from our institution's database. These were compared cytologically and immunophenotypically. RESULTS All 8 patients with SMARCA4-dNSCLC had a smoking history, and 4 of 8 cases had a prior cancer history. Cytologically, the tumors demonstrated predominantly loosely cohesive and high-grade epithelioid cells with markedly pleomorphic nuclei and prominent nucleoli. Binucleated/multinucleated cells were seen in 5 cases. Six cases showed focal plasmacytoid morphology, and 2 cases showed necrosis. In contrast, in all 8 cases of SMARCA4-rNSCLC, the aspirates were predominantly cohesive with focal, loosely cohesive epithelioid cells showing mild to moderate pleomorphism and lacked necrosis. Only 1 case showed multinucleated cells. All 8 cases of SMARCA4-dNSCLC showed an immunoprofile similar to that of the SMARCA4-rNSCLC cases, including immunoreactivity for AE1/AE3, a lack of immunoreactivity for thyroid transcription factor-1/Napsin A, and p40/p63 but with a loss of BRG1 expression. CONCLUSIONS SMARCA4-dNSCLCs exhibited high-grade cytologic features with marked pleomorphism and might show multinucleation and plasmacytoid morphology. In contrast, SMARCA4-rNSCLCs often show mild to moderate pleomorphism with round to polygonal shapes. Both characteristically lack expression of lung adenocarcinoma/squamous markers. Increased awareness of their cytomorphologic features on fine needle aspiration can ensure consideration of the diagnosis.
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Affiliation(s)
- Oluwaseun B Ogunbona
- Department of Pathology and Laboratory Medicine, Emory University Hospital Midtown, Emory University School of Medicine, Atlanta, Georgia; Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Xiaoqi Lin
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Jason L Hornick
- Department of Pathology, Harvard Medical School, Brigham & Women's Hospital, Boston, Massachusetts
| | - Daniel J Lubin
- Department of Pathology and Laboratory Medicine, Emory University Hospital Midtown, Emory University School of Medicine, Atlanta, Georgia
| | - Qun Wang
- Department of Pathology and Laboratory Medicine, Emory University Hospital Midtown, Emory University School of Medicine, Atlanta, Georgia
| | - Michelle D Reid
- Department of Pathology and Laboratory Medicine, Emory University Hospital Midtown, Emory University School of Medicine, Atlanta, Georgia
| | - Frank Schneider
- Department of Pathology and Laboratory Medicine, Emory University Hospital Midtown, Emory University School of Medicine, Atlanta, Georgia
| | - Dehong Li
- Department of Cancer Center and Drug Development, Clark Atlanta University, Atlanta, Georgia
| | - Dong M Shin
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Qiuying Shi
- Department of Pathology and Laboratory Medicine, Emory University Hospital Midtown, Emory University School of Medicine, Atlanta, Georgia.
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SMARCA4-deficient lung carcinoma is an aggressive tumor highly infiltrated by FOXP3+ cells and neutrophils. Lung Cancer 2022; 169:13-21. [DOI: 10.1016/j.lungcan.2022.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/25/2022] [Accepted: 05/01/2022] [Indexed: 11/19/2022]
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Kannan J, Mathews L, Wu Z, Young NS, Gao S. CAISC: A software to integrate copy number variations and single nucleotide mutations for genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing. BMC Bioinformatics 2022; 23:98. [PMID: 35313800 PMCID: PMC8939069 DOI: 10.1186/s12859-022-04625-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 03/02/2022] [Indexed: 11/26/2022] Open
Abstract
Background Although both copy number variations (CNVs) and single nucleotide variations (SNVs) detected by single-cell RNA sequencing (scRNA-seq) are used to study intratumor heterogeneity and detect clonal groups, a software that integrates these two types of data in the same cells is unavailable. Results We developed Clonal Architecture with Integration of SNV and CNV (CAISC), an R package for scRNA-seq data analysis that clusters single cells into distinct subclones by integrating CNV and SNV genotype matrices using an entropy weighted approach. The performance of CAISC was tested on simulation data and four real datasets, which confirmed its high accuracy in sub-clonal identification and assignment, including subclones which cannot be identified using one type of data alone. Furthermore, integration of SNV and CNV allowed for accurate examination of expression changes between subclones, as demonstrated by the results from trisomy 8 clones of the myelodysplastic syndromes (MDS) dataset. Conclusions CAISC is a powerful tool for integration of CNV and SNV data from scRNA-seq to identify clonal clusters with better accuracy than obtained from a single type of data. CAISC allows users to interactively examine clonal assignments. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04625-x.
