1
|
Goncharova IA, Zarubin AA, Babushkina NP, Koroleva IA, Nazarenko MS. Changes in DNA methylation profile in liver tissue during progression of HCV-induced fibrosis to hepatocellular carcinoma. Vavilovskii Zhurnal Genet Selektsii 2023; 27:72-82. [PMID: 36923478 PMCID: PMC10009477 DOI: 10.18699/vjgb-23-10] [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: 10/18/2022] [Revised: 12/08/2022] [Accepted: 12/15/2022] [Indexed: 03/11/2023] Open
Abstract
In this study we compared methylation levels of 27,578 CpG sites between paired samples of the tumor and surrounding liver tissues with various degrees of damage (fibrosis, cirrhosis) in HCV-induced hepatocellular carcinoma (HCC) patients, as well as between tumor and normal tissue in non-viral HCC patients, using GSE73003 and GSE37988 data from GEODataSets (https://www.ncbi.nlm.nih.gov/). A significantly lower number of differentially methylated sites (DMS) were found between HCC of non-viral etiology and normal liver tissue, as well as between HCC and fibrosis (32 and 40), than between HCC and cirrhosis (2450 and 2304, respectively, according to GSE73003 and GSE37988 datasets). As the pathological changes in the tissue surrounding the tumor progress, the ratio of hyper-/hypomethylated DMSs in the tumor decreases. Thus, in tumor tissues compared with normal/fibrosis/cirrhosis of the liver, 75/62.5/47.7 % (GSE73003) and 16 % (GSE37988) of CpG sites are hypermethylated, respectively. Persistent hypermethylation of the ZNF154 and ZNF540 genes, as well as CCL20 hypomethylation, were registered in tumor tissue in relation to both liver fibrosis and liver cirrhosis. Protein products of the EDG4, CCL20, GPR109A, and GRM8 genes, whose CpG sites are characterized by changes in DNA methylation level in tumor tissue in the setting of cirrhosis and fibrosis, belong to "Signaling by G-protein-coupled receptors (GPCRs)" category. However, changes in the methylation level of the "driver" genes for oncopathology (АРС, CDKN2B, GSTP1, ELF4, TERT, WT1) are registered in tumor tissue in the setting of liver cirrhosis but not fibrosis. Among the genes hypermethylated in tumor tissue in the setting of liver cirrhosis, the most represented biological pathways are developmental processes, cell-cell signaling, transcription regulation, Wnt-protein binding. Genes hypomethylated in liver tumor tissue in the setting of liver cirrhosis are related to olfactory signal transduction, neuroactive ligand-receptor interaction, keratinization, immune response, inhibition of serine proteases, and zinc metabolism. The genes hypermethylated in the tumor are located at the 7p15.2 locus in the HOXA cluster region, and the hypomethylated CpG sites occupy extended regions of the genome in the gene clusters of olfactory receptors (11p15.4), keratin and keratin-associated proteins (12q13.13, 17q21.2, and 21q22.11), epidermal differentiation complex (1q21.3), and immune system function loci 9p21.3 (IFNA, IFNB1, IFNW1 cluster) and 19q13.41-19q13.42 (KLK, SIGLEC, LILR, KIR clusters). Among the genes of fibrogenesis or DNA repair, cg14143055 (ADAMDEC1) is located in the binding region of the HOX gene family transcription factors (TFs), while cg05921699 (CD79A), cg06196379 (TREM1) and cg10990993 (MLH1) are located in the binding region of the ZNF protein family transcription factor (TF). Thus, the DNA methylation profile in the liver in HCV-induced HCC is unique and differs depending on the degree of surrounding tissue lesion - liver fibrosis or liver cirrhosis.
