1
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Mandal T, Shukla D, Khan MMA, Ganesan SK, Srivastava AK. The EXO1/Polη/Polι axis as a promising target for miR-3163-mediated attenuation of cancer stem-like cells in non-small cell lung carcinoma. Br J Cancer 2024:10.1038/s41416-024-02840-2. [PMID: 39369054 DOI: 10.1038/s41416-024-02840-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 08/21/2024] [Accepted: 08/27/2024] [Indexed: 10/07/2024] Open
Abstract
BACKGROUND Cancer stem-like cells (CSLCs) drive tumour progression and chemoresistance. The concerted efforts of EXO1 and TLS polymerases safeguard DNA integrity against chemotherapeutic drugs. In absence of potential drug targets, non-small cell lung carcinoma (NSCLC) patients have few therapeutic options. In current scenario, microRNAs offer a potential avenue for eradicating CSLCs. METHODS EXO1 downregulation impact on CSLCs expansion was assessed via flow cytometry. Co-localisation of EXO1, Polη and Polι was validated through co-immunoprecipitation and confocal-imaging. The effects of co-downregulation of Polη and Polι on CSLC survival, repair synthesis, and mutagenesis were evaluated using flow cytometry and immunohistochemistry in cell lines and xenografts. MicroRNA targeting EXO1 was studied for its role in CSLCs regulation. RESULTS EXO1 downregulation in NSCLC CSLCs induces DNA lesions, triggering apoptosis and enhances cisplatin sensitivity. It collaborates with Polη and Polι in DNA repair, contributing to cisplatin resistance in CSLCs. Absence of Polη and Polι impairs repair and reduces cisplatin-induced mutagenesis. Co-downregulation of Polη and Polι in xenografts reduces tumour proliferation significantly. MiR-3163 overexpression sensitises CSLCs to cisplatin via targeting EXO1/Polη/Polι axis, as shown in mechanistic studies. CONCLUSION This study unveils a novel regulatory pathway involving EXO1/Polη/Polι axis and miR-3163, providing insights into CSLCs regulation in NSCLC. EXO1/Polη/Polι axis targeted by miR-3163, resulting in the inhibition of cell growth and induction of apoptosis in NSCLC CSLCs.
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Affiliation(s)
- Tanima Mandal
- Cancer Biology & Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, Kolkata, WB, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Devendra Shukla
- Cancer Biology & Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, Kolkata, WB, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Md Maqsood Ahamad Khan
- Structural Biology & Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, WB, India
| | - Senthil Kumar Ganesan
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Structural Biology & Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, WB, India
| | - Amit Kumar Srivastava
- Cancer Biology & Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, Kolkata, WB, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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2
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Ren Y, Liang H, Huang Y, Miao Y, Li R, Qiang J, Wu L, Qi J, Li Y, Xia Y, Huang L, Wang S, Kong X, Zhou Y, Zhang Q, Zhu G. Key candidate genes and pathways in T lymphoblastic leukemia/lymphoma identified by bioinformatics and serological analyses. Front Immunol 2024; 15:1341255. [PMID: 38464517 PMCID: PMC10920334 DOI: 10.3389/fimmu.2024.1341255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/08/2024] [Indexed: 03/12/2024] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL)/T-cell lymphoblastic lymphoma (T-LBL) is an uncommon but highly aggressive hematological malignancy. It has high recurrence and mortality rates and is challenging to treat. This study conducted bioinformatics analyses, compared genetic expression profiles of healthy controls with patients having T-ALL/T-LBL, and verified the results through serological indicators. Data were acquired from the GSE48558 dataset from Gene Expression Omnibus (GEO). T-ALL patients and normal T cells-related differentially expressed genes (DEGs) were investigated using the online analysis tool GEO2R in GEO, identifying 78 upregulated and 130 downregulated genes. Gene Ontology (GO) and protein-protein interaction (PPI) network analyses of the top 10 DEGs showed enrichment in pathways linked to abnormal mitotic cell cycles, chromosomal instability, dysfunction of inflammatory mediators, and functional defects in T-cells, natural killer (NK) cells, and immune checkpoints. The DEGs were then validated by examining blood indices in samples obtained from patients, comparing the T-ALL/T-LBL group with the control group. Significant differences were observed in the levels of various blood components between T-ALL and T-LBL patients. These components include neutrophils, lymphocyte percentage, hemoglobin (HGB), total protein, globulin, erythropoietin (EPO) levels, thrombin time (TT), D-dimer (DD), and C-reactive protein (CRP). Additionally, there were significant differences in peripheral blood leukocyte count, absolute lymphocyte count, creatinine, cholesterol, low-density lipoprotein, folate, and thrombin times. The genes and pathways associated with T-LBL/T-ALL were identified, and peripheral blood HGB, EPO, TT, DD, and CRP were key molecular markers. This will assist the diagnosis of T-ALL/T-LBL, with applications for differential diagnosis, treatment, and prognosis.
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Affiliation(s)
- Yansong Ren
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Haoyue Liang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Yali Huang
- Clinical Laboratory of Zhengning County People's Hospital, Qingyang, Gansu, China
| | - Yuyang Miao
- Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin Geriatrics Institute, Tianjin, China
| | - Ruihua Li
- Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin Geriatrics Institute, Tianjin, China
| | - Junlian Qiang
- Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin Geriatrics Institute, Tianjin, China
| | - Lihong Wu
- Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin Geriatrics Institute, Tianjin, China
| | - Jinfeng Qi
- Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin Geriatrics Institute, Tianjin, China
| | - Ying Li
- Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin Geriatrics Institute, Tianjin, China
| | - Yonghui Xia
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Lunhui Huang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Shoulei Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Xiaodong Kong
- Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin Geriatrics Institute, Tianjin, China
| | - Yuan Zhou
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Qiang Zhang
- Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin Geriatrics Institute, Tianjin, China
| | - Guoqing Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
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3
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Lavi ES, Lin ZP, Ratner ES. Gene expression of non-homologous end-joining pathways in the prognosis of ovarian cancer. iScience 2023; 26:107934. [PMID: 37810216 PMCID: PMC10558711 DOI: 10.1016/j.isci.2023.107934] [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: 02/12/2023] [Revised: 04/04/2023] [Accepted: 09/13/2023] [Indexed: 10/10/2023] Open
Abstract
Ovarian cancer is the deadliest gynecologic malignancy in women, with a 46% five-year overall survival rate. The objective of the study was to investigate the effects of non-homologous end-joining (NHEJ) genes on clinical outcomes of ovarian cancer patients. To determine if these genes act as prognostic biomarkers of mortality and disease progression, the expression profiles of 48 NHEJ-associated genes were analyzed using an array of statistical and machine learning techniques: logistic regression models, decision trees, naive-Bayes, two sample t-tests, support vector machines, hierarchical clustering, principal component analysis, and neural networks. In this process, the correlation of genes with patient survival and disease progression and recurrence was noted. Also, multiple features from the gene set were found to have significant predictive capabilities. APTX, BRCA1, PAXX, LIG1, and TP53 were identified as most important out of all the candidate genes for predicting clinical outcomes of ovarian cancer patients.
