1
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Zhao M, Zhang X, Huan Q, Dong M. Metabolism-associated molecular classification of cervical cancer. BMC Womens Health 2023; 23:555. [PMID: 37884919 PMCID: PMC10605340 DOI: 10.1186/s12905-023-02712-6] [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: 05/22/2023] [Accepted: 10/16/2023] [Indexed: 10/28/2023] Open
Abstract
OBJECTIVE This study aimed to explore metabolic abnormalities in cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) for metabolism-related genes. METHODS We downloaded expression data for metabolism-related genes, performed differential expression analysis, and applied weighted gene co-expression network analysis (WGCNA) to identify metabolism-related functional modules. We obtained normalised miRNA expression data and identified master methylation regulators for metabolism-related genes. Cox regression of data on metabolism-related genes was performed to screen for genes that affect the prognosis of patients with CESC. Furthermore, we selected key genes for validation. RESULTS Our results identified 3620 metabolism-related genes in CESC, 2493 of which contained related mutations. The co-occurrence of CUBN, KALRN, and HERC1 was related to the prognosis of CESC. The fraction of genome altered (FGA) closely correlated with overall survival. In expression analysis, 374 genes were related to the occurrence and prognosis of CESC. We then identified four metabolic pathway modules in WGCNA. Further analysis revealed that glycolysis/gluconeogenesis was related to endothelial cells and that arachidonic acid metabolism was related to cell proliferation. These four modules were also related to the prognosis of CESC. Among CESC-related metabolic genes, two genes were found to be regulated by microRNAs (miRNAs) and methylation, whereas another two genes were coregulated by miRNAs and mutations. CONCLUSIONS Among metabolism-related genes, 15 genes were related to the prognosis of CESC. The co-occurrence of CUBN/KALRN/HERC1 was associated with CESC prognosis. Glycolysis/gluconeogenesis was related to endothelial cells, and arachidonic acid metabolism was related to cell proliferation.
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Affiliation(s)
- Min Zhao
- School of Medicine, Mianyang Central Hospital, University of Electronic Science and Technology of China, Mianyang, 621000, Sichuan, China.
| | - Xue Zhang
- School of Life Sciences, China Medical University, Shenyang, China
| | - Qing Huan
- Shandong Key Laboratory of Reproductive Medicine, Department of Obstetrics and Gynecology, Shandong Provincial Hospital, Shandong First Medical University, Jinan, 250021, Shandong, China
| | - Meng Dong
- School of Life Sciences, China Medical University, Shenyang, China
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2
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Tsai YS, Chareddy YS, Price BA, Parker JS, Pecot CV. An integrated model for predicting KRAS dependency. PLoS Comput Biol 2023; 19:e1011095. [PMID: 37141389 DOI: 10.1371/journal.pcbi.1011095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 05/16/2023] [Accepted: 04/10/2023] [Indexed: 05/06/2023] Open
Abstract
The clinical approvals of KRAS G12C inhibitors have been a revolutionary advance in precision oncology, but response rates are often modest. To improve patient selection, we developed an integrated model to predict KRAS dependency. By integrating molecular profiles of a large panel of cell lines from the DEMETER2 dataset, we built a binary classifier to predict a tumor's KRAS dependency. Monte Carlo cross validation via ElasticNet within the training set was used to compare model performance and to tune parameters α and λ. The final model was then applied to the validation set. We validated the model with genetic depletion assays and an external dataset of lung cancer cells treated with a G12C inhibitor. We then applied the model to several Cancer Genome Atlas (TCGA) datasets. The final "K20" model contains 20 features, including expression of 19 genes and KRAS mutation status. In the validation cohort, K20 had an AUC of 0.94 and accurately predicted KRAS dependency in both mutant and KRAS wild-type cell lines following genetic depletion. It was also highly predictive across an external dataset of lung cancer lines treated with KRAS G12C inhibition. When applied to TCGA datasets, specific subpopulations such as the invasive subtype in colorectal cancer and copy number high pancreatic adenocarcinoma were predicted to have higher KRAS dependency. The K20 model has simple yet robust predictive capabilities that may provide a useful tool to select patients with KRAS mutant tumors that are most likely to respond to direct KRAS inhibitors.
