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Yavas A, Ozcan K, Adsay NV, Balci S, Tarcan ZC, Hechtman JF, Luchini C, Scarpa A, Lawlor RT, Mafficini A, Reid MD, Xue Y, Yang Z, Haye K, Bellizzi AM, Vanoli A, Benhamida J, Balachandran V, Jarnagin W, Park W, O'Reilly EM, Klimstra DS, Basturk O. SWI/SNF Complex-Deficient Undifferentiated Carcinoma of the Pancreas: Clinicopathologic and Genomic Analysis. Mod Pathol 2024; 37:100585. [PMID: 39094734 DOI: 10.1016/j.modpat.2024.100585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 07/12/2024] [Accepted: 07/25/2024] [Indexed: 08/04/2024]
Abstract
Inactivating alterations in the SWItch/Sucrose NonFermentable (SWI/SNF) Chromatin Remodeling Complex subunits have been described in multiple tumor types. Recent studies focused on SMARC subunits of this complex to understand their relationship with tumor characteristics and therapeutic opportunities. To date, pancreatic cancer with these alterations has not been well studied, although isolated cases of undifferentiated carcinomas have been reported. Herein, we screened 59 pancreatic undifferentiated carcinomas for alterations in SWI/SNF complex-related (SMARCB1 [BAF47/INI1], SMARCA4 [BRG1], SMARCA2 [BRM]) proteins and/or genes using immunohistochemistry and/or next-generation sequencing. Cases with alterations in SWI/SNF complex-related proteins/genes were compared with cases without alterations, as well as with 96 conventional pancreatic ductal adenocarcinomas (PDAC). In all tumor groups, mismatch repair and PD-L1 protein expression were also evaluated. Thirty of 59 (51%) undifferentiated carcinomas had a loss of SWI/SNF complex-related protein expression or gene alteration. Twenty-seven of 30 (90%) SWI-/SNF-deficient undifferentiated carcinomas had rhabdoid morphology (vs 9/29 [31%] SWI-/SNF-retained undifferentiated carcinomas; P < .001) and all expressed cytokeratin, at least focally. Immunohistochemically, SMARCB1 protein expression was absent in 16/30 (53%) cases, SMARCA2 in 4/30 (13%), and SMARCA4 in 4/30 (13%); both SMARCB1 and SMARCA2 protein expressions were absent in 1/30 (3%). Five of 8 (62.5%) SWI-/SNF-deficient undifferentiated carcinomas that displayed loss of SMARCB1 protein expression by immunohistochemistry were found to have corresponding SMARCB1 deletions by next-generation sequencing. Analysis of canonical driver mutations for PDAC in these cases showed KRAS (2/5) and TP53 (2/5) abnormalities. Median combined positive score for PD-L1 (E1L3N) was significantly higher in the undifferentiated carcinomas with/without SWI/SNF deficiency compared with the conventional PDACs (P < .001). SWI-/SNF-deficient undifferentiated carcinomas were larger (P < .001) and occurred in younger patients (P < .001). Patients with SWI-/SNF-deficient undifferentiated carcinoma had worse overall survival compared with patients with SWI-/SNF-retained undifferentiated carcinoma (P = .004) and PDAC (P < .001). Our findings demonstrate that SWI-/SNF-deficient pancreatic undifferentiated carcinomas are frequently characterized by rhabdoid morphology, exhibit highly aggressive behavior, and have a negative prognostic impact. The ones with SMARCB1 deletions appear to be frequently KRAS wild type. Innovative developmental therapeutic strategies targeting this genomic basis of the SWI/SNF complex and the therapeutic implications of EZH2 inhibition (NCT03213665), SMARCA2 degrader (NCT05639751), or immunotherapy are currently under investigation.
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Affiliation(s)
- Aslihan Yavas
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Pathology, Now with Institute of Pathology, Heinrich Heine University and University Hospital of Düsseldorf, Düsseldorf, Germany
| | - Kerem Ozcan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Now with Department of Pathology and Laboratory Medicine, Henry Ford Hospital, Detroit, Michigan
| | - N Volkan Adsay
- The Department of Pathology, Koç University Hospital and Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Turkey
| | - Serdar Balci
- Department of Pathology, Memorial Healthcare Group, Istanbul, Turkey
| | - Zeynep C Tarcan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; David M. Rubenstein Center for Pancreatic Cancer Research, New York, New York
| | - Jaclyn F Hechtman
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Now with Caris Life Sciences, Miami, Florida
| | - Claudio Luchini
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy; ARC-Net Research Center, University and Hospital Trust of Verona, Verona, Italy
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Rita T Lawlor
- Department of Engineering for Innovation Medicine (DIMI), University of Verona, Verona, Italy
| | - Andrea Mafficini
- Department of Engineering for Innovation Medicine (DIMI), University of Verona, Verona, Italy
| | - Michelle D Reid
- Department of Pathology, School of Medicine, Emory University, Atlanta, Georgia
| | - Yue Xue
- Department of Pathology, University Hospitals, Cleveland, Ohio
| | - Zhaohai Yang
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Kester Haye
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Andrew M Bellizzi
- Department of Pathology, University of Iowa, Iowa City, Iowa; Department of Molecular Medicine, Unit of Anatomic Pathology, University of Pavia, Pavia, Italy
| | - Alessandro Vanoli
- Unit of Anatomic Pathology, Fondazione IRCCS San Matteo Hospital, Pavia, Italy
| | - Jamal Benhamida
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Vinod Balachandran
- David M. Rubenstein Center for Pancreatic Cancer Research, New York, New York; Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - William Jarnagin
- David M. Rubenstein Center for Pancreatic Cancer Research, New York, New York; Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Wungki Park
- David M. Rubenstein Center for Pancreatic Cancer Research, New York, New York; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Eileen M O'Reilly
- David M. Rubenstein Center for Pancreatic Cancer Research, New York, New York; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David S Klimstra
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Now with Paige.AI, New York, New York
| | - Olca Basturk
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; David M. Rubenstein Center for Pancreatic Cancer Research, New York, New York.
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Duan Y, Zhan H, Wang Q, Li B, Gao H, Liu D, Xu Q, Gao X, Liu Z, Gao P, Wei G, Wang Y. Integrated Lactylome Characterization Reveals the Molecular Dynamics of Protein Regulation in Gastrointestinal Cancers. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2400227. [PMID: 39018247 DOI: 10.1002/advs.202400227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 05/19/2024] [Indexed: 07/19/2024]
Abstract
Lysine lactylation (Kla) plays a vital role in several physiological processes. However, the cancer-specific modulation of Kla in gastrointestinal (GI) tumors requires systematic elucidation. Here, global lactylome profiling of cancerous and adjacent tissues is conducted from 40 patients with GI cancer and identified 11698 Kla sites. Lactylome integration revealed that Kla affects proteins involved in hallmark cancer processes, including epigenetic rewiring, metabolic perturbations, and genome instability. Moreover, the study revealed pan-cancer patterns of Kla alterations, among which 37 Kla sites are consistently upregulated in all four GI cancers and are involved in gene regulation. It is further verified that lactylation of CBX3 at K10 mediates its interaction of CBX3 with the epigenetic marker H3K9me3 and facilitates GI cancer progression. Overall, this study provides an invaluable resource for understanding the lactylome landscape in GI cancers, which may provide new paths for drug discovery for these devastating diseases.
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Affiliation(s)
- Yangmiao Duan
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Cell Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Hanxiang Zhan
- Division of Pancreatic Surgery, Department of General Surgery, Qilu Hospital, Shandong University, Jinan, Shandong, 250012, China
| | - Qin Wang
- Department of Anesthesiology, Qilu Hospital, Shandong University, Jinan, Shandong, 250012, China
| | - Bohao Li
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Cell Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Huiru Gao
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250033, China
| | - Duanrui Liu
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China
| | - Qinchen Xu
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250033, China
| | - Xin Gao
- Division of Pancreatic Surgery, Department of General Surgery, Qilu Hospital, Shandong University, Jinan, Shandong, 250012, China
| | - Zhenya Liu
- Division of Pancreatic Surgery, Department of General Surgery, Qilu Hospital, Shandong University, Jinan, Shandong, 250012, China
| | - Peng Gao
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Pathology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Guangwei Wei
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Cell Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Yunshan Wang
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China
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Davidson RK, Wu W, Kanojia S, George RM, Huter K, Sandoval K, Osmulski M, Casey N, Spaeth JM. The SWI/SNF chromatin remodelling complex regulates pancreatic endocrine cell expansion and differentiation in mice in vivo. Diabetologia 2024:10.1007/s00125-024-06211-7. [PMID: 38958700 DOI: 10.1007/s00125-024-06211-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 05/16/2024] [Indexed: 07/04/2024]
Abstract
AIMS/HYPOTHESIS Strategies to augment functional beta cell mass include directed differentiation of stem cells towards a beta cell fate, which requires extensive knowledge of transcriptional programs governing endocrine progenitor cell differentiation in vivo. We aimed to study the contributions of the Brahma-related gene-1 (BRG1) and Brahma (BRM) ATPase subunits of the SWI/SNF chromatin remodelling complex to endocrine cell development. METHODS We generated mice with endocrine progenitor-specific Neurog3-Cre BRG1 removal in the presence of heterozygous (Brg1Δendo;Brm+/-) or homozygous (double knockout: DKOΔendo) BRM deficiency. Whole-body metabolic phenotyping, islet function characterisation, islet quantitative PCR and histological characterisation were performed on animals and tissues postnatally. To test the mechanistic actions of SWI/SNF in controlling gene expression during endocrine cell development, single-cell RNA-seq was performed on flow-sorted endocrine-committed cells from embryonic day 15.5 control and mutant embryos. RESULTS Brg1Δendo;Brm+/- mice exhibit severe glucose intolerance, hyperglycaemia and hypoinsulinaemia, resulting, in part, from reduced islet number; diminished alpha, beta and delta cell mass; compromised islet insulin secretion; and altered islet gene expression programs, including reductions in MAFA and urocortin 3 (UCN3). DKOΔendo mice were not recovered at weaning; however, postnatal day 6 DKOΔendo mice were severely hyperglycaemic with reduced serum insulin levels and beta cell area. Single-cell RNA-seq of embryonic day 15.5 lineage-labelled cells revealed endocrine progenitor, alpha and beta cell populations from SWI/SNF mutants have reduced expression of Mafa, Gcg, Ins1 and Ins2, suggesting limited differentiation capacity. Reduced Neurog3 transcripts were discovered in DKOΔendo endocrine progenitor clusters, and the proliferative capacity of neurogenin 3 (NEUROG3)+ cells was reduced in Brg1Δendo;Brm+/- and DKOΔendo mutants. CONCLUSIONS/INTERPRETATION Loss of BRG1 from developing endocrine progenitor cells has a severe postnatal impact on glucose homeostasis, and loss of both subunits impedes animal survival, with both groups exhibiting alterations in hormone transcripts embryonically. Taken together, these data highlight the critical role SWI/SNF plays in governing gene expression programs essential for endocrine cell development and expansion. DATA AVAILABILITY Raw and processed data for scRNA-seq have been deposited into the NCBI Gene Expression Omnibus (GEO) database under the accession number GSE248369.
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Grants
- CA082709 Division of Cancer Prevention, National Cancer Institute
- DK097512 Division of Diabetes, Endocrinology, and Metabolic Diseases
- DK097771 Division of Diabetes, Endocrinology, and Metabolic Diseases
- DK106846 Division of Diabetes, Endocrinology, and Metabolic Diseases
- DK115633 Division of Diabetes, Endocrinology, and Metabolic Diseases
- DK127129 Division of Diabetes, Endocrinology, and Metabolic Diseases
- DK128918 Division of Diabetes, Endocrinology, and Metabolic Diseases
- DK129287 Division of Diabetes, Endocrinology, and Metabolic Diseases
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Affiliation(s)
- Rebecca K Davidson
- Center for Diabetes & Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN, USA
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Wenting Wu
- Center for Diabetes & Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sukrati Kanojia
- Center for Diabetes & Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN, USA
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Rajani M George
- Center for Diabetes & Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN, USA
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kayla Huter
- Center for Diabetes & Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN, USA
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kassandra Sandoval
- Center for Diabetes & Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN, USA
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Meredith Osmulski
- Center for Diabetes & Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN, USA
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Nolan Casey
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jason M Spaeth
- Center for Diabetes & Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN, USA.
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA.
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA.
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA.
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Wei CH, Sadimin E, Agulnik M, Yost SE, Longacre TA, Fadare O. SMARCA4 / BRG1 -deficient Uterine Neoplasm With Hybrid Adenosarcoma and Carcinoma Features: Expanding the Molecular-morphologic Spectrum of SMARCA4 -driven Gynecologic Malignancies. Int J Gynecol Pathol 2024; 43:354-361. [PMID: 38113031 PMCID: PMC11166733 DOI: 10.1097/pgp.0000000000000996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
SMARCA4 gene encodes BRG1 , a member of the SWItch/sucrose non-fermentable protein family involved in epigenetic transcriptional regulation of important cellular processes. In the uterine corpus, SMARCA4 / BRG1 deficiency is associated with a novel class of undifferentiated uterine sarcomas, characterized by younger age onset, rhabdoid histology, focal phyllodiform architecture, high-risk pathologic findings, and dismal prognosis. Herein, we report a case of a 34-year-old Asian woman with a SMARCA4 / BRG1 -deficient uterine tumor fulfilling the clinicopathologic features of an undifferentiated uterine sarcoma. However, the tumor exhibited several unique features that have not been previously emphasized, including (1) conspicuous phyllodiform architecture recapitulating conventional adenosarcoma, (2) rhabdoid tumor cells forming cords and keratin-positive cohesive epithelial islands, and (3) cooccurrence with a spatially distinct and discrete endometrial complex atypical hyperplasia from the rest of the proliferation. By immunohistochemistry, the tumor cells were diffusely positive for synaptophysin, whereas BRG1 was lost. Pertinent molecular findings included frameshift mutations in the SMARCA4 gene, mutations in histone modification and chromatin remodeling genes, including KMT2C , ARID1B , KAT6A , and NCOR1 , and mutations in Wnt signaling involving APC and CTNNB1 . Copy number gain in MDM2 and CDK4 were also identified. The tumor mutation burden was intermediate (6.8/MB) and it was microsatellite stable. On balance, our case exhibited morphologic and molecular features that overlap with (1) an undifferentiated uterine sarcoma, (2) an adenosarcoma with sarcomatous overgrowth, and (3) a mixed adenosarcoma and undifferentiated endometrial carcinoma. These hybrid features further expand the molecular-morphologic spectrum of SMARCA4 / BRG1 -deficient uterine neoplasms.
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Peng ZT, Hu R, Fu JY. Sulforaphane suppresses cell proliferation and induces apoptosis in glioma via the ACTL6A/PGK1 axis. Toxicol Mech Methods 2024; 34:507-516. [PMID: 38221767 DOI: 10.1080/15376516.2024.2306375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 01/11/2024] [Indexed: 01/16/2024]
Abstract
This study aimed to examine the expression and biological functions of ACTL6A in glioma cells (U251), the effects of sulforaphane on the growth of U251 cells and the involvement of the ACTL6A/PGK1 pathway in those effects. The U251 cell line was transfected with ACTL6A over-expression plasmids to upregulate the protein, or with ACTL6A inhibitor to underexpress it, then treated with different concentrations of sulforaphane. Cell viability, proliferation, and apoptosis were assessed using standard assays, and levels of mRNAs encoding ACTL6A, PGK1, cyclin D1, Myc, Bax or Bcl-2 were measured using quantitative real-time polymerase chain reaction (qRT-PCR). ACTL6A and PGK1 were expressed at higher levels in glioma cell lines than in normal HEB cells. ACTL6A overexpression upregulated PGK1, whereas ACTL6A inhibition had the opposite effect. ACTL6A overexpression induced proliferation, whereas its inhibition repressed proliferation, enhanced apoptosis, and halted the cell cycle. Moreover, sulforaphane suppressed the growth of U251 cells by inactivating the ACTL6A/PGK1 axis. ACTL6A acts via PGK1 to play a critical role in glioma cell survival and proliferation, and sulforaphane targets it to inhibit glioma.
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Affiliation(s)
- Zi-Tan Peng
- Department of Clinical Laboratory, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Hubei, People's Republic of China
- Hubei Key Laboratory of Kidney Disease Pathogenesis and Intervention, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Hubei, People's Republic of China
- Huangshi Key Laboratory of Assisted Reproduction and Reproductive Medicine, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Hubei, People's Republic of China
| | - Rong Hu
- Department of Clinical Laboratory, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Hubei, People's Republic of China
- Hubei Key Laboratory of Kidney Disease Pathogenesis and Intervention, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Hubei, People's Republic of China
- Huangshi Key Laboratory of Assisted Reproduction and Reproductive Medicine, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Hubei, People's Republic of China
| | - Jing-Yu Fu
- Department of Clinical Laboratory, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Hubei, People's Republic of China
- Hubei Key Laboratory of Kidney Disease Pathogenesis and Intervention, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Hubei, People's Republic of China
- Huangshi Key Laboratory of Assisted Reproduction and Reproductive Medicine, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Hubei, People's Republic of China
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Lehtinen N, Suhonen J, Rice K, Välimäki E, Toriseva M, Routila J, Halme P, Rahi M, Irjala H, Leivo I, Kallajoki M, Nees M, Kuopio T, Ventelä S, Rantala JK. Assessment of targeted therapy opportunities in sinonasal cancers using patient-derived functional tumor models. Transl Oncol 2024; 44:101935. [PMID: 38522153 PMCID: PMC10973676 DOI: 10.1016/j.tranon.2024.101935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/26/2024] [Accepted: 03/07/2024] [Indexed: 03/26/2024] Open
Abstract
Malignant tumors derived from the epithelium lining the nasal cavity region are termed sinonasal cancers, a highly heterogeneous group of rare tumors accounting for 3 - 5 % of all head and neck cancers. Progress with next-generation molecular profiling has improved our understanding of the complexity of sinonasal cancers and resulted in the identification of an increasing number of distinct tumor entities. Despite these significant developments, the treatment of sinonasal cancers has hardly evolved since the 1980s, and an advanced sinonasal cancer presents a poor prognosis as targeted therapies are usually not available. To gain insights into potential targeted therapeutic opportunities, we performed a multiomics profiling of patient-derived functional tumor models to identify molecular characteristics associated with pharmacological responses in the different subtypes of sinonasal cancer. METHODS Patient-derived ex vivo tumor models representing four distinct sinonasal cancer subtypes: sinonasal intestinal-type adenocarcinoma, sinonasal neuroendocrine carcinoma, sinonasal undifferentiated carcinoma and SMARCB1 deficient sinonasal carcinoma were included in the analyses. Results of functional drug screens of 160 anti-cancer therapies were integrated with gene panel sequencing and histological analyses of the tumor tissues and the ex vivo cell cultures to establish associations between drug sensitivity and molecular characteristics including driver mutations. RESULTS The different sinonasal cancer subtypes display considerable differential drug sensitivity. Underlying the drug sensitivity profiles, each subtype was associated with unique molecular features. The therapeutic vulnerabilities correlating with specific genomic background were extended and validated with in silico analyses of cancer cell lines representing different human cancers and with reported case studies of sinonasal cancers treated with targeted therapies. CONCLUSION The results demonstrate the importance of understanding the differential biology and the molecular features associated with the different subtypes of sinonasal cancers. Patient-derived ex vivo tumor models can be a powerful tool for investigating these rare cancers and prioritizing targeted therapeutic strategies for future clinical development and personalized medicine.
