TCGA database analysis of the tumor mutation burden and its clinical significance in colon cancer

BackgroundColon cancer is one of the most common malignant tumors, with high rates of incidence and death. The tumor mutational burden (TMB), which is characterized by microsatellite instability, has been becoming a powerful predictor which can show tumor behavior and response to immunotherapy.MethodsIn this study, we analyzed 437 mutation data of colon cancer samples obtained from The Cancer Genome Atlas (TCGA) and divided patients into low- and high-TMB groups according to the TMB value. Then we identified differentially-expressed genes (DEGs), conducted immune cell infiltration and survival analyses between groups.ResultsThe higher TMB of the patients with colon cancer predicts a poorer prognosis. Functional analysis was performed to assess the prognostic value of the top 30 core genes. The CIBER-SORT algorithm was used to investigate the correlation between the immune cells and TMB subtypes. An immune prognosis model was constructed to screen out immune genes related to prognosis, and the tumor immunity assessment resource (TIMER) was then used to determine the correlation between gene expression and the abundance of tumor-infiltrating immune cell subsets in colon cancer. We observed that APC, TP53, TTN, KRAS, MUC16, SYNE1, PIK3CA have higher somatic mutations. DEGs enrichment analysis showed that they are involved in the regulation of neuroactive ligand-receptor interaction, the Cyclic adenosine monophosphate (cAMP) signaling pathway, the calcium signaling pathway, and pantothenate and Coenzyme A (CoA) biosynthesis. The difference in the abundance of various white blood cell subtypes showed that Cluster of Differentiation 8 (CD8) T cells (P=0.008), activated CD4 memory T cells (P=0.019), M1 macrophages (P=0.002), follicular helper T cells (P=0.034), activated Natural killer (NK cell) cells (P=0.017) increased remarkably, while M0 macrophages significantly reduced (P=0.025). The two immune model genes showed that secretin (SCT) was negatively correlated with survival, while Guanylate cyclase activator 2A (GUCA2A) was positively correlated.ConclusionsThis study conducted a systematically comprehensive analysis of the prediction and clinical significance of TMB in colon cancer in identification, monitoring, and prognosis of colon cancer, and providing reference information for immunotherapy.     

The role of tumor-infiltrating B cells in the tumor microenvironment of hepatocellular carcinoma and its prognostic value: a bioinformatics analysis

BackgroundAccumulating evidence indicates that tumor heterogeneity is characterized by distinct immunosubtypes. However, prior studies have mainly focused on the functions of T cells. The role of tumor-infiltrating B cells in the microenvironment of hepatocellular carcinoma (HCC) requires further investigation.MethodsWe conducted an integrative analysis of single cell RNA sequencing (scRNA-seq) datasets in HCC tumor samples from Gene Expression Omnibus database. We analyzed the features of B cells in normal liver tissue and HCC. Additionally, we conducted a deconvolution analysis using the matrix of scRNA-seq datasets and the RNA-seq datasets in The Cancer Genome Atlas-Liver Hepatocellular Carcinoma (TCGA-LIHC) database. The survival analyses of the TCGA-LIHC cohort with different B cell infiltration rates and was further validated. Finally, we performed immunohistochemistry analysis of primary tumor tissue of HCC patients using antibodies against CD79A and validated the impact of tumor-infiltrating B cells in the prognosis of LIHC.ResultsWe identified several subtypes of B cells in the microenvironment of HCC, including the plasma cells and naïve B cells. The relative ratio of B cells, but not the plasma cells, was significantly decreased in HCC as compared to the normal liver tissue (P<0.05). In addition, genes related to antigen presentation and cell proliferation were decreased in tumor-infiltrating B cells (P<0.05). The observation of B cell infiltration was further validated with the TCGA-LIHC cohort. The overall survival and disease-free survival in HCC patients with higher B-cell infiltration rate were significantly longer than those in the lower infiltration group (P<0.05) in the TCGA-LIHC cohort. Moreover, we demonstrated higher infiltration rates of B cells were significantly associated with a better prognosis of HCC in our cohort.ConclusionsTumor-infiltrating B cells potentially exert a tumor-suppressive function in the microenvironment of HCC and the higher levels of B cell infiltration are associated with a favorable outcome of HCC. Targeted activation of B cells may improve the tumor immune-targeted therapy.     

