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Luan W, Cheng H, Xie H, Liu H, Wang Y, Wang S, Ye X, Zhu H, Tang F, Li Y, Chang X. PRKDC-Mediated NHEJ May Play a Crucial Role in Aneuploidy of Chromosome 8-Driven Progression of Ovarian Cancer. Int J Mol Sci 2024; 25:4825. [PMID: 38732044 PMCID: PMC11084440 DOI: 10.3390/ijms25094825] [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: 02/08/2024] [Revised: 04/15/2024] [Accepted: 04/20/2024] [Indexed: 05/13/2024] Open
Abstract
High malignancy is a prominent characteristic of epithelial ovarian cancer (EOC), emphasizing the necessity for further elucidation of the potential mechanisms underlying cancer progression. Aneuploidy and copy number variation (CNV) partially contribute to the heightened malignancy observed in EOC; however, the precise features of aneuploidy and their underlying molecular patterns, as well as the relationship between CNV and aneuploidy in EOC, remain unclear. In this study, we employed single-cell sequencing data along with The Cancer Genome Atlas (TCGA) to investigate aneuploidy and CNV in EOC. The technique of fluorescence in situ hybridization (FISH) was employed using specific probes. The copy number variation within the genomic region of chromosome 8 (42754568-47889815) was assessed and utilized as a representative measure for the ploidy status of individual cells in chromosome 8. Differential expression analysis was performed between different subgroups based on chromosome 8 ploidy. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), protein-protein interaction (PPI), and hub-gene analyses were subsequently utilized to identify crucial genes involved. By classifying enriched tumor cells into distinct subtypes based on chromosome 8 ploidy combined with TCGA data integration, we identified key genes driving chromosome 8 aneuploidy in EOC, revealing that PRKDC gene involvement through the mediated non-homologous end-joining pathway may play a pivotal role in disease progression. Further validation through analysis of the GEO and TCGA database and survival assessment, considering both mRNA expression levels and CNV status of PRKDC, has confirmed its involvement in the progression of EOC. Further functional analysis revealed an upregulation of PRKDC in both ovarian EOC cells and tissues, with its expression showing a significant correlation with the extent of copy number variation (CNV) on chromosome 8. Taken together, CNV amplification and aneuploidy of chromosome 8 are important characteristics of EOC. PRKDC and the mediated NHEJ pathway may play a crucial role in driving aneuploidy on chromosome 8 during the progression of EOC.
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Affiliation(s)
- Wenqing Luan
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing 100044, China; (W.L.); (H.C.); (H.X.); (H.L.); (Y.W.); (S.W.); (X.Y.); (H.Z.); (F.T.)
- Center of Gynecologic Oncology, Peking University People’s Hospital, Beijing 100044, China
| | - Hongyan Cheng
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing 100044, China; (W.L.); (H.C.); (H.X.); (H.L.); (Y.W.); (S.W.); (X.Y.); (H.Z.); (F.T.)
- Center of Gynecologic Oncology, Peking University People’s Hospital, Beijing 100044, China
| | - Haoling Xie
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing 100044, China; (W.L.); (H.C.); (H.X.); (H.L.); (Y.W.); (S.W.); (X.Y.); (H.Z.); (F.T.)
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, China
| | - Huiping Liu
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing 100044, China; (W.L.); (H.C.); (H.X.); (H.L.); (Y.W.); (S.W.); (X.Y.); (H.Z.); (F.T.)
- Center of Gynecologic Oncology, Peking University People’s Hospital, Beijing 100044, China
| | - Yicheng Wang
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing 100044, China; (W.L.); (H.C.); (H.X.); (H.L.); (Y.W.); (S.W.); (X.Y.); (H.Z.); (F.T.)
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, China
| | - Shang Wang
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing 100044, China; (W.L.); (H.C.); (H.X.); (H.L.); (Y.W.); (S.W.); (X.Y.); (H.Z.); (F.T.)
- Center of Gynecologic Oncology, Peking University People’s Hospital, Beijing 100044, China
| | - Xue Ye
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing 100044, China; (W.L.); (H.C.); (H.X.); (H.L.); (Y.W.); (S.W.); (X.Y.); (H.Z.); (F.T.)
- Center of Gynecologic Oncology, Peking University People’s Hospital, Beijing 100044, China
| | - Honglan Zhu
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing 100044, China; (W.L.); (H.C.); (H.X.); (H.L.); (Y.W.); (S.W.); (X.Y.); (H.Z.); (F.T.)
- Center of Gynecologic Oncology, Peking University People’s Hospital, Beijing 100044, China
| | - Fuchou Tang
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing 100044, China; (W.L.); (H.C.); (H.X.); (H.L.); (Y.W.); (S.W.); (X.Y.); (H.Z.); (F.T.)
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, China
| | - Yi Li
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing 100044, China; (W.L.); (H.C.); (H.X.); (H.L.); (Y.W.); (S.W.); (X.Y.); (H.Z.); (F.T.)
- Center of Gynecologic Oncology, Peking University People’s Hospital, Beijing 100044, China
| | - Xiaohong Chang
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing 100044, China; (W.L.); (H.C.); (H.X.); (H.L.); (Y.W.); (S.W.); (X.Y.); (H.Z.); (F.T.)
- Center of Gynecologic Oncology, Peking University People’s Hospital, Beijing 100044, China
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Ye L, Jiang Z, Zheng M, Pan K, Lian J, Ju B, Liu X, Tang S, Guo G, Zhang S, Hong X, Lu W. Fatty acid metabolism-related lncRNA prognostic signature for serous ovarian carcinoma. Epigenomics 2024; 16:309-329. [PMID: 38356435 DOI: 10.2217/epi-2023-0388] [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: 02/16/2024] Open
Abstract
Background: To explore the role of fatty acid metabolism (FAM)-related lncRNAs in the prognosis and antitumor immunity of serous ovarian cancer (SOC). Materials & methods: A SOC FAM-related lncRNA risk model was developed and evaluated by a series of analyses. Additional immune-related analyses were performed to further assess the associations between immune state, tumor microenvironment and the prognostic risk model. Results: Five lncRNAs associated with the FAM genes were found and used to create a predictive risk model. The patients with a low-risk profile exhibited favorable prognostic outcomes. Conclusion: The established prognostic risk model exhibits better predictive capabilities for the prognosis of patients with SOC and offers novel potential therapy targets for SOC.