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Affiliation(s)
- Ethan S. Lavi
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Z. Ping Lin
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Elena S. Ratner
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510, USA
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4
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Sun Y, Man Y, Cheng J, Li J, Liu Y. FAM60A promotes osteosarcoma development and progression. Cancer Med 2023; 12:17491-17503. [PMID: 37439040 PMCID: PMC10501228 DOI: 10.1002/cam4.6343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 07/02/2023] [Accepted: 07/03/2023] [Indexed: 07/14/2023] Open
Abstract
BACKGROUND Osteosarcoma (OS) is a highly malignant primary bone tumor. Family of homology 60A (FAM60A) reportedly contributes to the malignant growth of some tumors. METHODS Herein we investigated the mRNA expression level of FAM60A by combining OS and non-cancer samples from public databases. Immunohistochemistry was performed to determine protein expression levels of FAM60A in patients with OS. Further, RT-qPCR and western blotting were conducted to evaluate FAM60A expression in various OS cell lines. CCK-8 assay, colony formation assay, and flow cytometry were applied to determine the function of FAM60A. Finally, functional enrichment analysis was performed based on FAM60A co-expressed genes. RESULTS FAM60A mRNA expression level was found to be significantly upregulated (standardized mean difference = 1.27, 95% CI [0.67-1.88]). Survival analyses suggested that higher expression of FAM60A was indicative of poor prognoses. Similarly, FAM60A protein expression level was also observed to be upregulated. Knocking down FAM60A expression inhibited OS cell proliferation, increased apoptosis, and blocked cells from entering the S phase. Besides, cell cycle was the most prominently enriched pathway, and BUB1, DTL, and EXO1 were identified as hub genes. CONCLUSIONS FAM60A expression was found to be markedly upregulated in OS; furthermore, FAM60A was observed to promote OS cell proliferation, inhibit apoptosis, and participate in cell cycle regulation. Besides, FAM60A may interact with hub genes to participate in the progress of OS.
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Affiliation(s)
- Yu Sun
- Division of Spinal SurgeryThe First Affiliated Hospital of Guangxi Medical UniversityNanningGuangxi Zhuang Autonomous RegionP.R. China
| | - Yu‐Nan Man
- Division of Spinal SurgeryThe First Affiliated Hospital of Guangxi Medical UniversityNanningGuangxi Zhuang Autonomous RegionP.R. China
| | - Jin‐hui Cheng
- Jiangxi Provincial People's HospitalThe First Affiliated Hospital of Nanchang Medical CollegeNanchangJiangxiChina
| | - Jing‐tang Li
- Jiangxi Provincial People's HospitalThe First Affiliated Hospital of Nanchang Medical CollegeNanchangJiangxiChina
| | - Ya‐yun Liu
- Jiangxi Provincial People's HospitalThe First Affiliated Hospital of Nanchang Medical CollegeNanchangJiangxiChina
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5
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Xu W, Liu L, Cui Z, Li M, Ni J, Huang N, Zhang Y, Luo J, Sun L, Sun F. Identification of key enzalutamide-resistance-related genes in castration-resistant prostate cancer and verification of RAD51 functions. Open Med (Wars) 2023; 18:20230715. [PMID: 37251536 PMCID: PMC10224628 DOI: 10.1515/med-2023-0715] [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: 11/28/2022] [Revised: 03/16/2023] [Accepted: 04/17/2023] [Indexed: 05/31/2023] Open
Abstract
Patients with castration-resistant prostate cancer (CRPC) often develop drug resistance after treatment with enzalutamide. The goal of our study was to identify the key genes related to enzalutamide resistance in CRPC and to provide new gene targets for future research on improving the efficacy of enzalutamide. Differential expression genes (DEGs) associated with enzalutamide were obtained from the GSE151083 and GSE150807 datasets. We used R software, the DAVID database, protein-protein interaction networks, the Cytoscape program, and Gene Set Cancer Analysis for data analysis. The effect of RAD51 knockdown on prostate cancer (PCa) cell lines was demonstrated using Cell Counting Kit-8, clone formation, and transwell migration experiments. Six hub genes with prognostic values were screened (RAD51, BLM, DTL, RFC2, APOE, and EXO1), which were significantly associated with immune cell infiltration in PCa. High RAD51, BLM, EXO1, and RFC2 expression was associated with androgen receptor signaling pathway activation. Except for APOE, high expression of hub genes showed a significant negative correlation with the IC50 of Navitoclax and NPK76-II-72-1. RAD51 knockdown inhibited the proliferation and migration of PC3 and DU145 cell lines and promoted apoptosis. Additionally, 22Rv1 cell proliferation was more significantly inhibited with RAD51 knockdown than without RAD51 knockdown under enzalutamide treatment. Overall, six key genes associated with enzalutamide resistance were screened (RAD51, BLM, DTL, RFC2, APOE, and EXO1), which are potential therapeutic targets for enzalutamide-resistant PCa in the future.