Clinical significance and immunogenomic landscape analysis of glycolysis-associated prognostic model to guide clinical therapy in hepatocellular carcinoma

BackgroundHepatocellular carcinoma (HCC) is a common malignant tumor with a poor prognosis and high mortality rate worldwide. Glucose metabolism disorder is one of the most important characteristics of HCC. However, as the primary risk factors for the prognosis of HCC patients are unclear, the survival prognosis and therapy response of patients cannot be accurately predicted.MethodsFirst, gene sets of 29 cancer hallmarks were collected from public databases. The z-score of various cancer hallmarks were quantitively analyzed by a single-sample gene set enrichment analysis (ssGSEA) of HCC patients. Next, a glycolysis-related gene signature (GRS) was constructed using a series of bioinformatics methods, which were used to predict the survival prognosis of HCC patients and the immunotherapy benefits. The prediction accuracy of the GRS was validated in different HCC cohorts and clinical subgroups. Additionally, a decision tree and nomogram were also established based on the GRS and other clinical variables. Finally, the genomic alterations and tumor immune microenvironment of the HCC patients were examined.ResultsAmong the 29 cancer hallmarks, glycolysis was the most predominant risk factor for a poor prognosis in HCC. We subsequently constructed a novel GRS comprising 12 glycolysis-related genes. The high-GRS patients had a poorer survival prognosis than the low-GRS patients. The GRS exhibited a powerful ability to predict survival prognosis in different HCC cohorts and clinical feature subgroups. Additionally, the decision tree and nomogram aided in the risk stratification and prognosis evaluations of HCC patients. Further, we found that a high GRS was characterized by a severe tumor stage, pathological grade, and other clinical features. There were significant differences in the genomic alterations, immune cells, and immune checkpoints between the low- and high-GRS patients, especially in relation to the tumor protein p53 mutation and immunosuppressive cells. Notably, we also found that the GRS could be used to identify HCC patients who are more sensitive to chemotherapy and immunotherapy.ConclusionsIn summary, the GRS may be a useful tool for predicting the prognosis and guiding the clinical therapy of HCC patients.     

联合外周血循环肿瘤细胞评估索拉非尼治疗肝细胞癌疗效

目的 通过联合外周血循环肿瘤细胞（CTC）评估索拉非尼治疗肝细胞癌的疗效,提高对肝癌CTC临床应用的认识。方法 本科室基于BIOMARKERBOX平台,利用独特差减富集技术—肿瘤标示物免疫荧光染色—肿瘤细胞染色体荧光原位杂交整合技术平台（SET-iFISH）分离2例肝癌患者外周血,后将肿瘤标示物免疫荧光染色与染色体荧光原位杂交整合为同步进行的检测技术鉴别出CTC,并结合2例患者的临床表现及生存情况进行分析。结果 肝癌CTC经SET-iFISH标记为CK-/DAPI+/FISH（CEP8单体）+/CD45-。本科室采用连续3天分离患者外周血（7.5 ml）,病例1外周血中检测到CTC 2个,病例2外周血中未见CTC,病例2目前已无瘤生存13个月。结论 联合外周血CTC评估索拉非尼治疗肝细胞癌的疗效可能成为一种有效、无创的液体评估手段,为肝癌临床诊治提供新的思路。     

Bioinformatics analysis of immune infiltrates and tripartite motif (TRIM) family genes in hepatocellular carcinoma

BackgroundThe tripartite motif (TRIM) family are important members of the Gene-finger-containing E3 ubiquitin-conjugating enzyme and are involved in the progression of hepatocellular carcinoma (HCC). Previous studies have largely focused on gene expression and molecular pathways, while the underlying role of the TRIM family in the tumor immune microenvironment (TIME) remains poorly understood.MethodsWe systematically explored the correlations of prominent TRIM genes with immune checkpoints and immune infiltrates in 231 HCC samples [International Cancer Genome Consortium (ICGC) cohort (n=231); The Cancer Genome Atlas (TCGA) cohort (n=370)]. A prognostic risk model was constructed using the least absolute shrinkage and selection operator (LASSO) algorithm and multivariate Cox regression analysis in the ICGC cohort. Kaplan-Meier curves based on the overall survival (OS) were used to assess differences in survival between clusters. We utilized gene set variation analysis (GSVA) to characterize the differences in biological functions. Based on univariate and multivariate Cox progression analysis, we developed a risk score signature and verified its reliability and validity. The Tumor Immune Single-cell Hub (TISCH) single-cell database was employed to evaluate the correlation of TRIM genes with the tumor microenvironment.ResultsCluster 1 was preferentially associated with a favorable prognosis (P<0.001). The amino acid, fatty acid, and drug metabolism pathways were significantly enriched in cluster 2. A prognosis risk score project was established and evaluated based on the 9 independent prognostic genes (all P<0.05). The immune score and stromal scores of patients with low-risk scores were greater than those of patients with high-risk scores (all P<0.001). However, patients with a high-risk score exhibited lower responses to immune check-point inhibitors (ICIs), sorafenib, and transarterial chemoembolization (TACE) treatment (all P<0.05). Consistently, TRIM genes showed the same influence in the external TCGA cohort. TRIM gene-based signatures were implicated in TIME and their copy-number alterations dynamically impacted the abundance of tumor-infiltrating immune cells.ConclusionsOur findings revealed that MID1, TRIM5, TRIM22, TRIM28, TRIM 31, TRIM37, TRIM38, TRIM47, and TRIM74 could serve as efficient prognostic biomarkers and therapeutic targets in HCC. The identified TRIM gene-based signatures could serve as important TIME mediators in HCC, potentially increasing immune treatment efficacy.     

