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Chen C, Liu Y, Luo M, Yang J, Chen Y, Wang R, Zhou J, Zang Y, Diao L, Han L. PancanQTLv2.0: a comprehensive resource for expression quantitative trait loci across human cancers. Nucleic Acids Res 2024; 52:D1400-D1406. [PMID: 37870463 PMCID: PMC10767806 DOI: 10.1093/nar/gkad916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 10/24/2023] Open
Abstract
Expression quantitative trait locus (eQTL) analysis is a powerful tool used to investigate genetic variations in complex diseases, including cancer. We previously developed a comprehensive database, PancanQTL, to characterize cancer eQTLs using The Cancer Genome Atlas (TCGA) dataset, and linked eQTLs with patient survival and GWAS risk variants. Here, we present an updated version, PancanQTLv2.0 (https://hanlaboratory.com/PancanQTLv2/), with advancements in fine-mapping causal variants for eQTLs, updating eQTLs overlapping with GWAS linkage disequilibrium regions and identifying eQTLs associated with drug response and immune infiltration. Through fine-mapping analysis, we identified 58 747 fine-mapped eQTLs credible sets, providing mechanic insights of gene regulation in cancer. We further integrated the latest GWAS Catalog and identified a total of 84 592 135 linkage associations between eQTLs and the existing GWAS loci, which represents a remarkable ∼50-fold increase compared to the previous version. Additionally, PancanQTLv2.0 uncovered 659516 associations between eQTLs and drug response and identified 146948 associations between eQTLs and immune cell abundance, providing potentially clinical utility of eQTLs in cancer therapy. PancanQTLv2.0 expanded the resources available for investigating gene expression regulation in human cancers, leading to advancements in cancer research and precision oncology.
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Affiliation(s)
- Chengxuan Chen
- Brown Center for Immunotherapy, School of Medicine, Indiana University, Indianapolis, IN 46202, USA
- Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN 46202, USA
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Yuan Liu
- Brown Center for Immunotherapy, School of Medicine, Indiana University, Indianapolis, IN 46202, USA
- Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN 46202, USA
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Mei Luo
- Brown Center for Immunotherapy, School of Medicine, Indiana University, Indianapolis, IN 46202, USA
- Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN 46202, USA
| | - Jingwen Yang
- Brown Center for Immunotherapy, School of Medicine, Indiana University, Indianapolis, IN 46202, USA
- Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN 46202, USA
| | - Yamei Chen
- Brown Center for Immunotherapy, School of Medicine, Indiana University, Indianapolis, IN 46202, USA
- Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN 46202, USA
| | - Runhao Wang
- Brown Center for Immunotherapy, School of Medicine, Indiana University, Indianapolis, IN 46202, USA
- Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN 46202, USA
| | - Joseph Zhou
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Yong Zang
- Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN 46202, USA
| | - Lixia Diao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Leng Han
- Brown Center for Immunotherapy, School of Medicine, Indiana University, Indianapolis, IN 46202, USA
- Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN 46202, USA
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
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Li Z, Cai H, Zheng J, Chen X, Liu G, Lv Y, Ye H, Cai G. Mitochondrial-related genes markers that predict survival in patients with head and neck squamous cell carcinoma affect immunomodulation through hypoxia, glycolysis, and angiogenesis pathways. Aging (Albany NY) 2023; 15:10347-10369. [PMID: 37796226 PMCID: PMC10599748 DOI: 10.18632/aging.205081] [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: 04/14/2023] [Accepted: 09/08/2023] [Indexed: 10/06/2023]
Abstract
Mitochondria play a crucial role in the occurrence and development of tumors. We used mitochondria-related genes for consistent clustering to identify three stable molecular subtypes of head and neck squamous cell carcinoma (HNSCC) with different prognoses, mutations, and immune characteristics. Significant differences were observed in clinical characteristics, immune microenvironment, immune cell infiltration, and immune cell scores. TP53 was the most significantly mutated; cell cycle-related pathways and tumorigenesis-related pathways were activated in different subtypes. Risk modeling was conducted using a multifactor stepwise regression method, and nine genes were identified as mitochondria-related genes affecting prognosis (DKK1, EFNB2, ITGA5, AREG, EPHX3, CHGB, P4HA1, CCND1, and JCHAIN). Risk score calculations revealed significant differences in prognosis, immune cell scores, immune cell infiltration, and responses to conventional chemotherapy drugs. Glycolysis, angiogenesis, hypoxia, and tumor-related pathways were positively correlated with the RiskScore. Clinical samples were subjected to qPCR to validate the results. In this work, we constructed a prognostic model based on the mitochondrial correlation score, which well reflects the risk and positive factors for the prognosis of patients with HNSCC. This model can be used to guide individualized adjuvant and immunotherapy in patients with HNSCC.
