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2021 ◽  
Author(s):  
wenbo qi ◽  
Yuping Bai ◽  
Le Liu ◽  
Hao Chen

Abstract Background: Accurate assessment of the tumour immune microenvironment helps develop individualised immunotherapy regimens and screen dominant populations suitable for immunotherapy. Therefore, potential molecular markers were investigated to make an overall assessment of the immune microenvironment status of liver hepatocellular carcinoma (LIHC). Methods: Differentially expressed genes (DEGs) in LIHC were extracted from the International Cancer Genome Consortium and The Cancer Genome Atlas databases. Gene set enrichment analysis was employed to assess the function of DEGs. Hub genes were identified using the STRING tool. The prognostic value of the hub genes was evaluated through Kaplan–Meier analysis and Cox regression. The correlation between genes and immunity was analysed using the TIMER tool. Further, tissue samples from 42 LIHC patients were collected for immunohistochemistry. HuH7 and SKP1 cells were analysed via western blotting, Cell Counting kit-8 assay, and Transwell assay. Results: A total of 121 DEGs were identified, and DEGs were enriched in the epithelial-mesenchymal transition, hypoxia, myogenesis, and p53 pathways. A total of 20 hub genes were selected and a strong correlation was identified between these hub genes and prognosis. The expression of budding uninhibited by benzimidazoles 1 (BUB1), which is known to play a role in cancer progression, was found to be upregulated in LIHC (compared to normal tissues). Furthermore, BUB1 expression was strongly related to immune cells and immune checkpoint molecule expression. Immunohistochemistry indicated that BUB1 expression was higher in LIHC tissues than in normal liver tissues. Western blotting showed that BUB1 expression was the highest in HuH7 and SKP1 cells. BUB1 knockdown resulted in reduced proliferation and vertical migration ability of LIHC cells, and reduced the expression of phospho-SMAD family member 2 and phospho-SMAD family member 3 proteins. Immunohistochemistry showed that BUB1 expression was accompanied by immune cell infiltration into LIHC tissues.Conclusions: These results suggest that BUB1 may serve as a potential prognostic biomarker for LIHC and as an indicator of its immune status.


2021 ◽  
Author(s):  
Jinbo Wu ◽  
Taobo Hu ◽  
Shu Wang

Abstract Background: Breast cancer has remained the most common malignancy in women over the past two decades. As lifestyle and living environments have changed, alterations to the disease spectrum have inevitably occurred in this time. As molecular profiling has become a routine diagnostic and objective indicator of breast cancer etiology, we analyzed changes in gene expression in breast cancer populations over two decades using The Cancer Genome Atlas (TCGA). Methods: We performed Heatmap and Venn diagram analyses to identify constantly up- and down-regulated genes in this cohort. We used Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses to visualize associated functional pathways. Results: We determined that three oncogenes, PD-L2, ETV5, and MTOR and 113 long intergenic non-coding RNAs (lincRNAs) were constantly up-regulated, whereas two oncogenes, BCR and GTF2I, one tumor suppression gene (TSG) MEN1, and 30 lincRNAs were constantly down-regulated. Up-regulated genes were enriched in “focal adhesion” and “PI3K-Akt signaling” pathways, et al, and down-regulated genes were significantly enriched in “metabolic pathways” and “viral myocarditis”. Eight up-regulated genes exhibited doubled or higher expression, and the expression of three down-regulated genes was halved or lowered and correlated with long-term survival. Conclusions: In this study, we determined that genes and molecular pathways are constantly changing, importantly, some altered genes were associated with prognostics and are potential therapeutic targets, suggesting molecular typing technologies must keep pace with this dynamic situation.


Author(s):  
Fei Wang ◽  
Ran Liu ◽  
Jie Yang ◽  
Baoan Chen

2021 ◽  
Vol 2021 ◽  
pp. 1-9
Author(s):  
Hao Zhang ◽  
Renzheng Liu ◽  
Lin Sun ◽  
Xiao Hu

Hepatocellular carcinoma (HCC) is the most common primary liver malignancy and is a leading cause of cancer-related death worldwide. This study aimed to establish a reliable prognostic model for HCC using histological grades and the expression levels of related genes. The histological grade of a tumor provides prognostic information. The expression data of HCC samples were downloaded from The Cancer Genome Atlas (TCGA) database. We employed the univariate and multivariate Cox regression analyses, as well as the least absolute shrinkage and selection operator (LASSO) regression to establish the prognostic model. After verification of the proposed model using data downloaded from the International Cancer Genome Consortium (ICGC) database, we found that the model was highly reliable, and it was revealed that the prognosis in the high-risk group was significantly worse than that in the low-risk group. Next, we explored the correlation of RiskScore with patients’ clinicopathological characteristics, and we found that the RiskScore could be used as an independent prognostic factor, which further confirmed the reliability of our model. In summary, the proposed model could accurately predict the prognosis of HCC patients, assisting clinicians to study the roles of different histological grades of HCC.