TSC1/2 mutations—a unique type of mutation suitable for liver transplantation of Hepatocellular carcinoma

BackgroundThis study aimed to investigate the relationship between the prognosis of patients with hepatocellular carcinoma (HCC) after liver transplantation and mammalian target of rapamycin (mTOR) pathway-related genes-TSC1/2.MethodsWe retrospectively analyzed the clinical data of 46 patients who underwent liver transplantation for HCC and performed next generation sequencing to analyze the relationship between the efficacy of sirolimus after liver transplantation for HCC and mutations in mTOR pathway-related genes, especially tuberous sclerosis complex (TSC) mutations.ResultsThe average age of 46 patients with liver transplantation for HCC was 51±21 years. After surgery, 35 patients received an anti-rejection/anti-tumor regimen that included sirolimus, and 11 patients did not receive sirolimus. There was no significant difference in survival rate between the two groups (P=0.761). The gene sequencing results showed mTOR-related pathway mutations in 10 patients, of whom five (10.9%) had TSC1/2 mutations. Of the 35 patients using sirolimus, those with mTOR-related mutations had significantly better survival rates than patients without mTOR-related mutations (P=0.016).ConclusionsAccording to genetic sequencing results, a personalized treatment plan for specific genetic mutations should be selected in patients undergoing liver transplantation for HCC. Patients with mTOR-related gene mutations, especially TSC mutations, can gain significant benefits from the use of mTOR inhibitors such as sirolimus.     

High expression of aldolase A is associated with tumor progression and poor prognosis in hepatocellular carcinoma

BackgroundAldolase A (ALDOA), a key glycolytic enzyme, has been reported to play an important role in lung, pancreatic, and colorectal cancer. However, the role and mechanism of ALDOA in hepatocellular carcinoma (HCC) are still unclear. This study aimed to study the role and potential mechanism of ALDOA in HCC.MethodsThe changes in expression level and clinical implications of ALDOA in HCC were studied through bioinformatics and online databases. The prognostic role of ALDOA was investigated by Kaplan-Meier and Cox regression survival analysis. We explored the potential mechanism of ALDOA in the development of HCC by gene set enrichment analysis (GSEA).ResultsThe expression level of ALDOA was significantly increased in HCC compared with adjacent normal tissues (P<0.001). The expression level of ALDOA was significantly associated with tumor, node, metastasis (TNM) stage, histologic grade, and p53 mutation (all P<0.05). Prognostically, HCC patients with high expression of ALDOA indicated poorer prognosis and shorter survival time. In addition, univariate and multivariate Cox regression analysis further suggested that overexpression of ALDOA was an independent prognostic risk factor (P<0.05). Furthermore, the nomogram was developed based on ALDOA expression and tumor TNM stage. Besides, ALDOA DNA copy gain and methylation were associated with ALDOA upregulation in HCC. Finally, GSEA suggested that high expression of ALDOA was associated with glucose catabolic process, cell cycle, DNA replication, E2F1 pathways, protein kinase B/mammalian target of rapamycin (AKT/mTOR) pathways, and CD4 T cell related immune biological processes.ConclusionsThere is a close relationship between ALDOA and HCC progression, and ALDOA may be a novel prognostic biomarker and a promising drug target for the treatment of HCC.     

