1
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Kim SS, Moghe M, Rait A, Donaldson K, Harford JB, Chang EH. SMARCB1 Gene Therapy Using a Novel Tumor-Targeted Nanomedicine Enhances Anti-Cancer Efficacy in a Mouse Model of Atypical Teratoid Rhabdoid Tumors. Int J Nanomedicine 2024; 19:5973-5993. [PMID: 38895149 PMCID: PMC11185260 DOI: 10.2147/ijn.s458323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 06/11/2024] [Indexed: 06/21/2024] Open
Abstract
Purpose Atypical teratoid rhabdoid tumor (ATRT) is a deadly, fast-growing form of pediatric brain cancer with poor prognosis. Most ATRTs are associated with inactivation of SMARCB1, a subunit of the chromatin remodeling complex, which is involved in developmental processes. The recent identification of SMARCB1 as a tumor suppressor gene suggests that restoration of SMARCB1 could be an effective therapeutic approach. Methods We tested SMARCB1 gene therapy in SMARCB1-deficient rhabdoid tumor cells using a novel tumor-targeted nanomedicine (termed scL-SMARCB1) to deliver wild-type SMARCB1. Our nanomedicine is a systemically administered immuno-lipid nanoparticle that can actively cross the blood-brain barrier via transferrin receptor-mediated transcytosis and selectively target tumor cells via transferrin receptor-mediated endocytosis. We studied the antitumor activity of the scL-SMARCB1 nanocomplex either as a single agent or in combination with traditional treatment modalities in preclinical models of SMARCB1-deficient ATRT. Results Restoration of SMARCB1 expression by the scL-SMARCB1 nanocomplex blocked proliferation, and induced senescence and apoptosis in ATRT cells. Systemic administration of the scL-SMARCB1 nanocomplex demonstrated antitumor efficacy as monotherapy in mice bearing ATRT xenografts, where the expression of exogenous SMARCB1 modulates MYC-target genes. scL-SMARCB1 demonstrated even greater antitumor efficacy when combined with either cisplatin-based chemotherapy or radiation therapy, resulting in significantly improved survival of ATRT-bearing mice. Conclusion Collectively, our data suggest that restoring SMARCB1 function via the scL-SMARCB1 nanocomplex may lead to therapeutic benefits in ATRT patients when combined with traditional chemoradiation therapies.
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Affiliation(s)
- Sang-Soo Kim
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
- SynerGene Therapeutics, Inc, Potomac, MD, USA
| | - Manish Moghe
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Antonina Rait
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Kathryn Donaldson
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | | | - Esther H Chang
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
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2
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Land G, Van Haeringen B, Cooper C, Andelkovic V, O'Rourke T. A Rare Case of Rhabdoid Pancreatic Carcinoma: Prolonged Disease-Free Survival Following Upfront Resection and Adjuvant Chemotherapy. Cureus 2023; 15:e50145. [PMID: 38186431 PMCID: PMC10771581 DOI: 10.7759/cureus.50145] [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] [Accepted: 12/07/2023] [Indexed: 01/09/2024] Open
Abstract
The rhabdoid subtype of undifferentiated pancreatic carcinoma is rarely reported. The clinical course of this disease is therefore poorly understood, although it is apparently an aggressive malignancy. We herein discuss the case of a 69-year-old man presenting with a rapidly enlarging mass of the pancreatic body and tail who was diagnosed with locally advanced SMARCB1-deficient undifferentiated pancreatic carcinoma with rhabdoid features, treated with radical resection and adjuvant chemotherapy, and has achieved 18-month disease-free survival ongoing at the time of article publication. We identify and contrast our case with 15 similar tumors reported in the English literature, briefly discuss the biology of this tumor, its relationship to malignant rhabdoid tumors of childhood, the role of SMARCB1 and its parent complex switch/sucrose-non-fermentable chromatin remodeling complex (SWI/SNF) in modulating the behavior of pancreatic malignancy, and the potential therapeutic avenues available for SWI/SNF-mutated malignancies.
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Affiliation(s)
- Gabriel Land
- General Surgery, Princess Alexandra Hospital, Brisbane, AUS
| | | | - Caroline Cooper
- Anatomical Pathology, Princess Alexandra Hospital, Brisbane, AUS
| | | | - Thomas O'Rourke
- Hepatobiliary Surgery, Princess Alexandra Hospital, Brisbane, AUS
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3
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Giordano G, Ferioli E, Guareschi D, Tafuni A. Dedifferentiated Endometrial Carcinoma: A Rare Aggressive Neoplasm-Clinical, Morphological and Immunohistochemical Features. Cancers (Basel) 2023; 15:5155. [PMID: 37958329 PMCID: PMC10647464 DOI: 10.3390/cancers15215155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 10/22/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
Dedifferentiated endometrioid adenocarcinoma is characterised by the coexistence of an undifferentiated carcinoma and a low-grade endometrioid adenocarcinoma. The low-grade component in this subtype of endometrial carcinoma is Grade 1 or 2 according to the Federation of Gynaecology and Obstetrics (FIGO) grading system. The coexistence of low-grade endometrial carcinoma and solid undifferentiated carcinoma can cause diagnostic problems on histological examination. In fact, this combination can often be mistaken for a more common Grade 2 or Grade 3 endometrial carcinoma. Therefore, this subtype of uterine carcinoma can often go under-recognised. An accurate diagnosis of dedifferentiated endometrial carcinoma is mandatory because of its poorer prognosis compared to Grade 3 endometrial carcinoma, with a solid undifferentiated component that can amount to as much as 20% of the entire tumour. The aim of this review is to provide clinical, immunohistochemical, and molecular data to aid with making an accurate histological diagnosis and to establish whether there are any findings which could have an impact on the prognosis or therapeutic implications of this rare and aggressive uterine neoplasm.
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Affiliation(s)
- Giovanna Giordano
- Department of Medicine and Surgery, Pathology Unit, University of Parma, Viale A. Gramsci, 14, 43126 Parma, Italy; (E.F.); (A.T.)
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4
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Soto-Castillo JJ, Llavata-Marti L, Fort-Culillas R, Andreu-Cobo P, Moreno R, Codony C, García Del Muro X, Alemany R, Piulats JM, Martin-Liberal J. SWI/SNF Complex Alterations in Tumors with Rhabdoid Features: Novel Therapeutic Approaches and Opportunities for Adoptive Cell Therapy. Int J Mol Sci 2023; 24:11143. [PMID: 37446319 DOI: 10.3390/ijms241311143] [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: 05/31/2023] [Revised: 06/23/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
The SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin-remodeling complex is one of the most remarkably altered epigenetic regulators in cancer. Pathogenic mutations in genes encoding SWI/SNF-related proteins have been recently described in many solid tumors, including rare and aggressive malignancies with rhabdoid features with no standard therapies in advanced or metastatic settings. In recent years, clinical trials with targeted drugs aimed at restoring its function have shown discouraging results. However, preclinical data have found an association between these epigenetic alterations and response to immune therapy. Thus, the rationale for immunotherapy strategies in SWI/SNF complex alteration-related tumors is strong. Here, we review the SWI/SNF complex and how its dysfunction drives the oncogenesis of rhabdoid tumors and the proposed strategies to revert this alteration and promising novel therapeutic approaches, including immune checkpoint inhibition and adoptive cell therapy.
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Affiliation(s)
- Juan José Soto-Castillo
- Medical Oncology Department, Catalan Institute of Oncology (ICO), 08908 Hospitalet de Llobregat, Spain
| | - Lucía Llavata-Marti
- Medical Oncology Department, Catalan Institute of Oncology (ICO), 17007 Girona, Spain
| | - Roser Fort-Culillas
- Medical Oncology Department, Catalan Institute of Oncology (ICO), 17007 Girona, Spain
| | - Pablo Andreu-Cobo
- Medical Oncology Department, Parc Tauli Hospital Universitari, 08208 Sabadell, Spain
| | - Rafael Moreno
- Cancer Immunotherapy Group, iPROCURE Program, Bellvitge Biomedical Research Institute (IDIBELL), Catalan Institute of Oncology (ICO), 08908 Hospitalet de Llobregat, Spain
| | - Carles Codony
- Cancer Immunotherapy Group, iPROCURE Program, Bellvitge Biomedical Research Institute (IDIBELL), Catalan Institute of Oncology (ICO), 08908 Hospitalet de Llobregat, Spain
| | - Xavier García Del Muro
- Medical Oncology Department, Catalan Institute of Oncology (ICO), 08908 Hospitalet de Llobregat, Spain
| | - Ramon Alemany
- Cancer Immunotherapy Group, iPROCURE Program, Bellvitge Biomedical Research Institute (IDIBELL), Catalan Institute of Oncology (ICO), 08908 Hospitalet de Llobregat, Spain
| | - Josep M Piulats
- Medical Oncology Department, Catalan Institute of Oncology (ICO), 08908 Hospitalet de Llobregat, Spain
- Cancer Immunotherapy Group, iPROCURE Program, Bellvitge Biomedical Research Institute (IDIBELL), Catalan Institute of Oncology (ICO), 08908 Hospitalet de Llobregat, Spain
| | - Juan Martin-Liberal
- Medical Oncology Department, Catalan Institute of Oncology (ICO), 08908 Hospitalet de Llobregat, Spain
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5
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Gordillo GM, Guda PR, Singh K, Biswas A, Abouhashem AS, Rustagi Y, Sen A, Kumar M, Das A, Ghatak S, Khanna S, Sen CK, Roy S. Tissue nanotransfection causes tumor regression by its effect on nanovesicle cargo that alters microenvironmental macrophage state. Mol Ther 2023; 31:1402-1417. [PMID: 36380587 PMCID: PMC10188642 DOI: 10.1016/j.ymthe.2022.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 10/25/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Extracellular vesicles (EVs) are nanovesicles released by all eukaryotic cells. This work reports the first nanoscale fluorescent visualization of tumor-originating vesicles bearing an angiogenic microRNA (miR)-126 cargo. In a validated experimental model of lethal murine vascular neoplasm, tumor-originating EV delivered its miR-126 cargo to tumor-associated macrophages (TAMs). Such delivery resulted in an angiogenic (LYVE+) change of state in TAM that supported tumor formation. Study of the trafficking of tumor-originating fluorescently tagged EV revealed colocalization with TAM demonstrating uptake by these cells. Ex vivo treatment of macrophages with tumor-derived EVs led to gain of tumorigenicity in these isolated cells. Single-cell RNA sequencing of macrophages revealed that EV-borne miR-126 characterized the angiogenic change of state. Unique gene expression signatures of specific macrophage clusters responsive to miR-126-enriched tumor-derived EVs were revealed. Topical tissue nanotransfection (TNT) delivery of an oligonucleotide comprising an anti-miR against miR-126 resulted in significant knockdown of miR-126 in the tumor tissue. miR-126 knockdown resulted in complete involution of the tumor and improved survival rate of tumor-affected mice. This work identifies a novel tumorigenic mechanism that relies on tumorigenic state change of TAM caused by tumor-originating EV-borne angiomiR. This disease process can be effectively targeted by topical TNT of superficial tumors.
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Affiliation(s)
- Gayle M Gordillo
- Indiana Center for Regenerative Medicine and Engineering, Department of Surgery, Indiana University School of Medicine, 975 W Walnut Street, Suite 444, Indianapolis, IN 46202, USA.
| | - Poornachander Reddy Guda
- Indiana Center for Regenerative Medicine and Engineering, Department of Surgery, Indiana University School of Medicine, 975 W Walnut Street, Suite 444, Indianapolis, IN 46202, USA
| | - Kanhaiya Singh
- Indiana Center for Regenerative Medicine and Engineering, Department of Surgery, Indiana University School of Medicine, 975 W Walnut Street, Suite 444, Indianapolis, IN 46202, USA
| | - Ayan Biswas
- Indiana Center for Regenerative Medicine and Engineering, Department of Surgery, Indiana University School of Medicine, 975 W Walnut Street, Suite 444, Indianapolis, IN 46202, USA
| | - Ahmed S Abouhashem
- Indiana Center for Regenerative Medicine and Engineering, Department of Surgery, Indiana University School of Medicine, 975 W Walnut Street, Suite 444, Indianapolis, IN 46202, USA
| | - Yashika Rustagi
- Indiana Center for Regenerative Medicine and Engineering, Department of Surgery, Indiana University School of Medicine, 975 W Walnut Street, Suite 444, Indianapolis, IN 46202, USA
| | - Abhishek Sen
- Indiana Center for Regenerative Medicine and Engineering, Department of Surgery, Indiana University School of Medicine, 975 W Walnut Street, Suite 444, Indianapolis, IN 46202, USA
| | - Manishekhar Kumar
- Indiana Center for Regenerative Medicine and Engineering, Department of Surgery, Indiana University School of Medicine, 975 W Walnut Street, Suite 444, Indianapolis, IN 46202, USA
| | - Amitava Das
- Indiana Center for Regenerative Medicine and Engineering, Department of Surgery, Indiana University School of Medicine, 975 W Walnut Street, Suite 444, Indianapolis, IN 46202, USA
| | - Subhadip Ghatak
- Indiana Center for Regenerative Medicine and Engineering, Department of Surgery, Indiana University School of Medicine, 975 W Walnut Street, Suite 444, Indianapolis, IN 46202, USA
| | - Savita Khanna
- Indiana Center for Regenerative Medicine and Engineering, Department of Surgery, Indiana University School of Medicine, 975 W Walnut Street, Suite 444, Indianapolis, IN 46202, USA
| | - Chandan K Sen
- Indiana Center for Regenerative Medicine and Engineering, Department of Surgery, Indiana University School of Medicine, 975 W Walnut Street, Suite 444, Indianapolis, IN 46202, USA
| | - Sashwati Roy
- Indiana Center for Regenerative Medicine and Engineering, Department of Surgery, Indiana University School of Medicine, 975 W Walnut Street, Suite 444, Indianapolis, IN 46202, USA.
