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Choudhary A, Anand A, Singh A, Roy P, Singh N, Kumar V, Sharma S, Baranwal M. Machine learning-based ensemble approach in prediction of lung cancer predisposition using XRCC1 gene polymorphism. J Biomol Struct Dyn 2024; 42:7828-7837. [PMID: 37545160 DOI: 10.1080/07391102.2023.2242492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 07/23/2023] [Indexed: 08/08/2023]
Abstract
The employment of machine learning approaches has shown promising results in predicting cancer. In the current study, polymorphisms data of five single nucleotide polymorphisms (SNPs) of DNA repair gene XRCC1 (XRCC1 399, XRCC1 194, XRCC1 206, XRCC1 632, XRCC1 280) of the north Indian population along with four smoking status data is considered as an input to the proposed ensemble model to predict the risk of individual susceptibility to the lung cancer. The prediction accuracy of the proposed ensemble model for cancer predisposition was found to be 85%. The model performance is also evaluated using sensitivity, specificity, precision and the Gini index, which is found in the range of 0.83-0.87. The proposed model also outperformed in all evaluation parameters when compared with the individual Model (LM, SVM, RF, KNN and baseline neural net). Collectively, current results suggest the potential of the proposed ensemble model in predicting the risk of cancer based on XRCC1 SNPs data.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abhishek Choudhary
- Department of Computer Science, Thapar Institute of Engineering & Technology, India
| | - Adarsh Anand
- Department of Electronics & Communication Engineering, Thapar Institute of Engineering & Technology, India
| | - Amrita Singh
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
| | - Pratima Roy
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
| | - Navneet Singh
- Department of Pulmonary Medicine, Post Graduate Institute of Education and Medical Research (PGIMER), Chandigarh, India
| | - Vinay Kumar
- Department of Electronics & Communication Engineering, Thapar Institute of Engineering & Technology, India
| | - Siddharth Sharma
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
| | - Manoj Baranwal
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
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Bukhman YV, Morin PA, Meyer S, Chu LF, Jacobsen JK, Antosiewicz-Bourget J, Mamott D, Gonzales M, Argus C, Bolin J, Berres ME, Fedrigo O, Steill J, Swanson SA, Jiang P, Rhie A, Formenti G, Phillippy AM, Harris RS, Wood JMD, Howe K, Kirilenko BM, Munegowda C, Hiller M, Jain A, Kihara D, Johnston JS, Ionkov A, Raja K, Toh H, Lang A, Wolf M, Jarvis ED, Thomson JA, Chaisson MJP, Stewart R. A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography. Mol Biol Evol 2024; 41:msae036. [PMID: 38376487 PMCID: PMC10919930 DOI: 10.1093/molbev/msae036] [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: 03/08/2023] [Revised: 01/11/2024] [Accepted: 01/22/2024] [Indexed: 02/21/2024] Open
Abstract
The blue whale, Balaenoptera musculus, is the largest animal known to have ever existed, making it an important case study in longevity and resistance to cancer. To further this and other blue whale-related research, we report a reference-quality, long-read-based genome assembly of this fascinating species. We assembled the genome from PacBio long reads and utilized Illumina/10×, optical maps, and Hi-C data for scaffolding, polishing, and manual curation. We also provided long read RNA-seq data to facilitate the annotation of the assembly by NCBI and Ensembl. Additionally, we annotated both haplotypes using TOGA and measured the genome size by flow cytometry. We then compared the blue whale genome with other cetaceans and artiodactyls, including vaquita (Phocoena sinus), the world's smallest cetacean, to investigate blue whale's unique biological traits. We found a dramatic amplification of several genes in the blue whale genome resulting from a recent burst in segmental duplications, though the possible connection between this amplification and giant body size requires further study. We also discovered sites in the insulin-like growth factor-1 gene correlated with body size in cetaceans. Finally, using our assembly to examine the heterozygosity and historical demography of Pacific and Atlantic blue whale populations, we found that the genomes of both populations are highly heterozygous and that their genetic isolation dates to the last interglacial period. Taken together, these results indicate how a high-quality, annotated blue whale genome will serve as an important resource for biology, evolution, and conservation research.
