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De Lorenzo A, Dos Santos Fernandes MC, Romeiro F, Arpini AP, Dias GM. DNA damage and repair in patients undergoing myocardial perfusion single-photon emission computed tomography. Sci Rep 2024; 14:13079. [PMID: 38844507 PMCID: PMC11156974 DOI: 10.1038/s41598-024-63537-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/29/2024] [Indexed: 06/09/2024] Open
Abstract
As patient exposure to ionizing radiation from medical imaging and its risks are continuing issues, this study aimed to evaluate DNA damage and repair markers after myocardial perfusion single-photon emission computed tomography (MPS). Thirty-two patients undergoing Tc-99m sestamibi MPS were studied. Peripheral blood was collected before radiotracer injection at rest and 60-90 min after injection. The comet assay (single-cell gel electrophoresis) was performed with peripheral blood cells to detect DNA strand breaks. Three descriptors were evaluated: the percentage of DNA in the comet tail, tail length, and tail moment (the product of DNA tail percentage and tail length). Quantitative PCR (qPCR) was performed to evaluate the expression of five genes related to signaling pathways in response to DNA damage and repair (ATM, ATR, BRCA1, CDKN1A, and XPC). Mann-Whitney's test was employed for statistical analysis; p < 0.05 was considered significant. Mean Tc-99m sestamibi dose was 15.1 mCi. After radiotracer injection, comparing post-exposure to pre-exposure samples of each of the 32 patients, no statistically significant differences of the DNA percentage in the tail, tail length or tail moment were found. qPCR revealed increased expression of BRCA1 and XPC, without any significant difference regarding the other genes. No significant increase in DNA strand breaks was detected after a single radiotracer injection for MPS. There was activation of only two repair genes, which may indicate that, in the current patient sample, the effects of ionizing radiation on the DNA were not large enough to trigger intense repair responses, suggesting the absence of significant DNA damage.
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Affiliation(s)
- Andrea De Lorenzo
- Coordenação de Ensino e Pesquisa, Instituto Nacional de Cardiologia, Rua das Laranjeiras 374, Rio de Janeiro, RJ, Brazil.
| | | | - Francisco Romeiro
- Serviço de Medicina Nuclear, Instituto Nacional de Cardiologia, Rio de Janeiro, Brazil
| | - Anna Paula Arpini
- Coordenação de Ensino e Pesquisa, Instituto Nacional de Cardiologia, Rua das Laranjeiras 374, Rio de Janeiro, RJ, Brazil
| | - Glauber Monteiro Dias
- Laboratório de Biologia Celular e Tecidual, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Rio de Janeiro, Brazil
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2
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Yan LJ, Y. Lau AT, Xu YM. The regulation of microRNAs on chemoresistance in triple-negative breast cancer: a recent update. Epigenomics 2024; 16:571-587. [PMID: 38639712 PMCID: PMC11160456 DOI: 10.2217/epi-2023-0430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/07/2024] [Indexed: 04/20/2024] Open
Abstract
Triple-negative breast cancer (TNBC) has negative expressions of ER, PR and HER2. Due to the insensitivity to both endocrine therapy and HER2-targeted therapy, the main treatment method for TNBC is cytotoxic chemotherapy. However, the curative effect of chemotherapy is limited because of the existence of acquired or intrinsic multidrug resistance. MicroRNAs (miRNAs) are frequently dysregulated in malignant tumors and involved in tumor occurrence and progression. Interestingly, growing studies show that miRNAs are involved in chemoresistance in TNBC. Thus, targeting dysregulated miRNAs could be a plausible way for better treatment of TNBC. Here, we present the updated knowledge of miRNAs associated with chemoresistance in TNBC, which may be helpful for the early diagnosis, prognosis and treatment of this life-threatening disease.
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Affiliation(s)
- Li-Jun Yan
- Laboratory of Cancer Biology & Epigenetics, Department of Cell Biology & Genetics, Shantou University Medical College, Shantou, 515041, China
| | - Andy T. Y. Lau
- Laboratory of Cancer Biology & Epigenetics, Department of Cell Biology & Genetics, Shantou University Medical College, Shantou, 515041, China
| | - Yan-Ming Xu
- Laboratory of Cancer Biology & Epigenetics, Department of Cell Biology & Genetics, Shantou University Medical College, Shantou, 515041, China
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3
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Lu M, Gao Q, Jin R, Gu M, Wang Z, Li X, Li W, Wang J, Ma T. The Ribonuclease ZC3H12A is required for self-inflicted DNA breaks after DNA damage in small cell lung cancer cells. Cell Oncol (Dordr) 2024:10.1007/s13402-024-00941-x. [PMID: 38498096 DOI: 10.1007/s13402-024-00941-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2024] [Indexed: 03/20/2024] Open
Abstract
Radiotherapy is the first line treatment for small cell lung cancer (SCLC); However, radio-resistance accompanies with the treatment and hampers the prognosis for SCLC patients. The underlying mechanisms remains elusive. Here we discovered that self-inflicted DNA breaks exist in SCLC cells after radiation. Moreover, using nuclease siRNA screening combined with high-content ArrayScan™ cell analyzer, we identified that Ribonuclease ZC3H12A is required for the self-inflicted DNA breaks after radiation and for SCLC cell survival after DNA damage. ZC3H12A expression was increased in response to DNA damage and when ZC3H12A was knocked down, the DNA repair ability of the cells was impaired, as evidenced by decreased expression of the DNA damage repair protein BRCA1, and increased γH2AX at DNA damage sites. Colony formation assay demonstrates that ZC3H12A knocked down sensitized small cell lung cancer radiotherapy. Therefore, the Ribonuclease ZC3H12A regulates endogenous secondary breaks in small cell lung cancer and affects DNA damage repair. ZC3H12A may act as an important radiotherapy target in small cell lung cancer.
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Affiliation(s)
- Mingjun Lu
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Qing Gao
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Renjing Jin
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Meng Gu
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Ziyu Wang
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Xiaobo Li
- Department of Radiation Oncology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China
| | - Weiying Li
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Jinghui Wang
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Teng Ma
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China.
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4
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Liu W, Du Q, Mei T, Wang J, Huang D, Qin T. Comprehensive analysis the prognostic and immune characteristics of mitochondrial transport-related gene SFXN1 in lung adenocarcinoma. BMC Cancer 2024; 24:94. [PMID: 38233752 PMCID: PMC10795352 DOI: 10.1186/s12885-023-11646-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 11/15/2023] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND Mitochondria, which serve as the fundamental organelle for cellular energy and metabolism, are closely linked to the growth and survival of cancer cells. This study aims to identify and assess Sideroflexin1 (SFXN1), an unprecedented mitochondrial gene, as a potential prognostic biomarker for lung adenocarcinoma (LUAD). METHODS The mRNA and protein levels of SFXN1 were investigated based on the Cancer Genome Atlas (TCGA) LUAD dataset, and then validated by real-time quantitative PCR, Western Blotting and immunohistochemistry from our clinical samples. The clinical correlation and prognostic value were evaluated by the TCGA cohort and verified via our clinical dataset (n = 90). The somatic mutation, drug sensitivity data, immune cell infiltration and single-cell RNA sequencing data of SFXN1 were analyzed through public databases. RESULTS SFXN1 was markedly upregulated at both mRNA and protein levels in LUAD, and high expression of SFXN1 were correlated with larger tumor size, positive lymph node metastasis, and advanced clinical stage. Furthermore, SFXN1 upregulation was significantly associated with poor clinical prognosis. SFXN1 co-expressed genes were also analyzed, which were mainly involved in the cell cycle, central carbon metabolism, DNA repair, and the HIF-1α signaling pathway. Additionally, SFXN1 expression correlated with the expression of multiple immunomodulators, which act to regulate the tumor immune microenvironment. Results also demonstrated an association between SFXN1 expression and increased immune cell infiltration, such as activated CD8 + T cells, natural killer cells (NKs), activated dendritic cells (DCs), and macrophages. LUAD patients with high SFXN1 expression exhibited heightened sensitivity to multiple chemotherapies and targeted drugs and predicted a poor response to immunotherapy. SFXN1 represented an independent prognostic marker for LUAD patients with an improved prognostic value for overall survival when combined with clinical stage information. CONCLUSIONS SFXN1 is frequently upregulated in LUAD and has a significant impact on the tumor immune environment. Our study uncovers the potential of SFXN1 as a prognostic biomarker and as a novel target for intervention in LUAD.
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Affiliation(s)
- Wenting Liu
- Department of Thoracic Oncology, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Qingwu Du
- Department of Thoracic Oncology, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Ting Mei
- Department of Thoracic Oncology, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Jingya Wang
- Department of Thoracic Oncology, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Dingzhi Huang
- Department of Thoracic Oncology, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China.
| | - Tingting Qin
- Department of Thoracic Oncology, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China.
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5
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Li L, Li S, Zhang X, Mei L, Fu X, Dai M, Wei N. Establishing the role of BRCA1 in the diagnosis, prognosis and immune infiltrates of breast invasive cancer by bioinformatics analysis and experimental validation. Aging (Albany NY) 2024; 16:1077-1095. [PMID: 38224491 PMCID: PMC10866431 DOI: 10.18632/aging.205366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/16/2023] [Indexed: 01/17/2024]
Abstract
BACKGROUND Breast cancer susceptibility gene 1 (BRCA1) is a well-known gene that acts a vital role in suppressing the growth of tumors. Previous studies have primarily focused on the genetic mutations of BRCA1 and its association with hereditary breast invasive carcinoma (BRCA). However, little research has been done to investigate the relationship between BRCA1 and immune infiltrates and prognosis in BRCA. METHODS We obtained the expression profiles and clinical information of patients with BRCA from the Cancer Genome Atlas (TCGA) database. The levels of the BRCA1 gene between BRCA tissues and normal breast tissues were compared through the Wilcoxon rank-sum test. Additionally, we performed WB and RT-qPCR techniques to detect the expression of BRCA1. We conducted functional enrichment analyses. Furthermore, we assessed immune cell infiltration using a single-sample gene set enrichment analysis. The methylation status of the BRCA1 gene was analyzed using the UALCAN and MethSurv databases. The Cox regression analysis and (KM) Kaplan-Meier method were employed to determine the prognostic value of BRCA1. In order to provide a practical tool for predicting the overall survival rates at different time points, we also constructed a nomogram. RESULTS Our analysis revealed that the expression of BRCA1 was significantly higher in BRCA tissues compared to normal tissues. Furthermore, this increased level of BRCA1 was found to be associated with specific BRCA subtypes, including T2, stage II, ER positive, ect. Importantly, the overexpression of BRCA1 was shown to be a negative prognostic marker for the overall survival rates of BRCA patients. Moreover, low methylation status of the BRCA1 gene was related to a poorer prognosis. Furthermore, our results indicated that high levels of BRCA1 are related to a decrease in level of killer immune cells, such as natural killer (NK) cells, macrophages, CD8+ T cells, and plasma-like dendritic cells (pDCs) within the tumor microenvironment. CONCLUSIONS Our study is the first to provide evidence indicating that the presence of BRCA1 can serve as a reliable marker for both diagnosing and determining the prognosis of BRCA. Moreover, BRCA1 acts as a crucial indicator of the cancer's potential to infiltrate and invade the immune system, which has important implications for developing targeted therapies in BRCA.
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Affiliation(s)
- Leilei Li
- Department of Pathology, Kunming Medical University, Kunming 650500, Yunnan, China
| | - Shuangyan Li
- Department of Oncology, Kunming Medical University, Kunming 650500, Yunnan, China
| | - Xuyang Zhang
- Department of Hepatobiliary, Second Affiliated Hospital of Zunyi Medical University, Zunyi 563000, Guizhou, China
| | - Liying Mei
- Department of Breast Surgery, Guizhou Provincial People’s Hospital, Guiyang 550002, Guizhou, China
| | - Xueqin Fu
- Department of Breast Surgery, Guizhou Provincial People’s Hospital, Guiyang 550002, Guizhou, China
| | - Min Dai
- Department of Breast Surgery, Guizhou Provincial People’s Hospital, Guiyang 550002, Guizhou, China
| | - Na Wei
- Department of Breast Surgery, Guizhou Provincial People’s Hospital, Guiyang 550002, Guizhou, China
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6
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Misra G, Qaisar S, Singh P. CRISPR-based therapeutic targeting of signaling pathways in breast cancer. Biochim Biophys Acta Mol Basis Dis 2024; 1870:166872. [PMID: 37666438 DOI: 10.1016/j.bbadis.2023.166872] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/24/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023]
Abstract
Breast cancer remains a leading cause of death for women worldwide, and new treatment strategies are needed. There are innumerable anomalous genes that are responsible for the multi-factorial carcinogenesis pathway. Although several disease-causing mutations have been detected, therapy frequently focuses on attenuating the manifestation of the disease rather than harmonizing the mutation in the target area. The advent of CRISPR-Cas9 technology has revolutionized genome editing, allowing for precise and efficient manipulation of gene expression. The purpose of this review paper is to summarize recent progress in the use of CRISPR-based approaches to target key signaling pathways associated with breast cancer progression. The first section introduces basic concepts of CRISPR technology, focusing on its application in genome editing and transcriptional regulation followed by an overview of aspects involving complex signaling pathways in breast cancer such as P13K/AKT/mTOR, EPK/MAPK and Wnt/β catenin. An extensive literature search using PubMed and Google Scholar is performed for information retrieval. Further, the role of CRISPR-based interventions in regulating gene expression revealed, altered pathway activity and potential therapeutic consequences are discussed. This review will be a valuable addition to providing comprehensive knowledge of CRISPR-Cas-mediated therapeutic targeting in breast cancer.
