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Zhang F, Lee A, Freitas A, Herb J, Wang Z, Gupta S, Chen Z, Xu H. A transcription network underlies the dual genomic coordination of mitochondrial biogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.25.577217. [PMID: 38410491 PMCID: PMC10896348 DOI: 10.1101/2024.01.25.577217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Mitochondrial biogenesis requires the expression of genes encoded by both the nuclear and mitochondrial genomes. However, aside from a handful transcriptional factors regulating specific subsets of mitochondrial genes, the overall architecture of the transcriptional control of mitochondrial biogenesis remains to be elucidated. The mechanisms coordinating these two genomes are largely unknown. We performed a targeted RNAi screen in developing eyes with reduced mitochondrial DNA content, anticipating a synergistic disruption of tissue development due to impaired mitochondrial biogenesis and mtDNA deficiency. Among 638 transcription factors annotated in Drosophila genome, 77 were identified as potential regulators of mitochondrial biogenesis. Utilizing published ChIP-seq data of positive hits, we constructed a regulatory network revealing the logic of the transcription regulation of mitochondrial biogenesis. Multiple transcription factors in core layers had extensive connections, collectively governing the expression of nearly all mitochondrial genes, whereas factors sitting on the top layer may respond to cellular cues to modulate mitochondrial biogenesis through the underlying network. CG1603, a core component of the network, was found to be indispensable for the expression of most nuclear mitochondrial genes, including those required for mtDNA maintenance and gene expression, thus coordinating nuclear genome and mtDNA activities in mitochondrial biogenies. Additional genetics analyses validated YL-1, a transcription factor upstream of CG1603 in the network, as a regulator controlling CG1603 expression and mitochondrial biogenesis.
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Affiliation(s)
- Fan Zhang
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Annie Lee
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anna Freitas
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jake Herb
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zongheng Wang
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Snigdha Gupta
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhe Chen
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hong Xu
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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2
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Rich J, Bennaroch M, Notel L, Patalakh P, Alberola J, Issa F, Opolon P, Bawa O, Rondof W, Marchais A, Dessen P, Meurice G, Le-Gall M, Polrot M, Ser-Le Roux K, Mamchaoui K, Droin N, Raslova H, Maire P, Geoerger B, Pirozhkova I. DiPRO1 distinctly reprograms muscle and mesenchymal cancer cells. EMBO Mol Med 2024; 16:1840-1885. [PMID: 39009887 PMCID: PMC11319797 DOI: 10.1038/s44321-024-00097-z] [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: 01/10/2023] [Revised: 06/13/2024] [Accepted: 06/18/2024] [Indexed: 07/17/2024] Open
Abstract
We have recently identified the uncharacterized ZNF555 protein as a component of a productive complex involved in the morbid function of the 4qA locus in facioscapulohumeral dystrophy. Subsequently named DiPRO1 (Death, Differentiation, and PROliferation related PROtein 1), our study provides substantial evidence of its role in the differentiation and proliferation of human myoblasts. DiPRO1 operates through the regulatory binding regions of SIX1, a master regulator of myogenesis. Its relevance extends to mesenchymal tumors, such as rhabdomyosarcoma (RMS) and Ewing sarcoma, where DiPRO1 acts as a repressor via the epigenetic regulators TIF1B and UHRF1, maintaining methylation of cis-regulatory elements and gene promoters. Loss of DiPRO1 mimics the host defense response to virus, awakening retrotransposable repeats and the ZNF/KZFP gene family. This enables the eradication of cancer cells, reprogramming the cellular decision balance towards inflammation and/or apoptosis by controlling TNF-α via NF-kappaB signaling. Finally, our results highlight the vulnerability of mesenchymal cancer tumors to si/shDiPRO1-based nanomedicines, positioning DiPRO1 as a potential therapeutic target.
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Affiliation(s)
- Jeremy Rich
- UMR8126 CNRS, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Melanie Bennaroch
- UMR8126 CNRS, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Laura Notel
- UMR8126 CNRS, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Polina Patalakh
- UMR8126 CNRS, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Julien Alberola
- UMR8126 CNRS, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Fayez Issa
- INSERM U1016, CNRS UMR 8104, Institut Cochin, Université Paris-Cité, Paris, France
| | - Paule Opolon
- Pathology and Cytology Section, UMS AMMICA, CNRS, INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Olivia Bawa
- Pathology and Cytology Section, UMS AMMICA, CNRS, INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Windy Rondof
- Bioinformatics Platform, UMS AMMICA, CNRS, INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer campus, INSERM U1015, Université Paris-Saclay, Villejuif, France
| | - Antonin Marchais
- Bioinformatics Platform, UMS AMMICA, CNRS, INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer campus, INSERM U1015, Université Paris-Saclay, Villejuif, France
| | - Philippe Dessen
- Bioinformatics Platform, UMS AMMICA, CNRS, INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Guillaume Meurice
- Bioinformatics Platform, UMS AMMICA, CNRS, INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Morgane Le-Gall
- Proteom'IC facility, Université Paris Cité, CNRS, INSERM, Institut Cochin, F-75014, Paris, France
| | - Melanie Polrot
- Pre-clinical Evaluation Unit (PFEP), INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Karine Ser-Le Roux
- Pre-clinical Evaluation Unit (PFEP), INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Kamel Mamchaoui
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, F-75013, Paris, France
| | - Nathalie Droin
- Genomic Platform, UMS AMMICA US 23 INSERM UAR 3655 CNRS, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
- UMR1287 INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Hana Raslova
- UMR1287 INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Pascal Maire
- INSERM U1016, CNRS UMR 8104, Institut Cochin, Université Paris-Cité, Paris, France
| | - Birgit Geoerger
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer campus, INSERM U1015, Université Paris-Saclay, Villejuif, France
| | - Iryna Pirozhkova
- UMR8126 CNRS, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France.
- INSERM U1016, CNRS UMR 8104, Institut Cochin, Université Paris-Cité, Paris, France.
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Wang Q, Huang Y, Jiang M, Tang Y, Wang Q, Bai L, Yu C, Yang X, Ding K, Wang W, Bai J, Chen Y. The demethylase ALKBH5 mediates ZKSCAN3 expression through the m 6A modification to activate VEGFA transcription and thus participates in MNNG-induced gastric cancer progression. JOURNAL OF HAZARDOUS MATERIALS 2024; 473:134690. [PMID: 38781857 DOI: 10.1016/j.jhazmat.2024.134690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/04/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024]
Abstract
N-Nitroso compounds (NOCs) are recognized as important factors that promote gastric cancer development, but the specific effects and potential mechanisms by which NOC exposure promotes gastric cancer are still poorly understood. In this study, we explored the effects and potential molecular mechanisms of NOCs on the promotion of gastric cancer using methylnitronitrosoguanidine (MNNG), a classical direct carcinogen of NOC. The results of in vivo and in vitro experiments showed that chronic and low-concentration MNNG exposure significantly promoted the malignant progression of tumors, including cell migration, cell invasion, vasculogenic mimicry (VM) formation, cell spheroid formation, stem cell-like marker expression, and gastric cancer growth and metastasis. Mechanistically, we revealed that demethylase ALKBH5 regulated the level of the N6‑methyladenosine (m6A) modification in the 3'UTR and CDS region of the ZKSCAN3 mRNA to promote ZKSCAN3 expression, mediated the binding of ZKSCAN3 to the VEGFA promoter region to regulate VEGFA transcription, and participated in MNNG-induced gastric cancer cell migration, invasion, VM formation, cell spheroid formation, stem cell-like marker expression and ultimately gastric cancer progression. In addition, our study revealed that ALKBH5-ZKSCAN3-VEGFA signaling was significantly activated during MNNG-induced gastric carcinogenesis, and further studies in gastric cancer patients showed that ALKBH5, ZKSCAN3, and VEGFA expression were upregulated in cancers compared with paired gastric mucosal tissues, that ALKBH5, ZKSCAN3, and VEGFA could serve as important biomarkers for determining patient prognosis, and that the molecular combination showed greater prognostic value. These findings provide a theoretical basis for developing gastric cancer interventions for NOCs and for determining gastric cancer progression.
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Affiliation(s)
- Qing Wang
- School of Public Health, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China; Key Laboratory of Human Genetics and Environmental Medicine, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China
| | - Yefei Huang
- School of Public Health, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China; Key Laboratory of Human Genetics and Environmental Medicine, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China
| | - Min Jiang
- School of Public Health, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China; Key Laboratory of Human Genetics and Environmental Medicine, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China
| | - Yu Tang
- School of Public Health, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China; Key Laboratory of Human Genetics and Environmental Medicine, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China
| | - Qinzhi Wang
- School of Public Health, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China; Key Laboratory of Human Genetics and Environmental Medicine, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China
| | - Longlong Bai
- School of Public Health, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China; Key Laboratory of Human Genetics and Environmental Medicine, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China
| | - Chenglong Yu
- School of Public Health, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China; Key Laboratory of Human Genetics and Environmental Medicine, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China
| | - Xinyue Yang
- School of Public Health, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China; Key Laboratory of Human Genetics and Environmental Medicine, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China
| | - Kun Ding
- School of Public Health, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China; Key Laboratory of Human Genetics and Environmental Medicine, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China
| | - Weimin Wang
- Department of Oncology, Yixing Hospital Affiliated to Medical College of Yangzhou University, Yixing 214200, Jiangsu, China.
| | - Jin Bai
- Cancer Institute, Xuzhou Medical University̥, 84 West Huaihai Road, Xuzhou 221002, Jiangsu Province, China.
| | - Yansu Chen
- School of Public Health, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China; Key Laboratory of Human Genetics and Environmental Medicine, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China.
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Zeng H, Pan W, Xia Q, Shu H, Ji Z. Diagnostic, prognostic, and immunological roles of CDSN in ovarian cancer. Heliyon 2024; 10:e33357. [PMID: 39027431 PMCID: PMC11254609 DOI: 10.1016/j.heliyon.2024.e33357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 07/20/2024] Open
Abstract
Globally, ovarian cancer (OC) ranks as a principal cause of cancer-related mortality in females. Immunotherapy has revolutionized the treatment of OC, but the efficacy of immunotherapy is often limited by different immune microenvironments. The objective of this research was to pinpoint and validate candidate genes with potential value as diagnostic and prognostic biomarkers and therapeutic targets in OC. Data on genes associated with gene mutation, prognostic survival, and immune infiltration in OC were procured from the Cancer Genome Atlas (TCGA). Gene differential analysis, mutation site analysis, prognosis and survival analysis, and functional and signaling pathway enrichment analysis were conducted to identify and evaluate key genes. The genes were further investigated using immune infiltration analysis, receiver operating characteristic curves, and immunohistochemistry. The impact of CDSN on OC cell proliferation was investigated utilizing CCK-8, colony formation, and apoptosis detection assays. We identified a set of genes (CDSN, WARS, and CD38) that were highly expressed in OC and significantly associated with mutations and prognosis. Immune infiltration analysis and immunohistochemistry results indicated a correlation with immune infiltration in the tumor microenvironment, particularly in antigen-presenting cells. Receiver operating characteristic curve analysis demonstrated the diagnostic potential of these three genes in OC, with all three genes showing the area under the curve (AUC) above 0.8. In vitro studies suggested that knocked down CDSN expression resulted in a marked lower in the proliferative capacity of OC cells. The candidate gene CDSN identified through bioinformatics analysis and in vitro experiments is associated with mutation and immune infiltration, showing promise as a diagnostic and prognostic biomarker, as well as a therapeutic objective in OC.
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Affiliation(s)
- Huan Zeng
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, Nanning, 530021, China
| | - Wei Pan
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Qiuyi Xia
- Department of Clinical Laboratory, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Hong Shu
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, Nanning, 530021, China
| | - Zhaodong Ji
- Department of Clinical Laboratory, Huashan Hospital, Fudan University, Shanghai, 200040, China
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5
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Zhu Y, Zhao T, Wu Y, Xie S, Sun W, Wu J. ZNF862 induces cytostasis and apoptosis via the p21-RB1 and Bcl-xL-Caspase 3 signaling pathways in human gingival fibroblasts. J Periodontal Res 2024; 59:599-610. [PMID: 38482719 DOI: 10.1111/jre.13250] [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: 07/19/2023] [Revised: 12/06/2023] [Accepted: 02/15/2024] [Indexed: 05/24/2024]
Abstract
OBJECTIVE This study investigates the effects of ZNF862 on the proliferation and apoptosis of human gingival fibroblasts and their related mechanisms. BACKGROUND As a major transcription factor family, zinc finger proteins (ZFPs) regulate cell differentiation, growth, and apoptosis through their conserved zinc finger motifs, which allow high flexibility and specificity in gene regulation. In our previous study, ZNF862 mutation was associated with hereditary gingival fibromatosis. Nevertheless, little is known about the biological function of ZNF862. Therefore, this study was aimed to reveal intracellular localization of ZNF862, the influence of ZNF862 on the growth and apoptosis of human gingival fibroblasts (HGFs) and its potential related mechanisms. METHODS Immunohistochemistry, immunofluorescence staining, and western blotting were performed to determine the intracellular localization of ZNF862 in HGFs. HGFs were divided into three groups: ZNF862 overexpression group, ZNF862 interference group, and the empty vector control group. Then, the effects of ZNF862 on cell proliferation, migration, cell cycle, and apoptosis were evaluated. qRT-PCR and western blotting were performed to further explore the mechanism related to the proliferation and apoptosis of HGFs. RESULTS ZNF862 was found to be localized in the cytoplasm of HGFs. In vitro experiments revealed that ZNF862 overexpression inhibited HGFs proliferation and migration, induced cell cycle arrest at the G0/G1-phase and apoptosis. Whereas, ZNF862 knockdown promoted HGFs proliferation and migration, accelerated the transition from the G0/G1 phase into the S and G2/M phase and inhibited cell apoptosis. Mechanistically, the effects of ZNF862 on HGFs proliferation and apoptosis were noted to be dependent on inhibiting the cyclin-dependent kinase inhibitor 1A (p21)-retinoblastoma 1 (RB1) signaling pathway and enhancing the B-cell lymphoma-extra-large (Bcl-xL)-Caspase 3 signaling pathway. CONCLUSION Our results for the first time reveal that ZNF862 is localized in the cytoplasm of HGFs. ZNF862 can inhibit the proliferation of HGFs by inhibiting the p21-RB1 signaling pathway, and it also promotes the apoptosis of HGFs by enhancing the Bcl-xL-Caspase 3 signaling pathway.