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Affiliation(s)
- Wen Xu
- Shanghai Clinical College, Anhui Medical University, Shanghai, 200072, China
- The Fifth School of Clinical Medicine, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Li Liu
- Department of Clinical Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiaotong University, Shanghai, 200127, China
| | - Zhongqi Cui
- Department of Clinical Laboratory, Shanghai Tenth People’s Hospital of Tongji University, 200072, Shanghai, China
| | - Mingyang Li
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Jinliang Ni
- Shanghai Clinical College, Anhui Medical University, Shanghai, 200072, China
- The Fifth School of Clinical Medicine, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Nan Huang
- Department of Clinical Laboratory, Shanghai Tenth People’s Hospital of Tongji University, 200072, Shanghai, China
| | - Yue Zhang
- Department of Clinical Laboratory, Shanghai Tenth People’s Hospital of Tongji University, 200072, Shanghai, China
| | - Jie Luo
- Department of Clinical Laboratory, Shanghai Tenth People’s Hospital of Tongji University, 200072, Shanghai, China
| | - Limei Sun
- Department of Clinical Laboratory, Shanghai Tenth People’s Hospital of Tongji University, 200072, Shanghai, China
| | - Fenyong Sun
- The Fifth School of Clinical Medicine, Anhui Medical University, Hefei, 230032, Anhui, China
- Shanghai Clinical College, Anhui Medical University, No. 301, Yanchang Middle Road, Jingan District, Shanghai, 200072, China
- Department of Clinical Laboratory, Shanghai Tenth People’s Hospital of Tongji University, No. 301, Yanchang Middle Road, Jingan District, 200072, Shanghai, China
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6
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A CRISPR-Cas9 screen identifies EXO1 as a formaldehyde resistance gene. Nat Commun 2023; 14:381. [PMID: 36693839 PMCID: PMC9873647 DOI: 10.1038/s41467-023-35802-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 12/28/2022] [Indexed: 01/25/2023] Open
Abstract
Fanconi Anemia (FA) is a rare, genome instability-associated disease characterized by a deficiency in repairing DNA crosslinks, which are known to perturb several cellular processes, including DNA transcription, replication, and repair. Formaldehyde, a by-product of metabolism, is thought to drive FA by generating DNA interstrand crosslinks (ICLs) and DNA-protein crosslinks (DPCs). However, the impact of formaldehyde on global cellular pathways has not been investigated thoroughly. Herein, using a pangenomic CRISPR-Cas9 screen, we identify EXO1 as a critical regulator of formaldehyde-induced DNA lesions. We show that EXO1 knockout cell lines exhibit formaldehyde sensitivity leading to the accumulation of replicative stress, DNA double-strand breaks, and quadriradial chromosomes, a typical feature of FA. After formaldehyde exposure, EXO1 is recruited to chromatin, protects DNA replication forks from degradation, and functions in parallel with the FA pathway to promote cell survival. In vitro, EXO1-mediated exonuclease activity is proficient in removing DPCs. Collectively, we show that EXO1 limits replication stress and DNA damage to counteract formaldehyde-induced genome instability.
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7
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Hong MJ, Park JE, Lee SY, Lee JH, Choi JE, Kang HG, Do SK, Jeong JY, Shin KM, Lee WK, Seok Y, Choi SH, Lee YH, Seo H, Yoo SS, Lee J, Cha SI, Kim CH, Park JY. Exonuclease 1 genetic variant is associated with clinical outcomes of pemetrexed chemotherapy in lung adenocarcinoma. J Cancer 2022; 13:3701-3709. [PMID: 36606188 PMCID: PMC9809306 DOI: 10.7150/jca.78498] [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: 08/30/2022] [Accepted: 11/16/2022] [Indexed: 12/12/2022] Open
Abstract
Pemetrexed is an anti-folate agent which is one of the most frequently used chemotherapy agents for non-squamous non-small cell lung cancer (NSCLC) patients. However, clinical response to pemetrexed chemotherapy and survival outcome of patients varies significantly. We evaluated whether the genetic variants in miRNA target sites may affect the treatment outcome of pemetrexed chemotherapy in lung adenocarcinoma patients. One hundred SNPs in miRNA binding regions in cancer-related genes were obtained from the crosslinking, ligation, and sequencing of hybrids (CLASH) and CancerGenes database, and the associations with the response to pemetrexed chemotherapy and survival outcomes were investigated in 314 lung adenocarcinoma patients. Two polymorphisms, EXO1 rs1047840G>A and CAMKK2 rs1653586G>T, were significantly associated with worse chemotherapy response (adjusted odds ratio [aOR] = 0.41, 95% CI = 0.24-0.68, P = 0.001, under dominant model; and aOR = 0.33, 95% CI = 0.16-0.67, P = 0.002, under dominant model, respectively) and worse OS (adjusted hazard ratio [aHR] = 1.34, 95% CI = 1.01-1.77, P = 0.04, under dominant model; and aHR = 1.50, 95% CI = 1.06-2.13, P = 0.02, under dominant model, respectively) in multivariate analyses. Significantly increased luciferase activity was noted in EXO1 rs1047840 A allele compared to G allele. In conclusion, two SNPs in miRNA binding sites, especially EXO1 rs1047840G>A, were associated with the chemotherapy response and survival outcome in lung adenocarcinoma patients treated with pemetrexed.
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Affiliation(s)
- Mi Jeong Hong
- Department of Biochemistry, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.,Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Ji Eun Park
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Shin Yup Lee
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.,✉ Corresponding authors: Shin Yup Lee, MD, PhD, Lung Cancer Center, Kyungpook National University Chilgok Hospital, 807, Hoguk-ro, Buk-gu, Daegu 41404, Korea; Tel: +82-53-200-2632; Fax: +82-53-200-2027, E-mail: ; Jae Yong Park, MD, PhD, Lung Cancer Center, Kyungpook National University Chilgok Hospital, 807, Hoguk-ro, Buk-gu, Daegu 41404, Korea; Tel: +82-53-200-2631; Fax: +82-53-200-2027, E-mail:
| | - Jang Hyuck Lee
- Department of Biochemistry, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.,Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Jin Eun Choi
- Department of Biochemistry, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.,Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Hyo-Gyoung Kang
- Department of Biochemistry, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.,Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Sook Kyung Do
- Department of Biochemistry, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.,Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Ji Yun Jeong
- Department of Pathology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Kyung Min Shin
- Department of Radiology School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Won Ki Lee
- Medical Research Collaboration Center in Kyungpook National University Hospital and School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Yangki Seok
- Department of Thoracic Surgery, Soonchunhyang University Gumi Hospital, Gumi, Korea
| | - Sun Ha Choi
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Yong Hoon Lee
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Hyewon Seo
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Seung Soo Yoo
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Jaehee Lee
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Seung Ick Cha
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Chang Ho Kim
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Jae Yong Park
- Department of Biochemistry, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.,Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Korea.,Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.,BK21 Plus KNU Biomedical Convergence Program, Department of Biomedical Science, Kyungpook National University, Daegu, Korea.,✉ Corresponding authors: Shin Yup Lee, MD, PhD, Lung Cancer Center, Kyungpook National University Chilgok Hospital, 807, Hoguk-ro, Buk-gu, Daegu 41404, Korea; Tel: +82-53-200-2632; Fax: +82-53-200-2027, E-mail: ; Jae Yong Park, MD, PhD, Lung Cancer Center, Kyungpook National University Chilgok Hospital, 807, Hoguk-ro, Buk-gu, Daegu 41404, Korea; Tel: +82-53-200-2631; Fax: +82-53-200-2027, E-mail:
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8
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Manils J, Marruecos L, Soler C. Exonucleases: Degrading DNA to Deal with Genome Damage, Cell Death, Inflammation and Cancer. Cells 2022; 11:2157. [PMID: 35883600 PMCID: PMC9316158 DOI: 10.3390/cells11142157] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/30/2022] [Accepted: 07/07/2022] [Indexed: 01/27/2023] Open
Abstract
Although DNA degradation might seem an unwanted event, it is essential in many cellular processes that are key to maintaining genomic stability and cell and organism homeostasis. The capacity to cut out nucleotides one at a time from the end of a DNA chain is present in enzymes called exonucleases. Exonuclease activity might come from enzymes with multiple other functions or specialized enzymes only dedicated to this function. Exonucleases are involved in central pathways of cell biology such as DNA replication, repair, and death, as well as tuning the immune response. Of note, malfunctioning of these enzymes is associated with immune disorders and cancer. In this review, we will dissect the impact of DNA degradation on the DNA damage response and its links with inflammation and cancer.
