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Vitale DL, Parnigoni A, Viola M, Karousou E, Sevic I, Moretto P, Passi A, Alaniz L, Vigetti D. Deciphering Drug Resistance: Investigating the Emerging Role of Hyaluronan Metabolism and Signaling and Tumor Extracellular Matrix in Cancer Chemotherapy. Int J Mol Sci 2024; 25:7607. [PMID: 39062846 PMCID: PMC11276752 DOI: 10.3390/ijms25147607] [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: 06/07/2024] [Revised: 07/04/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
Hyaluronan (HA) has gained significant attention in cancer research for its role in modulating chemoresistance. This review aims to elucidate the mechanisms by which HA contributes to chemoresistance, focusing on its interactions within the tumor microenvironment. HA is abundantly present in the extracellular matrix (ECM) and binds to cell-surface receptors such as CD44 and RHAMM. These interactions activate various signaling pathways, including PI3K/Akt, MAPK, and NF-κB, which are implicated in cell survival, proliferation, and drug resistance. HA also influences the physical properties of the tumor stroma, enhancing its density and reducing drug penetration. Additionally, HA-mediated signaling contributes to the epithelial-mesenchymal transition (EMT), a process associated with increased metastatic potential and resistance to apoptosis. Emerging therapeutic strategies aim to counteract HA-induced chemoresistance by targeting HA synthesis, degradation, metabolism, or its binding to CD44. This review underscores the complexity of HA's role in chemoresistance and highlights the potential for HA-targeted therapies to improve the efficacy of conventional chemotherapeutics.
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Affiliation(s)
- Daiana L. Vitale
- Laboratorio de Microambiente Tumoral, Centro de Investigaciones Básicas y Aplicadas (CIBA), Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Junín B6000, Argentina; (D.L.V.); (I.S.); (L.A.)
- Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires (CITNOBA), UNNOBA-UNSAdA-CONICET, Junín 6000, Argentina
| | - Arianna Parnigoni
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden;
| | - Manuela Viola
- Dipartimento di Medicina e Chirurgia, Universitá degli Studi dell’Insubria, 21100 Varese, Italy; (M.V.); (E.K.); (P.M.); (A.P.)
| | - Evgenia Karousou
- Dipartimento di Medicina e Chirurgia, Universitá degli Studi dell’Insubria, 21100 Varese, Italy; (M.V.); (E.K.); (P.M.); (A.P.)
| | - Ina Sevic
- Laboratorio de Microambiente Tumoral, Centro de Investigaciones Básicas y Aplicadas (CIBA), Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Junín B6000, Argentina; (D.L.V.); (I.S.); (L.A.)
- Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires (CITNOBA), UNNOBA-UNSAdA-CONICET, Junín 6000, Argentina
| | - Paola Moretto
- Dipartimento di Medicina e Chirurgia, Universitá degli Studi dell’Insubria, 21100 Varese, Italy; (M.V.); (E.K.); (P.M.); (A.P.)
| | - Alberto Passi
- Dipartimento di Medicina e Chirurgia, Universitá degli Studi dell’Insubria, 21100 Varese, Italy; (M.V.); (E.K.); (P.M.); (A.P.)
| | - Laura Alaniz
- Laboratorio de Microambiente Tumoral, Centro de Investigaciones Básicas y Aplicadas (CIBA), Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Junín B6000, Argentina; (D.L.V.); (I.S.); (L.A.)
- Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires (CITNOBA), UNNOBA-UNSAdA-CONICET, Junín 6000, Argentina
| | - Davide Vigetti
- Dipartimento di Medicina e Chirurgia, Universitá degli Studi dell’Insubria, 21100 Varese, Italy; (M.V.); (E.K.); (P.M.); (A.P.)
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2
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Kosinski J, Sechi A, Hain J, Villwock S, Ha SA, Hauschulz M, Rose M, Steib F, Ortiz‐Brüchle N, Heij L, Maas SL, van der Vorst EPC, Knoesel T, Altendorf‐Hofmann A, Simon R, Sauter G, Bednarsch J, Jonigk D, Dahl E. ITIH5 as a multifaceted player in pancreatic cancer suppression, impairing tyrosine kinase signaling, cell adhesion and migration. Mol Oncol 2024; 18:1486-1509. [PMID: 38375974 PMCID: PMC11161730 DOI: 10.1002/1878-0261.13609] [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: 08/16/2023] [Revised: 01/19/2024] [Accepted: 02/06/2024] [Indexed: 02/21/2024] Open
Abstract
Inter-alpha-trypsin inhibitor heavy chain 5 (ITIH5) has been identified as a metastasis suppressor gene in pancreatic cancer. Here, we analyzed ITIH5 promoter methylation and protein expression in The Cancer Genome Atlas (TCGA) dataset and three tissue microarray cohorts (n = 618), respectively. Cellular effects, including cell migration, focal adhesion formation and protein tyrosine kinase activity, induced by forced ITIH5 expression in pancreatic cancer cell lines were studied in stable transfectants. ITIH5 promoter hypermethylation was associated with unfavorable prognosis, while immunohistochemistry demonstrated loss of ITIH5 in the metastatic setting and worsened overall survival. Gain-of-function models showed a significant reduction in migration capacity, but no alteration in proliferation. Focal adhesions in cells re-expressing ITIH5 exhibited a smaller and more rounded phenotype, typical for slow-moving cells. An impressive increase of acetylated alpha-tubulin was observed in ITIH5-positive cells, indicating more stable microtubules. In addition, we found significantly decreased activities of kinases related to focal adhesion. Our results indicate that loss of ITIH5 in pancreatic cancer profoundly affects its molecular profile: ITIH5 potentially interferes with a variety of oncogenic signaling pathways, including the PI3K/AKT pathway. This may lead to altered cell migration and focal adhesion formation. These cellular alterations may contribute to the metastasis-inhibiting properties of ITIH5 in pancreatic cancer.
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Affiliation(s)
- Jennifer Kosinski
- Institute of PathologyMedical Faculty of RWTH Aachen UniversityGermany
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD)Germany
| | - Antonio Sechi
- Department of Cell and Tumor BiologyRWTH Aachen UniversityGermany
| | - Johanna Hain
- Institute of PathologyMedical Faculty of RWTH Aachen UniversityGermany
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD)Germany
| | - Sophia Villwock
- Institute of PathologyMedical Faculty of RWTH Aachen UniversityGermany
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD)Germany
| | - Stefanie Anh Ha
- Institute of PathologyMedical Faculty of RWTH Aachen UniversityGermany
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD)Germany
| | - Maximilian Hauschulz
- Institute of PathologyMedical Faculty of RWTH Aachen UniversityGermany
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD)Germany
| | - Michael Rose
- Institute of PathologyMedical Faculty of RWTH Aachen UniversityGermany
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD)Germany
| | - Florian Steib
- Institute of PathologyMedical Faculty of RWTH Aachen UniversityGermany
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD)Germany
| | - Nadina Ortiz‐Brüchle
- Institute of PathologyMedical Faculty of RWTH Aachen UniversityGermany
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD)Germany
| | - Lara Heij
- Institute of PathologyUniversity Hospital EssenGermany
- Department of Surgery and Transplantation, Medical FacultyRWTH Aachen UniversityGermany
- Department of PathologyErasmus Medical Center RotterdamThe Netherlands
- NUTRIM School of Nutrition and Translational Research in MetabolismMaastricht UniversityThe Netherlands
| | - Sanne L. Maas
- Interdisciplinary Center for Clinical Research (IZKF), Institute for Molecular Cardiovascular Research (IMCAR)Medical Faculty of RWTH Aachen UniversityGermany
| | - Emiel P. C. van der Vorst
- Interdisciplinary Center for Clinical Research (IZKF), Institute for Molecular Cardiovascular Research (IMCAR)Medical Faculty of RWTH Aachen UniversityGermany
- Institute for Cardiovascular Prevention (IPEK)Ludwig‐Maximilians‐University MunichGermany
| | - Thomas Knoesel
- Institute of PathologyLudwig‐Maximilians‐University MunichGermany
| | | | - Ronald Simon
- Institute of PathologyUniversity Medical Center Hamburg‐EppendorfGermany
| | - Guido Sauter
- Institute of PathologyUniversity Medical Center Hamburg‐EppendorfGermany
| | - Jan Bednarsch
- Department of Surgery and Transplantation, Medical FacultyRWTH Aachen UniversityGermany
| | - Danny Jonigk
- Institute of PathologyMedical Faculty of RWTH Aachen UniversityGermany
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD)Germany
- RWTH centralized Biomaterial Bank (RWTH cBMB)Medical Faculty of the RWTH Aachen UniversityGermany
- German Center for Lung Research (DZL), BREATHHanoverGermany
| | - Edgar Dahl
- Institute of PathologyMedical Faculty of RWTH Aachen UniversityGermany
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD)Germany
- RWTH centralized Biomaterial Bank (RWTH cBMB)Medical Faculty of the RWTH Aachen UniversityGermany
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3
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Santarelli R, Evangelista L, Pompili C, Lo Presti S, Rossi A, Arena A, Gaeta A, Gonnella R, Gilardini Montani MS, Cirone M. EBV infection of primary colonic epithelial cells causes inflammation, DDR and autophagy dysregulation, effects that may predispose to IBD and carcinogenesis. Virus Res 2023; 338:199236. [PMID: 37797746 PMCID: PMC10582763 DOI: 10.1016/j.virusres.2023.199236] [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: 08/15/2023] [Revised: 09/29/2023] [Accepted: 10/02/2023] [Indexed: 10/07/2023]
Abstract
EBV is a gammaherpesvirus strongly associated to human cancer. The virus has been shown to play a role also in inflammatory diseases, including IBD, in the context of which colon cancer more frequently arise. In this study, we show for the first time that EBV infects primary colonic epithelial cells (HCoEpC), promotes pro-inflammatory cytokine secretion and activates molecular pathways bridging inflammation and cancer, such as ERK1/2. These effects, occurring in the course of the lytic phase of the viral life cycle, led to DDR and autophagy dysregulation. Such cellular responses, playing a key role in the maintenance of proteostasis and genome integrity, are essential to prevent carcinogenesis. Interestingly, we found that the use of the demethylating agent 5-AZA could counteract most of the effects induced by EBV infection in HCoEpC, suggesting that DNA hyper-methylation may strongly contribute to viral-driven inflammation and colon cancer predisposition.
