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Xi S, Jiang S, Li H, Huang Q, Lu J, Zhang X, Li Z, Zeng J. Adult epithelioid glioblastoma exhibits an extremely poor prognosis and high frequency of SWI/SNF complex mutation: Insights from a retrospective study. Int J Cancer 2024; 155:172-183. [PMID: 38411299 DOI: 10.1002/ijc.34854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/25/2023] [Accepted: 01/03/2024] [Indexed: 02/28/2024]
Abstract
Epithelioid glioblastoma (eGBM) is a rare subtype of GBM. Given the update of the definition of GBM, the understanding of the molecular characteristics and prognosis of "true" adult eGBM remains limited. Herein, we retrospectively analyzed the clinicopathological data of 39 adult eGBM cases. Adult eGBM primarily affected females, with a male-to-female ratio of 1:2.3. The average age of diagnosis was 53 years, and the tumor affected the temporal lobe in 41% of cases (16/39, 41%). Microscopically, the tumors consisted mainly or entirely of epithelioid cells. Perivascular infiltration (10/39, 25.6%) and leptomeningeal dissemination (7/39, 17.9%) were not uncommon. BRAF V600E mutation was detected in 40.9% of cases (n = 9/22). Next-generation sequencing revealed that CDKN2A/B homogeneous deletion was the most frequently mutated gene (8/10, 80%), followed by TERT promoter mutation (7/10, 70%), Cyclin-dependent kinases 4 or 6 (CDK4/6) amplification (5/10, 50%) and BRAF V600E mutation (50%, 5/10). Notably, the incidence of ARID1B mutation in eGBM was 50% (5/10), representing the first report of such a mutation in this subtype of GBM. ARID1B was known to be a subunit of the SWI/SNF chromatin remodeler. Chromosome analysis showed a 7+/10- signature in 90% (9/10) cases. Adult eGBM carried a dismal prognosis compared to GBM with IDH and H3 wild-type (typical GBM) (OS: 13.89 vs 24.30 months; P = .003) and even typical GBM without MGMT promoter methylation (OS: 13.89 vs 22.08 months; P = .036). Based on these findings, it can be concluded that adult eGBM harbors a high frequency of the 7+/10- signature and alterations in the MAPK pathway, SWI/SNF complex and cyclin-related genes and portends an extremely poor prognosis.
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Affiliation(s)
- Shaoyan Xi
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Shimeng Jiang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Hainan Li
- Department of Pathology, Guangdong Sanjiu Brain Hospital, Guangzhou, China
| | - Qitao Huang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jiabin Lu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xing Zhang
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co, Ltd, Nanjing, China
| | - Zhi Li
- Department of Pathology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Jing Zeng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
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2
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Yang S, Kim SH, Yang E, Kang M, Joo JY. Molecular insights into regulatory RNAs in the cellular machinery. Exp Mol Med 2024:10.1038/s12276-024-01239-6. [PMID: 38871819 DOI: 10.1038/s12276-024-01239-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/27/2024] [Accepted: 03/05/2024] [Indexed: 06/15/2024] Open
Abstract
It is apparent that various functional units within the cellular machinery are derived from RNAs. The evolution of sequencing techniques has resulted in significant insights into approaches for transcriptome studies. Organisms utilize RNA to govern cellular systems, and a heterogeneous class of RNAs is involved in regulatory functions. In particular, regulatory RNAs are increasingly recognized to participate in intricately functioning machinery across almost all levels of biological systems. These systems include those mediating chromatin arrangement, transcription, suborganelle stabilization, and posttranscriptional modifications. Any class of RNA exhibiting regulatory activity can be termed a class of regulatory RNA and is typically represented by noncoding RNAs, which constitute a substantial portion of the genome. These RNAs function based on the principle of structural changes through cis and/or trans regulation to facilitate mutual RNA‒RNA, RNA‒DNA, and RNA‒protein interactions. It has not been clearly elucidated whether regulatory RNAs identified through deep sequencing actually function in the anticipated mechanisms. This review addresses the dominant properties of regulatory RNAs at various layers of the cellular machinery and covers regulatory activities, structural dynamics, modifications, associated molecules, and further challenges related to therapeutics and deep learning.
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Affiliation(s)
- Sumin Yang
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea
| | - Sung-Hyun Kim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea
| | - Eunjeong Yang
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea
| | - Mingon Kang
- Department of Computer Science, University of Nevada, Las Vegas, NV, 89154, USA
| | - Jae-Yeol Joo
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea.
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Kraemer M, Zander T, Alakus H, Buettner R, Lyu SI, Simon AG, Schroeder W, Bruns CJ, Quaas A. Fetal gut cell-like differentiation in esophageal adenocarcinoma defines a rare tumor subtype with therapeutically relevant claudin-6 positivity and SWI/SNF gene alteration. Sci Rep 2024; 14:13474. [PMID: 38866822 PMCID: PMC11169473 DOI: 10.1038/s41598-024-64116-2] [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: 09/14/2023] [Accepted: 06/05/2024] [Indexed: 06/14/2024] Open
Abstract
Esophageal adenocarcinoma (EAC) is one of the deadliest tumor entities worldwide, with a 5-year survival rate of less than 25%. Unlike other tumor entities, personalized therapy options are rare, partly due to the lack of knowledge about specific subgroups. In this publication, we demonstrate a subgroup of patients with EAC in a large screening cohort of 826 patients, characterized by specific morphological and immunohistochemical features. This subgroup represents approximately 0.7% (6/826) of the total cohort. Morphological features of this subgroup show a striking clear cytoplasm of the tumour cells and the parallel existence of rare growth patterns like yolk sac-like differentiation and enteroblastic differentiation. Immunohistochemistry reveals expression of the fetal gut cell-like proteins Sal-like protein 4 (SALL4), claudin-6, and glypican 3. Interestingly, we find a correlation with alterations of SWI/SNF-complex associated genes, which are supposed to serve as tumor suppressor genes in various tumour entities. Our results suggest a possible implication of rare tumour subtypes in the WHO classification for EACs according to the classification for gastric cancer. Furthermore, claudin-6 positive tumors have shown promising efficacy of CAR T cell therapy in the recently published BNT-211-01 trial (NCT04503278). This represents a personalized therapeutic option for this tumor subtype.
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Affiliation(s)
- Max Kraemer
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Gastrointestinal Cancer Group Cologne GCGC, University of Cologne, Kerpener Str. 62, 50937, Cologne, Germany.
| | - Thomas Zander
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Gastrointestinal Cancer Group Cologne GCGC, University of Cologne, Kerpener Str. 62, 50937, Cologne, Germany
| | - Hakan Alakus
- Department of General, Visceral, Cancer and Transplantation Surgery, University Hospital Cologne, Cologne, Germany
| | - Reinhard Buettner
- Faculty of Medicine, University Hospital of Cologne, Institute of Pathology, University of Cologne, Cologne, Germany
| | - Su Ir Lyu
- Faculty of Medicine, University Hospital of Cologne, Institute of Pathology, University of Cologne, Cologne, Germany
| | - Adrian Georg Simon
- Faculty of Medicine, University Hospital of Cologne, Institute of Pathology, University of Cologne, Cologne, Germany
| | - Wolfgang Schroeder
- Department of General, Visceral, Cancer and Transplantation Surgery, University Hospital Cologne, Cologne, Germany
| | - Christiane J Bruns
- Department of General, Visceral, Cancer and Transplantation Surgery, University Hospital Cologne, Cologne, Germany
| | - Alexander Quaas
- Faculty of Medicine, University Hospital of Cologne, Institute of Pathology, University of Cologne, Cologne, Germany
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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] [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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Bakr A, Corte GD, Veselinov O, Kelekçi S, Chen MJM, Lin YY, Sigismondo G, Iacovone M, Cross A, Syed R, Jeong Y, Sollier E, Liu CS, Lutsik P, Krijgsveld J, Weichenhan D, Plass C, Popanda O, Schmezer P. ARID1A regulates DNA repair through chromatin organization and its deficiency triggers DNA damage-mediated anti-tumor immune response. Nucleic Acids Res 2024; 52:5698-5719. [PMID: 38587186 PMCID: PMC11162808 DOI: 10.1093/nar/gkae233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 02/27/2024] [Accepted: 03/21/2024] [Indexed: 04/09/2024] Open
Abstract
AT-rich interaction domain protein 1A (ARID1A), a SWI/SNF chromatin remodeling complex subunit, is frequently mutated across various cancer entities. Loss of ARID1A leads to DNA repair defects. Here, we show that ARID1A plays epigenetic roles to promote both DNA double-strand breaks (DSBs) repair pathways, non-homologous end-joining (NHEJ) and homologous recombination (HR). ARID1A is accumulated at DSBs after DNA damage and regulates chromatin loops formation by recruiting RAD21 and CTCF to DSBs. Simultaneously, ARID1A facilitates transcription silencing at DSBs in transcriptionally active chromatin by recruiting HDAC1 and RSF1 to control the distribution of activating histone marks, chromatin accessibility, and eviction of RNAPII. ARID1A depletion resulted in enhanced accumulation of micronuclei, activation of cGAS-STING pathway, and an increased expression of immunomodulatory cytokines upon ionizing radiation. Furthermore, low ARID1A expression in cancer patients receiving radiotherapy was associated with higher infiltration of several immune cells. The high mutation rate of ARID1A in various cancer types highlights its clinical relevance as a promising biomarker that correlates with the level of immune regulatory cytokines and estimates the levels of tumor-infiltrating immune cells, which can predict the response to the combination of radio- and immunotherapy.
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Affiliation(s)
- Ali Bakr
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Giuditta Della Corte
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Olivera Veselinov
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Simge Kelekçi
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Mei-Ju May Chen
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Yu-Yu Lin
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Gianluca Sigismondo
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), INF581, 69120 Heidelberg, Germany
| | - Marika Iacovone
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Alice Cross
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Rabail Syed
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Yunhee Jeong
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Etienne Sollier
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Chun- Shan Liu
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Jeroen Krijgsveld
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), INF581, 69120 Heidelberg, Germany
- Heidelberg University, Medical Faculty, Heidelberg, Germany
| | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), INF280, 69120 Heidelberg, Germany
| | - Odilia Popanda
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Peter Schmezer
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
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Onoprienko A, Hofstetter G, Muellauer L, Dorittke T, Polterauer S, Grimm C, Bartl T. Prognostic role of transcription factor ARID1A in patients with endometrial cancer of no specific molecular profile (NSMP) subtype. Int J Gynecol Cancer 2024; 34:840-846. [PMID: 38508586 DOI: 10.1136/ijgc-2023-005111] [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: 03/22/2024] Open
Abstract
OBJECTIVE As more than 50% of newly diagnosed endometrial cancers remain classified as 'no specific molecular subtype' (NSMP) due to a lack of established biomarkers to further improve molecular subtyping, this study aims to evaluate the prognostic value of ARID1A in endometrial cancers of NSMP subtype. METHODS Prospectively collected molecular profiling data of all consecutive patients with endometrial cancer who underwent primary surgery at our department between August 2017 and June 2022 and for whom both molecular profiling and clinical follow-up data were available were retrospectively evaluated. Tumor specimens were evaluated by combined mismatch repair protein immunohistochemistry and targeted next-generation hotspot sequencing. ARID1A mutational status, as defined by full-length gene sequencing, was matched with risk of recurrence, progression-free and disease-specific survival within the NSMP cohort. RESULTS A total of 127 patients with endometrial cancer were included. Among 72 patients with tumors of NSMP subtype (56.7%), ARID1A mutations were identified in 24 cases (33.3%). ARID1A mutations were significantly associated with a higher risk of recurrence (37.5% vs 12.5%, OR 4.20, 95% CI 1.28 to 13.80, p=0.018) and impaired progression-free survival (HR 3.96, 95% CI 1.41 to 11.15, p=0.009), but not with disease-specific survival. The results for both risk of recurrence (OR 3.70, 95% CI 1.04 to 13.13, p=0.043) and progression-free survival (HR 3.19, 95% CI 1.10 to 9.25, p=0.033) were confirmed in multivariable analysis compared with advanced tumor stage International Federation of Gynecology and Obstetrics (2009) (FIGO ≥III) and impaired Eastern Clinical Oncology Group performance status (ECOG ≥1). CONCLUSION ARID1A appears to identify patients with endometrial cancer of NSMP subtypes with a higher risk of recurrence and could be used as a future prognostic biomarker. After clinical validation, ARID1A assessment could help to further sub-classify selected endometrial cancers and improve personalized treatment strategies.
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Affiliation(s)
- Arina Onoprienko
- Department of Obstetrics and Gynecology, Division of General Gynecology and Gynecologic Oncology, Medical University of Vienna, Vienna, Austria
| | - Gerda Hofstetter
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | | | - Tim Dorittke
- Department of Obstetrics and Gynecology, Division of General Gynecology and Gynecologic Oncology, Medical University of Vienna, Vienna, Austria
| | - Stephan Polterauer
- Department of Obstetrics and Gynecology, Division of General Gynecology and Gynecologic Oncology, Medical University of Vienna, Vienna, Austria
| | - Christoph Grimm
- Department of Obstetrics and Gynecology, Division of General Gynecology and Gynecologic Oncology, Medical University of Vienna, Vienna, Austria
| | - Thomas Bartl
- Department of Obstetrics and Gynecology, Division of General Gynecology and Gynecologic Oncology, Medical University of Vienna, Vienna, Austria
- Translational Gynecology Group, Department of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
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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] [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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Garg S, Ni W, Chowdhury B, Weisberg EL, Sattler M, Griffin JD. BRD9 regulates normal human hematopoietic stem cell function and lineage differentiation. Cell Death Differ 2024:10.1038/s41418-024-01306-5. [PMID: 38816579 DOI: 10.1038/s41418-024-01306-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/23/2024] [Accepted: 04/25/2024] [Indexed: 06/01/2024] Open
Abstract
Bromodomain containing protein 9 (BRD9), a member of the non-canonical BRG1/BRM-associated factor (ncBAF) chromatin remodeling complex, has been implicated as a synthetic lethal target in AML but its function in normal human hematopoiesis is unknown. In hematopoietic stem and progenitor cells (HSPC) genomic or chemical inhibition of BRD9 led to a proliferative disadvantage and loss of stem cells in vitro. Human HSPCs with reduced BRD9 protein levels produced lower numbers of immature mixed multipotent GEMM colonies in semi-solid media. In lineage-promoting culture conditions, cells with reduced BRD9 levels failed to differentiate into the megakaryocytic lineage and showed delayed differentiation into erythroid cells but enhanced terminal myeloid differentiation. HSPCs with BRD9 knock down (KD) had reduced long-term multilineage engraftment in a xenotransplantation assay. An increased number of downregulated genes in RNAseq analysis after BRD9 KD coupled with a gain in chromatin accessibility at the promoters of several repressive transcription factors (TF) suggest that BRD9 functions in the maintenance of active transcription during HSC differentiation. In particular, the hematopoietic master regulator GATA1 was identified as one of the core TFs regulating the gene networks modulated by BRD9 loss in HSPCs. BRD9 inhibition reduced a GATA1-luciferase reporter signal, further suggesting a role for BRD9 in regulating GATA1 activity. BRD9 is therefore an additional example of epigenetic regulation of human hematopoiesis.
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Affiliation(s)
- Swati Garg
- Dana-Farber Cancer Institute, Dept. of Medical Oncology, Boston, MA, 02215, USA
- Harvard Medical School, Dept. of Medicine, Boston, MA, 02215, USA
| | - Wei Ni
- Dana-Farber Cancer Institute, Dept. of Medical Oncology, Boston, MA, 02215, USA
- Harvard Medical School, Dept. of Medicine, Boston, MA, 02215, USA
| | - Basudev Chowdhury
- Dana-Farber Cancer Institute, Dept. of Medical Oncology, Boston, MA, 02215, USA
- Harvard Medical School, Dept. of Medicine, Boston, MA, 02215, USA
| | - Ellen L Weisberg
- Dana-Farber Cancer Institute, Dept. of Medical Oncology, Boston, MA, 02215, USA
- Harvard Medical School, Dept. of Medicine, Boston, MA, 02215, USA
| | - Martin Sattler
- Dana-Farber Cancer Institute, Dept. of Medical Oncology, Boston, MA, 02215, USA
- Harvard Medical School, Dept. of Medicine, Boston, MA, 02215, USA
| | - James D Griffin
- Dana-Farber Cancer Institute, Dept. of Medical Oncology, Boston, MA, 02215, USA.