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Affiliation(s)
- Joan Manils
- Serra Húnter Programme, Immunology Unit, Department of Pathology and Experimental Therapy, School of Medicine, Universitat de Barcelona, Feixa Llarga s/n, 08907 L’Hospitalet de Llobregat, Spain;
- Immunity, Inflammation and Cancer Group, Oncobell Program, Institut d’Investigació Biomèdica de Bellvitge—IDIBELL, 08907 L’Hospitalet de Llobregat, Spain
| | - Laura Marruecos
- Breast Cancer Laboratory, Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia;
| | - Concepció Soler
- Immunity, Inflammation and Cancer Group, Oncobell Program, Institut d’Investigació Biomèdica de Bellvitge—IDIBELL, 08907 L’Hospitalet de Llobregat, Spain
- Immunology Unit, Department of Pathology and Experimental Therapy, School of Medicine, Universitat de Barcelona, 08007 Barcelona, Spain
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9
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Mao P, Wu S, Fan Y. Upregulation of EXO1 caused by homology-dependent repair confers cisplatin resistance to gastric cancer cells. Can J Physiol Pharmacol 2022; 100:903-914. [PMID: 35767882 DOI: 10.1139/cjpp-2022-0139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The homology-dependent repair (HDR) pathway is involved in DNA damage response (DDR), which is crucial to cancer cell survival after treatment with DNA damage agents, including cisplatin (CDDP). Here, we explored the interactions between EXO1, a core gene in the HDR pathway, and CDDP resistance in gastric cancer (GC). Using bioinformatics analysis, we identified the HDR pathway as the most amplified pathway in DDR in GC. In addition, EXO1 was the core gene in the HDR pathway and showed the most significant amplification in GC. The amplification of EXO1 resulted in higher EXO1 expression in cancerous tissues, with malignant prognostic effects. Moreover, we upregulated or downregulated EXO1 in GC cells to examine its effects on the cell malignant phenotype and CDDP resistance in vitro and in vivo. Depletion of EXO1 inhibited cell proliferatory, migratory and invasive activities, and provided apoptosis resistance to GC cells. EXO1 expression was elevated in CDDP-resistant cells. Ectopic expression of EXO1 increased the resistance of GC cells to CDDP, while downregulation of EXO1 increased the sensitivity of GC cells. Taken together, our study indicates that the HDR pathway is an important player in CDDP resistance in GC through the regulation of EXO1.
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Affiliation(s)
- Pengfei Mao
- Suzhou Hospital of Integrated Traditional Chinese and Western Medicine, Department of Gastroenterology, Suzhou, China;
| | - Suxiao Wu
- Suzhou Hospital of Integrated Traditional Chinese and Western Medicine, Department of Gastroenterology, Suzhou, China;
| | - Yuejuan Fan
- Suzhou Hospital of Integrated Traditional Chinese and Western Medicine, Department of Gastroenterology, Suzhou, China;
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10
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Zhang X, Min S, Yang Y, Ding D, Li Q, Liu S, Tao T, Zhang M, Li B, Zhao S, Ge R, Yang F, Li Y, He X, Ma X, Wang L, Wu T, Wang T, Wang G. A TP53 Related Immune Prognostic Model for the Prediction of Clinical Outcomes and Therapeutic Responses in Lung Adenocarcinoma. Front Immunol 2022; 13:876355. [PMID: 35837383 PMCID: PMC9275777 DOI: 10.3389/fimmu.2022.876355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/27/2022] [Indexed: 11/13/2022] Open
Abstract
TP53 is the most frequently mutated gene in lung adenocarcinoma (LUAD). The tumor immune microenvironment (TIM) is considered a vital factor that influences tumor progression and survival rate. The influence of TP53 mutation on TIM in LUAD has not been fully studied. Here we systematically investigated the relationship and potential mechanisms between TP53 mutation status and immune response in LUAD. We constructed an immune prognostic model (IPM) using immune associated genes, which were expressed differentially between the TP53 mutant and wild type LUAD patients. We discovered that TP53 mutations were significantly associated with 5 immune related biological processes. Thirty-six immune genes were expressed differentially between TP53 mutant and wild type LUAD patients. An IPM was constructed using 3 immune genes to differentiate the prognostic survival in LUAD. The high-risk LUAD group displayed significantly higher proportions of dendritic cell resting, T cell CD4 memory resting and mast cell resting, and significantly low proportions of dendritic cell activated, T cell CD4 memory activated, and mast cell activated. Moreover, IPM was found to be an independent clinical feature and can be used to predict immunotherapy responses. In summary, we constructed and validated an IPM using 3 immune related genes, which provides a better understanding of the mechanism from an immunological perspectives.