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Affiliation(s)
- Zhonghua Li
- Department of Otolaryngology Head and Neck Surgery, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou 362000, China
| | - Haoxi Cai
- School of Stomatology, Ningxia Medical University, Yinchuan 750004, China
| | - Jinyang Zheng
- Department of Pathology, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou 362000, China
| | - Xun Chen
- Department of Oral Surgery, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou 362000, China
| | - Guancheng Liu
- Department of Otolaryngology Head and Neck Surgery, The Hospital Affiliated of Guilin Medical College, Guilin 541000, China
| | - Yunxia Lv
- Department of Thyroid Surgery, The Second Affiliated Hospital to Nanchang University, Nanchang 330006, China
| | - Hui Ye
- Haicang Hospital Affiliated of Xiamen Medical College, Xiamen 361026, China
| | - Gengming Cai
- Haicang Hospital Affiliated of Xiamen Medical College, Xiamen 361026, China
- The School of Clinical Medicine, Fujian Medical University, Fuzhou 361026, China
- The Graduate School of Fujian Medical University, Fuzhou 361026, China
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Li M, Zhu C, Xue Y, Miao C, He R, Li W, Zhang B, Yu W, Huang X, Lv M, Xu Y, Huang Q. A DNA methylation signature for the prediction of tumour recurrence in stage II colorectal cancer. Br J Cancer 2023; 128:1681-1689. [PMID: 36828869 PMCID: PMC10133253 DOI: 10.1038/s41416-023-02155-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 01/05/2023] [Accepted: 01/11/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND A major challenge in stage II colorectal carcinoma is to identify patients with increased risk of recurrence. Biomarkers that distinguish patients with poor prognosis from patients without recurrence are currently lacking. This study aims to develop a robust DNA methylation classifier that allows the prediction of recurrence and chemotherapy benefit in patients with stage II colorectal cancer. We performed a genome-wide DNA methylation capture sequencing in 243 stage II colorectal carcinoma samples and identified a relapse-specific DNA methylation signature consisting of eight CpG sites. METHODS Two hundred and forty-three patients with stage II CRC were enrolled in this study. In order to select differential methylation sites among recurrence and non-recurrence stage II CRC samples, DNA methylation profiles of 62 tumour samples including 31 recurrence and 31 nonrecurrence samples were analysed using the Agilent SureSelectXT Human Methyl-Seq, a comprehensive target enrichment system to analyse CpG methylation. Pyrosequencing was applied to quantify the methylation level of candidate DNA methylation sites in 243 patients. Least absolute shrinkage and selection operator (LASSO) method was employed to build the disease recurrence prediction classifier. RESULTS We identified a relapse-related DNA methylation signature consisting of eight CpG sites in stage II CRC by DNA methylation capture sequencing. The classifier showed significantly higher prognostic accuracy than any clinicopathological risk factors. The Kaplan-Meier survival curve showed an association of high-risk score with poor prognosis. In multivariate analysis, the signature was the most significant prognosis factor, with an HR of 2.80 (95% CI, 1.71-4.58, P < 0.001). The signature could identify patients who are suitable candidates for adjuvant chemotherapy. CONCLUSIONS An eight-CpG DNA methylation signature is a reliable prognostic and predictive tool for disease recurrence in patients with stage II CRC.
