1
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Yavas A, Ozcan K, Adsay NV, Balci S, Tarcan ZC, Hechtman JF, Luchini C, Scarpa A, Lawlor RT, Mafficini A, Reid MD, Xue Y, Yang Z, Haye K, Bellizzi AM, Vanoli A, Benhamida J, Balachandran V, Jarnagin W, Park W, O'Reilly EM, Klimstra DS, Basturk O. SWI/SNF Complex-Deficient Undifferentiated Carcinoma of the Pancreas: Clinicopathologic and Genomic Analysis. Mod Pathol 2024; 37:100585. [PMID: 39094734 DOI: 10.1016/j.modpat.2024.100585] [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: 04/08/2024] [Revised: 07/12/2024] [Accepted: 07/25/2024] [Indexed: 08/04/2024]
Abstract
Inactivating alterations in the SWItch/Sucrose NonFermentable (SWI/SNF) Chromatin Remodeling Complex subunits have been described in multiple tumor types. Recent studies focused on SMARC subunits of this complex to understand their relationship with tumor characteristics and therapeutic opportunities. To date, pancreatic cancer with these alterations has not been well studied, although isolated cases of undifferentiated carcinomas have been reported. Herein, we screened 59 pancreatic undifferentiated carcinomas for alterations in SWI/SNF complex-related (SMARCB1 [BAF47/INI1], SMARCA4 [BRG1], SMARCA2 [BRM]) proteins and/or genes using immunohistochemistry and/or next-generation sequencing. Cases with alterations in SWI/SNF complex-related proteins/genes were compared with cases without alterations, as well as with 96 conventional pancreatic ductal adenocarcinomas (PDAC). In all tumor groups, mismatch repair and PD-L1 protein expression were also evaluated. Thirty of 59 (51%) undifferentiated carcinomas had a loss of SWI/SNF complex-related protein expression or gene alteration. Twenty-seven of 30 (90%) SWI-/SNF-deficient undifferentiated carcinomas had rhabdoid morphology (vs 9/29 [31%] SWI-/SNF-retained undifferentiated carcinomas; P < .001) and all expressed cytokeratin, at least focally. Immunohistochemically, SMARCB1 protein expression was absent in 16/30 (53%) cases, SMARCA2 in 4/30 (13%), and SMARCA4 in 4/30 (13%); both SMARCB1 and SMARCA2 protein expressions were absent in 1/30 (3%). Five of 8 (62.5%) SWI-/SNF-deficient undifferentiated carcinomas that displayed loss of SMARCB1 protein expression by immunohistochemistry were found to have corresponding SMARCB1 deletions by next-generation sequencing. Analysis of canonical driver mutations for PDAC in these cases showed KRAS (2/5) and TP53 (2/5) abnormalities. Median combined positive score for PD-L1 (E1L3N) was significantly higher in the undifferentiated carcinomas with/without SWI/SNF deficiency compared with the conventional PDACs (P < .001). SWI-/SNF-deficient undifferentiated carcinomas were larger (P < .001) and occurred in younger patients (P < .001). Patients with SWI-/SNF-deficient undifferentiated carcinoma had worse overall survival compared with patients with SWI-/SNF-retained undifferentiated carcinoma (P = .004) and PDAC (P < .001). Our findings demonstrate that SWI-/SNF-deficient pancreatic undifferentiated carcinomas are frequently characterized by rhabdoid morphology, exhibit highly aggressive behavior, and have a negative prognostic impact. The ones with SMARCB1 deletions appear to be frequently KRAS wild type. Innovative developmental therapeutic strategies targeting this genomic basis of the SWI/SNF complex and the therapeutic implications of EZH2 inhibition (NCT03213665), SMARCA2 degrader (NCT05639751), or immunotherapy are currently under investigation.
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Affiliation(s)
- Aslihan Yavas
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Pathology, Now with Institute of Pathology, Heinrich Heine University and University Hospital of Düsseldorf, Düsseldorf, Germany
| | - Kerem Ozcan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Now with Department of Pathology and Laboratory Medicine, Henry Ford Hospital, Detroit, Michigan
| | - N Volkan Adsay
- The Department of Pathology, Koç University Hospital and Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Turkey
| | - Serdar Balci
- Department of Pathology, Memorial Healthcare Group, Istanbul, Turkey
| | - Zeynep C Tarcan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; David M. Rubenstein Center for Pancreatic Cancer Research, New York, New York
| | - Jaclyn F Hechtman
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Now with Caris Life Sciences, Miami, Florida
| | - Claudio Luchini
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy; ARC-Net Research Center, University and Hospital Trust of Verona, Verona, Italy
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Rita T Lawlor
- Department of Engineering for Innovation Medicine (DIMI), University of Verona, Verona, Italy
| | - Andrea Mafficini
- Department of Engineering for Innovation Medicine (DIMI), University of Verona, Verona, Italy
| | - Michelle D Reid
- Department of Pathology, School of Medicine, Emory University, Atlanta, Georgia
| | - Yue Xue
- Department of Pathology, University Hospitals, Cleveland, Ohio
| | - Zhaohai Yang
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Kester Haye
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Andrew M Bellizzi
- Department of Pathology, University of Iowa, Iowa City, Iowa; Department of Molecular Medicine, Unit of Anatomic Pathology, University of Pavia, Pavia, Italy
| | - Alessandro Vanoli
- Unit of Anatomic Pathology, Fondazione IRCCS San Matteo Hospital, Pavia, Italy
| | - Jamal Benhamida
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Vinod Balachandran
- David M. Rubenstein Center for Pancreatic Cancer Research, New York, New York; Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - William Jarnagin
- David M. Rubenstein Center for Pancreatic Cancer Research, New York, New York; Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Wungki Park
- David M. Rubenstein Center for Pancreatic Cancer Research, New York, New York; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Eileen M O'Reilly
- David M. Rubenstein Center for Pancreatic Cancer Research, New York, New York; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David S Klimstra
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Now with Paige.AI, New York, New York
| | - Olca Basturk
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; David M. Rubenstein Center for Pancreatic Cancer Research, New York, New York.
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Chmykhalo VK, Deev RV, Tokarev AT, Polunina YA, Xue L, Shidlovskii YV. SWI/SNF Complex Connects Signaling and Epigenetic State in Cells of Nervous System. Mol Neurobiol 2024:10.1007/s12035-024-04355-6. [PMID: 39002058 DOI: 10.1007/s12035-024-04355-6] [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: 03/07/2024] [Accepted: 07/06/2024] [Indexed: 07/15/2024]
Abstract
SWI/SNF protein complexes are evolutionarily conserved epigenetic regulators described in all eukaryotes. In metameric animals, the complexes are involved in all processes occurring in the nervous system, from neurogenesis to higher brain functions. On the one hand, the range of roles is wide because the SWI/SNF complexes act universally by mobilizing the nucleosomes in a chromatin template at multiple loci throughout the genome. On the other hand, the complexes mediate the action of multiple signaling pathways that control most aspects of neural tissue development and function. The issues are discussed to provide insight into the molecular basis of the multifaceted role of SWI/SNFs in cell cycle regulation, DNA repair, activation of immediate-early genes, neurogenesis, and brain and connectome formation. An overview is additionally provided for the molecular basis of nervous system pathologies associated with the SWI/SNF complexes and their contribution to neuroinflammation and neurodegeneration. Finally, we discuss the idea that SWI/SNFs act as an integration platform to connect multiple signaling and genetic programs.
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Affiliation(s)
- Victor K Chmykhalo
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova St, Moscow, 119334, Russia.
| | - Roman V Deev
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova St, Moscow, 119334, Russia
| | - Artemiy T Tokarev
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova St, Moscow, 119334, Russia
| | - Yulia A Polunina
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova St, Moscow, 119334, Russia
| | - Lei Xue
- School of Life Science and Technology, The First Rehabilitation Hospital of Shanghai, Tongji University, Shanghai, China
| | - Yulii V Shidlovskii
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova St, Moscow, 119334, Russia
- Department of Biology and General Genetics, Sechenov University, Moscow, Russia
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3
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Skálová A, Agaimy A, Bradova M, Poorten VV, Hanna E, Guntinas-Lichius O, Franchi A, Hellquist H, Simpson RHW, Lopéz F, Nuyts S, Chiesa-Estomba C, Ng SP, Homma A, Teng Y, Leivo I, Ferlito A. Molecularly defined sinonasal malignancies: an overview with focus on the current WHO classification and recently described provisional entities. Virchows Arch 2024; 484:885-900. [PMID: 38491228 PMCID: PMC11186917 DOI: 10.1007/s00428-024-03775-y] [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: 01/06/2024] [Revised: 02/19/2024] [Accepted: 03/04/2024] [Indexed: 03/18/2024]
Abstract
Classification of tumors of the head and neck has evolved in recent decades including a widespread application of molecular testing in tumors of the sinonasal tract, salivary glands, and soft tissues with a predilection for the head and neck. The availability of new molecular techniques has allowed for the definition of multiple novel tumor types unique to head and neck sites. Moreover, an expanding spectrum of immunohistochemical markers specific to genetic alterations facilitates rapid identification of diagnostic molecular abnormalities. As such, it is currently possible for head and neck pathologists to benefit from a molecularly defined tumor classification while making diagnoses that are still based largely on histopathology and immunohistochemistry. This review covers the principal molecular alterations in sinonasal malignancies, such as alterations in DEK, AFF2, NUTM1, IDH1-2, and SWI/SNF genes in particular, that are important from a practical standpoint for diagnosis, prognosis, and prediction of response to treatment.
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Affiliation(s)
- Alena Skálová
- Sikl's Department of Pathology, Faculty of Medicine in Pilsen, Charles University, E. Benese 13, 305 99, Pilsen, Czech Republic.
- Bioptic Laboratory, Ltd., Pilsen, Czech Republic.
| | - Abbas Agaimy
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Martina Bradova
- Sikl's Department of Pathology, Faculty of Medicine in Pilsen, Charles University, E. Benese 13, 305 99, Pilsen, Czech Republic
- Bioptic Laboratory, Ltd., Pilsen, Czech Republic
| | - Vincent Vander Poorten
- Department of Otorhinolaryngology-Head and Neck Surgery, Leuven Cancer Institute, University Hospitals Leuven, 3000, Louvain, Belgium
- Department of Oncology, Section Head and Neck Oncology, Leuven Cancer Institute, KU Leuven, Louvain, Belgium
| | - Ehab Hanna
- Department of Head & Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Alessandro Franchi
- Department of Translational Research, School of Medicine, University of Pisa, Pisa, Italy
| | - Henrik Hellquist
- Faculty of Medicine and Biomedical Sciences (FMCB), Biomedical Center Research Institute (ABC-RI), University of Algarve, Faro, Portugal
| | | | - Fernando Lopéz
- Department of Otolaryngology, ISPA, IUOPA, CIBERONC, Hospital Universitario Central de Asturias, University of Oviedo, Oviedo, Spain
| | - Sandra Nuyts
- Laboratory of Experimental Radiotherapy, Department of Oncology, Leuven Cancer Institute, University Hospitals Leuven, 3000, Louvain, Belgium
- Department of Radiation Oncology, Leuven Cancer Institute, University Hospitals Leuven, 3000, Louvain, Belgium
| | - Carlos Chiesa-Estomba
- Department of Otorhinolaryngology-Head and Neck Surgery, Hospital Universitario Donostia, Donostia-San Sebastian, Guipuzkoa-Basque Country, Spain
| | - Sweet Ping Ng
- Department of Radiation Oncology, Olivia Newton-John Cancer Wellness and Research Centre, Austin Health, Melbourne, Australia
| | - Akihiro Homma
- Department of Otolaryngology-Head and Neck Surgery, Faculty of Medicine, Graduate School of Medicine, Hokkaido University, Hokkaido, Japan
| | - Yong Teng
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, USA
| | - Ilmo Leivo
- Institute of Biomedicine, Pathology, University of Turku, Turku, Finland
- Department of Pathology, Turku University Hospital, Turku, Finland
| | - Alfio Ferlito
- Coordinator of the International Head and Neck Scientific Group, Padua, Italy
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4
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Chaudhri A, Lizee G, Hwu P, Rai K. Chromatin Remodelers Are Regulators of the Tumor Immune Microenvironment. Cancer Res 2024; 84:965-976. [PMID: 38266066 DOI: 10.1158/0008-5472.can-23-2244] [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: 09/06/2023] [Revised: 11/24/2023] [Accepted: 01/17/2024] [Indexed: 01/26/2024]
Abstract
Immune checkpoint inhibitors show remarkable responses in a wide range of cancers, yet patients develop adaptive resistance. This necessitates the identification of alternate therapies that synergize with immunotherapies. Epigenetic modifiers are potent mediators of tumor-intrinsic mechanisms and have been shown to regulate immune response genes, making them prime targets for therapeutic combinations with immune checkpoint inhibitors. Some success has been observed in early clinical studies that combined immunotherapy with agents targeting DNA methylation and histone modification; however, less is known about chromatin remodeler-targeted therapies. Here, we provide a discussion on the regulation of tumor immunogenicity by the chromatin remodeling SWI/SNF complex through multiple mechanisms associated with immunotherapy response that broadly include IFN signaling, DNA damage, mismatch repair, regulation of oncogenic programs, and polycomb-repressive complex antagonism. Context-dependent targeting of SWI/SNF subunits can elicit opportunities for synthetic lethality and reduce T-cell exhaustion. In summary, alongside the significance of SWI/SNF subunits in predicting immunotherapy outcomes, their ability to modulate the tumor immune landscape offers opportunities for therapeutic intervention.
