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Yu Y, Lou Y, Zhu J, Wang X. Comprehensive analysis of diverse programmed cell death patterns in the prognosis, tumor microenvironment and drug sensitivity in hepatocellular carcinoma. Medicine (Baltimore) 2023; 102:e36239. [PMID: 38050240 PMCID: PMC10695610 DOI: 10.1097/md.0000000000036239] [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: 09/26/2023] [Accepted: 10/31/2023] [Indexed: 12/06/2023] Open
Abstract
Treatment failure in patients with liver hepatocellular carcinoma (LIHC) is primarily caused by tumor progression and therapy resistance. Tumor immunity plays a crucial role in regulating the homeostasis of cells through the process of programmed cell death (PCD). However, the expression profile and clinical significance of PCD-related genes in LIHC require further investigation. In this study, we analyzed twelve commonly observed PCD patterns to construct a prognostic model. We collected RNA-seq data, genomics, and clinical information from TCGA-LIHC and GSE14520 cohorts to validate the prognostic gene signature. We discovered 75 PCD-related differentially expressed genes (DEGs) with prognostic significance in LIHC. Using these genes, we constructed a PCD-related score (PCDscore) with an 11-gene signature through LASSO COX regression analysis. Validation in the GSE14520 cohort demonstrated that LIHC patients with high PCDscore had poorer prognoses. Unsupervised clustering based on the 11 model genes revealed 3 molecular subtypes of LIHC with distinct prognoses. By incorporating PCDscore with clinical features, we constructed a highly predictive nomogram. Additionally, PCDscore was correlated with immune checkpoint genes and immune cell infiltration. LIHC patients with high PCDscore exhibited sensitivity to common chemotherapy drugs (such as cisplatin and docetaxel). To summarize, our study developed a novel PCDscore model that comprehensively analyzed different cell death modes, providing an accurate prediction of clinical prognosis and drug sensitivity for LIHC patients.
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Affiliation(s)
- Youlin Yu
- Department of Hepatobiliary Surgery, Affiliated Hospital of Shaoxing University, Shaoxing, Zhejiang, China
| | - Yanglieguang Lou
- Department of Hepatobiliary Surgery, Affiliated Hospital of Shaoxing University, Shaoxing, Zhejiang, China
| | - Jinlong Zhu
- Department of Hepatobiliary Surgery, Affiliated Hospital of Shaoxing University, Shaoxing, Zhejiang, China
| | - Xiaobo Wang
- Department of Hepatobiliary Surgery, Affiliated Hospital of Shaoxing University, Shaoxing, Zhejiang, China
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Liao J, Wang J, Xu Y, Wu Y, Wang M, Zhao Q, Tan X, Meng Y, Wei L, Huang A. LAPTM4B-YAP loop feedback amplification enhances the stemness of hepatocellular carcinoma. iScience 2023; 26:106754. [PMID: 37213231 PMCID: PMC10197148 DOI: 10.1016/j.isci.2023.106754] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 02/10/2023] [Accepted: 04/23/2023] [Indexed: 05/23/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is highly heterogeneous, and stemness signatures are frequently elevated in HCC tumor cells to generate heterogeneous subtypes via multidirectional differentiation. However, the mechanisms affecting the regulation of stemness in HCC remain unclear. In this study, we identified that lysosome-associated protein transmembrane-4β (LAPTM4B) was significantly overexpressed in stem-like tumor cell populations with multidirectional differentiation potential at the single cell level, and verified that LAPTM4B was closely related to stemness of HCC using in vitro and in vivo experiments. Mechanistically, elevated LAPTM4B suppresses Yes-associated protein (YAP) phosphorylation and ubiquitination degradation. In turn, stabilized YAP localizes to the nucleus and binds to cAMP responsive element binding protein-1 (CREB1), which promotes transcription of LAPTM4B. Overall, our findings suggest that LAPTM4B forms a positive feedback loop with YAP, which maintains the stemness of HCC tumor cells and leads to an unfavorable prognosis for HCC patients.
