1
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Foley KG, Adli M, Kim JJ. Single-nuclei sequencing of uterine serous carcinoma reveals racial differences in immune signaling. Proc Natl Acad Sci U S A 2024; 121:e2402998121. [PMID: 39133838 PMCID: PMC11348309 DOI: 10.1073/pnas.2402998121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 07/15/2024] [Indexed: 08/29/2024] Open
Abstract
Significant racial disparities exist between Black and White patients with uterine serous carcinoma (USC). While the reasons for these disparities are unclear, several studies have demonstrated significantly different rates of driver mutations between racial groups, including TP53. However, limited research has investigated the transcriptional differences of tumors or the composition of the tumor microenvironment (TME) between these groups. Here, we report the single-nuclei RNA-sequencing profiles of primary USC tumors from diverse racial backgrounds. We find that there are significant differences between the tumors of Black and White patients. Tumors from Black patients exhibited higher expression of specific genes associated with aggressiveness, such as PAX8, and axon guidance and synaptic signaling pathways. We also demonstrated that T cell populations are reduced in the tumor tissue compared to matched benign, while anti-inflammatory macrophage populations are retained within the TME. Furthermore, we investigated the connection between PAX8 overexpression and immunosuppression in USC through regulation of several cytokines and chemokines. Notably, we show that PAX8 activity can influence macrophage gene expression and protein secretion. These studies provide a detailed understanding of the USC transcriptome and TME, and identify differences in tumor biology from patients of different racial backgrounds.
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Affiliation(s)
- K. Grace Foley
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Robert H. Lurie Cancer Center, Northwestern University, Chicago, IL60611
| | - Mazhar Adli
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Robert H. Lurie Cancer Center, Northwestern University, Chicago, IL60611
| | - J. Julie Kim
- Division of Reproductive Science in Medicine, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Robert H. Lurie Cancer Center, Northwestern University, Chicago, IL60611
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2
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Chen Y, Jiang Q, Xue Y, Chen W, Hua M. CRISPR-Cas9-mediated deletion enhancer of MECOM play a tumor suppressor role in ovarian cancer. Funct Integr Genomics 2024; 24:125. [PMID: 38995475 DOI: 10.1007/s10142-024-01399-8] [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: 05/03/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 07/13/2024]
Abstract
MDS1 and EVI1 complex locus (MECOM), a transcription factor encoding several variants, has been implicated in progression of ovarian cancer. The function of regulatory regions in regulating MECOM expression in ovarian cancer is not fully understood. In this study, MECOM expression was evaluated in ovarian cancer cell lines treated with bromodomain and extraterminal (BET) inhibitor JQ-1. Oncogenic phenotypes were assayed using assays of CCK-8, colony formation, wound-healing and transwell. Oncogenic phenotypes were estimated in stable sgRNA-transfected OVCAR3 cell lines. Xenograft mouse model was assayed via subcutaneous injection of enhancer-deleted OVCAR3 cell lines. The results displayed that expression of MECOM is downregulated in cell lines treated with JQ-1. Data from published ChIP-sequencing (H3K27Ac) in 3 ovarian cancer cell lines displayed a potential enhancer around the first exon. mRNA and protein expression were downregulated in OVCAR3 cells after deletion of the MECOM enhancer. Similarly, oncogenic phenotypes both in cells and in the xenograft mouse model were significantly attenuated. This study demonstrates that JQ-1 can inhibit the expression of MECOM and tumorigenesis. Deletion of the enhancer activity of MECOM has an indispensable role in inhibiting ovarian cancer progress, which sheds light on a promising opportunity for ovarian cancer treatment through the application of this non-coding DNA deletion.
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Affiliation(s)
- Yujie Chen
- Department of Gynecology and Obstetrics, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong, 226001, China
| | - Qiuwen Jiang
- Department of Gynecology and Obstetrics, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong, 226001, China
| | - Yingzhuo Xue
- Department of Gynecology and Obstetrics, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong, 226001, China
| | - Weiguan Chen
- Department of Rehabilitation Medicine, the first People's Hospital of Nantong, No. 666 Shengli Road, Nantong, 226001, China
| | - Minhui Hua
- Department of Gynecology and Obstetrics, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong, 226001, China.
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3
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Luo Y, Liu X, Chen Y, Tang Q, He C, Ding X, Hu J, Cai Z, Li X, Qiao H, Zou Z. Targeting PAX8 sensitizes ovarian cancer cells to ferroptosis by inhibiting glutathione synthesis. Apoptosis 2024:10.1007/s10495-024-01985-y. [PMID: 38853202 DOI: 10.1007/s10495-024-01985-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2024] [Indexed: 06/11/2024]
Abstract
Ovarian cancer is a malignant tumor originating from the ovary, characterized by its high mortality rate and propensity for recurrence. In some patients, especially those with recurrent cancer, conventional treatments such as surgical resection or standard chemotherapy yield suboptimal results. Consequently, there is an urgent need for novel anti-cancer therapeutic strategies. Ferroptosis is a distinct form of cell death separate from apoptosis. Ferroptosis inducers have demonstrated promising potential in the treatment of ovarian cancer, with evidence indicating their ability to enhance ovarian cancer cell sensitivity to cisplatin. However, resistance of cancer cells to ferroptosis still remains an inevitable challenge. Here, we analyzed genome-scale CRISPR-Cas9 loss-of function screens and identified PAX8 as a ferroptosis resistance protein in ovarian cancer. We identified PAX8 as a susceptibility gene in GPX4-dependent ovarian cancer. Depletion of PAX8 rendered GPX4-dependent ovarian cancer cells significantly more sensitive to GPX4 inhibitors. Additionally, we found that PAX8 inhibited ferroptosis in ovarian cancer cells. Combined treatment with a PAX8 inhibitor and RSL3 suppressed ovarian cancer cell growth, induced ferroptosis, and was validated in a xenograft mouse model. Further exploration of the molecular mechanisms underlying PAX8 inhibition of ferroptosis mutations revealed upregulation of glutamate-cysteine ligase catalytic subunit (GCLC) expression. GCLC mediated the ferroptosis resistance induced by PAX8 in ovarian cancer. In conclusion, our study underscores the pivotal role of PAX8 as a therapeutic target in GPX4-dependent ovarian cancer. The combination of PAX8 inhibitors such as losartan and captopril with ferroptosis inducers represents a promising new approach for ovarian cancer therapy.
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Affiliation(s)
- Yanlin Luo
- Institute of Clinical Pharmacology, School of Basic Medical Science, Zhengzhou University, Zhengzhou, 450001, China
- Department of Gynecologic Oncology, The Affiliated Cancer Hospital of Zhengzhou University (Henan Cancer Hospital), Zhengzhou, 450008, China
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Xiaoli Liu
- The Fourth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510631, China
| | - Yibing Chen
- Genetic and Prenatal Diagnosis Center, Department of Gynecology and Obstetrics, First Affiliated Hospital, Zhengzhou University, Zhengzhou, 450052, China
| | - Qing Tang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Chengsi He
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Xinyi Ding
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Jiachun Hu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Zheyou Cai
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Xiang Li
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Hailing Qiao
- Institute of Clinical Pharmacology, School of Basic Medical Science, Zhengzhou University, Zhengzhou, 450001, China.
| | - Zhengzhi Zou
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China.
- Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China.
- Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, 510631, China.
