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Chan YT, Zhang C, Wu J, Lu P, Xu L, Yuan H, Feng Y, Chen ZS, Wang N. Biomarkers for diagnosis and therapeutic options in hepatocellular carcinoma. Mol Cancer 2024; 23:189. [PMID: 39242496 PMCID: PMC11378508 DOI: 10.1186/s12943-024-02101-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: 07/30/2024] [Accepted: 08/23/2024] [Indexed: 09/09/2024] Open
Abstract
Liver cancer is a global health challenge, causing a significant social-economic burden. Hepatocellular carcinoma (HCC) is the predominant type of primary liver cancer, which is highly heterogeneous in terms of molecular and cellular signatures. Early-stage or small tumors are typically treated with surgery or ablation. Currently, chemotherapies and immunotherapies are the best treatments for unresectable tumors or advanced HCC. However, drug response and acquired resistance are not predictable with the existing systematic guidelines regarding mutation patterns and molecular biomarkers, resulting in sub-optimal treatment outcomes for many patients with atypical molecular profiles. With advanced technological platforms, valuable information such as tumor genetic alterations, epigenetic data, and tumor microenvironments can be obtained from liquid biopsy. The inter- and intra-tumoral heterogeneity of HCC are illustrated, and these collective data provide solid evidence in the decision-making process of treatment regimens. This article reviews the current understanding of HCC detection methods and aims to update the development of HCC surveillance using liquid biopsy. Recent critical findings on the molecular basis, epigenetic profiles, circulating tumor cells, circulating DNAs, and omics studies are elaborated for HCC diagnosis. Besides, biomarkers related to the choice of therapeutic options are discussed. Some notable recent clinical trials working on targeted therapies are also highlighted. Insights are provided to translate the knowledge into potential biomarkers for detection and diagnosis, prognosis, treatment response, and drug resistance indicators in clinical practice.
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Affiliation(s)
- Yau-Tuen Chan
- School of Chinese Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Cheng Zhang
- School of Chinese Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Junyu Wu
- School of Chinese Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Pengde Lu
- School of Chinese Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Lin Xu
- School of Chinese Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Hongchao Yuan
- School of Chinese Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Yibin Feng
- School of Chinese Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Zhe-Sheng Chen
- School of Chinese Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong.
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY, 11439, USA.
| | - Ning Wang
- School of Chinese Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong.
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Xu Z, Wu Y, Chen X, Jin B. Identification of tumor-antigen signatures and immune subtypes for messenger RNA vaccine selection in advanced clear cell renal cell carcinoma. Surgery 2024; 176:785-797. [PMID: 38851900 DOI: 10.1016/j.surg.2024.04.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/08/2024] [Accepted: 04/19/2024] [Indexed: 06/10/2024]
Abstract
BACKGROUND Advanced clear cell renal cell carcinoma still lacks reliable diagnostic and prognostic biomarkers. Recently, tumor vaccines targeting specific molecules have been proposed as a promising treatment in mitigating tumor progression, which was rekindled under the background of the COVID-19 pandemic. However, the application of messenger RNA vaccine against advanced clear cell renal cell carcinoma antigens remains stagnant, and no subgroup of patients deemed suitable for vaccination has been extensively studied or validated. Our study aims to explore novel advanced clear cell renal cell carcinoma antigen signatures to select suitable patients for vaccination. METHODS Gene expression profiles of advanced clear cell renal cell carcinoma samples and their corresponding clinical data were retrieved from The Cancer Genome Atlas. The least absolute shrinkage and selection operator model was applied to develop signatures to stratify patients with advanced clear cell renal cell carcinoma. Receiver operating characteristic analysis was used to compare the prognostic accuracy of each factor. Tumor Immune Estimation Resource was used to visualize the relationship between the proportion of antigen-presenting cells and the expression of filtered genes. The "CIBERSORT" and "WGCNA" R Packages were