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Affiliation(s)
- Yury V Bukhman
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Phillip A Morin
- Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration (NOAA), La Jolla, CA 92037, USA
| | - Susanne Meyer
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Li-Fang Chu
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Canada
| | | | | | - Daniel Mamott
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Maylie Gonzales
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Cara Argus
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Jennifer Bolin
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Mark E Berres
- University of Wisconsin Biotechnology Center, Bioinformatics Resource Center, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Olivier Fedrigo
- Vertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USA
| | - John Steill
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Scott A Swanson
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Peng Jiang
- Center for Gene Regulation in Health and Disease (GRHD), Cleveland State University, Cleveland, OH, USA
- Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH, USA
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Arang Rhie
- Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Giulio Formenti
- Laboratory of Neurogenetics of Language, The Rockefeller University/HHMI, New York, NY 10065, USA
| | - Adam M Phillippy
- Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Robert S Harris
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | | | - Kerstin Howe
- Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Bogdan M Kirilenko
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Institute of Cell Biology and Neuroscience, Faculty of Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Chetan Munegowda
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Institute of Cell Biology and Neuroscience, Faculty of Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Michael Hiller
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Institute of Cell Biology and Neuroscience, Faculty of Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Aashish Jain
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Alexander Ionkov
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Kalpana Raja
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Huishi Toh
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Aimee Lang
- Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration (NOAA), La Jolla, CA 92037, USA
| | - Magnus Wolf
- Institute for Evolution and Biodiversity (IEB), University of Muenster, 48149, Muenster, Germany
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
| | - Erich D Jarvis
- Vertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University/HHMI, New York, NY 10065, USA
| | - James A Thomson
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53726, USA
| | - Mark J P Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, Los Angeles, CA 90089, USA
| | - Ron Stewart
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
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Chiu TJ, Liu YW, Yong CC, Yin SM, Yeh CH, Chen YY. Combined Serum ALBUMIN with Neutrophil-to-Lymphocyte Ratio Predicts the Prognosis of Biliary Tract Cancer after Curative Resection. Cancers (Basel) 2023; 15:5474. [PMID: 38001734 PMCID: PMC10670262 DOI: 10.3390/cancers15225474] [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: 10/30/2023] [Revised: 11/15/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND The mainstay treatment of biliary tract cancer is complete tumor resection. Prior to surgery, risk stratification may help to predict and plan treatment approaches. In this study, we investigated the possibility of combining serum albumin concentrations and neutrophil-to-lymphocyte ratios (NLR) to create a score as ANS to predict the prognoses of biliary tract cancer before surgery. METHODS This study retrospectively collected serum albumin concentration, neutrophil, and lymphocyte data measured in biliary tract cancer patients slated to receive complete tumor resections within two weeks before surgery. From January 2013 to December 2019, 268 biliary tract cancer patients who had received tumor resections at our hospital were categorized into 3 ANS groups: ANS = 0 (high albumin and low NLR), ANS = 1 (low albumin or high NLR), and ANS = 2 (low albumin and high NLR). RESULTS Five-year survival rates were 70.1%, 47.6%, and 30.8% in the ANS = 0, 1, and 2 groups, respectively. The median overall survival time for the ANS = 0 group could not be determined by the end of the study, while those for ANS = 1 and ANS = 2 groups were 54.90 months and 16.62 months, respectively. The results of our multivariate analysis revealed that ANS could be used as an independent predictor of overall and recurrent-free survival. A high ANS was also correlated with other poor prognostic factors. CONCLUSIONS The ANS devised for this study can be used to predict postoperative survival in patients with BTC and to guide treatment strategies.
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Affiliation(s)
- Tai-Jan Chiu
- Division of Hematology-Oncology, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital, Taiwan and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan;
- Kaohsiung Chang Gung Cholangiocarcinoma and Pancreatic Cancer Group, Cancer Center, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan; (Y.-W.L.); (C.-C.Y.); (S.-M.Y.); (C.-H.Y.)
| | - Yueh-Wei Liu
- Kaohsiung Chang Gung Cholangiocarcinoma and Pancreatic Cancer Group, Cancer Center, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan; (Y.-W.L.); (C.-C.Y.); (S.-M.Y.); (C.-H.Y.)
- Department of Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan
| | - Chee-Chien Yong
- Kaohsiung Chang Gung Cholangiocarcinoma and Pancreatic Cancer Group, Cancer Center, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan; (Y.-W.L.); (C.-C.Y.); (S.-M.Y.); (C.-H.Y.)