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Affiliation(s)
- Yaoyao Zhu
- Department of Periodontology, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Research Institute of Stomatology, Nanjing University, Nanjing, China
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Research Institute of Stomatology, Nanjing University, Nanjing, China
| | - Tian Zhao
- Department of Periodontology, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Research Institute of Stomatology, Nanjing University, Nanjing, China
| | - Yongkang Wu
- Department of Periodontology, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Research Institute of Stomatology, Nanjing University, Nanjing, China
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Research Institute of Stomatology, Nanjing University, Nanjing, China
| | - Sijing Xie
- Department of Cariology and Endodontics, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Research Institute of Stomatology, Nanjing University, Nanjing, China
| | - Weibin Sun
- Department of Periodontology, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Research Institute of Stomatology, Nanjing University, Nanjing, China
| | - Juan Wu
- Department of Periodontology, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Research Institute of Stomatology, Nanjing University, Nanjing, China
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6
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Nonoyama K, Matsuo Y, Sugita S, Eguchi Y, Denda Y, Murase H, Kato T, Imafuji H, Saito K, Morimoto M, Ogawa R, Takahashi H, Mitsui A, Kimura M, Takiguchi S. Expression of ZKSCAN3 protein suppresses proliferation, migration, and invasion of pancreatic cancer through autophagy. Cancer Sci 2024; 115:1964-1978. [PMID: 38671550 PMCID: PMC11145104 DOI: 10.1111/cas.16173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 03/04/2024] [Accepted: 03/24/2024] [Indexed: 04/28/2024] Open
Abstract
Elevated autophagy activity enhances the malignancy of pancreatic cancer (PaCa), and autophagy is recognized as a novel therapeutic target. Zinc finger protein with KRAB and SCAN domains 3 (ZKSCAN3) is a transcription factor that suppresses autophagy, but its association with PaCa is unknown. We analyzed the function of ZKSCAN3 in PaCa and investigated whether autophagy regulation through ZKSCAN3 could become a new therapeutic target for PaCa. Using reverse transcription-quantitative polymerase chain reaction and western blotting, we observed that ZKSCAN3 expression was upregulated in several PaCa cell lines compared with normal pancreatic ductal epithelial cells. Additionally, comparing ZKSCAN3 expression with the prognosis of PaCa patients using web databases, we found that higher ZKSCAN3 expression in PaCa was associated with extended overall survival. Knocking down ZKSCAN3 promoted the proliferation of PaCa cells. Moreover, following ZKSCAN3 knockdown, PaCa cells exhibited significantly enhanced migratory and invasive properties. Conversely, overexpression of ZKSCAN3 significantly suppressed the proliferation, migration and invasion of PaCa cells. Additionally, the knockdown of ZKSCAN3 increased the expression of LC3-II, a marker of autophagy, whereas ZKSCAN3 overexpression decreased LC3-II expression. In a xenograft mouse model, tumors formed by MIA PaCa-2 cells in which ZKSCAN3 was knocked down significantly increased in size compared with the control group. In conclusion, ZKSCAN3 expression was upregulated in several pancreatic cancer cells. Additionally, it was revealed that ZKSCAN3 is negatively correlated with the malignancy of PaCa through autophagy. These results suggest that autophagy regulation via ZKSCAN3 may be a new therapeutic target for PaCa.
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Affiliation(s)
- Keisuke Nonoyama
- Department of Gastroenterological SurgeryNagoya City University Graduate School of Medical SciencesNagoyaAichiJapan
| | - Yoichi Matsuo
- Department of Gastroenterological SurgeryNagoya City University Graduate School of Medical SciencesNagoyaAichiJapan
| | - Saburo Sugita
- Department of Gastroenterological SurgeryNagoya City University Graduate School of Medical SciencesNagoyaAichiJapan
| | - Yuki Eguchi
- Department of Gastroenterological SurgeryNagoya City University Graduate School of Medical SciencesNagoyaAichiJapan
| | - Yuki Denda
- Department of Gastroenterological SurgeryNagoya City University Graduate School of Medical SciencesNagoyaAichiJapan
| | - Hiromichi Murase
- Department of Gastroenterological SurgeryNagoya City University Graduate School of Medical SciencesNagoyaAichiJapan
| | - Tomokatsu Kato
- Department of Gastroenterological SurgeryNagoya City University Graduate School of Medical SciencesNagoyaAichiJapan
| | - Hiroyuki Imafuji
- Department of Gastroenterological SurgeryNagoya City University Graduate School of Medical SciencesNagoyaAichiJapan
| | - Kenta Saito
- Department of Gastroenterological SurgeryNagoya City University Graduate School of Medical SciencesNagoyaAichiJapan
| | - Mamoru Morimoto
- Department of Gastroenterological SurgeryNagoya City University Graduate School of Medical SciencesNagoyaAichiJapan
| | - Ryo Ogawa
- Department of Gastroenterological SurgeryNagoya City University Graduate School of Medical SciencesNagoyaAichiJapan
| | - Hiroki Takahashi
- Department of Gastroenterological SurgeryNagoya City University Graduate School of Medical SciencesNagoyaAichiJapan
| | - Akira Mitsui
- Department of Gastroenterological SurgeryNagoya City University Graduate School of Medical SciencesNagoyaAichiJapan
| | - Masahiro Kimura
- Department of Gastroenterological SurgeryNagoya City University Graduate School of Medical SciencesNagoyaAichiJapan
| | - Shuji Takiguchi
- Department of Gastroenterological SurgeryNagoya City University Graduate School of Medical SciencesNagoyaAichiJapan
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7
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Tsitkov S, Valentine K, Kozareva V, Donde A, Frank A, Lei S, E Van Eyk J, Finkbeiner S, Rothstein JD, Thompson LM, Sareen D, Svendsen CN, Fraenkel E. Disease related changes in ATAC-seq of iPSC-derived motor neuron lines from ALS patients and controls. Nat Commun 2024; 15:3606. [PMID: 38697975 PMCID: PMC11066062 DOI: 10.1038/s41467-024-47758-8] [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: 01/05/2024] [Accepted: 04/09/2024] [Indexed: 05/05/2024] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS), like many other neurodegenerative diseases, is highly heritable, but with only a small fraction of cases explained by monogenic disease alleles. To better understand sporadic ALS, we report epigenomic profiles, as measured by ATAC-seq, of motor neuron cultures derived from a diverse group of 380 ALS patients and 80 healthy controls. We find that chromatin accessibility is heavily influenced by sex, the iPSC cell type of origin, ancestry, and the inherent variance arising from sequencing. Once these covariates are corrected for, we are able to identify ALS-specific signals in the data. Additionally, we find that the ATAC-seq data is able to predict ALS disease progression rates with similar accuracy to methods based on biomarkers and clinical status. These results suggest that iPSC-derived motor neurons recapitulate important disease-relevant epigenomic changes.
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Affiliation(s)
- Stanislav Tsitkov
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kelsey Valentine
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Velina Kozareva
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Aneesh Donde
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Aaron Frank
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Susan Lei
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jennifer E Van Eyk
- Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Steve Finkbeiner
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, USA
- Taube/Koret Center for Neurodegenerative Disease, Gladstone Institutes, San Francisco, CA, USA
- Departments of Neurology and Physiology, University of California, San Francisco, San Francisco, CA, USA
| | - Jeffrey D Rothstein
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Leslie M Thompson
- Department of Neurobiology and Behavior, University of California, Irvine, CA, USA
- Department of Psychiatry and Human Behavior, University of California, Irvine, CA, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA, USA
- Sue and Bill Gross Stem Cell Center, University of California, Irvine, CA, USA
| | - Dhruv Sareen
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- The Board of Governors Regenerative Medicine Institute and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Clive N Svendsen
- The Board of Governors Regenerative Medicine Institute and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ernest Fraenkel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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8
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Varghese JF, Kaskow BJ, von Glehn F, Case J, Li Z, Julé AM, Berdan E, Ho Sui SJ, Hu Y, Krishnan R, Chitnis T, Kuchroo VK, Weiner HL, Baecher-Allan CM. Human regulatory memory B cells defined by expression of TIM-1 and TIGIT are dysfunctional in multiple sclerosis. Front Immunol 2024; 15:1360219. [PMID: 38745667 PMCID: PMC11091236 DOI: 10.3389/fimmu.2024.1360219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/13/2024] [Indexed: 05/16/2024] Open
Abstract
Background Regulatory B cells (Bregs) play a pivotal role in suppressing immune responses, yet there is still a lack of cell surface markers that can rigorously identify them. In mouse models for multiple sclerosis (MS), TIM-1 or TIGIT expression on B cells is required for maintaining self-tolerance and regulating autoimmunity to the central nervous system. Here we investigated the activities of human memory B cells that differentially express TIM-1 and TIGIT to determine their potential regulatory function in healthy donors and patients with relapsing-remitting (RR) MS. Methods FACS-sorted TIM-1+/-TIGIT+/- memory B (memB) cells co-cultured with allogenic CD4+ T cells were analyzed for proliferation and induction of inflammatory markers using flow cytometry and cytokine quantification, to determine Th1/Th17 cell differentiation. Transcriptional differences were assessed by SMARTSeq2 RNA sequencing analysis. Results TIM-1-TIGIT- double negative (DN) memB cells strongly induce T cell proliferation and pro-inflammatory cytokine expression. The TIM-1+ memB cells enabled low levels of CD4+ T cell activation and gave rise to T cells that co-express IL-10 with IFNγ and IL-17A or FoxP3. T cells cultured with the TIM-1+TIGIT+ double positive (DP) memB cells exhibited reduced proliferation and IFNγ, IL-17A, TNFα, and GM-CSF expression, and exhibited strong regulation in Breg suppression assays. The functional activity suggests the DP memB cells are a bonafide Breg population. However, MS DP memB cells were less inhibitory than HC DP memB cells. A retrospective longitudinal study of anti-CD20 treated patients found that post-treatment DP memB cell frequency and absolute number were associated with response to therapy. Transcriptomic analyses indicated that the dysfunctional MS-derived DP memB/Breg population exhibited increased expression of genes associated with T cell activation and survival (CD80, ZNF10, PIK3CA), and had distinct gene expression compared to the TIGIT+ or TIM-1+ memB cells. Conclusion These findings demonstrate that TIM-1/TIGIT expressing memory B cell subsets have distinct functionalities. Co-expression of TIM-1 and TIGIT defines a regulatory memory B cell subset that is functionally impaired in MS.