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Affiliation(s)
- Lele Ye
- Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China
| | - Zhuofeng Jiang
- Department of Biochemistry, School of Medicine, Southern University of Science & Technology, Shenzhen, 518055, Guangdong, China
| | - Mengxia Zheng
- Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China
| | - Kan Pan
- First Clinical College, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Jingru Lian
- Department of Biochemistry, School of Medicine, Southern University of Science & Technology, Shenzhen, 518055, Guangdong, China
| | - Bing Ju
- Department of Biochemistry, School of Medicine, Southern University of Science & Technology, Shenzhen, 518055, Guangdong, China
| | - Xuefei Liu
- Department of Biochemistry, School of Medicine, Southern University of Science & Technology, Shenzhen, 518055, Guangdong, China
| | - Sangsang Tang
- Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China
| | - Gangqiang Guo
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research & Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens & Immunity, Department of Microbiology & Immunology, Institute of Molecular Virology & Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Songfa Zhang
- Department of Gynecologic Oncology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China
| | - Xin Hong
- Department of Biochemistry, School of Medicine, Southern University of Science & Technology, Shenzhen, 518055, Guangdong, China
- Key University Laboratory of Metabolism & Health of Guangdong, Southern University of Science & Technology, Shenzhen, 518055, Guangdong, China
- Guangdong Provincial Key Laboratory of Cell Microenvironment & Disease Research, Southern University of Science & Technology, Shenzhen, 518055, Guangdong, China
| | - Weiguo Lu
- Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China
- Department of Gynecologic Oncology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China
- Center of Uterine Cancer Diagnosis & Therapy of Zhejiang Province, Hangzhou, 310006, Zhejiang, China
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Wang XY, Xu YM, Lau ATY. Proteogenomics in Cancer: Then and Now. J Proteome Res 2023; 22:3103-3122. [PMID: 37725793 DOI: 10.1021/acs.jproteome.3c00196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
For years, the paths of sequencing technologies and mass spectrometry have occurred in isolation, with each developing its own unique culture and expertise. These two technologies are crucial for inspecting complementary aspects of the molecular phenotype across the central dogma. Integrative multiomics strives to bridge the analysis gap among different fields to complete more comprehensive mechanisms of life events and diseases. Proteogenomics is one integrated multiomics field. Here in this review, we mainly summarize and discuss three aspects: workflow of proteogenomics, proteogenomics applications in cancer research, and the SWOT (Strengths, Weaknesses, Opportunities, Threats) analysis of proteogenomics in cancer research. In conclusion, proteogenomics has a promising future as it clarifies the functional consequences of many unannotated genomic abnormalities or noncanonical variants and identifies driver genes and novel therapeutic targets across cancers, which would substantially accelerate the development of precision oncology.
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Affiliation(s)
- Xiu-Yun Wang
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, People's Republic of China
| | - Yan-Ming Xu
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, People's Republic of China
| | - Andy T Y Lau
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, People's Republic of China
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Khella CA, Franciosa L, Rodirguez-Rodriguez L, Rajkarnikar R, Mythreye K, Gatza ML. HCK Promotes High-Grade Serous Ovarian Cancer Tumorigenesis through CD44 and NOTCH3 Signaling. Mol Cancer Res 2023; 21:1037-1049. [PMID: 37342066 DOI: 10.1158/1541-7786.mcr-22-0496] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/05/2022] [Accepted: 06/15/2023] [Indexed: 06/22/2023]
Abstract
High-grade serous ovarian cancer (HGSOC) is a highly aggressive and lethal subtype of ovarian cancer. While most patients initially respond to standard-of-care treatment, the majority will eventually relapse and succumb to their disease. Despite significant advances in our understanding of this disease, the mechanisms that govern the distinctions between HGSOC with good and poor prognosis remain unclear. In this study, we implemented a proteogenomic approach to analyze gene expression, proteomic and phosphoproteomic profiles of HGSOC tumor samples to identify molecular pathways that distinguish HGSOC tumors relative to clinical outcome. Our analyses identify significant upregulation of hematopoietic cell kinase (HCK) expression and signaling in poor prognostic HGSOC patient samples. Analyses of independent gene expression datasets and IHC of patient samples confirmed increased HCK signaling in tumors relative to normal fallopian or ovarian samples and demonstrated aberrant expression in tumor epithelial cells. Consistent with the association between HCK expression and tumor aggressiveness in patient samples, in vitro phenotypic studies showed that HCK can, in part, promote cell proliferation, colony formation, and invasive capacity of cell lines. Mechanistically, HCK mediates these phenotypes, partly through CD44 and NOTCH3-dependent signaling, and inhibiting CD44 or NOTCH3 activity, either genetically or through gamma-secretase inhibitors, can revert HCK-driven phenotypes. IMPLICATIONS Collectively, these studies establish that HCK acts as an oncogenic driver of HGSOC through aberrant activation of CD44 and NOTCH3 signaling and identifies this network as a potential therapeutic opportunity in a subset of patients with aggressive and recurrent HGSOC.
