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Zhang Y, Yang Y, Hou Y, Yan W, Zhang X, Huang X, Song Q, He F, Wang J, Sun A, Tian C. ZNF8 promotes progression of gastrointestinal cancers via a p53-dependent mechanism. Cell Signal 2024; 123:111354. [PMID: 39173856 DOI: 10.1016/j.cellsig.2024.111354] [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: 03/20/2024] [Revised: 07/09/2024] [Accepted: 08/18/2024] [Indexed: 08/24/2024]
Abstract
p53 is a critical tumor suppressor, and the disruption of its normal function is often a prerequisite for the development or progression of tumors. Our previous works revealed that multiple members of Krüppel-associated box (KRAB) domain zinc-finger proteins (KZFPs) family regulate p53 transcriptional activity by interacting with it. But the tumor biology functions of these members have not been fully elucidated. Here, the pan-cancer analysis related to gastrointestinal cancers (GICs) revealed that ZNF8, a p53-interacting protein, is an unfavorable prognostic factor for patients with malignancies. ZNF8 interacts with p53 and further depresses its transcriptional activity in colon cancer cells. The knockdown of ZNF8 or the overexpression of ZNF8 inhibits or facilitates the in vitro colony formation, migration, invasion, and angiogenesis of p53+/+ colon cancer HCT116 cells, HepG2 cells and EC109 cells rather than p53-/- colon cancer HCT116 cells and p53-knockout HepG2 cells, respectively. Xenograft experiments conducted in vivo also showed that the knockdown of ZNF8 in p53+/+ but not in p53-/- HCT116 cells curbs the tumor growth and metastasis to lung, leading to an extended life span for tumor-bearing mice. Clinically, two independent immunohistochemistry cohorts of colon cancer and esophageal cancer also indicated that ZNF8 is higher expression in carcinoma tissues than adjacent tissues and this is associated with worse overall survival outcomes in patients without harboring p53 mutation. Together, our results provide insight into the p53-specific tumor oncogenic function of ZNF8. ZNF8 may prove to be a potential target for GICs treatment.
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Affiliation(s)
- Yiming Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; Research Unit of Proteomics Dirven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing 102206, China
| | - Yingchuan Yang
- College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Yushan Hou
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; Research Unit of Proteomics Dirven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing 102206, China
| | - Wei Yan
- The First Medical Center of Chinese PLA General Hospital, Beijing 100036, China
| | - Xiuyuan Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; Research Unit of Proteomics Dirven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing 102206, China
| | - Xiaofen Huang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; College of Life Sciences, Hebei University, Baoding 071002, Hebei, China
| | - Qin Song
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; College of Life Sciences, Hebei University, Baoding 071002, Hebei, China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; Research Unit of Proteomics Dirven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing 102206, China
| | - Jian Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; Research Unit of Proteomics Dirven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing 102206, China; College of Life Sciences, Hebei University, Baoding 071002, Hebei, China.
| | - Aihua Sun
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; Research Unit of Proteomics Dirven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing 102206, China; College of Life Sciences, Hebei University, Baoding 071002, Hebei, China.
| | - Chunyan Tian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; Research Unit of Proteomics Dirven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing 102206, China; College of Life Sciences, Hebei University, Baoding 071002, Hebei, China.
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Zhang D, Liang P, Xia B, Wu J, Hu X. Comprehensive pan-cancer analysis of ZNF337 as a potential diagnostic, immunological, and prognostic biomarker. BMC Cancer 2024; 24:987. [PMID: 39123194 PMCID: PMC11313096 DOI: 10.1186/s12885-024-12703-x] [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: 10/10/2023] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
BACKGROUND Zinc Finger Protein 337 (ZNF337) is a novel Zinc Finger (ZNF) protein family member. However, the roles of ZNF337 in human cancers have not yet been investigated. METHODS In this study, with the aid of TCGA databases, GTEx databases, and online websites, we determined the expression levels of ZNF337 in pan-cancer and its potential value as a diagnostic and prognostic marker for pan-cancer and analyzed the relationship between ZNF337 expression and immune cell infiltration and immune checkpoint genes. We then focused our research on the potential of ZNF337 as a biomarker for diagnostic and prognostic in KIRC (kidney renal clear cell carcinoma) and validated in the E-MTAB-1980 database. Moreover, the expression of ZNF337 was detected through qRT-PCR and Western blotting (WB). CCK-8 experiment, colony formation experiment, and EDU experiment were performed to evaluate cell proliferation ability. Wound healing assay and transwell assay were used to analyze its migration ability. The qRT-PCR and WB were used to detect the expression of ZNF337 in tumor tissues and paracancerous tissues of KIRC patients. RESULTS The pan-cancer analysis revealed that abnormal ZNF337 expression was found in multiple human cancer types. ZNF337 had a high diagnostic value in pan-cancer and a significant association with the prognosis of certain cancers, indicating that ZNF337 may be a valuable prognostic biomarker for multiple cancers. Further analysis demonstrated that the expression level of ZNF337 displayed significant correlations with cancer-associated fibroblasts, immune cell infiltration, and immune checkpoint genes in many tumors. Additionally, ZNF337 was observed to have a high expression in KIRC. Its expression was significantly associated with poor prognosis [overall survival (OS), disease-specific survival (DSS)], age, TNM stage, histologic grade, and pathologic stage. The high ZNF337 expression was associated with poor prognosis in the E-MTAB-1980 validation cohort. The in vitro experiments suggested that the expression of ZNF337 in KIRC tumor tissues was higher than in adjacent tissues, and ZNF337 knockdown inhibited the proliferation and migration of KIRC cells, whereas overexpression of ZNF337 had the opposite effects. CONCLUSIONS ZNF337 might be an important prognostic and immunotherapeutic biomarker for pan-cancer, especially in KIRC.
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Affiliation(s)
- Dongxu Zhang
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, NO. 8 Gongti South Road, Beijing, China
- Institute of Urology, Capital Medical University, Beijing, China
| | - Pu Liang
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- Beijing Institute of Infectious Diseases, Beijing, 100015, China
- National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, 100015, China
| | - Bowen Xia
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, NO. 8 Gongti South Road, Beijing, China
- Institute of Urology, Capital Medical University, Beijing, China
| | - Jitao Wu
- Department of Urology, Yantai Yuhuangding Hospital, Qingdao University, Yantai, Shandong, China
| | - Xiaopeng Hu
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, NO. 8 Gongti South Road, Beijing, China.
- Institute of Urology, Capital Medical University, Beijing, China.
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Xu F, Sun J, Gu X, Zhou Q. An innovative prognostic auxiliary for colon adenocarcinoma based on zinc finger protein genes. Transl Cancer Res 2024; 13:1623-1641. [PMID: 38737696 PMCID: PMC11082816 DOI: 10.21037/tcr-23-2158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 03/12/2024] [Indexed: 05/14/2024]
Abstract
Background The carcinogenesis and progression of colon adenocarcinoma (COAD) are intensively related to the abnormal expression of the zinc finger (ZNF) protein genes. We aimed to employ these genes to provide a reliable prognosis and treatment stratification tool for COAD patients. Methods Cox and the least absolute shrinkage and selection operator (LASSO) regression analysis were applied, utilizing The Cancer Genome Atlas (TCGA) metadata, to build a ZNF protein gene-based prognostic model. Using this model, patients in the training cohort and testing cohort (GSE17537) were labelled as either high or low risk. Kaplan-Meier (KM) survival analysis and time-dependent receiver operating characteristic (ROC) curve analysis were performed in the patients with opposite risk status to assess the predictive ability in each cohort. The potentiality of the mechanism was explored by the estimation of stromal and immune cells in malignant tumor tissues using expression data (ESTIMATE), single-sample gene set enrichment analysis (ssGSEA), gene set enrichment analysis (GSEA), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG). Finally, the degrees of expression of model genes were validated by immunohistochemistry (IHC). Results The prognostic model consisting of INSM1, PHF21B, RNF138, SYTL4, WRNIP1, ZNF585B, and ZNF514, classified patients into opposite risk statuses. Patients in the high-risk subset had a considerably lower chance of surviving compared to those in the low-risk subset. There is a high probability that these model genes were attached to immune-related biological processes, which can be confirmed by the results of the above mechanistic methods. Moreover, patients in the low-risk subset also significantly outperformed the patients in the high-risk subset when calculating immune cells and function scores. Drug sensitivity and tumor immune dysfunction and exclusion (TIDE) analyses showed a clear difference in the immunological and chemotherapeutic efficacy predictions within the two risk groups. Additionally, the degrees of expression of model genes in high-risk and low-risk subsets presented great discrepancies. Conclusions The signature may be applied as a predictive classifier to shepherd special medication for COAD patients.
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Affiliation(s)
- Fan Xu
- Department of Gastrointestinal Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jiahui Sun
- Department of Gastrointestinal Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xinyue Gu
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Qingxin Zhou
- Department of Gastrointestinal Oncology, Harbin Medical University Cancer Hospital, Harbin, China
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Sala C, Tarozzi M, Simonetti G, Pazzaglia M, Cammarata FP, Russo G, Acquaviva R, Cirrone GAP, Petringa G, Catalano R, Elia VC, Fede F, Manti L, Castellani G, Remondini D, Zironi I. Impact on the Transcriptome of Proton Beam Irradiation Targeted at Healthy Cardiac Tissue of Mice. Cancers (Basel) 2024; 16:1471. [PMID: 38672554 PMCID: PMC11048382 DOI: 10.3390/cancers16081471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/20/2024] [Accepted: 04/02/2024] [Indexed: 04/28/2024] Open
Abstract
Proton beam therapy is considered a step forward with respect to electromagnetic radiation, thanks to the reduction in the dose delivered. Among unwanted effects to healthy tissue, cardiovascular complications are a known long-term radiotherapy complication. The transcriptional response of cardiac tissue from xenografted BALB/c nude mice obtained at 3 and 10 days after proton irradiation covering both the tumor region and the underlying healthy tissue was analyzed as a function of dose and time. Three doses were used: 2 Gy, 6 Gy, and 9 Gy. The intermediate dose had caused the greatest impact at 3 days after irradiation: at 2 Gy, 219 genes were differently expressed, many of them represented by zinc finger proteins; at 6 Gy, there were 1109, with a predominance of genes involved in energy metabolism and responses to stimuli; and at 9 Gy, there were 105, mainly represented by zinc finger proteins and molecules involved in the regulation of cardiac function. After 10 days, no significant effects were detected, suggesting that cellular repair mechanisms had defused the potential alterations in gene expression. The nonlinear dose-response curve indicates a need to update the models built on photons to improve accuracy in health risk prediction. Our data also suggest a possible role for zinc finger protein genes as markers of proton therapy efficacy.
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Affiliation(s)
- Claudia Sala
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum University of Bologna, 40127 Bologna, Italy; (C.S.); (G.C.)
| | - Martina Tarozzi
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum University of Bologna, 40127 Bologna, Italy; (C.S.); (G.C.)
| | - Giorgia Simonetti
- Biosciences Laboratory, IRCCS Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (G.S.)
| | - Martina Pazzaglia
- Biosciences Laboratory, IRCCS Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (G.S.)
| | - Francesco Paolo Cammarata
- Institute of Bioimaging and Molecular Physiology, National Council of Research (IBFM-CNR), 90015 Cefalù, Italy (G.R.)
- Laboratori Nazionali del SUD, National Institute of Nuclear Physics, (LNS-INFN), 95125 Catania, Italy (G.P.)
| | - Giorgio Russo
- Institute of Bioimaging and Molecular Physiology, National Council of Research (IBFM-CNR), 90015 Cefalù, Italy (G.R.)
- Laboratori Nazionali del SUD, National Institute of Nuclear Physics, (LNS-INFN), 95125 Catania, Italy (G.P.)
| | - Rosaria Acquaviva
- Department of Drug Science, Section of Biochemistry, University of Catania, 95125 Catania, Italy;
| | | | - Giada Petringa
- Laboratori Nazionali del SUD, National Institute of Nuclear Physics, (LNS-INFN), 95125 Catania, Italy (G.P.)
| | - Roberto Catalano
- Laboratori Nazionali del SUD, National Institute of Nuclear Physics, (LNS-INFN), 95125 Catania, Italy (G.P.)
| | - Valerio Cosimo Elia
- Department of Physics “E. Pancini”, University of Naples Federico II, 80126 Naples, Italy; (V.C.E.); (F.F.); (L.M.)