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Affiliation(s)
- Johnna F. Varghese
- Harvard Medical School, Boston, MA, United States
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital, Boston, MA, United States
| | - Belinda J. Kaskow
- Harvard Medical School, Boston, MA, United States
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital, Boston, MA, United States
| | - Felipe von Glehn
- Harvard Medical School, Boston, MA, United States
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital, Boston, MA, United States
| | - Junning Case
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital, Boston, MA, United States
| | - Zhenhua Li
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital, Boston, MA, United States
| | - Amélie M. Julé
- Bioinformatics Core, Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Emma Berdan
- Bioinformatics Core, Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Shannan Janelle Ho Sui
- Bioinformatics Core, Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Yong Hu
- Harvard Medical School, Boston, MA, United States
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital, Boston, MA, United States
| | - Rajesh Krishnan
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital, Boston, MA, United States
- The Gene Lay Institute of Immunology and Inflammation, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, United States
| | - Tanuja Chitnis
- Harvard Medical School, Boston, MA, United States
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital, Boston, MA, United States
| | - Vijay K. Kuchroo
- Harvard Medical School, Boston, MA, United States
- The Gene Lay Institute of Immunology and Inflammation, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, United States
| | - Howard L. Weiner
- Harvard Medical School, Boston, MA, United States
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital, Boston, MA, United States
| | - Clare Mary Baecher-Allan
- Harvard Medical School, Boston, MA, United States
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital, Boston, MA, United States
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9
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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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10
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Li B, Liu S, He Z, Luo E, Liu H. The role of zinc finger proteins in the fate determination of mesenchymal stem cells during osteogenic and adipogenic differentiation. Int J Biochem Cell Biol 2024; 167:106507. [PMID: 38142772 DOI: 10.1016/j.biocel.2023.106507] [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: 09/11/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 12/26/2023]
Abstract
Zinc finger proteins (ZFPs) constitute a crucial group of transcription factors widely present in various organisms. They act as transcription factors, nucleases, and RNA-binding proteins, playing significant roles in cell differentiation, growth, and development. With extensive research on ZFPs, their roles in the determination of mesenchymal stem cells (MSCs) fate during osteogenic and adipogenic differentiation processes have become increasingly clear. ZFP521, for instance, is identified as an inhibitor of the Wnt signaling pathway and RUNX2's transcriptional activity, effectively suppressing osteogenic differentiation. Moreover, ZFP217 contributes to the inhibition of adipogenic differentiation by reducing the M6A level of the cell cycle regulator cyclin D1 (CCND1). In addition, other ZFPs can also influence the fate of mesenchymal stem cells (MSCs) during osteogenic and adipogenic differentiation through various signaling pathways, transcription factors, and epigenetic controls, participating in the subsequent differentiation and maturation of precursor cells. Given the prevalent occurrence of osteoporosis, obesity, and related metabolic disorders, a comprehensive understanding of the regulatory mechanisms balancing bone and fat metabolism is essential, with a particular focus on the fate determination of MSCs in osteogenic and adipogenic differentiation. In this review, we provide a detailed summary of how zinc finger proteins influence the osteogenic and adipogenic differentiation of MSCs through different signaling pathways, transcription factors, and epigenetic mechanisms. Additionally, we outline the regulatory mechanisms of ZFPs in controlling osteogenic and adipogenic differentiation based on various stages of MSC differentiation.
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Affiliation(s)
- Bolun Li
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan, China
| | - Shibo Liu
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan, China
| | - Ze He
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan, China
| | - En Luo
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan, China
| | - Hanghang Liu
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan, China.
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11
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Wang X, Yao L, Li Z, Zhang J, Ruan M, Mulati Y, Gan Y, Zhang Q. ZNF471 Interacts with BANP to Reduce Tumour Malignancy by Inactivating PI3K/AKT/mTOR Signalling but is Frequently Silenced by Aberrant Promoter Methylation in Renal Cell Carcinoma. Int J Biol Sci 2024; 20:643-663. [PMID: 38169650 PMCID: PMC10758100 DOI: 10.7150/ijbs.89785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 12/03/2023] [Indexed: 01/05/2024] Open
Abstract
Background: Renal cell carcinoma (RCC) is one of the most common malignant tumours of the urinary system. However, the aetiology and pathogenesis of RCC remain unclear. The C2H2 zinc finger protein (ZNF) family is the largest transcriptional regulatory factor family found in mammals, and Krüppel-associated box domain-containing zinc finger proteins (KRAB-ZFPs) constitute the largest subfamily of the C2H2 zinc finger protein family and play an important role in the occurrence and development of tumours. The aim of this study was to explore the role of abnormal methylation of ZNF471 in the development of renal carcinoma. Methods: In this study, we first used the TCGA and EWAS Data Hub databases to analyse the expression and methylation levels of ZNF471 in renal carcinoma tissues and adjacent normal tissues. Second, we collected samples of renal cancer and adjacent normal tissues at Peking University First Hospital to investigate the expression and methylation level of ZNF471 in renal cancer tissues and the relationships between these levels and the clinicopathological features and prognosis of patients with renal cancer. Next, we investigated the effects of ZNF471 on the proliferation, metastasis, cell cycle progression, and apoptosis of renal cell carcinoma cells by cell biology experiments. Finally, we elucidated the underlying molecular mechanisms of ZNF471 in renal cell carcinoma by transcriptome sequencing, bioinformatics analysis and molecular biology experiments. Results: The expression of ZNF471 in renal carcinoma tissues and cell lines was significantly lower than that in adjacent normal tissues and cell lines due to abnormal promoter CpG methylation. Furthermore, the expression of ZNF471 in renal carcinoma tissues was negatively correlated with tumour stage and grade in patients with renal carcinoma. The results of the cell biology experiments showed that ZNF471 could significantly inhibit the proliferation, migration and cell cycle progression of renal cell carcinoma cells and promote apoptosis in these cells. In addition, ZNF471 could interact with BANP and suppress the malignant phenotype of RCC by inactivating the PI3K/AKT/mTOR signalling pathway. Conclusions: As an important tumour suppressor, ZNF471 can interact with BANP in renal cancer cells and inhibit the activation of the PI3K/AKT/mTOR signalling pathway, thereby inhibiting the occurrence and development of renal cancer.
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Affiliation(s)
- Xiaofei Wang
- Department of Urology, Peking University First Hospital; Institute of Urology, Peking University; Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, National Urological Cancer Center, Beijing 100034, China
| | - Lin Yao
- Department of Urology, Peking University First Hospital; Institute of Urology, Peking University; Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, National Urological Cancer Center, Beijing 100034, China
| | - Zheng Li
- Department of Urology, Peking University First Hospital; Institute of Urology, Peking University; Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, National Urological Cancer Center, Beijing 100034, China
| | - Jiaen Zhang
- Department of Urology, Peking University First Hospital; Institute of Urology, Peking University; Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, National Urological Cancer Center, Beijing 100034, China
| | - Mingjian Ruan
- Department of Urology, Peking University First Hospital; Institute of Urology, Peking University; Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, National Urological Cancer Center, Beijing 100034, China
| | - Yelin Mulati
- Department of Urology, Peking University First Hospital; Institute of Urology, Peking University; Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, National Urological Cancer Center, Beijing 100034, China
| | - Ying Gan
- Department of Urology, Peking University First Hospital; Institute of Urology, Peking University; Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, National Urological Cancer Center, Beijing 100034, China
| | - Qian Zhang
- Department of Urology, Peking University First Hospital; Institute of Urology, Peking University; Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, National Urological Cancer Center, Beijing 100034, China
- Peking University Binhai Hospital, Tianjin 300450, China
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12
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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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13
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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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14
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Zhao J, Wen D, Zhang S, Jiang H, Di X. The role of zinc finger proteins in malignant tumors. FASEB J 2023; 37:e23157. [PMID: 37615242 DOI: 10.1096/fj.202300801r] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 07/19/2023] [Accepted: 08/10/2023] [Indexed: 08/25/2023]
Abstract
Zinc finger proteins (ZNFs) are the largest family of transcriptional factors in mammalian cells. Recently, their role in the development, progression, and metastasis of malignant tumors via regulating gene transcription and translation processes has become evident. Besides, their possible involvement in drug resistance has also been found, indicating that ZNFs have the potential to become new biological markers and therapeutic targets. In this review, we summarize the oncogenic and suppressive roles of various ZNFs in malignant tumors, including lung, breast, liver, gastric, colorectal, pancreatic, and other cancers, highlighting their role as prognostic markers, and hopefully provide new ideas for the treatment of malignant tumors in the future.
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Affiliation(s)
- Jia Zhao
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Doudou Wen
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Shubing Zhang
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Hao Jiang
- Department of Biomedical Informatics, School of Life Sciences, Central South University, Changsha, China
| | - Xiaotang Di
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
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15
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Li S, Chen D, Zhang H, Yang Y, Huai J, Huang L, Fan K, Lin T, Ding B. Clinical significance of expression level of ZNF471 in gastric cancer. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2023; 16:199-208. [PMID: 37693683 PMCID: PMC10492033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 07/12/2023] [Indexed: 09/12/2023]
Abstract
BACKGROUND As a tumor suppressor gene, zinc finger protein 471 (ZNF471) has an essential role in tumor occurrence and development. Due to promoter hypermethylation, it can be underexpressed or silenced in gastric cancer (GC) cell lines. In this study, we investigated relationships between clinical characteristics and ZNF471 expression levels in tissues of patients with GC. METHODS We used immunohistochemistry (IHC) to detect ZNF471 expression in paraffin tissue specimens, and quantitative real-time PCR (qRT-PCR) and western blot (WB) analysis to measure expression levels of ZNF471 in fresh tissue specimens. We analyzed relationships between ZNF471 expression levels and characteristics, such as tumor size, gender, age, TNM stage, and lymph node metastasis. RESULTS Immunohistochemistry revealed the expression of ZNF471 protein from paraffin blocks of GC tissues was significantly lower than that of adjacent tissues. Expression levels of ZNF471 mRNA and protein in fresh GC tissues were markedly lower than those in adjacent tissues and in normal gastric mucosal tissues from healthy subjects. ZNF471 expression was significantly correlated with tumor size, lymph node metastasis, and TNM stage (all P<0.05). There were no significant associations with gender, age, distant metastasis, or pathologic type. Expression of ZNF471 mRNA and protein was not significantly different between adjacent tissues of patients with GC and normal gastric mucosal tissue from healthy subjects. CONCLUSION ZNF471 functions as a tumor suppressor during the pathogenesis of GC. Thus, it is a promising biomarker for diagnosis and therapy of GC.
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Affiliation(s)
- Siyuan Li
- Postgraduate School, Wannan Medical CollegeWuhu 241000, Anhui, China
- Department of Gastroenterology, The First People’s Hospital of WuhuWuhu 241000, Anhui, China
| | - Diyang Chen
- Postgraduate School, Wannan Medical CollegeWuhu 241000, Anhui, China
| | - Huamin Zhang
- Health Services Policy and Management, Harbin Medical UniversityHarbin 150000, Heilongjiang, China
| | - Yong Yang
- Department of Gastroenterology, The First People’s Hospital of WuhuWuhu 241000, Anhui, China
| | - Jianguo Huai
- Department of Pathology, The First People’s Hospital of WuhuWuhu 241000, Anhui, China
| | - Linna Huang
- Department of Gastroenterology, The Second Affiliated Hospital of Wannan Medical CollegeWuhu 241000, Anhui, China
| | - Kai Fan
- Postgraduate School, Wannan Medical CollegeWuhu 241000, Anhui, China
| | - Tongyuan Lin
- Department of Pharmacy, Division of Science and Education, The First People’s Hospital of WuhuWuhu 241000, Anhui, China
| | - Baijing Ding
- Department of Gastroenterology, The First People’s Hospital of WuhuWuhu 241000, Anhui, China
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16
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Tovo PA, Galliano I, Parodi E, Calvi C, Gambarino S, Licciardi F, Dini M, Montanari P, Branca M, Ramenghi U, Bergallo M. Children with Chronic Immune Thrombocytopenia Exhibit High Expression of Human Endogenous Retroviruses TRIM28 and SETDB1. Genes (Basel) 2023; 14:1569. [PMID: 37628621 PMCID: PMC10454145 DOI: 10.3390/genes14081569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 07/26/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
Chronic immune thrombocytopenia (CITP) is an autoimmune disease whose underlying biologic mechanisms remain elusive. Human endogenous retroviruses (HERVs) derive from ancestral infections and constitute about 8% of our genome. A wealth of clinical and experimental studies highlights their pivotal pathogenetic role in autoimmune diseases. Epigenetic mechanisms, such as those modulated by TRIM28 and SETDB1, are involved in HERV activation and regulation of immune response. We assessed, through a polymerase chain reaction real-time Taqman amplification assay, the transcription levels of pol genes of HERV-H, HERV-K, and HERV-W; env genes of Syncytin (SYN)1, SYN2, and HERV-W; as well as TRIM28 and SETDB1 in whole blood from 34 children with CITP and age-matched healthy controls (HC). The transcriptional levels of all HERV sequences, with the exception of HERV-W-env, were significantly enhanced in children with CITP as compared to HC. Patients on eltrombopag treatment exhibited lower expression of SYN1, SYN2, and HERV-W-env as compared to untreated patients. The mRNA concentrations of TRIM28 and SETDB1 were significantly higher and were positively correlated with those of HERVs in CITP patients. The over-expressions of HERVs and TRIM28/SETDB1 and their positive correlations in patients with CITP are suggestive clues of their contribution to the pathogenesis of the disease and support innovative interventions to inhibit HERV and TRIM28/SETDB1 expressions in patients unresponsive to standard therapies.