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Affiliation(s)
- Apoorvi Chaudhri
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Gregory Lizee
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Kunal Rai
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
- MDACC Epigenomics Therapy Initiative, The University of Texas MD Anderson Cancer Center, Houston, Texas
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Spisak S, Chen D, Likasitwatanakul P, Doan P, Li Z, Bala P, Vizkeleti L, Tisza V, De Silva P, Giannakis M, Wolpin B, Qi J, Sethi NS. Identifying regulators of aberrant stem cell and differentiation activity in colorectal cancer using a dual endogenous reporter system. Nat Commun 2024; 15:2230. [PMID: 38472198 PMCID: PMC10933491 DOI: 10.1038/s41467-024-46285-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] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Aberrant stem cell-like activity and impaired differentiation are central to the development of colorectal cancer (CRC). To identify functional mediators of these key cellular programs, we engineer a dual endogenous reporter system by genome-editing the SOX9 and KRT20 loci of human CRC cell lines to express fluorescent reporters, broadcasting aberrant stem cell-like and differentiation activity, respectively. By applying a CRISPR screen targeting 78 epigenetic regulators with 542 sgRNAs to this platform, we identify factors that contribute to stem cell-like activity and differentiation in CRC. Perturbation single cell RNA sequencing (Perturb-seq) of validated hits nominate SMARCB1 of the BAF complex (also known as SWI/SNF) as a negative regulator of differentiation across an array of neoplastic colon models. SMARCB1 is a dependency and required for in vivo growth of human CRC models. These studies highlight the utility of biologically designed endogenous reporter platforms to uncover regulators with therapeutic potential.
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Affiliation(s)
- Sandor Spisak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - David Chen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Pornlada Likasitwatanakul
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Paul Doan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Zhixin Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Pratyusha Bala
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Laura Vizkeleti
- Department of Bioinformatics, Faculty of Medicine, Semmelweis University, 1094, Budapest, Hungary
| | - Viktoria Tisza
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Pushpamali De Silva
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
- Gastrointestinal Cancer Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Brian Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Gastrointestinal Cancer Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nilay S Sethi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA.
- Gastrointestinal Cancer Center, Dana-Farber Cancer Institute, Boston, MA, USA.
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6
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Hipólito A, Xavier R, Brito C, Tomás A, Lemos I, Cabaço LC, Silva F, Oliva A, Barral DC, Vicente JB, Gonçalves LG, Pojo M, Serpa J. BRD9 status is a major contributor for cysteine metabolic remodeling through MST and EAAT3 modulation in malignant melanoma. Biochim Biophys Acta Mol Basis Dis 2024; 1870:166983. [PMID: 38070581 DOI: 10.1016/j.bbadis.2023.166983] [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: 06/06/2023] [Revised: 10/31/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023]
Abstract
Cutaneous melanoma (CM) is the most aggressive skin cancer, showing globally increasing incidence. Hereditary CM accounts for a significant percentage (5-15 %) of all CM cases. However, most familial cases remain without a known genetic cause. Even though, BRD9 has been associated to CM as a susceptibility gene. The molecular events following BRD9 mutagenesis are still not completely understood. In this study, we disclosed BRD9 as a key regulator in cysteine metabolism and associated altered BRD9 to increased cell proliferation, migration and invasiveness, as well as to altered melanin levels, inducing higher susceptibility to melanomagenesis. It is evident that BRD9 WT and mutated BRD9 (c.183G>C) have a different impact on cysteine metabolism, respectively by inhibiting and activating MPST expression in the metastatic A375 cell line. The effect of the mutated BRD9 variant was more evident in A375 cells than in the less invasive WM115 line. Our data point out novel molecular and metabolic mechanisms dependent on BRD9 status that potentially account for the increased risk of developing CM and enhancing CM aggressiveness. Moreover, our findings emphasize the role of cysteine metabolism remodeling in melanoma progression and open new queues to follow to explore the role of BRD9 as a melanoma susceptibility or cancer-related gene.
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Affiliation(s)
- Ana Hipólito
- iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 130, 1169-056 Lisboa, Portugal; Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG), Rua Prof Lima Basto, 1099-023 Lisboa, Portugal
| | - Renato Xavier
- Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG), Rua Prof Lima Basto, 1099-023 Lisboa, Portugal
| | - Cheila Brito
- Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG), Rua Prof Lima Basto, 1099-023 Lisboa, Portugal
| | - Ana Tomás
- iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 130, 1169-056 Lisboa, Portugal; Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG), Rua Prof Lima Basto, 1099-023 Lisboa, Portugal
| | - Isabel Lemos
- Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG), Rua Prof Lima Basto, 1099-023 Lisboa, Portugal; Instituto de Tecnologia Química e Tecnológica (ITQB) António Xavier da Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Luís C Cabaço
- iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 130, 1169-056 Lisboa, Portugal
| | - Fernanda Silva
- iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 130, 1169-056 Lisboa, Portugal; Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG), Rua Prof Lima Basto, 1099-023 Lisboa, Portugal
| | - Abel Oliva
- Instituto de Tecnologia Química e Tecnológica (ITQB) António Xavier da Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Duarte C Barral
- iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 130, 1169-056 Lisboa, Portugal
| | - João B Vicente
- Instituto de Tecnologia Química e Tecnológica (ITQB) António Xavier da Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Luís G Gonçalves
- Instituto de Tecnologia Química e Tecnológica (ITQB) António Xavier da Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Marta Pojo
- Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG), Rua Prof Lima Basto, 1099-023 Lisboa, Portugal
| | - Jacinta Serpa
- iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 130, 1169-056 Lisboa, Portugal; Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG), Rua Prof Lima Basto, 1099-023 Lisboa, Portugal.
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7
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Skálová A, Bradová M, Michal M, Mosaieby E, Klubíčková N, Vaněček T, Leivo I. Molecular pathology in diagnosis and prognostication of head and neck tumors. Virchows Arch 2024; 484:215-231. [PMID: 38217715 PMCID: PMC10948559 DOI: 10.1007/s00428-023-03731-2] [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: 10/17/2023] [Revised: 12/26/2023] [Accepted: 12/28/2023] [Indexed: 01/15/2024]
Abstract
Classification of head and neck tumors has evolved in recent decades including a widespread application of molecular testing in tumors of the salivary glands, sinonasal tract, oropharynx, nasopharynx, and soft tissue. Availability of new molecular techniques allowed for the definition of multiple novel tumor types unique to head and neck sites. Moreover, the expanding spectrum of immunohistochemical markers facilitates a rapid identification of diagnostic molecular abnormalities. As such, it is currently possible for head and neck pathologists to benefit from a molecularly defined classifications, while making diagnoses that are still based largely on histopathology and immunohistochemistry. This review highlights some principal molecular alterations in head and neck neoplasms presently available to assist pathologists in the practice of diagnosis, prognostication and prediction of response to treatment.
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Affiliation(s)
- Alena Skálová
- Sikl's Department of Pathology, Faculty of Medicine in Pilsen, Charles University, E. Benese 13, 305 99, Pilsen, Czech Republic.
- Bioptic Laboratory, Ltd, Pilsen, Czech Republic.
| | - Martina Bradová
- Sikl's Department of Pathology, Faculty of Medicine in Pilsen, Charles University, E. Benese 13, 305 99, Pilsen, Czech Republic
- Bioptic Laboratory, Ltd, Pilsen, Czech Republic
| | - Michael Michal
- Sikl's Department of Pathology, Faculty of Medicine in Pilsen, Charles University, E. Benese 13, 305 99, Pilsen, Czech Republic
- Bioptic Laboratory, Ltd, Pilsen, Czech Republic
| | - Elaheh Mosaieby
- Molecular and Genetic Laboratory, Bioptic Laboratory, Ltd, Pilsen, Czech Republic
| | - Natálie Klubíčková
- Sikl's Department of Pathology, Faculty of Medicine in Pilsen, Charles University, E. Benese 13, 305 99, Pilsen, Czech Republic
- Bioptic Laboratory, Ltd, Pilsen, Czech Republic
| | - Tomáš Vaněček
- Molecular and Genetic Laboratory, Bioptic Laboratory, Ltd, Pilsen, Czech Republic
| | - Ilmo Leivo
- Institute of Biomedicine, Pathology, University of Turku and Department of Pathology, Turku University Hospital, Turku, Finland
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Klein DC, Lardo SM, Hainer SJ. The ncBAF Complex Regulates Transcription in AML Through H3K27ac Sensing by BRD9. CANCER RESEARCH COMMUNICATIONS 2024; 4:237-252. [PMID: 38126767 PMCID: PMC10831031 DOI: 10.1158/2767-9764.crc-23-0382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/02/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023]
Abstract
The non-canonical BAF complex (ncBAF) subunit BRD9 is essential for acute myeloid leukemia (AML) cell viability but has an unclear role in leukemogenesis. Because BRD9 is required for ncBAF complex assembly through its DUF3512 domain, precise bromodomain inhibition is necessary to parse the role of BRD9 as a transcriptional regulator from that of a scaffolding protein. To understand the role of BRD9 bromodomain function in regulating AML, we selected a panel of five AML cell lines with distinct driver mutations, disease classifications, and genomic aberrations and subjected these cells to short-term BRD9 bromodomain inhibition. We examined the bromodomain-dependent growth of these cell lines, identifying a dependency in AML cell lines but not HEK293T cells. To define a mechanism through which BRD9 maintains AML cell survival, we examined nascent transcription, chromatin accessibility, and ncBAF complex binding genome-wide after bromodomain inhibition. We identified extensive regulation of transcription by BRD9 bromodomain activity, including repression of myeloid maturation factors and tumor suppressor genes, while standard AML chemotherapy targets were repressed by inhibition of the BRD9 bromodomain. BRD9 bromodomain activity maintained accessible chromatin at both gene promoters and gene-distal putative enhancer regions, in a manner that qualitatively correlated with enrichment of BRD9 binding. Furthermore, we identified reduced chromatin accessibility at GATA, ETS, and AP-1 motifs and increased chromatin accessibility at SNAIL-, HIC-, and TP53-recognized motifs after BRD9 inhibition. These data suggest a role for BRD9 in regulating AML cell differentiation through modulation of accessibility at hematopoietic transcription factor binding sites. SIGNIFICANCE The bromodomain-containing protein BRD9 is essential for AML cell viability, but it is unclear whether this requirement is due to the protein's role as an epigenetic reader. We inhibited this activity and identified altered gene-distal chromatin regulation and transcription consistent with a more mature myeloid cell state.
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Affiliation(s)
- David C. Klein
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Santana M. Lardo
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Sarah J. Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
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Spisak S, Chen D, Likasitwatanakul P, Doan P, Li Z, Bala P, Vizkeleti L, Tisza V, De Silva P, Giannakis M, Wolpin B, Qi J, Sethi NS. Utilizing a dual endogenous reporter system to identify functional regulators of aberrant stem cell and differentiation activity in colorectal cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.21.545895. [PMID: 38293113 PMCID: PMC10827082 DOI: 10.1101/2023.06.21.545895] [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
Aberrant stem cell-like activity and impaired differentiation are central to the development of colorectal cancer (CRC). To identify functional mediators that regulate these key cellular programs in CRC, we developed an endogenous reporter system by genome-editing human CRC cell lines with knock-in fluorescent reporters at the SOX9 and KRT20 locus to report aberrant stem cell-like activity and differentiation, respectively, and then performed pooled genetic perturbation screens. Constructing a dual reporter system that simultaneously monitored aberrant stem cell-like and differentiation activity in the same CRC cell line improved our signal to noise discrimination. Using a focused-library CRISPR screen targeting 78 epigenetic regulators with 542 sgRNAs, we identified factors that contribute to stem cell-like activity and differentiation in CRC. Perturbation single cell RNA sequencing (Perturb-seq) of validated hits nominated SMARCB1 of the BAF complex (also known as SWI/SNF) as a negative regulator of differentiation across an array of neoplastic colon models. SMARCB1 is a dependency in CRC and required for in vivo growth of human CRC models. These studies highlight the utility of a biologically designed endogenous reporter system to uncover novel therapeutic targets for drug development.
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Affiliation(s)
- Sandor Spisak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - David Chen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Pornlada Likasitwatanakul
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Bangkok, Thailand
| | - Paul Doan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Zhixin Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Pratyusha Bala
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Laura Vizkeleti
- Department of Bioinformatics, Faculty of Medicine, Semmelweis University, 1094 Budapest, Hungary
| | - Viktoria Tisza
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Pushpamail De Silva
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
- Gastrointestinal Cancer Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Brian Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Gastrointestinal Cancer Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nilay S. Sethi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
- Gastrointestinal Cancer Center, Dana-Farber Cancer Institute, Boston, MA, USA
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10
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Deng H, Ding Y, Wang Z, Liang X, Liu Y. Novel Association of RAD54L Mutation with Müllerian Clear Cell Carcinoma of the Male Urethra: New Insights Regarding the Molecular Mechanisms of a Rare Tumour. Curr Cancer Drug Targets 2024; 24:1080-1087. [PMID: 38279717 DOI: 10.2174/0115680096260943231212043820] [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: 05/05/2023] [Revised: 09/19/2023] [Accepted: 10/12/2023] [Indexed: 01/28/2024]
Abstract
INTRODUCTION Müllerian clear cell carcinoma of the male urethra is similar to that of the female genital tract in terms of morphology and immunohistochemical expression but is rarely observed in clinical practice. CASE PRESENTATION Here, we report the case of a 65-year-old man diagnosed with Müllerian clear cell carcinoma who harboured a mutation in RAD54L. This patient was diagnosed by electrocautery and ultimately underwent prostatectomy. After a six-month follow-up period, no signs of recurrence or additional malignancy were found. Based on our analysis of the available literature, it appears that Müllerian clear cell carcinoma with RAD54L mutation has not been reported until now. CONCLUSION This case enhances our knowledge of the molecular biology of Müllerian clear cell carcinoma of the male urethra, which will help clinicians select optimal treatment options for this rare cancer in patients with specific driver mutations.
