1
|
Zhou Z, Zhang R, Zhou A, Lv J, Chen S, Zou H, Zhang G, Lin T, Wang Z, Zhang Y, Weng S, Han X, Liu Z. Proteomics appending a complementary dimension to precision oncotherapy. Comput Struct Biotechnol J 2024; 23:1725-1739. [PMID: 38689716 PMCID: PMC11058087 DOI: 10.1016/j.csbj.2024.04.044] [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: 02/06/2024] [Revised: 04/11/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
Recent advances in high-throughput proteomic profiling technologies have facilitated the precise quantification of numerous proteins across multiple specimens concurrently. Researchers have the opportunity to comprehensively analyze the molecular signatures in plentiful medical specimens or disease pattern cell lines. Along with advances in data analysis and integration, proteomics data could be efficiently consolidated and employed to recognize precise elementary molecular mechanisms and decode individual biomarkers, guiding the precision treatment of tumors. Herein, we review a broad array of proteomics technologies and the progress and methods for the integration of proteomics data and further discuss how to better merge proteomics in precision medicine and clinical settings.
Collapse
Affiliation(s)
- Zhaokai Zhou
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Henan 450052, China
| | - Ruiqi Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Aoyang Zhou
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Jinxiang Lv
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Shuang Chen
- Center of Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Haijiao Zou
- Center of Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Ge Zhang
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Ting Lin
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Zhan Wang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Henan 450052, China
| | - Yuyuan Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Siyuan Weng
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Interventional Institute of Zhengzhou University, Zhengzhou, Henan 450052, China
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan 450052, China
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Interventional Institute of Zhengzhou University, Zhengzhou, Henan 450052, China
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan 450052, China
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| |
Collapse
|
2
|
Valente LC, Bacil GP, Riechelmann-Casarin L, Barbosa GC, Barbisan LF, Romualdo GR. Exploring in vitro modeling in hepatocarcinogenesis research: morphological and molecular features and similarities to the corresponding human disease. Life Sci 2024; 351:122781. [PMID: 38848937 DOI: 10.1016/j.lfs.2024.122781] [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: 01/06/2024] [Revised: 04/04/2024] [Accepted: 06/04/2024] [Indexed: 06/09/2024]
Abstract
The hepatocellular carcinoma (HCC) features a remarkable epidemiological burden, ranking as the third most lethal cancer worldwide. As the HCC-related molecular and cellular complexity unfolds as the disease progresses, the use of a myriad of in vitro models available is mandatory in translational preclinical research setups. In this review paper, we will compile cutting-edge information on the in vitro bioassays for HCC research, (A) emphasizing their morphological and molecular parallels with human HCC; (B) delineating the advantages and limitations of their application; and (C) offering perspectives on their prospective applications. While bidimensional (2D) (co) culture setups provide a rapid low-cost strategy for metabolism and drug screening investigations, tridimensional (3D) (co) culture bioassays - including patient-derived protocols as organoids and precision cut slices - surpass some of the 2D strategies limitations, mimicking the complex microarchitecture and cellular and non-cellular microenvironment observed in human HCC. 3D models have become invaluable tools to unveil HCC pathophysiology and targeted therapy. In both setups, the recapitulation of HCC in different etiologies/backgrounds (i.e., viral, fibrosis, and fatty liver) may be considered as a fundamental guide for obtaining translational findings. Therefore, a "multimodel" approach - encompassing the advantages of different in vitro bioassays - is encouraged to circumvent "model-biased" outcomes in preclinical HCC research.
Collapse
Affiliation(s)
- Leticia Cardoso Valente
- São Paulo State University (UNESP), Medical School, Botucatu, Experimental Research Unit (UNIPEX), Brazil
| | - Gabriel Prata Bacil
- São Paulo State University (UNESP), Institute of Biosciences, Botucatu, Department of Structural and Functional Biology, Brazil
| | - Luana Riechelmann-Casarin
- São Paulo State University (UNESP), Medical School, Botucatu, Experimental Research Unit (UNIPEX), Brazil
| | | | - Luís Fernando Barbisan
- São Paulo State University (UNESP), Institute of Biosciences, Botucatu, Department of Structural and Functional Biology, Brazil
| | - Guilherme Ribeiro Romualdo
- São Paulo State University (UNESP), Medical School, Botucatu, Experimental Research Unit (UNIPEX), Brazil.
| |
Collapse
|
3
|
Jing SY, Liu D, Feng N, Dong H, Wang HQ, Yan X, Chen XF, Qu MC, Lin P, Yi B, Feng F, Chen L, Wang HY, Li H, He YF. Spatial multiomics reveals a subpopulation of fibroblasts associated with cancer stemness in human hepatocellular carcinoma. Genome Med 2024; 16:98. [PMID: 39138551 DOI: 10.1186/s13073-024-01367-8] [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: 11/14/2023] [Accepted: 07/23/2024] [Indexed: 08/15/2024] Open
Abstract
BACKGROUND Cancer-associated fibroblasts (CAFs) are the prominent cell type in the tumor microenvironment (TME), and CAF subsets have been identified in various tumors. However, how CAFs spatially coordinate other cell populations within the liver TME to promote cancer progression remains unclear. METHODS We combined multi-region proteomics (6 patients, 24 samples), 10X Genomics Visium spatial transcriptomics (11 patients, 25 samples), and multiplexed imaging (92 patients, 264 samples) technologies to decipher the expression heterogeneity, functional diversity, spatial distribution, colocalization, and interaction of fibroblasts. The newly identified CAF subpopulation was validated by cells isolated from 5 liver cancer patients and in vitro functional assays. RESULTS We identified a liver CAF subpopulation, marked by the expression of COL1A2, COL4A1, COL4A2, CTGF, and FSTL1, and named F5-CAF. F5-CAF is preferentially located within and around tumor nests and colocalizes with cancer cells with higher stemness in hepatocellular carcinoma (HCC). Multiplexed staining of 92 patients and the bulk transcriptome of 371 patients demonstrated that the abundance of F5-CAFs in HCC was associated with a worse prognosis. Further in vitro experiments showed that F5-CAFs isolated from liver cancer patients can promote the proliferation and stemness of HCC cells. CONCLUSIONS We identified a CAF subpopulation F5-CAF in liver cancer, which is associated with cancer stemness and unfavorable prognosis. Our results provide potential mechanisms by which the CAF subset in the TME promotes the development of liver cancer by supporting the survival of cancer stem cells.
Collapse
Affiliation(s)
- Si-Yu Jing
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, People's Republic of China
| | - Dan Liu
- Molecular Pathology Laboratory, National Center for Liver Cancer, Eastern Hepatobiliary Surgery Hospital, Shanghai, 201800, People's Republic of China
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, People's Republic of China
| | - Na Feng
- Molecular Pathology Laboratory, National Center for Liver Cancer, Eastern Hepatobiliary Surgery Hospital, Shanghai, 201800, People's Republic of China
| | - Hui Dong
- Department of Pathology, Eastern Hepatobiliary Surgery Hospital, Shanghai, 200438, People's Republic of China
| | - He-Qi Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, People's Republic of China
| | - Xi Yan
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, People's Republic of China
| | - Xu-Feng Chen
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, People's Republic of China
| | - Min-Cheng Qu
- Molecular Pathology Laboratory, National Center for Liver Cancer, Eastern Hepatobiliary Surgery Hospital, Shanghai, 201800, People's Republic of China
| | - Ping Lin
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, People's Republic of China
| | - Bin Yi
- Department of Organ Transplantation, Eastern Hepatobiliary Surgery Hospital, Shanghai, 201800, People's Republic of China
| | - Feiling Feng
- Department of Biliary Tract Surgery I, Eastern Hepatobiliary Surgery Hospital, Shanghai, 201800, People's Republic of China
| | - Lei Chen
- National Center for Liver Cancer and International Cooperation Laboratory On Signal Transduction, Eastern Hepatobiliary Surgery Institute/Hospital, Shanghai, 200438, People's Republic of China.
| | - Hong-Yang Wang
- National Center for Liver Cancer and International Cooperation Laboratory On Signal Transduction, Eastern Hepatobiliary Surgery Institute/Hospital, Shanghai, 200438, People's Republic of China.
- Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer, Ministry of Education and Shanghai Key Laboratory of Hepatobiliary Tumor Biology, Shanghai, 200438, People's Republic of China.
| | - Hong Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, People's Republic of China.
| | - Yu-Fei He
- Molecular Pathology Laboratory, National Center for Liver Cancer, Eastern Hepatobiliary Surgery Hospital, Shanghai, 201800, People's Republic of China.
| |
Collapse
|
4
|
Miao B, Ge L, He C, Wang X, Wu J, Li X, Chen K, Wan J, Xing S, Ren L, Shi Z, Liu S, Hu Y, Chen J, Yu Y, Feng L, Flores NM, Liang Z, Xu X, Wang R, Zhou J, Fan J, Xiang B, Li E, Mao Y, Cheng J, Zhao K, Mazur PK, Cai J, Lan F. SMYD5 is a ribosomal methyltransferase that catalyzes RPL40 lysine methylation to enhance translation output and promote hepatocellular carcinoma. Cell Res 2024:10.1038/s41422-024-01013-3. [PMID: 39103523 DOI: 10.1038/s41422-024-01013-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Accepted: 07/23/2024] [Indexed: 08/07/2024] Open
Abstract
While lysine methylation is well-known for regulating gene expression transcriptionally, its implications in translation have been largely uncharted. Trimethylation at lysine 22 (K22me3) on RPL40, a core ribosomal protein located in the GTPase activation center, was first reported 27 years ago. Yet, its methyltransferase and role in translation remain unexplored. Here, we report that SMYD5 has robust in vitro activity toward RPL40 K22 and primarily catalyzes RPL40 K22me3 in cells. The loss of SMYD5 and RPL40 K22me3 leads to reduced translation output and disturbed elongation as evidenced by increased ribosome collisions. SMYD5 and RPL40 K22me3 are upregulated in hepatocellular carcinoma (HCC) and negatively correlated with patient prognosis. Depleting SMYD5 renders HCC cells hypersensitive to mTOR inhibition in both 2D and 3D cultures. Additionally, the loss of SMYD5 markedly inhibits HCC development and growth in both genetically engineered mouse and patient-derived xenograft (PDX) models, with the inhibitory effect in the PDX model further enhanced by concurrent mTOR suppression. Our findings reveal a novel role of the SMYD5 and RPL40 K22me3 axis in translation elongation and highlight the therapeutic potential of targeting SMYD5 in HCC, particularly with concurrent mTOR inhibition. This work also conceptually broadens the understanding of lysine methylation, extending its significance from transcriptional regulation to translational control.
Collapse
Affiliation(s)
- Bisi Miao
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ling Ge
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chenxi He
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xinghao Wang
- China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Jibo Wu
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiang Li
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, China
| | - Kun Chen
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jinkai Wan
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Shenghui Xing
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lingnan Ren
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhennan Shi
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Shengnan Liu
- China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Yajun Hu
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jiajia Chen
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yanyan Yu
- China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Lijian Feng
- China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Natasha M Flores
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhihui Liang
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xinyi Xu
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ruoxin Wang
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jian Zhou
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jia Fan
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Bin Xiang
- China Novartis Institutes for BioMedical Research, Shanghai, China
| | - En Li
- China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Yuanhui Mao
- Department of Neurology of The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jingdong Cheng
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, China
| | - Kehao Zhao
- China Novartis Institutes for BioMedical Research, Shanghai, China
| | - Pawel K Mazur
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Jiabin Cai
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Fei Lan
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.
| |
Collapse
|
5
|
Liu Z, Yuan H, Wang Y, Li K, Suo C, Jin L, Ding C, Chen X. Proteogenomic Analysis Identifies a Causal Association between Plasma Apolipoprotein B Levels and Liver Cancer Risk. J Proteome Res 2024. [PMID: 39091241 DOI: 10.1021/acs.jproteome.4c00397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Liver oncogenesis is accompanied by discernible protein changes in the bloodstream. By employing plasma proteomic profiling, we can delve into the molecular mechanisms of liver cancer and pinpoint potential biomarkers. In this nested case-control study, we applied liquid chromatography-tandem mass spectrometry for proteome profiling in baseline plasma samples. Differential protein expression was determined and was subjected to functional enrichment, network, and Mendelian randomization (MR) analyses. We identified 193 proteins with notable differential levels between the groups. Of these proteins, MR analysis offered a compelling negative association between apolipoprotein B (APOB) and liver cancer. This association was further corroborated in the UK Biobank cohort: genetically predicted APOB levels were associated with a 31% (95% CI 19-42%) decreased risk of liver cancer; and phenotypic analysis indicated an 11% (95% CI 8-14%) decreased liver cancer risk for every 0.1 g/L increase of circulating APOB levels. Multivariable MR analysis suggested that the hepatic fat content might fully mediate the APOB-liver cancer connection. In summary, we identified some plasma proteins, particularly APOB, as potential biomarkers of liver cancer. Our findings underscore the intricate link between lipid metabolism and liver cancer, offering hints for targeted prophylactic strategies and early detection.
Collapse
Affiliation(s)
- Zhenqiu Liu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, Shanghai 200438, China
- Fudan University Taizhou Institute of Health Sciences, Taizhou 225316, China
| | - Huangbo Yuan
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, Shanghai 200438, China
- Fudan University Taizhou Institute of Health Sciences, Taizhou 225316, China
| | - Yunzhi Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Kai Li
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Chen Suo
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai 200032, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, Shanghai 200438, China
- Fudan University Taizhou Institute of Health Sciences, Taizhou 225316, China
| | - Chen Ding
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xingdong Chen
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| |
Collapse
|
6
|
Guo DZ, Zhang X, Zhang SQ, Zhang SY, Zhang XY, Yan JY, Dong SY, Zhu K, Yang XR, Fan J, Zhou J, Huang A. Single-cell tumor heterogeneity landscape of hepatocellular carcinoma: unraveling the pro-metastatic subtype and its interaction loop with fibroblasts. Mol Cancer 2024; 23:157. [PMID: 39095854 PMCID: PMC11295380 DOI: 10.1186/s12943-024-02062-3] [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: 02/01/2024] [Accepted: 07/05/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND Tumor heterogeneity presents a formidable challenge in understanding the mechanisms driving tumor progression and metastasis. The heterogeneity of hepatocellular carcinoma (HCC) in cellular level is not clear. METHODS Integration analysis of single-cell RNA sequencing data and spatial transcriptomics data was performed. Multiple methods were applied to investigate the subtype of HCC tumor cells. The functional characteristics, translation factors, clinical implications and microenvironment associations of different subtypes of tumor cells were analyzed. The interaction of subtype and fibroblasts were analyzed. RESULTS We established a heterogeneity landscape of HCC malignant cells by integrated 52 single-cell RNA sequencing data and 5 spatial transcriptomics data. We identified three subtypes in tumor cells, including ARG1+ metabolism subtype (Metab-subtype), TOP2A+ proliferation phenotype (Prol-phenotype), and S100A6+ pro-metastatic subtype (EMT-subtype). Enrichment analysis found that the three subtypes harbored different features, that is metabolism, proliferating, and epithelial-mesenchymal transition. Trajectory analysis revealed that both Metab-subtype and EMT-subtype originated from the Prol-phenotype. Translation factor analysis found that EMT-subtype showed exclusive activation of SMAD3 and TGF-β signaling pathway. HCC dominated by EMT-subtype cells harbored an unfavorable prognosis and a deserted microenvironment. We uncovered a positive loop between tumor cells and fibroblasts mediated by SPP1-CD44 and CCN2/TGF-β-TGFBR1 interaction pairs. Inhibiting CCN2 disrupted the loop, mitigated the transformation to EMT-subtype, and suppressed metastasis. CONCLUSION By establishing a heterogeneity landscape of malignant cells, we identified a three-subtype classification in HCC. Among them, S100A6+ tumor cells play a crucial role in metastasis. Targeting the feedback loop between tumor cells and fibroblasts is a promising anti-metastatic strategy.
Collapse
Affiliation(s)
- De-Zhen Guo
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 136 Yi Xue Yuan Road, Shanghai, 200032, China
- Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Xin Zhang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 136 Yi Xue Yuan Road, Shanghai, 200032, China
- Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Sen-Quan Zhang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 136 Yi Xue Yuan Road, Shanghai, 200032, China
- Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Shi-Yu Zhang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 136 Yi Xue Yuan Road, Shanghai, 200032, China
- Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Xiang-Yu Zhang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 136 Yi Xue Yuan Road, Shanghai, 200032, China
- Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Jia-Yan Yan
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 136 Yi Xue Yuan Road, Shanghai, 200032, China
- Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - San-Yuan Dong
- Department of Radiology, Zhongshan Hospital, Shanghai Institute of Medical Imaging, Fudan University, Shanghai, 200032, China
| | - Kai Zhu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 136 Yi Xue Yuan Road, Shanghai, 200032, China
- Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Xin-Rong Yang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 136 Yi Xue Yuan Road, Shanghai, 200032, China
- Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Jia Fan
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 136 Yi Xue Yuan Road, Shanghai, 200032, China
- Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Institute of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Jian Zhou
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 136 Yi Xue Yuan Road, Shanghai, 200032, China.
- Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
- Institute of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
- State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China.
| | - Ao Huang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, 136 Yi Xue Yuan Road, Shanghai, 200032, China.
- Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
| |
Collapse
|
7
|
Xie H, Huang G, Mai H, Chen J, Na R, Jiang D. Identification of pyroptosis subtypes and prognosis model of hepatocellular carcinoma based on pyroptosis-related genes. Cancer Med 2024; 13:e70081. [PMID: 39126216 PMCID: PMC11316015 DOI: 10.1002/cam4.70081] [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: 12/21/2023] [Revised: 04/25/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a common malignant tumor with poor prognosis. Pyroptosis, a type of programmed cell death, regulates tumor cell development. However, the role of pyroptosis-related genes (PRGs) in HCC and their association with prognosis are unclear. METHODS We conducted bioinformatics analysis to identify PRGs in The Cancer Genome Atlas-Liver Hepatocellular Carcinoma (TCGA-LIHC) patients. Consensus clustering classified patients into different subtypes. We used LASSO regression to established a pyroptosis subtype-related score (PSRS) related to prognosis. OncoPredict identified potential pharmaceuticals based on PSRS. RESULTS We found 20 HCC-related PRGs in 335 TCGA-LIHC patients. Consensus clustering classified patients into two subtypes. Subtype I had better overall survival and higher response to anti-PD1 treatment. The prognostic model involving 20 genes predicted poorer prognosis for high-PSRS group. The model was validated in two external cohorts. OncoPredict identified 65 potential pharmaceuticals based on PSRS. CONCLUSION Our investigation revealed a correlation between pyroptosis and HCC. We established PSRS as independent risk factors for predicting prognosis. The study paves the way for using PRGs as prognostic biomarkers and exploring personalized therapy for HCC.
Collapse
Affiliation(s)
- Haisheng Xie
- State Key Laboratory of Organ Failure Research, MOE Key Laboratory of Infectious Diseases Research in South China, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangdong Provincial Clinical Research Center for Viral Hepatitis, Guangdong Institute of Liver DiseasesDepartment of Infectious Diseases and Hepatology Unit, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
- The Key Laboratory of Molecular Pathology (Hepatic Diseases) of Guangxi, Department of PathologyThe Affiliated Hospital of Youjiang Medical University for NationalitiesBaiseGuangxiChina
| | - Guanlin Huang
- State Key Laboratory of Organ Failure Research, MOE Key Laboratory of Infectious Diseases Research in South China, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangdong Provincial Clinical Research Center for Viral Hepatitis, Guangdong Institute of Liver DiseasesDepartment of Infectious Diseases and Hepatology Unit, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
| | - Haoming Mai
- State Key Laboratory of Organ Failure Research, MOE Key Laboratory of Infectious Diseases Research in South China, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangdong Provincial Clinical Research Center for Viral Hepatitis, Guangdong Institute of Liver DiseasesDepartment of Infectious Diseases and Hepatology Unit, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
| | - Jiaxuan Chen
- State Key Laboratory of Organ Failure Research, MOE Key Laboratory of Infectious Diseases Research in South China, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangdong Provincial Clinical Research Center for Viral Hepatitis, Guangdong Institute of Liver DiseasesDepartment of Infectious Diseases and Hepatology Unit, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
| | - Rong Na
- Division of Urology, Department of Surgery, LKS Faculty of MedicineThe University of Hong KongHong KongChina
| | - De‐Ke Jiang
- State Key Laboratory of Organ Failure Research, MOE Key Laboratory of Infectious Diseases Research in South China, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangdong Provincial Clinical Research Center for Viral Hepatitis, Guangdong Institute of Liver DiseasesDepartment of Infectious Diseases and Hepatology Unit, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
- The Key Laboratory of Molecular Pathology (Hepatic Diseases) of Guangxi, Department of PathologyThe Affiliated Hospital of Youjiang Medical University for NationalitiesBaiseGuangxiChina
| |
Collapse
|
8
|
Yang Z, Zheng Y, Gao Q. Lysine lactylation in the regulation of tumor biology. Trends Endocrinol Metab 2024; 35:720-731. [PMID: 38395657 DOI: 10.1016/j.tem.2024.01.011] [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: 12/01/2023] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 02/25/2024]
Abstract
Lysine lactylation (Kla), a newly discovered post-translational modification (PTM) of lysine residues, is progressively revealing its crucial role in tumor biology. A growing body of evidence supports its capacity of transcriptional regulation through histone modification and modulation of non-histone protein function. It intricately participates in a myriad of events in the tumor microenvironment (TME) by orchestrating the transitions of immune states and augmenting tumor malignancy. Its preferential modification of metabolic proteins underscores its specific regulatory influence on metabolism. This review focuses on the effect and the probable mechanisms of Kla-mediated regulation of tumor metabolism, the upstream factors that determine Kla intensity, and its potential implications for the clinical diagnosis and treatment of tumors.
Collapse
Affiliation(s)
- Zijian Yang
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yingqi Zheng
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qiang Gao
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China; Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China; State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China.
| |
Collapse
|
9
|
Lyu P, Li F, Deng R, Wei Q, Lin B, Cheng L, Zhao B, Lu Z. Lnc-PIK3R1, transcriptionally suppressed by YY1, inhibits hepatocellular carcinoma progression via the Lnc-PIK3R1/miR-1286/GSK3β axis. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167233. [PMID: 38744342 DOI: 10.1016/j.bbadis.2024.167233] [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: 01/29/2024] [Revised: 05/03/2024] [Accepted: 05/09/2024] [Indexed: 05/16/2024]
Abstract
Hepatocellular carcinoma (HCC) poses a significant threat due to its highly aggressive and high recurrence characteristics, necessitating urgent advances in diagnostic and therapeutic approaches. Long non-coding RNAs exert vital roles in HCC tumorigenesis, however the mechanisms of their expression regulation and functions are not fully elucidated yet. Herein, we identify that a novel tumor suppressor 'lnc-PIK3R1' was significantly downregulated in HCC tissues, which was correlated with poor prognosis. Functionally, lnc-PIK3R1 played tumor suppressor roles to inhibit the proliferation and mobility of HCC cells, and to impede the distant implantation of xenograft in mice. Mechanistic studies revealed that lnc-PIK3R1 interacted with miR-1286 and alleviated the repression on GSK3B by miR-1286. Notably, pharmacological inhibition of GSK3β compromised the tumor suppression effect by lnc-PIK3R1, confirming their functional relevance. Moreover, we identified that oncogenic YY1 acts as a specific transcriptional repressor to downregulate the expression of lnc-PIK3R1 in HCC. In summary, this study highlights the tumor-suppressive effect of lnc-PIK3R1, and provides new insights into the regulation of GSK3β expression in HCC, which would benefit the development of innovative intervention strategies for HCC.
Collapse
Affiliation(s)
- Peng Lyu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, PR China
| | - Fengyue Li
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, PR China
| | - Runzhi Deng
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, PR China
| | - Qiliang Wei
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, PR China
| | - Bingkai Lin
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, PR China
| | - Lei Cheng
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, PR China
| | - Bixing Zhao
- The United Innovation of Mengchao Hepatobiliary Technology, Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, PR China.
| | - Zhonglei Lu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, PR China.
| |
Collapse
|
10
|
Zhang Y, Yang C, Wang J, Wang L, Zhao Y, Sun L, Sun W, Zhu Y, Li J, Wu S. BioLadder: A bioinformatic platform primarily focused on proteomic data analysis. IMETA 2024; 3:e215. [PMID: 39135688 PMCID: PMC11316921 DOI: 10.1002/imt2.215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/30/2024] [Accepted: 05/31/2024] [Indexed: 08/15/2024]
Abstract
BioLadder (https://www.bioladder.cn/) is an online data analysis platform designed for proteomics research, which includes three classes of experimental data analysis modules and four classes of common data analysis modules. It allows for a variety of proteomics analyses to be conducted easily and efficiently. Additionally, most modules can also be utilized for the analysis of other omics data. To facilitate user experience, we have carefully designed four different kinds of functions for customers to quickly and accurately utilize the relevant analysis modules.
Collapse
Affiliation(s)
| | - Chunyuan Yang
- State Key Laboratory of ProteomicsBeijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsBeijingChina
| | - Jinhao Wang
- Beijing Qinglian Biotech Co., Ltd.BeijingChina
| | - Lixin Wang
- Beijing Qinglian Biotech Co., Ltd.BeijingChina
| | - Yan Zhao
- Beijing Qinglian Biotech Co., Ltd.BeijingChina
| | | | - Wei Sun
- Beijing Qinglian Biotech Co., Ltd.BeijingChina
| | - Yunping Zhu
- State Key Laboratory of ProteomicsBeijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsBeijingChina
| | - Jingli Li
- Beijing Qinglian Biotech Co., Ltd.BeijingChina
| | - Songfeng Wu
- Beijing Qinglian Biotech Co., Ltd.BeijingChina
| |
Collapse
|
11
|
Tan S, Zhang X, Guo X, Pan G, Yan L, Ding Z, Li R, Wang D, Yan Y, Dong Z, Li T. DAP3 promotes mitochondrial activity and tumour progression in hepatocellular carcinoma by regulating MT-ND5 expression. Cell Death Dis 2024; 15:540. [PMID: 39080251 PMCID: PMC11289107 DOI: 10.1038/s41419-024-06912-2] [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: 01/17/2024] [Revised: 07/09/2024] [Accepted: 07/15/2024] [Indexed: 08/02/2024]
Abstract
Cancer cells often exhibit fragmented mitochondria and dysregulated mitochondrial dynamics, but the underlying mechanism remains elusive. Here, we found that the mitochondrial protein death-associated protein 3 (DAP3) is localized to mitochondria and promotes the progression of hepatocellular carcinoma (HCC) by regulating mitochondrial function. DAP3 can promote the proliferation, migration, and invasion of HCC cells in vitro and in vivo by increasing mitochondrial respiration, inducing the epithelial-mesenchymal transition (EMT), and slowing cellular senescence. Mechanistically, DAP3 can increase mitochondrial complex I activity in HCC cells by regulating the translation and expression of MT-ND5. The phosphorylation of DAP3 at Ser185 mediated by AKT is the key event mediating the mitochondrial localization and function of DAP3 in HCC cells. In addition, the DAP3 expression in HCC samples is inversely correlated with patient survival. Our results revealed a mechanism by which DAP3 promotes mitochondrial function and HCC progression by regulating MT-ND5 translation and expression, indicating that DAP3 may be a therapeutic target for HCC.
Collapse
Affiliation(s)
- Siyu Tan
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250012, China
- Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province and Department of Immunology, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Xiao Zhang
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250012, China
| | - Xiaowei Guo
- Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province and Department of Immunology, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Guoqiang Pan
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250012, China
| | - Lunjie Yan
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250012, China
| | - Ziniu Ding
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250012, China
| | - Ruizhe Li
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250012, China
| | - Dongxu Wang
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250012, China
| | - Yuchuan Yan
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250012, China
| | - Zhaoru Dong
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250012, China.
| | - Tao Li
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250012, China.
| |
Collapse
|
12
|
Du N, Yi L, Wang J, Lei Y, Bo X, Guo F, Wang R, Chai J, Liu G. High expression of YEATS2 as a predictive factor of poor prognosis in patients with hepatocellular carcinoma. Sci Rep 2024; 14:17246. [PMID: 39060453 PMCID: PMC11282058 DOI: 10.1038/s41598-024-68348-0] [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: 04/30/2024] [Accepted: 07/23/2024] [Indexed: 07/28/2024] Open
Abstract
YEATS domain containing 2 (YEATS2), it may function as a proto-oncogene. This study aims to investigate if YEATS2 correlates with prognosis in hepatocellular carcinoma. The prognostic landscape of YEATS2 and its relationship with expression in hepatocellular carcinoma were deciphered with public databases, RT-qPCR and western-blot in tissue samples. The expression profiling and prognostic value of YEATS2 were explored using UALCAN, TIMER, OncoLnc database. Transcription and survival analyses of YEATS2 in hepatocellular carcinoma were investigated with cBioPortal database. The STRING database was explored to identify molecular functions and signaling pathways downstream of YEATS2. YEATS2 expression was significantly higher in hepatocellular carcinoma compared with adjacent non-malignant tissues. Promoter methylation of YEATS2 exhibited different patterns in hepatocellular carcinoma. High expression of YEATS2 was associated with poorer survival. Mechanistically, YEATS2 was involved in mediating multiple biological processes including morphogenesis and migration.
Collapse
Affiliation(s)
- Ning Du
- Department of Hepatobiliary Surgery, Liaocheng People's Hospital, Liaocheng, 252000, China
| | - Lili Yi
- Joint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, 252000, China
| | - Jiamu Wang
- Department of Hepatobiliary Surgery, Liaocheng People's Hospital, Liaocheng, 252000, China
| | - Yongqiang Lei
- Joint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, 252000, China
| | - Xiaohui Bo
- Department of Hepatobiliary Surgery, Liaocheng People's Hospital, Liaocheng, 252000, China
| | - Fangjie Guo
- Joint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, 252000, China
| | - Ruhao Wang
- Joint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, 252000, China
| | - Jian Chai
- Joint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, 252000, China.
| | - Guijie Liu
- Department of Hepatobiliary Surgery, Liaocheng People's Hospital, Liaocheng, 252000, China.
| |
Collapse
|
13
|
Wang H, Liang Y, Liu Z, Zhang R, Chao J, Wang M, Liu M, Qiao L, Xuan Z, Zhao H, Lu L. POSTN + cancer-associated fibroblasts determine the efficacy of immunotherapy in hepatocellular carcinoma. J Immunother Cancer 2024; 12:e008721. [PMID: 39067872 DOI: 10.1136/jitc-2023-008721] [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] [Accepted: 06/08/2024] [Indexed: 07/30/2024] Open
Abstract
OBJECTIVE Hepatocellular carcinoma (HCC) poses a significant clinical challenge because the long-term benefits of immune checkpoint blockade therapy are limited. A comprehensive understanding of the mechanisms underlying immunotherapy resistance in HCC is imperative for improving patient prognosis. DESIGN In this study, to systematically investigate the characteristics of cancer-associated fibroblast (CAF) subsets and the dynamic communication among the tumor microenvironment (TME) components regulated by CAF subsets, we generated an HCC atlas by compiling single-cell RNA sequencing (scRNA-seq) datasets on 220 samples from six datasets. We combined spatial transcriptomics with scRNA-seq and multiplexed immunofluorescence to identify the specific CAF subsets in the TME that determine the efficacy of immunotherapy in HCC patients. RESULTS Our findings highlight the pivotal role of POSTN+ CAFs as potent immune response barriers at specific tumor locations, as they hinder effective T-cell infiltration and decrease the efficacy of immunotherapy. Additionally, we elucidated the interplay between POSTN+ CAFs and SPP1+ macrophages, whereby the former recruits the latter and triggers increased SPP1 expression via the IL-6/STAT3 signaling pathway. Moreover, we demonstrated a spatial correlation between POSTN+ CAFs and SPP1+ macrophages, revealing an immunosuppressive microenvironment that limits the immunotherapy response. Notably, we found that patients with elevated expression levels of both POSTN+ CAFs and SPP1+ macrophages achieved less therapeutic benefit in an immunotherapy cohort. CONCLUSION Our research elucidates light on the role of a particular subset of CAFs in immunotherapy resistance, emphasizing the potential benefits of targeting specific CAF subpopulations to improve clinical responses to immunotherapy.
Collapse
Affiliation(s)
- Hao Wang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital,Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University & Research Unit of Liver Transplantation and Transplant Immunology, Chinese Academy of Medical Sciences, Nanjing, Jiangsu, China
| | - Yuan Liang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University & Research Unit of Liver Transplantation and Transplant Immunology, Chinese Academy of Medical Sciences, Nanjing, Jiangsu, China
- School of Biological Science & Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Zheng Liu
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Rui Zhang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University & Research Unit of Liver Transplantation and Transplant Immunology, Chinese Academy of Medical Sciences, Nanjing, Jiangsu, China
| | - Jiashuo Chao
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital,Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University & Research Unit of Liver Transplantation and Transplant Immunology, Chinese Academy of Medical Sciences, Nanjing, Jiangsu, China
| | - Mingming Wang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital,Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University & Research Unit of Liver Transplantation and Transplant Immunology, Chinese Academy of Medical Sciences, Nanjing, Jiangsu, China
| | - Mu Liu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University & Research Unit of Liver Transplantation and Transplant Immunology, Chinese Academy of Medical Sciences, Nanjing, Jiangsu, China
| | - Lei Qiao
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University & Research Unit of Liver Transplantation and Transplant Immunology, Chinese Academy of Medical Sciences, Nanjing, Jiangsu, China
| | - Zhengfeng Xuan
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University & Research Unit of Liver Transplantation and Transplant Immunology, Chinese Academy of Medical Sciences, Nanjing, Jiangsu, China
| | - Haitao Zhao
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital,Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Ling Lu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University & Research Unit of Liver Transplantation and Transplant Immunology, Chinese Academy of Medical Sciences, Nanjing, Jiangsu, China
- Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| |
Collapse
|
14
|
Chen H, Chen Q, Chen J, Mao Y, Duan L, Ye D, Cheng W, Chen J, Gao X, Lin R, Lin W, Zhang M, Qi Y. Deciphering the Effects of the PYCR Family on Cell Function, Prognostic Value, Immune Infiltration in ccRCC and Pan-Cancer. Int J Mol Sci 2024; 25:8096. [PMID: 39125668 PMCID: PMC11311831 DOI: 10.3390/ijms25158096] [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: 07/08/2024] [Revised: 07/17/2024] [Accepted: 07/19/2024] [Indexed: 08/12/2024] Open
Abstract
Pyrroline-5-carboxylate reductase (PYCR) is pivotal in converting pyrroline-5-carboxylate (P5C) to proline, the final step in proline synthesis. Three isoforms, PYCR1, PYCR2, and PYCR3, existed and played significant regulatory roles in tumor initiation and progression. In this study, we first assessed the molecular and immune characteristics of PYCRs by a pan-cancer analysis, especially focusing on their prognostic relevance. Then, a kidney renal clear cell carcinoma (KIRC)-specific prognostic model was established, incorporating pathomics features to enhance predictive capabilities. The biological functions and regulatory mechanisms of PYCR1 and PYCR2 were investigated by in vitro experiments in renal cancer cells. The PYCRs' expressions were elevated in diverse tumors, correlating with unfavorable clinical outcomes. PYCRs were enriched in cancer signaling pathways, significantly correlating with immune cell infiltration, tumor mutation burden (TMB), and microsatellite instability (MSI). In KIRC, a prognostic model based on PYCR1 and PYCR2 was independently validated statistically. Leveraging features from H&E-stained images, a pathomics feature model reliably predicted patient prognosis. In vitro experiments demonstrated that PYCR1 and PYCR2 enhanced the proliferation and migration of renal carcinoma cells by activating the mTOR pathway, at least in part. This study underscores PYCRs' pivotal role in various tumors, positioning them as potential prognostic biomarkers and therapeutic targets, particularly in malignancies like KIRC. The findings emphasize the need for a broader exploration of PYCRs' implications in pan-cancer contexts.