Author(s):  
Ze-Bing Song ◽  
Yang Yu ◽  
Guo-Pei Zhang ◽  
Shao-Qiang Li

Hepatocellular carcinoma (HCC) is one of the major cancer-related deaths worldwide. Genomic instability is correlated with the prognosis of cancers. A biomarker associated with genomic instability might be effective to predict the prognosis of HCC. In the present study, data of HCC patients from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) databases were used. A total of 370 HCC patients from the TCGA database were randomly classified into a training set and a test set. A prognostic signature of the training set based on nine overall survival (OS)–related genomic instability–derived genes (SLCO2A1, RPS6KA2, EPHB6, SLC2A5, PDZD4, CST2, MARVELD1, MAGEA6, and SEMA6A) was constructed, which was validated in the test and TCGA and ICGC sets. This prognostic signature showed more accurate prediction for prognosis of HCC compared with tumor grade, pathological stage, and four published signatures. Cox multivariate analysis revealed that the risk score could be an independent prognostic factor of HCC. A nomogram that combines pathological stage and risk score performed well compared with an ideal model. Ultimately, paired differential expression profiles of genes in the prognostic signature were validated at mRNA and protein level using HCC and paratumor tissues obtained from our institute. Taken together, we constructed and validated a genomic instability–derived gene prognostic signature, which can help to predict the OS of HCC and help us to explore the potential therapeutic targets of HCC.


Author(s):  
Jiahao Yu ◽  
Shuoyi Ma ◽  
Siyuan Tian ◽  
Miao Zhang ◽  
Xiaopeng Ding ◽  
...  

Hepatocellular carcinoma (HCC), a highly aggressive tumor, has high incidence and mortality rates. Recently, immunotherapies have been shown to be a promising treatment in HCC. The results of either the CheckMate-040 or IMbrave 150 trials demonstrate the importance of immunotherapy in the systemic treatment of liver cancer. Thus, in this study, we tried to establish a reliable prognostic model for liver cancer based on immune-related genes (IRGs) and to provide a new insight for immunotherapy of HCC. In this study, we used four datasets that incorporated 851 HCC samples, including 340 samples with complete clinical information from the cancer genome atlas (TCGA) database, to establish an effective model for predicting the prognosis of HCC patients based on the differential expression of IRGs and validated the prognostic model using the data from International Cancer Genome Consortium (ICGC). The top 6 characteristic IRGs identified by protein-protein interaction (PPI) network analysis, MMP9, FOS, CAT, ESR1, ANGPTL3, and KLKB1, were selected for further study. In addition, we assessed the correlations of the six characteristic IRGs with the tumor immune microenvironment, clinical stage, and sensitivity to anti-cancer drugs. We also explored whether the differential expression of the characteristic IRGs was specific to HCC or present in pan-cancer. The expression levels of the six characteristic IRGs were significantly different between most tumor tissues and adjacent normal tissues. In addition, these characteristic IRGs showed a strong association with immune cell infiltration in HCC patients. We found that MMP9 and ESR1 were independent prognostic factors for HCC, while CAT, ESR1, and KLKB1 were associated with the clinical stage. We collected HCC paraffin sections from 24 patients from Xijing hospital to identify the differential expression of the five genes (MMP9, ESR1, CAT, FOS, and KLKB1). Finally, the results of decision curve analysis (DCA) and nomogram revealed that our models provided a prognostic benefit for most HCC patients and the predicted overall survival (OS) was consistent with the actual OS. In conclusion, we systemically constructed a novel prognostic model that provides new insights into HCC.


2021 ◽  
Vol 12 ◽  
Author(s):  
Linfeng Xu ◽  
Xingxing Jian ◽  
Zhenhao Liu ◽  
Jingjing Zhao ◽  
Siwen Zhang ◽  
...  

Background: Hepatocellular carcinoma (HCC) is the most common primary liver malignancy with high morbidity and mortality worldwide. Tumor immune microenvironment (TIME) plays a pivotal role in the outcome and treatment of HCC. However, the effect of immune cell signatures (ICSs) representing the characteristics of TIME on the prognosis and therapeutic benefit of HCC patients remains to be further studied.Materials and methods: In total, the gene expression profiles of 1,447 HCC patients from several databases, i.e., The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium, and Gene Expression Omnibus, were obtained and applied. Based on a comprehensive collection of marker genes, 182 ICSs were evaluated by single sample gene set enrichment analysis. Then, by performing univariate and multivariate Cox analysis and random forest modeling, four significant signatures were selected to fit an immune cell signature score (ICSscore).Results: In this study, an ICSscore-based prognostic model was constructed to stratify HCC patients into high-risk and low-risk groups in the TCGA-LIHC cohort, which was successfully validated in two independent cohorts. Moreover, the ICSscore values were found to positively correlate with the current American Joint Committee on Cancer staging system, indicating that ICSscore could act as a comparable biomarker for HCC risk stratification. In addition, when setting the four ICSs and ICSscores as features, the classifiers can significantly distinguish treatment-responding and non-responding samples in HCC. Also, in melanoma and breast cancer, the unified ICSscore could verify samples with therapeutic benefits.Conclusion: Overall, we simplified the tedious ICS to develop the ICSscore, which can be applied successfully for prognostic stratification and therapeutic evaluation in HCC. This study provides an insight into the therapeutic predictive efficacy of prognostic ICS, and a novel ICSscore was constructed to allow future expanded application.