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Affiliation(s)
- Pier-Angelo Tovo
- Department of Public Health and Pediatric Sciences, University of Turin, Piazza Polonia 94, 10126 Turin, Italy; (P.-A.T.); (U.R.)
| | - Ilaria Galliano
- Pediatric Laboratory, Department of Public Health and Pediatric Sciences, University of Turin, Regina Margherita Children’s Hospitalno, Piazza Polonia 94, 10126 Turin, Italy; (I.G.); (C.C.); (S.G.); (M.D.); (P.M.)
| | - Emilia Parodi
- Pediatric and Neonatology Unit, Ordine Mauriziano Hospital, Largo Filippo Turati 62, 10128 Turin, Italy;
| | - Cristina Calvi
- Pediatric Laboratory, Department of Public Health and Pediatric Sciences, University of Turin, Regina Margherita Children’s Hospitalno, Piazza Polonia 94, 10126 Turin, Italy; (I.G.); (C.C.); (S.G.); (M.D.); (P.M.)
| | - Stefano Gambarino
- Pediatric Laboratory, Department of Public Health and Pediatric Sciences, University of Turin, Regina Margherita Children’s Hospitalno, Piazza Polonia 94, 10126 Turin, Italy; (I.G.); (C.C.); (S.G.); (M.D.); (P.M.)
| | - Francesco Licciardi
- Regina Margherita Children’s Hospital, Piazza Polonia 94, 10126 Turin, Italy;
| | - Maddalena Dini
- Pediatric Laboratory, Department of Public Health and Pediatric Sciences, University of Turin, Regina Margherita Children’s Hospitalno, Piazza Polonia 94, 10126 Turin, Italy; (I.G.); (C.C.); (S.G.); (M.D.); (P.M.)
| | - Paola Montanari
- Pediatric Laboratory, Department of Public Health and Pediatric Sciences, University of Turin, Regina Margherita Children’s Hospitalno, Piazza Polonia 94, 10126 Turin, Italy; (I.G.); (C.C.); (S.G.); (M.D.); (P.M.)
| | - Margherita Branca
- Postgraduate School of Pediatrics, University of Turin, Piazza Polonia 94, 10126 Turin, Italy;
| | - Ugo Ramenghi
- Department of Public Health and Pediatric Sciences, University of Turin, Piazza Polonia 94, 10126 Turin, Italy; (P.-A.T.); (U.R.)
- Regina Margherita Children’s Hospital, Piazza Polonia 94, 10126 Turin, Italy;
- Postgraduate School of Pediatrics, University of Turin, Piazza Polonia 94, 10126 Turin, Italy;
| | - Massimiliano Bergallo
- Pediatric Laboratory, Department of Public Health and Pediatric Sciences, University of Turin, Regina Margherita Children’s Hospitalno, Piazza Polonia 94, 10126 Turin, Italy; (I.G.); (C.C.); (S.G.); (M.D.); (P.M.)
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17
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Fan W, Xiong R, Zhou Z, Zhang C, Han Y, Shi T, Qiu J, Zhang R. ZFP57 promotes ovarian cancer progression by transcriptionally regulating BRCA1 and managing G1 checkpoint. J Cancer 2023; 14:2039-2050. [PMID: 37497403 PMCID: PMC10367923 DOI: 10.7150/jca.84601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/12/2023] [Indexed: 07/28/2023] Open
Abstract
Ovarian cancer (OC) which is one of the frequently-occurring gynecologic malignant tumors, endangers the health of women. The zinc finger protein 57 (ZFP57) plays crucial functions during the progression of cancer and is reported as a prognostic and therapeutic candidate in a variety of cancer. However, the biological function as well as the underlying mechanism of ZFP57 during OC progression remains unknown. Here, ZFP57 expression was found prominently increased in OC tissues and correlated with the prognosis of OC patients. Knock down of ZFP57 in OC cells inhibited the cell proliferation and migration, and also arrested the cells at G1 phase as well as accelerated the apoptosis. Additionally, ZFP57 transcriptionally regulated BRCA1 expression in OC, indicating that ZFP57 may affect BRCA1 mediated G1 checkpoint to regulate the cell cycle of OC cells and further influence the progression of OC. Taken together, our present study discovered a novel function of ZFP57 in OC, suggesting that ZFP57 could be potentially treated as a prognostic biomarker and therapeutic target for OC patients.
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Affiliation(s)
- Weirong Fan
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
- Department of Obstetrics and Gynecology, Fengxian Hospital Affiliated to the Southern Medical University, Shanghai, China
| | - Rui Xiong
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
- Department of Obstetrics and Gynecology, Fengxian Hospital Affiliated to the Southern Medical University, Shanghai, China
| | - Ziyang Zhou
- Department of Obstetrics and Gynecology, Fengxian Hospital Affiliated to the Southern Medical University, Shanghai, China
| | - Cancan Zhang
- Department of Obstetrics and Gynecology, Fengxian Hospital Affiliated to the Southern Medical University, Shanghai, China
| | - Yanli Han
- Department of Obstetrics and Gynecology, Fengxian Hospital Affiliated to the Southern Medical University, Shanghai, China
| | - Tingyan Shi
- Department of Gynecologic Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jianping Qiu
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, China
| | - Rong Zhang
- Department of Obstetrics and Gynecology, Fengxian Hospital Affiliated to the Southern Medical University, Shanghai, China
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18
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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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19
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Ben Maamar M, Wang Y, Nilsson EE, Beck D, Yan W, Skinner MK. Transgenerational sperm DMRs escape DNA methylation erasure during embryonic development and epigenetic inheritance. ENVIRONMENTAL EPIGENETICS 2023; 9:dvad003. [PMID: 37346491 PMCID: PMC10281242 DOI: 10.1093/eep/dvad003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/10/2023] [Accepted: 06/01/2023] [Indexed: 06/23/2023]
Abstract
Germline transmission of epigenetic information is a critical component of epigenetic inheritance. Previous studies have suggested that an erasure of DNA methylation is required to develop stem cells in the morula embryo. An exception involves imprinted genes that escape this DNA methylation erasure. Transgenerational differential DNA methylation regions (DMRs) have been speculated to be imprinted-like and escape this erasure. The current study was designed to assess if morula embryos escape the erasure of dichlorodiphenyltrichloroethane-induced transgenerational sperm DMR methylation. Observations demonstrate that the majority (98%) of transgenerational sperm DMR sites retain DNA methylation and are not erased, so appearing similar to imprinted-like sites. Interestingly, observations also demonstrate that the majority of low-density CpG genomic sites had a significant increase in DNA methylation in the morula embryo compared to sperm. This is in contrast to the previously observed DNA methylation erasure of higher-density CpG sites. The general erasure of DNA methylation during embryogenesis appears applicable to high-density DNA methylation sites (e.g. CpG islands) but neither to transgenerational DMR methylation sites nor to low-density CpG deserts, which constitute the vast majority of the genome's DNA methylation sites. The role of epigenetics during embryogenesis appears more dynamic than the simple erasure of DNA methylation.
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Affiliation(s)
- Millissia Ben Maamar
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Yue Wang
- David Geffen School of Medicine at UCLA, The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Eric E Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Daniel Beck
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Wei Yan
- David Geffen School of Medicine at UCLA, The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
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20
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Bandyopadhayaya S, Yadav P, Sharma A, Dey SK, Nag A, Maheshwari R, Ford BM, Mandal CC. Oncogenic role of an uncharacterized cold-induced zinc finger protein 726 in breast cancer. J Cell Biochem 2023. [PMID: 37192271 DOI: 10.1002/jcb.30417] [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: 12/18/2022] [Revised: 03/29/2023] [Accepted: 04/18/2023] [Indexed: 05/18/2023]
Abstract
The unobtrusive cold environmental temperature can be linked to the development of cancer. This study, for the first time, envisaged cold stress-mediated induction of a zinc finger protein 726 (ZNF726) in breast cancer. However, the role of ZNF726 in tumorigenesis has not been defined. This study investigated the putative role of ZNF726 in breast cancer tumorigenic potency. Gene expression analysis using multifactorial cancer databases predicted overexpression of ZNF726 in various cancers, including breast cancer. Experimental observations found that malignant breast tissues and highly aggressive MDA-MB-231 cells showed an elevated ZNF726 expression as compared to benign and luminal A type (MCF-7), respectively. Furthermore, ZNF726 silencing decreased breast cancer cell proliferation, epithelial-mesenchymal transition, and invasion accompanied by the inhibition of colony-forming ability. Concordantly, ZNF726 overexpression significantly demonstrated opposite outcomes than ZNF726 knockdown. Taken together, our findings propose cold-inducible ZNF726 as a functional oncogene demonstrating its prominent role in facilitating breast tumorigenesis. An inverse correlation between environmental temperature and total serum cholesterol was observed in the previous study. Furthermore, experimental outcomes illustrate that cold stress elevated cholesterol content hinting at the involvement of the cholesterol regulatory pathway in cold-induced ZNF726 gene regulation. This observation was bolstered by a positive correlation between the expression of cholesterol-regulatory genes and ZNF726. Exogenous cholesterol treatment elevated ZNF726 transcript levels while knockdown of ZNF726 decreased the cholesterol content via downregulating various cholesterol regulatory gene expressions (e.g., SREBF1/2, HMGCoR, LDLR). Moreover, an underlying mechanism supporting cold-driven tumorigenesis is proposed through interdependent regulation of cholesterol regulatory pathway and cold-inducible ZNF726 expression.
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Affiliation(s)
- Shreetama Bandyopadhayaya
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Pooja Yadav
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Ankit Sharma
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Sanjay Kumar Dey
- Dr. B. R. Ambedkar Centre for Biomedical Research (ACBR), University of Delhi, Delhi, India
| | - Alo Nag
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Rekha Maheshwari
- Department of General Surgery, JLN Medical College, Ajmer, Rajasthan, India
| | - Bridget M Ford
- Department of Biology, University of the Incarnate Word, San Antonio, Texas, USA
| | - Chandi C Mandal
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
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21
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Joustra V, Hageman IL, Satsangi J, Adams A, Ventham NT, de Jonge WJ, Henneman P, D’Haens GR, Li Yim AYF. Systematic Review and Meta-analysis of Peripheral Blood DNA Methylation Studies in Inflammatory Bowel Disease. J Crohns Colitis 2023; 17:185-198. [PMID: 35998097 PMCID: PMC10024549 DOI: 10.1093/ecco-jcc/jjac119] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND AND AIMS Over the past decade, the DNA methylome has been increasingly studied in peripheral blood of inflammatory bowel disease [IBD] patients. However, a comprehensive summary and meta-analysis of peripheral blood leukocyte [PBL] DNA methylation studies has thus far not been conducted. Here, we systematically reviewed all available literature up to February 2022 and summarized the observations by means of meta-analysis. METHODS We conducted a systematic search and critical appraisal of IBD-associated DNA methylation studies in PBL using the biomarker-based cross-sectional studies [BIOCROSS] tool. Subsequently, we performed meta-analyses on the summary statistics obtained from epigenome-wide association studies [EWAS] that included patients with Crohn's disease [CD], ulcerative colitis [UC] and/or healthy controls [HC]. RESULTS Altogether, we included 15 studies for systematic review. Critical appraisal revealed large methodological and outcome heterogeneity between studies. Summary statistics were obtained from four studies based on a cumulative 552 samples [177 CD, 132 UC and 243 HC]. Consistent differential methylation was identified for 256 differentially methylated probes [DMPs; Bonferroni-adjusted p ≤ 0.05] when comparing CD with HC and 103 when comparing UC with HC. Comparing IBD [CD + UC] with HC resulted in 224 DMPs. Importantly, several of the previously identified DMPs, such as VMP1/TMEM49/MIR21 and RPS6KA2, were consistently differentially methylated across all studies. CONCLUSION Methodological homogenization of IBD epigenetic studies is needed to allow for easier aggregation and independent validation. Nonetheless, we were able to confirm previous observations. Our results can serve as the basis for future IBD epigenetic biomarker research in PBL.
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Affiliation(s)
| | | | - Jack Satsangi
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Alex Adams
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Nicholas T Ventham
- Institute of Genetics and Molecular Medicine, University of Edinburgh, UK
| | - Wouter J de Jonge
- Amsterdam UMC location University of Amsterdam, Department of Gastroenterology and Hepatology, Meibergdreef 9, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, Netherlands
- Amsterdam UMC location University of Amsterdam, Tytgat Institute for Liver and Intestinal Research, Amsterdam, Netherlands
| | - Peter Henneman
- Amsterdam UMC location University of Amsterdam, Department of Human Genetics, Genome Diagnostics Laboratory, Amsterdam, Netherlands
- Amsterdam Reproduction & Development, Amsterdam, Netherlands
| | - Geert R D’Haens
- Amsterdam UMC location University of Amsterdam, Department of Gastroenterology and Hepatology, Meibergdreef 9, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, Netherlands
| | - Andrew Y F Li Yim
- Corresponding author: Andrew Y. F. Li Yim, Amsterdam UMC location University of Amsterdam, Tytgat Institute for Liver and Intestinal Research, Amsterdam, Netherlands.