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Affiliation(s)
- Jeerthi Kannan
- Hematopoiesis and Bone Marrow Failure Laboratory, Hematology Branch, NHLBI, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Liza Mathews
- Hematopoiesis and Bone Marrow Failure Laboratory, Hematology Branch, NHLBI, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Zhijie Wu
- Hematopoiesis and Bone Marrow Failure Laboratory, Hematology Branch, NHLBI, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Neal S Young
- Hematopoiesis and Bone Marrow Failure Laboratory, Hematology Branch, NHLBI, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Shouguo Gao
- Hematopoiesis and Bone Marrow Failure Laboratory, Hematology Branch, NHLBI, National Institutes of Health, Bethesda, MD, 20892, USA.
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Garinet S, Wang P, Mansuet-Lupo A, Fournel L, Wislez M, Blons H. Updated Prognostic Factors in Localized NSCLC. Cancers (Basel) 2022; 14:cancers14061400. [PMID: 35326552 PMCID: PMC8945995 DOI: 10.3390/cancers14061400] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/06/2022] [Accepted: 03/08/2022] [Indexed: 12/25/2022] Open
Abstract
Lung cancer is the most common cause of cancer mortality worldwide, and non-small cell lung cancer (NSCLC) represents 80% of lung cancer subtypes. Patients with localized non-small cell lung cancer may be considered for upfront surgical treatment. However, the overall 5-year survival rate is 59%. To improve survival, adjuvant chemotherapy (ACT) was largely explored and showed an overall benefit of survival at 5 years < 7%. The evaluation of recurrence risk and subsequent need for ACT is only based on tumor stage (TNM classification); however, more than 25% of patients with stage IA/B tumors will relapse. Recently, adjuvant targeted therapy has been approved for EGFR-mutated resected NSCLC and trials are evaluating other targeted therapies and immunotherapies in adjuvant settings. Costs, treatment duration, emergence of resistant clones and side effects stress the need for a better selection of patients. The identification and validation of prognostic and theranostic markers to better stratify patients who could benefit from adjuvant therapies are needed. In this review, we report current validated clinical, pathological and molecular prognosis biomarkers that influence outcome in resected NSCLC, and we also describe molecular biomarkers under evaluation that could be available in daily practice to drive ACT in resected NSCLC.
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Affiliation(s)
- Simon Garinet
- Pharmacogenomics and Molecular Oncology Unit, Biochemistry Department, Assistance Publique—Hopitaux de Paris, Hôpital Européen Georges Pompidou, 75015 Paris, France;
- Centre de Recherche des Cordeliers, INSERM UMRS-1138, Sorbonne Université, Université de Paris, 75006 Paris, France
| | - Pascal Wang
- Oncology Thoracic Unit, Pulmonology Department, Assistance Publique—Hopitaux de Paris, Hôpital Cochin, 75014 Paris, France; (P.W.); (M.W.)
| | - Audrey Mansuet-Lupo
- Pathology Department, Assistance Publique—Hopitaux de Paris, Hôpital Cochin, 75014 Paris, France;
| | - Ludovic Fournel
- Thoracic Surgery Department, Assistance Publique—Hopitaux de Paris, Hôpital Cochin, 75014 Paris, France;
| | - Marie Wislez
- Oncology Thoracic Unit, Pulmonology Department, Assistance Publique—Hopitaux de Paris, Hôpital Cochin, 75014 Paris, France; (P.W.); (M.W.)
| | - Hélène Blons
- Pharmacogenomics and Molecular Oncology Unit, Biochemistry Department, Assistance Publique—Hopitaux de Paris, Hôpital Européen Georges Pompidou, 75015 Paris, France;
- Centre de Recherche des Cordeliers, INSERM UMRS-1138, Sorbonne Université, Université de Paris, 75006 Paris, France
- Correspondence:
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Abstract
Actin is a highly conserved protein in mammals. The actin dynamics is regulated by actin-binding proteins and actin-related proteins. Nuclear actin and these regulatory proteins participate in multiple nuclear processes, including chromosome architecture organization, chromatin remodeling, transcription machinery regulation, and DNA repair. It is well known that the dysfunctions of these processes contribute to the development of cancer. Moreover, emerging evidence has shown that the deregulated actin dynamics is also related to cancer. This chapter discusses how the deregulation of nuclear actin dynamics contributes to tumorigenesis via such various nuclear events.
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Affiliation(s)
- Yuanjian Huang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Shengzhe Zhang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jae-Il Park
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center and Health Science Center, Houston, TX, USA.
- Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Smith JJ, Xiao Y, Parsan N, Medwig-Kinney TN, Martinez MAQ, Moore FEQ, Palmisano NJ, Kohrman AQ, Chandhok Delos Reyes M, Adikes RC, Liu S, Bracht SA, Zhang W, Wen K, Kratsios P, Matus DQ. The SWI/SNF chromatin remodeling assemblies BAF and PBAF differentially regulate cell cycle exit and cellular invasion in vivo. PLoS Genet 2022; 18:e1009981. [PMID: 34982771 PMCID: PMC8759636 DOI: 10.1371/journal.pgen.1009981] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 01/14/2022] [Accepted: 12/07/2021] [Indexed: 12/15/2022] Open
Abstract
Chromatin remodelers such as the SWI/SNF complex coordinate metazoan development through broad regulation of chromatin accessibility and transcription, ensuring normal cell cycle control and cellular differentiation in a lineage-specific and temporally restricted manner. Mutations in genes encoding the structural subunits of chromatin, such as histone subunits, and chromatin regulating factors are associated with a variety of disease mechanisms including cancer metastasis, in which cancer co-opts cellular invasion programs functioning in healthy cells during development. Here we utilize Caenorhabditis elegans anchor cell (AC) invasion as an in vivo model to identify the suite of chromatin agents and chromatin regulating factors that promote cellular invasiveness. We demonstrate that the SWI/SNF ATP-dependent chromatin remodeling complex is a critical regulator of AC invasion, with pleiotropic effects on both G0 cell cycle arrest and activation of invasive machinery. Using targeted protein degradation and enhanced RNA interference (RNAi) vectors, we show that SWI/SNF contributes to AC invasion in a dose-dependent fashion, with lower levels of activity in the AC corresponding to aberrant cell cycle entry and increased loss of invasion. Our data specifically implicate the SWI/SNF BAF assembly in the regulation of the G0 cell cycle arrest in the AC, whereas the SWI/SNF PBAF assembly promotes AC invasion via cell cycle-independent mechanisms, including attachment to the basement membrane (BM) and activation of the pro-invasive fos-1/FOS gene. Together these findings demonstrate that the SWI/SNF complex is necessary for two essential components of AC invasion: arresting cell cycle progression and remodeling the BM. The work here provides valuable single-cell mechanistic insight into how the SWI/SNF assemblies differentially contribute to cellular invasion and how SWI/SNF subunit-specific disruptions may contribute to tumorigeneses and cancer metastasis. Cellular invasion is required for animal development and homeostasis. Inappropriate activation of invasion however can result in cancer metastasis. Invasion programs are orchestrated by complex gene regulatory networks (GRN) that function in a coordinated fashion to turn on and off pro-invasive genes. While the core of GRNs are DNA binding transcription factors, they require aid from chromatin remodelers to access the genome. To identify the suite of pro-invasive chromatin remodelers, we paired high resolution imaging with RNA interference to individually knockdown 269 chromatin factors, identifying the evolutionarily conserved SWItching defective/Sucrose Non-Fermenting (SWI/SNF) ATP-dependent chromatin remodeling complex as a new regulator of Caenorhabditis elegans anchor cell (AC) invasion. Using a combination of CRISPR/Cas9 genome engineering and targeted protein degradation we demonstrate that the core SWI/SNF complex functions in a dose-dependent manner to control invasion. Further, we determine that the accessory SWI/SNF complexes, BAF and PBAF, contribute to invasion via distinctive mechanisms: BAF is required to prevent inappropriate proliferation while PBAF promotes AC attachment and remodeling of the basement membrane. Together, our data provide insights into how the SWI/SNF complex, which is mutated in many human cancers, can function in a dose-dependent fashion to regulate switching from invasive to proliferative fates.
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Affiliation(s)
- Jayson J. Smith
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Yutong Xiao
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Nithin Parsan
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
- Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Taylor N. Medwig-Kinney
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Michael A. Q. Martinez
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Frances E. Q. Moore
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Nicholas J. Palmisano
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Abraham Q. Kohrman
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Mana Chandhok Delos Reyes
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Rebecca C. Adikes
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
- Biology Department, Siena College, Loudonville, New York, United States of America
| | - Simeiyun Liu
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
- Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Sydney A. Bracht
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
- Department of Cell Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Wan Zhang
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Kailong Wen
- The Grossman Institute for Neuroscience, Quantitative Biology, and Human Behavior, University of Chicago, Chicago, Illinois, United States of America
- Department of Neurobiology, University of Chicago, Chicago, Illinois, United States of America
| | - Paschalis Kratsios
- The Grossman Institute for Neuroscience, Quantitative Biology, and Human Behavior, University of Chicago, Chicago, Illinois, United States of America
- Department of Neurobiology, University of Chicago, Chicago, Illinois, United States of America
| | - David Q. Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
- * E-mail:
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