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4
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Xu X, Zhang X, Chen J, Du X, Sun Y, Zhan L, Wang W, Li Y. Exploring the molecular mechanisms by which per- and polyfluoroalkyl substances induce polycystic ovary syndrome through in silico toxicogenomic data mining. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 275:116251. [PMID: 38537477 DOI: 10.1016/j.ecoenv.2024.116251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 03/01/2024] [Accepted: 03/20/2024] [Indexed: 04/12/2024]
Abstract
The pathogeny of polycystic ovary syndrome (PCOS) is intricate, with endocrine disruptors (EDCs) being acknowledged as significant environmental factors. Research has shown a link between exposure to per- and polyfluoroalkyl substances (PFAS) and the development and progression of PCOS, although the precise mechanism is not fully understood. This study utilized toxicogenomics and comparative toxicogenomics databases to analyze data and investigate how PFAS mixtures may contribute to the development of PCOS. The results indicated that 74 genes are associated with both PFAS exposure and PCOS progression. Enrichment analysis suggested that cell cycle regulation and steroid hormone synthesis may be crucial pathways through which PFAS mixtures participate in the development of PCOS, involving important genes such as CCNB1 and SRD5A1. Furthermore, the study identified transcription factors (TFs) and miRNAs that may be involved in the onset and progression of PCOS, constructing regulatory networks encompassing TFs-mRNA interactions and miRNA-mRNA relationships to elucidate their regulatory roles in gene expression. By utilizing data mining techniques based on toxicogenomic databases, this study provides relatively comprehensive insights into the association between exposure factors and diseases compared to traditional toxicology studies. These findings offer new perspectives for further in vivo or in vitro investigations and contribute to understanding the pathogenesis of PCOS, thereby providing valuable references for identifying clinical treatment targets.
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Affiliation(s)
- Xueming Xu
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment factors and Cancer, Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, Fujian Province 350122, China
| | - Xiaoping Zhang
- Ganzhou Ganxian District Maternity and Child Health Hospital, Ganzhou, Jiangxi Province 341100, China
| | - Jiake Chen
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment factors and Cancer, Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, Fujian Province 350122, China
| | - Xiushuai Du
- School of Public Health, Fudan University, Shanghai 200032, China
| | - Yi Sun
- Research Center for Environment and Female Reproductive Health, the Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China
| | - Liqin Zhan
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment factors and Cancer, Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, Fujian Province 350122, China
| | - Wenxiang Wang
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment factors and Cancer, Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, Fujian Province 350122, China
| | - Yuchen Li
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment factors and Cancer, Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, Fujian Province 350122, China.
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5
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Ng-Blichfeldt JP, Stewart BJ, Clatworthy MR, Williams JM, Röper K. Identification of a core transcriptional program driving the human renal mesenchymal-to-epithelial transition. Dev Cell 2024; 59:595-612.e8. [PMID: 38340720 PMCID: PMC7616043 DOI: 10.1016/j.devcel.2024.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 11/28/2023] [Accepted: 01/17/2024] [Indexed: 02/12/2024]
Abstract
During kidney development, nephron epithelia arise de novo from fate-committed mesenchymal progenitors through a mesenchymal-to-epithelial transition (MET). Downstream of fate specification, transcriptional mechanisms that drive establishment of epithelial morphology are poorly understood. We used human iPSC-derived renal organoids, which recapitulate nephrogenesis, to investigate mechanisms controlling renal MET. Multi-ome profiling via snRNA-seq and ATAC-seq of organoids identified dynamic changes in gene expression and chromatin accessibility driven by activators and repressors throughout MET. CRISPR interference identified that paired box 8 (PAX8) is essential for initiation of MET in human renal organoids, contrary to in vivo mouse studies, likely by activating a cell-adhesion program. While Wnt/β-catenin signaling specifies nephron fate, we find that it must be attenuated to allow hepatocyte nuclear factor 1-beta (HNF1B) and TEA-domain (TEAD) transcription factors to drive completion of MET. These results identify the interplay between fate commitment and morphogenesis in the developing human kidney, with implications for understanding both developmental kidney diseases and aberrant epithelial plasticity following adult renal tubular injury.
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Affiliation(s)
- John-Poul Ng-Blichfeldt
- MRC-Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Benjamin J Stewart
- Molecular Immunity Unit, Department of Medicine, MRC-Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK; Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Menna R Clatworthy
- Molecular Immunity Unit, Department of Medicine, MRC-Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK; Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK
| | - Julie M Williams
- Bioscience Renal, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Katja Röper
- MRC-Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
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6
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Fujii M, Sekine S, Sato T. Decoding the basis of histological variation in human cancer. Nat Rev Cancer 2024; 24:141-158. [PMID: 38135758 DOI: 10.1038/s41568-023-00648-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/21/2023] [Indexed: 12/24/2023]
Abstract
Molecular abnormalities that shape human neoplasms dissociate their phenotypic landscape from that of the healthy counterpart. Through the lens of a microscope, tumour pathology optically captures such aberrations projected onto a tissue slide and has categorized human epithelial neoplasms into distinct histological subtypes based on the diverse morphogenetic and molecular programmes that they manifest. Tumour histology often reflects tumour aggressiveness, patient prognosis and therapeutic vulnerability, and thus has been used as a de facto diagnostic tool and for making clinical decisions. However, it remains elusive how the diverse histological subtypes arise and translate into pleiotropic biological phenotypes. Molecular analysis of clinical tumour tissues and their culture, including patient-derived organoids, and add-back genetic reconstruction of tumorigenic pathways using gene engineering in culture models and rodents further elucidated molecular mechanisms that underlie morphological variations. Such mechanisms include genetic mutations and epigenetic alterations in cellular identity codes that erode hard-wired morphological programmes and histologically digress tumours from the native tissues. Interestingly, tumours acquire the ability to grow independently of the niche-driven stem cell ecosystem along with these morphological alterations, providing a biological rationale for histological diversification during tumorigenesis. This Review comprehensively summarizes our current understanding of such plasticity in the histological and lineage commitment fostered cooperatively by molecular alterations and the tumour environment, and describes basic and clinical implications for future cancer therapy.
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Affiliation(s)
- Masayuki Fujii
- Department of Integrated Medicine and Biochemistry, Keio University School of Medicine, Tokyo, Japan.
| | - Shigeki Sekine
- Division of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan
| | - Toshiro Sato
- Department of Integrated Medicine and Biochemistry, Keio University School of Medicine, Tokyo, Japan.
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7
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Li A, Li M, Wang J, Zhou J, Yang T, Fan M, Zhang K, Gao H, Ren H, Chen M. MECOM: a bioinformatics and experimentally identified marker for the diagnosis and prognosis of lung adenocarcinoma. Biomark Med 2024; 18:79-91. [PMID: 38440890 DOI: 10.2217/bmm-2023-0600] [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] [Indexed: 03/06/2024] Open
Abstract
Objective: We aimed to explore the clinical value of MDS1 and EVI1 complex locus (MECOM) in lung adenocarcinoma (LUAD). Methods: Bioinformatics and experimental validation confirmed MECOM expression levels in LUAD. The value of MECOM was analyzed by receiver operating characteristic (ROC) curve and Cox regression analysis. Results: Serum MECOM levels were lower in LUAD and correlated with gender, TNM stage, tumor size, lymph node metastasis and distant metastasis. The ROC curve showed that the area under the curve of MECOM was 0.804 for LUAD and, of note, could reach 0.889 for advanced LUAD; specificity was up to 90%. Conclusion: MECOM may contribute to independently identifying LUAD patients, particularly in advanced stages.
