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Wang Z, Wang G, Zhao P, Sun P. The liquid-liquid phase separation signature predicts the prognosis and immunotherapy response in hepatocellular carcinoma. J Cell Mol Med 2024; 28:e18446. [PMID: 39072983 DOI: 10.1111/jcmm.18446] [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: 11/20/2023] [Revised: 03/28/2024] [Accepted: 05/13/2024] [Indexed: 07/30/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is a common and fatal malignancy characterized by poor patient prognosis and treatment outcome. The process of liquid-liquid phase separation in tumour cells alters the dysfunction of biomolecular condensation in tumour cells, which affects tumour progression and treatment. We downloaded the data of HCC samples from TCGA database and GEO database, and used a machine learning method to build a new liquid-liquid phase separation index (LLPSI) by liquid-liquid phase separation related genes. The LLPSI-related column line Figure was constructed to provide a quantitative tool for clinical practice. HCC patients were divided into high and low LLPSI groups based on LLPSI, and clinical features, tumour immune microenvironment, chemotherapeutic response, and immunotherapeutic response were systematically analysed. LLPSI, which consists of five liquid-liquid phase separation-associated genes (MAPT, WDR62, PLK1, CDCA8 and TOP2A), is a reliable predictor of survival in patients with HCC and has been validated in multiple external datasets. We found that the high LLPSI group showed higher levels of immune cell infiltration and better response to immunotherapy compared to the low LLPSI group, and LLPSI can also be used for prognostic prediction in various cancers other than HCC. In vitro experiments verified that knockdown of MAPT could inhibit the proliferation and migration of HCC. The LLPSI identified in this study can accurately assess the prognosis of patients with HCC and identify patient populations that will benefit from immunotherapy, providing valuable insights into the clinical management of HCC.
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Affiliation(s)
- Zhiyong Wang
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Guoliang Wang
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Peng Zhao
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ping Sun
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Luo H, Wang Z. Pan-cancer analysis reveals potential immunological and prognostic roles of COA6 in human cancers and preliminary exploration of COA6 in bladder cancer. Cell Signal 2024; 117:111111. [PMID: 38395184 DOI: 10.1016/j.cellsig.2024.111111] [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: 01/22/2024] [Revised: 02/15/2024] [Accepted: 02/19/2024] [Indexed: 02/25/2024]
Abstract
BACKGROUND Cytochrome C oxidase assembly factor 6 (COA6) is significantly involved in the progression of cancer and is aberrantly expressed in disease. Nevertheless, the comprehensive analysis of COA6 using many omics techniques, and its impact on the prognosis and immunological microenvironment of cancer patients, remains unexplored. METHODS We gathered data from 33 cancer cases and conducted a thorough analysis of abnormalities in COA6 gene expression. This analysis included examining its relevance to disease, its diagnostic and prognostic value, pathway enrichment, the immune microenvironment, its association with immune checkpoints, and its ability to predict patient response to immunotherapy and natural small molecule drugs that target the COA6 protein. Ultimately, we examined the function of COA6 in bladder cancer by in vitro research. RESULTS Our study revealed significant variations in gene expression and identified COA6 as a potential diagnostic biomarker for cancer. COA6 was also discovered to have a crucial function in pan-cancer involving the tumor microenvironment. COA6 has a strong correlation with well-known immunological checkpoints, including TMB and MSI. Molecular docking identified natural small chemical inhibitors that specifically target the COA6 protein. Ultimately, scientific evidence has verified that suppressing the expression of the COA6 gene hinders the growth and infiltration of bladder cancer cells. CONCLUSIONS Our study emphasizes the significant potential of COA6 as a predictive and immunotherapeutic response biomarker. This finding may lead to future investigation into the mechanism of tumor infiltration and the therapeutic possibilities of COA6 in cancer.
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Affiliation(s)
- Hong Luo
- Department of Oncology, Yancheng Branch of Nanjing Drum Tower Hospital, Yancheng 224001, Jiangsu Province, China
| | - Zhiyong Wang
- Gastrointestinal Surgery, Wuhan Union Hospital, Wuhan 430022, Hubei, China.
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Jiang F, Xu Y, Jiang Z, Hu B, Lv Q, Wang Z. Deciphering the immunological and prognostic features of hepatocellular carcinoma through ADP-ribosylation-related genes analysis and identify potential therapeutic target ARFIP2. Cell Signal 2024; 117:111073. [PMID: 38302034 DOI: 10.1016/j.cellsig.2024.111073] [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: 12/03/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 02/03/2024]
Abstract
BACKGROUND Hepatocellular carcinoma is one of the most common malignancies, and its prognosis and treatment outcome cannot be accurately predicted. ADP-ribosylation (ADPR) is a post-translationa modification of proteins involved in protein trafficking and immune response. Therefore, it is necessary to explore the ADPR-related genes associated with the prognosis and therapeutic efficacy of hepatocellular carcinoma treatments. METHODS We downloaded the data of hepatocellular carcinoma samples to identify ADPR-related genes as prognostic markers, and established a novel ADPR-related index (ADPRI) based on univariate and multivariate COX regression analyses. Patients' prognosis, clinical features, somatic variant, tumor immune microenvironment, chemotherapeutic response and immunotherapeutic response were systematically analyzed. Finally, the role of ARFIP2 in hepatocellular carcinoma cells was preliminarily explored in vitro. RESULTS The ADPRI consisting of four ADPR related genes (ARL8B, ARFIP2, PARP12, ADPRHL1) was established to be a reliable predictor of survival in patients with hepatocellular carcinoma and was validated using external datasets. Compared with the low ADPRI group, the high ADPRI group presented higher levels of mutation frequency, immune infiltration and patients in high ADPRI group benefit more from immune checkpoint inhibitor treatment. In addition, we predicted some natural small molecule drugs as potential therapeutic targets for hepatocellular carcinoma. Finally, Knockdown of ARFIP2 inhibits the proliferation and migration of hepatocellular carcinoma cells by inducing the G1/S phase cell cycle arrest in HCC cells. CONCLUSIONS The ADPRI can be used to accurately predict the prognosis and immunotherapeutic response of hepatocellular carcinoma patients and providing valuable insights for future precision treatment of patients with hepatocellular carcinoma.