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Affiliation(s)
- Gauri Misra
- National Institute of Biologicals, Noida 201309, UP, India.
| | - Sidra Qaisar
- National Institute of Biologicals, Noida 201309, UP, India
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7
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Miao X, Koch G, Shen S, Wang X, Li J, Shen X, Qu J, Straubinger RM, Jusko WJ. Systems Pharmacodynamic Model of Combined Gemcitabine and Trabectedin in Pancreatic Cancer Cells. Part II: Cell Cycle, DNA Damage Response, and Apoptosis Pathways. J Pharm Sci 2024; 113:235-245. [PMID: 37918792 PMCID: PMC10902796 DOI: 10.1016/j.xphs.2023.10.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/04/2023]
Abstract
Despite decades of research efforts, pancreatic adenocarcinoma (PDAC) continues to present a formidable clinical challenge, demanding innovative therapeutic approaches. In a prior study, we reported the synergistic cytotoxic effects of gemcitabine and trabectedin on pancreatic cancer cells. To investigate potential mechanisms underlying this synergistic pharmacodynamic interaction, liquid chromatography-mass spectrometry-based proteomic analysis was performed, and a systems pharmacodynamics model (SPD) was developed to capture pancreatic cancer cell responses to gemcitabine and trabectedin, alone and combined, at the proteome level. Companion report Part I describes the proteomic workflow and drug effects on the upstream portion of the SPD model related to cell growth and migration, specifically the RTK-, integrin-, GPCR-, and calcium-signaling pathways. This report presents Part II of the SPD model. Here we describe drug effects on pathways associated with cell cycle, DNA damage response (DDR), and apoptosis, and provide insights into underlying mechanisms. Drug combination effects on protein changes in the cell cycle- and apoptosis pathways contribute to the synergistic effects observed between gemcitabine and trabectedin. The SPD model was subsequently incorporated into our previously-established cell cycle model, forming a comprehensive, multi-scale quantification platform for evaluating drug effects across multiple scales, spanning the proteomic-, cellular-, and subcellular levels. This approach provides a quantitative mechanistic framework for evaluating drug-drug interactions in combination chemotherapy, and could potentially serve as a tool to predict combinatorial efficacy and assist in target selection.
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Affiliation(s)
- Xin Miao
- Department of Pharmaceutical Sciences, University at Buffalo, SUNY, Buffalo, NY, USA
| | - Gilbert Koch
- Pediatric Pharmacology and Pharmacometrics Research Center, University of Basel, Children's Hospital, Basel, Switzerland
| | - Shichen Shen
- Department of Biochemistry, School of Medicine and Biomedical Sciences, University at Buffalo, SUNY, Buffalo, NY, USA; New York State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, USA
| | - Xue Wang
- New York State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, USA; Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Jun Li
- New York State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, USA
| | - Xiaomeng Shen
- Department of Biochemistry, School of Medicine and Biomedical Sciences, University at Buffalo, SUNY, Buffalo, NY, USA; New York State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, USA
| | - Jun Qu
- Department of Pharmaceutical Sciences, University at Buffalo, SUNY, Buffalo, NY, USA; New York State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, USA
| | - Robert M Straubinger
- Department of Pharmaceutical Sciences, University at Buffalo, SUNY, Buffalo, NY, USA; New York State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, USA; Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - William J Jusko
- Department of Pharmaceutical Sciences, University at Buffalo, SUNY, Buffalo, NY, USA.
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Ho YF, Yajit NLM, Shiau JY, Malek SNA, Shyur LF, Karsani SA. Changes in the Proteome Profile of A549 Cells Following Helichrysetin-Induced Apoptosis Suggest the Involvement of DNA Damage Response and Cell Cycle Arrest-Associated Proteins. Appl Biochem Biotechnol 2023; 195:6867-6880. [PMID: 36947367 DOI: 10.1007/s12010-023-04384-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2023] [Indexed: 03/23/2023]
Abstract
Our previous findings demonstrated that Helichrysetin possessed promising anti-cancer activity. It was able to induce apoptosis in the A549 cell line. However, its mechanism of action is unknown. The present study aimed to unravel possible underlying molecular mechanisms of helichrysetin-induced apoptosis in A549 (human lung carcinoma) cells using comparative quantitative proteomics (iTRAQ labeled), followed by an exhaustive bioinformatics analysis. Our results suggested that DNA damage response (DDR) and cell cycle arrest were responsible for lung cancer cell death with helichrysetin treatment. Among proteins that changed in abundance were Nrf2 and HMOX1. They are oxidative stress-related proteins and were increased in abundance. BRAT1 was also increased in abundance, suggesting an increase in DNA damage repair, indicating the occurrence of DNA damage due to oxidative stress. However, several essential DDR downstream proteins such as p-ATM, BRCA1, FANCD2, and Rb1 that would further increase DNA damage were found to be dramatically decreased in relative abundance. Cell cycle-related proteins, p53, p21, and cyclin D1, were increased while cyclin A, cyclin E, and cdk2 were decreased. This is predicted to facilitate S-phase arrest. Furthermore, excessive DNA damage and prolonged arrest would in turn result in the induction of mitochondrial-mediated apoptosis. Based on these observations, we postulate that the effects of helichrysetin were in part via the suppression of DNA damage response which led to DNA damage and prolonged cell cycle arrest. Subsequently, this event initiated mitochondrial-mediated apoptosis in A549 lung cancer cells.
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Affiliation(s)
- Yen Fong Ho
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Noor Liana Mat Yajit
- University of Malaya Centre for Proteomics Research (UMCPR), Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Jeng-Yuan Shiau
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Sri Nurestri Abd Malek
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Lie-Fen Shyur
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan.
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan.
| | - Saiful Anuar Karsani
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
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Qiu L, Xu W, Lu X, Chen F, Chen Y, Tian Y, Zhu Q, Liu X, Wang Y, Pei XH, Xu X, Zhang J, Zhu WG. The HDAC6-RNF168 axis regulates H2A/H2A.X ubiquitination to enable double-strand break repair. Nucleic Acids Res 2023; 51:9166-9182. [PMID: 37503842 PMCID: PMC10516627 DOI: 10.1093/nar/gkad631] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/24/2023] [Accepted: 07/17/2023] [Indexed: 07/29/2023] Open
Abstract
Histone deacetylase 6 (HDAC6) mediates DNA damage signaling by regulating the mismatch repair and nucleotide excision repair pathways. Whether HDAC6 also mediates DNA double-strand break (DSB) repair is unclear. Here, we report that HDAC6 negatively regulates DSB repair in an enzyme activity-independent manner. In unstressed cells, HDAC6 interacts with H2A/H2A.X to prevent its interaction with the E3 ligase RNF168. Upon sensing DSBs, RNF168 rapidly ubiquitinates HDAC6 at lysine 116, leading to HDAC6 proteasomal degradation and a restored interaction between RNF168 and H2A/H2A.X. H2A/H2A.X is ubiquitinated by RNF168, precipitating the recruitment of DSB repair factors (including 53BP1 and BRCA1) to chromatin and subsequent DNA repair. These findings reveal novel regulatory machinery based on an HDAC6-RNF168 axis that regulates the H2A/H2A.X ubiquitination status. Interfering with this axis might be leveraged to disrupt a key mechanism of cancer cell resistance to genotoxic damage and form a potential therapeutic strategy for cancer.
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Affiliation(s)
- Lingyu Qiu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Wenchao Xu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Xiaopeng Lu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Feng Chen
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Yongcan Chen
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Yuan Tian
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Qian Zhu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Xiangyu Liu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Yongqing Wang
- Division of Rheumatology and Immunology, University of Toledo Medical Center, 3120 Glendale Avenue, Toledo 43614, OH, USA
| | - Xin-Hai Pei
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Anatomy and Histology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Xingzhi Xu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Cell Biology and Medical Genetics, Shenzhen University Medical School, Shenzhen 518055, China
| | - Jun Zhang
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Wei-Guo Zhu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
- School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, China
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
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10
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Al-Kafaji G, Jassim G, AlHajeri A, Alawadhi AMT, Fida M, Sahin I, Alali F, Fadel E. Investigation of germline variants in Bahraini women with breast cancer using next-generation sequencing based-multigene panel. PLoS One 2023; 18:e0291015. [PMID: 37656691 PMCID: PMC10473515 DOI: 10.1371/journal.pone.0291015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/20/2023] [Indexed: 09/03/2023] Open
Abstract
Germline variants in BRCA1 and BRCA2 (BRCA1/2) genes are the most common cause of hereditary breast cancer. However, a significant number of cases are not linked to these two genes and additional high-, moderate- and low-penetrance genes have been identified in breast cancer. The advent of next-generation sequencing (NGS) allowed simultaneous sequencing of multiple cancer-susceptibility genes and prompted research in this field. So far, cancer-predisposition genes other than BRCA1/2 have not been studied in the population of Bahrain. We performed a targeted NGS using a multi-panel covering 180 genes associated with cancer predisposition to investigate the spectrum and frequency of germline variants in 54 women with a positive personal and/or family history of breast cancer. Sequencing analysis revealed germline variants in 29 (53.7%) patients. Five pathogenic/likely pathogenic variants in four DNA repair pathway-related genes were identified in five unrelated patients (9.3%). Two BRCA1 variants, namely the missense variant c.287A>G (p.Asp96Gly) and the truncating variant c.1066C>T (p.Gln356Ter), were detected in two patients (3.7%). Three variants in non-BRCA1/2 genes were detected in three patients (1.85% each) with a strong family history of breast cancer. These included a monoallelic missense variant c.1187G>A (p.Gly396Asp) in MUTYH gene, and two truncating variants namely c.3343C>T (p.Arg1115Ter) in MLH3 gene and c.1826G>A (p.Trp609Ter) in PMS1 gene. Other variants of uncertain significance (VUS) were also detected, and some of them were found together with the deleterious variants. In this first application of NGS-based multigene testing in Bahraini women with breast cancer, we show that multigene testing can yield additional genomic information on low-penetrance genes, although the clinical significance of these genes has not been fully appreciated yet. Our findings also provide valuable epidemiological information for future studies and highlight the importance of genetic testing, and an NGS-based multigene analysis may be applied supplementary to traditional genetic counseling.
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Affiliation(s)
- Ghada Al-Kafaji
- Department of Molecular Medicine and Al-Jawhara Centre for Molecular Medicine, Genetics, and Inherited Disorders, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Kingdom of Bahrain
| | - Ghufran Jassim
- Department of Family Medicine, Royal College of Surgeons in Ireland-Bahrain, Manama, Kingdom of Bahrain
| | - Amani AlHajeri
- Department of Genetics, Salmaniya Medical Complex, Manama, Kingdom of Bahrain
| | | | - Mariam Fida
- Bahrain Oncology Center, King Hamad University Hospital, Manama, Kingdom of Bahrain
| | - Ibrahim Sahin
- Department of Molecular Medicine and Al-Jawhara Centre for Molecular Medicine, Genetics, and Inherited Disorders, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Kingdom of Bahrain
| | - Faisal Alali
- North western Hospital, Chicago Medical School, North Chicago, Illinois, United States of America
| | - Elias Fadel
- Bahrain Oncology Center, King Hamad University Hospital, Manama, Kingdom of Bahrain
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11
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Diabate M, Islam MM, Nagy G, Banerjee T, Dhar S, Smith N, Adamovich AI, Starita LM, Parvin JD. DNA repair function scores for 2172 variants in the BRCA1 amino-terminus. PLoS Genet 2023; 19:e1010739. [PMID: 37578980 PMCID: PMC10449183 DOI: 10.1371/journal.pgen.1010739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 08/24/2023] [Accepted: 07/16/2023] [Indexed: 08/16/2023] Open
Abstract
Single nucleotide variants are the most frequent type of sequence changes detected in the genome and these are frequently variants of uncertain significance (VUS). VUS are changes in DNA for which disease risk association is unknown. Thus, methods that classify the functional impact of a VUS can be used as evidence for variant interpretation. In the case of the breast and ovarian cancer specific tumor suppressor protein, BRCA1, pathogenic missense variants frequently score as loss of function in an assay for homology-directed repair (HDR) of DNA double-strand breaks. We previously published functional results using a multiplexed assay for 1056 amino acid substitutions residues 2-192 in the amino terminus of BRCA1. In this study, we have re-assessed the data from this multiplexed assay using an improved analysis pipeline. These new analysis methods yield functional scores for more variants in the first 192 amino acids of BRCA1, plus we report new results for BRCA1 amino acid residues 193-302. We now present the functional classification of 2172 BRCA1 variants in BRCA1 residues 2-302 using the multiplexed HDR assay. Comparison of the functional determinations of the missense variants with clinically known benign or pathogenic variants indicated 93% sensitivity and 100% specificity for this assay. The results from BRCA1 variants tested in this assay are a resource for clinical geneticists for evidence to evaluate VUS in BRCA1.
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Affiliation(s)
- Mariame Diabate
- The Ohio State University, Department of Biomedical Informatics, Columbus, Ohio, United States of America
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, United States of America
| | - Muhtadi M. Islam
- The Ohio State University, Department of Biomedical Informatics, Columbus, Ohio, United States of America
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, United States of America
| | - Gregory Nagy
- The Ohio State University, Department of Biomedical Informatics, Columbus, Ohio, United States of America
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, United States of America
| | - Tapahsama Banerjee
- The Ohio State University, Department of Biomedical Informatics, Columbus, Ohio, United States of America
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, United States of America
| | - Shruti Dhar
- The Ohio State University, Department of Biomedical Informatics, Columbus, Ohio, United States of America
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, United States of America
| | - Nahum Smith
- The University of Washington, Department of Genome Sciences, Seattle, Washington, United States of America
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, United States of America
| | - Aleksandra I. Adamovich
- The Ohio State University, Department of Biomedical Informatics, Columbus, Ohio, United States of America
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, United States of America
| | - Lea M. Starita
- The University of Washington, Department of Genome Sciences, Seattle, Washington, United States of America
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, United States of America
| | - Jeffrey D. Parvin
- The Ohio State University, Department of Biomedical Informatics, Columbus, Ohio, United States of America
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, United States of America
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12
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León-Mejía G, Vargas JE, Quintana-Sosa M, Rueda RA, Pérez JP, Miranda-Guevara A, Moreno OF, Trindade C, Acosta-Hoyos A, Dias J, da Silva J, Pêgas Henriques JA. Exposure to coal mining can lead to imbalanced levels of inorganic elements and DNA damage in individuals living near open-pit mining sites. ENVIRONMENTAL RESEARCH 2023; 227:115773. [PMID: 36966995 DOI: 10.1016/j.envres.2023.115773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/17/2023] [Accepted: 03/23/2023] [Indexed: 05/08/2023]
Abstract
Coal mining activities are considered harmful to living organisms. These activities release compounds to the environment, such as polycyclic aromatic hydrocarbons (PAHs), metals, and oxides, which can cause oxidative damage to DNA. In this study, we compared the DNA damage and the chemical composition of peripherical blood of 150 individuals exposed to coal mining residues and 120 non-exposed individuals. Analysis of coal particles revealed the presence of elements such as copper (Cu), aluminum (Al), chrome (Cr), silicon (Si) and iron (Fe). The exposed individuals in our study had significant concentrations of Al, sulfur (S), Cr, Fe, and Cu in their blood, as well as hypokalemia. Results from the enzyme-modified comet assay (FPG enzyme) suggest that exposure to coal mining residues caused oxidative DNA damage, particularly purine damage. Furthermore, particles with a diameter of <2.5 μm indicate that direct inhalation could promote these physiological alterations. Finally, a systems biology analysis was performed to investigate the effects of these elements on DNA damage and oxidative stress pathways. Interestingly, Cu, Cr, Fe, and K are key nodes that intensely modulate these pathways. Our results suggest that understanding the imbalance of inorganic elements caused by exposure to coal mining residues is crucial to understanding their effect on human health.
