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Gul S, Pang J, Yuan H, Chen Y, Yu Q, Wang H, Tang W. Stemness signature and targeted therapeutic drugs identification for Triple Negative Breast Cancer. Sci Data 2023; 10:815. [PMID: 37985782 PMCID: PMC10662149 DOI: 10.1038/s41597-023-02709-8] [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: 06/13/2023] [Accepted: 10/31/2023] [Indexed: 11/22/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer and carries the worst prognosis, characterized by the lack of progesterone, estrogen, and HER2 gene expression. This study aimed to analyze cancer stemness-related gene signature to determine patients' risk stratification and prognosis feature with TNBC. Here one-class logistic regression (OCLR) algorithm was applied to compute the stemness index of TNBC patients. Cox and LASSO regression analysis was performed on stemness-index related genes to establish 16 genes-based prognostic signature, and their predictive performance was verified in TCGA and METABERIC merged data cohort. We diagnosed the expression level of prognostic genes signature in the tumor immune microenvironment, analyzed the TNBC scRNA-seq GSE176078 dataset, and further validated the expression level of prognostic genes using the HPA database. Finally, the small molecular compounds targeted at the anti-tumor effect of predictive genes were screened by molecular docking; this novel stemness-based prognostic genes signature study could facilitate the prognosis of patients with TNBC and thus provide a feasible therapeutic target for TNBC.
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Affiliation(s)
- Samina Gul
- Laboratory of Molecular Genetics of Aging & Tumor, Medical School, Kunming University of Science and Technology, 727 jingming south road, Kunming city, Yunnan province, 650500, China
| | - Jianyu Pang
- Laboratory of Molecular Genetics of Aging & Tumor, Medical School, Kunming University of Science and Technology, 727 jingming south road, Kunming city, Yunnan province, 650500, China
| | - Hongjun Yuan
- Laboratory of Molecular Genetics of Aging & Tumor, Medical School, Kunming University of Science and Technology, 727 jingming south road, Kunming city, Yunnan province, 650500, China
| | - Yongzhi Chen
- Laboratory of Molecular Genetics of Aging & Tumor, Medical School, Kunming University of Science and Technology, 727 jingming south road, Kunming city, Yunnan province, 650500, China
| | - Qian Yu
- Laboratory of Molecular Genetics of Aging & Tumor, Medical School, Kunming University of Science and Technology, 727 jingming south road, Kunming city, Yunnan province, 650500, China
| | - Hui Wang
- Laboratory of Molecular Genetics of Aging & Tumor, Medical School, Kunming University of Science and Technology, 727 jingming south road, Kunming city, Yunnan province, 650500, China
| | - Wenru Tang
- Laboratory of Molecular Genetics of Aging & Tumor, Medical School, Kunming University of Science and Technology, 727 jingming south road, Kunming city, Yunnan province, 650500, China.
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Gu X, Mao Z, Pan H, Zou C, Ding G, Fan Y. <p>Case–Control Study on <em>TNFRSF6B</em> Gene Polymorphism and Susceptibility to Gastric Cancer in a Chinese Han Population</p>. Pharmgenomics Pers Med 2020; 13:749-756. [PMID: 33363398 PMCID: PMC7751833 DOI: 10.2147/pgpm.s283308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 12/04/2020] [Indexed: 12/26/2022] Open
Abstract
Purpose To explore the relationship between rs2297440 and rs2297441 polymorphisms of TNFRSF6B gene and susceptibility to gastric cancer. Methods A hospital-based case-control study was conducted. A total of 577 gastric cancer cases and 678 normal controls were recruited. Their genotypes were determined using the SnapShot method. Results The smoking rate in the case group (34.49%) was higher than that in the control group (27.29%). For TNFRSF6B rs2297440, among people <62 years old, the risk of gastric cancer in TC people was 1.84 times that in TT people. Among the non-drinking people, the risk of gastric cancer in the CC type was 0.66 times that in the TT+TC type. Among the drinking population, the risk of gastric cancer in the TC type was 1.67 times that in the TT type, and the risk in the TC+CC type was 1.70 times that in the TT type. As for TNFRSF6B rs2297441, in males and non-drinkers, the risk of gastric cancer in the AG type was less than that in the GG type. No matter how old the patient is, the risk of gastric cancer in the AA type was less than that in the AG+GG type. Conclusion A correlation exists between smoking and gastric cancer. For TNFRSF6B rs2297440, the TC genotype may be a risk factor for gastric cancer in people <62 years old. In the non-drinking population, the homozygous mutant of CC may be a protective factor for gastric cancer. In the drinking population, TC type may be a risk factor, whereas the TC+CC type dominated by C may be a protective factor. For TNFRSF6B rs2297441, the AG genotype may be a risk factor for gastric cancer in males and non-drinkers. The AA homozygous mutant may be a protective factor for gastric cancer.
