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Fudulu A, Diaconu CC, Iancu IV, Plesa A, Albulescu A, Bostan M, Socolov DG, Stoian IL, Balan R, Anton G, Botezatu A. Exploring the Role of E6 and E7 Oncoproteins in Cervical Oncogenesis through MBD2/3-NuRD Complex Chromatin Remodeling. Genes (Basel) 2024; 15:560. [PMID: 38790189 PMCID: PMC11121560 DOI: 10.3390/genes15050560] [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: 03/21/2024] [Revised: 04/18/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND Cervical cancer is among the highest-ranking types of cancer worldwide, with human papillomavirus (HPV) as the agent driving the malignant process. One aspect of the infection's evolution is given by epigenetic modifications, mainly DNA methylation and chromatin alteration. These processes are guided by several chromatin remodeling complexes, including NuRD. The purpose of this study was to evaluate the genome-wide binding patterns of the NuRD complex components (MBD2 and MBD3) in the presence of active HPV16 E6 and E7 oncogenes and to determine the potential of identified genes through an experimental model to differentiate between cervical precursor lesions, with the aim of establishing their utility as biomarkers. METHODS The experimental model was built using the CaSki cell line and shRNA for E6 and E7 HPV16 silencing, ChIP-seq, qRT-PCR, and Western blot analyses. Selected genes' expression was also assessed in patients. RESULTS Several genes have been identified to exhibit altered transcriptional activity due to the influence of HPV16 E6/E7 viral oncogenes acting through the MBD2/MBD3 NuRD complex, linking them to viral infection and cervical oncogenesis. CONCLUSIONS The impacted genes primarily play roles in governing gene transcription, mRNA processing, and regulation of translation. Understanding these mechanisms offers valuable insights into the process of HPV-induced oncogenesis.
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Affiliation(s)
- Alina Fudulu
- Stefan S. Nicolau Institute of Virology, Romanian Academy, 030304 Bucharest, Romania; (A.F.); (I.V.I.); (A.P.); (A.A.); (M.B.); (G.A.); (A.B.)
| | - Carmen Cristina Diaconu
- Stefan S. Nicolau Institute of Virology, Romanian Academy, 030304 Bucharest, Romania; (A.F.); (I.V.I.); (A.P.); (A.A.); (M.B.); (G.A.); (A.B.)
| | - Iulia Virginia Iancu
- Stefan S. Nicolau Institute of Virology, Romanian Academy, 030304 Bucharest, Romania; (A.F.); (I.V.I.); (A.P.); (A.A.); (M.B.); (G.A.); (A.B.)
| | - Adriana Plesa
- Stefan S. Nicolau Institute of Virology, Romanian Academy, 030304 Bucharest, Romania; (A.F.); (I.V.I.); (A.P.); (A.A.); (M.B.); (G.A.); (A.B.)
| | - Adrian Albulescu
- Stefan S. Nicolau Institute of Virology, Romanian Academy, 030304 Bucharest, Romania; (A.F.); (I.V.I.); (A.P.); (A.A.); (M.B.); (G.A.); (A.B.)
- Pharmacology Department, National Institute for Chemical Pharmaceutical Research and Development, 031299 Bucharest, Romania
| | - Marinela Bostan
- Stefan S. Nicolau Institute of Virology, Romanian Academy, 030304 Bucharest, Romania; (A.F.); (I.V.I.); (A.P.); (A.A.); (M.B.); (G.A.); (A.B.)
| | - Demetra Gabriela Socolov
- Department of Obstetrics and Gynecology, Grigore T. Popa University of Medicine and Pharmacy, 700115 Iasi, Romania; (D.G.S.); (I.L.S.); (R.B.)
| | - Irina Liviana Stoian
- Department of Obstetrics and Gynecology, Grigore T. Popa University of Medicine and Pharmacy, 700115 Iasi, Romania; (D.G.S.); (I.L.S.); (R.B.)
| | - Raluca Balan
- Department of Obstetrics and Gynecology, Grigore T. Popa University of Medicine and Pharmacy, 700115 Iasi, Romania; (D.G.S.); (I.L.S.); (R.B.)
| | - Gabriela Anton
- Stefan S. Nicolau Institute of Virology, Romanian Academy, 030304 Bucharest, Romania; (A.F.); (I.V.I.); (A.P.); (A.A.); (M.B.); (G.A.); (A.B.)
| | - Anca Botezatu
- Stefan S. Nicolau Institute of Virology, Romanian Academy, 030304 Bucharest, Romania; (A.F.); (I.V.I.); (A.P.); (A.A.); (M.B.); (G.A.); (A.B.)