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Affiliation(s)
- Min Li
- Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
- Institute of Clinical Sciences, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
| | - Congcong Zhu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'An Road, 200032, Shanghai, P. R. China
- Department of Oncology, Shanghai Medical College, Fudan University, 270 Dong'An Road, 200032, Shanghai, P. R. China
| | - Ying Xue
- Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
- Institute of Clinical Sciences, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
| | - Changhong Miao
- Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
| | - Ruiping He
- Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
- Institute of Clinical Sciences, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
| | - Wei Li
- Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Fudan University, 130 Dong'An Road, 200032, Shanghai, P. R. China
| | - Baolong Zhang
- Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Fudan University, 130 Dong'An Road, 200032, Shanghai, P. R. China
| | - Wenqiang Yu
- Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Fudan University, 130 Dong'An Road, 200032, Shanghai, P. R. China
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, P. R. China
| | - Minzhi Lv
- Institute of Clinical Sciences, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China.
- Department of Biostatistics, Clinical Research Unit, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China.
| | - Ye Xu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'An Road, 200032, Shanghai, P. R. China.
- Department of Oncology, Shanghai Medical College, Fudan University, 270 Dong'An Road, 200032, Shanghai, P. R. China.
| | - Qihong Huang
- Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China.
- Institute of Clinical Sciences, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China.
- Shanghai Respiratory Research Institute, 180 Fenglin Road, 200032, Shanghai, P. R. China.
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Cao M, Wang Y, Lu G, Qi H, Li P, Dai X, Lu J. Classical Angiogenic Signaling Pathways and Novel Anti-Angiogenic Strategies for Colorectal Cancer. Curr Issues Mol Biol 2022; 44:4447-4471. [PMID: 36286020 PMCID: PMC9601273 DOI: 10.3390/cimb44100305] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/17/2022] [Accepted: 09/21/2022] [Indexed: 11/17/2022] Open
Abstract
Although productive progress has been made in colorectal cancer (CRC) researchs, CRC is the second most frequent type of malignancy and the major cause of cancer-related death among gastrointestinal cancers. As angiogenesis constitutes an important point in the control of CRC progression and metastasis, understanding the key signaling pathways that regulate CRC angiogenesis is critical in elucidating ways to inhibit CRC. Herein, we comprehensively summarized the angiogenesis-related pathways of CRC, including vascular endothelial growth factor (VEGF), nuclear factor-kappa B (NF-κB), Janus kinase (JAK)/signal transducer and activator of transcription (STAT), Wingless and int-1 (Wnt), and Notch signaling pathways. We divided the factors influencing the specific pathway into promoters and inhibitors. Among these, some drugs or natural compounds that have antiangiogenic effects were emphasized. Furthermore, the interactions of these pathways in angiogenesis were discussed. The current review provides a comprehensive overview of the key signaling pathways that are involved in the angiogenesis of CRC and contributes to the new anti-angiogenic strategies for CRC.