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Affiliation(s)
- Yihsuan S Tsai
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Yogitha S Chareddy
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Brandon A Price
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Joel S Parker
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Chad V Pecot
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Division of Hematology & Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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3
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la Torre A, Lo Vecchio F, Greco A. Epigenetic Mechanisms of Aging and Aging-Associated Diseases. Cells 2023; 12:cells12081163. [PMID: 37190071 DOI: 10.3390/cells12081163] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 04/04/2023] [Accepted: 04/07/2023] [Indexed: 05/17/2023] Open
Abstract
Aging is an inevitable outcome of life, characterized by a progressive decline in tissue and organ function. At a molecular level, it is marked by the gradual alterations of biomolecules. Indeed, important changes are observed on the DNA, as well as at a protein level, that are influenced by both genetic and environmental parameters. These molecular changes directly contribute to the development or progression of several human pathologies, including cancer, diabetes, osteoporosis, neurodegenerative disorders and others aging-related diseases. Additionally, they increase the risk of mortality. Therefore, deciphering the hallmarks of aging represents a possibility for identifying potential druggable targets to attenuate the aging process, and then the age-related comorbidities. Given the link between aging, genetic, and epigenetic alterations, and given the reversible nature of epigenetic mechanisms, the precisely understanding of these factors may provide a potential therapeutic approach for age-related decline and disease. In this review, we center on epigenetic regulatory mechanisms and their aging-associated changes, highlighting their inferences in age-associated diseases.
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Affiliation(s)
- Annamaria la Torre
- Laboratory of Gerontology and Geriatrics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
| | - Filomena Lo Vecchio
- Laboratory of Gerontology and Geriatrics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
| | - Antonio Greco
- Complex Unit of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
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4
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Walker RR, Rentia Z, Chiappinelli KB. Epigenetically programmed resistance to chemo- and immuno-therapies. Adv Cancer Res 2023; 158:41-71. [PMID: 36990538 PMCID: PMC10184181 DOI: 10.1016/bs.acr.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Resistance to cancer treatments remains a major barrier in developing cancer cures. While promising combination chemotherapy treatments and novel immunotherapies have improved patient outcomes, resistance to these treatments remains poorly understood. New insights into the dysregulation of the epigenome show how it promotes tumor growth and resistance to therapy. By altering control of gene expression, tumor cells can evade immune cell recognition, ignore apoptotic cues, and reverse DNA damage induced by chemotherapies. In this chapter, we summarize the data on epigenetic remodeling during cancer progression and treatment that enable cancer cell survival and describe how these epigenetic changes are being targeted clinically to overcome resistance.
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Affiliation(s)
- Reddick R Walker
- The George Washington University Cancer Center (GWCC), Washington, DC, United States; Department of Microbiology, Immunology & Tropical Medicine, The George Washington University, Washington, DC, United States
| | - Zainab Rentia
- The George Washington University Cancer Center (GWCC), Washington, DC, United States
| | - Katherine B Chiappinelli
- The George Washington University Cancer Center (GWCC), Washington, DC, United States; Department of Microbiology, Immunology & Tropical Medicine, The George Washington University, Washington, DC, United States.