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Affiliation(s)
- Jianping Liao
- Department of Pathology, School of Basic Medical Sciences, Fujian Medical University, 88 Jiaotong Road, Fuzhou, Fujian 350004, China
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou 510060, China
| | - Jiahong Wang
- Department of Pathology, School of Basic Medical Sciences, Fujian Medical University, 88 Jiaotong Road, Fuzhou, Fujian 350004, China
| | - Yu Xu
- Department of Pathology, School of Basic Medical Sciences, Fujian Medical University, 88 Jiaotong Road, Fuzhou, Fujian 350004, China
| | - Yong Wu
- Department of Pathology, School of Basic Medical Sciences, Fujian Medical University, 88 Jiaotong Road, Fuzhou, Fujian 350004, China
| | - Meifeng Wang
- Department of Pathology, School of Basic Medical Sciences, Fujian Medical University, 88 Jiaotong Road, Fuzhou, Fujian 350004, China
| | - Qiudong Zhao
- Tumor Immunology and Gene Therapy Center, Third Affiliated Hospital of Second Military Medical University, 225 Changhai Road, Shanghai 200438, China
| | - Xiaodan Tan
- Department of Pathology, School of Basic Medical Sciences, Fujian Medical University, 88 Jiaotong Road, Fuzhou, Fujian 350004, China
| | - Yan Meng
- Tumor Immunology and Gene Therapy Center, Third Affiliated Hospital of Second Military Medical University, 225 Changhai Road, Shanghai 200438, China
- Department of Medical Ultrasound, Shanghai Tenth People’s Hospital, Tongji University Cancer Center, Tongji University School of Medicine, Shanghai 200072, China
- Corresponding author
| | - Lixin Wei
- Tumor Immunology and Gene Therapy Center, Third Affiliated Hospital of Second Military Medical University, 225 Changhai Road, Shanghai 200438, China
- Corresponding author
| | - Aimin Huang
- Department of Pathology, School of Basic Medical Sciences, Fujian Medical University, 88 Jiaotong Road, Fuzhou, Fujian 350004, China
- Corresponding author
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Liu YX, Li QZ, Cao YN. The effect of key DNA methylation in different regions on gene expression in hepatocellular carcinoma. Mol Omics 2021; 18:57-70. [PMID: 34782907 DOI: 10.1039/d1mo00282a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Hepatocellular carcinoma (HCC) is a common cancer with high morbidity and mortality. As we all know, the alteration of DNA methylation has a crucial impact on the occurrence of HCC. However, the mechanism of the effect of DNA methylation in different regions on gene expression is still unclear. Here, by computing and analyzing the distribution of differential methylation in 12 different regions in HCC tissues and adjacent normal tissues, not only the hypermethylation of CpG islands and global hypomethylation were found, but also a stable distribution pattern of differential methylation in HCC was found. Then the correlations between DNA methylations in different regions and gene expressions were calculated, and the diversity of correlations in different regions was determined. The key genes of differential methylation and differential expression related to the survival of HCC patients were obtained by using Cox regression analysis, a four-gene prognostic risk scoring model was constructed, and the prognostic performance was well verified. The regions of the differentially methylated CpG sites corresponding to the four key genes were located and their influences on the expression were analyzed. The results indicate that the promoter, first exon, 5'UTR, sixth exon, N_Shore, and S_Shore hypomethylation promotes the expression of key oncogenes, which together lead to the occurrence of HCC. These results might help to study the role of DNA methylation in HCC and provide potential biomarkers for the diagnosis of HCC.
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Affiliation(s)
- Yu-Xian Liu
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China.
| | - Qian-Zhong Li
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China. .,The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010070, China
| | - Yan-Ni Cao
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China.
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Roy G, Roy P, Bhattacharjee A, Shahid M, Misbah M, Gupta S, Husain M. Expression signature of lysosomal-associated transmembrane protein 4B in hepatitis C virus-induced hepatocellular carcinoma. Int J Biol Markers 2018; 33:283-292. [PMID: 29882487 DOI: 10.1177/1724600818773631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
INTRODUCTION Hepatocellular carcinoma is a lethal disease worldwide and therefore the establishment of novel diagnostic biomarkers is imperative. In this study, it was hypothesized that an abnormal expression of the lysosomal-associated protein transmembrane 4 beta ( LAPTM4B) gene is crucial in the pathogenesis of hepatitis C virus-mediated hepatocellular carcinoma; hence we investigated the expression profile of LAPTM4B in hepatitis C virus-induced hepatocellular carcinoma. METHODS A group of 189 consecutive patients (hepatitis C virus-related hepatocellular carcinoma as tumor cases; n=93, hepatitis C virus-related cirrhotics as disease controls; n=96) opting for living donor liver transplantation as a therapeutic surgical regimen were recruited with informed consent. Additionally, paired adjacent non-tumorous tissues (n=93) obtained from cases were also included. Serum LAPTM4B protein concentrations were assessed by third-generation enzyme-linked immunosorbent assay and LAPTM4B mRNA, and protein expressions at tissue level were determined by quantitative real time reverse transcription-polymerase chain reaction (qRT-PCR) and immunohistochemistry techniques, respectively. RESULTS LAPTM4B protein concentrations in sera of patients were higher ( p<0.001) in tumor cases (1.25±0.25 ng/ml) compared to disease controls (0.53±0.28 ng/ml). Our study also depicts positive clinicopathological correlations between alpha-fetoprotein titers (b=0.65; p<0.001), quantitative hepatitis C virus RNA copies (b=0.33; p<0.001), and LAPTM4B protein concentrations, all in sera of patients. In addition, qRT-PCR and immunohistochemistry analyses revealed a significantly higher ( p<0.05) tissue LAPTM4B mRNA and protein expression, respectively, in tumor cases rather than in non-tumorous tissues and disease controls. CONCLUSIONS Together, our results illustrate the LAPTM4B gene as a diagnostic biomarker in patients with hepatocellular carcinoma having documented evidence of chronic hepatitis C virus infection.
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Affiliation(s)
- Gaurav Roy
- 1 Department of Biotechnology, Molecular Virology Laboratory, Jamia Millia Islamia, New Delhi, India
| | - Papai Roy
- 2 Molecular Genetics and Development, Institut de Recherches Cliniques de Montreal, Montreal, Canada
| | - Atanu Bhattacharjee
- 3 Centre for Cancer Epidemiology, The Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, India
| | - Mudassar Shahid
- 1 Department of Biotechnology, Molecular Virology Laboratory, Jamia Millia Islamia, New Delhi, India
| | - Mohammad Misbah
- 1 Department of Biotechnology, Molecular Virology Laboratory, Jamia Millia Islamia, New Delhi, India
| | - Subash Gupta
- 4 Max Centre for Liver and Biliary Sciences, Max Super Speciality Hospital, New Delhi, India
| | - Mohammad Husain
- 1 Department of Biotechnology, Molecular Virology Laboratory, Jamia Millia Islamia, New Delhi, India
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