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Affiliation(s)
- Roberta Santarelli
- Department of Experimental Medicine, "Sapienza" University of Rome, 00161 Rome, Italy
| | - Lorenzo Evangelista
- Department of Experimental Medicine, "Sapienza" University of Rome, 00161 Rome, Italy
| | - Chiara Pompili
- Department of Experimental Medicine, "Sapienza" University of Rome, 00161 Rome, Italy
| | - Salvatore Lo Presti
- Department of Experimental Medicine, "Sapienza" University of Rome, 00161 Rome, Italy
| | - Alberto Rossi
- Department of Experimental Medicine, "Sapienza" University of Rome, 00161 Rome, Italy
| | - Andrea Arena
- Department of Experimental Medicine, "Sapienza" University of Rome, 00161 Rome, Italy
| | - Aurelia Gaeta
- Department of Molecular Medicine, "Sapienza" University of Rome, 00161 Rome, Italy
| | - Roberta Gonnella
- Department of Experimental Medicine, "Sapienza" University of Rome, 00161 Rome, Italy
| | | | - Mara Cirone
- Department of Experimental Medicine, "Sapienza" University of Rome, 00161 Rome, Italy.
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Tayanloo-Beik A, Hamidpour SK, Nikkhah A, Arjmand R, Mafi AR, Rezaei-Tavirani M, Larijani B, Gilany K, Arjmand B. DNA Damage Responses, the Trump Card of Stem Cells in the Survival Game. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023. [PMID: 37923882 DOI: 10.1007/5584_2023_791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2023]
Abstract
Stem cells, as a group of undifferentiated cells, are enriched with self-renewal and high proliferative capacity, which have attracted the attention of many researchers as a promising approach in the treatment of many diseases over the past years. However, from the cellular and molecular point of view, the DNA repair system is one of the biggest challenges in achieving therapeutic goals through stem cell technology. DNA repair mechanisms are an advantage for stem cells that are constantly multiplying to deal with various types of DNA damage. However, this mechanism can be considered a trump card in the game of cell survival and treatment resistance in cancer stem cells, which can hinder the curability of various types of cancer. Therefore, getting a deep insight into the DNA repair system can bring researchers one step closer to achieving major therapeutic goals. The remarkable thing about the DNA repair system is that this system is not only under the control of genetic factors, but also under the control of epigenetic factors. Therefore, it is necessary to investigate the role of the DNA repair system in maintaining the survival of cancer stem cells from both aspects.
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Affiliation(s)
- Akram Tayanloo-Beik
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Amirabbas Nikkhah
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Rasta Arjmand
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmad Rezazadeh Mafi
- Department of Radiation Oncology, Imam Hossein Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical sciences, Tehran, Iran
| | - Kambiz Gilany
- Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
- Reproductive Immunology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Babak Arjmand
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
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5
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An N, Yang X. Prediction of disease-free survival of N1/2 non-small cell lung cancer after adjuvant chemotherapy by the biomarker RPMB. Heliyon 2023; 9:e18266. [PMID: 37501955 PMCID: PMC10368914 DOI: 10.1016/j.heliyon.2023.e18266] [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: 05/10/2022] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 07/29/2023] Open
Abstract
No molecular biomarkers have been proven applicable in clinical practice to identify patients who can benefit from adjuvant chemotherapy in non-small cell lung cancer (NSCLC). In this study, we established a biomarker, RPMB, short for promotor methylation burden of DNA repair genes (DRGs), to identify the subgroup of patients who might benefit from adjuvant chemotherapy in NSCLC. Methylation profiles of 828 NSCLC primary tumors and their clinical information were downloaded from The Cancer Genome Atlas (TCGA) database. The RPMB for each patient after radical resection was calculated and its correlation with the prognosis of NSCLC was extensively investigated. DRGs of NSCLC were much more hypomethylated than the other genes (all p<0.001). RPMB was defined as the ratio of methylated DRGs to the total number of all the DRGs. Patients with higher RPMB values tended to be nonsmokers, had adenocarcinoma, were female and had peripheral tumors. Subgroup analysis of forest plot among different clinical factors showed that high RPMB was significantly correlated to better disease-free survival (DFS) in pathologic N-positive patients after adjuvant chemotherapy (HR = 0.404, n = 62, p = 0.034). Notably, more superior DFS was exhibited in high RPMB NSCLCs with N1 nodal stage compared with those with low RPMB values (HR = 0.348, n = 47, p = 0.043). High RPMB might be used as a potential predictor to identify suitable N-positive NSCLC patients who can benefit from adjuvant chemotherapy after radical surgery.
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Affiliation(s)
- Ning An
- Department of Radiation Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, 266003, China
| | - Xue Yang
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, 266003, China
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6
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Sergeeva A, Davydova K, Perenkov A, Vedunova M. Mechanisms of human DNA methylation, alteration of methylation patterns in physiological processes and oncology. Gene 2023:147487. [PMID: 37211289 DOI: 10.1016/j.gene.2023.147487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/05/2023] [Accepted: 05/11/2023] [Indexed: 05/23/2023]
Abstract
DNA methylation is one of the epigenetic modifications of the genome, the essence of which is the attachment of a methyl group to nitrogenous bases. In the eukaryote genome, cytosine is methylated in the vast majority of cases. About 98% of cytosines are methylated as part of CpG dinucleotides. They, in turn, form CpG islands, which are clusters of these dinucleotides. Islands located in the regulatory elements of genes are in particular interest. They are assumed to play an important role in the regulation of gene expression in humans. Besides that, cytosine methylation serves the functions of genomic imprinting, transposon suppression, epigenetic memory maintenance, X- chromosome inactivation, and embryonic development. Of particular interest are the enzymatic processes of methylation and demethylation. The methylation process always depends on the work of enzymatic complexes and is very precisely regulated. The methylation process largely depends on the functioning of three groups of enzymes: writers, readers and erasers. Writers include proteins of the DNMT family, readers are proteins containing the MBD, BTB/POZ or SET- and RING-associated domains and erasers are proteins of the TET family. Whereas demethylation can be performed not only by enzymatic complexes, but also passively during DNA replication. Hence, the maintenance of DNA methylation is important. Changes in methylation patterns are observed during embryonic development, aging, and cancers. In both aging and cancer, massive hypomethylation of the genome with local hypermethylation is observed. In this review, we will review the current understanding of the mechanisms of DNA methylation and demethylation in humans, the structure and distribution of CpG islands, the role of methylation in the regulation of gene expression, embryogenesis, aging, and cancer development.
