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Carey-Smith SL, Kotecha RS, Cheung LC, Malinge S. Insights into the Clinical, Biological and Therapeutic Impact of Copy Number Alteration in Cancer. Int J Mol Sci 2024; 25:6815. [PMID: 38999925 PMCID: PMC11241182 DOI: 10.3390/ijms25136815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/15/2024] [Accepted: 06/17/2024] [Indexed: 07/14/2024] Open
Abstract
Copy number alterations (CNAs), resulting from the gain or loss of genetic material from as little as 50 base pairs or as big as entire chromosome(s), have been associated with many congenital diseases, de novo syndromes and cancer. It is established that CNAs disturb the dosage of genomic regions including enhancers/promoters, long non-coding RNA and gene(s) among others, ultimately leading to an altered balance of key cellular functions. In cancer, CNAs have been associated with almost all steps of the disease: predisposition, initiation, development, maintenance, response to treatment, resistance, and relapse. Therefore, understanding how specific CNAs contribute to tumourigenesis may provide prognostic insight and ultimately lead to the development of new therapeutic approaches to improve patient outcomes. In this review, we provide a snapshot of what is currently known about CNAs and cancer, incorporating topics regarding their detection, clinical impact, origin, and nature, and discuss the integration of innovative genetic engineering strategies, to highlight the potential for targeting CNAs using novel, dosage-sensitive and less toxic therapies for CNA-driven cancer.
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Affiliation(s)
- Shannon L. Carey-Smith
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA 6009, Australia; (S.L.C.-S.); (R.S.K.); (L.C.C.)
- Curtin Medical School, Curtin University, Perth, WA 6102, Australia
| | - Rishi S. Kotecha
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA 6009, Australia; (S.L.C.-S.); (R.S.K.); (L.C.C.)
- Curtin Medical School, Curtin University, Perth, WA 6102, Australia
- Department of Clinical Haematology, Oncology, Blood and Marrow Transplantation, Perth Children’s Hospital, Perth, WA 6009, Australia
- UWA Medical School, University of Western Australia, Perth, WA 6009, Australia
| | - Laurence C. Cheung
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA 6009, Australia; (S.L.C.-S.); (R.S.K.); (L.C.C.)
- Curtin Medical School, Curtin University, Perth, WA 6102, Australia
- Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
| | - Sébastien Malinge
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA 6009, Australia; (S.L.C.-S.); (R.S.K.); (L.C.C.)
- Curtin Medical School, Curtin University, Perth, WA 6102, Australia
- UWA Medical School, University of Western Australia, Perth, WA 6009, Australia
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Aljahdali MO, Molla MHR. Multi-omics prognostic signatures of IPO11 mRNA expression and clinical outcomes in colorectal cancer using bioinformatics approaches. Health Inf Sci Syst 2023; 11:57. [PMID: 38028961 PMCID: PMC10678892 DOI: 10.1007/s13755-023-00259-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 11/05/2023] [Indexed: 12/01/2023] Open
Abstract
The most prevalent malignant illness of the gastrointestinal system, colorectal cancer, is the third most prevalent cancer in males and the second most prevalent cancer in women. Importin-11 is a protein that acts as a regulator of cancer cell proliferation in colorectal tumours by conveying β -catenin to the cell nucleus. However, the IPO11 gene was found to encode a protein called Importin-11, which functions as a nucleus importer for the cell. As a result, preventing β -catenin from entering the nucleus requires blocking Importin-11. As a result, we conducted a multi-omics investigation to assess IPO11 gene potential as a therapeutic biomarker for human colorectal cancer (CC). Oncomine, GEPIA2, immunohisto-chemistry, and UALCAN databases were used to analyses the mRNA expression profiles of IPO11 in CC. The investigation has yielded clear evidence of the increase of IPO11 expression in CC subtypes, as indicated by the data acquired. Analysing CC research from the cBioPortal database, the study discovered three new missense mutations in the importin-11 protein sequence at a frequency of 0.00-1.50% copy number changes. Additionally, the Kaplan-Meier plots demonstrated a strong connection concerning IPO11 downregulation and a poorer CC patient survival rate. The co-expressed gene profile of IPO11 was likewise associated with the onset of CC. IPO11 co-expressed gene profile was also linked to CC development. Moreover, the correlation analysis using bc-GenExMiner and the UCSC Xena server identified KIF2A as the most positively co-expressed gene. The study found that KIF2A and its co-expressed genes were involved in a wide variety of cancer progression pathways using the Enrichr database. Cumulatively, this result will not only provide new information about the expression of IPO11 associated with CC progression and patient survival, but could also serve as a therapeutic biomarker for treating CC in a significant and worthwhile manner. Supplementary Information The online version contains supplementary material available at 10.1007/s13755-023-00259-2.