employed to ascertain disparities in immune infiltration levels between advanced clear cell renal cell carcinoma subgroups. The Search Tools for the Retrieval of Interacting Genes database and Cytoscape were used to construct the protein-protein interaction network. CCK-8 and colony formation assays were included in the invitro experiment. RESULTS In total, 244 potential tumor antigens were identified. Using the least absolute shrinkage and selection operator Cox regression, 21 tumor antigens were selected for developing a risk evaluation signature. The risk score signature can be a useful tool to predict the outcome of advanced clear cell renal cell carcinoma patients. According to the differential clinical, molecular, and immune-related genes, we divided advanced clear cell renal cell carcinoma patients into the immune "cold" subtype and immune "hot" subtype. By developing a logistic score, the immune subtype signature can better distinguish a patient more likely to be immune "cold" subtype or immune "hot" subtype. Interestingly, patients with high risk scores had a higher proportion of immune "hot" subtype than those with a low risk score. Furthermore, the prognostic value was significantly improved when combining risk score and immune subtype. Distinct immune landscapes and signal pathways were observed between different tumor subtypes. Finally, novel tumor antigens related to oxidative stress were identified. CONCLUSION The tumor-antigens-based risk score and immune subtype signatures identified potentially effective neo-antigens for advanced clear cell renal cell carcinoma messenger RNA vaccine development, and patients with low risk scores and immune "cold" subtype tumors are more prone to benefit from messenger RNA vaccination. Furthermore, our study highlights the significant role of oxidative stress in determining the efficacy of the messenger RNA vaccine.
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Affiliation(s)
- Zhijie Xu
- Department of Urology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Engineering Research Center for Bladder Tumor Innovation Diagnosis and Treatment, Hangzhou, China.
| | - Yunfei Wu
- Department of Urology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Engineering Research Center for Bladder Tumor Innovation Diagnosis and Treatment, Hangzhou, China
| | - Xiaoyi Chen
- Department of Urology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Engineering Research Center for Bladder Tumor Innovation Diagnosis and Treatment, Hangzhou, China
| | - Baiye Jin
- Department of Urology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Zhejiang Engineering Research Center for Bladder Tumor Innovation Diagnosis and Treatment, Hangzhou, China
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Zhang X, Zhang B, Zhang Y, Zhang F. Association analysis of hepatocellular carcinoma-related hub proteins and hub genes. Proteomics Clin Appl 2023; 17:e2200090. [PMID: 37050894 DOI: 10.1002/prca.202200090] [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: 10/26/2022] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 04/14/2023]
Abstract
PURPOSE Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide. The occurrence and development of HCC are closely related to epigenetic modifications. Epigenetic modifications can regulate gene expression and related functions through DNA methylation. This paper presents an association analysis method of HCC-related hub proteins and hub genes. EXPERIMENTAL DESIGN Bioinformatics analysis of HCC-related DNA methylation data is carried out to clarify the molecular mechanism of HCC-related genes and to find hub genes (genes with more connections in the network) by constructing in the gene interaction network. This paper proposes an accurate prediction method of protein-protein interaction (PPI) based on deep learning model DeepSG2PPI. The trained DeepSG2PPI model predicts the interaction relationship between the synthetic proteins regulated by HCC-related genes. RESULTS This paper finds that four genes are the intersection of hub genes and hub proteins. The four genes are: FBL, CCNB2, ALDH18A1, and RPLP0. The association of RPLP0 gene with HCC is a new finding of this study. RPLP0 is expected to become a new biomarker for the treatment, diagnosis, and prognosis of HCC. The four proteins corresponding to the four genes are: ENSP00000221801, ENSP00000288207, ENSP00000360268, and ENSP00000449328. CONCLUSIONS AND CLINICAL RELEVANCE The association between the hub genes with the hub proteins is analyzed. The mutual verification of the hub genes and the hub proteins can obtain more credible HCC-related genes and proteins, which is helpful for the diagnosis, treatment, and drug development of HCC.