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6
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Nguyen VT, Tessema M, Weissman BE. The SWI/SNF Complex: A Frequently Mutated Chromatin Remodeling Complex in Cancer. Cancer Treat Res 2023; 190:211-244. [PMID: 38113003 DOI: 10.1007/978-3-031-45654-1_7] [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: 12/21/2023]
Abstract
The switch/sucrose non-fermenting (SWI/SNF) chromatin remodeling complex is a global regulator of gene expression known to maintain nucleosome-depleted regions at active enhancers and promoters. The mammalian SWI/SNF protein subunits are encoded by 29 genes and 11-15 subunits including an ATPase domain of either SMARCA4 (BRG1) or SMARCA2 (BRM) are assembled into a complex. Based on the distinct subunits, SWI/SNF are grouped into 3 major types (subfamilies): the canonical BRG1/BRM-associated factor (BAF/cBAF), polybromo-associated BAF (PBAF), and non-canonical BAF (GBAF/ncBAF). Pan-cancer genome sequencing studies have shown that nearly 25% of all cancers bear mutations in subunits of the SWI/SNF complex, many of which are loss of function (LOF) mutations, suggesting a tumor suppressor role. Inactivation of SWI/SNF complex subunits causes widespread epigenetic dysfunction, including increased dependence on antagonistic components such as polycomb repressor complexes (PRC1/2) and altered enhancer regulation, likely promoting an oncogenic state leading to cancer. Despite the prevalence of mutations, most SWI/SNF-mutant cancers lack targeted therapeutic strategies. Defining the dependencies created by LOF mutations in SWI/SNF subunits will identify better targets for these cancers.
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Affiliation(s)
- Vinh The Nguyen
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Curriculum in Toxicology and Environmental Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Mathewos Tessema
- Lung Cancer Program, Lovelace Biomedical Research Institute, Albuquerque, NM, USA
| | - Bernard Ellis Weissman
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA.
- Curriculum in Toxicology and Environmental Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA.
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA.
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7
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Mina M, Iyer A, Ciriello G. Epistasis and evolutionary dependencies in human cancers. Curr Opin Genet Dev 2022; 77:101989. [PMID: 36182742 DOI: 10.1016/j.gde.2022.101989] [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: 04/21/2022] [Revised: 08/29/2022] [Accepted: 08/31/2022] [Indexed: 01/27/2023]
Abstract
Cancer evolution is driven by the concerted action of multiple molecular alterations, which emerge and are selected during tumor progression. An alteration is selected when it provides an advantage to the tumor cell. However, the advantage provided by a specific alteration depends on the tumor lineage, cell epigenetic state, and presence of additional alterations. In this case, we say that an evolutionary dependency exists between an alteration and what influences its selection. Epistatic interactions between altered genes lead to evolutionary dependencies (EDs), by favoring or vetoing specific combinations of events. Large-scale cancer genomics studies have discovered examples of such dependencies, and showed that they influence tumor progression, disease phenotypes, and therapeutic response. In the past decade, several algorithmic approaches have been proposed to infer EDs from large-scale genomics datasets. These methods adopt diverse strategies to address common challenges and shed new light on cancer evolutionary trajectories. Here, we review these efforts starting from a simple conceptualization of the problem, presenting the tackled and still unmet needs in the field, and discussing the implications of EDs in cancer biology and precision oncology.
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Affiliation(s)
- Marco Mina
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Swiss Cancer Center Leman, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Arvind Iyer
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Swiss Cancer Center Leman, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Giovanni Ciriello
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Swiss Cancer Center Leman, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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8
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Zhang FL, Li DQ. Targeting Chromatin-Remodeling Factors in Cancer Cells: Promising Molecules in Cancer Therapy. Int J Mol Sci 2022; 23:12815. [PMID: 36361605 PMCID: PMC9655648 DOI: 10.3390/ijms232112815] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/12/2022] [Accepted: 10/19/2022] [Indexed: 03/28/2024] Open
Abstract
ATP-dependent chromatin-remodeling complexes can reorganize and remodel chromatin and thereby act as important regulator in various cellular processes. Based on considerable studies over the past two decades, it has been confirmed that the abnormal function of chromatin remodeling plays a pivotal role in genome reprogramming for oncogenesis in cancer development and/or resistance to cancer therapy. Recently, exciting progress has been made in the identification of genetic alteration in the genes encoding the chromatin-remodeling complexes associated with tumorigenesis, as well as in our understanding of chromatin-remodeling mechanisms in cancer biology. Here, we present preclinical evidence explaining the signaling mechanisms involving the chromatin-remodeling misregulation-induced cancer cellular processes, including DNA damage signaling, metastasis, angiogenesis, immune signaling, etc. However, even though the cumulative evidence in this field provides promising emerging molecules for therapeutic explorations in cancer, more research is needed to assess the clinical roles of these genetic cancer targets.
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Affiliation(s)
- Fang-Lin Zhang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Cancer Institute, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Da-Qiang Li
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Cancer Institute, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Department of Breast Surgery, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Shanghai Key Laboratory of Breast Cancer, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
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9
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Johnson RM, Qu X, Lin CF, Huw LY, Venkatanarayan A, Sokol E, Ou FS, Ihuegbu N, Zill OA, Kabbarah O, Wang L, Bourgon R, de Sousa E Melo F, Bolen C, Daemen A, Venook AP, Innocenti F, Lenz HJ, Bais C. ARID1A mutations confer intrinsic and acquired resistance to cetuximab treatment in colorectal cancer. Nat Commun 2022; 13:5478. [PMID: 36117191 PMCID: PMC9482920 DOI: 10.1038/s41467-022-33172-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 09/05/2022] [Indexed: 11/25/2022] Open
Abstract
Most colorectal (CRC) tumors are dependent on EGFR/KRAS/BRAF/MAPK signaling activation. ARID1A is an epigenetic regulator mutated in approximately 5% of non-hypermutated CRC tumors. Here we show that anti-EGFR but not anti-VEGF treatment enriches for emerging ARID1A mutations in CRC patients. In addition, we find that patients with ARID1A mutations, at baseline, are associated with worse outcome when treated with cetuximab- but not bevacizumab-containing therapies; thus, this suggests that ARID1A mutations may provide both an acquired and intrinsic mechanism of resistance to anti-EGFR therapies. We find that, ARID1A and EGFR-pathway genetic alterations are mutually exclusive across lung and colorectal cancers, further supporting a functional connection between these pathways. Our results not only suggest that ARID1A could be potentially used as a predictive biomarker for cetuximab treatment decisions but also provide a rationale for exploring therapeutic MAPK inhibition in an unexpected but genetically defined segment of CRC patients. ARID1A is an epigenetic regulator mutated in approximately 5% of non-hypermutated colorectal cancer tumors, however, its relationship with treatment response remains to be explored. Here, the authors suggest that ARID1A mutations may confer intrinsic and acquired resistance to cetuximab treatment.
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Affiliation(s)
- Radia M Johnson
- Bioinformatics & Computational Biology, Genentech, Inc., South San Francisco, CA, USA.
| | - Xueping Qu
- Oncology Biomarker Development, Genentech, Inc., South San Francisco, CA, USA.
| | - Chu-Fang Lin
- Real World Data Science Analytics, Genentech, Inc., South San Francisco, CA, USA
| | - Ling-Yuh Huw
- Oncology Biomarker Development, Genentech, Inc., South San Francisco, CA, USA
| | | | - Ethan Sokol
- Cancer Genomics Research, Foundation Medicine, Inc., Cambridge, MA, USA
| | - Fang-Shu Ou
- Alliance Statistics and Data Management Center, Mayo Clinic, Rochester, MN, USA
| | | | - Oliver A Zill
- Bioinformatics & Computational Biology, Genentech, Inc., South San Francisco, CA, USA
| | - Omar Kabbarah
- Oncology Biomarker Development, Genentech, Inc., South San Francisco, CA, USA
| | - Lisa Wang
- Real World Data Science Analytics, Genentech, Inc., South San Francisco, CA, USA
| | - Richard Bourgon
- Bioinformatics & Computational Biology, Genentech, Inc., South San Francisco, CA, USA
| | | | - Chris Bolen
- Bioinformatics & Computational Biology, Genentech, Inc., South San Francisco, CA, USA
| | - Anneleen Daemen
- Bioinformatics & Computational Biology, Genentech, Inc., South San Francisco, CA, USA
| | - Alan P Venook
- University of California, San Francisco, San Francisco, CA, USA
| | | | | | - Carlos Bais
- Oncology Biomarker Development, Genentech, Inc., South San Francisco, CA, USA.
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10
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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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11
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Rasmussen SV, Jin JX, Bickford LR, Woods AD, Sahm F, Crawford KA, Nagamori K, Goto H, Torres KE, Sidoni A, Rudzinski ER, Thway K, Jones RL, Ciulli A, Wright H, Lathara M, Srinivasa G, Kannan K, Huang PH, Grünewald TGP, Berlow NE, Keller C. Functional genomic analysis of epithelioid sarcoma reveals distinct proximal and distal subtype biology. Clin Transl Med 2022; 12:e961. [PMID: 35839307 PMCID: PMC9286527 DOI: 10.1002/ctm2.961] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/13/2022] [Accepted: 06/17/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Metastatic epithelioid sarcoma (EPS) remains a largely unmet clinical need in children, adolescents and young adults despite the advent of EZH2 inhibitor tazemetostat. METHODS In order to realise consistently effective drug therapies, a functional genomics approach was used to identify key signalling pathway vulnerabilities in a spectrum of EPS patient samples. EPS biopsies/surgical resections and cell lines were studied by next-generation DNA exome and RNA deep sequencing, then EPS cell cultures were tested against a panel of chemical probes to discover signalling pathway targets with the most significant contributions to EPS tumour cell maintenance. RESULTS Other biologically inspired functional interrogations of EPS cultures using gene knockdown or chemical probes demonstrated only limited to modest efficacy in vitro. However, our molecular studies uncovered distinguishing features (including retained dysfunctional SMARCB1 expression and elevated GLI3, FYN and CXCL12 expression) of distal, paediatric/young adult-associated EPS versus proximal, adult-associated EPS. CONCLUSIONS Overall results highlight the complexity of the disease and a limited chemical space for therapeutic advancement. However, subtle differences between the two EPS subtypes highlight the biological disparities between younger and older EPS patients and emphasise the need to approach the two subtypes as molecularly and clinically distinct diseases.
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Affiliation(s)
| | - Jia Xiang Jin
- Division of Translational Pediatric Sarcoma Research, Hopp Children's Cancer Center (KiTZ), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | | | - Andrew D Woods
- Children's Cancer Therapy Development Institute, Beaverton, Oregon, USA
| | - Felix Sahm
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | | | - Kiyo Nagamori
- Children's Cancer Therapy Development Institute, Beaverton, Oregon, USA
| | - Hiroaki Goto
- Division of Hematology/Oncology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Keila E Torres
- Sarcoma Surgical Oncology, MD Anderson Cancer Center, Houston, Texas, USA
| | - Angelo Sidoni
- Section of Pathology, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Erin R Rudzinski
- Department of Pathology, Seattle Children's Hospital, Seattle, Washington, USA
| | - Khin Thway
- Sarcoma Unit, Royal Marsden Hospital, Belmont, UK.,Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | - Robin L Jones
- Sarcoma Unit, Royal Marsden Hospital, Belmont, UK.,Division of Clinical Studies, Institute of Cancer Research, London, UK
| | - Alessio Ciulli
- School of Life Sciences, University of Dundee, Dundee, UK
| | | | | | | | | | - Paul H Huang
- Sarcoma Unit, Royal Marsden Hospital, Belmont, UK.,Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | - Thomas G P Grünewald
- Division of Translational Pediatric Sarcoma Research, Hopp Children's Cancer Center (KiTZ), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Noah E Berlow
- Children's Cancer Therapy Development Institute, Beaverton, Oregon, USA
| | - Charles Keller
- Children's Cancer Therapy Development Institute, Beaverton, Oregon, USA
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12
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Rechberger JS, Nesvick CL, Daniels DJ. Atypical teratoid rhabdoid tumor (ATRT): disease mechanisms and potential drug targets. Expert Opin Ther Targets 2022; 26:187-192. [PMID: 35142587 DOI: 10.1080/14728222.2022.2040017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Julian S Rechberger
- Mayo Clinic Graduate School of Biomedical Sciences, Department of Molecular Pharmacology and Experimental Therapeutics, Rochester, MN, United States.,Department of Neurologic Surgery, Mayo Clinic, Rochester, MN, United States
| | - Cody L Nesvick
- Department of Neurologic Surgery, Mayo Clinic, Rochester, MN, United States
| | - David J Daniels
- Department of Neurologic Surgery, Mayo Clinic, Rochester, MN, United States
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13
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Ding H, Huang Y, Shi J, Wang L, Liu S, Zhao B, Liu Y, Yang J, Chen Z. Attenuated expression of SNF5 facilitates progression of bladder cancer via STAT3 activation. Cancer Cell Int 2021; 21:655. [PMID: 34876150 PMCID: PMC8650342 DOI: 10.1186/s12935-021-02363-3] [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: 07/25/2021] [Accepted: 11/24/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND SWI/SNF, a well-known ATP-dependent chromatin-remodeling complex, plays an essential role in several biological processes. SNF5, the core subunit of the SWI/SNF remodeling complex, inactivated in 95% of malignant rhabdoid tumors (MRT), highlighting its significance in tumorigenesis. However, the role of SNF5 in bladder cancer (BC) remains unknown. In this study, we aimed to investigate the function and potential clinical applicability of SNF5 in BC. METHODS Data from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) and Cancer Cell Line Encyclopedia (CCLE) databases were used to evaluate the clinical significance of SNF5 in BC. We performed Gene Set Enrichment Analysis (GSEA) and functional assays to investigate the role of SNF5 in BC. Genomics of Drug Sensitivity in Cancer (GDSC) and drug-susceptibility tests were performed to identify the potential value of SNF5 in the treatment of BC. RESULTS Low SNF5 expression conferred a poor prognosis and was significantly associated with the N-stage in BC. ROC curves indicated that SNF5 could distinguish BC from the normal tissues. In vitro and in vivo functional assays demonstrated that attenuated SNF5 expression could promote cell proliferation and enhance migration by STAT3 activation. We imputed that low SNF5 expression could confer greater resistance against conventional first-line drugs, including cisplatin and gemcitabine in BC. GDSC and drug-resistance assays suggested that low SNF5 expression renders T24 and 5637 cells high sensitivity to EGFR inhibitor gefitinib, and combination of EZH2 inhibitor GSK126 and cisplatin. CONCLUSIONS To the best of our knowledge, the present study, for the first time, showed that low SNF5 expression could promote cell proliferation and migration by activating STAT3 and confer poor prognosis in BC. Importantly, SNF5 expression may be a promising candidate for identifying BC patients who could benefit from EGFR-targeted chemotherapy or cisplatin in combination with EZH2 inhibitor treatment regimens.