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Affiliation(s)
- Mohammed Othman Aljahdali
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah, 21598 Saudi Arabia
| | - Mohammad Habibur Rahman Molla
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah, 21598 Saudi Arabia
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Zhao H, Song N, Feng H, Lei Q, Zheng Y, Liu J, Liu C, Chai Z. Construction and validation of a prognostic model for gastrointestinal stromal tumors based on copy number alterations and clinicopathological characteristics. Front Oncol 2022; 12:1055174. [PMID: 36620561 PMCID: PMC9811389 DOI: 10.3389/fonc.2022.1055174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Background The increasing incidence of gastrointestinal stromal tumors (GISTs) has led to the discovery of more novel prognostic markers. We aim to establish an unsupervised prognostic model for the early prediction of the prognosis of future patients with GISTs and to guide clinical treatment. Methods We downloaded the GISTs dataset through the cBioPortal website. We extracted clinical information and pathological information, including the microsatellite instability (MSI) score, fraction genome altered (FGA) score, tumor mutational burden (TMB), and copy number alteration burden (CNAB), of patients with GISTs. For survival analysis, we used univariate Cox regression to analyze the contribution of each factor to prognosis and calculated a hazard ratio (HR) and 95% confidence interval (95% CI). For clustering groupings, we used the t-distributed stochastic neighbor embedding (t-SNE) method for data dimensionality reduction. Subsequently, the k-means method was used for clustering analysis. Results A total of 395 individuals were included in the study. After dimensionality reduction with t-SNE, all patients were divided into two subgroups. Cluster 1 had worse OS than cluster 2 (HR=3.45, 95% CI, 2.22-5.56, P<0.001). The median MSI score of cluster 1 was 1.09, and the median MSI score of cluster 2 was 0.24, which were significantly different (P<0.001). The FGA score of cluster 1 was 0.28, which was higher than that of cluster 2 (P<0.001). In addition, both the TMB and CNAB of cluster 1 were higher than those of cluster 2, and the P values were less than 0.001. Conclusion Based on the CNA of GISTs, patients can be divided into high-risk and low-risk groups. The high-risk group had a higher MSI score, FGA score, TMB and CNAB than the low-risk group. In addition, we established a prognostic nomogram based on the CNA and clinicopathological characteristics of patients with GISTs.
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Affiliation(s)
- Heng Zhao
- Department of Oncology, Shandong Key Laboratory of Rheumatic Disease and Translational Medicine, Shandong Provincial Qianfoshan Hospital, The First Affiliated Hospital of Shandong First Medical University, Jinan, China,Department of Research and Development, Shandong Benran Biotechnology Co., Ltd., Jinan, China
| | - Nuohan Song
- Department of Research and Development, Shandong Benran Biotechnology Co., Ltd., Jinan, China,China University of Political Science and Law, Beijing, China
| | - Hao Feng
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Qiang Lei
- Department of Research and Development, Shandong Benran Biotechnology Co., Ltd., Jinan, China
| | - Yingying Zheng
- Department of Oncology, Shandong Key Laboratory of Rheumatic Disease and Translational Medicine, Shandong Provincial Qianfoshan Hospital, The First Affiliated Hospital of Shandong First Medical University, Jinan, China
| | - Jing Liu
- Department of Clinical Laboratory Medicine, Shandong Public Health Clinical Center, Shandong University, Jinan, China
| | - Chunyan Liu
- Department of Oncology, Shandong Key Laboratory of Rheumatic Disease and Translational Medicine, Shandong Provincial Qianfoshan Hospital, The First Affiliated Hospital of Shandong First Medical University, Jinan, China,*Correspondence: Chunyan Liu, ; Zhengbin Chai,
| | - Zhengbin Chai
- Department of Clinical Laboratory Medicine, Shandong Public Health Clinical Center, Shandong University, Jinan, China,*Correspondence: Chunyan Liu, ; Zhengbin Chai,