- National Institute of Nuclear Physics, Napoli Section (INFN NA), 80126 Naples, Italy
| | - Francesca Fede
- Department of Physics “E. Pancini”, University of Naples Federico II, 80126 Naples, Italy; (V.C.E.); (F.F.); (L.M.)
- National Institute of Nuclear Physics, Napoli Section (INFN NA), 80126 Naples, Italy
| | - Lorenzo Manti
- Department of Physics “E. Pancini”, University of Naples Federico II, 80126 Naples, Italy; (V.C.E.); (F.F.); (L.M.)
- National Institute of Nuclear Physics, Napoli Section (INFN NA), 80126 Naples, Italy
| | - Gastone Castellani
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum University of Bologna, 40127 Bologna, Italy; (C.S.); (G.C.)
| | - Daniel Remondini
- National Institute for Nuclear Physics, Bologna Section (INFN BO), 40127 Bologna, Italy
- Department of Physics and Astronomy “Augusto Righi” (DIFA), Alma Mater Studiorum University of Bologna, 40127 Bologna, Italy
| | - Isabella Zironi
- National Institute for Nuclear Physics, Bologna Section (INFN BO), 40127 Bologna, Italy
- Department of Physics and Astronomy “Augusto Righi” (DIFA), Alma Mater Studiorum University of Bologna, 40127 Bologna, Italy
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Wang M, Tang L, Chen S, Wang L, Wu J, Zhong C, Li Y, Chen Y. ZNF217-activated Notch signaling mediates sulforaphane-suppressed stem cell properties in colorectal cancer. J Nutr Biochem 2024; 125:109551. [PMID: 38134973 DOI: 10.1016/j.jnutbio.2023.109551] [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: 05/13/2023] [Revised: 11/18/2023] [Accepted: 12/18/2023] [Indexed: 12/24/2023]
Abstract
Cancer stem cells (CSCs) are known to contribute to the progression of colorectal cancer (CRC). However, understanding of the molecular mechanisms and key factors involved in CRC is still insufficient to identify therapeutic targets against colorectal CSCs. In an effort to identify such mechanisms, we conducted bioinformatics analyses to evaluate the expression patterns in tumor and normal colorectal tissues, leading us to focus on the role of the ZNF217/Notch1 axis in mediating stem cell properties in CRC. Our findings revealed that ZNF217 overexpression activated self-renewal ability, expression of colorectal CSC markers, and Notch signaling in CRC. Dual-luciferase reporter assay suggested a role for ZNF217 in targeting Notch1 to activate Notch signaling. We observed that the promotional effects of Notch signaling, as well as CSC markers, under ZNF217 overexpression were attenuated after Notch1 knockdown. In addition to in vitro data, our in vivo results confirmed the inhibitory effect of sulforaphane on the tumorigenicity of CSCs, depicted the suppressive role of sulforaphane on colorectal CSCs mediated by the ZNF217/Notch1 axis, thereby providing new targetable vulnerabilities and therapeutic strategies for CRC.
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Affiliation(s)
- Menghuan Wang
- Department of Children Health Care, Children's Hospital of Nanjing Medical University, Nanjing, China; Department of Nutrition and Food Safety, School of Public Health, Nanjing Medical University, Nanjing, China
| | - LvYuwei Tang
- Department of Nutrition and Food Safety, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Siyu Chen
- Department of Fundamental and Community Nursing, School of Nursing, Nanjing Medical University, Nanjing, China
| | - Liudan Wang
- Department of Fundamental and Community Nursing, School of Nursing, Nanjing Medical University, Nanjing, China
| | - Jinyi Wu
- Department of Nutrition and Food Safety, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Caiyun Zhong
- Department of Nutrition and Food Safety, School of Public Health, Nanjing Medical University, Nanjing, China; Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.
| | - Yadong Li
- Department of Surgery, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Yue Chen
- Department of Fundamental and Community Nursing, School of Nursing, Nanjing Medical University, Nanjing, China.
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Oleksiewicz U, Machnik M, Sobocińska J, Molenda S, Olechnowicz A, Florczak A, Mierzejewska J, Adamczak D, Smolibowski M, Kaczmarek M, Mackiewicz A. ZNF643/ZFP69B Exerts Oncogenic Properties and Associates with Cell Adhesion and Immune Processes. Int J Mol Sci 2023; 24:16380. [PMID: 38003570 PMCID: PMC10671213 DOI: 10.3390/ijms242216380] [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: 08/30/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
The global cancer burden remains high; thus, a better understanding of the molecular mechanisms driving carcinogenesis is needed to improve current prevention and treatment options. We previously detected the ZNF643/ZFP69B gene upregulated in multiple tumors, and we speculated it may play a role in tumor biology. To test this hypothesis, we employed TCGA-centered databases to correlate ZNF643 status with various clinicopathological parameters. We also performed RNA-seq analysis and in vitro studies assessing cancer cell phenotypes, and we searched for ZNF643-bound genomic loci. Our data indicated higher levels of ZNF643 in most analyzed tumors compared to normal samples, possibly due to copy number variations. ZNF643 mRNA correlated with diverse molecular and immune subtypes and clinicopathological features (tumor stage, grade, patient survival). RNA-seq analysis revealed that ZNF643 silencing triggers the deregulation of the genes implicated in various cancer-related processes, such as growth, adhesion, and immune system. Moreover, we observed that ZNF643 positively influences cell cycle, migration, and invasion. Finally, our ChIP-seq analysis indicated that the genes associated with ZNF643 binding are linked to adhesion and immune signaling. In conclusion, our data confirm the oncogenic properties of ZNF643 and pinpoint its impact on cell adhesion and immune processes.
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Affiliation(s)
- Urszula Oleksiewicz
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, 15 Garbary Street, 61-866 Poznan, Poland
| | - Marta Machnik
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, 15 Garbary Street, 61-866 Poznan, Poland
| | - Joanna Sobocińska
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, 15 Garbary Street, 61-866 Poznan, Poland
| | - Sara Molenda
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, 15 Garbary Street, 61-866 Poznan, Poland
- Doctoral School, Poznan University of Medical Sciences, 70 Bukowska Street, 60-812 Poznan, Poland
| | - Anna Olechnowicz
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
- Doctoral School, Poznan University of Medical Sciences, 70 Bukowska Street, 60-812 Poznan, Poland
- Department of Histology and Embryology, Poznan University of Medical Sciences, 6 Święcickiego Street, 60-781 Poznan, Poland
| | - Anna Florczak
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, 15 Garbary Street, 61-866 Poznan, Poland
| | - Julia Mierzejewska
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
| | - Dominika Adamczak
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
| | - Mikołaj Smolibowski
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
| | - Mariusz Kaczmarek
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, 15 Garbary Street, 61-866 Poznan, Poland
| | - Andrzej Mackiewicz
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (U.O.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, 15 Garbary Street, 61-866 Poznan, Poland
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Oleksiewicz U, Machnik M, Sobocińska J, Molenda S, Olechnowicz A, Florczak A, Smolibowski M, Kaczmarek M. ZNF714 Supports Pro-Oncogenic Features in Lung Cancer Cells. Int J Mol Sci 2023; 24:15530. [PMID: 37958512 PMCID: PMC10649060 DOI: 10.3390/ijms242115530] [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: 09/07/2023] [Revised: 10/10/2023] [Accepted: 10/19/2023] [Indexed: 11/15/2023] Open
Abstract
Despite the ongoing progress in diagnosis and treatments, cancer remains a threat to more than one-third of the human population. The emerging data indicate that many Krüppel-associated box zinc finger proteins (KRAB-ZNF) belonging to a large gene family may be involved in carcinogenesis. Our previous study identified Zinc Finger Protein 714 (ZNF714), a KRAB-ZNF gene of unknown function, as being commonly overexpressed in many tumors, pointing to its hypothetical oncogenic role. Here, we harnessed The Cancer Genome Atlas (TCGA)-centered databases and performed functional studies with transcriptomic and methylomic profiling to explore ZNF714 function in cancer. Our pan-cancer analyses confirmed frequent ZNF714 overexpression in multiple tumors, possibly due to regional amplification, promoter hypomethylation, and Nuclear Transcription Factor Y Subunit Beta (NFYB) signaling. We also showed that ZNF714 expression correlates with tumor immunosuppressive features. The in vitro studies indicated that ZNF714 expression positively associates with proliferation, migration, and invasion. The transcriptomic analysis of ZNF714 knocked-down cells demonstrated deregulation of cell adhesion, migration, proliferation, apoptosis, and differentiation. Importantly, we provided evidence that ZNF714 negatively regulates the expression of several known TSGs indirectly via promoter methylation. However, as ZNF714 did not show nuclear localization in our research model, the regulatory mechanisms exerted by ZNF714 require further investigation. In conclusion, our results reveal, for the first time, that ZNF714 may support pro-oncogenic features in lung cancer cells.
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Affiliation(s)
- Urszula Oleksiewicz
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
| | - Marta Machnik
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
| | - Joanna Sobocińska
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
| | - Sara Molenda
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
- Doctoral School, Poznan University of Medical Sciences, 60-812 Poznan, Poland
| | - Anna Olechnowicz
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
- Doctoral School, Poznan University of Medical Sciences, 60-812 Poznan, Poland
- Department of Histology and Embryology, Poznan University of Medical Sciences, Swiecickiego 6 Street, 60-781 Poznan, Poland
| | - Anna Florczak
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
| | - Mikołaj Smolibowski
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
| | - Mariusz Kaczmarek
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
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Zhu Q, Liu Z, Cheng X, Liang W, Wang H, Li P, Zhang J, Chen Y, Gao Y, Qian R. ZNF480 influences the prognosis, pathogenesis, and immune microenvironment in patients with lower-grade glioma. Heliyon 2023; 9:e18185. [PMID: 37519705 PMCID: PMC10372659 DOI: 10.1016/j.heliyon.2023.e18185] [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: 08/21/2022] [Revised: 06/26/2023] [Accepted: 07/11/2023] [Indexed: 08/01/2023] Open
Abstract
ZNF480 has not yet attracted attention in the study of malignant tumors. Therefore, this study attempts to explain the significance of ZNF480 in the pathological process of lower-grade gliomas (LGG) based on large-scale samples from public database sources and in vitro experiments. Reverse transcription quantitative real-time polymerase chain reaction and immunohistochemistry confirmed that ZNF480 was highly expressed at both the mRNA and protein levels in LGG. Prognostic correlation analysis confirmed that the high expression of ZNF480, as an independent pathogenic gene, significantly correlates with poor survival in patients. Furthermore, the expression level of ZNF480 was significantly inhibited in SHG-44 cells treated with ademetionine disulfate tosylate. Gene set enrichment analysis showed that ZNF480 exists in multiple tumor-related signaling pathways, including the Notch signaling pathway. Immunological correlation analysis showed that ZNF480 can promote the LGG microenvironment to a high immune state and significantly enhance the infiltration of various immune cells, such as M2 macrophages. Finally, Spearman analysis showed a positive correlation of ZNF480 with many immune checkpoints, such as PD-L1. Overall, this study reveals for the first time the adverse effects of ZNF480 on the prognosis of tumor patients, which expands our understanding of the molecular mechanisms behind the regulation of ZNF480. We believe that the high expression of ZNF480 in LGG may be valuable for molecular targeted therapy or combined immunotherapy.