Collapse
MESH Headings
- Humans
- Pyrroline Carboxylate Reductases/metabolism
- Pyrroline Carboxylate Reductases/genetics
- Carcinoma, Renal Cell/immunology
- Carcinoma, Renal Cell/pathology
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/metabolism
- Prognosis
- Kidney Neoplasms/immunology
- Kidney Neoplasms/pathology
- Kidney Neoplasms/genetics
- Kidney Neoplasms/metabolism
- Biomarkers, Tumor/metabolism
- Biomarkers, Tumor/genetics
- Cell Line, Tumor
- Gene Expression Regulation, Neoplastic
- delta-1-Pyrroline-5-Carboxylate Reductase
- Cell Proliferation
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Signal Transduction
Collapse
Affiliation(s)
- Hongquan Chen
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China; (H.C.); (Q.C.); (Y.M.); (L.D.); (D.Y.); (W.C.); (J.C.); (X.G.); (R.L.); (W.L.)
| | - Qing Chen
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China; (H.C.); (Q.C.); (Y.M.); (L.D.); (D.Y.); (W.C.); (J.C.); (X.G.); (R.L.); (W.L.)
| | - Jinyang Chen
- College of Computer and Cyber Security, Fujian Normal University, Fuzhou 350009, China;
| | - Yazhen Mao
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China; (H.C.); (Q.C.); (Y.M.); (L.D.); (D.Y.); (W.C.); (J.C.); (X.G.); (R.L.); (W.L.)
| | - Lidi Duan
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China; (H.C.); (Q.C.); (Y.M.); (L.D.); (D.Y.); (W.C.); (J.C.); (X.G.); (R.L.); (W.L.)
| | - Dongjie Ye
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China; (H.C.); (Q.C.); (Y.M.); (L.D.); (D.Y.); (W.C.); (J.C.); (X.G.); (R.L.); (W.L.)
| | - Wenxiu Cheng
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China; (H.C.); (Q.C.); (Y.M.); (L.D.); (D.Y.); (W.C.); (J.C.); (X.G.); (R.L.); (W.L.)
| | - Jiaxi Chen
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China; (H.C.); (Q.C.); (Y.M.); (L.D.); (D.Y.); (W.C.); (J.C.); (X.G.); (R.L.); (W.L.)
| | - Xinrong Gao
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China; (H.C.); (Q.C.); (Y.M.); (L.D.); (D.Y.); (W.C.); (J.C.); (X.G.); (R.L.); (W.L.)
| | - Renxi Lin
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China; (H.C.); (Q.C.); (Y.M.); (L.D.); (D.Y.); (W.C.); (J.C.); (X.G.); (R.L.); (W.L.)
| | - Weibin Lin
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China; (H.C.); (Q.C.); (Y.M.); (L.D.); (D.Y.); (W.C.); (J.C.); (X.G.); (R.L.); (W.L.)
| | - Mingfang Zhang
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China; (H.C.); (Q.C.); (Y.M.); (L.D.); (D.Y.); (W.C.); (J.C.); (X.G.); (R.L.); (W.L.)
| | - Yuanlin Qi
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China; (H.C.); (Q.C.); (Y.M.); (L.D.); (D.Y.); (W.C.); (J.C.); (X.G.); (R.L.); (W.L.)
| |
Collapse
|
15
|
Xiang H, Luo R, Wang Y, Yang B, Xu S, Huang W, Tang S, Fang R, Chen L, Zhu N, Yu Z, Akesu S, Wei C, Xu C, Zhou Y, Gu J, Zhao J, Hou Y, Ding C. Proteogenomic insights into the biology and treatment of pan-melanoma. Cell Discov 2024; 10:78. [PMID: 39039072 PMCID: PMC11263678 DOI: 10.1038/s41421-024-00688-7] [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: 08/04/2023] [Accepted: 05/03/2024] [Indexed: 07/24/2024] Open
Abstract
Melanoma is one of the most prevalent skin cancers, with high metastatic rates and poor prognosis. Understanding its molecular pathogenesis is crucial for improving its diagnosis and treatment. Integrated analysis of multi-omics data from 207 treatment-naïve melanomas (primary-cutaneous-melanomas (CM, n = 28), primary-acral-melanomas (AM, n = 81), primary-mucosal-melanomas (MM, n = 28), metastatic-melanomas (n = 27), and nevi (n = 43)) provides insights into melanoma biology. Multivariate analysis reveals that PRKDC amplification is a prognostic molecule for melanomas. Further proteogenomic analysis combined with functional experiments reveals that the cis-effect of PRKDC amplification may lead to tumor proliferation through the activation of DNA repair and folate metabolism pathways. Proteome-based stratification of primary melanomas defines three prognosis-related subtypes, namely, the ECM subtype, angiogenesis subtype (with a high metastasis rate), and cell proliferation subtype, which provides an essential framework for the utilization of specific targeted therapies for particular melanoma subtypes. The immune classification identifies three immune subtypes. Further analysis combined with an independent anti-PD-1 treatment cohort reveals that upregulation of the MAPK7-NFKB signaling pathway may facilitate T-cell recruitment and increase the sensitivity of patients to immunotherapy. In contrast, PRKDC may reduce the sensitivity of melanoma patients to immunotherapy by promoting DNA repair in melanoma cells. These results emphasize the clinical value of multi-omics data and have the potential to improve the understanding of melanoma treatment.
Collapse
Affiliation(s)
- Hang Xiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Rongkui Luo
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yunzhi Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Bing Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Sha Xu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Wen Huang
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Shaoshuai Tang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Rundong Fang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lingli Chen
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Na Zhu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zixiang Yu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Sujie Akesu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chuanyuan Wei
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chen Xu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Yuhong Zhou
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Jianying Gu
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital (Xiamen), Fudan University, Shanghai, China.
| | - Jianyuan Zhao
- Institute for Developmental and Regenerative Cardiovascular Medicine, MOE-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Yingyong Hou
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Chen Ding
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.
| |
Collapse
|
16
|
Duan Y, Zhan H, Wang Q, Li B, Gao H, Liu D, Xu Q, Gao X, Liu Z, Gao P, Wei G, Wang Y. Integrated Lactylome Characterization Reveals the Molecular Dynamics of Protein Regulation in Gastrointestinal Cancers. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2400227. [PMID: 39018247 DOI: 10.1002/advs.202400227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 05/19/2024] [Indexed: 07/19/2024]
Abstract
Lysine lactylation (Kla) plays a vital role in several physiological processes. However, the cancer-specific modulation of Kla in gastrointestinal (GI) tumors requires systematic elucidation. Here, global lactylome profiling of cancerous and adjacent tissues is conducted from 40 patients with GI cancer and identified 11698 Kla sites. Lactylome integration revealed that Kla affects proteins involved in hallmark cancer processes, including epigenetic rewiring, metabolic perturbations, and genome instability. Moreover, the study revealed pan-cancer patterns of Kla alterations, among which 37 Kla sites are consistently upregulated in all four GI cancers and are involved in gene regulation. It is further verified that lactylation of CBX3 at K10 mediates its interaction of CBX3 with the epigenetic marker H3K9me3 and facilitates GI cancer progression. Overall, this study provides an invaluable resource for understanding the lactylome landscape in GI cancers, which may provide new paths for drug discovery for these devastating diseases.
Collapse
Affiliation(s)
- Yangmiao Duan
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Cell Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Hanxiang Zhan
- Division of Pancreatic Surgery, Department of General Surgery, Qilu Hospital, Shandong University, Jinan, Shandong, 250012, China
| | - Qin Wang
- Department of Anesthesiology, Qilu Hospital, Shandong University, Jinan, Shandong, 250012, China
| | - Bohao Li
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Cell Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Huiru Gao
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250033, China
| | - Duanrui Liu
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China
| | - Qinchen Xu
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250033, China
| | - Xin Gao
- Division of Pancreatic Surgery, Department of General Surgery, Qilu Hospital, Shandong University, Jinan, Shandong, 250012, China
| | - Zhenya Liu
- Division of Pancreatic Surgery, Department of General Surgery, Qilu Hospital, Shandong University, Jinan, Shandong, 250012, China
| | - Peng Gao
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Pathology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Guangwei Wei
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Cell Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Yunshan Wang
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China
| |
Collapse
|
17
|
Li Z, Wan J, Li S, Tang Y, Lin YCD, Ni J, Cai X, Yu J, Huang HD, Lee TY. Multi-Omics Characterization of E3 Regulatory Patterns in Different Cancer Types. Int J Mol Sci 2024; 25:7639. [PMID: 39062881 PMCID: PMC11276688 DOI: 10.3390/ijms25147639] [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: 05/14/2024] [Revised: 07/01/2024] [Accepted: 07/05/2024] [Indexed: 07/28/2024] Open
Abstract
Ubiquitination, a post-translational modification, refers to the covalent attachment of ubiquitin molecules to substrates. This modification plays a critical role in diverse cellular processes such as protein degradation. The specificity of ubiquitination for substrates is regulated by E3 ubiquitin ligases. Dysregulation of ubiquitination has been associated with numerous diseases, including cancers. In our study, we first investigated the protein expression patterns of E3 ligases across 12 cancer types. Our findings indicated that E3 ligases tend to be up-regulated and exhibit reduced tissue specificity in tumors. Moreover, the correlation of protein expression between E3 ligases and substrates demonstrated significant changes in cancers, suggesting that E3-substrate specificity alters in tumors compared to normal tissues. By integrating transcriptome, proteome, and ubiquitylome data, we further characterized the E3-substrate regulatory patterns in lung squamous cell carcinoma. Our analysis revealed that the upregulation of the SKP2 E3 ligase leads to excessive degradation of BRCA2, potentially promoting tumor cell proliferation and metastasis. Furthermore, the upregulation of E3 ubiquitin-protein ligase TRIM33 was identified as a biomarker associated with a favorable prognosis by inhibiting the cell cycle. This work exemplifies how leveraging multi-omics data to analyze E3 ligases across various cancers can unveil prognosis biomarkers and facilitate the identification of potential drug targets for cancer therapy.
Collapse
Affiliation(s)
- Zhongyan Li
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; (Z.L.); (J.W.)
| | - Jingting Wan
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; (Z.L.); (J.W.)
| | - Shangfu Li
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; (Z.L.); (J.W.)
| | - Yun Tang
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, No. 75, Boai Street, Hsinchu 300, Taiwan
| | - Yang-Chi-Dung Lin
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; (Z.L.); (J.W.)
| | - Jie Ni
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; (Z.L.); (J.W.)
| | - Xiaoxuan Cai
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; (Z.L.); (J.W.)
| | - Jinhan Yu
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; (Z.L.); (J.W.)
| | - Hsien-Da Huang
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; (Z.L.); (J.W.)
| | - Tzong-Yi Lee
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, No. 75, Boai Street, Hsinchu 300, Taiwan
| |
Collapse
|
18
|
He N, Zhao W, Tian W, Wu Y, Xu J, Lu Y, Chen X, Zhao H. A cellular senescence-related signature for predicting prognosis, immunotherapy response, and candidate drugs in patients treated with transarterial chemoembolization (TACE). Discov Oncol 2024; 15:271. [PMID: 38976093 PMCID: PMC11231123 DOI: 10.1007/s12672-024-01116-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 06/20/2024] [Indexed: 07/09/2024] Open
Abstract
BACKGROUND Cellular senescence is essential to TME development, progression, and remodeling. Few studies have examined cellular senescence in HCC after TACE. Investigating the relationship between cellular senescence, post-TACE prognosis, the TME, and immune treatment responses is crucial. METHODS We analyzed the GSE104580 dataset to identify DEGs. A cellular senescence-related signature was developed using LASSO Cox regression in the GSE14520 dataset and validated in the ICGC dataset. High- and low-risk subgroups were compared using GSVA and GSEA. Correlation studies were conducted to explore the relationship between the prognostic model, immune infiltration, immunotherapy response, and drug sensitivity. RESULTS A cellular senescence-related signature comprising FOXM1, CDK1, CHEK1, and SERPINE1 was created and validated. High-risk patients showed significantly lower OS than low-risk patients. High-risk patients had carcinogenetic pathways activated, immunosuppressive cells infiltrated, and immunomodulatory genes overexpressed. They also showed higher sensitivity to EPZ004777_1237 and MK-2206_1053 and potential benefits from GSK-3 inhibitor IX, nortriptyline, lestaurtinib, and JNK-9L. CONCLUSIONS This study constructed a cellular senescence-related signature that could be used to predict HCC patients' responses to and prognosis after TACE treatment, aiding in the development of personalized treatment plans.
Collapse
Affiliation(s)
- Ning He
- Department of Interventional and Vascular Surgery, Affiliated Hospital of Nantong University, Nantong, China
| | - Wenjing Zhao
- Cancer Research Center Nantong, Affiliated Tumor Hospital of Nantong University, Nantong, China
| | - Wenlong Tian
- Department of Interventional and Vascular Surgery, Affiliated Hospital of Nantong University, Nantong, China
| | - Ying Wu
- Department of Interventional and Vascular Surgery, Affiliated Hospital of Nantong University, Nantong, China
| | - Jian Xu
- Department of Oncology, The Second People's Hospital of Nantong, Nantong, China
| | - Yunyan Lu
- Department of Gynecology, Affiliated Tumor Hospital of Nantong University, Nantong, China
| | - Xudong Chen
- Department of Pathology, Affiliated Tumor Hospital of Nantong University, Nantong, China.
| | - Hui Zhao
- Department of Interventional and Vascular Surgery, Affiliated Hospital of Nantong University, Nantong, China.
| |
Collapse
|
19
|
He ZJ, He K, Cai SW, Zhang R, Shao ZB, Wang ST, Li XP, Li YC, Liu WJ, Zhu YQ, Zeng SJ, Su YB, Shi Z. Phase separation of RNF214 promotes the progression of hepatocellular carcinoma. Cell Death Dis 2024; 15:483. [PMID: 38969650 PMCID: PMC11226663 DOI: 10.1038/s41419-024-06869-2] [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: 02/22/2024] [Revised: 06/21/2024] [Accepted: 06/27/2024] [Indexed: 07/07/2024]
Abstract
Hepatocellular carcinoma (HCC) is one of the most common malignant tumors, and the expression and function of an uncharacterized protein RNF214 in HCC are still unknown. Phase separation has recently been observed to participate in the progression of HCC. In this study, we investigated the expression, function, and phase separation of RNF214 in HCC. We found that RNF214 was highly expressed in HCC and associated with poor prognosis. RNF214 functioned as an oncogene to promote the proliferation, migration, and metastasis of HCC. Mechanically, RNF214 underwent phase separation, and the coiled-coil (CC) domain of RNF214 mediated its phase separation. Furthermore, the CC domain was necessary for the oncogenic function of RNF214 in HCC. Taken together, our data favored that phase separation of RNF214 promoted the progression of HCC. RNF214 may be a potential biomarker and therapeutic target for HCC.
Collapse
Affiliation(s)
- Zheng-Jie He
- Cancer Minimally Invasive Therapies Centre, Guangdong Second Provincial General Hospital, Jinan University, Guangzhou, Guangdong, 510632, China
- Department of Cell Biology & Institute of Biomedicine, Guangdong Provincial Biotechnology & Engineering Technology Research Center, Guangdong Provincial Key Laboratory of Bioengineering Medicine, Genomic Medicine Engineering Research Center of Ministry of Education, MOE Key Laboratory of Tumor Molecular Biology, National Engineering Research Center of Genetic Medicine, State Key Laboratory of Bioactive Molecules and Druggability Assessment, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, 510632, China
| | - Ke He
- Cancer Minimally Invasive Therapies Centre, Guangdong Second Provincial General Hospital, Jinan University, Guangzhou, Guangdong, 510632, China
| | - Song-Wang Cai
- Department of Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, 510632, China
| | - Rui Zhang
- Department of Cell Biology & Institute of Biomedicine, Guangdong Provincial Biotechnology & Engineering Technology Research Center, Guangdong Provincial Key Laboratory of Bioengineering Medicine, Genomic Medicine Engineering Research Center of Ministry of Education, MOE Key Laboratory of Tumor Molecular Biology, National Engineering Research Center of Genetic Medicine, State Key Laboratory of Bioactive Molecules and Druggability Assessment, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, 510632, China
| | - Zhong-Bao Shao
- Department of Cell Biology & Institute of Biomedicine, Guangdong Provincial Biotechnology & Engineering Technology Research Center, Guangdong Provincial Key Laboratory of Bioengineering Medicine, Genomic Medicine Engineering Research Center of Ministry of Education, MOE Key Laboratory of Tumor Molecular Biology, National Engineering Research Center of Genetic Medicine, State Key Laboratory of Bioactive Molecules and Druggability Assessment, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, 510632, China
| | - Sheng-Te Wang
- Department of Cell Biology & Institute of Biomedicine, Guangdong Provincial Biotechnology & Engineering Technology Research Center, Guangdong Provincial Key Laboratory of Bioengineering Medicine, Genomic Medicine Engineering Research Center of Ministry of Education, MOE Key Laboratory of Tumor Molecular Biology, National Engineering Research Center of Genetic Medicine, State Key Laboratory of Bioactive Molecules and Druggability Assessment, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, 510632, China
| | - Xiao-Peng Li
- Department of Cell Biology & Institute of Biomedicine, Guangdong Provincial Biotechnology & Engineering Technology Research Center, Guangdong Provincial Key Laboratory of Bioengineering Medicine, Genomic Medicine Engineering Research Center of Ministry of Education, MOE Key Laboratory of Tumor Molecular Biology, National Engineering Research Center of Genetic Medicine, State Key Laboratory of Bioactive Molecules and Druggability Assessment, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, 510632, China
| | - Yan-Chi Li
- Department of Cell Biology & Institute of Biomedicine, Guangdong Provincial Biotechnology & Engineering Technology Research Center, Guangdong Provincial Key Laboratory of Bioengineering Medicine, Genomic Medicine Engineering Research Center of Ministry of Education, MOE Key Laboratory of Tumor Molecular Biology, National Engineering Research Center of Genetic Medicine, State Key Laboratory of Bioactive Molecules and Druggability Assessment, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, 510632, China
| | - Wei-Jing Liu
- Department of Cell Biology & Institute of Biomedicine, Guangdong Provincial Biotechnology & Engineering Technology Research Center, Guangdong Provincial Key Laboratory of Bioengineering Medicine, Genomic Medicine Engineering Research Center of Ministry of Education, MOE Key Laboratory of Tumor Molecular Biology, National Engineering Research Center of Genetic Medicine, State Key Laboratory of Bioactive Molecules and Druggability Assessment, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, 510632, China
| | - You-Qing Zhu
- Department of Cell Biology & Institute of Biomedicine, Guangdong Provincial Biotechnology & Engineering Technology Research Center, Guangdong Provincial Key Laboratory of Bioengineering Medicine, Genomic Medicine Engineering Research Center of Ministry of Education, MOE Key Laboratory of Tumor Molecular Biology, National Engineering Research Center of Genetic Medicine, State Key Laboratory of Bioactive Molecules and Druggability Assessment, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, 510632, China
| | - Shi-Jie Zeng
- Department of Cell Biology & Institute of Biomedicine, Guangdong Provincial Biotechnology & Engineering Technology Research Center, Guangdong Provincial Key Laboratory of Bioengineering Medicine, Genomic Medicine Engineering Research Center of Ministry of Education, MOE Key Laboratory of Tumor Molecular Biology, National Engineering Research Center of Genetic Medicine, State Key Laboratory of Bioactive Molecules and Druggability Assessment, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, 510632, China
| | - Yu-Bin Su
- Department of Cell Biology & Institute of Biomedicine, Guangdong Provincial Biotechnology & Engineering Technology Research Center, Guangdong Provincial Key Laboratory of Bioengineering Medicine, Genomic Medicine Engineering Research Center of Ministry of Education, MOE Key Laboratory of Tumor Molecular Biology, National Engineering Research Center of Genetic Medicine, State Key Laboratory of Bioactive Molecules and Druggability Assessment, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, 510632, China
| | - Zhi Shi
- Cancer Minimally Invasive Therapies Centre, Guangdong Second Provincial General Hospital, Jinan University, Guangzhou, Guangdong, 510632, China.