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Affiliation(s)
| | | | | | | | - Mervi Toriseva
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland; FICAN West Cancer Centre, Turku, Finland
| | - Johannes Routila
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland; Department for Otorhinolaryngology - Head and Neck Surgery, University of Turku and Turku University Hospital, Turku, Finland
| | - Perttu Halme
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland; Department for Otorhinolaryngology - Head and Neck Surgery, University of Turku and Turku University Hospital, Turku, Finland
| | - Melissa Rahi
- Department of Neurosurgery, Neurocenter, Turku University Hospital, Turku, Finland; Clinical Neurosciences, University of Turku, Turku, Finland
| | - Heikki Irjala
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland; Department for Otorhinolaryngology - Head and Neck Surgery, University of Turku and Turku University Hospital, Turku, Finland
| | - Ilmo Leivo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland; Department of Pathology, University of Turku and Turku University Hospital, Turku, Finland
| | - Markku Kallajoki
- Department of Pathology, University of Turku and Turku University Hospital, Turku, Finland
| | - Matthias Nees
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland; FICAN West Cancer Centre, Turku, Finland; Department of Biochemistry and Molecular Biology, Medical University of Lublin, Lublin, Poland
| | - Teijo Kuopio
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland; Wellbeing Services County of Central Finland, Jyväskylä, Finland
| | - Sami Ventelä
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland; FICAN West Cancer Centre, Turku, Finland; Department for Otorhinolaryngology - Head and Neck Surgery, University of Turku and Turku University Hospital, Turku, Finland
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7
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Singh AK, Allington G, Viviano S, McGee S, Kiziltug E, Ma S, Zhao S, Mekbib KY, Shohfi JP, Duy PQ, DeSpenza T, Furey CG, Reeves BC, Smith H, Sousa AMM, Cherskov A, Allocco A, Nelson-Williams C, Haider S, Rizvi SRA, Alper SL, Sestan N, Shimelis H, Walsh LK, Lifton RP, Moreno-De-Luca A, Jin SC, Kruszka P, Deniz E, Kahle KT. A novel SMARCC1 BAFopathy implicates neural progenitor epigenetic dysregulation in human hydrocephalus. Brain 2024; 147:1553-1570. [PMID: 38128548 PMCID: PMC10994532 DOI: 10.1093/brain/awad405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 10/01/2023] [Accepted: 10/26/2023] [Indexed: 12/23/2023] Open
Abstract
Hydrocephalus, characterized by cerebral ventriculomegaly, is the most common disorder requiring brain surgery in children. Recent studies have implicated SMARCC1, a component of the BRG1-associated factor (BAF) chromatin remodelling complex, as a candidate congenital hydrocephalus gene. However, SMARCC1 variants have not been systematically examined in a large patient cohort or conclusively linked with a human syndrome. Moreover, congenital hydrocephalus-associated SMARCC1 variants have not been functionally validated or mechanistically studied in vivo. Here, we aimed to assess the prevalence of SMARCC1 variants in an expanded patient cohort, describe associated clinical and radiographic phenotypes, and assess the impact of Smarcc1 depletion in a novel Xenopus tropicalis model of congenital hydrocephalus. To do this, we performed a genetic association study using whole-exome sequencing from a cohort consisting of 2697 total ventriculomegalic trios, including patients with neurosurgically-treated congenital hydrocephalus, that total 8091 exomes collected over 7 years (2016-23). A comparison control cohort consisted of 1798 exomes from unaffected siblings of patients with autism spectrum disorder and their unaffected parents were sourced from the Simons Simplex Collection. Enrichment and impact on protein structure were assessed in identified variants. Effects on the human fetal brain transcriptome were examined with RNA-sequencing and Smarcc1 knockdowns were generated in Xenopus and studied using optical coherence tomography imaging, in situ hybridization and immunofluorescence. SMARCC1 surpassed genome-wide significance thresholds, yielding six rare, protein-altering de novo variants localized to highly conserved residues in key functional domains. Patients exhibited hydrocephalus with aqueductal stenosis; corpus callosum abnormalities, developmental delay, and cardiac defects were also common. Xenopus knockdowns recapitulated both aqueductal stenosis and cardiac defects and were rescued by wild-type but not patient-specific variant SMARCC1. Hydrocephalic SMARCC1-variant human fetal brain and Smarcc1-variant Xenopus brain exhibited a similarly altered expression of key genes linked to midgestational neurogenesis, including the transcription factors NEUROD2 and MAB21L2. These results suggest de novo variants in SMARCC1 cause a novel human BAFopathy we term 'SMARCC1-associated developmental dysgenesis syndrome', characterized by variable presence of cerebral ventriculomegaly, aqueductal stenosis, developmental delay and a variety of structural brain or cardiac defects. These data underscore the importance of SMARCC1 and the BAF chromatin remodelling complex for human brain morphogenesis and provide evidence for a 'neural stem cell' paradigm of congenital hydrocephalus pathogenesis. These results highlight utility of trio-based whole-exome sequencing for identifying pathogenic variants in sporadic congenital structural brain disorders and suggest whole-exome sequencing may be a valuable adjunct in clinical management of congenital hydrocephalus patients.
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Affiliation(s)
- Amrita K Singh
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Garrett Allington
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Genetics, Yale University, New Haven, CT 06510, USA
| | - Stephen Viviano
- Department of Pediatrics, Yale University, New Haven, CT 06510, USA
| | | | - Emre Kiziltug
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Shaojie Ma
- Department of Genetics, Yale University, New Haven, CT 06510, USA
- Department of Neuroscience, Yale University, New Haven, CT 06510, USA
| | - Shujuan Zhao
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
- Departments of Genetics and Pediatrics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Kedous Y Mekbib
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - John P Shohfi
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Phan Q Duy
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Neuroscience, Yale University, New Haven, CT 06510, USA
| | - Tyrone DeSpenza
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Neuroscience, Yale University, New Haven, CT 06510, USA
| | - Charuta G Furey
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
| | - Benjamin C Reeves
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hannah Smith
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - André M M Sousa
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Adriana Cherskov
- Department of Neuroscience, Yale University, New Haven, CT 06510, USA
| | - August Allocco
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
| | | | - Shozeb Haider
- Department of Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, London, WC1N 1AX, UK
- UCL Centre for Advanced Research Computing, University College London, London, WC1H 9RN, UK
| | - Syed R A Rizvi
- Department of Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, London, WC1N 1AX, UK
| | - Seth L Alper
- Division of Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Division of Nephrology and Vascular Biology Research Center, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Nenad Sestan
- Department of Genetics, Yale University, New Haven, CT 06510, USA
- Department of Pediatrics, Yale University, New Haven, CT 06510, USA
| | - Hermela Shimelis
- Department of Radiology, Neuroradiology section, Kingston Health Sciences Centre, Queen's University Faculty of Health Sciences, Kingston, Ontario, Canada
| | - Lauren K Walsh
- Department of Radiology, Neuroradiology section, Kingston Health Sciences Centre, Queen's University Faculty of Health Sciences, Kingston, Ontario, Canada
| | - Richard P Lifton
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
| | - Andres Moreno-De-Luca
- Department of Radiology, Neuroradiology section, Kingston Health Sciences Centre, Queen's University Faculty of Health Sciences, Kingston, Ontario, Canada
- Department of Radiology, Diagnostic Medicine Institute, Geisinger, Danville, PA, 17822, USA
| | - Sheng Chih Jin
- Departments of Genetics and Pediatrics, Washington University School of Medicine, St Louis, MO 63110, USA
| | | | - Engin Deniz
- Department of Pediatrics, Yale University, New Haven, CT 06510, USA
| | - Kristopher T Kahle
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
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Wang D, Zhang Y, Zhang L, He D, Zhao L, Miao Z, Cheng W, Zhu C, Zhu L, Zhang W, Jin H, Zhu H, Pan H. IRF1 governs the expression of SMARCC1 via the GCN5-SETD2 axis and actively engages in the advancement of osteoarthritis. J Orthop Translat 2024; 45:211-225. [PMID: 38586591 PMCID: PMC10997872 DOI: 10.1016/j.jot.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/13/2023] [Accepted: 01/13/2024] [Indexed: 04/09/2024] Open
Abstract
Background Osteoarthritis (OA) is a degenerative joint disease characterized by the breakdown of joint cartilage and underlying bone. Macrophages are a type of white blood cell that plays a critical role in the immune system and can be found in various tissues, including joints. Research on the relationship between OA and macrophages is essential to understand the mechanisms underlying the development and progression of OA. Objective This study was performed to analyze the functions of the IRF1-GCN5-SETD2-SMARCC1 axis in osteoarthritis (OA) development. Methods A single-cell RNA sequencing (scRNA-seq) dataset, was subjected to a comprehensive analysis aiming to identify potential regulators implicated in the progression of osteoarthritis (OA). In order to investigate the role of IRF1 and SMARCC1, knockdown experiments were conducted in both OA-induced rats and interleukin (IL)-1β-stimulated chondrocytes, followed by the assessment of OA-like symptoms, secretion of inflammatory cytokines, and polarization of macrophages. Furthermore, the study delved into the identification of aberrant epigenetic modifications and functional enzymes responsible for the regulation of SMARCC1 by IRF1. To evaluate the clinical significance of the factors under scrutiny, a cohort comprising 13 patients diagnosed with OA and 7 fracture patients without OA was included in the analysis. Results IRF1 was found to exert regulatory control over the expression of SMARCC1, thus playing a significant role in the development of osteoarthritis (OA). The knockdown of either IRF1 or SMARCC1 disrupted the pro-inflammatory effects induced by IL-1β in chondrocytes, leading to a mitigation of OA-like symptoms, including inflammatory infiltration, cartilage degradation, and tissue injury, in rat models. Additionally, this intervention resulted in a reduction in the predominance of M1 macrophages both in vitro and in vivo. Significant epigenetic modifications, such as abundant H3K27ac and H3K4me3 marks, were observed near the SMARCC1 promoter and 10 kb upstream region. These modifications were attributed to the recruitment of GCN5 and SETD2, which are functional enzymes responsible for these modifications. Remarkably, the overexpression of either GCN5 or SETD2 restored SMARCC1 expression in rat cartilages or chondrocytes, consequently exacerbating the OA-like symptoms. Conclusion This research postulates that the transcriptional activity of SMARCC1 can be influenced by IRF1 through the recruitment of GCN5 and SETD2, consequently regulating the H3K27ac and H3K4me3 modifications in close proximity to the SMARCC1 promoter and 10 kb upstream region. These modifications, in turn, facilitate the M1 skewing of macrophages and contribute to the progression of osteoarthritis (OA). The Translational Potential of this Article The study demonstrated that the regulation of SMARCC1 by IRF1 plays a crucial role in the development of OA. Knocking down either IRF1 or SMARCC1 disrupted the pro-inflammatory effects induced by IL-1β in chondrocytes, leading to a mitigation of OA-like symptoms in rat models. These symptoms included inflammatory infiltration, cartilage degradation, and tissue injury. These findings suggest that targeting the IRF1-SMARCC1 regulatory axis, as well as the associated epigenetic modifications, could potentially be a novel approach in the development of OA therapies, offering new opportunities for disease management and improved patient outcomes.
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Affiliation(s)
- Dong Wang
- Department of Orthopaedics, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University (Hangzhou Hospital of Traditional Chinese Medicine), Hangzhou 310000, Zhejiang Province, PR China
- Department of Orthopaedics, Hangzhou Dingqiao Hospital, Huanding Road NO 1630, Hangzhou 310021, Zhejiang Province, PR China
- Institute of Orthopaedics and Traumatology, Hangzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, Tiyuchang Road NO 453, Hangzhou 310007, Zhejiang Province, PR China
- Hangzhou Lin'an District Traditional Chinese Medicine Hospital, Hangzhou, PR China
| | - Yujun Zhang
- Department of Orthopaedics, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University (Hangzhou Hospital of Traditional Chinese Medicine), Hangzhou 310000, Zhejiang Province, PR China
| | - Liangping Zhang
- Department of Orthopaedics, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University (Hangzhou Hospital of Traditional Chinese Medicine), Hangzhou 310000, Zhejiang Province, PR China
| | - Du He
- Department of Orthopaedics, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University (Hangzhou Hospital of Traditional Chinese Medicine), Hangzhou 310000, Zhejiang Province, PR China
| | - Lan Zhao
- Department of Orthopaedics, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University (Hangzhou Hospital of Traditional Chinese Medicine), Hangzhou 310000, Zhejiang Province, PR China
| | - Zhimin Miao
- Department of Orthopaedics, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University (Hangzhou Hospital of Traditional Chinese Medicine), Hangzhou 310000, Zhejiang Province, PR China
| | - Wei Cheng
- Department of Orthopaedics, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University (Hangzhou Hospital of Traditional Chinese Medicine), Hangzhou 310000, Zhejiang Province, PR China
- Department of Orthopaedics, Hangzhou Dingqiao Hospital, Huanding Road NO 1630, Hangzhou 310021, Zhejiang Province, PR China
| | - Chengyue Zhu
- Department of Orthopaedics, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University (Hangzhou Hospital of Traditional Chinese Medicine), Hangzhou 310000, Zhejiang Province, PR China
- Department of Orthopaedics, Hangzhou Dingqiao Hospital, Huanding Road NO 1630, Hangzhou 310021, Zhejiang Province, PR China
- Institute of Orthopaedics and Traumatology, Hangzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, Tiyuchang Road NO 453, Hangzhou 310007, Zhejiang Province, PR China
| | - Li Zhu
- Department of Orthopaedics, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University (Hangzhou Hospital of Traditional Chinese Medicine), Hangzhou 310000, Zhejiang Province, PR China
| | - Wei Zhang
- Department of Orthopaedics, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University (Hangzhou Hospital of Traditional Chinese Medicine), Hangzhou 310000, Zhejiang Province, PR China
- Department of Orthopaedics, Hangzhou Dingqiao Hospital, Huanding Road NO 1630, Hangzhou 310021, Zhejiang Province, PR China
| | - Hongting Jin
- Department of Orthopaedics, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University (Hangzhou Hospital of Traditional Chinese Medicine), Hangzhou 310000, Zhejiang Province, PR China
- Institute of Orthopaedics and Traumatology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, PR China
| | - Hang Zhu
- Department of Orthopaedics, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University (Hangzhou Hospital of Traditional Chinese Medicine), Hangzhou 310000, Zhejiang Province, PR China
| | - Hao Pan
- Department of Orthopaedics, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University (Hangzhou Hospital of Traditional Chinese Medicine), Hangzhou 310000, Zhejiang Province, PR China
- Department of Orthopaedics, Hangzhou Dingqiao Hospital, Huanding Road NO 1630, Hangzhou 310021, Zhejiang Province, PR China
- Institute of Orthopaedics and Traumatology, Hangzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, Tiyuchang Road NO 453, Hangzhou 310007, Zhejiang Province, PR China
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Zhou P, Fu Y, Tang Y, Jiang L, Wang W. Thoracic SMARCA4-deficient undifferentiated tumor: A clinicopathological and prognostic analysis of 35 cases and immunotherapy efficacy. Lung Cancer 2024; 189:107471. [PMID: 38306886 DOI: 10.1016/j.lungcan.2024.107471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 02/04/2024]
Abstract
BACKGROUND Thoracic SMARCA4-deficient undifferentiated tumor (SMARCA4-UT) is a recently recognized distinct clinicopathological entity according to the fifth edition of the 2021 World Health Organization Classification (WHO) for thoracic tumors. Thoracic SMARCA4-UTs are diagnostically challenging to diagnose, especially on small biopsies. METHODS We identified 35 thoracic SMARCA4-UTs from the Department of Pathology of West China Hospital, Sichuan University, between January 2017 and December 2022. In the present study, we summarized the clinicopathological features, prognostic significance and immunotherapy efficacy of thoracic SMARCA4-UTs. RESULTS All 35 patients were male, and 88.6 % were smokers. The left upper lobe (25.7 %) and mediastinum (20.0 %) were the most affected sites. 17.1 % of the patients received surgical treatment. 30.4 % of the patients were stage III, and 69.6 % were stage IV. Solid architecture (100 %), rhabdoid morphology (51.4 %) and necrosis (42.9 %) were the common histological features. Immunohistochemical staining revealed CD34 and synaptophysin positivity in most patients (76.9 % and 65.2 %, respectively). Patients had unfavorable outcomes. Patients who received immunotherapy had better OS and PFS than those who did not (p = 0.007 and p = 0.02, respectively). Five patients were evaluated for immunotherapy efficacy, and four of those patients were negative expression of PD-L1. Cases 1-4 presented TIL counts ranging from 20 to 1000/HPF. Case 5 presented TIL counts of 5-10/HPF. Mutations in SMARCA4 were confirmed in cases 4 and 5, and the TMB was 5.98 and 5.03 mutations/Mb, respectively. Case 1 achieved a CR, cases 2-4 achieved a PR, and case 5 had a PD. Five patients who received immunotherapy were all alive, with OS ranging from 10.7 to 33.6 months. CONCLUSIONS Thoracic SMARCA4-UTs exhibited an aggressive clinical course, presented solid architecture with or without necrosis and/or rhabdoid morphology, and frequently expressed CD34 and synaptophysin. Some thoracic SMARCA4-UTs appear to be associated with responsiveness to immunotherapy, suggesting the need for validation in larger series.
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Affiliation(s)
- Ping Zhou
- Department of Pathology, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, Sichuan 610041, China
| | - Yiyun Fu
- Department of Pathology, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, Sichuan 610041, China
| | - Yuan Tang
- Department of Pathology, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, Sichuan 610041, China
| | - Lili Jiang
- Department of Pathology, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, Sichuan 610041, China
| | - Weiya Wang
- Department of Pathology, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, Sichuan 610041, China.
