Comprehensive genomic profiling of small bowel adenocarcinoma by tissue and plasma biopsy
Genomics. 2023 Dec 21:110766. doi: 10.1016/j.ygeno.2023.110766. Online ahead of print.ABSTRACTSmall bowel adenocarcinoma (SBA) is a rare and aggressive malignancy with limited treatment options and poor prognosis. The molecular landscape and immunological characteristics of SBA are poorly understood. Here, we performed comprehensive mutation profiling of tissue and plasma biopsies from 143 and 42 patients with SBA. Analysis showed that SBA had a distinct mutation spectrum from left- and right-sided colorectal carcinoma. Plasma biopsy had high concordance with tissue biopsy for single nucleotide variants and structural vari...
Source: Genomics - December 23, 2023 Category: Genetics & Stem Cells Authors: Dan Yu Jianzheng Wang Bo Zheng Mingming Yuan Dejian Gu Rongrong Chen Xiao-Bing Chen Source Type: research
Systems genetics and bioinformatics analyses using ESR1-correlated genes identify potential candidates underlying female bone development
Genomics. 2023 Dec 21:110769. doi: 10.1016/j.ygeno.2023.110769. Online ahead of print.ABSTRACTEstrogen receptor α (ESR1) is involved in E2 signaling and plays a major role in postmenopausal bone loss. However, the molecular network underlying ESR1 has not been explored. We used systems genetics and bioinformatics to identify important genes associated with Esr1 in postmenopausal bone loss. We identified ~2300 Esr1-coexpressed genes in female BXD bone femur, functional analysis of which revealed 'osteoblast signaling' as the most enriched pathway. PPI network led to the identification of 25 'female bone candidates'. The ge...
Source: Genomics - December 23, 2023 Category: Genetics & Stem Cells Authors: Akhilesh K Bajpai Qingqing Gu Yan Jiao Athena Starlard-Davenport Weikuan Gu Leigh Darryl Quarles Zhousheng Xiao Lu Lu Source Type: research
Epigenomic analysis of the myometrium during late implantation revealed regulatory elements in genes related to the cellular zinc homeostasis pathway in pigs
In conclusion, the genes in the pathways of cellular zinc homeostasis and their regulatory elements identified have implications for pig reproduction trait improvement and warrant further investigations.PMID:38128703 | DOI:10.1016/j.ygeno.2023.110768 (Source: Genomics)
Source: Genomics - December 21, 2023 Category: Genetics & Stem Cells Authors: Weiwei Wang Yan Sun Pengfei Xu Hao Liang Yue Wang Dadong Deng Jianhua Cao Mei Yu Source Type: research
A comprehensive exploration of the heterogeneity of immune cells in Han and Zang systemic lupus erythematosus patients via single-cell RNA sequencing
CONCLUSIONS: In summary, the immune cellular heterogeneity of SLE patients both Han and Zang nationality was explored based on various bioinformatics approaches, providing new perspectives for immunological characteristics of SLE among different ethnic groups.PMID:38128704 | DOI:10.1016/j.ygeno.2023.110770 (Source: Genomics)
Source: Genomics - December 21, 2023 Category: Genetics & Stem Cells Authors: Yongzhuo Wu Chongjun Weng Yali Zhou Qinghuan Zhu Yingying Liu Junjuan Zheng Binbin Yang Wenting Cao Limei Yuan Meng Yang Danqi Deng Source Type: research
Integrative analysis of transcriptome and proteome in primary Sj ögren syndrome
CONCLUSION: Herein, we found critical processes and potential biomakers that may contribute to pSS pathogenesis by analyzing dysregulated genes and pathways. Additionally, the integrative multi-omics datasets provided additional insight into understanding complicated disease mechanisms.PMID:38128705 | DOI:10.1016/j.ygeno.2023.110767 (Source: Genomics)
Source: Genomics - December 21, 2023 Category: Genetics & Stem Cells Authors: Xiaoting Qiu Beijia Wang Hongxiao Gong Su Bu Pingping Li Runzhi Zhao Mingde Li Ling Zhu Xingxing Huo Source Type: research
Epigenomic analysis of the myometrium during late implantation revealed regulatory elements in genes related to the cellular zinc homeostasis pathway in pigs
In conclusion, the genes in the pathways of cellular zinc homeostasis and their regulatory elements identified have implications for pig reproduction trait improvement and warrant further investigations.PMID:38128703 | DOI:10.1016/j.ygeno.2023.110768 (Source: Genomics)