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Affiliation(s)
- Huiyan Deng
- Department of Pathology, the Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050011, China
| | - Yan Ding
- Department of Pathology, the Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050011, China
| | - Zhiyu Wang
- Department of Oncology Immunology, the Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050011, China
| | - Xiangdong Liang
- Department of Urology, the Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050011, China
| | - Yueping Liu
- Department of Pathology, the Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050011, China
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11
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Fagin JA, Krishnamoorthy GP, Landa I. Pathogenesis of cancers derived from thyroid follicular cells. Nat Rev Cancer 2023; 23:631-650. [PMID: 37438605 PMCID: PMC10763075 DOI: 10.1038/s41568-023-00598-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/08/2023] [Indexed: 07/14/2023]
Abstract
The genomic simplicity of differentiated cancers derived from thyroid follicular cells offers unique insights into how oncogenic drivers impact tumour phenotype. Essentially, the main oncoproteins in thyroid cancer activate nodes in the receptor tyrosine kinase-RAS-BRAF pathway, which constitutively induces MAPK signalling to varying degrees consistent with their specific biochemical mechanisms of action. The magnitude of the flux through the MAPK signalling pathway determines key elements of thyroid cancer biology, including differentiation state, invasive properties and the cellular composition of the tumour microenvironment. Progression of disease results from genomic lesions that drive immortalization, disrupt chromatin accessibility and cause cell cycle checkpoint dysfunction, in conjunction with a tumour microenvironment characterized by progressive immunosuppression. This Review charts the genomic trajectories of these common endocrine tumours, while connecting them to the biological states that they confer.
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Affiliation(s)
- James A Fagin
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Gnana P Krishnamoorthy
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Iñigo Landa
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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12
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Kuwahara Y, Iehara T, Matsumoto A, Okuda T. Recent insights into the SWI/SNF complex and the molecular mechanism of hSNF5 deficiency in rhabdoid tumors. Cancer Med 2023; 12:16323-16336. [PMID: 37317642 PMCID: PMC10469780 DOI: 10.1002/cam4.6255] [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: 10/11/2022] [Revised: 05/04/2023] [Accepted: 06/05/2023] [Indexed: 06/16/2023] Open
Abstract
Genetic information encoded by DNA is packaged in the nucleus using the chromatin structure. The accessibility of transcriptional elements in DNA is controlled by the dynamic structural changes of chromatin for the appropriate regulation of gene transcription. Chromatin structure is regulated by two general mechanisms, one is histone modification and the other is chromatin remodeling in an ATP-dependent manner. Switch/sucrose nonfermentable (SWI/SNF) complexes utilize the energy from ATP hydrolysis to mobilize nucleosomes and remodel the chromatin structure, contributing to conformational changes in chromatin. Recently, the inactivation of encoding genes for subunits of the SWI/SNF complexes has been documented in a series of human cancers, accounting for up to almost 20% of all human cancers. For example, human SNF5 (hSNF5), the gene that encodes a subunit of the SWI/SNF complexes, is the sole mutation target that drives malignant rhabdoid tumors (MRT). Despite remarkably simple genomes, the MRT has highly malignant characteristics. As a key to understanding MRT tumorigenesis, it is necessary to fully examine the mechanism of chromatin remodeling by the SWI/SNF complexes. Herein, we review the current understanding of chromatin remodeling by focusing on SWI/SNF complexes. In addition, we describe the molecular mechanisms and influences of hSNF5 deficiency in rhabdoid tumors and the prospects for developing new therapeutic targets to overcome the epigenetic drive of cancer that is caused by abnormal chromatin remodeling.
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Affiliation(s)
- Yasumichi Kuwahara
- Department of Biochemistry and Molecular Biology, Graduate School of Medical ScienceKyoto Prefectural University of MedicineKyotoJapan
| | - Tomoko Iehara
- Department of Pediatrics, Graduate School of Medical ScienceKyoto Prefectural University of MedicineKyotoJapan
| | - Akifumi Matsumoto
- Department of Ophthalmology, Graduate School of Medical ScienceKyoto Prefectural University of MedicineKyotoJapan
| | - Tsukasa Okuda
- Department of Biochemistry and Molecular Biology, Graduate School of Medical ScienceKyoto Prefectural University of MedicineKyotoJapan
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13
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Makabe S, Koguchi T, Matsuoka K, Hoshi S, Hata J, Sato Y, Akaihata H, Kataoka M, Uemura M, Kojima Y. SMARCB1-deficient basal cell carcinoma of the prostate controlled using radiation therapy. IJU Case Rep 2023; 6:248-252. [PMID: 37405037 PMCID: PMC10315236 DOI: 10.1002/iju5.12598] [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: 02/08/2023] [Accepted: 06/01/2023] [Indexed: 07/06/2023] Open
Abstract
Introduction Basal cell carcinoma of the prostate is rare, with no established treatment for its recurrence or metastasis. We report a case involving basal cell carcinoma of the prostate controlled using radiotherapy. Case presentation A 57-year-old man complained of perineal pain. Although his prostate-specific antigen was 0.657 ng/mL, a digital rectal examination revealed his prostate was stone hard. Prostate needle biopsy showed basal cell carcinoma of the prostate. The patient then underwent radical prostatectomy. Local recurrence and sacral bone metastasis appeared 2 months after surgery. OncoGuide™ NCC Oncopanel System showed deletion of SMARCB1; however no recommended treatment was identified. Thus, we decided to perform radiotherapy, which reduced all lesions. Conclusion Basal cell carcinoma of the prostate may have a poor prognosis with recurrence or metastasis, hence evaluation of prognostic factors is important. In this case, the genomic profiling test suggested that SMARCB1 deletion may be a prognostic factor associated with disease progression.
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Affiliation(s)
- Shunta Makabe
- Department of UrologyFukushima Medical University School of MedicineFukushimaJapan
| | - Tomoyuki Koguchi
- Department of UrologyFukushima Medical University School of MedicineFukushimaJapan
| | - Kanako Matsuoka
- Department of UrologyFukushima Medical University School of MedicineFukushimaJapan
| | - Seiji Hoshi
- Department of UrologyFukushima Medical University School of MedicineFukushimaJapan
| | - Junya Hata
- Department of UrologyFukushima Medical University School of MedicineFukushimaJapan
| | - Yuichi Sato
- Department of UrologyFukushima Medical University School of MedicineFukushimaJapan
| | - Hidenori Akaihata
- Department of UrologyFukushima Medical University School of MedicineFukushimaJapan
| | - Masao Kataoka
- Department of UrologyFukushima Medical University School of MedicineFukushimaJapan
| | - Motohide Uemura
- Department of UrologyFukushima Medical University School of MedicineFukushimaJapan
| | - Yoshiyuki Kojima
- Department of UrologyFukushima Medical University School of MedicineFukushimaJapan
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14
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Hu X, Tan C, Zhu G. Clinical Characteristics of Molecularly Defined Renal Cell Carcinomas. Curr Issues Mol Biol 2023; 45:4763-4777. [PMID: 37367052 DOI: 10.3390/cimb45060303] [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: 04/05/2023] [Revised: 05/23/2023] [Accepted: 05/26/2023] [Indexed: 06/28/2023] Open
Abstract
Kidney tumors comprise a broad spectrum of different histopathological entities, with more than 0.4 million newly diagnosed cases each year, mostly in middle-aged and older men. Based on the description of the 2022 World Health Organization (WHO) classification of renal cell carcinoma (RCC), some new categories of tumor types have been added according to their specific molecular typing. However, studies on these types of RCC are still superficial, many types of these RCC currently lack accurate diagnostic standards in the clinic, and treatment protocols are largely consistent with the treatment guidelines for clear cell RCC (ccRCC), which might result in worse treatment outcomes for patients with these types of molecularly defined RCC. In this article, we conduct a narrative review of the literature published in the last 15 years on molecularly defined RCC. The purpose of this review is to summarize the clinical features and the current status of research on the detection and treatment of molecularly defined RCC.
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Affiliation(s)
- Xinfeng Hu
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Congzhu Tan
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Guodong Zhu
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
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15
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Agaimy A. SWI/SNF-deficient Malignancies: Optimal Candidates for Immune-oncological Therapy? Adv Anat Pathol 2023; 30:211-217. [PMID: 36069856 DOI: 10.1097/pap.0000000000000366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Inactivation of different subunits of the SWItch/sucrose nonfermentable (SWI/SNF) chromatin remodeling complex has emerged as one of the most frequent genetic pathways driving a variety of neoplasms of diverse histogenesis, originating in different organs. With few exceptions, most SWI/SNF-deficient malignancies pursue a highly aggressive clinical course resulting in widespread disease dissemination either at or soon after diagnosis, ultimately causing patients' death soon after diagnosis, despite the apparently curative treatment intention. To date, no satisfactorily effective systemic chemotherapy has been established for treating these diseases. This disappointing finding underlines the urgent need for an effective systemic therapy that would enable sufficient intermediate to long-term disease control. Recently, SWI/SNF-deficiency has increasingly emerged as pivotal in cancer immunogenicity and hence a promising biomarker predicting response to immune-checkpoint inhibition therapy utilizing several recently established drugs. This review summarizes the most recent literature on this topic with emphasis on the entities that most likely represent suitable candidates for immune therapy.
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Affiliation(s)
- Abbas Agaimy
- Institute of Pathology, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
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16
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Meissner M, Napolitano A, Thway K, Huang P, Jones RL. Pharmacotherapeutic strategies for epithelioid sarcoma: are we any closer to a non-surgical cure? Expert Opin Pharmacother 2023; 24:1395-1401. [PMID: 37326105 DOI: 10.1080/14656566.2023.2224500] [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: 12/05/2022] [Accepted: 06/08/2023] [Indexed: 06/17/2023]
Abstract
INTRODUCTION Epithelioid sarcoma (ES) is a rare soft tissue sarcoma subtype, predominantly occurring in children and young adults. Despite optimal management of localized disease, approximately 50% of patients develop advanced disease. The management of advanced ES remains challenging due to limited response to conventional chemotherapy and despite novel oral EZH2 inhibitors that have better tolerability but similar efficacy to chemotherapy. AREAS COVERED We performed a literature review using the PubMed (MEDLINE) and Web of Science databases. We have focused on the role of chemotherapy, targeted agents such as EZH2 inhibitors, potential new targets and immune checkpoint inhibitors and combinations of therapies currently undergoing clinical investigation. EXPERT OPINION ES is a soft tissue sarcoma with a heterogeneous pathological, clinical, and molecular presentation. In the current era of precision medicine, more trials with targeted therapies and a combination of chemotherapy or immunotherapy with targeted therapies are required to establish optimal treatment for ES.
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Affiliation(s)
- Magdalena Meissner
- Velindre Cancer Centre, Cardiff, UK
- Department of Cancer and Genetics, Cardiff University, Cardiff, UK
| | | | - Khin Thway
- Sarcoma Unit, The Royal Marsden NHS Foundation Trust, London, UK
- Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | - Paul Huang
- Sarcoma Unit, The Royal Marsden NHS Foundation Trust, London, UK
- Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | - Robin L Jones
- Sarcoma Unit, The Royal Marsden NHS Foundation Trust, London, UK
- Division of Clinical Studies, The Institute of Cancer Research, London, UK
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17
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Czegle I, Huang C, Soria PG, Purkiss DW, Shields A, Wappler-Guzzetta EA. The Role of Genetic Mutations in Mitochondrial-Driven Cancer Growth in Selected Tumors: Breast and Gynecological Malignancies. Life (Basel) 2023; 13:996. [PMID: 37109525 PMCID: PMC10145875 DOI: 10.3390/life13040996] [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: 12/28/2022] [Revised: 03/15/2023] [Accepted: 03/31/2023] [Indexed: 04/29/2023] Open
Abstract
There is an increasing understanding of the molecular and cytogenetic background of various tumors that helps us better conceptualize the pathogenesis of specific diseases. Additionally, in many cases, these molecular and cytogenetic alterations have diagnostic, prognostic, and/or therapeutic applications that are heavily used in clinical practice. Given that there is always room for improvement in cancer treatments and in cancer patient management, it is important to discover new therapeutic targets for affected individuals. In this review, we discuss mitochondrial changes in breast and gynecological (endometrial and ovarian) cancers. In addition, we review how the frequently altered genes in these diseases (BRCA1/2, HER2, PTEN, PIK3CA, CTNNB1, RAS, CTNNB1, FGFR, TP53, ARID1A, and TERT) affect the mitochondria, highlighting the possible associated individual therapeutic targets. With this approach, drugs targeting mitochondrial glucose or fatty acid metabolism, reactive oxygen species production, mitochondrial biogenesis, mtDNA transcription, mitophagy, or cell death pathways could provide further tailored treatment.
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Affiliation(s)
- Ibolya Czegle
- Department of Internal Medicine and Haematology, Semmelweis University, H-1085 Budapest, Hungary
| | - Chelsea Huang
- Department of Pathology and Laboratory Medicine, Loma Linda University Health, Loma Linda, CA 92354, USA
| | - Priscilla Geraldine Soria
- Department of Pathology and Laboratory Medicine, Loma Linda University Health, Loma Linda, CA 92354, USA
| | - Dylan Wesley Purkiss
- Department of Pathology and Laboratory Medicine, Loma Linda University Health, Loma Linda, CA 92354, USA
| | - Andrea Shields
- Department of Pathology and Laboratory Medicine, Loma Linda University Health, Loma Linda, CA 92354, USA
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18
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Baněčková M, Cox D. Top 10 Basaloid Neoplasms of the Sinonasal Tract. Head Neck Pathol 2023; 17:16-32. [PMID: 36928732 PMCID: PMC10063752 DOI: 10.1007/s12105-022-01508-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 10/28/2022] [Indexed: 03/18/2023]
Abstract
BACKGROUND Basaloid neoplasms of the sinonasal tract represent a significant group of tumors with histological overlap but often with different etiologies (i.e., viral, genetics), clinical management, and prognostic significance. METHODS Review. RESULTS "Basaloid" generally refers to cells with coarse chromatin in round nuclei and sparse cytoplasm, resembling cells of epithelial basal layers or imparting an "immature" appearance. Tumors with this characteristic in the sinonasal tract are represented by a spectrum of benign to high-grade malignant neoplasms, such as adenoid cystic carcinoma, NUT carcinoma, sinonasal undifferentiated carcinoma, SWI/SNF complex-deficient carcinomas, and adamantinoma-like Ewing sarcoma. CONCLUSION In some instances, histology alone may be sufficient for diagnosis. However, limited biopsy material or fine-needle aspiration specimens may be particularly challenging. Therefore, often other diagnostic procedures, including a combination of histology, immunohistochemistry (IHC), DNA and RNA testing, and molecular genetics are necessary to establish an accurate diagnosis.
