Project description:Although hepatocellular carcinoma (HCC) has been subjected to continuous investigation and its symptoms are well-known, early stage diagnosis of this disease remains difficult and the survival rate after diagnosis is typically very low (3−5%). Early and accurate detection of metabolic changes in the sera of patients with liver cirrhosis can help improve the prognosis of HCC and lead to a better understanding of its mechanism at the molecular level, thus providing patients with in-time treatment of the disease. In this study, we compared metabolite levels in sera of 40 HCC patients and 49 cirrhosis patients from Egypt by using ultraperformance liquid chromatography coupled with quadrupole time-of-flight mass spectrometer (UPLC-QTOF MS). Following data preprocessing, the most relevant ions in distinguishing HCC cases from cirrhotic controls are selected by statistical methods. Putative metabolite identifications for these ions are obtained through mass-based database search. The identities of some of the putative identifications are verified by comparing their MS/MS fragmentation patterns and retention times with those from authentic compounds. Finally, the serum samples are reanalyzed for quantitation of selected metabolites as candidate biomarkers of HCC. This quantitation was performed using isotope dilution by selected reaction monitoring (SRM) on a triple quadrupole linear ion trap (QqQLIT) coupled to UPLC. Statistical analysis of the UPLC-QTOF data identified 274 monoisotopic ion masses with statistically significant differences in ion intensities between HCC cases and cirrhotic controls. Putative identifications were obtained for 158 ions by mass based search against databases. We verified the identities of selected putative identifications including glycholic acid (GCA), glycodeoxycholic acid (GDCA), 3β, 6β-dihydroxy-5β-cholan-24-oic acid, oleoyl carnitine, and Phe-Phe. SRM-based quantitation confirmed significant differences between HCC and cirrhotic controls in metabolite levels of bile acid metabolites, long chain carnitines and small peptide. Our study provides useful insight into appropriate experimental design and computational methods for serum biomarker discovery using LC−MS/MS based metabolomics. This study has led to the identification of candidate biomarkers with significant changes in metabolite levels between HCC cases and cirrhotic controls. This is the first MS-based metabolic biomarker discovery study on Egyptian subjects that led to the identification of candidate metabolites that discriminate early stage HCC from patients with liver cirrhosis.

Project description:Background: Hepatocellular carcinoma (HCC) is one of the most common malignant tumors worldwide, with unclear pathogenesis. Sphingomyelin phodiesterase acid-like 3A (SMPDL3A) affects cell differentiation and participates in immune regulation. However, its molecular biological function in HCC has not yet been elucidated. Methods：Data from 180 HCC patients were analyzed the relationship between the expression of SMPDL3A in liver cancer tissues and the prognosis of liver cancer patients. Crispr-Cas9 dual vector lentivirus was used to knock out SMPDL3A in HCC cell lines. The effects of SMPDL3A on cell viability were determined by CCK8 assay, clone formation experiment, cell cycle assay, cell scratch, TUNEL experiment and flow cytometry. Xenograft tumor assays in BALB/c nude mice confirmed that SMPDL3A promoted tumor growth and in vivo. Preliminary exploration of SMPDL3A interacting protein by mass spectrometry analysis and co-immunoprecipitation. Results: This study showed that the expression of SMPDL3A in HCC tissue differed from that in tumor-adjacent tissues. Moreover, the overall survival rate and tumor-free survival rate of patients with high-SMPDL3A expression were significantly lower than those with low-SMPDL3A expression. SMPDL3A expression was closely related to the level of protein induced by PIVKA-II, liver cirrhosis, tumor diameter, microvascular invasion, and Barcelona clinic liver cancer staging. Thus, SMPDL3A is an independent risk factor that affects the tumor-free survival rate and overall survival rate of HCC patients. In vitro study using Crispr-Cas9 genome editing technology revealed the knockout effect of SMPDL3A on cell proliferation, apoptosis, and migration. Cell counting kit-8 assay and clone formation experiment showed that sgSMPDL3A inhibited tumor cell proliferation and migration. Flow cytometry and TUNEL assay showed that sgSMPDL3A promoted apoptosis in tumors. Moreover, sgSMPDL3A inhibited tumor growth during subcutaneous tumor formation in nude mice. Immunohistochemistry of Ki67 and PNCA also indicated that sgSMPDL3A inhibited subcutaneous tumor proliferation in tumor-bearing nude mice. Further experiments showed that SMPDL3A interacts with the enhancer of rudimentary homolog (ERH). Conclusions: High-SMPDL3A expression was related to poor prognosis of patients with HCC. Knockout of SMPDL3A inhibited the proliferation and migration and accelerated the migration of HCC cells. SMPDL3A interacted with ERH to affect the tumorigenesis and progression of HCC.