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Affiliation(s)
- Anqi Li
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Meng Li
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Jing Wang
- Department of Pulmonary & Critical Care Medicine, Shaanxi Provincial Second People's Hospital, Xi'an, 710005, China
| | - Jiejun Zhou
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Tian Yang
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Meng Fan
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Kun Zhang
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Hengxing Gao
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Hui Ren
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Mingwei Chen
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
- Department of Pulmonary & Critical Care Medicine, Shaanxi Provincial Second People's Hospital, Xi'an, 710005, China
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8
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Chen Z, Li P, Shen L, Jiang X. Heat shock protein B7 (HSPB7) inhibits lung adenocarcinoma progression by inhibiting glycolysis. Oncol Rep 2023; 50:196. [PMID: 37732539 PMCID: PMC10560864 DOI: 10.3892/or.2023.8633] [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: 05/24/2023] [Accepted: 09/04/2023] [Indexed: 09/22/2023] Open
Abstract
In the present study, it was aimed to investigate the effects and potential mechanisms of heat shock protein B7 (HSPB7) on lung adenocarcinoma (LUAD). Bioinformatic analysis was performed to explore the association between HSPB7 expression and patients with LUAD. MTT, colony formation, wound healing and Transwell assays were performed to examine the proliferative, migratory and invasive abilities of H1975 and A549 cells. Western blot analysis was conducted to determine the corresponding protein expression. Co‑Immunoprecipitation and Chromatin immunoprecipitation assays were carried out to reveal the interaction between HSPB7 and myelodysplastic syndrome 1 and ecotropic viral integration site 1 complex locus (MECOM). In addition, an animal model was conducted by the subcutaneous injection of A549 cells into BALB/c nude mice, and tumor weight and size were measured. HSPB7 was downregulated in LUAD tissues and cells, and its expression level correlated with patient prognosis. Cell functional data revealed that silencing of HSPB7 promoted lung cancer cell proliferation, migration, invasion and epithelial mesenchymal transition (EMT); whereas overexpression of HSPB7 led to the opposite results. Furthermore, bioinformatics analysis showed that HSPB7 inhibited glycolysis. HSPB7 decreased glucose consumption, lactic acid production, and lactate dehydrogenase A, hexokinase 2 and pyruvate kinase muscle isoform 2 protein levels. The results demonstrated that MECOM was a transcription factor of HSPB7. Collectively, these results suggested that HSPB7 is regulated by MECOM, and that HSPB7 attenuates LUAD cell proliferation, migration, invasion and EMT by inhibiting glycolysis.
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Affiliation(s)
- Zhitao Chen
- Department of Thoracic Surgery, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250013, P.R. China
| | - Peipei Li
- Department of General Surgery, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250013, P.R. China
| | - Lingguang Shen
- Department of General Surgery, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250013, P.R. China
| | - Xiuyu Jiang
- Health Management Center, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250013, P.R. China
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9
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Subramanian A, Su S, Moding EJ, Binkley MS. Investigating the tissue specificity and prognostic impact of cis-regulatory cancer risk variants. Hum Genet 2023; 142:1395-1405. [PMID: 37474751 DOI: 10.1007/s00439-023-02586-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/07/2023] [Indexed: 07/22/2023]
Abstract
The tissue-specific incidence of cancers and their genetic basis are poorly understood. Although prior studies have shown global correlation across tissues for cancer risk single-nucleotide polymorphisms (SNPs) identified through genome-wide association studies (GWAS), any shared functional regulation of gene expression on a per SNP basis has not been well characterized. We set to quantify cis-mediated gene regulation and tissue sharing for SNPs associated with eight common cancers. We identify significant tissue sharing for individual SNPs and global enrichment for breast, colorectal, and Hodgkin lymphoma cancer risk SNPs in multiple tissues. In addition, we observe increasing tissue sharing for cancer risk SNPs overlapping with super-enhancers for breast cancer and Hodgkin lymphoma providing further evidence of tissue specificity. Finally, for genes under cis-regulation by breast cancer SNPs, we identify a phenotype characterized by low expression of tumor suppressors and negative regulators of the WNT pathway associated with worse freedom from progression and overall survival in patients who eventually develop breast cancer. Our results introduce a paradigm for functionally annotating individual cancer risk SNPs and will inform the design of future translational studies aimed to personalize assessment of inherited cancer risk across tissues.
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Affiliation(s)
- Ajay Subramanian
- Department of Radiation Oncology, Stanford Cancer Institute and Stanford University School of Medicine, Stanford, CA, USA
| | - Shengqin Su
- Department of Radiation Oncology, Stanford Cancer Institute and Stanford University School of Medicine, Stanford, CA, USA
| | - Everett J Moding
- Department of Radiation Oncology, Stanford Cancer Institute and Stanford University School of Medicine, Stanford, CA, USA
| | - Michael Sargent Binkley
- Department of Radiation Oncology, Stanford Cancer Institute and Stanford University School of Medicine, Stanford, CA, USA.
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10
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Ara MG, Motalleb G, Velasco B, Rahdar A, Taboada P. Antineoplastic effect of paclitaxel-loaded polymeric nanocapsules on malignant human ovarian carcinoma cells (SKOV-3). J Mol Liq 2023; 384:122190. [DOI: 10.1016/j.molliq.2023.122190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/30/2023]
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11
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Jank P, Leichsenring J, Kolb S, Hoffmann I, Bischoff P, Kunze CA, Dragomir MP, Gleitsmann M, Jesinghaus M, Schmitt WD, Kulbe H, Sers C, Stenzinger A, Sehouli J, Braicu IE, Westhoff C, Horst D, Denkert C, Gröschel S, Taube ET. High EVI1 and PARP1 expression as favourable prognostic markers in high-grade serous ovarian carcinoma. J Ovarian Res 2023; 16:150. [PMID: 37525239 PMCID: PMC10388497 DOI: 10.1186/s13048-023-01239-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/16/2023] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND Mechanisms of development and progression of high-grade serous ovarian cancer (HGSOC) are poorly understood. EVI1 and PARP1, part of TGF-ß pathway, are upregulated in cancers with DNA repair deficiencies with DNA repair deficiencies and may influce disease progression and survival. Therefore we questioned the prognostic significance of protein expression of EVI1 alone and in combination with PARP1 and analyzed them in a cohort of patients with HGSOC. METHODS For 562 HGSOC patients, we evaluated EVI1 and PARP1 expression by immunohistochemical staining on tissue microarrays with QuPath digital semi-automatic positive cell detection. RESULTS High EVI1 expressing (> 30% positive tumor cells) HGSOC were associated with improved progression-free survival (PFS) (HR = 0.66, 95% CI: 0.504-0.852, p = 0.002) and overall survival (OS) (HR = 0.45, 95% CI: 0.352-0.563, p < 0.001), including multivariate analysis. Most interestingly, mutual high expression of both proteins identifies a group with particularly good prognosis. Our findings were proven technically and clinically using bioinformatical data sets for single-cell sequencing, copy number variation and gene as well as protein expression. CONCLUSIONS EVI1 and PARP1 are robust prognostic biomarkers for favorable prognosis in HGSOC and imply further research with respect to their reciprocity.