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Affiliation(s)
- Martina Baněčková
- Department of Pathology, Faculty of Medicine in Plzen, Charles University, Plzen, Czech Republic.
- Bioptic Laboratory Ltd, Plzen, Czech Republic.
- Sikl's Department of Pathology, Faculty of Medicine in Pilsen, Charles University, E. Benese 13, 305 99, Pilsen, Czech Republic.
| | - Darren Cox
- University of Pacific Arthur A. Dugoni School of Dentistry, San Francisco, CA, USA
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19
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Abstract
The classification of poorly differentiated sinonasal carcinomas and their nonepithelial mimics has experienced tremendous developments during the last 2 decades. These recent developments paved the way for an increasingly adopted approach to a molecular-based or etiology-based refined classification of the many carcinoma variants that have been historically lumped into the sinonasal undifferentiated carcinoma category. Among these new achievements, recognition of carcinoma subtypes driven by defects in the Switch/Sucrose nonfermentable (SWI/SNF) chromatin remodeling complex represents a major highlight. This resulted in a new definition of 4 sinonasal entities driven solely or predominantly by Switch/Sucrose nonfermentable complex deficiency: (1) SMARCB1(INI1)-deficient sinonasal carcinoma (lacking gland formation and frequently displaying a non-descript basaloid, and less frequently eosinophilic/oncocytoid morphology, but no features of other definable subtypes), (2) SMARCB1-deficient sinonasal adenocarcinoma (with unequivocal glands or yolk sac-like pattern), (3) SMARCA4-deficient undifferentiated (sinonasal undifferentiated carcinoma-like) carcinoma (lacking glandular or squamous immunophenotypes), and (4) SMARCA4-deficient subset (~80%) of sinonasal teratocarcinosarcoma. Fortunately, diagnostic loss of all these proteins can be detected by routine immunohistochemistry, so that genetic testing is not mandatory in routine practice. This review summarizes the main demographic, clinicopathological, and molecular features of these new entities.
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Affiliation(s)
- Abbas Agaimy
- Institute of Pathology, Friedrich-Alexander-University Erlangen-Nürnberg, University Hospital, Erlangen, Germany
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20
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Targeted next-generation sequencing reveals activating CTNNB1 mutations in SMARCA4/BRG1-deficient sinonasal carcinomas: a report of two new cases and a brief review of the literature with an emphasis on histogenesis. Virchows Arch 2023; 482:453-460. [PMID: 36396744 DOI: 10.1007/s00428-022-03449-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/20/2022] [Accepted: 10/27/2022] [Indexed: 11/19/2022]
Abstract
SMARCA4/BRG1 is a catalytic subunit of the SWItch/sucrose non-fermentable (SWI/SNF) complex and its inactivation is known to drive a variety of cancers across different organs. SMARCA4/BRG1-deficient carcinoma is a relatively new entity in the sinonasal region, and a comprehensive molecular investigation of the underlying genetic abnormalities is largely lacking. In this study, we report two new cases of SMARCA4/BRG1-deficient sinonasal carcinoma with targeted next-generation sequencing analysis, both of which revealed activating mutation of CTNNB1 in addition to somatic loss-of-function mutation of SMARCA4, providing further insights into its tumorigenesis and theoretical basis for the potential future targeted therapy. Activating CTNNB1 mutations in our cases may provide further evidence that SMARCA4-deficient sinonasal carcinoma, sinonasal teratocarcinosarcoma, and olfactory carcinoma are genetically closely related lesions, as recently proposed in the literature.
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21
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SMARCA4: Current status and future perspectives in non-small-cell lung cancer. Cancer Lett 2023; 554:216022. [PMID: 36450331 DOI: 10.1016/j.canlet.2022.216022] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/07/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022]
Abstract
SMARCA4, also known as transcription activator, is an ATP-dependent catalytic subunit of SWI/SNF (SWItch/Sucrose NonFermentable) chromatin-remodeling complexes that participates in the regulation of chromatin structure and gene expression by supplying energy. As a tumor suppressor that has aberrant expression in ∼10% of non-small-cell lung cancers (NSCLCs), SMARCA4 possesses many biological functions, including regulating gene expression, differentiation and transcription. Furthermore, NSCLC patients with SMARCA4 alterations have a weak response to conventional chemotherapy and poor prognosis. Therefore, the mechanisms of SMARCA4 in NSCLC development urgently need to be explored to identify novel biomarkers and precise therapeutic strategies for this subtype. This review systematically describes the biological functions of SMARCA4 and its role in NSCLC development, metastasis, functional epigenetics and potential therapeutic approaches for NSCLCs with SMARCA4 alterations. Additionally, this paper explores the relationship and regulatory mechanisms shared by SMARCA4 and its mutually exclusive catalytic subunit SMARCA2. We aim to provide innovative treatment strategies and improve clinical outcomes for NSCLC patients with SMARCA4 alterations.
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Kuo TL, Cheng KH, Chen LT, Hung WC. ARID1A loss in pancreas leads to islet developmental defect and metabolic disturbance. iScience 2023; 26:105881. [PMID: 36654862 PMCID: PMC9840936 DOI: 10.1016/j.isci.2022.105881] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 10/27/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
ARID1A is a tumor suppressor gene mutated in 7-10% of pancreatic cancer patients. However, its function in pancreas development and endocrine regulation is unclear. We generated mice that lack Arid1a expression in the pancreas. Our results showed that deletion of the Arid1a gene in mice caused a reduction in islet numbers and insulin production, both of which are associated with diabetes mellitus (DM) phenotype. RNA sequencing of isolated islets confirmed DM gene signature and decrease of developmental lineage genes. We identified neurogenin3, a transcription factor that controls endocrine fate specification, is a direct target of Aird1a. Gene set enrichment analysis indicated the enhancement of histone deacetylase (HDAC) pathway after Arid1a depletion and a clinically approved HDAC inhibitor showed therapeutic benefit by suppressing disease onset. Our data suggest that Arid1a is required for the development of pancreatic islets by regulating Ngn3+-mediated transcriptional program and is important in maintaining endocrine function.
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Affiliation(s)
- Tzu-Lei Kuo
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan
| | - Kuang-Hung Cheng
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
| | - Li-Tzong Chen
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan
- Division of Internal Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Wen-Chun Hung
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
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Wolf BK, Zhao Y, McCray A, Hawk WH, Deary LT, Sugiarto NW, LaCroix IS, Gerber SA, Cheng C, Wang X. Cooperation of chromatin remodeling SWI/SNF complex and pioneer factor AP-1 shapes 3D enhancer landscapes. Nat Struct Mol Biol 2023; 30:10-21. [PMID: 36522426 PMCID: PMC10513740 DOI: 10.1038/s41594-022-00880-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 10/25/2022] [Indexed: 12/23/2022]
Abstract
The mechanism controlling the dynamic targeting of SWI/SNF has long been postulated to be coordinated by transcription factors (TFs), yet demonstrating a specific TF influence has proven difficult. Here we take a multi-omics approach to interrogate transient SWI/SNF interactors, chromatin targeting and the resulting three-dimensional epigenetic landscape. We utilize the labeling technique TurboID to map the SWI/SNF interactome and identify the activator protein-1 (AP-1) family members as critical interacting partners for SWI/SNF complexes. CUT&RUN profiling demonstrates SWI/SNF targeting enrichment at AP-1 bound loci, as well as SWI/SNF-AP-1 cooperation in chromatin targeting. HiChIP reveals AP-1-SWI/SNF-dependent restructuring of the three-dimensional promoter-enhancer architecture and generation of enhancer hubs. Through interrogation of the SWI/SNF-AP-1 interaction, we demonstrate an SWI/SNF dependency on AP-1-mediated chromatin localization. We propose that pioneer factors, such as AP-1, bind and target SWI/SNF to inactive chromatin, where it restructures the genomic landscape into an active state through epigenetic rewiring spanning multiple dimensions.
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Affiliation(s)
- Bennett K Wolf
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
- Dartmouth Cancer Center, Dartmouth College, Lebanon, NH, USA
| | - Yanding Zhao
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Institute for Clinical and Translational Sciences, Baylor College of Medicine, Houston, TX, USA
| | - Andrew McCray
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
- Dartmouth Cancer Center, Dartmouth College, Lebanon, NH, USA
| | - William H Hawk
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
- Dartmouth Cancer Center, Dartmouth College, Lebanon, NH, USA
| | - Luke T Deary
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
- Dartmouth Cancer Center, Dartmouth College, Lebanon, NH, USA
| | - Nicholas W Sugiarto
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
| | - Ian S LaCroix
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
- Dartmouth Cancer Center, Dartmouth College, Lebanon, NH, USA
| | - Scott A Gerber
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
- Dartmouth Cancer Center, Dartmouth College, Lebanon, NH, USA
| | - Chao Cheng
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
- Institute for Clinical and Translational Sciences, Baylor College of Medicine, Houston, TX, USA.
| | - Xiaofeng Wang
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA.
- Dartmouth Cancer Center, Dartmouth College, Lebanon, NH, USA.
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Apurva, Abdul Sattar RS, Ali A, Nimisha, Kumar Sharma A, Kumar A, Santoshi S, Saluja SS. Molecular pathways in periampullary cancer: An overview. Cell Signal 2022; 100:110461. [PMID: 36096460 DOI: 10.1016/j.cellsig.2022.110461] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/19/2022] [Accepted: 08/29/2022] [Indexed: 11/22/2022]
Abstract
Molecular alterations in oncogenes and tumor suppressors in various signaling pathways are basis for personalized therapy in cancer. Periampullary carcinoma behaves differently from pancreatic carcinoma both in prognosis and outcome, therefore it needs special attention. Pancreatic cancer have higher incidence of nodal spread and perineural &lymphovascular invasion suggesting it biologically more aggressive tumor compared to periampullary cancer. Since PAC tumors consist of heterogenous tissue of origin, they might contain different mutations in tumor associated genes and other changes in tissue composition among different subgroups clubbed together. Significant progress has been made in understanding the molecular nature of PAC in the previous two decades, and a large number of mutations and other genetic changes have been identified as being responsible for the disease. This review article targets to collate and discuss the molecular evolution of PAC and their implication in its outcome. As per literature, mitogen-activated protein kinase (MAPK), phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K), and Wnt signaling are the most common pathways involved in PAC. Mutations in KRAS, TP53, CTNNB1, SMAD4 and APC genes were the most frequently reported. I-subtype resembles colorectal cancer while the morphology of PB-type shows close resemblance to pancreatic tumors. The frequency of driver gene mutations is higher in I-type compared to PB-type of PAC indicating I-type to be genetically more unstable. The genetic landscape of PAC obtained from WES data highlighted PI3/AKT pathway to be a primary target in I-type and RAS/RAF in PB-type.
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Affiliation(s)
- Apurva
- Central Molecular Lab, GovindBallabhPant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India; Amity University, Noida, India
| | - Real Sumayya Abdul Sattar
- Central Molecular Lab, GovindBallabhPant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Asgar Ali
- Central Molecular Lab, GovindBallabhPant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Nimisha
- Central Molecular Lab, GovindBallabhPant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Abhay Kumar Sharma
- Central Molecular Lab, GovindBallabhPant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Arun Kumar
- Central Molecular Lab, GovindBallabhPant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | | | - Sundeep Singh Saluja
- Central Molecular Lab, GovindBallabhPant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India; Department of GI Surgery, GovindBallabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India.
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25
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Li Y, Yang X, Zhu W, Xu Y, Ma J, He C, Wang F. SWI/SNF complex gene variations are associated with a higher tumor mutational burden and a better response to immune checkpoint inhibitor treatment: a pan-cancer analysis of next-generation sequencing data corresponding to 4591 cases. Cancer Cell Int 2022; 22:347. [DOI: 10.1186/s12935-022-02757-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 10/20/2022] [Indexed: 11/15/2022] Open
Abstract
Abstract
Background
Genes related to the SWItch/sucrose nonfermentable (SWI/SNF) chromatin remodeling complex are frequently mutated across cancers. SWI/SNF-mutant tumors are vulnerable to synthetic lethal inhibitors. However, the landscape of SWI/SNF mutations and their associations with tumor mutational burden (TMB), microsatellite instability (MSI) status, and response to immune checkpoint inhibitors (ICIs) have not been elucidated in large real-world Chinese patient cohorts.
Methods
The mutational rates and variation types of six SWI/SNF complex genes (ARID1A, ARID1B, ARID2, SMARCA4, SMARCB1, and PBRM1) were analyzed retrospectively by integrating next-generation sequencing data of 4591 cases covering 18 cancer types. Thereafter, characteristics of SWI/SNF mutations were depicted and the TMB and MSI status and therapeutic effects of ICIs in the SWI/SNF-mutant and SWI/SNF-non-mutant groups were compared.
Results
SWI/SNF mutations were observed in 21.8% of tumors. Endometrial (54.1%), gallbladder and biliary tract (43.4%), and gastric (33.9%) cancers exhibited remarkably higher SWI/SNF mutational rates than other malignancies. Further, ARID1A was the most frequently mutated SWI/SNF gene, and ARID1A D1850fs was identified as relatively crucial. The TMB value, TMB-high (TMB-H), and MSI-high (MSI-H) proportions corresponding to SWI/SNF-mutant cancers were significantly higher than those corresponding to SWI/SNF-non-mutant cancers (25.8 vs. 5.6 mutations/Mb, 44.3% vs. 10.3%, and 16.0% vs. 0.9%, respectively; all p < 0.0001). Furthermore, these indices were even higher for tumors with co-mutations of SWI/SNF genes and MLL2/3. Regarding immunotherapeutic effects, patients with SWI/SNF variations showed significantly longer progression-free survival (PFS) rates than their SWI/SNF-non-mutant counterparts (hazard ratio [HR], 0.56 [95% confidence interval {CI} 0.44–0.72]; p < 0.0001), and PBRM1 mutations were associated with relatively better ICI treatment outcomes than the other SWI/SNF gene mutations (HR, 0.21 [95% CI 0.12–0.37]; p = 0.0007). Additionally, patients in the SWI/SNF-mutant + TMB-H (HR, 0.48 [95% CI 0.37–0.54]; p < 0.0001) cohorts had longer PFS rates than those in the SWI/SNF-non-mutant + TMB-low cohort.