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Ding K, Zhou M, Wang H, Zhang S, Metaxas DN. Spatially aware graph neural networks and cross-level molecular profile prediction in colon cancer histopathology: a retrospective multi-cohort study. Lancet Digit Health 2022; 4:e787-e795. [DOI: 10.1016/s2589-7500(22)00168-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 06/28/2022] [Accepted: 08/15/2022] [Indexed: 11/05/2022]
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Shen MH, Huang CJ, Ho TF, Liu CY, Shih YY, Huang CS, Huang CC. Colorectal cancer concurrent gene signature based on coherent patterns between genomic and transcriptional alterations. BMC Cancer 2022; 22:590. [PMID: 35637462 PMCID: PMC9150289 DOI: 10.1186/s12885-022-09627-9] [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: 07/05/2021] [Accepted: 05/03/2022] [Indexed: 11/10/2022] Open
Abstract
Background The aim of the study was to enhance colorectal cancer prognostication by integrating single nucleotide polymorphism (SNP) and gene expression (GE) microarrays for genomic and transcriptional alteration detection; genes with concurrent gains and losses were used to develop a prognostic signature. Methods The discovery dataset comprised 32 Taiwanese colorectal cancer patients, of which 31 were assayed for GE and copy number variations (CNVs) with Illumina Human HT-12 BeadChip v4.0 and Omni 25 BeadChip v1.1. Concurrent gains and losses were declared if coherent manners were observed between GE and SNP arrays. Concurrent genes were also identified in The Cancer Genome Atlas Project (TCGA) as the secondary discovery dataset (n = 345). Results The “universal” concurrent genes, which were the combination of z-transformed correlation coefficients, contained 4022 genes. Candidate genes were evaluated within each of the 10 public domain microarray datasets, and 1655 (2000 probe sets) were prognostic in at least one study. Consensus across all datasets was used to build a risk predictive model, while distinct relapse-free/overall survival patterns between defined risk groups were observed among four out of five training datasets. The predictive accuracy of recurrence, metastasis, or death was between 61 and 86% (cross-validation area under the receiver operating characteristic (ROC) curve: 0.548-0.833) from five independent validation studies. Conclusion The colorectal cancer concurrent gene signature is prognostic in terms of recurrence, metastasis, or mortality among 1746 patients. Genes with coherent patterns between genomic and transcriptional contexts are more likely to provide prognostication for colorectal cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09627-9.
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Affiliation(s)
- Ming-Hung Shen
- Department of Surgery, Fu-Jen Catholic University Hospital, No. 69, Guizi Road, Taishan District, New Taipei City, 243, Taiwan.,Ph. D Program in Nutrition and Food Science, College of Human Ecology, Fu-Jen Catholic University, No. 510, Zhongzheng Rd., Xinzhuang Dist., New Taipei City, 242062, Taiwan.,School of Medicine, College of Medicine, Fu-Jen Catholic University, No. 510, Zhongzheng Rd., Xinzhuang Dist., New Taipei City, 242062, Taiwan
| | - Chi-Jung Huang
- Department of Biochemistry, National Defense Medical Center, No.161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City, 11490, Taiwan.,Department of Medical Research, Cathay General Hospital, No.280, Sec. 4, Renai Rd., Daan Dist., Taipei City, 106, Taiwan
| | - Thien-Fiew Ho
- Division of General Surgery, Cathay General Hospital Sijhih, No. 2, Ln. 59, Jiancheng Rd., Xizhi Dist., New Taipei City, 221, Taiwan
| | - Chih-Yi Liu
- Division of Pathology, Cathay General Hospital Sijhih, No. 2, Ln. 59, Jiancheng Rd., Xizhi Dist., New Taipei City, 221, Taiwan
| | - Ying-Yih Shih
- Division of Hematology and Oncology, Cathay General Hospital Sijhih, No. 2, Ln. 59, Jiancheng Rd., Xizhi Dist., New Taipei City, 221, Taiwan
| | - Ching-Shui Huang
- Department of Surgery, Cathay General Hospital, No.280, Sec. 4, Renai Rd., Daan Dist., Taipei City, 106, Taiwan. .,School of Medicine, College of Medicine, Taipei Medical University, 250 Wu-Hsing Street, Taipei City, 110, Taiwan.
| | - Chi-Cheng Huang
- Department of Surgery, Taipei Veterans General Hospital, No.201, Sec. 2, Shipai Rd., Beitou District, Taipei City, 11217, Taiwan. .,Comprehensive Breast Health Center, Taipei Veterans General Hospital, No.201, Sec. 2, Shipai Rd., Beitou District, Taipei City, Taiwan, 11217. .,Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, No.17, Xuzhou Rd., Taipei City, 100, Taiwan.