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Affiliation(s)
- Hua Ding
- Department of Urology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Yaqin Huang
- Department of Cell Biology, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Jiazhong Shi
- Department of Cell Biology, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Liwei Wang
- Department of Urology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China.,Unit 32357 of People's Liberation Army, Pujiang, 611630, China
| | - Sha Liu
- Department of Cell Biology, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Baixiong Zhao
- Department of Urology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Yuting Liu
- Department of Cell Biology, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Jin Yang
- Department of Cell Biology, Third Military Medical University (Army Medical University), Chongqing, 400038, China.
| | - Zhiwen Chen
- Department of Urology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China.
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14
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Preclinical In Vivo Modeling of Pediatric Sarcoma-Promises and Limitations. J Clin Med 2021; 10:jcm10081578. [PMID: 33918045 PMCID: PMC8069549 DOI: 10.3390/jcm10081578] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/05/2021] [Accepted: 04/06/2021] [Indexed: 02/07/2023] Open
Abstract
Pediatric sarcomas are an extremely heterogeneous group of genetically distinct diseases. Despite the increasing knowledge on their molecular makeup in recent years, true therapeutic advancements are largely lacking and prognosis often remains dim, particularly for relapsed and metastasized patients. Since this is largely due to the lack of suitable model systems as a prerequisite to develop and assess novel therapeutics, we here review the available approaches to model sarcoma in vivo. We focused on genetically engineered and patient-derived mouse models, compared strengths and weaknesses, and finally explored possibilities and limitations to utilize these models to advance both biological understanding as well as clinical diagnosis and therapy.
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15
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Interplay of BAF and MLL4 promotes cell type-specific enhancer activation. Nat Commun 2021; 12:1630. [PMID: 33712604 PMCID: PMC7955098 DOI: 10.1038/s41467-021-21893-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 02/10/2021] [Indexed: 01/05/2023] Open
Abstract
Cell type-specific enhancers are activated by coordinated actions of lineage-determining transcription factors (LDTFs) and chromatin regulators. The SWI/SNF chromatin remodeling complex BAF and the histone H3K4 methyltransferase MLL4 (KMT2D) are both implicated in enhancer activation. However, the interplay between BAF and MLL4 in enhancer activation remains unclear. Using adipogenesis as a model system, we identify BAF as the major SWI/SNF complex that colocalizes with MLL4 and LDTFs on active enhancers and is required for cell differentiation. In contrast, the promoter enriched SWI/SNF complex PBAF is dispensable for adipogenesis. By depleting BAF subunits SMARCA4 (BRG1) and SMARCB1 (SNF5) as well as MLL4 in cells, we show that BAF and MLL4 reciprocally regulate each other’s binding on active enhancers before and during adipogenesis. By focusing on enhancer activation by the adipogenic pioneer transcription factor C/EBPβ without inducing cell differentiation, we provide direct evidence for an interdependent relationship between BAF and MLL4 in activating cell type-specific enhancers. Together, these findings reveal a positive feedback between BAF and MLL4 in promoting LDTF-dependent activation of cell type-specific enhancers. The SWI/SNF complex BAF and the histone H3K4 methyltransferase MLL4 (KMT2D) play critical roles in enhancer activation, however the interplay between them has remained unclear. Here the authors show that BAF and MLL4 are interdependent in promoting enhancer activation by lineage-determining transcription factors during adipogenesis.
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16
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Hong SH, Son KH, Ha SY, Wee TI, Choi SK, Won JE, Han HD, Ro Y, Park YM, Eun JW, Nam SW, Han JW, Kang K, You JS. Nucleoporin 210 Serves a Key Scaffold for SMARCB1 in Liver Cancer. Cancer Res 2020; 81:356-370. [PMID: 33239431 DOI: 10.1158/0008-5472.can-20-0568] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 07/19/2020] [Accepted: 10/28/2020] [Indexed: 11/16/2022]
Abstract
The roles of chromatin remodelers and their underlying mechanisms of action in cancer remain unclear. In this study, SMARCB1, known initially as a bona fide tumor suppressor gene, was investigated in liver cancer. SMARCB1 was highly upregulated in patients with liver cancer and was associated with poor prognosis. Loss- and gain-of-function studies in liver cells revealed that SMARCB1 loss led to reduced cell proliferation, wound healing capacity, and tumor growth in vivo. Although upregulated SMARCB1 appeared to contribute to switch/sucrose nonfermentable (SWI/SNF) complex stability and integrity, it did not act using its known pathways antagonism with EZH2 or association between TP53 or AMPK. SMARCB1 knockdown induced a mild reduction in global H3K27 acetylation, and chromatin immunoprecipitation sequencing of SMARCB1 and acetylated histone H3K27 antibodies before and after SMARCB1 loss identified Nucleoporin210 (NUP210) as a critical target of SMARCB1, which bound its enhancer and changed H3K27Ac enrichment and downstream gene expression, particularly cholesterol homeostasis and xenobiotic metabolism. Notably, NUP210 was not only a putative tumor supporter involved in liver cancer but also acted as a key scaffold for SMARCB1 and P300 to chromatin. Furthermore, SMARCB1 deficiency conferred sensitivity to doxorubicin and P300 inhibitor in liver cancer cells. These findings provide insights into mechanisms underlying dysregulation of chromatin remodelers and show novel associations between nucleoporins and chromatin remodelers in cancer. SIGNIFICANCE: This study reveals a novel protumorigenic role for SMARCB1 and describes valuable links between nucleoporins and chromatin remodelers in cancer by identifying NUP210 as a critical coregulator of SMARCB1 chromatin remodeling activity.
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Affiliation(s)
| | - Keun Hong Son
- College of Natural Sciences, Dankook University, Cheonan, Korea
| | - Sang Yun Ha
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Tae In Wee
- School of Medicine, Konkuk University, Seoul, Korea
| | | | - Ji Eun Won
- School of Medicine, Konkuk University, Seoul, Korea
| | - Hee Dong Han
- School of Medicine, Konkuk University, Seoul, Korea
| | - Youngtae Ro
- School of Medicine, Konkuk University, Seoul, Korea
| | | | - Jung Woo Eun
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Korea
| | - Suk Woo Nam
- Department of Pathology, College of Medicine, Catholic University, Seoul, Korea
| | - Jeung-Whan Han
- Research Center for Epigenome Regulation, School of Pharmacy, Sungkyunkwan University, Suwon, Korea
| | - Keunsoo Kang
- College of Natural Sciences, Dankook University, Cheonan, Korea
| | - Jueng Soo You
- School of Medicine, Konkuk University, Seoul, Korea.
- Research Institute of Medical Science, Konkuk University, Seoul, Korea
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17
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Ng KL, Taguchi YH. Identification of miRNA signatures for kidney renal clear cell carcinoma using the tensor-decomposition method. Sci Rep 2020; 10:15149. [PMID: 32938959 PMCID: PMC7494921 DOI: 10.1038/s41598-020-71997-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 08/24/2020] [Indexed: 12/21/2022] Open
Abstract
Cancer is a highly complex disease caused by multiple genetic factors. MicroRNA (miRNA) and mRNA expression profiles are useful for identifying prognostic biomarkers for cancer. Kidney renal clear cell carcinoma (KIRC), which accounts for more than 70% of all renal malignant tumour cases, was selected for our analysis. Traditional methods of identifying cancer prognostic markers may not be accurate. Tensor decomposition (TD) is a useful method uncovering the underlying low-dimensional structures in the tensor. The TD-based unsupervised feature extraction method was applied to analyse mRNA and miRNA expression profiles. Biological annotations of the prognostic miRNAs and mRNAs were examined utilizing the pathway and oncogenic signature databases DIANA-miRPath and MSigDB. TD identified the miRNA signatures and the associated genes. These genes were found to be involved in cancer-related pathways, and 23 genes were significantly correlated with the survival of KIRC patients. We demonstrated that the results are robust and not highly dependent upon the databases we selected. Compared with traditional supervised methods tested, TD achieves much better performance in selecting prognostic miRNAs and mRNAs. These results suggest that integrated analysis using the TD-based unsupervised feature extraction technique is an effective strategy for identifying prognostic signatures in cancer studies.
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Affiliation(s)
- Ka-Lok Ng
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung, Taiwan
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Y-H Taguchi
- Department of Physics, Chuo University, 1-13-27 Kasuga Bunky-ku, Tokyo, 112-8551, Japan.
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18
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Heatley N, Kolson Kokohaare E, Strauss DC, Hallin M, Jones RL, Fisher C, Thway K. Epithelioid malignant peripheral nerve sheath tumor arising in schwannoma. Rare Tumors 2020; 12:2036361320950862. [PMID: 32913618 PMCID: PMC7443986 DOI: 10.1177/2036361320950862] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 06/18/2020] [Indexed: 11/15/2022] Open
Abstract
Epithelioid malignant peripheral nerve sheath tumor (EMPNST, malignant epithelioid schwannoma) is a rare variant of malignant peripheral nerve sheath tumor that has morphologic and immunophenotypic overlap with a variety of epithelioid neoplasms. Because of its rarity it may be potentially underrecognized. We describe a case arising in the subcutis of the thigh in a 25 year-old female, and discuss the pathologic features and differential diagnosis.
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Affiliation(s)
| | | | | | - Magnus Hallin
- Sarcoma Unit, The Royal Marsden Hospital, London, UK
| | - Robin L Jones
- Sarcoma Unit, The Royal Marsden Hospital, London, UK.,The Institute of Cancer Research, London, UK
| | - Cyril Fisher
- The Institute of Cancer Research, London, UK.,Department of Musculoskeletal Pathology, Royal Orthopaedic Hospital NHS Foundation Trust, Robert Aitken Institute for Clinical Research, University of Birmingham, Birmingham, UK
| | - Khin Thway
- Sarcoma Unit, The Royal Marsden Hospital, London, UK.,The Institute of Cancer Research, London, UK
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19
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Gamrekelashvili J, Kapanadze T, Sablotny S, Ratiu C, Dastagir K, Lochner M, Karbach S, Wenzel P, Sitnow A, Fleig S, Sparwasser T, Kalinke U, Holzmann B, Haller H, Limbourg FP. Notch and TLR signaling coordinate monocyte cell fate and inflammation. eLife 2020; 9:57007. [PMID: 32723480 PMCID: PMC7413669 DOI: 10.7554/elife.57007] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 07/28/2020] [Indexed: 12/14/2022] Open
Abstract
Conventional Ly6Chi monocytes have developmental plasticity for a spectrum of differentiated phagocytes. Here we show, using conditional deletion strategies in a mouse model of Toll-like receptor (TLR) 7-induced inflammation, that the spectrum of developmental cell fates of Ly6Chi monocytes, and the resultant inflammation, is coordinately regulated by TLR and Notch signaling. Cell-intrinsic Notch2 and TLR7-Myd88 pathways independently and synergistically promote Ly6Clo patrolling monocyte development from Ly6Chi monocytes under inflammatory conditions, while impairment in either signaling axis impairs Ly6Clo monocyte development. At the same time, TLR7 stimulation in the absence of functional Notch2 signaling promotes resident tissue macrophage gene expression signatures in monocytes in the blood and ectopic differentiation of Ly6Chi monocytes into macrophages and dendritic cells, which infiltrate the spleen and major blood vessels and are accompanied by aberrant systemic inflammation. Thus, Notch2 is a master regulator of Ly6Chi monocyte cell fate and inflammation in response to TLR signaling.
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Affiliation(s)
- Jaba Gamrekelashvili
- Vascular Medicine Research, Hannover Medical School, Hannover, Germany.,Department of Nephrology and Hypertension, Hannover Medical School, Hannover, Germany
| | - Tamar Kapanadze
- Vascular Medicine Research, Hannover Medical School, Hannover, Germany.,Department of Nephrology and Hypertension, Hannover Medical School, Hannover, Germany
| | - Stefan Sablotny
- Vascular Medicine Research, Hannover Medical School, Hannover, Germany.,Department of Nephrology and Hypertension, Hannover Medical School, Hannover, Germany
| | - Corina Ratiu
- Institut für Kardiovaskuläre Physiologie, Fachbereich Medizin der Goethe-Universität Frankfurt am Main, Frankfurt am Main, Germany
| | - Khaled Dastagir
- Vascular Medicine Research, Hannover Medical School, Hannover, Germany.,Department of Plastic, Aesthetic, Hand and Reconstructive Surgery, Hannover Medical School, Hannover, Germany
| | - Matthias Lochner
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany.,Mucosal Infection Immunology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Susanne Karbach
- Center for Cardiology, Cardiology I, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany.,Center for Thrombosis and Hemostasis, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Rhine Main, Mainz, Germany
| | - Philip Wenzel
- Center for Cardiology, Cardiology I, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany.,Center for Thrombosis and Hemostasis, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Rhine Main, Mainz, Germany
| | - Andre Sitnow
- Vascular Medicine Research, Hannover Medical School, Hannover, Germany.,Department of Nephrology and Hypertension, Hannover Medical School, Hannover, Germany
| | - Susanne Fleig
- Vascular Medicine Research, Hannover Medical School, Hannover, Germany.,Department of Nephrology and Hypertension, Hannover Medical School, Hannover, Germany
| | - Tim Sparwasser
- Department of Medical Microbiology and Hygiene, Medical Center of the Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research Braunschweig and the Hannover Medical School, Hannover, Germany.,Cluster of Excellence-Resolving Infection Susceptibility (RESIST), Hanover Medical School, Hannover, Germany
| | - Bernhard Holzmann
- Department of Surgery, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Hermann Haller
- Vascular Medicine Research, Hannover Medical School, Hannover, Germany
| | - Florian P Limbourg
- Vascular Medicine Research, Hannover Medical School, Hannover, Germany.,Department of Nephrology and Hypertension, Hannover Medical School, Hannover, Germany
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20
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Thakur S, Ruan Y, Zhang C, Lun X, Jayanthan A, Narendran A. Human SNF5 arming of double-deleted vaccinia virus shows oncolytic and cytostatic activity against central nervous system atypical teratoid/rhabdoid tumor cells. Cancer Gene Ther 2020; 28:739-744. [PMID: 32678303 DOI: 10.1038/s41417-020-0199-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/27/2020] [Accepted: 07/02/2020] [Indexed: 11/09/2022]
Abstract
Central nervous system (CNS) atypical teratoid/rhabdoid tumor (AT/RT) is a rare, aggressive tumor that most often affects very young children. The common decisive molecular defect in AT/RT has been shown to be a single genetic alteration, i.e., the loss of hSNF5 gene that encodes for a subunit of the SWI/SNF complex that modulates chromatin remodeling activities. As a result, AT/RT cells display unregulated cell proliferation due to the dysfunction of an important epigenetic control. We have previously demonstrated the preclinical efficacy of the oncolytic double-deleted vaccinia virus (VVDD) against AT/RT. Here we report the establishment of a modified VVDD engineered to express wild type hSNF5 gene. We show that this reconstructed vaccinia virus retains comparable infectivity and in vitro cytotoxicity of the parent strain. However, in addition, hSNF5-arming of VVDD results in a decreased cell cycle S phase population and down-regulation of cyclin D1. These findings suggest that hSNF5-arming of VVDD may increase the efficacy in the treatment of AT/RT and validates, as a proof-of-concept, an experimental approach to enhance the effective use of novel modified oncolytic viruses in the treatment of tumors with loss of a tumor suppressor gene function.