- Harvard Medical School, Dept. of Medicine, Boston, MA, 02215, USA.
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9
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Zhang M, Guo T, Pei F, Feng J, Jing J, Xu J, Yamada T, Ho TV, Du J, Sehgal P, Chai Y. ARID1B maintains mesenchymal stem cell quiescence via inhibition of BCL11B-mediated non-canonical Activin signaling. Nat Commun 2024; 15:4614. [PMID: 38816354 PMCID: PMC11139927 DOI: 10.1038/s41467-024-48285-2] [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: 08/11/2023] [Accepted: 04/24/2024] [Indexed: 06/01/2024] Open
Abstract
ARID1B haploinsufficiency in humans causes Coffin-Siris syndrome, associated with developmental delay, facial dysmorphism, and intellectual disability. The role of ARID1B has been widely studied in neuronal development, but whether it also regulates stem cells remains unknown. Here, we employ scRNA-seq and scATAC-seq to dissect the regulatory functions and mechanisms of ARID1B within mesenchymal stem cells (MSCs) using the mouse incisor model. We reveal that loss of Arid1b in the GLI1+ MSC lineage disturbs MSCs' quiescence and leads to their proliferation due to the ectopic activation of non-canonical Activin signaling via p-ERK. Furthermore, loss of Arid1b upregulates Bcl11b, which encodes a BAF complex subunit that modulates non-canonical Activin signaling by directly regulating the expression of activin A subunit, Inhba. Reduction of Bcl11b or non-canonical Activin signaling restores the MSC population in Arid1b mutant mice. Notably, we have identified that ARID1B suppresses Bcl11b expression via specific binding to its third intron, unveiling the direct inter-regulatory interactions among BAF subunits in MSCs. Our results demonstrate the vital role of ARID1B as an epigenetic modifier in maintaining MSC homeostasis and reveal its intricate mechanistic regulatory network in vivo, providing novel insights into the linkage between chromatin remodeling and stem cell fate determination.
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Affiliation(s)
- Mingyi Zhang
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA, 90033, USA
| | - Tingwei Guo
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA, 90033, USA
| | - Fei Pei
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA, 90033, USA
| | - Jifan Feng
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA, 90033, USA
| | - Junjun Jing
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA, 90033, USA
| | - Jian Xu
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA, 90033, USA
| | - Takahiko Yamada
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA, 90033, USA
| | - Thach-Vu Ho
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA, 90033, USA
| | - Jiahui Du
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA, 90033, USA
| | - Prerna Sehgal
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA, 90033, USA
| | - Yang Chai
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA, 90033, USA.
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10
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Liu W, Kurkewich JL, Stoddart A, Khan S, Anandan D, Gaubil AN, Wolfgeher DJ, Jueng L, Kron SJ, McNerney ME. CUX1 regulates human hematopoietic stem cell chromatin accessibility via the BAF complex. Cell Rep 2024; 43:114227. [PMID: 38735044 PMCID: PMC11163479 DOI: 10.1016/j.celrep.2024.114227] [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: 07/27/2023] [Revised: 03/16/2024] [Accepted: 04/26/2024] [Indexed: 05/14/2024] Open
Abstract
CUX1 is a homeodomain-containing transcription factor that is essential for the development and differentiation of multiple tissues. CUX1 is recurrently mutated or deleted in cancer, particularly in myeloid malignancies. However, the mechanism by which CUX1 regulates gene expression and differentiation remains poorly understood, creating a barrier to understanding the tumor-suppressive functions of CUX1. Here, we demonstrate that CUX1 directs the BAF chromatin remodeling complex to DNA to increase chromatin accessibility in hematopoietic cells. CUX1 preferentially regulates lineage-specific enhancers, and CUX1 target genes are predictive of cell fate in vivo. These data indicate that CUX1 regulates hematopoietic lineage commitment and homeostasis via pioneer factor activity, and CUX1 deficiency disrupts these processes in stem and progenitor cells, facilitating transformation.
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Affiliation(s)
- Weihan Liu
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA; Committee on Cancer Biology, The University of Chicago, Chicago, IL 60637, USA
| | | | - Angela Stoddart
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Saira Khan
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Dhivyaa Anandan
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Alexandre N Gaubil
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Donald J Wolfgeher
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Lia Jueng
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Stephen J Kron
- The University of Chicago Medicine Comprehensive Cancer Center, The University of Chicago, Chicago, IL 60637, USA; Committee on Cancer Biology, The University of Chicago, Chicago, IL 60637, USA; Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Megan E McNerney
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA; The University of Chicago Medicine Comprehensive Cancer Center, The University of Chicago, Chicago, IL 60637, USA; Committee on Cancer Biology, The University of Chicago, Chicago, IL 60637, USA; Department of Pediatrics, Section of Hematology/Oncology, The University of Chicago, Chicago, IL 60637, USA.
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11
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He T, Xiao L, Qiao Y, Klingbeil O, Young E, Wu XS, Mannan R, Mahapatra S, Eyunni S, Ching-Yi Tien J, Wang X, Zheng Y, Kim N, Zheng H, Hou S, Su F, Miner SJ, Mehra R, Cao X, Abbineni C, Samajdar S, Ramachandra M, Parolia A, Vakoc CR, Chinnaiyan AM. Targeting the mSWI/SNF Complex in POU2F-POU2AF Transcription Factor-Driven Malignancies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576669. [PMID: 38328238 PMCID: PMC10849552 DOI: 10.1101/2024.01.22.576669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The POU2F3-POU2AF2/3 (OCA-T1/2) transcription factor complex is the master regulator of the tuft cell lineage and tuft cell-like small cell lung cancer (SCLC). Here, we found that the POU2F3 molecular subtype of SCLC (SCLC-P) exhibits an exquisite dependence on the activity of the mammalian switch/sucrose non-fermentable (mSWI/SNF) chromatin remodeling complex. SCLC-P cell lines were sensitive to nanomolar levels of a mSWI/SNF ATPase proteolysis targeting chimera (PROTAC) degrader when compared to other molecular subtypes of SCLC. POU2F3 and its cofactors were found to interact with components of the mSWI/SNF complex. The POU2F3 transcription factor complex was evicted from chromatin upon mSWI/SNF ATPase degradation, leading to attenuation of downstream oncogenic signaling in SCLC-P cells. A novel, orally bioavailable mSWI/SNF ATPase PROTAC degrader, AU-24118, demonstrated preferential efficacy in the SCLC-P relative to the SCLC-A subtype and significantly decreased tumor growth in preclinical models. AU-24118 did not alter normal tuft cell numbers in lung or colon, nor did it exhibit toxicity in mice. B cell malignancies which displayed a dependency on the POU2F1/2 cofactor, POU2AF1 (OCA-B), were also remarkably sensitive to mSWI/SNF ATPase degradation. Mechanistically, mSWI/SNF ATPase degrader treatment in multiple myeloma cells compacted chromatin, dislodged POU2AF1 and IRF4, and decreased IRF4 signaling. In a POU2AF1-dependent, disseminated murine model of multiple myeloma, AU-24118 enhanced survival compared to pomalidomide, an approved treatment for multiple myeloma. Taken together, our studies suggest that POU2F-POU2AF-driven malignancies have an intrinsic dependence on the mSWI/SNF complex, representing a therapeutic vulnerability.
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Affiliation(s)
- Tongchen He
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- These authors contributed equally
| | - Lanbo Xiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- These authors contributed equally
| | - Yuanyuan Qiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Olaf Klingbeil
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Eleanor Young
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Xiaoli S. Wu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Rahul Mannan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Somnath Mahapatra
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Sanjana Eyunni
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Jean Ching-Yi Tien
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Xiaoju Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yang Zheng
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - NamHoon Kim
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Heng Zheng
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Siyu Hou
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Fengyun Su
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Stephanie J. Miner
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Rohit Mehra
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| | | | | | | | - Abhijit Parolia
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | | | - Arul M. Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Urology, University of Michigan, Ann Arbor, MI, USA
- Lead contact
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12
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An HR, Kim HD, Ryu MH, Park YS. SMARCA4-deficient undifferentiated gastric carcinoma: a case series and literature review. Gastric Cancer 2024:10.1007/s10120-024-01510-9. [PMID: 38772975 DOI: 10.1007/s10120-024-01510-9] [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: 03/20/2024] [Accepted: 05/14/2024] [Indexed: 05/23/2024]
Abstract
Undifferentiated gastric carcinoma, characterized by anaplastic cells lacking distinct features of cytological or architectural differentiation, poses diagnostic and therapeutic challenges. Recent studies have suggested an association between this carcinoma and deficiencies in the SWI/SNF complex, particularly mutations in subunits such as SMARCA4. We herein report six cases of SMARCA4-deficient undifferentiated gastric carcinoma with molecular findings, highlighting the rarity and diagnostic pitfalls of this malignancy. Predominantly occurring in males over 50 years, these cases presented with nonspecific symptoms and were often diagnosed at an advanced stage. Histologically, the tumors exhibited a sheet-like growth pattern, reduced or absent epithelial markers, and loss of BRG-1 expression, with molecular analysis confirming SMARCA4 gene mutations. The response to conventional chemotherapy was poor, underscoring the importance of complete surgical resection and the development of alternative treatment modalities.
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Affiliation(s)
- Hyeong Rok An
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, 88, Olympic-Ro 43-Gil, Songpa-Gu, Seoul, 05505, Republic of Korea
| | - Hyung-Don Kim
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, 88, Olympic-Ro 43-Gil, Songpa-Gu, Seoul, 05505, Republic of Korea
| | - Min-Hee Ryu
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, 88, Olympic-Ro 43-Gil, Songpa-Gu, Seoul, 05505, Republic of Korea
| | - Young Soo Park
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, 88, Olympic-Ro 43-Gil, Songpa-Gu, Seoul, 05505, Republic of Korea.
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13
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Cremosnik G, Mesrouze Y, Zueger P, Furkert D, Grandjean F, Argoti D, Mermet-Meillon F, Bauer MR, Brittain S, Rogemoser P, Yang W, Giovannoni J, McGregor L, Tang J, Knapp M, Holzinger S, Buhr S, Muller L, Leder L, Xie L, Fernandez C, Nieto-Oberhuber C, Chène P, Galli GG, Sesterhenn F. mRNA Display Identifies Potent, Paralog-Selective Peptidic Ligands for ARID1B. ACS Chem Biol 2024; 19:1142-1150. [PMID: 38655884 PMCID: PMC11106749 DOI: 10.1021/acschembio.4c00083] [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: 02/02/2024] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 04/26/2024]
Abstract
The ARID1A and ARID1B subunits are mutually exclusive components of the BAF variant of SWI/SNF chromatin remodeling complexes. Loss of function mutations in ARID1A are frequently observed in various cancers, resulting in a dependency on the paralog ARID1B for cancer cell proliferation. However, ARID1B has never been targeted directly, and the high degree of sequence similarity to ARID1A poses a challenge for the development of selective binders. In this study, we used mRNA display to identify peptidic ligands that bind with nanomolar affinities to ARID1B and showed high selectivity over ARID1A. Using orthogonal biochemical, biophysical, and chemical biology tools, we demonstrate that the peptides engage two different binding pockets, one of which directly involves an ARID1B-exclusive cysteine that could allow covalent targeting by small molecules. Our findings impart the first evidence of the ligandability of ARID1B, provide valuable tools for drug discovery, and suggest opportunities for the development of selective molecules to exploit the synthetic lethal relationship between ARID1A and ARID1B in cancer.
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Affiliation(s)
- Gregor
S. Cremosnik
- Global
Discovery Chemistry, Novartis Biomedical
Research, CH-4056 Basel, Switzerland
| | - Yannick Mesrouze
- Disease
area Oncology, Novartis Biomedical Research, CH-4056 Basel, Switzerland
| | - Patrik Zueger
- Global
Discovery Chemistry, Novartis Biomedical
Research, CH-4056 Basel, Switzerland
| | - David Furkert
- Discovery
Sciences, Novartis Biomedical Research, CH-4056 Basel, Switzerland
| | - Frédéric Grandjean
- Discovery
Sciences, Novartis Biomedical Research, CH-4056 Basel, Switzerland
| | - Dayana Argoti
- Global
Discovery Chemistry, Novartis Biomedical
Research, Emeryville, California 94608, United States
| | | | - Matthias R. Bauer
- Global
Discovery Chemistry, Novartis Biomedical
Research, CH-4056 Basel, Switzerland
| | - Scott Brittain
- Discovery
Sciences, Novartis Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Phuong Rogemoser
- Discovery
Sciences, Novartis Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Winnie Yang
- Discovery
Sciences, Novartis Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Jerome Giovannoni
- Discovery
Sciences, Novartis Biomedical Research, CH-4056 Basel, Switzerland
| | - Lynn McGregor
- Discovery
Sciences, Novartis Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Jenny Tang
- Global
Discovery Chemistry, Novartis Biomedical
Research, Emeryville, California 94608, United States
| | - Mark Knapp
- Global
Discovery Chemistry, Novartis Biomedical
Research, Emeryville, California 94608, United States
| | - Sandra Holzinger
- Discovery
Sciences, Novartis Biomedical Research, CH-4056 Basel, Switzerland
| | - Sylvia Buhr
- Discovery
Sciences, Novartis Biomedical Research, CH-4056 Basel, Switzerland
| | - Lionel Muller
- Discovery
Sciences, Novartis Biomedical Research, CH-4056 Basel, Switzerland
| | - Lukas Leder
- Discovery
Sciences, Novartis Biomedical Research, CH-4056 Basel, Switzerland
| | - Lili Xie
- Discovery
Sciences, Novartis Biomedical Research, Emeryville, California 94608, United States
| | - Cesar Fernandez
- Discovery
Sciences, Novartis Biomedical Research, CH-4056 Basel, Switzerland
| | | | - Patrick Chène
- Disease
area Oncology, Novartis Biomedical Research, CH-4056 Basel, Switzerland
| | - Giorgio G. Galli
- Disease
area Oncology, Novartis Biomedical Research, CH-4056 Basel, Switzerland
| | - Fabian Sesterhenn
- Discovery
Sciences, Novartis Biomedical Research, CH-4056 Basel, Switzerland
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14
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Zhao J, Wang L, Zhou A, Wen S, Fang W, Zhang L, Duan J, Bai H, Zhong J, Wan R, Sun B, Zhuang W, Lin Y, He D, Cui L, Wang Z, Wang J. Decision model for durable clinical benefit from front- or late-line immunotherapy alone or with chemotherapy in non-small cell lung cancer. MED 2024:S2666-6340(24)00204-6. [PMID: 38781965 DOI: 10.1016/j.medj.2024.04.011] [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: 12/14/2023] [Revised: 03/19/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND Predictive biomarkers and models of immune checkpoint inhibitors (ICIs) have been extensively studied in non-small cell lung cancer (NSCLC). However, evidence for many biomarkers remains inconclusive, and the opaqueness of machine learning models hinders practicality. We aimed to provide compelling evidence for biomarkers and develop a transparent decision tree model. METHODS We consolidated data from 3,288 ICI-treated patients with NSCLC across real-world multicenter, public cohorts and the Choice-01 trial (ClinicalTrials.gov: NCT03856411). Over 50 features were examined for predicting durable clinical benefits (DCBs) from ICIs. Noteworthy biomarkers were identified to establish a decision tree model. Additionally, we explored the tumor microenvironment and peripheral CD8+ programmed death-1 (PD-1)+ T cell receptor (TCR) profiles. FINDINGS Multivariate logistic regression analysis identified tumor histology, PD-ligand 1 (PD-L1) expression, tumor mutational burden, line, and regimen of ICI treatment as significant factors. Mutation subtypes of EGFR, KRAS, KEAP1, STK11, and disruptive TP53 mutations were associated with DCB. The decision tree (DT10) model, using the ten clinicopathological and genomic markers, showed superior performance in predicting DCB in the training set (area under the curve [AUC] = 0.82) and consistently outperformed other models in test sets. DT10-predicted-DCB patients manifested longer survival, an enriched inflamed tumor immune phenotype (67%), and higher peripheral TCR diversity, whereas the DT10-predicted-NDB (non-durable benefit) group showed an enriched desert immune phenotype (86%) and higher peripheral TCR clonality. CONCLUSIONS The model effectively predicted DCB after front-/subsequent-line ICI treatment, with or without chemotherapy, for squamous and non-squamous lung cancer, offering clinicians valuable insights into efficacy prediction using cost-effective variables. FUNDING This study was supported by the National Key R&D Program of China.