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Affiliation(s)
- A Sergeeva
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, 603022, Russia
| | - K Davydova
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, 603022, Russia
| | - A Perenkov
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, 603022, Russia
| | - M Vedunova
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, 603022, Russia
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7
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Seborova K, Hlavac V, Holy P, Bjørklund SS, Fleischer T, Rob L, Hruda M, Bouda J, Mrhalova M, Allah MMKAO, Vodicka P, Fiala O, Soucek P, Kristensen VN, Vodickova L, Vaclavikova R. Complex molecular profile of DNA repair genes in epithelial ovarian carcinoma patients with different sensitivity to platinum-based therapy. Front Oncol 2022; 12:1016958. [DOI: 10.3389/fonc.2022.1016958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/14/2022] [Indexed: 12/03/2022] Open
Abstract
Epithelial ovarian carcinoma (EOC) is known for high mortality due to diagnosis at advanced stages and frequent therapy resistance. Previous findings suggested that the DNA repair system is involved in the therapeutic response of cancer patients and DNA repair genes are promising targets for novel therapies. This study aimed to address complex inter-relations among gene expression levels, methylation profiles, and somatic mutations in DNA repair genes and EOC prognosis and therapy resistance status. We found significant associations of DUT expression with the presence of peritoneal metastases in EOC patients. The high-grade serous EOC subtype was enriched with TP53 mutations compared to other subtypes. Furthermore, somatic mutations in XPC and PRKDC were significantly associated with worse overall survival of EOC patients, and higher FAAP20 expression in platinum-resistant than platinum-sensitive patients was observed. We found higher methylation of RAD50 in platinum-resistant than in platinum-sensitive patients. Somatic mutations in BRCA1 and RAD9A were significantly associated with higher RBBP8 methylation in platinum-sensitive compared to platinum-resistant EOC patients. In conclusion, we discovered associations of several candidate genes from the DNA repair pathway with the prognosis and platinum resistance status of EOC patients, which deserve further validation as potential predictive biomarkers.
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Mohanad M, Yousef HF, Bahnassy AA. Epigenetic inactivation of DNA repair genes as promising prognostic and predictive biomarkers in urothelial bladder carcinoma patients. Mol Genet Genomics 2022; 297:1671-1687. [PMID: 36076047 PMCID: PMC9596572 DOI: 10.1007/s00438-022-01950-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/27/2022] [Indexed: 11/29/2022]
Abstract
We sought to examine epigenetic inactivation of DNA damage repair (DDR) genes as prognostic and predictive biomarkers for urothelial bladder cancer (UBC) as there are currently no reliable prognostic biomarkers that identify UBC patients who would benefit from chemotherapy. Genome-wide DNA methylome using the cancer genome atlas-bladder cancer (TCGA-BLCA) datasets (primary tumors = 374 and normal tissues = 37) was performed for 154 DDR genes. The most two significant differentially methylated genes, Retinoblastoma binding protein 8 (RBBP8) and MutS homologue 4 (MSH4), between primary tumors and normal tissues of TCGA–BLCA were validated by methylation-specific PCR (MSP) in UBC (n = 70) compared to normal tissues (n = 30). RBBP8 and MSH4 expression was measured using qRT-PCR. We developed a predictive model for therapeutic response based on the RBBP8- and MSH4-methylation along with patients’ clinical features. Then, we assessed the prognostic significance of RBBP8 and MSH4. RBBP8- and MSH4 methylation and corresponding gene downregulation significantly associated with muscle-invasive phenotype, prolonged progression-free survival (PFS) and increased susceptibility to cisplatin chemotherapy in UBC. Promoter methylation of RBBP8 and MSH4 was positively correlated with each other and with their corresponding gene repression. The best machine-learning classification model predicted UBC patients’ response to cisplatin-based chemotherapy with an accuracy of 90.05 ± 4.5%. Epigenetic inactivation of RBBP8 and MSH4 in UBC could sensitize patients to DNA-damaging agents. A predictive machine-learning modeling approach based on the clinical features along with RBBP8- and MSH4-methylation might be a promising tool for stratification of UBC responders from nonresponders to chemotherapy.
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Affiliation(s)
- Marwa Mohanad
- Biochemistry Department, College of Pharmaceutical Sciences and Drug Manufacturing, Misr University for Science and Technology, 6th of October, Giza, Egypt.
| | - Hend F Yousef
- Tissue Culture and Cytogenetics Unit, Pathology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Abeer A Bahnassy
- Tissue Culture and Cytogenetics Unit, Pathology Department, National Cancer Institute, Cairo University, Cairo, Egypt
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9
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Chughtai AA, Pannhausen J, Dinger P, Wirtz J, Knüchel R, Gaisa NT, Eble MJ, Rose M. Effective Radiosensitization of Bladder Cancer Cells by Pharmacological Inhibition of DNA-PK and ATR. Biomedicines 2022; 10:biomedicines10061277. [PMID: 35740300 PMCID: PMC9220184 DOI: 10.3390/biomedicines10061277] [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: 04/21/2022] [Revised: 05/24/2022] [Accepted: 05/27/2022] [Indexed: 12/09/2022] Open
Abstract
This study aims at analyzing the impact of the pharmacological inhibition of DNA damage response (DDR) targets (DNA-PK and ATR) on radiosensitization of bladder cancer cell lines of different molecular/histological subtypes. Applying DNA-PK (AZD7648) and ATR (Ceralasertib) inhibitors on SCaBER, J82 and VMCUB-1 bladder cancer cell lines, we revealed sensitization upon ionizing radiation (IR), i.e., the IC50 for each drug shifted to a lower drug concentration with increased IR doses. In line with this, drug exposure retarded DNA repair after IR-induced DNA damage visualized by a neutral comet assay. Western blot analyses confirmed specific inhibition of targeted DDR pathways in the analyzed bladder cancer cell lines, i.e., drugs blocked DNA-PK phosphorylation at Ser2056 and the ATR downstream mediator CHK1 at Ser317. Interestingly, clonogenic survival assays indicated a cell-line-dependent synergism of combined DDR inhibition upon IR. Calculating combined index (CI) values, with and without IR, according to the Chou–Talalay method, confirmed drug- and IR-dose-specific synergistic CI values. Thus, we provide functional evidence that DNA-PK and ATR inhibitors specifically target corresponding DDR pathways retarding the DNA repair process at nano-molar concentrations. This, in turn, leads to a strong radiosensitizing effect and impairs the survival of bladder cancer cells.
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Affiliation(s)
- Ahmed Ali Chughtai
- Department of Radiation Oncology, RWTH Aachen University, 52074 Aachen, Germany;
- Correspondence: (A.A.C.); (M.R.); Tel.: +49-241-8036863 (A.A.C.); +49-241-8089715 (M.R.); Fax: +49-241-8082425 (A.A.C.); +49-241-8082439 (M.R.)
| | - Julia Pannhausen
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (J.P.); (P.D.); (J.W.); (R.K.); (N.T.G.)
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), 52074 Aachen, Germany
| | - Pia Dinger
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (J.P.); (P.D.); (J.W.); (R.K.); (N.T.G.)
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), 52074 Aachen, Germany
| | - Julia Wirtz
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (J.P.); (P.D.); (J.W.); (R.K.); (N.T.G.)
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), 52074 Aachen, Germany
| | - Ruth Knüchel
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (J.P.); (P.D.); (J.W.); (R.K.); (N.T.G.)
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), 52074 Aachen, Germany
| | - Nadine T. Gaisa
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (J.P.); (P.D.); (J.W.); (R.K.); (N.T.G.)
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), 52074 Aachen, Germany
| | - Michael J. Eble
- Department of Radiation Oncology, RWTH Aachen University, 52074 Aachen, Germany;
| | - Michael Rose
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (J.P.); (P.D.); (J.W.); (R.K.); (N.T.G.)
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), 52074 Aachen, Germany
- Correspondence: (A.A.C.); (M.R.); Tel.: +49-241-8036863 (A.A.C.); +49-241-8089715 (M.R.); Fax: +49-241-8082425 (A.A.C.); +49-241-8082439 (M.R.)