Integrative immunogenomic analysis reveals transcriptional and immune-related differences in hepatocellular carcinoma patients with different disease-free survival

A comprehensive investigation of the neoantigen spectrum and immune infiltration in patients with hepatocellular carcinoma (HCC) is lacking. This study aimed to examine the molecular features correlating with better prognoses in HCC patients. 27 paired tumor and normal tissues from 27 HCC patients were collected and performed with whole-exome sequencing. The most frequently mutated gene in 27 HCC patients was TP53 (16/27, 59.26%). Based on the whole median disease-free survival (DFS), all patients were divided into ‘long-term’ (n = 14, median DFS = 318 weeks) and ‘short-term’ (n = 13, median DFS = 11 weeks) groups. RNA-seq was performed to compare differentially expressed genes, immune infiltration, and neoantigens. Immunohistochemistry was performed to evaluate the immune infiltration. There were no significant differences in tumor mutation burden, immune score, cytolytic activity score, or neoantigen load between two groups. Compared with the long-term group, significantly increased B lineage (P = 0.0463), myeloid dendritic cells (P = 0.0152), and fibroblast (P = 0.0244) infiltration levels were observed in the short-term group, in which genes involved in ribosome, proteasome, and ECM-receptor interaction pathways were also overexpressed. Additionally, 16 patients with tumor thrombus were explored to identify specific biomarkers for prognosis. We found that patients with tumor thrombus carrying TP53/ARID2 neoantigens had significantly longer DFS. In conclusion, higher B lineage, myeloid dendritic cells, and fibroblast infiltration levels might cause poor prognosis in the short-term group, which also showed higher expression of genes involved in ribosome, proteasome, and ECM-receptor interaction pathways. In patients with tumor thrombus, specific TP53/ARID2 neoantigens may be used as biomarkers toward personalized immunotherapy.     

Rapid and aggressive recurrence accompanied by portal tumor thrombus after radiofrequency ablation for hepatocellular carcinoma

Although radiofrequency ablation (RFA) has been reported to be a safe and effective procedure for the treatment of hepatocellular carcinoma (HCC), patterns of recurrence and complications following RFA treatment have not been fully identified. Recently, we have experienced two cases of HCC patients who developed rapid and aggressive recurrence accompanied by portal tumor thrombus after RFA therapy. The first was a 68-year-old woman with hepatitis C virus (HCV)-positive liver cirrhosis, who received percutaneous RFA therapy for a 27-mm-diameter HCC in segment VII. The other was a 64-year-old man with hepatitis B surface antigen (HBsAg)-positive liver cirrhosis and multiple bilobar HCCs, who underwent left hemihepatectomy and intraoperative RFA for the two tumors in the remnant liver. In both patients, though immediate imaging studies suggested complete necrosis of the tumors, recurrences with massive portal tumor thrombus occurred in 4 and 6 months, respectively. At present, it is unclear whether such a recurrence pattern is directly related to the RFA procedure. However, it is implied that RFA therapy may entail a risk of promoting portal venous invasion of HCC tumors.     

CXCL5/CXCL8 is a promising potential prognostic and tumor microenvironment-related cluster in hepatocellular carcinoma

BackgroundImmune checkpoint blockers (ICBs) are increasingly applied to treat patients with advanced HCC. However, the overall survival (OS) of HCC patients is still unsatisfactory, and there is no confirmed immune-related and prognostic gene to identify patients who could clinically benefit from this treatment. The tumor microenvironment (TME) is known to be closely related to immunotherapy and plays a pivotal role in the recurrence and progression of HCC. Our aim is to explore TME-related genes and identify the prognostic value in HCC patients.MethodsESTIMATE, immune, and stromal scores were calculated for HCC patients based on RNA expression data from The Cancer Genome Atlas database. Differential expression analysis was performed to screen the differentially expressed genes (DEGs). A protein-protein interaction (PPI) network was constructed to identify the key DEGs. Univariate and multivariate Cox analyses were adopted to validate hub DEGs associated with clinical prognosis, and a single-sample gene set enrichment analysis (ssGSEA) algorithm was used to dissect the landscape of tumor-infiltrating cells (TIC) in HCC. Finally, the relationship between hub immune-related genes and TIC was explored through difference and correlation analyses.ResultsESTIMATE, immune and stromal scores were all found to be associated with the OS of patients (P<0.05). A total of 1,112 DEGs were identified by comparing low and high score groups of immune and stromal scores. Most of DEGs were enriched in immune-related gene sets by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Additionally, the top 34 genes were included in the protein–protein interaction (PPI) network, and univariate Cox analysis focus on a novel prognosis-related gene cluster CXCL5/CXCL8 (P<0.001). Regarding the immune landscape of HCC, univariable Cox regression analysis showed six immune cells to be associated with OS. Finally, 21 immune cells were commonly determined between high and low expression of CXCL5/CXCL8, suggesting there is a close relationship between expression of CXCL5 and CXCL8 .ConclusionsOur study has revealed that the immune-related gene cluster of CXCL5 /CXCL8 could be a promising prognostic indicator for HCC and a potential novel biomarker to guide the selection of HCC patients for ICB immunotherapy.     

