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Zhu G, Wang X, Wang Y, Huang T, Zhang X, He J, Shi N, Chen J, Zhang J, Zhang M, Li J. Comparative transcriptomic study on the ovarian cancer between chicken and human. Poult Sci 2024; 103:104021. [PMID: 39002367 DOI: 10.1016/j.psj.2024.104021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/05/2024] [Accepted: 06/19/2024] [Indexed: 07/15/2024] Open
Abstract
The laying hen is the spontaneous model of ovarian tumor. A comprehensive comparison based on RNA-seq from hens and women may shed light on the molecular mechanisms of ovarian cancer. We performed next-generation sequencing of microRNA and mRNA expression profiles in 9 chicken ovarian cancers and 4 normal ovaries, which has been deposited in GSE246604. Together with 6 public datasets (GSE21706, GSE40376, GSE18520, GSE27651, GSE66957, TCGA-OV), we conducted a comparative transcriptomics study between chicken and human. In the present study, miR-451, miR-2188-5p, and miR-10b-5p were differentially expressed in normal ovaries, early- and late-stage ovarian cancers. We also disclosed 499 up-regulated genes and 1,061 down-regulated genes in chicken ovarian cancer. The molecular signals from 9 cancer hallmarks, 25 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and 369 Gene Ontology (GO) pathways exhibited abnormalities in ovarian cancer compared to normal ovaries via Gene Set Enrichment Analysis (GSEA). In the comparative analysis across species, we have uncovered the conservation of 5 KEGG and 76 GO pathways between chicken and human including the mismatch repair and ECM receptor interaction pathways. Moreover, a total of 174 genes contributed to the core enrichment for these KEGG and GO pathways were identified. Among these genes, the 22 genes were found to be associated with overall survival in patients with ovarian cancer. In general, we revealed the microRNA profiles of ovarian cancers in hens and updated the mRNA profiles previously derived from microarrays. And we also disclosed the molecular pathways and core genes of ovarian cancer shared between hens and women, which informs model animal studies and gene-targeted drug development.
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Affiliation(s)
- Guoqiang Zhu
- Key laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xinglong Wang
- Key laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yajun Wang
- Key laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
| | - Tianjiao Huang
- Key laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiao Zhang
- Key laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jiliang He
- Key laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
| | - Ningkun Shi
- Key laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
| | - Juntao Chen
- Key laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jiannan Zhang
- Key laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
| | - Mao Zhang
- Division of Vascular Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Juan Li
- Key laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China.
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Qian J, Jiang Y, Hu H. Ginsenosides: an immunomodulator for the treatment of colorectal cancer. Front Pharmacol 2024; 15:1408993. [PMID: 38939839 PMCID: PMC11208871 DOI: 10.3389/fphar.2024.1408993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 05/23/2024] [Indexed: 06/29/2024] Open
Abstract
Ginsenosides, the primary bioactive ingredients derived from the root of Panax ginseng, are eagerly in demand for tumor patients as a complementary and alternative drug. Ginsenosides have increasingly become a "hot topic" in recent years due to their multifunctional role in treating colorectal cancer (CRC) and regulating tumor microenvironment (TME). Emerging experimental research on ginsenosides in the treatment and immune regulation of CRC has been published, while no review sums up its specific role in the CRC microenvironment. Therefore, this paper systematically introduces how ginsenosides affect the TME, specifically by enhancing immune response, inhibiting the activation of stromal cells, and altering the hallmarks of CRC cells. In addition, we discuss their impact on the physicochemical properties of the tumor microenvironment. Furthermore, we discuss the application of ginsenosides in clinical treatment as their efficacy in enhancing tumor patient immunity and prolonging survival. The future perspectives of ginsenoside as a complementary and alternative drug of CRC are also provided. This review hopes to open up a new horizon for the cancer treatment of Traditional Chinese Medicine monomers.
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Affiliation(s)
- Jianan Qian
- Department of Gastroenterology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yanyu Jiang
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hongyi Hu
- Department of Gastroenterology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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Huang Z, Hu X, Wei Y, Lai Y, Qi J, Pang J, Huang K, Li H, Cai P. ADAMTSL2 is a potential prognostic biomarker and immunotherapeutic target for colorectal cancer: Bioinformatic analysis and experimental verification. PLoS One 2024; 19:e0303909. [PMID: 38814950 PMCID: PMC11139340 DOI: 10.1371/journal.pone.0303909] [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: 09/24/2023] [Accepted: 05/02/2024] [Indexed: 06/01/2024] Open
Abstract
The ADAMTS Like 2 (ADAMTSL2) mutation has been identified to be associated with different human genetic diseases. The role of ADAMTSL2 is unclear in colorectal cancer (CRC). The study investigated the expression of ADAMTSL2 in both pan cancer and CRC, using data from The Cancer Genome Atlas (TCGA) database to assess its diagnostic value. The study examined the correlation between ADAMTSL2 expression levels and clinical characteristics, as well as prognosis in CRC. The study explored potential regulatory networks involving ADAMTSL2, including its association with immune infiltration, immune checkpoint genes, tumor mutational burden (TMB) / microsatellite instability (MSI), tumor stemness index (mRNAsi), and drug sensitivity in CRC. ADAMTSL2 expression was validated using GSE71187 and quantitative real-time PCR (qRT-PCR). ADAMTSL2 was aberrantly expressed in pan cancer and CRC. An increased level of ADAMTSL2 expression in patients with CRC was significantly associated with the pathologic N stage (p < 0.001), pathologic stage (p < 0.001), age (p < 0.001), histological type (p < 0.001), and neoplasm type (p = 0.001). The high expression of ADAMTSL2 in patients with CRC was found to be significantly associated with a poorer overall survival (OS) (HR: 1.67; 95% CI: 1.18-2.38; p = 0.004), progression-free survival (PFS) (HR: 1.55; 95% CI: 1.14-2.11; p = 0.005) and disease-specific survival (DSS) (HR: 1.83; 95% CI: 1.16-2.89; p = 0.010). The expression of ADAMTSL2 in patients with CRC (p = 0.009) was identified as an independent prognostic determinant. ADAMTSL2 was associated with extracellular matrix receptor (ECM-receptor) interaction, transforming growth factor β (TGF-β) signaling pathway, and more. ADAMTSL2 expression was correlated with immune infiltration, immune checkpoint genes, TMB / MSI and mRNAsi in CRC. ADAMTSL2 expression was significantly and negatively correlated with 1-BET-762, Trametinib, and WZ3105 in CRC. ADAMTSL2 was significantly upregulated in CRC cell lines. The high expression of ADAMTSL2 is significantly correlated with lower OS and immune infiltration of CRC. ADAMTSL2 may be a potential prognostic biomarker and immunotherapeutic target for CRC patients.
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Affiliation(s)
- Zhe Huang
- Department of Anorectal Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Xu Hu
- Department of Anorectal Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Yiqiu Wei
- Department of Anorectal Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Yousheng Lai
- Department of Anorectal Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Jiaming Qi
- Department of Anorectal Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Jinglin Pang
- Department of Anorectal Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Kang Huang
- Department of Anorectal Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Huagui Li
- Department of Anorectal Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Pengzhu Cai
- Department of Anorectal Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
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Jung SY, Yu H, Tan X, Pellegrini M. Novel DNA methylation-based epigenetic signatures in colorectal cancer from peripheral blood leukocytes. Am J Cancer Res 2024; 14:2253-2271. [PMID: 38859857 PMCID: PMC11162685 DOI: 10.62347/mxwj1398] [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: 01/20/2024] [Accepted: 04/21/2024] [Indexed: 06/12/2024] Open
Abstract
Colorectal cancer (CRC) is a multifactorial disease characterized by accumulation of multiple genetic and epigenetic alterations, transforming colonic epithelial cells into adenocarcinomas. Alteration of DNA methylation (DNAm) is a promising biomarker for predicting cancer risk and prognosis, but its role in CRC tumorigenesis is inconclusive. Notably, few DNAm studies have used pre-diagnostic peripheral blood (PB) DNA, causing difficulty in postulating the underlying biologic mechanism of CRC initiation. We conducted epigenome-wide association (EWA) scans in postmenopausal women from Women's Health Initiative (WHI) with their pre-diagnostic DNAm in PB leukocytes (PBLs) to prospectively evaluate CRC development. Our site-specific DNAm analyses across the genome adjusted for DNAm-age, leukocyte heterogeneities, as well as body mass index, diabetes, and insulin resistance. We validated 20 top EWA-CpGs in 2 independent CRC tissue datasets. Also, we detected differentially methylated regions (DMRs) associated with CRC, further mapped to transcriptomic profile, and finally conducted a Gene Set Enrichment Analysis. We detected multiple novel CpGs validated across WHI and tissue datasets. In particular, 2 CpGs (B4GALNT4cg10321339, SV2Bcg18144285) had the strongest effect on CRC risk. Results from our DMR scans contained MIR663cg06007966, which was also validated in EWA analyses. Also, we detected 1 methylome region in PEG10 of Chr7 shared across datasets. Our findings reflect both novel and well-established epigenomic and transcriptomic sites in CRC, warranting further functional validations. Our study contributes to better understanding of the complex interrelated mechanisms on the methylome underlying CRC tumorigenesis and suggests novel preventive DNAm-targets in PBLs for detecting at-risk individuals for CRC development.
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Affiliation(s)
- Su Yon Jung
- Translational Sciences Section, School of Nursing, University of CaliforniaLos Angeles, CA 90095, USA
- Department of Epidemiology, Fielding School of Public Health, University of CaliforniaLos Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, University of CaliforniaLos Angeles, CA 90095, USA
| | - Herbert Yu
- Cancer Epidemiology Program, University of Hawaii Cancer CenterHonolulu, HI 96813, USA
| | - Xianglong Tan
- Department of Biological Chemistry, University of CaliforniaLos Angeles, CA 90095, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, Life Sciences Division, University of CaliforniaLos Angeles, CA 90095, USA
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Ding M, Gao J, Wang J, Li Z, Gong X, Cui Z, Li C, Xue H, Li D, Wang Y. Colorectal cancer subtyping and immune landscape analysis based on natural killer cell-related genes. Arab J Gastroenterol 2024; 25:150-159. [PMID: 38719664 DOI: 10.1016/j.ajg.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 01/29/2024] [Accepted: 03/20/2024] [Indexed: 06/03/2024]
Abstract
BACKGROUND AND STUDY AIMS The prognosis of colorectal cancer (CRC) is related to natural killer (NK) cells, but the molecular subtype features of CRC based on NK cells are still unknown. This study aimed to identify NK cell-related molecular subtypes of CRC and analyze the survival status and immune landscape of patients with different subtypes. PATIENTS/MATERIAL AND METHODS mRNA expression data, single nucleotide variant (SNV) data, and clinical information of CRC patients were obtained from The Cancer Genome Atlas. Differentially expressed genes (DEGs) were obtained through differential analysis, and the intersection was taken with NK cell-associated genes to obtain 103 NK cell-associated CRC DEGs (NCDEGs). Based on NCDEGs, CRC samples were divided into three clusters through unsupervised clustering analysis. Survival analysis, immune analysis, Gene Set Enrichment Analysis (GSEA), and tumor mutation burden (TMB) analysis were performed. Finally, NCDEG-related small-molecule drugs were screened using the CMap database. RESULTS Survival analysis revealed that cluster2 had a lower survival rate than cluster1 and cluster3 (p < 0.05). Immune infiltration analysis found that the immune infiltration levels and immune checkpoint expression levels of cluster1_3 were substantially higher than those of cluster2, and the tumor purity was the opposite (p < 0.05). GSEA presented that cluster1_3 was significantly enriched in the chemokine signaling pathway, ECM receptor interaction, and antigen processing and presentation pathways (p < 0.05). The TMB of cluster1_3 was significantly higher than that of cluster2 (p < 0.05). Genes with the highest mutation rate in CRC were APC, TP53, TTN, and KRAS. Drug prediction results showed that small-molecule drugs that reverse the upregulation of NCDEGs, deoxycholic acid, dipivefrine, phenformin, and other drugs may improve the prognosis of CRC. CONCLUSION NK cell-associated CRC subtypes can be used to evaluate the tumor characteristics of CRC patients and provide an important reference for CRC patients.