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Affiliation(s)
- Mengyuan Cao
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yunmeng Wang
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Guige Lu
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Haoran Qi
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Peiyu Li
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xiaoshuo Dai
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Jing Lu
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
- Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou University, Zhengzhou 450001, China
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou 450052, China
- Correspondence:
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Identification of Key Genes and Pathways in Genotoxic Stress Induced Endothelial Dysfunction: Results of Whole Transcriptome Sequencing. Biomedicines 2022; 10:biomedicines10092067. [PMID: 36140167 PMCID: PMC9495888 DOI: 10.3390/biomedicines10092067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 12/02/2022] Open
Abstract
Atherosclerosis is a leading cause of cardiovascular morbidity and mortality worldwide. Endothelial disfunction underlying the atherogenesis can be triggered by genotoxic stress in endothelial cells. In the presented research whole transcriptome sequencing (RNA-seq) of human coronary artery (HCAEC) and internal thoracic artery (HITAEC) endothelial cells in vitro exposed to 500 ng/mL mitomycin C (treatment group) or 0.9% NaCl (control group) was performed. Resulting to bioinformatic analysis, 56 upregulated differentially expressed genes (DEGs) and 6 downregulated DEGs with absolute fold change ≥ 2 and FDR p-value < 0.05 were selected in HCAEC exposed to mitomycin C compared to the control group; in HITAEC only one upregulated DEG was found. According to Gene Ontology enrichment analysis, DEGs in HCAEC were classified into 25 functional groups of biological processes, while in HITAEC we found no statistically significant (FDR p-value < 0.05) groups. The four largest groups containing more than 50% DEGs (“signal transduction”, “response to stimulus”, “biological regulation”, and “regulation of biological process”) were identified. Finally, candidate DEGs and pathways underlying the genotoxic stress induced endothelial disfunction have been discovered that could improve our understanding of fundamental basis of atherogenesis and help to justification of genotoxic stress as a novel risk factor for atherosclerosis.
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刘 俊, 石 宇, 吴 敏, 徐 梦, 张 凤, 何 志, 唐 敏. [JAG1 promotes migration, invasion, and adhesion of triple-negative breast cancer cells by promoting angiogenesis]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2022; 42:1100-1108. [PMID: 35869777 PMCID: PMC9308863 DOI: 10.12122/j.issn.1673-4254.2022.07.21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To investigate the effect of JAG1 on the malignant phenotype of triple-negative breast cancer (TNBC) and its role in angiogenesis in breast cancer microenvironment. METHODS The expressions of Notch molecules were detected in human TNBC 231 and 231B cells using RT-qPCR. Five female nude mice were inoculated with 231 cells and another 5 with 231B cells into the mammary fat pads, and 4-6 weeks later, the tumors were collected for immunohistochemical and immunofluorescence tests. 231 cells and 231B cells were treated with recombinant JAG (rJAG) protein and DAPT, respectively, and changes in their malignant phenotypes were assessed using CCK-8 assay, Hoechst 33258 staining, wound healing assay, Transwell chamber assay and endothelial cell adhesion assay. Western blotting was used to detect the changes in the expressions of proteins related with the malignant phenotypes of 231 and 231B cells. The effects of conditioned medium (CM) derived from untreated 231 and 231 B cells, rJAG1-treated 231 cells and DAPT-treated 231B cells on proliferation and tube formation ability of cultured human umbilical vein endothelial cells (HUVECs) were evaluated using CCK-8 assay and tube-forming assay. RESULTS The expression of JAG1 was higher in 231B cells than in 231 cells (P < 0.05). Tumor 231B showed higher expression of VEGFA and CD31. Compared with 231-Blank group, the migration, invasion and adhesion of 231 cells in 231-rJAG1 were significantly enhanced (P < 0.05). Protein levels of Twist1 and Snail increased (P < 0.01), anti-apoptotic protein Bcl-2 increased (P < 0.05), while DAPT inhibited the related phenomena and indicators of 231B. The 231-rJAG1-CM increased the cell number and tubule number of HUVEC (P < 0.05). CONCLUSION JAG1 may affect the malignant phenotype of TNBC and promote angiogenesis in the tumor microenvironment.
