MRPS31 loss is a key driver of mitochondrial deregulation and hepatocellular carcinoma aggressiveness

Abstract Deregulated mitochondrial energetics is a metabolic hallmark of cancer cells. However, the causative mechanism of the bioenergetic deregulation is not clear. In this study, we show that somatic copy number alteration (SCNA) of mitoribosomal protein (MRP) genes is a key mechanism of bioenergetic deregulation in hepatocellular carcinoma (HCC). Association analysis between the genomic and transcriptomic profiles of 82 MRPs using The Cancer Genome Atlas-Liver HCC database identified eight key SCNA-dependent MRPs: MRPS31, MRPL10, MRPL21, MRPL15, MRPL13, MRPL55, and DAP3. MRPS31 was the only downregulated MRP harboring a DNA copy number (DCN) loss. MRPS31 loss was associated specifically with the DCN losses of many genes on chromosome 13q. Survival analysis revealed a unique dependency of HCC on the MRPS31 deficiency, showing poor clinical outcome. Subclass prediction analysis using several public classifiers indicated that MRPS31 loss is linked to aggressive HCC phenotypes. By employing hepatoma cell lines with SCNA-dependent MRPS31 expression (JHH5, HepG2, Hep3B, and SNU449), we demonstrated that MRPS31 deficiency is the key mechanism, disturbing the whole mitoribosome assembly. MRPS31 suppression enhanced hepatoma cell invasiveness by augmenting MMP7 and COL1A1 expression. Unlike the action of MMP7 on extracellular matrix destruction, COL1A1 modulated invasiveness via the ZEB1-mediated epithelial-to-mesenchymal transition. Finally, MRPS31 expression further stratified the high COL1A1/DDR1-expressing HCC groups into high and low overall survival, indicating that MRPS31 loss is a promising prognostic marker. Significance Our results provide new mechanistic insight for mitochondrial deregulation in HCC and present MRPS31 as a novel biomarker of HCC malignancy.

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HDAC9 Is Preferentially Expressed in Dedifferentiated Hepatocellular Carcinoma Cells and Is Involved in an Anchorage-Independent Growth

Cancers ◽

10.3390/cancers12102734 ◽

2020 ◽

Vol 12 (10) ◽

pp. 2734

Author(s):

Keita Kanki ◽

Ryota Watanabe ◽

Le Nguyen Thai ◽

Chun-Hao Zhao ◽

Kyoko Naito

Keyword(s):

Hepatocellular Carcinoma ◽

Histone Deacetylases ◽

Epithelial Mesenchymal Transition ◽

Cell Transformation ◽

The Cancer Genome Atlas ◽

Hepatic Differentiation ◽

Differentiation Markers ◽

Mesenchymal Transition ◽

Cancer Genome Atlas ◽

Hcc Cells

Aberrant activation of histone deacetylases (HDACs) is one of the causes of tumor cell transformation in many types of cancer, however, the critical HDAC responsible for the malignant transformation remain unclear. To identify the HDAC related to the dedifferentiation of hepatocellular carcinoma (HCC) cells, we investigated the expression profile of HDACs in differentiated and undifferentiated hepatoma cells. We found that HDAC9, a member of the class II HDAC, is preferentially expressed in undifferentiated HCC cells. Analysis of 373 HCC patients in The Cancer Genome Atlas (TCGA) database revealed that the expression of HDAC9 mRNA positively correlated with the markers of mesenchymal phenotype and stemness, and conversely, negatively correlated with hepatic differentiation markers. HDAC9 was transcriptionally upregulated in epithelial–mesenchymal transition (EMT)-induced HCC cells treated with TGF-β. Genetic and pharmacological inhibition of HDAC9 in undifferentiated HCC cells showed decreased sphere-forming activity, which indicates an ability of anchorage-independent cell growth and self-renewal. We also showed that aldehyde dehydrogenase 1A3 (ALDH1A3) was downregulated in HDAC9-suppressing cells, and ALDH inhibitor disulfiram significantly decreased the sphere formation of undifferentiated HCC cells. Together, our data provide useful information for the development of HDAC9-specific inhibitors for the treatment of HCC progression.