2021 ◽  
Author(s):  
Yuanmei Chen ◽  
Xinyi Huang ◽  
Haiyan Peng ◽  
Guibin Weng ◽  
Zhengrong Huang ◽  
...  

Abstract Background. Esophageal cancer (EC) is the 7th most common neoplasm and the 6th most common cause of cancer-related death worldwide. Immunotherapy is an effective treatment for EC patients. However, there are no dependable markers for predicting prognosis and immunotherapy responses in EC. Our study aims to explore prognostic models and markers in EC as well as predictors for immunotherapy. Methods. The expression profiles of EC were obtained from The Cancer Genome Atlas (TCGA), the Gene Expression Omnibus (GEO), and International Cancer Genome Consortium (ICGC) databases. Cox regression analysis was performed to construct a prognostic model. Overall survival and receiver operating characteristic curve analyses were applied to verify the accuracy of the model. The CIBERSORT algorithm was conducted to quantify the infiltration of different immune cells, and EC was grouped into three immune cell infiltration (ICI) clusters. PD-1 and PD-L1 expressions were compared between the ICI clusters. Overall survival analysis between ICI score and tumor mutation burden was conducted. The immunotherapy response of patients in different ICI score clusters was also compared. The copy number variations, somatic mutations, and single nucleotide polymorphisms were analyzed. Enrichment analyses were also performed. Results. A prognostic model was successfully constructed. Three ICI clusters were identified, and the clusters with high immune and stromal scores tended to have more immune-activated phenotypes and higher expressions of PD-1 and PDL1. The ICI score may be used as a predictor independent of tumor mutation burden. Patients with higher ICI score tended to have better immunotherapeutic responses than those with lower scores. Enrichment analyses showed that the differentially expressed genes were mostly enriched in microvillus and the KRAS and IL6/JAK/STAT3 pathways. The top eight genes with the highest mutation frequencies in EC were identified and all related to the prognosis of EC patients. Conclusions. Our study established an effective prognostic model and identified markers for predicting the prognosis and immunotherapy response of EC patients.


2021 ◽  
Vol 12 ◽  
Author(s):  
Tingping Huang ◽  
Tao Yan ◽  
Gonghai Chen ◽  
Chunqing Zhang

Background: Genomic alteration is the basis of occurrence and development of carcinoma. Specific gene mutation may be associated with the prognosis of hepatocellular carcinoma (HCC) patients without distant or lymphatic metastases. Hence, we developed a nomogram based on prognostic gene mutations that could predict the overall survival of HCC patients at early stage and provide reference for immunotherapy.Methods: HCC cohorts were obtained from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) databases. The total patient was randomly assigned to training and validation sets. Univariate and multivariate cox analysis were used to select significant variables for construction of nomogram. The support vector machine (SVM) and principal component analysis (PCA) were used to assess the distinguished effect of significant genes. Besides, the nomogram model was evaluated by concordance index, time-dependent receiver operating characteristics (ROC) curve, calibration curve and decision curve analysis (DCA). Gene Set Enrichment Analysis (GSEA), CIBERSORT, Tumor Immune Dysfunction and Exclusion (TIDE) and Immunophenoscore (IPS) were utilized to explore the potential mechanism of immune-related process and immunotherapy.Results: A total of 695 HCC patients were selected in the process including 495 training patients and 200 validation patients. Nomogram was constructed based on T stage, age, country, mutation status of DOCK2, EYS, MACF1 and TP53. The assessment showed the nomogram has good discrimination and high consistence between predicted and actual data. Furthermore, we found T cell exclusion was the potential mechanism of malignant progression in high-risk group. Meanwhile, low-risk group might be sensitive to immunotherapy and benefit from CTLA-4 blocker treatment.Conclusion: Our research established a nomogram based on mutant genes and clinical parameters, and revealed the underlying association between these risk factors and immune-related process.


2021 ◽  
Vol 15 (5) ◽  
Author(s):  
Ryota Kondou ◽  
Yasuto Akiyama ◽  
Akira Iizuka ◽  
Haruo Miyata ◽  
Chie Maeda ◽  
...  

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