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Izumiya Y, Algalil A, Espera JM, Miura H, Izumiya C, Inagaki T, Kumar A. Kaposi's sarcoma-associated herpesvirus terminal repeat regulates inducible lytic gene promoters. J Virol 2024; 98:e0138623. [PMID: 38240593 PMCID: PMC10878276 DOI: 10.1128/jvi.01386-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/02/2024] [Indexed: 02/21/2024] Open
Abstract
The Kaposi's sarcoma-associated herpesvirus (KSHV) genome consists of an approximately 140-kb unique coding region flanked by 30-40 copies of a 0.8-kb terminal repeat (TR) sequence. A gene enhancer recruits transcription-related enzymes by having arrays of transcription factor binding sites. Here, we show that KSHV TR possesses transcription regulatory function with latency-associated nuclear antigen (LANA). Cleavage under targets and release using nuclease demonstrated that TR fragments were occupied by LANA-interacting histone-modifying enzymes in naturally infected cells. The TR was enriched with histone H3K27 acetylation (H3K27Ac) and H3K4 tri-methylation (H3K4me3) modifications and also expressed nascent RNAs. The sites of H3K27Ac and H3K4me3 modifications were also conserved in the KSHV unique region among naturally infected primary effusion lymphoma cells. KSHV origin of lytic replication (Ori-Lyt) showed similar protein and histone modification occupancies with that of TR. In the Ori-Lyt region, the LANA and LANA-interacting proteins colocalized with an H3K27Ac-modified nucleosome along with paused RNA polymerase II. The KSHV transactivator KSHV replication and transcription activator (K-Rta) recruitment sites franked the LANA-bound nucleosome, and reactivation evicted the LANA-bound nucleosome. Including TR fragments in reporter plasmid enhanced inducible viral gene promoter activities independent of the orientations. In the presence of TR in reporter plasmids, K-Rta transactivation was drastically increased, while LANA acquired the promoter repression function. KSHV TR, therefore, functions as an enhancer for KSHV inducible genes. However, in contrast to cellular enhancers bound by multiple transcription factors, perhaps the KSHV enhancer is predominantly regulated by the LANA nuclear body.IMPORTANCEEnhancers are a crucial regulator of differential gene expression programs. Enhancers are the cis-regulatory sequences determining target genes' spatiotemporal and quantitative expression. Here, we show that Kaposi's sarcoma-associated herpesvirus (KSHV) terminal repeats fulfill the enhancer definition for KSHV inducible gene promoters. The KSHV enhancer is occupied by latency-associated nuclear antigen (LANA) and its interacting proteins, such as CHD4. Neighboring terminal repeat (TR) fragments to lytic gene promoters drastically enhanced KSHV replication and transcription activator and LANA transcription regulatory functions. This study, thus, proposes a new latency-lytic switch model in which TR accessibility to the KSHV gene promoters regulates viral inducible gene expression.
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Affiliation(s)
- Yoshihiro Izumiya
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, California, USA
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Sacramento, California, USA
| | - Adhraa Algalil
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, California, USA
- Midwestern University College of Dental Medicine, Glendale, Arizona, USA
| | - Jonna M. Espera
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, California, USA
| | - Hiroki Miura
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, California, USA
| | - Chie Izumiya
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, California, USA
| | - Tomoki Inagaki
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, California, USA
| | - Ashish Kumar
- Department of Dermatology, School of Medicine, University of California Davis, Sacramento, California, USA
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Zhou P, Fu Y, Tang Y, Jiang L, Wang W. Thoracic SMARCA4-deficient tumors: a clinicopathological analysis of 52 cases with SMARCA4-deficient non-small cell lung cancer and 20 cases with thoracic SMARCA4-deficient undifferentiated tumor. PeerJ 2024; 12:e16923. [PMID: 38374950 PMCID: PMC10875988 DOI: 10.7717/peerj.16923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 01/19/2024] [Indexed: 02/21/2024] Open
Abstract
Background Thoracic SMARCA4-deficient undifferentiated tumor (SMARCA4-UT) is a distinct clinicopathological entity with an aggressive clinical course. Additionally, SMARCA4/BRG1 deficiency can be observed in a few patients with non-small cell lung cancer (NSCLC). We aimed to compare the clinicopathological, immunohistochemical and prognostic features of SMARCA4-deficient NSCLC (SMARCA4-dNSCLC) with those of thoracic SMARCA4-UT. Methods Patients with BRG1-deficient tumors in the lung or thorax were enrolled in the study from the Department of Pathology of West China Hospital, Sichuan University, from January 2014 to June 2022. We retrospectively collected the clinicopathological and immunohistochemical features and outcomes of these patients. Results Seventy-two patients had tumors in the lung or thorax with BRG1-deficient expression, including 52 patients with SMARCA4-dNSCLC and 20 patients with thoracic SMARCA4-UT. Among the patients with SMARCA4-dNSCLC, 98.1% were male, 85.7% were smokers, and 79.5% (35/44) had tumor-node-metas-tasis (TNM) III-IV tumors. Among the patients with thoracic SMARCA4-UT, all were males who smoked, and 93.75% (15/16) had TNM III-IV tumors. Pure solid architecture and necrosis were the predominant pathological features. Rhabdoid morphology was observed in some SMARCA4-dNSCLCs (10/52, 19.2%) and thoracic SMARCA4-UTs (11/20, 55%). In most patients with thoracic SMARCA4-UT, the tumors exhibited scattered weak expression or negative expression of epithelial markers, and positive expression of CD34 and Syn. Overall survival (OS) and progression-free survival (PFS) were not significantly different between patients with SMARCA4-dNSCLC and patients with thoracic SMARCA4-UT (p = 0.63 and p = 0.20, respectively). Conclusions Thoracic SMARCA4-DTs include SMARCA4-dNSCLC and thoracic SMARCA4-UT. Both have overlapping clinicopathological features and poor prognosis. We hypothesize that thoracic SMARCA4-UT may be the undifferentiated or dedifferentiated form of SMARCA4-dNSCLC. However, further studies with larger cohorts and longer follow-up periods are needed.
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Affiliation(s)
- Ping Zhou
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yiyun Fu
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yuan Tang
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lili Jiang
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Weiya Wang
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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12
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Wang Y, Sun J, Sun B, Zhang C, Tian Z, Wang L, Li J. The genetic and immune features of salivary gland secretory carcinoma with high-grade transformation. Oral Dis 2024. [PMID: 38263601 DOI: 10.1111/odi.14876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/26/2023] [Accepted: 01/11/2024] [Indexed: 01/25/2024]
Abstract
OBJECTIVES To compare the clinicopathological, molecular, and immune features of conventional and high-grade transformation (HGT) secretory carcinoma (SC) in salivary glands. MATERIALS AND METHODS The clinicopathological data of 88 cases including 74 conventional SCs and 14 SCs with HGT were reviewed. Targeted next-generation sequencing was performed in 11 SCs with HGT and 7 conventional SCs. The level of PD-L1 and CD8+ TILs was determined by immunohistochemistry. RESULTS Compared with the conventional group, the rates of nodal metastasis, local recurrence, distant metastasis and mortality were significantly higher in the HGT cohort. Mutations of ARID1A/B, KMT2A, HOXD13, NRG1 and ETV6 genes were identified in HGT SCs. A recurrent E307G mutation in GATA6 gene was also observed in two cases. Two deceased HGT patients with distant metastasis harboured NOTCH3 mutations. ETV6-RET translocation was prone to occur in the HGT SCs. Additionally, PD-L1 expression was low, and CD8+ TILs were sparse in most HGT cases. CONCLUSION Our findings reveal novel gene alterations involved in the progression of HGT in SCs. Most HGT SCs patients cannot benefit from PD-L1 blocking and may be approached with a distinct treatment strategy including the lymph node dissection and application of molecular target drugs in precision oncology.
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Affiliation(s)
- Yu Wang
- Shanghai Key Laboratory of Stomatology, Department of Oral Pathology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingjing Sun
- Shanghai Key Laboratory of Stomatology, Department of Oral Pathology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bao Sun
- Shanghai Key Laboratory of Stomatology, Department of Oral Pathology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chunye Zhang
- Shanghai Key Laboratory of Stomatology, Department of Oral Pathology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhen Tian
- Shanghai Key Laboratory of Stomatology, Department of Oral Pathology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lizhen Wang
- Shanghai Key Laboratory of Stomatology, Department of Oral Pathology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiang Li
- Shanghai Key Laboratory of Stomatology, Department of Oral Pathology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Sun L, Fu Q, Chen L, Di M, Cao J. SMARCA4‑deficient non‑small cell lung cancer with an EGFR mutation: A case report. Oncol Lett 2023; 26:513. [PMID: 37927421 PMCID: PMC10623088 DOI: 10.3892/ol.2023.14100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/20/2023] [Indexed: 11/07/2023] Open
Abstract
SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily a, member 4 (SMARCA4)-deficient non-small cell lung cancer (dNSCLC) is a rare malignant tumor that originates in the lungs. It occurs more frequently in male smokers, and the epidermal growth factor receptor (EGFR) gene is often mutation-free. In the present study, the case of a 60-year-old, non-smoking female patient diagnosed with SMARCA4-dNSCLC is reported. Biopsy of the tumor showed solid flaky, nest-like infiltrating growth. Immunohistochemistry revealed the following: SMARCA4/BRG1(-), SMARCB1/INI-1(+), cytokeratin7 (+), cytokeratin 5.2 (+), CK5/6(+) and calretinin(+). The Ki-67 positivity index was 75%, and the thyroid transcription factor-1, NapsinA, p40, nuclear protein in testis, CD34, Sal-like protein 4, SRY-box transcription factor 2 and synaptophysin were negative. Molecular analysis showed mutations in both EGFR and TP53. The pathological diagnosis was SMARCA4-dNSCLC with an EGFR gene mutation. The present case report could be used for broadening the pathological diagnosis of SMARCA4-dNSCLC and for selecting appropriate treatment approaches.
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Affiliation(s)
- Lijun Sun
- Department of Pathology, Xiaoshan Affiliated Hospital of Wenzhou Medical University, Hangzhou, Zhejiang 311200, P.R. China
| | - Qiong Fu
- Department of Pathology, Xiaoshan Affiliated Hospital of Wenzhou Medical University, Hangzhou, Zhejiang 311200, P.R. China
| | - Lijiang Chen
- Department of Pathology, Xiaoshan Affiliated Hospital of Wenzhou Medical University, Hangzhou, Zhejiang 311200, P.R. China
| | - Meijuan Di
- Department of Pathology, Xiaoshan Affiliated Hospital of Wenzhou Medical University, Hangzhou, Zhejiang 311200, P.R. China
| | - Jianhua Cao
- Department of Respiratory Medicine, Xiaoshan Affiliated Hospital of Wenzhou Medical University, Hangzhou, Zhejiang 311200, P.R. China
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14
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Yu Y, Wang S, Wang Z, Gao R, Lee J. Arabidopsis thaliana: a powerful model organism to explore histone modifications and their upstream regulations. Epigenetics 2023; 18:2211362. [PMID: 37196184 DOI: 10.1080/15592294.2023.2211362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 04/07/2023] [Accepted: 04/28/2023] [Indexed: 05/19/2023] Open
Abstract
Histones are subjected to extensive covalent modifications that affect inter-nucleosomal interactions as well as alter chromatin structure and DNA accessibility. Through switching the corresponding histone modifications, the level of transcription and diverse downstream biological processes can be regulated. Although animal systems are widely used in studying histone modifications, the signalling processes that occur outside the nucleus prior to histone modifications have not been well understood due to the limitations including non viable mutants, partial lethality, and infertility of survivors. Here, we review the benefits of using Arabidopsis thaliana as the model organism to study histone modifications and their upstream regulations. Similarities among histones and key histone modifiers such as the Polycomb group (PcG) and Trithorax group (TrxG) in Drosophila, Human, and Arabidopsis are examined. Furthermore, prolonged cold-induced vernalization system has been well-studied and revealed the relationship between the controllable environment input (duration of vernalization), its chromatin modifications of FLOWERING LOCUS C (FLC), following gene expression, and the corresponding phenotypes. Such evidence suggests that research on Arabidopsis can bring insights into incomplete signalling pathways outside of the histone box, which can be achieved through viable reverse genetic screenings based on the phenotypes instead of direct monitoring of histone modifications among individual mutants. The potential upstream regulators in Arabidopsis can provide cues or directions for animal research based on the similarities between them.
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Affiliation(s)
- Yang Yu
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Sihan Wang
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Ziqin Wang
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Renwei Gao
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Joohyun Lee
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
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15
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Abstract
Keratinocyte senescence contributes to skin ageing and epidermal dysfunction. According to the existing knowledge, the transcription factor ΔNp63α plays pivotal roles in differentiation and proliferation of keratinocytes. It is traditionally accepted that ΔNp63α exerts its functions via binding to promoter regions to activate or repress gene transcription. However, accumulating evidence demonstrates that ΔNp63α can bind to elements away from promoter regions of its target genes, mediating epigenetic regulation. On the other hand, several epigenetic alterations, including DNA methylation, histone modification and variation, chromatin remodelling, as well as enhancer-promoter looping, are found to be related to cell senescence. To systematically elucidate how ΔNp63α affects keratinocyte senescence via epigenetic regulation, we comprehensively compiled the literatures on the roles of ΔNp63α in keratinocyte senescence, epigenetics in cellular senescence, and the relation between ΔNp63α-mediated epigenetic regulation and keratinocyte senescence. Based on the published data, we conclude that ΔNp63α mediates epigenetic regulation via multiple mechanisms: recruiting epigenetic enzymes to modify DNA or histones, coordinating chromatin remodelling complexes (CRCs) or regulating their expression, and mediating enhancer-promoter looping. Consequently, the expression of genes related to cell cycle is modulated, and proliferation of keratinocytes and renewal of stem cells are maintained, by ΔNp63α. During skin inflammaging, the decline of ΔNp63α may lead to epigenetic dysregulation, resultantly deteriorating keratinocyte senescence.
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Affiliation(s)
- Linghan Kuang
- Department of Laboratory Medicine, West China Second University Hospital, Sichuan University, Chengdu 610041, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu 610041, China
| | - Chenghua Li
- Center of Growth, Metabolism and Aging, Key Laboratory of Biological Resources and Ecological Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
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16
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Liu NQ, Paassen I, Custers L, Zeller P, Teunissen H, Ayyildiz D, He J, Buhl JL, Hoving EW, van Oudenaarden A, de Wit E, Drost J. SMARCB1 loss activates patient-specific distal oncogenic enhancers in malignant rhabdoid tumors. Nat Commun 2023; 14:7762. [PMID: 38040699 PMCID: PMC10692191 DOI: 10.1038/s41467-023-43498-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 11/10/2023] [Indexed: 12/03/2023] Open
Abstract
Malignant rhabdoid tumor (MRT) is a highly malignant and often lethal childhood cancer. MRTs are genetically defined by bi-allelic inactivating mutations in SMARCB1, a member of the BRG1/BRM-associated factors (BAF) chromatin remodeling complex. Mutations in BAF complex members are common in human cancer, yet their contribution to tumorigenesis remains in many cases poorly understood. Here, we study derailed regulatory landscapes as a consequence of SMARCB1 loss in the context of MRT. Our multi-omics approach on patient-derived MRT organoids reveals a dramatic reshaping of the regulatory landscape upon SMARCB1 reconstitution. Chromosome conformation capture experiments subsequently reveal patient-specific looping of distal enhancer regions with the promoter of the MYC oncogene. This intertumoral heterogeneity in MYC enhancer utilization is also present in patient MRT tissues as shown by combined single-cell RNA-seq and ATAC-seq. We show that loss of SMARCB1 activates patient-specific epigenetic reprogramming underlying MRT tumorigenesis.
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Affiliation(s)
- Ning Qing Liu
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Hematology, Erasmus Medical Center (MC) Cancer Institute, Rotterdam, the Netherlands
| | - Irene Paassen
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Lars Custers
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Peter Zeller
- Oncode Institute, Utrecht, the Netherlands
- Hubrecht Institute-KNAW, Utrecht, the Netherlands
- University Medical Center Utrecht, Utrecht, the Netherlands
| | - Hans Teunissen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Dilara Ayyildiz
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Jiayou He
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Juliane Laura Buhl
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | | | - Alexander van Oudenaarden
- Oncode Institute, Utrecht, the Netherlands
- Hubrecht Institute-KNAW, Utrecht, the Netherlands
- University Medical Center Utrecht, Utrecht, the Netherlands
| | - Elzo de Wit
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Jarno Drost
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
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17
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Wei CH, Wang E, Sadimin E, Rodriguez-Rodriguez L, Agulnik M, Yoon J, LoBello J, Szelinger S, Anderson C. Underreporting of SMARCB1 alteration by clinical sequencing: Integrative patho-genomic analysis captured SMARCB1/INI-1 deficiency in a vulvar yolk sac tumor. Gynecol Oncol Rep 2023; 50:101294. [PMID: 37876879 PMCID: PMC10590733 DOI: 10.1016/j.gore.2023.101294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/07/2023] [Accepted: 10/14/2023] [Indexed: 10/26/2023] Open
Abstract
•SMARCB1/INI1-deficient gynecologic tumors are rare and clinically aggressive. A subset shows primitive yolk sac tumor features.•Due to technical limitation of next generation sequencing (NGS) and interlaboratory variability in sequencing methodologies and analytical pipelines, SMARCB1 deficiency caused by somatic copy number variations (SCNV) may be underreported by NGS.•To improve identification of SMARCB1/INI1-deficient neoplasm, we propose the following strategy: First, careful pathology slide review and detection of rhabdoid cells should raise the possibility of SMARCB1/INI1 deficiency. Second, INI1 IHC is a useful complementary test to exclude clinical suspicion of SMARCB1 deficiency in the context of negative molecular reporting. Third, knowledge of potential underreporting of SMARCB1 mutation would avoid underdiagnosis.