- Department of Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan
| | - Shih-Min Yin
- Kaohsiung Chang Gung Cholangiocarcinoma and Pancreatic Cancer Group, Cancer Center, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan; (Y.-W.L.); (C.-C.Y.); (S.-M.Y.); (C.-H.Y.)
- Department of Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan
| | - Cheng-His Yeh
- Kaohsiung Chang Gung Cholangiocarcinoma and Pancreatic Cancer Group, Cancer Center, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan; (Y.-W.L.); (C.-C.Y.); (S.-M.Y.); (C.-H.Y.)
- Department of Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan
| | - Yen-Yang Chen
- Division of Hematology-Oncology, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital, Taiwan and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan;
- Kaohsiung Chang Gung Cholangiocarcinoma and Pancreatic Cancer Group, Cancer Center, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan; (Y.-W.L.); (C.-C.Y.); (S.-M.Y.); (C.-H.Y.)
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Yang W, Liu W, Zhu L, Lin Y, Meng Z, Wang Y. Association Between the XRCC1, GSTM1, and GSTT1 Polymorphisms in Model of Thyroid Cancer: A Meta-Analysis. Horm Metab Res 2023; 55:625-633. [PMID: 37678329 DOI: 10.1055/a-2135-6659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Thyroid cancer is the most common malignant tumor of the endocrine system, and its incidence is increasing worldwide each year. This study aimed to explore the association between XRCC1, GSTM1, and GSTT1 polymorphisms in the model of thyroid cancer. The experiment was conducted by searching PubMed, Embase, and Web of Science, with the last search performed in March 2022. A total of 12 studies were included in this meta-analysis, with sample sizes ranging from 211 to 1124. The proportion of XRCC1 polymorphisms (rs25489, GG) in thyroid cancer was slightly lower than that of the normal control group, but the difference was not statistically significant (Mean difference=1.13, 95% CI: 0.99-1.28, p=0.08). The proportion of XRCC1 polymorphisms (rs25489, GA) in thyroid cancer was significantly lower than that of the normal control group (Mean difference=1.32, 95% CI: 1.16-1.52, p<0.00001). The proportion of XRCC1 polymorphisms (rs25489, AA) in thyroid cancer was slightly lower than that of the normal control group, but again, the difference was not statistically significant (Mean difference=0.78, 95% CI: 0.61-1.01, p=0.06). Similarly, the proportion of XRCC1 polymorphisms (rs25487, GG) and (rs25487, GA) in thyroid cancer was lower than that of the normal control group, but the differences were not statistically significant (p=0.22 and p=0.49, respectively). In conclusion, this study found that the proportion of XRCC1 polymorphisms (rs25489, AA) in thyroid cancer was lower than that of the normal control group.
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Affiliation(s)
- Wenhan Yang
- Department of Maxillofacial Surgery, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Wanyu Liu
- Department of Maxillofacial Surgery, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Lei Zhu
- Department of Maxillofacial Surgery, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Yaqi Lin
- Department of Maxillofacial Surgery, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Zilu Meng
- Department of Maxillofacial Surgery, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Yudong Wang
- Department of Maxillofacial Surgery, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
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Wu Z, Liu Z, Sun Y, Yuan Y, Zou Q, Wen Y, Luo J, Liu R. APEX1 predicts poor prognosis of gallbladder cancer and affects biological properties of CD133 + GBC-SD cells via upregulating Jagged1. J Cancer 2023; 14:1443-1457. [PMID: 37283798 PMCID: PMC10240672 DOI: 10.7150/jca.83356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/12/2023] [Indexed: 06/08/2023] Open
Abstract
Although APEX1 is associated with the tumorigenesis and progression of some human cancer types, the function of APEX1 in gallbladder cancer (GBC) is unclear. In this study, we found that APEX1 expression is up-regulated in GBC tissues, and APEX1 positive expression is related to aggressive clinicopathological features and poor prognosis of GBC. APEX1 was an independent risk factor of GBC prognosis, and presented some pathological diagnostic significance in GBC. Furthermore, APEX1 was overexpressed in CD133+ GBC-SD cells in comparison with GBC-SD cells. APEX1 knockdown increased the sensitivity of CD133+ GBC-SD cells to 5-Fluorouracil via facilitating cell necrosis and apoptosis. APEX1 knockdown in CD133+ GBC-SD cells dramatically inhibited cell proliferation, migration, and invasion, and promoted cell apoptosis in vitro. APEX1 knockdown in CD133+ GBC-SD cells accelerated tumor growth in the xenograft models. Mechanistically, APEX1 affected these malignant properties via upregulating Jagged1 in CD133+ GBC-SD cells. Thus, APEX1 is a promising prognostic biomarker, and a potential therapeutic target for GBC.