Source: Genomics - December 21, 2023 Category: Genetics & Stem Cells Authors: Weiwei Wang Yan Sun Pengfei Xu Hao Liang Yue Wang Dadong Deng Jianhua Cao Mei Yu Source Type: research
A comprehensive exploration of the heterogeneity of immune cells in Han and Zang systemic lupus erythematosus patients via single-cell RNA sequencing
CONCLUSIONS: In summary, the immune cellular heterogeneity of SLE patients both Han and Zang nationality was explored based on various bioinformatics approaches, providing new perspectives for immunological characteristics of SLE among different ethnic groups.PMID:38128704 | DOI:10.1016/j.ygeno.2023.110770 (Source: Genomics)
Source: Genomics - December 21, 2023 Category: Genetics & Stem Cells Authors: Yongzhuo Wu Chongjun Weng Yali Zhou Qinghuan Zhu Yingying Liu Junjuan Zheng Binbin Yang Wenting Cao Limei Yuan Meng Yang Danqi Deng Source Type: research
Integrative analysis of transcriptome and proteome in primary Sj ögren syndrome
CONCLUSION: Herein, we found critical processes and potential biomakers that may contribute to pSS pathogenesis by analyzing dysregulated genes and pathways. Additionally, the integrative multi-omics datasets provided additional insight into understanding complicated disease mechanisms.PMID:38128705 | DOI:10.1016/j.ygeno.2023.110767 (Source: Genomics)
Source: Genomics - December 21, 2023 Category: Genetics & Stem Cells Authors: Xiaoting Qiu Beijia Wang Hongxiao Gong Su Bu Pingping Li Runzhi Zhao Mingde Li Ling Zhu Xingxing Huo Source Type: research
Epigenomic analysis of the myometrium during late implantation revealed regulatory elements in genes related to the cellular zinc homeostasis pathway in pigs
In conclusion, the genes in the pathways of cellular zinc homeostasis and their regulatory elements identified have implications for pig reproduction trait improvement and warrant further investigations.PMID:38128703 | DOI:10.1016/j.ygeno.2023.110768 (Source: Genomics)
Source: Genomics - December 21, 2023 Category: Genetics & Stem Cells Authors: Weiwei Wang Yan Sun Pengfei Xu Hao Liang Yue Wang Dadong Deng Jianhua Cao Mei Yu Source Type: research
A comprehensive exploration of the heterogeneity of immune cells in Han and Zang systemic lupus erythematosus patients via single-cell RNA sequencing
CONCLUSIONS: In summary, the immune cellular heterogeneity of SLE patients both Han and Zang nationality was explored based on various bioinformatics approaches, providing new perspectives for immunological characteristics of SLE among different ethnic groups.PMID:38128704 | DOI:10.1016/j.ygeno.2023.110770 (Source: Genomics)
Source: Genomics - December 21, 2023 Category: Genetics & Stem Cells Authors: Yongzhuo Wu Chongjun Weng Yali Zhou Qinghuan Zhu Yingying Liu Junjuan Zheng Binbin Yang Wenting Cao Limei Yuan Meng Yang Danqi Deng Source Type: research
Integrative analysis of transcriptome and proteome in primary Sj ögren syndrome
CONCLUSION: Herein, we found critical processes and potential biomakers that may contribute to pSS pathogenesis by analyzing dysregulated genes and pathways. Additionally, the integrative multi-omics datasets provided additional insight into understanding complicated disease mechanisms.PMID:38128705 | DOI:10.1016/j.ygeno.2023.110767 (Source: Genomics)
Source: Genomics - December 21, 2023 Category: Genetics & Stem Cells Authors: Xiaoting Qiu Beijia Wang Hongxiao Gong Su Bu Pingping Li Runzhi Zhao Mingde Li Ling Zhu Xingxing Huo Source Type: research
CircPHKB decreases the sensitivity of liver cancer cells to sorafenib via miR-1234-3p/CYP2W1 axis
In this study, we provided initial evidence demonstrating that circPHKB, a novel circRNA markedly overexpressed in sorafenib-treated liver cancer cells, attenuated the sensitivity of liver cancer cells to sorafenib. Mechanically, circPHKB sequestered miR-1234-3p, resulting in the up-regulation of cytochrome P450 family 2 subfamily W member 1 (CYP2W1), thereby reducing the killing effect of sorafenib on liver cancer cells. Moreover, knockdown of circPHKB sensitized liver cancer cells to sorafenib in vivo. The findings reveal a novel circPHKB/miR-1234-3p/CYP2W1 pathway that decreases the sensitivity of liver cancer cells to ...