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10
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Wang J, Sheng Z, Dong Z, Wu Q, Cai Y. The mechanism of radiotherapy for lung adenocarcinoma in promoting protein SIRT6-mediated deacetylation of RBBP8 to enhance the sensitivity of targeted therapy. Int J Immunopathol Pharmacol 2022; 36:3946320221130727. [PMID: 36172813 PMCID: PMC9523831 DOI: 10.1177/03946320221130727] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Background Lung cancer has the fastest increase in morbidity and mortality, and is one of the most threatening malignant tumors to human health and life. Both radiotherapy and targeted therapy are typical treatments after lung cancer surgery. Radiotherapy is a means of locally killing cancer lesions, and it plays an important role in the entire management of lung cancer. Gefitinib is one of the most commonly used targeted therapy drugs in the treatment of lung cancer. The purpose of this project is to explore the mechanism by which deacetylation of RBBP8 mediated by radiotherapy-promoting protein SIRT6 in lung adenocarcinoma enhances the sensitivity of targeted therapy. Methods In both the cell experiments and the animal experiments, the samples were divided into five groups: Model group, RT group, CT group, RT+CT group, and RT+CT+inhibitor group. The CCK8 method was used to detect the viability of each group of cells. The flow cytometry experiment was used to analyze the apoptotic characteristics of each group of cells. The scratch test was used to detect the migration ability of each group of cells. Transwell invasion test was used to determine the invasion ability of each group of cells. The lung tumor tissues of each group of mice were collected to analyze the tumor size, volume, and metastasis characteristics. The TUNEL experiment was used to detect the apoptosis characteristics of the cells in the lung cancer tissues of each group mice. Immunohistochemistry experiments were used to analyze the distribution and relative expression characteristics of protein SIRT6 in mouse lung cancer tissues. The colorimetric experiments were used to detect the activity of Caspase 3 and Caspase 8 in each group. Western blot method was used to detect the expression of SIRT6, RBBP8, and MYC in each group. Results In each experiment, the results of the experiment have mutually proven consistency, and there is no contradiction. In addition to the Model group, the other 4 groups used different treatment methods. The better the curative effect, the lower the cell viability of cancer cells and the higher the apoptotic ratio. This is reflected in the CCK8 test, flow cytometry analysis, cell scratch test, Transwell cell migration test, and TUNEL detection. At the same time, colorimetric detection and Western blot analysis also analyzed the levels of SIRT6, RBBP8 and other cancer-related proteins in each group at the molecular level, implying the importance of SIRT6 protein in the treatment process. Conclusion Our project has proved that radiotherapy can promote the protein SIRT6 to deacetylate RBBP8 proteins, and ultimately enhance targeted therapy drug sensitivity.
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Affiliation(s)
- Jiying Wang
- Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhaoying Sheng
- Department of Radiation Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhiyi Dong
- Department of Traditional Chinese Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qiongya Wu
- Department of Radiation Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yong Cai
- Department of Radiation Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
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11
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Priya R, Das B. Global DNA methylation profile at LINE-1 repeats and promoter methylation of genes involved in DNA damage response and repair pathways in human peripheral blood mononuclear cells in response to γ-radiation. Mol Cell Biochem 2021; 477:267-281. [PMID: 34708334 DOI: 10.1007/s11010-021-04265-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 09/17/2021] [Indexed: 02/02/2023]
Abstract
DNA methylation is an epigenetic mechanism, which plays an important role in gene regulation. The present study evaluated DNA methylation profile of LINE1 repeats and promoter methylation of DNA damage response (DDR) and DNA repair (DR) genes (PARP1, ATM, BRCA1, MLH1, XPC, RAD23B, APC, TNFα, DNMT3A, MRE11A, MGMT, CDKN2A, MTHFR) in human peripheral blood mononuclear cells (PBMCs) of healthy donors in response to γ-radiation. Methylation level was correlated with gene expression profile of selected DDR and DR genes (APC, MLH1, PARP1, MRE11A, TNFα, MGMT) to understand their role in gene regulation. Blood samples were collected from 15 random healthy donors, PBMCs were isolated, exposed to 0.1 Gy (low) and 2.0 Gy (high) doses of γ-radiation and proliferated for 48 h and 72 h. Genomic DNA and total RNA were isolated from irradiated PBMCs along with un-irradiated control. Methylation profile was determined from bisulphite converted DNA and amplified by methylation sensitive high resolution melting (MS-HRM) method. Total RNA was converted to cDNA and relative expression was analysed using real time quantitative-PCR. Our results revealed that at 0.1 Gy, MRE11A and TNFα showed significant (P < 0.05) increase in methylation at 72 h. At 2.0 Gy, significant increase (P < 0.05) in methylation profile was observed at LINE1, MRE11A, PARP1, BRCA1, DNMT3A and RAD23B at 48 h and 72 h. PARP1 showed significant positive correlation of methylation status with gene expression. In conclusion, low and high doses of γ-radiation have significant influence on DNA methylation status of LINE1, DDR and DR genes suggesting their potential role as epigenetic signatures in human PBMCs, which can be further explored in human populations.
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Affiliation(s)
- Rashmi Priya
- Low Level Radiation Research Section, Radiation Biology and Health Sciences Division, Bio-Sciences Group, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India
| | - Birajalaxmi Das
- Low Level Radiation Research Section, Radiation Biology and Health Sciences Division, Bio-Sciences Group, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India. .,Homi Bhabha National Institute, Anushaktinagar, Trombay, Mumbai, 400 094, India.
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12
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Computational Probing the Methylation Sites Related to EGFR Inhibitor-Responsive Genes. Biomolecules 2021; 11:biom11071042. [PMID: 34356665 PMCID: PMC8302001 DOI: 10.3390/biom11071042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/09/2021] [Accepted: 07/15/2021] [Indexed: 12/31/2022] Open
Abstract
The emergence of drug resistance is one of the main obstacles to the treatment of lung cancer patients with EGFR inhibitors. Here, to further understand the mechanism of EGFR inhibitors in lung cancer and offer novel therapeutic targets for anti-EGFR-inhibitor resistance via the deep mining of pharmacogenomics data, we associated DNA methylation with drug sensitivities for uncovering the methylation sites related to EGFR inhibitor sensitivity genes. Specifically, we first introduced a grouped regularized regression model (Group Least Absolute Shrinkage and Selection Operator, group lasso) to detect the genes that were closely related to EGFR inhibitor effectiveness. Then, we applied the classical regression model (lasso) to identify the methylation sites associated with the above drug sensitivity genes. The new model was validated on the well-known cancer genomics resource: CTRP. GeneHancer and Encyclopedia of DNA Elements (ENCODE) database searches indicated that the predicted methylation sites related to EGFR inhibitor sensitivity genes were related to regulatory elements. Moreover, the correlation analysis on sensitivity genes and predicted methylation sites suggested that the methylation sites located in the promoter region were more correlated with the expression of EGFR inhibitor sensitivity genes than those located in the enhancer region and the TFBS. Meanwhile, we performed differential expression analysis of genes and predicted methylation sites and found that changes in the methylation level of some sites may affect the expression of the corresponding EGFR inhibitor-responsive genes. Therefore, we supposed that the effectiveness of EGFR inhibitors in lung cancer may be improved by methylation modification in their sensitivity genes.
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13
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Humayun-Zakaria N, Ward DG, Arnold R, Bryan RT. Trends in urine biomarker discovery for urothelial bladder cancer: DNA, RNA, or protein? Transl Androl Urol 2021; 10:2787-2808. [PMID: 34295762 PMCID: PMC8261432 DOI: 10.21037/tau-20-1327] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 04/23/2021] [Indexed: 02/01/2023] Open
Abstract
Urothelial bladder cancer is a complex disease displaying a landscape of heterogenous molecular subtypes, mutation profiles and clinical presentations. Diagnosis and surveillance rely on flexible cystoscopy which has high accuracy, albeit accompanied by a high-cost burden for healthcare providers and discomfort for patients. Advances in "omic" technologies and computational biology have provided insights into the molecular pathogenesis of bladder cancer and provided powerful tools to identify markers for disease detection, risk stratification, and predicting responses to therapy. To date, numerous attempts have been made to discover and validate diagnostic biomarkers that could be deployed as an adjunct to the cystoscopic diagnosis and long-term surveillance of bladder cancer. We report a comprehensive literature analysis using PubMed to assess the changing trends in investigating DNA, RNA, or proteins as diagnostic urinary biomarkers over a period of 5 decades: 1970-2020. A gradual shift has been observed in research away from protein biomarkers to nucleic acids including different classes of RNA, and DNA methylation and mutation markers. Until 2000, publications involving protein biomarker discovery constituted 87% of the total number of research articles with DNA comprising 6% and RNA 7%. Since 2000 the proportion of protein biomarker articles has fallen to 40%, and DNA and RNA studies increased to 32% and 28%, respectively. Clearly research focus, perhaps driven by technological innovation, has shifted from proteins to nucleic acids. We optimistically hypothesise that, following thorough validation, a clinically useful detection test for bladder cancer based on a panel of DNA or RNA markers could become reality within 5-10 years.