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Affiliation(s)
- Jie Zhao
- State Key Laboratory of Molecular Oncology, CAMS Key Laboratory of Translational Research on Lung Cancer, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences Peking Union Medical College, Beijing 100021, China
| | - Lu Wang
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
| | - Anda Zhou
- School of Informatics, The University of Edinburgh, Edinburgh EH8 9YL, UK
| | - Shidi Wen
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
| | - Wenfeng Fang
- Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou 510060, Guangdong, China
| | - Li Zhang
- Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou 510060, Guangdong, China
| | - Jianchun Duan
- State Key Laboratory of Molecular Oncology, CAMS Key Laboratory of Translational Research on Lung Cancer, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences Peking Union Medical College, Beijing 100021, China
| | - Hua Bai
- State Key Laboratory of Molecular Oncology, CAMS Key Laboratory of Translational Research on Lung Cancer, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences Peking Union Medical College, Beijing 100021, China
| | - Jia Zhong
- State Key Laboratory of Molecular Oncology, CAMS Key Laboratory of Translational Research on Lung Cancer, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences Peking Union Medical College, Beijing 100021, China
| | - Rui Wan
- State Key Laboratory of Molecular Oncology, CAMS Key Laboratory of Translational Research on Lung Cancer, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences Peking Union Medical College, Beijing 100021, China
| | - Boyang Sun
- State Key Laboratory of Molecular Oncology, CAMS Key Laboratory of Translational Research on Lung Cancer, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences Peking Union Medical College, Beijing 100021, China
| | - Wei Zhuang
- State Key Laboratory of Molecular Oncology, CAMS Key Laboratory of Translational Research on Lung Cancer, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences Peking Union Medical College, Beijing 100021, China
| | - Yiwen Lin
- State Key Laboratory of Molecular Oncology, CAMS Key Laboratory of Translational Research on Lung Cancer, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences Peking Union Medical College, Beijing 100021, China
| | - Danming He
- State Key Laboratory of Molecular Oncology, CAMS Key Laboratory of Translational Research on Lung Cancer, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences Peking Union Medical College, Beijing 100021, China
| | - Lina Cui
- Department of Clinical and Translational Medicine, 3D Medicines, Inc., Shanghai, China
| | - Zhijie Wang
- State Key Laboratory of Molecular Oncology, CAMS Key Laboratory of Translational Research on Lung Cancer, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences Peking Union Medical College, Beijing 100021, China.
| | - Jie Wang
- State Key Laboratory of Molecular Oncology, CAMS Key Laboratory of Translational Research on Lung Cancer, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences Peking Union Medical College, Beijing 100021, China.
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15
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Maxwell MB, Hom-Tedla MS, Yi J, Li S, Rivera SA, Yu J, Burns MJ, McRae HM, Stevenson BT, Coakley KE, Ho J, Gastelum KB, Bell JC, Jones AC, Eskander RN, Dykhuizen EC, Shadel GS, Kaech SM, Hargreaves DC. ARID1A suppresses R-loop-mediated STING-type I interferon pathway activation of anti-tumor immunity. Cell 2024:S0092-8674(24)00451-3. [PMID: 38754421 DOI: 10.1016/j.cell.2024.04.025] [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: 11/19/2022] [Revised: 02/26/2024] [Accepted: 04/19/2024] [Indexed: 05/18/2024]
Abstract
Clinical trials have identified ARID1A mutations as enriched among patients who respond favorably to immune checkpoint blockade (ICB) in several solid tumor types independent of microsatellite instability. We show that ARID1A loss in murine models is sufficient to induce anti-tumor immune phenotypes observed in ARID1A mutant human cancers, including increased CD8+ T cell infiltration and cytolytic activity. ARID1A-deficient cancers upregulated an interferon (IFN) gene expression signature, the ARID1A-IFN signature, associated with increased R-loops and cytosolic single-stranded DNA (ssDNA). Overexpression of the R-loop resolving enzyme, RNASEH2B, or cytosolic DNase, TREX1, in ARID1A-deficient cells prevented cytosolic ssDNA accumulation and ARID1A-IFN gene upregulation. Further, the ARID1A-IFN signature and anti-tumor immunity were driven by STING-dependent type I IFN signaling, which was required for improved responsiveness of ARID1A mutant tumors to ICB treatment. These findings define a molecular mechanism underlying anti-tumor immunity in ARID1A mutant cancers.
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Affiliation(s)
- Matthew B Maxwell
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Biological Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92092, USA; NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Marianne S Hom-Tedla
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Department of Gynecologic Oncology, University of California, San Diego, San Diego, CA, USA
| | - Jawoon Yi
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Shitian Li
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Biological Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92092, USA; NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Samuel A Rivera
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Biological Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92092, USA; NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jingting Yu
- Integrative Genomics and Bioinformatics Core, Salk Institute of Biological Studies, La Jolla, CA 92037, USA
| | - Mannix J Burns
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Helen M McRae
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Braden T Stevenson
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Katherine E Coakley
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Department of Gynecologic Oncology, University of California, San Diego, San Diego, CA, USA
| | - Josephine Ho
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | | | - Joshua C Bell
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Alexander C Jones
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Ramez N Eskander
- Center for Personalized Cancer Therapy and Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Sciences, UC San Diego Moores Cancer Center, La Jolla, CA, USA
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Gerald S Shadel
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Susan M Kaech
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Diana C Hargreaves
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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16
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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:jcp-2024-209394. [PMID: 38702192 DOI: 10.1136/jcp-2024-209394] [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: 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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17
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Li X, Tian S, Shi H, Ta N, Ni X, Bai C, Zhu Z, Chen Y, Shi D, Huang H, Chen L, Hu Z, Qu L, Fang Y, Bai C. The golden key to open mystery boxes of SMARCA4-deficient undifferentiated thoracic tumor: focusing immunotherapy, tumor microenvironment and epigenetic regulation. Cancer Gene Ther 2024; 31:687-697. [PMID: 38347129 PMCID: PMC11101339 DOI: 10.1038/s41417-024-00732-4] [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: 07/02/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 02/19/2024]
Abstract
SMARCA4-deficient undifferentiated thoracic tumor is extremely invasive. This tumor with poor prognosis is easily confused with SMARCA4-deficent non-small cell lung cancer or sarcoma. Standard and efficient treatment has not been established. In this review, we summarized the etiology, pathogenesis and diagnosis, reviewed current and proposed innovative strategies for treatment and improving prognosis. Immunotherapy, targeting tumor microenvironment and epigenetic regulator have improved the prognosis of cancer patients. We summarized clinicopathological features and immunotherapy strategies and analyzed the progression-free survival (PFS) and overall survival (OS) of patients with SMARCA4-UT who received immune checkpoint inhibitors (ICIs). In addition, we proposed the feasibility of epigenetic regulation in the treatment of SMARCA4-UT. To our knowledge, this is the first review that aims to explore innovative strategies for targeting tumor microenvironment and epigenetic regulation and identify potential benefit population for immunotherapy to improve the prognosis.
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Affiliation(s)
- Xiang Li
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Naval Medical University (Shanghai Changhai Hospital), Shanghai, China
- Department of Respiratory and Critical Care Medicine, General Hospital of Central Theater Command of the Chinese People's Liberation Army, Wuhan, China
| | - Sen Tian
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Naval Medical University (Shanghai Changhai Hospital), Shanghai, China
- Department of Respiratory and Critical Care Medicine, No. 906 Hospital of the Chinese People's Liberation Army Joint Logistic Support Force, Ningbo, China
| | - Hui Shi
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Naval Medical University (Shanghai Changhai Hospital), Shanghai, China.
| | - Na Ta
- Department of Pathology, the First Affiliated Hospital of Naval Medical University (Shanghai Changhai Hospital), Shanghai, China
| | - Xiang Ni
- Department of Pathology, the First Affiliated Hospital of Naval Medical University (Shanghai Changhai Hospital), Shanghai, China
| | - Chenguang Bai
- Department of Pathology, the First Affiliated Hospital of Naval Medical University (Shanghai Changhai Hospital), Shanghai, China
| | - Zhanli Zhu
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Naval Medical University (Shanghai Changhai Hospital), Shanghai, China
| | - Yilin Chen
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Naval Medical University (Shanghai Changhai Hospital), Shanghai, China
| | - Dongchen Shi
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Naval Medical University (Shanghai Changhai Hospital), Shanghai, China
| | - Haidong Huang
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Naval Medical University (Shanghai Changhai Hospital), Shanghai, China
| | - Longpei Chen
- Department of Oncology, the First Affiliated Hospital of Naval Medical University (Shanghai Changhai Hospital), Shanghai, China
| | - Zhenhong Hu
- Department of Respiratory and Critical Care Medicine, General Hospital of Central Theater Command of the Chinese People's Liberation Army, Wuhan, China
| | - Lei Qu
- Department of Respiratory and Critical Care Medicine, General Hospital of Central Theater Command of the Chinese People's Liberation Army, Wuhan, China
| | - Yao Fang
- Department of Respiratory and Critical Care Medicine, General Hospital of Central Theater Command of the Chinese People's Liberation Army, Wuhan, China
| | - Chong Bai
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Naval Medical University (Shanghai Changhai Hospital), Shanghai, China.
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18
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Bellone S, Jeong K, Halle MK, Krakstad C, McNamara B, Greenman M, Mutlu L, Demirkiran C, Hartwich TMP, Yang-Hartwich Y, Zipponi M, Buza N, Hui P, Raspagliesi F, Lopez S, Paolini B, Milione M, Perrone E, Scambia G, Altwerger G, Ravaggi A, Bignotti E, Huang GS, Andikyan V, Clark M, Ratner E, Azodi M, Schwartz PE, Quick CM, Angioli R, Terranova C, Zaidi S, Nandi S, Alexandrov LB, Siegel ER, Choi J, Schlessinger J, Santin AD. Integrated mutational landscape analysis of poorly differentiated high-grade neuroendocrine carcinoma of the uterine cervix. Proc Natl Acad Sci U S A 2024; 121:e2321898121. [PMID: 38625939 PMCID: PMC11046577 DOI: 10.1073/pnas.2321898121] [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: 12/13/2023] [Accepted: 03/15/2024] [Indexed: 04/18/2024] Open
Abstract
High-grade neuroendocrine cervical cancers (NETc) are exceedingly rare, highly aggressive tumors. We analyzed 64 NETc tumor samples by whole-exome sequencing (WES). Human papillomavirus DNA was detected in 65.6% (42/64) of the tumors. Recurrent mutations were identified in PIK3CA, KMT2D/MLL2, K-RAS, ARID1A, NOTCH2, and RPL10. The top mutated genes included RB1, ARID1A, PTEN, KMT2D/MLL2, and WDFY3, a gene not yet implicated in NETc. Somatic CNV analysis identified two copy number gains (3q27.1 and 19q13.12) and five copy number losses (1p36.21/5q31.3/6p22.2/9q21.11/11p15.5). Also, gene fusions affecting the ACLY-CRHR1 and PVT1-MYC genes were identified in one of the eight samples subjected to RNA sequencing. To resolve evolutionary history, multiregion WES in NETc admixed with adenocarcinoma cells was performed (i.e., mixed-NETc). Phylogenetic analysis of mixed-NETc demonstrated that adenocarcinoma and neuroendocrine elements derive from a common precursor with mutations typical of adenocarcinomas. Over one-third (22/64) of NETc demonstrated a mutator phenotype of C > T at CpG consistent with deficiencies in MBD4, a member of the base excision repair (BER) pathway. Mutations in the PI3K/AMPK pathways were identified in 49/64 samples. We used two patient-derived-xenografts (PDX) (i.e., NET19 and NET21) to evaluate the activity of pan-HER (afatinib), PIK3CA (copanlisib), and ATR (elimusertib) inhibitors, alone and in combination. PDXs harboring alterations in the ERBB2/PI3K/AKT/mTOR/ATR pathway were sensitive to afatinib, copanlisib, and elimusertib (P < 0.001 vs. controls). However, combinations of copanlisib/afatinib and copanlisib/elimusertib were significantly more effective in controlling NETc tumor growth. These findings define the genetic landscape of NETc and suggest that a large subset of these highly lethal malignancies might benefit from existing targeted therapies.
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Affiliation(s)
- Stefania Bellone
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT06510
| | - Kyungjo Jeong
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul02841, Korea
| | - Mari Kyllesø Halle
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen5021, Norway
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen5009, Norway
| | - Camilla Krakstad
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen5021, Norway
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen5009, Norway
| | - Blair McNamara
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT06510
| | - Michelle Greenman
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT06510
| | - Levent Mutlu
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT06510
| | - Cem Demirkiran
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT06510
| | - Tobias Max Philipp Hartwich
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT06510
| | - Yang Yang-Hartwich
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT06510
| | - Margherita Zipponi
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT06510
| | - Natalia Buza
- Department of Pathology, Yale University School of Medicine, New Haven, CT06510
| | - Pei Hui
- Department of Pathology, Yale University School of Medicine, New Haven, CT06510
| | - Francesco Raspagliesi
- First Pathology Division, Fondazione Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Nazionale dei Tumori di Milano, Milano20133, Italy
| | - Salvatore Lopez
- First Pathology Division, Fondazione Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Nazionale dei Tumori di Milano, Milano20133, Italy
| | - Biagio Paolini
- First Pathology Division, Fondazione Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Nazionale dei Tumori di Milano, Milano20133, Italy
| | - Massimo Milione
- First Pathology Division, Fondazione Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Nazionale dei Tumori di Milano, Milano20133, Italy
| | - Emanuele Perrone
- Unit of Gynecologic Oncology, Department Woman and Child Health Sciences and Public Health, Fondazione Policlinico Universitario A. Gemelli Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome00168, Italy
| | - Giovanni Scambia
- Unit of Gynecologic Oncology, Department Woman and Child Health Sciences and Public Health, Fondazione Policlinico Universitario A. Gemelli Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome00168, Italy
| | - Gary Altwerger
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT06510
| | - Antonella Ravaggi
- ”Angelo Nocivelli” Institute of Molecular Medicine, Department of Obstetrics and Gynecology, Azienda Socio Sanitaria Territoriale (ASST) Spedali Civili and University of Brescia, Brescia25123, Italy
| | - Eliana Bignotti
- ”Angelo Nocivelli” Institute of Molecular Medicine, Department of Obstetrics and Gynecology, Azienda Socio Sanitaria Territoriale (ASST) Spedali Civili and University of Brescia, Brescia25123, Italy
| | - Gloria S. Huang
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT06510
| | - Vaagn Andikyan
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT06510
| | - Mitchell Clark
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT06510
| | - Elena Ratner
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT06510
| | - Masoud Azodi
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT06510
| | - Peter E. Schwartz
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT06510
| | - Charles M. Quick
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR72205
| | - Roberto Angioli
- Department of Obstetrics and Gynecology, Università Campus Bio-Medico di Roma, Rome00128, Italy
| | - Corrado Terranova
- Department of Obstetrics and Gynecology, Università Campus Bio-Medico di Roma, Rome00128, Italy
| | - Samir Zaidi
- Department of Genitourinary Oncology, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY10069
| | - Shuvro Nandi
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA92093
| | - Ludmil B. Alexandrov
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA92093
| | - Eric R. Siegel
- Department of Biostatistics, University of Arkansas for Medical Sciences, Little Rock, AR72205
| | - Jungmin Choi
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul02841, Korea
| | - Joseph Schlessinger
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT06520
| | - Alessandro D. Santin
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT06510
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19
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Liang H, Zheng X, Zhang X, Zhang Y, Zheng J. The role of SWI/SNF complexes in digestive system neoplasms. Med Oncol 2024; 41:119. [PMID: 38630164 DOI: 10.1007/s12032-024-02343-3] [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: 01/08/2024] [Accepted: 02/22/2024] [Indexed: 04/19/2024]
Abstract
Chromatin remodeling is a critical step in the DNA damage response, and the ATP-dependent chromatin remodelers are a group of epigenetic regulators that alter nucleosome assembly and regulate transcription factor accessibility to DNA, preventing genomic instability and tumorigenesis caused by DNA damage. The SWI/SNF chromatin remodeling complex is one of them, and mutations in the gene encoding the SWI/SNF subunit are frequently found in digestive tumors. We review the most recent literature on the role of SWI/SNF complexes in digestive tumorigenesis, with different SWI/SNF subunits playing different roles. They regulate the biological behavior of tumor cells, participate in multiple signaling pathways, interact with multiple genes, and have some correlation with the prognosis of patients. Their carcinogenic properties may help discover new therapeutic targets. Understanding the mutations and defects of SWI/SNF complexes, as well as the underlying functional mechanisms, may lead to new strategies for treating the digestive system by targeting relevant genes or modulating the tumor microenvironment.
