Hepatitis B virus X protein promotes tumor glycolysis by downregulating lncRNA OIP5-AS1/HKDC1 in HCC.

Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related mortality worldwide, with Hepatitis B virus (HBV) infection being the leading cause. This study aims to investigate the role of HBV in HCC pathogenesis involving glucose metabolism. Long non-coding RNA (lncRNA) OIP5-AS1 was significantly downregulated in HBV-positive HCC patients, and its low expression indicated a poor prognosis. This lncRNA was primarily localized in the cytoplasm, acting as a tumor suppressor. HBV protein X (HBx) repressed OIP5-AS1 expression by inhibiting a ligand-activated transcriptional factor peroxisome proliferator-activated receptor α (PPARα). Furthermore, mechanistic studies revealed that OIP5-AS1 inhibited tumor growth by suppressing Hexokinase domain component 1 (HKDC1)-mediated glycolysis. The expression of HKDC1 could be enhanced by transcriptional factor sterol regulatory element-binding protein 1 (SREBP1). OIP5-AS1 facilitated the ubiquitination and degradation of SREBP1 to suppress HKDC1 transcription, which inhibited glycolysis. The results suggest that lncRNA OIP5-AS1 plays an anti-oncogenic role in HBV-positive HCC via the HBx/OIP5-AS1/HKDC1 axis, providing a promising diagnostic marker and therapeutic target for HBV-positive HCC patients.

Hepatitis B Virus-Mediated m6A Demethylation Increases Hepatocellular Carcinoma Stemness and Immune Escape.

Hepatitis B viral (HBV) persistent infection plays a significant role in hepatocellular carcinoma (HCC) tumorigenesis. Many studies have revealed the pivotal roles of N6-methyladenosine (m6A) in multiple cancers, while the regulatory mechanism in stemness maintenance of HBV persistent infection-related HCC remains elusive. Here, we demonstrated that the level of m6A modification was downregulated by HBV in HBV-positive HCC, through enhanced stability of ALKBH5 mRNA. More specifically, we also identified that ALKBH5 mRNA was functionally required for the stemness maintenance and self-renewal in the HBV-positive HCC, but dispensable in HBV-negative HCC. Mechanistically, ALKBH5 demethylated the m6A modification in the 3' untranslated region of the oncogenic gene SNAI2 to prevent the recognition of YTHDF2 therewith stabilize SNAI2 transcripts, contributing to cancer stem cell traits in HBV-positive HCC. Moreover, the expression of SNAI2 reversed the suppression of stemness properties by knocking down ALKBH5. In addition, ALKBH5/SNAI2 axis accelerates tumor immune evasion through activated ligand of immune checkpoint CD155. Our study unveiled that the ALKBH5 induces m6A demethylation of the SNAI2 as a key regulator in HBV-related HCC, and identifies the function of ALKBH5/SNAI2/YTHDF2 axis in promoting the stem-like cells phenotype and immune escape during HBV infection. IMPLICATIONS: HBV promotes HCC stemness maintenance through elevate m6A modification of SNAI2 in an ALKBH5-YTHDF2-dependent manner and increases the expression of the ligand of immune checkpoint CD155.

A High-Salt Diet Exacerbates Liver Fibrosis through Enterococcus-Dependent Macrophage Activation.