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Affiliation(s)
- Paul Jank
- Institute of Pathology, Philipps-University Marburg, University Hospital Marburg (UKGM), Marburg, Germany
| | - Jonas Leichsenring
- Institute of Pathology, Zytologie Und Molekulare Diagnostik, REGIOMED, Klinikum Coburg, Coburg, Germany
| | - Svenja Kolb
- Department of Gynecology, Vivantes Netzwerk Für Gesundheit GmbH Berlin, Vivantes Hospital Neukölln, Rudower Straße 48, 12351, Berlin, Germany
| | - Inga Hoffmann
- Institute of Pathology, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität Zu Berlin, CCM, Charitéplatz 1, 10117, Berlin, Germany
| | - Philip Bischoff
- Institute of Pathology, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität Zu Berlin, CCM, Charitéplatz 1, 10117, Berlin, Germany
| | - Catarina Alisa Kunze
- Institute of Pathology, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität Zu Berlin, CCM, Charitéplatz 1, 10117, Berlin, Germany
| | - Mihnea P Dragomir
- Institute of Pathology, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität Zu Berlin, CCM, Charitéplatz 1, 10117, Berlin, Germany
| | - Moritz Gleitsmann
- Institute of Pathology, Philipps-University Marburg, University Hospital Marburg (UKGM), Marburg, Germany
| | - Moritz Jesinghaus
- Institute of Pathology, Philipps-University Marburg, University Hospital Marburg (UKGM), Marburg, Germany
| | - Wolfgang D Schmitt
- Institute of Pathology, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität Zu Berlin, CCM, Charitéplatz 1, 10117, Berlin, Germany
| | - Hagen Kulbe
- Tumorbank Ovarian Cancer Network, Charité, Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany
- Department of Gynecology, European Competence Center for Ovarian Cancer, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany
| | - Christine Sers
- Institute of Pathology, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität Zu Berlin, CCM, Charitéplatz 1, 10117, Berlin, Germany
| | | | - Jalid Sehouli
- Tumorbank Ovarian Cancer Network, Charité, Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany
- Department of Gynecology, European Competence Center for Ovarian Cancer, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany
| | - Ioana Elena Braicu
- Tumorbank Ovarian Cancer Network, Charité, Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany
- Department of Gynecology, European Competence Center for Ovarian Cancer, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany
| | - Christina Westhoff
- Institute of Pathology, Philipps-University Marburg, University Hospital Marburg (UKGM), Marburg, Germany
| | - David Horst
- Institute of Pathology, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität Zu Berlin, CCM, Charitéplatz 1, 10117, Berlin, Germany
| | - Carsten Denkert
- Institute of Pathology, Philipps-University Marburg, University Hospital Marburg (UKGM), Marburg, Germany
| | | | - Eliane T Taube
- Institute of Pathology, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität Zu Berlin, CCM, Charitéplatz 1, 10117, Berlin, Germany.
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12
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Nameki RA, Chang H, Yu P, Abbasi F, Lin X, Reddy J, Haro M, Fonseca MAS, Freedman ML, Drapkin R, Corona RI, Lawrenson K. Rewiring of master transcription factor cistromes during high-grade serous ovarian cancer development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.11.536378. [PMID: 37090516 PMCID: PMC10120620 DOI: 10.1101/2023.04.11.536378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
The transcription factors MECOM, PAX8, SOX17 and WT1 are candidate master regulators of high-grade serous 'ovarian' cancer (HGSC), yet their cooperative role in the hypothesized tissue of origin, the fallopian tube secretory epithelium (FTSEC) is unknown. We generated 26 epigenome (CUT&TAG, CUT&RUN, ATAC-seq and HiC) data sets and 24 profiles of RNA-seq transcription factor knock-down followed by RNA sequencing in FTSEC and HGSC models to define binding sites and gene sets regulated by these factors in cis and trans. This revealed that MECOM, PAX8, SOX17 and WT1 are lineage-enriched, super-enhancer associated master regulators whose cooperative DNA-binding patterns and target genes are re-wired during tumor development. All four TFs were indispensable for HGSC clonogenicity and survival but only depletion of PAX8 and WT1 impaired FTSEC cell survival. These four TFs were pharmacologically inhibited by transcriptional inhibitors only in HGSCs but not in FTSECs. Collectively, our data highlights that tumor-specific epigenetic remodeling is tightly related to MECOM, PAX8, SOX17 and WT1 activity and these transcription factors are targetable in a tumor-specific manner through transcriptional inhibitors.
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Affiliation(s)
- Robbin A. Nameki
- Women’s Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Heidi Chang
- Women’s Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Pak Yu
- Women’s Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Forough Abbasi
- Women’s Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Xianzhi Lin
- Women’s Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jessica Reddy
- Women’s Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Marcela Haro
- Women’s Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Marcos AS Fonseca
- Women’s Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Matthew L. Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Ronny Drapkin
- Ovarian Cancer Research Center, Department of Obstetrics and Gynecology, University of Pennsylvania Perelman School of Medicine, PA, USA
| | - Rosario I. Corona
- Women’s Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kate Lawrenson
- Women’s Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Cancer Prevention and Control Program, Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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13
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Patient-specific identification of genome-wide DNA-methylation differences between intracranial and extracranial melanoma metastases. Sci Rep 2023; 13:444. [PMID: 36624125 PMCID: PMC9829750 DOI: 10.1038/s41598-022-24940-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/22/2022] [Indexed: 01/11/2023] Open
Abstract
Melanomas frequently metastasize to distant organs and especially intracranial metastases still represent a major clinical challenge. Epigenetic reprogramming of intracranial metastases is thought to be involved in therapy failure, but so far only little is known about patient-specific DNA-methylation differences between intra- and extracranial melanoma metastases. Hierarchical clustering of the methylomes of 24 patient-matched intra- and extracranial melanoma metastases pairs revealed that intra- and extracranial metastases of individual patients were more similar to each other than to metastases in the same tissue from other patients. Therefore, a personalized analysis of each metastases pair was done by a Hidden Markov Model to classify methylation levels of individual CpGs as decreased, unchanged or increased in the intra- compared to the extracranial metastasis. The predicted DNA-methylation alterations were highly patient-specific differing in the number and methylation states of altered CpGs. Nevertheless, four important general observations were made: (i) intracranial metastases of most patients mainly showed a reduction of DNA-methylation, (ii) cytokine signaling was most frequently affected by differential methylation in individual metastases pairs, but also MAPK, PI3K/Akt and ECM signaling were often altered, (iii) frequently affected genes were mainly involved in signaling, growth, adhesion or apoptosis, and (iv) an enrichment of functional terms related to channel and transporter activities supports previous findings for a brain-like phenotype. In addition, the derived set of 17 signaling pathway genes that distinguished intra- from extracranial metastases in more than 50% of patients included well-known oncogenes (e.g. PRKCA, DUSP6, BMP4) and several other genes known from neuronal disorders (e.g. EIF4B, SGK1, CACNG8). Moreover, associations of gene body methylation alterations with corresponding gene expression changes revealed that especially the three signaling pathway genes JAK3, MECOM, and TNXB differ strongly in their expression between patient-matched intra- and extracranial metastases. Our analysis contributes to an in-depth characterization of DNA-methylation differences between patient-matched intra- and extracranial melanoma metastases and may provide a basis for future experimental studies to identify targets for new therapeutic approaches.