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Affiliation(s)
- Christen A Khella
- Department of Radiation Oncology, Robert Wood Johnson Medical School, New Brunswick, New Jersey
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
- School of Graduate Studies, Rutgers University, New Brunswick, New Jersey
| | | | | | - Resha Rajkarnikar
- Department of Pathology and O'Neal Comprehensive Cancer Center, Heersink School of Medicine, University of Alabama, Birmingham, Alabama
| | - Karthikeyan Mythreye
- Department of Pathology and O'Neal Comprehensive Cancer Center, Heersink School of Medicine, University of Alabama, Birmingham, Alabama
| | - Michael L Gatza
- Department of Radiation Oncology, Robert Wood Johnson Medical School, New Brunswick, New Jersey
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
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5
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Wang X, Peng H, Zhang G, Li Z, Du Z, Peng B, Cao P. ADNP is associated with immune infiltration and radiosensitivity in hepatocellular carcinoma for predicting the prognosis. BMC Med Genomics 2023; 16:178. [PMID: 37525242 PMCID: PMC10391866 DOI: 10.1186/s12920-023-01592-x] [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: 03/04/2023] [Accepted: 06/26/2023] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is one of the most lethal diseases due to its high faculty of invasiveness and metastasis. Activity-dependent neuroprotective protein (ADNP) has been regarded as an oncogene in bladder cancer and ovarian cancer. However, the role of ADNP in the regulation of tumor immune response, development, and treatment resistance in HCC remains unknown and is worth exploring. METHODS The correlation between ADNP and prognosis, immune cell infiltration, immune checkpoints, chemokines, tumor mutation burden, microsatellite instability, and genomic mutation of pan-cancer cohorts in The Cancer Genome Atlas was analyzed. ADNP expression in HCC cell lines, HCC and the adjacent normal tissues was measured by western blotting and immunochemistry. Nomogram was constructed to predict the survival of patients with HCC based on the ADNP expression and significant clinical characteristics. The potential biological functions and impacts on radiotherapy of ADNP in HCC cell lines were verified by vitro experiments. RESULTS ADNP was upregulated in most cancers and patients with elevated ADNP expression were related to poor survival in several types of cancers including HCC. Functional enrichment analysis showed ADNP participated in the pathways correlated with coagulation cascades and DNA double strand break repair. Further, ADNP exhibited a negative correlation with the immune score, stromal score, estimated score, and chemokines, and a positive correlation with cancer-associated fibroblasts, myeloid-derived suppressor cells, neutrophils, regulatory T cells, and endothelial cells. Immunochemistry and western blotting results demonstrated ADNP was up-regulated in HCC. Vitro experiments verified that suppressing the ADNP expression significantly inhibited the proliferation, invasion and migration and elevated the radiosensitivity via decreasing DNA damage repair in HCC. CONCLUSION ADNP might play an oncogene and immunosuppression role in tumor immune infiltration and response, thus influencing the prognosis. Its downregulation could attenuate the proliferation, invasion, migration, radioresistance of HCC. Our results indicated the potential of ADNP as a promising biomarker to predict the survival of HCC patients, providing a theoretical basis for novel integrative strategies.
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Affiliation(s)
- Xuan Wang
- Department of Oncology, Third Xiangya Hospital, Central South University, No.138 Tongzipo Road, Yuelu District, Changsha, 410013, Hunan, People's Republic of China
| | - Honghua Peng
- Department of Oncology, Third Xiangya Hospital, Central South University, No.138 Tongzipo Road, Yuelu District, Changsha, 410013, Hunan, People's Republic of China
| | - Ganghua Zhang
- Department of Oncology, Third Xiangya Hospital, Central South University, No.138 Tongzipo Road, Yuelu District, Changsha, 410013, Hunan, People's Republic of China
| | - Zeyuan Li
- Department of General Practice, Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, People's Republic of China
| | - Zhangyan Du
- Department of Oncology, Third Xiangya Hospital, Central South University, No.138 Tongzipo Road, Yuelu District, Changsha, 410013, Hunan, People's Republic of China
| | - Bin Peng
- Department of Oncology, Third Xiangya Hospital, Central South University, No.138 Tongzipo Road, Yuelu District, Changsha, 410013, Hunan, People's Republic of China
| | - Peiguo Cao
- Department of Oncology, Third Xiangya Hospital, Central South University, No.138 Tongzipo Road, Yuelu District, Changsha, 410013, Hunan, People's Republic of China.
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D'Incal CP, Van Rossem KE, De Man K, Konings A, Van Dijck A, Rizzuti L, Vitriolo A, Testa G, Gozes I, Vanden Berghe W, Kooy RF. Chromatin remodeler Activity-Dependent Neuroprotective Protein (ADNP) contributes to syndromic autism. Clin Epigenetics 2023; 15:45. [PMID: 36945042 PMCID: PMC10031977 DOI: 10.1186/s13148-023-01450-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/16/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Individuals affected with autism often suffer additional co-morbidities such as intellectual disability. The genes contributing to autism cluster on a relatively limited number of cellular pathways, including chromatin remodeling. However, limited information is available on how mutations in single genes can result in such pleiotropic clinical features in affected individuals. In this review, we summarize available information on one of the most frequently mutated genes in syndromic autism the Activity-Dependent Neuroprotective Protein (ADNP). RESULTS Heterozygous and predicted loss-of-function ADNP mutations in individuals inevitably result in the clinical presentation with the Helsmoortel-Van der Aa syndrome, a frequent form of syndromic autism. ADNP, a zinc finger DNA-binding protein has a role in chromatin remodeling: The protein is associated with the pericentromeric protein HP1, the SWI/SNF core complex protein BRG1, and other members of this chromatin remodeling complex and, in murine stem cells, with the chromodomain helicase CHD4 in a ChAHP complex. ADNP has recently been shown to possess R-loop processing activity. In addition, many additional functions, for instance, in association with cytoskeletal proteins have been linked to ADNP. CONCLUSIONS We here present an integrated evaluation of all current aspects of gene function and evaluate how abnormalities in chromatin remodeling might relate to the pleiotropic clinical presentation in individual"s" with Helsmoortel-Van der Aa syndrome.
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Affiliation(s)
- Claudio Peter D'Incal
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Belgium
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Epigenetic Signaling Lab (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Kirsten Esther Van Rossem
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Belgium
| | - Kevin De Man
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Epigenetic Signaling Lab (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Anthony Konings
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Epigenetic Signaling Lab (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Anke Van Dijck
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Belgium
| | - Ludovico Rizzuti
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122, Milan, Italy
- Human Technopole, V. Le Rita Levi-Montalcini, 1, 20157, Milan, Italy
| | - Alessandro Vitriolo
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122, Milan, Italy
- Human Technopole, V. Le Rita Levi-Montalcini, 1, 20157, Milan, Italy
| | - Giuseppe Testa
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122, Milan, Italy
- Human Technopole, V. Le Rita Levi-Montalcini, 1, 20157, Milan, Italy
| | - Illana Gozes
- Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Adams Super Center for Brain Studies and Sagol School of Neuroscience, Tel Aviv University, Sackler School of Medicine, 727, 69978, Tel Aviv, Israel
| | - Wim Vanden Berghe
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Epigenetic Signaling Lab (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium.