People consume more salt than the recommended levels due to poor dietary practices. The effects of long-term consumption of high-salt diets (HSD) on liver fibrosis are unclear. This study aimed to explore the impact of HSD on liver fibrosis. In this study, a carbon tetrachloride (CCL4)-induced liver fibrosis mouse model was used to evaluate fibrotic changes in the livers of mice fed a normal diet (ND) and an HSD. The HSD exacerbated liver injury and fibrosis. Moreover, the protein expression levels of transforming growth factor ß (TGF-ß), tumor necrosis factor alpha (TNF-α), and monocyte chemoattractant protein 1 (MCP-1) were significantly higher in the HSD group than in the normal group. The proportion of macrophages and activation significantly increased in the livers of HSD-fed mice. Meanwhile, the number of macrophages significantly increased in the small intestinal lamina propria of HSD-fed mice. The levels of profibrotic factors also increased in the small intestine of HSD-fed mice. Additionally, HSD increased the profibrotic chemokines and monocyte chemoattractant levels in the portal vein blood. Further characterization suggested that the HSD decreased the expression of tight junction proteins (ZO-1 and CLDN1), enhancing the translocation of bacteria. Enterococcus promoted liver injury and inflammation. In vitro experiments demonstrated that Enterococcus induced macrophage activation through the NF-κB pathway, thus promoting the expression of fibrosis-related genes, leading to liver fibrogenesis. Similarly, Enterococcus disrupted the gut microbiome in vivo and significantly increased the fibrotic markers, TGF-ß, and alpha smooth muscle actin (α-SMA) expression in the liver. IMPORTANCE This study further confirms that Enterococcus induce liver fibrosis in mice. These results indicate that an HSD can exacerbate liver fibrosis by altering the gut microbiota composition, thus impairing intestinal barrier function. Therefore, this may serve as a new target for liver fibrosis therapy and gut microbiota management.

zVAD alleviates experimental autoimmune hepatitis in mice by increasing the sensitivity of macrophage to TNFR1-dependent necroptosis.

BACKGROUND & AIMS: Autoimmune hepatitis (AIH) is characterized by hepatocyte destruction, leading to lymphocyte and macrophage accumulation in the liver. Macrophages are key drivers of AIH. A membrane-permeable pan-caspase inhibitor, Z-Val-Ala-DL-Asp-fluoromethylketone (zVAD), induces macrophage necroptosis in response to certain stimuli. However, the function of zVAD in the pathogenesis of autoimmune hepatitis remains elusive. In this study, we aimed to evaluate the effect and explore the underlying mechanisms of zVAD against AIH. METHODS: Murine acute autoimmune liver injury was established by concanavalin A (ConA) injection. Bone marrow-derived macrophages (BMDMs) were used in adoptive cell transfer experiments. The mechanism of action of zVAD was examined using macrophage cell lines and BMDMs. Phosphorylation of mixed lineage kinase domain-like proteins was used as a marker of necroptosis. RESULTS: Treatment with zVAD increased necroptosis, reduced inflammatory cytokine production, and alleviated liver injury in a ConA-induced liver injury mouse model. Regardless of zVAD treatment, macrophage deletion resulted in reduced neutrophil accumulation and relieved ConA-induced liver injury. In vitro studies have shown that zVAD pretreatment promotes lipopolysaccharide-induced macrophage necroptosis and leads to reduced pro-inflammatory cytokine and chemokine secretion. Transferring zVAD-pretreated BMDMs in mice notably reduced ConA-associated liver inflammation and injury, resulting in lower mortality than that observed after transferring normal BMDMs. Mechanistically, zVAD treatment increased the expression of tumour necrosis factor receptor (TNFR)-1 and interleukin (IL)-10 in macrophages. TNFR1 expression decreased upon transfection with IL-10-specific small interfering RNAs and blocking of TNFR1 decreased macrophage necroptosis. CONCLUSIONS: We found that zVAD alleviated ConA-induced liver injury by increasing the sensitivity of macrophages to necroptosis via IL-10-induced TNFR1 expression. This study provides new insights into the treatment of autoimmune hepatitis via zVAD-induced macrophage necroptosis.

Secreted phosphoprotein 1 as a potential prognostic and immunotherapy biomarker in multiple human cancers.