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Affiliation(s)
- Zhengchun Wu
- Department of Hepatobiliary and Intestinal Surgery, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan410013, China
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, Hunan410011, China
| | - Ziru Liu
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, Hunan410011, China
| | - Yi Sun
- Department of Pathology, Second Xiangya Hospital, Central South University, Changsha, Hunan410011, China
| | - Yuan Yuan
- Department of Pathology, Third Xiangya Hospital, Central South University, Changsha, Hunan410013, China
| | - Qiong Zou
- Department of Pathology, Third Xiangya Hospital, Central South University, Changsha, Hunan410013, China
| | - Yun Wen
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, Hunan410011, China
| | - Jia Luo
- Department of Hepatobiliary and Intestinal Surgery, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan410013, China
| | - Rushi Liu
- Laboratory of Medical Molecular and Immunological Diagnostics, School of medicine, Hunan Normal University, Changsha, Hunan 410013, China
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Lai J, Yang S, Lin Z, Huang W, Li X, Li R, Tan J, Wang W. Update on Chemoresistance Mechanisms to First-Line Chemotherapy for Gallbladder Cancer and Potential Reversal Strategies. Am J Clin Oncol 2023; 46:131-141. [PMID: 36867653 PMCID: PMC10030176 DOI: 10.1097/coc.0000000000000989] [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] [Indexed: 03/04/2023]
Abstract
OBJECTIVE Gallbladder cancer (GBC) mortality remains high and chemoresistance is increasing. This review consolidates what is known about the mechanisms of chemoresistance to inform and accelerate the development of novel GBC-specific chemotherapies. METHODS Studies related to GBC-related chemoresistance were systematically screened in PubMed using the advanced search function. Search terms included GBC, chemotherapy, and signaling pathway. RESULTS Analysis of existing studies showed that GBC has poor sensitivity to cisplatin, gemcitabine (GEM), and 5-fluorouracil. DNA damage repair-related proteins, including CHK1, V-SCR, and H2AX, are involved in tumor adaptation to drugs. GBC-specific chemoresistance is often accompanied by changes in the apoptosis and autophagy-related molecules, BCL-2, CRT, and GBCDRlnc1. CD44 + and CD133 + GBC cells are less resistant to GEM, indicating that tumor stem cells are also involved in chemoresistance. In addition, glucose metabolism, fat synthesis, and glutathione metabolism can influence the development of drug resistance. Finally, chemosensitizers such as lovastatin, tamoxifen, chloroquine, and verapamil are able improve the therapeutic effect of cisplatin or GEM in GBC. CONCLUSIONS This review summarizes recent experimental and clinical studies of the molecular mechanisms of chemoresistance, including autophagy, DNA damage, tumor stem cells, mitochondrial function, and metabolism, in GBC. Information on potential chemosensitizers is also discussed. The proposed strategies to reverse chemoresistance should inform the clinical use of chemosensitizers and gene-based targeted therapy for this disease.