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Belgium.
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Sigismondo G, Arseni L, Palacio-Escat N, Hofmann TG, Seiffert M, Krijgsveld J. Multi-layered chromatin proteomics identifies cell vulnerabilities in DNA repair. Nucleic Acids Res 2023; 51:687-711. [PMID: 36629267 PMCID: PMC9881138 DOI: 10.1093/nar/gkac1264] [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: 09/07/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 01/12/2023] Open
Abstract
The DNA damage response (DDR) is essential to maintain genome stability, and its deregulation predisposes to carcinogenesis while encompassing attractive targets for cancer therapy. Chromatin governs the DDR via the concerted interplay among different layers, including DNA, histone post-translational modifications (hPTMs) and chromatin-associated proteins. Here, we employ multi-layered proteomics to characterize chromatin-mediated functional interactions of repair proteins, signatures of hPTMs and the DNA-bound proteome during DNA double-strand break (DSB) repair at high temporal resolution. Our data illuminate the dynamics of known and novel DDR-associated factors both at chromatin and at DSBs. We functionally attribute novel chromatin-associated proteins to repair by non-homologous end-joining (NHEJ), homologous recombination (HR) and DSB repair pathway choice. We reveal histone reader ATAD2, microtubule organizer TPX2 and histone methyltransferase G9A as regulators of HR and involved in poly-ADP-ribose polymerase-inhibitor sensitivity. Furthermore, we distinguish hPTMs that are globally induced by DNA damage from those specifically acquired at sites flanking DSBs (γH2AX foci-specific) and profiled their dynamics during the DDR. Integration of complementary chromatin layers implicates G9A-mediated monomethylation of H3K56 in DSBs repair via HR. Our data provide a dynamic chromatin-centered view of the DDR that can be further mined to identify novel mechanistic links and cell vulnerabilities in DSB repair.
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Affiliation(s)
- Gianluca Sigismondo
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Lavinia Arseni
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Nicolàs Palacio-Escat
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Thomas G Hofmann
- Institute of Toxicology, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
| | - Martina Seiffert
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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Chen Y, Liao X, Jing P, Hu L, Yang Z, Yao Y, Liao C, Zhang S. Linoleic Acid-Glucosamine Hybrid for Endogenous Iron-Activated Ferroptosis Therapy in High-Grade Serous Ovarian Cancer. Mol Pharm 2022; 19:3187-3198. [PMID: 35939328 DOI: 10.1021/acs.molpharmaceut.2c00333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
As the most common subtype in ovarian malignancies, high-grade serous ovarian cancer (HGSOC) made less therapeutic progress in past decades due to the lack of effective drug-able targets. Herein, an effective linoleic acid (LA) and glucosamine (GlcN) hybrid (LA-GlcN) was synthesized for the treatment of HGSOC. The GlcN was introduced to recognize the glucose transporter 1 (GLUT 1) overexpressed in tumor cells to enhance the uptake of LA-GlcN, and the unsaturated LA was employed to trigger ferroptosis by iron-dependent lipid peroxidation. Since the iron content of HGSOC was ∼5 and 2 times, respectively, higher than that of the normal ovarian cells and low-grade serous ovarian cancer cells, these excess irons make them a good target to enhance the ferroptosis of LA-GlcN. The in vitro study demonstrated that LA-GlcN could selectively kill HGSOC cells without affecting normal cells; the in vivo study revealed that LA-GlcN at the dose of 50 mg kg-1 achieved a comparable tumor inhibition as doxorubicin hydrochloride (4 mg kg-1) while the overall survival of mice was extended largely due to the low toxicity, and when the dose was increased to 100 mg kg-1, the therapeutic outcomes could be improved further. This dietary hybrid which targets the excess endogenous iron to activate ferroptosis represents a promising drug for HGSOC treatment.
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Affiliation(s)
- Ying Chen
- The State Key Laboratory of Functions and Applications of Medicinal Plants & College of Pharmacy, Guizhou Medical University, University Town, Guian New District, Guiyang 550025, China.,College of Biomedical Engineering and National Engineering Research Center for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu 610064, China
| | - Xiaoming Liao
- College of Biomedical Engineering and National Engineering Research Center for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu 610064, China
| | - Pei Jing
- Department of Pharmacy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province 646000, China
| | - Liangkui Hu
- College of Biomedical Engineering and National Engineering Research Center for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu 610064, China
| | - Zengqiu Yang
- The State Key Laboratory of Functions and Applications of Medicinal Plants & College of Pharmacy, Guizhou Medical University, University Town, Guian New District, Guiyang 550025, China
| | - Yongchao Yao
- College of Biomedical Engineering and National Engineering Research Center for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu 610064, China.,State Key Laboratory of Biotherapy and Cancer Center, West China Hospital Sichuan University, Chengdu 610041, China
| | - Chunyan Liao
- College of Biomedical Engineering and National Engineering Research Center for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu 610064, China
| | - Shiyong Zhang
- College of Biomedical Engineering and National Engineering Research Center for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu 610064, China
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9