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Affiliation(s)
- 俊平 刘
- />重庆医科大学检验医学院,临床检验诊断学教育部重点实验室,重庆 400016Key Laboratory of Clinical Laboratory and Diagnostics of Ministry of Education, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - 宇彤 石
- />重庆医科大学检验医学院,临床检验诊断学教育部重点实验室,重庆 400016Key Laboratory of Clinical Laboratory and Diagnostics of Ministry of Education, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - 敏敏 吴
- />重庆医科大学检验医学院,临床检验诊断学教育部重点实验室,重庆 400016Key Laboratory of Clinical Laboratory and Diagnostics of Ministry of Education, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - 梦岐 徐
- />重庆医科大学检验医学院,临床检验诊断学教育部重点实验室,重庆 400016Key Laboratory of Clinical Laboratory and Diagnostics of Ministry of Education, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - 凤梅 张
- />重庆医科大学检验医学院,临床检验诊断学教育部重点实验室,重庆 400016Key Laboratory of Clinical Laboratory and Diagnostics of Ministry of Education, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - 志强 何
- />重庆医科大学检验医学院,临床检验诊断学教育部重点实验室,重庆 400016Key Laboratory of Clinical Laboratory and Diagnostics of Ministry of Education, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - 敏 唐
- />重庆医科大学检验医学院,临床检验诊断学教育部重点实验室,重庆 400016Key Laboratory of Clinical Laboratory and Diagnostics of Ministry of Education, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
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Liu X, Yang K, Li Z, Liu J. MMP2 Polymorphisms and Colorectal Cancer Susceptibility in a Chinese Han Population. Int J Gen Med 2022; 15:6009-6019. [PMID: 35818579 PMCID: PMC9270925 DOI: 10.2147/ijgm.s364029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/15/2022] [Indexed: 11/23/2022] Open
Affiliation(s)
- Xu Liu
- Department of Hepato-Pancreato-Biliary Surgery, Peking University Shenzhen Hospital, Shenzhen, Guangdong, People’s Republic of China
| | - Kelaier Yang
- Department of Endocrinology and Metabolism, Shenzhen University General Hospital, Shenzhen, Guangdong, People’s Republic of China
| | - Zhangfu Li
- Department of Hepato-Pancreato-Biliary Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong, People’s Republic of China
| | - Jikui Liu
- Department of Hepato-Pancreato-Biliary Surgery, Peking University Shenzhen Hospital, Shenzhen, Guangdong, People’s Republic of China
- Correspondence: Jikui Liu, Department of Hepato-Pancreato-Biliary Surgery, Peking University Shenzhen Hospital, #1120, Lianhua Road, Futian District, Shenzhen, Guangdong, 518036, People’s Republic of China, Tel/Fax +86-13841498565, Email
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Papadakos SP, Petrogiannopoulos L, Pergaris A, Theocharis S. The EPH/Ephrin System in Colorectal Cancer. Int J Mol Sci 2022; 23:ijms23052761. [PMID: 35269901 PMCID: PMC8910949 DOI: 10.3390/ijms23052761] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/26/2022] [Accepted: 02/27/2022] [Indexed: 01/27/2023] Open
Abstract
The EPH/ephrin system constitutes a bidirectional signaling pathway comprised of a family of tyrosine kinase receptors in tandem with their plasma membrane-bound ligand (ephrins). Its significance in a wide variety of physiologic and pathologic processes has been recognized during the past decades. In carcinogenesis, EPH/ephrins coordinate a wide spectrum of pathologic processes, such as angiogenesis, vessel infiltration, and metastasis. Despite the recent advances in colorectal cancer (CRC) diagnosis and treatment, it remains a leading cause of death globally, accounting for 9.2% of all cancer deaths. A growing body of literature has been published lately revitalizing our scientific interest towards the role of EPH/ephrins in pathogenesis and the treatment of CRC. The aim of the present review is to present the recent CRC data which might lead to clinical practice changes in the future.