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Affiliation(s)
- Satbir Thakur
- Division of Pediatric Hematology, Oncology and Transplant, Alberta Children's Hospital, University of Calgary, Calgary, AB, Canada
| | - Yibing Ruan
- Division of Pediatric Hematology, Oncology and Transplant, Alberta Children's Hospital, University of Calgary, Calgary, AB, Canada
| | - Chunfen Zhang
- Division of Pediatric Hematology, Oncology and Transplant, Alberta Children's Hospital, University of Calgary, Calgary, AB, Canada
| | - Xueqing Lun
- Division of Pediatric Hematology, Oncology and Transplant, Alberta Children's Hospital, University of Calgary, Calgary, AB, Canada
| | | | - Aru Narendran
- Division of Pediatric Hematology, Oncology and Transplant, Alberta Children's Hospital, University of Calgary, Calgary, AB, Canada.
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21
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SMARCB1 Acts as a Quiescent Gatekeeper for Cell Cycle and Immune Response in Human Cells. Int J Mol Sci 2020; 21:ijms21113969. [PMID: 32492816 PMCID: PMC7312701 DOI: 10.3390/ijms21113969] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 05/26/2020] [Accepted: 05/27/2020] [Indexed: 12/20/2022] Open
Abstract
Switch/sucrose non-fermentable (SWI/SNF)-related matrix-associated actin-dependent regulator of chromatin (SMARC) subfamily B member 1 (SMARCB1) is a core subunit of the switch/sucrose non-fermentable (SWI/SNF) complex, one of the adenosine triphosphate (ATP)-dependent chromatin remodeler complexes. The unique role of SMARCB1 has been reported in various cellular contexts. Here, we focused on the general role of the ubiquitous expression of SMARCB1 in a normal cell state. We selected ARPE19 (human primary retinal pigment epithelium) and IMR90 (from human fetal lung fibroblasts) cell lines as they have completely different contexts. Furthermore, although these cell lines have been immortalized, they are relatively close to normal human cells. The loss of SMARCB1 in ARPE19 and IMR90 cells reduced cell cycle progression via the upregulation of P21. Transcriptome analysis followed by SMARCB1 knockdown in both cell lines revealed that SMARCB1 was not only involved in cell maintenance but also conferred immunomodulation. Of note, SMARCB1 bound to interleukin (IL) 6 promoter in a steady state and dissociated in an active immune response state, suggesting that SMARCB1 was a direct repressor of IL6, which was further confirmed via loss- and gain-of-function studies. Taken together, we demonstrated that SMARCB1 is a critical gatekeeper molecule of the cell cycle and immune response.
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22
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Cooperation between SS18-SSX1 and miR-214 in Synovial Sarcoma Development and Progression. Cancers (Basel) 2020; 12:cancers12020324. [PMID: 32019274 PMCID: PMC7072427 DOI: 10.3390/cancers12020324] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 02/07/2023] Open
Abstract
SS18-SSX fusion proteins play a central role in synovial sarcoma development, although, the genetic network and mechanisms of synovial sarcomagenesis remain unknown. We established a new ex vivo synovial sarcoma mouse model through retroviral-mediated gene transfer of SS18-SSX1 into mouse embryonic mesenchymal cells followed by subcutaneous transplantation into nude mice. This approach successfully induced subcutaneous tumors in 100% recipients, showing invasive proliferation of short spindle tumor cells with occasional biphasic appearance. Cytokeratin expression was observed in epithelial components in tumors and expression of TLE1 and BCL2 was also shown. Gene expression profiling indicated SWI/SNF pathway modulation by SS18-SSX1 introduction into mesenchymal cells and Tle1 and Atf2 upregulation in tumors. These findings indicate that the model exhibits phenotypes typical of human synovial sarcoma. Retroviral tagging of the tumor identified 15 common retroviral integration sites within the Dnm3 locus as the most frequent in 30 mouse synovial sarcomas. miR-199a2 and miR-214 upregulation within the Dnm3 locus was observed. SS18-SSX1 and miR-214 cointroduction accelerated sarcoma onset, indicating that miR-214 is a cooperative oncomiR in synovial sarcomagenesis. miR-214 functions in a cell non-autonomous manner, promoting cytokine gene expression (e.g., Cxcl15/IL8). Our results emphasize the role of miR-214 in tumor development and disease progression.
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23
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Finetti MA, Grabovska Y, Bailey S, Williamson D. Translational genomics of malignant rhabdoid tumours: Current impact and future possibilities. Semin Cancer Biol 2020; 61:30-41. [PMID: 31923457 DOI: 10.1016/j.semcancer.2019.12.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/15/2019] [Accepted: 12/16/2019] [Indexed: 12/24/2022]
Abstract
Malignant Rhabdoid Tumours (MRT) are the quintessential example of an epigenetic cancer. Mutation of a single gene, SMARCB1 or more rarely SMARCA4, is capable of causing one of the most aggressive and lethal cancers of early childhood and infancy. SMARCB1 encodes a core subunit of the SWI/SNF complex and its mutation evokes genome-wide downstream effects which may be counteracted therapeutically. Here we review and discuss the use of translational genomics in the study of MRT biology and the ways in which this has impacted clinical practice or may do so in the future. First, the diagnosis and definition of MRT and the transition from a histopathological to a molecular definition. Second, epigenetic and transcriptomic subgroups within MRT, their defining features and potential prognostic or therapeutic significance. Third, functional genomic studies of MRT by mouse modelling and forced re-expression of SMARCB1 in MRT cells. Fourth, studies of underlying epigenetic mechanisms (e.g. EZH2, HDACs) or deregulated kinases (e.g. PDGFR, FGFR1) and the potential therapeutic opportunities these provide. Finally, we discuss likely future directions and proffer opinion on how future translational genomics should be integrated into future biological/clinical studies to select and evaluate the best anti-MRT therapeutic agents.
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Affiliation(s)
- Martina A Finetti
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle Upon Tyne, UK
| | - Yura Grabovska
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle Upon Tyne, UK
| | - Simon Bailey
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle Upon Tyne, UK
| | - Daniel Williamson
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle Upon Tyne, UK.
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24
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An Y, Guan Y, Xu Y, Han Y, Wu C, Bao C, Zhou B, Wang H, Zhang M, Liu W, Qiu L, Han Z, Chen Y, Xia X, Wang J, Liu Z, Huang W, Yi X, Huang J. The diagnostic and prognostic usage of circulating tumor DNA in operable hepatocellular carcinoma. Am J Transl Res 2019; 11:6462-6474. [PMID: 31737198 PMCID: PMC6834494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/09/2019] [Indexed: 06/10/2023]
Abstract
Circulating tumor DNA (ctDNA) is a promising noninvasive biomarker for hepatocellular carcinoma (HCC). In this study, we aimed to assess the diagnostic and prognostic value of ctDNA in HCC. Twenty-six operable HCC, 10 hepatitis and 10 cirrhosis patients were enrolled in this study. Treatment-naïve blood samples were collected from all patients, nevertheless resected tissue and postoperative blood samples were only collected from HCC patients. A custom-designed sequencing panel covering 354 genes was used to identify somatic mutations. Collectively, we identified 139 somatic mutations from 25 HCC baseline plasma samples (96.2%). TP53 (50.00%) was the most common mutant gene, and R249S was the most recurrent mutation (19.2%). Twenty-three patients (88.5%) carried at least one ctDNA mutation validated in matched tissue, and the driver mutations exhibited an advanced concordance than non-driver mutations (67.6% vs. 33.8%, P = 0.0002). For HCC patients, the number of mutations in ctDNA (R2 = 0.1682, P = 0.0375), maximal variant allele frequency (VAF) in ctDNA (R2 = 0.4974, P < 0.0001) and ctDNA concentration (R2 = 0.2676, P = 0.0068) were linearly correlated with tumor size. Multiple circulating cell-free DNA (cfDNA) parameters could be used in differentiating malignant lesions from benign lesions, and the performance was no less than blood alpha-fetoprotein (AFP). HCC patients with detectable mutation in postoperative plasma had a poor DFS than those without (17.5 months vs. 6.7 months, HR = 7.655, P < 0.0001), and postoperative cfDNA status (HR = 10.293, P < 0.0001) was an independent risk factors for recurrence. In conclusion, ctDNA profiling is potentially valuable in differential diagnosis and prognostic evaluation of HCC.
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Affiliation(s)
- Yan An
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong UniversityShanghai 200240, China
| | - Yanfang Guan
- Geneplus-BeijingBeijing 102206, China
- Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi’an Jiaotong University28 West Xianning Road, Xi’an 710049, China
| | - Yaping Xu
- Geneplus-BeijingBeijing 102206, China
| | - Yingxin Han
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong UniversityShanghai 200240, China
| | - Chi Wu
- Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People’s Hospital, Guangdong Medical CollegeShenzhen 518112, China
| | - Chaohui Bao
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong UniversityShanghai 200240, China
| | - Boping Zhou
- Shenzhen People’s Hospital, Second Clinical Medical College of Jinan UniversityShenzhen 518109, China
| | - Haiyan Wang
- Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People’s Hospital, Guangdong Medical CollegeShenzhen 518112, China
| | - Mingxia Zhang
- Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People’s Hospital, Guangdong Medical CollegeShenzhen 518112, China
| | - Weilong Liu
- Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People’s Hospital, Guangdong Medical CollegeShenzhen 518112, China
| | - Lin Qiu
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong UniversityShanghai 200240, China
| | - Zeguang Han
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong UniversityShanghai 200240, China
- Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome at ShanghaiShanghai 201203, China
| | - Yongsheng Chen
- Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi’an Jiaotong University28 West Xianning Road, Xi’an 710049, China
| | | | - Jiayin Wang
- Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi’an Jiaotong University28 West Xianning Road, Xi’an 710049, China
| | | | - Wanqiu Huang
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong UniversityShanghai 200240, China
| | - Xin Yi
- Geneplus-BeijingBeijing 102206, China
| | - Jian Huang
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong UniversityShanghai 200240, China
- Shenzhen People’s Hospital, Second Clinical Medical College of Jinan UniversityShenzhen 518109, China
- Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People’s Hospital, Guangdong Medical CollegeShenzhen 518112, China
- Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome at ShanghaiShanghai 201203, China
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25
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Chabanon RM, Morel D, Postel-Vinay S. Exploiting epigenetic vulnerabilities in solid tumors: Novel therapeutic opportunities in the treatment of SWI/SNF-defective cancers. Semin Cancer Biol 2019; 61:180-198. [PMID: 31568814 DOI: 10.1016/j.semcancer.2019.09.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 09/23/2019] [Accepted: 09/24/2019] [Indexed: 12/12/2022]
Abstract
Mammalian switch/sucrose non-fermentable (mSWI/SNF) family complexes are pivotal elements of the chromatin remodeling machinery, which contribute to the regulation of several major cellular functions. Large-scale exome-wide sequencing studies have identified mutations in genes encoding mSWI/SNF subunits in 20% of all human cancers, establishing mSWI/SNF deficiency as a recurrent oncogenic alteration. Accumulating evidence now supports that several mSWI/SNF defects represent targetable vulnerabilities in cancer; notably, recent research advances have unveiled unexpected synthetic lethal opportunities that foster the development of novel biomarker-driven and mechanism-based therapeutic approaches for the treatment of mSWI/SNF-deficient tumors. Here, we review the latest breakthroughs and discoveries that inform our understanding of the mSWI/SNF complexes biology in carcinogenesis, and discuss the most promising therapeutic strategies to target mSWI/SNF defects in human solid malignancies.
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Affiliation(s)
- Roman M Chabanon
- Université Paris Saclay, Université Paris-Sud, Faculté de médicine, Le Kremlin Bicêtre, France; ATIP-Avenir Group, Inserm Unit U981, Gustave Roussy, Villejuif, France; The Breast Cancer Now Toby Robins Breast Cancer Research Centre, France; CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Daphné Morel
- Université Paris Saclay, Université Paris-Sud, Faculté de médicine, Le Kremlin Bicêtre, France; ATIP-Avenir Group, Inserm Unit U981, Gustave Roussy, Villejuif, France
| | - Sophie Postel-Vinay
- Université Paris Saclay, Université Paris-Sud, Faculté de médicine, Le Kremlin Bicêtre, France; ATIP-Avenir Group, Inserm Unit U981, Gustave Roussy, Villejuif, France; DITEP (Département d'Innovations Thérapeutiques et Essais Précoces), Gustave Roussy, Villejuif, France.