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Affiliation(s)
- Hanyun Liang
- Department of Diagnostic Pathology, Shandong Second Medical University, Weifang, 261053, China
| | - Xin Zheng
- Department of Diagnostic Pathology, Shandong Second Medical University, Weifang, 261053, China
| | - Xiao Zhang
- Department of Ultrasound, Weifang People's Hospital, Weifang, 261041, China
| | - Yan Zhang
- Department of Pathology, Affiliated Hospital of Shandong Second Medical University, Weifang, 261053, China.
| | - Jie Zheng
- Department of Diagnostic Pathology, Shandong Second Medical University, Weifang, 261053, China.
- Neurologic Disorders and Regenerative Repair Lab of Shandong Higher Education, Shandong Second Medical University, Weifang, 261053, China.
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20
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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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21
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Xu M, Lu X, Zhu F, Sun X, Yao H, Zhang J, Chen W, Zhu H, Liu F, Shi SL, Deng X. BRG1 mediates epigenetic regulation of TNFα-induced CCL2 expression in oral tongue squamous cell carcinoma cells. J Cell Biochem 2024; 125:e30535. [PMID: 38348687 DOI: 10.1002/jcb.30535] [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: 08/23/2023] [Revised: 12/02/2023] [Accepted: 01/30/2024] [Indexed: 04/11/2024]
Abstract
Strong evidence has indicated that upregulation of chemokine (CC motif) ligand-2 (CCL2) expression and the presence of an inflammatory tumor microenvironment significantly contribute to the migratory and invasive properties of oral squamous cell carcinoma, specifically oral tongue squamous cell carcinoma (OTSCC). However, the precise epigenetic mechanism responsible for enhanced CCL2 expression in response to the inflammatory mediator tumor necrosis factor alpha (TNF-α) in OTSCC remains inadequately elucidated. We have demonstrated that the production of CCL2 can be induced by TNF-α, and this induction is mediated by the chromatin remodel protein BRG1. Through the use of a chromatin immunoprecipitation (ChIP) assay, we have found that BRG1 was involved in the recruitment of acetylated histones H3 and H4 at the CCL2 promoter, thereby activating TNF-α-induced CCL2 transcription. Furthermore, we have observed that recruitment of NF-κB p65 to the CCL2 promoter was increased following BRG1 overexpression and decreased after BRG1 knockdown in OTSCC cells. Our Re-ChIP assay has shown that BRG1 knockdown completely inhibits the recruitment of both acetylated histone H3 or H4 and NF-κB to the CCL2 promoter. In summary, the findings of our study demonstrate that BRG1 plays a significant role in mediating the production of CCL2 in OTSCC cells in response to TNF-α stimulation. This process involves the cooperative action of acetylated histone and NF-κB recruitment to the CCL2 promoter site. Our data suggest that BRG1 serves as a critical epigenetic mediator in the regulation of TNF-α-induced CCL2 transcription in OTSCC cells.
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Affiliation(s)
- Mingyan Xu
- School of Stomatology, Fujian Medical University, Fuzhou, China
- Department of Implantology, Stomatological Hospital of Xiamen Medical College & Xiamen Key Laboratory of Stomatological Disease Diagnosis and Treatment, Xiamen, Fujian, China
| | - Xuemei Lu
- Department of Basic Medical Science, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Feixiang Zhu
- Department of Basic Medical Science, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Xue Sun
- Department of Basic Medical Science, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Hongfa Yao
- Department of Implantology, Stomatological Hospital of Xiamen Medical College & Xiamen Key Laboratory of Stomatological Disease Diagnosis and Treatment, Xiamen, Fujian, China
| | - Junling Zhang
- Department of Basic Medical Science, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Weishi Chen
- Department of Stomatology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, Zhejiang, China
| | - Haohao Zhu
- Department of Pathology, The 908th Hospital of Chinese People's Liberation Army Joint Logistic Support Force, Nanchang, Jiangxi, China
| | - Fan Liu
- Department of Basic Medical Science, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Song Lin Shi
- Department of Basic Medical Science, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Xiaoling Deng
- Department of Basic Medical Science, School of Medicine, Xiamen University, Xiamen, Fujian, China
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22
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Radko-Juettner S, Yue H, Myers JA, Carter RD, Robertson AN, Mittal P, Zhu Z, Hansen BS, Donovan KA, Hunkeler M, Rosikiewicz W, Wu Z, McReynolds MG, Roy Burman SS, Schmoker AM, Mageed N, Brown SA, Mobley RJ, Partridge JF, Stewart EA, Pruett-Miller SM, Nabet B, Peng J, Gray NS, Fischer ES, Roberts CWM. Targeting DCAF5 suppresses SMARCB1-mutant cancer by stabilizing SWI/SNF. Nature 2024; 628:442-449. [PMID: 38538798 DOI: 10.1038/s41586-024-07250-1] [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: 10/18/2022] [Accepted: 02/28/2024] [Indexed: 04/06/2024]
Abstract
Whereas oncogenes can potentially be inhibited with small molecules, the loss of tumour suppressors is more common and is problematic because the tumour-suppressor proteins are no longer present to be targeted. Notable examples include SMARCB1-mutant cancers, which are highly lethal malignancies driven by the inactivation of a subunit of SWI/SNF (also known as BAF) chromatin-remodelling complexes. Here, to generate mechanistic insights into the consequences of SMARCB1 mutation and to identify vulnerabilities, we contributed 14 SMARCB1-mutant cell lines to a near genome-wide CRISPR screen as part of the Cancer Dependency Map Project1-3. We report that the little-studied gene DDB1-CUL4-associated factor 5 (DCAF5) is required for the survival of SMARCB1-mutant cancers. We show that DCAF5 has a quality-control function for SWI/SNF complexes and promotes the degradation of incompletely assembled SWI/SNF complexes in the absence of SMARCB1. After depletion of DCAF5, SMARCB1-deficient SWI/SNF complexes reaccumulate, bind to target loci and restore SWI/SNF-mediated gene expression to levels that are sufficient to reverse the cancer state, including in vivo. Consequently, cancer results not from the loss of SMARCB1 function per se, but rather from DCAF5-mediated degradation of SWI/SNF complexes. These data indicate that therapeutic targeting of ubiquitin-mediated quality-control factors may effectively reverse the malignant state of some cancers driven by disruption of tumour suppressor complexes.
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Affiliation(s)
- Sandi Radko-Juettner
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
- St Jude Graduate School of Biomedical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Hong Yue
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jacquelyn A Myers
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Raymond D Carter
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Alexis N Robertson
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Priya Mittal
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Zhexin Zhu
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Baranda S Hansen
- Department of Cell and Molecular Biology, St Jude Children's Research Hospital, Memphis, TN, USA
- The Center for Advanced Genome Engineering, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Moritz Hunkeler
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Wojciech Rosikiewicz
- Center for Applied Bioinformatics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Zhiping Wu
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Meghan G McReynolds
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Shourya S Roy Burman
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Anna M Schmoker
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Nada Mageed
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Scott A Brown
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Robert J Mobley
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Janet F Partridge
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Elizabeth A Stewart
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
- Cancer Center, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology, St Jude Children's Research Hospital, Memphis, TN, USA
- The Center for Advanced Genome Engineering, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Behnam Nabet
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Junmin Peng
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, Stanford Medicine, Stanford, CA, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
| | - Charles W M Roberts
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA.
- Cancer Center, St Jude Children's Research Hospital, Memphis, TN, USA.
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23
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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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24
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Grunewald TGP, Postel-Vinay S, Nakayama RT, Berlow NE, Bolzicco A, Cerullo V, Dermawan JK, Frezza AM, Italiano A, Jin JX, Loarer FL, Martin-Broto J, Pecora A, Perez-Martinez A, Tam YB, Tirode F, Trama A, Pasquali S, Vescia M, ortmann L, Wortmann M, Yoshida A, Webb K, Huang PH, Keller C, Antonescu CR. Translational Aspects of Epithelioid Sarcoma: Current Consensus. Clin Cancer Res 2024; 30:1079-1092. [PMID: 37916971 PMCID: PMC10947972 DOI: 10.1158/1078-0432.ccr-23-2174] [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: 07/19/2023] [Revised: 09/12/2023] [Accepted: 10/20/2023] [Indexed: 11/03/2023]
Abstract
Epithelioid sarcoma (EpS) is an ultra-rare malignant soft-tissue cancer mostly affecting adolescents and young adults. EpS often exhibits an unfavorable clinical course with fatal outcome in ∼50% of cases despite aggressive multimodal therapies combining surgery, chemotherapy, and irradiation. EpS is traditionally classified in a more common, less aggressive distal (classic) type and a rarer aggressive proximal type. Both subtypes are characterized by a loss of nuclear INI1 expression, most often following homozygous deletion of its encoding gene, SMARCB1-a core subunit of the SWI/SNF chromatin remodeling complex. In 2020, the EZH2 inhibitor tazemetostat was the first targeted therapy approved for EpS, raising new hopes. Still, the vast majority of patients did not benefit from this drug or relapsed rapidly. Further, other recent therapeutic modalities, including immunotherapy, are only effective in a fraction of patients. Thus, novel strategies, specifically targeted to EpS, are urgently needed. To accelerate translational research on EpS and eventually boost the discovery and development of new diagnostic tools and therapeutic options, a vibrant translational research community has formed in past years and held two international EpS digital expert meetings in 2021 and 2023. This review summarizes our current understanding of EpS from the translational research perspective and points to innovative research directions to address the most pressing questions in the field, as defined by expert consensus and patient advocacy groups.
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Affiliation(s)
- Thomas G. P. Grunewald
- Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
| | - Sophie Postel-Vinay
- Département d’Innovation Thérapeutique et d’Essais Précoces (DITEP), Gustave Roussy, Université Paris Saclay, Villejuif, France
- U981 INSERM, ERC StG team, Gustave Roussy, Villejuif, France
| | - Robert T. Nakayama
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Noah E. Berlow
- Children’s Cancer Therapy Development Institute, Hillsboro, Oregon
| | - Andrea Bolzicco
- Patients association ‘Orchestra per la vita’ Aps, Rome, Italy
- Patients association: ‘MC4 in corsa per la vita!’ ETS, Milan, Italy
| | - Vincenzo Cerullo
- Drug Research Program, University of Helsinki, Helsinki, Finland
| | - Josephine K. Dermawan
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Anna Maria Frezza
- Department of Medical Oncology 2, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Antoine Italiano
- Early Phase Trials and Sarcoma Units, Institut Bergonie, Bordeaux, France
- Faculty of Medicine, University of Bordeaux, Bordeaux, France
| | - Jia xiang Jin
- Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
| | - Francois Le Loarer
- Faculty of Medicine, University of Bordeaux, Bordeaux, France
- Department of Pathology, Institut Bergonie, Bordeaux, France
| | - Javier Martin-Broto
- Medical Oncology Department, Fundacion Jimenez Diaz University Hospital; University Hospital General de Villalba, and Instituto de Investigacion Sanitaria Fundacion Jimenez Diaz (IIS/FJD; UAM), Madrid, Spain
| | - Andrew Pecora
- John Theurer Cancer Center, Georgetown Lombardi Comprehensive Cancer Center, Washington, DC
| | - Antonio Perez-Martinez
- Patients association: ‘MC4 in corsa per la vita!’ ETS, Milan, Italy
- Department of Pediatric Hemato-Oncology, Autonomous University of Madrid, Institute for Health Research, IdiPAZ, La Paz University Hospital, Madrid, Spain
| | - Yuen Bun Tam
- Division of Molecular Pathology, Institute of Cancer Research, London, United Kingdom
| | - Franck Tirode
- Universite Claude Bernard, INSERM 1052, CNRS 5286, Cancer Research Center of Lyon, Centre Leon Berard, Lyon, France
| | - Annalisa Trama
- Department of Epidemiology and Data Science; Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Sandro Pasquali
- Molecular Pharmacology, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Lukas ortmann
- Patients association “Smarcb1” e.V., Bergisch Gladbach, Germany
| | | | - Akihiko Yoshida
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Kim Webb
- Patients association “Smarcb1” e.V., Bergisch Gladbach, Germany
| | - Paul H. Huang
- Division of Molecular Pathology, Institute of Cancer Research, London, United Kingdom
- Sarcoma Unit, Royal Marsden Hospital, Belmont, United Kingdom
| | - Charles Keller
- Children’s Cancer Therapy Development Institute, Hillsboro, Oregon
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25
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D’Ambrosio A, Bressan D, Ferracci E, Carbone F, Mulè P, Rossi F, Barbieri C, Sorrenti E, Fiaccadori G, Detone T, Vezzoli E, Bianchi S, Sartori C, Corso S, Fukuda A, Bertalot G, Falqui A, Barbareschi M, Romanel A, Pasini D, Chiacchiera F. Increased genomic instability and reshaping of tissue microenvironment underlie oncogenic properties of Arid1a mutations. SCIENCE ADVANCES 2024; 10:eadh4435. [PMID: 38489371 PMCID: PMC10942108 DOI: 10.1126/sciadv.adh4435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 02/12/2024] [Indexed: 03/17/2024]
Abstract
Oncogenic mutations accumulating in many chromatin-associated proteins have been identified in different tumor types. With a mutation rate from 10 to 57%, ARID1A has been widely considered a tumor suppressor gene. However, whether this role is mainly due to its transcriptional-related activities or its ability to preserve genome integrity is still a matter of intense debate. Here, we show that ARID1A is largely dispensable for preserving enhancer-dependent transcriptional regulation, being ARID1B sufficient and required to compensate for ARID1A loss. We provide in vivo evidence that ARID1A is mainly required to preserve genomic integrity in adult tissues. ARID1A loss primarily results in DNA damage accumulation, interferon type I response activation, and chronic inflammation leading to tumor formation. Our data suggest that in healthy tissues, the increased genomic instability that follows ARID1A mutations and the selective pressure imposed by the microenvironment might result in the emergence of aggressive, possibly immune-resistant, tumors.