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Levine J, Hakim F, Kooy RF, Gozes I. Vineland Adaptive Behavior Scale in a Cohort of Four ADNP Syndrome Patients Implicates Age-Dependent Developmental Delays with Increased Impact of Activities of Daily Living. J Mol Neurosci 2022; 72:1531-1546. [PMID: 35920977 DOI: 10.1007/s12031-022-02048-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 07/07/2022] [Indexed: 02/07/2023]
Abstract
Activity-dependent neuroprotective protein (ADNP) is one of the lead genes in autism spectrum disorder/intellectual disability. Heterozygous, de novo ADNP mutations cause the ADNP syndrome. Here, to evaluate natural history of the syndrome, mothers of two ADNP syndrome boys aged 6 and a half and two adults aged 27 years (man and woman) were subjected to Vineland III questionnaire assessing adaptive behavior. The boys were assessed again about 2 years after the first measurements. The skill measures, presented as standard scores (SS) included domains of communication, daily living, socialization, motor skills and a sum of adaptive behavior composite. The age equivalent (AE) and growth scale values (GSV) encompassing 11 subdomains assess the age level at which the subject's raw score is found at a norm sample median and the individual temporal progression, respectively. The norm referenced standard scores age-matched, mean 100 ± 15 of the two children showed the lowest outcome in communication (SS: 20-30). Daily living skills presented SS of 50-60, with a possible potential loss of some activities as the child ages, especially in interpersonal relationships with people outside of the immediate family (boy A). In contrast, in socialization, both children were at the SS of 38, with some positive increase to SS of ~ 45 (interpersonal relations with family members and coping skills, depending on the particular individual), 2 years later. Interestingly, there was an apparent large difference in motor skills (gross and fine) at the young age, with subject B showing a relatively higher level of skills (SS: 70), decreasing to subject A level (SS: 40) 2 years later. Together, the adaptive behavior composite suggested a level of SS: 39-48 with B showing a potential increase (SS: 41-44) and A, a substantial decrease (SS: 48-39), suggesting a strong impact of daily living skills. Adults were at SS: 20, which is the lowest possible score. AE showed minor improvements for subject A and B, with all AE values being below 3 years. GSVs for subject A showed some improvement with age, especially in interpersonal, play and leisure, and gross motor subdomains. GSV for subject B showed minor improvements in the various subdomains. Notably, all subjects showed a percentile rank < 1 compared with age-matched norms except for subject B as to motor domain (2nd percentile) at the age of 6 years. In summary, the results, especially comparing SS and AEs between childhood and adulthood, implied a continuous deterioration of activities compared to the general population, encompassing a slower developmental process coupled to possible neurodegeneration, strongly supporting a great need for disease modifying medicinal procedures.
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Affiliation(s)
- Joseph Levine
- The Elton Laboratory for Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, 6997801, Tel Aviv, Israel.,Psychiatric Division, Ben Gurion University, Beersheba, Israel
| | | | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Illana Gozes
- The Elton Laboratory for Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, 6997801, Tel Aviv, Israel.
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10
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Matou-Nasri S, Najdi M, AlSaud NA, Alhaidan Y, Al-Eidi H, Alatar G, AlWadaani D, Trivilegio T, AlSubait A, AlTuwaijri A, Abudawood M, Almuzzaini B. Blockade of p38 MAPK overcomes AML stem cell line KG1a resistance to 5-Fluorouridine and the impact on miRNA profiling. PLoS One 2022; 17:e0267855. [PMID: 35511922 PMCID: PMC9071118 DOI: 10.1371/journal.pone.0267855] [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: 02/03/2022] [Accepted: 04/16/2022] [Indexed: 11/19/2022] Open
Abstract
Most of the AML patients in remission develop multidrug resistance after the first-line therapy and relapse. AML stem cells have gained attention for their chemoresistance potentials. Chemoresistance is a multifactorial process resulting from altered survival signaling pathways and apoptosis regulators such as MAPK, NF-κB activation and ROS production. We targeted the survival pathway p38 MAPK, NF-κB and ROS generation in human chemoresistant AML stem cell line KG1a, susceptible to enhance cell sensitivity to the chemotherapy drug 5-Fluorouridine, compared to the chemosensitive AML cell line HL60. After confirming the phenotypic characterization of KG1a and HL60 cells using flow cytometry and transcriptomic array analyses, cell treatment with the NF-κB inhibitor IKKVII resulted in a complete induction of apoptosis, and a few p38 MAPK inhibitor SB202190-treated cells underwent apoptosis. No change in the apoptosis status was observed in the ROS scavenger N-acetylcysteine-treated cells. The p38 MAPK pathway blockade enhanced the KG1a cell sensitivity to 5-Fluorouridine, which was associated with the upregulation of microribonucleic acid-(miR-)328-3p, as determined by the microarray-based miRNA transcriptomic analysis. The downregulation of the miR-210-5p in SB202190-treated KG1a cells exposed to FUrd was monitored using RT-qPCR. The miR-328-3p is known for the enhancement of cancer cell chemosensitivity and apoptosis induction, and the downregulation of miR-210-5p is found in AML patients in complete remission. In conclusion, we highlighted the key role of the p38 MAPK survival pathway in the chemoresistance capacity of the AML stem cells and potentially involved miRNAs, which may pave the way for the development of a new therapeutic strategy targeting survival signaling proteins and reduce the rate of AML relapse.