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26
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Phi JH, Sun CH, Lee SH, Lee S, Park I, Choi SA, Park SH, Lee JY, Wang KC, Kim SK, Yun H, Park CK. NPM1 as a potential therapeutic target for atypical teratoid/rhabdoid tumors. BMC Cancer 2019; 19:848. [PMID: 31462227 PMCID: PMC6714307 DOI: 10.1186/s12885-019-6044-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 08/16/2019] [Indexed: 01/10/2023] Open
Abstract
Background Atypical teratoid/rhabdoid tumors (AT/RTs) are highly malignant brain tumors with inactivation of the SMARCB1 gene, which play a critical role in genomic transcriptional control. In this study, we analyzed the genomic and transcriptomic profiles of human AT/RTs to discover new druggable targets. Methods Multiplanar sequencing analyses, including whole exome sequencing (WES), single nucleotide polymorphism (SNP) arrays, array comparative genomic hybridization (aCGH), and whole transcriptome sequencing (RNA-Seq), were performed on 4 AT/RT tissues. Validation of a druggable target was conducted using AT/RT cell lines. Results WES revealed that the AT/RT genome is extremely stable except for the inactivation of SMARCB1. However, we identified 897 significantly upregulated genes and 523 significantly downregulated genes identified using RNA-Seq, indicating that the transcriptional profiles of the AT/RT tissues changed substantially. Gene set enrichment assays revealed genes related to the canonical pathways of cancers, and nucleophosmin (NPM1) was the most significantly upregulated gene in the AT/RT samples. An NPM1 inhibitor (NSC348884) effectively suppressed the viability of 7 AT/RT cell lines. Network analyses showed that genes associated with NPM1 are mainly involved in cell cycle regulation. Upon treatment with an NPM1 inhibitor, cell cycle arrest at G1 phase was observed in AT/RT cells. Conclusions We propose that NPM1 is a novel therapeutic target for AT/RTs. Electronic supplementary material The online version of this article (10.1186/s12885-019-6044-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ji Hoon Phi
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, Republic of Korea.,Department of Neurosurgery, Seoul National University College of Medicine, 101 Daehak-ro Jongno-gu, Seoul, 110-744, Republic of Korea
| | - Choong-Hyun Sun
- Genome opinion Co., Ltd. 7, Yeonmujang 5ga-gil, Seongdong-gu, Seoul, Republic of Korea
| | - Se-Hoon Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.,Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Seungmook Lee
- Graduated, Department of Statistics, Seoul National University, Seoul, Republic of Korea
| | - Inho Park
- SD Genomics, Seoul, Republic of Korea
| | - Seung Ah Choi
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, Republic of Korea
| | - Sung-Hye Park
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ji Yeoun Lee
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, Republic of Korea.,Department of Neurosurgery, Seoul National University College of Medicine, 101 Daehak-ro Jongno-gu, Seoul, 110-744, Republic of Korea.,Department of Anatomy, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyu-Chang Wang
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, Republic of Korea.,Department of Neurosurgery, Seoul National University College of Medicine, 101 Daehak-ro Jongno-gu, Seoul, 110-744, Republic of Korea
| | - Seung-Ki Kim
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, Republic of Korea. .,Department of Neurosurgery, Seoul National University College of Medicine, 101 Daehak-ro Jongno-gu, Seoul, 110-744, Republic of Korea.
| | - Hongseok Yun
- Center for Precision Medicine, Seoul National University Hospital, 101 Daehak-ro Jongno-gu, Seoul, 110-744, Republic of Korea.
| | - Chul-Kee Park
- Department of Neurosurgery, Seoul National University College of Medicine, 101 Daehak-ro Jongno-gu, Seoul, 110-744, Republic of Korea.
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27
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Orlando KA, Nguyen V, Raab JR, Walhart T, Weissman BE. Remodeling the cancer epigenome: mutations in the SWI/SNF complex offer new therapeutic opportunities. Expert Rev Anticancer Ther 2019; 19:375-391. [PMID: 30986130 DOI: 10.1080/14737140.2019.1605905] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Cancer genome sequencing studies have discovered mutations in members of the SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin-remodeling complex in nearly 25% of human cancers. The SWI/SNF complex, first discovered in S. cerevisiae, shows strong conservation from yeast to Drosophila to mammals, contains approximately 10-12 subunits and regulates nucleosome positioning through the energy generated by its ATPase subunits. The unexpected finding of frequent mutations in the complex has fueled studies to identify the mechanisms that drive tumor development and the accompanying therapeutic vulnerabilities. Areas covered: In the review, we focus upon the potential roles different SWI/SNF subunit mutations play in human oncogenesis, their common and unique mechanisms of transformation and the potential for translating these mechanisms into targeted therapies for SWI/SNF-mutant tumors. Expert opinion: We currently have limited insights into how mutations in different SWI/SNF subunits drive the development of human tumors. Because the SWI/SNF complex participates in a broad range of normal cellular functions, defining specific oncogenic pathways has proved difficult. In addition, therapeutic options for SWI/SNF-mutant cancers have mainly evolved from high-throughput screens of cell lines with mutations in different subunits. Future studies should follow a more coherent plan to pinpoint common vulnerabilities among these tumors.
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Affiliation(s)
- Krystal A Orlando
- a Department of Pathology and Laboratory Medicine , University of North Carolina , Chapel Hill , NC , USA
| | - Vinh Nguyen
- b Curriculum in Toxicology and Environmental Medicine , University of North Carolina , Chapel Hill , NC , USA
| | - Jesse R Raab
- c Department of Genetics , University of North Carolina , Chapel Hill , NC , USA
| | - Tara Walhart
- d Lineberger Comprehensive Cancer Center , University of North Carolina , Chapel Hill , NC , USA
| | - Bernard E Weissman
- a Department of Pathology and Laboratory Medicine , University of North Carolina , Chapel Hill , NC , USA.,b Curriculum in Toxicology and Environmental Medicine , University of North Carolina , Chapel Hill , NC , USA.,d Lineberger Comprehensive Cancer Center , University of North Carolina , Chapel Hill , NC , USA
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28
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Carugo A, Minelli R, Sapio L, Soeung M, Carbone F, Robinson FS, Tepper J, Chen Z, Lovisa S, Svelto M, Amin S, Srinivasan S, Del Poggetto E, Loponte S, Puca F, Dey P, Malouf GG, Su X, Li L, Lopez-Terrada D, Rakheja D, Lazar AJ, Netto GJ, Rao P, Sgambato A, Maitra A, Tripathi DN, Walker CL, Karam JA, Heffernan TP, Viale A, Roberts CWM, Msaouel P, Tannir NM, Draetta GF, Genovese G. p53 Is a Master Regulator of Proteostasis in SMARCB1-Deficient Malignant Rhabdoid Tumors. Cancer Cell 2019; 35:204-220.e9. [PMID: 30753823 PMCID: PMC7876656 DOI: 10.1016/j.ccell.2019.01.006] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 10/12/2018] [Accepted: 01/09/2019] [Indexed: 12/11/2022]
Abstract
Alterations in chromatin remodeling genes have been increasingly implicated in human oncogenesis. Specifically, the biallelic inactivation of the SWI/SNF subunit SMARCB1 results in the emergence of extremely aggressive pediatric malignancies. Here, we developed embryonic mosaic mouse models of malignant rhabdoid tumors (MRTs) that faithfully recapitulate the clinical-pathological features of the human disease. We demonstrated that SMARCB1-deficient malignancies exhibit dramatic activation of the unfolded protein response (UPR) and ER stress response via a genetically intact MYC-p19ARF-p53 axis. As a consequence, these tumors display an exquisite sensitivity to agents inducing proteotoxic stress and inhibition of the autophagic machinery. In conclusion, our findings provide a rationale for drug repositioning trials investigating combinations of agents targeting the UPR and autophagy in SMARCB1-deficient MRTs.
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Affiliation(s)
- Alessandro Carugo
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Rosalba Minelli
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Luigi Sapio
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Melinda Soeung
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Federica Carbone
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Frederick S Robinson
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - James Tepper
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Ziheng Chen
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Sara Lovisa
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Maria Svelto
- Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, Pozzuoli 80078, Italy
| | - Samirkumar Amin
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA
| | - Sanjana Srinivasan
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Edoardo Del Poggetto
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Sara Loponte
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Francesca Puca
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Prasenjit Dey
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Gabriel G Malouf
- Centre Hospitalier Régional et Universitaire Strasbourg, Hôpital Civil, 1 Place de L'Hôpital, Strasbourg 67091, France; Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, Université de Strasbourg, Illkirch 67400, France
| | - Xiaoping Su
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Liren Li
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou 510060, China
| | - Dolores Lopez-Terrada
- Department of Pathology, Texas Children's Hospital, 6621 Fannin Street, Houston, TX 77030, USA
| | - Dinesh Rakheja
- Department of Pathology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Alexander J Lazar
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA; Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - George J Netto
- Department of Pathology, Johns Hopkins University, 600 N. Wolfe Street/Carnegie 417, Baltimore, MD 21287, USA
| | - Priya Rao
- Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Alessandro Sgambato
- Dipartimento di Patologia Generale, Policlinico Agostino Gemelli, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, Roma 00168, Italy
| | - Anirban Maitra
- Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA; Sheikh Ahmed Bin Zayed Al Nahyan Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Durga N Tripathi
- Center for Precision Environmental Health, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Cheryl L Walker
- Center for Precision Environmental Health, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Jose A Karam
- Department of Urology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA; Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Timothy P Heffernan
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Andrea Viale
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Charles W M Roberts
- Department of Oncology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38120, USA
| | - Pavlos Msaouel
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Nizar M Tannir
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA.
| | - Giulio F Draetta
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA.
| | - Giannicola Genovese
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA; Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA; David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA.
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29
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Shamir ER, Devine WP, Pekmezci M, Umetsu SE, Krings G, Federman S, Cho SJ, Saunders TA, Jen KY, Bergsland E, Jones K, Kim GE, Kakar S, Chiu CY, Joseph NM. Identification of high-risk human papillomavirus and Rb/E2F pathway genomic alterations in mutually exclusive subsets of colorectal neuroendocrine carcinoma. Mod Pathol 2019; 32:290-305. [PMID: 30237525 DOI: 10.1038/s41379-018-0131-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 08/05/2018] [Accepted: 08/07/2018] [Indexed: 12/15/2022]
Abstract
Colorectal neuroendocrine carcinomas, both small cell and large cell types, are highly aggressive tumors with poor prognosis compared with colorectal adenocarcinoma. The molecular drivers of neuroendocrine carcinoma are best defined in small cell lung cancer, which shows near-universal genomic alterations in TP53 and RB1. The genetics of colorectal neuroendocrine carcinoma remain poorly understood; recent studies demonstrated infrequent RB1 alterations and genetics closely resembling colorectal adenocarcinoma. To better define the molecular pathogenesis of colorectal neuroendocrine carcinoma, we performed capture-based next-generation sequencing on 25 cases and evaluated for expression of p53, Rb, p16, and high-risk human papillomavirus (HR-HPV) subtypes using immunohistochemistry, in situ hybridization, and polymerase chain reaction. Rb/E2F pathway dysregulation was identified in nearly all cases (23/25, 92%) and occurred via three distinct mechanisms. First, RB1 genomic alteration was present in 56% (14/25) of cases and was accompanied by Rb protein loss, high p16 expression, and absence of HR-HPV; these cases also had frequent genomic alterations in TP53, the PI3K/Ras and Wnt pathways, as well as in DNA repair genes, with 4/14 cases being hypermutated. Second, 16% (4/25) of cases, all left-sided, had TP53 alteration without RB1 alteration; half of these harbored high-level amplifications in CCNE1 and MYC or MYCN and arose in patients with ulcerative colitis. Finally, 28% (7/25) of cases, all rectal or anal, lacked genomic alterations in RB1 or TP53 but were positive for HR-HPV. Our data demonstrate that Rb/E2F pathway dysregulation is essential in the pathogenesis of colorectal neuroendocrine carcinoma, akin to neuroendocrine carcinomas in other anatomic sites. Moreover, colorectal neuroendocrine carcinomas stratify into three distinct molecular subgroups, which can be differentiated based on Rb protein and HR-HPV status. HR-HPV infection represents a distinct mechanism for Rb and p53 inactivation in cases lacking genomic alterations in either gene. Differential treatment strategies for hypermutated and HPV-driven cases could improve patient outcomes.
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Affiliation(s)
- Eliah R Shamir
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - W Patrick Devine
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Melike Pekmezci
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Sarah E Umetsu
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Gregor Krings
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Scot Federman
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Soo-Jin Cho
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Tara A Saunders
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Kuang-Yu Jen
- Department of Pathology, University of California Davis, Sacramento, CA, USA
| | - Emily Bergsland
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Kirk Jones
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Grace E Kim
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Sanjay Kakar
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Nancy M Joseph
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA.
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30
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Sun S, Wu Y, Zeng K, Zhao Y. Expression and potential role of SNF5 in endometrial carcinoma. BMC WOMENS HEALTH 2019; 19:16. [PMID: 30683081 PMCID: PMC6346509 DOI: 10.1186/s12905-019-0718-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 01/15/2019] [Indexed: 12/22/2022]
Abstract
Background SNF5 is a key protein in regulating cell proliferation and apoptosis in various cancers. However, the physiological roles of SNF5 in Endometrial carcinoma (EC), which is one of the most frequent malignancies of the female reproduction worldwide, remains unclear. This study aims to investigate the role of SNF5 and its correlation with clinicopathologic characteristics in EC. Methods We performed immunohistochemistry to detect the SNF5 expression in 46 endometrial carcinomas and 20 normal endometrium (non-EC) specimens, as well as analyzed the correlations between SNF5 expression and clinicopathologic features of patients using a statistics software (GraphPad Prism V6.0). Western blotting had been used to confirm the protein level of SNF5 in endometrial tissues. In addition, we evaluated the correlations between SNF5 and p21 in EC. Results The positive immunostaining rate for SNF5 in EC and non-EC specimens were 65% (30/46) and 25% (5/20) respectively, and the expression of SNF5 was dramatically increased in EC compared with the normal endometrium (P < 0.01). The overexpression of SNF5 was associated with the PR levels, but not with age, FIGO stage, grade, lymphatic metastasis, myometrial invasion or ER status. Knockdown of SNF5 inhibits the expression of p21. Conclusions Our results indicate that SNF5 plays an important role of promoting oncogenesis in EC. These findings open up the possibility for various novel and effective combination therapies targeting SNF5 in the EC.