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Affiliation(s)
- Qingyun Zhu
- People's Hospital of Henan University, Henan Provincial People's Hospital, Microbiome Laboratory, Zhengzhou 450003, Henan Province, China
| | - Zhendong Liu
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People's Hospital; People's Hospital of Zhengzhou University, People's Hospital of Henan University, No.7 Weiwu Road, Jinshui District, Zhengzhou 450003, Henan Province, China
| | - Xingbo Cheng
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People's Hospital; People's Hospital of Zhengzhou University, People's Hospital of Henan University, No.7 Weiwu Road, Jinshui District, Zhengzhou 450003, Henan Province, China
| | - Wenjia Liang
- People's Hospital of Henan University, Henan Provincial People's Hospital, Microbiome Laboratory, Zhengzhou 450003, Henan Province, China
| | - Hongbo Wang
- Department of Urology, Lanzhou University Second Hospital, Lanzhou 730030, Gansu, China
| | - Pengxu Li
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People's Hospital; People's Hospital of Zhengzhou University, People's Hospital of Henan University, No.7 Weiwu Road, Jinshui District, Zhengzhou 450003, Henan Province, China
| | - Jiangfen Zhang
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People's Hospital; People's Hospital of Zhengzhou University, People's Hospital of Henan University, No.7 Weiwu Road, Jinshui District, Zhengzhou 450003, Henan Province, China
| | - Yusheng Chen
- Department of Neurosurgery, Henan Provincial People's Hospital, People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou 450003, Henan Province, China
| | - Yanzheng Gao
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People's Hospital; People's Hospital of Zhengzhou University, People's Hospital of Henan University, No.7 Weiwu Road, Jinshui District, Zhengzhou 450003, Henan Province, China
| | - Rongjun Qian
- Department of Neurosurgery, Henan Provincial People's Hospital, People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou 450003, Henan Province, China
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9
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Dong X, Zhang Y, Sun Y, Nan Q, Li M, Ma L, Zhang L, Luo J, Qi Y, Miao Y. Promoter hypermethylation and comprehensive regulation of ncRNA lead to the down-regulation of ZNF880, providing a new insight for the therapeutics and research of colorectal cancer. BMC Med Genomics 2023; 16:148. [PMID: 37370088 PMCID: PMC10294494 DOI: 10.1186/s12920-023-01571-2] [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: 06/02/2022] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
The human genome encodes more than 350 kinds of Krüppel-associated box (KRAB) domain-containing zinc-finger proteins (KZFPs), KRAB-type ZNF transcription factor family (KZNF) plays a vital role in gene regulatory networks. The KZNF family members include a large number of highly homologous genes, gene subtypes and pseudogenes, and their expression has a high degree of tissue specificity and precision. Due to the high complexity of its regulatory network, the KZNF gene family has not been researched in sufficient, and the role of its members in the occurrence of cancer is mostly unexplored. In this study, ZNF880 was significantly associated with overall survival (OS) and disease-free survival (DFS) in colorectal carcinoma (CRC) patients. Low ZNF880 expression resulted in shorter OS and DFS. Combined with Colon adenocarcinoma (COAD) and Rectum adenocarcinoma (READ) data collection in the TCGA database, we found that ZNF880 was significantly down-regulated in CRC. Further analysis of the sequence variation of ZNF880 in CRC showed that ZNF880 accumulated a large number of SNV in the C2H2 domain and KRAB domain, while promoter region of ZNF880 also showed high methylation in COAD and READ. Combined with the Cbioportal and TIMER databases, the expression of mutant ZNF880 was significantly lower in COAD compared to the wild type. Simultaneously, the lncRNA-miRNA-ZNF880 ceRNA regulatory network was constructed through co-expression and miRNAs target gene prediction, demonstrating the precision of the ZNF880 regulatory network. In addition, the decreased expression of ZNF880 caused the significant immune infiltration decreases of CD8 + cells in COAD. In contrast, the immune infiltration of CD4 + cells and macrophages in COAD is positively correlated with ZNF880. Finally, through protein-protein interaction (PPI) network analysis and transcription factor target gene prediction, we screened out the genes most likely to be related to the function of ZNF880. CENPK, IFNGR2, REC8 and ZBTB17 were identified as the most closely functioning genes with ZNF880, which may indicate that ZNF880 has important links with the formation of cell centromere, tumor immunity, cell cycle and other pathways closely related to the occurrence of CRC. These studies show that the down-regulation of ZNF880 gene is closely related to CRC, and the targeted change of the expression of its regulatory molecules (miRNA and lncRNA) may be a new perspective for CRC treatment.
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Affiliation(s)
- Xiangqian Dong
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, NO.295 Xichang Road, Kunming, 650032, P.R. China
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, 650032, China
| | - Yinghui Zhang
- Department of Gastroenterology, Affiliated Hospital of Yunnan University, Kunming, 650021, China
| | - Yang Sun
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, NO.295 Xichang Road, Kunming, 650032, P.R. China
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, 650032, China
| | - Qiong Nan
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, NO.295 Xichang Road, Kunming, 650032, P.R. China
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, 650032, China
| | - Maojuan Li
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, NO.295 Xichang Road, Kunming, 650032, P.R. China
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, 650032, China
| | - Lanqing Ma
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, NO.295 Xichang Road, Kunming, 650032, P.R. China
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, 650032, China
| | - Lei Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, NO.295 Xichang Road, Kunming, 650032, P.R. China
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, 650032, China
| | - Juan Luo
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, NO.295 Xichang Road, Kunming, 650032, P.R. China
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, 650032, China
| | - Yating Qi
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, NO.295 Xichang Road, Kunming, 650032, P.R. China
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, 650032, China
| | - Yinglei Miao
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, NO.295 Xichang Road, Kunming, 650032, P.R. China.
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, 650032, China.
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10
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Salnikov MY, Wang E, Christensen E, Prusinkiewicz MA, Shooshtari P, Mymryk JS. The EBV Gastric Cancer Resource (EBV-GCR): A Suite of Tools for Investigating EBV-Associated Human Gastric Carcinogenesis. Viruses 2023; 15:v15040853. [PMID: 37112833 PMCID: PMC10145221 DOI: 10.3390/v15040853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Epstein-Barr virus (EBV) causes lifelong infection in over 90% of the world’s population. EBV infection leads to several types of B cell and epithelial cancers due to the viral reprogramming of host-cell growth and gene expression. EBV is associated with 10% of stomach/gastric adenocarcinomas (EBVaGCs), which have distinct molecular, pathological, and immunological characteristics compared to EBV-negative gastric adenocarcinomas (EBVnGCs). Publicly available datasets, such as The Cancer Genome Atlas (TCGA), contain comprehensive transcriptomic, genomic, and epigenomic data for thousands of primary human cancer samples, including EBVaGCs. Additionally, single-cell RNA-sequencing data are becoming available for EBVaGCs. These resources provide a unique opportunity to explore the role of EBV in human carcinogenesis, as well as differences between EBVaGCs and their EBVnGC counterparts. We have constructed a suite of web-based tools called the EBV Gastric Cancer Resource (EBV-GCR), which utilizes TCGA and single-cell RNA-seq data and can be used for research related to EBVaGCs. These web-based tools allow investigators to gain in-depth biological and clinical insights by exploring the effects of EBV on cellular gene expression, associations with patient outcomes, immune landscape features, and differential gene methylation, featuring both whole-tissue and single-cell analyses.
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Affiliation(s)
- Mikhail Y. Salnikov
- Department of Microbiology and Immunology, Western University, London, ON N6A 3K7, Canada
| | - Eric Wang
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Erik Christensen
- Department of Computer Science, Western University, London, ON N6A 5B7, Canada
- Children’s Health Research Institute, Lawson Health Research Institute, London, ON N6A 5W9, Canada
| | | | - Parisa Shooshtari
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
- Department of Computer Science, Western University, London, ON N6A 5B7, Canada
- Children’s Health Research Institute, Lawson Health Research Institute, London, ON N6A 5W9, Canada
- The Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Joe S. Mymryk
- Department of Microbiology and Immunology, Western University, London, ON N6A 3K7, Canada
- Department of Oncology, Western University, London, ON N6A 3K7, Canada
- London Regional Cancer Program, Lawson Health Research Institute, London, ON N6A 5W9, Canada
- Department of Otolaryngology, Western University, London, ON N6A 5W9, Canada
- Correspondence:
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11
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Yang B, Tang H, Wang N, Gu J, Wang Q. Targeted DNA demethylation of the ZNF334 promoter inhibits colorectal cancer growth. Cell Death Dis 2023; 14:210. [PMID: 36966142 PMCID: PMC10039945 DOI: 10.1038/s41419-023-05743-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 03/11/2023] [Accepted: 03/15/2023] [Indexed: 03/27/2023]
Abstract
Colorectal cancer (CRC) is a leading cause of cancer deaths worldwide. Aberrant regulation of DNA methylation in promoters of tumor suppressor genes or proto-oncogenes is one of the fundamental processes driving the initiation and progression of CRC. Zinc-finger proteins (ZNFs) are one of the most abundant groups of proteins and function in many important biological processes related to tumorigenesis. Herein, we detected abnormal hypermethylation of the ZNF334 gene in CRC tissues compared with normal tissues, and this modification downregulated the expression of ZNF334. Furthermore, ten-eleven translocation 1 (TET1) was identified to be involved in regulating the methylation level of ZNF334. Next, a dCas9-multiGCN4/scFv-TET1CD-sgZNF334-targeted demethylation system was constructed to reverse the expression of ZNF334 through sgRNA targeting the ZNF334 promoter. Both in vitro and in vivo experiments demonstrated the targeted demethylation system upregulated ZNF334 expression and inhibited CRC growth. Collectively, targeted DNA demethylation of the ZNF334 promoter sheds light on the precise treatment of CRC.
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Affiliation(s)
- Bin Yang
- School of Pharmacy, Southwest Minzu University, Chengdu, 610225, Sichuan, China
| | - Haiyu Tang
- School of Pharmacy, Southwest Minzu University, Chengdu, 610225, Sichuan, China
| | - Nan Wang
- School of Pharmacy, Southwest Minzu University, Chengdu, 610225, Sichuan, China
| | - Jian Gu
- School of Pharmacy, Southwest Minzu University, Chengdu, 610225, Sichuan, China
| | - Qin Wang
- School of Pharmacy, Southwest Minzu University, Chengdu, 610225, Sichuan, China.
- BMI Center for Biomass Materials and Nanointerfaces, College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, Sichuan, China.
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12
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Mohibi S, Chen M, Chen X, Zhang J. Poly zinc finger protein ZFP14 suppresses lymphomagenesis and abnormal inflammatory response via the HOXA gene cluster. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166587. [PMID: 36349645 PMCID: PMC10907336 DOI: 10.1016/j.bbadis.2022.166587] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/19/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022]
Abstract
Poly zinc finger proteins (ZFP) that contain a KRAB (Krüppel-associated box) domain represent the largest class of transcription factors in higher organisms, but their roles in development and pathogenesis are largely undefined. ZFP14 (also known as ZNF531) contains thirteen zinc fingers and is highly conserved across species. Notably, we found that ZFP14 is frequently down-regulated in a multitude of human cancers, which correlates with poor prognosis of patients. Since ZFP14 has never been characterized, we generated a Zfp14-deficient mouse model to investigate the role of ZFP14 in development and pathogenesis. We showed that the mice deficient in Zfp14 had a short lifespan and were prone to diffuse large B-cell lymphoma (DLBCL), hyperplasia in multiple organs, systemic chronic inflammation, liver steatosis, and pancreatitis. Additionally, several pro-inflammatory cytokines, including IL-1β, IL18, and TNFα, were highly expressed in inflamed Zfp14-/- mice spleens, livers, kidneys and lungs. To determine the underlying mechanism, RNA-seq analysis was performed and showed that the loss of ZFP14 led to increased expression of inflammatory and tumor-promoting genes. Out of the various tumor-promoting genes upregulated by ZFP14 loss, the HOXA gene cluster, which is known to promote lymphomagenesis and conserved between mouse and human, is consistently induced by loss of ZFP14. Moreover, we showed that the HOXA gene expression was inversely correlated with that of ZFP14 in human cancer patients and higher HOXA1 expression was correlated with poor patient prognosis. Together, we postulate that ZFP14 suppresses lymphomagenesis and abnormal inflammatory response by maintaining proper expression of the HOXA gene cluster.
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Affiliation(s)
- Shakur Mohibi
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California, Davis, CA, United States of America.
| | - Mingyi Chen
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Xinbin Chen
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California, Davis, CA, United States of America.
| | - Jin Zhang
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California, Davis, CA, United States of America.