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Affiliation(s)
- Christina H. Wei
- Department of Pathology, City of Hope Medical Center, Duarte, CA, USA
| | - Edward Wang
- Department of Medical Oncology & Therapeutics Research, City of Hope Medical Center, Duarte, CA, USA
| | - Evita Sadimin
- Department of Pathology, City of Hope Medical Center, Duarte, CA, USA
| | | | - Mark Agulnik
- Department of Medical Oncology & Therapeutics Research, City of Hope Medical Center, Duarte, CA, USA
| | - Janet Yoon
- Department of Pediatrics, City of Hope Medical Center, Duarte, CA, USA
| | | | | | - Clarke Anderson
- Department of Pediatrics, City of Hope Medical Center, Duarte, CA, USA
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18
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Pofi R, Caratti G, Ray DW, Tomlinson JW. Treating the Side Effects of Exogenous Glucocorticoids; Can We Separate the Good From the Bad? Endocr Rev 2023; 44:975-1011. [PMID: 37253115 PMCID: PMC10638606 DOI: 10.1210/endrev/bnad016] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/25/2023] [Accepted: 05/26/2023] [Indexed: 06/01/2023]
Abstract
It is estimated that 2% to 3% of the population are currently prescribed systemic or topical glucocorticoid treatment. The potent anti-inflammatory action of glucocorticoids to deliver therapeutic benefit is not in doubt. However, the side effects associated with their use, including central weight gain, hypertension, insulin resistance, type 2 diabetes (T2D), and osteoporosis, often collectively termed iatrogenic Cushing's syndrome, are associated with a significant health and economic burden. The precise cellular mechanisms underpinning the differential action of glucocorticoids to drive the desirable and undesirable effects are still not completely understood. Faced with the unmet clinical need to limit glucocorticoid-induced adverse effects alongside ensuring the preservation of anti-inflammatory actions, several strategies have been pursued. The coprescription of existing licensed drugs to treat incident adverse effects can be effective, but data examining the prevention of adverse effects are limited. Novel selective glucocorticoid receptor agonists and selective glucocorticoid receptor modulators have been designed that aim to specifically and selectively activate anti-inflammatory responses based upon their interaction with the glucocorticoid receptor. Several of these compounds are currently in clinical trials to evaluate their efficacy. More recently, strategies exploiting tissue-specific glucocorticoid metabolism through the isoforms of 11β-hydroxysteroid dehydrogenase has shown early potential, although data from clinical trials are limited. The aim of any treatment is to maximize benefit while minimizing risk, and within this review we define the adverse effect profile associated with glucocorticoid use and evaluate current and developing strategies that aim to limit side effects but preserve desirable therapeutic efficacy.
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Affiliation(s)
- Riccardo Pofi
- Oxford Centre for Diabetes, Endocrinology and Metabolism, NIHR Oxford Biomedical Research Centre, University of Oxford, Churchill Hospital, Oxford OX3 7LE, UK
| | - Giorgio Caratti
- Oxford Centre for Diabetes, Endocrinology and Metabolism, NIHR Oxford Biomedical Research Centre, University of Oxford, Churchill Hospital, Oxford OX3 7LE, UK
| | - David W Ray
- Oxford Centre for Diabetes, Endocrinology and Metabolism, NIHR Oxford Biomedical Research Centre, University of Oxford, Churchill Hospital, Oxford OX3 7LE, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
- Oxford Kavli Centre for Nanoscience Discovery, University of Oxford, Oxford OX37LE, UK
| | - Jeremy W Tomlinson
- Oxford Centre for Diabetes, Endocrinology and Metabolism, NIHR Oxford Biomedical Research Centre, University of Oxford, Churchill Hospital, Oxford OX3 7LE, UK
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19
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Cohen Y, Adar S. Novel insights into bulky DNA damage formation and nucleotide excision repair from high-resolution genomics. DNA Repair (Amst) 2023; 130:103549. [PMID: 37566959 DOI: 10.1016/j.dnarep.2023.103549] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023]
Abstract
DNA damages compromise cell function and fate. Cells of all organisms activate a global DNA damage response that includes a signaling stress response, activation of checkpoints, and recruitment of repair enzymes. Especially deleterious are bulky, helix-distorting damages that block transcription and replication. Due to their miscoding nature, these damages lead to mutations and cancer. In human cells, bulky DNA damages are repaired by nucleotide excision repair (NER). To date, the basic mechanism of NER in naked DNA is well defined. Still, there is a fundamental gap in our understanding of how repair is orchestrated despite the packaging of DNA in chromatin, and how it is coordinated with active transcription and replication. The last decade has brought forth huge advances in our ability to detect and assay bulky DNA damages and their repair at single nucleotide resolution across the human genome. Here we review recent findings on the effect of chromatin and DNA-binding proteins on the formation of bulky DNA damages, and novel insights on NER, provided by the recent application of genomic methods.
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Affiliation(s)
- Yuval Cohen
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Sheera Adar
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel.
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20
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Xin Q, Yu G, Feng I, Dean J. Chromatin remodeling of prostaglandin signaling in smooth muscle enables mouse embryo passage through the female reproductive tract. Dev Cell 2023; 58:1716-1732.e8. [PMID: 37714160 DOI: 10.1016/j.devcel.2023.08.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/10/2023] [Accepted: 08/22/2023] [Indexed: 09/17/2023]
Abstract
Early mammalian development occurs during embryo transit of the female reproductive tract. Transport is orchestrated by secreted oviduct fluid, unidirectional beating of epithelial cilia, and smooth muscle contractions. Using gene-edited mice, we document that conditional disruption of a component of the SWI/SNF chromatin remodeling complex in smooth muscle cells prevents transport through the oviduct without perturbing embryogenesis. Analysis with RNA sequencing (RNA-seq), transposase-accessible chromatin with sequencing (ATAC-seq), chromatin immunocleavage sequencing (ChIC-seq), and pharmacologic rescue experiments implicated prostaglandin signaling pathways. In comparison with controls, gene-edited mice had compromised chromatin accessibility at enhancer/promoters of Ptgs2, Pla2g16, Pla2r1, and Ptger3 (EP3) as well as decreased enhancer-promoter interactive looping critical for Ptgs2 (aka Cox-2) expression in a SWI/SNF complex-dependent manner. Treatment of wild-type mice with prostaglandin inhibitors phenocopied the genetically induced defect.
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Affiliation(s)
- Qiliang Xin
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Guoyun Yu
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Iris Feng
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jurrien Dean
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA.
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21
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de Traux de Wardin H, Dermawan JK, Merlin MS, Wexler LH, Orbach D, Vanoli F, Schleiermacher G, Geoerger B, Ballet S, Guillemot D, Frouin E, Cyrille S, Delattre O, Pierron G, Antonescu CR. Sequential genomic analysis using a multisample/multiplatform approach to better define rhabdomyosarcoma progression and relapse. NPJ Precis Oncol 2023; 7:96. [PMID: 37730754 PMCID: PMC10511463 DOI: 10.1038/s41698-023-00445-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 08/30/2023] [Indexed: 09/22/2023] Open
Abstract
The genomic spectrum of rhabdomyosarcoma (RMS) progression from primary to relapse is not fully understood. In this pilot study, we explore the sensitivity of various targeted and whole-genome NGS platforms in order to assess the best genomic approach of using liquid biopsy in future prospective clinical trials. Moreover, we investigate 35 paired primary/relapsed RMS from two contributing institutions, 18 fusion-positive (FP-RMS) and 17 fusion-negative RMS (FN-RMS) by either targeted DNA or whole exome sequencing (WES). In 10 cases, circulating tumor DNA (ctDNA) from multiple timepoints through clinical care and progression was analyzed for feasibility of liquid biopsy in monitoring treatment response/relapse. ctDNA alterations were evaluated using a targeted 36-gene custom RMS panel at high coverage for single-nucleotide variation and fusion detection, and a shallow whole-genome sequencing for copy number variation. FP-RMS have a stable genome with relapse, with common secondary alterations CDKN2A/B, MYCN, and CDK4 present at diagnosis and impacting survival. FP-RMS lacking major secondary events at baseline acquire recurrent MYCN and AKT1 alterations. FN-RMS acquire a higher number of new alterations, most commonly SMARCA2 missense mutations. ctDNA analyses detect pathognomonic variants in all RMS patients within our collection at diagnosis, regardless of type of alterations, and confirmed at relapse in 86% of FP-RMS and 100% FN-RMS. Moreover, a higher number of fusion reads is detected with increased disease burden and at relapse in patients following a fatal outcome. These results underscore patterns of tumor progression and provide rationale for using liquid biopsy to monitor treatment response.
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Affiliation(s)
- Henry de Traux de Wardin
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Unit of Somatic Genetics, Institut Curie, Paris, France
| | - Josephine K Dermawan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marie-Sophie Merlin
- University of Lorraine, Centre Hospitalier Régional Universitaire (CHRU), Childrens' Hospital, Department of Pediatric Oncology, Vandoeuvre-lès-Nancy, France
| | - Leonard H Wexler
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel Orbach
- SIREDO Oncology Center (Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer), PSL University, Institut Curie, Paris, France
| | - Fabio Vanoli
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gudrun Schleiermacher
- SIREDO Oncology Center (Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer), PSL University, Institut Curie, Paris, France
- U830 INSERM, Paris, France
| | - Birgit Geoerger
- Gustave Roussy Cancer Center, Department of Pediatric and Adolescent Oncology, Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Université Paris-Saclay, Villejuif, 94805, France
| | - Stelly Ballet
- Unit of Somatic Genetics, Institut Curie, Paris, France
| | | | | | - Stacy Cyrille
- Department of Biometrics, Institut Curie, Paris, France
| | - Olivier Delattre
- SIREDO Oncology Center (Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer), PSL University, Institut Curie, Paris, France
- U830 INSERM, Paris, France
| | - Gaelle Pierron
- Unit of Somatic Genetics, Institut Curie, Paris, France.
| | - Cristina R Antonescu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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22
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Xu C, Huang KK, Law JH, Chua JS, Sheng T, Flores NM, Pizzi MP, Okabe A, Tan ALK, Zhu F, Kumar V, Lu X, Benitez AM, Lian BSX, Ma H, Ho SWT, Ramnarayanan K, Anene-Nzelu CG, Razavi-Mohseni M, Abdul Ghani SAB, Tay ST, Ong X, Lee MH, Guo YA, Ashktorab H, Smoot D, Li S, Skanderup AJ, Beer MA, Foo RSY, Wong JSH, Sanghvi K, Yong WP, Sundar R, Kaneda A, Prabhakar S, Mazur PK, Ajani JA, Yeoh KG, So JBY, Tan P. Comprehensive molecular phenotyping of ARID1A-deficient gastric cancer reveals pervasive epigenomic reprogramming and therapeutic opportunities. Gut 2023; 72:1651-1663. [PMID: 36918265 DOI: 10.1136/gutjnl-2022-328332] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 02/27/2023] [Indexed: 03/16/2023]
Abstract
OBJECTIVE Gastric cancer (GC) is a leading cause of cancer mortality, with ARID1A being the second most frequently mutated driver gene in GC. We sought to decipher ARID1A-specific GC regulatory networks and examine therapeutic vulnerabilities arising from ARID1A loss. DESIGN Genomic profiling of GC patients including a Singapore cohort (>200 patients) was performed to derive mutational signatures of ARID1A inactivation across molecular subtypes. Single-cell transcriptomic profiles of ARID1A-mutated GCs were analysed to examine tumour microenvironmental changes arising from ARID1A loss. Genome-wide ARID1A binding and chromatin profiles (H3K27ac, H3K4me3, H3K4me1, ATAC-seq) were generated to identify gastric-specific epigenetic landscapes regulated by ARID1A. Distinct cancer hallmarks of ARID1A-mutated GCs were converged at the genomic, single-cell and epigenomic level, and targeted by pharmacological inhibition. RESULTS We observed prevalent ARID1A inactivation across GC molecular subtypes, with distinct mutational signatures and linked to a NFKB-driven proinflammatory tumour microenvironment. ARID1A-depletion caused loss of H3K27ac activation signals at ARID1A-occupied distal enhancers, but unexpectedly gain of H3K27ac at ARID1A-occupied promoters in genes such as NFKB1 and NFKB2. Promoter activation in ARID1A-mutated GCs was associated with enhanced gene expression, increased BRD4 binding, and reduced HDAC1 and CTCF occupancy. Combined targeting of promoter activation and tumour inflammation via bromodomain and NFKB inhibitors confirmed therapeutic synergy specific to ARID1A-genomic status. CONCLUSION Our results suggest a therapeutic strategy for ARID1A-mutated GCs targeting both tumour-intrinsic (BRD4-assocatiated promoter activation) and extrinsic (NFKB immunomodulation) cancer phenotypes.
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Affiliation(s)
- Chang Xu
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Kie Kyon Huang
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Jia Hao Law
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Joy Shijia Chua
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Taotao Sheng
- Epigenetic and Epigenomic Regulation, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Natasha M Flores
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Melissa Pool Pizzi
- Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Atsushi Okabe
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Angie Lay Keng Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Feng Zhu
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Vikrant Kumar
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Xiaoyin Lu
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ana Morales Benitez
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Haoran Ma
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Shamaine Wei Ting Ho
- Epigenetic and Epigenomic Regulation, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore
| | | | - Chukwuemeka George Anene-Nzelu
- Cardiovascular Research Institute, National University Health System, Singapore
- Human Genetics, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore
- Montreal Heart Institute, Quebec, Québec, Canada
- Department of Medicine, University of Montreal, Quebec, Québec, Canada
| | - Milad Razavi-Mohseni
- Department of Biomedical Engineering and McKusick-Nathans Department of Genetic Medicine, Baltimore, Maryland, USA
| | | | - Su Ting Tay
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Xuewen Ong
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Ming Hui Lee
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Yu Amanda Guo
- Computational and Systems Biology, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore
| | | | - Duane Smoot
- Department of Internal Medicine, Meharry Medical College, Nashville, Tennessee, USA
| | - Shang Li
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Anders Jacobsen Skanderup
- Computational and Systems Biology, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Michael A Beer
- Department of Biomedical Engineering and McKusick-Nathans Department of Genetic Medicine, Baltimore, Maryland, USA
| | - Roger Sik Yin Foo
- Cardiovascular Research Institute, National University Health System, Singapore
- Human Genetics, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore
| | | | - Kaushal Sanghvi
- Department of General Surgery, Tan Tock Seng Hospital, Singapore
| | - Wei Peng Yong
- Department of Haematology-Oncology, National University Health System, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Raghav Sundar
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Department of Haematology-Oncology, National University Cancer Institute, Singapore
- The N.1 Institute for Health, National University of Singapore, Singapore
- Singapore Gastric Cancer Consortium, Singapore
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Shyam Prabhakar
- Computational and Systems Biology, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Pawel Karol Mazur
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jaffer A Ajani
- Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Khay Guan Yeoh
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Singapore Gastric Cancer Consortium, Singapore
- Department of Gastroenterology and Hepatology, National University Health System, Singapore
| | - Jimmy Bok-Yan So
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Singapore Gastric Cancer Consortium, Singapore
- Division of Surgical Oncology, National University Cancer Institute, Singapore
| | - Patrick Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
- Epigenetic and Epigenomic Regulation, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Singapore Gastric Cancer Consortium, Singapore
- SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore
- Cellular and Molecular Research, National Cancer Centre, Singapore
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Yin Z, You B, Bai Y, Zhao Y, Liao S, Sun Y, Wu Y. Natural Compounds Derived from Plants on Prevention and Treatment of Renal Cell Carcinoma: A Literature Review. Adv Biol (Weinh) 2023:e2300025. [PMID: 37607316 DOI: 10.1002/adbi.202300025] [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: 01/26/2023] [Revised: 08/04/2023] [Indexed: 08/24/2023]
Abstract
Renal cell carcinoma (RCC) accounts for roughly 85% of all malignant kidney cancer. Therapeutic options for RCC have expanded rapidly over the past decade. Targeted therapy and immunotherapy have ushered in a new era of the treatment of RCC, which has facilitated the outcomes of RCC. However, the related adverse effects and drug resistance remain an urgent issue. Natural compounds are optional strategies to reduce mobility. Natural compounds are favored by clinicians and researchers due to their good tolerance and low economic burden. Many studies have explored the anti-RCC activity of natural products and revealed relevant mechanisms. In this article, the chemoprevention and therapeutic potential of natural compounds is reviewed and the mechanisms regarding natural compounds are explored.
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Affiliation(s)
- Zhenjie Yin
- Department of Urology, Affiliated Sanming First Hospital, Fujian Medical University, Sanming, Fujian, 365001, P. R. China
| | - Bingyong You
- Department of Urology, Affiliated Sanming First Hospital, Fujian Medical University, Sanming, Fujian, 365001, P. R. China
| | - Yuanyuan Bai
- Department of Urology, Affiliated Sanming First Hospital, Fujian Medical University, Sanming, Fujian, 365001, P. R. China
| | - Yu Zhao
- Department of Medical and Radiation Oncology, Affiliated Sanming First Hospital, Fujian Medical University, Sanming, Fujian, 365001, P. R. China
| | - Shangfan Liao
- Department of Urology, Affiliated Sanming First Hospital, Fujian Medical University, Sanming, Fujian, 365001, P. R. China
| | - Yingming Sun
- Department of Medical and Radiation Oncology, Affiliated Sanming First Hospital, Fujian Medical University, Sanming, Fujian, 365001, P. R. China
| | - Yongyang Wu
- Department of Urology, Affiliated Sanming First Hospital, Fujian Medical University, Sanming, Fujian, 365001, P. R. China
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24
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Meng X, Ma J, Meng N, Yun T, Niu B. Case Report: SMARCA4 (BRG1)-deficient undifferentiated carcinoma of gallbladder with genetic analysis. Front Oncol 2023; 13:1086266. [PMID: 37456262 PMCID: PMC10348478 DOI: 10.3389/fonc.2023.1086266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/26/2023] [Indexed: 07/18/2023] Open
Abstract
SMARCA4 (BRG1)-deficient undifferentiated carcinoma is a rare and highly aggressive malignancy. It has been reported to occur in a multiple range of organs. However, to the best of our knowledge, SMARCA4 (BRG1)-deficient undifferentiated carcinoma of gallbladder has not yet been reported. Here, we describe a case of SMARCA4 (BRG1)-deficient undifferentiated carcinoma of gallbladder. Through comprehensive genetic analysis, we hypothesized that in addition to SMARCA4 (BRG1) deficiency, other genetic changes might also be involved in the tumorigenesis of undifferentiated gallbladder cancer in this patient, particularly somatic mutations in the CTNNB1, KRAS, PIK3CA, TP53, CREBBP, and FANCI genes. To the best of our knowledge, this is the first report of SMARCA4 (BRG1)-deficient undifferentiated carcinoma of gallbladder with genetic analysis.