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Tan ES, Knepper TC, Wang X, Permuth JB, Wang L, Fleming JB, Xie H. Copy Number Alterations as Novel Biomarkers and Therapeutic Targets in Colorectal Cancer. Cancers (Basel) 2022; 14:2223. [PMID: 35565354 PMCID: PMC9101426 DOI: 10.3390/cancers14092223] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 04/21/2022] [Accepted: 04/24/2022] [Indexed: 12/10/2022] Open
Abstract
In colorectal cancer, somatic mutations have played an important role as prognostic and predictive biomarkers, with some also functioning as therapeutic targets. Another genetic aberration that has shown significance in colorectal cancer is copy number alterations (CNAs). CNAs occur when a change to the DNA structure propagates gain/amplification or loss/deletion in sections of DNA, which can often lead to changes in protein expression. Multiple techniques have been developed to detect CNAs, including comparative genomic hybridization with microarray, low pass whole genome sequencing, and digital droplet PCR. In this review, we summarize key findings in the literature regarding the role of CNAs in the pathogenesis of colorectal cancer, from adenoma to carcinoma to distant metastasis, and discuss the roles of CNAs as prognostic and predictive biomarkers in colorectal cancer.
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Affiliation(s)
- Elaine S. Tan
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA; (E.S.T.); (J.B.P.); (J.B.F.)
| | - Todd C. Knepper
- Department of Individualized Cancer Management, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA;
| | - Xuefeng Wang
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA;
| | - Jennifer B. Permuth
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA; (E.S.T.); (J.B.P.); (J.B.F.)
| | - Liang Wang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, 12901 USF Magnolia Drive Tampa, Tampa, FL 33612, USA;
| | - Jason B. Fleming
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA; (E.S.T.); (J.B.P.); (J.B.F.)
| | - Hao Xie
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA; (E.S.T.); (J.B.P.); (J.B.F.)
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Altered SERCA Expression in Breast Cancer. ACTA ACUST UNITED AC 2021; 57:medicina57101074. [PMID: 34684111 PMCID: PMC8539028 DOI: 10.3390/medicina57101074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 11/26/2022]
Abstract
Background and Objectives: Calcium (Ca2+) signaling is critical for the normal functioning of various cellular activities. However, abnormal changes in cellular Ca2+ can contribute to pathological conditions, including various types of cancer. The maintenance of intracellular Ca2+ levels is achieved through tightly regulated processes that help maintain Ca2+ homeostasis. Several types of regulatory proteins are involved in controlling intracellular Ca2+ levels, including the sarco/endoplasmic reticulum (SR/ER) Ca2+ ATPase pump (SERCA), which maintains Ca2+ levels released from the SR/ER. In total, three ATPase SR/ER Ca2+-transporting (ATP2A) 1-3 genes exist, which encode for several isoforms whose expression profiles are tissue-specific. Recently, it has become clear that abnormal SERCA expression and activity are associated with various types of cancer, including breast cancer. Breast carcinomas represent 40% of all cancer types that affect women, with a wide variety of pathological and clinical conditions. Materials and methods: Using cBioPortal breast cancer patient data, Kaplan–Meier plots demonstrated that high ATP2A1 and ATP2A3 expression was associated with reduced patient survival. Results: The present study found significantly different SERCA specific-type expressions in a series of breast cancer cell lines. Moreover, bioinformatics analysis indicated that ATP2A1 and ATP2A3 expression was highly altered in patients with breast cancer. Conclusion: Overall, the present data suggest that SERCA gene-specific expressioncan possibly be considered as a crucial target for the control of breast cancer development and progression.