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Affiliation(s)
- Jinbao Lai
- Yan’an Affiliated Hospital of Kunming Medical University
- Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province
- Kunming Key Laboratory of Biotherapy, Kunming, Yunnan, China
| | - Songlin Yang
- Yan’an Affiliated Hospital of Kunming Medical University
- Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province
- Kunming Key Laboratory of Biotherapy, Kunming, Yunnan, China
| | - Zhuying Lin
- Yan’an Affiliated Hospital of Kunming Medical University
- Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province
- Kunming Key Laboratory of Biotherapy, Kunming, Yunnan, China
| | - Wenwen Huang
- Yan’an Affiliated Hospital of Kunming Medical University
- Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province
- Kunming Key Laboratory of Biotherapy, Kunming, Yunnan, China
| | - Xiao Li
- Yan’an Affiliated Hospital of Kunming Medical University
- Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province
- Kunming Key Laboratory of Biotherapy, Kunming, Yunnan, China
| | - Ruhong Li
- Yan’an Affiliated Hospital of Kunming Medical University
- Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province
- Kunming Key Laboratory of Biotherapy, Kunming, Yunnan, China
| | - Jing Tan
- Yan’an Affiliated Hospital of Kunming Medical University
- Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province
- Kunming Key Laboratory of Biotherapy, Kunming, Yunnan, China
| | - Wenju Wang
- Yan’an Affiliated Hospital of Kunming Medical University
- Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province
- Kunming Key Laboratory of Biotherapy, Kunming, Yunnan, China
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Yang F, Zhou L, Chen J, Luo Y, Wang Y. Survival association of XRCC1 for patients with head and neck squamous cell carcinoma: A systematic review and meta-analysis. Front Genet 2023; 13:1035910. [PMID: 36685969 PMCID: PMC9849232 DOI: 10.3389/fgene.2022.1035910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/29/2022] [Indexed: 01/06/2023] Open
Abstract
Background: Epidemiologic studies have demonstrated that X-ray repair cross-complementary group 1 (XRCC1) is one of the susceptibility factors in head and neck squamous cell carcinoma (HNSCC) patients. However, its clinical prognostic impact remains controversial. Thus, a meta-analysis was performed to clarify the association between XRCC1 and the survival outcomes in HNSCC patients. Methods: Following the Preferred Reporting Items or Systematic Reviews Meta Analyses (PRISMA) 2020 guidelines, literature searches were systematically performed in PubMed, EMBASE, Web of Science, Wanfang, and Chinese National Knowledge Infrastructure (CNKI) databases with manual retrieval. Hazard ratios (HRs) and 95% confidence intervals (CIs) were collected to estimate the correlation between XRCC1 and the survival outcomes of HNSCC patients. Results: Ten studies including 1995 HNSCC patients who satisfied the inclusion and exclusion criteria were included in this meta-analysis. Pooled analysis indicated that XRCC1 Arg399Gln and XRCC1 high protein expression were significantly correlated with poor overall survival with HR of 1.31 (95% CIs: 1.03-1.66, p = 0.027) and 2.32 (95% CIs: 1.55-3.48 p = 0.000) in HNSCC patients. In addition, our results demonstrated that XRCC1 was significantly associated with poor progression-free survival (HR = 1.42, 95% CIs: 1.15-1.75, p = 0.001) in HNSCC patients. ConclusionThis meta-analysis demonstrated that XRCC1 Arg399Gln and XRCC1 high protein expression increase the risk of poor survival for HNSCC patients. XRCC1 is a potential therapeutic target for HNSCC.
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Kabziński J, Majsterek I. Association of base excision repair pathway genes OGG1, XRCC1 and MUTYH polymorphisms and the level of 8-oxo-guanine with increased risk of colorectal cancer occurrence. Int J Occup Med Environ Health 2022; 35:625-633. [PMID: 35770680 PMCID: PMC10464724 DOI: 10.13075/ijomeh.1896.01901] [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: 08/05/2021] [Accepted: 04/15/2022] [Indexed: 10/17/2022] Open
Abstract
OBJECTIVES Reduced efficiency of DNA repair systems has long been a suspected factor in increasing the risk of cancer. In this work authors investigate influence of selected polymorphisms of DNA repair genes (XRCC1, OGG1 and MUTYH) and level of oxidative damage (measured as level of 8-oxo-guanine, 8-oG) on modulation of the risk of colorectal cancer. MATERIAL AND METHODS In group of 324 patients with colorectal cancer the occurrence of polymorphic variants in Ser326Cys of OGG1, Arg399Gln of XRCC1 and Gln324His of MUTYH were studied with TaqMan technique. In addition level of 8-oG in isolated DNA was determined. RESULTS Studied polymorphisms of OGG1, XRCC1 and MUTYH genes influence the risk of CRC: OGG1 Ser326Cys (OR = 1.259, 95% CI: 1.058-1.499, p = 0.007), XRCC1 Arg399Gln (OR = 2.481, 95% CI: 1.745-3.529, p < 0.0001) and MUTYH Gln324His (OR = 1.421, 95% CI: 1.017-1.984, p = 0.039) increase the risk. At the same time, studies examined level of 8-oG for each of the genotypes in both the patient and control group, and have shown that OGG1 Ser326Cys and XRCC1 Arg399Gln are associated with elevated 8-oG level, while MUTYH Gln324His is not, suggesting, that in case of OGG1 Ser326Cys and XRCC1 Arg399Gln CRC risk modulation is connected to mechanisms associated with 8-oG levels. CONCLUSIONS This work shows that patients with CRC not only have an increased level of 8-oG and that the studied polymorphisms modulate risk of cancer, but also indicate a relationship between these 2 phenomena, which may contribute to a better understanding of the mechanism of neoplastic process in case of reduced effectiveness of DNA repair mechanisms. Int J Occup Med Environ Health. 2022;35(5):625-33.