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Affiliation(s)
- Stavros P Papadakos
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 157 72 Athens, Greece
| | - Leonidas Petrogiannopoulos
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 157 72 Athens, Greece
| | - Alexandros Pergaris
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 157 72 Athens, Greece
| | - Stamatios Theocharis
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 157 72 Athens, Greece
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Cai S, Guo X, Huang C, Deng Y, Du L, Liu W, Yang C, Zhao H, Ma K, Wang L, He J, Yu Z. Integrative analysis and experiments to explore angiogenesis regulators correlated with poor prognosis, immune infiltration and cancer progression in lung adenocarcinoma. J Transl Med 2021; 19:361. [PMID: 34419075 PMCID: PMC8380343 DOI: 10.1186/s12967-021-03031-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/07/2021] [Indexed: 02/07/2023] Open
Abstract
Angiogenesis is the process of capillary sprouting from pre-existing vessels and it plays a critical role in the carcinogenic process of lung adenocarcinoma (LUAD). However, the association of angiogenesis regulators with the prognosis and progression of LUAD needs to be further elucidated. In this study, we adopted differential expression analysis, Cox proportional hazards (PH) regression analysis and experimental validation to identify angiogenesis regulators correlated with a poor prognosis, immune infiltration and cancer progression in LUAD. These results showed that the diagnostic and prognostic models based on COL5A2 and EPHB2 served as independent biomarkers with superior predictive ability. The patients in the high-risk group exhibited a worse prognosis in the TCGA cohort (P < 0.001, HR = 1.72, 95% CI 1.28-2.30), GSE310210 cohort (P = 0.005, HR = 2.87, 95% CI 1.46-5.61), and GSE31019 cohort (P = 0.01, HR = 2.14, 95% CI 1.19-3.86) than patients in the low-risk group. The high prognostic risk patients had a higher TMB (P < 0.001); higher fractions of M0 macrophages, neutrophils, NK cells resting, and T cells CD4 memory activated (P < 0.05); and higher expression of immune checkpoints PD-1, PDL-1, PDL-2, and B7H3 (P < 0.001). Patients in the high-risk group were more sensitive to chemotherapeutic drugs and molecular targeted drugs such as cisplatin, doxorubicin, gefitinib, and bosutinib (P < 0.0001). In addition, inhibition of COL5A2 and EPHB2 effectively suppressed the proliferation and migration of LUAD cells. The current study identified angiogenesis regulators as potential biomarkers and therapeutic targets for LUAD and may help to further optimize cancer therapy.
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Affiliation(s)
- Songhua Cai
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, 518116, China
| | - Xiaotong Guo
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, 518116, China
| | - Chujian Huang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, 518116, China
| | - Youjun Deng
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, 518116, China
| | - Longde Du
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, 518116, China
| | - Wenyi Liu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, 518116, China
| | - Chenglin Yang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, 518116, China
| | - Hongbo Zhao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, 518116, China
| | - Kai Ma
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, 518116, China
| | - Lixu Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, 518116, China
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, 518116, China. .,Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Zhentao Yu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, 518116, China.
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Wang Y, Yan K, Wang L, Bi J. Genome instability-related long non-coding RNA in clear renal cell carcinoma determined using computational biology. BMC Cancer 2021; 21:727. [PMID: 34167490 PMCID: PMC8229419 DOI: 10.1186/s12885-021-08356-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/29/2021] [Indexed: 12/04/2022] Open
Abstract
Background There is evidence that long non-coding RNA (lncRNA) is related to genetic stability. However, the complex biological functions of these lncRNAs are unclear. Method TCGA - KIRC lncRNAs expression matrix and somatic mutation information data were obtained from TCGA database. “GSVA” package was applied to evaluate the genomic related pathway in each samples. GO and KEGG analysis were performed to show the biological function of lncRNAs-mRNAs. “Survival” package was applied to determine the prognostic significance of lncRNAs. Multivariate Cox proportional hazard regression analysis was applied to conduct lncRNA prognosis model. Results In the present study, we applied computational biology to identify genome-related long noncoding RNA and identified 26 novel genomic instability-associated lncRNAs in clear cell renal cell carcinoma. We identified a genome instability-derived six lncRNA-based gene signature that significantly divided clear renal cell samples into high- and low-risk groups. We validated it in test cohorts. To further elucidate the role of the six lncRNAs in the model’s genome stability, we performed a gene set variation analysis (GSVA) on the matrix. We performed Pearson correlation analysis between the GSVA scores of genomic stability-related pathways and lncRNA. It was determined that LINC00460 and LINC01234 could be used as critical factors in this study. They may influence the genome stability of clear cell carcinoma by participating in mediating critical targets in the base excision repair pathway, the DNA replication pathway, homologous recombination, mismatch repair pathway, and the P53 signaling pathway. Conclusion subsections These data suggest that LINC00460 and LINC01234 are crucial for the stability of the clear cell renal cell carcinoma genome. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08356-9.