Project description:Development of targeted therapeutics for hepatocellular carcinoma (HCC) remains a major challenge. We have previously demonstrated that constitutively photomorphogenic 1 (COP1), which regulates p53 activity by ubiquitination, is frequently overexpressed in human HCC. Here we examined whether molecular targeting of COP1 by small interfering (si) RNA can affect the course of HCC progression. COP1-1 was selected as the most effective target siRNAs in terms of growth inhibition and apoptotic induction in several HCC cell lines. Interestingly, the growth inhibition occurred both in HCC cells that retain wild-type p53 or express mutant p53 (Y220C or R249S). Next we have determined to investigate the molecular mechanisms underlying the phenotypic changes. Given the recent findings that COP1 functions as a negative regulator of p53, we addressed whether the phenotypic changes caused by COP1 silencing were due to alterations in p53 and/or p21 status. Indeed, in COP1-depleted HepG2 cells expressing wild type p53, induction of apoptosis was associated with restoration of p53 function as judged by a marked increase in the levels of p53 and its target p21, suggesting that cell death was p53-dependent. However, the COP1 silencing in Huh7 cells, which carry Y220C mutation, caused a strong induction of apoptosis without changing p53 levels. To further address this issue, we next looked for the global transcriptional changes underlying the antitumor effects of COP1 silencing in HCC cells [with different p53 status]. For this purpose, Huh7 and HepG2 were treated with NCsiRNA and COP1-1siRNA for 48 hours and subjected to illumina microarray analysis. We found that the number of differentially expressed genes which displayed more than a 2-fold change (P < 0.01 by Bootstrap t-test) was 462 (167 up- and 295 down-regulated genes) and 522 (179 up- and 343 down-regulated genes) in COP1siRNA-treated Huh7 and HepG2 cells, respectively. As expected, the expression levels of RFWD2 (COP1) mRNA were significantly reduced in both treated HCC cell lines. Consistent with phenotypic changes, COP1-depleted Huh7 cells also displayed changes in p53-associated group of genes functionally involved in regulation of apoptosis, growth and differentiation including CASP6, GLIPR1, FHL2, GADD45A, HMOX1 BCL6, FOXO3, GDF15, and SCNN1A genes. Finally, we generated the common COP1 knockdown gene signature which included 78 genes. The Ingenuity Pathway Analysis analysis revealed that the 5 top putative networks with high score (>19) were strongly associated with NF-ÎºB, HNF4Î±, TNF, and p53 pathways, suggesting that a common subset of molecular alterations in the diverse oncogenic pathways may cooperatively result in growth inhibition of HCC cells with wild type and mutant p53. Analysis of COP1 knockdown gene expression signatures by microarray revealed that the anti-proliferative effect was driven by a common subset of molecular alterations including p53-associated functional network. Systemic delivery of a modified COP1siRNA by stable-nucleic-acid-lipid-particles (SNALP) significantly suppressed neoplastic growth in liver, without unwanted immune response in an orthotopic xenograft model. These findings provide the first proof of principle that COP1 is a promising target for systemic therapy of HCC. Microarray was performed on human Ref-8v3 microarrays (illumina) as recommended by the manufacture. In detail, total RNAs were isolated 48 h after the transfection of NCsiRNA or COP1-1siRNA to Huh7, HepG2 or Hep3B cells. Biotin-labeled cRNA was linearly amplified according to manufacturerâs specification (AMIL1791; Ambion, Austin, TX). As input, 200 ng total RNA from tumor was used for the in vitro transcription (IVT) reactions which were incubated for 16 h at 37 ÂºC. The efficiency of this single round amplification was measured by NanoDrop (ND1000, Thermo Scientific). Hybridization, washing, detection (Cy3-streptavidin, Amersham Biosciences, GE Healthcare) and scanning were performed on an Illumina iScan system (Illumina) using reagents and following protocols supplied by the manufacturer. Briefly, the biotinylated cRNA (750 ng/sample) was hybridized on Sentrix whole genome beadchips human Ref-8v3 for 18 h at 58ÂºC while rocking (5 rpm). The beadchip covers ~ 24,000 RefSeq transcripts. Image analysis and data extraction were performed automatically using Illumina GenomeScan Software. To explore the functional relationships among the genes with altered expression in the HCC cells treated with COP1-1siRNA, a pathway analysis was carried out with the Ingenuity Pathway Analysis tool (Ingenuity Systems). Using the approach, we examined functional associations among genes and generated the gene networks with high significance on the basis that they had more of the interconnected genes present than would be expected by chance. The significance of each network was estimated by scoring system provided by Ingenuity. The scores are determined by the number of differentially expressed genes within each of the networks and the strength of the associations among network members. Once over-represented genes that are functionally relevant in gene networks are identified, we validated their functional association by using the independent pathway analysis tool PathwayStudio (Ariadne Genomics).