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5
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Nan H, Guo P, Fan J, Zeng W, Hu C, Zheng C, Pan B, Cao Y, Ge Y, Xue X, Li W, Lin K. Comprehensive analysis of the prognosis, tumor microenvironment, and immunotherapy response of SDHs in colon adenocarcinoma. Front Immunol 2023; 14:1093974. [PMID: 36949947 PMCID: PMC10025334 DOI: 10.3389/fimmu.2023.1093974] [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: 11/09/2022] [Accepted: 02/13/2023] [Indexed: 03/08/2023] Open
Abstract
Background Succinate dehydrogenase (SDH), one of the key enzymes in the tricarboxylic acid cycle, is mainly found in the mitochondria. SDH consists of four subunits encoding SDHA, SDHB, SDHC, and SDHD. The biological function of SDH is significantly related to cancer progression. Colorectal cancer (CRC) is one of the most common malignant tumors globally, whose most common histological subtype is colon adenocarcinoma (COAD). However, the correlation between SDH factors and COAD remains unclear. Methods The data on pan-cancer was obtained from The Cancer Genome Atlas (TCGA) database. Kaplan-Meier survival analysis showed the prognostic ability of SDHs. The cBioPortal database reflected genetic variations of SDHs. The correlation analysis was conducted between SDHs and mitochondrial energy metabolism genes (MMGs) and the protein-protein interaction (PPI) network was built. Consequently, Univariate and Multivariate Cox Regression Analysis on SDHs and other clinical characteristics were conducted. A nomogram was established. The ssGSEA analysis visualized the association between SDHs and immune infiltration. Immunophenoscore (IPS) explored the correlation between SDHs and immunotherapy, and the correlation between SDHs and targeted therapy was investigated through Genomics of Drug Sensitivity in Cancer. Finally, qPCR and immunohistochemistry detected SDHs' expression. Results After assessing SDHs differential expression in pan-cancer, we found that SDHB, SDHC, and SDHD benefit COAD patients. The cBioPortal database demonstrated that SDHA was the top gene in mutation frequency rank. Correlation analysis mirrored a strong link between SDHs and MMGs. We formulated a nomogram and found that SDHB, SDHC, SDHD, and clinical characteristics correlated with COAD patients' survival. For T helper cells, Th2 cells, and Tem, SDHA, SDHB, SDHC, and SDHD were significantly enriched in the high expression group. Moreover, COAD patients with high SDHA expression were more suitable for immunotherapy. And COAD patients with different SDHs' expression have different sensitivity to targeted drugs. Further verifying the gene and protein expression levels of SDHs, we found that the tissues were consistent with the bioinformatics analysis. Conclusions Our study analyzed the expression and prognostic value of SDHs in COAD, explored the pathway mechanisms involved, and the immune cell correlations, indicating that SDHs might be biomarkers for COAD patients.
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Affiliation(s)
- Han Nan
- School and Hospital of Stomatology, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Pengkun Guo
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jianing Fan
- School of Second Clinical Medical, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Wen Zeng
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Chonghan Hu
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Can Zheng
- The First School of Medicine, School of Information and Engineering, Wenzhou Medical University, Wenzhou, China
| | - Bujian Pan
- Department of Hepatobiliary Surgery, Wenzhou Central Hospital, The Dingli Clinical Institute of Wenzhou Medical University, Wenzhou, China
| | - Yu Cao
- School and Hospital of Stomatology, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yiwen Ge
- School of Second Clinical Medical, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiangyang Xue
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Experiemtial Center of Basic Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
- Department of General Surgery, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
- *Correspondence: Xiangyang Xue, ; Wenshu Li, ; Kezhi Lin,
| | - Wenshu Li
- Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
- *Correspondence: Xiangyang Xue, ; Wenshu Li, ; Kezhi Lin,
| | - Kezhi Lin
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Experiemtial Center of Basic Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
- *Correspondence: Xiangyang Xue, ; Wenshu Li, ; Kezhi Lin,
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6
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Khan MZI, Tam MSY, Azam Z, Law HKW. Proteomic profiling of metabolic proteins as potential biomarkers of radioresponsiveness for colorectal cancer. J Proteomics 2022; 262:104600. [DOI: 10.1016/j.jprot.2022.104600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 04/25/2022] [Accepted: 05/01/2022] [Indexed: 12/24/2022]
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7
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Zhang M, Wang HZ, Peng RY, Xu F, Wang F, Zhao Q. Metabolism-Associated Molecular Classification of Colorectal Cancer. Front Oncol 2020; 10:602498. [PMID: 33344254 PMCID: PMC7746835 DOI: 10.3389/fonc.2020.602498] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 10/28/2020] [Indexed: 12/11/2022] Open
Abstract
The high heterogeneity of colorectal cancer (CRC) is the main clinical challenge for individualized therapies. Molecular classification will contribute to drug discovery and personalized management optimizing. Here, we aimed to characterize the molecular features of CRC by a classification system based on metabolic gene expression profiles. 435 CRC samples from the Genomic Data Commons data portal were chosen as training set while 566 sample in GSE39582 were selected as testing set. Then, a non-negative matrix factorization clustering was performed, and three subclasses of CRC (C1, C2, and C3) were identified in both training set and testing set. Results showed that subclass C1 displayed high metabolic activity and good prognosis. Subclass C2 was associated with low metabolic activities and displayed high immune signatures as well as high expression of immune checkpoint genes. C2 had the worst prognosis among the three subtypes. Subclass C3 displayed intermediate metabolic activity, high gene mutation numbers and good prognosis. Finally, a 27-gene metabolism-related signature was identified for prognosis prediction. Our works deepened the understanding of metabolic hallmarks of CRC, and provided valuable information for “multi-molecular” based personalized therapies.