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Affiliation(s)
- Mei Ding
- Surgical Research Division, Tangshan Vocational & Technical College, Tangshan, Hebei 063000, China; Department of Laparoscopy and Colorectal Surgery, Tangshan Central Hospital, Tangshan, Hebei 063000, China
| | - Jianchao Gao
- Department of Laparoscopy and Colorectal Surgery, Tangshan Central Hospital, Tangshan, Hebei 063000, China
| | - Jinyan Wang
- Department of Laparoscopy and Colorectal Surgery, Tangshan Central Hospital, Tangshan, Hebei 063000, China
| | - Zongfu Li
- Surgical Research Division, Tangshan Vocational & Technical College, Tangshan, Hebei 063000, China
| | - Xiangliang Gong
- Department of Laparoscopy and Colorectal Surgery, Tangshan Central Hospital, Tangshan, Hebei 063000, China
| | - Zhiyu Cui
- Department of Laparoscopy and Colorectal Surgery, Tangshan Central Hospital, Tangshan, Hebei 063000, China
| | - Changjun Li
- Department of Laparoscopy and Colorectal Surgery, Tangshan Central Hospital, Tangshan, Hebei 063000, China
| | - Hongjun Xue
- Department of Laparoscopy and Colorectal Surgery, Tangshan Central Hospital, Tangshan, Hebei 063000, China
| | - Dandan Li
- Department of Pathology, Tangshan Central Hospital, Tangshan, Hebei 063000, China
| | - Yigang Wang
- Department of Laparoscopy and Colorectal Surgery, Tangshan Central Hospital, Tangshan, Hebei 063000, China.
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Wang Q, Jiang Y, Li J, Li J, He Y. Genetic structural analysis of different breeds and geographical groups of Fenneropenaeus chinensis reveals population diversity. Genomics 2024; 116:110843. [PMID: 38608736 DOI: 10.1016/j.ygeno.2024.110843] [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: 11/07/2023] [Revised: 03/30/2024] [Accepted: 04/09/2024] [Indexed: 04/14/2024]
Abstract
Fenneropenaeus chinensis is a commercially important shrimp species cultured in China. This study investigated eight F. chinensis populations in China, including four geographical populations, three commercial breeds, and one wild population captured from the Yellow Sea. Population stratification analysis revealed that the Hebei geographical population and commercial breeding "Huanghai No. 4" were relatively independent and stable, reflecting a relatively closed breeding environment, whereas gene introgression was present between other populations. Selective signature analysis detected artificial selection for vision, growth, and disease resistance in the Hebei population. Neuronal development-related genes were detected to be under selection in the Changyi and Rizhao populations. Fertility of the Rizhao population was also investigated. Additionally, genes in the glycosaminoglycan biosynthesis-chondroitin sulfate/dermatan sulfate pathway were involved in the high pH tolerance of the "Huanghai No. 4" population. This study provided support for the genetic mechanism of parsing economic traits and the development of molecular breeding technologies.
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Affiliation(s)
- Qiong Wang
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266200, China
| | - Yuhan Jiang
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Jian Li
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266200, China
| | - Jitao Li
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266200, China.
| | - Yuying He
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266200, China.
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Zhou H, Shen Y, Zheng G, Zhang B, Wang A, Zhang J, Hu H, Lin J, Liu S, Luan X, Zhang W. Integrating single-cell and spatial analysis reveals MUC1-mediated cellular crosstalk in mucinous colorectal adenocarcinoma. Clin Transl Med 2024; 14:e1701. [PMID: 38778448 PMCID: PMC11111627 DOI: 10.1002/ctm2.1701] [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: 11/28/2023] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Mucinous colorectal adenocarcinoma (MCA) is a distinct subtype of colorectal cancer (CRC) with the most aggressive pattern, but effective treatment of MCA remains a challenge due to its vague pathological characteristics. An in-depth understanding of transcriptional dynamics at the cellular level is critical for developing specialised MCA treatment strategies. METHODS We integrated single-cell RNA sequencing and spatial transcriptomics data to systematically profile the MCA tumor microenvironment (TME), particularly the interactome of stromal and immune cells. In addition, a three-dimensional bioprinting technique, canonical ex vivo co-culture system, and immunofluorescence staining were further applied to validate the cellular communication networks within the TME. RESULTS This study identified the crucial intercellular interactions that engaged in MCA pathogenesis. We found the increased infiltration of FGF7+/THBS1+ myofibroblasts in MCA tissues with decreased expression of genes associated with leukocyte-mediated immunity and T cell activation, suggesting a crucial role of these cells in regulating the immunosuppressive TME. In addition, MS4A4A+ macrophages that exhibit M2-phenotype were enriched in the tumoral niche and high expression of MS4A4A+ was associated with poor prognosis in the cohort data. The ligand-receptor-based intercellular communication analysis revealed the tight interaction of MUC1+ malignant cells and ZEB1+ endothelial cells, providing mechanistic information for MCA angiogenesis and molecular targets for subsequent translational applications. CONCLUSIONS Our study provides novel insights into communications among tumour cells with stromal and immune cells that are significantly enriched in the TME during MCA progression, presenting potential prognostic biomarkers and therapeutic strategies for MCA. KEY POINTS Tumour microenvironment profiling of MCA is developed. MUC1+ tumour cells interplay with FGF7+/THBS1+ myofibroblasts to promote MCA development. MS4A4A+ macrophages exhibit M2 phenotype in MCA. ZEB1+ endotheliocytes engage in EndMT process in MCA.
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Affiliation(s)
- Haiyang Zhou
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
- Department of Colorectal SurgeryChangzheng HospitalNaval Medical UniversityShanghaiChina
| | - Yiwen Shen
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Guangyong Zheng
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Beibei Zhang
- Department of DermatologyTongren HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Anqi Wang
- Department of Colorectal SurgeryChangzheng HospitalNaval Medical UniversityShanghaiChina
| | - Jing Zhang
- Department of PathologyChangzheng HospitalNaval Medical UniversityShanghaiChina
| | - Hao Hu
- Department of PathologyChanghai HospitalNaval Medical UniversityShanghaiChina
| | - Jiayi Lin
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Sanhong Liu
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Xin Luan
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Weidong Zhang
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
- Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- School of PharmacyNaval Medical UniversityShanghaiChina
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Xiong K, Fang Y, Qiu B, Chen C, Huang N, Liang F, Huang C, Lu T, Zheng L, Zhao J, Zhu B. Investigation of cellular communication and signaling pathways in tumor microenvironment for high TP53-expressing osteosarcoma cells through single-cell RNA sequencing. Med Oncol 2024; 41:93. [PMID: 38526643 DOI: 10.1007/s12032-024-02318-4] [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: 12/18/2023] [Accepted: 01/29/2024] [Indexed: 03/27/2024]
Abstract
Osteosarcoma (OS) stands as the most prevalent primary bone cancer in children and adolescents, and its limited treatment options often result in unsatisfactory outcomes, particularly for metastatic cases. The tumor microenvironment (TME) has been recognized as a crucial determinant in OS progression. However, the intercellular dynamics between high TP53-expressing OS cells and neighboring cell types within the TME are yet to be thoroughly understood. In our study, we harnessed the single-cell RNA sequencing (scRNA-seq) technology in combination with the computational tool-Cellchat, aiming to elucidate the intercellular communication networks present within OS. Through meticulous quantitative inference and subsequent analysis of these networks, we succeeded in identifying significant signaling pathways connecting high TP53-expressing OS cells with proximate cell types, namely Macrophages, Monocytes, Endothelial Cells, and PVLs. This research brings forth a nuanced understanding of the intricate patterns and coordination involved in the TME's intercellular communication signals. These findings not only provide profound insights into the molecular mechanisms underpinning OS but also indicate potential therapeutic targets that could revolutionize treatment strategies.
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Affiliation(s)
- Kai Xiong
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, 530021, China
- Department of Orthopaedics Trauma and HandSurgery, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China
- Department of Orthopaedics Trauma and HandSurgery, The Third Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530031, China
| | - Yuqi Fang
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, 530021, China
| | - Boyuan Qiu
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, 530021, China
| | - Chaotao Chen
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, 530021, China
- Department of Orthopaedics Trauma and HandSurgery, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China
| | - Nanchang Huang
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, 530021, China
- Department of Orthopaedics Trauma and HandSurgery, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China
| | - Feiyuan Liang
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, 530021, China
- Department of Orthopaedics Trauma and HandSurgery, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China
| | - Chuangming Huang
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, 530021, China
- Department of Orthopaedics Trauma and HandSurgery, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China
- Department of Bone and Soft Tissue Surgery, Guangxi Medical University Cancer Hospital, Guangxi Medical University, Nanning, 530021, China
| | - Tiantian Lu
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, 530021, China
| | - Li Zheng
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China.
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, 530021, China.
- International Joint Laboratory of Ministry of Education for Regeneration of Bone and Soft Tissues, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China.
| | - Jinmin Zhao
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China.
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, 530021, China.
- Department of Orthopaedics Trauma and HandSurgery, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China.
- International Joint Laboratory of Ministry of Education for Regeneration of Bone and Soft Tissues, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China.
- Guangxi Key Laboratory of Regenerative Medicine, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China.
| | - Bo Zhu
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China.
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, 530021, China.
- Guangxi Key Laboratory of Regenerative Medicine, The First Affiliated Hospital of Guangxi Medical University, Guangxi Medical University, Nanning, 530021, China.