Collapse
Affiliation(s)
- I A Goncharova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - A A Zarubin
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - N P Babushkina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - I A Koroleva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - M S Nazarenko
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| |
Collapse
|
2
|
Li SR, Man QW, Liu B. Development and validation of a novel hypoxia-related signature for prognostic and immunogenic evaluation in head and neck squamous cell carcinoma. Front Oncol 2022; 12:943945. [PMID: 36452497 PMCID: PMC9702068 DOI: 10.3389/fonc.2022.943945] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 10/26/2022] [Indexed: 10/15/2023] Open
Abstract
Hypoxia plays a critical role in head and neck squamous cell carcinoma (HNSCC) prognosis. However, till now, robust and reliable hypoxia-related prognostic signatures have not been established for an accurate prognostic evaluation in HNSCC patients. This article focused on establishing a risk score model to evaluate the prognosis and guide treatment for HNSCC patients. RNA-seq data and clinical information of 502 HNSCC patients and 44 normal samples were downloaded from The Cancer Genome Atlas (TCGA) database. 433 samples from three Gene Expression Omnibus (GEO) datasets were incorporated as an external validation cohort. In the training cohort, prognostic-related genes were screened and LASSO regression analyses were performed for signature establishment. A scoring system based on SRPX, PGK1, STG1, HS3ST1, CDKN1B, and HK1 showed an excellent prediction capacity for an overall prognosis for HNSCC patients. Patients were divided into high- and low-risk groups, and the survival status of the two groups exhibited a statistically significant difference. Subsequently, gene set enrichment analysis (GSEA) was carried out to explore the underlying mechanisms for the prognosis differences between the high- and low-risk groups. The tumor immune microenvironment was evaluated by CIBERSORT, ESTIMATE, TIDE, and xCell algorithm, etc. Then, we explored the relationships between this prognostic model and the levels of immune checkpoint-related genes. Cox regression analysis and nomogram plot indicated the scoring system was an independent predictor for HNSCC. Moreover, a comparison of predictive capability has been made between the present signature and existing prognostic signatures for HNSCC patients. Finally, we detected the expression levels of proteins encoded by six-HRGs via immunohistochemical analysis in tissue microarray. Collectively, a novel integrated signature considering both HRGs and clinicopathological parameters will serve as a prospective candidate for the prognostic evaluation of HNSCC patients.
Collapse
Affiliation(s)
- Su-Ran Li
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Qi-Wen Man
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China
- Department of Oral Maxillofacial Head Neck Oncology, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei, China
| | - Bing Liu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China
- Department of Oral Maxillofacial Head Neck Oncology, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei, China
| |
Collapse
|
3
|
Huang S, Li D, Zhuang L, Zhang J, Wu J. Identification of an Epithelial-Mesenchymal Transition-Related Long Non-coding RNA Prognostic Signature to Determine the Prognosis and Drug Treatment of Hepatocellular Carcinoma Patients. Front Med (Lausanne) 2022; 9:850343. [PMID: 35685422 PMCID: PMC9170944 DOI: 10.3389/fmed.2022.850343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 05/02/2022] [Indexed: 12/11/2022] Open
Abstract
Introduction Hepatocellular carcinoma (HCC) is one of the most common malignant tumors with poor prognosis. Epithelial–mesenchymal transition (EMT) is crucial for cancer progression and metastasis. Thus, we aimed to construct an EMT-related lncRNA signature for predicting the prognosis of HCC patients. Methods Cox regression analysis and LASSO regression method were used to build an EMT-related lncRNAs risk signature based on TCGA database. Kaplan-Meier survival analysis was conducted to compare the overall survival (OS) in different risk groups. ROC curves and Cox proportional-hazards analysis were performed to evaluate the performance of the risk signature. RT-qPCR was conducted in HCC cell lines and tissue samples to detect the expression of some lncRNAs in this risk model. Furthermore, a nomogram involving the risk score and clinicopathological features was built and validated with calibration curves and ROC curves. In addition, we explored the association between risk signature and tumor immunity, somatic mutations status, and drugs sensitivity. Results Twelve EMT-related lncRNAs were obtained to construct the prognostic risk signature for patients with HCC. The Kaplan-Meier curve analysis revealed that patients in the high-risk group had worse overall survival (OS) than those in low-risk group. ROC curves and Cox regression analysis suggested the risk signature could predict HCC survival exactly and independently. The prognostic value of the risk model was confirmed in the testing and entire groups. We also found AC099850.3 and AC092171.2 were highly expressed in HCC cells and HCC tissues. The nomogram could accurately predict survival probability of HCC patients. Gene set enrichment analysis (GSEA) and gene ontology (GO) analysis showed that cancer-related pathways and cell division activity were enriched in high-risk group. The SNPs showed that the prevalence of TP53 mutations was significantly different between high- and low-risk groups; the TP53 mutations and the high TMB were both associated with a worse prognosis in patients with HCC. We also observed widely associations between risk signature and drugs sensitivity in HCC. Conclusion A novel EMT-related lncRNAs risk signature, including 12 lncRNAs, was established and identified in patients with HCC, which can accurately predict the prognosis of HCC patients and may be used to guide individualized treatment in the clinical practice.