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Analysis of the Cancer Genome Atlas Data Reveals Novel Putative ncRNAs Targets in Hepatocellular Carcinoma

BioMed Research International ◽

10.1155/2018/2864120 ◽

2018 ◽

Vol 2018 ◽

pp. 1-9 ◽

Cited By ~ 9

Author(s):

Tiago Falcon ◽

Martiela Freitas ◽

Ana Carolina Mello ◽

Laura Coutinho ◽

Mario R. Alvares-da-Silva ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

The Cancer Genome Atlas ◽

R Software ◽

Liver Malignancy ◽

Regulate Gene Expression ◽

Cancer Genome Atlas ◽

Cell Invasiveness ◽

Cell Dissemination ◽

Solid Tumor Tissue ◽

Shed Light

Hepatocellular carcinoma (HCC) is the prevalent type of primary liver malignancy. Different noncoding RNAs (ncRNAs) that negatively regulate gene expression, such as the microRNAs and the long ncRNAs (lncRNAs), have been associated with cell invasiveness and cell dissemination, tumor recurrence, and metastasis in HCC. To evaluate which regulatory ncRNAs might be good candidates to disrupt HCC proliferation pathways, we performed both unsupervised and supervised analyses of HCC expression data, comparing samples of solid tumor tissue (TP) and adjacent tissue (NT) of a set of patients, focusing on ncRNAs and searching for common mechanisms that may shed light in future therapeutic options. All analyses were performed using the R software. Differential expression (total RNA and miRNA) and enrichment analyses (Gene Ontology + Pathways) were performed using the package TCGABiolinks. As a result, we improved the set of lncRNAs that could be the target of future studies in HCC, highlighting the potential ofFAM170B-AS1andTTN-AS1.

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FXR silencing in human colon cancer by DNA methylation and KRAS signaling

AJP Gastrointestinal and Liver Physiology ◽

10.1152/ajpgi.00234.2013 ◽

2014 ◽

Vol 306 (1) ◽

pp. G48-G58 ◽

Cited By ~ 34

Author(s):

Ann M. Bailey ◽

Le Zhan ◽

Dipen Maru ◽

Imad Shureiqi ◽

Curtis R. Pickering ◽

...

Keyword(s):

Dna Methylation ◽

Colon Cancer ◽

Epithelial To Mesenchymal Transition ◽

Human Colon ◽

Cancer Genome ◽

The Cancer Genome Atlas ◽

Human Colon Cancer ◽

Mesenchymal Transition ◽

Cancer Genome Atlas ◽

Genome Atlas

Farnesoid X receptor (FXR) is a bile acid nuclear receptor described through mouse knockout studies as a tumor suppressor for the development of colon adenocarcinomas. This study investigates the regulation of FXR in the development of human colon cancer. We used immunohistochemistry of FXR in normal tissue ( n = 238), polyps ( n = 32), and adenocarcinomas, staged I–IV ( n = 43, 39, 68, and 9), of the colon; RT-quantitative PCR, reverse-phase protein array, and Western blot analysis in 15 colon cancer cell lines; NR1H4 promoter methylation and mRNA expression in colon cancer samples from The Cancer Genome Atlas; DNA methyltransferase inhibition; methyl-DNA immunoprecipitation (MeDIP); bisulfite sequencing; and V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS) knockdown assessment to investigate FXR regulation in colon cancer development. Immunohistochemistry and quantitative RT-PCR revealed that expression and function of FXR was reduced in precancerous lesions and silenced in a majority of stage I-IV tumors. FXR expression negatively correlated with phosphatidylinositol-4, 5-bisphosphate 3 kinase signaling and the epithelial-to-mesenchymal transition. The NR1H4 promoter is methylated in ∼12% colon cancer The Cancer Genome Atlas samples, and methylation patterns segregate with tumor subtypes. Inhibition of DNA methylation and KRAS silencing both increased FXR expression. FXR expression is decreased early in human colon cancer progression, and both DNA methylation and KRAS signaling may be contributing factors to FXR silencing. FXR potentially suppresses epithelial-to-mesenchymal transition and other oncogenic signaling cascades, and restoration of FXR activity, by blocking silencing mechanisms or increasing residual FXR activity, represents promising therapeutic options for the treatment of colon cancer.