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Affiliation(s)
- Fenfen Jiang
- Laboratory of Hepatobiliary and Pancreas Surgery, Affiliated Hospital of Guilin Medical University, Guilin 541004, Guangxi, China
| | - Yan Xu
- Department of Urology, The First Hospital of China Medical University, Shenyang 110001, China
| | - Zhuang Jiang
- Traditional Chinese Medicine department, Shanghai Haijiang Hospital, 200434 Shanghai, China
| | - Bin Hu
- General Department, Shanghai Yangpu District Central Hospital, 200090 Shanghai, China
| | - Qing Lv
- Gastrointestinal surgery, Wuhan Union Hospital, Wuhan 430022, Hubei, China
| | - Zhiyong Wang
- Gastrointestinal surgery, Wuhan Union Hospital, Wuhan 430022, Hubei, China.
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Gu Y, Huang Q, Wang Y, Wang H, Xiang Z, Xu Y, Wang X, Liu W, Wang A. The vasculogenic mimicry related signature predicts the prognosis and immunotherapy response in renal clear cell carcinoma. BMC Cancer 2024; 24:420. [PMID: 38580922 PMCID: PMC10996246 DOI: 10.1186/s12885-024-12107-x] [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: 07/22/2023] [Accepted: 03/12/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND Clear cell carcinoma of the kidney is a common urological malignancy characterized by poor patient prognosis and treatment outcomes. Modulation of vasculogenic mimicry in tumor cells alters the tumor microenvironment and the influx of tumor-infiltrating lymphocytes, and the combination of its inducers and immune checkpoint inhibitors plays a synergistic role in enhancing antitumor effects. METHODS We downloaded the data from renal clear cell carcinoma samples and vasculogenic mimicry-related genes to establish a new vasculogenic mimicry-related index (VMRI) using a machine learning approach. Based on VMRI, patients with renal clear cell carcinoma were divided into high VMRI and low VMRI groups, and patients' prognosis, clinical features, tumor immune microenvironment, chemotherapeutic response, and immunotherapeutic response were systematically analyzed. Finally, the function of CDH5 was explored in renal clear cell carcinoma cells. RESULTS VMRI can be used for prognostic and immunotherapy efficacy prediction in a variety of cancers, which consists of four vasculogenic mimicry-related genes (CDH5, MMP9, MAPK1, and MMP13), is a reliable predictor of survival and grade in patients with clear cell carcinoma of the kidney and has been validated in multiple external datasets. We found that the high VMRI group presented higher levels of immune cell infiltration, which was validated by pathological sections. We performed molecular docking prediction of vasculogenic mimicry core target proteins and identified natural small molecule drugs with the highest affinity for the target protein. Knockdown of CDH5 inhibited the proliferation and migration of renal clear cell carcinoma. CONCLUSIONS The VMRI identified in this study allows for accurate prognosis assessment of patients with renal clear cell carcinoma and identification of patient populations that will benefit from immunotherapy, providing valuable insights for future precision treatment of patients with renal clear cell carcinoma.
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Affiliation(s)
- Yuming Gu
- Department of Traditional Chinese medicine, School of Clinical Medicine, Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong Province, 261042, China
- Weifang Medical University, Weifang, Shandong Province, 261042, China
- Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, Shandong Province, 261042, China
| | - Qinqin Huang
- Department of Traditional Chinese medicine, School of Clinical Medicine, Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong Province, 261042, China
- Weifang Medical University, Weifang, Shandong Province, 261042, China
- Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, Shandong Province, 261042, China
| | - Yun Wang
- Department of Traditional Chinese medicine, School of Clinical Medicine, Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong Province, 261042, China
- Weifang Medical University, Weifang, Shandong Province, 261042, China
- Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, Shandong Province, 261042, China
| | - Haixia Wang
- Department of Traditional Chinese medicine, School of Clinical Medicine, Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong Province, 261042, China
- Weifang Medical University, Weifang, Shandong Province, 261042, China
| | - Zhenhua Xiang
- Department of Traditional Chinese medicine, School of Clinical Medicine, Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong Province, 261042, China
| | - Yu Xu
- Department of Traditional Chinese medicine, School of Clinical Medicine, Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong Province, 261042, China
| | - Xin Wang
- Changchun University of Chinese Medicine, Changchun, Jilin Province, 130117, China
| | - Weiguo Liu
- Department of Traditional Chinese medicine, School of Clinical Medicine, Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong Province, 261042, China
| | - Aiju Wang
- Department of Traditional Chinese medicine, School of Clinical Medicine, Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong Province, 261042, China.
- Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, Shandong Province, 261042, China.
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