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14
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Salvi A, Hardy LR, Heath KN, Watry S, Pergande MR, Cologna SM, Burdette JE. PAX8 modulates the tumor microenvironment of high grade serous ovarian cancer through changes in the secretome. Neoplasia 2022; 36:100866. [PMID: 36586182 PMCID: PMC9816987 DOI: 10.1016/j.neo.2022.100866] [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: 10/18/2022] [Revised: 12/05/2022] [Accepted: 12/13/2022] [Indexed: 12/31/2022] Open
Abstract
High grade serous ovarian cancer (HGSC) arises from the fimbriated end of the fallopian tube epithelium (FTE), and in some cases, the ovarian surface epithelium (OSE). PAX8 is a commonly used biomarker for HGSC and is expressed in ∼90% of HGSC. Although the OSE does not express PAX8, murine models of HGSC derived from the OSE acquire PAX8, suggesting that it is not only a marker of Müllerian origin, but also an essential part of cancer progression, potentially from both the OSE and FTE. Previously, we have shown that PAX8 loss in HGSC cells causes tumor cell death and reduces cell migration and invasion. Herein, secretome analysis was performed in PAX8 deleted cells and we identified a reduction of the extracellular matrix (ECM) components, collagen and fibronectin. Immunoblotting and immunofluorescence in PAX8 deleted HGSC cells further validated the results from the secretome analysis. PAX8 loss reduced the amount of secreted TGFbeta, a cytokine that plays a crucial role in remodelling the tumor microenvironment. Furthermore, PAX8 loss reduced the integrity of 3D spheroids and caused a reduction of ECM proteins fibronectin and collagen in 3D cultures. Due to the ubiquitous nature of PAX8 in HGSC, regardless of cell origin, and the association of its reduced expression with decreasing tumor burden, a PAX8 inhibitor could be a promising drug target against various types of HGSC. To accomplish this, we generated a murine oviductal epithelial (MOE) cell line stably expressing PAX8 promoter-luciferase. Using this cell line, we performed a screening assay with a library of FDA-approved drugs (Prestwick Library) and quantitatively assessed these compounds for their inhibition of PAX8. We identified two hits: losartan and captropril, both inhibitors of the renin-angiotensin pathway that inhibit PAX8 expression and function. Overall, this study validates PAX8 as a regulator of ECM deposition in the tumor microenvironment.
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Affiliation(s)
- Amrita Salvi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Laura R. Hardy
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Kimberly N. Heath
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Samantha Watry
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Melissa R. Pergande
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Stephanie M. Cologna
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Joanna E. Burdette
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA,Corresponding author.
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15
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Di Palma T, Zannini M. PAX8 as a Potential Target for Ovarian Cancer: What We Know so Far. Onco Targets Ther 2022; 15:1273-1280. [PMID: 36275185 PMCID: PMC9584354 DOI: 10.2147/ott.s361511] [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: 06/30/2022] [Accepted: 10/13/2022] [Indexed: 11/22/2022] Open
Abstract
The Fallopian tube epithelium harbors the origin cells for the majority of high-grade serous ovarian carcinomas (HGSCs), the most lethal form of gynecologic malignancies. PAX8 belongs to the paired-box gene family of transcription factors and it is a marker of the FTE secretory cell lineage. Its role has been investigated in migration, invasion, proliferation, cell survival, stem cell maintenance, angiogenesis and tumor growth. In this review, we focus on the pro-tumorigenic role of PAX8 in ovarian cancer; in this context, PAX8 possibly continues to exert its transcriptional activity on its physiological targets but may also function on newly available targets after the tumorigenic hits. Acquiring new insights into the different PAX8 mechanism(s) of action in the tumor microenvironment could uncover new viable therapeutic targets and thus improve the current treatment regimen.
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Affiliation(s)
- Tina Di Palma
- IEOS - Institute of Experimental Endocrinology and Oncology ‘G. Salvatore’, National Research Council, Napoli, 80131, Italy
| | - Mariastella Zannini
- IEOS - Institute of Experimental Endocrinology and Oncology ‘G. Salvatore’, National Research Council, Napoli, 80131, Italy,Correspondence: Mariastella Zannini, IEOS - Institute of Experimental Endocrinology and Oncology ‘G. Salvatore’, National Research Council, via S. Pansini 5, Napoli, 80131, Italy, Tel +39-081-5465530, Fax +39-081-2296674, Email
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16
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Hu S, Gan H, Yang F. Significance analysis of PAX8 expression in endometrial carcinoma. Medicine (Baltimore) 2022; 101:e31159. [PMID: 36281161 PMCID: PMC9592497 DOI: 10.1097/md.0000000000031159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
To analyze the expression and prognostic value of paired-box 8 (PAX8) expression in uterine corpus endometrial carcinoma (UCEC) by bioinformatics. The expression of PAX8 gene in UCEC was analyzed by R language and immunohistochemistry. The correlation between PAX8 expression and clinicopathological features was analyzed by R language. The prognostic factors was analyzed by univariate/multivariate regression. The survival curve of patients was analyzed by Kaplan-Meier Plotter (K-M Plotter). The diagnostic value of PAX8 in UCEC was analyzed by receiver operating characteristic curve, and the relationship between PAX8 expression and methylation was analyzed by Ualcan. The relationship between methylation and prognosis was analyzed by MethSurv database. The expression of PAX8 in cancer tissues was significantly higher than that in normal tissues. The expression of PAX8 was related to clinical stage, age, histological type, histologic grade, tumor invasion and disease-specific survival event. Univariate/multivariate regression analysis showed that clinical stage, tumor invasion, and PAX8 expression were the influence factors of overall survival (OS), while histologic grade and PAX8 expression were the influence factors of disease-specific survival, and patients with low expression had a longer OS. The area under the curve of receiver operating characteristic curve was 0.81 for PAX8 diagnosis of UCEC. PAX8 was hypomethylated in cancer tissue, and patients with hypermethylated PAX8 had a longer OS. The high expression of PAX8 induced by hypomethylation may play an important role in the occurrence and prognosis of UCEC.
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Affiliation(s)
- Shan Hu
- Department of Obstetrics and Gynecology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, P.R. China
| | - Hua Gan
- Department of Orthopaedic, XiangZhou District Renmin Hospital, Xiangyang, Hubei, P.R. China
| | - Fengmei Yang
- Department of Obstetrics and Gynecology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, P.R. China
- * Correspondence: Fengmei Yang, Department of Obstetrics and Gynecology, Taihe Hospital, Hubei University of Medicine, Renmin Southern 32, Shiyan, Hubei 442000, P.R. China (e-mail: )
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17
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Nameki R, Shetty A, Dareng E, Tyrer J, Lin X, Pharoah P, Corona RI, Kar S, Lawrenson K. chromMAGMA: regulatory element-centric interrogation of risk variants. Life Sci Alliance 2022; 5:e202201446. [PMID: 35777959 PMCID: PMC9251535 DOI: 10.26508/lsa.202201446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 11/24/2022] Open
Abstract
Candidate causal risk variants from genome-wide association studies reside almost exclusively in noncoding regions of the genome and innovative approaches are necessary to understand their biological function. Multi-marker analysis of genomic annotation (MAGMA) is a widely used program that nominates candidate risk genes by mapping single-nucleotide polymorphism summary statistics from genome-wide association studies to gene bodies. We augmented MAGMA to create chromatin-MAGMA (chromMAGMA), a method to nominate candidate risk genes based on the presence of risk variants within noncoding regulatory elements (REs). We applied chromMAGMA to a genetic susceptibility dataset for epithelial ovarian cancer (EOC), a rare gynecologic malignancy characterized by high mortality. This identified 155 unique candidate EOC risk genes across five EOC histotypes; 83% (105/127) of high-grade serous ovarian cancer risk genes had not previously been implicated in this EOC histotype. Risk genes nominated by chromMAGMA converged on mRNA splicing and transcriptional dysregulation pathways. chromMAGMA is a pipeline that nominates candidate risk genes through a gene regulation-focused approach and helps interpret the biological mechanism of noncoding risk variants for complex diseases.