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Affiliation(s)
- Xiaonan Zhang
- Department of Pathophysiology, Bengbu Medical College, Bengbu, China
- Bengbu Medical College Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Bengbu, China
| | - Simin Min
- Department of Pathophysiology, Bengbu Medical College, Bengbu, China
- Bengbu Medical College Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Bengbu, China
| | - Yifan Yang
- Department of Thoracic Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Dushan Ding
- Department of Pathophysiology, Bengbu Medical College, Bengbu, China
- Bengbu Medical College Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Bengbu, China
| | - Qicai Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Saisai Liu
- Department of Pathophysiology, Bengbu Medical College, Bengbu, China
- Bengbu Medical College Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Bengbu, China
| | - Tao Tao
- Department of Thoracic Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Ming Zhang
- Bengbu Medical College Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Bengbu, China
| | - Baiqing Li
- Department of Immunology, Bengbu Medical College, Bengbu, China
| | - Shidi Zhao
- Department of Pathophysiology, Bengbu Medical College, Bengbu, China
- Bengbu Medical College Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Bengbu, China
| | - Rongjing Ge
- Department of Pathophysiology, Bengbu Medical College, Bengbu, China
- Bengbu Medical College Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Bengbu, China
| | - Fan Yang
- Bengbu Medical College Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Bengbu, China
| | - Yan Li
- Bengbu Medical College Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Bengbu, China
| | - Xiaoyu He
- Bengbu Medical College Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Bengbu, China
| | - Xiaoxiao Ma
- Department of Thoracic Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Lian Wang
- Department of Pathophysiology, Bengbu Medical College, Bengbu, China
| | - Tianyu Wu
- Department of Preventive Medicine, Bengbu Medical College, Bengbu, China
| | - Tao Wang
- College of Life and Health Sciences, Northeastern University, Shenyang, China
- *Correspondence: Guowen Wang, ; Tao Wang,
| | - Guowen Wang
- Department of Thoracic Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
- *Correspondence: Guowen Wang, ; Tao Wang,
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11
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Bioinformatics Analysis and Experimental Study of Exonuclease 1 Gene in Lung Adenocarcinoma. Biochem Genet 2022; 60:1934-1945. [PMID: 35169964 DOI: 10.1007/s10528-022-10190-y] [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: 04/14/2021] [Accepted: 01/13/2022] [Indexed: 12/24/2022]
Abstract
The objective of this study is to examine the role of Human Exonuclease 1(EXO1) gene in the diagnosis and prognosis of lung adenocarcinoma (LUAD), and predict the signal pathways EXO1 involved in. The clinical parameters and EXO1 expression datasets of LUAD patients were obtained from The Cancer Genome Atlas (TCGA), Oncomine and Gene Expression Omnibus (GEO) database. Wilcoxon rank-sum test was performed to determine whether EXO1 expression was upregulated in LUAD. The correlation between EXO1 expression and clinicopathological parameters was analyzed by Chi-square test, and Kaplan-Meier survival analysis and COX regression models were adopted to analyze and verify the correlation of EXO1 expression with OS of LUAD patients for the exploration of prognostic value of EXO1 in LUAD patients. The signaling pathway related to EXO1 was predicted by gene set enrichment analysis (GSEA). In addition, sera from LUAD patients and healthy subjects were collected, and real-time fluorescence quantitative polymerase chain reaction (RT-qPCR) was conducted to detect EXO1 expression. EXO1 expression was upregulated in LUAD patients with respect to normal individuals. EXO1 expression was negatively correlated with the prognosis and thus could independently predict the prognosis of LUAD patients. EXO1 gene was involved in 128 signal pathways, of which 9 pathways may be closely related. EXO1 was highly expressed in the blood of LUAD patients. High EXO1 expression can serve as an independent risk factor for poor prognosis, and the expression of serum EXO1 has certain diagnostic value for LUAD.
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12
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Wang W, Yang C, Deng H. Overexpression of 15-Hydroxyprostaglandin Dehydrogenase Inhibits A549 Lung Adenocarcinoma Cell Growth via Inducing Cell Cycle Arrest and Inhibiting Epithelial-Mesenchymal Transition. Cancer Manag Res 2021; 13:8887-8900. [PMID: 34876851 PMCID: PMC8643138 DOI: 10.2147/cmar.s331222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/20/2021] [Indexed: 01/22/2023] Open
Abstract
Purpose Lung cancer is one of the most commonly diagnosed cancer as well as the leading cause of cancer-related mortality worldwide, among which lung adenocarcinoma (LUAD) is the most frequent form of lung cancer. Previous studies have shown that 15-hydroxyprostaglandin dehydrogenase (15-PGDH) catalyzes the oxidation of prostaglandins to reduce their biological activities and behaves as a tumor suppressor in various cancers. Thus, we aimed to systematically examine the effects of 15-PGDH overexpression on cellular processes in lung adenocarcinoma cells. Methods The stable 15-PGDH-overexpressing A549 cell line was constructed using lentivirus particles. CCK-8 assay was used to determine the cell proliferation rate and sensitivity to cisplatin. Tandem mass tag (TMT)-based quantitative proteomic analysis was used to identify differentially expressed proteins between control and 15-PGDH-overexpression cells. The cell cycle was determined by a flow cytometer. The expression levels of mesenchymal and epithelial markers were measured using Western blotting. Wound healing and transwell assays were used to detect the cell migration and cell invasion ability, respectively. Results Analysis of datasets in The Cancer Genome Atlas revealed that the PGDH gene expression level in the lung adenocarcinoma tissues was significantly lower than that in the pericarcinous tissues. 15-PGDH overexpression in A549 cells reduced cell proliferation rate. Quantitative proteomics revealed that 15-PGDH overexpression inhibited PI3K/AKT/mTOR signaling pathway, which is a signaling pathway driving tumor cell growth and epithelial-mesenchymal transition (EMT) process. In addition, both cell cycle and DNA repair-related proteins were down-regulated in 15-PGDH overexpressed cells. 15-PGDH overexpression induced G1/S cell cycle arrest and increased susceptibility to DNA damaging reagent cisplatin. Importantly, overexpression of 15-PGDH inhibited EMT process with the downregulation of β-catenin and Snail-1 as well as upregulation of E-cadherin and ZO-1. Conclusion 15-PGDH is a tumor suppressor in lung cancer and may serve as a potential therapeutic target to prevent lung adenocarcinoma.