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Guo J, Zhou M, Li J, Yang Y, Hu Y, Tang T, Quan Y. The Prognosis and Immunotherapy Prediction Model of Ovarian Serous Cystadenocarcinoma Patient was Constructed Based on Cuproptosis-Related LncRNA. TOHOKU J EXP MED 2024; 262:63-74. [PMID: 37438122 DOI: 10.1620/tjem.2023.j056] [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] [Indexed: 07/14/2023]
Abstract
Cuproptosis can serve as potential prognostic predictors in patients with cancer. However, the role of this relationship in ovarian serous cystadenocarcinoma (OV) remains unclear. 376 OV tumor samples were obtained from the Cancer Genome Atlas (TCGA) database, and long non-coding RNAs (lncRNAs) related to cuproptosis were obtained through correlation analysis. The risk assessment model was further constructed by univariate Cox regression analysis and LASSO Cox regression. Bioinformatics was used to analyze the regulatory effect of relevant risk assessment models on tumor mutational burden (TMB) and immune microenvironment. We obtained 5 lncRNAs (AC025287.2, AC092718.4, AC112721.2, LINC00996, and LINC01639) and incorporated them into the Cox proportional hazards model. Kaplan-Meier (KM) curve analysis of the prognosis found that the high-risk group was associated with a poorer prognosis. The receiver operating characteristic (ROC) curve showed stronger predictive power compared to other clinicopathological features. Immune infiltration analysis showed that high-risk scores were inversely correlated with CD8+ T cells, CD4+ T cells, macrophages, NK cells, and B cells. Functional enrichment analysis found that they may act via the extracellular matrix (ECM)-interacting proteins and other pathways. We successfully constructed a reliable cuproptosis-related lncRNA model for the prognosis of OV.
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Affiliation(s)
- Junliang Guo
- Department of Obstetrics and Gynaecology, Centre for Reproductive Medicine, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University
- Sichuan Provincial Key Laboratory of Development and Related Diseases of Women and Children
| | - Muchuan Zhou
- Department of Anesthesia, Sichuan Integrative Medicine Hospital, Sichuan Academy of Chinese Medicine Science (SACMS)
- Sichuan Provincial Key Laboratory of Quality of Chinese Medicinal Materials and Research on Innovative Chinese Medicine
| | - Jinhong Li
- Department of Obstetrics and Gynaecology, Centre for Reproductive Medicine, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University
- Sichuan Provincial Key Laboratory of Development and Related Diseases of Women and Children
| | - Yihong Yang
- Department of Obstetrics and Gynaecology, Centre for Reproductive Medicine, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University
- Sichuan Provincial Key Laboratory of Development and Related Diseases of Women and Children
| | - Yang Hu
- West China School of Medicine, Sichuan University
| | - Tian Tang
- Department of Obstetrics and Gynaecology, Centre for Reproductive Medicine, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University
- Sichuan Provincial Key Laboratory of Development and Related Diseases of Women and Children
| | - Yi Quan
- Department of Obstetrics and Gynaecology, Centre for Reproductive Medicine, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University
- Sichuan Provincial Key Laboratory of Development and Related Diseases of Women and Children
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10
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Lian W, Ge S, Pang Q. Platycodin D ameliorates ammonia-induced pulmonary fibrosis by repressing TGF-β1-mediated extracellular matrix remodeling. Chem Biol Drug Des 2024; 103:e14446. [PMID: 38230787 DOI: 10.1111/cbdd.14446] [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: 09/11/2023] [Revised: 12/18/2023] [Accepted: 12/27/2023] [Indexed: 01/18/2024]
Abstract
Ammonia can induce pulmonary fibrosis in humans and animals. Platycodin D (PLD) possesses various bioactive activities including anti-fibrotic properties. In this study, we aimed to explore the activity and mechanism of PLD in pulmonary fibrosis induced by ammonia. The mouse model of ammonia-induced lung fibrosis was established, and the role of PLD was assessed by H&E and Masson's trichrome staining. The differentially expressed genes (DEGs) were identified by RNA-seq and subjected to GO and KEGG pathway analyses. BEAS-2B cells were treated with NH4 Cl alone or along with PLD. Results showed that PLD attenuated ammonia-induced pulmonary inflammation and fibrosis in vivo. The extracellular matrix (ECM)-receptor interaction pathway was predicted as a prominent pathway underlying the anti-fibrotic function of PLD. In ammonia-induced mouse models and NH4 Cl-treated BEAS-2B cells, PLD could repress the activation of the TGF-β1 pathway. By incubating lung fibroblast HFL1 cells with the conditioned medium of BEAS-2B cells treated with NH4Cl alone or along with PLD, PLD was confirmed to attenuate NH4 Cl-induced ECM deposition in HFL1 cells. Our findings demonstrate that PLD exerts a protective function in ammonia-induced pulmonary fibrosis by repressing TGF-β1-mediated ECM remodeling, suggesting the potential therapeutic value of PLD in this disease.
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Affiliation(s)
- Wenqi Lian
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Shihao Ge
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Quanhai Pang
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi, China
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11
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Wang D, Yang F, Han G, Zhang J, Wang H, Xiao Z, Chen W, Li P. Identification of a 5-Gene Cuproptosis Signature Predicting the Prognosis for Colon Adenocarcinoma Based on WGCNA. Technol Cancer Res Treat 2024; 23:15330338241250285. [PMID: 38802999 PMCID: PMC11135095 DOI: 10.1177/15330338241250285] [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: 01/29/2024] [Revised: 03/11/2024] [Accepted: 04/08/2024] [Indexed: 05/29/2024] Open
Abstract
Background: Colorectal cancer is a highly aggressive malignant tumor that primarily affects the digestive system. It is frequently diagnosed at an advanced stage. Cuproptosis is a copper-dependent form cell death mechanism, distinct from all other known pathways underlying cell death, tumor progression, prognosis, and immune response. Although the role of cuproptosis in colorectal cancer has been investigated over time, there is still an urgent need to explore new methods and insights to understand its potential function. Methods: The Gene Expression Omnibus and The Cancer Genome Atlas gene expression data were systematically explored to investigate the role of cuproptosis in colon adenocarcinoma. The weighted gene coexpression network analysis was used to construct a gene coexpression network and identify the critical module and cuproptosis-related genes correlated with colon adenocarcinoma prognosis. A cuproptosis-related genes prognostic signature for colon adenocarcinoma was identified and validated. To validate the identified gene signature, quantitative reverse transcription-polymerase chain reaction was performed. Cell proliferation assays were analyzed by CCK8 and cell cycle detection. In addition, reactive oxygen species assay was also analyzed. Results: Five hub cuproptosis-related genes (Dihydrolipoamide S-acetyltransferase, Cyclin-dependent kinase inhibitor 2A, ATOX1, VEGFA, and ULK1) were screened and a prognostic risk model for predicting overall survival was established based on these genes. The model was successfully tested in the validation cohort and the GEPIA database. Colon adenocarcinoma patients were categorized into high-risk and low-risk groups based on risk scores. The study revealed that patients with higher risk scores were more likely to have a poor prognosis. Moreover, Dihydrolipoamide S-acetyltransferase was a tumor suppressor gene that can induce cell death and affected the redox reactions in the colon cancer cell line. Conclusions: These findings suggest that the newly identified 5-gene signature may serve as a more reliable prognostic factor than clinical factors such as age and stage of disease. These findings offer a theoretical foundation for further investigation into potential cuproptosis-related biomarkers for predicting colon adenocarcinoma prognosis in the future.
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Affiliation(s)
- Dongxue Wang
- Department of Radiology and Nuclear Medicine, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Funing Yang
- Department of Radiology and Nuclear Medicine, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Guiping Han
- Department of Pathology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Jifeng Zhang
- Department of Radiology and Nuclear Medicine, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Hongjia Wang
- Department of Radiology and Nuclear Medicine, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Zunyu Xiao
- Department of Nuclear Medicine, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Weiyu Chen
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, Zhejiang, China
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Ping Li
- Department of Radiology and Nuclear Medicine, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
- Heilongjiang Key Laboratory for Accurate Diagnosis and Treatment of Coronary Heart Disease, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
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12
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Sun J, Zhang X, Zhu B, Chen Y, Wang H. A pan-cancer analysis of TNFAIP8L1 in human tumors. Medicine (Baltimore) 2023; 102:e36291. [PMID: 38065896 PMCID: PMC10713146 DOI: 10.1097/md.0000000000036291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 11/02/2023] [Indexed: 12/18/2023] Open
Abstract
TNFAIP8L1, as a recently identified member in TNFAIP8 family, plays an important role in tumorigenesis. However, a pan-cancer analysis of TNFAIP8L1 in human tumors has not been conducted until now. The main purpose of study is to investigate TNFAIP8L1 during 33 different types of human tumors by using TCGA and GTEx. The pan-cancer analysis showed that TNFAIP8L1 was significantly over-expressed in 15 cancers and low-expressed in 9 cancers. There were distinct relations between TNFAIP8L1 expression and prognosis of patients with cancer. Furthermore, we also found that DNA methylation and RNA modification of TNFAIP8L1 were associated with many cancers. And then, we detected that TNFAIP8L1 level was positively associated with cancer-associated fibroblasts (CAFs) in many tumors. And, we obtained that TNFAIP8L1 expression was related with most of immune inhibitory and stimulatory genes in multiple types of tumors. We also found TNFAIP8L1 expression was correlated with most of chemokine, receptor, MHC, immunoinhibitor and immunostimulator gens in most of cancers. Moreover, we detected TNFAIP8L1 expression was associated with TMB and MSI in several tumors. Finally, TNFAIP8L1 gene had a significant positive association with 5 genes including BCL6B, DLL4, PCDH12, COL4A1 and DLL4 in the majority of tumors. GO enrichment and KEGG pathway analyses showed that TNFAIP8L1 in thepathogenesis of cancer may be related to "purine nucleoside binding," "purine ribonucleoside binding," "ECM-receptor interaction," etc. Our first pan-cancer study may provide a deep comprehending of TNFAIP8L1 in tumoeigenesis from different tumors.
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Affiliation(s)
- Jinghui Sun
- Department of Dermatology, Shengli Oilfield Central Hospital, Dongying, Shandong, China
| | - Xuezhong Zhang
- Department of Laboratory Medicine, Zibo Central Hospital, Zibo, Shandong, China
| | - Bin Zhu
- Department of Laboratory Medicine, Zibo Central Hospital, Zibo, Shandong, China
| | - Yingjun Chen
- Department of Infectious Diseases, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Hui Wang
- Department of Gynaecology and Obstetrics, Shengli Oilfield Central Hospital, Dongying, Shandong, China
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13
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Wang Q, Zhang YF, Li CL, Wang Y, Wu L, Wang XR, Huang T, Liu GL, Chen X, Yu Q, He PF. Integrating scRNA-seq and bulk RNA-seq to characterize infiltrating cells in the colorectal cancer tumor microenvironment and construct molecular risk models. Aging (Albany NY) 2023; 15:13799-13821. [PMID: 38054820 PMCID: PMC10756133 DOI: 10.18632/aging.205263] [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: 08/04/2023] [Accepted: 10/19/2023] [Indexed: 12/07/2023]
Abstract
Colorectal cancer (CRC) is a malignancy that is both highly lethal and heterogeneous. Although the correlation between intra-tumoral genetic and functional heterogeneity and cancer clinical prognosis is well-established, the underlying mechanism in CRC remains inadequately understood. Utilizing scRNA-seq data from GEO database, we re-isolated distinct subsets of cells, constructed a CRC tumor-related cell differentiation trajectory, and conducted cell-cell communication analysis to investigate potential interactions across cell clusters. A prognostic model was built by integrating scRNA-seq results with TCGA bulk RNA-seq data through univariate, LASSO, and multivariate Cox regression analyses. Eleven distinct cell types were identified, with Epithelial cells, Fibroblasts, and Mast cells exhibiting significant differences between CRC and healthy controls. T cells were observed to engage in extensive interactions with other cell types. Utilizing the 741 signature genes, prognostic risk score model was constructed. Patients with high-risk scores exhibited a significant correlation with unfavorable survival outcomes, high-stage tumors, metastasis, and low responsiveness to chemotherapy. The model demonstrated a strong predictive performance across five validation cohorts. Our investigation involved an analysis of the cellular composition and interactions of infiltrates within the microenvironment, and we developed a prognostic model. This model provides valuable insights into the prognosis and therapeutic evaluation of CRC.