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Affiliation(s)
- Nada Humayun-Zakaria
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Douglas G Ward
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Roland Arnold
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Richard T Bryan
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
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14
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Börcsök J, Diossy M, Sztupinszki Z, Prosz A, Tisza V, Spisak S, Rusz O, Stormoen DR, Pappot H, Csabai I, Brunak S, Mouw KW, Szallasi Z. Detection of Molecular Signatures of Homologous Recombination Deficiency in Bladder Cancer. Clin Cancer Res 2021; 27:3734-3743. [PMID: 33947694 DOI: 10.1158/1078-0432.ccr-20-5037] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/11/2021] [Accepted: 04/29/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Poly (ADP ribose)-polymerase (PARP) inhibitors are approved for use in breast, ovarian, prostate, and pancreatic cancers, which are the solid tumor types that most frequently have alterations in key homologous recombination (HR) genes, such as BRCA1/2. However, the frequency of HR deficiency (HRD) in other solid tumor types, including bladder cancer, is less well characterized. EXPERIMENTAL DESIGN Specific DNA aberration profiles (mutational signatures) are induced by HRD, and the presence of these "genomic scars" can be used to assess the presence or absence of HRD in a given tumor biopsy even in the absence of an observed alteration of an HR gene. Using whole-exome and whole-genome data, we measured various HRD-associated mutational signatures in bladder cancer. RESULTS We found that a subset of bladder tumors have evidence of HRD. In addition to a small number of tumors with biallelic BRCA1/2 events, approximately 10% of bladder tumors had significant evidence of HRD-associated mutational signatures. Increased levels of HRD signatures were associated with promoter methylation of RBBP8, which encodes CtIP, a key protein involved in HR. CONCLUSIONS A subset of bladder tumors have genomic features suggestive of HRD and therefore may be more likely to benefit from therapies such as platinum agents and PARP inhibitors that target tumor HRD.
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Affiliation(s)
- Judit Börcsök
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Miklos Diossy
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Zsofia Sztupinszki
- Danish Cancer Society Research Center, Copenhagen, Denmark.,Computational Health Informatics Program, Boston Children's Hospital, Boston, Massachusetts
| | - Aurel Prosz
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Viktoria Tisza
- Computational Health Informatics Program, Boston Children's Hospital, Boston, Massachusetts
| | - Sandor Spisak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Orsolya Rusz
- 2nd Department of Pathology, SE NAP, Brain Metastasis Research Group, Semmelweis University, Budapest, Hungary
| | - Dag R Stormoen
- Department of Oncology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Helle Pappot
- Department of Oncology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Istvan Csabai
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Kent W Mouw
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Zoltan Szallasi
- Danish Cancer Society Research Center, Copenhagen, Denmark. .,Computational Health Informatics Program, Boston Children's Hospital, Boston, Massachusetts.,2nd Department of Pathology, SE NAP, Brain Metastasis Research Group, Semmelweis University, Budapest, Hungary
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15
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Arora M, Kumari S, Singh J, Chopra A, Chauhan SS. PAXX, Not NHEJ1 Is an Independent Prognosticator in Colon Cancer. Front Mol Biosci 2020; 7:584053. [PMID: 33195430 PMCID: PMC7649742 DOI: 10.3389/fmolb.2020.584053] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/09/2020] [Indexed: 12/24/2022] Open
Abstract
Classical Non-homologous End Joining (NHEJ) pathway is the mainstay of cellular response to DNA double strand breaks. While aberrant expression of genes involved in this pathway has been linked with genomic instability and drug resistance in several cancers, limited information is available about its clinical significance in colon cancer. We performed a comprehensive analysis of seven essential genes, including XRCC5, XRCC6, PRKDC, LIG4, XRCC4, NHEJ1, and PAXX of this pathway, in colon cancer using multi-omics datasets, and studied their associations with molecular and clinicopathological features, including age, gender, stage, KRAS mutation, BRAF mutation, microsatellite instability status and promoter DNA methylation in TCGA colon cancer dataset. This analysis revealed upregulation of XRCC5, PRKDC, and PAXX in colon cancer compared to normal colon tissues, while LIG4 and NHEJ1 (XLF) displayed downregulation. The expression of these genes was independent of age and KRAS status, while XRCC5, PRKDC, and LIG4 exhibited reduced expression in BRAF mutant tumors. Interestingly, we observed a strong association between XRCC6, XRCC5, PRKDC and LIG4 overexpression and microsatellite instability status of the tumors. In multivariate analysis, high PAXX expression emerged as an independent prognostic marker for poor overall and disease specific survival. We also observed hypomethylation of PAXX promoter in tumors, which exhibited a strong correlation with its overexpression. Furthermore, PAXX overexpression was also associated with several oncogenic pathways as well as a reduction in numbers of tumor-infiltrating lymphocytes.
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Affiliation(s)
- Mohit Arora
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Sarita Kumari
- Laboratory Oncology Unit, Dr. BRA-IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Jay Singh
- Laboratory Oncology Unit, Dr. BRA-IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Anita Chopra
- Laboratory Oncology Unit, Dr. BRA-IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Shyam S Chauhan
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
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16
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Mozaffari NL, Pagliarulo F, Sartori AA. Human CtIP: A 'double agent' in DNA repair and tumorigenesis. Semin Cell Dev Biol 2020; 113:47-56. [PMID: 32950401 DOI: 10.1016/j.semcdb.2020.09.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/20/2020] [Accepted: 09/02/2020] [Indexed: 12/14/2022]
Abstract
Human CtIP was originally identified as an interactor of the retinoblastoma protein and BRCA1, two bona fide tumour suppressors frequently mutated in cancer. CtIP is renowned for its role in the resection of DNA double-strand breaks (DSBs) during homologous recombination, a largely error-free DNA repair pathway crucial in maintaining genome integrity. However, CtIP-dependent DNA end resection is equally accountable for alternative end-joining, a mutagenic DSB repair mechanism implicated in oncogenic chromosomal translocations. In addition, CtIP contributes to transcriptional regulation of G1/S transition, DNA damage checkpoint signalling, and replication fork protection pathways. In this review, we present a perspective on the current state of knowledge regarding the tumour-suppressive and oncogenic properties of CtIP and provide an overview of their relevance for cancer development, progression, and therapy.
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Affiliation(s)
- Nour L Mozaffari
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Fabio Pagliarulo
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Alessandro A Sartori
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland.
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17
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Havusha-Laufer S, Kosenko A, Kisliouk T, Barash I. H2AX Promoter Demethylation at Specific Sites Plays a Role in STAT5-Induced Tumorigenesis. J Mammary Gland Biol Neoplasia 2020; 25:205-218. [PMID: 32748326 DOI: 10.1007/s10911-020-09455-2] [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: 03/25/2020] [Accepted: 07/27/2020] [Indexed: 10/23/2022] Open
Abstract
Deregulated STAT5 activity in the mammary gland of transgenic mice results in parity-dependent latent tumorigenesis. The trigger for cell transformation was previously associated with hyperactivation of the H2AX proximal promoter in a small basal cell population during pregnancy. The current study focuses on the latent activation of tumor development. H2AX was highly expressed in carcinoma and adenocarcinoma as compared to the multiparous mammary gland, whereas pSTAT5 expression decreased in a tumor type-dependent manner. In contrast to the pregnant gland, no positive correlation between H2AX and pSTAT5 expression could be defined in carcinoma and adenocarcinoma. Using targeted methylation analysis, the methylation profile of the H2AX promoter was characterized in the intact gland and tumors. Average H2AX promoter methylation in the tumors was relatively high (~90%), but did not exceed that of the multiparous gland; 5mC methylation was higher in the differentiated tumors and negatively correlated with its oxidative product 5hmC and H2AX expression. Individual analysis of 25 H2AX promoter-methylation sites revealed two consecutive CpGs at positions -77 and - 54 that were actively demethylated in the multiparous gland, but not in their age-matched virgin counterpart. The different methylation profiles at these sites distinguished tumor types and may assume a prognostic role. In-silico and ChIP analyses revealed overlapping methylation-independent SP1-binding and methylation-dependent p53-binding to these sites. We propose that interference with SP1-assisted p53-binding to these sites abrogates H2AX's ability to arrest the cell cycle upon DNA damage, and contributes to triggering latent development of STAT5-induced tumors in estrapausal multiparous mice.
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Affiliation(s)
- Sharon Havusha-Laufer
- Institute of Animal Science, Agricultural Research Organization (ARO), The Volcani Center, Bet Dagan, Israel
| | - Ana Kosenko
- Institute of Animal Science, Agricultural Research Organization (ARO), The Volcani Center, Bet Dagan, Israel
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tatiana Kisliouk
- Institute of Animal Science, Agricultural Research Organization (ARO), The Volcani Center, Bet Dagan, Israel
| | - Itamar Barash
- Institute of Animal Science, Agricultural Research Organization (ARO), The Volcani Center, Bet Dagan, Israel.