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Tovo PA, Marozio L, Abbona G, Calvi C, Frezet F, Gambarino S, Dini M, Benedetto C, Galliano I, Bergallo M. Pregnancy Is Associated with Impaired Transcription of Human Endogenous Retroviruses and of TRIM28 and SETDB1, Particularly in Mothers Affected by Multiple Sclerosis. Viruses 2023; 15:v15030710. [PMID: 36992419 PMCID: PMC10051116 DOI: 10.3390/v15030710] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/01/2023] [Accepted: 03/06/2023] [Indexed: 03/12/2023] Open
Abstract
Accumulating evidence highlights the pathogenetic role of human endogenous retroviruses (HERVs) in eliciting and maintaining multiple sclerosis (MS). Epigenetic mechanisms, such as those regulated by TRIM 28 and SETDB1, are implicated in HERV activation and in neuroinflammatory disorders, including MS. Pregnancy markedly improves the course of MS, but no study explored the expressions of HERVs and of TRIM28 and SETDB1 during gestation. Using a polymerase chain reaction real-time Taqman amplification assay, we assessed and compared the transcriptional levels of pol genes of HERV-H, HERV-K, HERV-W; of env genes of Syncytin (SYN)1, SYN2, and multiple sclerosis associated retrovirus (MSRV); and of TRIM28 and SETDB1 in peripheral blood and placenta from 20 mothers affected by MS; from 27 healthy mothers, in cord blood from their neonates; and in blood from healthy women of child-bearing age. The HERV mRNA levels were significantly lower in pregnant than in nonpregnant women. Expressions of all HERVs were downregulated in the chorion and in the decidua basalis of MS mothers compared to healthy mothers. The former also showed lower mRNA levels of HERV-K-pol and of SYN1, SYN2, and MSRV in peripheral blood. Significantly lower expressions of TRIM28 and SETDB1 also emerged in pregnant vs. nonpregnant women and in blood, chorion, and decidua of mothers with MS vs. healthy mothers. In contrast, HERV and TRIM28/SETDB1 expressions were comparable between their neonates. These results show that gestation is characterized by impaired expressions of HERVs and TRIM28/SETDB1, particularly in mothers with MS. Given the beneficial effects of pregnancy on MS and the wealth of data suggesting the putative contribution of HERVs and epigenetic processes in the pathogenesis of the disease, our findings may further support innovative therapeutic interventions to block HERV activation and to control aberrant epigenetic pathways in MS-affected patients.
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Affiliation(s)
- Pier-Angelo Tovo
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
- Correspondence: (P.-A.T.); (M.B.)
| | - Luca Marozio
- Department of Surgical Sciences, Obstetrics and Gynecology 1, University of Turin, 10126 Turin, Italy
| | - Giancarlo Abbona
- Pathology Unit, Department Laboratory Medicine, AOU Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Cristina Calvi
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
- Pediatric Laboratory, Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
| | - Federica Frezet
- Department of Surgical Sciences, Obstetrics and Gynecology 1, University of Turin, 10126 Turin, Italy
| | - Stefano Gambarino
- Pediatric Laboratory, Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
| | - Maddalena Dini
- Pediatric Laboratory, Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
| | - Chiara Benedetto
- Department of Surgical Sciences, Obstetrics and Gynecology 1, University of Turin, 10126 Turin, Italy
| | - Ilaria Galliano
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
- Pediatric Laboratory, Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
| | - Massimiliano Bergallo
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
- Pediatric Laboratory, Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
- Correspondence: (P.-A.T.); (M.B.)
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23
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Idriss S, Hallal M, El-Kurdi A, Zalzali H, El-Rassi I, Ehli EA, Davis CM, Chung PED, Gendoo DMA, Zacksenhaus E, Saab R, Khoueiry P. A temporal in vivo catalog of chromatin accessibility and expression profiles in pineoblastoma reveals a prevalent role for repressor elements. Genome Res 2023; 33:269-282. [PMID: 36650051 PMCID: PMC10069464 DOI: 10.1101/gr.277037.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 01/11/2023] [Indexed: 01/19/2023]
Abstract
Pediatric pineoblastomas (PBs) are rare and aggressive tumors of grade IV histology. Although some oncogenic drivers are characterized, including germline mutations in RB1 and DICER1, the role of epigenetic deregulation and cis-regulatory regions in PB pathogenesis and progression is largely unknown. Here, we generated genome-wide gene expression, chromatin accessibility, and H3K27ac profiles covering key time points of PB initiation and progression from pineal tissues of a mouse model of CCND1-driven PB. We identified PB-specific enhancers and super-enhancers, and found that in some cases, the accessible genome dynamics precede transcriptomic changes, a characteristic that is underexplored in tumor progression. During progression of PB, newly acquired open chromatin regions lacking H3K27ac signal become enriched for repressive state elements and harbor motifs of repressor transcription factors like HINFP, GLI2, and YY1. Copy number variant analysis identified deletion events specific to the tumorigenic stage, affecting, among others, the histone gene cluster and Gas1, the growth arrest specific gene. Gene set enrichment analysis and gene expression signatures positioned the model used here close to human PB samples, showing the potential of our findings for exploring new avenues in PB management and therapy. Overall, this study reports the first temporal and in vivo cis-regulatory, expression, and accessibility maps in PB.
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Affiliation(s)
- Salam Idriss
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Mohammad Hallal
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon.,Biomedical Engineering Program, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Abdullah El-Kurdi
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon.,Pillar Genomics Institute, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Hasan Zalzali
- Department of Pediatric and Adolescent Medicine, American University of Beirut, Beirut 1107 2020, Lebanon.,Department of Anatomy, Cell Biology, and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Inaam El-Rassi
- Biomedical Engineering Program, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Erik A Ehli
- Avera Institute for Human Genetics, Sioux Falls, South Dakota 57108, USA
| | - Christel M Davis
- Avera Institute for Human Genetics, Sioux Falls, South Dakota 57108, USA
| | - Philip E D Chung
- Toronto General Research Institute, University Health Network, Toronto, Ontario M5G 1L7, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Deena M A Gendoo
- Centre for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2SY, United Kingdom
| | - Eldad Zacksenhaus
- Toronto General Research Institute, University Health Network, Toronto, Ontario M5G 1L7, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Raya Saab
- Department of Pediatric and Adolescent Medicine, American University of Beirut, Beirut 1107 2020, Lebanon.,Department of Anatomy, Cell Biology, and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Pierre Khoueiry
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon; .,Pillar Genomics Institute, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
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24
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The role and application of transcriptional repressors in cancer treatment. Arch Pharm Res 2023; 46:1-17. [PMID: 36645575 DOI: 10.1007/s12272-023-01427-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/03/2023] [Indexed: 01/17/2023]
Abstract
Gene expression is modulated through the integration of many regulatory elements and their associated transcription factors (TFs). TFs bind to specific DNA sequences and either activate or repress transcriptional activity. Through decades of research, it has been established that aberrant expression or functional abnormalities of TFs can lead to uncontrolled cell division and the development of cancer. Initial studies on transcriptional regulation in cancer have focused on TFs as transcriptional activators. However, recent studies have demonstrated several different mechanisms of transcriptional repression in cancer, which could be potential therapeutic targets for the development of specific anti-cancer agents. In the first section of this review, "Emerging roles of transcriptional repressors in cancer development," we summarize the current understanding of transcriptional repressors and their involvement in the molecular processes of cancer progression. In the subsequent section, "Therapeutic applications," we provide an updated overview of the available therapeutic targets for drug discovery and discuss the new frontier of such applications.
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25
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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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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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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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High Expression of POGK Predicts Poor Prognosis in Patients with Hepatocellular Carcinoma. Curr Oncol 2022; 29:8650-8667. [PMID: 36421335 PMCID: PMC9688978 DOI: 10.3390/curroncol29110682] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVE Kruppel-associated box (KRAB) proteins reportedly play a dual role in neoplastic transformation. At present, little is known about the function of the proteins encoded by the human pogo transposable element derived with KRAB domain (POGK) gene. Herein, we evaluated the prognostic significance of POGK expression in patients with hepatocellular carcinoma (HCC). METHODS The data of HCC patients was downloaded from The Cancer Genome Atlas (TCGA) database. To determine the relationship between POGK and clinical features, logistic regression was applied. Cox regression and Kaplan-Meier analyses were used to evaluate the correlation between POGK and survival rates. Gene ontology (GO) analysis and Gene set enrichment analysis (GSEA) were conducted to identify the enriched pathways and functions associated with POGK. RESULTS A total of 374 HCC patients were identified in TCGA. POGK was significantly upregulated in HCC and correlated with tumor status (p = 0.036), race (p = 0.025), weight (p = 0.002), body mass index (p = 0.033), histologic grade (p < 0.001), and alpha-fetoprotein (p < 0.001). High POGK expression in HCC patients correlated with a poor outcome in terms of overall survival (p = 0.0018), progression-free survival (p = 0.0087), relapse-free survival (p = 0.045), and disease-specific survival (p = 0.014), according to Kaplan-Meier analysis. Receiver operating characteristic curve analysis showed that the area under the curve of POGK expression for HCC diagnosis was 0.891. GSEA showed that high POGK expression might activate mitotic prometaphase, kinesins, homologous DNA pairing and strand exchange, MET activates PTK2 signaling pathway, G1 to S cell cycle control, Aurora B pathway, ncRNAs involved in WNT signaling pathway, hepatitis C, and ncRNAs involved in the STAT3 signaling pathway. POGK expression correlated with the abundance of adaptive and innate immunocytes in HCC. CONCLUSION High expression of POGK has high diagnostic and prognostic values in patients with HCC. Moreover, POGK expression is correlated with immune infiltration in HCC.
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Catapano R, Sepe L, Toscano E, Paolella G, Chiurazzi F, Barbato SP, Bruzzese D, Arianna R, Grosso M, Romano S, Romano MF, Costanzo P, Cesaro E. Biological relevance of ZNF224 expression in chronic lymphocytic leukemia and its implication IN NF-kB pathway regulation. Front Mol Biosci 2022; 9:1010984. [PMID: 36425656 PMCID: PMC9681601 DOI: 10.3389/fmolb.2022.1010984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/20/2022] [Indexed: 12/21/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a heterogeneous disease, whose presentation and clinical course are highly variable. Identification of novel prognostic factors may contribute to improving the CLL classification and providing indications for treatment options. The zinc finger protein ZNF224 plays a key role in cell transformation, through the control of apoptotic and survival pathways. In this study, we evaluated the potential application of ZNF224 as a novel marker of CLL progression and therapy responsiveness. To this aim, we analyzed ZNF224 expression levels in B lymphocytes from CLL patients at different stages of the disease and in patients showing different treatment outcomes. The expression of ZNF224 was significantly increased in disease progression and dramatically decreased in patients in complete remission after chemotherapy. Gene expression correlation analysis performed on datasets of CLL patients revealed that ZNF224 expression was well correlated with that of some prognostic and predictive markers. Moreover, bioinformatic analysis coupled ZNF224 to NF-κB pathway, and experimental data demonstrated that RNA interference of ZNF224 reduced the activity of the NF-κB survival pathway in CLL cells. Consistently with a pro-survival role, ZNF224 knockdown raised spontaneous and drug-induced apoptosis and inhibited the proliferation of peripheral blood mononuclear cells from CLL patients. Our findings provide evidence for the involvement of ZNF224 in the survival of CLL cells via NF-κB pathway modulation, and also suggest ZNF224 as a prognostic and predictive molecular marker of CLL disease.
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Affiliation(s)
- Rosa Catapano
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Leandra Sepe
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
- Ceinge Advanced Technologies, Naples, Italy
| | - Elvira Toscano
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
- Ceinge Advanced Technologies, Naples, Italy
| | - Giovanni Paolella
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
- Ceinge Advanced Technologies, Naples, Italy
| | - Federico Chiurazzi
- Division of Hematology, Department of Clinical and Experimental Medicine, University of Naples Federico II, Naples, Italy
| | - Serafina Patrizia Barbato
- Division of Hematology, Department of Clinical and Experimental Medicine, University of Naples Federico II, Naples, Italy
| | - Dario Bruzzese
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Rosa Arianna
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Michela Grosso
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
- Ceinge Advanced Technologies, Naples, Italy
| | - Simona Romano
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Maria Fiammetta Romano
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Paola Costanzo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Elena Cesaro
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
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miR-193a-5p Enhances the Radioresistance of Pancreatic Cancer Cells by Targeting ZFP57 and Activating the Wnt Pathway. JOURNAL OF ONCOLOGY 2022; 2022:8071343. [PMID: 36276285 PMCID: PMC9586754 DOI: 10.1155/2022/8071343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 09/20/2022] [Indexed: 11/18/2022]
Abstract
This study was to investigate whether miR-193a-5p and ZFP57 are involved in the radioresistance of pancreatic cancer and to explore its working mechanism. Pancreatic cancer tissues were harvested from patients who achieved CR (complete remission) and PR (partial remission) and those who achieved PD (progressive disease) and SD (stable disease). The mRNA and protein expressions of ZFP57 and miR-193a-5p were determined by RT-qPCR and WB (Western blot), respectively. For in vitro experiments, the parental BxPC-3 cell line was irradiated by X-ray at a total dose of 40 Gy to induce the irradiation-resistant subtype BxPC-3-RR. ZFP57 was downregulated in radioresistant pancreatic cancer cells. The results of dual-luciferase reporter gene assay, RNA pull-down assay, RT-qPCR, and WB confirmed that miR-193a-5p targeted ZFP57 and inhibited ZFP57 expression. The MTT assay and the colony formation assay showed that the radioresistant pancreatic cancer cells had higher viability and survival fraction. The results of WB indicated that in the radioresistant pancreatic cancer cells, the cyclin D1, Bax, CDk4, cleaved caspase-3, Bcl-2, and γ-H2AX proteins were upregulated to varying degrees. The results of the in vitro nude mouse experiment were consistent with those of in vivo experiments. According to the cell transfection and salvage experiments, miR-193a-5p down regulated ZFP57 after radiotherapy. As a result, the Wnt pathway was activated, which further induced radioresistance of pancreatic cancer cells. Our experiments showed that the miR-193a-5p/ZFP57/Wnt pathway mediated the radioresistance of pancreatic cancer cells, providing novel clues for the treatment of pancreatic cancer.