Experimental study on enhancement of the metastatic potential of portal vein tumor thrombus-originated hepatocellular carcinoma cells using portal vein serum

Objective： Portal vein metastasis of hepatocellular carcinoma（HCC） results in a poor prognosis and seriously affects the survival rate of patients. The mechanism underlying the formation of portal vein tumor thrombus（PVTT） is complex and is not yet fully understood. This study was conducted to investigate the impact of portal vein blood on the proliferation, metastasis, invasion and apoptosis of PVTT cells and to explore its possible mechanisms, which was expected to lay a foundation for ascertaining the mechanism underlying the portal vein metastasis of HCC.
Methods： Peripheral blood and portal vein blood were collected from patients with HCC, and the sera from these two sources were used to culture the PVTT-originated HCC cell line CSQT-2. The cells were collected after 24 h, and flow cytometry was performed to detect cell proliferation, cell cycle stages and apoptosis. Transwell migration and invasion assays were applied to detect the metastasis and invasion of the cells in each group. The changes in the expression of MMP-2 and MMP-9 in cells were detected via Western blotting. The contents of IL-12, IFN-γ, IL-1β, IL-2 and TNF-α in the two groups of sera were quantified using corresponding kits.
Results： Compared with the group of cells cultured with peripheral serum, the cells cultured with portal vein serum showed significantly lower apoptosis（P〈0.01）, significantly enhanced cell metastasis and invasion（P〈0.01）, whereas cell proliferation and the stages of the cell cycle did not differ significantly（P〉0.05）. A significantly increased expression level of MMP-2 has been observed in tumor cells treated portal vein serum. In addition, compared with peripheral serum, the content of IL-12 was significantly decreased in portal vein serum（P〈0.05）, while the contents of IFN-γ, IL-1β, IL-2, and TNF-α did not differ significantly（P〈0.05）.
Conclusions： Portal vein serum from HCC patients could inhibit the apoptosis of PVTT-originated HCC cells and promote cell met     

奥沙利铂治疗肝细胞癌耐药的相关机制研究进展

奥沙利铂在我国已被批准用于晚期肝细胞癌（HCC）的治疗,以奥沙利铂为基础的FOLFOX 4方案已成为晚期HCC的标准治疗之一,显著延长了患者的生存期,展现出安全有效、耐受性良好等特点。尽管如此,奥沙利铂治疗HCC的临床疗效仍十分有限,其治疗失败与HCC产生耐药密切相关。本文就奥沙利铂治疗HCC的耐药机制研究进展作一综述,希望能帮助临床和科研工作者了解最新动态,并为他们的工作拓宽思路。     

肿瘤负荷评分在肝细胞癌患者预后预测中的价值

目的 探讨肿瘤负荷评分（tumor burden score,TBS）预测肝细胞癌患者预后的价值。方法 回顾性收集487例行肝切除术肝细胞癌患者的临床资料。采用时间依赖的ROC曲线及曲线下面积（area under the ROC curve,AUC）评价TBS预测总生存率和无瘤生存率的准确性。多因素Cox回归筛选影响肝细胞癌患者预后的独立因素。结果 ROC曲线分析显示,TBS预测肝细胞癌患者术后5年生存率的AUC为0.722,高于肿瘤最大直径的AUC （0.711）和肿瘤数目的AUC（0.548）。TBS可将患者分成4个不同预后风险组,即TBS≤3组（n=70,14.4%）、3n=175,35.9%）、5n=150,30.8%）、TBS>8组（n=92,18.9%）,各组患者5年总生存率依次为87.5%、75.7%、62.9%和36.3%;5年无瘤生存率依次为62.4%、44.2%、31.1%和12.9%。组间总生存率和无瘤生存率比较差异均有统计学意义（P<0.001）。Cox多因素分析显示,TBS是影响肝细胞癌患者术后总生存率和无瘤生存率的独立因素。结论 TBS可较好地预测肝细胞癌患者肝切除术后的预后情况。