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13
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ZNF3 regulates proliferation, migration and invasion through MMP1 and TWIST in colorectal cancer. Acta Biochim Biophys Sin (Shanghai) 2022; 54:1889-1896. [PMID: 36789689 PMCID: PMC10157515 DOI: 10.3724/abbs.2022187] [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: 12/12/2022] Open
Abstract
Colorectal cancer (CRC) is a malignant tumor with a high incidence and mortality worldwide. Currently, the underlying molecular mechanisms of CRC are still unclear. Zinc finger protein 3 (ZNF3) is a zinc-finger transcription factor that has been reported as a candidate for breast cancer prognosis, suggesting its involvement in the regulation of tumorigenesis. However, the association between ZNF3 and CRC remains unknown. To investigate the role of ZNF3 in CRC, we first analyze the correlation between ZNF3 expression and CRC, and the results demonstrate that ZNF3 is highly expressed in CRC tissue and cells, which is associated with the age of CRC patients. In vitro studies show that ZNF3 overexpression promotes CRC cell migration. Compared to control cells, knockdown of ZNF3 markedly suppresses CRC cell proliferation, migration and invasion and promotes G0/G1 phase cell cycle arrest. The expressions of the EMT-related markers TWIST and MMP1 are significantly decreased when ZNF3 is silenced. Additionally, overexpression of MMP1 and TWIST exacerbates CRC cell proliferation, accelerates the S phase cell cycle in ZNF3-knockdown SW480 cells, and increases cell migration and invasion through Transwell chambers. These data suggest that ZNF3 is involved in cellular proliferation, migration and invasion by regulating MMP1 and TWIST in CRC cells.
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14
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Arora I, Li S, Crowley MR, Li Y, Tollefsbol TO. Genome-Wide Analysis on Transcriptome and Methylome in Prevention of Mammary Tumor Induced by Early Life Combined Botanicals. Cells 2022; 12:cells12010014. [PMID: 36611809 PMCID: PMC9818885 DOI: 10.3390/cells12010014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Breast cancer (BC) is the most common malignancy and the second leading cause of cancer death among women in the United States. The consumption of natural dietary components such as broccoli sprouts (BSp) and green tea polyphenols (GTPs) has demonstrated exciting potential in reducing the risk of BC through the regulation of epigenetic mechanisms. However, little is known about their impacts on reversing epigenomic aberrations that are centrally involved in the initiation and progression of BC. Previously, we have determined the efficacy of combined BSp and GTPs treatment on the inhibition of the growth of a mammary tumor in a transgenic Her2/neu mouse model. We sought to extend our previous study to identify universal biomarkers that represent common mechanistic changes among different mouse models in response to this dietary regime by including a new transgenic mouse model, C3(1)-SV40 TAg (SV40). As a result, we identified novel target genes that were differentially expressed and methylated in response to dietary botanicals when administered singly (BSp and GTPs) and in combination (BSp + GTPs) in both mouse models. We discovered more differentially expressed and methylated genes in the combination treatment group compared to the singly administered groups. Subsequently, several biological pathways related to epigenetic regulations were identified in response to the combination treatment. Furthermore, when compared to the BSp and GTPs treatment alone, the combinatorial treatment showed a more significant impact on the regulation of the epigenetic modifier activities involved in DNA methylation and histone modifications. Our study provides key insights about the impact of the combined administration of BSp and GTPs on BC using a multi-omics analysis, suggesting a combinatorial approach is more efficacious in preventing and inhibiting BC by impacting key tumor-related genes at transcriptomic and methylomic levels. Our findings could be further extrapolated as a comprehensive source for understanding the epigenetic modifications that are associated with the effects of these dietary botanicals on BC prevention.
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Affiliation(s)
- Itika Arora
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Shizhao Li
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Michael R. Crowley
- Heflin Center for Genomic Science, Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Yuanyuan Li
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA
- Correspondence: (Y.L.); (T.O.T.)
| | - Trygve O. Tollefsbol
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Integrative Center for Aging Research, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Correspondence: (Y.L.); (T.O.T.)
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15
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Sobocińska J, Nowakowska J, Molenda S, Olechnowicz A, Guglas K, Kozłowska-Masłoń J, Kazimierczak U, Machnik M, Oleksiewicz U, Teresiak A, Lamperska K, Kolenda T. Zinc Finger Proteins in Head and Neck Squamous Cell Carcinomas: ZNF540 May Serve as a Biomarker. Curr Oncol 2022; 29:9896-9915. [PMID: 36547193 PMCID: PMC9776630 DOI: 10.3390/curroncol29120779] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/05/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is one of the ten most common cancers. Most cancer cases originate from alcohol and tobacco consumption. However, studies have demonstrated that human papillomavirus (HPV) infection, particularly HPV-16, may also significantly influence disease progression. The KRAB-ZNF family of genes is involved in epigenetic suppression, and its involvement in carcinogenesis is the subject of extensive studies. The available literature data demonstrate that they may play different roles, both as tumor suppressors and oncogenes. In this study, six ZNF genes, ZFP28, ZNF132, ZNF418, ZNF426, ZNF540, and ZNF880, were tested using several in silico approaches based on the TCGA and GEO datasets. Our analyses indicate that the expression of the analyzed ZNFs was significantly downregulated in tumor tissues and depended on tumor localization. The expression levels of ZNFs differed between HPV-positive vs. HPV-negative patients depending on the clinical-pathological parameters. More specifically, the patients with higher levels of ZNF418 and ZNF540 showed better survival rates than those with a lower expression. In addition, the level of ZNF540 expression in HPV-positive (HPV(+)) patients was higher than in HPV-negative (HPV(-)) patients (p < 0.0001) and was associated with better overall survival (OS). In conclusion, we demonstrate that ZNF540 expression highly correlates with HPV infection, which renders ZNF540 a potential biomarker for HNSCC prognosis and treatment.
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Affiliation(s)
- Joanna Sobocińska
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
| | - Joanna Nowakowska
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
- Molecular and Cell Biology Unit, Poznan University of Medical Sciences, 60-572 Poznan, Poland
| | - Sara Molenda
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
| | - Anna Olechnowicz
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
- Department of Histology and Embryology, Poznan University of Medical Sciences, Święcickiego 6 Street, 60-781 Poznan, Poland
| | - Kacper Guglas
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Zwirki and Wigury Street 61, 02-091 Warsaw, Poland
| | - Joanna Kozłowska-Masłoń
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznan, Poland
| | - Urszula Kazimierczak
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
| | - Marta Machnik
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
| | - Urszula Oleksiewicz
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
| | - Anna Teresiak
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
| | - Katarzyna Lamperska
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
| | - Tomasz Kolenda
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
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16
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Kleinbielen T, Olasagasti F, Azcarate D, Beristain E, Viguri-Díaz A, Guerra-Merino I, García-Orad Á, de Pancorbo MM. In silico identification and in vitro expression analysis of breast cancer-related m 6A-SNPs. Epigenetics 2022; 17:2144-2156. [PMID: 35971775 PMCID: PMC9665143 DOI: 10.1080/15592294.2022.2111137] [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: 04/05/2022] [Accepted: 08/01/2022] [Indexed: 12/24/2022] Open
Abstract
Research on m6A-associated SNPs (m6A-SNPs) has emerged recently due to their possible critical roles in many key biological processes. In this sense, several investigations have identified m6A-SNPs in different diseases. In order to gain a more complete understanding of the role that m6A-SNPs can play in breast cancer, we performed an in silico analysis to identify the m6A-SNPs associated with breast cancer and to evaluate their possible effects. For this purpose, we downloaded SNPs related to breast cancer and a list of m6A-SNPs from public databases in order to identify which ones appear in both. Subsequently, we assessed the identified m6A-SNPs in silico by expression quantitative trait loci (eQTL) analysis and differential gene expression analysis. We genotyped the m6A-SNPs found in the in silico analysis in 35 patients with breast cancer, and we carried out a gene expression analysis experimentally on those that showed differences. Our results identified 981 m6A-SNPs related to breast cancer. Four m6A-SNPs showed an eQTL effect and only three were in genes that presented an altered gene expression. When the three m6A-SNPs were evaluated in the tissue sample of our breast cancer patients, only the m6A-SNP rs76563149 located in ZNF354A gene presented differences in allele frequencies and a low gene expression in breast cancer tissues, especially in luminal B HER2+ subtype. Future investigations of these m6A-SNPs should expand the study in different ethnic groups and increase the sample sizes to test their association with breast cancer and elucidate their molecular function.
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Affiliation(s)
- Tamara Kleinbielen
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU. Postal code: 01006. Vitoria-Gasteiz, Araba, Spain
- Department of Zoology and Animal Biology. University of the Basque Country (UPV/EHU). Postal code: 48940. Leioa, Bizkaia, Spain
- Bioaraba Health Research Institute. Postal Code: 01009, Vitoria-Gasteiz, Araba, Spain
| | - Felix Olasagasti
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU. Postal code: 01006. Vitoria-Gasteiz, Araba, Spain
- Bioaraba Health Research Institute. Postal Code: 01009, Vitoria-Gasteiz, Araba, Spain
- Department of Biochemistry and Molecular Biology, University of the Basque Country, UPV/EHU. Postal code: 01006. Vitoria-Gasteiz, Araba, Spain
| | - Daniel Azcarate
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU. Postal code: 01006. Vitoria-Gasteiz, Araba, Spain
- Department of Zoology and Animal Biology. University of the Basque Country (UPV/EHU). Postal code: 48940. Leioa, Bizkaia, Spain
- Bioaraba Health Research Institute. Postal Code: 01009, Vitoria-Gasteiz, Araba, Spain
| | - Elena Beristain
- Bioaraba Health Research Institute. Postal Code: 01009, Vitoria-Gasteiz, Araba, Spain
- Molecular Genetics Laboratory, Araba University Hospital, Osakidetza Basque Health Service. Postal code: 01009. Vitoria-Gasteiz, Araba, Spain
| | - Amparo Viguri-Díaz
- Pathology Department, Araba University Hospital. Postal code: 01009. Vitoria-Gasteiz, Araba, Spain
| | - Isabel Guerra-Merino
- Bioaraba Health Research Institute. Postal Code: 01009, Vitoria-Gasteiz, Araba, Spain
- Pathology Department, Araba University Hospital. Postal code: 01009. Vitoria-Gasteiz, Araba, Spain
| | - África García-Orad
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU). Postal code: 48940. Leioa, Bizkaia, Spain
- BioCruces Bizkaia Health Research Institute. Postal code: 48903. Barakaldo, Bizkaia, Spain
| | - Marian M. de Pancorbo
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU. Postal code: 01006. Vitoria-Gasteiz, Araba, Spain
- Department of Zoology and Animal Biology. University of the Basque Country (UPV/EHU). Postal code: 48940. Leioa, Bizkaia, Spain
- Bioaraba Health Research Institute. Postal Code: 01009, Vitoria-Gasteiz, Araba, Spain
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Zhen J, Ke Y, Pan J, Zhou M, Zeng H, Song G, Yu Z, Fu B, Liu Y, Huang D, Wu H. ZNF320 is a hypomethylated prognostic biomarker involved in immune infiltration of hepatocellular carcinoma and associated with cell cycle. Aging (Albany NY) 2022; 14:8411-8436. [PMID: 36287187 PMCID: PMC9648795 DOI: 10.18632/aging.204350] [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: 06/30/2022] [Accepted: 10/03/2022] [Indexed: 11/26/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the most deadly and common malignant cancers around the world, and the prognosis of HCC patients is not optimistic. ZNF320 belongs to Krüppel like zinc finger gene family. However, no studies have focused on the influence of ZNF320 in HCC. We first analyzed ZNF320 expression in HCC by using data from TCGA and ICGC, then conducted a joint analysis with TIMER and UALCAN, and validated by immunohistochemistry in clinical HCC samples. Then we applied UALCAN to explore the correlation between ZNF320 expression and clinicopathological characteristics. Consequently, using Kaplan-Meier Plotter analysis and the Cox regression, we can predict the prognostic value of ZNF320 for HCC patients. Next, the analysis by GO, KEGG, and GSEA revealed that ZNF320 was significantly correlated to cell cycle and immunity. Finally, TIMER and GEPIA analysis verified that ZNF320 expression is closely related to tumor infiltrating immune cells (TIIC), including B cells, CD8+ T cells, CD4+ T cells, macrophages, neutrophils, and dendritic cells. The analysis of the TCGA and ICGC data sets revealed that ZNF320 expression was significantly correlated with m6A related genes (RBMX, YTHDF1, and METTL3). In conclusion, ZNF320 may be a prognostic biomarker related to immunity as a candidate for liver cancer.