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Affiliation(s)
- Grethel León-Mejía
- Centro de Investigaciones en Ciencias de La Vida (CICV), Universidad Simón Bolívar, Barranquilla, 080002, Colombia.
| | - Jose Eduardo Vargas
- Departamento de Biologia Celular. Universidade Federal de Paraná, Curitiba, Brazil
| | - Milton Quintana-Sosa
- Centro de Investigaciones en Ciencias de La Vida (CICV), Universidad Simón Bolívar, Barranquilla, 080002, Colombia
| | - Robinson Alvarez Rueda
- Centro de Investigaciones en Ciencias de La Vida (CICV), Universidad Simón Bolívar, Barranquilla, 080002, Colombia
| | - Jose Pérez Pérez
- Centro de Investigaciones en Ciencias de La Vida (CICV), Universidad Simón Bolívar, Barranquilla, 080002, Colombia
| | - Alvaro Miranda-Guevara
- Centro de Investigaciones en Ciencias de La Vida (CICV), Universidad Simón Bolívar, Barranquilla, 080002, Colombia
| | - Ornella Fiorillo Moreno
- Centro de Investigaciones en Ciencias de La Vida (CICV), Universidad Simón Bolívar, Barranquilla, 080002, Colombia
| | - Cristiano Trindade
- Centro de Investigaciones en Ciencias de La Vida (CICV), Universidad Simón Bolívar, Barranquilla, 080002, Colombia
| | - Antonio Acosta-Hoyos
- Centro de Investigaciones en Ciencias de La Vida (CICV), Universidad Simón Bolívar, Barranquilla, 080002, Colombia
| | - Johnny Dias
- Laboratório de Implantação Iônica, Instituto de Física, Universidade Federal Do Rio Grande Do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Juliana da Silva
- Laboratório de Genética Toxicológica, Universidade Luterana Do Brasil (ULBRA)& Universidade La Salle (UniaSalle), Canoas, RS, Brazil
| | - João Antonio Pêgas Henriques
- Departamento de Biofísica, Centro de Biotecnologia, Universidade Federal Do Rio Grande Do Sul (UFRGS), Porto Alegre, RS, Brazil; Programa de Pós-Graduação Em Biotecnologia e Em Ciências Médicas, Universidade Do Vale Do Taquari - UNIVATES, Lajeado, RS, Brazil
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13
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Chen JK, Wiedemann J, Nguyen L, Lin Z, Tahir M, Hui CC, Plikus MV, Andersen B. IRX5 promotes DNA damage repair and activation of hair follicle stem cells. Stem Cell Reports 2023; 18:1227-1243. [PMID: 37084727 PMCID: PMC10202659 DOI: 10.1016/j.stemcr.2023.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 04/23/2023] Open
Abstract
The molecular mechanisms allowing hair follicles to periodically activate their stem cells (HFSCs) are incompletely characterized. Here, we identify the transcription factor IRX5 as a promoter of HFSC activation. Irx5-/- mice have delayed anagen onset, with increased DNA damage and diminished HFSC proliferation. Open chromatin regions form near cell cycle progression and DNA damage repair genes in Irx5-/- HFSCs. DNA damage repair factor BRCA1 is an IRX5 downstream target. Inhibition of FGF kinase signaling partially rescues the anagen delay in Irx5-/- mice, suggesting that the Irx5-/- HFSC quiescent phenotype is partly due to failure to suppress Fgf18 expression. Interfollicular epidermal stem cells also show decreased proliferation and increased DNA damage in Irx5-/-mice. Consistent with a role for IRX5 as a promoter of DNA damage repair, we find that IRX genes are upregulated in many cancer types and that there is a correlation between IRX5 and BRCA1 expression in breast cancer.
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Affiliation(s)
- Jefferson K Chen
- Departments of Biological Chemistry and Medicine, Division of Endocrinology, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Julie Wiedemann
- Departments of Biological Chemistry and Medicine, Division of Endocrinology, School of Medicine, University of California, Irvine, Irvine, CA, USA; Mathematical, Computational and Systems Biology (MCSB) Program, University of California, Irvine, Irvine, CA, USA
| | - Ly Nguyen
- Departments of Biological Chemistry and Medicine, Division of Endocrinology, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Zhongqi Lin
- Departments of Biological Chemistry and Medicine, Division of Endocrinology, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Mahum Tahir
- Departments of Biological Chemistry and Medicine, Division of Endocrinology, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Chi-Chung Hui
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Maksim V Plikus
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Bogi Andersen
- Departments of Biological Chemistry and Medicine, Division of Endocrinology, School of Medicine, University of California, Irvine, Irvine, CA, USA.
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14
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Czegle I, Huang C, Soria PG, Purkiss DW, Shields A, Wappler-Guzzetta EA. The Role of Genetic Mutations in Mitochondrial-Driven Cancer Growth in Selected Tumors: Breast and Gynecological Malignancies. Life (Basel) 2023; 13:life13040996. [PMID: 37109525 PMCID: PMC10145875 DOI: 10.3390/life13040996] [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: 12/28/2022] [Revised: 03/15/2023] [Accepted: 03/31/2023] [Indexed: 04/29/2023] Open
Abstract
There is an increasing understanding of the molecular and cytogenetic background of various tumors that helps us better conceptualize the pathogenesis of specific diseases. Additionally, in many cases, these molecular and cytogenetic alterations have diagnostic, prognostic, and/or therapeutic applications that are heavily used in clinical practice. Given that there is always room for improvement in cancer treatments and in cancer patient management, it is important to discover new therapeutic targets for affected individuals. In this review, we discuss mitochondrial changes in breast and gynecological (endometrial and ovarian) cancers. In addition, we review how the frequently altered genes in these diseases (BRCA1/2, HER2, PTEN, PIK3CA, CTNNB1, RAS, CTNNB1, FGFR, TP53, ARID1A, and TERT) affect the mitochondria, highlighting the possible associated individual therapeutic targets. With this approach, drugs targeting mitochondrial glucose or fatty acid metabolism, reactive oxygen species production, mitochondrial biogenesis, mtDNA transcription, mitophagy, or cell death pathways could provide further tailored treatment.
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Affiliation(s)
- Ibolya Czegle
- Department of Internal Medicine and Haematology, Semmelweis University, H-1085 Budapest, Hungary
| | - Chelsea Huang
- Department of Pathology and Laboratory Medicine, Loma Linda University Health, Loma Linda, CA 92354, USA
| | - Priscilla Geraldine Soria
- Department of Pathology and Laboratory Medicine, Loma Linda University Health, Loma Linda, CA 92354, USA
| | - Dylan Wesley Purkiss
- Department of Pathology and Laboratory Medicine, Loma Linda University Health, Loma Linda, CA 92354, USA
| | - Andrea Shields
- Department of Pathology and Laboratory Medicine, Loma Linda University Health, Loma Linda, CA 92354, USA
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15
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Diabate M, Islam MM, Nagy G, Banerjee T, Dhar S, Smith N, Adamovich AI, Starita LM, Parvin JD. DNA Repair Function Scores for 2172 Variants in the BRCA1 Amino-Terminus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.10.536331. [PMID: 37090572 PMCID: PMC10120616 DOI: 10.1101/2023.04.10.536331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Single nucleotide variants are the most frequent type of sequence changes detected in the genome and these are frequently variants of uncertain significance (VUS). VUS are changes in DNA for which disease risk association is unknown. Thus, methods that classify the functional impact of a VUS can be used as evidence for variant interpretation. In the case of the breast and ovarian cancer specific tumor suppressor protein, BRCA1, pathogenic missense variants frequently score as loss of function in an assay for homology-directed repair (HDR) of DNA double-strand breaks. We previously published functional results using a multiplexed assay for 1056 amino acid substitutions residues 2-192 in the amino terminus of BRCA1. In this study, we have re-assessed the data from this multiplexed assay using an improved analysis pipeline. These new analysis methods yield functional scores for more variants in the first 192 amino acids of BRCA1, plus we report new results for BRCA1 amino acid residues 193-302. We now present the functional classification of 2172 BRCA1 variants in BRCA1 residues 2-302 using the multiplexed HDR assay. Comparison of the functional determinations of the missense variants with clinically known benign or pathogenic variants indicated 93% sensitivity and 100% specificity for this assay. The results from BRCA1 variants tested in this assay are a resource for clinical geneticists for evidence to evaluate VUS in BRCA1 . AUTHOR SUMMARY Most missense substitutions in BRCA1 are variants of unknown significance (VUS), and individuals with a VUS in BRCA1 cannot know from genetic information alone whether this variant predisposes to breast or ovarian cancer. We apply a multiplexed functional assay for homology directed repair of DNA double strand breaks to assess variant impact on this important BRCA1 protein function. We analyzed 2172 variants in the amino-terminus of BRCA1 and demonstrate that variants that are known as pathogenic have a loss of function in the DNA repair assay. Conversely, variants that are known to be benign are functionally normal in the multiplexed assay. We suggest that these functional determinations of BRCA1 variants can be used to augment the information that clinical cancer geneticists provide to patients who have a VUS in BRCA1 .
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Affiliation(s)
- Mariame Diabate
- The Ohio State University, Department of Biomedical Informatics, and The Ohio State University Comprehensive Center, Columbus, OH 43210
| | - Muhtadi M Islam
- The Ohio State University, Department of Biomedical Informatics, and The Ohio State University Comprehensive Center, Columbus, OH 43210
| | - Gregory Nagy
- The Ohio State University, Department of Biomedical Informatics, and The Ohio State University Comprehensive Center, Columbus, OH 43210
| | - Tapahsama Banerjee
- The Ohio State University, Department of Biomedical Informatics, and The Ohio State University Comprehensive Center, Columbus, OH 43210
| | - Shruti Dhar
- The Ohio State University, Department of Biomedical Informatics, and The Ohio State University Comprehensive Center, Columbus, OH 43210
| | - Nahum Smith
- The University of Washington, Department of Genome Sciences, Seattle, WA 98195
- Brotman Baty Institute for Precision Medicine, Seattle WA, 98195
| | - Aleksandra I Adamovich
- The Ohio State University, Department of Biomedical Informatics, and The Ohio State University Comprehensive Center, Columbus, OH 43210
| | - Lea M Starita
- The University of Washington, Department of Genome Sciences, Seattle, WA 98195
- Brotman Baty Institute for Precision Medicine, Seattle WA, 98195
| | - Jeffrey D Parvin
- The Ohio State University, Department of Biomedical Informatics, and The Ohio State University Comprehensive Center, Columbus, OH 43210
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16
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Divya KP, Keerthana S, Viswanathan C, Ponpandian N. MXene supported biomimetic bilayer lipid membrane biosensor for zeptomole detection of BRCA1 gene. Mikrochim Acta 2023; 190:116. [PMID: 36877256 DOI: 10.1007/s00604-023-05694-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/08/2023] [Indexed: 03/07/2023]
Abstract
A biomimetic bilayer lipid membrane supported MXene based biosensor is reported for electrochemical hybridization detection of the most prevalent and potential BC biomarker BRCA1. 2D MXene nanosheet-anchored gold nanoparticle-decorated biomimetic bilayer lipid membrane (AuNP@BLM) biosensor is used for the attachment of thiolated single-stranded DNA (HS-ssDNA) targeting hybridization detection. The interaction of biomimetic bilayer lipid membrane with 2D MXene nanosheets is explored in this work for the first time. The synergistic combination of MXene and AuNP@BLM has proven to efficiently improve the detection signal to several folds. The sensor provides hybridization signals only to the complementary DNA (cDNA) sequence with a linearity range 10 zM to 1 µM and LOD of 1 zM without the need of any further amplification. The specificity of the biosensor is validated using non-complementary (ncDNA) and double base mis-match oligonucleotide DNA (dmmDNA) sequences. The sensor successfully distinguishes the signal for different target DNAs with good reproducibility indicated by the RSD value of 4.9%. Hence, we envision that the reported biosensor can be used to construct efficient diagnostic point-of-care tools based on molecular affinity interactions.
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Affiliation(s)
- Karutha Pandian Divya
- Bharathiar Cancer Theranostics Research Centre (BCTRC), RUSA 2.0, Bharathiar University, Coimbatore, 641 046, India.,Department of Nanoscience and Technology, Bharathiar University, Coimbatore, 641 046, India
| | | | | | - Nagamony Ponpandian
- Department of Nanoscience and Technology, Bharathiar University, Coimbatore, 641 046, India.