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Affiliation(s)
- Xiangpeng Meng
- Pancreatic Endocrinology Ward, Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jia Ma
- Department of Gastroenterology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Nan Meng
- Beijing ChosenMed Clinical Laboratory Co. Ltd., Beijing, China
| | - Tianyu Yun
- Beijing ChosenMed Clinical Laboratory Co. Ltd., Beijing, China
| | - Beifang Niu
- Beijing ChosenMed Clinical Laboratory Co. Ltd., Beijing, China
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
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25
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Wang L, Tang J. SWI/SNF complexes and cancers. Gene 2023; 870:147420. [PMID: 37031881 DOI: 10.1016/j.gene.2023.147420] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 04/11/2023]
Abstract
Epigenetics refers to the study of genetic changes that can affect gene expression without altering the underlying DNA sequence, including DNA methylation, histone modification, chromatin remodelling, X chromosome inactivation and non-coding RNA regulation. Of these, DNA methylation, histone modification and chromatin remodelling constitute the three classical modes of epigenetic regulation. These three mechanisms alter gene transcription by adjusting chromatin accessibility, thereby affecting cell and tissue phenotypes in the absence of DNA sequence changes. In the presence of ATP hydrolases, chromatin remodelling alters the structure of chromatin and thus changes the transcription level of DNA-guided RNA. To date, four types of ATP-dependent chromatin remodelling complexes have been identified in humans, namely SWI/SNF, ISWI, INO80 and NURD/MI2/CHD. SWI/SNF mutations are prevalent in a wide variety of cancerous tissues and cancer-derived cell lines as discovered by next-generation sequencing technologies.. SWI/SNF can bind to nucleosomes and use the energy of ATP to disrupt DNA and histone interactions, sliding or ejecting histones, altering nucleosome structure, and changing transcriptional and regulatory mechanisms. Furthermore, mutations in the SWI/SNF complex have been observed in approximately 20% of all cancers. Together, these findings suggest that mutations targeting the SWI/SNF complex may have a positive impact on tumorigenesis and cancer progression.
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Affiliation(s)
- Liyuan Wang
- The Second Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Department of Oncology and Hematology, Jinan 250000, Shandong Province, China
| | - Jinglong Tang
- Adicon Medical Laboratory Center, Molecular Genetic Diagnosis Center, Pathological Diagnosis Center, Jinan 250014, Shandong Province, China.
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26
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Choi JH, Ro JY. The Recent Advances in Molecular Diagnosis of Soft Tissue Tumors. Int J Mol Sci 2023; 24:ijms24065934. [PMID: 36983010 PMCID: PMC10051446 DOI: 10.3390/ijms24065934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/17/2023] [Accepted: 03/19/2023] [Indexed: 03/30/2023] Open
Abstract
Soft tissue tumors are rare mesenchymal tumors with divergent differentiation. The diagnosis of soft tissue tumors is challenging for pathologists owing to the diversity of tumor types and histological overlap among the tumor entities. Present-day understanding of the molecular pathogenesis of soft tissue tumors has rapidly increased with the development of molecular genetic techniques (e.g., next-generation sequencing). Additionally, immunohistochemical markers that serve as surrogate markers for recurrent translocations in soft tissue tumors have been developed. This review aims to provide an update on recently described molecular findings and relevant novel immunohistochemical markers in selected soft tissue tumors.
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Affiliation(s)
- Joon Hyuk Choi
- Department of Pathology, Yeungnam University College of Medicine, 170 Hyeonchung-ro, Namgu, Daegu 42415, Republic of Korea
| | - Jae Y Ro
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Medical College, Cornell University, Houston, TX 77030, USA
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Singh AK, Viviano S, Allington G, McGee S, Kiziltug E, Mekbib KY, Shohfi JP, Duy PQ, DeSpenza T, Furey CG, Reeves BC, Smith H, Ma S, Sousa AMM, Cherskov A, Allocco A, Nelson-Williams C, Haider S, Rizvi SRA, Alper SL, Sestan N, Shimelis H, Walsh LK, Lifton RP, Moreno-De-Luca A, Jin SC, Kruszka P, Deniz E, Kahle KT. A novel SMARCC1 -mutant BAFopathy implicates epigenetic dysregulation of neural progenitors in hydrocephalus. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.19.23287455. [PMID: 36993720 PMCID: PMC10055611 DOI: 10.1101/2023.03.19.23287455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Importance Hydrocephalus, characterized by cerebral ventriculomegaly, is the most common disorder requiring brain surgery. A few familial forms of congenital hydrocephalus (CH) have been identified, but the cause of most sporadic cases of CH remains elusive. Recent studies have implicated SMARCC1 , a component of the B RG1- a ssociated factor (BAF) chromatin remodeling complex, as a candidate CH gene. However, SMARCC1 variants have not been systematically examined in a large patient cohort or conclusively linked with a human syndrome. Moreover, CH-associated SMARCC1 variants have not been functionally validated or mechanistically studied in vivo . Objectives The aims of this study are to (i) assess the extent to which rare, damaging de novo mutations (DNMs) in SMARCC1 are associated with cerebral ventriculomegaly; (ii) describe the clinical and radiographic phenotypes of SMARCC1 -mutated patients; and (iii) assess the pathogenicity and mechanisms of CH-associated SMARCC1 mutations in vivo . Design setting and participants A genetic association study was conducted using whole-exome sequencing from a cohort consisting of 2,697 ventriculomegalic trios, including patients with neurosurgically-treated CH, totaling 8,091 exomes collected over 5 years (2016-2021). Data were analyzed in 2023. A comparison control cohort consisted of 1,798 exomes from unaffected siblings of patients with autism spectrum disorder and their unaffected parents sourced from the Simons simplex consortium. Main outcomes and measures Gene variants were identified and filtered using stringent, validated criteria. Enrichment tests assessed gene-level variant burden. In silico biophysical modeling estimated the likelihood and extent of the variant impact on protein structure. The effect of a CH-associated SMARCC1 mutation on the human fetal brain transcriptome was assessed by analyzing RNA-sequencing data. Smarcc1 knockdowns and a patient-specific Smarcc1 variant were tested in Xenopus and studied using optical coherence tomography imaging, in situ hybridization, and immunofluorescence microscopy. Results SMARCC1 surpassed genome-wide significance thresholds in DNM enrichment tests. Six rare protein-altering DNMs, including four loss-of-function mutations and one recurrent canonical splice site mutation (c.1571+1G>A) were detected in unrelated patients. DNMs localized to the highly conserved DNA-interacting SWIRM, Myb-DNA binding, Glu-rich, and Chromo domains of SMARCC1 . Patients exhibited developmental delay (DD), aqueductal stenosis, and other structural brain and heart defects. G0 and G1 Smarcc1 Xenopus mutants exhibited aqueductal stenosis and cardiac defects and were rescued by human wild-type SMARCC1 but not a patient-specific SMARCC1 mutant. Hydrocephalic SMARCC1 -mutant human fetal brain and Smarcc1 -mutant Xenopus brain exhibited a similarly altered expression of key genes linked to midgestational neurogenesis, including the transcription factors NEUROD2 and MAB21L2 . Conclusions SMARCC1 is a bona fide CH risk gene. DNMs in SMARCC1 cause a novel human BAFopathy we term " S MARCC1- a ssociated D evelopmental D ysgenesis S yndrome (SaDDS)", characterized by cerebral ventriculomegaly, aqueductal stenosis, DD, and a variety of structural brain or cardiac defects. These data underscore the importance of SMARCC1 and the BAF chromatin remodeling complex for human brain morphogenesis and provide evidence for a "neural stem cell" paradigm of human CH pathogenesis. These results highlight the utility of trio-based WES for identifying risk genes for congenital structural brain disorders and suggest WES may be a valuable adjunct in the clinical management of CH patients. KEY POINTS Question: What is the role of SMARCC1 , a core component of the B RG1- a ssociated factor (BAF) chromatin remodeling complex, in brain morphogenesis and congenital hydrocephalus (CH)? Findings: SMARCC1 harbored an exome-wide significant burden of rare, protein-damaging de novo mutations (DNMs) (p = 5.83 × 10 -9 ) in the largest ascertained cohort to date of patients with cerebral ventriculomegaly, including treated CH (2,697 parent-proband trios). SMARCC1 contained four loss-of-function DNMs and two identical canonical splice site DNMs in a total of six unrelated patients. Patients exhibited developmental delay, aqueductal stenosis, and other structural brain and cardiac defects. Xenopus Smarcc1 mutants recapitulated core human phenotypes and were rescued by the expression of human wild-type but not patient-mutant SMARCC1 . Hydrocephalic SMARCC1 -mutant human brain and Smarcc1 -mutant Xenopus brain exhibited similar alterationsin the expression of key transcription factors that regulate neural progenitor cell proliferation. Meaning: SMARCC1 is essential for human brain morphogenesis and is a bona fide CH risk gene. SMARCC1 mutations cause a novel human BAFopathy we term " S MARCC1- a ssociated D evelopmental D ysgenesis S yndrome (SaDDS)". These data implicate epigenetic dysregulation of fetal neural progenitors in the pathogenesis of hydrocephalus, with diagnostic and prognostic implications for patients and caregivers.
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Ali MM, Naz S, Ashraf S, Knapp S, Ul-Haq Z. Epigenetic modulation by targeting bromodomain containing protein 9 (BRD9): Its therapeutic potential and selective inhibition. Int J Biol Macromol 2023; 230:123428. [PMID: 36709803 DOI: 10.1016/j.ijbiomac.2023.123428] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/20/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023]
Abstract
The bromodomain-containing protein 9, a component of the SWI/SNF chromatin remodeling complex, functions as an 'epigenetic reader' selectively recognizing acetyl-lysine marks. It regulates chromatin structure and gene expression by recruitment of acetylated transcriptional regulators and by modulating the function of remodeling complexes. Recent data suggests that BRD9 plays an important role in regulating cellular growth and it has been suggested to drive progression of several malignant diseases such as cervical cancer, and acute myeloid leukemia. Its role in tumorigenesis suggests that selective BRD9 inhibitors may have therapeutic value in cancer therapy. Currently, there has been increasing interest in developing small molecules that can specifically target BRD9 or the closely related bromodomain protein BRD7. Available chemical probes will help to clarify biological functions of BRD9 and its potential for cancer therapy. Since the report of the first BRD9 inhibitor LP99 in 2015, numerous inhibitors have been developed. In this review, we summarized the biological roles of BRD9, structural details and the progress made in the development of BRD9 inhibitors.
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Affiliation(s)
- Maria Mushtaq Ali
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Sehrish Naz
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Sajda Ashraf
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Goethe University Frankfurt, Max von Lauestrasse 9, 60438 Frankfurt, Germany; Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe University Frankfurt, Max von Lauestrasse 15, 60438 Frankfurt, Germany
| | - Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan.
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Liu W, Wang Z, Liu S, Zhang X, Cao X, Jiang M. RNF138 inhibits late inflammatory gene transcription through degradation of SMARCC1 of the SWI/SNF complex. Cell Rep 2023; 42:112097. [PMID: 36800290 DOI: 10.1016/j.celrep.2023.112097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 06/09/2022] [Accepted: 01/25/2023] [Indexed: 02/17/2023] Open
Abstract
As one of the core components of the switching or sucrose non-fermentable (SWI/SNF) complex, SMARCC1 (BAF155, SRG3) plays essential roles in activation of late inflammatory genes in response to microbial challenge. However, little is known about the mechanism of how SMARCC1 regulates the inflammatory innate response. Via functional screening, we identify the nuclear E3 ubiquitin ligase RNF138 as a negative regulator in the inflammatory innate response and show that RNF138 interacts with SMARCC1 and mediates its K48-linked polyubiquitination at position Lys643 and proteasomal degradation. As a result, the catalytic activity of RNF138 fine-tunes the kinetics of late inflammatory gene transcription by inhibiting chromatin remodeling at SWI/SNF-regulated gene loci. Reduced RNF138 and increased SMARCC1 in monocytes of rheumatoid arthritis patients are observed. These results provide mechanistic insight into the interplay among nucleosome remodeling, inflammation, and ubiquitylation and underscore the important role of the E3 ubiquitin ligases in controlling the extent and duration of inflammatory responses.
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Affiliation(s)
- Wei Liu
- Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China; Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Ziqiao Wang
- Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Shuo Liu
- Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Xuan Zhang
- Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Xuetao Cao
- Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China.
| | - Minghong Jiang
- Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China.
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Zare A, Salehpour A, Khoradmehr A, Bakhshalizadeh S, Najafzadeh V, Almasi-Turk S, Mahdipour M, Shirazi R, Tamadon A. Epigenetic Modification Factors and microRNAs Network Associated with Differentiation of Embryonic Stem Cells and Induced Pluripotent Stem Cells toward Cardiomyocytes: A Review. Life (Basel) 2023; 13:life13020569. [PMID: 36836926 PMCID: PMC9965891 DOI: 10.3390/life13020569] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 02/22/2023] Open
Abstract
More research is being conducted on myocardial cell treatments utilizing stem cell lines that can develop into cardiomyocytes. All of the forms of cardiac illnesses have shown to be quite amenable to treatments using embryonic (ESCs) and induced pluripotent stem cells (iPSCs). In the present study, we reviewed the differentiation of these cell types into cardiomyocytes from an epigenetic standpoint. We also provided a miRNA network that is devoted to the epigenetic commitment of stem cells toward cardiomyocyte cells and related diseases, such as congenital heart defects, comprehensively. Histone acetylation, methylation, DNA alterations, N6-methyladenosine (m6a) RNA methylation, and cardiac mitochondrial mutations are explored as potential tools for precise stem cell differentiation.
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Affiliation(s)
- Afshin Zare
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr 7514633196, Iran
| | - Aria Salehpour
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr 7514633196, Iran
| | - Arezoo Khoradmehr
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr 7514633196, Iran
| | - Shabnam Bakhshalizadeh
- Reproductive Development, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Vahid Najafzadeh
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
| | - Sahar Almasi-Turk
- Department of Basic Sciences, School of Medicine, Bushehr University of Medical Sciences, Bushehr 7514633341, Iran
| | - Mahdi Mahdipour
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz 5166653431, Iran
- Department of Reproductive Biology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz 5166653431, Iran
- Correspondence: (M.M.); (R.S.); (A.T.)
| | - Reza Shirazi
- Department of Anatomy, School of Medical Sciences, Medicine & Health, UNSW Sydney, Sydney, NSW 2052, Australia
- Correspondence: (M.M.); (R.S.); (A.T.)
| | - Amin Tamadon
- PerciaVista R&D Co., Shiraz 7135644144, Iran
- Correspondence: (M.M.); (R.S.); (A.T.)
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Kobayashi T, Matsui Y, Miki H, Hatta M, Ishida M, Satake H, Sekimoto M. Case report: administration of immune checkpoint inhibitor for SMARCB1 (INI1)-negative rhabdoid carcinoma with microsatellite instability (MSI)-high in the right colon. Surg Case Rep 2023; 9:17. [PMID: 36732357 PMCID: PMC9895154 DOI: 10.1186/s40792-023-01594-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 01/22/2023] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Malignant tumors with rhabdoid features are rare, highly aggressive, and some of them are characterized by SMARCB1 (INI1) loss. Although cases of rhabdoid carcinoma are extremely rare, its occurrence in the colon has been reported previously. CASE PRESENTATION A 71-year-old Japanese female patient presented with loss of appetite, fatigue, and weight loss. Computed tomography demonstrated a tumor in the right colon that infiltrated the surrounding kidneys and swelling of the left supraclavicular and periaortic lymph nodes. Laparotomy revealed that the tumor was unresectable because it had directly invaded the head of the pancreas and duodenum. Therefore, ileocecal vascularized bulky lymph nodes were sampled, and gastrojejunostomy with Braun's anastomosis and ileotransversostomy were performed as palliative procedures. Histopathological examination of the lymph nodes revealed that the neoplastic cells had rich eosinophilic cytoplasm and eccentrically located large nuclei characteristic of rhabdoid carcinoma. In addition, these neoplastic cells lacked SMARCB1 expression; therefore, the patient was diagnosed with SMARCB1-negative rhabdoid carcinoma. The postoperative course was uneventful. Molecular analysis confirmed that the neoplastic cells had high microsatellite instability (MSI); therefore, two cycles of pembrolizumab were administered. However, no clinical benefit was noted, and the patient died 3 months postoperatively. CONCLUSION This is the first report of a case of SMARCB1-negative rhabdoid colon carcinoma with high MSI treated with pembrolizumab. Rhabdoid carcinoma is highly aggressive; therefore, additional studies are required to determine the therapeutic strategy for SMARCB1-negative rhabdoid colorectal carcinoma.
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Affiliation(s)
- Toshinori Kobayashi
- grid.410783.90000 0001 2172 5041Department of Surgery, Kansai Medical University, 2-5-1, Shinmachi, Hirakata, Osaka 573-1010 Japan
| | - Yuki Matsui
- grid.410783.90000 0001 2172 5041Department of Surgery, Kansai Medical University, 2-5-1, Shinmachi, Hirakata, Osaka 573-1010 Japan
| | - Hisanori Miki
- grid.410783.90000 0001 2172 5041Department of Surgery, Kansai Medical University, 2-5-1, Shinmachi, Hirakata, Osaka 573-1010 Japan
| | - Masahiko Hatta
- grid.410783.90000 0001 2172 5041Department of Surgery, Kansai Medical University, 2-5-1, Shinmachi, Hirakata, Osaka 573-1010 Japan
| | - Mitsuaki Ishida
- grid.410783.90000 0001 2172 5041Department of Surgery, Kansai Medical University, 2-5-1, Shinmachi, Hirakata, Osaka 573-1010 Japan ,Department of Pathology, Osaka Medical and Pharmaceutical University, 2-7, Daigaku-Machi, Takatsuki, Osaka 569-8686 Japan
| | - Hironaga Satake
- grid.410783.90000 0001 2172 5041Department of Surgery, Kansai Medical University, 2-5-1, Shinmachi, Hirakata, Osaka 573-1010 Japan ,grid.278276.e0000 0001 0659 9825Department of Medical Oncology, Kochi Medical School, Nankoku, 7838505 Japan
| | - Mitsugu Sekimoto
- grid.410783.90000 0001 2172 5041Department of Surgery, Kansai Medical University, 2-5-1, Shinmachi, Hirakata, Osaka 573-1010 Japan
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Tabuloc CA, Cai YD, Kwok RS, Chan EC, Hidalgo S, Chiu JC. CLOCK and TIMELESS regulate rhythmic occupancy of the BRAHMA chromatin-remodeling protein at clock gene promoters. PLoS Genet 2023; 19:e1010649. [PMID: 36809369 PMCID: PMC9983840 DOI: 10.1371/journal.pgen.1010649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 03/03/2023] [Accepted: 02/02/2023] [Indexed: 02/23/2023] Open
Abstract
Circadian clock and chromatin-remodeling complexes are tightly intertwined systems that regulate rhythmic gene expression. The circadian clock promotes rhythmic expression, timely recruitment, and/or activation of chromatin remodelers, while chromatin remodelers regulate accessibility of clock transcription factors to the DNA to influence expression of clock genes. We previously reported that the BRAHMA (BRM) chromatin-remodeling complex promotes the repression of circadian gene expression in Drosophila. In this study, we investigated the mechanisms by which the circadian clock feeds back to modulate daily BRM activity. Using chromatin immunoprecipitation, we observed rhythmic BRM binding to clock gene promoters despite constitutive BRM protein expression, suggesting that factors other than protein abundance are responsible for rhythmic BRM occupancy at clock-controlled loci. Since we previously reported that BRM interacts with two key clock proteins, CLOCK (CLK) and TIMELESS (TIM), we examined their effect on BRM occupancy to the period (per) promoter. We observed reduced BRM binding to the DNA in clk null flies, suggesting that CLK is involved in enhancing BRM occupancy to initiate transcriptional repression at the conclusion of the activation phase. Additionally, we observed reduced BRM binding to the per promoter in flies overexpressing TIM, suggesting that TIM promotes BRM removal from DNA. These conclusions are further supported by elevated BRM binding to the per promoter in flies subjected to constant light and experiments in Drosophila tissue culture in which the levels of CLK and TIM are manipulated. In summary, this study provides new insights into the reciprocal regulation between the circadian clock and the BRM chromatin-remodeling complex.