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Affiliation(s)
- Weixuan Wang
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Changmei Yang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, Beijing, People's Republic of China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, Beijing, People's Republic of China
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13
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Identification of DNA Damage Repair-Associated Prognostic Biomarkers for Prostate Cancer Using Transcriptomic Data Analysis. Int J Mol Sci 2021; 22:ijms222111771. [PMID: 34769200 PMCID: PMC8584064 DOI: 10.3390/ijms222111771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/19/2021] [Accepted: 10/29/2021] [Indexed: 02/08/2023] Open
Abstract
In the recent decade, the importance of DNA damage repair (DDR) and its clinical application have been firmly recognized in prostate cancer (PC). For example, olaparib was just approved in May 2020 to treat metastatic castration-resistant PC with homologous recombination repair-mutated genes; however, not all patients can benefit from olaparib, and the treatment response depends on patient-specific mutations. This highlights the need to understand the detailed DDR biology further and develop DDR-based biomarkers. In this study, we establish a four-gene panel of which the expression is significantly associated with overall survival (OS) and progression-free survival (PFS) in PC patients from the TCGA-PRAD database. This panel includes DNTT, EXO1, NEIL3, and EME2 genes. Patients with higher expression of the four identified genes have significantly worse OS and PFS. This significance also exists in a multivariate Cox regression model adjusting for age, PSA, TNM stages, and Gleason scores. Moreover, the expression of the four-gene panel is highly correlated with aggressiveness based on well-known PAM50 and PCS subtyping classifiers. Using publicly available databases, we successfully validate the four-gene panel as having the potential to serve as a prognostic and predictive biomarker for PC specifically based on DDR biology.
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14
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Yılmaz H, Toy HI, Marquardt S, Karakülah G, Küçük C, Kontou PI, Logotheti S, Pavlopoulou A. In Silico Methods for the Identification of Diagnostic and Favorable Prognostic Markers in Acute Myeloid Leukemia. Int J Mol Sci 2021; 22:ijms22179601. [PMID: 34502522 PMCID: PMC8431757 DOI: 10.3390/ijms22179601] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/13/2021] [Accepted: 08/20/2021] [Indexed: 12/13/2022] Open
Abstract
Acute myeloid leukemia (AML), the most common type of acute leukemia in adults, is mainly asymptomatic at early stages and progresses/recurs rapidly and frequently. These attributes necessitate the identification of biomarkers for timely diagnosis and accurate prognosis. In this study, differential gene expression analysis was performed on large-scale transcriptomics data of AML patients versus corresponding normal tissue. Weighted gene co-expression network analysis was conducted to construct networks of co-expressed genes, and detect gene modules. Finally, hub genes were identified from selected modules by applying network-based methods. This robust and integrative bioinformatics approach revealed a set of twenty-four genes, mainly related to cell cycle and immune response, the diagnostic significance of which was subsequently compared against two independent gene expression datasets. Furthermore, based on a recent notion suggesting that molecular characteristics of a few, unusual patients with exceptionally favorable survival can provide insights for improving the outcome of individuals with more typical disease trajectories, we defined groups of long-term survivors in AML patient cohorts and compared their transcriptomes versus the general population to infer favorable prognostic signatures. These findings could have potential applications in the clinical setting, in particular, in diagnosis and prognosis of AML.
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Affiliation(s)
- Hande Yılmaz
- Izmir Biomedicine and Genome Center, Balcova, 35340 Izmir, Turkey; (H.Y.); (H.I.T.); (G.K.); (C.K.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balcova, 35340 Izmir, Turkey
- Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, 18057 Rostock, Germany;
| | - Halil Ibrahim Toy
- Izmir Biomedicine and Genome Center, Balcova, 35340 Izmir, Turkey; (H.Y.); (H.I.T.); (G.K.); (C.K.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balcova, 35340 Izmir, Turkey
| | - Stephan Marquardt
- Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, 18057 Rostock, Germany;
| | - Gökhan Karakülah
- Izmir Biomedicine and Genome Center, Balcova, 35340 Izmir, Turkey; (H.Y.); (H.I.T.); (G.K.); (C.K.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balcova, 35340 Izmir, Turkey
| | - Can Küçük
- Izmir Biomedicine and Genome Center, Balcova, 35340 Izmir, Turkey; (H.Y.); (H.I.T.); (G.K.); (C.K.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balcova, 35340 Izmir, Turkey
- Department of Medical Biology, Faculty of Medicine, Dokuz Eylül University, Balcova, 35340 Izmir, Turkey
| | - Panagiota I. Kontou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece;
| | - Stella Logotheti
- Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, 18057 Rostock, Germany;
- Correspondence: (S.L.); (A.P.)
| | - Athanasia Pavlopoulou
- Izmir Biomedicine and Genome Center, Balcova, 35340 Izmir, Turkey; (H.Y.); (H.I.T.); (G.K.); (C.K.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balcova, 35340 Izmir, Turkey
- Correspondence: (S.L.); (A.P.)
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15
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Moura DS, Peña‐Chilet M, Cordero Varela JA, Alvarez‐Alegret R, Agra‐Pujol C, Izquierdo F, Ramos R, Ortega‐Medina L, Martin‐Davila F, Castilla‐Ramirez C, Hernandez‐Leon CN, Romagosa C, Vaz Salgado MA, Lavernia J, Bagué S, Mayodormo‐Aranda E, Vicioso L, Hernández Barceló JE, Rubio‐Casadevall J, de Juan A, Fiaño‐Valverde MC, Hindi N, Lopez‐Alvarez M, Lacerenza S, Dopazo J, Gutierrez A, Alvarez R, Valverde C, Martinez‐Trufero J, Martín‐Broto J. A DNA damage repair gene-associated signature predicts responses of patients with advanced soft-tissue sarcoma to treatment with trabectedin. Mol Oncol 2021; 15:3691-3705. [PMID: 33983674 PMCID: PMC8637557 DOI: 10.1002/1878-0261.12996] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/13/2021] [Accepted: 05/10/2021] [Indexed: 11/29/2022] Open
Abstract
Predictive biomarkers of trabectedin represent an unmet need in advanced soft‐tissue sarcomas (STS). DNA damage repair (DDR) genes, involved in homologous recombination or nucleotide excision repair, had been previously described as biomarkers of trabectedin resistance or sensitivity, respectively. The majority of these studies only focused on specific factors (ERCC1, ERCC5, and BRCA1) and did not evaluate several other DDR‐related genes that could have a relevant role for trabectedin efficacy. In this retrospective translational study, 118 genes involved in DDR were evaluated to determine, by transcriptomics, a predictive gene signature of trabectedin efficacy. A six‐gene predictive signature of trabectedin efficacy was built in a series of 139 tumor samples from patients with advanced STS. Patients in the high‐risk gene signature group showed a significantly worse progression‐free survival compared with patients in the low‐risk group (2.1 vs 6.0 months, respectively). Differential gene expression analysis defined new potential predictive biomarkers of trabectedin sensitivity (PARP3 and CCNH) or resistance (DNAJB11 and PARP1). Our study identified a new gene signature that significantly predicts patients with higher probability to respond to treatment with trabectedin. Targeting some genes of this signature emerges as a potential strategy to enhance trabectedin efficacy.