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18
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Yan YL, Huang ZN, Zhu Z, Cui YY, Li MQ, Huang RM, Yan J, Shen B. Downregulation of TET1 Promotes Bladder Cancer Cell Proliferation and Invasion by Reducing DNA Hydroxymethylation of AJAP1. Front Oncol 2020; 10:667. [PMID: 32528872 PMCID: PMC7253684 DOI: 10.3389/fonc.2020.00667] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 04/09/2020] [Indexed: 12/20/2022] Open
Abstract
Ten-eleven translocation 1 (TET1) is a member of methylcytosine dioxygenase, which catalyzes 5-methylcytosine (5 mC) to 5-hydroxymethylcytosine (5 hmC) to promote the demethylation process. The dysregulated TET1 protein and 5 hmC level were reported to either suppress or promote carcinogenesis in a cancer type-dependent manner. Currently, the role of TET1 in the development of urinary bladder cancer (UBC) and its underlying molecular mechanisms remain unclear. Herein, we found that TET1 expression was downregulated in UBC specimens compared with normal urothelium and was inversely related to tumor stage and grade and overall survival, suggesting its negative association with UBC progression. TET1 silencing in UBC cells increased cell proliferation and invasiveness while the ectopic expression of wild-type TET1-CD, but not its enzymatic inactive mutant, reversed these effects and suppressed tumorigenicity in vivo. In addition, as a direct regulator of TET1 activity, vitamin C treatment increased 5 hmC level and inhibited the anchorage-independent growth and tumorigenicity of UBC cells. Furthermore, we found that TET1 maintained the hypomethylation in the promoter of the AJAP1 gene, which codes for adherens junction-associated protein 1. The downregulation of AJAP1 reversed TET1-CD-induced nuclear translocation of β-catenin, thus inhibiting the expression of its downstream genes. In human UBC specimens, AJAP1 is frequently downregulated and positively associated with TET1. Notably, low expression levels of both TET1 and AJAP1 predict poor prognosis in UBC patients. In conclusion, we found that the frequently downregulated TET1 level reduces the hydroxymethylation of AJAP1 promoter and subsequently activates β-catenin signaling to promote UBC development. The downregulation of both TET1 and AJAP1 might be a promising prognostic biomarker for UBC patients.
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Affiliation(s)
- Yi-Lin Yan
- Department of Urology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zheng-Nan Huang
- Department of Urology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhen Zhu
- Model Animal Research Center of Nanjing University, Nanjing, China
| | - Yang-Yan Cui
- Model Animal Research Center of Nanjing University, Nanjing, China
| | - Mei-Qian Li
- Model Animal Research Center of Nanjing University, Nanjing, China
| | - Rui-Min Huang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jun Yan
- Department of Laboratory Animal Science, Fudan University, Shanghai, China
| | - Bing Shen
- Department of Urology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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19
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Rose M, Bringezu S, Godfrey L, Fiedler D, Gaisa NT, Koch M, Bach C, Füssel S, Herr A, Hübner D, Ellinger J, Pfister D, Knüchel R, Wirth MP, Böhme M, Dahl E. ITIH5 and ECRG4 DNA Methylation Biomarker Test (EI-BLA) for Urine-Based Non-Invasive Detection of Bladder Cancer. Int J Mol Sci 2020; 21:ijms21031117. [PMID: 32046186 PMCID: PMC7036997 DOI: 10.3390/ijms21031117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/05/2020] [Accepted: 02/05/2020] [Indexed: 02/07/2023] Open
Abstract
Bladder cancer is one of the more common malignancies in humans and the most expensive tumor for treating in the Unites States (US) and Europe due to the need for lifelong surveillance. Non-invasive tests approved by the FDA have not been widely adopted in routine diagnosis so far. Therefore, we aimed to characterize the two putative tumor suppressor genes ECRG4 and ITIH5 as novel urinary DNA methylation biomarkers that are suitable for non-invasive detection of bladder cancer. While assessing the analytical performance, a spiking experiment was performed by determining the limit of RT112 tumor cell detection (range: 100-10,000 cells) in the urine of healthy donors in dependency of the processing protocols of the RWTH cBMB. Clinically, urine sediments of 474 patients were analyzed by using quantitative methylation-specific PCR (qMSP) and Methylation Sensitive Restriction Enzyme (MSRE) qPCR techniques. Overall, ECRG4-ITIH5 showed a sensitivity of 64% to 70% with a specificity ranging between 80% and 92%, i.e., discriminating healthy, benign lesions, and/or inflammatory diseases from bladder tumors. When comparing single biomarkers, ECRG4 achieved a sensitivity of 73%, which was increased by combination with the known biomarker candidate NID2 up to 76% at a specificity of 97%. Hence, ITIH5 and, in particular, ECRG4 might be promising candidates for further optimizing current bladder cancer biomarker panels and platforms.
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Affiliation(s)
- Michael Rose
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (S.B.); (L.G.); (D.F.); (N.T.G.); (M.K.); (R.K.)
- RWTH Centralized Biomaterial Bank (RWTH cBMB), Medical Faculty, RWTH Aachen University, 52074 Aachen, Germany
- Correspondence: (M.R.); (E.D.); Tel.: +49-241-808-9715 (M.R.); +49-241-808-8431 (E.D.); Fax: +49-241-808-2439 (M.R.); +49-241-808-2439 (E.D.)
| | - Sarah Bringezu
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (S.B.); (L.G.); (D.F.); (N.T.G.); (M.K.); (R.K.)
| | - Laura Godfrey
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (S.B.); (L.G.); (D.F.); (N.T.G.); (M.K.); (R.K.)
| | - David Fiedler
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (S.B.); (L.G.); (D.F.); (N.T.G.); (M.K.); (R.K.)
| | - Nadine T. Gaisa
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (S.B.); (L.G.); (D.F.); (N.T.G.); (M.K.); (R.K.)
| | - Maximilian Koch
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (S.B.); (L.G.); (D.F.); (N.T.G.); (M.K.); (R.K.)
| | - Christian Bach
- Department of Urology, RWTH Aachen University, 52074 Aachen, Germany; (C.B.); (D.P.)
| | - Susanne Füssel
- Department of Urology, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany; (S.F.); (D.H.); (M.P.W.)
| | | | - Doreen Hübner
- Department of Urology, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany; (S.F.); (D.H.); (M.P.W.)
| | - Jörg Ellinger
- Department of Urology, University Hospital Bonn, 53105 Bonn, Germany;
| | - David Pfister
- Department of Urology, RWTH Aachen University, 52074 Aachen, Germany; (C.B.); (D.P.)
- Department of Urology, Uro-Oncology, Robot Assisted and Reconstructive Urologic Surgery, University Hospital Cologne, 50937 Cologne, Germany
| | - Ruth Knüchel
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (S.B.); (L.G.); (D.F.); (N.T.G.); (M.K.); (R.K.)
| | - Manfred P. Wirth
- Department of Urology, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany; (S.F.); (D.H.); (M.P.W.)
| | - Manja Böhme
- Biotype GmbH, 01109 Dresden, Germany; (A.H.); (M.B.)
| | - Edgar Dahl
- Institute of Pathology, RWTH Aachen University, 52074 Aachen, Germany; (S.B.); (L.G.); (D.F.); (N.T.G.); (M.K.); (R.K.)
- RWTH Centralized Biomaterial Bank (RWTH cBMB), Medical Faculty, RWTH Aachen University, 52074 Aachen, Germany
- Correspondence: (M.R.); (E.D.); Tel.: +49-241-808-9715 (M.R.); +49-241-808-8431 (E.D.); Fax: +49-241-808-2439 (M.R.); +49-241-808-2439 (E.D.)
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20
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You W, Xu Z, Shan T. Regulatory Roles of GADD45α in Skeletal Muscle and Adipocyte. Curr Protein Pept Sci 2020; 20:918-925. [PMID: 31232235 DOI: 10.2174/1389203720666190624143503] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 06/02/2019] [Accepted: 06/11/2019] [Indexed: 02/07/2023]
Abstract
GADD45α, a member of the GADD45 family proteins, is involved in various cellular processes including the maintenance of genomic integrity, growth arrest, apoptosis, senescence, and signal transduction. In skeletal muscle, GADD45α plays an important role in regulating mitochondrial biogenesis and muscle atrophy. In adipocytes, GADD45α regulates preadipocyte differentiation, lipid accumulation, and thermogenesis metabolism. Moreover, it has been recently demonstrated that GADD45α promotes gene activation by inducing DNA demethylation. The epigenetic function of GADD45α is important for preadipocyte differentiation and transcriptional regulation during development. This article mainly reviews and discusses the regulatory roles of GADD45α in skeletal muscle development, adipocyte progenitor differentiation, and DNA demethylation.