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17
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Dalberto D, Garcia ALH, De Souza MR, Picinini J, Soares S, De Souza GMS, Chytry P, Dias JF, Salvador M, Da Silva FR, Da Silva J. Dry tobacco leaves: an in vivo and in silico approach to the consequences of occupational exposure. Mutagenesis 2023; 38:120-130. [PMID: 36738258 DOI: 10.1093/mutage/gead003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
Exposure of tobacco workers handling dried tobacco leaves has been linked to an increased risk of toxicity and respiratory illness due to the presence of nicotine and other chemicals. This study aimed to evaluate the DNA damage caused by the exposure of tobacco growers during the dry leaf classification process and the relation to cellular mechanisms. A total of 86 individuals participated in the study, divided into a group exposed to dry tobacco (n = 44) and a control group (n = 42). Genotoxicity was evaluated using the alkaline comet assay and lymphocyte micronucleus (MN) assay (CBMN-Cyt), and measurement of telomere length. The levels of oxidative and nitrosative stress were evaluated through the formation of thiobarbituric acid reactive species, and nitric oxide levels, respectively. The inorganic elements were measured in the samples using particle-induced X-ray emission method. The combination of variables was demonstrated through principal component analysis and the interactions were expanded through systems biology. Comet assay, MN, death cells, thiobarbituric acid reactive species, and nitrosative stress showed a significant increase for all exposed groups in relation to the control. Telomere length showed a significant decrease for exposed women and total exposed group in relation to men and control groups, respectively. Bromine (Br) and rubidium (Rb) in the exposed group presented higher levels than control groups. Correlations between nitrate and apoptosis; Br and MN and necrosis; and Rb and telomeres; besides age and DNA damage and death cells were observed. The systems biology analysis demonstrated that tobacco elements can increase the nuclear translocation of NFKB dimers inducing HDAC2 expression, which, associated with BRCA1 protein, can potentially repress transcription of genes that promote DNA repair. Dry tobacco workers exposed to dry leaves and their different agents showed DNA damage by different mechanisms, including redox imbalance.
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Affiliation(s)
- Daiana Dalberto
- Laboratory of Genetic Toxicology, PPGBioSaúde, Lutheran University of Brazil (ULBRA), Canoas, RS, Brazil
| | - Ana L H Garcia
- Laboratory of Genetic Toxicology, PPGBioSaúde, Lutheran University of Brazil (ULBRA), Canoas, RS, Brazil.,Laboratory of Genetic Toxicology, PPGSDH, La Salle University (UniLaSalle), Canoas, RS, Brazil
| | - Melissa R De Souza
- Laboratory of Genetic Toxicology, PPGBioSaúde, Lutheran University of Brazil (ULBRA), Canoas, RS, Brazil
| | - Juliana Picinini
- Laboratory of Genetic Toxicology, PPGBioSaúde, Lutheran University of Brazil (ULBRA), Canoas, RS, Brazil
| | - Solange Soares
- Laboratory of Genetic Toxicology, PPGBioSaúde, Lutheran University of Brazil (ULBRA), Canoas, RS, Brazil
| | - Guilherme M S De Souza
- Ion Implantation Laboratory, Institute of Physics, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Paola Chytry
- Ion Implantation Laboratory, Institute of Physics, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Johnny F Dias
- Ion Implantation Laboratory, Institute of Physics, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Mirian Salvador
- Biotechnology Institute, University of Caxias do Sul, Caxias do Sul (UCS), RS, Brazil
| | - Fernanda R Da Silva
- Laboratory of Genetic Toxicology, PPGSDH, La Salle University (UniLaSalle), Canoas, RS, Brazil
| | - Juliana Da Silva
- Laboratory of Genetic Toxicology, PPGBioSaúde, Lutheran University of Brazil (ULBRA), Canoas, RS, Brazil.,Laboratory of Genetic Toxicology, PPGSDH, La Salle University (UniLaSalle), Canoas, RS, Brazil
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18
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Manunu B, Serafin AM, Akudugu JM. BAG1, MGMT, FOXO1, and DNAJA1 as potential drug targets for radiosensitizing cancer cell lines. Int J Radiat Biol 2023; 99:292-307. [PMID: 35511481 DOI: 10.1080/09553002.2022.2074164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
BACKGROUND AND PURPOSE Activation of some signaling pathways can promote cell survival and have a negative impact on tumor response to radiotherapy. Here, the role of differences in expression levels of genes related to the poly(ADP-ribose) polymerase-1 (PARP-1), heat shock protein 90 (Hsp90), B-cell lymphoma 2 (Bcl-2), and phosphoinositide 3-kinase (PI3K) pathways in the survival or death of cells following X-ray exposure was investigated. METHODS Eight human cell cultures (MCF-7 and MDA-MB-231: breast cancers; MCF-12A: apparently normal breast; A549: lung cancer; L132: normal lung; G28, G44 and G112: glial cancers) were irradiated with X-rays. The colony-forming and real-time PCR based on a custom human pathway RT2 Profiler PCR Array assays were used to evaluate cell survival and gene expression, respectively. RESULTS The surviving fractions at 2 Gy for the cell lines, in order of increasing radioresistance, were found to be as follows: MCF-7 (0.200 ± 0.011), G44 (0.277 ± 0.065), L132 (0.367 ± 0.023), MDA-MB-231 (0.391 ± 0.057), G112 (0.397 ± 0.113), A549 (0.490 ± 0.048), MCF-12A (0.526 ± 0.004), and G28 (0.633 ± 0.094). The rank order of radioresistance at 6 Gy was: MCF-7 < L132 < G44 < MDA-MB-231 < A549 < G28 < G112 < MCF-12A. PCR array data analysis revealed that several genes were differentially expressed between irradiated and unirradiated cell cultures. The following genes, with fold changes: BCL2A1 (21.91), TP53 (8743.75), RAD51 (11.66), FOX1 (65.86), TCP1 (141.32), DNAJB1 (3283.64), RAD51 (51.52), and HSPE1 (12887.29) were highly overexpressed, and BAX (-127.21), FOX1 (-81.79), PDPK1 (-1241.78), BRCA1 (-8.70), MLH1 (-12143.95), BCL2 (-18.69), CCND1 (-46475.98), and GJA1 (-2832.70) were highly underexpressed in the MDA-MB-231, MCF-7, MCF-12A, A549, L132, G28, G44, and G112 cell lines, respectively. The radioresistance in the malignant A549 and G28 cells was linked to upregulation in the apoptotic, DNA repair, PI3K, and Hsp90 pathway genes BAG1, MGMT, FOXO1, and DNAJA1, respectively, and inhibition of these genes resulted in significant radiosensitization. CONCLUSIONS Targeting BAG1, MGMT, FOXO1, and DNAJA1 with specific inhibitors might effectively sensitize radioresistant tumors to radiotherapy.
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Affiliation(s)
- Bayanika Manunu
- Division of Radiobiology, Department of Medical Imaging and Clinical Oncology, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
| | - Antonio M Serafin
- Division of Radiobiology, Department of Medical Imaging and Clinical Oncology, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
| | - John M Akudugu
- Division of Radiobiology, Department of Medical Imaging and Clinical Oncology, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
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19
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Choi E, Mun GI, Lee J, Lee H, Cho J, Lee YS. BRCA1 deficiency in triple-negative breast cancer: Protein stability as a basis for therapy. Biomed Pharmacother 2023; 158:114090. [PMID: 36493696 DOI: 10.1016/j.biopha.2022.114090] [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: 10/24/2022] [Revised: 11/24/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Mutations in breast cancer-associated 1 (BRCA1) increase the lifetime risk of developing breast cancer by up to 51% over the risk of the general population. Many aspects of this multifunctional protein have been revealed, including its essential role in homologous recombination repair, E3 ubiquitin ligase activity, transcriptional regulation, and apoptosis. Although most studies have focused on BRCA1 deficiency due to mutations, only a minority of patients carry BRCA1 mutations. A recent study has suggested an expanded definition of BRCA1 deficiency with reduced BRCA1 levels, which accounts for almost half of all triple-negative breast cancer (TNBC) patients. Reduced BRCA1 levels can result from epigenetic modifications or increased proteasomal degradation. In this review, we discuss how this knowledge of BRCA1 function and regulation of BRCA1 protein stability can help overcome the challenges encountered in the clinic and advance current treatment strategies for BRCA1-related breast cancer patients, especially focusing on TNBC.
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Affiliation(s)
- Eun Choi
- Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Gil-Im Mun
- Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Joohyun Lee
- Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Hanhee Lee
- Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jaeho Cho
- Department of Radiation Oncology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Yun-Sil Lee
- Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea.
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20
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Sukumaran S, Zochedh A, Viswanathan TM, Sultan AB, Kathiresan T. Theoretical Investigation of 5-Fluorouracil and Tamoxifen Complex – Structural, Spectrum, DFT, ADMET and Docking Simulation. Polycycl Aromat Compd 2023. [DOI: 10.1080/10406638.2022.2164018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Sureba Sukumaran
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil, Tamil Nadu, India
| | - Azar Zochedh
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil, Tamil Nadu, India
| | - Thimma Mohan Viswanathan
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil, Tamil Nadu, India
| | - Asath Bahadur Sultan
- Department of Physics, Condensed Matter Physics Laboratory, Kalasalingam Academy of Research and Education, Krishnankoil, Tamil Nadu, India
| | - Thandavarayan Kathiresan
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil, Tamil Nadu, India
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21
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Barszczewska-Pietraszek G, Drzewiecka M, Czarny P, Skorski T, Śliwiński T. Polθ Inhibition: An Anticancer Therapy for HR-Deficient Tumours. Int J Mol Sci 2022; 24:ijms24010319. [PMID: 36613762 PMCID: PMC9820168 DOI: 10.3390/ijms24010319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/15/2022] [Accepted: 12/17/2022] [Indexed: 12/28/2022] Open
Abstract
DNA polymerase theta (Polθ)-mediated end joining (TMEJ) is, along with homologous recombination (HR) and non-homologous end-joining (NHEJ), one of the most important mechanisms repairing potentially lethal DNA double-strand breaks (DSBs). Polθ is becoming a new target in cancer research because it demonstrates numerous synthetically lethal interactions with other DNA repair mechanisms, e.g., those involving PARP1, BRCA1/2, DNA-PK, ATR. Inhibition of Polθ could be achieved with different methods, such as RNA interference (RNAi), CRISPR/Cas9 technology, or using small molecule inhibitors. In the context of this topic, RNAi and CRISPR/Cas9 are still more often applied in the research itself rather than clinical usage, different than small molecule inhibitors. Several Polθ inhibitors have been already generated, and two of them, novobiocin (NVB) and ART812 derivative, are being tested in clinical trials against HR-deficient tumors. In this review, we describe the significance of Polθ and the Polθ-mediated TMEJ pathway. In addition, we summarize the current state of knowledge about Polθ inhibitors and emphasize the promising role of Polθ as a therapeutic target.
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Affiliation(s)
| | - Małgorzata Drzewiecka
- Laboratory of Medical Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 90-236 Lodz, Poland
| | - Piotr Czarny
- Department of Medical Biochemistry, Medical University of Lodz, 92-216 Lodz, Poland
| | - Tomasz Skorski
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Tomasz Śliwiński
- Laboratory of Medical Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 90-236 Lodz, Poland
- Correspondence: ; Tel.: +48-42-635-44-86
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22
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Malacrida A, Erriquez J, Hashemi M, Rodriguez-Menendez V, Cassetti A, Cavaletti G, Miloso M. Evaluation of antitumoral effect of Hibiscus sabdariffa extract on human breast cancer cells. Biochem Biophys Rep 2022; 32:101353. [PMID: 36186735 PMCID: PMC9519930 DOI: 10.1016/j.bbrep.2022.101353] [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: 04/29/2022] [Revised: 08/17/2022] [Accepted: 09/19/2022] [Indexed: 11/22/2022] Open
Abstract
BackgroundBreast cancer is the most frequent tumor in women. Natural substances represent an important source of innovative therapeutic solutions, eventually integrating or substituting conventional drugs and chemicals. Hibiscus sabdariffa L. is a plant of the Malvaceae family that has raised interest thanks to its anti-inflammatory, antioxidant and anticancer effects. In this work, we evaluated the antitumoral effects of an enriched fraction of Hibiscus sabdariffa L. extract (HsEF) in two human breast cancer cell lines, MCF-7(ERα +) and MDA-MB-231 (triple negative). Methods and resultsCell viability was assessed by MTT and Trypan blue assays. HsEF reduced both cell lines viability in a dose and time dependent manner and this effect results irreversible. In MCF-7 cells immunofluorescence experiments, demonstrated that HsEF induced ERα trans-location from nucleus to perinuclear area and in cytoplasmic compartment. qRT-PCR and western blotting high-lighted that HsEF reduced ERα, BRCA1 and caveolin1 gene and protein expression in MCF-7 cells, but not in MDA-MB-231 cells. Moreover, we demonstrated that HsEF reduced proteasome activity, an increased autophagy, impair migration and invasion in both cell lines. ConclusionsOur data suggest HsEF has an antitumoral effects on both breast tumor cells examined and that ERα involvement could explain the differences observed between the two cell lines. Breast cancer conventional treatments have some limitations, such as drug resistance, metastasis and high heterogeneity. Natural products and their metabolites represent an alternative and an interesting therapeutic option. H. sabdariffa reduce cell viability, cell migration and cell invasion of breast cancer cell lines MCF-7 and MDA-MB-231. H. sabdariffa inhibits proteasome and induces autophagy. H.sabdariffa induce estrogen receptor downregulation and intracellular de-localization.
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23
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Qi H, Kikuchi M, Yoshino Y, Fang Z, Ohashi K, Gotoh T, Ideta R, Ui A, Endo S, Otsuka K, Shindo N, Gonda K, Ishioka C, Miki Y, Iwabuchi T, Chiba N. BRCA1 transports the DNA damage signal for CDDP-induced centrosome amplification through the centrosomal Aurora A. Cancer Sci 2022; 113:4230-4243. [PMID: 36082621 DOI: 10.1111/cas.15573] [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: 06/23/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 12/15/2022] Open
Abstract
Breast cancer gene 1 (BRCA1) plays roles in DNA repair and centrosome regulation and is involved in DNA damage-induced centrosome amplification (DDICA). Here, the centrosomal localization of BRCA1 and the kinases involved in centrosome duplication were analyzed in each cell cycle phase after treatment with DNA crosslinker cisplatin (CDDP). CDDP treatment increased the centrosomal localization of BRCA1 in early S-G2 phase. BRCA1 contributed to the increased centrosomal localization of Aurora A in S phase and that of phosphorylated Polo-like kinase 1 (PLK1) in late S phase after CDDP treatment, resulting in centriole disengagement and overduplication. The increased centrosomal localization of BRCA1 and Aurora A induced by CDDP treatment involved the nuclear export of BRCA1 and BRCA1 phosphorylation by ataxia telangiectasia mutated (ATM). Patient-derived variants and mutations at phosphorylated residues of BRCA1 suppressed the interaction between BRCA1 and Aurora A, as well as the CDDP-induced increase in the centrosomal localization of BRCA1 and Aurora A. These results suggest that CDDP induces the phosphorylation of BRCA1 by ATM in the nucleus and its transport to the cytoplasm, thereby promoting the centrosomal localization Aurora A, which phosphorylates PLK1. The function of BRCA1 in the translocation of the DNA damage signal from the nucleus to the centrosome to induce centrosome amplification after CDDP treatment might support its role as a tumor suppressor.