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Affiliation(s)
- Xinhong Zhang
- School of Software, Henan University, Kaifeng, China
| | - Boyan Zhang
- School of Software, Henan University, Kaifeng, China
| | - Yawei Zhang
- Henan Key Laboratory of Big Data Analysis and Processing, Henan University, Kaifeng, China
| | - Fan Zhang
- Henan Key Laboratory of Big Data Analysis and Processing, Henan University, Kaifeng, China
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Zhang M, Ding Q, Bian C, Su J, Xin Y, Jiang X. Progress on the molecular mechanism of portal vein tumor thrombosis formation in hepatocellular carcinoma. Exp Cell Res 2023; 426:113563. [PMID: 36944406 DOI: 10.1016/j.yexcr.2023.113563] [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: 12/06/2022] [Revised: 03/01/2023] [Accepted: 03/18/2023] [Indexed: 03/22/2023]
Abstract
Hepatocellular carcinoma (HCC) is one of the most common malignant tumors, with poor prognosis and high mortality. Early-stage HCC has no obvious clinical symptoms, and most patients are already at an advanced stage when they are diagnosed. Portal vein tumor thrombus (PVTT) is the most common complication and a poor prognostic factor for HCC, which frequently leads to portal vein hypertension, ascites, gastrointestinal bleeding, and tumor metastasis. The formation of PVTT is related to the complex structure and hemodynamic changes of the portal vein and is closely related to changes at the cellular and molecular levels. The differentially-expressed genes (DEGs) between PVTT and primary tumor (PT) suggest that the two tissues may have different clonal origins. Epigenetic and proteomic analyses also suggest complex and diverse mechanisms for the formation of PVTT. In addition, the tumor microenvironment and energy metabolism pathways are interrelated in regulating the invasion and progression of PVTT. Aerobic glycolysis and the tumor immune microenvironment have been the focus of recent studies on PVTT. In this review, we summarize the mechanism of PVTT formation at the cellular and molecular levels to provide information to guide better prevention and treatment of PVTT in the clinic.
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Affiliation(s)
- Min Zhang
- Jilin Provincial Key Laboratory of Radiation Oncology & Therapy, Changchun, 130021, China; Department of Radiation Oncology, The First Hospital of Jilin University, Changchun, 130021, China; NHC Key Laboratory of Radiobiology, School of Public Health of Jilin University, Changchun, 130021, China.
| | - Qiuhui Ding
- Jilin Provincial Key Laboratory of Radiation Oncology & Therapy, Changchun, 130021, China; Department of Radiation Oncology, The First Hospital of Jilin University, Changchun, 130021, China; NHC Key Laboratory of Radiobiology, School of Public Health of Jilin University, Changchun, 130021, China.
| | - Chenbin Bian
- Jilin Provincial Key Laboratory of Radiation Oncology & Therapy, Changchun, 130021, China; Department of Radiation Oncology, The First Hospital of Jilin University, Changchun, 130021, China; NHC Key Laboratory of Radiobiology, School of Public Health of Jilin University, Changchun, 130021, China.
| | - Jing Su
- Jilin Provincial Key Laboratory of Radiation Oncology & Therapy, Changchun, 130021, China; Department of Radiation Oncology, The First Hospital of Jilin University, Changchun, 130021, China; NHC Key Laboratory of Radiobiology, School of Public Health of Jilin University, Changchun, 130021, China.
| | - Ying Xin
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun, 130021, China.
| | - Xin Jiang
- Jilin Provincial Key Laboratory of Radiation Oncology & Therapy, Changchun, 130021, China; Department of Radiation Oncology, The First Hospital of Jilin University, Changchun, 130021, China; NHC Key Laboratory of Radiobiology, School of Public Health of Jilin University, Changchun, 130021, China.