Project description:Development of targeted therapeutics for hepatocellular carcinoma (HCC) remains a major challenge. We have previously demonstrated that constitutively photomorphogenic 1 (COP1), which regulates p53 activity by ubiquitination, is frequently overexpressed in human HCC. Here we examined whether molecular targeting of COP1 by small interfering (si) RNA can affect the course of HCC progression. COP1-1 was selected as the most effective target siRNAs in terms of growth inhibition and apoptotic induction in several HCC cell lines. Interestingly, the growth inhibition occurred both in HCC cells that retain wild-type p53 or express mutant p53 (Y220C or R249S). Next we have determined to investigate the molecular mechanisms underlying the phenotypic changes. Given the recent findings that COP1 functions as a negative regulator of p53, we addressed whether the phenotypic changes caused by COP1 silencing were due to alterations in p53 and/or p21 status. Indeed, in COP1-depleted HepG2 cells expressing wild type p53, induction of apoptosis was associated with restoration of p53 function as judged by a marked increase in the levels of p53 and its target p21, suggesting that cell death was p53-dependent. However, the COP1 silencing in Huh7 cells, which carry Y220C mutation, caused a strong induction of apoptosis without changing p53 levels. To further address this issue, we next looked for the global transcriptional changes underlying the antitumor effects of COP1 silencing in HCC cells [with different p53 status]. For this purpose, Huh7 and HepG2 were treated with NCsiRNA and COP1-1siRNA for 48 hours and subjected to illumina microarray analysis. We found that the number of differentially expressed genes which displayed more than a 2-fold change (P < 0.01 by Bootstrap t-test) was 462 (167 up- and 295 down-regulated genes) and 522 (179 up- and 343 down-regulated genes) in COP1siRNA-treated Huh7 and HepG2 cells, respectively. As expected, the expression levels of RFWD2 (COP1) mRNA were significantly reduced in both treated HCC cell lines. Consistent with phenotypic changes, COP1-depleted Huh7 cells also displayed changes in p53-associated group of genes functionally involved in regulation of apoptosis, growth and differentiation including CASP6, GLIPR1, FHL2, GADD45A, HMOX1 BCL6, FOXO3, GDF15, and SCNN1A genes. Finally, we generated the common COP1 knockdown gene signature which included 78 genes. The Ingenuity Pathway Analysis analysis revealed that the 5 top putative networks with high score (>19) were strongly associated with NF-κB, HNF4α, TNF, and p53 pathways, suggesting that a common subset of molecular alterations in the diverse oncogenic pathways may cooperatively result in growth inhibition of HCC cells with wild type and mutant p53. Analysis of COP1 knockdown gene expression signatures by microarray revealed that the anti-proliferative effect was driven by a common subset of molecular alterations including p53-associated functional network. Systemic delivery of a modified COP1siRNA by stable-nucleic-acid-lipid-particles (SNALP) significantly suppressed neoplastic growth in liver, without unwanted immune response in an orthotopic xenograft model. These findings provide the first proof of principle that COP1 is a promising target for systemic therapy of HCC.

Project description:Characterizing the metabolic changes pertaining to hepatocellular carcinoma (HCC) in patients with liver cirrhosis is believed to contribute towards early detection, treatment, and understanding of the molecular mechanisms of HCC. In this study, we compare metabolite levels in sera of 78 HCC cases with 184 cirrhotic controls by using ultra performance liquid chromatography coupled with a hybrid quadrupole time-of-flight mass spectrometry (UPLC-QTOF MS). Following data preprocessing, the most relevant ions in distinguishing HCC cases from patients with cirrhosis are selected by parametric and non-parametric statistical methods. Putative metabolite identifications for these ions are obtained through mass-based database search. Verification of the identities of selected metabolites is conducted by comparing their MS/MS fragmentation patterns and retention time with those from authentic compounds. Quantitation of these metabolites is performed in a subset of the serum samples (10 HCC and 10 cirrhosis) using isotope dilution by selected reaction monitoring (SRM) on triple quadrupole linear ion trap (QqQLIT) and triple quadrupole (QqQ) mass spectrometers. The results of this analysis confirm that metabolites involved in sphingolipid metabolism and phospholipid catabolism such as sphingosine-1-phosphate (S-1-P) and lysophosphatidylcholine (lysoPC 17:0) are up-regulated in sera of HCC vs. those with liver cirrhosis. Down-regulated metabolites include those involved in bile acid biosynthesis (specifically cholesterol metabolism) such as glycochenodeoxycholic acid 3-sulfate (3-sulfo-GCDCA), glycocholic acid (GCA), glycodeoxycholic acid (GDCA), taurocholic acid (TCA), and taurochenodeoxycholate (TCDCA). These results provide useful insights into HCC biomarker discovery utilizing metabolomics as an efficient and cost-effective platform. Our work shows that metabolomic profiling is a promising tool to identify candidate metabolic biomarkers for early detection of HCC cases in high risk population of cirrhotic patients.

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Effects of ARHGEF2 knockdown on gene expression in Hepatocellular Carcinoma HepG2 cells

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