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Affiliation(s)
- Huicheng Qi
- Department of Cancer Biology; Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.,Department of Cancer Biology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Megumi Kikuchi
- Department of Cancer Biology; Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.,Laboratory of Cancer Biology, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Yuki Yoshino
- Department of Cancer Biology; Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.,Department of Cancer Biology, Tohoku University Graduate School of Medicine, Sendai, Japan.,Laboratory of Cancer Biology, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Zhenzhou Fang
- Department of Cancer Biology; Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.,Department of Cancer Biology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kazune Ohashi
- Department of Cancer Biology; Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.,Laboratory of Cancer Biology, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Takato Gotoh
- Department of Cancer Biology; Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.,Laboratory of Cancer Biology, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Ryo Ideta
- Department of Cancer Biology; Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.,Tohoku University School of Medicine, Sendai, Japan
| | - Ayako Ui
- Department of Molecular Oncology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Shino Endo
- Department of Cancer Biology; Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.,Department of Cancer Biology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kei Otsuka
- Department of Cancer Biology; Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.,Laboratory of Cancer Biology, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Norihisa Shindo
- Division of Molecular and Cellular Oncology, Miyagi Cancer Center Research Institute, Natori, Japan
| | - Kohsuke Gonda
- Department of Medical Physics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Chikashi Ishioka
- Department of Clinical Oncology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoshio Miki
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tokuro Iwabuchi
- Faculty of Bioscience and Biotechnology, Tokyo University of Technology, Tokyo, Japan
| | - Natsuko Chiba
- Department of Cancer Biology; Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.,Department of Cancer Biology, Tohoku University Graduate School of Medicine, Sendai, Japan.,Laboratory of Cancer Biology, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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24
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Mathur R, Jha NK, Saini G, Jha SK, Shukla SP, Filipejová Z, Kesari KK, Iqbal D, Nand P, Upadhye VJ, Jha AK, Roychoudhury S, Slama P. Epigenetic factors in breast cancer therapy. Front Genet 2022; 13:886487. [PMID: 36212140 PMCID: PMC9539821 DOI: 10.3389/fgene.2022.886487] [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: 02/28/2022] [Accepted: 07/20/2022] [Indexed: 11/17/2022] Open
Abstract
Epigenetic modifications are inherited differences in cellular phenotypes, such as cell gene expression alterations, that occur during somatic cell divisions (also, in rare circumstances, in germ line transmission), but no alterations to the DNA sequence are involved. Histone alterations, polycomb/trithorax associated proteins, short non-coding or short RNAs, long non—coding RNAs (lncRNAs), & DNA methylation are just a few biological processes involved in epigenetic events. These various modifications are intricately linked. The transcriptional potential of genes is closely conditioned by epigenetic control, which is crucial in normal growth and development. Epigenetic mechanisms transmit genomic adaptation to an environment, resulting in a specific phenotype. The purpose of this systematic review is to glance at the roles of Estrogen signalling, polycomb/trithorax associated proteins, DNA methylation in breast cancer progression, as well as epigenetic mechanisms in breast cancer therapy, with an emphasis on functionality, regulatory factors, therapeutic value, and future challenges.
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Affiliation(s)
- Runjhun Mathur
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, India
- Dr. A.P.J Abdul Kalam Technical University, Lucknow, India
| | - Niraj Kumar Jha
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, India
- Department of Biotechnology, School of Applied and Life Sciences (SALS), Uttaranchal University, Dehradun, India
- Department of Biotechnology Engineering and Food Technology, Chandigarh University, Mohali, India
| | - Gaurav Saini
- Department of Civil Engineering, Netaji Subhas University of Technology, Delhi, India
| | - Saurabh Kumar Jha
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, India
- Department of Biotechnology Engineering and Food Technology, Chandigarh University, Mohali, India
| | - Sheo Prasad Shukla
- Department of Civil Engineering, Rajkiya Engineering College, Banda, India
| | - Zita Filipejová
- Small Animal Clinic, University of Veterinary Sciences Brno, Brno, Czechia
| | | | - Danish Iqbal
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majma'ah, Saudi Arabia
- Health and Basic Sciences Research Center, Majmaah University, Al Majma'ah, Saudi Arabia
| | - Parma Nand
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, India
| | - Vijay Jagdish Upadhye
- Center of Research for Development (CR4D), Parul Institute of Applied Sciences (PIAS), Parul University, Vadodara, Gujarat
| | - Abhimanyu Kumar Jha
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, India
- *Correspondence: Abhimanyu Kumar Jha, ; Shubhadeep Roychoudhury,
| | - Shubhadeep Roychoudhury
- Department of Life Science and Bioinformatics, Assam University, Silchar, India
- *Correspondence: Abhimanyu Kumar Jha, ; Shubhadeep Roychoudhury,
| | - Petr Slama
- Department of Animal Morphology, Physiology, and Genetics, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia
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25
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Hill RM, Rocha S, Parsons JL. Overcoming the Impact of Hypoxia in Driving Radiotherapy Resistance in Head and Neck Squamous Cell Carcinoma. Cancers (Basel) 2022; 14:4130. [PMID: 36077667 PMCID: PMC9454974 DOI: 10.3390/cancers14174130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 12/24/2022] Open
Abstract
Hypoxia is very common in most solid tumours and is a driving force for malignant progression as well as radiotherapy and chemotherapy resistance. Incidences of head and neck squamous cell carcinoma (HNSCC) have increased in the last decade and radiotherapy is a major therapeutic technique utilised in the treatment of the tumours. However, effectiveness of radiotherapy is hindered by resistance mechanisms and most notably by hypoxia, leading to poor patient prognosis of HNSCC patients. The phenomenon of hypoxia-induced radioresistance was identified nearly half a century ago, yet despite this, little progress has been made in overcoming the physical lack of oxygen. Therefore, a more detailed understanding of the molecular mechanisms of hypoxia and the underpinning radiobiological response of tumours to this phenotype is much needed. In this review, we will provide an up-to-date overview of how hypoxia alters molecular and cellular processes contributing to radioresistance, particularly in the context of HNSCC, and what strategies have and could be explored to overcome hypoxia-induced radioresistance.
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Affiliation(s)
- Rhianna M. Hill
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool L7 8TX, UK
| | - Sonia Rocha
- Department of Molecular Physiology and Cell Signalling, University of Liverpool, Liverpool L69 7ZB, UK
| | - Jason L. Parsons
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool L7 8TX, UK
- Clatterbridge Cancer Centre NHS Foundation Trust, Clatterbridge Road, Bebington CH63 4JY, UK
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26
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Zheng K, Gao L, Hao J, Zou X, Hu X. An immunotherapy response prediction model derived from proliferative CD4+ T cells and antigen-presenting monocytes in ccRCC. Front Immunol 2022; 13:972227. [PMID: 36091022 PMCID: PMC9452905 DOI: 10.3389/fimmu.2022.972227] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Most patients with clear cell renal cell carcinoma (ccRCC) have an impaired response to immune checkpoint blockade (ICB) therapy. Few biomarkers can predict responsiveness, and there is insufficient evidence to extend them to ccRCC clinical use. To explore subtypes and signatures of immunocytes with good predictive performance for ICB outcomes in the ccRCC context, we reanalyzed two ccRCC single-cell RNA sequencing (scRNA-seq) datasets from patients receiving ICB treatment. A subtype of proliferative CD4+ T cells and regulatory T cells and a subtype of antigen-presenting monocytes that have good predictive capability and are correlated with ICB outcomes were identified. These findings were corroborated in independent ccRCC ICB pretreatment bulk RNA-seq datasets. By incorporating the cluster-specific marker genes of these three immunocyte subtypes, we developed a prediction model, which reached an AUC of 93% for the CheckMate cohort (172 samples). Our study shows that the ICB response prediction model can serve as a valuable clinical decision-making tool for guiding ICB treatment of ccRCC patients.
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Affiliation(s)
- Kun Zheng
- Department of Urology, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Lianchong Gao
- Yantai Institute, China Agricultural University, Yantai, China
| | - Jie Hao
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai, China
- *Correspondence: Jie Hao, ; Xin Zou, ; Xiaoyong Hu,
| | - Xin Zou
- Center for Tumor Diagnosis & Therapy, Jinshan Hospital, Fudan University, Shanghai, China
- Department of Pathology, Jinshan Hospital, Fudan University, Shanghai, China
- *Correspondence: Jie Hao, ; Xin Zou, ; Xiaoyong Hu,
| | - Xiaoyong Hu
- Department of Urology, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
- *Correspondence: Jie Hao, ; Xin Zou, ; Xiaoyong Hu,
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27
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Farrow SL, Schierding W, Gokuladhas S, Golovina E, Fadason T, Cooper AA, O’Sullivan JM. Establishing gene regulatory networks from Parkinson's disease risk loci. Brain 2022; 145:2422-2435. [PMID: 35094046 PMCID: PMC9373962 DOI: 10.1093/brain/awac022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 12/02/2021] [Accepted: 12/20/2021] [Indexed: 11/25/2022] Open
Abstract
The latest meta-analysis of genome-wide association studies identified 90 independent variants across 78 genomic regions associated with Parkinson's disease, yet the mechanisms by which these variants influence the development of the disease remains largely elusive. To establish the functional gene regulatory networks associated with Parkinson's disease risk variants, we utilized an approach combining spatial (chromosomal conformation capture) and functional (expression quantitative trait loci) data. We identified 518 genes subject to regulation by 76 Parkinson's variants across 49 tissues, whicih encompass 36 peripheral and 13 CNS tissues. Notably, one-third of these genes were regulated via trans-acting mechanisms (distal; risk locus-gene separated by >1 Mb, or on different chromosomes). Of particular interest is the identification of a novel trans-expression quantitative trait loci-gene connection between rs10847864 and SYNJ1 in the adult brain cortex, highlighting a convergence between familial studies and Parkinson's disease genome-wide association studies loci for SYNJ1 (PARK20) for the first time. Furthermore, we identified 16 neurodevelopment-specific expression quantitative trait loci-gene regulatory connections within the foetal cortex, consistent with hypotheses suggesting a neurodevelopmental involvement in the pathogenesis of Parkinson's disease. Through utilizing Louvain clustering we extracted nine significant and highly intraconnected clusters within the entire gene regulatory network. The nine clusters are enriched for specific biological processes and pathways, some of which have not previously been associated with Parkinson's disease. Together, our results not only contribute to an overall understanding of the mechanisms and impact of specific combinations of Parkinson's disease variants, but also highlight the potential impact gene regulatory networks may have when elucidating aetiological subtypes of Parkinson's disease.
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Affiliation(s)
- Sophie L Farrow
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | - William Schierding
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | | | - Evgeniia Golovina
- Liggins Institute, The University of Auckland, Auckland, New Zealand
| | - Tayaza Fadason
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | - Antony A Cooper
- Australian Parkinson’s Mission, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St Vincent’s Clinical School, UNSW Sydney, Sydney, New South Wales, Australia
| | - Justin M O’Sullivan
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
- Australian Parkinson’s Mission, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Brain Research New Zealand, The University of Auckland, Auckland, New Zealand
- MRC Lifecourse Epidemiology Unit, University of Southampton, UK
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28
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Lian BJ, Zhang K, Fang XD, Li F, Dai Z, Chen WY, Qi XP. Clinical Benefit of Niraparib to TKI/mTORi-Resistance Metastatic ccRCC With BAP1-Frame Shift Mutation: Case Report and Literature Review. Front Oncol 2022; 12:927250. [PMID: 35875073 PMCID: PMC9299075 DOI: 10.3389/fonc.2022.927250] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common subtype of renal cancer. The top four mutant genes affecting the occurrence and progression of ccRCC are VHL, PBRM1, BAP1, and SETD2, respectively. Tyrosine kinase/mammalian target of rapamycin inhibitors (TKI/mTORis) with or without immunotherapy are the standard and effective therapy to metastatic ccRCC. Once TKI/mTORis fail to ccRCC, there is still a lack of other effective therapies. In this study, we reported a case in which a metastatic ccRCC patient (T2aN1M1) presented resistance after a 28-month treatment by sorafenib–axitinib–everolimus (TKI-TKI-mTORi). Subsequently, a frame shift pathogenic mutation, c.799_800del (p.Q267fs) in the exon10 of BAP1 in ccRCC, was revealed by targeted sequencing. Oral administration of nilapanib (PARP inhibitor) was further given, which may provide a new therapy for TKI/mTORi-resistance metastatic ccRCC. Fortunately, a partial response has been achieved and lasted for 5 months. Since the frequency of BAP1 mutations in ccRCC patients was approximately 10%–20%, as reported previously, we also tried to explore the potential mechanisms benefitting from the nilapanib. Moreover, the literature concerning BAP1 mutation and associated cancers including ccRCC is reviewed.