- Department of Cell Biology & Institute of Biomedicine, Guangdong Provincial Biotechnology & Engineering Technology Research Center, Guangdong Provincial Key Laboratory of Bioengineering Medicine, Genomic Medicine Engineering Research Center of Ministry of Education, MOE Key Laboratory of Tumor Molecular Biology, National Engineering Research Center of Genetic Medicine, State Key Laboratory of Bioactive Molecules and Druggability Assessment, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, 510632, China.
| |
Collapse
|
20
|
Padarath K, Deroubaix A, Naicker P, Stoychev S, Kramvis A. Comparison of the Proteome of Huh7 Cells Transfected with Hepatitis B Virus Subgenotype A1, with or without G1862T. Curr Issues Mol Biol 2024; 46:7032-7047. [PMID: 39057060 PMCID: PMC11275860 DOI: 10.3390/cimb46070419] [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: 06/14/2024] [Revised: 07/01/2024] [Accepted: 07/03/2024] [Indexed: 07/28/2024] Open
Abstract
HBeAg is a non-structural, secreted protein of hepatitis B virus (HBV). Its p25 precursor is post-translationally modified in the endoplasmic reticulum. The G1862T precore mutation leads to the accumulation of P25 in the endoplasmic reticulum and activation of unfolded protein response. Using mass spectrometry, comparative proteome profiling of Huh-7 cells transfected with wildtype (WT) or G1862T revealed significantly differentially expressed proteins resulting in 12 dysregulated pathways unique to WT-transfected cells and 7 shared between cells transfected with either WT or G1862T. Except for the p38 MAPK signalling pathway, WT showed a higher number of DEPs than G1862T-transfected cells in all remaining six shared pathways. Two signalling pathways: oxidative stress and cell cycle signalling were differentially expressed only in cells transfected with G1862T. Fifteen pathways were dysregulated in G1862T-transfected cells compared to WT. The 15 dysregulated pathways were involved in the following processes: MAPK signalling, DNA synthesis and methylation, and extracellular matrix organization. Moreover, proteins involved in DNA synthesis signalling (replication protein A (RPA) and DNA primase (PRIM2)) were significantly upregulated in G1862T compared to WT. This upregulation was confirmed by mRNA quantification of both genes and immunofluorescent confocal microscopy for RPA only. The dysregulation of the pathways involved in these processes may lead to immune evasion, persistence, and uncontrolled proliferation, which are hallmarks of cancer.
Collapse
Affiliation(s)
- Kiyasha Padarath
- Hepatitis Virus Diversity Unit, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Science, University of Witwatersrand, 7 York Road, Johannesburg 2193, South Africa
| | - Aurélie Deroubaix
- Hepatitis Virus Diversity Unit, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Science, University of Witwatersrand, 7 York Road, Johannesburg 2193, South Africa
- Life Sciences Imaging Facility, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Johannesburg 2193, South Africa
| | - Previn Naicker
- Future Production Chemicals, Council for Scientific and Industrial Research, Pretoria 0001, South Africa;
| | - Stoyan Stoychev
- ReSyn Biosciences, Johannesburg 2194, South Africa;
- Evosep Biosystems, 5230 Odense, Denmark
| | - Anna Kramvis
- Hepatitis Virus Diversity Unit, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Science, University of Witwatersrand, 7 York Road, Johannesburg 2193, South Africa
| |
Collapse
|
21
|
Huo Z, Duan Y, Zhan D, Xu X, Zheng N, Cai J, Sun R, Wang J, Cheng F, Gao Z, Xu C, Liu W, Dong Y, Ma S, Zhang Q, Zheng Y, Lou L, Kuang D, Chu Q, Qin J, Wang G, Wang Y. Proteomic Stratification of Prognosis and Treatment Options for Small Cell Lung Cancer. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzae033. [PMID: 38961535 DOI: 10.1093/gpbjnl/qzae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 10/24/2023] [Accepted: 01/22/2024] [Indexed: 07/05/2024]
Abstract
Small cell lung cancer (SCLC) is a highly malignant and heterogeneous cancer with limited therapeutic options and prognosis prediction models. Here, we analyzed formalin-fixed, paraffin-embedded (FFPE) samples of surgical resections by proteomic profiling, and stratified SCLC into three proteomic subtypes (S-I, S-II, and S-III) with distinct clinical outcomes and chemotherapy responses. The proteomic subtyping was an independent prognostic factor and performed better than current tumor-node-metastasis or Veterans Administration Lung Study Group staging methods. The subtyping results could be further validated using FFPE biopsy samples from an independent cohort, extending the analysis to both surgical and biopsy samples. The signatures of the S-II subtype in particular suggested potential benefits from immunotherapy. Differentially overexpressed proteins in S-III, the worst prognostic subtype, allowed us to nominate potential therapeutic targets, indicating that patient selection may bring new hope for previously failed clinical trials. Finally, analysis of an independent cohort of SCLC patients who had received immunotherapy validated the prediction that the S-II patients had better progression-free survival and overall survival after first-line immunotherapy. Collectively, our study provides the rationale for future clinical investigations to validate the current findings for more accurate prognosis prediction and precise treatments.
Collapse
Affiliation(s)
- Zitian Huo
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- National Health Commission Key Laboratory of Respiratory Diseases, Tongji Hosptial, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yaqi Duan
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- National Health Commission Key Laboratory of Respiratory Diseases, Tongji Hosptial, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Dongdong Zhan
- Beijing Pineal Diagnostics Co., Ltd., Beijing 102206, China
| | - Xizhen Xu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Nairen Zheng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Jing Cai
- Institution of Pathology, The First Affiliated Hospital of Henan University, Kaifeng 475001, China
| | - Ruifang Sun
- Department of Tumor Biobank, Shanxi Cancer Hospital, Taiyuan 030013, China
| | - Jianping Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- Chongqing Key Laboratory of Big Data for Bio Intelligence, School of Bioinformation, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Fang Cheng
- Beijing Pineal Diagnostics Co., Ltd., Beijing 102206, China
| | - Zhan Gao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Caixia Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Wanlin Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yuting Dong
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Sailong Ma
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- National Health Commission Key Laboratory of Respiratory Diseases, Tongji Hosptial, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Qian Zhang
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yiyun Zheng
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Liping Lou
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Dong Kuang
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Qian Chu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jun Qin
- Beijing Pineal Diagnostics Co., Ltd., Beijing 102206, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Guoping Wang
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- National Health Commission Key Laboratory of Respiratory Diseases, Tongji Hosptial, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yi Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| |
Collapse
|
22
|
Luo R, Le H, Wu Q, Gong C. Nanoplatform-Based In Vivo Gene Delivery Systems for Cancer Therapy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2312153. [PMID: 38441386 DOI: 10.1002/smll.202312153] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/05/2024] [Indexed: 07/26/2024]
Abstract
Gene therapy uses modern molecular biology methods to repair disease-causing genes. As a burgeoning therapeutic, it has been widely applied for cancer therapy. Since 1989, there have been numerous clinical gene therapy cases worldwide. However, a few are successful. The main challenge of clinical gene therapy is the lack of efficient and safe vectors. Although viral vectors show high transfection efficiency, their application is still limited by immune rejection and packaging capacity. Therefore, the development of non-viral vectors is overwhelming. Nanoplatform-based non-viral vectors become a hotspot in gene therapy. The reasons are mainly as follows. 1) Non-viral vectors can be engineered to be uptaken by specific types of cells or tissues, providing effective targeting capability. 2) Non-viral vectors can protect goods that need to be delivered from degradation. 3) Nanoparticles can transport large-sized cargo such as CRISPR/Cas9 plasmids and nucleoprotein complexes. 4) Nanoparticles are highly biosafe, and they are not mutagenic in themselves compared to viral vectors. 5) Nanoparticles are easy to scale preparation, which is conducive to clinical conversion and application. Here, an overview of the categories of nanoplatform-based non-viral gene vectors, the limitations on their development, and their applications in cancer therapy.
Collapse
Affiliation(s)
- Rui Luo
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Hao Le
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Qinjie Wu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Changyang Gong
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| |
Collapse
|
23
|
Padarath K, Deroubaix A, Naicker P, Stoychev S, Kramvis A. Comparative Proteomic Analysis of Huh7 Cells Transfected with Sub-Saharan African Hepatitis B Virus (Sub)genotypes Reveals Potential Oncogenic Factors. Viruses 2024; 16:1052. [PMID: 39066215 PMCID: PMC11281506 DOI: 10.3390/v16071052] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
In sub-Saharan Africa (SSA), the (sub)genotypes A1, D3, and E of the hepatitis B virus (HBV) prevail. Individuals infected with subgenotype A1 have a 4.5-fold increased risk of HCC compared to those infected with other (sub)genotypes. The effect of (sub)genotypes on protein expression and host signalling has not been studied. Mass spectrometry was used to analyse the proteome of Huh7 cells transfected with replication-competent clones. Proteomic analysis revealed significantly differentially expressed proteins between SSA (sub)genotypes. Different (sub)genotypes have the propensity to dysregulate specific host signalling pathways. Subgenotype A1 resulted in dysregulation within the Ras pathway. Ras-associated protein, RhoC, was significantly upregulated in cells transfected with subgenotype A1 compared to those transfected with other (sub)genotypes, on both a proteomic (>1.5-fold) and mRNA level (p < 0.05). Two of the main cellular signalling pathways involving RHOC, MAPK and PI3K/Akt/mTOR, regulate cell growth, motility, and survival. Downstream signalling products of these pathways have been shown to increase MMP2 and MMP9 expression. An extracellular MMP2 and MMP9 ELISA revealed a non-significant increase in MMP2 and MMP9 in the cells transfected with A1 compared to the other (sub)genotypes (p < 0.05). The upregulated Ras-associated proteins have been implicated as oncoproteins in various cancers and could contribute to the increased hepatocarcinogenic potential of A1.
Collapse
Affiliation(s)
- Kiyasha Padarath
- Hepatitis Virus Diversity Unit, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Science, University of Witwatersrand, 7 York Road, Parktown, Johannesburg 2193, South Africa (A.D.)
| | - Aurélie Deroubaix
- Hepatitis Virus Diversity Unit, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Science, University of Witwatersrand, 7 York Road, Parktown, Johannesburg 2193, South Africa (A.D.)
- Life Sciences Imaging Facility, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Parktown, Johannesburg 2193, South Africa
| | - Previn Naicker
- Future Production Chemicals, Council for Scientific and Industrial Research, Pretoria 0184, South Africa;
| | - Stoyan Stoychev
- ReSyn Biosciences, Johannesburg 2000, South Africa;
- Evosep Biosystems, 5230 Odense, Denmark
| | - Anna Kramvis
- Hepatitis Virus Diversity Unit, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Science, University of Witwatersrand, 7 York Road, Parktown, Johannesburg 2193, South Africa (A.D.)
| |
Collapse
|
24
|
Gao D, Yam JWP. Reversal of lipid metabolism as a therapeutic approach for HCC. Hepatology 2024:01515467-990000000-00936. [PMID: 38935863 DOI: 10.1097/hep.0000000000001000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Accepted: 06/17/2024] [Indexed: 06/29/2024]
Affiliation(s)
- Daming Gao
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
- Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Judy Wai Ping Yam
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
| |
Collapse
|
25
|
Li Q, Guo W, Qian Y, Li S, Li L, Zhu Z, Wang F, Tong Y, Xia Q, Liu Y. Protein O-fucosyltransferase 1 promotes PD-L1 stability to drive immune evasion and directs liver cancer to immunotherapy. J Immunother Cancer 2024; 12:e008917. [PMID: 38908854 DOI: 10.1136/jitc-2024-008917] [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] [Accepted: 05/30/2024] [Indexed: 06/24/2024] Open
Abstract
BACKGROUND AND AIMS The immunosuppressive tumor microenvironment (TME) plays an essential role in cancer progression and immunotherapy response. Despite the considerable advancements in cancer immunotherapy, the limited response to immune checkpoint blockade (ICB) therapies in patients with hepatocellular carcinoma (HCC) remains a major challenge for its clinical implications. Here, we investigated the molecular basis of the protein O-fucosyltransferase 1 (POFUT1) that drives HCC immune evasion and explored a potential therapeutic strategy for enhancing ICB efficacy. METHODS De novo MYC/Trp53-/- liver tumor and the xenograft tumor models were used to evaluate the function of POFUT1 in immune evasion. Biochemical assays were performed to elucidate the underlying mechanism of POFUT1-mediated immune evasion. RESULTS We identified POFUT1 as a crucial promoter of immune evasion in liver cancer. Notably, POFUT1 promoted HCC progression and inhibited T-cell infiltration in the xenograft tumor and de novo MYC/Trp53-/- mouse liver tumor models. Mechanistically, we demonstrated that POFUT1 stabilized programmed death ligand 1 (PD-L1) protein by preventing tripartite motif containing 21-mediated PD-L1 ubiquitination and degradation independently of its protein-O-fucosyltransferase activity. In addition, we further demonstrated that PD-L1 was required for the tumor-promoting and immune evasion effects of POFUT1 in HCC. Importantly, inhibition of POFUT1 could synergize with anti-programmed death receptor 1 therapy by remodeling TME in the xenograft tumor mouse model. Clinically, POFUT1 high expression displayed a lower response rate and worse clinical outcome to ICB therapies. CONCLUSIONS Our findings demonstrate that POFUT1 functions as a novel regulator of tumor immune evasion and inhibition of POFUT1 may be a potential therapeutic strategy to enhance the efficacy of immune therapy in HCC.
Collapse
Affiliation(s)
- Qianyu Li
- Department of Liver Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Renji-Med-X Clinical Stem Cell Research Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenyun Guo
- Department of Liver Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Renji-Med-X Clinical Stem Cell Research Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yifei Qian
- Department of Liver Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Renji-Med-X Clinical Stem Cell Research Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Songling Li
- School of Biomedical Engineering & Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Linfeng Li
- Renji-Med-X Clinical Stem Cell Research Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zijun Zhu
- Department of Liver Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Renji-Med-X Clinical Stem Cell Research Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fan Wang
- Renji-Med-X Clinical Stem Cell Research Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Tong
- Renji-Med-X Clinical Stem Cell Research Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qiang Xia
- Department of Liver Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Engineering Research Center of Transplantation and Immunology, Shanghai Institute of Transplantation, Shanghai, China
| | - Yanfeng Liu
- Department of Liver Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Engineering Research Center of Transplantation and Immunology, Shanghai Institute of Transplantation, Shanghai, China
| |
Collapse
|
26
|
Wang QF, Li ZW, Zhou HF, Zhu KZ, Wang YJ, Wang YQ, Zhang YW. Predicting the prognosis of hepatic arterial infusion chemotherapy in hepatocellular carcinoma. World J Gastrointest Oncol 2024; 16:2380-2393. [PMID: 38994149 PMCID: PMC11236234 DOI: 10.4251/wjgo.v16.i6.2380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/19/2024] [Accepted: 04/03/2024] [Indexed: 06/14/2024] Open
Abstract
Hepatic artery infusion chemotherapy (HAIC) has good clinical efficacy in the treatment of advanced hepatocellular carcinoma (HCC); however, its efficacy varies. This review summarized the ability of various markers to predict the efficacy of HAIC and provided a reference for clinical applications. As of October 25, 2023, 51 articles have been retrieved based on keyword predictions and HAIC. Sixteen eligible articles were selected for inclusion in this study. Comprehensive literature analysis found that methods used to predict the efficacy of HAIC include serological testing, gene testing, and imaging testing. The above indicators and their combined forms showed excellent predictive effects in retrospective studies. This review summarized the strategies currently used to predict the efficacy of HAIC in middle and advanced HCC, analyzed each marker's ability to predict HAIC efficacy, and provided a reference for the clinical application of the prediction system.