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Affiliation(s)
- Sabine Matou-Nasri
- Cell and Gene Therapy Group, Medical Genomics Research Department, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
- * E-mail: (SMN); (BA)
| | - Maria Najdi
- Cell and Gene Therapy Group, Medical Genomics Research Department, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
- Postgraduate program, King Saud University, Riyadh, Saudi Arabia
| | - Nouran Abu AlSaud
- Department of Cellular Therapy and Cancer Research, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - Yazeid Alhaidan
- Medical Genomics Research Department, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - Hamad Al-Eidi
- Cell and Gene Therapy Group, Medical Genomics Research Department, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - Ghada Alatar
- Cell and Gene Therapy Group, Medical Genomics Research Department, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - Deemah AlWadaani
- Medical Genomics Research Department, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - Thadeo Trivilegio
- Medical Research Core Facility and Platforms, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - Arwa AlSubait
- Medical Research Core Facility and Platforms, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - Abeer AlTuwaijri
- Medical Genomics Research Department, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - Manal Abudawood
- Department of Clinical Laboratory Sciences, Chair of Medical and Molecular Genetics Research, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Bader Almuzzaini
- Medical Genomics Research Department, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
- * E-mail: (SMN); (BA)
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11
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Wu Q, Tang X, Zhu W, Li Q, Zhang X, Li H. The Potential Prognostic Role of Oligosaccharide-Binding Fold-Containing Protein 2A (OBFC2A) in Triple-Negative Breast Cancer. Front Oncol 2021; 11:751430. [PMID: 34868954 PMCID: PMC8634334 DOI: 10.3389/fonc.2021.751430] [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: 08/01/2021] [Accepted: 10/28/2021] [Indexed: 11/13/2022] Open
Abstract
Background Patients with triple-negative breast cancer (TNBC) have poor overall survival. The present study aimed to investigate the potential prognostics of TNBC by analyzing breast cancer proteomic and transcriptomic datasets. Methods Candidate proteins selected from CPTAC (the National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium) were validated using datasets from METABRIC (Molecular Taxonomy of Breast Cancer International Consortium). Kaplan-Meier analysis and ROC (receiver operating characteristic) curve analysis were performed to explore the prognosis of candidate genes. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis were performed on the suspected candidate genes. Single-cell RNA-seq (scRNA-seq) data from GSE118389 were used to analyze the cell clusters in which OBFC2A (Oligosaccharide-Binding Fold-Containing Protein 2A) was mainly distributed. TIMER (Tumor Immune Estimation Resource) was used to verify the correlation between OBFC2A expression and immune infiltration. Clone formation assays and wound healing assays were used to detect the role of OBFC2A expression on the proliferation, invasion, and migration of breast cancer cells. Flow cytometry was used to analyze the effects of silencing OBFC2A on breast cancer cell cycle and apoptosis. Results Six candidate proteins were found to be differentially expressed in non-TNBC and TNBC groups from CPTAC. However, only OBFC2A was identified as an independently poor prognostic gene marker in METABRIC (HR=3.658, 1.881-7.114). And OBFC2A was associated with immune functions in breast cancer. Biological functional experiments showed that OBFC2A might promote the proliferation and migration of breast cancer cells. The inhibition of OBFC2A expression blocked the cell cycle in G1 phase and inhibited the transformation from G1 phase to S phase. Finally, downregulation of OBFC2A also increased the total apoptosis rate of cells. Conclusion On this basis, OBFC2A may be a potential prognostic biomarker for TNBC.
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Affiliation(s)
- Qianxue Wu
- Department of the Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, Chongqing, China
| | - Xin Tang
- Department of Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Wenming Zhu
- Department of the Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, Chongqing, China
| | - Qing Li
- Department of the Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, Chongqing, China
| | - Xiang Zhang
- Department of the Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, Chongqing, China
| | - Hongyuan Li
- Department of the Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, Chongqing, China
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12
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Yee SS, Risinger AL. Efficacy of a Covalent Microtubule Stabilizer in Taxane-Resistant Ovarian Cancer Models. Molecules 2021; 26:molecules26134077. [PMID: 34279417 PMCID: PMC8271594 DOI: 10.3390/molecules26134077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/23/2021] [Accepted: 06/30/2021] [Indexed: 11/25/2022] Open
Abstract
Ovarian cancer often has a poor clinical prognosis because of late detection, frequently after metastatic progression, as well as acquired resistance to taxane-based therapy. Herein, we evaluate a novel class of covalent microtubule stabilizers, the C-22,23-epoxytaccalonolides, for their efficacy against taxane-resistant ovarian cancer models in vitro and in vivo. Taccalonolide AF, which covalently binds β-tubulin through its C-22,23-epoxide moiety, demonstrates efficacy against taxane-resistant models and shows superior persistence in clonogenic assays after drug washout due to irreversible target engagement. In vivo, intraperitoneal administration of taccalonolide AF demonstrated efficacy against the taxane-resistant NCI/ADR-RES ovarian cancer model both as a flank xenograft, as well as in a disseminated orthotopic disease model representing localized metastasis. Taccalonolide-treated animals had a significant decrease in micrometastasis of NCI/ADR-RES cells to the spleen, as detected by quantitative RT-PCR, without any evidence of systemic toxicity. Together, these findings demonstrate that taccalonolide AF retains efficacy in taxane-resistant ovarian cancer models in vitro and in vivo and that its irreversible mechanism of microtubule stabilization has the unique potential for intraperitoneal treatment of locally disseminated taxane-resistant disease, which represents a significant unmet clinical need in the treatment of ovarian cancer patients.
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Affiliation(s)
- Samantha S. Yee
- Department of Pharmacology, The University of Texas Health Science Center at San Antonio, Floyd Curl Drive, San Antonio, TX 78229, USA;
- Mays Cancer Center, 7979 Wurzbach Road, San Antonio, TX 78229, USA
| | - April L. Risinger
- Department of Pharmacology, The University of Texas Health Science Center at San Antonio, Floyd Curl Drive, San Antonio, TX 78229, USA;
- Mays Cancer Center, 7979 Wurzbach Road, San Antonio, TX 78229, USA
- Correspondence: ; Tel.: +1-210-567-6267
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13
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Xie Y, Zhu S, Zang J, Wu G, Wen Y, Liang Y, Long Y, Guo W, Zang C, Hu X, Fan G, Xiang S, Zhang J. ADNP prompts the cisplatin-resistance of bladder cancer via TGF-β-mediated epithelial-mesenchymal transition (EMT) pathway. J Cancer 2021; 12:5114-5124. [PMID: 34335928 PMCID: PMC8317519 DOI: 10.7150/jca.58049] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/19/2021] [Indexed: 12/31/2022] Open
Abstract
Activity-dependent neuroprotective protein (ADNP) is vital for embryonic development and brain formation. Besides, the upregulated expression of ADNP enhances tumorigenesis in some human tumors like bladder cancer (BC). However, the potential roles of ADNP in drug resistance and the related mechanisms in BC is unknown. We performed this study to elucidate the influence of ADNP in the chemoresistance of BC and tried to explore the underlying molecular mechanism. The expressions of ADNP in BC from progression and non-progression patient specimens were measured by quantitative real-time PCR (qRT-PCR) and immunohistochemistry (IHC). In vitro experiments including colony formation, cell counting kit-8 (CCK-8), wound healing, and in vivo tumorigenesis assay were performed to explore the effects of ADNP on chemoresistance of BC. The impacts of ADNP on TGF-β/Smad signaling pathways were explored by western blot. Our results showed that the expression of ADNP mRNA and protein were significantly upregulated in BC tissues of the patients who suffered tumor-progression via RT-PCR and western blot. Cox regression survival analysis revealed that patients with high ADNP expression closely linked to shorter tumor-free survival. ADNP downregulation in BC showed more sensitive to cisplatin in vivo, while ADNP overexpression showed the opposite results. Additionally, we confirmed that ADNP promoted cell migration and EMT, thereby inducing cisplatin resistance, which may be related to TGF-β / Smad signaling pathway.