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Affiliation(s)
- Bi-Jun Lian
- Department of Oncologic and Urologic Surgery, The 903rd People's Liberation Army (PLA) Hospital, Wenzhou Medical University, Hangzhou, China
| | - Ke Zhang
- Center for Radiation Oncology, Affiliated Hangzhou Cancer Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xu-Dong Fang
- Department of Oncologic and Urologic Surgery, The 903rd People's Liberation Army (PLA) Hospital, Wenzhou Medical University, Hangzhou, China
| | - Feng Li
- Department of Oncologic and Urologic Surgery, The 903rd People's Liberation Army (PLA) Hospital, Wenzhou Medical University, Hangzhou, China
| | - Zhao Dai
- Department of Neurology, The 903rd People's Liberation Army (PLA) Hospital, Wenzhou Medical University, Hangzhou, China
| | - Wei-Ying Chen
- Department of Urology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Enze Hospital, Taizhou Enze Medical Center (Group), Taizhou, China
| | - Xiao-Ping Qi
- Department of Oncologic and Urologic Surgery, The 903rd People's Liberation Army (PLA) Hospital, Wenzhou Medical University, Hangzhou, China
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29
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Loh D, Reiter RJ. Melatonin: Regulation of Viral Phase Separation and Epitranscriptomics in Post-Acute Sequelae of COVID-19. Int J Mol Sci 2022; 23:8122. [PMID: 35897696 PMCID: PMC9368024 DOI: 10.3390/ijms23158122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/09/2022] [Accepted: 07/20/2022] [Indexed: 01/27/2023] Open
Abstract
The relentless, protracted evolution of the SARS-CoV-2 virus imposes tremendous pressure on herd immunity and demands versatile adaptations by the human host genome to counter transcriptomic and epitranscriptomic alterations associated with a wide range of short- and long-term manifestations during acute infection and post-acute recovery, respectively. To promote viral replication during active infection and viral persistence, the SARS-CoV-2 envelope protein regulates host cell microenvironment including pH and ion concentrations to maintain a high oxidative environment that supports template switching, causing extensive mitochondrial damage and activation of pro-inflammatory cytokine signaling cascades. Oxidative stress and mitochondrial distress induce dynamic changes to both the host and viral RNA m6A methylome, and can trigger the derepression of long interspersed nuclear element 1 (LINE1), resulting in global hypomethylation, epigenetic changes, and genomic instability. The timely application of melatonin during early infection enhances host innate antiviral immune responses by preventing the formation of "viral factories" by nucleocapsid liquid-liquid phase separation that effectively blockades viral genome transcription and packaging, the disassembly of stress granules, and the sequestration of DEAD-box RNA helicases, including DDX3X, vital to immune signaling. Melatonin prevents membrane depolarization and protects cristae morphology to suppress glycolysis via antioxidant-dependent and -independent mechanisms. By restraining the derepression of LINE1 via multifaceted strategies, and maintaining the balance in m6A RNA modifications, melatonin could be the quintessential ancient molecule that significantly influences the outcome of the constant struggle between virus and host to gain transcriptomic and epitranscriptomic dominance over the host genome during acute infection and PASC.
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Affiliation(s)
- Doris Loh
- Independent Researcher, Marble Falls, TX 78654, USA;
| | - Russel J. Reiter
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229, USA
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T helper cell-mediated epitranscriptomic regulation via m6A RNA methylation bridges link between coronary artery disease and invasive ductal carcinoma. J Cancer Res Clin Oncol 2022; 148:3421-3436. [PMID: 35776197 DOI: 10.1007/s00432-022-04130-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 06/08/2022] [Indexed: 12/09/2022]
Abstract
PURPOSE Invasive ductal carcinoma (IDC) and coronary artery disease (CAD), remains the greatest cause of death annually in women, driven by complex signalling pathways and shared several predisposing risk factors together. Therefore, it is important to find out the common epigenetic modifications which are responsible for possible disease progression from CAD to IDC. METHODS CD4+T cell isolation by MACS, RT2 profiler PCR array, Gene ontology study, m6A RNA methylation, ChIP-qPCR, Q-PCR, CRISPR/Cas9-mediated knockout/overexpression, Lactate dehydrogenase release assay, RDIP-qPCR. RESULTS We have identified several epigenetic regulators (e.g., VEGFA, AIMP1, etc.) which are mainly involved in inflammatory pathways in both the diseased conditions. Epitranscriptomic alterations such as m6A RNA methylation found abnormal in CD4+T helper cells in both IDC as well as CAD. CRISPR-Cas9 mediated knockout/overexpression of specific gene (BRCA1) are promising therapeutic approaches in diseased conditions by regulating m6A RNA methylation and also tumor suppressor gene P53. It also affected the R-loop formation which is vulnerable to DNA damage and BRCA1 can also induce CTL mediated cytotoxicity in breast cancer cells. CONCLUSIONS Therefore, by understanding the modifications of epigenetic mechanisms, their alterations and interactions will aid in the development of newer therapeutic approaches to stop the possible spread from one disease to another.
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31
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Vaghari-Tabari M, Hassanpour P, Sadeghsoltani F, Malakoti F, Alemi F, Qujeq D, Asemi Z, Yousefi B. CRISPR/Cas9 gene editing: a new approach for overcoming drug resistance in cancer. Cell Mol Biol Lett 2022; 27:49. [PMID: 35715750 PMCID: PMC9204876 DOI: 10.1186/s11658-022-00348-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 05/24/2022] [Indexed: 12/18/2022] Open
Abstract
The CRISPR/Cas9 system is an RNA-based adaptive immune system in bacteria and archaea. Various studies have shown that it is possible to target a wide range of human genes and treat some human diseases, including cancers, by the CRISPR/Cas9 system. In fact, CRISPR/Cas9 gene editing is one of the most efficient genome manipulation techniques. Studies have shown that CRISPR/Cas9 technology, in addition to having the potential to be used as a new therapeutic approach in the treatment of cancers, can also be used to enhance the effectiveness of existing treatments. Undoubtedly, the issue of drug resistance is one of the main obstacles in the treatment of cancers. Cancer cells resist anticancer drugs by a variety of mechanisms, such as enhancing anticancer drugs efflux, enhancing DNA repair, enhancing stemness, and attenuating apoptosis. Mutations in some proteins of different cellular signaling pathways are associated with these events and drug resistance. Recent studies have shown that the CRISPR/Cas9 technique can be used to target important genes involved in these mechanisms, thereby increasing the effectiveness of anticancer drugs. In this review article, studies related to the applications of this technique in overcoming drug resistance in cancer cells will be reviewed. In addition, we will give a brief overview of the limitations of the CRISP/Cas9 gene-editing technique.
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Affiliation(s)
- Mostafa Vaghari-Tabari
- Department of Clinical Biochemistry and Laboratory Medicine, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Parisa Hassanpour
- Department of Clinical Biochemistry and Laboratory Medicine, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Fatemeh Sadeghsoltani
- Department of Clinical Biochemistry and Laboratory Medicine, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Faezeh Malakoti
- Department of Clinical Biochemistry and Laboratory Medicine, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Forough Alemi
- Department of Clinical Biochemistry and Laboratory Medicine, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Durdi Qujeq
- Cellular and Molecular Biology Research Center (CMBRC), Health Research Institute, Babol University of Medical Sciences, Babol, Iran.,Department of Clinical Biochemistry, Babol University of Medical Sciences, Babol, Iran
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran.
| | - Bahman Yousefi
- Department of Clinical Biochemistry and Laboratory Medicine, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran. .,Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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32
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Ng CS, Lai CK, Ke HM, Lee HH, Chen CF, Tang PC, Cheng HC, Lu MJ, Li WH, Tsai IJ. Genome assembly and evolutionary analysis of the mandarin duck Aix galericulata reveal strong genome conservation among ducks. Genome Biol Evol 2022; 14:6594746. [PMID: 35640266 PMCID: PMC9189614 DOI: 10.1093/gbe/evac083] [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] [Accepted: 05/25/2022] [Indexed: 11/13/2022] Open
Abstract
The mandarin duck, Aix galericulata, is popular in East Asian cultures and displays exaggerated sexual dimorphism, especially in feather traits during breeding seasons. We generated and annotated the first mandarin duck de novo assembly, which was 1.08 Gb in size and encoded 16,615 proteins. Using a phylogenomic approach calibrated with fossils and molecular divergences, we inferred that the last common ancestor of ducks occurred 13.3–26.7 Ma. The majority of the mandarin duck genome repetitive sequences belonged to the chicken repeat 1 (CR1) retroposon CR1-J2_Pass, which underwent a duck lineage-specific burst. Synteny analyses among ducks revealed infrequent chromosomal rearrangements in which breaks were enriched in LINE retrotransposons and DNA transposons. The calculation of the dN/dS ratio revealed that the majority of duck genes were under strong purifying selection. The expanded gene families in the mandarin duck are primarily involved in olfactory perception as well as the development and morphogenesis of feather and branching structures. This new reference genome will improve our understanding of the morphological and physiological characteristics of ducks and provide a valuable resource for functional genomics studies to investigate the feather traits of the mandarin duck.
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Affiliation(s)
- Chen Siang Ng
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan.,Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan.,Bioresource Conservation Research Center, National Tsing Hua University, Hsinchu, Taiwan.,The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Cheng-Kuo Lai
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | - Huei-Mien Ke
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Hsin-Han Lee
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Chih-Feng Chen
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.,Department of Animal Science, National Chung Hsing University, Taichung, Taiwan
| | - Pin-Chi Tang
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.,Department of Animal Science, National Chung Hsing University, Taichung, Taiwan
| | - Hsu-Chen Cheng
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.,Department of Life Science, National Chung Hsing University, Taichung, Taiwan
| | - Meiyeh J Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Wen-Hsiung Li
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Department of Ecology and Evolution, University of Chicago, Chicago, USA
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Humayun A, Fornace AJ. GADD45 in Stress Signaling, Cell Cycle Control, and Apoptosis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1360:1-22. [PMID: 35505159 DOI: 10.1007/978-3-030-94804-7_1] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
GADD45 is a gene family consisting of GADD45A, GADD45B, and GADD45G that is often induced by DNA damage and other stress signals associated with growth arrest and apoptosis. Many of these roles are carried out via signaling mediated by p38 mitogen-activated protein kinases (MAPKs). The GADD45 proteins can contribute to p38 activation either by activation of upstream kinase(s) or by direct interaction, as well as suppression of p38 activity in certain cases. In vivo, there are important tissue and cell type specific differences in the roles for GADD45 in MAPK signaling. In addition to being p53-regulated, GADD45A has also been found to contribute to p53 activation via p38. Like other stress and signaling proteins, GADD45 proteins show complex regulation and numerous effectors. More recently, aberrant GADD45 expression has been found in several human cancers, but the mechanisms behind these findings largely remain to be understood.
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Affiliation(s)
- Arslon Humayun
- Lombardi Comprehensive Cancer Center, Washington, DC, USA
| | - Albert J Fornace
- Lombardi Comprehensive Cancer Center, Washington, DC, USA.
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC, USA.
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34
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Kissling VM, Reginato G, Bianco E, Kasaciunaite K, Tilma J, Cereghetti G, Schindler N, Lee SS, Guérois R, Luke B, Seidel R, Cejka P, Peter M. Mre11-Rad50 oligomerization promotes DNA double-strand break repair. Nat Commun 2022; 13:2374. [PMID: 35501303 PMCID: PMC9061753 DOI: 10.1038/s41467-022-29841-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 04/01/2022] [Indexed: 11/08/2022] Open
Abstract
The conserved Mre11-Rad50 complex is crucial for the detection, signaling, end tethering and processing of DNA double-strand breaks. While it is known that Mre11-Rad50 foci formation at DNA lesions accompanies repair, the underlying molecular assembly mechanisms and functional implications remained unclear. Combining pathway reconstitution in electron microscopy, biochemical assays and genetic studies, we show that S. cerevisiae Mre11-Rad50 with or without Xrs2 forms higher-order assemblies in solution and on DNA. Rad50 mediates such oligomerization, and mutations in a conserved Rad50 beta-sheet enhance or disrupt oligomerization. We demonstrate that Mre11-Rad50-Xrs2 oligomerization facilitates foci formation, DNA damage signaling, repair, and telomere maintenance in vivo. Mre11-Rad50 oligomerization does not affect its exonuclease activity but drives endonucleolytic cleavage at multiple sites on the 5'-DNA strand near double-strand breaks. Interestingly, mutations in the human RAD50 beta-sheet are linked to hereditary cancer predisposition and our findings might provide insights into their potential role in chemoresistance.
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Affiliation(s)
- Vera M Kissling
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8093, Zürich, Switzerland
| | - Giordano Reginato
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8093, Zürich, Switzerland
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500, Bellinzona, Switzerland
| | - Eliana Bianco
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8093, Zürich, Switzerland
| | - Kristina Kasaciunaite
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103, Leipzig, Germany
| | - Janny Tilma
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8093, Zürich, Switzerland
| | - Gea Cereghetti
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8093, Zürich, Switzerland
| | - Natalie Schindler
- Institute for Developmental and Neurobiology (IDN), Johannes Gutenberg University, 55128, Mainz, Germany
| | - Sung Sik Lee
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8093, Zürich, Switzerland
- Scientific Center for Optical and Electron Microscopy, Eidgenössische Technische Hochschule (ETH), 8093, Zürich, Switzerland
| | - Raphaël Guérois
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Brian Luke
- Institute for Developmental and Neurobiology (IDN), Johannes Gutenberg University, 55128, Mainz, Germany
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany
| | - Ralf Seidel
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103, Leipzig, Germany
| | - Petr Cejka
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8093, Zürich, Switzerland.
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500, Bellinzona, Switzerland.
| | - Matthias Peter
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8093, Zürich, Switzerland.
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35
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Czajkowski D, Szmyd R, Gee HE. Impact of DNA damage response defects in cancer cells on response to immunotherapy and radiotherapy. J Med Imaging Radiat Oncol 2022; 66:546-559. [PMID: 35460184 PMCID: PMC9321602 DOI: 10.1111/1754-9485.13413] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/03/2022] [Accepted: 04/06/2022] [Indexed: 11/30/2022]
Abstract
The DNA damage response (DDR) is a complex set of downstream pathways triggered in response to DNA damage to maintain genomic stability. Many tumours exhibit mutations which inactivate components of the DDR, making them prone to the accumulation of DNA defects. These can both facilitate the development of tumours and provide potential targets for novel therapeutic interventions. The inhibition of the DDR has been shown to induce radiosensitivity in certain cancers, rendering them susceptible to treatment with radiotherapy and improving the therapeutic window. Moreover, DDR defects are a strong predictor of patient response to immune checkpoint inhibition (ICI). The ability to target the DDR selectively has the potential to expand the tumour neoantigen repertoire, thus increasing tumour immunogenicity and facilitating a CD8+ T and NK cell response against cancer cells. Combinatorial approaches, which seek to integrate DDR inhibition with radiotherapy and immunotherapy, have shown promise in early trials. Further studies are necessary to understand these synergies and establish reliable biomarkers.
