Gang Liu

Hsa_circ_0001649: A circular RNA and potential novel biomarker for hepatocellular carcinoma

BACKGROUNDnIt has been shown that circular RNA (circRNA) is associated with human cancers, however, few studies have been reported in hepatocellular carcinoma (HCC).nnnOBJECTIVEnTo estimate clinical values of a circular RNA, Hsa_circ_0001649, in HCC.nnnMETHODSnExpression level of hsa_circ_0001649 was detected in HCC and paired adjacent liver tissues by real-time quantitative reverse transcription-polymerase chain reactions (qRT-PCRs). Differences in expression level of hsa_circ_0001649 were analyzed using the paired t-test. Tests were performed between clinical information and hsa_circ_0001649 expression level by analysis of variance (ANOVA) or welch t-test and a receiver operating characteristics (ROC) curve was established to estimate the value of hsa_circ_0001649 expression as a biomarker in HCC.nnnRESULTSnhsa_circ_0001649 expression was significantly downregulated in HCC tissues (p = 0.0014) based on an analysis of 89 paired samples of HCC and adjacent liver tissues and the area under the ROC curve (AUC) was 0.63. Furthermore, hsa_circ_0001649 expression was correlated with tumor size (p = 0.045) and the occurrence of tumor embolus (p = 0.017) in HCC.nnnCONCLUSIONSnWe first found hsa_circ_0001649 was significantly downregulated in HCC. Our findings indicate hsa_circ_0001649 might serve as a novel potential biomarker for HCC and may function in tumorigenesis and metastasis of HCC.

Potential diagnostic and prognostic marker dimethylglycine dehydrogenase (DMGDH) suppresses hepatocellular carcinoma metastasis in vitro and in vivo.

Key metabolic enzymes regulatethe fluxes of small compounds to provide the basal substrates for cellular architecture and energy. Some of them are reported to be important carcinogenesis- and metastasis-related genes. In our work, we performed RNA-seq for50 pairs of normal-tumor of hepatocellular carcinoma (HCC) samples and found that the expression of dimethylglycine dehydrogenase (DMGDH) is decreased in HCC. The analysis of protein levels with Western blotting and immunohistochemistry also conformed our findings. It is proven to be a valuable biomarker for both diagnosis and prognosis in three independent datasets. Furthermore, we revealed that DMGDH suppresses migration, invasion and metastasis both in vitro and in vivo. By utilizing gene expression microarray for DMGDH, we identified several possible pathways altered in a DMGDH over-expressing cell line. Among these pathways, we noted that the phosphorylation of Akt-308/473 was significantly suppressed when DMGDH was over-expressed. In summary, our work reveals that DMGDH is a potential valuable biomarker for both diagnosis and prognosisfor HCC, and DMGDH gene expression suppresses metastasis through the Akt signaling pathway.

Aldehyde dehydrogenase‐2 (ALDH2) opposes hepatocellular carcinoma progression by regulating AMP‐activated protein kinase signaling in mice

Potential biomarkers that can be used to determine prognosis and perform targeted therapies are urgently needed to treat patients with hepatocellular carcinoma (HCC). To meet this need, we performed a screen to identify functional genes associated with hepatocellular carcinogenesis and its progression at the transcriptome and proteome levels. We identified aldehyde dedydrogenase‐2 (ALDH2) as a gene of interest for further study. ALDH2 levels were significantly lower at the mRNA and protein level in tumor tissues than in normal tissues, and they were even lower in tissues that exhibited increased migratory capacity. A study of clinical associations showed that ALDH2 is correlated with survival and multiple migration‐associated clinicopathological traits, including the presence of metastasis and portal vein tumor thrombus. The result of overexpressing or knocking down ALDH2 showed that this gene inhibited migration and invasion both in vivo and in vitro. We also found that ALDH2 altered the redox status of cells by regulating acetaldehyde levels and that it further activated the AMP‐activated protein kinase (AMPK) signaling pathway. Conclusion: Decreased levels of ALDH2 may indicate a poor prognosis in HCC patients, while forcing the expression of ALDH2 in HCC cells inhibited their aggressive behavior in vitro and in mice largely by modulating the activity of the ALDH2‐acetaldehyde‐redox‐AMPK axis. Therefore, identifying ALDH2 expression levels in HCC might be a useful strategy for classifying HCC patients and for developing potential therapeutic strategies that specifically target metastatic HCC. (Hepatology 2017;65:1628‐1644).

Integrated Multiple "-omics" Data Reveal Subtypes of Hepatocellular Carcinoma.