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Hedgehog Signal Inhibitor GANT61 Inhibits the Malignant Behavior of Undifferentiated Hepatocellular Carcinoma Cells by Targeting Non-Canonical GLI Signaling

International Journal of Molecular Sciences ◽

10.3390/ijms21093126 ◽

2020 ◽

Vol 21 (9) ◽

pp. 3126

Author(s):

Kensuke Harada ◽

Ryuya Ohashi ◽

Kyoko Naito ◽

Keita Kanki

Keyword(s):

Hepatocellular Carcinoma ◽

Molecular Mechanisms ◽

Epithelial Mesenchymal Transition ◽

Hepatoma Cell ◽

Mek Inhibitor ◽

Specific Expression ◽

Mesenchymal Transition ◽

Hepatoma Cell Lines ◽

And Migration ◽

Sphere Formation

The Hedgehog (HH)–GLI pathway plays an important role in cell dedifferentiation and is therefore pivotally involved in the malignant transformation of cancer cells. GANT61, a selective inhibitor of GLI1 and GLI2, was reported as a promising treatment for cancer in various tissues; however, the biological impact of GANT61 in hepatocellular carcinoma (HCC), especially in undifferentiated HCC cells, remains unclear. In this study, we investigated the antitumor effect of GANT61 using two undifferentiated hepatoma cell lines: HLE and HLF. Quantitative PCR and RT-PCR analyses revealed that these cells express GLI transcripts, showing mesenchymal phenotypes characterized by the loss of epithelial and hepatic markers and specific expression of epithelial–mesenchymal transition (EMT)-related genes. GANT61 significantly reduced the proliferation and cell viability after drug treatment using 5-FU and Mitomycin C. We showed that GLI transcript levels were down-regulated by the MEK inhibitor U0126 and the Raf inhibitor sorafenib, suggesting that non-canonical signaling including the Ras–Raf–MEK–ERK pathway is involved. Sphere formation and migration were significantly decreased by GANT61 treatment, and it is suggested that the underlying molecular mechanisms are the down-regulation of stemness-related genes (Oct4, Bmi1, CD44, and ALDH) and the EMT-related gene Snail1. The data presented here showed that direct inhibition of GLI might be beneficial for the treatment of dedifferentiated HCC.

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Molecular and Clinical Characterization of a Claudin-Low Subtype of Gastric Cancer

JCO Precision Oncology ◽

10.1200/po.17.00047 ◽

2017 ◽

pp. 1-10 ◽

Cited By ~ 1

Author(s):

Tomohiro F. Nishijima ◽

Jordan Kardos ◽

Shengjie Chai ◽

Christof C. Smith ◽

Dante S. Bortone ◽

...

Keyword(s):

Gastric Cancer ◽

Epithelial To Mesenchymal Transition ◽

The Cancer Genome Atlas ◽

Data Set ◽

Mesenchymal Transition ◽

Gene Sets ◽

Hazard Ratios ◽

Gene Predictor ◽

Cancer Genome Atlas

Purpose Claudin-low molecular subtypes have been identified in breast and bladder cancers and are characterized by low expression of claudins, enrichment for epithelial-to-mesenchymal transition (EMT), and tumor-initiating cell (TIC) features. We evaluated whether the claudin-low subtype also exists in gastric cancer. Materials and Methods Four hundred fifteen tumors from The Cancer Genome Atlas (TCGA) gastric cancer mRNA data set were clustered on the claudin, EMT, and TIC gene sets to identify claudin-low tumors. We derived a 24-gene predictor that classifies gastric cancer into claudin-low and non–claudin-low subtypes. This predictor was validated with the Asian Cancer Research Group (ACRG) data set. We characterized molecular and clinical features of claudin-low tumors. Results We identified 46 tumors that had consensus enrichment for claudin-low features in TCGA data set. Claudin-low tumors were most commonly diffuse histologic type (82%) and originally classified as TCGA genomically stable (GS) subtype (78%). Compared with GS subtype, claudin-low subtype had significant activation in Rho family of GTPases signaling, which appears to play a key role in its EMT and TIC properties. In the ACRG data set, 28 of 300 samples were classified as claudin-low tumors by the 24-gene predictor and were phenotypically similar to the initially derived claudin-low tumors. Clinically, claudin-low subtype had the worst overall survival. Of note, the hazard ratios that compared claudin-low versus GS subtype were 2.10 (95% CI, 1.07 to 4.11) in TCGA and 2.32 (95% CI, 1.18 to 4.55) in the ACRG cohorts, with adjustment for age and pathologic stage. Conclusion We identified a gastric claudin-low subtype that carries a poor prognosis likely related to therapeutic resistance as a result of its EMT and TIC phenotypes.