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Affiliation(s)
- Qi Wang
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
- Shanxi Key Laboratory of Big Data for Clinical Decision Research, Taiyuan, China
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, China
| | - Yi-Fan Zhang
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, China
- The First clinical Medical College, Shanxi medical University, Taiyuan, China
| | - Chen-Long Li
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
- Shanxi Key Laboratory of Big Data for Clinical Decision Research, Taiyuan, China
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, China
| | - Yang Wang
- Shanxi Key Laboratory of Big Data for Clinical Decision Research, Taiyuan, China
- School of Management, Shanxi Medical University, Taiyuan, China
| | - Li Wu
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
- Department of Anesthesiology, Shanxi Provincial People's Hospital (Fifth Hospital) of Shanxi Medical University, Taiyuan, China
| | - Xing-Ru Wang
- The Fifth Clinical Medical School, Shanxi Medical University, Taiyuan, China
| | - Tai Huang
- Shanxi Key Laboratory of Big Data for Clinical Decision Research, Taiyuan, China
- School of Management, Shanxi Medical University, Taiyuan, China
| | - Ge-Liang Liu
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
- Shanxi Key Laboratory of Big Data for Clinical Decision Research, Taiyuan, China
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, China
| | - Xing Chen
- Department of Gastroenterology, The First Hospital of Shanxi Medical University, Taiyuan, China
| | - Qi Yu
- Shanxi Key Laboratory of Big Data for Clinical Decision Research, Taiyuan, China
- School of Management, Shanxi Medical University, Taiyuan, China
| | - Pei-Feng He
- Shanxi Key Laboratory of Big Data for Clinical Decision Research, Taiyuan, China
- School of Management, Shanxi Medical University, Taiyuan, China
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14
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Liu Y, Pang Z, Wang J, Wang J, He J, Ji B, Zhang L, Ren M. Heat shock protein family A member 8 is a prognostic marker for bladder cancer: Evidences based on experiments and machine learning. J Cell Mol Med 2023; 27:3995-4008. [PMID: 37771276 PMCID: PMC10746959 DOI: 10.1111/jcmm.17977] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/03/2023] [Accepted: 09/16/2023] [Indexed: 09/30/2023] Open
Abstract
Heat shock protein member 8 (HSPA8) is one of the most abundant chaperones in eukaryotic cells, but its biological roles in bladder cancer (BC) are largely unclear. First, we observed that HSPA8 was abundant in both cell lines and tissues of BC, and the HSPA8-high group had poorer T stages and overall survival (OS) than the HSPA8-low group in the TCGA patients. Next, when we knocked down HSPA8 in BC cells, the growth and migration abilities were significantly decreased, the apoptosis rates were significantly increased, and the Ki67 fluorescence intensity was decreased in BC cells. Moreover, caspase 3 was significantly decreased with overexpression of HSPA8 in BC cells. After that, a machine learning prognostic model was created based on the expression of HSPA8 by applying LASSO Cox regression in TCGA and GEO patients. The model indicated that the low-risk (LR) group with BC had better tumour stages, lymphovascular invasion, and OS than the high-risk (HR) group. Additionally, the risk score was demonstrated to be an independent risk factor for the prognosis of BC by univariate and multivariate Cox analyses. Moreover, the HR group showed a greater rate of TP53 mutations and was mostly enriched in the ECM-receptor interaction pathway than the LR group. Importantly, lower CD8+ T-cell and NK cell infiltration, higher immune exclusion scores, higher expression of PD-L1 and CTLA4 and poorer immune checkpoint therapy effects were found in the HR group. These findings demonstrated how crucial HSPA8 plays a role in determining the prognosis of bladder cancer.
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Affiliation(s)
- Yang Liu
- Department of Urinary SurgeryFirst Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiangChina
| | - Zhong‐qi Pang
- Department of Urinary SurgeryFirst Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiangChina
| | - Jian‐she Wang
- Department of Urinary SurgeryFirst Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiangChina
| | - Jin‐feng Wang
- Department of Urinary SurgeryFirst Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiangChina
| | - Jia‐xin He
- Department of Urinary SurgeryFirst Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiangChina
| | - Bo Ji
- Department of Urinary SurgeryFirst Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiangChina
| | - Lu Zhang
- Department of Urinary SurgeryFirst Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiangChina
| | - Ming‐hua Ren
- Department of Urinary SurgeryFirst Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiangChina
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15
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Lu T, Wang Y, Liu F, Zhang L, Huang S, Zhou Y, Wu H, Mao Y, Jin C, Song W. Synergistic Inhibitory Effect of Berberine and Low-Temperature Plasma on Non-Small-Cell Lung Cancer Cells via PI3K-AKT-Driven Signaling Axis. Molecules 2023; 28:7797. [PMID: 38067530 PMCID: PMC10708101 DOI: 10.3390/molecules28237797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/28/2023] [Accepted: 11/14/2023] [Indexed: 12/18/2023] Open
Abstract
Low-temperature plasma (LTP) is an emerging biomedical technique that has been proposed as a potential approach for cancer therapy. Meanwhile, berberine (BER), an active ingredient extracted from various medical herbs, such as Coptischinesis, has been proven antitumor effects in a broad spectrum of cancer cells. In this study, we seek to develop a novel dual cancer therapeutic method by integrating pre-administration of BER and LTP exposure and evaluating its comprehensive antitumor effect on the human non-small-cell lung cancer (NSCLC) cell lines (A549 and H1299) in vitro. Cell viability, cell cycle, cell apoptosis, and intracellular and extracellular ROS were investigated. The results showed that cotreatment of BER and LTP significantly decreased the cell viability, arrested the cell cycle in the S phase, promoted cell apoptosis, and increased intracellular and extracellular ROS. Additionally, RNA Sequencing (RNA-Seq) technology was used to explore potential mechanisms. The differentially expressed genes among different treatment groups of NSCLC cells were analyzed and were mainly enriched in the phosphatidylinositol-3-kinase (PI3K)/protein kinase B (AKT) signaling pathway. Moreover, cotreatment of BER and LTP notably depressed the total protein expression level of PI3K and AKT with immunoblotting. In conclusion, BER and LTP have a synergistic inhibitory effect on NSCLC cells via the PI3K-AKT signaling pathway, which could provide a promising strategy for supplementary therapy in the anti-NSCLC battle.
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Affiliation(s)
- Tingting Lu
- Key Laboratory for the Application and Transformation of Traditional Chinese Medicine in the Prevention and Treatment of Major Pulmonary Diseases, Anhui University of Chinese Medicine, Hefei 230012, China; (T.L.); (Y.W.); (L.Z.); (S.H.); (Y.M.)
- Anhui Province Key Laboratory of Medical Physics, Institute of Health & Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China; (F.L.); (Y.Z.); (H.W.)
- Key Laboratory of Xin’an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Yu Wang
- Key Laboratory for the Application and Transformation of Traditional Chinese Medicine in the Prevention and Treatment of Major Pulmonary Diseases, Anhui University of Chinese Medicine, Hefei 230012, China; (T.L.); (Y.W.); (L.Z.); (S.H.); (Y.M.)
- Key Laboratory of Xin’an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Fang Liu
- Anhui Province Key Laboratory of Medical Physics, Institute of Health & Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China; (F.L.); (Y.Z.); (H.W.)
| | - Lu Zhang
- Key Laboratory for the Application and Transformation of Traditional Chinese Medicine in the Prevention and Treatment of Major Pulmonary Diseases, Anhui University of Chinese Medicine, Hefei 230012, China; (T.L.); (Y.W.); (L.Z.); (S.H.); (Y.M.)
- Key Laboratory of Xin’an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Simin Huang
- Key Laboratory for the Application and Transformation of Traditional Chinese Medicine in the Prevention and Treatment of Major Pulmonary Diseases, Anhui University of Chinese Medicine, Hefei 230012, China; (T.L.); (Y.W.); (L.Z.); (S.H.); (Y.M.)
- Key Laboratory of Xin’an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Yuanyuan Zhou
- Anhui Province Key Laboratory of Medical Physics, Institute of Health & Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China; (F.L.); (Y.Z.); (H.W.)
| | - Hui Wu
- Anhui Province Key Laboratory of Medical Physics, Institute of Health & Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China; (F.L.); (Y.Z.); (H.W.)
| | - Yanmei Mao
- Key Laboratory for the Application and Transformation of Traditional Chinese Medicine in the Prevention and Treatment of Major Pulmonary Diseases, Anhui University of Chinese Medicine, Hefei 230012, China; (T.L.); (Y.W.); (L.Z.); (S.H.); (Y.M.)
- Key Laboratory of Xin’an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Chufeng Jin
- Key Laboratory of Neutronics and Radiation Safety, Chinese Academy of Sciences, Hefei 230031, China
- International Academy of Neutron Science, Qingdao 266199, China
| | - Wencheng Song
- Anhui Province Key Laboratory of Medical Physics, Institute of Health & Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China; (F.L.); (Y.Z.); (H.W.)
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16
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Zhang P, Zhang H, Tang J, Ren Q, Zhang J, Chi H, Xiong J, Gong X, Wang W, Lin H, Li J, Huang C. The integrated single-cell analysis developed an immunogenic cell death signature to predict lung adenocarcinoma prognosis and immunotherapy. Aging (Albany NY) 2023; 15:10305-10329. [PMID: 37796202 PMCID: PMC10599752 DOI: 10.18632/aging.205077] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/06/2023] [Indexed: 10/06/2023]
Abstract
BACKGROUND Research on immunogenic cell death (ICD) in lung adenocarcinoma (LUAD) has been relatively limited. This study aims to create ICD-related signatures for accurate survival prognosis prediction in LUAD patients, addressing the challenge of lacking reliable early prognostic indicators for this type of cancer. METHODS Using single-cell RNA sequencing (scRNA-seq) analysis, ICD activity in cells was calculated by AUCell algorithm, divided into high- and low-ICD groups according to median values, and key ICD regulatory genes were identified through differential analysis, and these genes were integrated into TCGA data to construct prognostic signatures using LASSO and COX regression analysis, and multi-dimensional analysis of ICD-related signatures in terms of prognosis, immunotherapy, tumor microenvironment (TME), and mutational landscape. RESULTS The constructed signature reveals a pronounced disparity in prognosis between the high- and low-risk groups of LUAD patients. The statistical discrepancies in survival times among LUAD patients from both the TCGA and GEO databases further corroborate this observation. Additionally, heightened levels of immune cell infiltration expression are evidenced in the low-risk group, suggesting a potential benefit from immunotherapeutic interventions for these patients. The expression levels of pivotal risk-associated genes in tissue samples were assessed utilizing qRT-PCR, thereby unveiling PITX3 as a plausible therapeutic target in the context of LUAD. CONCLUSIONS Our constructed ICD-related signatures provide help in predicting the prognosis and immunotherapy of LUAD patients, and to some extent guide the clinical treatment of LUAD patients.