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Zhou W, Fang DL, He Y. Screening potential prognostic biomarkers for portal vein emboli in patients with hepatocellular carcinoma. J Gastrointest Oncol 2021; 12:1927-1938. [PMID: 34532139 DOI: 10.21037/jgo-21-433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/10/2021] [Indexed: 01/27/2023] Open
Abstract
Background The formation of portal vein tumor thrombus (PVTT) is closely related to the prognosis of patients with hepatocellular carcinoma (HCC). However, the mechanisms by which PVTTs form and the biomarkers involved are still little understood. Methods The Genome Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases were used to obtain transcriptome data from normal tissue, HCC tissue, primary tumors (PTs) of HCC, and paired PVTT tissue. Differentially expressed genes (DEGs) in PTs and PVTTs were analyzed. The differentially expressed immune genes were further investigated in terms of their prognostic significance, immune infiltration, function. Finally, we explored the relationship between risk scores and drug sensitivity based on the R package. Results In the two datasets, there were 458 DEGs identified in the PT and PVTT tissues, of which, 58 were immune-related genes. The differentially expressed immune genes may promote the progression of PVTT by participating in the regulation of non-cellular components such as the extracellular matrix, inflammatory factors, and chemokines. Furthermore, the immune genes KDR, AKT3, FCGR2B, KIAA1429, and TPT1 were correlated with the prognosis of HCC in patients with PVTT. Using this data, a model was constructed to predict the prognosis of patients, thus allowing for the identification of high- and low-risk patients. Conclusions This study demonstrated that immune-related genes may be involved in the regulation of the extracellular matrix and acellular components, and subsequently, in the formation of PVTT. These five genes KDR, AKT3, FCGR2B, KIAA1429, and TPT1 may be potential prognostic biomarkers and treatment targets for HCC patients with PVTT.
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Affiliation(s)
- Weijie Zhou
- Clinical Laboratory, Baise People's Hospital, Baise, China
| | - Da Lang Fang
- Department of Breast and Thyroid Surgery, the Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Yongfei He
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
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Sun M, Cao Y, Yang X, An F, Wu H, Wang J. DNA methylation in the OPG/RANK/RANKL pathway is associated with steroid-induced osteonecrosis of the femoral head. BMC Musculoskelet Disord 2021; 22:599. [PMID: 34187427 PMCID: PMC8240366 DOI: 10.1186/s12891-021-04472-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 06/10/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Dysregulation of the OPG/RANK/RANKL signalling pathway is a key step in the occurrence of steroid-induced osteonecrosis of the femoral head (ONFH). This study aims to understand the degree of methylation of the OPG, RANK, and RANKL genes in steroid-related ONFH. METHODS A case-control study was designed, including 50 patients (25 males and 25 females) and 50 matched controls. The European Molecular Biology Open Software Suite (EMBOSS) was used to predict the existence and location of CpG islands in the OPG, RANK, and RANKL genes. The Agena MassARRAY platform was used to detect the methylation status of the above genes in the blood of subjects. The relationship between the methylation level of CpG sites in each gene and steroid-related ONFH was analysed by the chi-square test, logistic regression analysis, and other statistical methods. RESULTS In the CpG islands of the OPG, RANK, and RANKL genes in patients with steroid-related ONFH, several CpG sites with high methylation rates and high methylation levels were found. Some hypermethylated CpG sites increase the risk of steroid-related ONFH. In addition, a few hypermethylated CpG sites have predictive value for the early diagnosis of steroid-related ONFH. CONCLUSION Methylation of certain sites in the OPG/RANK/RANKL signalling pathway increases the risk of steroid-related ONFH. Some hypermethylated CpG sites may be used as early prediction and diagnostic targets for steroid-related ONFH.
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Affiliation(s)
- Menghu Sun
- Department of Orthopedics and Traumatology, The Second Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010030, Inner Mongolia, China
- Inner Mongolia Medical University, Hohhot, 010050, Inner Mongolia, China
| | - Yuju Cao
- Zhengzhou Traditional Chinese Medicine (TCM) Traumatology Hospital, Zhengzhou, 450016, Henan Province, China
| | - Xiaolong Yang
- Department of Orthopedics and Traumatology, The Second Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010030, Inner Mongolia, China
| | - Feimeng An
- Inner Mongolia Autonomous Region Hospital of Traditional Chinese Medicine, Hohhot, 010110, Inner Mongolia, China
| | - Huiqiang Wu
- Inner Mongolia Autonomous Region Hospital of Traditional Chinese Medicine, Hohhot, 010110, Inner Mongolia, China
| | - Jianzhong Wang
- Department of Orthopedics and Traumatology, The Second Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010030, Inner Mongolia, China.