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Affiliation(s)
- Christine A. Tabuloc
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, California, United States of America
| | - Yao D. Cai
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, California, United States of America
| | - Rosanna S. Kwok
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, California, United States of America
| | - Elizabeth C. Chan
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, California, United States of America
| | - Sergio Hidalgo
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, California, United States of America
| | - Joanna C. Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, California, United States of America
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Chung SY, Kenee P, Mitton T, Halderman A. SMARCB1(INI-1)-Deficient Sinonasal Carcinoma: An Evolving Entity. J Neurol Surg Rep 2023; 84:e1-e5. [PMID: 36712411 PMCID: PMC9883109 DOI: 10.1055/a-1996-1283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022] Open
Abstract
SMARCB1(INI-1)-deficient sinonasal carcinoma is a rare, poorly differentiated neoplasm with a poor prognosis. Though historically most were identified as sinonasal undifferentiated carcinoma, we now understand it to be a distinct entity. There is currently a general consensus supporting multimodal therapy, though the optimal sequence of surgery, chemotherapy, and radiation has yet to be defined.
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Affiliation(s)
- Sei Y. Chung
- Department of Otolaryngology-Head and Neck Surgery, The University of Texas Southwestern Medical Center Ringgold Standard Institution, Dallas, Texas, United States,Address for correspondence Sei Y. Chung, MD Department of Otolaryngology-Head and Neck SurgeryThe University of Texas Southwestern Medical Center Ringgold Standard Institution, Dallas, TX 75219United States
| | - Parker Kenee
- Department of Otolaryngology-Head and Neck Surgery, The University of Texas Southwestern Medical Center Ringgold Standard Institution, Dallas, Texas, United States
| | - Tanner Mitton
- Department of Otolaryngology-Head and Neck Surgery, The University of Texas Southwestern Medical Center Ringgold Standard Institution, Dallas, Texas, United States
| | - Ashleigh Halderman
- Department of Otolaryngology-Head and Neck Surgery, The University of Texas Southwestern Medical Center Ringgold Standard Institution, Dallas, Texas, United States
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Hoellerbauer P, Biery MC, Arora S, Rao Y, Girard EJ, Mitchell K, Dighe P, Kufeld M, Kuppers DA, Herman JA, Holland EC, Soroceanu L, Vitanza NA, Olson JM, Pritchard JR, Paddison PJ. Functional genomic analysis of adult and pediatric brain tumor isolates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.05.522885. [PMID: 36711964 PMCID: PMC9881972 DOI: 10.1101/2023.01.05.522885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Background Adult and pediatric tumors display stark differences in their mutation spectra and chromosome alterations. Here, we attempted to identify common and unique gene dependencies and their associated biomarkers among adult and pediatric tumor isolates using functional genetic lethal screens and computational modeling. Methods We performed CRISRP-Cas9 lethality screens in two adult glioblastoma (GBM) tumor isolates and five pediatric brain tumor isolates representing atypical teratoid rhabdoid tumors (ATRT), diffuse intrinsic pontine glioma, GBM, and medulloblastoma. We then integrated the screen results with machine learning-based gene-dependency models generated from data from >900 cancer cell lines. Results We found that >50% of candidate dependencies of 280 identified were shared between adult GBM tumors and individual pediatric tumor isolates. 68% of screen hits were found as nodes in our network models, along with shared and tumor-specific predictors of gene dependencies. We investigated network predictors associated with ADAR, EFR3A, FGFR1 (pediatric-specific), and SMARCC2 (ATRT-specific) gene dependency among our tumor isolates. Conclusions The results suggest that, despite harboring disparate genomic signatures, adult and pediatric tumor isolates share a preponderance of genetic dependences. Further, combining data from primary brain tumor lethality screens with large cancer cell line datasets produced valuable insights into biomarkers of gene dependency, even for rare cancers. Importance of the Study Our results demonstrate that large cancer cell lines data sets can be computationally mined to identify known and novel gene dependency relationships in adult and pediatric human brain tumor isolates. Gene dependency networks and lethality screen results represent a key resource for neuro-oncology and cancer research communities. We also highlight some of the challenges and limitations of this approach.
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Affiliation(s)
- Pia Hoellerbauer
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA USA
| | - Matt C Biery
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA USA
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Yiyun Rao
- Huck Institute for the Life Sciences, Pennsylvania State University, State College, PA, USA
| | - Emily J Girard
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Kelly Mitchell
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Pratiksha Dighe
- California Pacific Medical Center Research Institute, San Francisco, CA 94107, USA
| | - Megan Kufeld
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Daniel A Kuppers
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Jacob A Herman
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Liliana Soroceanu
- California Pacific Medical Center Research Institute, San Francisco, CA 94107, USA
| | - Nicholas A Vitanza
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - James M Olson
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA USA
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Justin R Pritchard
- Huck Institute for the Life Sciences, Pennsylvania State University, State College, PA, USA
| | - Patrick J Paddison
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA USA
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Passeri T, Dahmani A, Masliah-Planchon J, El Botty R, Courtois L, Vacher S, Marangoni E, Nemati F, Roman-Roman S, Adle-Biassette H, Mammar H, Froelich S, Bièche I, Decaudin D. In vivo efficacy assessment of the CDK4/6 inhibitor palbociclib and the PLK1 inhibitor volasertib in human chordoma xenografts. Front Oncol 2022; 12:960720. [PMID: 36505864 PMCID: PMC9732546 DOI: 10.3389/fonc.2022.960720] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 10/18/2022] [Indexed: 11/26/2022] Open
Abstract
Background Management of advanced chordomas remains delicate considering their insensitivity to chemotherapy. Homozygous deletion of the regulatory gene CDKN2A has been described as the most frequent genetic alteration in chordomas and may be considered as a potential theranostic marker. Here, we evaluated the tumor efficacy of the CDK4/6 inhibitor palbociclib, as well as the PLK1 inhibitor volasertib, in three chordoma patient-derived xenograft (PDX) models to validate and identify novel therapeutic approaches. Methods From our chordoma xenograft panel, we selected three models, two of them harboring a homozygous deletion of CDKN2A/2B genes, and the last one a PBRM1 pathogenic variant (as control). For each model, we tested the palbociclib and volasertib drugs with pharmacodynamic studies together with RT-PCR and RNAseq analyses. Results For palbociclib, we observed a significant tumor response for one of two models harboring the deletion of CDKN2A/2B (p = 0.02), and no significant tumor response in the PBRM1-mutated PDX; for volasertib, we did not observe any response in the three tested models. RT-PCR and RNAseq analyses showed a correlation between cell cycle markers and responses to palbociclib; finally, RNAseq analyses showed a natural enrichment of the oxidative phosphorylation genes (OxPhos) in the palbociclib-resistant PDX (p = 0.02). Conclusion CDK4/6 inhibition appears as a promising strategy to manage advanced chordomas harboring a loss of CDKN2A/2B. However, further preclinical studies are strongly requested to confirm it and to understand acquired or de novo resistance to palbociclib, in the peculiar view of a targeting of the oxidative phosphorylation genes.
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Affiliation(s)
- Thibault Passeri
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, University of Paris Saclay, Paris, France,Department of Genetics, Institut Curie, University of Paris Saclay, Paris, France,Department of Neurosurgery, Lariboisière Hospital, Assistance Publique des Hôpitaux de Paris, University of Paris, Paris, France,*Correspondence: Thibault Passeri,
| | - Ahmed Dahmani
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, University of Paris Saclay, Paris, France
| | | | - Rania El Botty
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, University of Paris Saclay, Paris, France
| | - Laura Courtois
- Department of Genetics, Institut Curie, University of Paris Saclay, Paris, France
| | - Sophie Vacher
- Department of Genetics, Institut Curie, University of Paris Saclay, Paris, France
| | - Elisabetta Marangoni
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, University of Paris Saclay, Paris, France
| | - Fariba Nemati
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, University of Paris Saclay, Paris, France
| | - Sergio Roman-Roman
- Department of Translational Research, Institut Curie, University of Paris Saclay, Paris, France
| | - Homa Adle-Biassette
- Department of Pathology, Lariboisière Hospital, Assistance Publique des Hôpitaux de Paris, University of Paris, Paris, France
| | - Hamid Mammar
- Department of Radiotherapy - Proton Therapy Center, Institut Curie, Paris-Saclay University, Orsay, France
| | - Sébastien Froelich
- Department of Neurosurgery, Lariboisière Hospital, Assistance Publique des Hôpitaux de Paris, University of Paris, Paris, France
| | - Ivan Bièche
- Department of Genetics, Institut Curie, University of Paris Saclay, Paris, France
| | - Didier Decaudin
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, University of Paris Saclay, Paris, France,Department of Medical Oncology, Institut Curie, Paris, France
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He X, Xu J, Niu N, Xu G, Zhu H, Liu Z, Mou Y, Qian Z, Wang H, Hu J, Ma T, Ma J, Tao H. PBRM1 presents a potential prognostic marker and therapeutic target in duodenal papillary carcinoma. Clin Transl Med 2022; 12:e1062. [PMID: 36178086 PMCID: PMC9523678 DOI: 10.1002/ctm2.1062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Due to its rarity, duodenal papillary carcinoma (DPC) is seldom studied as a unique disease and no specific molecular features or treatment guidelines are provided. METHODS Whole-exome sequencing was performed to gain new insights into the DPC mutation landscape and to identify potential signalling pathways and therapeutic targets. Mechanistically, immunohistochemistry (IHC), immunofluorescence, RNA-seq, ATAC-seq and in vitro cell function experiments were performed to confirm the underlying mechanisms. RESULTS We described the mutational landscape of DPC for the first time as a group of rare tumours with a high frequency of dysregulation in the chromatin remodelling pathway, particularly PBRM1-inactivating mutations that are significantly higher than duodenal adenocarcinomas and ampullary adenocarcinoma (27% vs. 0% vs. 7%, p < .01). In vitro cell experiments showed that downregulation of PBRM1 expression could significantly promote the cancer progression and epithelial-to-mesenchymal transition via the PBRM1-c-JUN-VIM axis. The IHC data indicated that PBRM1 deficiency (p = .047) and c-JUN expression (p < .001) were significantly associated with poor prognosis. Meanwhile, the downregulation of PBRM1 expression in HUTU-80 cells was sensitive to radiation, which may be due to the suppression of c-JUN by irradiation. CONCLUSIONS Our findings define a novel molecular subgroup of PBRM1-inactivating mutations in DPC. PBRM1 play an important role in DPC progression and may serve as a potential therapeutic target and prognostic indicator.
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Affiliation(s)
- Xujun He
- Key Laboratory of Gastroenterology of Zhejiang ProvinceZhejiang Provincial People's Hospital (Affiliated People's HospitalHangzhou Medical College)HangzhouZhejiangChina,Department of Genetic and Genome MedicineZhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College)HangzhouZhejiangChina,Department of Gastrointestinal and Pancreatic SurgeryZhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College)HangzhouZhejiangChina
| | - Ji Xu
- Key Laboratory of Gastroenterology of Zhejiang ProvinceZhejiang Provincial People's Hospital (Affiliated People's HospitalHangzhou Medical College)HangzhouZhejiangChina,Department of Gastrointestinal and Pancreatic SurgeryZhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College)HangzhouZhejiangChina
| | - Nan Niu
- The Second Clinical Medical College of Zhejiang Chinese Medical UniversityHangzhouZhejiangChina
| | - Guoxi Xu
- Department of Gastrointestinal SurgeryJinjiang HospitalQuanzhouFujianChina
| | - Honglin Zhu
- Genetron Health (Beijing) TechnologyCo. Ltd.BeijingChina
| | - Zhengchuang Liu
- Key Laboratory of Gastroenterology of Zhejiang ProvinceZhejiang Provincial People's Hospital (Affiliated People's HospitalHangzhou Medical College)HangzhouZhejiangChina
| | - Yiping Mou
- Key Laboratory of Gastroenterology of Zhejiang ProvinceZhejiang Provincial People's Hospital (Affiliated People's HospitalHangzhou Medical College)HangzhouZhejiangChina,Department of Gastrointestinal and Pancreatic SurgeryZhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College)HangzhouZhejiangChina
| | - Zhengyuan Qian
- Key Laboratory of Gastroenterology of Zhejiang ProvinceZhejiang Provincial People's Hospital (Affiliated People's HospitalHangzhou Medical College)HangzhouZhejiangChina,Department of Gastrointestinal and Pancreatic SurgeryZhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College)HangzhouZhejiangChina
| | - Huiju Wang
- Key Laboratory of Gastroenterology of Zhejiang ProvinceZhejiang Provincial People's Hospital (Affiliated People's HospitalHangzhou Medical College)HangzhouZhejiangChina,Department of Gastrointestinal and Pancreatic SurgeryZhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College)HangzhouZhejiangChina
| | - Junfeng Hu
- Key Laboratory of Gastroenterology of Zhejiang ProvinceZhejiang Provincial People's Hospital (Affiliated People's HospitalHangzhou Medical College)HangzhouZhejiangChina,Department of Gastrointestinal and Pancreatic SurgeryZhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College)HangzhouZhejiangChina
| | - Tonghui Ma
- Genetron Health (Beijing) TechnologyCo. Ltd.BeijingChina
| | - Jie Ma
- Department of PathologyZhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College)HangzhouZhejiangChina
| | - Houquan Tao
- Key Laboratory of Gastroenterology of Zhejiang ProvinceZhejiang Provincial People's Hospital (Affiliated People's HospitalHangzhou Medical College)HangzhouZhejiangChina,Department of Gastrointestinal and Pancreatic SurgeryZhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College)HangzhouZhejiangChina
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37
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Ng JKM, Chan JYK, Li JJX, Tang K, Yeung DCM, Chan ABW. SMARCB1 (INI1)-Deficient Sinonasal Carcinoma with Yolk Sac differentiation Showing Co-loss of SMARCA4 Immunostaining - A Case Report and Literature Review. Head Neck Pathol 2022; 16:934-941. [PMID: 35257325 PMCID: PMC9424504 DOI: 10.1007/s12105-022-01423-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 01/30/2022] [Indexed: 02/09/2023]
Abstract
SMARCB1 (INI1)-deficient carcinoma of the sinonasal tract is a rare and distinct entity characterized by the loss of INI1 immunostain expression. These tumors are morphologically diverse, with isolated cases of yolk sac differentiation reported. We report the first case of SMARCB1-deficient sinonasal carcinoma that demonstrated co-loss of SMARCA4 immunostain, and reduced SMARCA2 and ARID1A staining, with the entire tumor showing histological and immunohistochemical evidence of yolk sac differentiation. The clinical, histological, immunohistochemical and molecular features were discussed and compared against SMARCB1-deficient sinonasal carcinomas with yolk sac differentiation and SMARCA4-deficeint sinonasal carcinomas reported in the literature. With a highly aggressive clinical course leading to mortality two months after presentation, the behavior of this tumor appears to be more comparable to that of SMARCA4-deficient sinonasal carcinomas. A comprehensive immunopanel including SMARCB1, SMARCA4, SMARCA2 and ARID1A may be advisable for assessment and prognostication of SWI/SNF-deficient tumors.
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Affiliation(s)
- Joanna K M Ng
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, 1/F, Clinical Sciences Building, New Territories, Hong Kong
| | - Jason Y K Chan
- Department of Otorhinolaryngology, Head and Neck Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, New Territories, Hong Kong
| | - Joshua J X Li
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, 1/F, Clinical Sciences Building, New Territories, Hong Kong
| | - Kinglam Tang
- Department of Otorhinolaryngology, Head and Neck Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, New Territories, Hong Kong
| | - David C M Yeung
- Department of Otorhinolaryngology, Head and Neck Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, New Territories, Hong Kong
| | - Amy B W Chan
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, 1/F, Clinical Sciences Building, New Territories, Hong Kong.
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Deng J, Hua L, Bian L, Chen H, Chen L, Cheng H, Dou C, Geng D, Hong T, Ji H, Jiang Y, Lan Q, Li G, Liu Z, Qi S, Qu Y, Shi S, Sun X, Wang H, You Y, Yu H, Yue S, Zhang J, Zhang X, Wang S, Mao Y, Zhong P, Gong Y. Molecular diagnosis and treatment of meningiomas: an expert consensus (2022). Chin Med J (Engl) 2022; 135:1894-1912. [PMID: 36179152 PMCID: PMC9746788 DOI: 10.1097/cm9.0000000000002391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Indexed: 11/27/2022] Open
Abstract
ABSTRACT Meningiomas are the most common primary intracranial neoplasm with diverse pathological types and complicated clinical manifestations. The fifth edition of the WHO Classification of Tumors of the Central Nervous System (WHO CNS5), published in 2021, introduces major changes that advance the role of molecular diagnostics in meningiomas. To follow the revision of WHO CNS5, this expert consensus statement was formed jointly by the Group of Neuro-Oncology, Society of Neurosurgery, Chinese Medical Association together with neuropathologists and evidence-based experts. The consensus provides reference points to integrate key biomarkers into stratification and clinical decision making for meningioma patients. REGISTRATION Practice guideline REgistration for transPAREncy (PREPARE), IPGRP-2022CN234.