Secreted phosphoprotein 1 (SPP1) is involved in immune regulation, cell survival, and tumor progression. Studies have demonstrated that SPP1 plays an important role in certain individual tumors. However, the expression profile and oncogenic features of SPP1 in diverse cancers are remaining unknown. Therefore, we performed a comprehensive analysis using The Cancer Genome Atlas (TCGA) database. Raw data of 33 cancer types were download from the University of California Santa Cruz (UCSC) Xena website. The expression of SPP1 and its relationship with tumor prognosis, immune invasion, tumor microenvironment, and immunotherapy were analyzed using the R language. The function analysis was conducted using Gene Set Enrichment Analysis (GSEA). The oncogenic features of SPP1 was validated by wound-healing assay and EdU staining assay. SPP1 highly expressed in most cancers. The expression of SPP1 was significant related to prognosis, tumor mutation burden (TMB), microsatellite instability (MSI), and immune checkpoint genes, suggested that SPP1 plays an essential role in the tumor immune microenvironment and immune cell infiltration. The immune/stromal scores correlated positively with the SPP1 expression, and the relationship was affected by tumor heterogeneity and immunotherapy. In addition, SPP1 could predict the response of tumor immunotherapy. Functional analysis revealed the SPP1-associated terms and pathways. Finally, SPP1 significantly elevated cell proliferation and migration in A549, Huh7, HT-29, A2780 tumor cell lines. In conclusion, this study indicated that SPP1 involved in tumorigenesis, tumor progression, and regulated tumor immune microenvironment, revealing SPP1 might be a potential target for evaluating prognosis and immunotherapy in multiple cancers.

Interleukin-33 as an early predictor of cetuximab treatment efficacy in patients with colorectal cancer.

BACKGROUND: Cetuximab is used for colorectal cancer (CRC) treatment. However, the early biomarker of treatment efficacy of cetuximab has not been identified. METHODS: After 1 year of cetuximab treatment, patients were divided into an effective group and an ineffective group. The interleukin-33 (IL-33) level and the distribution of lymphatic cells in patients were investigated by analyzing the peripheral blood mononuclear cells via flow cytometry analysis and ELISA. The correlation between IL-33 immunomodulatory effect and cetuximab treatment efficacy was determined through experiments in vivo and in vitro. RESULTS: The IL-33 level in the peripheral blood was increased at 4 weeks after cetuximab administration of effective group, meanwhile, the osteopontin (OPN) was reduced. Whereas neither IL-33 level nor OPN level of ineffective patients changed. In the effective group, the number of natural killer (NK) and CD8+ T cells were increased. Moreover, CD137 and CD107a expression on NK cells were higher in the effective group compared to the ineffective group. In vitro cetuximab treatment also increased the number of NK and CD8+ T cells as well as CD137 and CD107a expression upon IL-33 stimulation. Moreover, the secretion of OPN was inhibited by IL-33 administration in cetuximab-treated PBMCs from the effective group patients. IL-33 upregulated the cytotoxicity of NK cells and inhibited tumor cells growth in the effective cetuximab treatment mice. CONCLUSION: Effective cetuximab treatment induced a change of IL-33 and OPN at the early stage and triggered the NK cells antitumor activity. Consequently, significantly increased IL-33 level and decreased OPN level in the peripheral blood at the early treatment are proposed as potential predictors of cetuximab treatment efficacy.

The Salivary Microbiota of Patients With Primary Biliary Cholangitis Is Distinctive and Pathogenic.