Collapse
Affiliation(s)
- Qi-Feng Wang
- Department of Hepatobiliary Pancreatic Center, Beijing Tsinghua Changgung Hospital Affiliated to Tsinghua University, Beijing 102218, China
- Department of Hepatobiliary and Pancreatic Surgery, Qinghai University Affiliated Hospital, Xining 810000, Qinghai Province, China
| | - Zong-Wei Li
- Department of Hepatobiliary and Pancreatic Surgery, Qinghai University Affiliated Hospital, Xining 810000, Qinghai Province, China
| | - Hai-Feng Zhou
- Department of Hepatobiliary and Pancreatic Surgery, Qinghai University Affiliated Hospital, Xining 810000, Qinghai Province, China
| | - Kun-Zhong Zhu
- Department of Hepatobiliary and Pancreatic Surgery, Qinghai University Affiliated Hospital, Xining 810000, Qinghai Province, China
| | - Ya-Jing Wang
- Department of Hepatobiliary Pancreatic Center, Beijing Tsinghua Changgung Hospital Affiliated to Tsinghua University, Beijing 102218, China
| | - Ya-Qin Wang
- Department of Hepatobiliary Pancreatic Center, Beijing Tsinghua Changgung Hospital Affiliated to Tsinghua University, Beijing 102218, China
| | - Yue-Wei Zhang
- Department of Hepatobiliary Pancreatic Center, Beijing Tsinghua Changgung Hospital Affiliated to Tsinghua University, Beijing 102218, China
| |
Collapse
|
27
|
Wang QF, Li ZW, Zhou HF, Zhu KZ, Wang YJ, Wang YQ, Zhang YW. Predicting the prognosis of hepatic arterial infusion chemotherapy in hepatocellular carcinoma. World J Gastrointest Oncol 2024; 16:2368-2381. [DOI: 10.4251/wjgo.v16.i6.2368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/19/2024] [Accepted: 04/03/2024] [Indexed: 06/13/2024] Open
Abstract
Hepatic artery infusion chemotherapy (HAIC) has good clinical efficacy in the treatment of advanced hepatocellular carcinoma (HCC); however, its efficacy varies. This review summarized the ability of various markers to predict the efficacy of HAIC and provided a reference for clinical applications. As of October 25, 2023, 51 articles have been retrieved based on keyword predictions and HAIC. Sixteen eligible articles were selected for inclusion in this study. Comprehensive literature analysis found that methods used to predict the efficacy of HAIC include serological testing, gene testing, and imaging testing. The above indicators and their combined forms showed excellent predictive effects in retrospective studies. This review summarized the strategies currently used to predict the efficacy of HAIC in middle and advanced HCC, analyzed each marker's ability to predict HAIC efficacy, and provided a reference for the clinical application of the prediction system.
Collapse
Affiliation(s)
- Qi-Feng Wang
- Department of Hepatobiliary Pancreatic Center, Beijing Tsinghua Changgung Hospital Affiliated to Tsinghua University, Beijing 102218, China
- Department of Hepatobiliary and Pancreatic Surgery, Qinghai University Affiliated Hospital, Xining 810000, Qinghai Province, China
| | - Zong-Wei Li
- Department of Hepatobiliary and Pancreatic Surgery, Qinghai University Affiliated Hospital, Xining 810000, Qinghai Province, China
| | - Hai-Feng Zhou
- Department of Hepatobiliary and Pancreatic Surgery, Qinghai University Affiliated Hospital, Xining 810000, Qinghai Province, China
| | - Kun-Zhong Zhu
- Department of Hepatobiliary and Pancreatic Surgery, Qinghai University Affiliated Hospital, Xining 810000, Qinghai Province, China
| | - Ya-Jing Wang
- Department of Hepatobiliary Pancreatic Center, Beijing Tsinghua Changgung Hospital Affiliated to Tsinghua University, Beijing 102218, China
| | - Ya-Qin Wang
- Department of Hepatobiliary Pancreatic Center, Beijing Tsinghua Changgung Hospital Affiliated to Tsinghua University, Beijing 102218, China
| | - Yue-Wei Zhang
- Department of Hepatobiliary Pancreatic Center, Beijing Tsinghua Changgung Hospital Affiliated to Tsinghua University, Beijing 102218, China
| |
Collapse
|
28
|
Lin M, Zheng X, Yan J, Huang F, Chen Y, Ding R, Wan J, Zhang L, Wang C, Pan J, Cao X, Fu K, Lou Y, Feng XH, Ji J, Zhao B, Lan F, Shen L, He X, Qiu Y, Jin J. The RNF214-TEAD-YAP signaling axis promotes hepatocellular carcinoma progression via TEAD ubiquitylation. Nat Commun 2024; 15:4995. [PMID: 38862474 PMCID: PMC11167002 DOI: 10.1038/s41467-024-49045-y] [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: 04/22/2023] [Accepted: 05/22/2024] [Indexed: 06/13/2024] Open
Abstract
RNF214 is an understudied ubiquitin ligase with little knowledge of its biological functions or protein substrates. Here we show that the TEAD transcription factors in the Hippo pathway are substrates of RNF214. RNF214 induces non-proteolytic ubiquitylation at a conserved lysine residue of TEADs, enhances interactions between TEADs and YAP, and promotes transactivation of the downstream genes of the Hippo signaling. Moreover, YAP and TAZ could bind polyubiquitin chains, implying the underlying mechanisms by which RNF214 regulates the Hippo pathway. Furthermore, RNF214 is overexpressed in hepatocellular carcinoma (HCC) and inversely correlates with differentiation status and patient survival. Consistently, RNF214 promotes tumor cell proliferation, migration, and invasion, and HCC tumorigenesis in mice. Collectively, our data reveal RNF214 as a critical component in the Hippo pathway by forming a signaling axis of RNF214-TEAD-YAP and suggest that RNF214 is an oncogene of HCC and could be a potential drug target of HCC therapy.
Collapse
Affiliation(s)
- Mengjia Lin
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, and National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang, China
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Xiaoyun Zheng
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Jianing Yan
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, Zhejiang, China
| | - Fei Huang
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Yilin Chen
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Ran Ding
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Jinkai Wan
- International Co-laboratory of Medical Epigenetics and Metabolism of Ministry of Science and Technology, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, and Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Lei Zhang
- International Co-laboratory of Medical Epigenetics and Metabolism of Ministry of Science and Technology, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Chenliang Wang
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Jinchang Pan
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Xiaolei Cao
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Kaiyi Fu
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Yan Lou
- Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, Department of Clinical Pharmacy, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang, China
| | - Xin-Hua Feng
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, Zhejiang, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, 321000, China
| | - Junfang Ji
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, Zhejiang, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, 321000, China
| | - Bin Zhao
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, Zhejiang, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, 321000, China
| | - Fei Lan
- International Co-laboratory of Medical Epigenetics and Metabolism of Ministry of Science and Technology, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, and Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Li Shen
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, Zhejiang, China
- Department of Orthopedics Surgery, School of Medicine, The Second Affiliated Hospital, Zhejiang University, Hangzhou, 310009, Zhejiang, China
| | - Xianglei He
- Department of Pathology, Zhejiang Provincial People's Hospital, Hangzhou, 3100014, Zhejiang, China
| | - Yunqing Qiu
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, and National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang, China.
- Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, Department of Clinical Pharmacy, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang, China.
| | - Jianping Jin
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
- Cancer Center, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
- Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, Department of Clinical Pharmacy, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang, China.
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, 321000, China.
| |
Collapse
|
29
|
Chamrád I, Simerský R, Lenobel R, Novák O. Exploring affinity chromatography in proteomics: A comprehensive review. Anal Chim Acta 2024; 1306:342513. [PMID: 38692783 DOI: 10.1016/j.aca.2024.342513] [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: 12/12/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 05/03/2024]
Abstract
Over the past decades, the proteomics field has undergone rapid growth. Progress in mass spectrometry and bioinformatics, together with separation methods, has brought many innovative approaches to the study of the molecular biology of the cell. The potential of affinity chromatography was recognized immediately after its first application in proteomics, and since that time, it has become one of the cornerstones of many proteomic protocols. Indeed, this chromatographic technique exploiting the specific binding between two molecules has been employed for numerous purposes, from selective removal of interfering (over)abundant proteins or enrichment of scarce biomarkers in complex biological samples to mapping the post-translational modifications and protein interactions with other proteins, nucleic acids or biologically active small molecules. This review presents a comprehensive survey of this versatile analytical tool in current proteomics. To navigate the reader, the haphazard space of affinity separations is classified according to the experiment's aims and the separated molecule's nature. Different types of available ligands and experimental strategies are discussed in further detail for each of the mentioned procedures.
Collapse
Affiliation(s)
- Ivo Chamrád
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic.
| | - Radim Simerský
- Department of Chemical Biology, Faculty of Science, Palacký University, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
| | - René Lenobel
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
| |
Collapse
|
30
|
Yang S, Zheng L, Li L, Zhang J, Wang J, Zhao H, Chen Y, Liu X, Gan H, Chen J, Yan M, He C, Li K, Ding C, Li Y. Integrative multiomics analysis identifies molecular subtypes and potential targets of hepatocellular carcinoma. Clin Transl Med 2024; 14:e1727. [PMID: 38804617 PMCID: PMC11131356 DOI: 10.1002/ctm2.1727] [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: 01/17/2024] [Revised: 05/10/2024] [Accepted: 05/15/2024] [Indexed: 05/29/2024] Open
Abstract
BACKGROUND The liver is anatomically divided into eight segments based on the distribution of Glisson's triad. However, the molecular mechanisms underlying each segment and its association with hepatocellular carcinoma (HCC) heterogeneity are not well understood. In this study, our objective is to conduct a comprehensive multiomics profiling of the segmentation atlas in order to investigate potential subtypes and therapeutic approaches for HCC. METHODS A high throughput liquid chromatography-tandem mass spectrometer strategy was employed to comprehensively analyse proteome, lipidome and metabolome data, with a focus on segment-resolved multiomics profiling. To classify HCC subtypes, the obtained data with normal reference profiling were integrated. Additionally, potential therapeutic targets for HCC were identified using immunohistochemistry assays. The effectiveness of these targets were further validated through patient-derived organoid (PDO) assays. RESULTS A multiomics profiling of 8536 high-confidence proteins, 1029 polar metabolites and 3381 nonredundant lipids was performed to analyse the segmentation atlas of HCC. The analysis of the data revealed that in normal adjacent tissues, the left lobe was primarily involved in energy metabolism, while the right lobe was associated with small molecule metabolism. Based on the normal reference atlas, HCC patients with segment-resolved classification were divided into three subtypes. The C1 subtype showed enrichment in ribosome biogenesis, the C2 subtype exhibited an intermediate phenotype, while the C3 subtype was closely associated with neutrophil degranulation. Furthermore, using the PDO assay, exportin 1 (XPO1) and 5-lipoxygenase (ALOX5) were identified as potential targets for the C1 and C3 subtypes, respectively. CONCLUSION Our extensive analysis of the segmentation atlas in multiomics profiling defines molecular subtypes of HCC and uncovers potential therapeutic strategies that have the potential to enhance the prognosis of HCC.
Collapse
Affiliation(s)
- Shuai Yang
- Department of Hematology & OncologyJiangbei CampusThe First Affiliated Hospital of Army Medical UniversityChongqingChina
| | - Lu Zheng
- Department of Hepatobiliary SurgeryXinqiao HospitalArmy Medical UniversityChongqingChina
| | - Lingling Li
- State Key Laboratory of Genetic EngineeringInstitutes of Biomedical SciencesHuman Phenome InstituteSchool of Life SciencesZhongshan HospitalFudan UniversityShanghaiChina
| | - Jiangang Zhang
- Department of Medical OncologyChongqing University Cancer HospitalChongqingChina
| | - Jingchun Wang
- Department of GastroenterologyXinqiao Hospital, Army Medical UniversityChongqingChina
| | - Huakan Zhao
- Department of Medical OncologyChongqing University Cancer HospitalChongqingChina
| | - Yu Chen
- Department of Medical OncologyChongqing University Cancer HospitalChongqingChina
| | - Xudong Liu
- Department of Medical OncologyChongqing University Cancer HospitalChongqingChina
| | - Hui Gan
- Department of RadiologyXinqiao HospitalArmy Medical UniversityChongqingChina
| | - Junying Chen
- Department of PathologyJiangbei CampusThe First Affiliated Hospital of Army Medical UniversityChongqingChina
| | - Mei Yan
- Department of PathologyJiangbei CampusThe First Affiliated Hospital of Army Medical UniversityChongqingChina
| | - Chuanyin He
- Department of PathologyJiangbei CampusThe First Affiliated Hospital of Army Medical UniversityChongqingChina
| | - Kai Li
- State Key Laboratory of Genetic EngineeringInstitutes of Biomedical SciencesHuman Phenome InstituteSchool of Life SciencesZhongshan HospitalFudan UniversityShanghaiChina
| | - Chen Ding
- State Key Laboratory of Genetic EngineeringInstitutes of Biomedical SciencesHuman Phenome InstituteSchool of Life SciencesZhongshan HospitalFudan UniversityShanghaiChina
| | - Yongsheng Li
- Department of Medical OncologyChongqing University Cancer HospitalChongqingChina
| |
Collapse
|
31
|
Peng H, Feng K, Jia W, Li Y, Lv Q, Zhang Y. An integrated investigation of sulfotransferases (SULTs) in hepatocellular carcinoma and identification of the role of SULT2A1 on stemness. Apoptosis 2024; 29:898-919. [PMID: 38411862 DOI: 10.1007/s10495-024-01938-5] [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] [Accepted: 01/09/2024] [Indexed: 02/28/2024]
Abstract
The cytosolic sulfotransferases (SULTs) are phase II conjugating enzymes, which are widely expressed in the liver and mainly mediate the sulfation of numerous xenobiotics and endogenous compounds. However, the role of various SULTs genes has not been reported in hepatocellular carcinoma (HCC). This study aims to analyze the expression and potential functional roles of SULTs genes in HCC and to identify the role of SULT2A1 in HCC stemness as well as the possible mechanism. We found that all of the 12 SULTs genes were differentially expressed in HCC. Moreover, clinicopathological features and survival rates were also investigated. Multivariate regression analysis showed that SULT2A1 and SULT1C2 could be used as independent prognostic factors in HCC. SULT1C4, SULT1E1, and SULT2A1 were significantly associated with immune infiltration. SULT2A1 deficiency in HCC promoted chemotherapy resistance and stemness maintenance. Mechanistically, silencing of SULT2A1 activated the AKT signaling pathway, on the one hand, promoted the expression of downstream stemness gene c-Myc, on the other hand, facilitated the NRF2 expression to reduce the accumulation of ROS, and jointly increased HCC stemness. Moreover, knockdown NR1I3 was involved in the transcriptional regulation of SULT2A1 in stemness maintenance. In addition, SULT2A1 knockdown HCC cells promoted the proliferation and activation of hepatic stellate cells (HSCs), thereby exerting a potential stroma remodeling effect. Our study revealed the expression and role of SULTs genes in HCC and identified the contribution of SULT2A1 to the initiation and progression of HCC.
Collapse
Affiliation(s)
- Hao Peng
- Medical School, Southeast University, Nanjing, 210009, China
| | - Kun Feng
- Hepatopancreatobiliary Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210009, China
| | - Weilu Jia
- Medical School, Southeast University, Nanjing, 210009, China
| | - Yunxin Li
- Hepatopancreatobiliary Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210009, China
| | - Qingpeng Lv
- Hepatopancreatobiliary Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210009, China
| | - Yewei Zhang
- Medical School, Southeast University, Nanjing, 210009, China.
- Hepatopancreatobiliary Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210009, China.
| |
Collapse
|
32
|
Liu Y, Li D, Zhang X, Xia S, Qu Y, Ling X, Li Y, Kong X, Zhang L, Cui CP, Li D. A protein sequence-based deep transfer learning framework for identifying human proteome-wide deubiquitinase-substrate interactions. Nat Commun 2024; 15:4519. [PMID: 38806474 PMCID: PMC11133436 DOI: 10.1038/s41467-024-48446-3] [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: 07/17/2023] [Accepted: 04/26/2024] [Indexed: 05/30/2024] Open
Abstract
Protein ubiquitination regulates a wide range of cellular processes. The degree of protein ubiquitination is determined by the delicate balance between ubiquitin ligase (E3)-mediated ubiquitination and deubiquitinase (DUB)-mediated deubiquitination. In comparison to the E3-substrate interactions, the DUB-substrate interactions (DSIs) remain insufficiently investigated. To address this challenge, we introduce a protein sequence-based ab initio method, TransDSI, which transfers proteome-scale evolutionary information to predict unknown DSIs despite inadequate training datasets. An explainable module is integrated to suggest the critical protein regions for DSIs while predicting DSIs. TransDSI outperforms multiple machine learning strategies against both cross-validation and independent test. Two predicted DUBs (USP11 and USP20) for FOXP3 are validated by "wet lab" experiments, along with two predicted substrates (AR and p53) for USP22. TransDSI provides new functional perspective on proteins by identifying regulatory DSIs, and offers clues for potential tumor drug target discovery and precision drug application.