Conclusions
SWI/SNF complex genes are frequently mutated and are closely associated with TMB-H status, MSI-H status, and superior ICI treatment response in several cancers, such as colorectal cancer, gastric cancer, and non-small cell lung cancer. These findings emphasize the necessity and importance of molecular-level detection and interpretation of SWI/SNF complex mutations.
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26
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Yu L, Sun M, Zhang Q, Zhou Q, Wang Y. Harnessing the immune system by targeting immune checkpoints: Providing new hope for Oncotherapy. Front Immunol 2022; 13:982026. [PMID: 36159789 PMCID: PMC9498063 DOI: 10.3389/fimmu.2022.982026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
With the goal of harnessing the host's immune system to provide long-lasting remission and cures for various cancers, the advent of immunotherapy revolutionized the cancer therapy field. Among the current immunotherapeutic strategies, immune checkpoint blockades have greatly improved the overall survival rates in certain patient populations. Of note, CTLA4 and PD-1/PD-L1 are two major non-redundant immune checkpoints implicated in promoting cancer immune evasion, and ultimately lead to relapse. Antibodies or inhibitors targeting these two c+heckpoints have achieved some encouraging clinical outcomes. Further, beyond the canonical immune checkpoints, more inhibitory checkpoints have been identified. Herein, we will summarize recent progress in immune checkpoint blockade therapies, with a specific focus on key pre-clinical and clinical results of new immune checkpoint therapies for cancer. Given the crucial roles of immune checkpoint blockade in oncotherapy, drugs targeting checkpoint molecules expressed by both cancer and immune cells are in clinical trials, which will be comprehensively summarized in this review. Taken together, investigating combinatorial therapies targeting immune checkpoints expressed by cancer cells and immune cells will greatly improve immunotherapies that enhance host elimination of tumors.
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Affiliation(s)
- Lu Yu
- Department of Pulmonary and Critical Care Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Minghan Sun
- Central of Reproductive Medicine, Department of Obstetrics and Gynecology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Qi Zhang
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Qiao Zhou
- Department of Rheumatology and Immunology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Clinical Immunology Translational Medicine Key Laboratory of Sichuan Province, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Institute of Organ Transplantation, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Yi Wang
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
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Del Savio E, Maestro R. Beyond SMARCB1 Loss: Recent Insights into the Pathobiology of Epithelioid Sarcoma. Cells 2022; 11:cells11172626. [PMID: 36078034 PMCID: PMC9454995 DOI: 10.3390/cells11172626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
Epithelioid sarcoma (ES) is a very rare and aggressive mesenchymal tumor of unclear origin and uncertain lineage characterized by a prevalent epithelioid morphology. The only recurrent genetic alteration reported in ES as yet is the functional inactivation of SMARCB1 (SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1), a key component of the SWI/SNF (SWItch/Sucrose Non-Fermentable) chromatin remodeling complexes. How SMARCB1 deficiency dictates the clinicopathological characteristics of ES and what other molecular defects concur to its malignant progression is still poorly understood. This review summarizes the recent findings about ES pathobiology, including defects in chromatin remodeling and other signaling pathways and their role as therapeutic vulnerabilities.
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28
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Taylor AM, Bailey C, Belmont LD, Campbell R, Cantone N, Côté A, Crawford TD, Cummings R, DeMent K, Duplessis M, Flynn M, Good AC, Huang HR, Joshi S, Leblanc Y, Murray J, Nasveschuk CG, Neiss A, Poy F, Romero FA, Sandy P, Tang Y, Tsui V, Zawadzke L, Sims RJ, Audia JE, Bellon SF, Magnuson SR, Albrecht BK, Cochran AG. GNE-064: A Potent, Selective, and Orally Bioavailable Chemical Probe for the Bromodomains of SMARCA2 and SMARCA4 and the Fifth Bromodomain of PBRM1. J Med Chem 2022; 65:11177-11186. [PMID: 35930799 DOI: 10.1021/acs.jmedchem.2c00662] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bromodomains are acetyllysine recognition domains present in a variety of human proteins. Bromodomains also bind small molecules that compete with acetyllysine, and therefore bromodomains have been targets for drug discovery efforts. Highly potent and selective ligands with good cellular permeability have been proposed as chemical probes for use in exploring the functions of many of the bromodomain proteins. We report here the discovery of a class of such inhibitors targeting the family VIII bromodomains of SMARCA2 (BRM) and SMARCA4 (BRG1), and PBRM1 (polybromo-1) bromodomain 5. We propose one example from this series, GNE-064, as a chemical probe for the bromodomains SMARCA2, SMARCA4, and PBRM1(5) with the potential for in vivo use.
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Affiliation(s)
- Alexander M Taylor
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Chris Bailey
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Lisa D Belmont
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Robert Campbell
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Nico Cantone
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Alexandre Côté
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Terry D Crawford
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Richard Cummings
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Kevin DeMent
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Martin Duplessis
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Megan Flynn
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Andrew C Good
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Hon-Ren Huang
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Shivangi Joshi
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Yves Leblanc
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Jeremy Murray
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Christopher G Nasveschuk
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Adrianne Neiss
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Florence Poy
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - F Anthony Romero
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Peter Sandy
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Yong Tang
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Vickie Tsui
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Laura Zawadzke
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Robert J Sims
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - James E Audia
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Steven F Bellon
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Steven R Magnuson
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Brian K Albrecht
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Andrea G Cochran
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
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Ren T, Wang J, Tang W, Chen D, Wang S, Zhang X, Yang D. ARID1A has prognostic value in acute myeloid leukemia and promotes cell proliferation via TGF-β1/SMAD3 signaling. Clin Exp Med 2022:10.1007/s10238-022-00863-8. [PMID: 35867200 DOI: 10.1007/s10238-022-00863-8] [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: 12/14/2021] [Accepted: 07/04/2022] [Indexed: 11/03/2022]
Abstract
Previous studies have shown that the gene AT-rich interactive domain-containing protein 1A (ARID1A) is a subunit of SWI/SNF chromatin remodeling complex that acts as a tumor suppressor gene in several cancers and plays a vital role in tumorigenesis. However, its biological functions in acute myeloid leukemia (AML) are still unclear. Here, we tried to elaborate the expression of ARID1A in patients with AML, in leukemia cells, as well as the molecular mechanisms. Our results indicated that the expression of ARID1A was significantly downregulated in the bone marrow of patients with AML and relapsed patients compared with healthy subjects and patients in complete remission. Meantime, receiver operating characteristic curve analysis showed that the expression of ARID1A could be used to discriminate between patients with AML and patients in complete remission. We further constructed a knockdown cell model to determine the regulatory mechanisms of ARID1A in AML cells. We found that the decreased expression of ARID1A promoted cell proliferation, suppressed cellular apoptosis, and impeded cell cycle arrest via TGF-β1/SMAD3 signaling pathway. These results revealed that the reduced expression of ARID1A promoted cell proliferation via the TGF-β1/SMAD3 cascade and served as a prognostic biomarker for AML and therapeutic targets.
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Affiliation(s)
- Tianying Ren
- Zhong Yuan Academy of Biological Medicine, Liaocheng People's Hospital, Liaocheng, 252000, Shandong, People's Republic of China
| | - Jing Wang
- Key Laboratory for Pediatrics of Integrated Traditional and Western Medicine, Liaocheng People's Hospital, Liaocheng, 252000, Shandong, People's Republic of China
| | - Wenqiang Tang
- Central Laboratory, Liaocheng People's Hospital, Liaocheng, 252000, Shandong, People's Republic of China
| | - Dongliang Chen
- Zhong Yuan Academy of Biological Medicine, Liaocheng People's Hospital, Liaocheng, 252000, Shandong, People's Republic of China
| | - Shuang Wang
- Zhong Yuan Academy of Biological Medicine, Liaocheng People's Hospital, Liaocheng, 252000, Shandong, People's Republic of China
| | - Xiaole Zhang
- Department of Hematology, Liaocheng People's Hospital, Liaocheng, 252000, Shandong, People's Republic of China.
| | - Dawei Yang
- Zhong Yuan Academy of Biological Medicine, Liaocheng People's Hospital, Liaocheng, 252000, Shandong, People's Republic of China.
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Epigenetic gene alterations in metastatic solid tumours: results from the prospective precision medicine MOSCATO and MATCH-R trials. Eur J Cancer 2022; 173:133-145. [PMID: 35872509 DOI: 10.1016/j.ejca.2022.06.014] [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: 04/28/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 11/23/2022]
Abstract
INTRODUCTION Although the role of epigenetic alterations in oncogenesis has been well studied, their prevalence in metastatic solid tumours is still poorly described. We therefore aimed at: (i) describing the presence of epigenetic gene alterations (EGA) - defined by an alteration in a gene encoding an epigenetic regulator; and (ii) evaluating their relationship with clinical characteristics and outcome in patients (pts) included in prospective molecular profiling trials. MATERIALS AND METHODS On-purpose tumour biopsies from pts with metastatic solid tumours enrolled in the Gustave Roussy-sponsored MOSCATO (NCT01566019) and MATCHR (NCT02517892) trials were molecularly profiled using whole exome sequencing (WES). Alterations in 176 epigenetic genes were assessed and classified as pathogenic variants (PV) or non-pathogenic variants by a molecular tumour board. Clinical characteristics and outcome were collected. RESULTS Between Dec 2011 and Oct 2016, WES was successfully performed in 292 pts presenting various solid tumours. We found 496 epigenetic gene alterations in 134 patients (49%), including 237 pathogenic variants in 86 patients; 63 tumour samples (47%) presented ≥3 EGAs. The median number of previous treatment lines was 3 (1-10). The most frequently altered genes were KMT2D and KMT2C (16% each), ARID1A and SETD2 (10% each) and KMT2A (8%).; 31% of EGA co-occurred with a driver gene alteration (p < 0.001). Outcome was not correlated with the presence of EGA. CONCLUSIONS Epigenetic alterations occur frequently in metastatic solid tumours. With the current development of epigenetic modifiers, they increasingly represent actionable targets. Such genes should now be systematically analysed in molecular profiling studies.
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Beon J, Han S, Yang H, Park SE, Hyun K, Lee SY, Rhee HW, Seo JK, Kim J, Kim S, Lee D. Inositol polyphosphate multikinase physically binds to the SWI/SNF complex and modulates BRG1 occupancy in mouse embryonic stem cells. eLife 2022; 11:73523. [PMID: 35551737 PMCID: PMC9098221 DOI: 10.7554/elife.73523] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 04/26/2022] [Indexed: 11/13/2022] Open
Abstract
Inositol polyphosphate multikinase (IPMK), a key enzyme in inositol polyphosphate (IP) metabolism, is a pleiotropic signaling factor involved in major biological events, including transcriptional control. In the yeast, IPMK and its IP products promote the activity of the chromatin remodeling complex SWI/SNF, which plays a critical role in gene expression by regulating chromatin accessibility. However, the direct link between IPMK and chromatin remodelers remains unclear, raising the question of how IPMK contributes to transcriptional regulation in mammals. By employing unbiased screening approaches and in vivo/in vitro immunoprecipitation, here we demonstrate that mammalian IPMK physically interacts with the SWI/SNF complex by directly binding to SMARCB1, BRG1, and SMARCC1. Furthermore, we identified the specific domains required for IPMK-SMARCB1 binding. Notably, using CUT&RUN and ATAC-seq assays, we discovered that IPMK co-localizes with BRG1 and regulates BRG1 localization as well as BRG1-mediated chromatin accessibility in a genome-wide manner in mouse embryonic stem cells. Together, these findings show that IPMK regulates the promoter targeting of the SWI/SNF complex, thereby contributing to SWI/SNF-meditated chromatin accessibility, transcription, and differentiation in mouse embryonic stem cells.
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Affiliation(s)
- Jiyoon Beon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Sungwook Han
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Hyeokjun Yang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Seung Eun Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Kwangbeom Hyun
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Song-Yi Lee
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Jeong Kon Seo
- UNIST Central Research Facilities (UCRF), Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Jaehoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Seyun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,KAIST Stem Cell Center, KAIST, Daejeon, Republic of Korea.,KAIST Institute for the BioCentury, KAIST, Daejeon, Republic of Korea
| | - Daeyoup Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
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Agaimy A. Proceedings of the North American Society of Head and Neck Pathology, Los Angeles, CA, March 20, 2022: SWI/SNF-deficient Sinonasal Neoplasms: An Overview. Head Neck Pathol 2022; 16:168-178. [PMID: 35307773 PMCID: PMC9018903 DOI: 10.1007/s12105-022-01416-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 01/15/2022] [Indexed: 11/27/2022]
Abstract
The pathology of poorly differentiated sinonasal malignancies has been the subject of extensive studies during the last decade, which resulted into significant developments in the definitions and histo-/pathogenetic classification of several entities included in the historical spectrum of "sinonasal undifferentiated carcinomas (SNUC)" and poorly differentiated unclassified carcinomas. In particular, genetic defects leading to inactivation of different protein subunits in the SWI/SNF chromatin remodeling complex have continuously emerged as the major (frequently the only) genetic player driving different types of sinonasal carcinomas. The latter display distinctive demographic, phenotypic and genotypic characteristics. To date, four different SWI/SNF-driven sinonasal tumor types have been recognized: SMARCB1(INI1)-deficient carcinoma (showing frequently non-descript basaloid, and less frequently eosinophilic, oncocytoid or rhabdoid undifferentiated morphology), SMARCB1-deficient adenocarcinomas (showing variable gland formation or yolk sac-like morphology), SMARCA4-deficient carcinoma (lacking any differentiation markers and variably overlapping with large cell neuroendocrine carcinoma and SNUC), and lastly, SMARCA4-deficient sinonasal teratocarcinosarcoma. These different tumor types display highly variable immunophenotypes with SMARCB1-deficient carcinomas showing variable squamous immunophenotype, while their SMARCA4-related counterparts lack such features altogether. While sharing same genetic defect, convincing evidence is still lacking that SMARCA4-deficient carcinoma and SMARCA4-deficient teratocracinosarcoma might belong to the spectrum of same entity. Available molecular studies revealed no additional drivers in these entities, confirming the central role of SWI/SNF deficiency as the sole driver genetic event in these aggressive malignancies. Notably, all studied cases lacked oncogenic IDH2 mutations characteristic of genuine SNUC. Identification and precise classification of these entities and separating them from SNUC, NUT carcinoma and other poorly differentiated neoplasms of epithelial melanocytic, hematolymphoid or mesenchymal origin is mandatory for appropriate prognostication and tailored therapies. Moreover, drugs targeting the SWI/SNF vulnerabilities are emerging in clinical trials.