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Affiliation(s)
- Yu Xie
- Key Laboratory of Protein Chemistry and Developmental Biology of the Ministry of Education, Hunan Normal University, 410081 Changsha, China.,Department of Urology, the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan Cancer Hospital, 410013 Changsha, China
| | - Shuai Zhu
- Department of Urology, the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan Cancer Hospital, 410013 Changsha, China
| | - Jinglei Zang
- Changsha Health Vocational College, 410600 Changsha, China
| | - Guanlin Wu
- Department of Pathology, School of Basic Medical Sciences, Fudan University, 200433 Shanghai, China
| | - Yuheng Wen
- Department of Urology, the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan Cancer Hospital, 410013 Changsha, China
| | - Yu Liang
- Department of Urology, the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan Cancer Hospital, 410013 Changsha, China.,Pingxiang Maternal and Child Care Hospital, 337000 Pingxiang, China
| | - Ying Long
- Clinical Translational Research Center, the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan Cancer Hospital, 410013 Changsha, China
| | - Weiming Guo
- The 2nd Affiliated Hospital of South China University, 421001 Hengyang, China
| | - Chuanbing Zang
- Medizinische Klinik m. S. Hämatologie u. Onkologie, Campus Bejamin Franklin, Unviersitätsmedizin Berlin Charité, 12203 Berlin, Germany
| | - Xiang Hu
- Key Laboratory of Protein Chemistry and Developmental Biology of the Ministry of Education, Hunan Normal University, 410081 Changsha, China
| | - Gang Fan
- Department of Urology, the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan Cancer Hospital, 410013 Changsha, China.,Department of Urology, Huazhong University of Science and Technology Union Shenzhen Hospital; the 6th Affiliated Hospital of Shenzhen University Health Science Center, 518060 Shenzhen, China
| | - Shuanglin Xiang
- Key Laboratory of Protein Chemistry and Developmental Biology of the Ministry of Education, Hunan Normal University, 410081 Changsha, China
| | - Jian Zhang
- Key Laboratory of Protein Chemistry and Developmental Biology of the Ministry of Education, Hunan Normal University, 410081 Changsha, China
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14
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Li X, Duan Y, Hao Y. Identification of super enhancer-associated key genes for prognosis of germinal center B-cell type diffuse large B-cell lymphoma by integrated analysis. BMC Med Genomics 2021; 14:69. [PMID: 33663517 PMCID: PMC7934469 DOI: 10.1186/s12920-021-00916-z] [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: 08/31/2020] [Accepted: 02/21/2021] [Indexed: 01/01/2023] Open
Abstract
Background The pathogenesis of germinal center B-cell type diffuse large B-cell lymphoma (GCB-DLBCL) is not fully elucidated. This study aims to explore the regulation of super enhancers (SEs) on GCB-DLBCL by identifying specific SE-target gene. Methods Weighted gene co-expression network analysis (WGCNA) was used to screen modules associated with GCB subtype. Functional analysis was performed by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment. H3K27ac peaks were used to identify SEs. Overall survival analysis was performed using Kaplan–Meier curve with log-rank and Breslow test. The effect of ADNP, ANKRD28 and RTN4IP1 knockdown on Karpas 422 and SUDHL-4 cells proliferation was analyzed by CCK-8. Karpas 422 and SUDHL-4 cells were treated with bromodomain and extra-terminal domain (BET) inhibitor JQ1, and the expression of ADNP, ANKRD28 and RTN4IP1was measured by qRT-PCR. Results A total of 26 modules were screened in DLBCL. Turquoise module was closely related to GCB-DLBCL, and its eigengenes were mainly related to autophagy. There were 971 SEs in Karpas 422 cell and 1088 SEs in SUDHL-4 cell. Function of the nearest genes of overall SEs were related to cancer. Six SE-related genes associated with GCB-DLBCL were identified as prognostic markers. Knockdown of ADNP, ANKRD28 and RTN4IP1 inhibited the proliferation of Karpas 422 and SUDHL-4 cells. JQ1 treatment suppressed ADNP, ANKRD28 and RTN4IP1 expression in Karpas 422 and SUDHL-4 cells. Conclusions A total of 6 SE-related genes associated with GCB-DLBCL overall survival were identified in this study. These results will serve as a theoretical basis for further study of gene regulation and function of GCB-DLBCL.
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Affiliation(s)
- Xi Li
- Department of Lymphoma, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Taiyuan, Shanxi, People's Republic of China
| | - Yan Duan
- Department of Critical Care Medicine, Shanxi Provincial Cancer Hospital, Taiyuan, Shanxi, People's Republic of China
| | - Yuxia Hao
- Department of Gastroenterology, Shanxi Provincial People's Hospital, 29 shuangtasi Rd, Taiyuan, 030012, People's Republic of China.
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15
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Khella CA, Mehta GA, Mehta RN, Gatza ML. Recent Advances in Integrative Multi-Omics Research in Breast and Ovarian Cancer. J Pers Med 2021; 11:149. [PMID: 33669749 PMCID: PMC7922242 DOI: 10.3390/jpm11020149] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/13/2021] [Accepted: 02/14/2021] [Indexed: 02/07/2023] Open
Abstract
The underlying molecular heterogeneity of cancer is responsible for the dynamic clinical landscape of this disease. The combination of genomic and proteomic alterations, including both inherited and acquired mutations, promotes tumor diversity and accounts for variable disease progression, therapeutic response, and clinical outcome. Recent advances in high-throughput proteogenomic profiling of tumor samples have resulted in the identification of novel oncogenic drivers, tumor suppressors, and signaling networks; biomarkers for the prediction of drug sensitivity and disease progression; and have contributed to the development of novel and more effective treatment strategies. In this review, we will focus on the impact of historical and recent advances in single platform and integrative proteogenomic studies in breast and ovarian cancer, which constitute two of the most lethal forms of cancer for women, and discuss the molecular similarities of these diseases, the impact of these findings on our understanding of tumor biology as well as the clinical applicability of these discoveries.