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Identification and Characterization of the Copy Number Dosage-Sensitive Genes in Colorectal Cancer. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 18:501-510. [PMID: 32775488 PMCID: PMC7390836 DOI: 10.1016/j.omtm.2020.06.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 06/22/2020] [Indexed: 02/07/2023]
Abstract
Dosage effect is one of the common mechanisms of somatic copy number alteration in the development of colorectal cancer, yet the roles of dosage-sensitive genes (DSGs) in colorectal cancer (CRC) remain to be characterized more deeply. In this study, we developed a five-step pipeline to identify DSGs and analyzed their characterization in CRC. Results showed that our pipeline performed better than existing methods, and the result was significantly overlapped between solid tumor and cell line. We also found that the top five DSGs (PSMF1, RAF1, PTPRA, MKRN2, and ELP3) were associated with the progression of CRC. By analyzing the characterization, DSGs were enriched in driver genes and they drove sub-pathways of CRC. In addition, immune-related DSGs are associated with CRC progression. Our results also showed that the CRC samples affected by high microsatellites have fewer DSGs, but a higher overlap with DSGs in microsatellite low instability and microsatellite stable samples. In addition, we applied DSGs to identify potential drug targets, with the results showing that 22 amplified DSGs were more sensitive to four drugs. In conclusion, DSGs play an important role in CRC, and our pipeline is effective to identify them.
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Chang Z, Miao X, Zhao W. Identification of Prognostic Dosage-Sensitive Genes in Colorectal Cancer Based on Multi-Omics. Front Genet 2020; 10:1310. [PMID: 31998369 PMCID: PMC6962299 DOI: 10.3389/fgene.2019.01310] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 11/27/2019] [Indexed: 01/13/2023] Open
Abstract
Several studies have already identified the prognostic markers in colorectal cancer (CRC) based on somatic copy number alteration (SCNA). However, very little information is available regarding their value as a prognostic marker. Gene dosage effect is one important mechanism of copy number and dosage-sensitive genes are more likely to behave like driver genes. In this work, we propose a new pipeline to identify the dosage-sensitive prognostic genes in CRC. The RNAseq data, the somatic copy number of CRC from TCGA were assayed to screen out the SCNAs. Wilcoxon rank-sum test was used to identify the differentially expressed genes in alteration samples with |SCNA| > 0.3. Cox-regression was used to find the candidate prognostic genes. An iterative algorithm was built to identify the stable prognostic genes. Finally, the Pearson correlation coefficient was calculated between gene expression and SCNA as the dosage effect score. The cell line data from CCLE was used to test the consistency of the dosage effect. The differential co-expression network was built to discover their function in CRC. A total of six amplified genes (NDUFB4, WDR5B, IQCB1, KPNA1, GTF2E1, and SEC22A) were found to be associated with poor prognosis. They demonstrate a stable prognostic classification in more than 50% threshold of SCNA. The average dosage effect score was 0.5918 ± 0.066, 0.5978 ± 0.082 in TCGA and CCLE, respectively. They also show great stability in different data sets. In the differential co-expression network, these six genes have the top degree and are connected to the driver and tumor suppressor genes. Function enrichment analysis revealed that gene NDUFB4 and GTF2E1 affect cancer-related functions such as transmembrane transport and transformation factors. In conclusion, the pipeline for identifying the prognostic dosage-sensitive genes in CRC was proved to be stable and reliable.
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Affiliation(s)
- Zhiqiang Chang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xiuxiu Miao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Wenyuan Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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Wang L, Wei CY, Xu YY, Deng XY, Wang Q, Ying JH, Zhang SM, Yuan X, Xuan TF, Pan YY, Gu JY. Prognostic genes of melanoma identified by weighted gene co-expression network analysis and drug repositioning using a network-based method. Oncol Lett 2019; 18:6066-6078. [PMID: 31788081 PMCID: PMC6864934 DOI: 10.3892/ol.2019.10961] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 08/21/2019] [Indexed: 12/19/2022] Open
Abstract
Melanoma is one of the most malignant types of skin cancer. However, the efficacy and utility of available drug therapies for melanoma are limited. The objective of the present study was to identify potential genes associated with melanoma progression and to explore approved therapeutic drugs that target these genes. Weighted gene co-expression network analysis was used to construct a gene co-expression network, explore the associations between genes and clinical characteristics and identify potential biomarkers. Gene expression profiles of the GSE65904 dataset were obtained from the Gene Expression Omnibus database. RNA-sequencing data and clinical information associated with melanoma obtained from The Cancer Genome Atlas were used for biomarker validation. A total of 15 modules were identified through average linkage hierarchical clustering. In the two significant modules, three network hub genes associated with melanoma prognosis were identified: C-X-C motif chemokine receptor 4 (CXCR4), interleukin 7 receptor (IL7R) and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit γ (PIK3CG). The receiver operating characteristic curve indicated that the mRNA levels of these genes exhibited excellent prognostic efficiency for primary and metastatic tumor tissues. In addition, the proximity between candidate genes associated with melanoma progression and drug targets obtained from DrugBank was calculated in the protein interaction network, and the top 15 drugs that may be suitable for treating melanoma were identified. In summary, co-expression network analysis led to the selection of CXCR4, IL7R and PIK3CG for further basic and clinical research on melanoma. Utilizing a network-based method, 15 drugs that exhibited potential for the treatment of melanoma were identified.