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Affiliation(s)
- David S. Moura
- Institute of Biomedicine of Seville (IBIS, HUVR, CSIC, Universidad de Sevilla)Spain
| | - Maria Peña‐Chilet
- Institute of Biomedicine of Seville (IBIS, HUVR, CSIC, Universidad de Sevilla)Spain
- Clinical Bioinformatics AreaFundación Progreso y Salud (FPS)CDCAHospital Virgen del RocioSevilleSpain
- Bioinformatics in Rare Diseases (BiER)Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)FPSHospital Virgen del RocioSevilleSpain
| | | | | | | | | | - Rafael Ramos
- Pathology DepartmentSon Espases University HospitalMallorcaSpain
| | | | | | | | | | - Cleofe Romagosa
- Pathology DepartmentVall d'Hebron University HospitalBarcelonaSpain
| | | | - Javier Lavernia
- Medical Oncology DepartmentInstituto Valenciano de OncologiaValenciaSpain
| | - Silvia Bagué
- Pathology ServiceHospital de la Santa Creu i Sant PauBarcelonaSpain
| | | | - Luis Vicioso
- Pathology DepartmentVirgen de la Victoria University HospitalMalagaSpain
| | | | - Jordi Rubio‐Casadevall
- Medical Oncology DepartmentHospital Josep TruetaCatalan Institute of OncologyGironaSpain
| | - Ana de Juan
- Medical Oncology DepartmentMarqués de Valdecilla University HospitalSantanderSpain
| | | | - Nadia Hindi
- Institute of Biomedicine of Seville (IBIS, HUVR, CSIC, Universidad de Sevilla)Spain
- Medical Oncology DepartmentUniversity Hospital Fundación Jimenez DiazMadridSpain
- University Hospital General de VillalbaMadridSpain
- Instituto de Investigacion Sanitaria Fundacion Jimenez Diaz (IIS/FJD)MadridSpain
| | - Maria Lopez‐Alvarez
- Institute of Biomedicine of Seville (IBIS, HUVR, CSIC, Universidad de Sevilla)Spain
| | - Serena Lacerenza
- Institute of Biomedicine of Seville (IBIS, HUVR, CSIC, Universidad de Sevilla)Spain
| | - Joaquin Dopazo
- Institute of Biomedicine of Seville (IBIS, HUVR, CSIC, Universidad de Sevilla)Spain
- Clinical Bioinformatics AreaFundación Progreso y Salud (FPS)CDCAHospital Virgen del RocioSevilleSpain
- Bioinformatics in Rare Diseases (BiER)Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)FPSHospital Virgen del RocioSevilleSpain
- INB‐ELIXIR‐esFPSHospital Virgen del RocíoSevilleSpain
| | | | - Rosa Alvarez
- Medical Oncology DepartmentGregorio Marañon University HospitalMadridSpain
| | - Claudia Valverde
- Medical Oncology DepartmentVall d'Hebron University HospitalBarcelonaSpain
| | | | - Javier Martín‐Broto
- Institute of Biomedicine of Seville (IBIS, HUVR, CSIC, Universidad de Sevilla)Spain
- Medical Oncology DepartmentUniversity Hospital Fundación Jimenez DiazMadridSpain
- University Hospital General de VillalbaMadridSpain
- Instituto de Investigacion Sanitaria Fundacion Jimenez Diaz (IIS/FJD)MadridSpain
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16
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Zhou CS, Feng MT, Chen X, Gao Y, Chen L, Li LD, Li DH, Cao YQ. Exonuclease 1 (EXO1) is a Potential Prognostic Biomarker and Correlates with Immune Infiltrates in Lung Adenocarcinoma. Onco Targets Ther 2021; 14:1033-1048. [PMID: 33623391 PMCID: PMC7894803 DOI: 10.2147/ott.s286274] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/16/2021] [Indexed: 12/16/2022] Open
Abstract
Background Exonuclease 1 (EXO1) has been identified to be highly expressed in different human malignancies, but its expression and prognostic role in lung adenocarcinoma (LUAD) remain unknown. Materials and Methods Two independent cohorts extracted from public databases and one cohort from our center were analyzed in this study. Expression levels of EXO1 in LUAD tissues and paired para-cancer tissues were detected. The prognostic value of EXO1 in LUAD patients was evaluated in the three cohorts. Enrichment analyses were performed to explore the possible underlying biological pathways. Moreover, we also explored the correlations between EXO1 and tumor-infiltrating immune cells and evaluated the impact of EXO1 knock-down on the migration of lung cancer cells. Results In this study, we found that EXO1 was highly expressed in LUAD tissues compared with para-cancerous tissues in public databases (p < 0.01), which was consistent with our data (p < 0.01). Survival analysis indicated that high expression of EXO1 was associated with poor prognosis in LUAD (p < 0.01). Enrichment analyses indicated that biological pathways like cell cycle regulation, DNA damage and repair, immune response, neuroactive ligand-receptor interaction, may be associated with EXO1 aberrant expression. Moreover, high expression of EXO1 was correlated with decreased infiltrating B cells (p < 0.01) and CD4+ T cells (p < 0.01) levels, and low infiltrating levels of B cells (p < 0.01) and dendritic cells (DCs) (p < 0.05) indicated poor overall survival (OS) in LUAD. Additionally, in vitro experiments suggested that knockdown of EXO1 may inhibit the migratory ability of lung cancer cells. Conclusion In conclusion, EXO1 is a potential prognostic biomarker in LUAD, and correlates with infiltrating levels of immune cells in the tumor microenvironment. Further prospective validation of EXO1 in lung cancer is warranted.