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Affiliation(s)
- Xuyu Gu
- School of Medicine, Southeast University, Nanjing, Jiangsu 210009, People's Republic of China
| | - Zhenwei Mao
- Cancer Institute, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu 212002, People's Republic of China
| | - Huiwen Pan
- Cancer Institute, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu 212002, People's Republic of China
| | - Chen Zou
- Cancer Institute, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu 212002, People's Republic of China
| | - Guowen Ding
- Cancer Institute, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu 212002, People's Republic of China
| | - Yu Fan
- Cancer Institute, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu 212002, People's Republic of China
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Zhang H, Cheng J, Li Z, Xi Y. Identification of hub genes and molecular mechanisms in infant acute lymphoblastic leukemia with MLL gene rearrangement. PeerJ 2019; 7:e7628. [PMID: 31523525 PMCID: PMC6717502 DOI: 10.7717/peerj.7628] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 08/06/2019] [Indexed: 12/17/2022] Open
Abstract
Infant acute lymphoblastic leukemia (ALL) with the mixed lineage leukemia (MLL) gene rearrangement (MLL-R) is considered a distinct leukemia from childhood or non-MLL-R infant ALL. To detect key genes and elucidate the molecular mechanisms of MLL-R infant ALL, microarray expression data were downloaded from the Gene Expression Omnibus (GEO) database, and differentially expressed genes (DEGs) between MLL-R and non-MLL-R infant ALL were identified. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were carried out. Then, we constructed a protein-protein interaction (PPI) network and identified the hub genes. Finally, drug-gene interactions were mined. A total of 139 cases of MLL-R infant ALL including 77 (55.4%) fusions with AF4, 38 (27.3%) with ENL, 14 (10.1%) with AF9, and 10 (7.2%) other gene fusions were characterized. A total of 236 up-regulated and 84 down-regulated DEGs were identified. The up-regulated DEGs were mainly involved in homophilic cell adhesion, negative regulation of apoptotic process and cellular response to drug GO terms, while down-regulated DEGs were mainly enriched in extracellular matrix organization, protein kinase C signaling and neuron projection extension GO terms. The up-regulated DEGs were enriched in seven KEGG pathways, mainly involving transcriptional regulation and signaling pathways, and down-regulated DEGs were involved in three main KEGG pathways including Alzheimer’s disease, TGF-beta signaling pathway, and hematopoietic cell lineage. The PPI network included 297 nodes and 410 edges, with MYC, ALB, CD44, PTPRC and TNF identified as hub genes. Twenty-three drug-gene interactions including four up-regulated hub genes and 24 drugs were constructed by Drug Gene Interaction database (DGIdb). In conclusion, MYC, ALB, CD44, PTPRC and TNF may be potential bio-markers for the diagnosis and therapy of MLL-R infant ALL.
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Affiliation(s)
- Hao Zhang
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Juan Cheng
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Zijian Li
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Yaming Xi
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu, China
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Kim S, Wyckoff J, Morris AT, Succop A, Avery A, Duncan GE, Jazwinski SM. DNA methylation associated with healthy aging of elderly twins. GeroScience 2018; 40:469-484. [PMID: 30136078 PMCID: PMC6294724 DOI: 10.1007/s11357-018-0040-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/09/2018] [Indexed: 12/21/2022] Open
Abstract
Variation in healthy aging and lifespan is ascribed more to various non-genetic factors than to inherited genetic determinants, and a major goal in aging research is to reveal the epigenetic basis of aging. One approach to this goal is to find genomic sites or regions where DNA methylation correlates with biological age. Using health data from 134 elderly twins, we calculated a frailty index as a quantitative indicator of biological age, and by applying the Infinium HumanMethylation450K BeadChip technology to their leukocyte DNA samples, we obtained quantitative DNA methylation data on genome-wide CpG sites. We analyzed the health and epigenome data by taking two independent associative approaches: the parametric regression-based approach and a non-parametric machine learning approach followed by GO ontology analysis. Our results indicate that DNA methylation at CpG sites in the promoter region of PCDHGA3 is associated with biological age. PCDHGA3 belongs to clustered protocadherin genes, which are all located in a single locus on chromosome 5 in human. Previous studies of the clustered protocadherin genes showed that (1) DNA methylation is associated with age or age-related phenotypes; (2) DNA methylation can modulate gene expression; (3) dysregulated gene expression is associated with various pathologies; and (4) DNA methylation patterns at this locus are associated with adverse lifetime experiences. All these observations suggest that DNA methylation at the clustered protocadherin genes, including PCDHGA3, is a key mediator of healthy aging.