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Affiliation(s)
- Abbas Agaimy
- Institute of Pathology, Friedrich-Alexander-University Erlangen-Nürnberg, University Hospital, Erlangen, Germany
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Hemogen /BRG1 cooperativity modulates promoter and enhancer activation during erythropoiesis. Blood 2022; 139:3532-3545. [PMID: 35297980 DOI: 10.1182/blood.2021014308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 03/15/2022] [Indexed: 11/20/2022] Open
Abstract
Hemogen, also known as EDAG, is a hematopoietic tissue-specific gene that regulates the proliferation and differentiation of hematopoietic cells. However, the mechanism underlying hemogen function in erythropoiesis is unknown. We found that depletion of hemogen in human CD34+ erythroid progenitor cells and HUDEP2 cells significantly reduced the expression of genes associated with heme and hemoglobin synthesis, supporting a positive role of hemogen in erythroid maturation. In human K562 cells, hemogen antagonized the occupancy of co-repressors NuRD complex and facilitated LDB1 complex-mediated chromatin looping. Hemogen recruited SWI/SNF complex ATPase BRG1 as a co-activator to regulate nucleosome accessibility and H3K27ac enrichment for promoter and enhancer activity. To ask if hemogen/BRG1 cooperativity is conserved in mammalian systems, we generated hemogen KO/KI mice and investigated hemogen/BRG1 function in murine erythropoiesis. Loss of hemogen in E12.5-E16.5 fetal liver cells impeded erythroid differentiation through reducing the production of mature erythroblasts. ChIP-seq in WT and hemogen KO animal revealed BRG1 is largely dependent on hemogen to regulate chromatin accessibility at erythroid gene promoters and enhancers. In summary, hemogen/BRG1 interaction in mammals is essential for fetal erythroid maturation and hemoglobin production through its active role in promoter and enhancer activity and chromatin organization.
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Xu W, Dong H, Ru G, Zhao M. ARID1A deficient undifferentiated spindle cell and rhabdoid sarcoma of the prostate: report of a unique case with emphasis on diagnostic implications. Diagn Pathol 2022; 17:22. [PMID: 35125107 PMCID: PMC8818209 DOI: 10.1186/s13000-022-01198-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 01/18/2022] [Indexed: 11/10/2022] Open
Abstract
Background SWItch Sucrose Non-Fermentable (SWI/SNF) chromatin-remodeling complex functions collectively as a tumor suppressor and the inactivation of any of its constituent components is frequently associated with tumor initiation and/or progression. Most SWI/SNF deficient tumors share common rhabdoid morphology. ARID1A is the most frequently dysregulated SWI/SNF subunit in human cancer and inactivation of ARID1A is frequent across carcinomatous types while very rarely drives the tumorigenesis of sarcomas. Herein, we report a rare case of primary prostatic undifferentiated spindle cell sarcoma with focal rhabdoid morphology, harboring biallelic inactivation of ARID1A detected by next-generation sequencing with complete loss of ARID1A expression by immunohistochemistry. Case presentation The patient is a 58-year-old man who presented with dysuria and obstructive voiding symptoms for 3 month and was found to have a large, ill-defined, prostatic mass lesion with circumferential extension into the rectal wall on imaging studies. A needle biopsy showed a spindle cell undifferentiated sarcoma of the prostate and the patient was treated by chemotherapy of combined etoposide and cisplatin for 2 months. A subsequent imaging study showed that the tumor was significantly enlarged, and the patient underwent laparoscopically radical prostatectomy. Gross examination showed a disrupted, 10 × 7 × 5 cm, solid and cystic mass involving almost the entire prostate and sparing the seminal vesicle glands. Histologic examination showed that tumor was composed mainly of mildly atypical, oval to spindle-shaped cells, arranged in sheets and fascicles or herringbone-like patterns within a small amount of edematous to myxoid, vascularized stroma. Notably, groups of discohesive rhabdoid tumor cells with eccentric nuclei, prominent nucleoli, and abundant globular cytoplasm were observed. There were prominent mitotic figures, multifocal geographic necroses, and foci of lymphovascular invasion. Immunohistochemistry showed that the tumor cells were diffusely positive for TLE-1 and vimentin and focally positive for epithelial membrane antigen, AE1/3, Cam5.2, SATB2, and CD34 (all in less than 10% tumor cells). Next-generation sequencing showed biallelic inactivation mutation of ARID1A; the predicted inactivating effect of ARID1A deletion was confirmed by immunohistochemical staining. After the surgery, the patient received an alternative combined chemotherapy of doxorubicin and ifosfamide for 5 months. The patient died 9 months after initial presentation due to extensive abdominal metastases. Conclusions We report an ARID1A deficient undifferentiated spindle cell and rhabdoid sarcoma of the prostate, adding to the growing spectrum of SWI/SNF driven undifferentiated sarcoma. Rhabdoid cells can be a helpful morphological clue for promoting molecular and immunohistochemical analyses for deficiency of SWI/SNF subunits, in the diagnostic workup of undifferentiated neoplasms featuring epithelioid or rhabdoid morphology. Supplementary Information The online version contains supplementary material available at 10.1186/s13000-022-01198-4.
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Duan Z, Yao K, Yang S, Qu Y, Ren M, Zhang Y, Fan T, Zhao H, Gao J, Feng J, Fan X, Qi X. Primary adult sellar SMARCB1/INI1-deficient tumor represents a subtype of atypical teratoid/rhabdoid tumor. Mod Pathol 2022; 35:1910-1920. [PMID: 35804041 PMCID: PMC9708584 DOI: 10.1038/s41379-022-01127-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/01/2022] [Accepted: 06/06/2022] [Indexed: 12/24/2022]
Abstract
Loss of function in SMARCB1/INI1 has been observed in a group of malignancies collectively defined as SMARCB1/INI1-deficient neoplasms. Primary intracranial SMARCB1/INI1-deficient tumors in adults are extremely rare. We collected eight primary adult sellar SMARCB1/INI1-deficient tumors to study their clinicopathological and (epi)genetic characteristics. We performed a comprehensive assessment of the clinical, radiological, morphological and immunohistochemical features. FISH analysis for the SMARCB1 locus and target exome sequencing for 425 cancer relevant genes were performed. Furthermore, six bona fide proximal epithelioid sarcoma (PES), fourteen atypical teratoid/rhabdoid tumors (ATRT) in brain and five pediatric poorly differentiated chordomas (PDC) in the clivus were collected for comparative analysis of differential diagnostic maker expression and DNA methylation profile. The median age was 47.1 years, ranging from 26 to 73 years. On morphology, tumors were characterized by sheets of monomorphic larger epithelioid-like cells, in two cases with rhabdoid cells. "Stag-horn" vasculatures were observed in five cases. The loss of INI1 protein expression, co-expression of epithelial makers and mesenchymal markers were observed in all cases. CD34 expression was observed in six cases. Heterozygous deletion of SMARCB1/INI1 was confirmed using FISH in six cases. The results of target exome sequencing showed three patients harbored heterozygous point mutations in SMARCB1. The epigenetic features of the primary adult sellar SMARCB1/INI1-deficient tumors resembled the ATRT-MYC subgroup, but clustered apart from PES and PDC. Based on epigenetic characteristics, primary adult sellar SMARCB1/INI1-deficient tumors represent a subtype of ATRT with similar epigenetic characteristics of ATRT-MYC subgroup. Our findings suggest that DNA methylation profiling should be utilized for differential diagnosis for the majority of epithelioid sarcoma and (sellar) rhabdoid tumor.
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Affiliation(s)
- Zejun Duan
- grid.24696.3f0000 0004 0369 153XDepartment of Pathology, Sanbo Brain Hospital, Capital Medical University, Beijing, 100093 China
| | - Kun Yao
- grid.24696.3f0000 0004 0369 153XDepartment of Pathology, Sanbo Brain Hospital, Capital Medical University, Beijing, 100093 China
| | - Shaomin Yang
- grid.11135.370000 0001 2256 9319Department of Pathology, School of Basic Medical Sciences, Third Hospital, Peking University Health Science Center, Beijing, 100191 China
| | - Yanming Qu
- grid.24696.3f0000 0004 0369 153XDepartment of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, 100093 China
| | - Ming Ren
- grid.24696.3f0000 0004 0369 153XDepartment of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, 100093 China
| | - Yongli Zhang
- grid.24696.3f0000 0004 0369 153XDepartment of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, 100093 China
| | - Tao Fan
- grid.24696.3f0000 0004 0369 153XDepartment of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, 100093 China
| | - Heqian Zhao
- grid.24696.3f0000 0004 0369 153XDepartment of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, 100093 China
| | - Jie Gao
- grid.24696.3f0000 0004 0369 153XDepartment of Radiology, Sanbo Brain Hospital, Capital Medical University, Beijing, 100093 China
| | - Jing Feng
- grid.20513.350000 0004 1789 9964Beijing Key Laboratory of Gene Resource and Molecular Development, Laboratory of Neuroscience and Brain Development, School of Life Sciences, Beijing Normal University, Beijing, 100875 China
| | - Xiaolong Fan
- grid.20513.350000 0004 1789 9964Beijing Key Laboratory of Gene Resource and Molecular Development, Laboratory of Neuroscience and Brain Development, School of Life Sciences, Beijing Normal University, Beijing, 100875 China
| | - Xueling Qi
- Department of Pathology, Sanbo Brain Hospital, Capital Medical University, Beijing, 100093, China.
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Dihowm H, Amin M, Ballentine S. SMARCB1(INI1)-deficient undifferentiated carcinoma with rhabdoid features of anorectal origin. CURRENT PROBLEMS IN CANCER: CASE REPORTS 2021. [DOI: 10.1016/j.cpccr.2021.100095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Mardinian K, Adashek JJ, Botta GP, Kato S, Kurzrock R. SMARCA4: Implications of an Altered Chromatin-Remodeling Gene for Cancer Development and Therapy. Mol Cancer Ther 2021; 20:2341-2351. [PMID: 34642211 PMCID: PMC8643328 DOI: 10.1158/1535-7163.mct-21-0433] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/20/2021] [Accepted: 10/07/2021] [Indexed: 01/04/2023]
Abstract
The SWI/SNF chromatin remodeling complex, via nucleosome topology modulation, regulates transcription. The SMARCA4 (BRG1) subunit codes for the ATPase energy engine of the SWI/SNF complex. SMARCA4 is a tumor suppressor that is aberrant in ∼5% to 7% of human malignancies. Class I SMARCA4 alterations (truncating mutations, fusions, and homozygous deletion) lead to loss of function whereas class II alterations (missense mutations) have a dominant negative/gain-of-function effect and/or loss-of function. SMARCA4 alterations typify the ultra-rare small cell carcinomas of the ovary hypercalcemic type (SCCOHT) and SMARCA4-deficient thoracic and uterine sarcomas; they are also found in a subset of more common tumors, for example, lung, colon, bladder, and breast carcinomas. Germline variants in the SMARCA4 gene lead to various hereditary conditions: rhabdoid tumor predisposition syndrome-2 (RTPS2), characterized by loss-of-function alterations and aggressive rhabdoid tumors presenting in infants and young children; and Coffin-Siris syndrome, characterized by dominant negative/gain-of function alterations and developmental delays, microcephaly, unique facies, and hypoplastic nails of the fifth fingers or toes. A minority of rhabdoid tumors have a germline SMARCA4 variant as do >40% of women with SCCOHT. Importantly, immune checkpoint blockade has shown remarkable, albeit anecdotal, responses in SCCOHT. In addition, there is ongoing research into BET, EZH2, HDAC, CDK4/6, and FGFR inhibitors, as well as agents that might induce synthetic lethality via DNA damage repair impairment (ATR inhibitors and platinum chemotherapy), or via the exploitation of mitochondrial oxidative phosphorylation inhibitors or AURKA inhibitors, in SMARCA4-aberrant cancers.
