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Ma Y, Field NR, Xie T, Briscas S, Kokinogoulis EG, Skipper TS, Alghalayini A, Sarker FA, Tran N, Bowden NA, Dickson KA, Marsh DJ. Aberrant SWI/SNF Complex Members Are Predominant in Rare Ovarian Malignancies-Therapeutic Vulnerabilities in Treatment-Resistant Subtypes. Cancers (Basel) 2024; 16:3068. [PMID: 39272926 PMCID: PMC11393890 DOI: 10.3390/cancers16173068] [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: 08/09/2024] [Revised: 08/30/2024] [Accepted: 09/02/2024] [Indexed: 09/15/2024] Open
Abstract
SWI/SNF (SWItch/Sucrose Non-Fermentable) is the most frequently mutated chromatin-remodelling complex in human malignancy, with over 20% of tumours having a mutation in a SWI/SNF complex member. Mutations in specific SWI/SNF complex members are characteristic of rare chemoresistant ovarian cancer histopathological subtypes. Somatic mutations in ARID1A, encoding one of the mutually exclusive DNA-binding subunits of SWI/SNF, occur in 42-67% of ovarian clear cell carcinomas (OCCC). The concomitant somatic or germline mutation and epigenetic silencing of the mutually exclusive ATPase subunits SMARCA4 and SMARCA2, respectively, occurs in Small cell carcinoma of the ovary, hypercalcaemic type (SCCOHT), with SMARCA4 mutation reported in 69-100% of SCCOHT cases and SMARCA2 silencing seen 86-100% of the time. Somatic ARID1A mutations also occur in endometrioid ovarian cancer (EnOC), as well as in the chronic benign condition endometriosis, possibly as precursors to the development of the endometriosis-associated cancers OCCC and EnOC. Mutation of the ARID1A paralogue ARID1B can also occur in both OCCC and SCCOHT. Mutations in other SWI/SNF complex members, including SMARCA2, SMARCB1 and SMARCC1, occur rarely in either OCCC or SCCOHT. Abrogated SWI/SNF raises opportunities for pharmacological inhibition, including the use of DNA damage repair inhibitors, kinase and epigenetic inhibitors, as well as immune checkpoint blockade.
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Affiliation(s)
- Yue Ma
- Translational Oncology Group, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Natisha R Field
- Translational Oncology Group, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Tao Xie
- Translational Oncology Group, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Sarina Briscas
- Translational Oncology Group, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Emily G Kokinogoulis
- Translational Oncology Group, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Tali S Skipper
- Translational Oncology Group, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Amani Alghalayini
- Translational Oncology Group, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Farhana A Sarker
- Translational Oncology Group, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Nham Tran
- School of Biomedical Engineering, Faculty of Engineering and IT, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Nikola A Bowden
- Drug Repurposing and Medicines Research Program, Hunter Medical Research Institute, Newcastle, NSW 2289, Australia
- School of Medicine and Public Health, University of Newcastle, Newcastle, NSW 2289, Australia
| | - Kristie-Ann Dickson
- Translational Oncology Group, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Deborah J Marsh
- Translational Oncology Group, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW 2007, Australia
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Zhou W, Chi H, Zhao X, Tao G, Gan J. A mutational signature and ARID1A mutation associated with outcome in hepatocellular carcinoma. Clin Transl Oncol 2024:10.1007/s12094-024-03669-0. [PMID: 39179940 DOI: 10.1007/s12094-024-03669-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 08/09/2024] [Indexed: 08/26/2024]
Abstract
OBJECTIVE The prognosis of hepatocellular carcinoma (HCC) is poor and there is no stable and reliable molecular biomarker for evaluation. This study attempted to find reliable prognostic markers from tumor mutational profiles. METHODS A total of 362 HCC samples with whole-exome sequencing were collected as discovery datasets, and 200 samples with targeted sequencing were used for validation of the relevant results. All HCC samples were obtained from previously published studies. Bayesian non-negative matrix factorization was used to extract mutational signatures, and multivariate Cox regression models were utilized to identify the prognostic role of mutational factors. Gene set enrichment analysis was employed to discover potential signaling pathways associated with specific mutational groups. RESULTS In the HCC discovery dataset, a total of four mutational signatures (i.e., signatures 4, 6, 16, and 22) were extracted, of which signature 16 characterized by T>C mutations was observed to be associated with favorable HCC prognosis, and this correlation was also found in the validation dataset. Further analysis showed that patients with ARID1A mutations exhibited inferior survival outcomes in both discovery and validation datasets. Mechanistic exploration revealed that the presence of signature 16 was associated with better immune infiltration and tumor immunogenicity, while patients with ARID1A mutations were away from these favorable immunological features. CONCLUSION By integrating somatic mutation data and clinical information of HCC, this study identified that signature 16 and ARID1A mutations were associated with better and worse outcomes respectively, providing a basis for prognosis prediction and clinical treatment strategies of HCC.