The role of host-microbiota interactions in primary biliary cholangitis (PBC) has received increased attention. However, the impact of PBC on the oral microbiota and contribution of the oral microbiota to PBC are unclear. In this study, thirty-nine PBC patients without other diseases and 37 healthy controls (HCs) were enrolled and tested for liver functions and haematological variables. Saliva specimens were collected before and after brushing, microbiota was determined using 16S rDNA sequencing, metabolomics was profiled using Gas Chromatography-Mass Spectrometer (GC-MS), 80 cytokines were assayed using biochips, and inflammation inducibility was evaluated using OKF6 keratinocytes and THP-1 macrophages. Finally, the effect of ultrasonic scaling on PBC was estimated. Compared with HCs, PBC saliva had enriched taxa such as Bacteroidetes, Campylobacter, Prevotella and Veillonella and depleted taxa such as Enterococcaceae, Granulicatella, Rothia and Streptococcus. PBC saliva also had enriched sCD163, enriched metabolites such as 2-aminomalonic acid and 1-dodecanol, and depleted metabolites such as dodecanoic acid and propylene glycol. sCD163, 4-hydroxybenzeneacetic acid and 2-aminomalonic acid were significantly correlated with salivary cytokines, bacteria and metabolites. Salivary Veillonellaceae members, 2-aminomalonic acid, and sCD163 were positively correlated with liver function indicators such as serum alkaline phosphatase (ALP), aspartate aminotransferase (AST) and alanine aminotransferase (ALT). PBC salivary microbes induced more soluble interleukin (IL)-6 receptor α (sIL-6Rα), sIL-6Rß and tumour necrosis factor ligand superfamily (TNFSF)13B from OKF6 keratinocytes, and PBC salivary supernatant induced more IL-6, IL-10, granulocyte-macrophage colony-stimulating factor (GM-CSF), chemokine (C-C motif) ligand (CCL)13, C-X-C motif chemokine (CXC)L1 and CXCL16 from THP-1 macrophages. Toothbrushing significantly reduced the expression of inflammatory cytokines such as IL-1ß, IL-8 and TNF-α and harmful metabolites such as cadaverine and putrescine in PBC but not HC saliva after P-value correction. The levels of ALP and bilirubin in PBC serum were decreased after ultrasonic scaling. Together, PBC patients show significant alterations in their salivary microbiota, likely representing one cause and treatment target of oral inflammation and worsening liver functions.

RBM15-mediated N6-methyladenosine modification affects COVID-19 severity by regulating the expression of multitarget genes.

Severe coronavirus disease 2019 (COVID-19) is characterized by symptoms of lymphopenia and multiorgan damage, but the underlying mechanisms remain unclear. To explore the function of N6-methyladenosine (m6A) modifications in COVID-19, we performed microarray analyses to comprehensively characterize the m6A epitranscriptome. The results revealed distinct global m6A profiles in severe and mild COVID-19 patients. Programmed cell death and inflammatory response were the major biological processes modulated by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Further, RBM15, a major m6A methyltransferase, was significantly elevated and positively correlated with disease severity. Silencing RBM15 drastically reduced lymphocyte death in vitro. Knockdown of RBM15 remarkably suppressed the expression levels of multitarget genes related to programmed cell death and inflammatory response. This study shows that SARS-CoV-2 infection alters the m6A epitranscriptome of lymphocytes, particularly in the case of severe patients. RBM15 regulated host immune response to SARS-CoV-2 by elevating m6A modifications of multitarget genes. These findings indicate that RBM15 can serve as a target for the treatment of COVID-19.

A narrative review of the role of necroptosis in liver disease: a double-edged sword.

Acute and chronic liver injuries lead to hepatocyte death and turnover. When injuries become chronic, continuous cell death and transformation lead to chronic inflammation, fibrosis, cirrhosis, and eventually carcinoma. A therapeutic strategy of great significance for liver disease is to control hepatocyte death in acute and chronic injuries. This strategy prevents hepatocytes from causing liver failure and inhibits both secondary inflammation and fibrosis. Both apoptosis and necrosis have been proven to occur in the liver, but the role of necroptosis in liver diseases is controversial. Necroptosis, which has features of necrosis and apoptosis, is a regulatory process that occurs in some cell types when caspases are inhibited. The signaling pathway of necroptosis is characterized by the activation of receptor-interacting proteins kinase (RIPK) and mixed lineage kinase domain-like (MLKL). Necroptosis is associated with a variety of inflammatory diseases and has been the focus of research in recent years. The incidence of necroptosis in liver tissues has been studied recently in several liver injury models, but the results of the studies are not consistent. The purpose of this review is to summarize the published data on the involvement of necroptosis in liver injury, focusing on the controversies, issues remaining to be discussed, and potential therapeutic applications in this area.

Hepatitis B virus P protein initiates glycolytic bypass in HBV-related hepatocellular carcinoma via a FOXO3/miRNA-30b-5p/MINPP1 axis.

