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Zhang Y, Tong GH, Wei XX, Chen HY, Liang T, Tang HP, Wu CA, Wen GM, Yang WK, Liang L, Shen H. Identification of Five Cytotoxicity-Related Genes Involved in the Progression of Triple-Negative Breast Cancer. Front Genet 2022; 12:723477. [PMID: 35046993 PMCID: PMC8762060 DOI: 10.3389/fgene.2021.723477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 10/29/2021] [Indexed: 12/15/2022] Open
Abstract
Background: Breast cancer is one of the deadly tumors in women, and its incidence continues to increase. This study aimed to identify novel therapeutic molecules using RNA sequencing (RNA-seq) data of breast cancer from our hospital. Methods: 30 pairs of human breast cancer tissue and matched normal tissue were collected and RNA sequenced in our hospital. Differentially expressed genes (DEGs) were calculated with raw data by the R package "edgeR", and functionally annotated using R package "clusterProfiler". Tumor-infiltrating immune cells (TIICs) were estimated using a website tool TIMER 2.0. Effects of key genes on therapeutic efficacy were analyzed using RNA-seq data and drug sensitivity data from two databases: the Cancer Cell Line Encyclopedia (CCLE) and the Cancer Therapeutics Response Portal (CTRP). Results: There were 2,953 DEGs between cancerous and matched normal tissue, as well as 975 DEGs between primary breast cancer and metastatic breast cancer. These genes were primarily enriched in PI3K-Akt signaling pathway, calcium signaling pathway, cAMP signaling pathway, and cell cycle. Notably, CD8+ T cell, M0 macrophage, M1 macrophage, regulatory T cell and follicular helper T cell were significantly elevated in cancerous tissue as compared with matched normal tissue. Eventually, we found five genes (GALNTL5, MLIP, HMCN2, LRRN4CL, and DUOX2) were markedly corelated with CD8+ T cell infiltration and cytotoxicity, and associated with therapeutic response. Conclusion: We found five key genes associated with tumor progression, CD8+ T cell and therapeutic efficacy. The findings would provide potential molecular targets for the treatment of breast cancer.
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Affiliation(s)
- Yan Zhang
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University/Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, The First Affiliated Hospital of Guangdong University Of Pharmacy, Guangzhou, China.,Department of Pathology, Shenzhen Longhua District Maternity & Child Healthcare Hospital, Shenzhen, China
| | - Gui-Hui Tong
- Department of Pathology,The first Affiliated Hospital,Guangzhou Medical University, Guangzhou, China
| | - Xu-Xuan Wei
- Department of Pathology, The First Affiliated Hospital of Guangdong University Of Pharmacy, Guangzhou, China
| | - Hai-Yang Chen
- Department of Pathology, The First Affiliated Hospital of Guangdong University Of Pharmacy, Guangzhou, China
| | - Tian Liang
- Department of Pathology, The First Affiliated Hospital of Guangdong University Of Pharmacy, Guangzhou, China
| | - Hong-Ping Tang
- Department of Pathology, Shenzhen Maternity & Child Healthcare Hospital, Shenzhen, China
| | - Chuan-An Wu
- Department of Prevention and Health Care, Shenzhen Longhua District Maternity & Child Healthcare Hospital, Shenzhen, China
| | - Guo-Ming Wen
- Department of Prevention and Health Care, Shenzhen Longhua District Maternity & Child Healthcare Hospital, Shenzhen, China
| | - Wei-Kang Yang
- Department of Prevention and Health Care, Shenzhen Longhua District Maternity & Child Healthcare Hospital, Shenzhen, China
| | - Li Liang
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University/Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, China
| | - Hong Shen
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University/Nanfang Hospital, Southern Medical University, Guangzhou, China
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Li YL, Xing TF, Liu JX. Genome-wide association analyses based on whole-genome sequencing of Protosalanx hyalocranius provide insights into sex determination of Salangid fishes. Mol Ecol Resour 2020; 20:1038-1049. [PMID: 32315505 DOI: 10.1111/1755-0998.13172] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 03/28/2020] [Accepted: 04/09/2020] [Indexed: 12/22/2022]
Abstract
Identification of sex determination system and sex-determining genes have important implications in conservation, ecology and evolution. However, much remains to be discovered about the evolution of different sexual determination systems in teleost fishes, of which the mechanisms of sex determination are remarkably variable. In the present study, the whole genomes of 20 males and 20 females of a Salangid fish, Protosalanx hyalocranius, were sequenced and genome wide association analyses were conducted to uncover its sex determination system and putative sex-determining genes. A total of 150 SNPs were significantly associated with sex, which showed high differentiation between sexes (FST ranged from 0.245 to 0.556). Of the 150 sex-associated SNPs, 76 SNPs