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Affiliation(s)
- Meng Zhang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Clinical Center & Key Lab of Intestinal & Colorectal Diseases, Wuhan University, Wuhan, China
| | - Hai-Zhou Wang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Clinical Center & Key Lab of Intestinal & Colorectal Diseases, Wuhan University, Wuhan, China
| | - Ru-Yi Peng
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Clinical Center & Key Lab of Intestinal & Colorectal Diseases, Wuhan University, Wuhan, China
| | - Fei Xu
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Clinical Center & Key Lab of Intestinal & Colorectal Diseases, Wuhan University, Wuhan, China
| | - Fan Wang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Clinical Center & Key Lab of Intestinal & Colorectal Diseases, Wuhan University, Wuhan, China
| | - Qiu Zhao
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Clinical Center & Key Lab of Intestinal & Colorectal Diseases, Wuhan University, Wuhan, China
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8
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Zhang J, Hou C, Dou S, Li G, Wang Z, Liu Y, Zhang Y, Wang R, Shen B, Han G. T cell immunoglobulin and mucin domain protein 3 inhibits glycolysis in RAW 264.7 macrophages through Hexokinase 2. Scand J Immunol 2020; 93:e12981. [PMID: 33031600 DOI: 10.1111/sji.12981] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 09/17/2020] [Accepted: 09/25/2020] [Indexed: 12/27/2022]
Abstract
T cell immunoglobulin and mucin domain-3 (Tim-3), an immune checkpoint molecule, plays critical roles in maintaining innate immune homeostasis; however, the mechanisms underlying these roles remain to be determined. Here, we determined that Tim-3 controls glycolysis in macrophages and thus contributes to phenotype shifting. Tim-3 signal blockade significantly increases lactate production by macrophages, but does not influence cell proliferation or apoptosis. Tim-3 attenuates glucose uptake by inhibiting hexokinase 2 (HK2) expression in macrophages. Tim-3-mediated inhibition of macrophage glycolysis and the expression of proinflammatory cytokines, tumour necrosis factor (TNF)-α and interleukin (IL)-1β are reversed by HK2 silencing. Finally, we demonstrated that Tim-3 inhibits HK2 expression via the STAT1 pathway. We have thus discovered a new way by which Tim-3 modulates macrophage function.
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Affiliation(s)
- Jiacheng Zhang
- The Sixth Medical Center, the General Hospital of PLA, Beijing, China.,Institute of Military Cognitive and Brain Sciences, Beijing, China
| | - Chunmei Hou
- Institute of Military Cognitive and Brain Sciences, Beijing, China
| | - Shuaijie Dou
- Institute of Military Cognitive and Brain Sciences, Beijing, China
| | - Ge Li
- Institute of Military Cognitive and Brain Sciences, Beijing, China
| | - Zhiding Wang
- Institute of Military Cognitive and Brain Sciences, Beijing, China
| | - Yiqiong Liu
- Institute of Military Cognitive and Brain Sciences, Beijing, China
| | - Yanling Zhang
- Institute of Military Cognitive and Brain Sciences, Beijing, China
| | - Renxi Wang
- Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Beijing Institute of Brain Disorders, Capital Medical University, Beijing, China
| | - Beifen Shen
- Institute of Military Cognitive and Brain Sciences, Beijing, China
| | - Gencheng Han
- Institute of Military Cognitive and Brain Sciences, Beijing, China
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9
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Zhao Z, He B, Cai Q, Zhang P, Peng X, Zhang Y, Xie H, Wang X. A model of twenty-three metabolic-related genes predicting overall survival for lung adenocarcinoma. PeerJ 2020; 8:e10008. [PMID: 33024640 PMCID: PMC7520091 DOI: 10.7717/peerj.10008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/31/2020] [Indexed: 01/27/2023] Open