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Affiliation(s)
- Kristina Mardinian
- Center for Personalized Cancer Therapy, University of California San Diego, Moores Cancer Center, La Jolla, California
| | - Jacob J Adashek
- Department of Internal Medicine, University of South Florida, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida.
| | - Gregory P Botta
- Center for Personalized Cancer Therapy, University of California San Diego, Moores Cancer Center, La Jolla, California
| | - Shumei Kato
- Center for Personalized Cancer Therapy, University of California San Diego, Moores Cancer Center, La Jolla, California
| | - Razelle Kurzrock
- Center for Personalized Cancer Therapy, University of California San Diego, Moores Cancer Center, La Jolla, California. .,WIN Consortium, Paris, France
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Balasubramanian S, Hodkinson B, Schuster SJ, Fowler NH, Trotman J, Hess G, Cheson BD, Schaffer M, Sun S, Deshpande S, Vermeulen J, Salles G, Gopal AK. Identification of a genetic signature enriching for response to ibrutinib in relapsed/refractory follicular lymphoma in the DAWN phase 2 trial. Cancer Med 2021; 11:61-73. [PMID: 34791836 PMCID: PMC8704158 DOI: 10.1002/cam4.4422] [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: 12/22/2020] [Revised: 09/13/2021] [Accepted: 10/26/2021] [Indexed: 11/08/2022] Open
Abstract
Background The single‐arm DAWN trial (NCT01779791) of ibrutinib monotherapy in patients with relapsed/refractory follicular lymphoma (FL) showed an overall response rate (ORR) of 20.9% and a median response duration of 19.4 months. This biomarker analysis of the DAWN dataset sought to determine genetic classifiers for prediction of response to ibrutinib treatment. Methods Whole exome sequencing was performed on baseline tumor samples. Potential germline variants were excluded; a custom set of 1216 cancer‐related genes was examined. Responder‐ versus nonresponder‐associated variants were identified using Fisher's exact test. Classifiers with increasing numbers of genes were created using a greedy algorithm that repeatedly selected genes, adding the most nonresponders to the existing “predicted nonresponders” set and were evaluated with 10‐fold cross‐validation. Results Exome data were generated from 88 patient samples and 13,554 somatic mutation variants were inferred. Response data were available for 83 patients (17 responders, 66 nonresponders). Each sample showed 100 to >500 mutated genes, with greater variance across nonresponders. The overall variant pattern was consistent with previous FL studies; 75 genes had mutations in >10% of patients, including genes previously reported as associated with FL. Univariate analysis yielded responder‐associated genes FANCA, HISTH1B, ANXA6, BTG1, and PARP10, highlighting the importance of functions outside of B‐cell receptor signaling, including epigenetic processes, DNA damage repair, cell cycle/proliferation, and cell motility/invasiveness. While nonresponder‐associated genes included well‐known TP53 and CARD11, genetic classifiers developed using nonresponder‐associated genes included ATP6AP1, EP400, ARID1A, SOCS1, and TBL1XR1, suggesting resistance to ibrutinib may be related to broad biological functions connected to epigenetic modification, telomere maintenance, and cancer‐associated signaling pathways (mTOR, JAK/STAT, NF‐κB). Conclusion The results from univariate and genetic classifier analyses provide insights into genes associated with response or resistance to ibrutinib in FL and identify a classifier developed using nonresponder‐associated genes, which warrants further investigation. Trial registration: NCT01779791.
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Affiliation(s)
| | | | - Stephen J Schuster
- Lymphoma Program, Abramson Cancer Center of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nathan H Fowler
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Judith Trotman
- Haematology Department, Concord Hospital, University of Sydney, Sydney, New South Wales, Australia
| | - Georg Hess
- Department of Hematology/Oncology, Johannes Gutenberg-University, Mainz, Germany
| | - Bruce D Cheson
- Lombardi Comprehensive Cancer Center, Georgetown University Hospital, Washington, District of Columbia, USA
| | | | - Steven Sun
- Janssen Research & Development, Raritan, New Jersey, USA
| | | | | | - Gilles Salles
- Hospices Civils de Lyon, Université de Lyon, Pierre-Bénite Cedex, Lyon, France
| | - Ajay K Gopal
- Division of Medical Oncology, Department of Medicine, The University of Washington, Seattle, Washington, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Lymphoma Program, Seattle Cancer Care Alliance, Seattle, Washington, USA
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Agaimy A, Hartmann A. [SMARCB1(INI1)-deficient renal cell carcinoma: medullary and beyond : Evolving concepts]. DER PATHOLOGE 2021; 42:571-577. [PMID: 34609565 DOI: 10.1007/s00292-021-00985-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/11/2021] [Indexed: 10/20/2022]
Abstract
During the last decades, the SWI/SNF chromatin-remodeling complex has received enormous recognition as a major player in the molecular pathogenesis of diverse neoplasms. Accordingly, SWI/SNF defects affecting different subunits of the complex became defining genetic features in the nosology of different neoplastic entities. In the kidney, loss of SMARCB1(INI1) as a major component of the SWI/SNF complex has emerged as the defining genetic marker for renal medullary carcinoma and pediatric malignant rhabdoid tumor. Diagnosis of these two rare entities is based on a set of defined demographic, clinicopathological, immunophenotypic, and genetic (SMARCB1 loss) criteria. Moreover, the sickle cell trait is considered a prerequisite for renal medullary carcinoma. Current knowledge illustrates that SMARCB1 loss is encountered in three major tumor categories in the kidney: (1) histologically defined neoplasms that are primarily driven by de novo SMARCB1 loss (renal medullary carcinoma and malignant rhabdoid tumor); (2) SMRACB1-deficient renal cell carcinoma (RCC) with variable non-specific histology ranging from collecting duct-like, papillary high-grade (papillary type 2), or medullary-like (lacking sickle cell trait), to fully undifferentiated; and (3) biphasic (dedifferentiated) RCC showing a variable SMARCB1-deficient undifferentiated component. The latter variant most frequently originates from pre-existing clear cell RCC but may rarely superimpose on papillary or chromophobe RCC. This review summarizes the major defining features of the emerging SMARCB1-deficient renal neoplasms. All SMARCB1-deficient carcinomas have a poor prognosis in common. Therefore, exact diagnosis of these tumors is a prerequisite for studies investigating new therapies.
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Affiliation(s)
- Abbas Agaimy
- Institut für Pathologie, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Krankenhausstraße 8-10, 91054, Erlangen, Deutschland.
| | - Arndt Hartmann
- Institut für Pathologie, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Krankenhausstraße 8-10, 91054, Erlangen, Deutschland
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Histologic and genomic features of breast cancers with alterations affecting the SWI/SNF (SMARC) genes. Mod Pathol 2021; 34:1850-1859. [PMID: 34079072 PMCID: PMC8448940 DOI: 10.1038/s41379-021-00837-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 05/04/2021] [Accepted: 05/05/2021] [Indexed: 02/04/2023]
Abstract
The SWI/SNF family of proteins is a multisubunit ATPase complex frequently altered in human cancer. Inactivating mutations in SWI/SNF-related matrix-associated actin-dependent regulator of chromatin (SMARCs) underpin a subset of tumors such as the malignant rhabdoid tumor and small cell carcinoma of the ovary, hypercalcemic type. Here, we investigated the genotypic and phenotypic characteristics of breast cancers harboring somatic genetic alterations affecting genes of the SMARC family. We analyzed a series of 6026 primary and metastatic breast cancers subjected to targeted-capture sequencing. SMARC core subunit (SMARCA4, SMARCB1, and SMARCA2) alterations were identified in <1% of all breast cancers, consisting of 27 primary and 30 recurrent/metastatic tumors. The majority of SMARC alterations were monoallelic mutations (47/57, 82%) and thus categorized into two groups: Class 1 alterations consisting of potentially pathogenic mutations and rearrangements and Class 2 alterations consisting of missense mutations and small in-frame deletions of unknown significance. Biallelic events in a SMARC gene were present in a minority of cases (10/57, 18%). Histologic patterns in the form of rhabdoid, composite rhabdoid, sarcomatoid or anaplastic features were observed in a subset of Class 1 primary and metastatic tumors (7/57, 12%). SMARC protein was preserved in nearly all tumors analyzed with immunohistochemistry (26/30, 87%). Four Class 1 tumors demonstrated altered SMARC protein expression in the form of loss (1/30, 3%) or mosaic pattern (3/30, 10%). Complete loss of SMARCA2 (BRM) was observed in a sole tumor with composite rhabdoid morphology, and biallelic hits in the SMARCA2 gene. The genomic landscape of both primary Class 1 and 2 breast cancers did not reveal any characteristic findings. In summary, SMARC alterations likely contribute to the biology of a rare subset of breast cancers in the form of biallelic or pathogenic alterations in SMARC, as evidenced by SMARC-deficient phenotype or altered expression of SMARC protein.
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Chen C, Yin W, Wang X, Li P, Chen Y, Jin X, Yang P, Wu H. Synchronous Malignant Gastrointestinal Neuroectodermal Tumor and SMARCA4-Deficient Undifferentiated Carcinoma With Independent Origins in the Small Intestine: A Case Report. Front Oncol 2021; 11:665056. [PMID: 34513665 PMCID: PMC8429901 DOI: 10.3389/fonc.2021.665056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/05/2021] [Indexed: 01/14/2023] Open
Abstract
Background Malignant gastrointestinal neuroectodermal tumor (GNET) is a rare malignant mesenchymal neoplasm that commonly arises in the small bowel, stomach or colon. Meanwhile, SMARCA4-deficient undifferentiated carcinoma is a rarely reported entity with highly aggressive behavior that may involve the ovary, lung, gastrointestinal (GI) tract, endometrium and other organs. To our knowledge, we describe for the first time, an extremely rare case of synchronous GNET and SMARCA4-deficient undifferentiated carcinoma with independent origins in the small intestine. Case Presentation A 46-year-old woman presented with multiple small intestine masses and underwent surgical resection. Two distinct entities, GNET and SMARCA4-deficient undifferentiated carcinoma, were identified. GNET was composed of epithelioid and spindle cells with clear or eosinophilic cytoplasm arranged in sheets, nest, papillary, fascicular, palisade, rosette like or pseudoalveolar pattern. The neoplastic cells were positive for S-100 and SOX-10. Ewing sarcoma breakpoint region 1 gene (EWSR1) rearrangement was confirmed by fluorescence in situ hybridization (FISH), and EWSR1-CREB1 fusion was revealed by next-generation sequencing (NGS). SMARCA4-deficient undifferentiated carcinoma was composed mainly of poorly adhesive rhabdoid cells with eosinophilic cytoplasm arranged in a diffuse pattern. Multifocal necrosis, brisk mitotic figures as well as multinucleated tumor cells were observed. The neoplastic cells diffusely expressed pancytokeratin and vimentin, and was negative for SMARCA4(BRG1). Frame shift mutation of SMARCA4 was detected by NGS. Conclusions This is the first report that GNET and SMARCA4-deficient undifferentiated carcinoma occurred simultaneously in the small intestine, with the latter showing multiple involvement of the jejunum and ileum. The potential mechanism underlying co-existence of these two rare malignancies is unknown and need further investigations and concern.
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Affiliation(s)
- Cuimin Chen
- Department of Pathology, Shenzhen Hospital of Peking University, Shenzhen, China
| | - Weihua Yin
- Department of Pathology, Shenzhen Hospital of Peking University, Shenzhen, China
| | - Xingen Wang
- Department of Pathology, Shenzhen Hospital of Peking University, Shenzhen, China
| | - Ping Li
- Department of Pathology, Shenzhen Hospital of Peking University, Shenzhen, China
| | - Yaoli Chen
- Department of Pathology, Shenzhen Hospital of Peking University, Shenzhen, China
| | - Xianglan Jin
- Department of Pathology, Shenzhen Hospital of Peking University, Shenzhen, China
| | - Ping Yang
- Department of Pathology, Shenzhen Hospital of Peking University, Shenzhen, China
| | - Huanwen Wu
- Department of Pathology, Peking Union Medical College Hospital, Peking, China
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42
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Alves A, Constantinidou A, Thway K, Fisher C, Huang P, Jones RL. The evolving management of epithelioid sarcoma. Eur J Cancer Care (Engl) 2021; 30:e13489. [PMID: 34278633 PMCID: PMC9285437 DOI: 10.1111/ecc.13489] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/15/2021] [Accepted: 06/23/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Anneke Alves
- Sarcoma Unit, Royal Marsden Hospital, London, UK
| | | | - Khin Thway
- Sarcoma Unit, Royal Marsden Hospital, London, UK.,Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | - Cyril Fisher
- Department of Musculoskeletal Pathology, Robert Aitken Institute for Clinical Research, Birmingham, UK
| | - Paul Huang
- Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | - Robin L Jones
- Sarcoma Unit, Royal Marsden Hospital, London, UK.,Division of Clinical Studies, Institute of Cancer Research, London, UK
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Mehta A, Bansal D, Tripathi R, Jajodia A. SMARCA4/BRG1 protein-deficient thoracic tumors dictate re-examination of small biopsy reporting in non-small cell lung cancer. J Pathol Transl Med 2021; 55:307-316. [PMID: 34147056 PMCID: PMC8476316 DOI: 10.4132/jptm.2021.05.11] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/10/2021] [Indexed: 12/23/2022] Open
Abstract
Background SMARCA4/BRG1 protein–deficient lung adenocarcinomas and thoracic sarcoma are recently described entities that lack distinctive histological features, transcription termination factor 1 (TTF1) reactivity, and actionable driver mutations. The current diagnostic path for small lung biopsies as recommended by the World Health Organization (WHO, 2015) is likely to categorize these as non–small cell carcinoma–not otherwise specified (NSCC-NOS). The present study attempts to define the subtle but distinctive clinicopathologic features of SMARCA4/BRG1 protein-deficient thoracic tumors; highlight their unique biology; and addresses the unmet need to segregate these using a new, tissue-proficient diagnostic pathway. Methods All lung biopsies and those from metastatic sites in patients with suspected advanced lung cancer and classified as NSCC-NOS as per WHO (2015) guidelines were subjected to BRG1 testing by immunohistochemistry. SMARCA4/BRG1 protein–deficient thoracic tumors were evaluated by an extended immunohistochemistry panel. Predictive biomarker and programmed death–ligand 1 testing was conducted in all cases. Results Of 110 cases, nine were found to be SMARCA4/BRG1 protein-deficient; six were identified as SMARCA4/BRG1 protein–deficient lung adenocarcinomas, and three were SMARCA4/BRG1 protein-deficient thoracic sarcomas. The histology ranged from poorly differentiated to undifferentiated to rhabdoid. None of the cases showed significant expression of TTF1 or p40, and no actionable mutation was identified. Conclusions It is difficult to separate BRG1-deficient lung adenocarcinomas and thoracic sarcomas based on morphology alone. We propose a diagnostic pathway for small biopsies of thoracic tumors to segregate these distinct entities so that they can be studied more efficaciously for new biomarkers and therapeutic options.