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Affiliation(s)
- Shiying Sun
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, Anhui, China.
| | - Yi Wu
- Department of Pathogenic Biology, Shenyang Medical College, Shenyang, 110034, Liaoning, China
| | - Kai Zeng
- Department of Cell Biology, Key laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang, 110122, Liaoning, China
| | - Yue Zhao
- Department of Cell Biology, Key laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang, 110122, Liaoning, China.
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31
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Nesvick CL, Nageswara Rao AA, Raghunathan A, Biegel JA, Daniels DJ. Case-based review: atypical teratoid/rhabdoid tumor. Neurooncol Pract 2018; 6:163-178. [PMID: 31386032 DOI: 10.1093/nop/npy037] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Atypical teratoid/rhabdoid tumor (AT/RT) is a rare CNS cancer that typically occurs in children younger than 3 years of age. Histologically, AT/RTs are embryonal tumors that contain a rhabdoid component as well as areas with primitive neuroectodermal, mesenchymal, and epithelial features. Compared to other CNS tumors of childhood, AT/RTs are characterized by their rapid growth, short symptomatic prodrome, and large size upon presentation, often leading to brain compression and intracranial hypertension requiring urgent intervention. For decades, the mainstay of care has been a combination of maximal safe surgical resection followed by adjuvant chemotherapy and radiotherapy. Despite advances in each of these modalities, the relative paucity of data on these tumors, their inherently aggressive course, and a lack of molecular data have limited advances in treatment over the past 3 decades. Recent large-scale, multicenter interdisciplinary studies, however, have significantly advanced our understanding of the molecular pathogenesis of these tumors. Multiple clinical trials testing molecularly targeted therapies are underway, offering hope for patients with AT/RT and their families.
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Affiliation(s)
- Cody L Nesvick
- Department of Neurological Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Amulya A Nageswara Rao
- Department of Pediatric and Adolescent Medicine, Division of Pediatric Hematology/Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Aditya Raghunathan
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Jaclyn A Biegel
- Department of Pathology and Laboratory Medicine, Children's Hospital of Los Angeles, Keck School of Medicine of University of Southern California, USA
| | - David J Daniels
- Department of Neurological Surgery, Mayo Clinic, Rochester, Minnesota, USA
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32
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Garczyk S, Schneider U, Lurje I, Becker K, Vögeli TA, Gaisa NT, Knüchel R. ARID1A-deficiency in urothelial bladder cancer: No predictive biomarker for EZH2-inhibitor treatment response? PLoS One 2018; 13:e0202965. [PMID: 30138427 PMCID: PMC6107234 DOI: 10.1371/journal.pone.0202965] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 08/13/2018] [Indexed: 01/21/2023] Open
Abstract
Bladder cancer therapy relies on aggressive treatments highlighting the need for new, targeted therapies with reduced side effects. SWI/SNF complexes are mutated in ~20% across human cancers and dependency of SWI/SNF-deficient tumors on EZH2 has been uncovered recently. To systematically dissect the frequency of genetic alterations in SWI/SNF complexes potentially contributing to their inactivation, mutations and copy number variations in 25 SWI/SNF subunit genes were analyzed making use of publicly available sequencing data for 408 muscle-invasive bladder carcinoma samples. ARID1A truncating mutations were identified as the by far most common alterations of SWI/SNF complexes in urothelial bladder cancer. As current ARID1A protein expression data in bladder cancer are inconsistent and incomplete we examined if the frequency of truncating ARID1A mutations translates into a similar frequency of cases showing ARID1A protein loss. We applied a validated ARID1A antibody conducting a comprehensive immunohistochemistry-based expression analysis in urothelial bladder cancer (n = 362) including carcinoma in situ (CIS) cases. While observing increased median ARID1A protein levels in all carcinoma subgroups compared to normal urothelial controls (n = 21), the percentage of cases showing ARID1A protein loss was positively correlated with increasing stage and grade culminating in a rate of 14.1% in muscle-invasive disease. ARID1A-depletion did neither increase EZH2 protein or trimethylated H3K27 levels in vitro nor did ARID1A expression correlate with EZH2 or H3K27me3 amounts in human bladder carcinomas. Importantly, ARID1A-deficiency was neither associated with enhanced sensitivity towards inhibition of EZH2 enzymatic activity nor depletion of EZH2 protein. In summary, ARID1A truncating mutations, potentially translating into ARID1A protein loss in a subset of high-grade bladder cancers, are the most common SWI/SNF genetic alterations in bladder cancer. Our data do not support ARID1A-deficiency as predictive biomarker for EZH2-inhibitor treatment response in bladder cancer underlining the need for future bladder cancer-specific, drug screens for successfull discovery of ARID1A-deficiency-based targeted drugs.
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Affiliation(s)
- Stefan Garczyk
- Uropathology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
- * E-mail:
| | - Ursula Schneider
- Uropathology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Isabella Lurje
- Uropathology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Katharina Becker
- Uropathology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Thomas A. Vögeli
- Department of Urology, University Hospital RWTH Aachen, Aachen, Germany
| | - Nadine T. Gaisa
- Uropathology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Ruth Knüchel
- Uropathology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
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33
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Bögershausen N, Wollnik B. Mutational Landscapes and Phenotypic Spectrum of SWI/SNF-Related Intellectual Disability Disorders. Front Mol Neurosci 2018; 11:252. [PMID: 30123105 PMCID: PMC6085491 DOI: 10.3389/fnmol.2018.00252] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 07/03/2018] [Indexed: 12/29/2022] Open
Abstract
Mutations in genes that encode proteins of the SWI/SNF complex, called BAF complex in mammals, cause a spectrum of disorders that ranges from syndromic intellectual disability to Coffin-Siris syndrome (CSS) to Nicolaides-Baraitser syndrome (NCBRS). While NCBRS is known to be a recognizable and restricted phenotype, caused by missense mutations in SMARCA2, the term CSS has been used lately for a more heterogeneous group of phenotypes that are caused by mutations in either of the genes ARID1B, ARID1A, ARID2, SMARCA4, SMARCB1, SMARCE1, SOX11, or DPF2. In this review, we summarize the current knowledge on the phenotypic traits and molecular causes of the above named conditions, consider the question whether a clinical distinction of the phenotypes is still adequate, and suggest the term "SWI/SNF-related intellectual disability disorders" (SSRIDDs). We will also outline important features to identify the ARID1B-related phenotype in the absence of classic CSS features, and discuss distinctive and overlapping features of the SSRIDD subtypes. Moreover, we will briefly review the function of the SWI/SNF complex in development and describe the mutational landscapes of the genes involved in SSRIDD.
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Affiliation(s)
- Nina Bögershausen
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
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Abstract
Defects in chromatin modifiers and remodelers have been described both for hematological and solid malignancies, corroborating and strengthening the role of epigenetic aberrations in the etiology of cancer. Furthermore, epigenetic marks-DNA methylation, histone modifications, chromatin remodeling, and microRNA-can be considered potential markers of cancer development and progression. Here, we review whether altered epigenetic landscapes are merely a consequence of chromatin modifier/remodeler aberrations or a hallmark of cancer etiology. We critically evaluate current knowledge on causal epigenetic aberrations and examine to what extent the prioritization of (epi)genetic deregulations can be assessed in cancer as some type of genetic lesion characterizing solid cancer progression. We also discuss the multiple challenges in developing compounds targeting epigenetic enzymes (named epidrugs) for epigenetic-based therapies. The implementation of acquired knowledge of epigenetic biomarkers for patient stratification, together with the development of next-generation epidrugs and predictive models, will take our understanding and use of cancer epigenetics in diagnosis, prognosis, and treatment of cancer patients to a new level.
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Affiliation(s)
- Angela Nebbioso
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania "L. Vanvitelli," Napoli, Italy
| | - Francesco Paolo Tambaro
- Struttura Semplice Dipartimentale Trapianto di Midollo Osseo-Azienda Ospedialiera di Rilievo Nazionale, Santobono-Pausilipon, Napoli, Italy
| | - Carmela Dell'Aversana
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania "L. Vanvitelli," Napoli, Italy
| | - Lucia Altucci
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania "L. Vanvitelli," Napoli, Italy
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35
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Sing TL, Hung MP, Ohnuki S, Suzuki G, San Luis BJ, McClain M, Unruh JR, Yu Z, Ou J, Marshall-Sheppard J, Huh WK, Costanzo M, Boone C, Ohya Y, Jaspersen SL, Brown GW. The budding yeast RSC complex maintains ploidy by promoting spindle pole body insertion. J Cell Biol 2018; 217:2445-2462. [PMID: 29875260 PMCID: PMC6028538 DOI: 10.1083/jcb.201709009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 02/13/2018] [Accepted: 05/09/2018] [Indexed: 01/31/2023] Open
Abstract
Sing et al. characterize an unanticipated role for the Saccharomyces cerevisiae RSC complex in ploidy maintenance. They show that RSC promotes the distribution of Nbp1 and Ndc1 to the spindle pole body (SPB) to facilitate SPB maturation and accurate chromosome segregation. Ploidy is tightly regulated in eukaryotic cells and is critical for cell function and survival. Cells coordinate multiple pathways to ensure replicated DNA is segregated accurately to prevent abnormal changes in chromosome number. In this study, we characterize an unanticipated role for the Saccharomyces cerevisiae “remodels the structure of chromatin” (RSC) complex in ploidy maintenance. We show that deletion of any of six nonessential RSC genes causes a rapid transition from haploid to diploid DNA content because of nondisjunction events. Diploidization is accompanied by diagnostic changes in cell morphology and is stably maintained without further ploidy increases. We find that RSC promotes chromosome segregation by facilitating spindle pole body (SPB) duplication. More specifically, RSC plays a role in distributing two SPB insertion factors, Nbp1 and Ndc1, to the new SPB. Thus, we provide insight into a role for a SWI/SNF family complex in SPB duplication and ploidy maintenance.
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Affiliation(s)
- Tina L Sing
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Minnie P Hung
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
| | - Godai Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
| | - Bryan-Joseph San Luis
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Jay R Unruh
- Stowers Institute for Medical Research, Kansas City, MO
| | - Zulin Yu
- Stowers Institute for Medical Research, Kansas City, MO
| | - Jiongwen Ou
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Jesse Marshall-Sheppard
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Won-Ki Huh
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Michael Costanzo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Charles Boone
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
| | - Sue L Jaspersen
- Stowers Institute for Medical Research, Kansas City, MO.,Department of Molecular and Integrative Physiology, University of Kansas Medical Centre, Kansas City, KS
| | - Grant W Brown
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada .,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
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36
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Giancotti V, Bergamin N, Cataldi P, Rizzi C. Epigenetic Contribution of High-Mobility Group A Proteins to Stem Cell Properties. Int J Cell Biol 2018; 2018:3698078. [PMID: 29853899 PMCID: PMC5941823 DOI: 10.1155/2018/3698078] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 03/01/2018] [Accepted: 03/18/2018] [Indexed: 02/07/2023] Open
Abstract
High-mobility group A (HMGA) proteins have been examined to understand their participation as structural epigenetic chromatin factors that confer stem-like properties to embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs), and cancer stem cells (CSCs). The function of HMGA was evaluated in conjunction with that of other epigenetic factors such as histones and microRNAs (miRs), taking into consideration the posttranscriptional modifications (PTMs) of histones (acetylation and methylation) and DNA methylation. HMGA proteins were coordinated or associated with histone and DNA modification and the expression of the factors related to pluripotency. CSCs showed remarkable differences compared with ESCs and iPSCs.
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Affiliation(s)
- Vincenzo Giancotti
- Department of Life Science, University of Trieste, Trieste, Italy
- Trieste Proteine Ricerche, Palmanova, Udine, Italy
| | - Natascha Bergamin
- Division of Pathology, Azienda Ospedaliero-Universitaria, Udine, Italy
| | - Palmina Cataldi
- Division of Pathology, Azienda Ospedaliero-Universitaria, Udine, Italy
| | - Claudio Rizzi
- Division of Pathology, Azienda Ospedaliero-Universitaria, Udine, Italy
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37
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Lang JD, Hendricks WPD, Orlando KA, Yin H, Kiefer J, Ramos P, Sharma R, Pirrotte P, Raupach EA, Sereduk C, Tang N, Liang WS, Washington M, Facista SJ, Zismann VL, Cousins EM, Major MB, Wang Y, Karnezis AN, Sekulic A, Hass R, Vanderhyden BC, Nair P, Weissman BE, Huntsman DG, Trent JM. Ponatinib Shows Potent Antitumor Activity in Small Cell Carcinoma of the Ovary Hypercalcemic Type (SCCOHT) through Multikinase Inhibition. Clin Cancer Res 2018; 24:1932-1943. [PMID: 29440177 DOI: 10.1158/1078-0432.ccr-17-1928] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 11/27/2017] [Accepted: 02/02/2018] [Indexed: 11/16/2022]
Abstract
Purpose: Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is a rare, aggressive ovarian cancer in young women that is universally driven by loss of the SWI/SNF ATPase subunits SMARCA4 and SMARCA2. A great need exists for effective targeted therapies for SCCOHT.Experimental Design: To identify underlying therapeutic vulnerabilities in SCCOHT, we conducted high-throughput siRNA and drug screens. Complementary proteomics approaches profiled kinases inhibited by ponatinib. Ponatinib was tested for efficacy in two patient-derived xenograft (PDX) models and one cell-line xenograft model of SCCOHT.Results: The receptor tyrosine kinase (RTK) family was enriched in siRNA screen hits, with FGFRs and PDGFRs being overlapping hits between drug and siRNA screens. Of multiple potent drug classes in SCCOHT cell lines, RTK inhibitors were only one of two classes with selectivity in SCCOHT relative to three SWI/SNF wild-type ovarian cancer cell lines. We further identified ponatinib as the most effective clinically approved RTK inhibitor. Reexpression of SMARCA4 was shown to confer a 1.7-fold increase in resistance to ponatinib. Subsequent proteomic assessment of ponatinib target modulation in SCCOHT cell models confirmed inhibition of nine known ponatinib target kinases alongside 77 noncanonical ponatinib targets in SCCOHT. Finally, ponatinib delayed tumor doubling time 4-fold in SCCOHT-1 xenografts while reducing final tumor volumes in SCCOHT PDX models by 58.6% and 42.5%.Conclusions: Ponatinib is an effective agent for SMARCA4-mutant SCCOHT in both in vitro and in vivo preclinical models through its inhibition of multiple kinases. Clinical investigation of this FDA-approved oncology drug in SCCOHT is warranted. Clin Cancer Res; 24(8); 1932-43. ©2018 AACR.