Hepatocellular carcinoma is one of the most heterogeneous cancers, as reflected by its multiple grades and difficulty to subtype. In this study, we integrated copy number variation, DNA methylation, mRNA, and miRNA data with the developed “cluster of cluster” method and classified 256 HCC samples from TCGA (The Cancer Genome Atlas) into five major subgroups (S1-S5). We observed that this classification was associated with specific mutations and protein expression, and we detected that each subgroup had distinct molecular signatures. The subclasses were associated not only with survival but also with clinical observations. S1 was characterized by bulk amplification on 8q24, TP53 mutation, low lipid metabolism, highly expressed onco-proteins, attenuated tumor suppressor proteins and a worse survival rate. S2 and S3 were characterized by telomere hypomethylation and a low expression of TERT and DNMT1/3B. Compared to S2, S3 was associated with less copy number variation and some good prognosis biomarkers, including CRP and CYP2E1. In contrast, the mutation rate of CTNNB1 was higher in S3. S4 was associated with bulk amplification and various molecular characteristics at different biological levels. In summary, we classified the HCC samples into five subgroups using multiple “-omics” data. Each subgroup had a distinct survival rate and molecular signature, which may provide information about the pathogenesis of subtypes in HCC.

Neuraminidase 1 (NEU1) promotes proliferation and migration as a diagnostic and prognostic biomarker of hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is among the most malignant cancers worldwide, lacking biomarkers for subtyping and the reliable prognostication. Herein, we report a novel biomarker, NEU1 (neuraminidase 1), is up-regulated in most samples of HCC. The diagnostic value of NEU1 was evaluated by ROC, and the AUC (area under curve) reached 0.87 and 0.96 in two independent datasets, respectively. The survival differences of HCC patients with high or low expression of NEU1 were statistically significant, and a significant correlation between NEU1 expression and clinical information including stage, differentiation, AFP and embolus were observed. NEU1 expression, at both the mRNA and protein levels, were also higher in the portal vein tumor thrombus than tumor tissues. We also measured the proliferation and migration ability of two HCC cell lines following NEU1 interference and over-expression. Migration and proliferation rate were increased in NEU1 high expression groups. Moreover, gene expression studies identified pathways significantly associated with NEU1 expression. Among them, all the genes involved in spliceosomepathway were up regulated in NEU1-high group. In summary, our work identified NEU1 as a novel biomarker for both diagnosis and prognosis in HCC, and one of the most altered pathway of NEU1 is spliceosome.

Upregulate KIF4A Enhances Proliferation, Invasion of Hepatocellular Carcinoma and Indicates poor prognosis Across Human Cancer Types

Hepatocellular carcinoma (HCC) is one of the most aggressive and heterogeneous cancers worldwide. Herein, we demonstrate KIF4A (Chromosome-associated kinesin KIF4A) as a potential biomarker, is up-regulated in most samples of HCC. The expression level of KIF4A in tumor tissue is significantly associated with the survival time, and a significant correlation between KIF4A expression and clinical information stage, metastasis and tumor dimension was observed. We further measured the proliferation and migration ability of two HCC cell lines, HCC-LM3 and PLC/PRF/5, following KIF4A-siRNA transfection. Knocking down of KIF4A significantly reduced migration and proliferation ability. Moreover, we also measured the proliferation and migration ability of two HCC cell lines through KIF4A overexpression, and found that KIF4A overexpression could enhance migration and proliferation ability, indicating that KIF4A exhibits oncogenic effects. Besides, study based on TCGA cohorts also reveals high KIF4A mRNA expression are significantly associated with shorter overall survival in multiple cancer types. Gene sets enrichment analysis exhibited that cell cycle related pathways and p53 signaling pathways to be top altered pathways of in KIF4A-high expression group in HCC, suggesting the potential role of KIF4A in mediating tumor initiation and progression. In summary, our work identified KIF4A as a potential predictive and prognostic marker for hepatocellular carcinoma.