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Affiliation(s)
- Robbin Nameki
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Anamay Shetty
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Eileen Dareng
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jonathan Tyrer
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Xianzhi Lin
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Paul Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Rosario I Corona
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Siddhartha Kar
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Kate Lawrenson
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Cancer Prevention and Control Program, Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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18
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Kakun RR, Melamed Z, Perets R. PAX8 in the Junction between Development and Tumorigenesis. Int J Mol Sci 2022; 23:ijms23137410. [PMID: 35806410 PMCID: PMC9266416 DOI: 10.3390/ijms23137410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/25/2022] [Accepted: 06/28/2022] [Indexed: 12/17/2022] Open
Abstract
Normal processes of embryonic development and abnormal transformation to cancer have many parallels, and in fact many aberrant cancer cell capabilities are embryonic traits restored in a distorted, unorganized way. Some of these capabilities are cell autonomous, such as proliferation and resisting apoptosis, while others involve a complex interplay with other cells that drives significant changes in neighboring cells. The correlation between embryonic development and cancer is driven by shared proteins. Some embryonic proteins disappear after embryogenesis in adult differentiated cells and are restored in cancer, while others are retained in adult cells, acquiring new functions upon transformation to cancer. Many embryonic factors embraced by cancer cells are transcription factors; some are master regulators that play a major role in determining cell fate. The paired box (PAX) domain family of developmental transcription factors includes nine members involved in differentiation of various organs. All paired box domain proteins are involved in different cancer types carrying pro-tumorigenic or anti-tumorigenic roles. This review focuses on PAX8, a master regulator of transcription in embryonic development of the thyroid, kidney, and male and female genital tracts. We detail the role of PAX8 in each of these organ systems, describe its role during development and in the adult if known, and highlight its pro-tumorigenic role in cancers that emerge from PAX8 expressing organs.
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Affiliation(s)
- Reli Rachel Kakun
- Bruce and Ruth Rappaport Faculty of Medicine, Technion–Israel Institute of Technology, Haifa 3109601, Israel;
- Clinical Research Institute at Rambam, Rambam Health Care Campus, Haifa 3109601, Israel
| | - Zohar Melamed
- Division of Oncology, Rambam Health Care Campus, Haifa 3109601, Israel;
| | - Ruth Perets
- Bruce and Ruth Rappaport Faculty of Medicine, Technion–Israel Institute of Technology, Haifa 3109601, Israel;
- Clinical Research Institute at Rambam, Rambam Health Care Campus, Haifa 3109601, Israel
- Division of Oncology, Rambam Health Care Campus, Haifa 3109601, Israel;
- Correspondence:
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19
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Zhu EY, Dupuy AJ. Machine learning approach informs biology of cancer drug response. BMC Bioinformatics 2022; 23:184. [PMID: 35581546 PMCID: PMC9112473 DOI: 10.1186/s12859-022-04720-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 05/03/2022] [Indexed: 12/12/2022] Open
Abstract
Background The mechanism of action for most cancer drugs is not clear. Large-scale pharmacogenomic cancer cell line datasets offer a rich resource to obtain this knowledge. Here, we present an analysis strategy for revealing biological pathways that contribute to drug response using publicly available pharmacogenomic cancer cell line datasets. Methods We present a custom machine-learning based approach for identifying biological pathways involved in cancer drug response. We test the utility of our approach with a pan-cancer analysis of ML210, an inhibitor of GPX4, and a melanoma-focused analysis of inhibitors of BRAFV600. We apply our approach to reveal determinants of drug resistance to microtubule inhibitors. Results Our method implicated lipid metabolism and Rac1/cytoskeleton signaling in the context of ML210 and BRAF inhibitor response, respectively. These findings are consistent with current knowledge of how these drugs work. For microtubule inhibitors, our approach implicated Notch and Akt signaling as pathways that associated with response. Conclusions Our results demonstrate the utility of combining informed feature selection and machine learning algorithms in understanding cancer drug response. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04720-z.
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Affiliation(s)
- Eliot Y Zhu
- Department of Anatomy and Cell Biology, The University of Iowa, Iowa City, IA, USA.,Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA, USA.,Cancer Biology Graduate Program, The University of Iowa, Iowa City, IA, USA.,The Medical Scientist Training Program, The University of Iowa, Iowa City, IA, USA
| | - Adam J Dupuy
- Department of Anatomy and Cell Biology, The University of Iowa, Iowa City, IA, USA. .,Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA, USA.
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20
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Curcumol Targeting PAX8 Inhibits Ovarian Cancer Cell Migration and Invasion and Increases Chemotherapy Sensitivity of Niraparib. JOURNAL OF ONCOLOGY 2022; 2022:3941630. [PMID: 35548853 PMCID: PMC9085303 DOI: 10.1155/2022/3941630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/22/2022] [Accepted: 02/07/2022] [Indexed: 11/18/2022]
Abstract
Objective. To investigate the effects of Curcumol on invasion, migration and epithelial-mesenchymal transformation of IGROV-1 and OVCAR-3 cells in ovarian cancer and its potential mechanism. Meanwhile, the effect of Curcumol on the antitumor activity of Niraparib was analyzed. Methods. Cell Counting Kit 8 (CCK-8) was used to detect the effects of Curcumol on the activity of IGROV-1 and OVCAR 3 cells. In vitro invasion assay (Transwell) was used to test the invasiveness of cells. Cell migration was detected by scratch assay. The inhibitory effect of Curcumol on PAX8 was detected by QRT-PCR. To evaluate the antitumor effect of Curcumol in subcutaneous tumor-bearing animal model. Results. Knockdown of PAX8 could inhibit the proliferation, invasion and migration of ovarian cancer cells. After Curcumol treated IGROV-1 and OVCAR-3 cells, the cell proliferation ability was decreased, the number of invasive cells was significantly reduced, and the scratch closure rate was significantly reduced, in a dose-dependent manner. Mechanism studies showed that Curcumol increased the antitumor activity of Niraparib by inhibiting PAX8. Conclusion. Curcumol can inhibit the invasion, migration and epithelial-mesenchymal transformation of IGROV-1 and OVCAR-3 cells in ovarian cancer, and its mechanism is related to the targeted inhibition of PAX8. Curcumol also increased the sensitivity of Niraparib chemotherapy by inhibiting PAX8.
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21
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Shi X, Li Y, Yuan Q, Tang S, Guo S, Zhang Y, He J, Zhang X, Han M, Liu Z, Zhu Y, Gao S, Wang H, Xu X, Zheng K, Jing W, Chen L, Wang Y, Jin G, Gao D. Integrated profiling of human pancreatic cancer organoids reveals chromatin accessibility features associated with drug sensitivity. Nat Commun 2022; 13:2169. [PMID: 35449156 PMCID: PMC9023604 DOI: 10.1038/s41467-022-29857-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 03/31/2022] [Indexed: 12/16/2022] Open
Abstract
Chromatin accessibility plays an essential role in controlling cellular identity and the therapeutic response of human cancers. However, the chromatin accessibility landscape and gene regulatory network of pancreatic cancer are largely uncharacterized. Here, we integrate the chromatin accessibility profiles of 84 pancreatic cancer organoid lines with whole-genome sequencing data, transcriptomic sequencing data and the results of drug sensitivity analysis of 283 epigenetic-related chemicals and 5 chemotherapeutic drugs. We identify distinct transcription factors that distinguish molecular subtypes of pancreatic cancer, predict numerous chromatin accessibility peaks associated with gene regulatory networks, discover regulatory noncoding mutations with potential as cancer drivers, and reveal the chromatin accessibility signatures associated with drug sensitivity. These results not only provide the chromatin accessibility atlas of pancreatic cancer but also suggest a systematic approach to comprehensively understand the gene regulatory network of pancreatic cancer in order to advance diagnosis and potential personalized medicine applications.