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Wang X, Wei X, Cao Y, Xing P. ZNF33A Promotes Tumor Progression and BET Inhibitor Resistance in Triple-Negative Breast Cancer. THE AMERICAN JOURNAL OF PATHOLOGY 2022; 192:1458-1469. [PMID: 35843263 DOI: 10.1016/j.ajpath.2022.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 06/04/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Overexpression of ZNF33A (Krüppel-type zinc finger 33A) promotes carcinogenesis in several malignant tumors. However, the biochemical role and clinical importance of ZNF33A in triple-negative breast cancer (TNBC) still need to be explored. In this study, overexpression of ZNF33A in TNBC patient tissues and cell lines led to a worse prognosis. ZNF33A promoted cell growth and facilitated the resistance of cancer cells to inhibitors of bromodomain and extraterminal domain (BET) in TNBC. ZNF33A also promoted the induction of c-Myc, the primary player for the resistance to BET inhibitors in TNBC. In conclusion, ZNF33A may be a tumor growth-promoting factor associated with TNBC prognosis, and ZNF33A repression may sensitize TNBC cells to BET inhibitors.
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Affiliation(s)
- Xu Wang
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xiaolin Wei
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yu Cao
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Peng Xing
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China.
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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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Enhanced Expression of Human Endogenous Retroviruses, TRIM28 and SETDB1 in Autism Spectrum Disorder. Int J Mol Sci 2022; 23:ijms23115964. [PMID: 35682642 PMCID: PMC9180946 DOI: 10.3390/ijms23115964] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/12/2022] [Accepted: 05/23/2022] [Indexed: 02/01/2023] Open
Abstract
Human endogenous retroviruses (HERVs) are relics of ancestral infections and represent 8% of the human genome. They are no longer infectious, but their activation has been associated with several disorders, including neuropsychiatric conditions. Enhanced expression of HERV-K and HERV-H envelope genes has been found in the blood of autism spectrum disorder (ASD) patients, but no information is available on syncytin 1 (SYN1), SYN2, and multiple sclerosis-associated retrovirus (MSRV), which are thought to be implicated in brain development and immune responses. HERV activation is regulated by TRIM28 and SETDB1, which are part of the epigenetic mechanisms that organize the chromatin architecture in response to external stimuli and are involved in neural cell differentiation and brain inflammation. We assessed, through a PCR realtime Taqman amplification assay, the transcription levels of pol genes of HERV-H, -K, and -W families, of env genes of SYN1, SYN2, and MSRV, as well as of TRIM28 and SETDB1 in the blood of 33 ASD children (28 males, median 3.8 years, 25–75% interquartile range 3.0–6.0 y) and healthy controls (HC). Significantly higher expressions of TRIM28 and SETDB1, as well as of all the HERV genes tested, except for HERV-W-pol, were found in ASD, as compared with HC. Positive correlations were observed between the mRNA levels of TRIM28 or SETDB1 and every HERV gene in ASD patients, but not in HC. Overexpression of TRIM28/SETDB1 and several HERVs in children with ASD and the positive correlations between their transcriptional levels suggest that these may be main players in pathogenetic mechanisms leading to ASD.
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Stroggilos R, Frantzi M, Zoidakis J, Mokou M, Moulavasilis N, Mavrogeorgis E, Melidi A, Makridakis M, Stravodimos K, Roubelakis MG, Mischak H, Vlahou A. Gene Expression Monotonicity across Bladder Cancer Stages Informs on the Molecular Pathogenesis and Identifies a Prognostic Eight-Gene Signature. Cancers (Basel) 2022; 14:cancers14102542. [PMID: 35626146 PMCID: PMC9140126 DOI: 10.3390/cancers14102542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/14/2022] [Accepted: 05/17/2022] [Indexed: 01/27/2023] Open
Abstract
Despite advancements in molecular classification, tumor stage and grade still remain the most relevant prognosticators used by clinicians to decide on patient management. Here, we leverage publicly available data to characterize bladder cancer (BLCA)’s stage biology based on increased sample sizes, identify potential therapeutic targets, and extract putative biomarkers. A total of 1135 primary BLCA transcriptomes from 12 microarray studies were compiled in a meta-cohort and analyzed for monotonal alterations in pathway activities, gene expression, and co-expression patterns with increasing stage (Ta–T1–T2–T3–T4), starting from the non-malignant tumor-adjacent urothelium. The TCGA-2017 and IMvigor-210 RNA-Seq data were used to validate our findings. Wnt, MTORC1 signaling, and MYC activity were monotonically increased with increasing stage, while an opposite trend was detected for the catabolism of fatty acids, circadian clock genes, and the metabolism of heme. Co-expression network analysis highlighted stage- and cell-type-specific genes of potentially synergistic therapeutic value. An eight-gene signature, consisting of the genes AKAP7, ANLN, CBX7, CDC14B, ENO1, GTPBP4, MED19, and ZFP2, had independent prognostic value in both the discovery and validation sets. This novel eight-gene signature may increase the granularity of current risk-to-progression estimators.
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Affiliation(s)
- Rafael Stroggilos
- Systems Biology Center, Biomedical Research Foundation of the Academy of Athens, Soranou Efessiou 4, 11527 Athens, Greece; (R.S.); (J.Z.); (E.M.); (A.M.); (M.M.)
| | - Maria Frantzi
- Mosaiques Diagnostics GmbH, 30659 Hannover, Germany; (M.F.); (M.M.); (H.M.)
| | - Jerome Zoidakis
- Systems Biology Center, Biomedical Research Foundation of the Academy of Athens, Soranou Efessiou 4, 11527 Athens, Greece; (R.S.); (J.Z.); (E.M.); (A.M.); (M.M.)
| | - Marika Mokou
- Mosaiques Diagnostics GmbH, 30659 Hannover, Germany; (M.F.); (M.M.); (H.M.)
| | - Napoleon Moulavasilis
- 1st Department of Urology, Laiko Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece; (N.M.); (K.S.)
| | - Emmanouil Mavrogeorgis
- Systems Biology Center, Biomedical Research Foundation of the Academy of Athens, Soranou Efessiou 4, 11527 Athens, Greece; (R.S.); (J.Z.); (E.M.); (A.M.); (M.M.)
| | - Anna Melidi
- Systems Biology Center, Biomedical Research Foundation of the Academy of Athens, Soranou Efessiou 4, 11527 Athens, Greece; (R.S.); (J.Z.); (E.M.); (A.M.); (M.M.)
| | - Manousos Makridakis
- Systems Biology Center, Biomedical Research Foundation of the Academy of Athens, Soranou Efessiou 4, 11527 Athens, Greece; (R.S.); (J.Z.); (E.M.); (A.M.); (M.M.)
| | - Konstantinos Stravodimos
- 1st Department of Urology, Laiko Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece; (N.M.); (K.S.)
| | - Maria G. Roubelakis
- Laboratory of Biology, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece;
- Cell and Gene Therapy Laboratory, Biomedical Research Foundation of the Academy of Athens, Soranou Efessiou 4, 11527 Athens, Greece
| | - Harald Mischak
- Mosaiques Diagnostics GmbH, 30659 Hannover, Germany; (M.F.); (M.M.); (H.M.)
| | - Antonia Vlahou
- Systems Biology Center, Biomedical Research Foundation of the Academy of Athens, Soranou Efessiou 4, 11527 Athens, Greece; (R.S.); (J.Z.); (E.M.); (A.M.); (M.M.)
- Correspondence: ; Tel.: +30-210-659-7506; Fax: +30-210-659-7545
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Heyliger SO, Soliman KFA, Saulsbury MD, Reams RR. Prognostic Relevance of ZNF844 and Chr 19p13.2 KRAB-Zinc Finger Proteins in Clear Cell Renal Carcinoma. Cancer Genomics Proteomics 2022; 19:305-327. [PMID: 35430565 DOI: 10.21873/cgp.20322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/05/2022] [Accepted: 02/11/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND/AIM Clear-cell renal cell carcinoma (ccRCC) is the most common and aggressive form of all urological cancers, with poor prognosis and high mortality. Despite growing evidence of involvement in carcinogenesis, the role of KRAB-ZFP in ccRCC has not been fully explored. KRAB Zinc finger proteins (KRAB-ZFPs) are the largest family of mammalian transcription regulators. They are differentially expressed in various tissues during cellular development and phenotypic differentiation. MATERIALS AND METHODS 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. RESULTS Using bioinformatics techniques, we demonstrate that approximately 60% of KRAB zinc finger proteins located on chromosome 19p13.2 are differentially expressed, with all but two being down-regulated in ccRCC. Moreover, ZNF844, a paralog of ZNF433, was the most down-regulated across all histological grades and pathological stages (p<0.001). In addition, the decrease in ZNF844 expression was associated with poor patient survival (HR=0.41; 95% CI=0.3-0.56; p<0.0001). Gene Set Enrichment Analysis of genes inversely co-expressed with ZNF844 revealed that enriched pathways were consistently related to immune and translation processes (p<0.05, FDR <0.05). Lastly, ZNF844 expression showed moderate, inverse correlation to Helper T-cell (CD4 or Th1) subtype 1 (R=-0.558, p=5.15×10-39) infiltration and with the exhausted T-cell phenotype (R=-0.37; p=4.1×10-21). CONCLUSION Down-regulation of KRAB-ZFPs at 19p13.2 may represent a signature for ccRCC. Moreover, ZNF844 is a prognostic marker for ccRCC and may serve as a putative immune-related tumor suppressor gene.
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Affiliation(s)
- Simone O Heyliger
- Department of Pharmaceutical Sciences, Hampton University, Hampton, VA, U.S.A
| | - Karam F A Soliman
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, U.S.A
| | - Marilyn D Saulsbury
- Department of Pharmaceutical Sciences, Hampton University, Hampton, VA, U.S.A
| | - R Renee Reams
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, U.S.A.
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Wilanowski T, Dworkin S. Transcription Factors in Cancer. Int J Mol Sci 2022; 23:ijms23084434. [PMID: 35457252 PMCID: PMC9029932 DOI: 10.3390/ijms23084434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 04/14/2022] [Accepted: 04/14/2022] [Indexed: 11/16/2022] Open
Abstract
This Special Issue comprises three original studies and five review articles [...].
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Affiliation(s)
- Tomasz Wilanowski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 1 Miecznikowa St., 02-096 Warsaw, Poland;
| | - Sebastian Dworkin
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Bundoora, VIC 3086, Australia
- Correspondence: ; Tel.: +61-3-9479-5728
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Sun M, Ju J, Ding Y, Zhao C, Tian C. The signaling pathways regulated by KRAB zinc-finger proteins in cancer. Biochim Biophys Acta Rev Cancer 2022; 1877:188731. [DOI: 10.1016/j.bbcan.2022.188731] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 03/23/2022] [Accepted: 04/20/2022] [Indexed: 12/11/2022]
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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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Tovo P, Monti G, Daprà V, Montanari P, Calvi C, Alliaudi C, Sardo A, Galliano I, Bergallo M. Enhanced expression of endogenous retroviruses and of TRIM28 and SETDB1 in children with food allergy. Clin Transl Allergy 2022; 12:e12124. [PMID: 35344298 PMCID: PMC8967271 DOI: 10.1002/clt2.12124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 01/19/2022] [Accepted: 01/27/2022] [Indexed: 11/20/2022] Open
Abstract
Background Human endogenous retroviruses (HERVs) represent 8% of our genome. They originate from ancestral infections and although no longer contagious they can regulate transcription of adjacent cellular genes, produce viral RNAs sensed as non‐self by pattern recognition receptors, and encode viral proteins, such as Syncytin (SYN) 1 and 2, that exhibit potent immunomodulatory properties. Based on this, HERVs have been studied and proposed as relevant cofactors in several chronic inflammatory and immune‐mediated diseases. HERV transcription is regulated by host TRIM28 and SET domain bifurcated histone lysine methyltransferase 1 (SETDB1), which in turn exert crucial regulatory functions on the host immune system. No studies explored the expression of HERVs, TRIM28, and SETDB1 in allergic patients. Methods We assessed, through a polymerase chain reaction real time Taqman amplification assay, the transcription levels of pol genes of HERV‐H, HERV‐K, HERV‐W, and of env genes of SYN1 and SYN2, as well as of TRIM28 and SETDB1 in whole blood from 32 children with IgE‐mediated food allergy, 19 with food protein‐induced enterocolitis syndrome (FPIES), and in healthy control children. Results The expression levels of pol genes of HERV‐H, ‐K, and ‐W were significantly enhanced in patients with IgE‐mediated FA or FPIES as compared to control subjects, while the mRNA concentrations of SYN1 and SYN2 were comparable in each group of children. Both TRIM28 and SETDB1 mRNA levels were significantly higher in allergic patients. Conclusions Given the influence of HERVs and of TRIM28 and SETDB1 on innate and adaptive immune responses, their transcriptional activation in children with food allergies suggest that they might play important roles in the development of these diseases.