Collapse
Affiliation(s)
- Shenglan Huang
- Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Key Laboratory of Clinical and Translational Cancer Research, Nanchang, China
| | - Dan Li
- Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Key Laboratory of Clinical and Translational Cancer Research, Nanchang, China
| | - Lingling Zhuang
- Jiangxi Key Laboratory of Clinical and Translational Cancer Research, Nanchang, China
- Department of Gynaecology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jian Zhang
- Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Key Laboratory of Clinical and Translational Cancer Research, Nanchang, China
| | - Jianbing Wu
- Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Key Laboratory of Clinical and Translational Cancer Research, Nanchang, China
- *Correspondence: Jianbing Wu,
| |
Collapse
|
4
|
Feng C, Liu S, Shang Z. Identification and Validation of an EMT-Related LncRNA Signature for HNSCC to Predict Survival and Immune Landscapes. Front Cell Dev Biol 2022; 9:798898. [PMID: 35273966 PMCID: PMC8902443 DOI: 10.3389/fcell.2021.798898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/30/2021] [Indexed: 12/24/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are increasingly recognized as decisive factors in the progression of head and neck squamous cell carcinoma (HNSCC), and they participate in the epithelial–mesenchymal transformation (EMT) of HNSCC. LncRNAs are closely related to the prognosis of patients with HNSCC; thus, it is essential to identify EMT-related lncRNAs with prognostic value for HNSCC. The coexpression network of EMT-related lncRNAs was constructed using The Cancer Genome Atlas (TCGA). An EMT-related eight-lncRNA-based prognostic signature was constructed using LASSO Cox regression and Cox proportional hazards analyses. Univariate and multivariate analyses and stratified prognosis confirmed that the prognostic signature was an independent predictive factor. Subsequently, we performed immune cell infiltration analysis, gene set enrichment analysis (GSEA), and single-sample GSEA (ssGSEA) pathway enrichment analysis to uncover the potential molecular mechanisms of prognostic differences in the high- and low-risk groups. Next, we discussed the relationship between the prognostic signature and immune checkpoint-related genes, their TIDE scores, and the sensitivity of common chemotherapeutics. Finally, we further verified the expression differences in lncRNAs that were included in our signature via RT–qPCR in eighteen paired tissues. In summary, this prognostic signature provides powerful prognostic biomarkers for HNSCC and could serve as a predictor for the sensitivity of common chemotherapeutics and immunotherapy responses as well as providing a reference for further personalized treatment.
Collapse
Affiliation(s)
- Chunyu Feng
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Shaopeng Liu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Zhengjun Shang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China
- Department of Oral and Maxillofacial Head and Neck Oncology, School and Hospital of Stomatology, Wuhan University, Wuhan, China
- *Correspondence: Zhengjun Shang,
| |
Collapse
|
5
|
Li K, Song Y, Qin L, Li A, Jiang S, Ren L, Zang C, Sun J, Zhao Y, Zhang Y. A CpG Methylation Signature as a Potential Marker for Early Diagnosis of Hepatocellular Carcinoma From HBV-Related Liver Disease Using Multiplex Bisulfite Sequencing. Front Oncol 2021; 11:756326. [PMID: 34745991 PMCID: PMC8564137 DOI: 10.3389/fonc.2021.756326] [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: 08/11/2021] [Accepted: 09/27/2021] [Indexed: 12/04/2022] Open
Abstract
Background Aberrant methylation of CpG sites served as an epigenetic marker for building diagnostic, prognostic, and recurrence models for hepatocellular carcinoma (HCC). Methods Using Illumina 450K and EPIC Beadchip, we identified 34 CpG sites in peripheral blood mononuclear cell (PBMC) DNA that were differentially methylated in early HCC versus HBV-related liver diseases (HBVLD). We employed multiplex bisulfite sequencing (MBS) based on next-generation sequencing (NGS) to measure methylation of 34 CpG sites in PBMC DNA from 654 patients that were divided into a training set (n = 442) and a test set (n = 212). Using the training set, we selected and built a six-CpG-scorer (namely, cg14171514, cg07721852, cg05166871, cg18087306, cg05213896, and cg18772205), applying least absolute shrinkage and selection operator (LASSO) regression. We performed multivariable analyses of four candidate risk predictors (namely, six-CpG-scorer, age, sex, and AFP level), using 20 times imputation of missing data, non-linearly transformed, and backwards feature selection with logistic regression. The final model’s regression coefficients were calculated according to “Rubin’s Rules”. The diagnostic accuracy of the model was internally validated with a 10,000 bootstrap validation dataset and then applied to the test set for validation. Results The area under the receiver operating characteristic curve (AUROC) of the model was 0.81 (95% CI, 0.77–0.85) and it showed good calibration and decision curve analysis. Using enhanced bootstrap validation, adjusted C-statistics and adjusted Brier score were 0.809 and 0.199, respectively. The model also showed an AUROC value of 0.84 (95% CI 0.79–0.88) of diagnosis for early HCC in the test set. Conclusions Our model based on the six-CpG-scorer was a reliable diagnosis tool for early HCC from HBVLD. The usage of the MBS method can realize large-scale detection of CpG sites in clinical diagnosis of early HCC and benefit the majority of patients.