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Affiliation(s)
- Xiaohan Shi
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Second Military Medical University (Naval Medical University), Shanghai, China
| | - Yunguang Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiuyue Yuan
- CEMS, NCMIS, HCMS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100080, China
- School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shijie Tang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shiwei Guo
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Second Military Medical University (Naval Medical University), Shanghai, China
| | - Yehan Zhang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juan He
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoyu Zhang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ming Han
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhuang Liu
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiqin Zhu
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Suizhi Gao
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Second Military Medical University (Naval Medical University), Shanghai, China
| | - Huan Wang
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Second Military Medical University (Naval Medical University), Shanghai, China
| | - Xiongfei Xu
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Second Military Medical University (Naval Medical University), Shanghai, China
| | - Kailian Zheng
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Second Military Medical University (Naval Medical University), Shanghai, China
| | - Wei Jing
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Second Military Medical University (Naval Medical University), Shanghai, China
| | - Luonan Chen
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China.
- Guangdong Institute of Intelligence Science and Technology, Hengqin, Zhuhai, Guangdong, 519031, China.
| | - Yong Wang
- CEMS, NCMIS, HCMS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100080, China.
- School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China.
| | - Gang Jin
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Second Military Medical University (Naval Medical University), Shanghai, China.
| | - Dong Gao
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
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22
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Chaves-Moreira D, Mitchell MA, Arruza C, Rawat P, Sidoli S, Nameki R, Reddy J, Corona RI, Afeyan LK, Klein IA, Ma S, Winterhoff B, Konecny GE, Garcia BA, Brady DC, Lawrenson K, Morin PJ, Drapkin R. The transcription factor PAX8 promotes angiogenesis in ovarian cancer through interaction with SOX17. Sci Signal 2022; 15:eabm2496. [PMID: 35380877 DOI: 10.1126/scisignal.abm2496] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
PAX8 is a master transcription factor that is essential during embryogenesis and promotes neoplastic growth. It is expressed by the secretory cells lining the female reproductive tract, and its deletion during development results in atresia of reproductive tract organs. Nearly all ovarian carcinomas express PAX8, and its knockdown results in apoptosis of ovarian cancer cells. To explore the role of PAX8 in these tissues, we purified the PAX8 protein complex from nonmalignant fallopian tube cells and high-grade serous ovarian carcinoma cell lines. We found that PAX8 was a member of a large chromatin remodeling complex and preferentially interacted with SOX17, another developmental transcription factor. Depleting either PAX8 or SOX17 from cancer cells altered the expression of factors involved in angiogenesis and functionally disrupted tubule and capillary formation in cell culture and mouse models. PAX8 and SOX17 in ovarian cancer cells promoted the secretion of angiogenic factors by suppressing the expression of SERPINE1, which encodes a proteinase inhibitor with antiangiogenic effects. The findings reveal a non-cell-autonomous function of these transcription factors in regulating angiogenesis in ovarian cancer.
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Affiliation(s)
- Daniele Chaves-Moreira
- Ovarian Cancer Research Center, Department of Obstetrics and Gynecology, University of Pennsylvania Perelman School of Medicine, Biomedical Research Building II/III, Suite 1224, Philadelphia, PA 19104, USA
| | - Marilyn A Mitchell
- Ovarian Cancer Research Center, Department of Obstetrics and Gynecology, University of Pennsylvania Perelman School of Medicine, Biomedical Research Building II/III, Suite 1224, Philadelphia, PA 19104, USA
| | - Cristina Arruza
- Ovarian Cancer Research Center, Department of Obstetrics and Gynecology, University of Pennsylvania Perelman School of Medicine, Biomedical Research Building II/III, Suite 1224, Philadelphia, PA 19104, USA
| | - Priyanka Rawat
- Ovarian Cancer Research Center, Department of Obstetrics and Gynecology, University of Pennsylvania Perelman School of Medicine, Biomedical Research Building II/III, Suite 1224, Philadelphia, PA 19104, USA
| | - Simone Sidoli
- Epigenetics Institute, Department of Biochemistry and Biophysics, Smilow Center for Translational Research, University of Pennsylvania Perelman School of Medicine, Suite 9-124, Philadelphia, PA 19104, USA
| | - Robbin Nameki
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.,Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jessica Reddy
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.,Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Rosario I Corona
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.,Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Lena K Afeyan
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Isaac A Klein
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Sisi Ma
- Institute for Health Informatics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Boris Winterhoff
- Department of Obstetrics, Gynecology and Women's Health, Division of Gynecologic Oncology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gottfried E Konecny
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Benjamin A Garcia
- Epigenetics Institute, Department of Biochemistry and Biophysics, Smilow Center for Translational Research, University of Pennsylvania Perelman School of Medicine, Suite 9-124, Philadelphia, PA 19104, USA
| | - Donita C Brady
- Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Biomedical Research Building II/III, Suite 612, Philadelphia, PA 19104, USA.,Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Biomedical Research Building II/III, Suite 612, Philadelphia, PA 19104, USA
| | - Kate Lawrenson
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.,Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Patrice J Morin
- Ovarian Cancer Research Center, Department of Obstetrics and Gynecology, University of Pennsylvania Perelman School of Medicine, Biomedical Research Building II/III, Suite 1224, Philadelphia, PA 19104, USA
| | - Ronny Drapkin
- Ovarian Cancer Research Center, Department of Obstetrics and Gynecology, University of Pennsylvania Perelman School of Medicine, Biomedical Research Building II/III, Suite 1224, Philadelphia, PA 19104, USA
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23
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Lin L, Shi K, Zhou S, Cai MC, Zhang C, Sun Y, Zang J, Cheng L, Ye K, Ma P, Shen P, Zhang M, Cheng Y, Qi C, Li Y, Yin X, Zheng Y, Tan L, Zhuang G, Zang R. SOX17 and PAX8 constitute an actionable lineage-survival transcriptional complex in ovarian cancer. Oncogene 2022; 41:1767-1779. [DOI: 10.1038/s41388-022-02210-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 01/04/2022] [Accepted: 01/24/2022] [Indexed: 12/22/2022]
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24
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Huang J, Wang G, Liao K, Xie N, Deng K. UCP1 modulates immune infiltration level and survival outcome in ovarian cancer patients. J Ovarian Res 2022; 15:16. [PMID: 35090503 PMCID: PMC8800348 DOI: 10.1186/s13048-022-00951-z] [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: 09/08/2021] [Accepted: 01/18/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
The uncoupling proteins (UCPs) are critical genes associated with tumorigenesis and chemoresistance. However, little is known about the molecular mechanism of the UCPs in ovarian cancer (OV).
Material and methods
UCPs expression analysis was conducted using Gene Expression Profiling Interactive Analysis (GEPIA), and its potential in clinical prognosis was analyzed using Kaplan- Meier analyses. The influence of UCPs on immune infiltration was analyzed by TIMER. In addition, the correlation between UCPs expression and molecular mechanisms was investigated by TIMER and Cancer Single-cell State Atlas (CancerSEA).