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Affiliation(s)
- Lu Wang
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Chuan-Yuan Wei
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Yuan-Yuan Xu
- Department of Surgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Xin-Yi Deng
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Qiang Wang
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Jiang-Hui Ying
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Si-Min Zhang
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Xin Yuan
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Tian-Fan Xuan
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Yu-Yan Pan
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Jian-Ying Gu
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
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Savage SR, Shi Z, Liao Y, Zhang B. Graph Algorithms for Condensing and Consolidating Gene Set Analysis Results. Mol Cell Proteomics 2019; 18:S141-S152. [PMID: 31142576 PMCID: PMC6692773 DOI: 10.1074/mcp.tir118.001263] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 03/22/2019] [Indexed: 01/04/2023] Open
Abstract
Gene set analysis plays a critical role in the functional interpretation of omics data. Although this is typically done for one omics experiment at a time, there is an increasing need to combine gene set analysis results from multiple experiments performed on the same or different omics platforms, such as in multi-omics studies. Integrating results from multiple experiments is challenging, and annotation redundancy between gene sets further obscures clear conclusions. We propose to use a weighted set cover algorithm to reduce redundancy of gene sets identified in a single experiment. Next, we use affinity propagation to consolidate similar gene sets identified from multiple experiments into clusters and to automatically determine the most representative gene set for each cluster. Using three examples from over representation analysis and gene set enrichment analysis, we showed that weighted set cover outperformed a previously published set cover method and reduced the number of gene sets by 52-77%. Focusing on overlapping genes between the list of input genes and the enriched gene sets in over-representation analysis and leading-edge genes in gene set enrichment analysis further reduced the number of gene sets. A use case combining enrichment analysis results from RNA-Seq and proteomics data comparing basal and luminal A breast cancer samples highlighted the known difference in proliferation and DNA damage response. Finally, we used these algorithms for a pan-cancer survival analysis. Our analysis clearly revealed prognosis-related pathways common to multiple cancer types or specific to individual cancer types, as well as pathways associated with prognosis in different directions in different cancer types. We implemented these two algorithms in an R package, Sumer, which generates tables and static and interactive plots for exploration and publication. Sumer is publicly available at https://github.com/bzhanglab/sumer.
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Affiliation(s)
- Sara R Savage
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Zhiao Shi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Yuxing Liao
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.
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Xi M, Chen T, Wu C, Gao X, Wu Y, Luo X, Du K, Yu L, Cai T, Shen R, Sun H. CDK8 as a therapeutic target for cancers and recent developments in discovery of CDK8 inhibitors. Eur J Med Chem 2018; 164:77-91. [PMID: 30594029 DOI: 10.1016/j.ejmech.2018.11.076] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 11/08/2018] [Accepted: 11/09/2018] [Indexed: 02/08/2023]
Abstract
Cyclin-dependent kinases 8 (CDK8) regulates transcriptional process via associating with the mediator complex or phosphorylating transcription factors (TF). Overexpression of CDK8 has been observed in various cancers. It mediates aberrant activation of Wnt/β-catenin signaling pathway, which is initially recognized and best studied in colorectal cancer (CRC). CDK8 acts as an oncogene and represents a potential target for developing novel CDK8 inhibitors in cancer therapeutics. However, other study has revealed its contrary role. The function of CDK8 is context dependent. Even so, a variety of potent and selective CDK8 inhibitors have been discovered after crystal structures were resolved in two states (active or inactive). In this review, we summarize co-crystal structures, biological mechanisms, dysregulation in cancers and recent progress in the field of CDK8 inhibitors, trying to offer an outlook of CDK8 inhibitors in cancer therapy in future.
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Affiliation(s)
- Meiyang Xi
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Tingkai Chen
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, China
| | - Chunlei Wu
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Xiaozhong Gao
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Yonghua Wu
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Xiang Luo
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Kui Du
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Lemao Yu
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Tao Cai
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Runpu Shen
- College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, 312000, China
| | - Haopeng Sun
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, China.
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