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Affiliation(s)
- Wenjing You
- College of Animal Sciences, Zhejiang University; The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang Provincial Laboratory of Feed and Animal Nutrition, No. 866 Yuhangtang Road, Hangzhou, Zhejiang, 310058, China
| | - Ziye Xu
- College of Animal Sciences, Zhejiang University; The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang Provincial Laboratory of Feed and Animal Nutrition, No. 866 Yuhangtang Road, Hangzhou, Zhejiang, 310058, China
| | - Tizhong Shan
- College of Animal Sciences, Zhejiang University; The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang Provincial Laboratory of Feed and Animal Nutrition, No. 866 Yuhangtang Road, Hangzhou, Zhejiang, 310058, China
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21
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Klinakis A, Karagiannis D, Rampias T. Targeting DNA repair in cancer: current state and novel approaches. Cell Mol Life Sci 2020; 77:677-703. [PMID: 31612241 PMCID: PMC11105035 DOI: 10.1007/s00018-019-03299-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 08/06/2019] [Accepted: 09/09/2019] [Indexed: 12/12/2022]
Abstract
DNA damage response, DNA repair and genomic instability have been under study for their role in tumor initiation and progression for many years now. More recently, next-generation sequencing on cancer tissue from various patient cohorts have revealed mutations and epigenetic silencing of various genes encoding proteins with roles in these processes. These findings, together with the unequivocal role of DNA repair in therapeutic response, have fueled efforts toward the clinical exploitation of research findings. The successful example of PARP1/2 inhibitors has also supported these efforts and led to numerous preclinical and clinical trials with a large number of small molecules targeting various components involved in DNA repair singularly or in combination with other therapies. In this review, we focus on recent considerations related to DNA damage response and new DNA repair inhibition agents. We then discuss how immunotherapy can collaborate with these new drugs and how epigenetic drugs can rewire the activity of repair pathways and sensitize cancer cells to DNA repair inhibition therapies.
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Affiliation(s)
- Apostolos Klinakis
- Biomedical Research Foundation of the Academy of Athens, 11527, Athens, Greece.
| | - Dimitris Karagiannis
- Department of Genetics and Development, Columbia University Medical Center, New York, NY, 10032, USA
| | - Theodoros Rampias
- Biomedical Research Foundation of the Academy of Athens, 11527, Athens, Greece.
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22
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Kumar SU, Kumar DT, Siva R, Doss CGP, Zayed H. Integrative Bioinformatics Approaches to Map Potential Novel Genes and Pathways Involved in Ovarian Cancer. Front Bioeng Biotechnol 2019; 7:391. [PMID: 31921802 PMCID: PMC6927934 DOI: 10.3389/fbioe.2019.00391] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/19/2019] [Indexed: 12/14/2022] Open
Abstract
Background and aims: Ovarian cancer (OC) is the seventh most commonly detected cancer among women. This study aimed to map the hub and core genes and potential pathways that might be involved in the molecular pathogenesis of OC. Methods: In the present work, we analyzed a microarray dataset (GSE126519) from the Gene Expression Omnibus (GEO) database and used the GEO2R tool to screen OC cells and ovarian SINE-resistant cancer cells for differentially expressed genes (DEGs). For the functional annotation of the DEGs, we conducted Gene Ontology (GO) and pathway enrichment analyses (KEGG) using the DAVID v6.8 online server and GenoGo Metacore™, Cortellis Solution software. Protein–protein interaction (PPI) networks were constructed using the STRING database, and Cytoscape software was used for visualization. The survival analysis was performed using the online platform GEPIA2 to determine the prognostic value of the expression of hub genes in cell lines from OC patients. Results: We identified a total of 809 upregulated and 700 downregulated DEGs. GO analysis revealed that the genes with statistically significant differences in expression were mainly associated with biological processes involved in the cell cycle, the mitotic cell cycle, mitotic nuclear division, organ morphogenesis, cell development, and cell morphogenesis. By using the Analyze Networks (AN) algorithm in GeneGo, we identified the most relevant biological networks involving DEGs that were mainly enriched in the cell cycle (in metaphase checkpoints) and revealed the role of APC in cell cycle regulation pathways. We found 10 hub genes and four core genes (FZD6, FZD8, CDK2, and RBBP8) that are strongly linked to OC. Conclusion: This study sheds light on the molecular pathogenesis of OC and is expected to provide potential molecular biomarkers that are beneficial for the treatment and clinical molecular diagnosis of OC.
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Affiliation(s)
- S Udhaya Kumar
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - D Thirumal Kumar
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - R Siva
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - C George Priya Doss
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, Doha, Qatar
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23
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Martinez VG, Munera-Maravilla E, Bernardini A, Rubio C, Suarez-Cabrera C, Segovia C, Lodewijk I, Dueñas M, Martínez-Fernández M, Paramio JM. Epigenetics of Bladder Cancer: Where Biomarkers and Therapeutic Targets Meet. Front Genet 2019; 10:1125. [PMID: 31850055 PMCID: PMC6902278 DOI: 10.3389/fgene.2019.01125] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 10/17/2019] [Indexed: 12/12/2022] Open
Abstract
Bladder cancer (BC) is the most common neoplasia of the urothelial tract. Due to its high incidence, prevalence, recurrence and mortality, it remains an unsolved clinical and social problem. The treatment of BC is challenging and, although immunotherapies have revealed potential benefit in a percentage of patients, it remains mostly an incurable disease at its advanced state. Epigenetic alterations, including aberrant DNA methylation, altered chromatin remodeling and deregulated expression of non-coding RNAs are common events in BC and can be driver events in BC pathogenesis. Accordingly, these epigenetic alterations are now being used as potential biomarkers for these disorders and are being envisioned as potential therapeutic targets for the future management of BC. In this review, we summarize the recent findings in these emerging and exciting new aspects paving the way for future clinical treatment of this disease.
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Affiliation(s)
- Victor G. Martinez
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
| | - Ester Munera-Maravilla
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Alejandra Bernardini
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Carolina Rubio
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Cristian Suarez-Cabrera
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
| | - Cristina Segovia
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
| | - Iris Lodewijk
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
| | - Marta Dueñas
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Mónica Martínez-Fernández
- Genomes & Disease Lab, CiMUS (Center for Research in Molecular Medicine and Chronic Diseases), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Jesus Maria Paramio
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
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24
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Mijnes J, Tiedemann J, Eschenbruch J, Gasthaus J, Bringezu S, Bauerschlag D, Maass N, Arnold N, Weimer J, Anzeneder T, Fasching PA, Rübner M, Bruno B, Heindrichs U, Freres J, Schulz H, Hilgers RD, Ortiz-Brüchle N, von Serenyi S, Knüchel R, Kloten V, Dahl E. SNiPER: a novel hypermethylation biomarker panel for liquid biopsy based early breast cancer detection. Oncotarget 2019; 10:6494-6508. [PMID: 31741713 PMCID: PMC6849652 DOI: 10.18632/oncotarget.27303] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 10/19/2019] [Indexed: 01/02/2023] Open
Abstract
Introduction Mammography is the gold standard for early breast cancer detection, but shows important limitations. Blood-based approaches on basis of cell-free DNA (cfDNA) provide minimally invasive screening tools to characterize epigenetic alterations of tumor suppressor genes and could serve as a liquid biopsy, complementing mammography. Methods Potential biomarkers were identified from The Cancer Genome Atlas (TCGA), using HumanMethylation450-BeadChip data. Promoter methylation status was evaluated quantitatively by pyrosequencing in a serum test cohort (n = 103), a serum validation cohort (n = 368) and a plasma cohort (n = 125). Results SPAG6, NKX2-6 and PER1 were identified as novel biomarker candidates. ITIH5 was included on basis of our previous work. In the serum test cohort, a panel of SPAG6 and ITIH5 showed 63% sensitivity for DCIS and 51% sensitivity for early invasive tumor (pT1, pN0) detection at 80% specificity. The serum validation cohort revealed 50% sensitivity for DCIS detection on basis of NKX2-6 and ITIH5. Furthermore, an inverse correlation between methylation frequency and cfDNA concentration was uncovered. Therefore, markers were tested in a plasma cohort, achieving a 64% sensitivity for breast cancer detection using SPAG6, PER1 and ITIH5. Conclusions Although liquid biopsy remains challenging, a combination of SPAG6, NKX2-6, ITIH5 and PER1 (SNiPER) provides a promising tool for blood-based breast cancer detection.