Results
UCP1, UCP2, UCP3 and UCP5 expression levels correlated with a favorable prognosis and tumor progression. Moreover, UCP1 expression correlated to several immune cell markers and regulated tumorigenesis, such as tumor invasion, EMT, metastasis and DNA repair. In addition, UCP1 potentially involved in genes expression of SNAI2, MMP2, BRCA1 and PARP1.
Conclusions
These results implied a critical role of UCP1 in the prognosis and immune infiltration of ovarian cancer. In addition, UCP1 expression participated in regulating multiple oncogenes and tumorigenesis.
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25
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Magaletta ME, Lobo M, Kernfeld EM, Aliee H, Huey JD, Parsons TJ, Theis FJ, Maehr R. Integration of single-cell transcriptomes and chromatin landscapes reveals regulatory programs driving pharyngeal organ development. Nat Commun 2022; 13:457. [PMID: 35075189 PMCID: PMC8786836 DOI: 10.1038/s41467-022-28067-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 01/07/2022] [Indexed: 12/13/2022] Open
Abstract
Maldevelopment of the pharyngeal endoderm, an embryonic tissue critical for patterning of the pharyngeal region and ensuing organogenesis, ultimately contributes to several classes of human developmental syndromes and disorders. Such syndromes are characterized by a spectrum of phenotypes that currently cannot be fully explained by known mutations or genetic variants due to gaps in characterization of critical drivers of normal and dysfunctional development. Despite the disease-relevance of pharyngeal endoderm, we still lack a comprehensive and integrative view of the molecular basis and gene regulatory networks driving pharyngeal endoderm development. To close this gap, we apply transcriptomic and chromatin accessibility single-cell sequencing technologies to generate a multi-omic developmental resource spanning pharyngeal endoderm patterning to the emergence of organ-specific epithelia in the developing mouse embryo. We identify cell-type specific gene regulation, distill GRN models that define developing organ domains, and characterize the role of an immunodeficiency-associated forkhead box transcription factor.
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Affiliation(s)
- Margaret E Magaletta
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
- Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, USA
| | - Macrina Lobo
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
- Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, USA
| | - Eric M Kernfeld
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
- Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, USA
| | - Hananeh Aliee
- Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany
| | - Jack D Huey
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
- Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, USA
| | - Teagan J Parsons
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
- Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, USA
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany
- Department of Mathematics, Technische Universität München, Munich, Germany
- School of Life Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | - René Maehr
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.
- Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, USA.
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26
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EVI1 Promotes the Proliferation and Invasive Properties of Human Head and Neck Squamous Cell Carcinoma Cells. Int J Mol Sci 2022; 23:ijms23031050. [PMID: 35162973 PMCID: PMC8835242 DOI: 10.3390/ijms23031050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 01/27/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is a frequent malignancy with a poor prognosis. So far, the EGFR inhibitor cetuximab is the only approved targeted therapy. A deeper understanding of the molecular and genetic basis of HNSCC is needed to identify additional targets for rationally designed, personalized therapeutics. The transcription factor EVI1, the major product of the MECOM locus, is an oncoprotein with roles in both hematological and solid tumors. In HNSCC, high EVI1 expression was associated with an increased propensity to form lymph node metastases, but its effects in this tumor entity have not yet been determined experimentally. We therefore overexpressed or knocked down EVI1 in several HNSCC cell lines and determined the impact of these manipulations on parameters relevant to tumor growth and invasiveness, and on gene expression patterns. Our results revealed that EVI1 promoted the proliferation and migration of HNSCC cells. Furthermore, it augmented tumor spheroid formation and the ability of tumor spheroids to displace an endothelial cell layer. Finally, EVI1 altered the expression of numerous genes in HNSCC cells, which were enriched for Gene Ontology terms related to its cellular functions. In summary, EVI1 represents a novel oncogene in HNSCC that contributes to cellular proliferation and invasiveness.
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27
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Feng L, Wang J, Zhang J, Diao J, He L, Fu C, Liao H, Xu X, Gao Y, Zhou C. Comprehensive Analysis of E3 Ubiquitin Ligases Reveals Ring Finger Protein 223 as a Novel Oncogene Activated by KLF4 in Pancreatic Cancer. Front Cell Dev Biol 2021; 9:738709. [PMID: 34722520 PMCID: PMC8551701 DOI: 10.3389/fcell.2021.738709] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/15/2021] [Indexed: 12/22/2022] Open
Abstract
Pancreatic cancer is one of the major malignancies and causes of mortality worldwide. E3 ubiquitin-protein ligases transfer activated ubiquitin from ubiquitin-conjugating enzymes to protein substrates and confer substrate specificity in cancer. In this study, we first downloaded data from The Cancer Genome Atlas pancreatic adenocarcinoma dataset, acquired all 27 differentially expressed genes (DEGs), and identified genomic alterations. Then, the prognostic significance of DEGs was analyzed, and eight DEGs (MECOM, CBLC, MARCHF4, RNF166, TRIM46, LONRF3, RNF39, and RNF223) and two clinical parameters (pathological N stage and T stage) exhibited prognostic significance. RNF223 showed independent significance as an unfavorable prognostic marker and was chosen for subsequent analysis. Next, the function of RNF223 in the pancreatic cancer cell lines ASPC-1 and PANC-1 was investigated, and RNF223 silencing promoted pancreatic cancer growth and migration. To explore the potential targets and pathways of RNF223 in pancreatic cancer, quantitative proteomics was applied to analyze differentially expressed proteins, and metabolism-related pathways were primarily enriched. Finally, the reason for the elevated expression of RNF223 was analyzed, and KLF4 was shown to contribute to the increased expression of RNF233. In conclusion, this study comprehensively analyzed the clinical significance of E3 ligases. Functional assays revealed that RNF223 promotes cancer by regulating cell metabolism. Finally, the elevated expression of RNF223 was attributed to KLF4-mediated transcriptional activation. This study broadens our knowledge regarding E3 ubiquitin ligases and signal transduction and provides novel markers and therapeutic targets in pancreatic cancer.
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Affiliation(s)
- Lei Feng
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center for Artificial Organ and Tissue Engineering, Guangzhou Clinical Research and Transformation Center for Artificial Liver, Institute of Regenerative Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jieqing Wang
- The First Affiliated Hospital, Sun Yat-sen university, Guangzhou, China
| | - Jianmin Zhang
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center for Artificial Organ and Tissue Engineering, Guangzhou Clinical Research and Transformation Center for Artificial Liver, Institute of Regenerative Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jingfang Diao
- Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China
| | | | - Chaoyi Fu
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center for Artificial Organ and Tissue Engineering, Guangzhou Clinical Research and Transformation Center for Artificial Liver, Institute of Regenerative Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Hui Liao
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center for Artificial Organ and Tissue Engineering, Guangzhou Clinical Research and Transformation Center for Artificial Liver, Institute of Regenerative Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaoping Xu
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center for Artificial Organ and Tissue Engineering, Guangzhou Clinical Research and Transformation Center for Artificial Liver, Institute of Regenerative Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yi Gao
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center for Artificial Organ and Tissue Engineering, Guangzhou Clinical Research and Transformation Center for Artificial Liver, Institute of Regenerative Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China.,State Key Laboratory of Organ Failure Research, Southern Medical University, Guangzhou, China
| | - Chenjie Zhou
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center for Artificial Organ and Tissue Engineering, Guangzhou Clinical Research and Transformation Center for Artificial Liver, Institute of Regenerative Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
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