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Affiliation(s)
- Christen A Khella
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Gaurav A Mehta
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Rushabh N Mehta
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Michael L Gatza
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
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16
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Zhang Y, Wang X, Chen X. Identification of core genes for early diagnosis and the EMT modulation of ovarian serous cancer by bioinformatics perspective. Aging (Albany NY) 2021; 13:3112-3145. [PMID: 33493131 PMCID: PMC7880353 DOI: 10.18632/aging.202524] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 11/30/2020] [Indexed: 02/05/2023]
Abstract
Ovarian serous carcinoma (OSC), as a common malignant tumor, poses a serious threat to women's health in that epithelial-mesenchymal transformation (EMT)-related modulation becomes heavily implicated in the invasion and progression of OSC. In this study, two core genes (BUB1B and NDC80) among the 16 hub genes have been identified to be involved in the molecular regulation of EMT and associated with the poor early survival of OSC at stages I+II. Through the Gene Regulatory Networks (GRN) analysis of 15 EMT regulators and core genes, it was revealed that TFAP2A and hsa-miR-655 could elaborately modulate EMT development of OSC. Next genetic variation analysis indicated that EMT regulator ELF3 would also serve as a crucial part in the occurrence and progression of OSC. Eventually, survival investigation suggested that TFAP2A, ELF3 and hsa-miR-655 were significantly associated with the overall survival of progressive OSC patients. Thus, combined with diversified bioinformatic analyses, BUB1B, NDC80, TFAP2A, ELF3 and hsa-miR-655 may act as the key biomarkers for early clinical diagnosis and prognosis evaluation of OSC patients as well as potential therapeutic target-points.
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Affiliation(s)
- Yanna Zhang
- State Key Laboratory of Biotherapy, Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, High Technological Development Zone, Chengdu 610041, Sichuan, People's Republic of China
| | - Xun Wang
- State Key Laboratory of Biotherapy, Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, High Technological Development Zone, Chengdu 610041, Sichuan, People's Republic of China
| | - Xiancheng Chen
- State Key Laboratory of Biotherapy, Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, High Technological Development Zone, Chengdu 610041, Sichuan, People's Republic of China
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17
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Zhu S, Xu Z, Zeng Y, Long Y, Fan G, Ding Q, Wen Y, Cao J, Dai T, Han W, Xie Y. ADNP Upregulation Promotes Bladder Cancer Cell Proliferation via the AKT Pathway. Front Oncol 2020; 10:491129. [PMID: 33240802 PMCID: PMC7680929 DOI: 10.3389/fonc.2020.491129] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 09/18/2020] [Indexed: 01/09/2023] Open
Abstract
Background Activity-dependent neuroprotective protein (ADNP), which is involved in embryonic development and neurogenesis, has been proven to be upregulated in some human tumors. However, its role in bladder cancer (BC) has never been studied. Objective We aimed to investigate the mechanisms by which ADNP promotes the progression of BC. Methods ADNP expressions in BC cell lines and paired BC and adjacent normal tissues were measured by quantitative real-time PCR (qRT-PCR), Western blot, and immunohistochemistry. Colony formation, Cell Counting Kit-8 (CCK-8), trypan blue exclusion assay, flow cytometry, and nude mice tumorigenesis assay were performed to explore the effects of ADNP on growth of BC in vivo and in vitro. The impacts of ADNP on AKT signaling pathways were measured by Western blot. Results The expression of ADNP mRNA and protein was significantly upregulated in BC tissues compared with adjacent normal tissues. Immunohistochemical analysis of 221 BC and 51 adjacent normal tissue paraffin sections indicated that ADNP expression was significantly associated with histological classification and pathological T and N stages. Survival analysis revealed that patients with high ADNP expression have worse prognosis with respect to overall survival and progression-free disease. ADNP knockdown markedly delayed propagation of BC in vitro and the development of BC in vivo. ADNP overexpression showed the opposite effect. In addition, ADNP can markedly promote G1-S cell cycle transition in BC cells. On the molecular level, we confirmed that ADNP mediated acceleration of G1-S transition was associated with activation of the AKT pathways in BC. Conclusion ADNP is overexpressed in BC and promotes BC growth partly through AKT pathways. ADNP is crucial in predicting the outcome of BC patients and may be a potential therapeutic target in BC.
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Affiliation(s)
- Shuai Zhu
- Department of Urology, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan Cancer Hospital, Changsha, China
| | - Zhenzhou Xu
- Department of Urology, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan Cancer Hospital, Changsha, China
| | - Yong Zeng
- Clinical Translational Research Center, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan Cancer Hospital, Changsha, China
| | - Ying Long
- Clinical Translational Research Center, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan Cancer Hospital, Changsha, China
| | - Gang Fan
- Department of Urology, Huazhong University of Science and Technology Union Shenzhen Hospital, The 6th Affliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Qi Ding
- Clinical Translational Research Center, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan Cancer Hospital, Changsha, China
| | - Yuheng Wen
- Department of Urology, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan Cancer Hospital, Changsha, China
| | - Jian Cao
- Department of Urology, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan Cancer Hospital, Changsha, China
| | - Tao Dai
- Department of Urology, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan Cancer Hospital, Changsha, China
| | - Weiqing Han
- Department of Urology, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan Cancer Hospital, Changsha, China
| | - Yu Xie
- Department of Urology, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan Cancer Hospital, Changsha, China
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Turashvili G. ADNP (Activity Dependent Neuroprotector Homeobox): A novel oncogene driving poor prognosis in high-grade serous carcinoma. EBioMedicine 2020; 51:102589. [PMID: 31901854 PMCID: PMC6940605 DOI: 10.1016/j.ebiom.2019.11.050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 11/29/2019] [Indexed: 11/12/2022] Open
Affiliation(s)
- Gulisa Turashvili
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital and University of Toronto, 600 University Avenue, Toronto, ON M5G 1X5, Canada.
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