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Affiliation(s)
- Pengpeng Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Lung Cancer Surgery, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Haotian Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Junjie Tang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qianhe Ren
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jieying Zhang
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Hao Chi
- Clinical Medical College, Southwest Medical University, Luzhou, China
| | - Jingwen Xiong
- Department of Sports Rehabilitation, Southwest Medical University, Luzhou, China
| | - Xiangjin Gong
- Department of Sports Rehabilitation, Southwest Medical University, Luzhou, China
| | - Wei Wang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Haoran Lin
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jun Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chenjun Huang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Yang L, Wei Q, Sun Y, Guo J, Xu X, Zhang Z, Zhu L, Zheng X, Liu F, Wu J, Xie X, Lin S, Li H, Wu S. Hyperuricemia and coronary heart disease: The mediating role of blood pressure and thrombospondin 3. Nutr Metab Cardiovasc Dis 2023; 33:1969-1980. [PMID: 37524613 DOI: 10.1016/j.numecd.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/07/2023] [Accepted: 06/01/2023] [Indexed: 08/02/2023]
Abstract
BACKGROUND & AIMS Although hyperuricemia is a known risk factor for coronary heart disease (CHD), little is known about the role of blood pressure in mediating this association. The purpose of this study is to investigate the role of blood pressure-related indicators and Thrombospondin 3 (THBS3) in the association between hyperuricemia and CHD. METHODS AND RESULTS Our observational epidemiology study included 593 CHD cases and 760 controls from a residential stable sample. We also chose 43 new CHD patients and 43 controls to test the expression levels of THBS3 using ELISA kits. We used logistic regression models and mediating effect analysis to investigate the relationships between hyperuricemia and CHD, as well as the mediating role of blood pressure-related indicators and THBS3. In the general population (OR: 2.001 [95% CI: 1.528-2.622]), male population (OR: 1.591 [95% CI: 1.119-2.262]), and female population (OR: 2.813 [95% CI: 1.836-4.310]), hyperuricemia is an independent risk factor for CHD. In general, average systolic blood pressure (SBP) and average pulse pressure difference (PPD) mediated 3.35% and 4.59%, respectively, of the association between hyperuricemia and CHD, and 6.60% and 6.60% in women. However, in the male population, we have not yet found that blood pressure-related indicators had a significant mediating effect. Meanwhile, we found that THBS3 mediated 19.23% of the association between hyperuricemia and CHD. CONCLUSIONS Average SBP, PPD, and THBS3 all play a role in the association of hyperuricemia and CHD. In the female population, similar mediating results in blood pressure-related indicators were observed.
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Affiliation(s)
- Le Yang
- School of Public Health, Fujian Medical University, Fujian, China
| | - Qinfei Wei
- School of Public Health, Fujian Medical University, Fujian, China
| | - Yu Sun
- School of Public Health, Fujian Medical University, Fujian, China
| | - Jianhui Guo
- School of Public Health, Fujian Medical University, Fujian, China
| | - Xingyan Xu
- School of Public Health, Fujian Medical University, Fujian, China
| | - Zhiyu Zhang
- School of Public Health, Fujian Medical University, Fujian, China
| | - Li Zhu
- School of Public Health, Fujian Medical University, Fujian, China
| | - Xiaofeng Zheng
- School of Public Health, Fujian Medical University, Fujian, China
| | - Fang Liu
- School of Public Health, Fujian Medical University, Fujian, China
| | - Jiadong Wu
- School of Public Health, Fujian Medical University, Fujian, China
| | - XiaoXu Xie
- School of Public Health, Fujian Medical University, Fujian, China
| | - Shaowei Lin
- School of Public Health, Fujian Medical University, Fujian, China
| | - Huangyuan Li
- School of Public Health, Fujian Medical University, Fujian, China
| | - Siying Wu
- School of Public Health, Fujian Medical University, Fujian, China.
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Xu X, Zhang X, Lin Q, Qin Y, Liu Y, Tang W. Integrated single-cell and bulk RNA sequencing analysis identifies a prognostic signature related to ferroptosis dependence in colorectal cancer. Sci Rep 2023; 13:12653. [PMID: 37542061 PMCID: PMC10403602 DOI: 10.1038/s41598-023-39412-y] [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: 11/02/2022] [Accepted: 07/25/2023] [Indexed: 08/06/2023] Open
Abstract
Ferroptosis is an iron-dependent form of cell death induced by lipid oxidation with an essential role in diseases, including cancer. Since prognostic value of ferroptosis-dependent related genes (FDRGs) in colorectal cancer (CRC) remains unclear, we explored the significance of FDRGs in CRC through comprehensive single-cell analysis. We downloaded the GSE161277 dataset for single-cell analyses and calculated the ferroptosis-dependent gene score (FerrScore) for each cell type. According to each cell type-specific median FerrScore, we categorized the cells into low- and high-ferroptosis groups. By analyzing differentially-expressed genes across the two groups, we identified FDRGs. We further screened these prognosis-related genes used to develop a prognostic signature and calculated its correlation with immune infiltration. We also compared immune checkpoint gene efficacy among different risk groups, and qRT-PCR was performed in colorectal normal and cancer cell lines to explore whether the signature genes could be used as clinical prognostic indicators. In total, 523 FDRGs were identified. A prognostic signature including five signature genes was constructed, and patients were divided into two risk groups. The high-risk group had poor survival rates and displayed high levels of immune infiltration. Our newly developed ferroptosis-based prognostic signature possessed a high predictive ability for CRC.
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Affiliation(s)
- Xiaochen Xu
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
| | - Xinwen Zhang
- Department of Gastrointestinal Surgery, Affiliated Hospital of Guilin Medical University, Guilin, 541001, Guangxi Zhuang Autonomous Region, China
| | - Qiumei Lin
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
| | - Yuling Qin
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
| | - Yihao Liu
- Department of Gastrointestinal Surgery, Affiliated Hospital of Guilin Medical University, Guilin, 541001, Guangxi Zhuang Autonomous Region, China
| | - Weizhong Tang
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi Zhuang Autonomous Region, China.
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Lausten MA, Boman BM. A Review of IsomiRs in Colorectal Cancer. Noncoding RNA 2023; 9:34. [PMID: 37368334 DOI: 10.3390/ncrna9030034] [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: 04/29/2023] [Revised: 05/26/2023] [Accepted: 06/02/2023] [Indexed: 06/28/2023] Open
Abstract
As advancements in sequencing technology rapidly continue to develop, a new classification of microRNAs has occurred with the discovery of isomiRs, which are relatively common microRNAs with sequence variations compared to their established template microRNAs. This review article seeks to compile all known information about isomiRs in colorectal cancer (CRC), which has not, to our knowledge, been gathered previously to any great extent. A brief overview is given of the history of microRNAs, their implications in colon cancer, the canonical pathway of biogenesis and isomiR classification. This is followed by a comprehensive review of the literature that is available on microRNA isoforms in CRC. The information on isomiRs presented herein shows that isomiRs hold great promise for translation into new diagnostics and therapeutics in clinical medicine.
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Affiliation(s)
- Molly A Lausten
- Cawley Center for Translational Cancer Research, Helen F. Graham Cancer Center & Research Institute, Newark, DE 19713, USA
- Department of Biological Sciences, University of Delaware, Newark, DE 19713, USA
| | - Bruce M Boman
- Cawley Center for Translational Cancer Research, Helen F. Graham Cancer Center & Research Institute, Newark, DE 19713, USA
- Department of Biological Sciences, University of Delaware, Newark, DE 19713, USA
- Department of Pharmacology & Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA 19107, USA
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Zhao Y, Liang X, Duan X, Zhang C. Exploring the prognostic function of TMB-related prognostic signature in patients with colon cancer. BMC Med Genomics 2023; 16:116. [PMID: 37237274 DOI: 10.1186/s12920-023-01555-2] [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: 02/27/2023] [Accepted: 05/21/2023] [Indexed: 05/28/2023] Open
Abstract
Tumor mutation burden (TMB) level is identified as a useful predictor in multiple tumors including colon adenocarcinoma (COAD). However, the function of TMB related genes has not been explored previously. In this study, we obtained patients' expression and clinical data from The Cancer Genome Atlas (TCGA) and the National Center for Biotechnology Information (NCBI). TMB genes were screened and subjected to differential expression analysis. Univariate Cox and LASSO analyses were utilized to construct the prognostic signature. The efficiency of the signature was tested by using a receiver operating characteristic (ROC) curve. A nomogram was further plotted to assess the overall survival (OS) time of patients with COAD. In addition, we compared the predictive performance of our signature with other four published signatures. Functional analyses indicated that patients in the low-risk group have obviously different enrichment of tumor related pathways and tumor infiltrating immune cells from that of high-risk patients. Our findings suggested that the ten genes' prognostic signature could exert undeniable prognostic functions in patients with COAD, which might provide significant clues for the development of personalized management of these patients.
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Affiliation(s)
- Yan Zhao
- Department of Nuclear Medicine, Zigong First People's Hospital, Zigong, 643000, Sichuan, PR China
| | - Xiaolong Liang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, PR China
| | - Xudong Duan
- Oncology Department, Zigong First People's Hospital, Zigong, 643000, Sichuan, PR China.
| | - Chengli Zhang
- Department of Nuclear Medicine, Zigong First People's Hospital, Zigong, 643000, Sichuan, PR China.