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Affiliation(s)
- Chang-Shuai Zhou
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Ming-Tao Feng
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Xin Chen
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Yang Gao
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Lei Chen
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Liang-Dong Li
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - De-Heng Li
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Yi-Qun Cao
- Department of Neurosurgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
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17
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Li Y, Qi D, Zhu B, Ye X. Analysis of m6A RNA Methylation-Related Genes in Liver Hepatocellular Carcinoma and Their Correlation with Survival. Int J Mol Sci 2021; 22:ijms22031474. [PMID: 33540684 PMCID: PMC7867233 DOI: 10.3390/ijms22031474] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/18/2021] [Accepted: 01/27/2021] [Indexed: 02/06/2023] Open
Abstract
N6-methyladenosine (m6A) modification on RNA plays an important role in tumorigenesis and metastasis, which could change gene expression and even function at multiple levels such as RNA splicing, stability, translocation, and translation. In this study, we aim to conduct a comprehensive analysis on m6A RNA methylation-related genes, including m6A RNA methylation regulators and m6A RNA methylation-modified genes, in liver hepatocellular carcinoma, and their relationship with survival and clinical features. Data, which consist of the expression of widely reported m6A RNA methylation-related genes in liver hepatocellular carcinoma from The Cancer Genome Atlas (TCGA), were analyzed by one-way ANOVA, Univariate Cox regression, a protein–protein interaction network, gene enrichment analysis, feature screening, a risk prognostic model, correlation analysis, and consensus clustering analysis. In total, 405 of the m6A RNA methylation-related genes were found based on one-way ANOVA. Among them, DNA topoisomerase 2-alpha (TOP2A), exodeoxyribonuclease 1 (EXO1), ser-ine/threonine-protein kinase Nek2 (NEK2), baculoviral IAP repeat-containing protein 5 (BIRC5), hyaluronan mediated motility receptor (HMMR), structural maintenance of chromosomes protein 4 (SMC4), bloom syndrome protein (BLM), ca-sein kinase I isoform epsilon (CSNK1E), cytoskeleton-associated protein 5 (CKAP5), and inner centromere protein (INCENP), which were m6A RNA methylation-modified genes, were recognized as the hub genes based on the protein–protein interaction analysis. The risk prognostic model showed that gender, AJCC stage, grade, T, and N were significantly different between the subgroup with the high and low risk groups. The AUC, the evaluation parameter of the prediction model which was built by RandomForest, was 0.7. Furthermore, two subgroups were divided by consensus clustering analysis, in which stage, grade, and T differed. We identified the important genes expressed significantly among two clusters, including uridine-cytidine kinase 2 (UCK2), filensin (BFSP1), tubulin-specific chaperone D (TBCD), histone-lysine N-methyltransferase PRDM16 (PRDM16), phosphorylase b ki-nase regulatory subunit alpha (PHKA2), serine/threonine-protein kinase BRSK2 (BRSK2), Arf-GAP with coiled-coil (ACAP3), general transcription factor 3C polypep-tide 2 (GTF3C2), and guanine nucleotide exchange factor MSS4 (RABIF). In our study, the m6A RNA methylation-related genes in liver hepatocellular carcinoma were analyzed systematically, including the expression, interaction, function, and prognostic values, which provided an important theoretical basis for m6A RNA methylation in liver cancer. The nine important m6A-related genes could be prognostic markers in the survival time of patients.
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Affiliation(s)
- Yong Li
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Y.L.); (B.Z.)
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China;
| | - Dandan Qi
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China;
| | - Baoli Zhu
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Y.L.); (B.Z.)
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China;
| | - Xin Ye
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Y.L.); (B.Z.)
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China;
- Correspondence: ; Tel.: +86-010-6480-7513
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18
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Zhang X, Zheng Y, Li G, Yu C, Ji T, Miao S. Identifying four DNA methylation gene sites signature for predicting prognosis of osteosarcoma. Transl Cancer Res 2020; 9:7299-7309. [PMID: 35117331 PMCID: PMC8798623 DOI: 10.21037/tcr-20-3204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 11/18/2020] [Indexed: 01/22/2023]
Abstract
BACKGROUND Osteosarcoma (OS) is a common malignant bone tumor in children and adolescents. DNA methylation plays a crucial role in the prognosis prediction of cancer. Identification of novel DNA methylation sites biomarkers could be beneficial for the prognosis of OS patients. In this study, we aim to find an efficient methylated site model for predicting survival in OS. METHODS DNA methylation data were downloaded from the Cancer Genome Atlas database (TCGA) and the GEO database. Cox proportional hazard regression and random survival forest algorithm (RSFVH) were applied to identify DNA methylated site signature in the samples randomly assigned to the training subset and the other samples as the test subset. By randomizing 71 clinical samples into two individual groups and a series of statistical analyses between the two groups, a DNA methylation signature is verified. RESULTS This signature comprises four methylation sites (cg04533248, cg12401425, cg13997435, and cg15075357) associated with the patient training group from the univariate Cox proportional hazards regression analysis, RSFVH, and multivariate Cox regression analysis. Kaplan-Meier survival curves showed the OS patients in the high-risk group have a poor 5-year overall survival compared with the low-risk group, and this finding was identified in the test data set. A ROC analysis was performed in the current research. The results revealed that this signature was an independent predictor of patient survival by investigating the AUC of the four methylation sites signature in the training data set (AUC =0.861) and test data set, respectively (AUC =0.920). The nomogram described in the current study placed a great guiding value for predicting 1-, 2-, 3-year survival of the OS by combining age, gender, grade, and TNM stage as covariates with the RS of patients' methylation related signatures. CONCLUSIONS Our study proved that this signature might be a powerful prognostic tool for survival rate evaluation and guide tailored therapy for OS patients.
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Affiliation(s)
- Xijun Zhang
- Department of Laboratory of Jiayuguan City First People’s Hospital, Jiayuguan, China
| | - Yongjun Zheng
- The 984th Hospital of the People’s Liberation Army, Shangzhuang Township, Beijing, China
| | - Gaoshan Li
- Department of Orthopaedics, 968 Hospital of Joint Service Support Force of Chinese People’s Liberation Army, Jinzhou, China
| | - Changying Yu
- Department of Laboratory Medicine, the 965 Hospital of the PLA, Jilin, China
| | - Ting Ji
- Shenzhen Mindray Bio-Medical Electronics Co., Ltd, Shenzhen, China
| | - Shenghu Miao
- Department of Laboratory Medicine, Wuwei People’s Hospital, Wuwei, China
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