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Affiliation(s)
- Jing Zhen
- Second Affiliated Hospital of Nanchang University, Nanchang, China
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Yun Ke
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Jingying Pan
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Minqin Zhou
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Hong Zeng
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Gelin Song
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Zichuan Yu
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Bidong Fu
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Yue Liu
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Da Huang
- Department of Thyroid Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Honghu Wu
- Department of Science and Technology, Second Affiliated Hospital of Nanchang University, Nanchang, China
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18
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Zhou Z, Hu F, Huang D, Chi Q, Tang NLS. Nonsense-Mediated Decay Targeted RNA (ntRNA): Proposal of a ntRNA–miRNA–lncRNA Triple Regulatory Network Usable as Biomarker of Prognostic Risk in Patients with Kidney Cancer. Genes (Basel) 2022; 13:genes13091656. [PMID: 36140823 PMCID: PMC9498815 DOI: 10.3390/genes13091656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/05/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022] Open
Abstract
The most prevalent subtype of renal cell carcinoma (RCC), kidney renal clear cell carcinoma (KIRC) may be associated with a poor prognosis in a high number of cases, with a stage-specific prognostic stratification currently in use. No reliable biomarkers have been utilized so far in clinical practice despite the efforts in biomarker research in the last years. Nonsense-mediated mRNA decay (NMD) is a critical safeguard against erroneous transcripts, particularly mRNA transcripts containing premature termination codons (called nonsense-mediated decay targeted RNA, ntRNA). In this study, we first characterized 296 differentially expressed ntRNAs that were independent of the corresponding gene, 261 differentially expressed miRNAs, and 4653 differentially expressed lncRNAs. Then, we constructed a hub ntRNA–miRNA–lncRNA triple regulatory network associated with the prognosis of KIRC. Moreover, the results of immune infiltration analysis indicated that this network may influence the changes of the tumor immune microenvironment. A prognostic model derived from the genes and immune cells associated with the network was developed to distinguish between high- and low-risk patients, which was a better prognostic than other models, constructed using different biomarkers. Additionally, correlation of methylation and ntRNAs in the network suggested that some ntRNAs were regulated by methylation, which is helpful to further study the causes of abnormal expression of ntRNAs. In conclusion, this study highlighted the possible clinical implications of ntRNA functions in KIRC, proposing potential significant biomarkers that could be utilized to define the prognosis and design personalized treatment plans in kidney cancer management in the next future.
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Affiliation(s)
- Zhiyue Zhou
- Department of Statistics, School of Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China
| | - Fuyan Hu
- Department of Statistics, School of Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China
- Correspondence: (F.H.); (N.L.S.T.)
| | - Dan Huang
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Qingjia Chi
- Department of Engineering Structure and Mechanics, School of Science, Wuhan University of Technology, Wuhan 430070, China
| | - Nelson L. S. Tang
- Department of Chemical Pathology and Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Functional Genomics and Biostatistical Computing Laboratory, CUHK Shenzhen Research Institute, Shenzhen 518000, China
- Hong Kong Branch of CAS Center for Excellence in Animal Evolution and Genetics, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- Correspondence: (F.H.); (N.L.S.T.)
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19
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Chen CY, Wu JJ, Lin YJ, Hsu CH, Hu JM, Chang PK, Sun CA, Yang T, Su JQ, Chou YC. Significance of Hypermethylation of Tumor-Suppressor Genes PTGER4 and ZNF43 at CpG Sites in the Prognosis of Colorectal Cancer. Int J Mol Sci 2022; 23:ijms231810225. [PMID: 36142151 PMCID: PMC9499344 DOI: 10.3390/ijms231810225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/26/2022] Open
Abstract
The status of DNA methylation in primary tumor tissue and adjacent tumor-free tissue is associated with the occurrence of aggressive colorectal cancer (CRC) and can aid personalized cancer treatments at early stages. Tumor tissue and matched adjacent nontumorous tissue were extracted from 208 patients with CRC, and the correlation between the methylation levels of PTGER4 and ZNF43 at certain CpG loci and the prognostic factors of CRC was determined using the MassARRAY System testing platform. The Wilcoxon signed-rank test, a Chi-square test, and McNemar’s test were used for group comparisons, and Kaplan–Meier curves and a log-rank test were used for prediction. The hypermethylation of PTGER4 at the CpG_4, CpG_5, CpG_15, and CpG_17 tumor tissue sites was strongly correlated with shorter recurrence-free survival (RFS), progression-free survival (PFS), and overall survival (OS) [hazard ratio (HR) = 3.26, 95% confidence interval (CI) = 1.38–7.73 for RFS, HR = 2.35 and 95% CI = 1.17–4.71 for PFS, HR = 4.32 and 95% CI = 1.8–10.5 for OS]. By contrast, RFS and PFS were significantly longer in the case of increased methylation of ZNF43 at the CpG_5 site of normal tissue [HR = 2.33, 95% CI = 1.07–5.08 for RFS, HR = 2.42 and 95% CI = 1.19–4.91 for PFS]. Aberrant methylation at specific CpG sites indicates tissue with aggressive behavior. Therefore, the differential methylation of PTGER4 and ZNF43 at specific loci can be employed for the prognosis of patients with CRC.
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Affiliation(s)
- Chao-Yang Chen
- Division of Colorectal Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan
| | - Jia-Jheng Wu
- School of Public Health, National Defense Medical Center, Taipei 114, Taiwan
| | - Yu-Jyun Lin
- School of Public Health, National Defense Medical Center, Taipei 114, Taiwan
| | - Chih-Hsiung Hsu
- School of Public Health, National Defense Medical Center, Taipei 114, Taiwan
| | - Je-Ming Hu
- Division of Colorectal Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 114, Taiwan
| | - Pi-Kai Chang
- Division of Colorectal Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 114, Taiwan
| | - Chien-An Sun
- Department of Public Health, College of Medicine, Fu-Jen Catholic University, New Taipei City 242, Taiwan
- Data Science Center, College of Medicine, Fu-Jen Catholic University, New Taipei City 242, Taiwan
| | - Tsan Yang
- Department of Health Business Administration, Meiho University, Pingtung 912, Taiwan
| | - Jing-Quan Su
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan
- Correspondence: (J.-Q.S.); (Y.-C.C.); Tel.: +886-7-3422121 (ext. 78058) (J.-Q.S.); +886-2-87923100 (ext. 18437) (Y.-C.C.); Fax: +886-7-3468056 (J.-Q.S.); +886-2-87923147 (Y.-C.C.)
| | - Yu-Ching Chou
- School of Public Health, National Defense Medical Center, Taipei 114, Taiwan
- Correspondence: (J.-Q.S.); (Y.-C.C.); Tel.: +886-7-3422121 (ext. 78058) (J.-Q.S.); +886-2-87923100 (ext. 18437) (Y.-C.C.); Fax: +886-7-3468056 (J.-Q.S.); +886-2-87923147 (Y.-C.C.)
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20
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Research on the Expression Level of Matrin-Type Zinc Finger Protein 4 Gene in T Cells of Thyroid Carcinoma Tissue. CONTRAST MEDIA & MOLECULAR IMAGING 2022; 2022:9884155. [PMID: 36051924 PMCID: PMC9410845 DOI: 10.1155/2022/9884155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/21/2022] [Accepted: 07/26/2022] [Indexed: 11/17/2022]
Abstract
In order to analyze the expression level of zinc finger matrin-type protein 4 (ZMAT4) gene in T cells of thyroid carcinoma (TC) tissue and its clinical significance to prognosis of patients based on bioinformatics and reverse transcription polymerase chain reaction (RT-PCR), 389 TC patients with ZMAT4 gene and its corresponding survival and prognosis are searched by the Cancer Genome Atlas database. The expression of ZMAT4 gene is compared between normal thyroid tissue and TC tissue by RT-PCR. The relationship between ZMAT4 expression levels and clinicopathological parameters and baseline data is analyzed. The experimental results show that the low expression of ZMAT4 gene has an important relationship with the development of thyroid cancer, and real-time monitoring of ZMAT4 gene in TC patients can effectively evaluate the prognosis of patients.
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21
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Fuchs Weizman N, Wyse BA, Montbriand J, Jahangiri S, Librach CL. Cannabis significantly alters DNA methylation of the human ovarian follicle in a concentration-dependent manner. Mol Hum Reprod 2022; 28:gaac022. [PMID: 35674367 PMCID: PMC9247704 DOI: 10.1093/molehr/gaac022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
Cannabis is increasingly consumed by women of childbearing age, and the reproductive and epigenetic effects are unknown. The purpose of this study was to evaluate the potential epigenetic implications of cannabis use on the female ovarian follicle. Whole-genome methylation was assessed in granulosa cells from 14 matched case-control patients. Exposure status was determined by liquid chromatography-mass spectrometry (LC-MS/MS) measurements of five cannabis-derived phytocannabinoids in follicular fluid. DNA methylation was measured using the Illumina TruSeq Methyl Capture EPIC kit. Differential methylation, pathway analysis and correlation analysis were performed. We identified 3679 differentially methylated sites, with two-thirds affecting coding genes. A hotspot region on chromosome 9 was associated with two genomic features, a zinc-finger protein (ZFP37) and a long non-coding RNA (FAM225B). There were 2214 differentially methylated genomic features, 19 of which have been previously implicated in cannabis-related epigenetic modifications in other organ systems. Pathway analysis revealed enrichment in G protein-coupled receptor signaling, cellular transport, immune response and proliferation. Applying strict criteria, we identified 71 differentially methylated regions, none of which were previously annotated in this context. Finally, correlation analysis revealed 16 unique genomic features affected by cannabis use in a concentration-dependent manner. Of these, the histone methyltransferases SMYD3 and ZFP37 were hypomethylated, possibly implicating histone modifications as well. Herein, we provide the first DNA methylation profile of human granulosa cells exposed to cannabis. With cannabis increasingly legalized worldwide, further investigation into the heritability and functional consequences of these effects is critical for clinical consultation and for legalization guidelines.
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Affiliation(s)
- Noga Fuchs Weizman
- CReATe Fertility Centre, Toronto, ON, Canada
- Racine IVF Unit, Lis Maternity Hospital, Tel Aviv Sourasky Medical Center, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | | | - Sahar Jahangiri
- CReATe Fertility Centre, Toronto, ON, Canada
- CReATe BioBank, Toronto, Canada
| | - Clifford L Librach
- CReATe Fertility Centre, Toronto, ON, Canada
- CReATe BioBank, Toronto, Canada
- Department of Obstetrics and Gynecology, University of Toronto, Toronto, ON, Canada
- Department of Physiology, University of Toronto, Toronto, ON, Canada
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22
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Ma B, Chai B, Dong H, Qi J, Wang P, Xiong T, Gong Y, Li D, Liu S, Song F. Diagnostic classification of cancers using DNA methylation of paracancerous tissues. Sci Rep 2022; 12:10646. [PMID: 35739223 PMCID: PMC9226137 DOI: 10.1038/s41598-022-14786-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/13/2022] [Indexed: 11/09/2022] Open
Abstract
The potential role of DNA methylation from paracancerous tissues in cancer diagnosis has not been explored until now. In this study, we built classification models using well-known machine learning models based on DNA methylation profiles of paracancerous tissues. We evaluated our methods on nine cancer datasets collected from The Cancer Genome Atlas (TCGA) and utilized fivefold cross-validation to assess the performance of models. Additionally, we performed gene ontology (GO) enrichment analysis on the basis of the significant CpG sites selected by feature importance scores of XGBoost model, aiming to identify biological pathways involved in cancer progression. We also exploited the XGBoost algorithm to classify cancer types using DNA methylation profiles of paracancerous tissues in external validation datasets. Comparative experiments suggested that XGBoost achieved better predictive performance than the other four machine learning methods in predicting cancer stage. GO enrichment analysis revealed key pathways involved, highlighting the importance of paracancerous tissues in cancer progression. Furthermore, XGBoost model can accurately classify nine different cancers from TCGA, and the feature sets selected by XGBoost can also effectively predict seven cancer types on independent GEO datasets. This study provided new insights into cancer diagnosis from an epigenetic perspective and may facilitate the development of personalized diagnosis and treatment strategies.