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Affiliation(s)
- Pier‐Angelo Tovo
- Department of Pediatric Sciences and Public Health University of Turin Turin Italy
| | - Giovanna Monti
- Pediatric Allergy Unit Regina Margherita Children's Hospital Turin Italy
| | - Valentina Daprà
- Pediatric Laboratory Department of Pediatric Sciences and Public Health University of Turin Turin Italy
| | - Paola Montanari
- Department of Pediatric Sciences and Public Health University of Turin Turin Italy
- Pediatric Laboratory Department of Pediatric Sciences and Public Health University of Turin Turin Italy
| | - Cristina Calvi
- Department of Pediatric Sciences and Public Health University of Turin Turin Italy
- Pediatric Laboratory Department of Pediatric Sciences and Public Health University of Turin Turin Italy
| | - Carla Alliaudi
- Department of Pediatric Sciences and Public Health University of Turin Turin Italy
- Pediatric Laboratory Department of Pediatric Sciences and Public Health University of Turin Turin Italy
| | - Allegra Sardo
- Department of Pediatric Sciences and Public Health University of Turin Turin Italy
| | - Ilaria Galliano
- Department of Pediatric Sciences and Public Health University of Turin Turin Italy
- Pediatric Laboratory Department of Pediatric Sciences and Public Health University of Turin Turin Italy
| | - Massimiliano Bergallo
- Department of Pediatric Sciences and Public Health University of Turin Turin Italy
- Pediatric Laboratory Department of Pediatric Sciences and Public Health University of Turin Turin Italy
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Wu X, Ren Y, Wen Y, Lu S, Li H, Yu H, Li W, Zou F. Deacetylation of ZKSCAN3 by SIRT1 induces autophagy and protects SN4741 cells against MPP +-induced oxidative stress. Free Radic Biol Med 2022; 181:82-97. [PMID: 35124181 DOI: 10.1016/j.freeradbiomed.2022.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/28/2021] [Accepted: 02/01/2022] [Indexed: 11/20/2022]
Abstract
Mitochondrial dysfunction, oxidative stress and misfolded protein aggregation are related to autophagy-lysosomal dysregulation and contribute to the pathogenesis of Parkinson' s disease (PD). ZKSCAN3, a transcriptional repressor, plays a crucial role in autophagy and lysosomal biogenesis. However, the role and modification of ZKSCAN3 in the defection of ALP, along with the molecular mechanism involved in pathogenesis of PD, still remain unclear. In this study, we demonstrated that cellular reactive oxygen species (ROS) generated by MPP+ exposure and the resulting oxidative damage were counteracted by SIRT1-ZKSCAN3 pathway induction. Here we showed that nuclear ZKSCAN3 significantly increased in ventral midbrain of MPTP-treated mice and MPP+-treated SN4741 cells. Knockdown of ZKSCAN3 alleviated MPP+-induced ALP defect, Tyrosine Hydroxylase (TH) declination and neuronal death. NAC, a ROS scavenger, reduced the nuclear translocation of ZKSCAN3 and sequentially improved ALP function in MPP+-treated SN4741 cells. SRT2104, a SIRT1 activator, attenuated impairment of ALP in MPP+-treated SN47417 cells through decreasing nuclear accumulation of ZKSCAN3 and protected dopaminergic neurons from MPTP injury. Moreover, SRT2104 relieved impairment in locomotor activities and coordination skills upon treatment of MPTP in C57/BL6J mice through behavior tests including rotarod, pole climbing and grid. Furthermore, ZKSCAN3 was a novel substrate of SIRT1 which was deacetylated at lysine 148 residues by SIRT1. This subsequently facilitated the shuttling of ZKSCAN3 to the cytoplasm. Therefore, our study identifies a novel acetylation-dependent regulatory mechanism of nuclear translocation of ZKSCAN3. It results in autophagy-lysosomal dysfunction and then leads to DA neuronal death in MPTP/MPP+ model of PD.
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Affiliation(s)
- Xian Wu
- Department of Occupational Health and Occupational Medicine, Guangdong Province Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China.
| | - Yixian Ren
- Department of Occupational Health and Occupational Medicine, Guangdong Province Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China; Evaluation and Monitoring Center of Occupational Health, Guangzhou Twelfth People's Hospital, Guangzhou, PR China.
| | - Yue Wen
- Department of Occupational Health and Occupational Medicine, Guangdong Province Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China.
| | - Sixin Lu
- Department of Occupational Health and Occupational Medicine, Guangdong Province Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China.
| | - Huihui Li
- Department of Occupational Health and Occupational Medicine, Guangdong Province Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China.
| | - Honglin Yu
- Department of Occupational Health and Occupational Medicine, Guangdong Province Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China.
| | - Wenjun Li
- Department of Occupational Health and Occupational Medicine, Guangdong Province Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China.
| | - Fei Zou
- Department of Occupational Health and Occupational Medicine, Guangdong Province Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China.
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Lorenz P, Steinbeck F, Krause L, Thiesen HJ. The KRAB Domain of ZNF10 Guides the Identification of Specific Amino Acids That Transform the Ancestral KRAB-A-Related Domain Present in Human PRDM9 into a Canonical Modern KRAB-A Domain. Int J Mol Sci 2022; 23:1072. [PMID: 35162997 PMCID: PMC8835667 DOI: 10.3390/ijms23031072] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 12/14/2022] Open
Abstract
Krüppel-associated box (KRAB) zinc finger proteins are a large class of tetrapod transcription factors that usually exert transcriptional repression through recruitment of TRIM28/KAP1. The evolutionary root of modern KRAB domains (mKRAB) can be traced back to an ancestral motif (aKRAB) that occurs even in invertebrates. Here, we first stratified three subgroups of aKRAB sequences from the animal kingdom (PRDM9, SSX and coelacanth KZNF families) and defined ancestral subdomains for KRAB-A and KRAB-B. Using human ZNF10 mKRAB-AB as blueprints for function, we then identified the necessary amino acid changes that transform the inactive aKRAB-A of human PRDM9 into an mKRAB domain capable of mediating silencing and complexing TRIM28/KAP1 in human cells when employed as a hybrid with ZNF10-B. Full gain of function required replacement of residues KR by the conserved motif MLE (positionsA32-A34), which inserted an additional residue, and exchange of A9/S for F, A20/M for L, and A27/R for V. AlphaFold2 modelling documented an evolutionary conserved L-shaped body of two α-helices in all KRAB domains. It is transformed into a characteristic spatial arrangement typical for mKRAB-AB upon the amino acid replacements and in conjunction with a third helix supplied by mKRAB-B. Side-chains pointing outward from the core KRAB 3D structure may reveal a protein-protein interaction code enabling graded binding of TRIM28 to different KRAB domains. Our data provide basic insights into structure-function relationships and emulate transitions of KRAB during evolution.
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Affiliation(s)
- Peter Lorenz
- Rostock University Medical Center, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany; (F.S.); (L.K.); (H.-J.T.)
| | - Felix Steinbeck
- Rostock University Medical Center, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany; (F.S.); (L.K.); (H.-J.T.)
| | - Ludwig Krause
- Rostock University Medical Center, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany; (F.S.); (L.K.); (H.-J.T.)
| | - Hans-Jürgen Thiesen
- Rostock University Medical Center, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany; (F.S.); (L.K.); (H.-J.T.)
- Gesellschaft für Individualisierte Medizin (IndyMed) mbH, 17, 18055 Rostock, Germany
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Valentini S, Gandolfi F, Carolo M, Dalfovo D, Pozza L, Romanel A. OUP accepted manuscript. Nucleic Acids Res 2022; 50:1335-1350. [PMID: 35061909 PMCID: PMC8860573 DOI: 10.1093/nar/gkac024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/03/2022] [Accepted: 01/07/2022] [Indexed: 11/21/2022] Open
Abstract
In the last years, many studies were able to identify associations between common genetic variants and complex diseases. However, the mechanistic biological links explaining these associations are still mostly unknown. Common variants are usually associated with a relatively small effect size, suggesting that interactions among multiple variants might be a major genetic component of complex diseases. Hence, elucidating the presence of functional relations among variants may be fundamental to identify putative variants’ interactions. To this aim, we developed Polympact, a web-based resource that allows to explore functional relations among human common variants by exploiting variants’ functional element landscape, their impact on transcription factor binding motifs, and their effect on transcript levels of protein-coding genes. Polympact characterizes over 18 million common variants and allows to explore putative relations by combining clustering analysis and innovative similarity and interaction network models. The properties of the network models were studied and the utility of Polympact was demonstrated by analysing the rich sets of Breast Cancer and Alzheimer's GWAS variants. We identified relations among multiple variants, suggesting putative interactions. Polympact is freely available at bcglab.cibio.unitn.it/polympact.
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Affiliation(s)
- Samuel Valentini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Francesco Gandolfi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Mattia Carolo
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Davide Dalfovo
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Lara Pozza
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Alessandro Romanel
- To whom correspondence should be addressed. Tel: +39 0461 285217; Fax: +39 0461 283937;
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Siraj AK, Parvathareddy SK, Siraj N, Al-Obaisi K, Aldughaither SM, AlManea HM, AlHussaini HF, Al-Dayel F, Al-Kuraya KS. Loss of ZNF677 expression is a predictive biomarker for lymph node metastasis in Middle Eastern Colorectal Cancer. Sci Rep 2021; 11:22346. [PMID: 34785764 PMCID: PMC8595636 DOI: 10.1038/s41598-021-01869-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 11/02/2021] [Indexed: 11/22/2022] Open
Abstract
Zinc-finger proteins are transcription factors with a “finger-like” domain that are widely involved in many biological processes. The zinc-finger protein 677 (ZNF677) belongs to the zinc-finger protein family. Previous reports have highlighted the tumor suppressive role of ZNF677 in thyroid and lung cancer. However, its role in colorectal cancer (CRC) has not been explored. ZNF677 protein expression was analyzed by immunohistochemistry in a large cohort of 1158 CRC patients. ZNF677 loss of expression was more frequent in CRC tissues (45.3%, 525/1158), when compared to that of normal tissue (5.1%, 11/214) (p < 0.0001) and was associated with mucinous histology (p = 0.0311), advanced pathological stage (p < 0.0001) and lymph node (LN) metastasis (p = 0.0374). Further analysis showed ZNF677 loss to be significantly enriched in LN metastatic CRC compared to overall cohort (p = 0.0258). More importantly, multivariate logistic regression analysis showed that ZNF677 loss is an independent predictor of LN metastasis in CRC (Odds ratio = 1.41; 95% confidence interval 1.05–1.87; p = 0.0203).The gain- and loss-of-function studies in CRC cell lines demonstrated that loss of ZNF677 protein expression prominently increased cell proliferation, progression of epithelial-mesenchymal transition and conferred chemoresistance, whereas its overexpression reversed the effect. In conclusion, loss of ZNF677 protein expression is common in Middle Eastern CRC and contributes to the prediction of biological aggressiveness of CRC. Therefore, ZNF677 could not only serve as a marker in predicting clinical prognosis in patient with CRC but also as a potential biomarker for personalized targeted therapy.
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Affiliation(s)
- Abdul K Siraj
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, MBC#98-16, P.O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Sandeep Kumar Parvathareddy
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, MBC#98-16, P.O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Nabil Siraj
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, MBC#98-16, P.O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Khadija Al-Obaisi
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, MBC#98-16, P.O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Saud M Aldughaither
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, MBC#98-16, P.O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Hadeel M AlManea
- Department of Pathology, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Hussah F AlHussaini
- Department of Pathology, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Fouad Al-Dayel
- Department of Pathology, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Khawla S Al-Kuraya
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, MBC#98-16, P.O. Box 3354, Riyadh, 11211, Saudi Arabia.