Abstract
Background The highest rate of cancer-related deaths worldwide is from lung adenocarcinoma (LUAD) annually. Metabolism was associated with tumorigenesis and cancer development. Metabolic-related genes may be important biomarkers and metabolic therapeutic targets for LUAD. Materials and Methods In this study, the gleaned cohort included LUAD RNA-SEQ data from the Cancer Genome Atlas (TCGA) and corresponding clinical data (n = 445). The training cohort was utilized to model construction, and data from the Gene Expression Omnibus (GEO, GSE30219 cohort, n = 83; GEO, GSE72094, n = 393) were regarded as a testing cohort and utilized for validation. First, we used a lasso-penalized Cox regression analysis to build a new metabolic-related signature for predicting the prognosis of LUAD patients. Next, we verified the metabolic gene model by survival analysis, C-index, receiver operating characteristic (ROC) analysis. Univariate and multivariate Cox regression analyses were utilized to verify the gene signature as an independent prognostic factor. Finally, we constructed a nomogram and performed gene set enrichment analysis to facilitate subsequent clinical applications and molecular mechanism analysis. Result Patients with higher risk scores showed significantly associated with poorer survival. We also verified the signature can work as an independent prognostic factor for LUAD survival. The nomogram showed better clinical application performance for LUAD patient prognostic prediction. Finally, KEGG and GO pathways enrichment analyses suggested several especially enriched pathways, which may be helpful for us investigative the underlying mechanisms.
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Affiliation(s)
- Zhenyu Zhao
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China
| | - Boxue He
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China
| | - Qidong Cai
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China
| | - Pengfei Zhang
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China
| | - Xiong Peng
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China
| | - Yuqian Zhang
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China
| | - Hui Xie
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China
| | - Xiang Wang
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China
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10
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Zhang Q, Huang R, Hu H, Yu L, Tang Q, Tao Y, Liu Z, Li J, Wang G. Integrative Analysis of Hypoxia-Associated Signature in Pan-Cancer. iScience 2020; 23:101460. [PMID: 32861996 PMCID: PMC7476856 DOI: 10.1016/j.isci.2020.101460] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/18/2020] [Accepted: 08/12/2020] [Indexed: 02/06/2023] Open
Abstract
Hypoxia is serving crucial roles in cancers. This study aims to comprehensively analyze the molecular features and clinical relevance of a well-defined hypoxia-associated signature in pan-cancer using multi-omics data. Data were acquired from TCGA, CCLE, GDSC, and GEO. RNA expression pattern, copy number variation (CNV), methylation, and mutation of the signature were analyzed. The majority of the 15 genes were upregulated in cancer tissues compared with normal tissue, and RNA expression was negatively associated with methylation level. CNV occurred in almost all the cancers, whereas mutation frequency was low across different cancer types. The signature was also closely related to cancer hallmarks and cancer-related metabolism pathways. NDRG1 was upregulated in kidney cancer tissues as indicated by immunohistochemistry. Besides, most of the 15 genes were risk factors for patients' overall survival. Our results provide a valuable resource that will guide both mechanistic and therapeutic analyses of the hypoxia signature in cancers.