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Gudmundsson S, Carlston CM, O'Donnell-Luria A. Interpreting variants in genes affected by clonal hematopoiesis in population data. Hum Genet 2024; 143:545-549. [PMID: 36739343 PMCID: PMC10400727 DOI: 10.1007/s00439-023-02526-4] [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: 08/29/2022] [Accepted: 01/18/2023] [Indexed: 02/05/2023]
Abstract
Reference population databases like the Genome Aggregation Database (gnomAD) have improved our ability to interpret the human genome. Variant frequencies and frequency-derived tools (such as depletion scores) have become fundamental to variant interpretation and the assessment of variant-gene-disease relationships. Clonal hematopoiesis (CH) obstructs variant interpretation as somatic variants that provide proliferative advantage will affect variant frequencies, depletion scores, and downstream filtering. Further, default filtering of variants or genes associated with CH risks filtering bona fide germline variants as variants associated with CH can also cause Mendelian conditions. Here, we provide our insights on interpreting population variant data in genes affected by clonal hematopoiesis, as well as recommendations for careful review of 36 established CH genes associated with neurodevelopmental conditions.
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Affiliation(s)
- Sanna Gudmundsson
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Colleen M Carlston
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Center for Genomic Medicine, Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Anne O'Donnell-Luria
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Genomic Medicine, Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
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Li J, Xi J. Exploring Immune-Related Gene Profiling and Infiltration of Immune Cells in Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma. Genes (Basel) 2024; 15:121. [PMID: 38275602 PMCID: PMC10815177 DOI: 10.3390/genes15010121] [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: 12/07/2023] [Revised: 01/08/2024] [Accepted: 01/12/2024] [Indexed: 01/27/2024] Open
Abstract
Cervical cancer is a widespread malignancy among women, leading to a substantial global health impact. Despite extensive research, our understanding of the basic molecules and pathogenic processes of cervical squamous cell carcinoma is still insufficient. This investigation aims to uncover immune-related genes linked to CESC and delineate their functions. Leveraging data from the GEO and ImmPort databases, a total of 22 immune-related genes were identified. Multiple tools, including DAVID, the human protein atlas, STRING, GeneMANIA, and TCGA, were employed to delve into the expression and roles of these immune genes in CESC, alongside their connections to the disease's pathological features. Through RT-PCR, the study confirmed notable disparities in CXCL8 and CXCL10 mRNA expression between CESC and normal cervical tissue. The TCGA dataset's immune-related information reinforced the association of CXCL8 and CXCL10 with immune infiltration in CESC. This research sheds light on the potential of CXCL8 and CXCL10 as promising therapeutic targets and essential prognostic factors for individuals diagnosed with CESC.
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Affiliation(s)
- Jialu Li
- School of Medicine, Institute of Translational Medicine, Yangzhou University, Yangzhou 225012, China;
| | - Juqun Xi
- School of Medicine, Institute of Translational Medicine, Yangzhou University, Yangzhou 225012, China;
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou 225009, China
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Liu H, Ma H, Li Y, Zhao H. Advances in epigenetic modifications and cervical cancer research. Biochim Biophys Acta Rev Cancer 2023; 1878:188894. [PMID: 37011697 DOI: 10.1016/j.bbcan.2023.188894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/19/2023] [Accepted: 03/31/2023] [Indexed: 04/03/2023]
Abstract
Cervical cancer (CC) is an important public health problem for women, and perspectives and information regarding its prevention and treatment are quickly evolving. Human papilloma virus (HPV) has been recognized as a major contributor to CC development; however, HPV infection is not the only cause of CC. Epigenetics refers to changes in gene expression levels caused by non-gene sequence changes. Growing evidence suggests that the disruption of gene expression patterns which were governed by epigenetic modifications can result in cancer, autoimmune diseases, and various other maladies. This article mainly reviews the current research status of epigenetic modifications in CC based on four aspects, respectively DNA methylation, histone modification, noncoding RNA regulation and chromatin regulation, and we also discuss their functions and molecular mechanisms in the occurrence and progression of CC. This review provides new ideas for early screening, risk assessment, molecular targeted therapy and prognostic prediction of CC.