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Affiliation(s)
- Alessandro D’Ambrosio
- Laboratory of stem cells and cancer genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
- SEMM, University of Milan, 20142 Milan, Italy
| | - Davide Bressan
- Laboratory of stem cells and cancer genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Elisa Ferracci
- Laboratory of stem cells and cancer genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Francesco Carbone
- Unità Operativa Multizonale di Anatomia Patologica, APSS, 38122 Trento, Italy
| | - Patrizia Mulè
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, 20139 Milan, Italy
| | - Federico Rossi
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, 20139 Milan, Italy
| | - Caterina Barbieri
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, 20139 Milan, Italy
| | - Elisa Sorrenti
- Laboratory of stem cells and cancer genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Gaia Fiaccadori
- Laboratory of stem cells and cancer genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Thomas Detone
- Unità Operativa Multizonale di Anatomia Patologica, APSS, 38122 Trento, Italy
| | - Elena Vezzoli
- Department of Biomedical sciences for Health, University of Milan, 20133 Milan, Italy
| | - Salvatore Bianchi
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
| | - Chiara Sartori
- Unità Operativa Multizonale di Anatomia Patologica, APSS, 38122 Trento, Italy
| | - Simona Corso
- Department of Oncology, University of Torino, 10060 Candiolo, Italy
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy
| | - Akihisa Fukuda
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Giovanni Bertalot
- Unità Operativa Multizonale di Anatomia Patologica, APSS, 38122 Trento, Italy
- Centre for Medical Sciences–CISMed, University of Trento, 38122 Trento, Italy
| | - Andrea Falqui
- Department of Physics, University of Milan, 20133 Milan, Italy
| | - Mattia Barbareschi
- Unità Operativa Multizonale di Anatomia Patologica, APSS, 38122 Trento, Italy
- Centre for Medical Sciences–CISMed, University of Trento, 38122 Trento, Italy
| | - Alessandro Romanel
- Laboratory of Bioinformatics and Computational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Diego Pasini
- Department of Experimental Oncology, European Institute of Oncology (IEO), IRCCS, 20139 Milan, Italy
- Department of Health Sciences, University of Milan, 20142 Milan, Italy
| | - Fulvio Chiacchiera
- Laboratory of stem cells and cancer genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
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26
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Voutsadakis IA. Targeting super-enhancer activity for colorectal cancer therapy. Am J Transl Res 2024; 16:700-719. [PMID: 38586095 PMCID: PMC10994804 DOI: 10.62347/qkhb5897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/28/2024] [Indexed: 04/09/2024]
Abstract
In addition to genetic variants and copy number alterations, epigenetic deregulation of oncogenes and tumor suppressors is a major contributor in cancer development and propagation. Regulatory elements for gene transcription regulation can be found in promoters which are located in the vicinity of transcription start sites but also at a distance, in enhancer sites, brought to interact with proximal sites when occupied by enhancer protein complexes. These sites provide most of the specific regulatory sequences recognized by transcription factors. A sub-set of enhancers characterized by a longer structure and stronger activity, called super-enhancers, are critical for the expression of specific genes, usually associated with individual cell type identity and function. Super-enhancers show deregulation in cancer, which may have profound repercussions for cancer cell survival and response to therapy. Dysfunction of super-enhancers may result from multiple mechanisms that include changes in their sequence, alterations in the topological neighborhoods where they belong, and alterations in the proteins that mediate their function, such as transcription factors and epigenetic modifiers. These can become potential targets for therapeutic interventions. Genes that are targets of super-enhancers are cell and cancer type specific and could also be of interest for therapeutic targeting. In colorectal cancer, a super-enhancer regulated and over-expressed oncogene is MYC, under the influence of the WNT/β-catenin pathway. Identification and targeting of additional oncogenes regulated by super-enhancers in colorectal cancer may pave the way for combination therapies targeting the super-enhancer machinery and signal transduction pathways that regulate the specific transcription factors operative on them.
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Affiliation(s)
- Ioannis A Voutsadakis
- Algoma District Cancer Program, Sault Area HospitalSault Ste. Marie, ON, Canada
- Division of Clinical Sciences, Section of Internal Medicine, Northern Ontario School of MedicineSudbury, ON, Canada
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27
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d’Amati A, Bargiacchi L, Rossi S, Carai A, Bertero L, Barresi V, Errico ME, Buccoliero AM, Asioli S, Marucci G, Del Baldo G, Mastronuzzi A, Miele E, D’Antonio F, Schiavello E, Biassoni V, Massimino M, Gessi M, Antonelli M, Gianno F. Pediatric CNS tumors and 2021 WHO classification: what do oncologists need from pathologists? Front Mol Neurosci 2024; 17:1268038. [PMID: 38544524 PMCID: PMC10966132 DOI: 10.3389/fnmol.2024.1268038] [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: 07/27/2023] [Accepted: 02/23/2024] [Indexed: 05/14/2024] Open
Abstract
The fifth edition of the WHO Classification of Tumors of the Central Nervous System (CNS), published in 2021, established new approaches to both CNS tumor nomenclature and grading, emphasizing the importance of integrated diagnoses and layered reports. This edition increased the role of molecular diagnostics in CNS tumor classification while still relying on other established approaches such as histology and immunohistochemistry. Moreover, it introduced new tumor types and subtypes based on novel diagnostic technologies such as DNA methylome profiling. Over the past decade, molecular techniques identified numerous key genetic alterations in CSN tumors, with important implications regarding the understanding of pathogenesis but also for prognosis and the development and application of effective molecularly targeted therapies. This review summarizes the major changes in the 2021 fifth edition classification of pediatric CNS tumors, highlighting for each entity the molecular alterations and other information that are relevant for diagnostic, prognostic, or therapeutic purposes and that patients' and oncologists' need from a pathology report.
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Affiliation(s)
- Antonio d’Amati
- Unit of Anatomical Pathology, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari “Aldo Moro”, Bari, Italy
- Unit of Human Anatomy and Histology, Department of Translational Biomedicine and Neuroscience (DiBraiN), University of Bari “Aldo Moro”, Bari, Italy
- Unit of Anatomical Pathology, Department of Radiology, Oncology and Anatomical Pathology, University La Sapienza, Rome, Italy
- Neuropathology Unit, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Università Cattolica S. Cuore, Roma, Italy
| | - Lavinia Bargiacchi
- Unit of Anatomical Pathology, Department of Radiology, Oncology and Anatomical Pathology, University La Sapienza, Rome, Italy
| | - Sabrina Rossi
- Pathology Unit, Department of Laboratories, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Andrea Carai
- Department of Neuroscience and Neurorehabilitation, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Luca Bertero
- Pathology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Valeria Barresi
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Maria Elena Errico
- Department of Pathology, AORN Santobono Pausilipon, Pediatric Hospital, Naples, Italy
| | | | - Sofia Asioli
- Department of Biomedical and Neuromotor Sciences (DIBINEM), Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Gianluca Marucci
- Neuropathology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Giada Del Baldo
- Department of Paediatric Haematology/Oncology, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Angela Mastronuzzi
- Department of Paediatric Haematology/Oncology, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Evelina Miele
- Department of Paediatric Haematology/Oncology, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Federica D’Antonio
- Department of Paediatric Haematology/Oncology, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Elisabetta Schiavello
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Veronica Biassoni
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Maura Massimino
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Marco Gessi
- Neuropathology Unit, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Università Cattolica S. Cuore, Roma, Italy
| | - Manila Antonelli
- Unit of Anatomical Pathology, Department of Radiology, Oncology and Anatomical Pathology, University La Sapienza, Rome, Italy
- IRCCS Neuromed, Pozzilli, Isernia, Italy
| | - Francesca Gianno
- Unit of Anatomical Pathology, Department of Radiology, Oncology and Anatomical Pathology, University La Sapienza, Rome, Italy
- IRCCS Neuromed, Pozzilli, Isernia, Italy
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Szczepanski A, Tsuboyama N, Lyu H, Wang P, Beytullahoglu O, Zhang T, Singer BD, Yue F, Zhao Z, Wang L. A SWI/SNF-dependent transcriptional regulation mediated by POU2AF2/C11orf53 at enhancer. Nat Commun 2024; 15:2067. [PMID: 38453939 PMCID: PMC10920751 DOI: 10.1038/s41467-024-46492-5] [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: 06/15/2023] [Accepted: 02/13/2024] [Indexed: 03/09/2024] Open
Abstract
Recent studies have identified a previously uncharacterized protein C11orf53 (now named POU2AF2/OCA-T1), which functions as a robust co-activator of POU2F3, the master transcription factor which is critical for both normal and neoplastic tuft cell identity and viability. Here, we demonstrate that POU2AF2 dictates opposing transcriptional regulation at distal enhance elements. Loss of POU2AF2 leads to an inhibition of active enhancer nearby genes, such as tuft cell identity genes, and a derepression of Polycomb-dependent poised enhancer nearby genes, which are critical for cell viability and differentiation. Mechanistically, depletion of POU2AF2 results in a global redistribution of the chromatin occupancy of the SWI/SNF complex, leading to a significant 3D genome structure change and a subsequent transcriptional reprogramming. Our genome-wide CRISPR screen further demonstrates that POU2AF2 depletion or SWI/SNF inhibition leads to a PTEN-dependent cell growth defect, highlighting a potential role of POU2AF2-SWI/SNF axis in small cell lung cancer (SCLC) pathogenesis. Additionally, pharmacological inhibition of SWI/SNF phenocopies POU2AF2 depletion in terms of gene expression alteration and cell viability decrease in SCLC-P subtype cells. Therefore, impeding POU2AF2-mediated transcriptional regulation represents a potential therapeutic approach for human SCLC therapy.
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Affiliation(s)
- Aileen Szczepanski
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Natsumi Tsuboyama
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Huijue Lyu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Ping Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Oguzhan Beytullahoglu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Te Zhang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Benjamin David Singer
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Zibo Zhao
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
| | - Lu Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
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29
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Ou J, Deng S, Ding C, Cai Z, Chen J, Huang Z, Xu X, Li J, Wu Z, Tang B, Zhang T, Wang Z, Zhou Y, Xuan L, Liu Q, Zhou H. Mutations of epigenetic modifier genes predict poor outcome in adult acute lymphoblastic leukemia. Ann Hematol 2024:10.1007/s00277-024-05681-4. [PMID: 38451293 DOI: 10.1007/s00277-024-05681-4] [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: 12/03/2023] [Accepted: 02/25/2024] [Indexed: 03/08/2024]
Abstract
Epigenetic modifier (EM) genes play important roles in the occurrence and progression of acute lymphoblastic leukemia (ALL). However, the prognostic significance of EM mutations in ALL has not yet been thoroughly investigated. This retrospective study included 205 adult patients with ALL engaged in a pediatric-type regimen. Based on targeted next-generation sequencing, they were divided into EM mutation group (EM-mut, n = 75) and EM wild-type group (EM-wt, n = 130). The EM-mut group showed a higher positive rate of minimal residual disease (MRD) on treatment day24 and before consolidation therapy (P = 0.026, 0.020). Multivariate Cox regression analysis showed that EM-mut was an independent adverse factor for overall survival (OS) and event-free survival (EFS) (HR = 2.123, 1.742; P = 0.009, 0.007). Survival analysis revealed that the OS and EFS rates were significantly lower in the EM-mut group than in the EM-wt group (3-year OS rate, 45.8% vs. 65.0%, P = 0.0041; 3-year EFS rate, 36.7% vs. 53.2%, P = 0.011). In conclusion, EM was frequently mutated in adult ALL and was characterized by poor response to induction therapy and inferior clinical outcomes.
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Affiliation(s)
- Jiawang Ou
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Shiyu Deng
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Chenhao Ding
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zihong Cai
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Junjie Chen
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zicong Huang
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiuli Xu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jia Li
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zhengwei Wu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Bingqing Tang
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ting Zhang
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zhixiang Wang
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ya Zhou
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Li Xuan
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qifa Liu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hongsheng Zhou
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
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30
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Lambert GS, Rice BL, Kaddis Maldonado RJ, Chang J, Parent LJ. Comparative analysis of retroviral Gag-host cell interactions: focus on the nuclear interactome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.18.575255. [PMID: 38293010 PMCID: PMC10827203 DOI: 10.1101/2024.01.18.575255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Retroviruses exploit a variety of host proteins to assemble and release virions from infected cells. To date, most studies that examined possible interacting partners of retroviral Gag proteins focused on host proteins that localize primarily to the cytoplasm or plasma membrane. Given the recent findings that several full-length Gag proteins localize to the nucleus, identifying the Gag-nuclear interactome has high potential for novel findings that reveal previously unknown host processes. In this study, we systematically compared nuclear factors identified in published HIV-1 proteomic studies which had used a variety of experimental approaches. In addition, to contribute to this body of knowledge, we report results from a mass spectrometry approach using affinity-tagged (His6) HIV-1 and RSV Gag proteins mixed with nuclear extracts. Taken together, the previous studies-as well as our own-identified potential binding partners of HIV-1 and RSV Gag involved in several nuclear processes, including transcription, splicing, RNA modification, and chromatin remodeling. Although a subset of host proteins interacted with both Gag proteins, there were also unique host proteins belonging to each interactome dataset. To validate one of the novel findings, we demonstrated the interaction of RSV Gag with a member of the Mediator complex, Med26, which is required for RNA polymerase II-mediated transcription. These results provide a strong premise for future functional studies to investigate roles for these nuclear host factors that may have shared functions in the biology of both retroviruses, as well as functions specific to RSV and HIV-1, given their distinctive hosts and molecular pathology.
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Affiliation(s)
- Gregory S. Lambert
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - Breanna L. Rice
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - Rebecca J. Kaddis Maldonado
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA
- Department of Microbiology and Immunology, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - Jordan Chang
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - Leslie J. Parent
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA
- Department of Microbiology and Immunology, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA
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31
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Sun M, Gu Y, Fang H, Shao F, Lin C, Zhang H, Li H, He H, Li R, Wang J, Liu H, Xu J. Clinical outcome and molecular landscape of patients with ARID1A-loss gastric cancer. Cancer Sci 2024; 115:905-915. [PMID: 38148578 PMCID: PMC10920992 DOI: 10.1111/cas.16057] [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: 10/11/2023] [Revised: 12/05/2023] [Accepted: 12/09/2023] [Indexed: 12/28/2023] Open
Abstract
Chromatin remodelers are commonly altered in human cancer. The mutation of AT-rich interactive domain 1A (ARID1A) in gastric cancer (GC), a component of the SWI/SNF chromatin remodeling complex, was proven associated with treatment response in our previous study. However, ARID1A loss of function was caused not only by mutations but also copy number deletions. The clinicopathologic, genomic, and immunophenotypic correlates of ARID1A loss is largely uncharacterized in GC. Here, 819 patients with clinicopathological information and sequencing data or formalin-fixed paraffin-embedded tissues from four cohorts, Zhongshan Hospital (ZSHS) cohort (n = 375), The Cancer Genome Atlas (TCGA) cohort (n = 371), Samsung Medical Center (SMC) cohort (n = 53), and ZSHS immunotherapy cohort (n = 20), were enrolled. ARID1A loss was defined by genome sequencing or deficient ARID1A expression by immunohistochemistry. We found that ARID1A mutation and copy number deletion were enriched in GC with microsatellite instability (MSI) and chromosomal-instability (CIN), respectively. In the TCGA and ZSHS cohorts, only CIN GC with ARID1A loss could benefit from fluorouracil-based adjuvant chemotherapy. In the SMC and ZSHS immunotherapy cohorts, ARID1A loss exhibited a tendency of superior responsiveness and indicated favorable overall survival after anti-PD-1 immunotherapy. ARID1A-loss tumors demonstrated elevated mutation burden, neoantigen load, and interferon gamma pathway activation. Moreover, in CIN GC, ARID1A loss was correlated with higher homologous recombination deficiency. ARID1A loss defines a distinct subtype of GC characterized by high levels of genome instability, neoantigen formation, and immune activation. These tumors show sensitivity to both chemotherapy and anti-PD-1 immunotherapy. This study provides valuable insights for precision treatment strategies in GC.