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Affiliation(s)
- Anurag Mehta
- Department of Laboratory, Molecular and Transfusion Services, Rajiv Gandhi Cancer Institute and Research Centre (RGCIRC), New Delhi, India
| | - Divya Bansal
- Department of Pathology, Rajiv Gandhi Cancer Institute and Research Centre (RGCIRC), New Delhi, India
| | - Rupal Tripathi
- Department of Research, Rajiv Gandhi Cancer Institute and Research Centre (RGCIRC), New Delhi, India
| | - Ankush Jajodia
- Department of Radiology, Rajiv Gandhi Cancer Institute and Research Centre (RGCIRC), New Delhi, India
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Kenny C, O’Meara E, Ulaş M, Hokamp K, O’Sullivan MJ. Global Chromatin Changes Resulting from Single-Gene Inactivation-The Role of SMARCB1 in Malignant Rhabdoid Tumor. Cancers (Basel) 2021; 13:cancers13112561. [PMID: 34071089 PMCID: PMC8197137 DOI: 10.3390/cancers13112561] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/02/2021] [Accepted: 05/10/2021] [Indexed: 01/08/2023] Open
Abstract
Simple Summary Malignant rhabdoid tumors (MRT), one of the most lethal, treatment-resistant human cancers, arises in young children within brain, kidney, liver and/or soft tissues. Generally, cancer arises in older adults, and results from multiple significant changes (mutations) accumulating in the genetic blueprint (DNA) of a person’s tissues. This blueprint is composed of a 4-letter alphabet. Together, the multiple significant changes in the blueprint then allow a cell to go “out of control”, becoming a cancer cell. The striking thing about MRT is that it has only a single spelling change, so that mutation must be very powerful to lead to such a lethal cancer. Using a model system that we developed, we show herein how this single mutation alters how the whole of the DNA is arranged, thereby having its profound and lethal effects. We present insights into how this mutation arrests maturation of the cells, keeping them in a cancer “state”. Abstract Human cancer typically results from the stochastic accumulation of multiple oncogene-activating and tumor-suppressor gene-inactivating mutations. However, this process takes time and especially in the context of certain pediatric cancer, fewer but more ‘impactful’ mutations may in short order produce the full-blown cancer phenotype. This is well exemplified by the highly aggressive malignant rhabdoid tumor (MRT), where the only gene classically showing recurrent inactivation is SMARCB1, a subunit member of the BAF chromatin-remodeling complex. This is true of all three presentations of MRT including MRT of kidney (MRTK), MRT of the central nervous system (atypical teratoid rhabdoid tumor—ATRT) and extracranial, extrarenal rhabdoid tumor (EERT). Our reverse modeling of rhabdoid tumors with isogenic cell lines, either induced or not induced, to express SMARCB1 showed widespread differential chromatin remodeling indicative of altered BAF complex activity with ensuant histone modifications when tested by chromatin immunoprecipitation followed by sequencing (ChIP-seq). The changes due to reintroduction of SMARCB1 were preponderantly at typical enhancers with tandem BAF complex occupancy at these sites and related gene activation, as substantiated also by transcriptomic data. Indeed, for both MRTK and ATRT cells, there is evidence of an overlap between SMARCB1-dependent enhancer activation and tissue-specific lineage-determining genes. These genes are inactive in the tumor state, conceivably arresting the cells in a primitive/undifferentiated state. This epigenetic dysregulation from inactivation of a chromatin-remodeling complex subunit contributes to an improved understanding of the complex pathophysiological basis of MRT, one of the most lethal and aggressive human cancers.
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Affiliation(s)
- Colin Kenny
- School of Medicine, Trinity College, University of Dublin, Dublin 2, Ireland;
| | - Elaine O’Meara
- School of Medicine, Trinity College, University of Dublin, Dublin 2, Ireland;
| | - Mevlüt Ulaş
- The National Children’s Research Centre, O’Sullivan Research Laboratory, Oncology Division, Gate 5, Children’s Health Ireland at Crumlin, D12N512 Dublin, Ireland; (E.O.); (M.U.)
| | - Karsten Hokamp
- School of Genetics and Microbiology, Trinity College, University of Dublin, Dublin 2, Ireland;
| | - Maureen J. O’Sullivan
- School of Medicine, Trinity College, University of Dublin, Dublin 2, Ireland;
- The National Children’s Research Centre, O’Sullivan Research Laboratory, Oncology Division, Gate 5, Children’s Health Ireland at Crumlin, D12N512 Dublin, Ireland; (E.O.); (M.U.)
- Histology Laboratory, Pathology Department, Children’s Health Ireland at Crumlin, D12N512 Dublin, Ireland
- Correspondence:
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The Genomic Landscape of Thyroid Cancer Tumourigenesis and Implications for Immunotherapy. Cells 2021; 10:cells10051082. [PMID: 34062862 PMCID: PMC8147376 DOI: 10.3390/cells10051082] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 12/13/2022] Open
Abstract
Thyroid cancer is the most prevalent endocrine malignancy that comprises mostly indolent differentiated cancers (DTCs) and less frequently aggressive poorly differentiated (PDTC) or anaplastic cancers (ATCs) with high mortality. Utilisation of next-generation sequencing (NGS) and advanced sequencing data analysis can aid in understanding the multi-step progression model in the development of thyroid cancers and their metastatic potential at a molecular level, promoting a targeted approach to further research and development of targeted treatment options including immunotherapy, especially for the aggressive variants. Tumour initiation and progression in thyroid cancer occurs through constitutional activation of the mitogen-activated protein kinase (MAPK) pathway through mutations in BRAF, RAS, mutations in the phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K) pathway and/or receptor tyrosine kinase fusions/translocations, and other genetic aberrations acquired in a stepwise manner. This review provides a summary of the recent genetic aberrations implicated in the development and progression of thyroid cancer and implications for immunotherapy.
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Mou PK, Yang EJ, Shi C, Ren G, Tao S, Shim JS. Aurora kinase A, a synthetic lethal target for precision cancer medicine. Exp Mol Med 2021; 53:835-847. [PMID: 34050264 PMCID: PMC8178373 DOI: 10.1038/s12276-021-00635-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 02/01/2023] Open
Abstract
Recent advances in high-throughput sequencing technologies and data science have facilitated the development of precision medicine to treat cancer patients. Synthetic lethality is one of the core methodologies employed in precision cancer medicine. Synthetic lethality describes the phenomenon of the interplay between two genes in which deficiency of a single gene does not abolish cell viability but combined deficiency of two genes leads to cell death. In cancer treatment, synthetic lethality is leveraged to exploit the dependency of cancer cells on a pathway that is essential for cell survival when a tumor suppressor is mutated. This approach enables pharmacological targeting of mutant tumor suppressors that are theoretically undruggable. Successful clinical introduction of BRCA-PARP synthetic lethality in cancer treatment led to additional discoveries of novel synthetic lethal partners of other tumor suppressors, including p53, PTEN, and RB1, using high-throughput screening. Recent work has highlighted aurora kinase A (AURKA) as a synthetic lethal partner of multiple tumor suppressors. AURKA is a serine/threonine kinase involved in a number of central biological processes, such as the G2/M transition, mitotic spindle assembly, and DNA replication. This review introduces synthetic lethal interactions between AURKA and its tumor suppressor partners and discusses the potential of AURKA inhibitors in precision cancer medicine.
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Affiliation(s)
- Pui Kei Mou
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Eun Ju Yang
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Changxiang Shi
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Guowen Ren
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Shishi Tao
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Joong Sup Shim
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China.
- MoE Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macau SAR, China.
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Odnokoz O, Wavelet-Vermuse C, Hophan SL, Bulun S, Wan Y. ARID1 proteins: from transcriptional and post-translational regulation to carcinogenesis and potential therapeutics. Epigenomics 2021; 13:809-823. [PMID: 33890484 PMCID: PMC8738980 DOI: 10.2217/epi-2020-0414] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The ARID1 proteins are mutually exclusive subunits of the BRG1/BRM-associated factor (BAF) complexes that play an important role in chromatin remodeling and regulate many fundamental cell functions. The role of ARID1s is well defined as a tumor-suppressive. The cancer cells evolve different mechanisms to downregulate ARID1s and inactivate their functions. ARID1s are frequently mutated in human cancer. The recent findings of ARID1A/B downregulation at transcriptional and translational levels along with their low levels in human cancers indicate the significance of regulatory mechanisms of ARID1s in cancers. In this review, we present the current knowledge on the regulation and alterations of ARID1 protein expression in human cancers and indicate the importance of regulators of ARID1s as a prognostic marker and in potential therapeutic strategies.
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Affiliation(s)
- Olena Odnokoz
- Department of Obstetrics & Gynecology & Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Pharmacology & Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Cindy Wavelet-Vermuse
- Department of Obstetrics & Gynecology & Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Pharmacology & Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Shelby L Hophan
- Department of Obstetrics & Gynecology & Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Pharmacology & Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Serdar Bulun
- Department of Obstetrics & Gynecology & Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Yong Wan
- Department of Obstetrics & Gynecology & Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Pharmacology & Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Author for correspondence: Tel.: +1 312 503 2769;
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Sirohi D, Ohe C, Smith SC, Amin MB. SWI/SNF-deficient neoplasms of the genitourinary tract. Semin Diagn Pathol 2021; 38:212-221. [PMID: 33840529 DOI: 10.1053/j.semdp.2021.03.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 03/30/2021] [Accepted: 03/30/2021] [Indexed: 12/13/2022]
Abstract
Since the discovery of association of SMARCB1 mutations with malignant rhabdoid tumors and renal medullary carcinoma, mutations in genes of the SWI/SNF chromatin remodeling complex have been increasingly identified across a diverse spectrum of neoplasms. As a group, SWI/SNF complex subunit mutations are now recognized to be the second most frequent type of mutations across tumors. SMARCB1 mutations were originally reported in malignant rhabdoid tumors of the kidney and thought to be pathognomonic for this tumor. However, more broadly, recognition of typical rhabdoid cytomorphology and SMARCB1 mutations beyond rhabdoid tumors has changed our understanding of the pathobiology of these tumors. While mutations of SWI/SNF complex are diagnostic of rhabdoid tumors and renal medullary carcinoma, their clinical relevance extends to potential prognostic and predictive utility in other tumors as well. Beyond SMARCB1, the PBRM1 and ARID1A genes are the most frequently altered members of the SWI/SNF complex in genitourinary neoplasms, especially in clear cell renal cell carcinoma and urothelial carcinoma. In this review, we provide an overview of alterations in the SWI/SNF complex encountered in genitourinary neoplasms and discuss their increasing clinical importance.
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Affiliation(s)
- Deepika Sirohi
- Department of Pathology, University of Utah and ARUP Laboratories, Salt Lake City, UT, USA
| | - Chisato Ohe
- Department of Pathology, Kansai Medical University, Osaka, Japan
| | - Steven C Smith
- Departments of Pathology and Urology, Virginia Commonwealth University, School of Medicine, PO Box 980662, Richmond, VA 23298, USA.
| | - Mahul B Amin
- Department of Pathology and Laboratory Medicine, University of Tennessee Health Sciences, Memphis, TN, USA; Department of Urology, USC Keck School of Medicine, Los Angeles, CA, USA
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49
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Agaimy A, Bishop JA. SWI/SNF-deficient head and neck neoplasms: An overview. Semin Diagn Pathol 2021; 38:175-182. [PMID: 33663878 DOI: 10.1053/j.semdp.2021.02.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 02/24/2021] [Indexed: 11/11/2022]
Abstract
With wide-spread use of next generation sequencing tools in surgical pathology, a variety of neoplasms have been increasingly recognized to be associated with specific recurrent defining genetic abnormalities. This has led to recognition of new genetically defined entities and refinements of preexisting heterogeneous neoplastic categories. Among these, neoplasms associated with inactivating mutations involving different subunits of the SWI/SNF chromatin remodeling complex have received special attention. In the head and neck area, SMARCB1 (INI1) and SMARCA4 (BRG1) are the main two SWI/SNF components responsible for several recently described highly aggressive undifferentiated malignancies with predilection for the soft tissue of the neck (SMARCB1-deficient malignant rhabdoid tumors in children and rare epithelioid sarcoma cases in adults) and the sinonasal tract (SMARCB1-deficient sinonasal carcinoma including a small subset of adenocarcinomas, SMARCA4-deficient sinonasal undifferentiated carcinoma and SMARCA4-deficient sinonasal teratocarcinosarcoma). Molecular studies confirmed paucity of additional genetic abnormalities in these diseases underlining the central role of SWI/SNF deficiency as the primary and frequently sole genetic driver of these lethal diseases. Initiation of clinical trials using drugs that target the SWI/SNF collapse encourages recognition and correct classification of these morphologically frequently overlapping malignancies and underpins the role of SWI/SNF immunohistochemistry as emerging powerful adjunct tool in surgical pathology of the head and neck.
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Affiliation(s)
- Abbas Agaimy
- Institute of Pathology, Friedrich-Alexander-University Erlangen-Nürnberg, University Hospital, Erlangen, Germany.
| | - Justin A Bishop
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
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50
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Abstract
PURPOSE OF REVIEW Pediatric renal tumors account for 7% of new cancer diagnoses in children. Here, we will review results from recently completed clinical trials informing the current standard of care and discuss targeted and immune therapies being explored for the treatment of high risk or relapsed/refractory pediatric renal malignancies. RECENT FINDINGS Cooperative group trials have continued to make improvements in the care of children with pediatric tumors. In particular, trials that standardize treatment of rare cancers (e.g., bilateral Wilms tumor) have improved outcomes significantly. We have seen improvements in event free and overall survival in recently completed clinical trials for many pediatric renal tumors. Still, there are subsets of rarer cancers where outcomes remain poor and new therapeutic strategies are needed. Future trials aim to balance treatment toxicity with treatment efficacy for those with excellent outcomes while identifying novel therapeutics for those with poor outcomes.
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Affiliation(s)
- Juhi Jain
- Aflac Cancer and Blood Disorders Center, Children Healthcare of Atlanta, Atlanta, GA, USA.,Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA.,Emory Children's Center, 2015 Uppergate Drive NE , 400, Atlanta, GA, 30322, USA
| | - Kathryn S Sutton
- Aflac Cancer and Blood Disorders Center, Children Healthcare of Atlanta, Atlanta, GA, USA.,Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA.,Emory Children's Center, 2015 Uppergate Drive NE, 434B, Atlanta, GA, 30322, USA
| | - Andrew L Hong
- Aflac Cancer and Blood Disorders Center, Children Healthcare of Atlanta, Atlanta, GA, USA. .,Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA. .,Winship Cancer Institute, Atlanta, GA, USA. .,Health Sciences Research Building, 1760 Haygood Drive NE, E-370, Atlanta, GA, 30322, USA.
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