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Affiliation(s)
- Baoshan Ma
- School of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China.
| | - Bingjie Chai
- School of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China
| | - Heng Dong
- School of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China
| | - Jishuang Qi
- School of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China
| | - Pengcheng Wang
- Department of Mechanical Engineering, University of Houston, Houston, TX, 77204, USA
| | - Tong Xiong
- School of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China
| | - Yi Gong
- School of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China
| | - Di Li
- Department of Neuro Intervention, Dalian Medical University Affiliated Dalian Municipal Central Hospital, Dalian, 116033, China
| | - Shuxin Liu
- Department of Nephrology, Dalian Medical University Affiliated Dalian Municipal Central Hospital, Dalian, 116033, China.
| | - Fengju Song
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Tianjin, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China.
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23
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Hernández-Gómez C, Hernández-Lemus E, Espinal-Enríquez J. The Role of Copy Number Variants in Gene Co-Expression Patterns for Luminal B Breast Tumors. Front Genet 2022; 13:806607. [PMID: 35432489 PMCID: PMC9010943 DOI: 10.3389/fgene.2022.806607] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/03/2022] [Indexed: 12/20/2022] Open
Abstract
Gene co-expression networks have become a usual approach to integrate the vast amounts of information coming from gene expression studies in cancer cohorts. The reprogramming of the gene regulatory control and the molecular pathways depending on such control are central to the characterization of the disease, aiming to unveil the consequences for cancer prognosis and therapeutics. There is, however, a multitude of factors which have been associated with anomalous control of gene expression in cancer. In the particular case of co-expression patterns, we have previously documented a phenomenon of loss of long distance co-expression in several cancer types, including breast cancer. Of the many potential factors that may contribute to this phenomenology, copy number variants (CNVs) have been often discussed. However, no systematic assessment of the role that CNVs may play in shaping gene co-expression patterns in breast cancer has been performed to date. For this reason we have decided to develop such analysis. In this study, we focus on using probabilistic modeling techniques to evaluate to what extent CNVs affect the phenomenon of long/short range co-expression in Luminal B breast tumors. We analyzed the co-expression patterns in chromosome 8, since it is known to be affected by amplifications/deletions during cancer development. We found that the CNVs pattern in chromosome 8 of Luminal B network does not alter the co-expression patterns significantly, which means that the co-expression program in this cancer phenotype is not determined by CNV structure. Additionally, we found that region 8q24.3 is highly dense in interactions, as well as region p21.3. The most connected genes in this network belong to those cytobands and are associated with several manifestations of cancer in different tissues. Interestingly, among the most connected genes, we found MAF1 and POLR3D, which may constitute an axis of regulation of gene transcription, in particular for non-coding RNA species. We believe that by advancing on our knowledge of the molecular mechanisms behind gene regulation in cancer, we will be better equipped, not only to understand tumor biology, but also to broaden the scope of diagnostic, prognostic and therapeutic interventions to ultimately benefit oncologic patients.
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Affiliation(s)
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
- *Correspondence: Jesús Espinal-Enríquez, ; Enrique Hernández-Lemus,
| | - Jesús Espinal-Enríquez
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
- *Correspondence: Jesús Espinal-Enríquez, ; Enrique Hernández-Lemus,
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24
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Olechnowicz A, Oleksiewicz U, Machnik M. KRAB-ZFPs and cancer stem cells identity. Genes Dis 2022. [PMID: 37492743 PMCID: PMC10363567 DOI: 10.1016/j.gendis.2022.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Studies on carcinogenesis continue to provide new information about different disease-related processes. Among others, much research has focused on the involvement of cancer stem cells (CSCs) in tumor initiation and progression. Studying the similarities and differences between CSCs and physiological stem cells (SCs) allows for a better understanding of cancer biology. Recently, it was shown that stem cell identity is partially governed by the Krϋppel-associated box domain zinc finger proteins (KRAB-ZFPs), the biggest family of transcription regulators. Several KRAB-ZFP factors exert a known effect in tumor cells, acting as tumor suppressor genes (TSGs) or oncogenes, yet their role in CSCs is still poorly characterized. Here, we review recent studies regarding the influence of KRAB-ZFPs and their cofactor protein TRIM28 on CSCs phenotype, stemness features, migration and invasion potential, metastasis, and expression of parental markers.
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25
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Zhang X, Zheng Q, Yue X, Yuan Z, Ling J, Yuan Y, Liang Y, Sun A, Liu Y, Li H, Xu K, He F, Wang J, Wu J, Zhao C, Tian C. ZNF498 promotes hepatocellular carcinogenesis by suppressing p53-mediated apoptosis and ferroptosis via the attenuation of p53 Ser46 phosphorylation. J Exp Clin Cancer Res 2022; 41:79. [PMID: 35227287 PMCID: PMC8883630 DOI: 10.1186/s13046-022-02288-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 02/14/2022] [Indexed: 02/08/2023] Open
Abstract
Background Dysfunctional p53 signaling is one of the major causes of hepatocellular carcinoma (HCC) tumorigenesis and development, but the mechanisms underlying p53 inactivation in HCC have not been fully clarified. The role of Krüppel-associated box (KRAB)-type zinc-finger protein ZNF498 in tumorigenesis and the underlying mechanisms are poorly understood. Methods Clinical HCC samples were used to assess the association of ZNF498 expression with clinicopathological characteristics and patient outcomes. A mouse model in which HCC was induced by diethylnitrosamine (DEN) was used to explore the role of ZNF498 in HCC initiation and progression. ZNF498 overexpression and knockdown HCC cell lines were employed to examine the effects of ZNF498 on cellular proliferation, apoptosis, ferroptosis and tumor growth. Western blotting, immunoprecipitation, qPCR, luciferase assays and flow cytometry were also conducted to determine the underlying mechanisms related to ZNF498 function. Results ZNF498 was found to be highly expressed in HCC, and increased ZNF498 expression was positively correlated with advanced pathological grade and poor survival in HCC patients. Furthermore, ZNF498 promoted DEN-induced hepatocarcinogenesis and progression in mice. Mechanistically, ZNF498 directly interacted with p53 and suppressed p53 transcriptional activation by inhibiting p53 Ser46 phosphorylation. ZNF498 competed with p53INP1 for p53 binding and suppressed PKCδ- and p53INP1-mediated p53 Ser46 phosphorylation. In addition, functional assays revealed that ZNF498 promoted liver cancer cell growth in vivo and in vitro in a p53-dependent manner. Moreover, ZNF498 inhibited p53-mediated apoptosis and ferroptosis by attenuating p53 Ser46 phosphorylation. Conclusions Our results strongly suggest that ZNF498 suppresses apoptosis and ferroptosis by attenuating p53 Ser46 phosphorylation in hepatocellular carcinogenesis, revealing a novel ZNF498-PKCδ-p53INP1-p53 axis in HCC cells that would enrich the non-mutation p53-inactivating mechanisms in HCC. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-022-02288-3.
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Affiliation(s)
- Xiuyuan Zhang
- School of Life science and Technology, Weifang Medical University, Weifang, 261053, Shandong Province, China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Qijian Zheng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Xiuying Yue
- Tianjin Baodi Hospital, Baodi Clinical College of Tianjin Medical University, Tianjin, 301800, China
| | - Zhanna Yuan
- Tianjin Baodi Hospital, Baodi Clinical College of Tianjin Medical University, Tianjin, 301800, China
| | - Jiming Ling
- School of Life science and Technology, Weifang Medical University, Weifang, 261053, Shandong Province, China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Yanzhi Yuan
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Yanying Liang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.,School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271016, Shandong, China
| | - Aihua Sun
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Yuchen Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Hui Li
- Shanghai University of Medicine & Health Sciences, Shanghai, 201318, China
| | - Kaikun Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Jian Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
| | - Jin Wu
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200092, China. .,Department of Gastroenterology and Nutrition, Shanghai Institute for Pediatric Research, School of Medicine, Shanghai Jiaotong University, Shanghai, 200092, China.
| | - Chunling Zhao
- School of Life science and Technology, Weifang Medical University, Weifang, 261053, Shandong Province, China.
| | - Chunyan Tian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
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Zinc-finger protein 382 antagonises CDC25A and ZEB1 signaling pathway in breast cancer. Genes Dis 2022; 10:568-582. [DOI: 10.1016/j.gendis.2021.12.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 11/13/2021] [Accepted: 12/22/2021] [Indexed: 11/23/2022] Open
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27
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Ganini C, Amelio I, Bertolo R, Bove P, Buonomo OC, Candi E, Cipriani C, Di Daniele N, Juhl H, Mauriello A, Marani C, Marshall J, Melino S, Marchetti P, Montanaro M, Natale ME, Novelli F, Palmieri G, Piacentini M, Rendina EA, Roselli M, Sica G, Tesauro M, Rovella V, Tisone G, Shi Y, Wang Y, Melino G. Global mapping of cancers: The Cancer Genome Atlas and beyond. Mol Oncol 2021; 15:2823-2840. [PMID: 34245122 PMCID: PMC8564642 DOI: 10.1002/1878-0261.13056] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/04/2021] [Accepted: 07/09/2021] [Indexed: 12/20/2022] Open
Abstract
Cancer genomes have been explored from the early 2000s through massive exome sequencing efforts, leading to the publication of The Cancer Genome Atlas in 2013. Sequencing techniques have been developed alongside this project and have allowed scientists to bypass the limitation of costs for whole-genome sequencing (WGS) of single specimens by developing more accurate and extensive cancer sequencing projects, such as deep sequencing of whole genomes and transcriptomic analysis. The Pan-Cancer Analysis of Whole Genomes recently published WGS data from more than 2600 human cancers together with almost 1200 related transcriptomes. The application of WGS on a large database allowed, for the first time in history, a global analysis of features such as molecular signatures, large structural variations and noncoding regions of the genome, as well as the evaluation of RNA alterations in the absence of underlying DNA mutations. The vast amount of data generated still needs to be thoroughly deciphered, and the advent of machine-learning approaches will be the next step towards the generation of personalized approaches for cancer medicine. The present manuscript wants to give a broad perspective on some of the biological evidence derived from the largest sequencing attempts on human cancers so far, discussing advantages and limitations of this approach and its power in the era of machine learning.
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Affiliation(s)
- Carlo Ganini
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
- IDI‐IRCCSRomeItaly
| | - Ivano Amelio
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | - Riccardo Bertolo
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
- San Carlo di Nancy HospitalRomeItaly
| | - Pierluigi Bove
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
- San Carlo di Nancy HospitalRomeItaly
| | - Oreste Claudio Buonomo
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | - Eleonora Candi
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
- IDI‐IRCCSRomeItaly
| | - Chiara Cipriani
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
- San Carlo di Nancy HospitalRomeItaly
| | - Nicola Di Daniele
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | | | - Alessandro Mauriello
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | - Carla Marani
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
- San Carlo di Nancy HospitalRomeItaly
| | - John Marshall
- Medstar Georgetown University HospitalGeorgetown UniversityWashingtonDCUSA
| | - Sonia Melino
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | | | - Manuela Montanaro
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | - Maria Emanuela Natale
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
- San Carlo di Nancy HospitalRomeItaly
| | - Flavia Novelli
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | - Giampiero Palmieri
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | - Mauro Piacentini
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | | | - Mario Roselli
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | - Giuseppe Sica
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | - Manfredi Tesauro
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | - Valentina Rovella
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | - Giuseppe Tisone
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | - Yufang Shi
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
- CAS Key Laboratory of Tissue Microenvironment and TumorShanghai Institute of Nutrition and HealthShanghai Institutes for Biological SciencesUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghaiChina
- The First Affiliated Hospital of Soochow University and State Key Laboratory of Radiation Medicine and ProtectionInstitutes for Translational MedicineSoochow UniversityChina
| | - Ying Wang
- CAS Key Laboratory of Tissue Microenvironment and TumorShanghai Institute of Nutrition and HealthShanghai Institutes for Biological SciencesUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghaiChina
| | - Gerry Melino
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
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28
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Feng G, Wang T, Xue F, Qi Y, Wang R, Yuan H. Identification of enhancer RNAs for the prognosis of head and neck squamous cell carcinoma. Head Neck 2021; 43:3820-3831. [PMID: 34569097 DOI: 10.1002/hed.26877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/10/2021] [Accepted: 09/08/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Enhancer RNAs (eRNAs) play an important role in carcinogenesis. The landscape of eRNAs in head and neck squamous cell carcinoma (HNSCC) remains largely unknown. METHODS The eRNA expression matrix was obtained from the enhancer RNA in the cancer database. Functional enrichment analyses were performed using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG). Prognostic eRNAs were identified using Cox regression analysis, and a prognostic prediction model was constructed based on coefficients. RESULTS KEGG analysis showed that eRNA-related transcription factors were mainly enriched in herpes simplex virus 1 (HSV1) infection. The zinc finger (ZNF) family may play an essential role in HNSCC. ENSR00000188847, ENSR00000250663, ENSR00000313345, ENSR00000317887, and ENSR00000336429 were identified. The prediction model was robust. CONCLUSIONS We constructed a robust 5-eRNA prognostic prediction model, and these eRNAs are potential biomarkers for HNSCC prognosis.