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Affiliation(s)
- Jiaojiao Deng
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai 200040, China
- National Center for Neurological Disorders, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Lingyang Hua
- Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Shanghai 200040, China
- Neurosurgical Institute of Fudan University, Shanghai 200040, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai 200040, China
| | - Liuguan Bian
- Department of Neurosurgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Hong Chen
- Department of Pathology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Ligang Chen
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Hongwei Cheng
- Department of Neurosurgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China
| | - Changwu Dou
- Department of Neurosurgery, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia 750306, China
| | - Dangmurenjiapu Geng
- Department of Neurosurgery, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830011, China
| | - Tao Hong
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Hongming Ji
- Department of Neurosurgery, Shanxi Medical University Shanxi Provincial People's Hospital, Taiyuan, Shanxi 030012, China
| | - Yugang Jiang
- Department of Neurosurgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Qing Lan
- Department of Neurosurgery, The Second Affiliated Hospital of Soochow University, Soochow, Jiangsu 215004, China
| | - Gang Li
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250063, China
| | - Zhixiong Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Songtao Qi
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Yan Qu
- Department of Neurosurgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi 710038, China
| | - Songsheng Shi
- Department of Neurosurgery, Fujian Medical University Affiliated Union Hospital, Fuzhou, Fujian 350001, China
| | - Xiaochuan Sun
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, China
| | - Haijun Wang
- Department of Neurosurgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510080, China
| | - Yongping You
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Hualin Yu
- Department of Neurosurgery, Kunming Medical University First Affiliated Hospital, Kunming, Yunnan 650032, China
| | - Shuyuan Yue
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Jianming Zhang
- Department of Neurosurgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China
| | - Xiaohua Zhang
- Department of Neurosurgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Shuo Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, China
| | - Ying Mao
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Ping Zhong
- Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Shanghai 200040, China
- Neurosurgical Institute of Fudan University, Shanghai 200040, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai 200040, China
| | - Ye Gong
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai 200040, China
- National Center for Neurological Disorders, Huashan Hospital, Fudan University, Shanghai 200040, China
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Ren T, Wang J, Tang W, Chen D, Wang S, Zhang X, Yang D. ARID1A has prognostic value in acute myeloid leukemia and promotes cell proliferation via TGF-β1/SMAD3 signaling. Clin Exp Med 2022:10.1007/s10238-022-00863-8. [PMID: 35867200 DOI: 10.1007/s10238-022-00863-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 07/04/2022] [Indexed: 11/03/2022]
Abstract
Previous studies have shown that the gene AT-rich interactive domain-containing protein 1A (ARID1A) is a subunit of SWI/SNF chromatin remodeling complex that acts as a tumor suppressor gene in several cancers and plays a vital role in tumorigenesis. However, its biological functions in acute myeloid leukemia (AML) are still unclear. Here, we tried to elaborate the expression of ARID1A in patients with AML, in leukemia cells, as well as the molecular mechanisms. Our results indicated that the expression of ARID1A was significantly downregulated in the bone marrow of patients with AML and relapsed patients compared with healthy subjects and patients in complete remission. Meantime, receiver operating characteristic curve analysis showed that the expression of ARID1A could be used to discriminate between patients with AML and patients in complete remission. We further constructed a knockdown cell model to determine the regulatory mechanisms of ARID1A in AML cells. We found that the decreased expression of ARID1A promoted cell proliferation, suppressed cellular apoptosis, and impeded cell cycle arrest via TGF-β1/SMAD3 signaling pathway. These results revealed that the reduced expression of ARID1A promoted cell proliferation via the TGF-β1/SMAD3 cascade and served as a prognostic biomarker for AML and therapeutic targets.
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Affiliation(s)
- Tianying Ren
- Zhong Yuan Academy of Biological Medicine, Liaocheng People's Hospital, Liaocheng, 252000, Shandong, People's Republic of China
| | - Jing Wang
- Key Laboratory for Pediatrics of Integrated Traditional and Western Medicine, Liaocheng People's Hospital, Liaocheng, 252000, Shandong, People's Republic of China
| | - Wenqiang Tang
- Central Laboratory, Liaocheng People's Hospital, Liaocheng, 252000, Shandong, People's Republic of China
| | - Dongliang Chen
- Zhong Yuan Academy of Biological Medicine, Liaocheng People's Hospital, Liaocheng, 252000, Shandong, People's Republic of China
| | - Shuang Wang
- Zhong Yuan Academy of Biological Medicine, Liaocheng People's Hospital, Liaocheng, 252000, Shandong, People's Republic of China
| | - Xiaole Zhang
- Department of Hematology, Liaocheng People's Hospital, Liaocheng, 252000, Shandong, People's Republic of China.
| | - Dawei Yang
- Zhong Yuan Academy of Biological Medicine, Liaocheng People's Hospital, Liaocheng, 252000, Shandong, People's Republic of China.
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Zhu H, Zhao H, Wang J, Zhao S, Ma C, Wang D, Gao H, Yang F, Ni Q, Li H, Zhou X, Zhang C, Lu J. Potential prognosis index for m 6A-related mRNA in cholangiocarcinoma. BMC Cancer 2022; 22:620. [PMID: 35672673 PMCID: PMC9170563 DOI: 10.1186/s12885-022-09665-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/12/2022] [Indexed: 12/12/2022] Open
Abstract
Background Cholangiocarcinoma (CHOL) is a malignant tumor that originates in the extrahepatic bile duct and can extend from the hilar region to the lower end of the common bile duct. The prognosis of CHOL patients is particularly poor; therefore, in this study, we screened mRNAs correlated with N6-methyladenosine (m6A) to construct a risk model for prognosis in CHOL. Methods The TCGA-CHOL dataset was applied to obtain and analyze the coexpression of 1281 m6A-related mRNAs, from which 14 were selected for further analysis through univariate proportional hazards (cox) regression analysis. Aryl hydrocarbon receptor interacting protein (AIP), CCAAT/enhancer binding protein beta (CEBPB), syndecan1 (SDC1), vacuolar protein sorting 25 homolog (VPS25) and syntaxin binding protein 2 (STXBP2) were then screened out through the least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression analysis to develop a precise m6A-related mRNA prognosis risk model (MRMRPM) with an area under curve (AUC) of 0.908 and 0.923 after 1 and 2 years, respectively. We divided the samples into high-risk and low-risk groups using the m6A-related mRNA prognosis risk model. Results Kaplan–Meier analysis indicated poor overall survival (OS) for the high-risk group. Two Gene Expression Omnibus (GEO) datasets (GSE89748 and GSE107943) were used to validate the risk model. The results of drug sensitivity and immune cell infiltration analysis showed that the risk model could serve as a prognosis index of potential immunotherapeutic characteristics and drug sensitivity. Furthermore, the proportion of resting dendritic cells and regulatory T cells was positively associated with an increased expression of four m6A-related mRNAs — AIP, CEBPB, SDC1, and VPS25 — in the high-risk CHOL group. Conclusions Our findings suggest that this model can be a prognostic indicator for CHOL patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09665-3.
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Affiliation(s)
- Huaqiang Zhu
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, Shandong, China.,Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
| | - Haini Zhao
- Jinan Health Publicity and Education Center, Jinan, 250021, Shandong, China
| | - Jianlu Wang
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, Shandong, China.,Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
| | - Shuchao Zhao
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
| | - Chaoqun Ma
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, Shandong, China.,Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
| | - Dongliang Wang
- ChosenMed Technology (Beijing) Co., Ltd., Beijing, 100176, China
| | - Hengjun Gao
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, Shandong, China.,Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
| | - Faji Yang
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, Shandong, China.,Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
| | - Qingqiang Ni
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, Shandong, China.,Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
| | - Hongguang Li
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, Shandong, China.,Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
| | - Xu Zhou
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, Shandong, China.,Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
| | - Chunqing Zhang
- Department of Gastroenterology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, Shandong, China.
| | - Jun Lu
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, Shandong, China. .,Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China.
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Cao L, Luo Y, Guo X, Liu S, Li S, Li J, Zhang Z, Zhao Y, Zhang Q, Gao F, Ji X, Gao X, Li Y, You F. SAFA facilitates chromatin opening of immune genes through interacting with anti-viral host RNAs. PLoS Pathog 2022; 18:e1010599. [PMID: 35658050 PMCID: PMC9200321 DOI: 10.1371/journal.ppat.1010599] [Citation(s) in RCA: 8] [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: 11/12/2021] [Revised: 06/15/2022] [Accepted: 05/17/2022] [Indexed: 12/19/2022] Open
Abstract
Regulation of chromatin structure and accessibility determines the transcription activities of genes, which endows the host with function-specific patterns of gene expression. Upon viral infection, the innate immune responses provide the first line of defense, allowing rapid production of variegated antiviral cytokines. Knowledge on how chromatin accessibility is regulated during host defense against viral infection remains limited. Our previous work found that the nuclear matrix protein SAFA surveilled viral RNA and regulated antiviral immune genes expression. However, how SAFA regulates the specific induction of antiviral immune genes remains unknown. Here, through integration of RNA-seq, ATAC-seq and ChIP-seq assays, we found that the depletion of SAFA specifically decreased the chromatin accessibility, activation and expression of virus induced genes. And mutation assays suggested that the RNA-binding ability of SAFA was essential for its function in regulating antiviral chromatin accessibility. RIP-seq results showed that SAFA exclusively bound with antiviral related RNAs following viral infection. Further, we combined the CRISPR-Cas13d mediated RNA knockdown system with ATAC-qPCR, and demonstrated that the binding between SAFA and according antiviral RNAs specifically mediated the openness of the corresponding chromatin and following robust transcription of antiviral genes. Moreover, knockdown of these associated RNAs dampened the accessibility of related genes in an extranuclear signaling pathway dependent manner. Interestingly, VSV infection cleaved SAFA protein at the C-terminus which deprived its RNA binding ability for immune evasion. Thus, our results demonstrated that SAFA and the interacting RNA products collaborated and remodeled chromatin accessibility to facilitate antiviral innate immune responses. Regulation of chromatin opening and gene expression underlies a key point during host defense against viral infection, which endows the host with timely and effective antiviral gene expression patterns. We previously reported that the nuclear matrix protein SAFA surveils viral RNA and regulates antiviral immune genes expression. However, how SAFA regulates the expression and what determines the specific induction of antiviral immune genes remains unclear. Here, we used a combination of high-throughput sequencing technologies and found that SAFA and the interacting RNA products collaborated and specifically remodeled chromatin accessibility to facilitate antiviral immune genes expression. We also found that VSV infection cleaved SAFA protein at the C-terminus and deprived its RNA binding ability for immune evasion. Our study provides new insights into the mechanism by which chromatin remodeling facilitates the induction of antiviral immune genes.
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Affiliation(s)
- Lili Cao
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Yujie Luo
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
| | - Xuefei Guo
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
| | - Shengde Liu
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing, China
| | - Siji Li
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
| | - Junhong Li
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Zeming Zhang
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
| | - Yingchi Zhao
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
| | - Qiao Zhang
- School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Feng Gao
- School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Xiong Ji
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Xiang Gao
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, School of life science, Shandong University, Qingdao, China
| | - Yunfei Li
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
- * E-mail: (YL); (FY)
| | - Fuping You
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
- * E-mail: (YL); (FY)
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Molecular features of primary hepatic undifferentiated carcinoma. Mod Pathol 2022; 35:680-687. [PMID: 34949765 DOI: 10.1038/s41379-021-00970-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/26/2021] [Accepted: 10/26/2021] [Indexed: 11/09/2022]
Abstract
The clinicopathological and molecular characteristics of primary hepatic undifferentiated carcinoma are poorly defined. It is speculated that primary hepatic undifferentiated carcinoma develops in the setting of preceding primary hepatic carcinoma. We investigated 14 primary hepatic undifferentiated carcinomas through targeted next-generation sequencing and immunohistochemistry. A panel of genes commonly mutated in primary liver carcinomas were examined. We found a similar clinical context as primary hepatic carcinoma, including a high prevalence of chronic viral hepatitis (86%), cirrhosis (57%), and elevated alpha-fetoprotein (29%). Tumors had sheet-like and poorly cohesive growth patterns. Rhabdoid cytomorphology was observed in four samples. Notably, the most common genetic mutations in primary hepatic undifferentiated carcinoma were in the promoter of TERT (n = 8, 57%) and TP53 (n = 8, 57%), which are common in hepatocellular carcinoma. The mutation rate of TP53 was elevated compared with hepatocellular carcinoma. No other typical genetic features of intrahepatic cholangiocarcinoma were identified, such as an IDH1/IDH2 mutation, FGFR2 fusions, or aberrant BAP1 expression. Furthermore, novel switch/sucrose nonfermenting complex inactivation was found, including SMARCA4/SMARCA2 (n = 1) and PBRM1 deficiency (n = 2). The three tumors demonstrated poorly cohesive histology, including rhabdoid features. High PD-L1 expression (57%) was observed in a majority of the tumors. Primary hepatic undifferentiated carcinoma shares clinical and genetic features with hepatocellular carcinoma but harbors progressive molecular characteristics that may initiate tumor dedifferentation. High PD-L1 expression in primary hepatic undifferentiated carcinoma may be a useful biomarker for potential immunotherapeutic strategies.
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Sun T, Gilani SM, Podany P, Harigopal M, Zhong M, Wang H. Cytomorphologic features of SMARCA4-deficient non-small cell lung carcinoma and correlation with immunohistochemical and molecular features. Cancer Cytopathol 2022; 130:620-629. [PMID: 35468657 DOI: 10.1002/cncy.22581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/19/2022] [Accepted: 03/22/2022] [Indexed: 11/08/2022]
Abstract
BACKGROUND SMARCA4/BRG1-deficient tumors and those that have loss of SMARCA/BRG1 have been described as various aggressive carcinomas and sarcomas, including a subset of non-small cell lung carcinoma (NSCLC). Cytomorphologic features of NSCLCs are yet to be described. The objective of this study was to evaluate the cytomorphologic features, immunohistochemical profile, and molecular profile of SMARCA4/BRG1-deficient NSCLC (SMARCA4-dNSCLC). METHODS The authors retrospectively searched for cases with SMARCA4/BRG1 functional loss alterations, which were identified in molecular studies and further confirmed by immunocytochemistry, and they reviewed the cytomorphologic features. Tumors with BRG1 loss were also stained with an extensive antibody panel. Molecular profiling and clinical information of the identified cases were scrutinized. RESULTS In total, 12 cytopathology cases from different anatomic sites were included. All cases showed variable expression of cytokeratin irrespective of type. One-half of cases had glandular features, followed by squamoid features, and poorly differentiated features. The most common cytologic features included sheets or papillary architecture, round or oval cell shapes, nuclear enlargement, moderate-to-marked pleomorphism, and coarse chromatin. Two cases with poorly differentiated cytomorphology had a predominance of single cells, scant cytoplasm, and macronucleoli. Variable expression of epithelial markers was noted in all cases. TP53 was the most frequently co-mutated gene in SMARCA4-dNSLCs. CONCLUSIONS This study demonstrates that SMARCA4-dNSCLCs can have a wide spectrum of cytomorphologic features, ranging from a relatively well differentiated adenocarcinoma to a poorly differentiated/undifferentiated carcinoma, with the majority of cases exhibiting some high-grade features, such as mitosis, apoptosis, necrosis, and marked pleomorphism.
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Affiliation(s)
- Tong Sun
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Syed M Gilani
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Peter Podany
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Malini Harigopal
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Minghao Zhong
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - He Wang
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
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Tung HJ, Wu RC, Lin CY, Lai CH. Rare Subtype of Endometrial Cancer: Undifferentiated/Dedifferentiated Endometrial Carcinoma, from Genetic Aspects to Clinical Practice. Int J Mol Sci 2022; 23:ijms23073794. [PMID: 35409155 PMCID: PMC8999061 DOI: 10.3390/ijms23073794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 02/01/2023] Open
Abstract
Endometrial cancer (EC) is one of the most common gynecologic cancers worldwide. There were 417,367 newly diagnosed cases and 97,370 deaths due to this disease worldwide in 2020. The incidence rates have increased over time, especially in countries with rapid socioeconomic transitions, and EC has been the most prevalent gynecologic malignancy in Taiwan since 2012. The new EC molecular classifications of The Cancer Genome Atlas (TCGA) Research Network include clear-cell carcinoma, serous carcinoma, and carcinosarcoma, while undifferentiated/dedifferentiated EC (UDEC) is not mentioned, and most previous clinical trials for EC have not included UDEC. UDEC is rare, has an aggressive growth pattern, tends to be diagnosed at an advanced stage, and is resistant to conventional chemotherapy. In this review, case series or case reports on the clinical features and genomic/epigenetic and expression profiles on UDEC data are summarized in order to identify potential molecular targets for current and future research.
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Affiliation(s)
- Hsiu-Jung Tung
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital, Linkou Branch and Chang Gung University College of Medicine, Taoyuan 333, Taiwan; (H.-J.T.); (C.-Y.L.)
- Gynecologic Cancer Research Center, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan 333, Taiwan;
| | - Ren-Chin Wu
- Gynecologic Cancer Research Center, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan 333, Taiwan;
- Department of Pathology, Chang Gung Memorial Hospital, Linkou Branch and Chang Gung University College of Medicine, Taoyuan 333, Taiwan
| | - Chiao-Yun Lin
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital, Linkou Branch and Chang Gung University College of Medicine, Taoyuan 333, Taiwan; (H.-J.T.); (C.-Y.L.)
- Gynecologic Cancer Research Center, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan 333, Taiwan;
| | - Chyong-Huey Lai
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital, Linkou Branch and Chang Gung University College of Medicine, Taoyuan 333, Taiwan; (H.-J.T.); (C.-Y.L.)
- Gynecologic Cancer Research Center, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan 333, Taiwan;
- Correspondence: ; Tel.: +886-(3)-328-1200; Fax: +886-(3)-328-8252
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Zhang L, Zhang L, Wang XI, Katz G, Tandon N, Zhao B, Lucci J, Ding J, Zhang S. The value of SOX2 in the differential diagnosis of SMARCA4 (BRG1)-deficient uterine neoplasms. Hum Pathol 2022; 124:45-55. [PMID: 35331811 DOI: 10.1016/j.humpath.2022.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/11/2022] [Accepted: 03/16/2022] [Indexed: 11/26/2022]
Abstract
SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 4 (SMARCA4/BRG1) deficient undifferentiated uterine sarcoma (SDUS) is a recently described uterine sarcoma. It is characterized by predominantly rhabdoid or large epithelioid cells with abundant cytoplasm and varying components of small and spindle cells, resembling the "large cell variant" of small cell carcinoma of ovary, hypercalcemic type (SCCOHT). In addition, SMARCA4 inactivating mutations have been described as the driver mutations in SDUS. However, undifferentiated (UDEC) and dedifferentiated endometrial carcinomas (DDEC) may show some clinical and morphological overlaps with SDUS, and about 20% reported UDEC/DDEC cases also have loss expression of SMARCA4. SDUS is a very aggressive disease and universally lethal in all reported cases. Differentiating SDUS from UDEC/DDEC is relevant for the prognosis, pathogenesis and possible targeted therapies for the disease. In this study, we compared the clinical, morphological, immunohistochemical and molecular characteristics of 10 tumors including 2 SDUS, 2 SCCOHT, 1 uterine carcinoma with neuroendocrine differentiation (UDEC?) and 5 UDEC/DDEC. All 5 UDEC/DDEC cases showed strong and diffuse nuclear positivity for SOX2, while all SCCOHT and SDUS cases were completely negative. We concluded that SOX2 could be a useful marker for the differential diagnosis between SDUS and UDEC/DDEC.