Collapse
Affiliation(s)
- Yuan Liu
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Dianke Li
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xin Zhang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Simin Xia
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
- School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, China
| | - Yingjie Qu
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Xinping Ling
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
- College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Yang Li
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Xiangren Kong
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Lingqiang Zhang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Chun-Ping Cui
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
| | - Dong Li
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
| |
Collapse
|
33
|
Hu D, Zhang Z, Liu X, Wu Y, An Y, Wang W, Yang M, Pan Y, Qiao K, Du C, Zhao Y, Li Y, Bao J, Qin T, Pan Y, Xia Z, Zhao X, Sun K. Generalizable transcriptome-based tumor malignant level evaluation and molecular subtyping towards precision oncology. J Transl Med 2024; 22:512. [PMID: 38807223 PMCID: PMC11134716 DOI: 10.1186/s12967-024-05326-0] [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: 02/21/2024] [Accepted: 05/19/2024] [Indexed: 05/30/2024] Open
Abstract
In cancer treatment, therapeutic strategies that integrate tumor-specific characteristics (i.e., precision oncology) are widely implemented to provide clinical benefits for cancer patients. Here, through in-depth integration of tumor transcriptome and patients' prognoses across cancers, we investigated dysregulated and prognosis-associated genes and catalogued such important genes in a cancer type-dependent manner. Utilizing the expression matrices of these genes, we built models to quantitatively evaluate the malignant levels of tumors across cancers, which could add value to the clinical staging system for improved prediction of patients' survival. Furthermore, we performed a transcriptome-based molecular subtyping on hepatocellular carcinoma, which revealed three subtypes with significantly diversified clinical outcomes, mutation landscapes, immune microenvironment, and dysregulated pathways. As tumor transcriptome was commonly profiled in clinical practice with low experimental complexity and cost, this work proposed easy-to-perform approaches for practical clinical promotion towards better healthcare and precision oncology of cancer patients.
Collapse
Affiliation(s)
- Dingxue Hu
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518132, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Ziteng Zhang
- Hepato-Biliary Surgery Division, The Second Affiliated Hospital, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518100, China
| | - Xiaoyi Liu
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518132, China
| | - Youchun Wu
- Hepato-Biliary Surgery Division, The Second Affiliated Hospital, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518100, China
| | - Yunyun An
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518132, China
| | - Wanqiu Wang
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518132, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Mengqi Yang
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518132, China
| | - Yuqi Pan
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518132, China
- Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Kun Qiao
- Thoracic Surgical Department, Shenzhen Third People's Hospital, The Second Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518100, China
| | - Changzheng Du
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518132, China
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China
- Beijing Tsinghua Changgung Hospital, Tsinghua University School of Medicine, Beijing, 102218, China
| | - Yu Zhao
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, 518107, China
| | - Yan Li
- Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China
- Integrative Microecology Clinical Center, Shenzhen Key Laboratory of Gastrointestinal Microbiota and Disease, Shenzhen Clinical Research Center for Digestive Disease, Shenzhen Technology Research Center of Gut Microbiota Transplantation, Shenzhen Hospital, Southern Medical University, Shenzhen, 510086, China
| | - Jianqiang Bao
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Tao Qin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat- Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Yue Pan
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat- Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Zhaohua Xia
- Thoracic Surgical Department, Shenzhen Third People's Hospital, The Second Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518100, China.
| | - Xin Zhao
- Hepato-Biliary Surgery Division, The Second Affiliated Hospital, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518100, China.
| | - Kun Sun
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518132, China.
| |
Collapse
|
34
|
Zhu Y, Zhao Y, Ning Z, Deng Y, Li B, Sun Y, Meng Z. Metabolic self-feeding in HBV-associated hepatocarcinoma centered on feedback between circulation lipids and the cellular MAPK/mTOR axis. Cell Commun Signal 2024; 22:280. [PMID: 38773448 PMCID: PMC11106961 DOI: 10.1186/s12964-024-01619-5] [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: 02/05/2024] [Accepted: 04/17/2024] [Indexed: 05/23/2024] Open
Abstract
INTRODUCTION Hepatitis B Virus (HBV) is widely recognized as a "metabolic virus" that disrupts hepatic metabolic homeostasis, rendering it one of the foremost risk factors for hepatocellular carcinoma (HCC). Except for antiviral therapy, the fundamental principles underlying HBV- and HBV+ HCC have remained unchanged, limiting HCC treatment options. OBJECTIVES In this study, we aim to identify the distinctive metabolic profile of HBV-associated HCC, with the promise of identifying novel metabolic targets that confer survival advantages and ultimately impede cancer progression. METHODS We employed a comprehensive methodology to evaluate metabolic alterations systematically. Initially, we analyzed transcriptomic and proteomic data obtained from a public database, subsequently validating these findings within our test cohort at both the proteomic and transcriptomic levels. Additionally, we conducted a comprehensive analysis of tissue metabolomics profiles, lipidomics, and the activity of the MAPK and AKT signaling pathway to corroborate the abovementioned changes. RESULTS Our multi-omics approach revealed distinct metabolic dysfunctions associated with HBV-associated HCC. Specifically, we observed upregulated steroid hormone biosynthesis, primary bile acid metabolism, and sphingolipid metabolism in HBV-associated HCC patients' serum. Notably, metabolites involved in primary bile acid and sphingolipids can activate the MAPK/mTOR pathway. Tissue metabolomics and lipidomics analyses further validated the serum metabolic alterations, particularly alterations in lipid composition and accumulation of unsaturated fatty acids. CONCLUSION Our findings emphasize the pivotal role of HBV in HCC metabolism, elucidating the activation of a unique MAPK/mTOR signaling axis by primary bile acids and sphingolipids. Moreover, the hyperactive MAPK/mTOR signaling axis transduction leads to significant reprogramming in lipid metabolism within HCC cells, further triggering the activation of the MAPK/mTOR pathway in turn, thereby establishing a self-feeding circle driven by primary bile acids and sphingolipids.
Collapse
Affiliation(s)
- Ying Zhu
- Minimally invasive therapy center, Shanghai Cancer Center, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Yingke Zhao
- Minimally invasive therapy center, Shanghai Cancer Center, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China
| | - Zhouyu Ning
- Minimally invasive therapy center, Shanghai Cancer Center, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Yong Deng
- Department of Research and Development, Department of Nuclear Medicine, Shanghai Proton and Heavy Ion Center, Fudan University Shanghai Cancer Center, Shanghai, 201321, China
- Shanghai Key Laboratory of radiation oncology (20dz2261000), Shanghai, 201321, China
- Shanghai Engineering Research Center of Proton and Heavy Ion Radiation Therapy, Shanghai, 201321, China
| | - Bing Li
- Department of Research and Development, Department of Nuclear Medicine, Shanghai Proton and Heavy Ion Center, Fudan University Shanghai Cancer Center, Shanghai, 201321, China
- Shanghai Key Laboratory of radiation oncology (20dz2261000), Shanghai, 201321, China
- Shanghai Engineering Research Center of Proton and Heavy Ion Radiation Therapy, Shanghai, 201321, China
| | - Yun Sun
- Department of Research and Development, Department of Nuclear Medicine, Shanghai Proton and Heavy Ion Center, Fudan University Shanghai Cancer Center, Shanghai, 201321, China.
- Shanghai Key Laboratory of radiation oncology (20dz2261000), Shanghai, 201321, China.
- Shanghai Engineering Research Center of Proton and Heavy Ion Radiation Therapy, Shanghai, 201321, China.
| | - Zhiqiang Meng
- Minimally invasive therapy center, Shanghai Cancer Center, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.
| |
Collapse
|
35
|
Gao M, Liu T, Hu K, Chen S, Wang S, Gan D, Li Z, Lin X. Ribosomal Dysregulation in Metastatic Laryngeal Squamous Cell Carcinoma: Proteomic Insights and CX-5461's Therapeutic Promise. TOXICS 2024; 12:363. [PMID: 38787142 PMCID: PMC11126056 DOI: 10.3390/toxics12050363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024]
Abstract
One of the main barriers to the successful treatment of laryngeal squamous cell carcinoma (LSCC) is postoperative progression, primarily due to tumor cell metastasis. To systematically investigate the molecular characteristics and potential mechanisms underlying the metastasis in laryngeal cancer, we carried out a TMT-based proteomic analysis of both cancerous and adjacent non-cancerous tissues from 10 LSCC patients with lymph node metastasis (LNM) and 10 without. A total of 5545 proteins were quantified across all samples. We identified 57 proteins that were downregulated in LSCC with LNM, which were enriched in cell adhesion pathways, and 69 upregulated proteins predominantly enriched in protein production pathways. Importantly, our data revealed a strong correlation between increased ribosomal activity and the presence of LNM, as 18 ribosomal subunit proteins were found to be upregulated, with RPS10 and RPL24 being the most significantly overexpressed. The potential of ribosomal proteins, including RPS10 and RPL24, as biomarkers for LSCC with LNM was confirmed in external validation samples (six with LNM and six without LNM) using Western blotting and immunohistochemistry. Furthermore, we have confirmed that the RNA polymerase I inhibitor CX-5461, which impedes ribosome biogenesis in LSCC, also decreases the expression of RPS10, RPL24, and RPS26. In vitro experiments have revealed that CX-5461 moderately reduces cell viability, while it significantly inhibits the invasion and migration of LSCC cells. It can enhance the expression of the epithelial marker CDH1 and suppress the expression of the mesenchymal markers CDH2, VIM, and FN at a dose that does not affect cell viability. Our study broadens the scope of the proteomic data on laryngeal cancer and suggests that ribosome targeting could be a supplementary therapeutic strategy for metastatic LSCC.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Xiaohuang Lin
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350108, China; (M.G.); (T.L.); (K.H.); (S.C.); (S.W.); (D.G.); (Z.L.)
| |
Collapse
|
36
|
Niu MY, Liu YJ, Shi JJ, Chen RY, Zhang S, Li CY, Cao JF, Yang GJ, Chen J. The Emerging Role of Ubiquitin-Specific Protease 36 (USP36) in Cancer and Beyond. Biomolecules 2024; 14:572. [PMID: 38785979 PMCID: PMC11118191 DOI: 10.3390/biom14050572] [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: 03/28/2024] [Revised: 05/07/2024] [Accepted: 05/11/2024] [Indexed: 05/25/2024] Open
Abstract
The balance between ubiquitination and deubiquitination is instrumental in the regulation of protein stability and maintenance of cellular homeostasis. The deubiquitinating enzyme, ubiquitin-specific protease 36 (USP36), a member of the USP family, plays a crucial role in this dynamic equilibrium by hydrolyzing and removing ubiquitin chains from target proteins and facilitating their proteasome-dependent degradation. The multifaceted functions of USP36 have been implicated in various disease processes, including cancer, infections, and inflammation, via the modulation of numerous cellular events, including gene transcription regulation, cell cycle regulation, immune responses, signal transduction, tumor growth, and inflammatory processes. The objective of this review is to provide a comprehensive summary of the current state of research on the roles of USP36 in different pathological conditions. By synthesizing the findings from previous studies, we have aimed to increase our understanding of the mechanisms underlying these diseases and identify potential therapeutic targets for their treatment.
Collapse
Affiliation(s)
- Meng-Yao Niu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China; (M.-Y.N.); (Y.-J.L.); (J.-J.S.); (R.-Y.C.); (C.-Y.L.); (J.-F.C.)
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Meishan Campus, Ningbo University, Ningbo 315832, China
| | - Yan-Jun Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China; (M.-Y.N.); (Y.-J.L.); (J.-J.S.); (R.-Y.C.); (C.-Y.L.); (J.-F.C.)
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Meishan Campus, Ningbo University, Ningbo 315832, China
| | - Jin-Jin Shi
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China; (M.-Y.N.); (Y.-J.L.); (J.-J.S.); (R.-Y.C.); (C.-Y.L.); (J.-F.C.)
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Meishan Campus, Ningbo University, Ningbo 315832, China
| | - Ru-Yi Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China; (M.-Y.N.); (Y.-J.L.); (J.-J.S.); (R.-Y.C.); (C.-Y.L.); (J.-F.C.)
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Meishan Campus, Ningbo University, Ningbo 315832, China
| | - Shun Zhang
- Ningbo No.2 Hospital, Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Meishan Campus, Ningbo University, Ningbo 315832, China;
| | - Chang-Yun Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China; (M.-Y.N.); (Y.-J.L.); (J.-J.S.); (R.-Y.C.); (C.-Y.L.); (J.-F.C.)
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Meishan Campus, Ningbo University, Ningbo 315832, China
| | - Jia-Feng Cao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China; (M.-Y.N.); (Y.-J.L.); (J.-J.S.); (R.-Y.C.); (C.-Y.L.); (J.-F.C.)
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Meishan Campus, Ningbo University, Ningbo 315832, China
| | - Guan-Jun Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China; (M.-Y.N.); (Y.-J.L.); (J.-J.S.); (R.-Y.C.); (C.-Y.L.); (J.-F.C.)
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Meishan Campus, Ningbo University, Ningbo 315832, China
| | - Jiong Chen
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Meishan Campus, Ningbo University, Ningbo 315832, China
- Ningbo No.2 Hospital, Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Meishan Campus, Ningbo University, Ningbo 315832, China;
| |
Collapse
|
37
|
Wu Z, Dong Z, Luo J, Hu W, Tong Y, Gao X, Yao W, Tian H, Wang X. A comprehensive comparison of molecular and phenotypic profiles between hepatitis B virus (HBV)-infected and non-HBV-infected hepatocellular carcinoma by multi-omics analysis. Genomics 2024; 116:110831. [PMID: 38513875 DOI: 10.1016/j.ygeno.2024.110831] [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: 08/01/2023] [Revised: 11/22/2023] [Accepted: 03/14/2024] [Indexed: 03/23/2024]
Abstract
Hepatitis B virus (HBV) infection is a major etiology of hepatocellular carcinoma (HCC). An interesting question is how different are the molecular and phenotypic profiles between HBV-infected (HBV+) and non-HBV-infected (HBV-) HCCs? Based on the publicly available multi-omics data for HCC, including bulk and single-cell data, and the data we collected and sequenced, we performed a comprehensive comparison of molecular and phenotypic features between HBV+ and HBV- HCCs. Our analysis showed that compared to HBV- HCCs, HBV+ HCCs had significantly better clinical outcomes, higher degree of genomic instability, higher enrichment of DNA repair and immune-related pathways, lower enrichment of stromal and oncogenic signaling pathways, and better response to immunotherapy. Furthermore, in vitro experiments confirmed that HBV+ HCCs had higher immunity, PD-L1 expression and activation of DNA damage response pathways. This study may provide insights into the profiles of HBV+ and HBV- HCCs, and guide rational therapeutic interventions for HCC patients.
Collapse
Affiliation(s)
- Zijie Wu
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China
| | - Zehua Dong
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
| | - Jiangti Luo
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
| | - Weiwei Hu
- Center for New Drug Safety Evaluation and Research, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China
| | - Yue Tong
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China
| | - Xiangdong Gao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China
| | - Wenbing Yao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China.
| | - Hong Tian
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China.
| | - Xiaosheng Wang
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China.
| |
Collapse
|
38
|
Das D, Wang X, Chiu YC, Bouamar H, Sharkey FE, Lopera JE, Lai Z, Weintraub ST, Han X, Zou Y, Chen HIH, Zeballos Torrez CR, Gu X, Cserhati M, Michalek JE, Halff GA, Chen Y, Zheng S, Cigarroa FG, Sun LZ. Integrative multi-omics characterization of hepatocellular carcinoma in Hispanic patients. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.27.24306447. [PMID: 38746245 PMCID: PMC11092709 DOI: 10.1101/2024.04.27.24306447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Background The incidence and mortality rates of hepatocellular carcinoma (HCC) among Hispanics in the United States are much higher than those of non-Hispanic whites. We conducted comprehensive multi-omics analyses to understand molecular alterations in HCC among Hispanic patients. Methods Paired tumor and adjacent non-tumor samples were collected from 31 Hispanic HCC in South Texas (STX-Hispanic) for genomic, transcriptomic, proteomic, and metabolomic profiling. Additionally, serum lipids were profiled in 40 Hispanic and non-Hispanic patients with or without clinically diagnosed HCC. Results Exome sequencing revealed high mutation frequencies of AXIN2 and CTNNB1 in STX Hispanic HCCs, suggesting a predominant activation of the Wnt/β-catenin pathway. The TERT promoter mutation frequency was also remarkably high in the Hispanic cohort. Cell cycles and liver functions were identified as positively- and negatively-enriched, respectively, with gene set enrichment analysis. Gene sets representing specific liver metabolic pathways were associated with dysregulation of corresponding metabolites. Negative enrichment of liver adipogenesis and lipid metabolism corroborated with a significant reduction in most lipids in the serum samples of HCC patients. Two HCC subtypes from our Hispanic cohort were identified and validated with the TCGA liver cancer cohort. The subtype with better overall survival showed higher activity of immune and angiogenesis signatures, and lower activity of liver function-related gene signatures. It also had higher levels of immune checkpoint and immune exhaustion markers. Conclusions Our study revealed some specific molecular features of Hispanic HCC and potential biomarkers for therapeutic management of HCC and provides a unique resource for studying Hispanic HCC.
Collapse
|
39
|
Li X, Pan YF, Chen YB, Wan QQ, Lin YK, Shang TY, Xu MY, Jiang TY, Pei MM, Tan YX, Dong LW, Wan XY. Arsenic trioxide augments immunogenic cell death and induces cGAS-STING-IFN pathway activation in hepatocellular carcinoma. Cell Death Dis 2024; 15:300. [PMID: 38684648 PMCID: PMC11058202 DOI: 10.1038/s41419-024-06685-8] [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: 11/09/2023] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024]
Abstract
The treatment of hepatocellular carcinoma (HCC) is particularly challenging due to the inherent tumoral heterogeneity and easy resistance towards chemotherapy and immunotherapy. Arsenic trioxide (ATO) has emerged as a cytotoxic agent effective for treating solid tumors, including advanced HCC. However, its effectiveness in HCC treatment remains limited, and the underlying mechanisms are still uncertain. Therefore, this study aimed to characterize the effects and mechanisms of ATO in HCC. By evaluating the susceptibilities of human and murine HCC cell lines to ATO treatment, we discovered that HCC cells exhibited a range of sensitivity to ATO treatment, highlighting their inherent heterogeneity. A gene signature comprising 265 genes was identified to distinguish ATO-sensitive from ATO-insensitive cells. According to this signature, HCC patients have also been classified and exhibited differential features of ATO response. Our results showed that ATO treatment induced reactive oxygen species (ROS) accumulation and the activation of multiple cell death modalities, including necroptosis and ferroptosis, in ATO-sensitive HCC cells. Meanwhile, elevated tumoral immunogenicity was also observed in ATO-sensitive HCC cells. Similar effects were not observed in ATO-insensitive cells. We reported that ATO treatment induced mitochondrial injury and mtDNA release into the cytoplasm in ATO-sensitive HCC tumors. This subsequently activated the cGAS-STING-IFN axis, facilitating CD8+ T cell infiltration and activation. However, we found that the IFN pathway also induced tumoral PD-L1 expression, potentially antagonizing ATO-mediated immune attack. Additional anti-PD1 therapy promoted the anti-tumor response of ATO in ATO-sensitive HCC tumors. In summary, our data indicate that heterogeneous ATO responses exist in HCC tumors, and ATO treatment significantly induces immunogenic cell death (ICD) and activates the tumor-derived mtDNA-STING-IFN axis. These findings may offer a new perspective on the clinical treatment of HCC and warrant further study.
