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Liu YX, Song JL, Li XM, Lin H, Cao YN. Identification of target genes co-regulated by four key histone modifications of five key regions in hepatocellular carcinoma. Methods 2024; 231:165-177. [PMID: 39349287 DOI: 10.1016/j.ymeth.2024.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 08/27/2024] [Accepted: 09/27/2024] [Indexed: 10/02/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is a cancer with high morbidity and mortality. Studies have shown that histone modification plays an important regulatory role in the occurrence and development of HCC. However, the specific regulatory effects of histone modifications on gene expression in HCC are still unclear. This study focuses on HepG2 cell lines and hepatocyte cell lines. First, the distribution of histone modification signals in the two cell lines was calculated and analyzed. Then, using the random forest algorithm, we analyzed the effects of different histone modifications and their modified regions on gene expression in the two cell lines, four key histone modifications (H3K36me3, H3K4me3, H3K79me2, and H3K9ac) and five key regions that co-regulate gene expression were obtained. Subsequently, target genes regulated by key histone modifications in key regions were screened. Combined with clinical data, Cox regression analysis and Kaplan-Meier survival analysis were performed on the target genes, and four key target genes (CBX2, CEBPZOS, LDHA, and UMPS) related to prognosis were identified. Finally, through immune infiltration analysis and drug sensitivity analysis of key target genes, the potential role of key target genes in HCC was confirmed. Our results provide a theoretical basis for exploring the occurrence of HCC and propose potential biomarkers associated with histone modifications, which may be potential drug targets for the clinical treatment of HCC.
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Affiliation(s)
- Yu-Xian Liu
- School of Artificial Intelligence, Anhui University of Science and Technology, Huainan 232001, China.
| | - Jia-Le Song
- School of Artificial Intelligence, Anhui University of Science and Technology, Huainan 232001, China
| | - Xiao-Ming Li
- School of Artificial Intelligence, Anhui University of Science and Technology, Huainan 232001, China
| | - Hao Lin
- Key Laboratory for Neuro-Information of Ministry of Education, Center for Informational Biology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China.
| | - Yan-Ni Cao
- School of Artificial Intelligence, Anhui University of Science and Technology, Huainan 232001, China.
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Ruishi X, Linyi X, Yunfan B, Wenbo Y, Xiaoying Z, Xiaoxue F, Difu Z, Xintian L, Ming Z, Haoming L. New perspectives on chemokines in hepatocellular carcinoma therapy: a critical pathway for natural products regulation of the tumor microenvironment. Front Immunol 2024; 15:1456405. [PMID: 39206194 PMCID: PMC11349538 DOI: 10.3389/fimmu.2024.1456405] [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: 06/28/2024] [Accepted: 07/26/2024] [Indexed: 09/04/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common primary neoplasms of the liver and one of the most common solid tumors in the world. Its global incidence is increasing and it has become the third leading cause of cancer-related deaths. There is growing evidence that chemokines play an important role in the tumor microenvironment, regulating the migration and localization of immune cells in tissues and are critical for the function of the immune system. This review comprehensively analyses the expression and activity of chemokines in the TME of HCC and describes their interrelationship with hepatocarcinogenesis and progression. Special attention is given to the role of chemokine-chemokine receptors in the regulation of immune cell accumulation in the TME. Therapeutic strategies targeting tumor-promoting chemokines or the induction/release of beneficial chemokines are reviewed, highlighting the potential value of natural products in modulating chemokines and their receptors in the treatment of HCC. The in-depth discussion in this paper provides a theoretical basis for the treatment of HCC. It is an important reference for new drug development and clinical research.
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Affiliation(s)
- Xie Ruishi
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, Jilin, China
| | - Xu Linyi
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, Jilin, China
| | - Bai Yunfan
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, Jilin, China
| | - Yu Wenbo
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, Jilin, China
| | - Zhang Xiaoying
- The First Hospital of Jilin University, Changchun, China
| | - Fang Xiaoxue
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, Jilin, China
| | - Zhu Difu
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, Jilin, China
| | - Lan Xintian
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, Jilin, China
| | - Zhu Ming
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, Jilin, China
| | - Luo Haoming
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, Jilin, China
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Hao L, Li S, Deng J, Li N, Yu F, Jiang Z, Zhang J, Shi X, Hu X. The current status and future of PD-L1 in liver cancer. Front Immunol 2023; 14:1323581. [PMID: 38155974 PMCID: PMC10754529 DOI: 10.3389/fimmu.2023.1323581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 11/27/2023] [Indexed: 12/30/2023] Open
Abstract
The application of immunotherapy in tumor, especially immune checkpoint inhibitors (ICIs), has played an important role in the treatment of advanced unresectable liver cancer. However, the efficacy of ICIs varies greatly among different patients, which has aroused people's attention to the regulatory mechanism of programmed death ligand-1 (PD-L1) in the immune escape of liver cancer. PD-L1 is regulated by multiple levels and signaling pathways in hepatocellular carcinoma (HCC), including gene variation, epigenetic inheritance, transcriptional regulation, post-transcriptional regulation, and post-translational modification. More studies have also found that the high expression of PD-L1 may be the main factor affecting the immunotherapy of liver cancer. However, what is the difference of PD-L1 expressed by different types of cells in the microenvironment of HCC, and which type of cells expressed PD-L1 determines the effect of tumor immunotherapy remains unclear. Therefore, clarifying the regulatory mechanism of PD-L1 in liver cancer can provide more basis for liver cancer immunotherapy and combined immune treatment strategy. In addition to its well-known role in immune regulation, PD-L1 also plays a role in regulating cancer cell proliferation and promoting drug resistance of tumor cells, which will be reviewed in this paper. In addition, we also summarized the natural products and drugs that regulated the expression of PD-L1 in HCC.
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Affiliation(s)
- Liyuan Hao
- School of Clinical Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- Department of Infectious Diseases, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Shenghao Li
- School of Clinical Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- Clinical Research Center, Shijiazhuang Fifth Hospital, Shijiazhuang, Hebei, China
| | - Jiali Deng
- School of Clinical Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- Department of Infectious Diseases, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Na Li
- School of Clinical Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- Department of Infectious Diseases, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Fei Yu
- School of Clinical Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- Department of Infectious Diseases, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Zhi Jiang
- School of Clinical Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- Department of Infectious Diseases, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Junli Zhang
- Department of Infectious Diseases, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, China
| | - Xinli Shi
- Center of Experimental Management, Shanxi University of Chinese Medicine, Jinzhong, China
| | - Xiaoyu Hu
- Department of Infectious Diseases, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
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