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Affiliation(s)
- Mengyao Sun
- NHC Key Laboratory of Glycoconjugate Research, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Yun Gu
- NHC Key Laboratory of Glycoconjugate Research, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesFudan UniversityShanghaiChina
- Department of General Surgery, Shanghai Sixth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Hanji Fang
- NHC Key Laboratory of Glycoconjugate Research, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesFudan UniversityShanghaiChina
- Department of General Surgery, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Fei Shao
- Department of Oncology, Shanghai General HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Chao Lin
- Department of General Surgery, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Heng Zhang
- Department of General Surgery, Zhongshan HospitalFudan UniversityShanghaiChina
| | - He Li
- Department of General Surgery, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Hongyong He
- Department of General Surgery, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Ruochen Li
- Department of General Surgery, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Jieti Wang
- Department of EndoscopyFudan University Shanghai Cancer CenterShanghaiChina
| | - Hao Liu
- Department of General Surgery, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Jiejie Xu
- NHC Key Laboratory of Glycoconjugate Research, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesFudan UniversityShanghaiChina
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An L, Dong K, Chi S, Wei S, Zhang J, Yu Z, Zhang Q, Zhang T, Cheng S, Shi R, Jin Z, Zhou X, Zhao Y, Wang H. lncRNA UCA1 promotes tumor progression by targeting SMARCD3 in cervical cancer. Mol Carcinog 2024; 63:384-399. [PMID: 38116886 DOI: 10.1002/mc.23659] [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: 08/26/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 12/21/2023]
Abstract
Long noncoding RNA urothelial carcinoma associated 1 (UCA1) has been identified as a key molecule in human cancers. However, its functional implications remain unspecified in the context of cervical cancer (CC). This research aims to identify the regulatory mechanism of UCA1 in CC. UCA1 was identified through microarray and confirmed through a quantitative real-time polymerase chain reaction. Proteins that bind with UCA1 were recognized using RNA pull-down assays along with RNA immunoprecipitation. Ubiquitination assays and coimmunoprecipitation were performed to explore the molecular mechanisms of the SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily d, member 3 (SMARCD3) downregulated in CC. The effects of UCA1 and SMARCD3 on the progression of CC were investigated through gain- and loss-of-function assays and xenograft tumor formation in vivo. In this study, UCA1 was found to be upregulated in CC cells as well as in human plasma exosomes for the first time. Functional studies indicated that UCA1 promotes CC progression. Mechanically, UCA1 downregulated the SMARCD3 protein stabilization by promoting SMARCD3 ubiquitination. Taken together, we revealed that the UCA1/SMARCD3 axis promoted CC progression, which could provide a new therapeutic target for CC.
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Affiliation(s)
- Lanfen An
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Plastic Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Kejun Dong
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shuqi Chi
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, China
| | - Sitian Wei
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jun Zhang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhicheng Yu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qian Zhang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tangansu Zhang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shuangshuang Cheng
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Rui Shi
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhishan Jin
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xing Zhou
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yingchao Zhao
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hongbo Wang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Li Z, Wang Y, Zhao L, Li Y. Epidemiology, Characteristics, and Prognostic Factors of Primary Atypical Teratoid/Rhabdoid Tumors in the Spinal Canal: A Systematic Review. Neurospine 2024; 21:182-203. [PMID: 38317556 PMCID: PMC10992646 DOI: 10.14245/ns.2347096.548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 12/09/2023] [Accepted: 12/11/2023] [Indexed: 02/07/2024] Open
Abstract
Primary atypical teratoid/rhabdoid tumors (AT/RTs) in the spinal canal are rare central nervous system (CNS) neoplasms that are challenging to diagnose and treat. To date, there has been no standard treatment regimen for these challenging malignant tumors. Thus, we conducted this research to explore potential prognostic factors and feasible treatment modalities for improving the prognosis of these tumors. Articles were retrieved from the PubMed, MEDLINE, and Embase databases, using the keywords "atypical teratoid/rhabdoid tumor," "rhabdoid tumor," "spine," "spinal," "spinal neoplasm", and "spinal cord neoplasm." All eligible cases demonstrated SMARCB1-deficient expression validated by pathological examination. We collected and analyzed data related to clinical presentation, radiological features, pathological characteristics, treatment modalities and prognosis via Kaplan-Meier and Cox regression analyses. Thirty-six articles comprising 58 spinal AT/RT patients were included in the study. The median progression-free survival (PFS) and overall survival (OS) were 18 and 22 months, respectively. Kaplan-Meier analysis demonstrated significant survival improvements for OS in the nonmetastasis, male, radiotherapy and intrathecal chemotherapy groups as well as for PFS in the chemotherapy and radiotherapy groups. Multivariate analysis revealed that chemotherapy and radiotherapy were prognostic factors for improved PFS, and that intrathecal chemotherapy reduced the risk of mortality. Spinal AT/RTs are uncommon malignant entities with a dismal survival rate. Although our review is limited by variability between cases, there is some evidence revealing potential risk factors and the importance of systematic chemotherapy, intrathecal chemotherapy and radiotherapy in spinal AT/RT treatment modalities.
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Affiliation(s)
- Zhibin Li
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, China
| | - Yubo Wang
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, China
| | - Liyan Zhao
- Department of Clinical Laboratory, The Second Hospital of Jilin University, Changchun, China
| | - Yunqian Li
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, China
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Nguyen V, Schrank TP, Major MB, Weissman BE. ARID1A loss is associated with increased NRF2 signaling in human head and neck squamous cell carcinomas. PLoS One 2024; 19:e0297741. [PMID: 38358974 PMCID: PMC10868765 DOI: 10.1371/journal.pone.0297741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/11/2024] [Indexed: 02/17/2024] Open
Abstract
Prior to the next generation sequencing and characterization of the tumor genome landscape, mutations in the SWI/SNF chromatin remodeling complex and the KEAP1-NRF2 signaling pathway were underappreciated. While these two classes of mutations appeared to independently contribute to tumor development, recent reports have demonstrated a mechanistic link between these two regulatory mechanisms in specific cancer types and cell models. In this work, we expand upon these data by exploring the relationship between mutations in BAF and PBAF subunits of the SWI/SNF complex and activation of NRF2 signal transduction across many cancer types. ARID1A/B mutations were strongly associated with NRF2 transcriptional activity in head and neck squamous carcinomas (HNSC). Many additional tumor types showed significant association between NRF2 signaling and mutation of specific components of the SWI/SNF complex. Different effects of BAF and PBAF mutations on the polarity of NRF2 signaling were observed. Overall, our results support a context-dependent functional link between SWI/SNF and NRF2 mutations across human cancers and implicate ARID1A inactivation in HPV-negative HNSC in promoting tumor progression and survival through activation of the KEAP1-NRF2 signaling pathway. The tumor-specific effects of these mutations open a new area of study for how mutations in the KEAP1-NRF2 pathway and the SWI/SNF complex contribute to cancer.
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Affiliation(s)
- Vinh Nguyen
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, United States of America
- Curriculum in Toxicology and Environmental Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Travis P. Schrank
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, United States of America
- Department of Otolaryngology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Michael B. Major
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, United States of America
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Bernard E. Weissman
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, United States of America
- Curriculum in Toxicology and Environmental Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, United States of America
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35
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Akinjiyan FA, Nassief G, Phillipps J, Adeyelu T, Elliott A, Abdulla F, Zhou AY, Souroullas G, Kim KB, Vanderwalde A, Park SJ, Ansstas G. ARID2 mutations may relay a distinct subset of cutaneous melanoma patients with different outcomes. Sci Rep 2024; 14:3444. [PMID: 38341515 PMCID: PMC10858967 DOI: 10.1038/s41598-024-54136-3] [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: 12/06/2023] [Accepted: 02/08/2024] [Indexed: 02/12/2024] Open
Abstract
ARID genes encode subunits of SWI/SNF chromatin remodeling complexes and are frequently mutated in human cancers. We investigated the correlation between ARID mutations, molecular features, and clinical outcomes in melanoma patients. Cutaneous melanoma samples (n = 1577) were analyzed by next-generation sequencing. Samples were stratified by pathogenic/likely pathogenic mutation in ARID genes (ARID1A/2/1B/5B). PD-L1 expression was assessed using IHC (SP142; positive (+): ≥ 1%). Tumor mutation burden (TMB)-high was defined as ≥ 10 mutations/Mb. Transcriptomic signatures predictive of response to immune checkpoint inhibitors-interferon gamma and T-cell inflamed score were calculated. Real-world overall survival (OS) information was obtained from insurance claims data, with Kaplan-Meier estimates calculated from time of tissue collection until last date of contact. Mann-Whitney U, Chi-square, and Fisher exact tests were applied where appropriate, with p values adjusted for multiple comparisons. ARID2 mutations were more prevalent in cutaneous melanoma compared to ARID1A (11.0%: n = 451 vs 2.8%: n = 113), with concurrent ARID1A/ARID2 mutation in 1.1% (n = 46) of samples. ARID mutations were associated with a high prevalence of RAS pathway mutations-NF1 (ARID1A, 52.6%; ARID2, 48.5%; ARID1A/2, 63.6%; and ARID-WT, 13.3%; p < 0.0001) and KRAS (ARID1A, 3.5%; ARID2, 3.1%; ARID1A/2, 6.5%; and ARID-WT, 1.0%; p = 0.018)), although BRAF mutations were less common in ARID-mutated cohorts (ARID1A, 31.9%; ARID2, 35.6%; ARID1A/2, 26.1%; and ARID-WT, 50.4%; p < 0.0001). TMB-high was more common in ARID-mutated samples (ARID1A, 80.9%; ARID2, 89.9%; ARID1A/2, 100%; and ARID-WT, 49.4%; p < 0.0001), while PD-L1 positivity was similar across subgroups (ARID1A, 43.8%; ARID2, 51.1%; ARID1A/2, 52.5%; and ARID-WT, 44.9%; p = 0.109). Patients with ARID1A mutations had a higher prevalence of dMMR/MSI-H compared to those with ARID-WT (2.7% vs 0.2%, p = 0.030). Median IFN-γ and T-cell signatures were higher in ARID2-mutated samples compared to ARID-WT (IFN-γ: - 0.15 vs - 0.21, p = 0.0066; T-cell: 23.5 vs - 18.5, p = 0.041). ARID2-mutated patients had improved survival compared to ARID-WT; (HR: 1.22 (95% CI 1.0-1.5), p = 0.022). No additional OS benefit was observed with anti-PD-1 therapy for ARID2 mutation compared to ARID-WT. Melanoma patients with ARID mutations exhibited higher prevalence of markers associated with ICI response, including TMB-H, and immune-related signatures. Our data also suggests improved survival outcome in patients with ARID2 mutations, irrespective of anti-PD1 therapy.
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Affiliation(s)
- Favour A Akinjiyan
- Division of Medical Oncology, Department of Medicine, Washington University in Saint Louis, 4921 Parkview Place, Saint Louis, MO, 63110, USA
| | - George Nassief
- Division of Medical Oncology, Department of Medicine, Washington University in Saint Louis, 4921 Parkview Place, Saint Louis, MO, 63110, USA
| | - Jordan Phillipps
- Division of Medical Oncology, Department of Medicine, Washington University in Saint Louis, 4921 Parkview Place, Saint Louis, MO, 63110, USA
| | | | | | | | - Alice Y Zhou
- Division of Medical Oncology, Department of Medicine, Washington University in Saint Louis, 4921 Parkview Place, Saint Louis, MO, 63110, USA
| | - George Souroullas
- Division of Medical Oncology, Department of Medicine, Washington University in Saint Louis, 4921 Parkview Place, Saint Louis, MO, 63110, USA
| | - Kevin B Kim
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | | | - Soo J Park
- Division of Hematology/Oncology, Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - George Ansstas
- Division of Medical Oncology, Department of Medicine, Washington University in Saint Louis, 4921 Parkview Place, Saint Louis, MO, 63110, USA.
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Davis RB, Supakar A, Ranganath AK, Moosa MM, Banerjee PR. Heterotypic interactions can drive selective co-condensation of prion-like low-complexity domains of FET proteins and mammalian SWI/SNF complex. Nat Commun 2024; 15:1168. [PMID: 38326345 PMCID: PMC10850361 DOI: 10.1038/s41467-024-44945-5] [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: 04/12/2023] [Accepted: 01/08/2024] [Indexed: 02/09/2024] Open
Abstract
Prion-like domains (PLDs) are low-complexity protein sequences enriched within nucleic acid-binding proteins including those involved in transcription and RNA processing. PLDs of FUS and EWSR1 play key roles in recruiting chromatin remodeler mammalian SWI/SNF (mSWI/SNF) complex to oncogenic FET fusion protein condensates. Here, we show that disordered low-complexity domains of multiple SWI/SNF subunits are prion-like with a strong propensity to undergo intracellular phase separation. These PLDs engage in sequence-specific heterotypic interactions with the PLD of FUS in the dilute phase at sub-saturation conditions, leading to the formation of PLD co-condensates. In the dense phase, homotypic and heterotypic PLD interactions are highly cooperative, resulting in the co-mixing of individual PLD phases and forming spatially homogeneous condensates. Heterotypic PLD-mediated positive cooperativity in protein-protein interaction networks is likely to play key roles in the co-phase separation of mSWI/SNF complex with transcription factors containing homologous low-complexity domains.
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Affiliation(s)
- Richoo B Davis
- Department of Physics, University at Buffalo, Buffalo, NY, 14260, USA
| | - Anushka Supakar
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | | | | | - Priya R Banerjee
- Department of Physics, University at Buffalo, Buffalo, NY, 14260, USA.
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA.
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, NY, 14260, USA.
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Chen Y, Gao Z, Mohd‐Ibrahim I, Yang H, Wu L, Fu Y, Deng Y. Pan-cancer analyses of bromodomain containing 9 as a novel therapeutic target reveals its diagnostic, prognostic potential and biological mechanism in human tumours. Clin Transl Med 2024; 14:e1543. [PMID: 38303608 PMCID: PMC10835192 DOI: 10.1002/ctm2.1543] [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: 07/10/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Mutations in one or more genes responsible for encoding subunits within the SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin-remodelling complexes are found in approximately 25% of cancer patients. Bromodomain containing 9 (BRD9) is a more recently identified protein coding gene, which can encode SWI/SNF chromatin-remodelling complexes subunits. Although initial evaluations of the potential of BRD9-based targeted therapy have been explored in the clinical application of a small number of cancer types, more detailed study of the diagnostic and prognostic potential, as well as the detailed biological mechanism of BRD9 remains unreported. METHODS We used various bioinformatics tools to generate a comprehensive, pan-cancer analyses of BRD9 expression in multiple disease types described in The Cancer Genome Atlas (TCGA). Experimental validation was conducted in tissue microarrays and cell lines derived from lung and colon cancers. RESULTS Our study revealed that BRD9 exhibited elevated expression in a wide range of tumours. Analysis of survival data and DNA methylation for BRD9 indicated distinct conclusions for multiple tumours. mRNA splicing and molecular binding were involved in the functional mechanism of BRD9. BRD9 may affect cancer progression through different phosphorylation sites or N6 -methyladenosine site modifications. BRD9 could potentially serve as a novel biomarker for diagnosing different cancer types, especially could accurately forecast the prognosis of melanoma patients receiving anti-programmed cell death 1 immunotherapy. BRD9 has the potential to serve as a therapeutic target, when pairing with etoposide in patients with melanoma. The BRD9/SMARCD1 axis exhibited promising discriminative performance in forecasting the prognosis of patients afflicted with liver hepatocellular carcinoma (LIHC) and mesothelioma. Additionally, this axis appears to potentially influence the immune response in LIHC by regulating the programmed death-ligand 1 immune checkpoint. For experimental validation, high expression levels of BRD9 were observed in tumour tissue samples from both lung and colon cancer patients. Knocking down BRD9 led to the inhibition of lung and colon cancer development, likely via the Wnt/β-catenin signalling pathway. CONCLUSIONS These pan-cancer study revealed the diagnostic and prognostic potential, along with the biological mechanism of BRD9 as a novel therapeutic target in human tumours.