Panel of seven long noncoding RNA as a candidate prognostic biomarker for ovarian cancer

Ovarian cancer is one of the most common and lethal gynecological malignancies. The diagnosis of ovarian cancer is often at an advanced stage. Accumulated evidence suggests that long noncoding RNAs (lncRNAs) play important roles during ovarian tumorigenesis. In this study, using the lncRNA-mining approach, we analyzed lncRNA expression profiles of 493 ovarian cancer patients from Gene Expression Omnibus datasets, and identified a signature group of seven lncRNAs (BC037530, AK021924, AK094536, AK094536, BC062365, BC004123 and BC007937) associated with patient survival in the training dataset GSE9891. We also formulated a risk score model to divide patients into low-risk and high-risk groups based on the expression of these seven lncRNAs. We further validated the predictive power of our risk score model in two other datasets, GSE26193 and GSE63885. Our analysis showed that the seven-lncRNA signature can serve as an independent predictor apart from Federation of Gynecology and Obstetrics (FIGO) stage and patient age. Further investigation revealed the seven-lncRNA signature correlated with few critical signaling pathways involved in cancer. Combined, all these findings strongly support that the seven-lncRNA signature can serve as a strong prognosis biomarker.

Comparative Transcriptomic Analysis of Primary Duck Hepatocytes Provides Insight into Differential Susceptibility to DHBV Infection.

Primary duck hepatocytes (PDH) displays differential susceptibility to duck hepatitis B virus when maintained in the media supplemented with fetal bovine serum or dimethyl sulfoxide (DMSO) which has been widely used for the maintenance of hepatocytes, and prolonging susceptibility to hepadnavirus. However the mechanism underlying maintenance of susceptibility to hepadnavirus by DMSO treatment remains unclear. In this study, a global transcriptome analysis of PDHs under different culture conditions was conducted for investigating the effects of DMSO on maintenance of susceptibility of PDH to DHBV in vitro. The 384 differential expressed genes (DEGs) were identified by comparisons between each library pair (PDHs cultured with or without DMSO or fresh isolated PDH). We analyzed canonical pathways in which the DEGs were enriched in Hepatic Fibrosis / Hepatic Stellate Cell Activation, Bile Acid Biosynthesis and Tight Junction signaling. After re-annotation against human genome data, the 384 DEGs were pooled together with proteins belonging to hepatitis B pathway to construct a protein-protein interaction network. The combination of decreased expression of liver-specific genes (CYP3A4, CYP1E1, CFI, RELN and GSTA1 et al) with increased expression of hepatocyte-dedifferentiation-associated genes (PLA2G4A and PLCG1) suggested that in vitro culture conditions results in the fading of hepatocyte phenotype in PDHs. The expression of seven DEGs associated with tight junction formation (JAM3, PPP2R2B, PRKAR1B, PPP2R2C, MAGI2, ACTA2 and ACTG2) was up-regulated after short-term culture in vitro, which was attenuated in the presence of DMSO. Those results could shed light on DHBV infection associated molecular events affected by DMSO.

Cancer stem cell associated eight gene‑based signature predicts clinical outcomes of colorectal cancer

Previous studies have suggested that cancer stem cells serve crucial functions in tumorigenesis, metastasis and therapy failure. Stem cell signaling transduction pathways are frequently dysregulated in cancer and associated with tumorigenesis, metastasis and the cell cycle, which are necessary for cancer proliferation. However, cancer stem cell-associated gene signatures have not been established for predicting patient outcomes in colorectal cancer. Using a gene-mining approach, the present study performed mRNA expression profiling in large colorectal cancer cohorts from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) database, including a TCGA colorectal cancer cohort (n=383) and three independent validation series GSE39582 (n=582), GSE17536 (n=177) and GSE17537 (n=55). The present study identified that an eight-gene signature in cancer stem cell signaling was associated with the overall survival and disease/recurrence-free survival of patients with colorectal. On the basis of this signature, patients in the TCGA training sets were divided into high-risk and low-risk subgroups with a significantly different overall survival rate (hazard ratio, 2.38; P=0.0005). The prognostic value of this signature was confirmed using three independent GEO colorectal cancer sets. Identifying this prognostic stem cell signaling signature may provide an efficient classification tool for clinical prognosis evaluation, and facilitate cancer stem cell-targeted therapy.

Genomics alterations of metastatic and primary tissues across 15 cancer types

Metastasis is an important event for cancer evolution and prognosis. In this article, we analyzed the differences in genomic alterations between primary and metastatic tissues at hotspot regions in 15 cancer types and 10,456 samples. Differential somatic mutations at the amino acid, protein domain and gene levels, mutational exclusiveness, and copy number variations were identified in these cancers, while no significant nucleotide and gene fusion differences were detected. The homogeneity and heterogeneity of these differences in cancers were also detected. By characterizing the genomic alterations of these genes, important signaling pathways during metastasis were also identified. In summary, the metastatic cancer tissues retained most genomic features of the primary tumor at the biological level and acquired new signatures during cancer cell migration.