BACKGROUND: Hepatitis B virus (HBV) infection is a crucial risk factor for hepatocellular carcinoma (HCC). However, its underlying mechanism remains understudied. METHODS: Microarray analysis was conducted to compare the genes and miRNAs in liver tissue from HBV-positive and HBV-negative HCC patients. Biological functions of these biomarkers in HBV-related HCC were validated via in vitro and in vivo experiments. Furthermore, we investigated the effect of HBV on the proliferation and migration of tumor cells in HBV-positive HCC tissue. Bioinformatics analysis was then performed to validate the clinical value of the biomarkers in a large HCC cohort. RESULTS: We found that a gene, MINPP1 from the glycolytic bypass metabolic pathway, has an important biological function in the development of HBV-positive HCC. MINPP1 is down-regulated in HBV-positive HCC and could inhibit the proliferation and migration of the tumor cells. Meanwhile, miRNA-30b-5p was found to be a stimulator for the proliferation of tumor cell through glycolytic bypass in HBV-positive HCC. More importantly, miRNA-30b-5p could significantly downregulate MINPP1 expression. Metabolic experiments showed that the miRNA-30b-5p/MINPP1 axis is able to accelerate the conversion of glucose to lactate and 2,3-bisphosphoglycerate (2,3-BPG). In the HBV-negative HCC cells, miRNA-30b-5p/MINPP1 could not regulate the glycolytic bypass to promote the tumorigenesis. However, once HBV was introduced into these cells, miRNA-30b-5p/MINPP1 significantly enhanced the proliferation, migration of tumor cells, and promoted the glycolytic bypass. We further revealed that HBV infection promoted the expression of miRNA-30b-5p through the interaction of HBV protein P (HBp) with FOXO3. Bioinformatics analysis on a large cohort dataset showed that high expression of MINPP1 was associated with favorable survival of HBV-positive HCC patients, which could lead to a slower progress of this disease. CONCLUSION: Our study found that the HBp/FOXO3/miRNA-30b-5p/MINPP1 axis contributes to the development of HBV-positive HCC cells through the glycolytic bypass. We also presented miRNA-30b-5p/MINPP1 as a novel biomarker for HBV-positive HCC early diagnosis and a potential pharmaceutical target for antitumor therapy.

Comprehensive Study of Tumor Immune Microenvironment and Relevant Genes in Hepatocellular Carcinoma Identifies Potential Prognostic Significance.

Background: The tumor immune microenvironment (TIME) is an external immune system that regulates tumorigenesis. However, cellular interactions involving the TIME in hepatocellular carcinoma (HCC) are poorly characterized. Methods: In this study, we used multidimensional bioinformatic methods to comprehensively analyze cellular TIME characteristics in 735 HCC patients. Additionally, we explored associations involving TIME molecular subtypes and gene types and clinicopathological features to construct a prognostic signature. Results: Based on their characteristics, we classified TIME and gene signatures into three phenotypes (TIME T1-3) and two gene clusters (Gene G1-2), respectively. Further analysis revealed that Gene G1 was associated with immune activation and surveillance and included CD8+ T cells, natural killer cell activation, and activated CD4+ memory T cells. In contrast, Gene G2 was characterized by increased M0 macrophage and regulatory T cell levels. After calculation of principal component algorithms, a TIME score (TS) model, including 78 differentially expressed genes, was constructed based on TIME phenotypes and gene clusters. Furthermore, we observed that the Gene G2 cluster was characterized by high TS, and Gene G1 was characterized by low TS, which correlated with poor and favorable prognosis of HCC, respectively. Correlation analysis showed that TS had a positive association with several clinicopathologic signatures [such as grade, stage, tumor (T), and node (N)] and known somatic gene mutations (such as TP53 and CTNNB1). The prognostic value of the TS model was verified using external data sets. Conclusion: We constructed a TS model based on differentially expressed genes and involving immune phenotypes and demonstrated that the TS model is an effective prognostic biomarker and predictor for HCC patients.