Source: Genomics - December 19, 2023 Category: Genetics & Stem Cells Authors: Lingxi Chen Hanxi Xiao Yaran Wu Dongjing Yan Meihua Shan Liangbo Sun Xiaojing Yan Dong Liu Tao Li Yang Zhang Li Xiang An Chen Shuhui Li Wei Xiang Zhenhong Ni Fengtian He Mingzhen Yang Jiqin Lian Source Type: research
Genomic and transcriptomic characteristics of 12 novel primary cell lines derived from three patients with cholangiocarcinoma
Genomics. 2023 Dec 17:110765. doi: 10.1016/j.ygeno.2023.110765. Online ahead of print.ABSTRACTCholangiocarcinoma (CCA) is an aggressive bile duct malignancy with poor prognosis. To improve our understanding of the biological characteristics of CCA and develop effective therapies, appropriate preclinical models are required. Here, we established and characterized 12 novel patient-derived primary cancer cell (PDPC) models using multi-region sampling. At the genomic level of PDPCs, we observed not only commonly mutated genes, such as TP53, JAK3, and KMT2C, consistent with the reports in CCA, but also specific mutation pattern...
Source: Genomics - December 19, 2023 Category: Genetics & Stem Cells Authors: Feiling Feng Xianglei Xing Guojuan Jiang Xiaoya Xu Bin Li Zhizhen Li Zhenghua Xie Yue Wu Xiaofang Li Qingxiang Gao Dongyu Liu Yang Shen Jianyang Ao Dadong Zhang Yanxin Chang Xiaoqing Jiang Source Type: research
CircPHKB decreases the sensitivity of liver cancer cells to sorafenib via miR-1234-3p/CYP2W1 axis
In this study, we provided initial evidence demonstrating that circPHKB, a novel circRNA markedly overexpressed in sorafenib-treated liver cancer cells, attenuated the sensitivity of liver cancer cells to sorafenib. Mechanically, circPHKB sequestered miR-1234-3p, resulting in the up-regulation of cytochrome P450 family 2 subfamily W member 1 (CYP2W1), thereby reducing the killing effect of sorafenib on liver cancer cells. Moreover, knockdown of circPHKB sensitized liver cancer cells to sorafenib in vivo. The findings reveal a novel circPHKB/miR-1234-3p/CYP2W1 pathway that decreases the sensitivity of liver cancer cells to ...
Source: Genomics - December 19, 2023 Category: Genetics & Stem Cells Authors: Lingxi Chen Hanxi Xiao Yaran Wu Dongjing Yan Meihua San Liangbo Sun Xiaojing Yan Dong Liu Tao Li Yang Zhang Li Xiang An Chen Shuhui Li Wei Xiang Zhenhong Ni Fengtian He Mingzhen Yang Jiqin Lian Source Type: research
Genomic and transcriptomic characteristics of 12 novel primary cell lines derived from three patients with cholangiocarcinoma
Genomics. 2023 Dec 17:110765. doi: 10.1016/j.ygeno.2023.110765. Online ahead of print.ABSTRACTCholangiocarcinoma (CCA) is an aggressive bile duct malignancy with poor prognosis. To improve our understanding of the biological characteristics of CCA and develop effective therapies, appropriate preclinical models are required. Here, we established and characterized 12 novel patient-derived primary cancer cell (PDPC) models using multi-region sampling. At the genomic level of PDPCs, we observed not only commonly mutated genes, such as TP53, JAK3, and KMT2C, consistent with the reports in CCA, but also specific mutation pattern...
Source: Genomics - December 19, 2023 Category: Genetics & Stem Cells Authors: Feiling Feng Xianglei Xing Guojuan Jiang Xiaoya Xu Bin Li Zhizhen Li Zhenghua Xie Yue Wu Xiaofang Li Qingxiang Gao Dongyu Liu Yang Shen Jianyang Ao Dadong Zhang Yanxin Chang Xiaoqing Jiang Source Type: research