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Affiliation(s)
- Yutao Wang
- Department of Urology, China Medical University, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Kexin Yan
- Department of Dermatology, China Medical University, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Linhui Wang
- Department of Urology, China Medical University, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Jianbin Bi
- Department of Urology, China Medical University, The First Hospital of China Medical University, Shenyang, Liaoning, China.
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11
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Artemaki PI, Kontos CK. Editorial for the Special Issue "Molecular Biomarkers in Colorectal Adenocarcinoma". Int J Mol Sci 2021; 22:ijms22042052. [PMID: 33669582 PMCID: PMC7922430 DOI: 10.3390/ijms22042052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 02/14/2021] [Accepted: 02/15/2021] [Indexed: 12/15/2022] Open
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12
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Song, BA Y, Wang, MA F, Wei, MA Y, Chen, BA D, Deng, BA G. ATP5A1 Participates in Transcriptional and Posttranscriptional Regulation of Cancer-Associated Genes by Modulating Their Expression and Alternative Splicing Profiles in HeLa Cells. Technol Cancer Res Treat 2021; 20:15330338211039126. [PMID: 34520292 PMCID: PMC8445539 DOI: 10.1177/15330338211039126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 07/26/2021] [Indexed: 12/13/2022] Open
Abstract
Background: Aberrant expression and alternative splicing of oncogenes are the driving events in tumor initiation and development. But how these events are regulated in cancer cells is largely unknown. Functions of ATP5A1, an important mitochondrial ATP synthase gene, in transcriptional and posttranscriptional regulation were explored in this study. Methods: ATP5A1 was overexpressed using plasmid-transformed HeLa cells, and its influence on cell apoptosis and proliferation is evaluated. Transcriptome sequencing was then performed using RNA-seq to study the changes in gene expression and regulation of alternative splicing events. Validation of the implicated genes was achieved using RT-qPCR analysis. Results: It was found that ATP5A1 could significantly promote cellular apoptosis, but it had no influence on cell proliferation. ATP5A1 overexpression significantly increased the expression levels of genes associated with the innate immune response, angiogenesis, and collagen catabolic processes. This included enrichment of MMP2 and MMP19. It was also found that ATP5A1 could interfere with the alternative splicing of hundreds of genes associated with glucose homeostasis, HIF-1 signaling activation, and several pathways associated with cancers. Eight ATP5A1-regulated differentially expressed genes and 3 genes altered by splicing were selected and validated using RT-qPCR analysis. Conclusions: In summary, we illustrate the regulatory functions of ATP5A1 on the transcriptome of HeLa cells by exploring its influence on gene expression and alternative splicing. The results suggest that ATP5A1 may play an important regulatory role in cervical cancer cells by regulating expression and alternative splicing of cancer-associated genes. This study provides novel insights into the current understanding of the mechanisms of ATP5A1 on carcinogenesis and cancer progression.