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Affiliation(s)
- Jolein Mijnes
- Molecular Oncology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Janina Tiedemann
- Molecular Oncology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Julian Eschenbruch
- Molecular Oncology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Janina Gasthaus
- Molecular Oncology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Sarah Bringezu
- Molecular Oncology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Dirk Bauerschlag
- Department of Gynecology and Obstetrics, University Medical Centre Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Nicolai Maass
- Department of Gynecology and Obstetrics, University Medical Centre Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Norbert Arnold
- Department of Gynecology and Obstetrics, University Medical Centre Schleswig-Holstein, Campus Kiel, Kiel, Germany.,Institute of Clinical Molecular Biology, University Medical Centre Schleswig-Holstein, Campus Kiel, Christian-Albrechts-University, Kiel, Germany
| | - Jörg Weimer
- Department of Gynecology and Obstetrics, University Medical Centre Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Tobias Anzeneder
- Patients' Tumor Bank of Hope (PATH-Biobank) Foundation, München, Germany
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Erlangen, Germany
| | - Matthias Rübner
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Erlangen, Germany
| | - Benjamin Bruno
- Department of Gynecology and Obstetrics Luisenhospital, Aachen, Germany
| | - Uwe Heindrichs
- Department of Gynecology and Obstetrics Luisenhospital, Aachen, Germany
| | - Jennifer Freres
- Department of Gynecology and Obstetrics Luisenhospital, Aachen, Germany
| | - Hanna Schulz
- Molecular Oncology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Ralf-Dieter Hilgers
- Institute of Medical Statistics, University Hospital RWTH Aachen, Aachen, Germany
| | - Nadina Ortiz-Brüchle
- Molecular Oncology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Sonja von Serenyi
- Molecular Oncology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Ruth Knüchel
- Molecular Oncology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Vera Kloten
- Molecular Oncology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany.,Current address: Bayer AG, Pharmaceuticals Division, Biomarker Research, Wuppertal, Germany.,Share equal senior authorship
| | - Edgar Dahl
- Molecular Oncology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany.,RWTH centralized Biomaterial Bank (RWTH cBMB) at the Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany.,Share equal senior authorship
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25
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Zhou B, Guo R. Integrative Analysis of Genomic and Clinical Data Reveals Intrinsic Characteristics of Bladder Urothelial Carcinoma Progression. Genes (Basel) 2019; 10:genes10060464. [PMID: 31212967 PMCID: PMC6628253 DOI: 10.3390/genes10060464] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/12/2019] [Accepted: 06/14/2019] [Indexed: 12/14/2022] Open
Abstract
The progression of bladder cancer is generally a complex and dynamic process, involving a variety of biological factors. Here, we aimed to identify a set of survival-related genes that play an important role in the progression of bladder cancer and uncover their synergistic patterns. Based on the large-scale genomic profiling data and clinical information of 404 bladder cancer patients derived from The Cancer Genome Atlas (TCGA) database, we first discovered 1078 survival-related genes related to their survival states using univariate and multivariate Cox proportional hazardous regression. We then investigated the dynamic changes of the cooperative behaviors of these 1078 genes by analyzing their respective genomic features, including copy number variations, DNA methylations, somatic mutations, and microRNA regulatory networks. Our analyses showed that during the progression of bladder cancer, the biological disorder involving the identified survival-related genes can be reflected by multiple levels of abnormal gene regulation, ranging from genomic alteration to post-transcriptional dysregulation. In particular, the stage-specific co-expression networks of these genes undergo a series of structural variations. Our findings provide useful hints on understanding the underlying complex molecular mechanisms related to the evolution of bladder cancer and offer a new perspective on clinical diagnosis and treatment of bladder cancer.
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Affiliation(s)
- Bin Zhou
- School of Life Science, Tsinghua University, Beijing 100084, China.
| | - Rui Guo
- Department of Biochemistry and Molecular biology, Shanxi Medical University, Taiyuan 030001, China.
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26
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Larsen LK, Lind GE, Guldberg P, Dahl C. DNA-Methylation-Based Detection of Urological Cancer in Urine: Overview of Biomarkers and Considerations on Biomarker Design, Source of DNA, and Detection Technologies. Int J Mol Sci 2019; 20:ijms20112657. [PMID: 31151158 PMCID: PMC6600406 DOI: 10.3390/ijms20112657] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 12/11/2022] Open
Abstract
Changes in DNA methylation have been causally linked with cancer and provide promising biomarkers for detection in biological fluids such as blood, urine, and saliva. The field has been fueled by genome-wide characterization of DNA methylation across cancer types as well as new technologies for sensitive detection of aberrantly methylated DNA molecules. For urological cancers, urine is in many situations the preferred "liquid biopsy" source because it contains exfoliated tumor cells and cell-free tumor DNA and can be obtained easily, noninvasively, and repeatedly. Here, we review recent advances made in the development of DNA-methylation-based biomarkers for detection of bladder, prostate, renal, and upper urinary tract cancers, with an emphasis on the performance characteristics of biomarkers in urine. For most biomarkers evaluated in independent studies, there was great variability in sensitivity and specificity. We discuss issues that impact the outcome of DNA-methylation-based detection of urological cancer and account for the great variability in performance, including genomic location of biomarkers, source of DNA, and technical issues related to the detection of rare aberrantly methylated DNA molecules. Finally, we discuss issues that remain to be addressed to fully exploit the potential of DNA-methylation-based biomarkers in the clinic, including the need for prospective trials and careful selection of control groups.
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Affiliation(s)
| | - Guro Elisabeth Lind
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, the Norwegian Radium Hospital, NO-0424 Oslo, Norway.
| | - Per Guldberg
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark.
| | - Christina Dahl
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark.
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27
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Prognosis value of RBBP8 expression in plasma cell myeloma. Cancer Gene Ther 2019; 27:22-29. [PMID: 30622325 PMCID: PMC7027984 DOI: 10.1038/s41417-018-0069-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/30/2018] [Accepted: 11/02/2018] [Indexed: 12/01/2022]
Abstract
Plasma cell myeloma (PCM) secretes monoclonal immunoglobulin (Ig) by clonal plasma cells of abnormal proliferation in the bone marrow. As PCM is incurable, it is necessary to find new biomarkers to predict the prognosis and recurrence of PCM. The relationship between cancer and RBBP8 has not been fully studied. The role of RBBP8 in tumorigenesis remains inconsistent. We described the expression of RBBP8 in the gene expression profile of 1930 PCM samples (1878 PCM patients) from seven independent data sets. We analyzed the relationship between RBBP8 and survival prognosis, recurrence, and treatment response in patients with PCM, and the biological significance of RBBP8 in PCM. The gene expression level of RBBP8 was significantly related to the International staging system (ISS) grade of PCM (P = 0.0012). RBBP8 expression in different molecular subtypes was different (P < 2.2e-16). High RBBP8 expression is associated with poor survival in PCM (P < 0.0001). High expression of RBBP8 indicates that PCM patients are more likely to relapse (P = 0.0078). The biological significance of RBBP8 in PCM is related to the cell cycle (P < 0.05). High RBBP8 expression predicts poorer survival and more likely relapse in PCM. RBBP8 plays an important role in the cell cycle of PCM. RBBP8 can be considered an independent prognostic factor for PCM. RBBP8 can be used as a potential biomarker for assessing the prognosis of PCM patients.
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28
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Combined Targeted Resequencing of Cytosine DNA Methylation and Mutations of DNA Repair Genes with Potential Use for Poly(ADP-Ribose) Polymerase 1 Inhibitor Sensitivity Testing. J Mol Diagn 2018; 21:198-213. [PMID: 30576872 DOI: 10.1016/j.jmoldx.2018.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/31/2018] [Accepted: 10/16/2018] [Indexed: 02/08/2023] Open
Abstract
Current molecular tumor diagnostics encompass panel sequencing to detect mutations, copy number alterations, and rearrangements. However, tumor suppressor genes can also be inactivated by methylation within their promoter region. These epigenetic alterations are so far rarely assessed in the clinical setting. Therefore, we established the AllCap protocol facilitating the combined detection of mutations and DNA methylation at the coding and promoter regions of 342 DNA repair genes in one experiment. We demonstrate the use of the protocol by applying it to ovarian cancer cell lines with different responsiveness to poly(ADP-ribose) polymerase inhibition. BRCA1, ATM, ATR, and EP300 mutations and methylation of the BRCA1 promoter were detected as potential predictors for therapy response. The required amount of input DNA was optimized, and the application to formalin-fixed, paraffin-embedded tissue samples was verified to improve the clinical applicability. Thus, by adding DNA methylation values to panel resequencings, the AllCap assay will add another important level of information to clinical tests and will improve stratification of patients for systemic therapies.
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