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21
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Liu T, Sun L, Li ZZ, Yang K, Chen JM, Han XY, Qi LM, Zhou XG, Wang P. The m6A/m5C/m1A regulator genes signature reveals the prognosis and is related with immune microenvironment for hepatocellular carcinoma. BMC Gastroenterol 2023; 23:147. [PMID: 37170222 PMCID: PMC10173529 DOI: 10.1186/s12876-023-02776-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 04/20/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND RNA methylation is a crucial in many biological functions, and its aberrant regulation is associated with cancer progression. N6-Methyladenosine (m6A), 5-Methylcytosine (m5C), N1-methyladenosine (m1A) are common modifications of RNA methylation. However, the effect of methylation of m6A/m5C/m1A in hepatocellular carcinoma (HCC) remains unclear. METHOD The transcriptome datasets, clinic information, and mutational data of 48 m6A/m5C/m1A regulator genes were acquired from the TCGA database, and the prognostic hazard model was established by univariate and Least absolute shrinkage and selection operator (Lasso) regression. The multivariate regression was performed to determine whether the risk score was an independent prognostic indicator. Kaplan-Meier survival analysis and ROC curve analysis were used to evaluate the predictive ability of the risk model. Decision curve analysis(DCA)analysis was conducted to estimate the clinical utility of the risk model. We further analyzed the association between risk score and functional enrichment, tumor immune microenvironment, and somatic mutation. RESULT The four-gene (YTHDF1, YBX1, TRMT10C, TRMT61A) risk signature was constructed. The high-risk group had shorter overall survival (OS) than the low-risk group. Univariate and multivariate regression analysis indicated that risk score was an independent prognostic indicator. Risk scores in male group, T3 + T4 group and Stage III + IV group were higher in female group, T1 + T2 group and stage I + II group. The AUC values for 1-, 2-, and 3-year OS in the TCGA dataset were 0.764, 0.693, and 0.689, respectively. DCA analysis showed that the risk score had a higher clinical net benefit in 1- and 2-year OS than other clinical features.The risk score was positively related to some immune cell infiltration and most immune checkpoints. CONCLUSION We developed a novel m6A/m5C/m1A regulator genes' prognostic model, which could be applied as a latent prognostic tool for HCC and might guide the choice of immunotherapies.
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Affiliation(s)
- Ting Liu
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, People's Republic of China
| | - Lei Sun
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, People's Republic of China
| | - Zhi-Zhao Li
- Department of Cardiovascular, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, People's Republic of China
| | - Kun Yang
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, People's Republic of China
| | - Jia-Min Chen
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, People's Republic of China
| | - Xiao-Yi Han
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, People's Republic of China
| | - Li-Ming Qi
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, People's Republic of China
| | - Xin-Gang Zhou
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, People's Republic of China.
| | - Peng Wang
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, No. 8 Jing Shun East Street, Chaoyang District, Beijing, 100015, People's Republic of China.
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Huang Y, Lei X, Sun L, Liu Y, Yang J. Leveraging various extracellular matrix levels to assess prognosis and sensitivity to immunotherapy in patients with ovarian cancer. Front Oncol 2023; 13:1163695. [PMID: 37228494 PMCID: PMC10203472 DOI: 10.3389/fonc.2023.1163695] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 04/18/2023] [Indexed: 05/27/2023] Open
Abstract
Background Ovarian cancer (OC) is the fifth leading cause of cancer-related deaths among women. Late diagnosis and heterogeneous treatment result in a poor prognosis for patients with OC. Therefore, we aimed to develop new biomarkers to predict accurate prognoses and provide references for individualized treatment strategies. Methods We constructed a co-expression network applying the "WGCNA" package and identified the extracellular matrix-associated gene modules. We figured out the best model and generated the extracellular matrix score (ECMS). The ECMS' ability to predict accurate OC patients' prognoses and responses to immunotherapy was evaluated. Results The ECMS was an independent prognostic factor in the training [hazard ratio (HR) = 3.132 (2.068-4.744), p< 0.001] and testing sets [HR = 5.514 (2.084-14.586), p< 0.001]. The receiver operating characteristic curve (ROC) analysis showed that the AUC values for 1, 3, and 5 years were 0.528, 0.594, and 0.67 for the training set, respectively, and 0.571, 0.635, and 0.684 for the testing set, respectively. It was found that the high ECMS group had shorter overall survival than the low ECMS group [HR = 2 (1.53-2.61), p< 0.001 in the training set; HR = 1.62 (1.06-2.47), p = 0.021 in the testing set; HR = 1.39 (1.05-1.86), p = 0.022 in the training set]. The ROC values of the ECMS model for predicting immune response were 0.566 (training set) and 0.572 (testing set). The response rate to immunotherapy was higher in patients with low ECMS. Conclusion We created an ECMS model to predict the prognosis and immunotherapeutic benefits in OC patients and provided references for individualized treatment of OC patients.
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Affiliation(s)
- Youqun Huang
- Department of Nephrology-2, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Xingxing Lei
- Department of Endocrinology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Lisha Sun
- Department of Endocrinology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Yu Liu
- Department of Nephrology, South China Hospital, Health Science Center, Shenzhen University, Shenzhen, China
| | - Jiao Yang
- Department of Endocrinology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
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Ye J, Feng JW, Wu WX, Qi GF, Wang F, Hu J, Hong LZ, Liu SY, Jiang Y. Microarray profiling identifies hsa_circ_0082003 as a novel tumor promoter for papillary thyroid carcinoma. J Endocrinol Invest 2023; 46:509-522. [PMID: 36115894 DOI: 10.1007/s40618-022-01922-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/11/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Circular RNAs (circRNAs) are non-coding RNAs that have essential regulatory roles in the development of various tumors. This study explored whether circRNAs are involved in the progression of papillary thyroid carcinoma (PTC). METHODS Differentially expressed circRNAs (DECs) in four pairs of PTC and matched normal thyroid tissues were screened using a circRNA microarray. The potential functions of dysregulated circRNAs were predicted by bioinformatic analyses. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) was used to determine hsa_circ_0082003 expression in 80 pairs of PTC and matched normal thyroid tissues. Cell counting kit-8, colony formation, wound healing, and Transwell assays were performed to evaluate the biological functions of hsa_circ_0082003 in PTC cells. The role of hsa_circ_0082003 in PTC tumorigenesis in vivo was validated in nude mice. RESULTS In total, 3150 DECs (2317 upregulated and 833 downregulated) were identified. Pathway enrichment analyses indicated that the dysregulated circRNAs may play roles in PTC development. RT-qPCR validation demonstrated that hsa_circ_0082003 expression was significantly increased in PTC tissues and correlated with poor clinicopathological parameters. Receiver operating characteristic curve analysis showed that hsa_circ_0082003 had good performance for diagnosing PTC and judging whether it was accompanied by lymph node metastasis. Knockdown of hsa_circ_0082003 inhibited PTC cell proliferation, migration, and invasion. Tumor formation assays in vivo showed that downregulation of hsa_circ_0082003 significantly suppressed the growth of PTC. CONCLUSION Hsa_circ_0082003 may serve as a novel diagnostic biomarker and potential therapeutic target for PTC.
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Affiliation(s)
- J Ye
- Department of Thyroid Surgery, The Third Affiliated Hospital of Soochow University, Changzhou First People's Hospital, Changzhou, Jiangsu, China
| | - J-W Feng
- Department of Thyroid Surgery, The Third Affiliated Hospital of Soochow University, Changzhou First People's Hospital, Changzhou, Jiangsu, China
| | - W-X Wu
- Department of Thyroid Surgery, The Third Affiliated Hospital of Soochow University, Changzhou First People's Hospital, Changzhou, Jiangsu, China
| | - G-F Qi
- Department of Thyroid Surgery, The Third Affiliated Hospital of Soochow University, Changzhou First People's Hospital, Changzhou, Jiangsu, China
| | - F Wang
- Department of Thyroid Surgery, The Third Affiliated Hospital of Soochow University, Changzhou First People's Hospital, Changzhou, Jiangsu, China
| | - J Hu
- Department of Thyroid Surgery, The Third Affiliated Hospital of Soochow University, Changzhou First People's Hospital, Changzhou, Jiangsu, China
| | - L-Z Hong
- Department of Thyroid Surgery, The Third Affiliated Hospital of Soochow University, Changzhou First People's Hospital, Changzhou, Jiangsu, China
| | - S-Y Liu
- Department of Thyroid Surgery, The Third Affiliated Hospital of Soochow University, Changzhou First People's Hospital, Changzhou, Jiangsu, China
| | - Y Jiang
- Department of Thyroid Surgery, The Third Affiliated Hospital of Soochow University, Changzhou First People's Hospital, Changzhou, Jiangsu, China.
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Qin H, Zhang H, Li H, Xu Q, Sun W, Zhang S, Zhang X, Zhu S, Wang H. Prognostic risk analysis related to radioresistance genes in colorectal cancer. Front Oncol 2023; 12:1100481. [PMID: 36741692 PMCID: PMC9890073 DOI: 10.3389/fonc.2022.1100481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/29/2022] [Indexed: 01/19/2023] Open
Abstract
Background Radiotherapy (RT) is one of the most important treatments for patients with colorectal cancer (CRC). Radioresistance is the crucial cause of poor therapeutic outcomes in colorectal cancer. However, the underlying mechanism of radioresistance in colorectal cancer is still poorly defined. Herein we established a radioresistant colorectal cancer cell line and performed transcriptomics analyses to search for the underlying genes that contribute to radioresistance and investigate its association with the prognosis of CRC patients. Methods The radioresistant cell line was developed from the parental HCT116 cell by a stepwise increased dose of irradiation. Differential gene analysis was performed using cellular transcriptome data to identify genes associated with radioresistance, from which extracellular matrix (ECM) and cell adhesion-related genes were screened. Survival data from a CRC cohort in the TCGA database were used for further model gene screening and validation. The correlation between the risk score model and tumor microenvironment, clinical phenotype, drug treatment sensitivity, and tumor mutation status were also investigated. Results A total of 493 different expression genes were identified from the radioresistant and wild-type cell line, of which 94 genes were associated with ECM and cell adhesion-related genes. The five model genes TNFRSF13C, CD36, ANGPTL4, LAMB3, and SERPINA1 were identified for CRC radioresistance via screening using the best model. A ROC curve indicated that the AUC of the resulting prognostic model (based on the 5-gene risk score and other clinical parameters, including age, sex, and tumor stages) was 0.79, 0.77, and 0.78 at 1, 2, and 3 years, respectively. The calibration curve showed high agreement between the risk score prediction and actual survival probability. The immune microenvironment, drug treatment sensitivity, and tumor mutation status significantly differed between the high- and low-risk groups. Conclusions The risk score model built with five radioresistance genes in this study, including TNFRSF13C, CD36, ANGPTL4, LAMB3, and SERPINA1, showed favorable performance in prognosis prediction after radiotherapy for CRC.