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The Diagnostic Value of Serum PIVKA-II Alone or in Combination with AFP in Chinese Hepatocellular Carcinoma Patients. DISEASE MARKERS 2021; 2021:8868370. [PMID: 33628341 PMCID: PMC7884179 DOI: 10.1155/2021/8868370] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 10/13/2020] [Accepted: 01/31/2021] [Indexed: 01/02/2023]
Abstract
Background At present, the diagnostic accuracy of alpha-fetoprotein (AFP) for hepatocellular carcinoma (HCC) surveillance is insufficient. It remains controversial whether prothrombin induced by vitamin K absence II (PIVKA-II) has a better diagnostic value than AFP for HCC patients. Objective To investigate the diagnostic role of PIVKA-II alone or in combination with AFP in Chinese HCC patients. Methods Serum AFP and PIVKA-II levels were detected and analyzed in 308 HCC afflicted patients and 120 unafflicted controls. The receiver operator curve (ROC) and area under the curve (AUC) were conducted to evaluate the clinical value of AFP and PIVKA-II for diagnosing HCC and early HCC. Results In the whole HCC cohort, the diagnostic values of PIVKA-II were better than that of AFP. The AUC of PIVKA-II and AFP was 0.90 (95% CI 0.87-0.94) and 0.79 (95% CI 0.74-0.84), respectively. “AFP + PIVKA-II” yielded a high sensitivity of 95.1% and a specificity of 83.3%, with the AUC 0.89 (95% CI 0.85-0.93). In the early stage HCC group, the diagnostic accuracy of PIVKA-II was also better than that of AFP. The AUC of PIVKA-II and AFP was 0.83 (95% CI 0.77-0.89) and 0.75 (95% CI 0.68-0.81), respectively. “AFP + PIVKA-II” achieved the sensitivity of 83.3% and specificity of 89.1%, with an AUC of 0.86 (95% CI 0.81-0.91). Moreover, for AFP-negative HCC patients, serum PIVKA-II showed good diagnostic performance, with an AUC of 0.804 (95% CI 0.720-0.887). Besides, elevated PIVKA-II level was a strong independent risk factor for HCC patients with portal vein tumor thrombus (PVTT) (OR = 4.890, P = 0.020). Conclusion PIVKA-II is superior to AFP in HCC screening, and AFP in combination with PIVKA-II significantly improves the diagnostic value for Chinese HCC patients. PIVKA-II could effectively indicate HCC accompanied by PVTT and help to optimize the therapeutic strategy.
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Hepigenetics: A Review of Epigenetic Modulators and Potential Therapies in Hepatocellular Carcinoma. BIOMED RESEARCH INTERNATIONAL 2020; 2020:9593254. [PMID: 33299889 PMCID: PMC7707949 DOI: 10.1155/2020/9593254] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/13/2020] [Accepted: 11/05/2020] [Indexed: 12/13/2022]
Abstract
Hepatocellular carcinoma is the fifth most common cancer worldwide and the second most lethal, following lung cancer. Currently applied therapeutic practices rely on surgical resection, chemotherapy and radiotherapy, or a combination thereof. These treatment options are associated with extreme adversities, and risk/benefit ratios do not always work in patients' favor. Anomalies of the epigenome lie at the epicenter of aberrant molecular mechanisms by which the disease develops and progresses. Modulation of these anomalous events poses a promising prospect for alternative treatment options, with an abundance of felicitous results reported in recent years. Herein, the most recent epigenetic modulators in hepatocellular carcinoma are recapitulated on.
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