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Affiliation(s)
- Yu Chen
- Department of Quantitative Health SciencesJohn A. Burns School of MedicineUniversity of Hawaii at ManoaHonoluluHawaiiUSA
- Department of Molecular Biosciences and BioengineeringCollege of Tropical Agriculture and Human ResourcesAgricultural SciencesUniversity of Hawaii at ManoaHonoluluHawaiiUSA
| | - Zitong Gao
- Department of Quantitative Health SciencesJohn A. Burns School of MedicineUniversity of Hawaii at ManoaHonoluluHawaiiUSA
- Department of Molecular Biosciences and BioengineeringCollege of Tropical Agriculture and Human ResourcesAgricultural SciencesUniversity of Hawaii at ManoaHonoluluHawaiiUSA
| | - Isam Mohd‐Ibrahim
- Department of Quantitative Health SciencesJohn A. Burns School of MedicineUniversity of Hawaii at ManoaHonoluluHawaiiUSA
- Department of Molecular Biosciences and BioengineeringCollege of Tropical Agriculture and Human ResourcesAgricultural SciencesUniversity of Hawaii at ManoaHonoluluHawaiiUSA
| | - Hua Yang
- Department of Quantitative Health SciencesJohn A. Burns School of MedicineUniversity of Hawaii at ManoaHonoluluHawaiiUSA
| | - Lang Wu
- Cancer Epidemiology DivisionPopulation Sciences in the Pacific ProgramUniversity of Hawaii Cancer CenterUniversity of Hawaii at ManoaHonoluluHawaiiUSA
| | - Yuanyuan Fu
- Department of Quantitative Health SciencesJohn A. Burns School of MedicineUniversity of Hawaii at ManoaHonoluluHawaiiUSA
| | - Youping Deng
- Department of Quantitative Health SciencesJohn A. Burns School of MedicineUniversity of Hawaii at ManoaHonoluluHawaiiUSA
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Liu S. Bioinformatics analysis identifies GLUD1 as a prognostic indicator for clear cell renal cell carcinoma. Eur J Med Res 2024; 29:70. [PMID: 38245763 PMCID: PMC10799526 DOI: 10.1186/s40001-024-01649-2] [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: 12/06/2023] [Accepted: 01/08/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Renal cell carcinoma (RCC) is a common primary tumor of the kidney and is divided into three major subtypes, of which clear cell renal cell carcinoma (ccRCC) has the highest incidence. Glutamate dehydrogenase 1 (GLUD1) encodes glutamate dehydrogenase 1, which catalyzes the oxidative deamination of glutamate. METHODS We analyzed TCGA data using R language software and used multiple online databases to explore the relationship of GLUD1 with signaling pathways and drug sensitivity as well as GLUD1 protein expression and methylation. RESULTS The results showed that GLUD1 mRNA expression was reduced in tumor tissues and correlated with the progression of ccRCC. Univariate and multivariate Cox analysis showed that GLUD1 could be used as a prognostic marker for ccRCC. GLUD1 expression in ccRCC was associated with immune cells infiltration and multiple classical signaling pathways. In addition, GLUD1 mRNA expression was related to drug sensitivity. CONCLUSIONS These findings provide new ideas for finding new prognostic molecular markers and therapeutic targets for ccRCC.
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Affiliation(s)
- Shuang Liu
- Department of Clinical Laboratory, Institute of Translational Medicine, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, People's Republic of China.
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Abraham A, Samaniego-Castruita D, Paladino J, Han I, Ramesh P, Tran MT, Southern RM, Shukla A, Shukla V. Arid1a-dependent canonical BAF complex suppresses inflammatory programs to drive efficient Germinal Center B cell responses. RESEARCH SQUARE 2024:rs.3.rs-3871185. [PMID: 38313292 PMCID: PMC10836118 DOI: 10.21203/rs.3.rs-3871185/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Differentiating B cells in germinal centers (GC) require tightly coordinated transcriptional and epigenetic transitions to generate efficient humoral immune responses. The mammalian Brg1/Brm-associated factor (BAF) complexes are major regulators of nucleosomal remodeling, crucial for cellular differentiation and development, and are commonly mutated in several cancers, including GC-derived B cell lymphomas. However, the specific roles of distinct BAF complexes in GC B cell biology and generation of functional humoral immune responses are not well understood. Here, we show that the A-T Rich Interaction Domain 1a (Arid1a) containing canonical BAF (cBAF) complex is required for maintenance of GCs and therefore high affinity antibody responses. While Arid1a-deficient B cells undergo activation to initiate GC responses, they fail to sustain the GC program resulting in premature GC collapse. We discovered that Arid1a-dependent cBAF activity establishes permissive chromatin landscapes during B cell activation and is concomitantly required to suppress inflammatory gene programs to maintain transcriptional fidelity in early GC B cells. Interestingly, the inflammatory signatures instigated by Arid1a deficiency in early GC B cells recruited neutrophils and inflammatory monocytes and eventually disrupted GC homeostasis. Dampening of inflammatory cues with anti-inflammatory glucocorticoid receptor signaling rescued GC B cell differentiation of Arid1a-deficient B cells, thus highlighting a critical role of inflammation in impeding GC responses. In sum, our work identifies essential functions of Arid1a-dependent BAF activity in promoting efficient GC responses. These findings further support an emerging paradigm in which unrestrained inflammation limits GC-derived humoral responses, as reported in the context of severe bacterial and viral infections.
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Affiliation(s)
- Ajay Abraham
- Department of Cell and Developmental Biology, Northwestern University, Chicago, Illinois, USA, 60611
- Center for Human Immunobiology, Northwestern University, Chicago, Illinois, USA, 60611
| | | | - Jillian Paladino
- Department of Cell and Developmental Biology, Northwestern University, Chicago, Illinois, USA, 60611
| | - Isabella Han
- Department of Cell and Developmental Biology, Northwestern University, Chicago, Illinois, USA, 60611
| | - Prathyaya Ramesh
- Department of Cell and Developmental Biology, Northwestern University, Chicago, Illinois, USA, 60611
| | - Mi Thao Tran
- Department of Cell and Developmental Biology, Northwestern University, Chicago, Illinois, USA, 60611
| | - Rebecca M Southern
- Department of Cell and Developmental Biology, Northwestern University, Chicago, Illinois, USA, 60611
| | - Ashima Shukla
- Department of Cell and Developmental Biology, Northwestern University, Chicago, Illinois, USA, 60611
| | - Vipul Shukla
- Department of Cell and Developmental Biology, Northwestern University, Chicago, Illinois, USA, 60611
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois, USA, 60611
- Center for Human Immunobiology, Northwestern University, Chicago, Illinois, USA, 60611
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Ahmad K, Brahma S, Henikoff S. Epigenetic pioneering by SWI/SNF family remodelers. Mol Cell 2024; 84:194-201. [PMID: 38016477 PMCID: PMC10842064 DOI: 10.1016/j.molcel.2023.10.045] [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: 07/06/2023] [Revised: 09/20/2023] [Accepted: 10/31/2023] [Indexed: 11/30/2023]
Abstract
In eukaryotic genomes, transcriptional machinery and nucleosomes compete for binding to DNA sequences; thus, a crucial aspect of gene regulatory element function is to modulate chromatin accessibility for transcription factor (TF) and RNA polymerase binding. Recent structural studies have revealed multiple modes of TF engagement with nucleosomes, but how initial "pioneering" results in steady-state DNA accessibility for further TF binding and RNA polymerase II (RNAPII) engagement has been unclear. Even less well understood is how distant sites of open chromatin interact with one another, such as when developmental enhancers activate promoters to release RNAPII for productive elongation. Here, we review evidence for the centrality of the conserved SWI/SNF family of nucleosome remodeling complexes, both in pioneering and in mediating enhancer-promoter contacts. Consideration of the nucleosome unwrapping and ATP hydrolysis activities of SWI/SNF complexes, together with their architectural features, may reconcile steady-state TF occupancy with rapid TF dynamics observed by live imaging.
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Affiliation(s)
- Kami Ahmad
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Sandipan Brahma
- University of Nebraska Medical Center, Department of Genetics, Cell Biology & Anatomy, Omaha, NE, USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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Dillon MT, Guevara J, Mohammed K, Patin EC, Smith SA, Dean E, Jones GN, Willis SE, Petrone M, Silva C, Thway K, Bunce C, Roxanis I, Nenclares P, Wilkins A, McLaughlin M, Jayme-Laiche A, Benafif S, Nintos G, Kwatra V, Grove L, Mansfield D, Proszek P, Martin P, Moore L, Swales KE, Banerji U, Saunders MP, Spicer J, Forster MD, Harrington KJ. Durable responses to ATR inhibition with ceralasertib in tumors with genomic defects and high inflammation. J Clin Invest 2024; 134:e175369. [PMID: 37934611 PMCID: PMC10786692 DOI: 10.1172/jci175369] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/02/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUNDPhase 1 study of ATRinhibition alone or with radiation therapy (PATRIOT) was a first-in-human phase I study of the oral ATR (ataxia telangiectasia and Rad3-related) inhibitor ceralasertib (AZD6738) in advanced solid tumors.METHODSThe primary objective was safety. Secondary objectives included assessment of antitumor responses and pharmacokinetic (PK) and pharmacodynamic (PD) studies. Sixty-seven patients received 20-240 mg ceralasertib BD continuously or intermittently (14 of a 28-day cycle).RESULTSIntermittent dosing was better tolerated than continuous, which was associated with dose-limiting hematological toxicity. The recommended phase 2 dose of ceralasertib was 160 mg twice daily for 2 weeks in a 4-weekly cycle. Modulation of target and increased DNA damage were identified in tumor and surrogate PD. There were 5 (8%) confirmed partial responses (PRs) (40-240 mg BD), 34 (52%) stable disease (SD), including 1 unconfirmed PR, and 27 (41%) progressive disease. Durable responses were seen in tumors with loss of AT-rich interactive domain-containing protein 1A (ARID1A) and DNA damage-response defects. Treatment-modulated tumor and systemic immune markers and responding tumors were more immune inflamed than nonresponding.CONCLUSIONCeralasertib monotherapy was tolerated at 160 mg BD intermittently and associated with antitumor activity.TRIAL REGISTRATIONClinicaltrials.gov: NCT02223923, EudraCT: 2013-003994-84.FUNDINGCancer Research UK, AstraZeneca, UK Department of Health (National Institute for Health Research), Rosetrees Trust, Experimental Cancer Medicine Centre.
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Affiliation(s)
- Magnus T. Dillon
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Jeane Guevara
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Kabir Mohammed
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | | | | | - Emma Dean
- Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | | | | | - Marcella Petrone
- Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
| | - Carlos Silva
- Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
| | - Khin Thway
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Catey Bunce
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | | | | | - Anna Wilkins
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | | | - Adoracion Jayme-Laiche
- UCL Cancer Institute and University College London Hospital NHS Foundation Trust, London, United Kingdom
| | - Sarah Benafif
- UCL Cancer Institute and University College London Hospital NHS Foundation Trust, London, United Kingdom
| | - Georgios Nintos
- King’s College London, and Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Vineet Kwatra
- King’s College London, and Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Lorna Grove
- The Institute of Cancer Research, London, United Kingdom
| | | | - Paula Proszek
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Philip Martin
- Oncology R&D, AstraZeneca, Gaithersburg, Maryland, USA
| | - Luiza Moore
- Oncology R&D, AstraZeneca, Gaithersburg, Maryland, USA
| | | | - Udai Banerji
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | | | - James Spicer
- King’s College London, and Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Martin D. Forster
- UCL Cancer Institute and University College London Hospital NHS Foundation Trust, London, United Kingdom
| | - Kevin J. Harrington
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
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Xing T, Li L, Rao X, Zhao J, Chen Y, Ju G, Xu Y, Gao X, Dong G, Xia X, Guan Y, Zhang L, Wen Z, Liang J. ARID1A deficiency promotes progression and potentiates therapeutic antitumour immunity in hepatitis B virus-related hepatocellular carcinoma. BMC Gastroenterol 2024; 24:11. [PMID: 38166741 PMCID: PMC10759659 DOI: 10.1186/s12876-023-03059-w] [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: 04/20/2023] [Accepted: 11/22/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Exploring predictive biomarkers and therapeutic strategies of ICBs has become an urgent need in clinical practice. Increasing evidence has shown that ARID1A deficiency might play a critical role in sculpting tumor environments in various tumors and might be used as pan-cancer biomarkers for immunotherapy outcomes. The current study aims to explored the immune-modulating role of ARID1A deficiency in Hepatitis B virus (HBV) related hepatocellular carcinoma (HBV-HCC) and its potential immunotherapeutic implications. METHODS In the current study, we performed a comprehensive analysis using bioinformatics approaches and pre-clinical experiments to evaluate the ARID1A regulatory role on the biological behavior, and immune landscape of Hepatitis B virus (HBV) related hepatocellular carcinoma (HBV-HCC). A total of 425 HBV-related hepatocellular carcinoma patients from TCGA-LIHC, AMC and CHCC-HBV cohort were enrolled in bioinformatics analysis. Immunohistochemical staining of HBV-HCC specimens and ARID1A deficiency cellular models were used to validate the results of the analysis. RESULTS Our results have shown that ARID1A deficiency promoted tumor proliferation and metastasis. More importantly, ARID1A deficiency in HBV-HCC was associated with the higher TMB, elevated immune activity, and up-regulated expression of immune checkpoint proteins, especially TIM-3 in HBV-HCC. Further, the expression of Galectin-9, which is the ligand of TIM-3, was elevated in the ARID1A knockout HBV positive cell line. CONCLUSION To conclude, we have shown that the ARID1A deficiency was correlated with more active immune signatures and higher expression of immune checkpoints in HBV-HCC. Additionally, the present study provides insights to explore the possibility of the predictive role of ARID1A in HBV-HCC patients responsive to immunotherapy.
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Affiliation(s)
- Tao Xing
- Departments of Oncology, Peking University International Hospital, 1 Life Park Road, Life Science Park of Zhongguancun, Changping, Beijing, 102206, China
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, No. 52, Fucheng Road, Haidian District, Beijing, 100142, China
| | - Li Li
- Departments of Oncology, Peking University International Hospital, 1 Life Park Road, Life Science Park of Zhongguancun, Changping, Beijing, 102206, China
| | - Xiaosong Rao
- HAINAN YILING Medical Industry Development Co.,Ldt, Qionghai, Hainan, 571442, China
| | - Jing Zhao
- Department of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, 72074, Germany
| | - Yiran Chen
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, 350014, China
| | - Gaoda Ju
- Departments of Oncology, Peking University International Hospital, 1 Life Park Road, Life Science Park of Zhongguancun, Changping, Beijing, 102206, China
| | - Yaping Xu
- Geneplus-Beijing Institute, Beijing, 102206, China
| | - Xuan Gao
- Geneplus-Beijing Institute, Beijing, 102206, China
| | - Guilan Dong
- Tangshan People's Hospital, Tangshan, Hebei, 063001, China
| | - Xuefeng Xia
- Geneplus-Beijing Institute, Beijing, 102206, China
| | - Yanfang Guan
- Geneplus-Beijing Institute, Beijing, 102206, China
| | - Lingling Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, No. 52, Fucheng Road, Haidian District, Beijing, 100142, China.
| | - Zhenping Wen
- Inner Mongolia Cancer Hospital, 42 Zhaowuda Road, Saihan District, Hohhot, Inner Mongolia, 010020, P. R. China.
| | - Jun Liang
- Departments of Oncology, Peking University International Hospital, 1 Life Park Road, Life Science Park of Zhongguancun, Changping, Beijing, 102206, China.
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, No. 52, Fucheng Road, Haidian District, Beijing, 100142, China.
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Hernández-Oliveras A, Zarain-Herzberg A. The role of Ca 2+-signaling in the regulation of epigenetic mechanisms. Cell Calcium 2024; 117:102836. [PMID: 37988873 DOI: 10.1016/j.ceca.2023.102836] [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: 07/04/2023] [Revised: 11/10/2023] [Accepted: 11/16/2023] [Indexed: 11/23/2023]
Abstract
Epigenetic mechanisms regulate multiple cell functions like gene expression and chromatin conformation and stability, and its misregulation could lead to several diseases including cancer. Epigenetic drugs are currently under investigation in a broad range of diseases, but the cellular processes involved in regulating epigenetic mechanisms are not fully understood. Calcium (Ca2+) signaling regulates several cellular mechanisms such as proliferation, gene expression, and metabolism, among others. Moreover, Ca2+ signaling is also involved in diseases such as neurological disorders, cardiac, and cancer. Evidence indicates that Ca2+ signaling and epigenetics are involved in the same cellular functions, which suggests a possible interplay between both mechanisms. Ca2+-activated transcription factors regulate the recruitment of chromatin remodeling complexes into their target genes, and Ca2+-sensing proteins modulate their activity and intracellular localization. Thus, Ca2+ signaling is an important regulator of epigenetic mechanisms. Moreover, Ca2+ signaling activates epigenetic mechanisms that in turn regulate genes involved in Ca2+ signaling, suggesting possible feedback between both mechanisms. The understanding of how epigenetics are regulated could lead to developing better therapeutical approaches.