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

Epigenomics ◽

10.2217/epi-2019-0385 ◽

2020 ◽

Vol 12 (15) ◽

pp. 1303-1315

Author(s):

Weibo Du ◽

Wenbiao Chen ◽

Zheyue Shu ◽

Dairong Xiang ◽

Kefan Bi ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Copy Number ◽

Noncoding Rna ◽

Noncoding Rnas ◽

The Cancer Genome Atlas ◽

Differentially Expressed ◽

Prognostic Biomarkers ◽

Copy Number Alterations ◽

Sequencing Data ◽

Cancer Genome Atlas

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.

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Genomic characterization of rare molecular subclasses of hepatocellular carcinoma

Communications Biology ◽

10.1038/s42003-021-02674-1 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Jeffrey S. Damrauer ◽

Markia A. Smith ◽

Vonn Walter ◽

Aatish Thennavan ◽

Lisle E. Mose ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Copy Number ◽

Primary Liver Cancer ◽

Progression Free Survival ◽

The Cancer Genome Atlas ◽

Mutational Signatures ◽

Disease Biology ◽

Cancer Genome Atlas ◽

Genomic Characterization

AbstractPrimary liver cancer, consisting of both cholangiocarcinoma (CCA) and hepatocellular carcinoma (HCC), is the second leading cause of cancer deaths worldwide. Our goal is to genomically characterize rare HCC subclasses to provide insight into disease biology. Leveraging The Cancer Genome Atlas (TCGA) to perform a combined analysis of CCA (n = 36) and HCC (n = 275), we integrated multiple genomic platforms, to assess transcriptional profiles, mutational signatures, and copy number patterns to uncover underlying etiology and linage specific patterns. We identified two molecular classes distinct from prototypical HCC tumors. The first, CCA-Like, although histologically indistinguishable from HCC, had enrichment of CCA mutations (IDH1, BAP1), mutational signatures, and transcriptional patterns (SOX9, KRT19). CCA-Like, however, retained a copy number landscape similar to HCC, suggesting a hepatocellular linage. The second, Blast-Like, is enriched in TP53 mutations, HBV infection, exposure related mutational signatures and transcriptionally similar to hepatoblasts. Although these subclasses are molecularly distinct, they both have a worse progression-free survival compared to classical HCC tumors, yet are clinically treated the same. The identification of and characterization of CCA-Like and Blast-Like subclasses advance our knowledge of HCC as well as represents an urgent need for the identification of class specific biomarkers and targeted therapy.

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Sulfatase 2-Induced Cancer-Associated Fibroblasts Promote Hepatocellular Carcinoma Progression via Inhibition of Apoptosis and Induction of Epithelial-to-Mesenchymal Transition

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.631931 ◽

2021 ◽

Vol 9 ◽

Author(s):

Cong Wang ◽

Chuzhi Shang ◽

Xiaohong Gai ◽

Tao Song ◽

Shaoshan Han ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Signaling Pathway ◽