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Affiliation(s)
- Jessica D Lang
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, Arizona
| | - William P D Hendricks
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, Arizona
| | - Krystal A Orlando
- Department of Pathology and Laboratory Medicine, Lineberger Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Hongwei Yin
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, Arizona
| | - Jeffrey Kiefer
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, Arizona
| | - Pilar Ramos
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, Arizona
| | - Ritin Sharma
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute (TGen), Phoenix, Arizona
| | - Patrick Pirrotte
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute (TGen), Phoenix, Arizona
| | - Elizabeth A Raupach
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, Arizona.,Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute (TGen), Phoenix, Arizona
| | - Chris Sereduk
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, Arizona
| | - Nanyun Tang
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, Arizona
| | - Winnie S Liang
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, Arizona
| | - Megan Washington
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, Arizona
| | - Salvatore J Facista
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, Arizona
| | - Victoria L Zismann
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, Arizona
| | - Emily M Cousins
- Department of Cell Biology and Physiology, Lineberger Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Michael B Major
- Department of Cell Biology and Physiology, Lineberger Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Yemin Wang
- Department of Pathology and Laboratory Medicine, University of British Columbia and Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Anthony N Karnezis
- Department of Pathology and Laboratory Medicine, University of British Columbia and Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Aleksandar Sekulic
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, Arizona.,Department of Dermatology, Mayo Clinic, Scottsdale, Arizona
| | - Ralf Hass
- Department of Obstetrics and Gynecology, Hannover Medical School, Hannover, Germany
| | - Barbara C Vanderhyden
- Department of Cellular and Molecular Medicine, University of Ottawa, and Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | | | - Bernard E Weissman
- Department of Pathology and Laboratory Medicine, Lineberger Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - David G Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia and Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.,Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jeffrey M Trent
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, Arizona.
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38
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Li Y, Wang J, Yu M, Wang Y, Zhang H, Yin J, Li Z, Li T, Yan H, Li F, Wang X. SNF5 deficiency induces apoptosis resistance by repressing SATB1 expression in Sézary syndrome. Leuk Lymphoma 2018; 59:2405-2413. [PMID: 29334836 DOI: 10.1080/10428194.2017.1422861] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
SNF5, is a core member of the SWI/SNF chromatin remodeling complex. It's deficiency leads to multiple types of aggressive cancer. Sézary syndrome, a leukemic variant of cutaneous T-cell lymphoma, is characterized by its resistance to apoptosis. Although the cause of apoptosis resistance is still poorly understood, recent evidence has revealed the importance of SATB1 in the apoptosis resistance of Sézary syndrome. In this study, we show that SNF5 is an upstream regulator of SATB1 in several conditions and that both are deficient in Sézary cells. Additionally, SNF5 not only controls the expression of SATB1, but also utilizes SATB1 to recruit itself to specific sites. Overexpression of SNF5 induces SATB1 expression and partially reverse apoptosis resistance phenotype in Sézary cells. These results suggest that both SNF5 and SATB1 may regulate apoptosis-related genes in Sézary syndrome. Thus, targeting SWI/SNF complex may represent a promising approach for Sézary syndrome therapy.
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Affiliation(s)
- Yang Li
- a Department of Cell Biology , 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Laboratory of Epigenetics in Development and Tumorigenesis, Tianjin Research Center of Basic Medical Sciences, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University , Tianjin , China
| | - Jin Wang
- a Department of Cell Biology , 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Laboratory of Epigenetics in Development and Tumorigenesis, Tianjin Research Center of Basic Medical Sciences, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University , Tianjin , China
| | - Minghang Yu
- a Department of Cell Biology , 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Laboratory of Epigenetics in Development and Tumorigenesis, Tianjin Research Center of Basic Medical Sciences, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University , Tianjin , China
| | - Yang Wang
- b Department of Dermatology and Venerology , Peking University First Hospital , Beijing , China
| | - Huilai Zhang
- c Departments of Lymphoma , Sino-US Center for Lymphoma and Leukemia, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy , Tianjin , China
| | - Jie Yin
- a Department of Cell Biology , 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Laboratory of Epigenetics in Development and Tumorigenesis, Tianjin Research Center of Basic Medical Sciences, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University , Tianjin , China
| | - Zexing Li
- a Department of Cell Biology , 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Laboratory of Epigenetics in Development and Tumorigenesis, Tianjin Research Center of Basic Medical Sciences, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University , Tianjin , China
| | - Ting Li
- a Department of Cell Biology , 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Laboratory of Epigenetics in Development and Tumorigenesis, Tianjin Research Center of Basic Medical Sciences, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University , Tianjin , China
| | - Han Yan
- a Department of Cell Biology , 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Laboratory of Epigenetics in Development and Tumorigenesis, Tianjin Research Center of Basic Medical Sciences, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University , Tianjin , China
| | - Fajin Li
- d School of Biomedical Engineering and Technology , Tianjin Medical University , Tianjin , China
| | - Xi Wang
- a Department of Cell Biology , 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Laboratory of Epigenetics in Development and Tumorigenesis, Tianjin Research Center of Basic Medical Sciences, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University , Tianjin , China.,e Department of Immunology, School of Basic Medical Sciences , Capital Medical University , Beijing , P. R. China
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39
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Yan HX, Zhang YJ, Zhang Y, Ren X, Shen YF, Cheng MB, Zhang Y. CRIF1 enhances p53 activity via the chromatin remodeler SNF5 in the HCT116 colon cancer cell lines. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:516-522. [DOI: 10.1016/j.bbagrm.2017.02.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 02/17/2017] [Accepted: 02/18/2017] [Indexed: 12/28/2022]
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40
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Genovese G, Carugo A, Tepper J, Robinson FS, Li L, Svelto M, Nezi L, Corti D, Minelli R, Pettazzoni P, Gutschner T, Wu CC, Seth S, Akdemir KC, Leo E, Amin S, Molin MD, Ying H, Kwong LN, Colla S, Takahashi K, Ghosh P, Giuliani V, Muller F, Dey P, Jiang S, Garvey J, Liu CG, Zhang J, Heffernan TP, Toniatti C, Fleming JB, Goggins MG, Wood LD, Sgambato A, Agaimy A, Maitra A, Roberts CWM, Wang H, Viale A, DePinho RA, Draetta GF, Chin L. Synthetic vulnerabilities of mesenchymal subpopulations in pancreatic cancer. Nature 2017; 542:362-366. [PMID: 28178232 DOI: 10.1038/nature21064] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 12/16/2016] [Indexed: 12/11/2022]
Abstract
Malignant neoplasms evolve in response to changes in oncogenic signalling. Cancer cell plasticity in response to evolutionary pressures is fundamental to tumour progression and the development of therapeutic resistance. Here we determine the molecular and cellular mechanisms of cancer cell plasticity in a conditional oncogenic Kras mouse model of pancreatic ductal adenocarcinoma (PDAC), a malignancy that displays considerable phenotypic diversity and morphological heterogeneity. In this model, stochastic extinction of oncogenic Kras signalling and emergence of Kras-independent escaper populations (cells that acquire oncogenic properties) are associated with de-differentiation and aggressive biological behaviour. Transcriptomic and functional analyses of Kras-independent escapers reveal the presence of Smarcb1-Myc-network-driven mesenchymal reprogramming and independence from MAPK signalling. A somatic mosaic model of PDAC, which allows time-restricted perturbation of cell fate, shows that depletion of Smarcb1 activates the Myc network, driving an anabolic switch that increases protein metabolism and adaptive activation of endoplasmic-reticulum-stress-induced survival pathways. Increased protein turnover renders mesenchymal sub-populations highly susceptible to pharmacological and genetic perturbation of the cellular proteostatic machinery and the IRE1-α-MKK4 arm of the endoplasmic-reticulum-stress-response pathway. Specifically, combination regimens that impair the unfolded protein responses block the emergence of aggressive mesenchymal subpopulations in mouse and patient-derived PDAC models. These molecular and biological insights inform a potential therapeutic strategy for targeting aggressive mesenchymal features of PDAC.
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Affiliation(s)
- Giannicola Genovese
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Alessandro Carugo
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,European Institute of Oncology, Milano 20141, Italy
| | - James Tepper
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Frederick Scott Robinson
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Liren Li
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou, 510060, China
| | - Maria Svelto
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Istituto di Patologia Generale, Universitá Cattolica del Sacro Cuore, Rome 00168, Italy
| | - Luigi Nezi
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Denise Corti
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Rosalba Minelli
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Piergiorgio Pettazzoni
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Tony Gutschner
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Chia-Chin Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Sahil Seth
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Kadir Caner Akdemir
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Elisabetta Leo
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Samirkumar Amin
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Graduate program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Marco Dal Molin
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Haoqiang Ying
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Lawrence N Kwong
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Simona Colla
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Koichi Takahashi
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Papia Ghosh
- Office of Technology Commercialization, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Virginia Giuliani
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Florian Muller
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Prasenjit Dey
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Shan Jiang
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jill Garvey
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Chang-Gong Liu
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jianhua Zhang
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Timothy P Heffernan
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Carlo Toniatti
- ORBIT Platform, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jason B Fleming
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Michael G Goggins
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Laura D Wood
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Alessandro Sgambato
- Istituto di Patologia Generale, Universitá Cattolica del Sacro Cuore, Rome 00168, Italy
| | - Abbas Agaimy
- Department of Pathology, Friedrich Alexander University Erlangen-Nuremberg, University Hospital, Erlangen 91054, Germany
| | - Anirban Maitra
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Sheikh Ahmed Bin Zayed Al Nahyan Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Charles W M Roberts
- Comprehensive Cancer Center and Department of Oncology, St Jude Children's Research Hospital, Memphis, Tennessee 77027, USA
| | - Huamin Wang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Andrea Viale
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Ronald A DePinho
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Giulio F Draetta
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Lynda Chin
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
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41
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WU S, WANG J, LI F. Role of SNF5 in rheumatoid arthritis by upregulation ofp16 and inactivation of JNK pathway. Turk J Biol 2017. [DOI: 10.3906/biy-1610-40] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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42
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Wang X, Lee RS, Alver BH, Haswell JR, Wang S, Mieczkowski J, Drier Y, Gillespie SM, Archer TC, Wu JN, Tzvetkov EP, Troisi EC, Pomeroy SL, Biegel JA, Tolstorukov MY, Bernstein BE, Park PJ, Roberts CWM. SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation. Nat Genet 2016; 49:289-295. [PMID: 27941797 PMCID: PMC5285474 DOI: 10.1038/ng.3746] [Citation(s) in RCA: 220] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 11/18/2016] [Indexed: 02/07/2023]
Abstract
SMARCB1 (also known as SNF5, INI1, and BAF47), a core subunit of the SWI/SNF (BAF) chromatin-remodeling complex, is inactivated in nearly all pediatric rhabdoid tumors. These aggressive cancers are among the most genomically stable, suggesting an epigenetic mechanism by which SMARCB1 loss drives transformation. Here we show that, despite having indistinguishable mutational landscapes, human rhabdoid tumors exhibit distinct enhancer H3K27ac signatures, which identify remnants of differentiation programs. We show that SMARCB1 is required for the integrity of SWI/SNF complexes and that its loss alters enhancer targeting-markedly impairing SWI/SNF binding to typical enhancers, particularly those required for differentiation, while maintaining SWI/SNF binding at super-enhancers. We show that these retained super-enhancers are essential for rhabdoid tumor survival, including some that are shared by all subtypes, such as SPRY1, and other lineage-specific super-enhancers, such as SOX2 in brain-derived rhabdoid tumors. Taken together, our findings identify a new chromatin-based epigenetic mechanism underlying the tumor-suppressive activity of SMARCB1.
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Affiliation(s)
- Xiaofeng Wang
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Ryan S Lee
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Burak H Alver
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Jeffrey R Haswell
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Su Wang
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Jakub Mieczkowski
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Yotam Drier
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Shawn M Gillespie
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Tenley C Archer
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jennifer N Wu
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Evgeni P Tzvetkov
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Emma C Troisi
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Scott L Pomeroy
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jaclyn A Biegel
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine at the University of Southern California, Los Angeles, California, USA
| | - Michael Y Tolstorukov
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Bradley E Bernstein
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Charles W M Roberts
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA.,Comprehensive Cancer Center and Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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43
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Brok J, Treger TD, Gooskens SL, van den Heuvel-Eibrink MM, Pritchard-Jones K. Biology and treatment of renal tumours in childhood. Eur J Cancer 2016; 68:179-195. [PMID: 27969569 DOI: 10.1016/j.ejca.2016.09.005] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 08/25/2016] [Accepted: 09/01/2016] [Indexed: 02/08/2023]
Abstract
In Europe, almost 1000 children are diagnosed with a malignant renal tumour each year. The vast majority of cases are nephroblastoma, also known as Wilms' tumour (WT). Most children are treated according to Société Internationale d'Oncologie Pédiatrique Renal Tumour Study Group (SIOP-RTSG) protocols with pre-operative chemotherapy, surgery, and post-operative treatment dependent on stage and histology. Overall survival approaches 90%, but a subgroup of WT, with high-risk histology and/or relapsed disease, still have a much poorer prognosis. Outcome is similarly poor for the rare non-WT, particularly for malignant rhabdoid tumour of the kidney, metastatic clear cell sarcoma of the kidney (CCSK), and metastatic renal cell carcinoma (RCC). Improving outcome and long-term quality of life requires more accurate risk stratification through biological insights. Biomarkers are also needed to signpost potential targeted therapies for high-risk subgroups. Our understanding of Wilms' tumourigenesis is evolving and several signalling pathways, microRNA processing and epigenetics are now known to play pivotal roles. Most rhabdoid tumours display somatic and/or germline mutations in the SMARCB1 gene, whereas CCSK and paediatric RCC reveal a more varied genetic basis, including characteristic translocations. Conducting early-phase trials of targeted therapies is challenging due to the scarcity of patients with refractory or relapsed disease, the rapid progression of relapse and the genetic heterogeneity of the tumours with a low prevalence of individual somatic mutations. A further consideration in improving population survival rates is the geographical variation in outcomes across Europe. This review provides a comprehensive overview of the current biological knowledge of childhood renal tumours alongside the progress achieved through international collaboration. Ongoing collaboration is needed to ensure consistency of outcomes through standardised diagnostics and treatment and incorporation of biomarker research. Together, these objectives constitute the rationale for the forthcoming SIOP-RTSG 'UMBRELLA' study.