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Affiliation(s)
- Andrés Hernández-Oliveras
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Angel Zarain-Herzberg
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico.
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Lee J, Shin DY, Jang Y, Han JP, Cho EM, Seo YR. Cadmium-induced Carcinogenesis in Respiratory Organs and the Prostate: Insights from Three Perspectives on Toxicogenomic Approach. J Cancer Prev 2023; 28:150-159. [PMID: 38205367 PMCID: PMC10774485 DOI: 10.15430/jcp.2023.28.4.150] [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: 12/15/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
Cadmium (Cd) exposure primarily occurs through inhalation, either by smoking or occupational exposure to contaminated air. Upon inhalation, Cd ultimately reaches the prostate through the bloodstream. In this review, we investigate the carcinogenic potential of Cd in both respiratory organs and the prostate. Specifically, this review examines cellular metabolism, comprehensive toxicity, and carcinogenic mechanisms by exploring gene ontology, biological networks, and adverse outcome pathways. In the respiratory organs, Cd induces lung cancer by altering the expression of IL1B and FGF2, causing DNA damage, reducing cell junction integrity, and promoting apoptosis. In the prostate, Cd induces prostate cancer by modifying the expression of EDN1 and HMOX1, leading to abnormal protein activities and maturation, suppressing tumor suppressors, and inducing apoptosis. Collectively, this review provides a comprehensive understanding of the carcinogenic mechanisms of Cd in two different organs by adopting toxicogenomic approaches. These insights can serve as a foundation for further research on cadmium-induced cancer, contributing to the establishment of future cancer prevention strategies.
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Affiliation(s)
- Jun Lee
- Department of Life Science, Institute of Environmental Medicine for Green Chemistry, Dongguk University Biomedi Campus, Goyang, Korea
| | - Dong Yeop Shin
- Department of Life Science, Institute of Environmental Medicine for Green Chemistry, Dongguk University Biomedi Campus, Goyang, Korea
| | - Yujin Jang
- Department of Life Science, Institute of Environmental Medicine for Green Chemistry, Dongguk University Biomedi Campus, Goyang, Korea
| | - Jun Pyo Han
- Department of Life Science, Institute of Environmental Medicine for Green Chemistry, Dongguk University Biomedi Campus, Goyang, Korea
| | - Eun-Min Cho
- Department of Nano, Chemical & Biological Engineering, College of Natural Science and Engineering, Seokyeong University, Seoul, Korea
| | - Young Rok Seo
- Department of Life Science, Institute of Environmental Medicine for Green Chemistry, Dongguk University Biomedi Campus, Goyang, Korea
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Wang A, Jin Y, Cao Z, Lu L, Li Z. Clinicopathological characteristics and treatment outcomes of advanced SMARCA4-deficient thoracic tumors. Cancer Med 2023; 13:e6809. [PMID: 38124509 PMCID: PMC10807565 DOI: 10.1002/cam4.6809] [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: 08/24/2023] [Revised: 11/16/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
PURPOSE SMARCA4-deficient thoracic tumors, characterized by distinct clinicopathological, morphological, immunohistochemical, and genetic features, differ significantly from conventional non-small-cell lung carcinomas (NSCLCs). This group encompasses both SMARCA4-deficient NSCLCs (SMARCA4-NSCLCs) and SMARCA4-deficient undifferentiated tumors (SMARCA4-UTs). The efficacy of PD-1 inhibitors in treating SMARCA4-deficient thoracic tumors remains uncertain. METHODS Medical records of 36 patients diagnosed with stage IIIB, IIIC, or IV SMARCA4-deficient thoracic tumors were analyzed. We assessed the clinical, pathological, and genetic features of these patients through immunohistochemistry (IHC) and a 68-gene panel next-generation sequencing (NGS). We compared the differences between SMARCA4-NSCLCs and SMARCA4-UTs, and evaluated the impact of chemotherapy and immunotherapy on patient outcomes. RESULTS The majority of patients with SMARCA4-deficient thoracic tumors were heavy-smoking males, averaging 64.6 years in age. IHC predominantly showed weak or negative staining for markers such as TTF-1, CK5/6, p40, synaptophysin, chromogranin A, and CD56, which are often associated with adenocarcinoma, squamous cell carcinoma, and neuroendocrine tumors. The most common genetic mutations identified via NGS included TP53, CDKN2A, KRAS, STK11, NF1, and PTEN. No significant overall survival (OS) difference was observed between SMARCA4-NSCLCs and SMARCA4-UTs (p = 0.366). The median OS for patients treated with chemotherapy (n = 9) was 447 days, while the median OS for patients undergoing PD-1-inhibitor-based therapy (n = 16) was not reached (p = 0.105). CONCLUSION SMARCA4-deficient thoracic tumors exhibit distinct characteristics from conventional NSCLCs, and PD-1 inhibitors show promise in treating advanced SMARCA4-deficient thoracic tumors.
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Affiliation(s)
- Anni Wang
- Shanghai Lung Cancer Center, Shanghai Chest HospitalShanghai Jiao Tong University, School of MedicineShanghaiChina
| | - Yueping Jin
- Shanghai Lung Cancer Center, Shanghai Chest HospitalShanghai Jiao Tong University, School of MedicineShanghaiChina
| | - Zhengqi Cao
- Shanghai Lung Cancer Center, Shanghai Chest HospitalShanghai Jiao Tong University, School of MedicineShanghaiChina
| | - Li Lu
- Shanghai Lung Cancer Center, Shanghai Chest HospitalShanghai Jiao Tong University, School of MedicineShanghaiChina
| | - Ziming Li
- Shanghai Lung Cancer Center, Shanghai Chest HospitalShanghai Jiao Tong University, School of MedicineShanghaiChina
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Li JJ, Lee CS. The Role of the AT-Rich Interaction Domain 1A Gene ( ARID1A) in Human Carcinogenesis. Genes (Basel) 2023; 15:5. [PMID: 38275587 PMCID: PMC10815128 DOI: 10.3390/genes15010005] [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: 11/13/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024] Open
Abstract
The switch/sucrose non-fermentable (SWI/SNF) (SWI/SNF) complex uses energy from ATP hydrolysis to mobilise nucleosomes on chromatin. Components of SWI/SNF are mutated in 20% of all human cancers, of which mutations in AT-rich binding domain protein 1A (ARID1A) are the most common. ARID1A is mutated in nearly half of ovarian clear cell carcinoma and around one-third of endometrial and ovarian carcinomas of the endometrioid type. This review will examine in detail the molecular functions of ARID1A, including its role in cell cycle control, enhancer regulation, and the prevention of telomerase activity. ARID1A has key roles in the maintenance of genomic integrity, including DNA double-stranded break repair, DNA decatenation, integrity of the cohesin complex, and reduction in replication stress, and is also involved in mismatch repair. The role of ARID1A loss in the pathogenesis of some of the most common human cancers is discussed, with a particular emphasis on gynaecological cancers. Finally, several promising synthetic lethal strategies, which exploit the specific vulnerabilities of ARID1A-deficient cancer cells, are briefly mentioned.
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Affiliation(s)
- Jing Jing Li
- Department of Anatomical Pathology, Liverpool Hospital, Liverpool, NSW 2170, Australia;
- Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia
| | - Cheok Soon Lee
- Department of Anatomical Pathology, Liverpool Hospital, Liverpool, NSW 2170, Australia;
- Discipline of Pathology, School of Medicine, Western Sydney University, Sydney, NSW 2560, Australia
- South Western Sydney Clinical School, University of New South Wales, Liverpool, NSW 2170, Australia
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW 2010, Australia
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Shafi O, Siddiqui G, Jaffry HA. The benign nature and rare occurrence of cardiac myxoma as a possible consequence of the limited cardiac proliferative/ regenerative potential: a systematic review. BMC Cancer 2023; 23:1245. [PMID: 38110859 PMCID: PMC10726542 DOI: 10.1186/s12885-023-11723-3] [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: 08/08/2023] [Accepted: 12/05/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND Cardiac Myxoma is a primary tumor of heart. Its origins, rarity of the occurrence of primary cardiac tumors and how it may be related to limited cardiac regenerative potential, are not yet entirely known. This study investigates the key cardiac genes/ transcription factors (TFs) and signaling pathways to understand these important questions. METHODS Databases including PubMed, MEDLINE, and Google Scholar were searched for published articles without any date restrictions, involving cardiac myxoma, cardiac genes/TFs/signaling pathways and their roles in cardiogenesis, proliferation, differentiation, key interactions and tumorigenesis, with focus on cardiomyocytes. RESULTS The cardiac genetic landscape is governed by a very tight control between proliferation and differentiation-related genes/TFs/pathways. Cardiac myxoma originates possibly as a consequence of dysregulations in the gene expression of differentiation regulators including Tbx5, GATA4, HAND1/2, MYOCD, HOPX, BMPs. Such dysregulations switch the expression of cardiomyocytes into progenitor-like state in cardiac myxoma development by dysregulating Isl1, Baf60 complex, Wnt, FGF, Notch, Mef2c and others. The Nkx2-5 and MSX2 contribute predominantly to both proliferation and differentiation of Cardiac Progenitor Cells (CPCs), may possibly serve roles based on the microenvironment and the direction of cell circuitry in cardiac tumorigenesis. The Nkx2-5 in cardiac myxoma may serve to limit progression of tumorigenesis as it has massive control over the proliferation of CPCs. The cardiac cell type-specific genetic programming plays governing role in controlling the tumorigenesis and regenerative potential. CONCLUSION The cardiomyocytes have very limited proliferative and regenerative potential. They survive for long periods of time and tightly maintain the gene expression of differentiation genes such as Tbx5, GATA4 that interact with tumor suppressors (TS) and exert TS like effect. The total effect such gene expression exerts is responsible for the rare occurrence and benign nature of primary cardiac tumors. This prevents the progression of tumorigenesis. But this also limits the regenerative and proliferative potential of cardiomyocytes. Cardiac Myxoma develops as a consequence of dysregulations in these key genes which revert the cells towards progenitor-like state, hallmark of CM. The CM development in carney complex also signifies the role of TS in cardiac cells.
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Affiliation(s)
- Ovais Shafi
- Sindh Medical College - Jinnah Sindh Medical University / Dow University of Health Sciences, Karachi, Pakistan.
| | - Ghazia Siddiqui
- Sindh Medical College - Jinnah Sindh Medical University / Dow University of Health Sciences, Karachi, Pakistan
| | - Hassam A Jaffry
- Sindh Medical College - Jinnah Sindh Medical University / Dow University of Health Sciences, Karachi, Pakistan
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48
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Epp S, Chuah SM, Halasz M. Epigenetic Dysregulation in MYCN-Amplified Neuroblastoma. Int J Mol Sci 2023; 24:17085. [PMID: 38069407 PMCID: PMC10707345 DOI: 10.3390/ijms242317085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
Neuroblastoma (NB), a childhood cancer arising from the neural crest, poses significant clinical challenges, particularly in cases featuring amplification of the MYCN oncogene. Epigenetic factors play a pivotal role in normal neural crest and NB development, influencing gene expression patterns critical for tumorigenesis. This review delves into the multifaceted interplay between MYCN and known epigenetic modifications during NB genesis, shedding light on the intricate regulatory networks underlying the disease. We provide an extensive survey of known epigenetic mechanisms, encompassing DNA methylation, histone modifications, non-coding RNAs, super-enhancers (SEs), bromodomains (BET), and chromatin modifiers in MYCN-amplified (MNA) NB. These epigenetic changes collectively contribute to the dysregulated gene expression landscape observed in MNA NB. Furthermore, we review emerging therapeutic strategies targeting epigenetic regulators, including histone deacetylase inhibitors (HDACi), histone methyltransferase inhibitors (HMTi), and DNA methyltransferase inhibitors (DNMTi). We also discuss and summarize current drugs in preclinical and clinical trials, offering insights into their potential for improving outcomes for MNA NB patients.
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Affiliation(s)
- Soraya Epp
- Systems Biology Ireland, UCD School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland; (S.E.)
| | - Shin Mei Chuah
- Systems Biology Ireland, UCD School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland; (S.E.)
| | - Melinda Halasz
- Systems Biology Ireland, UCD School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland; (S.E.)
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland
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Yu Y, Wang S, Wang Z, Gao R, Lee J. Arabidopsis thaliana: a powerful model organism to explore histone modifications and their upstream regulations. Epigenetics 2023; 18:2211362. [PMID: 37196184 DOI: 10.1080/15592294.2023.2211362] [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: 11/24/2022] [Revised: 04/07/2023] [Accepted: 04/28/2023] [Indexed: 05/19/2023] Open
Abstract
Histones are subjected to extensive covalent modifications that affect inter-nucleosomal interactions as well as alter chromatin structure and DNA accessibility. Through switching the corresponding histone modifications, the level of transcription and diverse downstream biological processes can be regulated. Although animal systems are widely used in studying histone modifications, the signalling processes that occur outside the nucleus prior to histone modifications have not been well understood due to the limitations including non viable mutants, partial lethality, and infertility of survivors. Here, we review the benefits of using Arabidopsis thaliana as the model organism to study histone modifications and their upstream regulations. Similarities among histones and key histone modifiers such as the Polycomb group (PcG) and Trithorax group (TrxG) in Drosophila, Human, and Arabidopsis are examined. Furthermore, prolonged cold-induced vernalization system has been well-studied and revealed the relationship between the controllable environment input (duration of vernalization), its chromatin modifications of FLOWERING LOCUS C (FLC), following gene expression, and the corresponding phenotypes. Such evidence suggests that research on Arabidopsis can bring insights into incomplete signalling pathways outside of the histone box, which can be achieved through viable reverse genetic screenings based on the phenotypes instead of direct monitoring of histone modifications among individual mutants. The potential upstream regulators in Arabidopsis can provide cues or directions for animal research based on the similarities between them.
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Affiliation(s)
- Yang Yu
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Sihan Wang
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Ziqin Wang
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Renwei Gao
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Joohyun Lee
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
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Kamal M, Atwi D, Pang H, Li S, Hassell L. Dedifferentiated Ovarian Carcinoma with ARID1A and ARID1B Mutations: A Clinicopathological Report and Literature Review. Int J Surg Pathol 2023; 31:1526-1531. [PMID: 36843546 DOI: 10.1177/10668969231157776] [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: 02/28/2023]
Abstract
Dedifferentiated carcinoma of the female genital tract is a relatively recently recognized aggressive tumor affecting predominantly perimenopausal and postmenopausal women. In addition to having an undifferentiated component, dedifferentiated carcinoma includes a juxtaposed endometrioid adenocarcinoma, FIGO grade 1 or 2. Molecular characterization of these tumors has been a subject of discussion in multiple recent articles. We present a case of dedifferentiated carcinoma of the ovary in a 70-year-old female demonstrating concurrent inactivation of ARID1A and ARID1B. To the best of our knowledge, this is the second clinical report demonstrating dedifferentiated carcinoma of the ovary with concurrent inactivation of ARID1A and ARID1B. ARID1A and ARID1B inactivation seems to represent an alternate mechanism of switch/sucrose nonfermentable complex inactivation in the development of dedifferentiated carcinoma. Additional studies are warranted to precisely understand the molecular mechanism of cellular dedifferentiation in the dedifferentiated endometrial/ovarian carcinomas, thus guiding the development of targeted therapy.
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Affiliation(s)
- Maria Kamal
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Doaa Atwi
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Hui Pang
- Genetics Lab, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Shibo Li
- Genetics Lab, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Lewis Hassell
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
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