Collapse
Affiliation(s)
- Kang Li
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| | - Yi Song
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Ling Qin
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| | - Ang Li
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| | | | - Lei Ren
- Pharmacology Department, Air Force Medical Center, People's Liberation Army of China (PLA), Beijing, China
| | - Chaoran Zang
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| | - Jianping Sun
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| | - Yan Zhao
- Clinical Laboratory Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| | - Yonghong Zhang
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| |
Collapse
|
6
|
Construction and Validation of a Prognostic Gene-Based Model for Overall Survival Prediction in Hepatocellular Carcinoma Using an Integrated Statistical and Bioinformatic Approach. Int J Mol Sci 2021; 22:ijms22041632. [PMID: 33562824 PMCID: PMC7915780 DOI: 10.3390/ijms22041632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common lethal cancers worldwide and is often related to late diagnosis and poor survival outcome. More evidence is demonstrating that gene-based prognostic models can be used to predict high-risk HCC patients. Therefore, our study aimed to construct a novel prognostic model for predicting the prognosis of HCC patients. We used multivariate Cox regression model with three hybrid penalties approach including least absolute shrinkage and selection operator (Lasso), adaptive lasso and elastic net algorithms for informative prognostic-related genes selection. Then, the best subset regression was used to identify the best prognostic gene signature. The prognostic gene-based risk score was constructed using the Cox coefficient of the prognostic gene signature. The model was evaluated by Kaplan-Meier (KM) and receiver operating characteristic curve (ROC) analyses. A novel four-gene signature associated with prognosis was identified and the risk score was constructed based on the four-gene signature. The risk score efficiently distinguished the patients into a high-risk group with poor prognosis. The time-dependent ROC analysis revealed that the risk model had a good performance with an area under the curve (AUC) of 0.780, 0.732, 0.733 in 1-, 2- and 3-year prognosis prediction in The Cancer Genome Atlas (TCGA) dataset. Moreover, the risk score revealed a high diagnostic performance to classify HCC from normal samples. The prognosis and diagnosis prediction performances of risk scores were verified in external validation datasets. Functional enrichment analysis of the four-gene signature and its co-expressed genes involved in the metabolic and cell cycle pathways was constructed. Overall, we developed a novel-gene-based prognostic model to predict high-risk HCC patients and we hope that our findings can provide promising insight to explore the role of the four-gene signature in HCC patients and aid risk classification.
Collapse
|
7
|
Guo Y, Yang PT, Wang ZW, Xu K, Kou WH, Luo H. Identification of Three Autophagy-Related Long Non-Coding RNAs as a Novel Head and Neck Squamous Cell Carcinoma Prognostic Signature. Front Oncol 2021; 10:603864. [PMID: 33575215 PMCID: PMC7871905 DOI: 10.3389/fonc.2020.603864] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 11/09/2020] [Indexed: 01/08/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) has a poor prognosis. Considerable evidence indicates that autophagy and non-coding RNA play essential roles in the biological processes involved in cancers, but associations between autophagy-related long non-coding RNAs (lncRNAs) and HNSCC remain unclear. In the present study, HNSCC RNA sequences and autophagy-related gene data were extracted from The Cancer Genome Atlas database and the Human Autophagy Database. A total of 1,153 autophagy-related lncRNAs were selected via calculating Pearson’s correlation coefficient. Three prognosis-related autophagy lncRNAs were identified via univariate Cox regression, least absolute shrinkage and selection operator analysis, and multivariate Cox regression analysis. We also constructed a prognostic model based on these autophagy-related lncRNAs and evaluated its ability to accurately and independently predict the prognosis of HNSCC patients. The area under the curve (AUC) was 0.864 (3-year) and 0.836 (5-year), and our model can independently predict the prognosis of HNSCC. The prognostic value of the three autophagy lncRNAs was confirmed via analysis of samples from five databases. To further identify the functions of the three lncRNAs, a co-expression network was constructed and pathway analysis was performed. In that analysis the lncRNAs were correlated with 189 related genes and 20 autophagy-related genes, and these lncRNAs mainly involved homologous recombination, the Fanconi anemia pathway, the autophagy-related pathway, and immune-related pathways. In addition, we validated the expression levels of three lncRNAs and autophagy markers (ATG12, BECN1, and MAP1LC3B) based on TIMER, Oncomine, and HPA database analysis. Our results indicated that TTTY15 was increased in HPV positive and HPV negative HNSCC patients, and three autophagy markers were up-regulated in all HNSCCC patients. Lastly, association between three lncRNAs and autophagy markers was performed, and our results showed that TTTY15 and MIF-AS1 were associated with autophagy markers. Collectively, these results suggested that three autophagy-related lncRNAs have prognostic value in HNSCC patients.
Collapse
Affiliation(s)
- Ya Guo
- Department of Radiation Oncology, Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Peng Tao Yang
- Department of Radiation Oncology, Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Zhong Wei Wang
- Department of Radiation Oncology, Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Kun Xu
- Department of Radiation Oncology, Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Wei Hua Kou
- Department of Radiation Oncology, Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Heng Luo
- Department of Radiation Oncology, Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| |
Collapse
|