Collapse
Affiliation(s)
- Xin Li
- Department of Integrated Chinese and Western Medicine, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Yu-Fei Pan
- National Center for Liver Cancer, Naval Medical University, Shanghai, China
| | - Yi-Bin Chen
- National Center for Liver Cancer, Naval Medical University, Shanghai, China
- Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Qian-Qian Wan
- Department of Integrated Chinese and Western Medicine, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Yun-Kai Lin
- National Center for Liver Cancer, Naval Medical University, Shanghai, China
| | - Tai-Yu Shang
- National Center for Liver Cancer, Naval Medical University, Shanghai, China
- School of Life Sciences, Fudan University, Shanghai, China
| | - Meng-You Xu
- National Center for Liver Cancer, Naval Medical University, Shanghai, China
- Peking University Cancer Hospital, Beijing, China
| | - Tian-Yi Jiang
- National Center for Liver Cancer, Naval Medical University, Shanghai, China
| | - Meng-Miao Pei
- Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Ye-Xiong Tan
- National Center for Liver Cancer, Naval Medical University, Shanghai, China.
| | - Li-Wei Dong
- National Center for Liver Cancer, Naval Medical University, Shanghai, China.
| | - Xu-Ying Wan
- Department of Integrated Chinese and Western Medicine, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China.
| |
Collapse
|
40
|
Zhao J, Liu Z, Yang K, Shen S, Peng J. DNA methylation regulator-based molecular subtyping and tumor microenvironment characterization in hepatocellular carcinoma. Front Immunol 2024; 15:1333923. [PMID: 38736884 PMCID: PMC11082416 DOI: 10.3389/fimmu.2024.1333923] [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: 11/06/2023] [Accepted: 04/16/2024] [Indexed: 05/14/2024] Open
Abstract
Backgroud Although recent studies have reported the regulation of the immune response in hepatocellular carcinoma (HCC) through DNA methylation, the comprehensive impact methylation modifications on tumor microenvironment characteristics and immunotherapy efficacy has not been fully elucidated. Methods In this research, we conducted a comprehensive assessment of the patterns of DNA methylation regulators and the profiles of the tumor microenvironment (TME) in HCC, focusing on 21 specific DNA methylation regulators. We subsequently developed a unique scoring system, a DNA methylation score (DMscore), to assess the individual DNA methylation modifications among the three distinct methylation patterns for differentially expressed genes (DEGs). Results Three distinct methylation modification patterns were identified with distinct TME infiltration characteristics. We demonstrated that the DMscore could predict patient subtype, TME infiltration, and patient prognosis. A low DMscore, characterized by an elevated tumor mutation burden (TMB), hepatitis B virus (HBV)/hepatitis C virus (HCV) infection, and immune activation, indicates an inflamed tumor microenvironment phenotype with a 5-year survival rate of 7.8%. Moreover, a low DMscore appeared to increase the efficacy of immunotherapy in the anti-CTLA-4/PD-1/PD-L1 cohort. Conclusions In brief, this research has enhanced our understanding of the correlation between modifications in DNA methylation patterns and the profile of the tumor microenvironment in individuals diagnosed with HCC. The DMscore may serve as an alternative biomarker for survival and efficacy of immunotherapy in patients with HCC.
Collapse
Affiliation(s)
- Junsheng Zhao
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhengtao Liu
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Keda Yang
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Sijia Shen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Shulan (Hangzhou) Hospital Affiliated to Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Jing Peng
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
41
|
Zhao D, Guo Y, Wei H, Jia X, Zhi Y, He G, Nie W, Huang L, Wang P, Laster KV, Liu Z, Wang J, Lee MH, Dong Z, Liu K. Multi-omics characterization of esophageal squamous cell carcinoma identifies molecular subtypes and therapeutic targets. JCI Insight 2024; 9:e171916. [PMID: 38652547 PMCID: PMC11141925 DOI: 10.1172/jci.insight.171916] [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: 05/02/2023] [Accepted: 04/12/2024] [Indexed: 04/25/2024] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is the predominant form of esophageal cancer and is characterized by an unfavorable prognosis. To elucidate the distinct molecular alterations in ESCC and investigate therapeutic targets, we performed a comprehensive analysis of transcriptomics, proteomics, and phosphoproteomics data derived from 60 paired treatment-naive ESCC and adjacent nontumor tissue samples. Additionally, we conducted a correlation analysis to describe the regulatory relationship between transcriptomic and proteomic processes, revealing alterations in key metabolic pathways. Unsupervised clustering analysis of the proteomics data stratified patients with ESCC into 3 subtypes with different molecular characteristics and clinical outcomes. Notably, subtype III exhibited the worst prognosis and enrichment in proteins associated with malignant processes, including glycolysis and DNA repair pathways. Furthermore, translocase of inner mitochondrial membrane domain containing 1 (TIMMDC1) was validated as a potential prognostic molecule for ESCC. Moreover, integrated kinase-substrate network analysis using the phosphoproteome nominated candidate kinases as potential targets. In vitro and in vivo experiments further confirmed casein kinase II subunit α (CSNK2A1) as a potential kinase target for ESCC. These underlying data represent a valuable resource for researchers that may provide better insights into the biology and treatment of ESCC.
Collapse
Affiliation(s)
- Dengyun Zhao
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou, Henan, China
| | - Yaping Guo
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
- The Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou, Henan, China
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan, China
| | - Huifang Wei
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
| | - Xuechao Jia
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
| | - Yafei Zhi
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
| | - Guiliang He
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
| | - Wenna Nie
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
| | - Limeng Huang
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
| | - Penglei Wang
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
| | | | - Zhicai Liu
- Linzhou Cancer Hospital, Anyang, Henan, China
| | - Jinwu Wang
- Linzhou Cancer Hospital, Anyang, Henan, China
| | - Mee-Hyun Lee
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
- College of Korean Medicine, Dongshin University, Naju, Jeonnam, Republic of Korea
| | - Zigang Dong
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou, Henan, China
- The Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou, Henan, China
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan, China
- Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou University, Zhengzhou, Henan, China
| | - Kangdong Liu
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou, Henan, China
- The Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou, Henan, China
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan, China
- Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou University, Zhengzhou, Henan, China
| |
Collapse
|
42
|
Zheng S, Chan SW, Liu F, Liu J, Chow PKH, Toh HC, Hong W. Hepatocellular Carcinoma: Current Drug Therapeutic Status, Advances and Challenges. Cancers (Basel) 2024; 16:1582. [PMID: 38672664 PMCID: PMC11048862 DOI: 10.3390/cancers16081582] [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: 03/16/2024] [Revised: 04/12/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common form of liver cancer, accounting for ~90% of liver neoplasms. It is the second leading cause of cancer-related deaths and the seventh most common cancer worldwide. Although there have been rapid developments in the treatment of HCC over the past decade, the incidence and mortality rates of HCC remain a challenge. With the widespread use of the hepatitis B vaccine and antiviral therapy, the etiology of HCC is shifting more toward metabolic-associated steatohepatitis (MASH). Early-stage HCC can be treated with potentially curative strategies such as surgical resection, liver transplantation, and radiofrequency ablation, improving long-term survival. However, most HCC patients, when diagnosed, are already in the intermediate or advanced stages. Molecular targeted therapy, followed by immune checkpoint inhibitor immunotherapy, has been a revolution in HCC systemic treatment. Systemic treatment of HCC especially for patients with compromised liver function is still a challenge due to a significant resistance to immune checkpoint blockade, tumor heterogeneity, lack of oncogenic addiction, and lack of effective predictive and therapeutic biomarkers.
Collapse
Affiliation(s)
- Shunzhen Zheng
- Key Laboratory of Biopharmaceuticals, Postdoctoral Scientific Research Workstation, Shandong Academy of Pharmaceutical Science, Jinan 250098, China;
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore 138673, Singapore; (S.W.C.); (W.H.)
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, China;
| | - Siew Wee Chan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore 138673, Singapore; (S.W.C.); (W.H.)
| | - Fei Liu
- Key Laboratory of Biopharmaceuticals, Postdoctoral Scientific Research Workstation, Shandong Academy of Pharmaceutical Science, Jinan 250098, China;
| | - Jun Liu
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, China;
| | - Pierce Kah Hoe Chow
- Division of Surgery and Surgical Oncology, National Cancer Centre, Singapore 169610, Singapore;
- Academic Clinical Programme for Surgery, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Han Chong Toh
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 168583, Singapore;
| | - Wanjin Hong
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore 138673, Singapore; (S.W.C.); (W.H.)
| |
Collapse
|
43
|
Guo Z, Liu Y, Ling Q, Xu L, Wang T, Zhu J, Lin Y, Lu X, Qu W, Zhang F, Zhu Z, Zhang J, Jia Z, Zeng P, Wang W, Sun Q, Luo Q, Hu Z, Zheng Z, Jia Y, Li J, Zheng Y, Wang M, Wang S, Han Z, Yu S, Li C, Zhang S, Xiong J, Deng F, Liu Y, Chen H, Wang Y, Li L, Liang W, Schlegel A, Björn N, Liu C, Zheng S, He X. Pre-transplant Use of Immune Checkpoint Inhibitors for Hepatocellular Carcinoma: A Multicenter, Retrospective Cohort Study. Am J Transplant 2024:S1600-6135(24)00278-8. [PMID: 38642712 DOI: 10.1016/j.ajt.2024.04.007] [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: 12/19/2023] [Revised: 03/24/2024] [Accepted: 04/15/2024] [Indexed: 04/22/2024]
Abstract
Immune checkpoint inhibitors (ICIs) as a downstaging or bridging therapy for liver transplantation (LT) in hepatocellular carcinoma (HCC) patients is rapidly increasing. However, the evidence about the feasibility and safety of pre-LT ICIs therapy is limited and controversial. To this end, a multicenter, retrospective cohort study was conducted in 11 Chinese centers. The results showed that 83 recipients received pre-LT ICIs therapy during the study period. The median post-LT follow up was 8.1 (interquartile range [IQR] 3.3-14.6) months. During the short follow-up, 23 (27.7%) recipients developed allograft rejection, and 7 of them (30.4%) was diagnosed by liver biopsy. Multivariate logistics regression analysis showed that time interval between the last administration of ICIs therapy and LT (TLAT) ≥ 30 days was an independent protective factor for allograft rejection (OR = 0.096, 95%CI 0.026-0.357; P < 0.001). Multivariate Cox analysis showed that allograft rejection was an independent risk factor for overall survival (OS) (HR = 9.960, 95%CI 1.006-98.610; P = 0.043). We conclude that patients who receive a pre-LT ICIs therapy with a TLAT shorter than 30 days have a much higher risk of allograft rejection than those with a TLAT longer than 30 days. The presence of rejection episodes might be associated with a higher post-LT mortality.
Collapse
Affiliation(s)
- Zhiyong Guo
- Organ Transplant Centre, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou 510080, China; Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou 510080, China; NHC key Laboratory of Assisted Circulation (Sun Yat-sen University), Guangzhou 510080, China
| | - Yao Liu
- Organ Transplant Centre, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou 510080, China; Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou 510080, China
| | - Qi Ling
- Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 311121, China; Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou 311121, China
| | - Leibo Xu
- Department of Pancreato-Biliary Surgery and Liver Transplantation Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Tielong Wang
- Organ Transplant Centre, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou 510080, China; Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou 510080, China
| | - Jiaxing Zhu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510120, China
| | - Yimou Lin
- Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 311121, China; Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou 311121, China
| | - Xinjun Lu
- Department of Pancreato-Biliary Surgery and Liver Transplantation Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Wei Qu
- Liver Transplantation Center, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing100000, China; Clinical Center for Pediatric Liver Transplantation, Capital Medical University, Beijing100000, China
| | - Fan Zhang
- Liver Transplantation Center, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing100000, China; Clinical Center for Pediatric Liver Transplantation, Capital Medical University, Beijing100000, China
| | - Zhijun Zhu
- Liver Transplantation Center, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing100000, China; Clinical Center for Pediatric Liver Transplantation, Capital Medical University, Beijing100000, China
| | - Jian Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangzhou 510080, China
| | - Zehua Jia
- Organ Transplant Centre, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou 510080, China; Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou 510080, China
| | - Ping Zeng
- Organ Transplant Centre, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou 510080, China; Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou 510080, China
| | - Wenjing Wang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510120, China
| | - Qiang Sun
- Department of General Surgery, Zhongshan People's Hospital, Zhongshan 528403, China
| | - Qijie Luo
- Department of General Surgery, Zhongshan People's Hospital, Zhongshan 528403, China
| | - Zemin Hu
- Department of General Surgery, Zhongshan People's Hospital, Zhongshan 528403, China
| | - Zhouying Zheng
- Department of Hepatobiliary Surgery, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China
| | - Yingbin Jia
- Department of Urology, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China
| | - Jian Li
- Department of Hepatobiliary Surgery, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China
| | - Yujian Zheng
- Department of Hepatobiliary Surgery & Liver Transplantation Center, General Hospital of Southern Theater Command, Guangzhou 510010, China
| | - Mengchao Wang
- Department of Hepatobiliary Surgery & Liver Transplantation Center, General Hospital of Southern Theater Command, Guangzhou 510010, China
| | - Shaoping Wang
- Department of Hepatobiliary Surgery & Liver Transplantation Center, General Hospital of Southern Theater Command, Guangzhou 510010, China
| | - Zemin Han
- Division of Hepatobiliopancreatic Surgery, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Sheng Yu
- Division of Hepatobiliopancreatic Surgery, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Chuanjiang Li
- Division of Hepatobiliopancreatic Surgery, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Shuhua Zhang
- Department of Hepatobiliary Surgery of General Surgery, Liver transplant center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Jun Xiong
- Department of Hepatobiliary Surgery of General Surgery, Liver transplant center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Feiwen Deng
- Liver Surgery Department, The First People's Hospital of Foshan, Foshan 528010, China
| | - Ying Liu
- Liver Surgery Department, The First People's Hospital of Foshan, Foshan 528010, China
| | - Huanwei Chen
- Liver Surgery Department, The First People's Hospital of Foshan, Foshan 528010, China
| | - Yanfeng Wang
- Zhongnan Hospital of Wuhan University, Institute of Hepatobiliary Diseases of Wuhan University, Transplant Center of Wuhan University, Hubei Key Laboratory of Medical Technology on Transplantation, Wuhan 430071, China
| | - Ling Li
- Zhongnan Hospital of Wuhan University, Institute of Hepatobiliary Diseases of Wuhan University, Transplant Center of Wuhan University, Hubei Key Laboratory of Medical Technology on Transplantation, Wuhan 430071, China
| | - Wenjin Liang
- Zhongnan Hospital of Wuhan University, Institute of Hepatobiliary Diseases of Wuhan University, Transplant Center of Wuhan University, Hubei Key Laboratory of Medical Technology on Transplantation, Wuhan 430071, China
| | - Andrea Schlegel
- Transplantation Center, Digestive Disease and Surgery Institute, Department of Immunity and Inflammation, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Nashan Björn
- Organ Transplantation Center, The First Affiliated Hospital of the University of Science and Technology of China, Hefei 230001, China
| | - Chao Liu
- Department of Pancreato-Biliary Surgery and Liver Transplantation Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.
| | - Shusen Zheng
- Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 311121, China; Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou 311121, China.
| | - Xiaoshun He
- Organ Transplant Centre, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou 510080, China; Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou 510080, China.
| |
Collapse
|
44
|
Liu S, Meng Y, Zhang Y, Qiu L, Wan X, Yang X, Zhang Y, Liu X, Wen L, Lei X, Zhang B, Han J. Integrative analysis of senescence-related genes identifies robust prognostic clusters with distinct features in hepatocellular carcinoma. J Adv Res 2024:S2090-1232(24)00150-4. [PMID: 38614215 DOI: 10.1016/j.jare.2024.04.007] [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: 11/15/2023] [Revised: 04/09/2024] [Accepted: 04/09/2024] [Indexed: 04/15/2024] Open
Abstract
INTRODUCTION Senescence refers to a state of permanent cell growth arrest and is regarded as a tumor suppressive mechanism, whereas accumulative evidence demonstrate that senescent cells play an adverse role during cancer progression. The scarcity of specific and reliable markers reflecting senescence level in cancer impede our understanding of this biological basis. OBJECTIVES Senescence-related genes (SRGs) were collected for integrative analysis to reveal the role of senescence in hepatocellular carcinoma (HCC). METHODS Consensus clustering was used to subtype HCC based on SRGs. Several computational methods, including single sample gene set enrichment analysis (ssGSEA), fuzzy c-means algorithm, were performed. Data of drug sensitivities were utilized to screen potential therapeutic agents for different senescence patients. Additionally, we developed a method called signature-related gene analysis (SRGA) for identification of markers relevant to phenotype of interest. Experimental strategies consisting quantitative real-time PCR (qRT-PCR), β-galactosidase assay, western blot, and tumor-T cell co-culture system were used to validate the findings in vitro. RESULTS We identified three robust prognostic clusters of HCC patients with distinct survival outcome, mutational landscape, and immune features. We further extracted signature genes of senescence clusters to construct the senescence scoring system and profile senescence level in HCC at bulk and single-cell resolution. Senescence-induced stemness reprogramming was confirmed both in silico and in vitro. HCC patients with high senescence were immune suppressed and sensitive to Tozasertib and other drugs. We suggested that MAFG, PLIN3, and 4 other genes were pertinent to HCC senescence, and MAFG potentially mediated immune suppression, senescence, and stemness. CONCLUSION Our findings provide insights into the role of SRGs in patients stratification and precision medicine.