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Affiliation(s)
- Wei Zhou
- Department of Infectious Diseases, The First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, China
| | - Hao Chi
- Department of Medical Laboratory, Huaian Hospital of Huaian City, Huaian, China
| | - Xiaohu Zhao
- Department of Infectious Diseases, Huaian Hospital of Huaian City, Huaian, China
| | - Guangrong Tao
- Department of Infectious Diseases, Huaian Hospital of Huaian City, Huaian, China
| | - Jianhe Gan
- Department of Infectious Diseases, The First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, China.
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Zhang R, Yang X, Shi X, Xing E, Wang L, Hao C, Zhang Z. Bortezomib modulated the autophagy-lysosomal pathway in a TFEB-dependent manner in multiple myeloma. Leuk Res 2024; 138:107455. [PMID: 38368721 DOI: 10.1016/j.leukres.2024.107455] [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: 11/25/2023] [Revised: 01/29/2024] [Accepted: 02/05/2024] [Indexed: 02/20/2024]
Abstract
OBJECTIVE To explore the involvement of TFEB-mediated autophagy-lysosomal mechanisms in multiple myeloma (MM) during bortezomib treatment. METHODS MM cells were exposed to bortezomib or subjected to TFEB knockdown. CCK assay was used to assess the cell proliferation. Western blotting and fluorescent staining were conducted to examine autophagy and lysosomes. The TFEB expression pattern was analyzed, and whole transcriptome sequencing was carried out. Additionally, TFEB target genes were predicted using the GTRD(http://gtrd.biouml.org/) website, and pathway analysis was performed. RESULTS Bortezomib demonstrated a dose-dependent and time dependent inhibition of cell proliferation. In MM cells treated with bortezomib, LC3B, Beclin-1, TFEB, and Lamp1 exhibited upregulation in a time- and concentration-dependent manner. LysoTracker dye labeling showed an increase in lysosomes in the bortezomib-treated group. Moreover, bortezomib elevated the expression of lysosome-associated factor Lamp1. Bortezomib promoted the nuclear translocation of TFEB, leading to decreased cytoplasmic TFEB and increased nuclear TFEB. TFEB gene silencing reversed bortezomib's inhibitory effect on MM cell lines, significantly reducing autophagosome expression and lysosome numbers. Furthermore, bioinformatic analysis identified the MAPK pathway as a potential downstream target of TFEB. CONCLUSION Bortezomib effectively inhibits MM cell proliferation and induces autophagy, partly through TFEB-mediated mechanisms, with potential involvement of the MAPK pathway.
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Affiliation(s)
- Rongjuan Zhang
- Department of Internal Medicine, Hebei Medical University, Shijiazhaung 050000, China
| | - Xinhong Yang
- Department of Hematology, The Affiliated Hospital of Chengde Medical College, Chengde 067000, China
| | - Xiaomin Shi
- Department of Hematology, The Affiliated Hospital of Chengde Medical College, Chengde 067000, China
| | - Enhong Xing
- Department of central laboratory, The Affiliated Hospital of Chengde Medical College, Chengde 067000, China
| | - Lihong Wang
- Department of Hematology, The Affiliated Hospital of Chengde Medical College, Chengde 067000, China
| | - Changlai Hao
- Department of Internal Medicine, Hebei Medical University, Shijiazhaung 050000, China; Department of Hematology, The Affiliated Hospital of Chengde Medical College, Chengde 067000, China.
| | - Zhihua Zhang
- Department of Hematology, The Affiliated Hospital of Chengde Medical College, Chengde 067000, China.
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