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Affiliation(s)
- Qian Zhang
- Department of Colorectal Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province 150086, China
| | - Rui Huang
- Department of Colorectal Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province 150086, China
| | - Hanqing Hu
- Department of Colorectal Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province 150086, China
| | - Lei Yu
- Department of Colorectal Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province 150086, China
| | - Qingchao Tang
- Department of Colorectal Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province 150086, China
| | - Yangbao Tao
- Department of Colorectal Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province 150086, China
| | - Zheng Liu
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100000, China
| | - Jiaying Li
- Department of Colorectal Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province 150086, China
| | - Guiyu Wang
- Department of Colorectal Surgery, the Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province 150086, China
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11
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Orlov YL, Baranova AV. Editorial: Bioinformatics of Genome Regulation and Systems Biology. Front Genet 2020; 11:625. [PMID: 32849761 PMCID: PMC7399369 DOI: 10.3389/fgene.2020.00625] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 05/26/2020] [Indexed: 12/31/2022] Open
Affiliation(s)
- Yuriy L Orlov
- Institute of Digital Medicine, I.M.Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,Life Sciences Department, Novosibirsk State University, Novosibirsk, Russia.,Agrobiotechnology Department, Agrarian and Technological Institute, Peoples' Friendship University of Russia, Moscow, Russia
| | - Ancha V Baranova
- School of Systems Biology, George Mason University, Fairfax, VA, United States
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12
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Yan XM, Zhang Z, Meng Y, Li HB, Gao L, Luo D, Jiang H, Gao Y, Yuan B, Zhang JB. Genome-wide identification and analysis of circular RNAs differentially expressed in the longissimus dorsi between Kazakh cattle and Xinjiang brown cattle. PeerJ 2020; 8:e8646. [PMID: 32211228 PMCID: PMC7081781 DOI: 10.7717/peerj.8646] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 01/27/2020] [Indexed: 12/18/2022] Open
Abstract
Xinjiang brown cattle have better meat quality than Kazakh cattle. Circular RNAs (circRNAs) are a type of RNA that can participate in the regulation of gene transcription. Whether circRNAs are differentially expressed in the longissimus dorsi between these two types of cattle and whether differentially expressed circRNAs regulate muscle formation and differentiation are still unknown. In this study, we established two RNA-seq libraries, each of which consisted of three samples. A total of 5,177 circRNAs were identified in longissimus dorsi samples from Kazakh cattle and Xinjiang brown cattle using the Illumina platform, 46 of which were differentially expressed. Fifty-five Gene Ontology terms were significantly enriched, and 12 Kyoto Encyclopedia of Genes and Genomes pathways were identified for the differentially expressed genes. Muscle biological processes were associated with the origin genes of the differentially expressed circRNAs. In addition, we randomly selected six overexpressed circRNAs and compared their levels in longissimus dorsi tissue from Kazakh cattle and Xinjiang brown cattle using RT-qPCR. Furthermore, we predicted 66 interactions among 65 circRNAs and 14 miRNAs using miRanda and established a coexpression network. A few microRNAs known for their involvement in myoblast regulation, such as miR-133b and miR-664a, were identified in this network. Notably, bta_circ_03789_1 and bta_circ_05453_1 are potential miRNA sponges that may regulate insulin-like growth factor 1 receptor expression. These findings provide an important reference for prospective investigations of the role of circRNA in longissimus muscle growth and development. This study provides a theoretical basis for targeting circRNAs to improve beef quality and taste.
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Affiliation(s)
- Xiang-Min Yan
- Department of Laboratory Animals, Jilin University, Changchun, Jilin, China.,Institute of Animal Husbandry, Xinjiang Academy of Animal Husbandry, Ürümqi, Xinjiang, China
| | - Zhe Zhang
- Department of Laboratory Animals, Jilin University, Changchun, Jilin, China
| | - Yu Meng
- Department of Laboratory Animals, Jilin University, Changchun, Jilin, China
| | - Hong-Bo Li
- Institute of Animal Husbandry, Xinjiang Academy of Animal Husbandry, Ürümqi, Xinjiang, China
| | - Liang Gao
- Yili Vocational and Technical College, Yili, Xinjiang, China
| | - Dan Luo
- Department of Laboratory Animals, Jilin University, Changchun, Jilin, China
| | - Hao Jiang
- Department of Laboratory Animals, Jilin University, Changchun, Jilin, China
| | - Yan Gao
- Department of Laboratory Animals, Jilin University, Changchun, Jilin, China
| | - Bao Yuan
- Department of Laboratory Animals, Jilin University, Changchun, Jilin, China
| | - Jia-Bao Zhang
- Department of Laboratory Animals, Jilin University, Changchun, Jilin, China
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Baranova AV, Skoblov MY, Voropaeva EN, Shanmughavel P, Orlov YL. Medical genetics studies at BGRS conference series. BMC MEDICAL GENETICS 2019; 20:50. [PMID: 30967129 PMCID: PMC6454589 DOI: 10.1186/s12881-019-0769-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Ancha V. Baranova
- School of Systems Biology, George Mason University, Fairfax, VA USA
- Research Centre for Medical Genetics, 115478 Moscow, Russia
| | | | - Elena N. Voropaeva
- Research Institute of Internal and Preventive Medicine - Branch of the Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | | | - Yuriy L. Orlov
- Research Institute of Internal and Preventive Medicine - Branch of the Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
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