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Affiliation(s)
| | - Radosław Szmyd
- Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Sydney, New South Wales, Australia.,Sydney West Radiation Oncology Network, Crown Princess Mary Cancer Centre Westmead, Sydney, New South Wales, Australia
| | - Harriet E Gee
- University of Sydney, Sydney, New South Wales, Australia.,Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Sydney, New South Wales, Australia.,Sydney West Radiation Oncology Network, Crown Princess Mary Cancer Centre Westmead, Sydney, New South Wales, Australia
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36
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Ho JCW, Chen J, Cheuk IWY, Siu MT, Shin VY, Kwong A. MicroRNA-199a-3p promotes drug sensitivity in triple negative breast cancer by down-regulation of BRCA1. Am J Transl Res 2022; 14:2021-2036. [PMID: 35422914 PMCID: PMC8991114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/07/2021] [Indexed: 06/14/2023]
Abstract
MiR-199a-3p was previously predicted to target tumor suppressor gene BRCA1, which has been linked to cancer onset and therapeutic response. In this study, the effects of miR-199a-3p-mediated BRCA1 dysfunction on triple-negative breast cancer (TNBC) progression and chemosensitivity were assessed. The association between miR-199a-3p and BRCA1 expression was examined in TNBC tumors and verified with luciferase reporter and protein assays. Tumorigenic functions of miR-199a-3p in TNBC cells were investigated by cell proliferation, clonogenic and migration assays. The sensitivities to chemotherapeutic drugs were tested with cisplatin and PARP inhibitor (veliparib) treatments. Mouse xenograft model was used to examine the effects of miR-199a-3p on tumor growth and drug response in vivo. MiR-199a-3p was shown to directly target BRCA1 in TNBC cells, resulting its downregulation and reduced luciferase reporter activity mediated by BRCA1 3'-UTR. Ectopic miR-199a-3p in TNBC cells exerted inhibitory effects on cell proliferation, migration and xenograft tumor growth. Moreover, miR-199a-3p was shown to reverse cisplatin-resistance and sensitize TNBC cells to veliparib, which might be due to repressed DNA repair ability and induced cell apoptosis. Our results demonstrated the tumor suppressive effects of miR-199a-3p on TNBC and induction on chemotherapeutic sensitivities, which were correlated with BRCA1 gene dysfunction. These findings may provide insights into the potential prognostic and therapeutic values of miR-199a-3p in patients with TNBC.
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Affiliation(s)
- John Chi-Wang Ho
- Department of Surgery, The University of Hong Kong and The University of Hong Kong-Shenzhen HospitalHong Kong, China
| | - Jiawei Chen
- Department of Surgery, The University of Hong Kong and The University of Hong Kong-Shenzhen HospitalHong Kong, China
| | - Isabella Wai-Yin Cheuk
- Department of Surgery, The University of Hong Kong and The University of Hong Kong-Shenzhen HospitalHong Kong, China
| | - Man-Ting Siu
- Department of Surgery, The University of Hong Kong and The University of Hong Kong-Shenzhen HospitalHong Kong, China
| | - Vivian Yvonne Shin
- Department of Surgery, The University of Hong Kong and The University of Hong Kong-Shenzhen HospitalHong Kong, China
| | - Ava Kwong
- Department of Surgery, The University of Hong Kong and The University of Hong Kong-Shenzhen HospitalHong Kong, China
- Department of Surgery, Hong Kong Sanatorium & HospitalHong Kong, China
- Hong Kong Hereditary Breast Cancer Family RegistryHong Kong, China
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37
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Han S, Zhang Y, Zhang X, Zhang H, Meng S, Kong M, Liu X, Ma X. Single-Cell RNA Sequencing of the Nucleus Pulposus Reveals Chondrocyte Differentiation and Regulation in Intervertebral Disc Degeneration. Front Cell Dev Biol 2022; 10:824771. [PMID: 35265617 PMCID: PMC8899542 DOI: 10.3389/fcell.2022.824771] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/10/2022] [Indexed: 01/07/2023] Open
Abstract
The nucleus pulposus (NP), a heterogeneous tissue, is an essential functional component of the intervertebral disc. However, NP cell development route and regulation mechanism in intervertebral disc degeneration (IVDD) remain unknown. Here, we performed single-cell RNA sequencing of six NP samples with normal control, mild degeneration, and severe degeneration. Based on unbiased clustering of gene expression patterns from 30,300 single-cell RNA sequencing, we identified three cell lineage families of macrophages, endothelial, and chondrocyte cells and characterized seven chondrocyte subtypes, and defined two developmental pathways of the chondrocyte cell lineage families in the process of IVDD. Additionally, CellPhoneDB analysis revealed potential interactions between chondrocyte cells and other cells in IVDD. Chondrocytes in one of the differentiated orientations interact with macrophages and endothelial cells and have an inflammatory amplification effect, which were key factors causing IVDD. Collectively, these results revealed the dynamic cell landscape of IVDD development and offered new insights into the influence of NP cells differentiation on extracellular matrix homeostasis during degeneration, providing potential treatment targets for IVDD.
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Affiliation(s)
- Shuo Han
- Department of Spinal Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China.,Department of Medicine, Qingdao University, Qingdao, China
| | - Yiran Zhang
- Medical Research Center, Shandong Institute of Orthopaedics and Traumatology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xianjuan Zhang
- Department of Medicine, Qingdao University, Qingdao, China.,Department of Pathogenic Biology, Qingdao University Medical College, Qingdao, China
| | - Hao Zhang
- Department of Spinal Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China.,Department of Medicine, Qingdao University, Qingdao, China
| | - Shengwei Meng
- Department of Spinal Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China.,Department of Medicine, Qingdao University, Qingdao, China
| | - Meng Kong
- Department of Spinal Surgery, Qingdao Municipal Hospital, Qingdao, China
| | - Xiaojie Liu
- Department of Medicine, Qingdao University, Qingdao, China.,970 Hospital of the PLA Joint Logistic Support Force, Weihai, China
| | - Xuexiao Ma
- Department of Spinal Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
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Ebner S, Winkelmann R, Martin S, Köllermann J, Wild PJ, Demes M. Sequencing of BRCA1/2-alterations using NGS-based technology: annotation as a challenge. Oncotarget 2022; 13:464-475. [PMID: 35251494 PMCID: PMC8893798 DOI: 10.18632/oncotarget.28213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 02/24/2022] [Indexed: 11/26/2022] Open
Abstract
In this study, the molecular profile of different BRCA-associated tumor types was assessed with regard to the classification and annotation of detected BRCA1/2 variants. The aim was to establish guidelines in order to facilitate the interpretation of BRCA1/2 alterations in routine diagnostics. Annotation of detected variants was evaluated compared to background mutations found in normal tissue samples and manually reviewed according to distinct online databases. This retrospective study included 48 samples (45 tumors, three non-tumors), which were sequenced with the GeneReader (QIAGEN). Thereof ten samples were additionally analyzed with the Ion S5™ (Thermo Fisher) and 20 samples with the MiSeq™ (Illumina®) to compare the different NGS devices, as well as the sequencing results and their quality. The analysis showed that the individual NGS platforms detected different numbers of BRCA1/2 alterations in the respective tumor sample. In addition, the GeneReader revealed variability in the detection and classification of pathogenic alterations within the platform itself as well as in comparison with the other platforms or online databases. The study concluded that the Ion S5™ in combination with the Oncomine™ Comprehensive Assay v3 is most recommendable for current and prospective requirements of molecular analysis in routine diagnostics. In addition to the two BRCA1/2 genes, a broad number of other genes (BRCAness genes and genes involved in the repair pathway) is covered by the panel, which may open up new treatment options for patients depending on the respective eligibility criteria.
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Affiliation(s)
- Silvana Ebner
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Ria Winkelmann
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Saskia Martin
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Jens Köllermann
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Peter J Wild
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main, Germany.,Wildlab, University Hospital MVZ GmbH, Frankfurt am Main, Germany
| | - Melanie Demes
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main, Germany.,Wildlab, University Hospital MVZ GmbH, Frankfurt am Main, Germany
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Core Homologous Recombination Mutations and Improved Survival in Nonpancreatic GI Cancers. Am J Clin Oncol 2022; 45:137-141. [DOI: 10.1097/coc.0000000000000901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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40
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Puri S, Chiu YH, Draczkowski P, Ko KT, Yang TJ, Wang YS, Uchiyama S, Danny Hsu ST. Impacts of cancer-associated mutations on the structure-activity relationship of BAP1. J Mol Biol 2022; 434:167553. [DOI: 10.1016/j.jmb.2022.167553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 02/24/2022] [Accepted: 03/15/2022] [Indexed: 10/18/2022]
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41
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Pharmacometabolomics Applied to Personalized Medicine in Urological Cancers. Pharmaceuticals (Basel) 2022; 15:ph15030295. [PMID: 35337093 PMCID: PMC8952371 DOI: 10.3390/ph15030295] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 02/06/2023] Open
Abstract
Prostate cancer (PCa), bladder cancer (BCa), and renal cell carcinoma (RCC) are the most common urological cancers, and their incidence has been rising over time. Surgery is the standard treatment for these cancers, but this procedure is only effective when the disease is localized. For metastatic disease, PCa is typically treated with androgen deprivation therapy, while BCa is treated with chemotherapy, and RCC is managed primarily with targeted therapies. However, response rates to these therapeutic options remain unsatisfactory due to the development of resistance and treatment-related toxicity. Thus, the discovery of biomarkers with prognostic and predictive value is needed to stratify patients into different risk groups, minimizing overtreatment and the risk of drug resistance development. Pharmacometabolomics, a branch of metabolomics, is an attractive tool to predict drug response in an individual based on its own metabolic signature, which can be collected before, during, and after drug exposure. Hence, this review focuses on the application of pharmacometabolomic approaches to identify the metabolic responses to hormone therapy, targeted therapy, immunotherapy, and chemotherapy for the most prevalent urological cancers.
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Póti Á, Szikriszt B, Gervai JZ, Chen D, Szüts D. Characterisation of the spectrum and genetic dependence of collateral mutations induced by translesion DNA synthesis. PLoS Genet 2022; 18:e1010051. [PMID: 35130276 PMCID: PMC8870599 DOI: 10.1371/journal.pgen.1010051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 02/24/2022] [Accepted: 01/21/2022] [Indexed: 11/18/2022] Open
Abstract
Translesion DNA synthesis (TLS) is a fundamental damage bypass pathway that utilises specialised polymerases with relaxed template specificity to achieve replication through damaged DNA. Misinsertions by low fidelity TLS polymerases may introduce additional mutations on undamaged DNA near the original lesion site, which we termed collateral mutations. In this study, we used whole genome sequencing datasets of chicken DT40 and several human cell lines to obtain evidence for collateral mutagenesis in higher eukaryotes. We found that cisplatin and UVC radiation frequently induce close mutation pairs within 25 base pairs that consist of an adduct-associated primary and a downstream collateral mutation, and genetically linked their formation to TLS activity involving PCNA ubiquitylation and polymerase κ. PCNA ubiquitylation was also indispensable for close mutation pairs observed amongst spontaneously arising base substitutions in cell lines with disrupted homologous recombination. Collateral mutation pairs were also found in melanoma genomes with evidence of UV exposure. We showed that collateral mutations frequently copy the upstream base, and extracted a base substitution signature that describes collateral mutagenesis in the presented dataset regardless of the primary mutagenic process. Using this mutation signature, we showed that collateral mutagenesis creates approximately 10–20% of non-paired substitutions as well, underscoring the importance of the process. DNA base substitutions are the most common form of genomic mutations, formed both spontaneously and in response to environmental mutagens. One of the main mechanisms of base substitution mutagenesis is translesion synthesis, a process that relies on specialised DNA polymerases to replicate damaged DNA templates. In addition to incorrect base insertions at the site of lesions in the template, translesion polymerases may also generate ‘collateral’ mutations away from the lesion due to their lower accuracy in selecting the correct incoming nucleotide. In this study, we surveyed the whole genome sequence of experimental cell clones to examine the extent and genetic dependence of collateral mutagenesis in higher eukaryotes. Looking for close mutation pairs, we found that collateral mutations frequently occur near primary lesions generated by cisplatin or ultraviolet radiation in chicken and human cells, but are restricted to a short distance of approximately 25 base pairs. By analysing their sequence context, we showed that collateral mutations can also occur near correctly bypassed primary lesions and may be responsible for a considerable proportion of all base substitution mutations.
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Affiliation(s)
- Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Bernadett Szikriszt
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | | | - Dan Chen
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
- * E-mail:
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43
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Hsieh YP, Naler LB, Ma S, Lu C. Cell-type-specific epigenomic variations associated with BRCA1 mutation in pre-cancer human breast tissues. NAR Genom Bioinform 2022; 4:lqac006. [PMID: 35118379 PMCID: PMC8808540 DOI: 10.1093/nargab/lqac006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 12/13/2021] [Accepted: 01/24/2022] [Indexed: 11/24/2022] Open
Abstract
BRCA1 germline mutation carriers are predisposed to breast cancers. Epigenomic regulations have been known to strongly interact with genetic variations and potentially mediate biochemical cascades involved in tumorigenesis. Due to the cell-type specificity of epigenomic features, profiling of individual cell types is critical for understanding the molecular events in various cellular compartments within complex breast tissue. Here, we produced cell-type-specific profiles of genome-wide histone modifications including H3K27ac and H3K4me3 in basal, luminal progenitor, mature luminal and stromal cells extracted from a small pilot cohort of pre-cancer BRCA1 mutation carriers (BRCA1mut/+) and non-carriers (BRCA1+/+), using a low-input ChIP-seq technology that we developed. We discovered that basal and stromal cells present the most extensive epigenomic differences between mutation carriers (BRCA1mut/+) and non-carriers (BRCA1+/+), while luminal progenitor and mature luminal cells are relatively unchanged with the mutation. Furthermore, the epigenomic changes in basal cells due to BRCA1 mutation appear to facilitate their transformation into luminal progenitor cells. Taken together, epigenomic regulation plays an important role in the case of BRCA1 mutation for shaping the molecular landscape that facilitates tumorigenesis.