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Czerwinska P, Mackiewicz AA. Low Levels of TRIM28-Interacting KRAB-ZNF Genes Associate with Cancer Stemness and Predict Poor Prognosis of Kidney Renal Clear Cell Carcinoma Patients. Cancers (Basel) 2021; 13:cancers13194835. [PMID: 34638319 PMCID: PMC8508054 DOI: 10.3390/cancers13194835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/16/2021] [Accepted: 09/22/2021] [Indexed: 12/23/2022] Open
Abstract
Simple Summary This is the first report investigating the involvement of TRIM28-interacting KRAB-ZNFs in kidney cancer progression. We demonstrate a significant negative association between KRAB-ZNFs and cancer stemness followed by an attenuated immune-suppressive response and reveal the prognostic role for several KRAB-ZNFs. Our findings may help better understand the molecular basis of kidney cancer and ultimately pave the way to more appropriate prognostic tools and novel therapeutic strategies directly eradicating the dedifferentiated compartment of the tumor. Abstract Krüppel-associated box zinc finger (KRAB-ZNF) proteins are known to regulate diverse biological processes, such as embryonic development, tissue-specific gene expression, and cancer progression. However, their involvement in the regulation of cancer stemness-like phenotype acquisition and maintenance is scarcely explored across solid tumor types, and to date, there are no data for kidney renal clear cell cancer (KIRC). We have harnessed The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) database transcriptomic data and used several bioinformatic tools (i.e., GEPIA2, GSCALite, TISIDB, GSEA, CIBERSORT) to verify the relation between the expression and genomic alterations in KRAB-ZNFs and kidney cancer, focusing primarily on tumor dedifferentiation status and antitumor immune response. Our results demonstrate a significant negative correlation between KRAB-ZNFs and kidney cancer dedifferentiation status followed by an attenuated immune-suppressive response. The transcriptomic profiles of high KRAB-ZNF-expressing kidney tumors are significantly enriched with stem cell markers and show a depletion of several inflammatory pathways known for favoring cancer stemness. Moreover, we show for the first time the prognostic role for several KRAB-ZNFs in kidney cancer. Our results provide new insight into the role of selected KRAB-ZNF proteins in kidney cancer development. We believe that our findings may help better understand the molecular basis of KIRC.
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Affiliation(s)
- Patrycja Czerwinska
- Department of Cancer Immunology, Poznan University of Medical Sciences, 15 Garbary St., 61-866 Poznan, Poland; or
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 15 Garbary St., 61-866 Poznan, Poland
- Correspondence: or
| | - Andrzej Adam Mackiewicz
- Department of Cancer Immunology, Poznan University of Medical Sciences, 15 Garbary St., 61-866 Poznan, Poland; or
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 15 Garbary St., 61-866 Poznan, Poland
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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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Tovo PA, Garazzino S, Daprà V, Pruccoli G, Calvi C, Mignone F, Alliaudi C, Denina M, Scolfaro C, Zoppo M, Licciardi F, Ramenghi U, Galliano I, Bergallo M. COVID-19 in Children: Expressions of Type I/II/III Interferons, TRIM28, SETDB1, and Endogenous Retroviruses in Mild and Severe Cases. Int J Mol Sci 2021; 22:7481. [PMID: 34299101 PMCID: PMC8303145 DOI: 10.3390/ijms22147481] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/07/2021] [Accepted: 07/10/2021] [Indexed: 02/07/2023] Open
Abstract
Children with the new coronavirus disease 2019 (COVID-19) have milder symptoms and a better prognosis than adult patients. Several investigations assessed type I, II, and III interferon (IFN) signatures in SARS-CoV-2 infected adults, however no data are available for pediatric patients. TRIM28 and SETDB1 regulate the transcription of multiple genes involved in the immune response as well as of human endogenous retroviruses (HERVs). Exogenous viral infections can trigger the activation of HERVs, which in turn can induce inflammatory and immune reactions. Despite the potential cross-talks between SARS-CoV-2 infection and TRIM28, SETDB1, and HERVs, information on their expressions in COVID-19 patients is lacking. We assessed, through a PCR real time Taqman amplification assay, the transcription levels of six IFN-I stimulated genes, IFN-II and three of its sensitive genes, three IFN-lIIs, as well as of TRIM28, SETDB1, pol genes of HERV-H, -K, and -W families, and of env genes of Syncytin (SYN)1, SYN2, and multiple sclerosis-associated retrovirus (MRSV) in peripheral blood from COVID-19 children and in control uninfected subjects. Higher expression levels of IFN-I and IFN-II inducible genes were observed in 36 COVID-19 children with mild or moderate disease as compared to uninfected controls, whereas their concentrations decreased in 17 children with severe disease and in 11 with multisystem inflammatory syndrome (MIS-C). Similar findings were found for the expression of TRIM-28, SETDB1, and every HERV gene. Positive correlations emerged between the transcriptional levels of type I and II IFNs, TRIM28, SETDB1, and HERVs in COVID-19 patients. IFN-III expressions were comparable in each group of subjects. This preserved induction of IFN-λs could contribute to the better control of the infection in children as compared to adults, in whom IFN-III deficiency has been reported. The upregulation of IFN-I, IFN-II, TRIM28, SETDB1, and HERVs in children with mild symptoms, their declines in severe cases or with MIS-C, and the positive correlations of their transcription in SARS-CoV-2-infected children suggest that they may play important roles in conditioning the evolution of the infection.
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Affiliation(s)
- Pier-Angelo Tovo
- Department of Pediatric Sciences and Public Health, University of Turin, Piazza Polonia 94, 10126 Turin, Italy; (G.P.); (C.C.); (C.A.); (M.D.); (F.L.); (U.R.); (I.G.)
| | - Silvia Garazzino
- Infectious Diseases Unit, Department of Pediatrics, Regina Margherita Children’s Hospital, Piazza Polonia 94, 10126 Turin, Italy; (S.G.); (F.M.); (C.S.); (M.Z.)
| | - Valentina Daprà
- Pediatric Laboratory, Department of Pediatric Sciences and Public Health, University of Turin, 10126 Turin, Italy;
| | - Giulia Pruccoli
- Department of Pediatric Sciences and Public Health, University of Turin, Piazza Polonia 94, 10126 Turin, Italy; (G.P.); (C.C.); (C.A.); (M.D.); (F.L.); (U.R.); (I.G.)
| | - Cristina Calvi
- Department of Pediatric Sciences and Public Health, University of Turin, Piazza Polonia 94, 10126 Turin, Italy; (G.P.); (C.C.); (C.A.); (M.D.); (F.L.); (U.R.); (I.G.)
- Pediatric Laboratory, Department of Pediatric Sciences and Public Health, University of Turin, 10126 Turin, Italy;
| | - Federica Mignone
- Infectious Diseases Unit, Department of Pediatrics, Regina Margherita Children’s Hospital, Piazza Polonia 94, 10126 Turin, Italy; (S.G.); (F.M.); (C.S.); (M.Z.)
| | - Carla Alliaudi
- Department of Pediatric Sciences and Public Health, University of Turin, Piazza Polonia 94, 10126 Turin, Italy; (G.P.); (C.C.); (C.A.); (M.D.); (F.L.); (U.R.); (I.G.)
- Pediatric Laboratory, Department of Pediatric Sciences and Public Health, University of Turin, 10126 Turin, Italy;
| | - Marco Denina
- Department of Pediatric Sciences and Public Health, University of Turin, Piazza Polonia 94, 10126 Turin, Italy; (G.P.); (C.C.); (C.A.); (M.D.); (F.L.); (U.R.); (I.G.)
| | - Carlo Scolfaro
- Infectious Diseases Unit, Department of Pediatrics, Regina Margherita Children’s Hospital, Piazza Polonia 94, 10126 Turin, Italy; (S.G.); (F.M.); (C.S.); (M.Z.)
| | - Marisa Zoppo
- Infectious Diseases Unit, Department of Pediatrics, Regina Margherita Children’s Hospital, Piazza Polonia 94, 10126 Turin, Italy; (S.G.); (F.M.); (C.S.); (M.Z.)
| | - Francesco Licciardi
- Department of Pediatric Sciences and Public Health, University of Turin, Piazza Polonia 94, 10126 Turin, Italy; (G.P.); (C.C.); (C.A.); (M.D.); (F.L.); (U.R.); (I.G.)
| | - Ugo Ramenghi
- Department of Pediatric Sciences and Public Health, University of Turin, Piazza Polonia 94, 10126 Turin, Italy; (G.P.); (C.C.); (C.A.); (M.D.); (F.L.); (U.R.); (I.G.)
| | - Ilaria Galliano
- Department of Pediatric Sciences and Public Health, University of Turin, Piazza Polonia 94, 10126 Turin, Italy; (G.P.); (C.C.); (C.A.); (M.D.); (F.L.); (U.R.); (I.G.)
- Pediatric Laboratory, Department of Pediatric Sciences and Public Health, University of Turin, 10126 Turin, Italy;
| | - Massimiliano Bergallo
- Department of Pediatric Sciences and Public Health, University of Turin, Piazza Polonia 94, 10126 Turin, Italy; (G.P.); (C.C.); (C.A.); (M.D.); (F.L.); (U.R.); (I.G.)
- Pediatric Laboratory, Department of Pediatric Sciences and Public Health, University of Turin, 10126 Turin, Italy;
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Ye Q, Mohamed R, Dakhlallah D, Gencheva M, Hu G, Pearce MC, Kolluri SK, Marsh CB, Eubank TD, Ivanov AV, Guo NL. Molecular Analysis of ZNF71 KRAB in Non-Small-Cell Lung Cancer. Int J Mol Sci 2021; 22:3752. [PMID: 33916522 PMCID: PMC8038441 DOI: 10.3390/ijms22073752] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 02/07/2023] Open
Abstract
Our previous study found that zinc finger protein 71 (ZNF71) mRNA expression was associated with chemosensitivity and its protein expression was prognostic of non-small-cell lung cancer (NSCLC). The Krüppel associated box (KRAB) transcriptional repression domain is commonly present in human zinc finger proteins, which are linked to imprinting, silencing of repetitive elements, proliferation, apoptosis, and cancer. This study revealed that ZNF71 KRAB had a significantly higher expression than the ZNF71 KRAB-less isoform in NSCLC tumors (n = 197) and cell lines (n = 117). Patients with higher ZNF71 KRAB expression had a significantly worse survival outcome than patients with lower ZNF71 KRAB expression (log-rank p = 0.04; hazard ratio (HR): 1.686 [1.026, 2.771]), whereas ZNF71 overall and KRAB-less expression levels were not prognostic in the same patient cohort. ZNF71 KRAB expression was associated with epithelial-to-mesenchymal transition (EMT) in both patient tumors and cell lines. ZNF71 KRAB was overexpressed in NSCLC cell lines resistant to docetaxel and paclitaxel treatment compared to chemo-sensitive cell lines, consistent with its association with poor prognosis in patients. Therefore, ZNF71 KRAB isoform is a more effective prognostic factor than ZNF71 overall and KRAB-less expression for NSCLC. Functional analysis using CRISPR-Cas9 and RNA interference (RNAi) screening data indicated that a knockdown/knockout of ZNF71 did not significantly affect NSCLC cell proliferation in vitro.
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Affiliation(s)
- Qing Ye
- WVU Cancer Institute, West Virginia University, Morgantown, WV 26506, USA; (Q.Y.); (R.M.); (D.D.); (G.H.); (T.D.E.); (A.V.I.)
- Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV 26506, USA
| | - Rehab Mohamed
- WVU Cancer Institute, West Virginia University, Morgantown, WV 26506, USA; (Q.Y.); (R.M.); (D.D.); (G.H.); (T.D.E.); (A.V.I.)
| | - Duaa Dakhlallah
- WVU Cancer Institute, West Virginia University, Morgantown, WV 26506, USA; (Q.Y.); (R.M.); (D.D.); (G.H.); (T.D.E.); (A.V.I.)
- Department of Microbiology, Immunology & Cell Biology, West Virginia University, Morgantown, WV 26506, USA;
- Institute of Global Health and Human Ecology, School of Sciences & Engineering, The American University of Cairo, New Cairo 11835, Egypt
| | - Marieta Gencheva
- Department of Microbiology, Immunology & Cell Biology, West Virginia University, Morgantown, WV 26506, USA;
| | - Gangqing Hu
- WVU Cancer Institute, West Virginia University, Morgantown, WV 26506, USA; (Q.Y.); (R.M.); (D.D.); (G.H.); (T.D.E.); (A.V.I.)
- Department of Microbiology, Immunology & Cell Biology, West Virginia University, Morgantown, WV 26506, USA;
| | - Martin C. Pearce
- Cancer Research Laboratory, Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA; (M.C.P.); (S.K.K.)
| | - Siva Kumar Kolluri
- Cancer Research Laboratory, Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA; (M.C.P.); (S.K.K.)
| | - Clay B. Marsh
- Department of Medicine, West Virginia University, Morgantown, WV 26506, USA;
| | - Timothy D. Eubank
- WVU Cancer Institute, West Virginia University, Morgantown, WV 26506, USA; (Q.Y.); (R.M.); (D.D.); (G.H.); (T.D.E.); (A.V.I.)
- Department of Microbiology, Immunology & Cell Biology, West Virginia University, Morgantown, WV 26506, USA;
| | - Alexey V. Ivanov
- WVU Cancer Institute, West Virginia University, Morgantown, WV 26506, USA; (Q.Y.); (R.M.); (D.D.); (G.H.); (T.D.E.); (A.V.I.)
- Department of Biochemistry, West Virginia University, Morgantown, WV 26506, USA
| | - Nancy Lan Guo
- WVU Cancer Institute, West Virginia University, Morgantown, WV 26506, USA; (Q.Y.); (R.M.); (D.D.); (G.H.); (T.D.E.); (A.V.I.)
- Department of Occupational and Environmental Health Sciences, West Virginia University, Morgantown, WV 26506, USA
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