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Affiliation(s)
- Sangkyu Kim
- Tulane Center for Aging and Department of Medicine, Tulane University Health Sciences Center, New Orleans, LA, 70112, USA.
| | - Jennifer Wyckoff
- Tulane Center for Aging and Department of Medicine, Tulane University Health Sciences Center, New Orleans, LA, 70112, USA
| | - Anne-T Morris
- Virginia Commonwealth University, Mid-Atlantic Twin Registry, Richmond, VA, USA
| | | | - Ally Avery
- University of Washington Twin Registry, Seattle, WA, USA
- Washington State Twin Registry, Washington State University - Health Sciences Spokane, Spokane, WA, USA
| | - Glen E Duncan
- University of Washington Twin Registry, Seattle, WA, USA
- Washington State Twin Registry, Washington State University - Health Sciences Spokane, Spokane, WA, USA
| | - S Michal Jazwinski
- Tulane Center for Aging and Department of Medicine, Tulane University Health Sciences Center, New Orleans, LA, 70112, USA
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Liu Y, Peng K, Xie R, Zheng J, Guo J, Wei R, Yang H, Cai C, Wei Q. Protocadherin γ-A7 is down-regulated in colorectal cancer and associated with the prognosis in patients with wild-type KRAS. Hum Pathol 2018; 83:14-21. [PMID: 30121367 DOI: 10.1016/j.humpath.2018.08.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 08/10/2018] [Accepted: 08/12/2018] [Indexed: 12/13/2022]
Abstract
Many clustered protocadherin genes (PCDHs) within chromosome 5q31 are frequently down-regulated in colorectal cancer (CRC) due to the hypermethylation of this region, and some of them have been identified as tumor suppressors. However, the association between the expression of the clustered PCDHs and prognosis of CRC patients is still unclear. Here, we identified multiple PCDHs that were significantly down-regulated in CRC by analyzing the RNA-seq data of the Cancer Genome Atlas (TCGA) cohort. Among them, one γ-PCDH subfamily member, PCDHGA7, was found to be associated with overall survival in the patients with wild-type KRAS. Next, we experimentally validated the decrease of PCDHGA7 mRNA and protein levels in tumor tissues of 20 CRC patients by using quantitative real-time polymerase chain reaction (qRT-PCR) and immunohistochemistry assay (IHC). To further investigate whether the expression of PCDHGA7 could predict clinical outcomes, an independent cohort of 138 patients, whose tumors carried wild-type KRAS, was enrolled. In-house tissue microarrays (TMAs) were developed to facilitate the protein detection, and prognostic significance was analyzed. The result showed low PCDHGA7 expression was associated with advanced TNM stage, high risk of tumor recurrence and short overall survival. In conclusion, this study demonstrates that PCDHGA7 is down-regulated in CRC, and its expression level is correlated with clinical outcomes in patients with wild-type KRAS. Our finding indicates PCDHGA7 could serve as a potential novel biomarker to predict prognosis by combining certain tumor genotypes in patients of CRC.
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Affiliation(s)
- Yingdi Liu
- Department of Pathology, Shanghai clinical college Anhui Medical University, Hefei 230032, China; Department of Pathology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Kangsheng Peng
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Ruting Xie
- Department of Pathology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Jiayi Zheng
- Department of Pathology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Jing Guo
- Department of Pathology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Rong Wei
- Department of Pathology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Huiqiong Yang
- Department of Pathology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Chunmiao Cai
- Department of Pathology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China.
| | - Qing Wei
- Department of Pathology, Shanghai clinical college Anhui Medical University, Hefei 230032, China; Department of Pathology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China.
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