In-depth characterization of the biomarkers based on tumor-infiltrated immune cells reveals implications for diagnosis and prognosis in hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is an immune-related tumor, that the type and number of tumor-infiltrated immune cells can serve as biomarkers for the clinical application. In this study, we constructed the immune model for diagnostic and prognostic prediction of HCC based on the systematic bioinformatics analyses on the component of immune cells from large samples transcriptome. CIBERSORT analysis found that the component of immune cells between 513 HCC and 473 adjacent normal tissues was different. M0 macrophages and regulatory T cells were mainly enriched in tumor tissues, whereas the CD8+ T cell and activated CD4+ memory T cells were the most in normal tissues. Using random forest and LASSO analyses, eleven immune cell types were mined out to construct the immune diagnostic model (IDG), which showed high efficiency in distinguishing cancer from normal tissues both in testing and validation groups. In addition, the immune prognostic model (IPG) consisting of five types of immune cells was constructed using the LASSO-Cox algorithm. It showed that HCC patients of the high-risk group had a significantly shorter survival time than those of low-risk group in testing, validation, and entire cohorts. Besides, Nomogram plots and decision curve analyses revealed that the IPG was positively associated with the HCC clinical classification of the Barcelona Clinic Liver Cancer (BCLC) stage, and showing more accuracy of prediction than independent BCLC stage. Related analyses found that IDG positively correlated with epithelial-mesenchymal transition (EMT) and cytotoxic factor-related genes and negatively correlated with immune checkpoint regulators related genes. From the GSEA analysis of the biological function of genes related to IPG, it was found that the genes of the high-risk group were enriched in some tumorigenesis related pathways, such as DNA replication, cell cycle, and PPARA. Therefore, this study identified IDG and IPG as efficient biomarkers for the diagnosis and prognosis of HCC.

The Contradictory Role of Interleukin-33 in Immune Cells and Tumor Immunity.

Interleukin (IL)-33 is a member of the IL-1 superfamily and is a crucial cytokine playing the role of a dual-function molecule. IL-33 mediates its function by interacting with its receptor suppression of tumorigenicity 2 (ST2), which is constitutively expressed on T helper (Th)1 cells, Th2 cells, and other immune cells. Previously, we summarized findings on IL-33 and performed an intensive study of the correlation between IL-33 and tumor. IL-33 enables anti-tumor immune responses through Th1 cells and natural killer (NK) cells and plays a role in tumor immune escape in cancers via Th2 cells and regulatory T cells. Herein, we discuss the contradictory role of IL-33 in immune cells in different cancer, and our summaries may be helpful for better understanding of the development of research on IL-33 and tumor immunity.

Identification of prognostic biomarkers of hepatocellular carcinoma via long noncoding RNA expression and copy number alterations.

Aim: This study aimed to identify long noncoding RNAs (lncRNAs) with potential to be prognostic biomarkers of hepatocellular carcinoma (HCC) by analyzing copy number alterations (CNAs). Methods: RNA Sequencing data of 369 HCC patients was downloaded from The Cancer Genome Atlas database and analyzed with a series of systematic bioinformatics methods. Results: LncRNA-CNA association analysis revealed that many lncRNAs were located in sites frequently amplified or deleted. Three upregulated lncRNAs (LINC00689, SNHG20 and MAFG-AS1) with copy amplification and one downregulated lncRNA TMEM220-AS1 with copy deletion were associated with poor prognosis of HCC. Conclusion: This study reveals that differentially expressed lncRNAs correlate with CNAs in HCC. Moreover, the differentially expressed lncRNAs and their copy amplification/deletions could be promising prognostic biomarkers of HCC.

Sodium butyrate modulates gut microbiota and immune response in colorectal cancer liver metastatic mice.