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Affiliation(s)
- Jesper Brok
- Cancer Section, University College London, Institute of Child Health, UK; Department of Paediatric Haematology and Oncology, Rigshospitalet, Copenhagen University Hospital, Denmark.
| | - Taryn D Treger
- Cancer Section, University College London, Institute of Child Health, UK
| | - Saskia L Gooskens
- Department of Paediatric Oncology, Princess Máxima Center for Pediatric Oncology and University of Utrecht, The Netherlands; Department of Paediatric Haematology and Oncology, Erasmus MC - Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Marry M van den Heuvel-Eibrink
- Department of Paediatric Oncology, Princess Máxima Center for Pediatric Oncology and University of Utrecht, The Netherlands
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44
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Abstract
Since its foundation by remarkably talented and insightful individuals, prominently including Pepper Dehner, pediatric soft tissue tumor pathology has developed at an immense rate. The morphologic classification of tumoral entities has extensively been corroborated, but has also evolved with refinement or realignment of these classifications, through accruing molecular data, with many derivative ancillary diagnostic assays now already well-established. Tumors of unclear histogenesis, classically morphologically undifferentiated, are prominent amongst pediatric sarcomas, however, the classes of undifferentiated round- or spindle-cell-tumors-not-otherwise-specified are being dismantled gradually with the identification of their molecular underpinnings. Within recent years, for example, numerous subcategories of 'Ewing-like' round cell sarcoma have emerged. Such advances have provided the basis for novel diagnostic and prognostic sub-classifications. Efforts at defining cell- or lineage-of-origin for several tumor types have produced interesting insights especially for rhabdomyosarcoma. The remarkably early onset of pediatric sarcomas defies the theory necessitating stochastic accumulation of several somatic mutations for cancer development and indeed, these tumors may be remarkably genomically stable, often belying their aggressive nature. Much is coming to light recently regarding the role of epigenetic modifications in the evolution of these sarcomas. Indeed the morphologic features of embryonal tumors generally (not just sarcomas) may be highly reminiscent of arrested differentiation, and given the tight epigenetic regulation of cell fate determination and cell identity maintenance, a theory of epigenetically-driven oncogenesis sits easily with these tumors. The age-delimited distinct biologies of 'pediatric' and adult GIST are intriguing, particularly, the SDH-deficient 'pediatric' form, driven by a metabolic defect, but resulting in epigenetic dysregulation with genome-wide DNA methylation changes. There is little doubt that many of the gaps in our understanding of pediatric sarcoma biology will be filled by a deeper appreciation of the role of dysregulated epigenetics including chromatin biology, perhaps best exemplified in malignant rhabdoid tumor. The field of pediatric soft tissue tumor pathology grows ever more interesting. Importantly though, it must be emphasized, that none of this progress could have occurred, or indeed continue, without the initial step of accurate diagnosis, founded solidly on morphology - thank you Pepper for your unparalleled contributions to this field! The opportunity to be your apprentice for five years has been a bigger and more positive influence than words can express.
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Affiliation(s)
- Maureen O'Sullivan
- National Children's Research Centre, Crumlin, Dublin, Ireland; Our Lady's Children's Hospital Crumlin, Dublin, Ireland; Trinity College, Dublin, Ireland.
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45
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Abstract
Rhabdoid tumor is a rare, highly aggressive malignancy that primarily affects infants and young children. These tumors typically arise in the brain and kidney, although extrarenal, non-central nervous system tumors in almost all soft-tissue sites have been described. SMARCB1 is a member of the SWI/SNF chromatin-remodeling complex and functions as a tumor suppressor in the vast majority of rhabdoid tumors. Patients with germline mutations or deletions affecting SMARCB1 are predisposed to the development of rhabdoid tumors, as well as the genetic disorder schwannomatosis. The current hypothesis is that rhabdoid tumors are driven by epigenetic dysregulation, as opposed to the alteration of a specific biologic pathway. The strategies for novel therapeutic approaches based on what is currently known about rhabdoid tumor biology are presented.
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Affiliation(s)
- James I Geller
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Jacquelyn J Roth
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Jaclyn A Biegel
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles; Keck School of Medicine, University of Southern California, Los Angeles, Ca
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46
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Stojanova A, Tu WB, Ponzielli R, Kotlyar M, Chan PK, Boutros PC, Khosravi F, Jurisica I, Raught B, Penn LZ. MYC interaction with the tumor suppressive SWI/SNF complex member INI1 regulates transcription and cellular transformation. Cell Cycle 2016; 15:1693-705. [PMID: 27267444 PMCID: PMC4957596 DOI: 10.1080/15384101.2016.1146836] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
MYC is a key driver of cellular transformation and is deregulated in most human cancers. Studies of MYC and its interactors have provided mechanistic insight into its role as a regulator of gene transcription. MYC has been previously linked to chromatin regulation through its interaction with INI1 (SMARCB1/hSNF5/BAF47), a core member of the SWI/SNF chromatin remodeling complex. INI1 is a potent tumor suppressor that is inactivated in several types of cancers, most prominently as the hallmark alteration in pediatric malignant rhabdoid tumors. However, the molecular and functional interaction of MYC and INI1 remains unclear. Here, we characterize the MYC-INI1 interaction in mammalian cells, mapping their minimal binding domains to functionally significant regions of MYC (leucine zipper) and INI1 (repeat motifs), and demonstrating that the interaction does not interfere with MYC-MAX interaction. Protein-protein interaction network analysis expands the MYC-INI1 interaction to the SWI/SNF complex and a larger network of chromatin regulatory complexes. Genome-wide analysis reveals that the DNA-binding regions and target genes of INI1 significantly overlap with those of MYC. In an INI1-deficient rhabdoid tumor system, we observe that with re-expression of INI1, MYC and INI1 bind to common target genes and have opposing effects on gene expression. Functionally, INI1 re-expression suppresses cell proliferation and MYC-potentiated transformation. Our findings thus establish the antagonistic roles of the INI1 and MYC transcriptional regulators in mediating cellular and oncogenic functions.
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Affiliation(s)
- Angelina Stojanova
- a Department of Medical Biophysics , Faculty of Medicine, University of Toronto , Toronto , Ontario , Canada.,b Princess Margaret Cancer Centre, University Health Network , Toronto , Ontario , Canada
| | - William B Tu
- a Department of Medical Biophysics , Faculty of Medicine, University of Toronto , Toronto , Ontario , Canada.,b Princess Margaret Cancer Centre, University Health Network , Toronto , Ontario , Canada
| | - Romina Ponzielli
- b Princess Margaret Cancer Centre, University Health Network , Toronto , Ontario , Canada
| | - Max Kotlyar
- b Princess Margaret Cancer Centre, University Health Network , Toronto , Ontario , Canada
| | - Pak-Kei Chan
- b Princess Margaret Cancer Centre, University Health Network , Toronto , Ontario , Canada
| | - Paul C Boutros
- a Department of Medical Biophysics , Faculty of Medicine, University of Toronto , Toronto , Ontario , Canada.,b Princess Margaret Cancer Centre, University Health Network , Toronto , Ontario , Canada.,c Informatics and Biocomputing Program, Ontario Institute for Cancer Research , Toronto , Ontario , Canada
| | - Fereshteh Khosravi
- b Princess Margaret Cancer Centre, University Health Network , Toronto , Ontario , Canada
| | - Igor Jurisica
- a Department of Medical Biophysics , Faculty of Medicine, University of Toronto , Toronto , Ontario , Canada.,b Princess Margaret Cancer Centre, University Health Network , Toronto , Ontario , Canada.,d Department of Computer Science , University of Toronto , Toronto , Ontario , Canada
| | - Brian Raught
- a Department of Medical Biophysics , Faculty of Medicine, University of Toronto , Toronto , Ontario , Canada.,b Princess Margaret Cancer Centre, University Health Network , Toronto , Ontario , Canada
| | - Linda Z Penn
- a Department of Medical Biophysics , Faculty of Medicine, University of Toronto , Toronto , Ontario , Canada.,b Princess Margaret Cancer Centre, University Health Network , Toronto , Ontario , Canada
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47
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Abstract
SMARCB1 is the core subunit of the SWI/sucrose non-fermenting ATP-dependent chromatin remodelling complex located on the long arm of chromosome 22 (22q11.2). Since discovering genetic alterations of the SMARCB1 gene in malignant rhabdoid tumours, the family of tumours harbouring loss of SMARCB1 expression has been steadily expanding. In this review, we give a general overview of SMARCB1, its role in various cancers including germline mutations, association with genetic syndromes and role in future targeted therapies.
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Affiliation(s)
- Sangeetha N Kalimuthu
- Department of Pathology, Laboratory Medicine Program, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Runjan Chetty
- Department of Pathology, Laboratory Medicine Program, University Health Network, University of Toronto, Toronto, Ontario, Canada
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48
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Porrello A, Piergentili RB. Contextualizing the Genes Altered in Bladder Neoplasms in Pediatric andTeen Patients Allows Identifying Two Main Classes of Biological ProcessesInvolved and New Potential Therapeutic Targets. Curr Genomics 2016; 17:33-61. [PMID: 27013923 PMCID: PMC4780474 DOI: 10.2174/1389202916666151014222603] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 06/29/2015] [Accepted: 07/08/2015] [Indexed: 12/19/2022] Open
Abstract
Research on bladder neoplasms in pediatric and teen patients (BNPTP) has described 21 genes, which are variously involved in this disease and are mostly responsible for deregulated cell proliferation. However, due to the limited number of publications on this subject, it is still unclear what type of relationships there are among these genes and which are the chances that, while having different molecular functions, they i) act as downstream effector genes of well-known pro- or anti- proliferative stimuli and/or interplay with biochemical pathways having oncological relevance or ii) are specific and, possibly, early biomarkers of these pathologies. A Gene Ontology (GO)-based analysis showed that these 21 genes are involved in biological processes, which can be split into two main classes: cell regulation-based and differentiation/development-based. In order to understand the involvement/overlapping with main cancer-related pathways, we performed a meta-analysis dependent on the 189 oncogenic signatures of the Molecular Signatures Database (OSMSD) curated by the Broad Institute. We generated a binary matrix with 53 gene signatures having at least one hit; this analysis i) suggests that some genes of the original list show inconsistencies and might need to be experimentally re- assessed or evaluated as biomarkers (in particular, ACTA2) and ii) allows hypothesizing that important (proto)oncogenes (E2F3, ERBB2/HER2, CCND1, WNT1, and YAP1) and (putative) tumor suppressors (BRCA1, RBBP8/CTIP, and RB1-RBL2/p130) may participate in the onset of this disease or worsen the observed phenotype, thus expanding the list of possible molecular targets for the treatment of BNPTP.
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Affiliation(s)
- A. Porrello
- Comprehensive Cancer Center (LCCC), University of North Carolina (UNC)-Chapel Hill, Chapel Hill, 27599 NC, USA
| | - R. b Piergentili
- Institute of Molecular Biology and Pathology at CNR (CNR-IBPM); Department of Biology and Biotechnologies, Sapienza – Università di Roma, Italy
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49
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Tamayo P, Steinhardt G, Liberzon A, Mesirov JP. The limitations of simple gene set enrichment analysis assuming gene independence. Stat Methods Med Res 2016; 25:472-87. [PMID: 23070592 PMCID: PMC3758419 DOI: 10.1177/0962280212460441] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Since its first publication in 2003, the Gene Set Enrichment Analysis method, based on the Kolmogorov-Smirnov statistic, has been heavily used, modified, and also questioned. Recently a simplified approach using a one-sample t-test score to assess enrichment and ignoring gene-gene correlations was proposed by Irizarry et al. 2009 as a serious contender. The argument criticizes Gene Set Enrichment Analysis's nonparametric nature and its use of an empirical null distribution as unnecessary and hard to compute. We refute these claims by careful consideration of the assumptions of the simplified method and its results, including a comparison with Gene Set Enrichment Analysis's on a large benchmark set of 50 datasets. Our results provide strong empirical evidence that gene-gene correlations cannot be ignored due to the significant variance inflation they produced on the enrichment scores and should be taken into account when estimating gene set enrichment significance. In addition, we discuss the challenges that the complex correlation structure and multi-modality of gene sets pose more generally for gene set enrichment methods.
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Affiliation(s)
- Pablo Tamayo
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - George Steinhardt
- Boston University Bioinformatics Program, Boston University, Boston, MA, USA
| | - Arthur Liberzon
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Jill P Mesirov
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA Boston University Bioinformatics Program, Boston University, Boston, MA, USA
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50
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Epigenomic regulation of oncogenesis by chromatin remodeling. Oncogene 2016; 35:4423-36. [PMID: 26804164 DOI: 10.1038/onc.2015.513] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/27/2015] [Accepted: 12/07/2015] [Indexed: 02/08/2023]
Abstract
Disruption of the intricate gene expression program represents one of major driving factors for the development, progression and maintenance of human cancer, and is often associated with acquired therapeutic resistance. At the molecular level, cancerous phenotypes are the outcome of cellular functions of critical genes, regulatory interactions of histones and chromatin remodeling complexes in response to dynamic and persistent upstream signals. A large body of genetic and biochemical evidence suggests that the chromatin remodelers integrate the extracellular and cytoplasmic signals to control gene activity. Consequently, widespread dysregulation of chromatin remodelers and the resulting inappropriate expression of regulatory genes, together, lead to oncogenesis. We summarize the recent developments and current state of the dysregulation of the chromatin remodeling components as the driving mechanism underlying the growth and progression of human tumors. Because chromatin remodelers, modifying enzymes and protein-protein interactions participate in interpreting the epigenetic code, selective chromatin remodelers and bromodomains have emerged as new frontiers for pharmacological intervention to develop future anti-cancer strategies to be used either as single-agent or in combination therapies with chemotherapeutics or radiotherapy.
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