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Affiliation(s)
- Jacek Kabziński
- Medical University of Lodz, Department of Clinical Chemistry and Biochemistry, Łódź, Poland
| | - Ireneusz Majsterek
- Medical University of Lodz, Department of Clinical Chemistry and Biochemistry, Łódź, Poland
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Wright GM, Gassman NR. Glucose Increases STAT3 Activation, Promoting Sustained XRCC1 Expression and Increasing DNA Repair. Int J Mol Sci 2022; 23:ijms23084314. [PMID: 35457130 PMCID: PMC9029887 DOI: 10.3390/ijms23084314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/28/2022] [Accepted: 04/10/2022] [Indexed: 02/05/2023] Open
Abstract
Dysregulation of DNA repair is a hallmark of cancer, though few cancer-specific mechanisms that drive the overexpression of DNA repair proteins are known. We previously identified STAT3 as a novel transcriptional regulator of X-ray cross-complementing group 1 (XRCC1), an essential scaffold protein in base excision repair in triple-negative breast cancers. We also identified an inducible response to IL-6 and epidermal growth factor stimulation in the non-tumorigenic embryonic kidney cell line HEK293T. As IL-6 and EGF signaling are growth and inflammatory-inducible responses, we examined if glucose challenge can increase STAT3 activation, promoting adaptive changes in XRCC1 expression in different cell types. Acute high glucose exposure promoted XRCC1 expression through STAT3 activation, increasing the repair of methyl methanesulfonate-induced DNA damage in HEK293T cells and the osteosarcoma cell line U2OS. Sustained exposure to high glucose promoted the overexpression of XRCC1, which can be reversed upon glucose restriction and down-regulation of STAT3 activation. Thus, we have identified a novel link between XRCC1 expression and STAT3 activation following exogenous exposures, which could play a critical role in dictating a cancer cell’s response to DNA-damaging agents.
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Affiliation(s)
- Griffin M. Wright
- College of Medicine Depart of Physiology & Cell Biology, University of South Alabama, Mobile, AL 36688, USA;
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36607, USA
| | - Natalie R. Gassman
- Department of Pharmacology and Toxicology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Correspondence:
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Wright G, Sonavane M, Gassman NR. Activated STAT3 Is a Novel Regulator of the XRCC1 Promoter and Selectively Increases XRCC1 Protein Levels in Triple Negative Breast Cancer. Int J Mol Sci 2021; 22:ijms22115475. [PMID: 34067421 PMCID: PMC8196947 DOI: 10.3390/ijms22115475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/18/2021] [Accepted: 05/20/2021] [Indexed: 02/07/2023] Open
Abstract
Base Excision Repair (BER) addresses base lesions and abasic sites induced by exogenous and endogenous stressors. X-ray cross complementing group 1 (XRCC1) functions as a scaffold protein in BER and single-strand break repair (SSBR), facilitating and coordinating repair through its interaction with a host of critical repair proteins. Alterations of XRCC1 protein and gene expression levels are observed in many cancers, including colorectal, ovarian, and breast cancer. While increases in the expression level of XRCC1 are reported, the transcription factors responsible for this up-regulation are not known. In this study, we identify the signal transducer and activator of transcription 3 (STAT3) as a novel regulator of XRCC1 through chromatin immunoprecipitation. Activation of STAT3 through phosphorylation at Y705 by cytokine (IL-6) signaling increases the expression of XRCC1 and the occupancy of STAT3 within the XRCC1 promoter. In triple negative breast cancer, the constitutive activation of STAT3 upregulates XRCC1 gene and protein expression levels. Increased expression of XRCC1 is associated with aggressiveness and resistance to DNA damaging chemotherapeutics. Thus, we propose that activated STAT3 regulates XRCC1 under stress and growth conditions, but constitutive activation in cancers results in dysregulation of XRCC1 and subsequently BER and SSBR.
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Affiliation(s)
- Griffin Wright
- Department of Physiology and Cell Biology, University of South Alabama College of Medicine, 307 N University Blvd, Mobile, AL 36688, USA; (G.W.); (M.S.)
- Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, AL 36604-1405, USA
| | - Manoj Sonavane
- Department of Physiology and Cell Biology, University of South Alabama College of Medicine, 307 N University Blvd, Mobile, AL 36688, USA; (G.W.); (M.S.)
- Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, AL 36604-1405, USA
| | - Natalie R. Gassman
- Department of Physiology and Cell Biology, University of South Alabama College of Medicine, 307 N University Blvd, Mobile, AL 36688, USA; (G.W.); (M.S.)
- Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, AL 36604-1405, USA
- Correspondence:
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Lin Y, Chen H, Pan F. Prognostic Nomograms to Predict Survival of Patients with Resectable Gallbladder Cancer: A Surveillance, Epidemiology, and End Results (SEER)-Based Analysis. Med Sci Monit 2021; 27:e929106. [PMID: 33784268 PMCID: PMC8019267 DOI: 10.12659/msm.929106] [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] [Indexed: 11/24/2022] Open
Abstract
Background Gallbladder adenocarcinoma (GBAC) is globally acknowledged as one of the most common malignancies among all gastrointestinal cancers. Despite prognosis of GBAC patients remains poor, patients with early-stage disease can be observed with long-term survival. Material/Methods In this study, 2556 patients with pathological GBAC between 2010 and 2015 were derived from the Surveillance, Epidemiology, and End Results (SEER) database. The prognostic nomograms containing all independent prognostic factors for predicting overall survival (OS) and cancer-specific survival (CSS) were constructed to achieve superior prognostic discriminatory ability. Results Based on the AJCC 7th TNM staging system, we found the TNM substaging was not accurate enough to predict the survival and stratify the risk. Based on the results of univariate and multivariate analyses, a more precise prognostic nomogram was constructed containing all significant independent prognostic factors (age, grade, TNM stage, bone metastasis, and chemotherapy) for OS, while age, grade, TNM stage, bone metastasis and radiotherapy significant independent prognostic factors for CSS. The C-index of the constructed nomogram for predicting OS and CSS was 0.740 and 0.737 higher than that of TNM staging alone (0.667 for OS and 0.689 for CSS), respectively. In addition, the calibration curves and decision curve analysis further showed its robust power in survival prediction. Conclusions The constructed nomograms showed better discrimination abilities to predict OS and CSS rates at 1, 3, and 5 years. In the future, these constructed models for this disease will assist in risk stratification to guide GBAC treatment.
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Affiliation(s)
- Yan Lin
- Department of Gastroenterology, Fuzhou Second Hospital Affiliated to Xiamen University, Fuzhou, Fujian, China (mainland)
| | - Hua Chen
- Department of General Surgery, Ningde Medical District, 900th Hospital of the Joint Logistics Team, People's Liberation Army (PLA), Ningde, Fujian, China (mainland)
| | - Fan Pan
- Department of Hepatobiliary Surgery, 900th Hospital of the Joint Logistics Team, People's Liberation Army (PLA), Fuzhou, Fujian, China (mainland)
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A trifunctional Pt(II) complex alleviates the NHEJ/HR-related DSBs repairs to evade cisplatin-resistance in NSCLC. Bioorg Chem 2020; 104:104210. [PMID: 32920356 DOI: 10.1016/j.bioorg.2020.104210] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/29/2020] [Accepted: 08/17/2020] [Indexed: 01/26/2023]
Abstract
Cisplatin, a representative of platinum-based drug, is clinically and widely used in the treatment of various types of malignant cancer. However, its non-selectivity to almost all the cell lines and resistance in long-term use severely limit its scope of use. As biotin-specific uptake systems are overexpressed in many types of tumors but rarely occur in normal tissues, making biotin a promising target for cancer treatment. In the study, we synthesized the Pt(II) complex C2 and determined its biological activities. The existence of biotin enhanced the ability of the complex to target tumors, while the introduction of a naphthalimide compound makes it possible to diagnose tumors and monitor their progress. We have also introduced a known Pt(II) complex DN604, which not only retains the excellent cytotoxicity of platinum drugs, but also inhibits the expression of DNA double-strand breaks (DSBs) repair-related NHEJ protein Ku70 and HR protein Rad51. In summary, we report a novel trifunctional Pt(II) complex that could target tumor cells, monitor tumor progression, and reverse DSBs repair-induced cisplatin-resistance.
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