Colorectal cancer (CRC) liver metastasis (CLM) is the leading death cause of CRC patients, but there is no satisfied approach to treat CLM. Gut microbiota plays a pivotal role in CRC initiation and development. Targeting dysbiosis of the gut microbiota might open up new opportunities for CLM treatment. Here, we investigated the efficacy of sodium butyrate (NaB), a major product of gut microbial fermentation, in modulating gut microbiota in CLM mice. NaB supplement decreased mouse colon cancer CT26 cell liver metastasis in intrasplenic tumor injection model of BALB/c mice. Using 16S rRNA gene sequencing, we found altered microbiota composition in CLM mice, characterized by increases of Firmicutes and Proteobacteria. NaB beneficially changed dysbiosis in CLM mice. Functional analysis of the KEGG pathways showed that NaB changed pathways related to immune system diseases and primary immunodeficiency in CLM mice. In addition, NaB decreased T regulatory cells and increased natural killer T cells and T helper 17 cells, accordingly decreased IL-10 and increased IL-17 secretion in CLM mice liver. In conclusion, NaB beneficially modulated gut microbiota and improved host immune response in CLM mice. These findings demonstrate the therapeutic potential of NaB in CLM treatment.

No difference in TCRß repertoire of CD4+ naive T cell between patients with primary biliary cholangitis and healthy control subjects.

Primary biliary cholangitis (PBC) is considered as a model of organ-specific autoimmune disease based on the serological findings of anti-mitochondrial antibodies (AMA), infiltrates of T cells, and selective destruction of epithelial cells in the liver. T-cell-mediated autoimmune mechanisms are considered to be involved in the pathogenesis of primary biliary cholangitis (PBC). In this context, we used a combination of multiplex-PCR, Illumina sequencing and IMGT/HighV-QUEST for a standardized analysis of the T cell receptor ß-chain (TCRß) repertoire of CD4＋naive T cells in PBC patients compared with healthy volunteers. Nonfunctional TCRs were used to study the pre-selection TCR repertoire, as they are not subject to functional selection (positive and negative selection). Functional TCRs were used to study the post-selection TCR repertoire. The results showed that there was not significant difference between PBC patients and healthy volunteers in TCRß diversity, CDR3 length distributions, degree of sequence sharing, and usage frequency of TRBV and TRBJ segments, no matter in Pre-selection or Post-selection repertoires. In conclusion, early events in thymic T cell development and repertoire generation are not abnormality in PBC patients. The breakdown of self-tolerance to autoantigen may be derived from other immunological dysregulation or environmental agents.

Identifying Hepatocellular Carcinoma Driver Genes by Integrative Pathway Crosstalk and Protein Interaction Network.

In this study, we mined out hepatocellular carcinoma (HCC) driver genes from MEDLINE literatures by bioinformatics methods of pathway crosstalk and protein interaction network. Furthermore, the relationship between driver genes and their clinicopathological characteristics, as well as classification effectiveness was verified in the public databases. We identified 560 human genes reported to be associated with HCC in 1074 published articles. Functional analysis revealed that biological processes and biochemical pathways relating to tumor pathogenesis, cancer disease, tumor cell molecule, and hepatic disease were enriched in these genes. Pathway crosstalk analysis indicated that significant pathways could be divided into three modules: cancer disease, virus infection, and tumor signaling pathway. The HCC-related protein-protein interaction network comprised 10,212 nodes, and 56,400 edges were mined out to identify 18 modules corresponding to 14 driver genes. We verified that these 14 driver genes have high classification effectiveness to distinguish cancer samples from normal samples and the classification effectiveness was better than that of randomly selected genes. Present study provided pathway crosstalk and protein interaction network for understanding potential tumorigenesis genes underlying HCC. The 14 driver genes identified from this study are of great translational value in HCC diagnosis and treatment, as well as in clinical study on the pathogenesis of HCC.

DNA methylation-based classification and identification of renal cell carcinoma prognosis-subgroups.