Collapse
Affiliation(s)
- Sicheng Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yang Meng
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yaguang Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Lei Qiu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiaowen Wan
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xuyang Yang
- Research Laboratory of Cancer Epigenetics and Genomics, Department of General Surgery, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yang Zhang
- Research Laboratory of Cancer Epigenetics and Genomics, Department of General Surgery, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xueqin Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Linda Wen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xue Lei
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Bo Zhang
- Research Laboratory of Cancer Epigenetics and Genomics, Department of General Surgery, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Junhong Han
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China.
| |
Collapse
|
45
|
Fu Y, Maccioni L, Wang XW, Greten TF, Gao B. Alcohol-associated liver cancer. Hepatology 2024:01515467-990000000-00837. [PMID: 38607725 DOI: 10.1097/hep.0000000000000890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024]
Abstract
Heavy alcohol intake induces a wide spectrum of liver diseases ranging from steatosis, steatohepatitis, cirrhosis, and HCC. Although alcohol consumption is a well-known risk factor for the development, morbidity, and mortality of HCC globally, alcohol-associated hepatocellular carcinoma (A-HCC) is poorly characterized compared to viral hepatitis-associated HCC. Most A-HCCs develop after alcohol-associated cirrhosis (AC), but the direct carcinogenesis from ethanol and its metabolites to A-HCC remains obscure. The differences between A-HCC and HCCs caused by other etiologies have not been well investigated in terms of clinical prognosis, genetic or epigenetic landscape, molecular mechanisms, and heterogeneity. Moreover, there is a huge gap between basic research and clinical practice due to the lack of preclinical models of A-HCC. In the current review, we discuss the pathogenesis, heterogeneity, preclinical approaches, epigenetic, and genetic profiles of A-HCC, and discuss the current insights into and the prospects for future research on A-HCC. The potential effect of alcohol on cholangiocarcinoma and liver metastasis is also discussed.
Collapse
Affiliation(s)
- Yaojie Fu
- Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland, USA
| | - Luca Maccioni
- Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland, USA
| | - Xin Wei Wang
- Liver Carcinogenesis Section, Laboratory of Human Carcinogenesis, National Cancer Institute, NIH, Bethesda, Maryland, USA
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Tim F Greten
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
- Gastrointestinal Malignancies Section, Thoracic and Gastrointestinal Malignancies Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Bin Gao
- Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland, USA
| |
Collapse
|
46
|
Liu G, Li M, Zeng Z, Fan Q, Ren X, Wang Z, Sun Y, He Y, Sun L, Deng Y, Liu S, Zhong C, Gao J. Tyrosine hydroxylase inhibits HCC progression by downregulating TGFβ/Smad signaling. Eur J Med Res 2024; 29:228. [PMID: 38610044 PMCID: PMC11015545 DOI: 10.1186/s40001-024-01703-z] [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: 12/06/2023] [Accepted: 01/31/2024] [Indexed: 04/14/2024] Open
Abstract
The alteration of metabolic processes has been found to have significant impacts on the development of hepatocellular carcinoma (HCC). Nevertheless, the effects of dysfunction of tyrosine metabolism on the development of HCC remains to be discovered. This research demonstrated that tyrosine hydroxylase (TH), which responsible for the initial and limiting step in the bio-generation of the neuro-transmitters dopamine and adrenaline, et al. was shown to be reduced in HCC. Increased expression of TH was found facilitates the survival of HCC patients. In addition, decreased TH indicated larger tumor size, much more numbers of tumor, higher level of AFP, and the presence of cirrhosis. TH effectively impairs the growth and metastasis of HCC cells, a process dependent on the phosphorylation of serine residues (S19/S40). TH directly binds to Smad2 and hinders the cascade activation of TGFβ/Smad signaling with the treatment of TGFβ1. In summary, our study uncovered the non-metabolic functions of TH in the development of HCC and proposes that TH might be a promising biomarker for diagnosis as well as an innovative target for metastatic HCC.
Collapse
Affiliation(s)
- Guoqian Liu
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha, 410008, Hunan, China
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Mengwei Li
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha, 410008, Hunan, China
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Zimei Zeng
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Qi Fan
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Xinxin Ren
- Cancer Center, Department of Pathology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China
| | - Zhexin Wang
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Yaoqi Sun
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China
- Institute of Gynecological Minimally Invasive Medicine, Tongji University School of Medicine, Shanghai, 200072, China
| | - Yulin He
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Lunquan Sun
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha, 410008, Hunan, China
| | - Yuezhen Deng
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
| | - Shupeng Liu
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China.
- Institute of Gynecological Minimally Invasive Medicine, Tongji University School of Medicine, Shanghai, 200072, China.
| | - Chenxi Zhong
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
| | - Jie Gao
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha, 410008, Hunan, China.
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
- Xiangya Cancer Center, Xiangya Hospital, Central South University, 87th of Xiangya Road, Changsha, 410008, China.
| |
Collapse
|
47
|
Gonvers S, Martins-Filho SN, Hirayama A, Calderaro J, Phillips R, Uldry E, Demartines N, Melloul E, Park YN, Paradis V, Thung SN, Alves V, Sempoux C, Labgaa I. Macroscopic Characterization of Hepatocellular Carcinoma: An Underexploited Source of Prognostic Factors. J Hepatocell Carcinoma 2024; 11:707-719. [PMID: 38605975 PMCID: PMC11007400 DOI: 10.2147/jhc.s447848] [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: 11/02/2023] [Accepted: 02/29/2024] [Indexed: 04/13/2024] Open
Abstract
The macroscopic appearance of a tumor such as hepatocellular carcinoma (HCC) may be defined as its phenotype which is de facto dictated by its genotype. Therefore, macroscopic characteristics of HCC are unlikely random but rather reflect genomic traits of cancer, presumably acting as a valuable source of information that can be retrieved and exploited to infer prognosis. This review aims to provide a comprehensive overview of the available data on the prognostic value of macroscopic characterization in HCC. A total of 57 studies meeting eligible criteria were identified, including patients undergoing liver resection (LR; 47 studies, 83%) or liver transplant (LT; 9 studies, 16%). The following macroscopic variables were investigated: tumor size (n = 42 studies), number of nodules (n = 28), vascular invasion (n = 24), bile duct invasion (n = 6), growth pattern (n = 15), resection margin (n = 11), tumor location (n = 6), capsule (n = 2) and satellite (n = 1). Although the selected studies provided insightful data with notable prognostic performances, a lack of standardization and substantial gaps were noted in the report and the analysis of gross findings. This topic remains incompletely covered. While the available studies underscored the value of macroscopic variables in HCC prognostication, important lacks were also observed. Macroscopic characterization of HCC is likely an underexploited source of prognostic factors that must be actively explored by future multidisciplinary research.
Collapse
Affiliation(s)
- Stéphanie Gonvers
- Department of Visceral Surgery, Lausanne University Hospital (CHUV), Lausanne, Switzerland
- Faculty of Biology & Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland
| | | | - André Hirayama
- Department of Pathology, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Julien Calderaro
- Department of Pathology, APHP, Henri Mondor University Hospital, Creteil, Val-de-Marne, France
| | - Rebecca Phillips
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Emilie Uldry
- Department of Visceral Surgery, Lausanne University Hospital (CHUV), Lausanne, Switzerland
- Faculty of Biology & Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Nicolas Demartines
- Department of Visceral Surgery, Lausanne University Hospital (CHUV), Lausanne, Switzerland
- Faculty of Biology & Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Emmanuel Melloul
- Department of Visceral Surgery, Lausanne University Hospital (CHUV), Lausanne, Switzerland
- Faculty of Biology & Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Young Nyun Park
- Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Valérie Paradis
- Department of Pathology, APHP, Beaujon University Hospital, Clichy, France
| | - Swan N Thung
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Venancio Alves
- Department of Pathology, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Christine Sempoux
- Faculty of Biology & Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland
- Department of Pathology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Ismail Labgaa
- Department of Visceral Surgery, Lausanne University Hospital (CHUV), Lausanne, Switzerland
- Faculty of Biology & Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland
| |
Collapse
|
48
|
Yang Y, Huang L, Zhang N, Deng YN, Cao X, Liang Y, Hou H, Luo Y, Yang Y, Li Q, Liang S. SUMOylation of annexin A6 retards cell migration and tumor growth by suppressing RHOU/AKT1-involved EMT in hepatocellular carcinoma. Cell Commun Signal 2024; 22:206. [PMID: 38566133 PMCID: PMC10986105 DOI: 10.1186/s12964-024-01573-2] [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: 11/30/2023] [Accepted: 03/16/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND The protein annexin A6 (AnxA6) is involved in numerous membrane-related biological processes including cell migration and invasion by interacting with other proteins. The dysfunction of AnxA6, including protein expression abundance change and imbalance of post-translational modification, is tightly related to multiple cancers. Herein we focus on the biological function of AnxA6 SUMOylation in hepatocellular carcinoma (HCC) progression. METHODS The modification sites of AnxA6 SUMOylation were identified by LC-MS/MS and amino acid site mutation. AnxA6 expression was assessed by immunohistochemistry and immunofluorescence. HCC cells were induced into the epithelial-mesenchymal transition (EMT)-featured cells by 100 ng/mL 12-O-tetradecanoylphorbol-13-acetate exposure. The ability of cell migration was evaluated under AnxA6 overexpression by transwell assay. The SUMO1 modified AnxA6 proteins were enriched from total cellular proteins by immunoprecipitation with anti-SUMO1 antibody, then the SUMOylated AnxA6 was detected by Western blot using anti-AnxA6 antibody. The nude mouse xenograft and orthotopic hepatoma models were established to determine HCC growth and tumorigenicity in vivo. The HCC patient's overall survival versus AnxA6 expression level was evaluated by the Kaplan-Meier method. RESULTS Lys579 is a major SUMO1 modification site of AnxA6 in HCC cells, and SUMOylation protects AnxA6 from degradation via the ubiquitin-proteasome pathway. Compared to the wild-type AnxA6, its SUMO site mutant AnxA6K579R leads to disassociation of the binding of AnxA6 with RHOU, subsequently RHOU-mediated p-AKT1ser473 is upregulated to facilitate cell migration and EMT progression in HCC. Moreover, the SENP1 deSUMOylates AnxA6, and AnxA6 expression is negatively correlated with SENP1 protein expression level in HCC tissues, and a high gene expression ratio of ANXA6/SENP1 indicates a poor overall survival of patients. CONCLUSIONS AnxA6 deSUMOylation contributes to HCC progression and EMT phenotype, and the combination of AnxA6 and SENP1 is a better tumor biomarker for diagnosis of HCC grade malignancy and prognosis.
Collapse
Affiliation(s)
- Yanfang Yang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No.17, 3rd Section of People's South Road, Chengdu, 610041, People's Republic of China
| | - Lan Huang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No.17, 3rd Section of People's South Road, Chengdu, 610041, People's Republic of China
| | - Nan Zhang
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ya-Nan Deng
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No.17, 3rd Section of People's South Road, Chengdu, 610041, People's Republic of China
| | - Xu Cao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No.17, 3rd Section of People's South Road, Chengdu, 610041, People's Republic of China
| | - Yue Liang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No.17, 3rd Section of People's South Road, Chengdu, 610041, People's Republic of China
| | - Huijin Hou
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No.17, 3rd Section of People's South Road, Chengdu, 610041, People's Republic of China
| | - Yinheng Luo
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No.17, 3rd Section of People's South Road, Chengdu, 610041, People's Republic of China
| | - Yang Yang
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Qiu Li
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Shufang Liang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No.17, 3rd Section of People's South Road, Chengdu, 610041, People's Republic of China.
| |
Collapse
|
49
|
Yang L, Du M, Liu K, Wang P, Zhu J, Li F, Wang Z, Huang K, Liang M. Pimpinellin ameliorates macrophage inflammation by promoting RNF146-mediated PARP1 ubiquitination. Phytother Res 2024; 38:1783-1798. [PMID: 38323338 DOI: 10.1002/ptr.8135] [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: 08/08/2023] [Revised: 12/17/2023] [Accepted: 01/13/2024] [Indexed: 02/08/2024]
Abstract
Macrophage inflammation plays a central role during the development and progression of sepsis, while the regulation of macrophages by parthanatos has been recently identified as a novel strategy for anti-inflammatory therapies. This study was designed to investigate the therapeutic potential and mechanism of pimpinellin against LPS-induced sepsis. PARP1 and PAR activation were detected by western blot or immunohistochemistry. Cell death was assessed by flow cytometry and western blot. Cell metabolism was measured with a Seahorse XFe24 extracellular flux analyzer. C57, PARP1 knockout, and PARP1 conditional knock-in mice were used in a model of sepsis caused by LPS to assess the effect of pimpinellin. Here, we found that pimpinellin can specifically inhibit LPS-induced macrophage PARP1 and PAR activation. In vitro studies showed that pimpinellin could inhibit the expression of inflammatory cytokines and signal pathway activation in macrophages by inhibiting overexpression of PARP1. In addition, pimpinellin increased the survival rate of LPS-treated mice, thereby preventing LPS-induced sepsis. Further research confirmed that LPS-induced sepsis in PARP1 overexpressing mice was attenuated by pimpinellin, and PARP1 knockdown abolished the protective effect of pimpinellin against LPS-induced sepsis. Further study found that pimpinellin can promote ubiquitin-mediated degradation of PARP1 through RNF146. This is the first study to demonstrate that pimpinellin inhibits excessive inflammatory responses by promoting the ubiquitin-mediated degradation of PARP1.
Collapse
Affiliation(s)
- Liuye Yang
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Meng Du
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Metabolic Abnormalities and Vascular Aging Huazhong University of Science and Technology, Wuhan, China
- Hubei Clinical Research Center for Metabolic and Cardiovascular Disease, Huazhong University of Science and Technology, Wuhan, China
| | - Kaiyuan Liu
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Pengchao Wang
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jingbo Zhu
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fengcen Li
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ze Wang
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of science and technology, Wuhan, China
| | - Kai Huang
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Metabolic Abnormalities and Vascular Aging Huazhong University of Science and Technology, Wuhan, China
- Hubei Clinical Research Center for Metabolic and Cardiovascular Disease, Huazhong University of Science and Technology, Wuhan, China
| | - Minglu Liang
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Metabolic Abnormalities and Vascular Aging Huazhong University of Science and Technology, Wuhan, China
- Hubei Clinical Research Center for Metabolic and Cardiovascular Disease, Huazhong University of Science and Technology, Wuhan, China
| |
Collapse
|
50
|
Zheng L, Wang Y, Liu Z, Wang Z, Tao C, Wu A, Li H, Xiao T, Li Z, Rong W. Identification of molecular characteristics of hepatocellular carcinoma with microvascular invasion based on deep targeted sequencing. Cancer Med 2024; 13:e7043. [PMID: 38572921 PMCID: PMC10993708 DOI: 10.1002/cam4.7043] [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: 09/19/2023] [Revised: 01/29/2024] [Accepted: 02/13/2024] [Indexed: 04/05/2024] Open
Abstract
BACKGROUND As an indicator of tumor invasiveness, microvascular invasion (MVI) is a crucial risk factor for postoperative relapse, metastasis, and unfavorable prognosis in hepatocellular carcinoma (HCC). Nevertheless, the genetic mechanisms underlying MVI, particularly for Chinese patients, remain mostly uncharted. METHODS We applied deep targeted sequencing on 66 Chinese HCC samples. Focusing on the telomerase reverse transcriptase (TERT) promoter (TERTp) and TP53 co-mutation (TERTp+/TP53+) group, gene set enrichment analysis (GSEA) was used to explore the potential molecular mechanisms of the TERTp+/TP53+ group on tumor progression and metastasis. Additionally, we evaluated the tumor immune microenvironment of the TERTp+/TP53+ group in HCC using multiplex immunofluorescence (mIF) staining. RESULTS Among the 66 HCC samples, the mutated genes that mostly appeared were TERT, TP53, and CTNNB1. Of note, we found 10 cases with TERTp+/TP53+, of which nine were MVI-positive and one was MVI-negative, and there was a co-occurrence of TERTp and TP53 (p < 0.05). Survival analysis demonstrated that patients with the TERTp+/TP53+ group had lower the disease-free survival (DFS) (p = 0.028). GSEA results indicated that telomere organization, telomere maintenance, DNA replication, positive regulation of cell cycle, and negative regulation of immune response were significantly enriched in the TERTp+/TP53+ group (all adjusted p-values (p.adj) < 0.05). mIF revealed that the TERTp+/TP53+ group decreased CD8+ T cells infiltration (p = 0.25) and enhanced PDL1 expression (p = 0.55). CONCLUSIONS TERTp+/TP53+ was significantly enriched in MVI-positive patients, leading to poor prognosis for HCC patients by promoting proliferation of HCC cell and inhibiting infiltration of immune cell surrounding HCC. TERTp+/TP53+ can be utilized as a potential indicator for predicting MVI-positive patients and poor prognosis, laying a preliminary foundation for further exploration of co-mutation in HCC with MVI and clinical treatment.
Collapse
Affiliation(s)
- Linlin Zheng
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Yaru Wang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Zhenrong Liu
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Zhihao Wang
- Department of Hepatobiliary Hernia SurgeryLiaocheng Dongcangfu People's HospitalLiaochengChina
| | - Changcheng Tao
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Anke Wu
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Haiyang Li
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Ting Xiao
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Zhuo Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Weiqi Rong
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| |
Collapse
|