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Feng D, Li W, Wu W, Kahlert UD, Gao P, Hu G, Huang X, Shi W, Li H. Chromatin Regulator-Related Gene Signature for Predicting Prognosis and Immunotherapy Efficacy in Breast Cancer. JOURNAL OF ONCOLOGY 2023; 2023:2736932. [PMID: 36755810 PMCID: PMC9902130 DOI: 10.1155/2023/2736932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 10/22/2022] [Accepted: 11/24/2022] [Indexed: 02/01/2023]
Abstract
BACKGROUND Many studies have found that chromatin regulators (CRs) are correlated with tumorigenesis and disease prognosis. Here, we attempted to build a new CR-related gene model to predict breast cancer (BC) survival status. METHODS First, the CR-related differentially expressed genes (DEGs) were screened in normal and tumor breast tissues, and the potential mechanism of CR-related DEGs was determined by function analysis. Based on the prognostic DEGs, the Cox regression model was applied to build a signature for BC. Then, survival and receiver operating characteristic (ROC) curves were performed to validate the signature's efficacy and identify its independent prognostic value. The CIBERSORT and tumor immune dysfunction and exclusion (TIDE) algorithms were used to assess the immune cells infiltration and immunotherapy efficacy for this signature, respectively. Additionally, a novel nomogram was also built for clinical decisions. RESULTS We identified 98 CR-related DEGs in breast tissues and constructed a novel 6 CR-related gene signature (ARID5A, ASCL1, IKZF3, KDM4B, PRDM11, and TFF1) to predict the outcome of BC patients. The prognostic value of this CR-related gene signature was validated with outstanding predictive performance. The TIDE analysis revealed that the high-risk group patients had a better response to immune checkpoint blockade (ICB) therapy. CONCLUSION A new CR-related gene signature was built, and this signature could provide the independent predictive capability of prognosis and immunotherapy efficacy for BC patients.
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Affiliation(s)
- Dongxu Feng
- Department of General Surgery, Chongming Hospital Affiliated to Shanghai University of Medicine and Health Sciences, Chongming District, Shanghai 202150, China
| | - Wenbing Li
- Department of General Surgery, Chongming Hospital Affiliated to Shanghai University of Medicine and Health Sciences, Chongming District, Shanghai 202150, China
| | - Wei Wu
- Department of General Surgery, Chongming Hospital Affiliated to Shanghai University of Medicine and Health Sciences, Chongming District, Shanghai 202150, China
| | - Ulf Dietrich Kahlert
- University Clinic for General, Visceral, Vascular-and Transplantation Surgery, Faculty of Medicine, Otto-von-Guericke-University, Magdeburg 39120, Germany
| | - Pingfa Gao
- Department of General Surgery, Chongming Hospital Affiliated to Shanghai University of Medicine and Health Sciences, Chongming District, Shanghai 202150, China
| | - Gangfeng Hu
- Department of General Surgery, Chongming Hospital Affiliated to Shanghai University of Medicine and Health Sciences, Chongming District, Shanghai 202150, China
| | - Xia Huang
- Department of General Surgery, Chongming Hospital Affiliated to Shanghai University of Medicine and Health Sciences, Chongming District, Shanghai 202150, China
| | - Wenjie Shi
- University Clinic for General, Visceral, Vascular-and Transplantation Surgery, Faculty of Medicine, Otto-von-Guericke-University, Magdeburg 39120, Germany
- University Hospital for Gynaecology, Pius-Hospital, University Medicine Oldenburg, Oldenburg 26121, Germany
| | - Huichao Li
- Department of Thyroid Surgery, The Affiliated Hospital of Qingdao University, Qingdao 266555, Shandong, China
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