BACKGROUND: Renal cell carcinoma (RCC) is the most common kidney cancer and includes several molecular and histological subtypes with different clinical characteristics. The combination of DNA methylation and gene expression data can improve the classification of tumor heterogeneity, by incorporating differences at the epigenetic level and clinical features. METHODS: In this study, we identified the prognostic methylation and constructed specific prognosis-subgroups based on the DNA methylation spectrum of RCC from the TCGA database. RESULTS: Significant differences in DNA methylation profiles among the seven subgroups were revealed by consistent clustering using 3389 CpGs that indicated that were significant differences in prognosis. The specific DNA methylation patterns reflected differentially in the clinical index, including TNM classification, pathological grade, clinical stage, and age. In addition, 437 CpGs corresponding to 477 genes of 151 samples were identified as specific hyper/hypomethylation sites for each specific subgroup. A total of 277 and 212 genes corresponding to DNA methylation at promoter sites were enriched in transcription factor of GKLF and RREB-1, respectively. Finally, Bayesian network classifier with specific methylation sites was constructed and was used to verify the test set of prognoses into DNA methylation subgroups, which was found to be consistent with the classification results of the train set. DNA methylation-based classification can be used to identify the distinct subtypes of renal cell carcinoma. CONCLUSIONS: This study shows that DNA methylation-based classification is highly relevant for future diagnosis and treatment of renal cell carcinoma as it identifies the prognostic value of each epigenetic subtype.

Investigating the dysfunctional pathogenesis of Wilms' tumor through a multidimensional integration strategy.

BACKGROUND: Wilms' tumor (WT) is a common kidney tumor in early childhood which is characterized by multiple congenital anomalies and syndromes. With the continuous improvement of medical standards, the cure rate and survival period of WT have increased. However, its molecular mechanism is still elusive. METHODS: A comprehensive multidimensional integration strategy was used to comprehensively analyze the mechanisms of WT. RESULTS: By integrating the potential pathogenic genes of kidney cancer and performing co-expression analysis on the disease-related genes, 23 functional modules were obtained. All the genes were differentially expressed in WT, and were mainly involved in many biological processes and signaling pathways, such as Wnt/ß-catenin, mTOR/ERK and calcineurin. Additionally, based on the relationship between transcriptional and post-transcriptional regulatory systems, in functional modules, transcription factors (TFs) including STAT3, HDAC1 and SP1 as well as non-coding RNAs (ncRNAs) such as miR-335-5p, miR-21-5p and TUG1 were identified. Finally, potential drugs for these multifactor regulated dysfunctional modules which may have certain pharmacological or toxicological effects on WT such as cisplatin, sorafenib, and zinc were predicted. CONCLUSIONS: A multidimensional dysfunction mechanism, involving disease-related genes, TFs and ncRNAs was revealed in the pathogenesis of WT. Functional modules were used to predict potential drugs which can be used in personalized therapy and drug delivery. This study explored the pathogenesis of WT from a new perspective, and provides new candidate targets and therapeutic drugs for improving the cure rate of WT.

Thrombin cleavage of osteopontin controls activation of hepatic stellate cells and is essential for liver fibrogenesis.

Liver biopsy is the current reliable way of evaluating liver fibrosis. However, no specific sera biomarker could be applied in clinical diagnosis. As the pivotal role of osteopontin (OPN) reported in numerous liver diseases, thrombin-cleaved OPN (Thr-OPN) exposes an integrin-binding motif that promoted biological functions. Herein, we investigated the potential of Thr-OPN in liver fibrosis. Using patient samples, mouse models and hepatic stellate cells (HSCs), we analyzed the involvement of Thr-OPN in liver fibrosis. The result showed that, first, Thr-OPN level was significantly higher in patients with liver cirrhosis than that in patients with chronic hepatitis B and healthy controls. Thr-OPN level was positively correlated with liver fibrosis degree in clinical samples. Then in mouse models, it showed a similar correlation between hepatic Thr-OPN levels and liver fibrosis degree. Thr-OPN peptides exacerbated liver fibrosis in OPN-deficient mice, whereas the neutralization of Thr-OPN alleviated liver fibrosis in wild-type mice. Furthermore, when compared with full-length OPN (FL-OPN), Thr-OPN exhibited a greater ability to promote HSC activation, proliferation, and migration via mitogen-activated protein (MAP) kinase and nuclear factor (NF)-κB pathways. In conclusion, Thr-OPN, not FL-OPN, was critically involved in the exacerbation of liver fibrosis by α9 and α4 integrins via MAP kinase and NF-κB signaling pathway, thus representing a novel diagnostic biomarker and treatment target for liver cirrhosis.