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Affiliation(s)
- Yisa Song, BA
- Qinghai People's Hospital Xining, Xining, Qinghai, P.R. China
| | - Fei Wang, MA
- Qinghai People's Hospital Xining, Xining, Qinghai, P.R. China
| | | | - Dong Chen, BA
- ABLife Inc., Wuhan, P.R. China
- ABLife BioBigData Institute, Wuhan, P.R. China
| | - Gang Deng, BA
- Wuhan Hospital of Traditional Chinese and Western Medicine, Wuhan, Hubei, P.R. China
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Deutelmoser H, Lorenzo Bermejo J, Benner A, Weigl K, Park HA, Haffa M, Herpel E, Schneider M, Ulrich CM, Hoffmeister M, Chang-Claude J, Brenner H, Scherer D. Genotype-Based Gene Expression in Colon Tissue-Prediction Accuracy and Relationship with the Prognosis of Colorectal Cancer Patients. Int J Mol Sci 2020; 21:E8150. [PMID: 33142733 PMCID: PMC7662650 DOI: 10.3390/ijms21218150] [Citation(s) in RCA: 2] [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: 09/30/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) survival has environmental and inherited components. The expression of specific genes can be inferred based on individual genotypes-so called expression quantitative trait loci. In this study, we used the PrediXcan method to predict gene expression in normal colon tissue using individual genotype data from 91 CRC patients and examined the correlation ρ between predicted and measured gene expression levels. Out of 5434 predicted genes, 58% showed a negative ρ value and only 16% presented a ρ higher than 0.10. We subsequently investigated the association between genotype-based gene expression in colon tissue for genes with ρ > 0.10 and survival of 4436 CRC patients. We identified an inverse association between the predicted expression of ARID3B and CRC-specific survival for patients with a body mass index greater than or equal to 30 kg/m2 (HR (hazard ratio) = 0.66 for an expression higher vs. lower than the median, p = 0.005). This association was validated using genotype and clinical data from the UK Biobank (HR = 0.74, p = 0.04). In addition to the identification of ARID3B expression in normal colon tissue as a candidate prognostic biomarker for obese CRC patients, our study illustrates the challenges of genotype-based prediction of gene expression, and the advantage of reassessing the prediction accuracy in a subset of the study population using measured gene expression data.
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Affiliation(s)
- Heike Deutelmoser
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany; (H.D.); (M.H.); (C.M.U.); (H.B.)
- Institute of Medical Biometry and Informatics, Medical Faculty, Heidelberg University, Im Neuenheimer Feld 130.3, 69120 Heidelberg, Germany;
| | - Justo Lorenzo Bermejo
- Institute of Medical Biometry and Informatics, Medical Faculty, Heidelberg University, Im Neuenheimer Feld 130.3, 69120 Heidelberg, Germany;
| | - Axel Benner
- Division of Biostatistics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69121 Heidelberg, Germany;
| | - Korbinian Weigl
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69121 Heidelberg, Germany; (K.W.); (M.H.)
| | - Hanla A. Park
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69121 Heidelberg, Germany; (H.A.P.); (J.C.-C.)
| | - Mariam Haffa
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany; (H.D.); (M.H.); (C.M.U.); (H.B.)
- Division of Translational Functional Cancer Genomics, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Esther Herpel
- NCT Tissue Bank, National Center for Tumor Diseases (NCT) and University Hospital Heidelberg, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany;
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
| | - Martin Schneider
- Department of General, Visceral, and Transplantation Surgery, University Hospital Heidelberg, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany;
| | - Cornelia M. Ulrich
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany; (H.D.); (M.H.); (C.M.U.); (H.B.)
- Huntsman Cancer Institute, 2000 Cir of Hope Dr 1950, Salt Lake City, UT 84112, USA
- Department of Population Health Sciences, School of Medicine, University of Utah, Salt Lake City, UT 84112, USA
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69121 Heidelberg, Germany; (K.W.); (M.H.)
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69121 Heidelberg, Germany; (H.A.P.); (J.C.-C.)
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf (UKE), Martinstraße 52, 20246 Hamburg, Germany
| | - Hermann Brenner
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany; (H.D.); (M.H.); (C.M.U.); (H.B.)
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69121 Heidelberg, Germany; (K.W.); (M.H.)
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Dominique Scherer
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany; (H.D.); (M.H.); (C.M.U.); (H.B.)
- Institute of Medical Biometry and Informatics, Medical Faculty, Heidelberg University, Im Neuenheimer Feld 130.3, 69120 Heidelberg, Germany;
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