Epithelial To Mesenchymal Transition ◽

Akt Signaling ◽

The Cancer Genome Atlas ◽

Luciferase Reporter ◽

Akt Signaling Pathway ◽

Mesenchymal Transition ◽

Hcc Cells

BackgroundSulfatase 2 (SULF2) removes the 6-O-sulfate groups from heparan sulfate proteoglycans (HSPG) and consequently alters the binding sites for various signaling molecules. Here, we elucidated the role of SULF2 in the differentiation of hepatic stellate cells (HSCs) into carcinoma-associated fibroblasts (CAFs) in the hepatocellular carcinoma (HCC) microenvironment and the mechanism underlying CAF-mediated HCC growth.MethodsThe clinical relevance of SULF2 and CAFs was examined using in silico and immunohistochemical (IHC) analyses. Functional studies were performed to evaluate the role of SULF2 in the differentiation of HSCs into CAFs and elucidate the mechanism underlying CAF-mediated HCC growth. Mechanistic studies were performed using the chromatin immunoprecipitation, luciferase reporter, and RNA immunoprecipitation assays. The in vitro findings were verified using the nude HCC xenograft mouse model.ResultsThe Cancer Genome Atlas (TCGA) database and IHC analyses revealed that the expression of CAF markers, which was positively correlated with that of SULF2 in the HCC tissues, predicted unfavorable postsurgical outcomes. Co-culturing HSCs with HCC cells expressing SULF2 promoted CAF differentiation. Additionally, CAFs repressed HCC cell apoptosis by activating the SDF-1/CXCR4/PI3K/AKT signaling pathway. Meanwhile, SULF2-induced CAFs promoted epithelial-to-mesenchymal transition (EMT) of HCC cells by modulating the SDF-1/CXCR4/OIP5-AS1/miR-153-3p/SNAI1 axis. Studies using HCC xenograft mouse models demonstrated that OIP5-AS1 induced EMT by upregulating SNAI1 and promoted HCC growth in vivo.ConclusionThese data indicated that SULF2 secreted by the HCC cells induced the differentiation of HSCs into CAFs through the TGFβ1/SMAD3 signaling pathway. SULF2-induced CAFs attenuated HCC apoptosis by activating the SDF-1/CXCR4/PI3K/AKT signaling pathway and induced EMT through the SDF-1/CXCR4/OIP5-AS1/miR-153-3p/SNAI1 axis. This study revealed a novel mechanism involved in the crosstalk between HCC cells and CAFs in the tumor microenvironment, which can aid in the development of novel and efficient therapeutic strategies for primary liver cancer.

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A Four-Methylated lncRNAs-Based Prognostic Signature for Hepatocellular Carcinoma

Genes ◽

10.3390/genes11080908 ◽

2020 ◽

Vol 11 (8) ◽

pp. 908

Author(s):

Le-En Liao ◽

Dan-Dan Hu ◽

Yun Zheng

Keyword(s):

Hepatocellular Carcinoma ◽

Prediction Model ◽

Cell Lines ◽

Prediction Models ◽

Hepatoma Cell ◽

Critical Role ◽

The Cancer Genome Atlas ◽

Roc Curve Analysis ◽

Data Set ◽

Hepatoma Cell Lines

Currently, an increasing number of studies suggest that long non-coding RNAs (lncRNAs) and methylation-regulated lncRNAs play a critical role in the pathogenesis of various cancers including hepatocellular carcinoma (HCC). Therefore, methylated differentially expressed lncRNAs (MDELs) may be critical biomarkers of HCC. In this study, 63 MDELs were identified by screening The Cancer Genome Atlas (TCGA) HCC lncRNAs expression data set and lncRNAs methylation data set. Based on univariate and multivariate survival analysis, four MDELs (AC025016.1, LINC01164, LINC01183 and LINC01269) were selected to construct the survival prognosis prediction model. Through the PI formula, the study indicates that our new prediction model performed well and is superior to the traditional staging method. At the same time, compared with the previous prediction models reported in the literature, the results of time-dependent receiver operating characteristic (ROC) curve analysis show that our 4-MDELs model predicted overall survival (OS) stability and provided better prognosis. In addition, we also applied the prognostic model to Cancer Cell Line Encyclopedia (CCLE) cell lines and classified different hepatoma cell lines through the model to evaluate the sensitivity of different hepatoma cell lines to different drugs. In conclusion, we have established a new risk scoring system to predict the prognosis, which may have a very important guiding significance for the individualized treatment of HCC patients.

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