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Affiliation(s)
- Guanying Feng
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Tianxiao Wang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Feifei Xue
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Yibo Qi
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Ruixia Wang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Hua Yuan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
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29
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Developing ZNF Gene Signatures Predicting Radiosensitivity of Patients with Breast Cancer. JOURNAL OF ONCOLOGY 2021; 2021:9255494. [PMID: 34504527 PMCID: PMC8423582 DOI: 10.1155/2021/9255494] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/22/2021] [Accepted: 08/16/2021] [Indexed: 12/13/2022]
Abstract
Adjuvant radiotherapy is one of the main treatment methods for breast cancer, but its clinical benefit depends largely on the characteristics of the patient. This study aimed to explore the relationship between the expression of zinc finger (ZNF) gene family proteins and the radiosensitivity of breast cancer patients. Clinical and gene expression data on a total of 976 breast cancer samples were obtained from The Cancer Genome Atlas (TCGA) database. ZNF gene expression was dichotomized into groups with a higher or lower level than the median level of expression. Univariate and multivariate Cox regression analyses were used to evaluate the relationship between ZNF gene expression levels and radiosensitivity. The Molecular Taxonomy Data of the International Federation of Breast Cancer (METABRIC) database was used for validation. The results revealed that 4 ZNF genes were possible radiosensitivity markers. High expression of ZNF644 and low expression levels of the other 3 genes (ZNF341, ZNF541, and ZNF653) were related to the radiosensitivity of breast cancer. Hierarchical cluster, Cox, and CoxBoost analysis based on these 4 ZNF genes indicated that patients with a favorable 4-gene signature had better overall survival on radiotherapy. Thus, this 4-gene signature may have value for selecting those patients most likely to benefit from radiotherapy. ZNF gene clusters could act as radiosensitivity signatures for breast cancer patients and may be involved in determining the radiosensitivity of cancer.
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The Identification of Zinc-Finger Protein 433 as a Possible Prognostic Biomarker for Clear-Cell Renal Cell Carcinoma. Biomolecules 2021; 11:biom11081193. [PMID: 34439859 PMCID: PMC8392881 DOI: 10.3390/biom11081193] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/31/2021] [Accepted: 08/06/2021] [Indexed: 11/18/2022] Open
Abstract
Clear-cell renal cell carcinoma (ccRCC) is the most common and aggressive form of all urological cancers, with poor prognosis and high mortality. At late stages, ccRCC is known to be mainly resistant to chemotherapy and radiotherapy. Therefore, it is urgent and necessary to identify biomarkers that can facilitate the early detection of ccRCC in patients. In this study, the levels of transcripts of ccRCC from The Cancer Genome Atlas (TCGA) dataset were used to identify prognostic biomarkers in this disease. Analyzing the data obtained indicated that the KRAB-ZNF protein is significantly suppressed in clear-cell carcinomas. Furthermore, ZNF433 is differentially expressed in ccRCC in a stage- and histological-grade-specific manner. In addition, ZNF433 expression was correlated with metastasis, with greater node involvement associated with lower ZNF433 expression (p < 0.01) and with a more unsatisfactory overall survival outcome (HR, 0.45; 95% CI, 0.33–0.6; p = 8.5 × 10−8). Since ccRCC is characterized by mutations in proteins that alter epigenetic modifications and /or chromatin remodeling, we examined the expression of ZNF433 transcripts in ccRCC with wildtype and mutated forms of BAP1, KDMC5, MTOR, PBRM1, SETD2, and VHL. Analysis revealed that ZNF433 expression was significantly reduced in ccRCC with mutations in the BAP1, SETD2, and KDM5C genes (p < 0.05). In addition, the ZNF433 promoter region was highly methylated, and hypermethylation was significantly associated with mRNA suppression (p < 2.2 × 10−16). In silico analysis of potential ZNF target genes found that the largest group of target genes are involved in cellular metabolic processes, which incidentally are particularly impaired in ccRCC. It was concluded from this study that gene expression of ZNF433 is associated with cancer progression and poorer prognosis, and that ZNF433 behaves in a manner that suggests that it is a prognostic marker and a possible tumor-suppressor gene in clear-cell renal cell carcinoma.
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31
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Aberrant expression of WDR4 affects the clinical significance of cancer immunity in pan-cancer. Aging (Albany NY) 2021; 13:18360-18375. [PMID: 34282052 PMCID: PMC8351698 DOI: 10.18632/aging.203284] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 06/22/2021] [Indexed: 12/24/2022]
Abstract
Recent publications have presented research showing that WD repeat domain 4 (WDR4) plays a significant role in various kinds of malignant tumours. However, the expression profile of WDR4 is still unspecified, as is its significance in the analysis of human pan-cancer. We conducted an in-depth analysis of three aspects of WDR4 expression patterns from 33 types of cancer and determined the value of WDR4 for prognostic prediction and carcinoma drug resistance prediction. WDR4 was expressed in different cancer cell lines at inconsistent levels. Aberrant expression of WDR4 has been observed in various malignant cancers and is significantly implicated in overall survival outcomes. The expression level of WDR4 is also strongly associated with tumour immunity, such as immune scores and tumour-infiltrating immune cells. The level of WDR4 is related to microsatellite instability and tumour mutation burden in several types of malignancy, and validation studies implied that WDR4-associated terms and pathways are involved in malignancy. We explored the expression level of WDR4 across 33 types of cancer and showed that WDR4 plays a significant role during cancer development. More crucially, WDR4 is associated with immune infiltration, which suggests that WDR4 could be an immunotherapy target in cancers. In summary, our research showed that WDR4 plays a vital role in tumorigenesis and has the potential for to be targeted with treatments.
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32
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KRAB-ZFP Transcriptional Regulators Acting as Oncogenes and Tumor Suppressors: An Overview. Int J Mol Sci 2021; 22:ijms22042212. [PMID: 33672287 PMCID: PMC7926519 DOI: 10.3390/ijms22042212] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/18/2021] [Accepted: 02/20/2021] [Indexed: 12/17/2022] Open
Abstract
Krüppel-associated box zinc finger proteins (KRAB-ZFPs) constitute the largest family of transcriptional factors exerting co-repressor functions in mammalian cells. In general, KRAB-ZFPs have a dual structure. They may bind to specific DNA sequences via zinc finger motifs and recruit a repressive complex through the KRAB domain. Such a complex mediates histone deacetylation, trimethylation of histone 3 at lysine 9 (H3K9me3), and subsequent heterochromatization. Nevertheless, apart from their repressive role, KRAB-ZFPs may also co-activate gene transcription, likely through interaction with other factors implicated in transcriptional control. KRAB-ZFPs play essential roles in various biological processes, including development, imprinting, retroelement silencing, and carcinogenesis. Cancer cells possess multiple genomic, epigenomic, and transcriptomic aberrations. A growing number of data indicates that the expression of many KRAB-ZFPs is altered in several tumor types, in which they may act as oncogenes or tumor suppressors. Hereby, we review the available literature describing the oncogenic and suppressive roles of various KRAB-ZFPs in cancer. We focused on their association with the clinicopathological features and treatment response, as well as their influence on the cancer cell phenotype. Moreover, we summarized the identified upstream and downstream molecular mechanisms that may govern the functioning of KRAB-ZFPs in a cancer setting.
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33
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Oleksiewicz U, Machnik M. Causes, effects, and clinical implications of perturbed patterns within the cancer epigenome. Semin Cancer Biol 2020; 83:15-35. [PMID: 33359485 DOI: 10.1016/j.semcancer.2020.12.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 02/06/2023]
Abstract
Somatic mutations accumulating over a patient's lifetime are well-defined causative factors that fuel carcinogenesis. It is now clear, however, that epigenomic signature is also largely perturbed in many malignancies. These alterations support the transcriptional program crucial for the acquisition and maintenance of cancer hallmarks. Epigenetic instability may arise due to the genetic mutations or transcriptional deregulation of the proteins implicated in epigenetic signaling. Moreover, external stimulation and physiological aging may also participate in this phenomenon. The epigenomic signature is frequently associated with a cell of origin, as well as with tumor stage and differentiation, which all reflect its high heterogeneity across and within various tumors. Here, we will overview the current understanding of the causes and effects of the altered and heterogeneous epigenomic landscape in cancer. We will focus mainly on DNA methylation and post-translational histone modifications as the key regulatory epigenetic signaling marks. In addition, we will describe how this knowledge is translated into the clinic. We will particularly concentrate on the applicability of epigenetic alterations as biomarkers for improved diagnosis, prognosis, and prediction. Finally, we will also review current developments regarding epi-drug usage in clinical and experimental settings.
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Affiliation(s)
- Urszula Oleksiewicz
- Department of Cancer Immunology, Poznan University of Medical Sciences, Poznan, Poland; Department of Cancer Diagnostics and Immunology, Greater Poland Cancer Centre, Poznan, Poland.
| | - Marta Machnik
- Department of Cancer Immunology, Poznan University of Medical Sciences, Poznan, Poland; Department of Cancer Diagnostics and Immunology, Greater Poland Cancer Centre, Poznan, Poland
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34
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Iacobas DA. Powerful quantifiers for cancer transcriptomics. World J Clin Oncol 2020; 11:679-704. [PMID: 33033692 PMCID: PMC7522543 DOI: 10.5306/wjco.v11.i9.679] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 06/06/2020] [Accepted: 07/01/2020] [Indexed: 02/06/2023] Open
Abstract
Every day, investigators find a new link between a form of cancer and a particular alteration in the sequence or/and expression level of a key gene, awarding this gene the title of “biomarker”. The clinician may choose from numerous available panels to assess the type of cancer based on the mutation or expression regulation (“transcriptomic signature”) of “driver” genes. However, cancer is not a “one-gene show” and, together with the alleged biomarker, hundreds other genes are found as mutated or/and regulated in cancer samples. Regardless of the platform, a well-designed transcriptomic study produces three independent features for each gene: Average expression level, expression variability and coordination with expression of each other gene. While the average expression level is used in all studies to identify what genes were up-/down-regulated or turn on/off, the other two features are unfairly ignored. We use all three features to quantify the transcriptomic change during the progression of the disease and recovery in response to a treatment. Data from our published microarray experiments on cancer nodules and surrounding normal tissue from surgically removed tumors prove that the transcriptomic topologies are not only different in histopathologically distinct regions of a tumor but also dynamic and unique for each human being. We show also that the most influential genes in cancer nodules [the Gene Master Regulators (GMRs)] are significantly less influential in the normal tissue. As such, “smart” manipulation of the cancer GMRs expression may selectively kill cancer cells with little consequences on the normal ones. Therefore, we strongly recommend a really personalized approach of cancer medicine and present the experimental procedure and the mathematical algorithm to identify the most legitimate targets (GMRs) for gene therapy.