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Affiliation(s)
- Haoren Qin
- Department of Oncology, Tianjin Union Medical Center, Nankai University, Tianjin, China,School of Medicine, Nankai University, Tianjin, China
| | - Heng Zhang
- Department of Oncology, Tianjin Union Medical Center, Nankai University, Tianjin, China
| | - Haipeng Li
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Qiong Xu
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Wanjun Sun
- Department of Oncology, Tianjin Union Medical Center, Nankai University, Tianjin, China
| | - Shiwu Zhang
- Department of Pathology, Tianjin Union Medical Center, Nankai University, Tianjin, China
| | - Xipeng Zhang
- Department of Colorectal Surgery, Tianjin Union Medical Center, Nankai University, Tianjin, China
| | - Siwei Zhu
- Department of Oncology, Tianjin Union Medical Center, Nankai University, Tianjin, China
| | - Hui Wang
- Department of Oncology, Tianjin Union Medical Center, Nankai University, Tianjin, China,*Correspondence: Hui Wang,
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Deng Y, Lu L, Liang X, Li J, Zhu D, Huang H, Zhang Y, Zhang X, Chen Y, Liu X, Fu Y. DNA methylation-mediated silencing of Neuronatin promotes hepatocellular carcinoma proliferation through the PI3K-Akt signaling pathway. Life Sci 2023; 312:121266. [PMID: 36473542 DOI: 10.1016/j.lfs.2022.121266] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
AIMS To explore the methylation status, function, and underlying mechanism of the imprinted gene Neuronatin (NNAT) in hepatocellular carcinoma (HCC) progression. MAIN METHODS Immunohistochemistry (IHC) was performed to evaluate the expression of NNAT in HCC samples. Bisulfite genomic sequencing PCR (BSP) was applied to examine the methylation status of the NNAT promoter. In addition, colony formation, 5-Ethynyl-20-deoxyuridine (EdU) assays and subcutaneous xenograft nude models were used to explore the roles of NNAT in HCC cell proliferation. Furthermore, RNA-seq and phospho-specific protein microarray assays were conducted to illustrate the underlying mechanism by which NNAT regulates HCC progression. KEY FINDINGS NNAT was obviously downregulated in HCC tissues, and its expression level was closely associated with tumor growth and patient prognosis. The downregulation of NNAT in HCC was induced by hypermethylation of CpG islands in the promoter region, and hypermethylation was correlated with overall survival of HCC. Moreover, the enforced expression of NNAT significantly inhibited HCC cell proliferation in vitro and in vivo. Transcriptome analysis showed that the alteration of NNAT expression was mainly related to dysregulation of the PI3K-Akt signaling pathway. Finally, phospho-specific antibody microarray detection further revealed that overexpressed NNAT can increase the phosphorylation levels of LKB1, Met, and elF4E and decrease the phosphorylation levels of PTEN, which are all involved in the PI3K-Akt signaling pathway. SIGNIFICANCE Our research provides new insights into the epigenetic regulation of imprinted genes in tumorigenesis and implies that the imprinted gene NNAT may act as a prognostic biomarker and tumor suppressor in HCC.
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Affiliation(s)
- Yalan Deng
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Liqing Lu
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Xujun Liang
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Jingzhi Li
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; Department of Obstetrics, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Dandan Zhu
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Huichao Huang
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; Department of Infectious Disease, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Ye Zhang
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Xiangqian Zhang
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Yongheng Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Xiaojin Liu
- Department of Plastic Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
| | - Ying Fu
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
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Ning Y, Lin K, Fang J, Ding Y, Zhang Z, Chen X, Zhao Q, Wang H, Wang F. Gastrointestinal pan-cancer landscape of tumor matrix heterogeneity identifies biologically distinct matrix stiffness subtypes predicting prognosis and chemotherapy efficacy. Comput Struct Biotechnol J 2023; 21:2744-2758. [PMID: 37181656 PMCID: PMC10173364 DOI: 10.1016/j.csbj.2023.04.016] [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: 01/15/2023] [Revised: 04/18/2023] [Accepted: 04/18/2023] [Indexed: 05/16/2023] Open
Abstract
Gastrointestinal (GI) cancers are a heterogeneous group of primary solid tumors, arising in GI tract from the esophagus to rectum. Matrix stiffness (MS) is a critical physical factor for cancer progression; however, its importance in tumor progression remains to be comprehensively recognized. Herein, we conducted a comprehensive pan-cancer analysis of MS subtypes across seven GI-cancer types. Using unsupervised clustering based on literature-derived MS-specific pathway signatures, the GI-tumor samples were divided into three MS subtypes, termed as the Soft, Mixed and Stiff. Then, distinct prognoses, biological features, tumor microenvironments and mutation landscapes among three MS subtypes were revealed. The Stiff tumor subtype was associated with the poorest prognosis, the most malignant biological behaviors, and the immunosuppressive tumor stromal microenvironment. Furthermore, multiple machine learning algorithms were used to develop an 11-gene MS-signature to identify the MS subtypes of GI-caner and predict chemotherapy sensitivity, which were further validated in two external GI-cancer cohorts. This novel MS-based classification on GI-cancers could enhance our understanding of the important role of MS in tumor progression, and may have implications for the optimization of individualized cancer management.
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Affiliation(s)
- Yumei Ning
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Kun Lin
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jun Fang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yang Ding
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Zhang Zhang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Xiaojia Chen
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Qiu Zhao
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
- Corresponding authors at: Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Haizhou Wang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
- Corresponding authors at: Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Fan Wang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
- Corresponding authors at: Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
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TGF-β Pathways Stratify Colorectal Cancer into Two Subtypes with Distinct Cartilage Oligomeric Matrix Protein (COMP) Expression-Related Characteristics. Biomolecules 2022; 12:biom12121877. [PMID: 36551305 PMCID: PMC9775768 DOI: 10.3390/biom12121877] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Colorectal cancers (CRCs) continue to be the leading cause of cancer-related deaths worldwide. The exact landscape of the molecular features of TGF-β pathway-inducing CRCs remains uncharacterized. METHODS Unsupervised hierarchical clustering was performed to stratify samples into two clusters based on the differences in TGF-β pathways. Weighted gene co-expression network analysis was applied to identify the key gene modules mediating the different characteristics between two subtypes. An algorithm integrating the least absolute shrinkage and selection operator (LASSO), XGBoost, and random forest regression was performed to narrow down the candidate genes. Further bioinformatic analyses were performed focusing on COMP-related immune infiltration and functions. RESULTS The integrated machine learning algorithm identified COMP as the hub gene, which exhibited a significant predictive value for two subtypes with an area under the curve (AUC) value equaling 0.91. Further bioinformatic analysis revealed that COMP was significantly upregulated in various cancers, especially in advanced CRCs, and regulated the immune infiltration, especially M2 macrophages and cancer-associated fibroblasts in CRCs. CONCLUSIONS Comprehensive immune analysis and experimental validation demonstrate that COMP is a reliable signature for subtype prediction. Our results could provide a new point for TGFβ-targeted anticancer drugs and contribute to guiding clinical decision making for CRC patients.
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Wu J, Zhang L, Kuchi A, Otohinoyi D, Hicks C. CpG Site-Based Signature Predicts Survival of Colorectal Cancer. Biomedicines 2022; 10:biomedicines10123163. [PMID: 36551919 PMCID: PMC9776399 DOI: 10.3390/biomedicines10123163] [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: 10/29/2022] [Revised: 11/26/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND A critical unmet medical need in clinical management of colorectal cancer (CRC) pivots around lack of noninvasive and or minimally invasive techniques for early diagnosis and prognostic prediction of clinical outcomes. Because DNA methylation can capture the regulatory landscape of tumors and can be measured in body fluids, it provides unparalleled opportunities for the discovery of early diagnostic and prognostics markers predictive of clinical outcomes. Here we investigated use of DNA methylation for the discovery of potential clinically actionable diagnostic and prognostic markers for predicting survival in CRC. METHODS We analyzed DNA methylation patterns between tumor and control samples to discover signatures of CpG sites and genes associated with CRC and predictive of survival. We conducted functional analysis to identify molecular networks and signaling pathways driving clinical outcomes. RESULTS We discovered a signature of aberrantly methylated genes associated with CRC and a signature of thirteen (13) CpG sites predictive of survival. We discovered molecular networks and signaling pathways enriched for CpG sites likely to drive clinical outcomes. CONCLUSIONS The investigation revealed that CpG sites can predict survival in CRC and that DNA methylation can capture the regulatory state of tumors through aberrantly methylated molecular networks and signaling pathways.
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Affiliation(s)
- Jiande Wu
- Department of Genetics and the Bioinformatics and Genomics Program, School of Medicine, Louisiana State University Health Sciences Center, Bolivar 533, New Orleans, LA 70112, USA
| | - Lu Zhang
- Department of Public Health Sciences, Clemson University, Clemson, SC 29634, USA
| | - Aditi Kuchi
- Department of Genetics and the Bioinformatics and Genomics Program, School of Medicine, Louisiana State University Health Sciences Center, Bolivar 533, New Orleans, LA 70112, USA
| | - David Otohinoyi
- Department of Genetics and the Bioinformatics and Genomics Program, School of Medicine, Louisiana State University Health Sciences Center, Bolivar 533, New Orleans, LA 70112, USA
| | - Chindo Hicks
- Department of Genetics and the Bioinformatics and Genomics Program, School of Medicine, Louisiana State University Health Sciences Center, Bolivar 533, New Orleans, LA 70112, USA
- Correspondence:
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Cheng J, Chen F, Cheng Y. Construction and Evaluation of a Risk Score Model for Lymph Node Metastasis-Associated Circadian Clock Genes in Esophageal Squamous Carcinoma. Cells 2022; 11:cells11213432. [PMID: 36359828 PMCID: PMC9655457 DOI: 10.3390/cells11213432] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/19/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022] Open
Abstract
Background: Studies suggested that circadian clock genes (CCGs) in human esophageal squamous carcinoma (ESCC) samples are dysregulated. However, the relevance of CCGs to lymph node metastasis (LNM) and prognosis of ESCC remains unclear. Methods: The differentially expressed genes (DEGs) between normal and ESCC samples in The Cancer Genome Atlas database (TCGA) database were intersected with the genes associated with LNM (LNMGs) in ESCC samples and 300 CCGs to obtain the differentially expressed LNM-associated CCGs (DE-LNM-CCGs). The risk model was constructed by Cox regression analysis in the TCGA-ESCC training set, and the accuracy of the risk model was verified by risk profile and overall survival profile. Furthermore, differences of 23 immune cells, 13 immune functions, and immune checkpoint molecules between the high- and low-risk groups were assessed using the single-sample gene set enrichment analysis (ssGSEA) algorithm. Gene set enrichment analysis (GSEA) was conducted to investigate the functional differences between low- and high-risk groups. Finally, we validated the mRNA expression levels of prognostic model genes by quantitative real-time polymerase chain reaction (qRT-PCR). Results: A total of six DE-LNM-CCGs were identified in TCGA-ESCC. TP53 and NAGLU were selected by Cox regression analysis to construct the risk model. Risk profile plots, overall survival plots, and validation results of the risk model in the validation set indicated that the constructed risk model was reliable. The result of ssGSEA showed that the percentages of activated B cells, activated dendritic cells, effector memory CD8 T cells, immune function in neutrophils, plasmacytoid dendritic cells, T cell co-inhibition, and Type 17 T helper cells were different between the high- and low-risk groups. In addition, the expression of CD274, PDCD1, TNFRSF18, and TNFRSF9 was dysregulated between the high- and low-risk groups. GSEA revealed that the high-risk group was associated with cell differentiation, oxidative phosphorylation, and steroid biosynthesis pathways, while the low-risk group was associated with chromosome, ECM–receptor interaction, and other pathways. Finally, qRT-PCR results showed that the mRNA expression levels of two prognostic genes were consistent with TCGA. Conclusion: In conclusion, the risk model constructed based on TP53 and NAGLU could accurately predict the prognosis.