displayed sex specificity with even coverage of depth and were female heterogametic, which suggested a ZZ/ZW sex determination system. Interestingly, one scaffold containing sex-specific SNPs displayed synteny to the sex chromosome of medaka. Annotations of sex-associated loci suggested that both transcriptional regulators (e.g., FOX genes) and secreted hormones and their receptors might be involved in the sex determination/differentiation of P. hyalocranius. More strikingly, we found a nonsense mutation in one copy of GALNT homology gene of all females, which suggested that "Z dosage" effect might play a vital role in the processes of sex determination/differentiation. These sex-specific loci could be a valuable resource for further research on sex determination of Salangid fishes and the results could contribute to the understanding of sex determination mechanisms and the evolution of sex chromosome in teleost fishes.
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Affiliation(s)
- Yu-Long Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Teng-Fei Xing
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jin-Xian Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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Zhou L, Liu Z, Dong Y, Sun X, Wu B, Yu T, Zheng Y, Yang A, Zhao Q, Zhao D. Transcriptomics analysis revealing candidate genes and networks for sex differentiation of yesso scallop (Patinopecten yessoensis). BMC Genomics 2019; 20:671. [PMID: 31443640 PMCID: PMC6708199 DOI: 10.1186/s12864-019-6021-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 08/09/2019] [Indexed: 02/06/2023] Open
Abstract
Background The Yesso scallop, Patinopecten (Mizuhopecten) yessoensis, is a commercially important bivalve in the coastal countries of Northeast Asia. It has complex modes of sex differentiation, but knowledge of the mechanisms underlying this sex determination and differentiation is limited. Results In this study, the gonad tissues from females and males at three developmental stages were used to investigate candidate genes and networks for sex differentiation via RNA-Req. A total of 901,980,606 high quality clean reads were obtained from 18 libraries, of which 417 expressed male-specific genes and 754 expressed female-specific genes. Totally, 10,074 genes differentially expressed in females and males were identified. Weighted gene co-expression network analysis (WGCNA) revealed that turquoise and green gene modules were significantly positively correlated with male gonads, while coral1 and black modules were significantly associated with female gonads. The most important gene for sex determination and differentiation was Pydmrt 1, which was the only gene discovered that determined the male sex phenotype during early gonadal differentiation. Enrichment analyses of GO terms and KEGG pathways revealed that genes involved in metabolism, genetic and environmental information processes or pathways are sex-biased. Forty-nine genes in the five modules involved in sex differentiation or determination were identified and selected to construct a gene co-expression network and a hypothesized sex differentiation pathway. Conclusions The current study focused on screening genes of sex differentiation in Yesso scallop, highlighting the potential regulatory mechanisms of gonadal development in P. yessoensis. Our data suggested that WCGNA can facilitate identification of key genes for sex differentiation and determination. Using this method, a hypothesized P. yessoensis sex determination and differentiation pathway was constructed. In this pathway, Pydmrt 1 may have a leading function. Electronic supplementary material The online version of this article (10.1186/s12864-019-6021-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Liqing Zhou
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Qingdao, China.,Labortory for Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhihong Liu
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Qingdao, China.,Labortory for Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | | | - Xiujun Sun
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Qingdao, China.,Labortory for Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Biao Wu
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Qingdao, China.,Labortory for Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Tao Yu
- Changdao Enhancement and Experiment Station, Chinese Academy of Fishery Science, Changdao, China
| | - Yanxin Zheng
- Changdao Enhancement and Experiment Station, Chinese Academy of Fishery Science, Changdao, China
| | - Aiguo Yang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Qingdao, China. .,Labortory for Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Qing Zhao
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Qingdao, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Dan Zhao
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Qingdao, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
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