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Affiliation(s)
- Dumitru Andrei Iacobas
- Personalized Genomics Laboratory, CRI Center for Computational Systems Biology, Roy G Perry College of Engineering, Prairie View A&M University, Prairie View, TX 77446, United States
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35
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Cylwa R, Kiełczewski K, Machnik M, Oleksiewicz U, Biecek P. KRAB ZNF explorer-the online tool for the exploration of the transcriptomic profiles of KRAB-ZNF factors in The Cancer Genome Atlas. Bioinformatics 2020; 36:980-981. [PMID: 31392309 DOI: 10.1093/bioinformatics/btz624] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 08/01/2019] [Accepted: 08/06/2019] [Indexed: 12/31/2022] Open
Abstract
SUMMARY Krüppel-associated box domain zinc finger protein (KRAB ZNF) explorer is a web-based tool for comprehensive characterization of the mRNA expression status of KRAB-ZNF transcription factors in the data from The Cancer Genome Atlas study. Key functionalities cover a comparative analysis of KRAB-ZNF expression between normal and cancer tissues, an association of KRAB-ZNF expression with various pathological features, including survival analysis, association with global DNA methylation status, analyses of KRAB-ZNF isoform expressions and analysis of KRAB-ZNF levels in normal tissues. AVAILABILITY AND IMPLEMENTATION KRAB ZNF explorer is available at http://mi2.mini.pw.edu.pl: 8080/KRAB_ZNF/. The source code for shiny application is available at: https://github.com/MI2DataLab/KRAB_ZNF/tree/master/app and the source code for analyses and precalculations are available at: https://github.com/MI2DataLab/KRAB_ZNF/tree/master/work.
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Affiliation(s)
- Rafał Cylwa
- Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, 02-097 Warsaw, Poland
| | - Kornel Kiełczewski
- Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662 Warsaw, Poland
| | - Marta Machnik
- Department of Cancer Immunology, Poznan University of Medical Sciences, Poznan 60-408, Poland.,Department of Cancer Diagnostics and Immunology, Greater Poland Cancer Centre, Poznan 61-866, Poland
| | - Urszula Oleksiewicz
- Department of Cancer Immunology, Poznan University of Medical Sciences, Poznan 60-408, Poland.,Department of Cancer Diagnostics and Immunology, Greater Poland Cancer Centre, Poznan 61-866, Poland
| | - Przemysław Biecek
- Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, 02-097 Warsaw, Poland.,Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662 Warsaw, Poland
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36
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Zhang B, Wang Y, Li H, Feng L, Li W, Cheng S. Identification of Prognostic Biomarkers for Multiple Solid Tumors Using a Human Villi Development Model. Front Cell Dev Biol 2020; 8:492. [PMID: 32656211 PMCID: PMC7325693 DOI: 10.3389/fcell.2020.00492] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/25/2020] [Indexed: 01/03/2023] Open
Abstract
The processes of embryonic development that rely on epithelial-mesenchymal transition (EMT) for the implantation of trophoblast cells are co-opted by tumors, reflecting their inherent uncontrolled characteristics and leading to invasion and metastasis. Although tumorigenesis and embryogenesis have similar EMT characteristics, trophoblasts have been shown to exhibit "physiological metastasis" or be "pseudo-malignant," resulting in different outcomes. The gene co-expression network is the basis of embryonic development and tumorigenesis. We hypothesize that if the gene co-expression network in tumors is "off-track" from that in villi, it is more likely to develop into malignant tumors and have a worse prognosis, and we proposed the "off-track theory" for the first time. In this study, we examined gene co-expression networks in villi and multiple solid tumors. Through network functional enrichment analyses, we found that most tumors and villi exhibited a significantly enriched EMT, but the genes that performed this function were not identical. Then, we identified the "off-track genes" in the EMT-related gene interaction network using the "off-track theory," and through survival analysis, we discovered that the risk score of "off-track genes" was associated with poor survival of cancer patients. Our study indicated that villi development is a reliable and strictly regulated model that can illuminate the trajectory of human cancer development and that the gene co-expression networks in tumor development are "off-track" from those in villi. These "off-track genes" may have a substantial impact on tumor development and could reveal novel prognostic biomarkers.
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Affiliation(s)
- Botao Zhang
- Department of Neuro-oncology, Neurosurgery Center, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuanjing Wang
- Department of Gynecological Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Hongxia Li
- Department of Obstetrics and Gynecology, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Lin Feng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenbin Li
- Department of Neuro-oncology, Neurosurgery Center, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Shujun Cheng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Endogenous retroviruses are a source of enhancers with oncogenic potential in acute myeloid leukaemia. Nat Commun 2020; 11:3506. [PMID: 32665538 PMCID: PMC7360734 DOI: 10.1038/s41467-020-17206-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 06/10/2020] [Indexed: 02/07/2023] Open
Abstract
Acute myeloid leukemia (AML) is characterised by a series of genetic and epigenetic alterations that result in deregulation of transcriptional networks. One understudied source of transcriptional regulators are transposable elements (TEs), whose aberrant usage could contribute to oncogenic transcriptional circuits. However, the regulatory influence of TEs and their links to AML pathogenesis remain unexplored. Here we identify six endogenous retrovirus (ERV) families with AML-associated enhancer chromatin signatures that are enriched in binding of key regulators of hematopoiesis and AML pathogenesis. Using both locus-specific genetic editing and simultaneous epigenetic silencing of multiple ERVs, we demonstrate that ERV deregulation directly alters the expression of adjacent genes in AML. Strikingly, deletion or epigenetic silencing of an ERV-derived enhancer suppresses cell growth by inducing apoptosis in leukemia cell lines. This work reveals that ERVs are a previously unappreciated source of AML enhancers that may be exploited by cancer cells to help drive tumour heterogeneity and evolution. Transposable elements are a potential source of transcriptional regulators, but how these sequences contribute to oncogenesis remains poorly understood. Here, the authors identify endogenous retroviruses (ERVs) with acute myeloid leukemia (AML)-associated enhancer chromatin signatures, and provide evidence that ERV activation provides an additional layer of gene regulation in AML.
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Machnik M, Oleksiewicz U. Dynamic Signatures of the Epigenome: Friend or Foe? Cells 2020; 9:cells9030653. [PMID: 32156057 PMCID: PMC7140607 DOI: 10.3390/cells9030653] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/24/2020] [Accepted: 03/04/2020] [Indexed: 12/12/2022] Open
Abstract
Highly dynamic epigenetic signaling is influenced mainly by (micro)environmental stimuli and genetic factors. The exact mechanisms affecting particular epigenomic patterns differ dependently on the context. In the current review, we focus on the causes and effects of the dynamic signatures of the human epigenome as evaluated with the high-throughput profiling data and single-gene approaches. We will discuss three different aspects of phenotypic outcomes occurring as a consequence of epigenetics interplaying with genotype and environment. The first issue is related to the cases of environmental impacts on epigenetic profile, and its adverse and advantageous effects related to human health and evolutionary adaptation. The next topic will present a model of the interwoven co-evolution of genetic and epigenetic patterns exemplified with transposable elements (TEs) and their epigenetic repressors Krüppel-associated box zinc finger proteins (KRAB–ZNFs). The third aspect concentrates on the mitosis-based microevolution that takes place during carcinogenesis, leading to clonal diversity and expansion of tumor cells. The whole picture of epigenome plasticity and its role in distinct biological processes is still incomplete. However, accumulating data define epigenomic dynamics as an essential co-factor driving adaptation at the cellular and inter-species levels with a benefit or disadvantage to the host.
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Affiliation(s)
- Marta Machnik
- Department of Cancer Immunology, Poznan University of Medical Sciences, 60-806 Poznan, Poland;
- Department of Cancer Diagnostics and Immunology, Greater Poland Cancer Centre, 61-866 Poznan, Poland
| | - Urszula Oleksiewicz
- Department of Cancer Immunology, Poznan University of Medical Sciences, 60-806 Poznan, Poland;
- Department of Cancer Diagnostics and Immunology, Greater Poland Cancer Centre, 61-866 Poznan, Poland
- Correspondence:
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Lakiotaki K, Georgakopoulos G, Castanas E, Røe OD, Borboudakis G, Tsamardinos I. A data driven approach reveals disease similarity on a molecular level. NPJ Syst Biol Appl 2019; 5:39. [PMID: 31666984 PMCID: PMC6814739 DOI: 10.1038/s41540-019-0117-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 09/26/2019] [Indexed: 02/06/2023] Open
Abstract
Could there be unexpected similarities between different studies, diseases, or treatments, on a molecular level due to common biological mechanisms involved? To answer this question, we develop a method for computing similarities between empirical, statistical distributions of high-dimensional, low-sample datasets, and apply it on hundreds of -omics studies. The similarities lead to dataset-to-dataset networks visualizing the landscape of a large portion of biological data. Potentially interesting similarities connecting studies of different diseases are assembled in a disease-to-disease network. Exploring it, we discover numerous non-trivial connections between Alzheimer's disease and schizophrenia, asthma and psoriasis, or liver cancer and obesity, to name a few. We then present a method that identifies the molecular quantities and pathways that contribute the most to the identified similarities and could point to novel drug targets or provide biological insights. The proposed method acts as a "statistical telescope" providing a global view of the constellation of biological data; readers can peek through it at: http://datascope.csd.uoc.gr:25000/.
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Affiliation(s)
| | | | - Elias Castanas
- Laboratory of Experimental Endocrinology, School of Medicine, University of Crete, Heraklion, Greece
| | - Oluf Dimitri Røe
- Norwegian University of Science and Technology, Department of Clinical Research and Molecular Medicine, Trondheim, Norway
- Levanger Hospital, Nord-Trøndelag Hospital Trust, Cancer Clinic, Norway
- Clinical Cancer Research Center, Department of Clinical Medicine, Aalborg, Denmark
| | | | - Ioannis Tsamardinos
- Computer Science Department, University of Crete, Heraklion, Greece
- Gnosis Data Analysis PC, Heraklion Crete, Greece
- Institute of Computational and Applied Mathematics, Foundation for Research and Technology, Heraklion, Greece
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Sabara PH, Jakhesara SJ, Panchal KJ, Joshi CG, Koringa PG. Transcriptomic analysis to affirm the regulatory role of long non-coding RNA in horn cancer of Indian zebu cattle breed Kankrej (Bos indicus). Funct Integr Genomics 2019; 20:75-87. [PMID: 31368028 DOI: 10.1007/s10142-019-00700-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/15/2019] [Accepted: 07/01/2019] [Indexed: 01/08/2023]
Abstract
Long non-coding RNA (lncRNA) was previously considered as a non-functional transcript, which now established as part of regulatory elements of biological events such as chromosome structure, remodeling, and regulation of gene expression. The study presented here showed the role of lncRNA through differential expression analysis on cancer-related coding genes in horn squamous cell carcinoma of Indian zebu cattle. A total of 10,360 candidate lncRNAs were identified and further analyzed for its coding potential ability using three tools (CPC, CPAT, and PLEK) that provide 8862 common lncRNAs. Pfam analysis of these common lncRNAs gave 8612 potential candidates for lncRNA differential expression analysis. Differential expression analysis showed a total of 59 significantly differentially expressed genes and 19 lncRNAs. Pearson's correlation analysis was used to identify co-expressed mRNA-lncRNAs to established relation of the regulatory role of lncRNAs in horn cancer. We established a positive relation of seven upregulated (XLOC_000016, XLOC_002198, XLOC_002851, XLOC_ 007383, XLOC_010701, XLOC_010272, and XLOC_011517) and one downregulated (XLOC_011302) lncRNAs with eleven genes that are related to keratin family protein, keratin-associated protein family, cornifelin, corneodesmosin, serpin family protein, and metallothionein that have well-established role in squamous cell carcinoma through cellular communication, cell growth, cell invasion, and cell migration. These biological events were found to be related to the MAPK pathway of cell cycle regulation indicating the role of lncRNAs in manipulating cell cycle regulation during horn squamous cell carcinomas that will be useful in identifying molecular portraits related to the development of horn cancer.
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Affiliation(s)
- Pritesh H Sabara
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Subhash J Jakhesara
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Ketankumar J Panchal
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Prakash G Koringa
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India.
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