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Affiliation(s)
- Lan Zhang
- Department of Pathology and Laboratory Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Lin Zhang
- Department of Pathology and Laboratory Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Xiaohong Iris Wang
- Department of Pathology and Laboratory Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Guy Katz
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Nidhi Tandon
- Department of Pathology and Laboratory Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Bihong Zhao
- Department of Pathology and Laboratory Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Joseph Lucci
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jianmin Ding
- Department of Pathology and Laboratory Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Songlin Zhang
- Department of Pathology and Laboratory Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA.
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Passeri T, Dahmani A, Masliah-Planchon J, Naguez A, Michou M, El Botty R, Vacher S, Bouarich R, Nicolas A, Polivka M, Franck C, Schnitzler A, Némati F, Roman-Roman S, Bourdeaut F, Adle-Biassette H, Mammar H, Froelich S, Bièche I, Decaudin D. Dramatic In Vivo Efficacy of the EZH2-Inhibitor Tazemetostat in PBRM1-Mutated Human Chordoma Xenograft. Cancers (Basel) 2022; 14:cancers14061486. [PMID: 35326637 PMCID: PMC8946089 DOI: 10.3390/cancers14061486] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/08/2022] [Accepted: 03/10/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Chordomas are rare bone tumors characterized by a high recurrence rate. Presently, no medical treatment is available for advanced diseases due to the lack of molecular data and preclinical models. The current study showed the establishment and characterization of the largest panel chordoma xenografts, allowing pharmacological studies. In one PBRM1-mutated model, we demonstrated a strong therapeutic efficacy of the EZH2-inhibitor tazemetostat, encouraging further research on EZH2-inhibitors in chordomas. Abstract Chordomas are rare neoplasms characterized by a high recurrence rate and a poor long-term prognosis. Considering their chemo-/radio-resistance, alternative treatment strategies are strongly required, but their development is limited by the paucity of relevant preclinical models. Mutations affecting genes of the SWI/SNF complexes are frequently found in chordomas, suggesting a potential therapeutic effect of epigenetic regulators in this pathology. Twelve PDX models were established and characterized on histological and biomolecular features. Patients whose tumors were able to grow into mice had a statistically significant lower progression-free survival than those whose tumors did not grow after in vivo transplantation (p = 0.007). All PDXs maintained the same histopathological features as patients’ tumors. Homozygous deletions of CDKN2A/2B (58.3%) and PBRM1 (25%) variants were the most common genomic alterations found. In the tazemetostat treated PDX model harboring a PBRM1 variant, an overall survival of 100% was observed. Our panel of chordoma PDXs represents a useful preclinical tool for both pharmacologic and biological assessments. The first demonstration of a high antitumor activity of tazemetostat in a PDX model harboring a PBRM1 variant supports further evaluation for EZH2-inhibitors in this subgroup of chordomas.
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Affiliation(s)
- Thibault Passeri
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, University of Paris Saclay, 75005 Paris, France; (T.P.); (A.D.); (A.N.); (M.M.); (R.E.B.); (F.N.)
- Department of Genetics, Institut Curie, University of Paris Saclay, 75005 Paris, France; (J.M.-P.); (S.V.); (C.F.); (A.S.); (I.B.)
- Department of Neurosurgery, Lariboisière Hospital, Assistance Publique des Hôpitaux de Paris, University of Paris, 75010 Paris, France;
| | - Ahmed Dahmani
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, University of Paris Saclay, 75005 Paris, France; (T.P.); (A.D.); (A.N.); (M.M.); (R.E.B.); (F.N.)
| | - Julien Masliah-Planchon
- Department of Genetics, Institut Curie, University of Paris Saclay, 75005 Paris, France; (J.M.-P.); (S.V.); (C.F.); (A.S.); (I.B.)
| | - Adnan Naguez
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, University of Paris Saclay, 75005 Paris, France; (T.P.); (A.D.); (A.N.); (M.M.); (R.E.B.); (F.N.)
| | - Marine Michou
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, University of Paris Saclay, 75005 Paris, France; (T.P.); (A.D.); (A.N.); (M.M.); (R.E.B.); (F.N.)
| | - Rania El Botty
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, University of Paris Saclay, 75005 Paris, France; (T.P.); (A.D.); (A.N.); (M.M.); (R.E.B.); (F.N.)
| | - Sophie Vacher
- Department of Genetics, Institut Curie, University of Paris Saclay, 75005 Paris, France; (J.M.-P.); (S.V.); (C.F.); (A.S.); (I.B.)
| | - Rachida Bouarich
- Integrated Cancer Research Site, Institut Curie, 75005 Paris, France; (R.B.); (F.B.)
| | - André Nicolas
- Department of Tumor Biology, Institut Curie, 75005 Paris, France;
| | - Marc Polivka
- Department of Pathology, Lariboisière Hospital, Assistance Publique des Hôpitaux de Paris, University of Paris, UMR 1141 Inserm, 75010 Paris, France; (M.P.); (H.A.-B.)
| | - Coralie Franck
- Department of Genetics, Institut Curie, University of Paris Saclay, 75005 Paris, France; (J.M.-P.); (S.V.); (C.F.); (A.S.); (I.B.)
| | - Anne Schnitzler
- Department of Genetics, Institut Curie, University of Paris Saclay, 75005 Paris, France; (J.M.-P.); (S.V.); (C.F.); (A.S.); (I.B.)
| | - Fariba Némati
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, University of Paris Saclay, 75005 Paris, France; (T.P.); (A.D.); (A.N.); (M.M.); (R.E.B.); (F.N.)
| | - Sergio Roman-Roman
- Department of Translational Research, Institut Curie, University of Paris Saclay, 75005 Paris, France;
| | - Franck Bourdeaut
- Integrated Cancer Research Site, Institut Curie, 75005 Paris, France; (R.B.); (F.B.)
| | - Homa Adle-Biassette
- Department of Pathology, Lariboisière Hospital, Assistance Publique des Hôpitaux de Paris, University of Paris, UMR 1141 Inserm, 75010 Paris, France; (M.P.); (H.A.-B.)
| | - Hamid Mammar
- Proton Therapy Center, Institut Curie, 91400 Orsay, France;
| | - Sébastien Froelich
- Department of Neurosurgery, Lariboisière Hospital, Assistance Publique des Hôpitaux de Paris, University of Paris, 75010 Paris, France;
| | - Ivan Bièche
- Department of Genetics, Institut Curie, University of Paris Saclay, 75005 Paris, France; (J.M.-P.); (S.V.); (C.F.); (A.S.); (I.B.)
| | - Didier Decaudin
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, University of Paris Saclay, 75005 Paris, France; (T.P.); (A.D.); (A.N.); (M.M.); (R.E.B.); (F.N.)
- Department of Medical Oncology, Institut Curie, 75005 Paris, France
- Correspondence: ; Tel.: +33-1-56-24-62-40
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Gañez-Zapater A, Mackowiak SD, Guo Y, Tarbier M, Jordán-Pla A, Friedländer MR, Visa N, Östlund Farrants AK. The SWI/SNF subunit BRG1 affects alternative splicing by changing RNA binding factor interactions with nascent RNA. Mol Genet Genomics 2022; 297:463-484. [PMID: 35187582 PMCID: PMC8960663 DOI: 10.1007/s00438-022-01863-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 01/23/2022] [Indexed: 11/29/2022]
Abstract
BRG1 and BRM are ATPase core subunits of the human SWI/SNF chromatin remodelling complexes mainly associated with transcriptional initiation. They also have a role in alternative splicing, which has been shown for BRM-containing SWI/SNF complexes at a few genes. Here, we have identified a subset of genes which harbour alternative exons that are affected by SWI/SNF ATPases by expressing the ATPases BRG1 and BRM in C33A cells, a BRG1- and BRM-deficient cell line, and analysed the effect on splicing by RNA sequencing. BRG1- and BRM-affected sub-sets of genes favouring both exon inclusion and exon skipping, with only a minor overlap between the ATPase. Some of the changes in alternative splicing induced by BRG1 and BRM expression did not require the ATPase activity. The BRG1-ATPase independent included exons displayed an exon signature of a high GC content. By investigating three genes with exons affected by the BRG-ATPase-deficient variant, we show that these exons accumulated phosphorylated RNA pol II CTD, both serine 2 and serine 5 phosphorylation, without an enrichment of the RNA polymerase II. The ATPases were recruited to the alternative exons, together with both core and signature subunits of SWI/SNF complexes, and promoted the binding of RNA binding factors to chromatin and RNA at the alternative exons. The interaction with the nascent RNP, however, did not reflect the association to chromatin. The hnRNPL, hnRNPU and SAM68 proteins associated with chromatin in cells expressing BRG1 and BRM wild type, but the binding of hnRNPU to the nascent RNP was excluded. This suggests that SWI/SNF can regulate alternative splicing by interacting with splicing-RNA binding factor and influence their binding to the nascent pre-mRNA particle.
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Affiliation(s)
- Antoni Gañez-Zapater
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, The Arrhenius Laboratories F4, 106 91, Stockholm, Sweden
- Center for Genomic Regulation, 08003, Barcelona, Spain
| | - Sebastian D Mackowiak
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91, Stockholm, Sweden
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany
| | - Yuan Guo
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, The Arrhenius Laboratories F4, 106 91, Stockholm, Sweden
| | - Marcel Tarbier
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91, Stockholm, Sweden
| | - Antonio Jordán-Pla
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, The Arrhenius Laboratories F4, 106 91, Stockholm, Sweden
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencies Biológicas, Valencia University, C/Dr. Moliner, 50, 46100, Burjassot, Spain
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91, Stockholm, Sweden
| | - Neus Visa
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, The Arrhenius Laboratories F4, 106 91, Stockholm, Sweden
| | - Ann-Kristin Östlund Farrants
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, The Arrhenius Laboratories F4, 106 91, Stockholm, Sweden.
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Xu W, Dong H, Ru G, Zhao M. ARID1A deficient undifferentiated spindle cell and rhabdoid sarcoma of the prostate: report of a unique case with emphasis on diagnostic implications. Diagn Pathol 2022; 17:22. [PMID: 35125107 PMCID: PMC8818209 DOI: 10.1186/s13000-022-01198-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 01/18/2022] [Indexed: 11/10/2022] Open
Abstract
Background SWItch Sucrose Non-Fermentable (SWI/SNF) chromatin-remodeling complex functions collectively as a tumor suppressor and the inactivation of any of its constituent components is frequently associated with tumor initiation and/or progression. Most SWI/SNF deficient tumors share common rhabdoid morphology. ARID1A is the most frequently dysregulated SWI/SNF subunit in human cancer and inactivation of ARID1A is frequent across carcinomatous types while very rarely drives the tumorigenesis of sarcomas. Herein, we report a rare case of primary prostatic undifferentiated spindle cell sarcoma with focal rhabdoid morphology, harboring biallelic inactivation of ARID1A detected by next-generation sequencing with complete loss of ARID1A expression by immunohistochemistry. Case presentation The patient is a 58-year-old man who presented with dysuria and obstructive voiding symptoms for 3 month and was found to have a large, ill-defined, prostatic mass lesion with circumferential extension into the rectal wall on imaging studies. A needle biopsy showed a spindle cell undifferentiated sarcoma of the prostate and the patient was treated by chemotherapy of combined etoposide and cisplatin for 2 months. A subsequent imaging study showed that the tumor was significantly enlarged, and the patient underwent laparoscopically radical prostatectomy. Gross examination showed a disrupted, 10 × 7 × 5 cm, solid and cystic mass involving almost the entire prostate and sparing the seminal vesicle glands. Histologic examination showed that tumor was composed mainly of mildly atypical, oval to spindle-shaped cells, arranged in sheets and fascicles or herringbone-like patterns within a small amount of edematous to myxoid, vascularized stroma. Notably, groups of discohesive rhabdoid tumor cells with eccentric nuclei, prominent nucleoli, and abundant globular cytoplasm were observed. There were prominent mitotic figures, multifocal geographic necroses, and foci of lymphovascular invasion. Immunohistochemistry showed that the tumor cells were diffusely positive for TLE-1 and vimentin and focally positive for epithelial membrane antigen, AE1/3, Cam5.2, SATB2, and CD34 (all in less than 10% tumor cells). Next-generation sequencing showed biallelic inactivation mutation of ARID1A; the predicted inactivating effect of ARID1A deletion was confirmed by immunohistochemical staining. After the surgery, the patient received an alternative combined chemotherapy of doxorubicin and ifosfamide for 5 months. The patient died 9 months after initial presentation due to extensive abdominal metastases. Conclusions We report an ARID1A deficient undifferentiated spindle cell and rhabdoid sarcoma of the prostate, adding to the growing spectrum of SWI/SNF driven undifferentiated sarcoma. Rhabdoid cells can be a helpful morphological clue for promoting molecular and immunohistochemical analyses for deficiency of SWI/SNF subunits, in the diagnostic workup of undifferentiated neoplasms featuring epithelioid or rhabdoid morphology. Supplementary Information The online version contains supplementary material available at 10.1186/s13000-022-01198-4.
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Wang R, Wang L, Fang J, Zhong Q, Hou L, Ma H, Feng L, He S, Wang C, Zhang L. Clinical diagnosis and treatment analyses on SMARCB1 (INI-1)-deficient sinonasal carcinoma: case series with systematic review of the literature. World Neurosurg 2022; 161:e229-e243. [PMID: 35123020 DOI: 10.1016/j.wneu.2022.01.114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/26/2022] [Accepted: 01/26/2022] [Indexed: 11/29/2022]
Abstract
OBJECTIVE This study aims to improve the understanding of SMARCB1 (INI-1)-deficient sinonasal carcinoma (SDSC) by analyzing its clinical features, treatment strategies and prognosis. METHODS Sixty-nine patients were included in this research: 15 new cases from Beijing Tongren Hospital, and 54 previously reported cases. We analyzed and summarized patients' epidemiological data, clinical features, and treatment regimens. Main outcomes were overall survival (OS) and recurrence-free survival (RFS). Univariate and multivariate analyses were performed using a Cox regression model for OS and RFS. RESULTS SDSC was more common in men than womanwith a median age of 52 (ranged from 21 to 89 years). Epistaxis (40.0%) and headache (36.7%) were the major complaints. The most common affected paranasal sinus was the ethmoid sinus (58.0%). For TNM stage, 66.7% cases were first diagnosed as T4N0M0. The tumor cells were complete loss of INI-1 in all cases by immunohistochemical analysis. However, 72.5% cases were first misdiagnosed initially. The 1-year, 3-year, and 5-year OS and RFS were 85.3%, 51.8%, 47.8%; and 56.8%, 38.2%, 35.3% respectively. The RFS of comprehensive treatment based on surgery was better than that of systemic therapy without surgery (P<0.05), Additionally, the OS and RFS of surgery with chemoradiotherapy was better than that of surgery with radiotherapy (P<0.05). Univariate and multivariate analysis identified treatment modality as an independent prognostic factor for SDSC patients. CONCLUSION Immunohistochemical analysis of SDSC during initial biopsy can prevent delays in diagnosis and treatment. Radical surgery resection combined with chemoradiotherapy may be the preferred treatment modality.
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Affiliation(s)
- Ru Wang
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Lingwa Wang
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Jugao Fang
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China.
| | - Qi Zhong
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Lizhen Hou
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Hongzhi Ma
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Ling Feng
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Shizhi He
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Chengshuo Wang
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China; Key Laboratory of Otolaryngology-Head and Neck Surgery, Capital Medical University, Beijing, PR China
| | - Luo Zhang
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China; Key Laboratory of Otolaryngology-Head and Neck Surgery, Capital Medical University, Beijing, PR China
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He DD, Shang XY, Wang N, Wang GX, He KY, Wang L, Han ZG. BRD4 inhibition induces synthetic lethality in ARID2-deficient hepatocellular carcinoma by increasing DNA damage. Oncogene 2022; 41:1397-1409. [PMID: 35017665 DOI: 10.1038/s41388-022-02176-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 12/02/2021] [Accepted: 01/04/2022] [Indexed: 02/06/2023]
Abstract
Hepatocellular carcinoma (HCC) has emerged as the third cause of cancer-related death owing to lacking effective systemic therapies. Genomic DNA sequencing revealed the high frequency of loss-of-function mutations in ARID2, which encodes a subunit of SWI/SNF chromatin remodeling complex, however, the therapeutic strategy for the HCC patients with ARID2 mutations is still completely unclear. In this study, we first performed a high-throughput screening approach using a compound library consisting of 2 180 FDA-approved drugs and other compounds, to elicit the potential drugs for synthetic lethality to target ARID2-deficient HCC cells. Interestingly, JQ1, a selective inhibitor of bromodomain protein BRD4, uniquely suppressed the growth of ARID2- deficient HCC cells. Next JQ1 is further confirmed to predominantly induce cell lethality upon ARID2 depletion through exacerbating DNA damage, especially double strand breaks (DSBs). Functional assays demonstrated that both BRD4 inhibition and ARID2 deficiency synergistically impede two main DNA damage repair pathways, homologous recombination (HR) and non-homologous end-joining (NHEJ), through attenuating the transcription of BRCA1, RAD51, and 53BP1, which encode the core molecules responsible for DSB repair. Mechanistically, both ARID2 and BRD4 exert a synergistic effect for maintaining transcriptional enhancer-promoter loops of these genes within chromatin conformation. However, as both ARID2 and BRD4 are disrupted, the expression of these DNA repair-related genes in response to DNA damage are hindered, resulting in DSB accumulation and cell apoptosis. Taken together, this study discloses that BRD4 inhibition may induce synthetic lethality in ARID2-deficient HCC cells, which might provide a potential therapeutic strategy for HCC patients with ARID2 mutations.
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Affiliation(s)
- Dan-Dan He
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xue-Ying Shang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Na Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Guang-Xing Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Kun-Yan He
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lan Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ze-Guang Han
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China. .,Hangzhou Innovation Institute for Systems Oncology (HIISCO), 3F Building 1, 2636 Yuhangtang Rd, Yuhang District, Hangzhou, 311121, Zhejiang Province, China.
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