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Affiliation(s)
- Jian Cheng
- Department of Cancer Center, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan 250033, China
| | - Fang Chen
- Department of Pharmacy, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan 250033, China
| | - Yufeng Cheng
- Department of Radiation Oncology, Qilu Hospital of Shandong University, No. 107 West Wenhua Road, Jinan 250012, China
- Correspondence:
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Li M, Zhang T, Chen W. Development of necroptosis-related gene signature to predict the prognosis of colon adenocarcinoma. Front Genet 2022; 13:1051800. [DOI: 10.3389/fgene.2022.1051800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 10/10/2022] [Indexed: 12/24/2022] Open
Abstract
Colon adenocarcinoma (COAD) is a common malignancy and has a high mortality rate. However, the current tumor node metastasis (TNM) staging system is inadequate for prognostic assessment of COAD patients. Therefore, there is an urgent need to identify reliable biomarkers for the prognosis COAD patients. The aberrant expression of necroptosis-related genes (NRGs) is reported to be associated with tumorigenesis and metastasis. In the present work, we compared the expression profiles of NRGs between COAD patients and normal individuals. Based on seven differentially expressed NRGs, a risk score was defined to predict the prognosis of COAD patients. The validation results from both training and independent external cohorts demonstrated that the risk score is able to distinguish the high and low risk COAD patients with higher accuracies, and is independent of the other clinical factors. To facilitate its clinical use, by integrating the proposed risk score, a nomogram was built to predict the risk of individual COAD patients. The C-index of the nomogram is 0.75, indicating the reliability of the nomogram in predicting survival rates. Furthermore, two candidate drugs, namely dapsone and xanthohumol, were screed out and validated by molecular docking, which hold the potential for the treatment of COAD. These results will provide novel clues for the diagnosis and treatment of COAD.
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Luan L, Dai Y, Shen T, Yang C, Chen Z, Liu S, Jia J, Li Z, Fang S, Qiu H, Cheng X, Yang Z. Development of a novel hypoxia-immune–related LncRNA risk signature for predicting the prognosis and immunotherapy response of colorectal cancer. Front Immunol 2022; 13:951455. [PMID: 36189298 PMCID: PMC9516397 DOI: 10.3389/fimmu.2022.951455] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/22/2022] [Indexed: 11/21/2022] Open
Abstract
Background Colorectal cancer (CRC) is one of the most common digestive system tumors worldwide. Hypoxia and immunity are closely related in CRC; however, the role of hypoxia-immune–related lncRNAs in CRC prognosis is unknown. Methods Data used in the current study were sourced from the Gene Expression Omnibus and The Cancer Genome Atlas (TCGA) databases. CRC patients were divided into low- and high-hypoxia groups using the single-sample gene set enrichment analysis (ssGSEA) algorithm and into low- and high-immune groups using the Estimation of STromal and Immune cells in MAlignant Tumours using Expression data (ESTIMATE) algorithm. Differentially expressed lncRNAs (DElncRNAs) between low- and high-hypoxia groups, low- and high-immune groups, and tumor and control samples were identified using the limma package. Hypoxia-immune–related lncRNAs were obtained by intersecting these DElncRNAs. A hypoxia-immune–related lncRNA risk signature was developed using univariate Cox regression and least absolute shrinkage and selection operator (LASSO) analyses. The tumor microenvironments in the low- and high-risk groups were evaluated using ssGSEA, ESTIMATE, and the expression of immune checkpoints. The therapeutic response in the two groups was assessed using TIDE, IPS, and IC50. A ceRNA network based on signature lncRNAs was constructed. Finally, we used RT-qPCR to verify the expression of hypoxia-immune–related lncRNA signatures in normal and cancer tissues. Results Using differential expression analysis, and univariate Cox and LASSO regression analyses, ZNF667-AS1, LINC01354, LINC00996, DANCR, CECR7, and LINC01116 were selected to construct a hypoxia-immune–related lncRNA signature. The performance of the risk signature in predicting CRC prognosis was validated in internal and external datasets, as evidenced by receiver operating characteristic curves. In addition, we observed significant differences in the tumor microenvironment and immunotherapy response between low- and high-risk groups and constructed a CECR7–miRNA–mRNA regulatory network in CRC. Furthermore, RT-qPCR results confirmed that the expression patterns of the six lncRNA signatures were consistent with those in TCGA-CRC cohort. Conclusion Our study identified six hypoxia-immune–related lncRNAs for predicting CRC survival and sensitivity to immunotherapy. These findings may enrich our understanding of CRC and help improve CRC treatment. However, large-scale long-term follow-up studies are required for verification.
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Affiliation(s)
- Likun Luan
- Department of Gastric and Intestinal Surgery, The Third Affiliated Hospital of Kunming Medical University/Yunnan Tumor Hospital, Kunming, China
| | - Youguo Dai
- Department of Gastric and Intestinal Surgery, The Third Affiliated Hospital of Kunming Medical University/Yunnan Tumor Hospital, Kunming, China
| | - Tao Shen
- Department of Colorectal Surgery, The Third Affiliated Hospital of Kunming Medical University/Yunnan Tumor Hospital, Kunming, China
| | - Changlong Yang
- Department of Gastric and Intestinal Surgery, The Third Affiliated Hospital of Kunming Medical University/Yunnan Tumor Hospital, Kunming, China
| | - Zhenpu Chen
- Tumor Institute, The Third Affiliated Hospital of Kunming Medical University/Yunnan Tumor Hospital, Kunming, China
| | - Shan Liu
- Departments of Combination of Traditional Chinese and Western Medicine, The Third Affiliated Hospital of Kunming Medical University/Yunnan Tumor Hospital, Kunming, China
| | - Junyi Jia
- Department of Gastric and Intestinal Surgery, The Third Affiliated Hospital of Kunming Medical University/Yunnan Tumor Hospital, Kunming, China
| | - Zhenhui Li
- Department of Radiology, The Third Affiliated Hospital of Kunming Medical University/Yunnan Tumor Hospital, Kunming, China
| | - Shaojun Fang
- Department of Colorectal Surgery, The Third Affiliated Hospital of Kunming Medical University/Yunnan Tumor Hospital, Kunming, China
| | - Hengqiong Qiu
- Department of Surgery Teaching Management, The Third Affiliated Hospital of Kunming Medical University/Yunnan Tumor Hospital, Kunming, China
| | - Xianshuo Cheng
- Department of Colorectal Surgery, The Third Affiliated Hospital of Kunming Medical University/Yunnan Tumor Hospital, Kunming, China
- *Correspondence: Xianshuo Cheng, ; Zhibin Yang,
| | - Zhibin Yang
- Department of Colorectal Surgery, The Third Affiliated Hospital of Kunming Medical University/Yunnan Tumor Hospital, Kunming, China
- *Correspondence: Xianshuo Cheng, ; Zhibin Yang,
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Prognostic and tumor immunity implication of inflammatory bowel disease-associated genes in colorectal cancer. Eur J Med Res 2022; 27:91. [PMID: 35698180 PMCID: PMC9190109 DOI: 10.1186/s40001-022-00720-0] [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: 04/13/2022] [Accepted: 05/31/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Epidemiologic studies continue to emphasize that increasing patients with inflammatory bowel disease (IBD) develop to colorectal cancer (CRC). Although the function and mechanisms of IBD-associated genes (IBDGs) in CRC tumorigenesis have been extensively researched, the implications of IBDGs in the prognosis value and tumor immunity of CRC remain unclear. RESULTS In this study, the expression, pathological stages and prognostic value of IBDGs in CRC were systematically analyzed, and 7 prognostic genes including CDH1, CCL11, HLA-DRA, NOS2, NAT2, TIMP1 and TP53 were screened through LASSO-Cox regression analysis. Then, a prognostic signature was established based on the 7 prognostic genes, and the model exhibited a good ability in risk stratification of CRC patients. Subsequent results showed that the genetic alterations of the 7 prognostic genes exhibited more significant and extensive influence on immune cells infiltration in colon adenocarcinoma than that in rectal adenocarcinoma. Meanwhile, immune cells infiltration also showed a significant difference between low-risk group and high-risk group. What's more, 7 prognostic genes-based risk stratification was associated with microsatellite instability, and its prognostic characteristics were significantly negatively correlated with mismatch repair genes. CONCLUSIONS This study provided a promising insight that the 7 IBDGs could be used as valuable biomarkers for prognostic diagnosis and personalized immunotherapy of CRC patients.
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Nersisyan S, Novosad V, Galatenko A, Sokolov A, Bokov G, Konovalov A, Alekseev D, Tonevitsky A. ExhauFS: exhaustive search-based feature selection for classification and survival regression. PeerJ 2022; 10:e13200. [PMID: 35378930 PMCID: PMC8976470 DOI: 10.7717/peerj.13200] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/09/2022] [Indexed: 01/12/2023] Open
Abstract
Feature selection is one of the main techniques used to prevent overfitting in machine learning applications. The most straightforward approach for feature selection is an exhaustive search: one can go over all possible feature combinations and pick up the model with the highest accuracy. This method together with its optimizations were actively used in biomedical research, however, publicly available implementation is missing. We present ExhauFS-the user-friendly command-line implementation of the exhaustive search approach for classification and survival regression. Aside from tool description, we included three application examples in the manuscript to comprehensively review the implemented functionality. First, we executed ExhauFS on a toy cervical cancer dataset to illustrate basic concepts. Then, multi-cohort microarray breast cancer datasets were used to construct gene signatures for 5-year recurrence classification. The vast majority of signatures constructed by ExhauFS passed 0.65 threshold of sensitivity and specificity on all datasets, including the validation one. Moreover, a number of gene signatures demonstrated reliable performance on independent RNA-seq dataset without any coefficient re-tuning, i.e., turned out to be cross-platform. Finally, Cox survival regression models were used to fit isomiR signatures for overall survival prediction for patients with colorectal cancer. Similarly to the previous example, the major part of models passed the pre-defined concordance index threshold 0.65 on all datasets. In both real-world scenarios (breast and colorectal cancer datasets), ExhauFS was benchmarked against state-of-the-art feature selection models, including L1-regularized sparse models. In case of breast cancer, we were unable to construct reliable cross-platform classifiers using alternative feature selection approaches. In case of colorectal cancer not a single model passed the same 0.65 threshold. Source codes and documentation of ExhauFS are available on GitHub: https://github.com/s-a-nersisyan/ExhauFS.
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Affiliation(s)
- Stepan Nersisyan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Victor Novosad
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
| | - Alexei Galatenko
- Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, Russia,Moscow Center for Fundamental and Applied Mathematics, Moscow, Russia
| | - Andrey Sokolov
- Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, Russia,Moscow Center for Fundamental and Applied Mathematics, Moscow, Russia
| | - Grigoriy Bokov
- Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, Russia,Moscow Center for Fundamental and Applied Mathematics, Moscow, Russia
| | - Alexander Konovalov
- Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, Russia,Moscow Center for Fundamental and Applied Mathematics, Moscow, Russia
| | - Dmitry Alekseev
- Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, Russia,Moscow Center for Fundamental and Applied Mathematics, Moscow, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia,Institute of Nanotechnologies of Microelectronics RAS, Moscow, Russia
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