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Affiliation(s)
- Yuan-Pang Hsieh
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Lynette B Naler
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Sai Ma
- Department of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA 24061, USA
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA
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Orozco CA, González-Giraldo Y, Bonilla DA, Forero DA. An in silico analysis of genome-wide expression profiles of the effects of exhaustive exercise identifies heat shock proteins as the key players. Meta Gene 2022. [DOI: 10.1016/j.mgene.2022.101012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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45
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Rajan A, Varghese GR, Yadev I, Anandan J, Latha NR, Patra D, Krishnan N, Kuppusamy K, Warrier AV, Bhushan S, Nadhan R, Ram Kumar RM, Srinivas P. Modulation of BRCA1 mediated DNA damage repair by deregulated ER-α signaling in breast cancers. Am J Cancer Res 2022; 12:17-47. [PMID: 35141003 PMCID: PMC8822286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/16/2021] [Indexed: 06/14/2023] Open
Abstract
BRCA1 mutation carriers have a greater risk of developing cancers in hormone-responsive tissues like breasts and ovaries. However, this tissue-specific incidence of BRCA1 related cancers remains elusive. The majority of the BRCA1 mutated breast cancers exhibit typical histopathological features of high-grade tumors, with basal epithelial phenotype, classified as triple-negative molecular subtype and have a higher percentage of DNA damage and chromosomal abnormality. Though there are many studies relating BRCA1 with ER-α (Estrogen receptor-α), it has not been reported whether E2 (Estrogen) -ER-α signaling can modulate the DNA repair activities of BRCA1. The present study analyzes whether deregulation of ER-α signaling, arising as a result of E2/ER-α deficiency, could impact the BRCA1 dependent DDR (DNA Damage Response) pathways, predominantly those of DNA-DSB (Double Strand break) repair and oxidative damage response. We demonstrate that E2/E2-stimulated ER-α can augment BRCA1 mediated high fidelity repairs like HRR (Homologous Recombination Repair) and BER (Base Excision Repair) in breast cancer cells. Conversely, a condition of ER-α deficiency itself or any interruption in ligand-dependent ER-α transactivation resulted in delayed DNA damage repair, leading to persistent activation of γH2AX and retention of unrepaired DNA lesions, thereby triggering tumor progression. ER-α deficiency not only limited the HRR in cells but also facilitated the DSB repair through error prone pathways like NHEJ (Non Homologous End Joining). ER-α deficiency associated persistence of DNA lesions and reduced expression of DDR proteins were validated in human mammary tumors.
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Affiliation(s)
- Arathi Rajan
- Cancer Research Program, Rajiv Gandhi Centre for BiotechnologyThiruvananthapuram 695014, Kerala, India
- Department of Biotechnology, University of KeralaThiruvananthapuram 695011, Kerala, India
| | - Geetu R Varghese
- Cancer Research Program, Rajiv Gandhi Centre for BiotechnologyThiruvananthapuram 695014, Kerala, India
| | - Induprabha Yadev
- Goverment Medical CollegeThiruvananthapuram 695011, Kerala, India
| | - Jaimie Anandan
- Goverment Medical CollegeThiruvananthapuram 695011, Kerala, India
| | - Neetha R Latha
- Cancer Research Program, Rajiv Gandhi Centre for BiotechnologyThiruvananthapuram 695014, Kerala, India
| | - Dipyaman Patra
- Cancer Research Program, Rajiv Gandhi Centre for BiotechnologyThiruvananthapuram 695014, Kerala, India
| | - Neethu Krishnan
- Cancer Research Program, Rajiv Gandhi Centre for BiotechnologyThiruvananthapuram 695014, Kerala, India
| | - Krithiga Kuppusamy
- Cancer Research Program, Rajiv Gandhi Centre for BiotechnologyThiruvananthapuram 695014, Kerala, India
| | - Arathy V Warrier
- Cancer Research Program, Rajiv Gandhi Centre for BiotechnologyThiruvananthapuram 695014, Kerala, India
| | - Satej Bhushan
- Cancer Research Program, Rajiv Gandhi Centre for BiotechnologyThiruvananthapuram 695014, Kerala, India
| | - Revathy Nadhan
- Cancer Research Program, Rajiv Gandhi Centre for BiotechnologyThiruvananthapuram 695014, Kerala, India
- OU Health Stephenson Cancer CentreOklahoma, United State
| | - Ram Mohan Ram Kumar
- Cancer Research Program, Rajiv Gandhi Centre for BiotechnologyThiruvananthapuram 695014, Kerala, India
| | - Priya Srinivas
- Cancer Research Program, Rajiv Gandhi Centre for BiotechnologyThiruvananthapuram 695014, Kerala, India
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46
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High BRCA1 gene expression increases the risk of early distant metastasis in ER + breast cancers. Sci Rep 2022; 12:77. [PMID: 34996912 PMCID: PMC8741892 DOI: 10.1038/s41598-021-03471-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 10/11/2021] [Indexed: 12/24/2022] Open
Abstract
Although the function of the BRCA1 gene has been extensively studied, the relationship between BRCA1 gene expression and tumor aggressiveness remains controversial in sporadic breast cancers. Because the BRCA1 protein is known to regulate estrogen signaling, we selected microarray data of ER+ breast cancers from the GEO public repository to resolve previous conflicting findings. The BRCA1 gene expression level in highly proliferative luminal B tumors was shown to be higher than that in luminal A tumors. Survival analysis using a cure model indicated that patients of early ER+ breast cancers with high BRCA1 expression developed rapid distant metastasis. In addition, the proliferation marker genes MKI67 and PCNA, which are characteristic of aggressive tumors, were also highly expressed in patients with high BRCA1 expression. The associations among high BRCA1 expression, high proliferation marker expression, and high risk of distant metastasis emerged in independent datasets, regardless of tamoxifen treatment. Tamoxifen therapy could improve the metastasis-free fraction of high BRCA1 expression patients. Our findings link BRCA1 expression with proliferation and possibly distant metastasis via the ER signaling pathway. We propose a testable hypothesis based on these consistent results and offer an interpretation for our reported associations.
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47
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Creeden JF, Nanavaty NS, Einloth KR, Gillman CE, Stanbery L, Hamouda DM, Dworkin L, Nemunaitis J. Homologous recombination proficiency in ovarian and breast cancer patients. BMC Cancer 2021; 21:1154. [PMID: 34711195 PMCID: PMC8555001 DOI: 10.1186/s12885-021-08863-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 10/11/2021] [Indexed: 02/07/2023] Open
Abstract
Homologous recombination and DNA repair are important for genome maintenance. Genetic variations in essential homologous recombination genes, including BRCA1 and BRCA2 results in homologous recombination deficiency (HRD) and can be a target for therapeutic strategies including poly (ADP-ribose) polymerase inhibitors (PARPi). However, response is limited in patients who are not HRD, highlighting the need for reliable and robust HRD testing. This manuscript will review BRCA1/2 function and homologous recombination proficiency in respect to breast and ovarian cancer. The current standard testing methods for HRD will be discussed as well as trials leading to approval of PARPi's. Finally, standard of care treatment and synthetic lethality will be reviewed.
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Affiliation(s)
- Justin Fortune Creeden
- Department of Neurosciences, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA.,Department of Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA.,Department of Surgery, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Nisha S Nanavaty
- Department of Medicine, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Katelyn R Einloth
- Department of Medicine, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Cassidy E Gillman
- Department of Medicine, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | | | - Danae M Hamouda
- Department of Medicine, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Lance Dworkin
- Department of Medicine, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
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Tarpey MD, Amorese AJ, LaFave ER, Minchew EC, Fisher-Wellman KH, McClung JM, Hvastkovs EG, Spangenburg EE. Skeletal Muscle Function Is Dependent Upon BRCA1 to Maintain Genomic Stability. Exerc Sport Sci Rev 2021; 49:267-273. [PMID: 34091499 PMCID: PMC8495729 DOI: 10.1249/jes.0000000000000265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Breast Cancer gene 1 (BRCA1) is a large, multifunctional protein that regulates a variety of mechanisms in multiple different tissues. Our work established that Brca1 is expressed in skeletal muscle and localizes to the mitochondria and nucleus. Here, we propose BRCA1 expression is critical for the maintenance of force production and mitochondrial respiration in skeletal muscle.
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Affiliation(s)
- Michael D. Tarpey
- East Carolina University, Department of Physiology, Brody School of Medicine, Greenville, NC 27834
| | - Adam J. Amorese
- East Carolina University, Department of Physiology, Brody School of Medicine, Greenville, NC 27834
| | - Elizabeth R. LaFave
- East Carolina University, Department of Chemistry, 300 Science and Technology Bldg., Greenville, NC 27858
| | - Everett C. Minchew
- East Carolina University, Department of Physiology, Brody School of Medicine, Greenville, NC 27834
| | - Kelsey H. Fisher-Wellman
- East Carolina University, Department of Physiology, Brody School of Medicine, Greenville, NC 27834
- East Carolina Diabetes and Obesity Institute, 115 Heart Dr, East Carolina University, Greenville NC, 27834
| | - Joseph M. McClung
- East Carolina University, Department of Physiology, Brody School of Medicine, Greenville, NC 27834
- East Carolina Diabetes and Obesity Institute, 115 Heart Dr, East Carolina University, Greenville NC, 27834
| | - Eli G. Hvastkovs
- East Carolina University, Department of Chemistry, 300 Science and Technology Bldg., Greenville, NC 27858
| | - Espen E. Spangenburg
- East Carolina University, Department of Physiology, Brody School of Medicine, Greenville, NC 27834
- East Carolina Diabetes and Obesity Institute, 115 Heart Dr, East Carolina University, Greenville NC, 27834
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49
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Garrido-Cano I, Pattanayak B, Adam-Artigues A, Lameirinhas A, Torres-Ruiz S, Tormo E, Cervera R, Eroles P. MicroRNAs as a clue to overcome breast cancer treatment resistance. Cancer Metastasis Rev 2021; 41:77-105. [PMID: 34524579 PMCID: PMC8924146 DOI: 10.1007/s10555-021-09992-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 09/02/2021] [Indexed: 12/31/2022]
Abstract
Breast cancer is the most frequent cancer in women worldwide. Despite the improvement in diagnosis and treatments, the rates of cancer relapse and resistance to therapies remain higher than desirable. Alterations in microRNAs have been linked to changes in critical processes related to cancer development and progression. Their involvement in resistance or sensitivity to breast cancer treatments has been documented by different in vivo and in vitro experiments. The most significant microRNAs implicated in modulating resistance to breast cancer therapies are summarized in this review. Resistance to therapy has been linked to cellular processes such as cell cycle, apoptosis, epithelial-to-mesenchymal transition, stemness phenotype, or receptor signaling pathways, and the role of microRNAs in their regulation has already been described. The modulation of specific microRNAs may modify treatment response and improve survival rates and cancer patients' quality of life. As a result, a greater understanding of microRNAs, their targets, and the signaling pathways through which they act is needed. This information could be useful to design new therapeutic strategies, to reduce resistance to the available treatments, and to open the door to possible new clinical approaches.
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Affiliation(s)
| | | | | | - Ana Lameirinhas
- INCLIVA Biomedical Research Institute, 46010, Valencia, Spain
| | | | - Eduardo Tormo
- INCLIVA Biomedical Research Institute, 46010, Valencia, Spain.,Center for Biomedical Network Research On Cancer, CIBERONC-ISCIII, 28029, Madrid, Spain
| | | | - Pilar Eroles
- INCLIVA Biomedical Research Institute, 46010, Valencia, Spain. .,Center for Biomedical Network Research On Cancer, CIBERONC-ISCIII, 28029, Madrid, Spain. .,Department of Physiology, University of Valencia, 46010, Valencia, Spain.
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50
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Alemi F, Raei Sadigh A, Malakoti F, Elhaei Y, Ghaffari SH, Maleki M, Asemi Z, Yousefi B, Targhazeh N, Majidinia M. Molecular mechanisms involved in DNA repair in human cancers: An overview of PI3k/Akt signaling and PIKKs crosstalk. J Cell Physiol 2021; 237:313-328. [PMID: 34515349 DOI: 10.1002/jcp.30573] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 12/14/2022]
Abstract
The cellular genome is frequently subjected to abundant endogenous and exogenous factors that induce DNA damage. Most of the Phosphatidylinositol 3-kinase-related kinases (PIKKs) family members are activated in response to DNA damage and are the most important DNA damage response (DDR) proteins. The DDR system protects the cells against the wrecking effects of these genotoxicants and repairs the DNA damage caused by them. If the DNA damage is severe, such as when DNA is the goal of chemo-radiotherapy, the DDR drives cells toward cell cycle arrest and apoptosis. Some intracellular pathways, such as PI3K/Akt, which is overactivated in most cancers, could stimulate the DDR process and failure of chemo-radiotherapy with the increasing repair of damaged DNA. This signaling pathway induces DNA repair through the regulation of proteins that are involved in DDR like BRCA1, HMGB1, and P53. In this review, we will focus on the crosstalk of the PI3K/Akt and PIKKs involved in DDR and then discuss current achievements in the sensitization of cancer cells to chemo-radiotherapy by PI3K/Akt inhibitors.
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Affiliation(s)
- Forough Alemi
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Aydin Raei Sadigh
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Faezeh Malakoti
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yusuf Elhaei
- Department of Clinical Biochemistry, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Seyed Hamed Ghaffari
- Department of Orthopedics, Shohada Medical Research & Training Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Masomeh Maleki
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran
| | - Bahman Yousefi
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Niloufar Targhazeh
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Maryam Majidinia
- Solid Tumor Research Center, Urmia University of Medical Sciences, Urmia, Iran
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