A replication study of genome-wide CNV association for hepatic biomarkers identifies nine genes associated with liver function

Kim, Hyo‐Young; Byun, Mi-Jeong; Kim, Heebal

doi:10.5483/bmbrep.2011.44.9.578

Cited by 6 publications

(3 citation statements)

References 33 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Consistent with previous studies, the hepatic histological damage was observed in DSS-induced murine colitis model ( 43 , 44 ). AST and ALT always seemed like sensitive indicators to access the hepatic damage ( 45 , 46 ). Here our results revealed the increased plasma and hepatic levels of AST and ALT in acute colitis mice.…”

Section: Discussionmentioning

confidence: 99%

Milk Fat Globule Membrane Attenuates Acute Colitis and Secondary Liver Injury by Improving the Mucus Barrier and Regulating the Gut Microbiota

Liu

Huang

et al. 2022

Front. Immunol.

View full text Add to dashboard Cite

ObjectiveInflammatory bowel disease (IBD) often occurs along with extraintestinal manifestations, including hepatic injury. Milk fat globule membrane (MFGM) is an active substance with a potential anti-inflammation activity. However, its alleviated effect and mechanisms in IBD as well as the IBD-induced secondary liver injury are still unclear.MethodsC57BL/6J mice were administered with a 21-day oral gavage of MFGM, followed by 7 days of drinking water with 4% dextran sulfate sodium (DSS). Disease activity index (DAI), histological features, and cytokines of the colon and liver were evaluated. Then, RNA-seq of the colon and liver was conducted. The gut microbiota was assessed by analyzing 16S rRNA gene sequences, and finally the integrity and the function of the mucus barrier were evaluated by Alcian blue staining, real-time quantitative PCR, and ELISA.ResultsProphylactic MFGM treatment was effective against colitis to include effects in body weight loss, DAI score, colonic length, intestinal pathology, and histological score. Additionally, prophylactic MFGM decreased the levels of interleukin (IL)-1β, IL-6, and myeloperoxidase in colonic tissue, while it increased the IL-10 level. Moreover, the gene expressions of MUC2, MUC4, Reg3b, and Reg3g associated with the production of the molecular mediator of immune response, membrane invagination, and response to protozoan were strikingly upregulated when administered with MFGM. On the other hand, the beneficial effects of MFGM were related to the enriched abundance of genera such as Faccalibacumum and Roseburia in feces samples. Consistently, the administration of MFGM was also found to alleviate DSS-induced hepatic injury. Furthermore, the glutathione transferase activity pathway was enriched in the liver of MFGM-treated mice after DSS administration. Mechanistically, prophylactic MFGM enhanced the mucosal barrier by increasing the gene levels of Reg3b and Reg3g. Meanwhile, the alleviation of MFGM on liver injury was dependent on the reduced hepatic oxidative stress.ConclusionsMFGM attenuated colitis and hepatic injury by maintaining the mucosal barrier and bacterial community while inhibiting oxidative stress, which might be an effective therapy of hepatic injury secondary to IBD.

show abstract

Section: Discussionmentioning

confidence: 99%

Milk Fat Globule Membrane Attenuates Acute Colitis and Secondary Liver Injury by Improving the Mucus Barrier and Regulating the Gut Microbiota

Liu

Huang

et al. 2022

Front. Immunol.

View full text Add to dashboard Cite

show abstract

“…The VCS tool provides a graphical view of the physical distribution of CNV or SNP on chromosomes. Any marker contained information of chromosomal position by point (SNP) or specific ranges (CNV, miRNA, and repeat sequence) can be used in this tool ( Kim et al, 2010 ; 2011 ; 2013 ). This menu is useful for comparing the physical distribution of your own CNV or SNP.…”

Section: Program Overviewmentioning

confidence: 99%

VCS: Tool for Visualizing Copy Number Variation and Single Nucleotide Polymorphism

Kim

Sung

Cho

et al. 2014

Asian Australas. J. Anim. Sci

View full text Add to dashboard Cite

Copy number variation (CNV) or single nucleotide phlyorphism (SNP) is useful genetic resource to aid in understanding complex phenotypes or deseases susceptibility. Although thousands of CNVs and SNPs are currently avaliable in the public databases, they are somewhat difficult to use for analyses without visualization tools. We developed a web-based tool called the VCS (visualization of CNV or SNP) to visualize the CNV or SNP detected. The VCS tool can assist to easily interpret a biological meaning from the numerical value of CNV and SNP. The VCS provides six visualization tools: i) the enrichment of genome contents in CNV; ii) the physical distribution of CNV or SNP on chromosomes; iii) the distribution of log2 ratio of CNVs with criteria of interested; iv) the number of CNV or SNP per binning unit; v) the distribution of homozygosity of SNP genotype; and vi) cytomap of genes within CNV or SNP region.

show abstract

“…It manifests divergent expression patterns in conditions such as pulmonary adenocarcinoma (9) and cerebral glioma (10) , demonstrating a correlation with immune in ltration within tumour cells. Concurrently, extant studies have shown an association between PSMC6 and aspartate aminotransferase (AST), indicating that PSMC6 is a pivotal factor in uencing disease onset within the hepatic milieu (11) . Nevertheless, the PSMC6 domain remains a lacuna in HCC.…”

Section: Introductionmentioning

confidence: 99%

PSMC6 as a Potential Novel Prognostic and Diagnostic Marker in Hepatocellular Carcinoma Associated with Immune Infiltration and Drug Sensitivity

Li,

Wei

et al. 2023

Preprint

View full text Add to dashboard Cite

Objective: ATPase proteasome 26S subunit 6(PSMC6), a member of the 19S regulatory subunit of the 26S proteasome. It catalyszes bears the responsibility of catalyzing the unfolding and translocation of substrates into the confines of the 20S proteasome. It has shown its ascending significance in multiple cancers such as Lung adenocarcinoma, Glioma, and Breast invasive carcinoma. However, no systematic analysis has been conducted to explore its function hepatocellular carcinoma (HCC). in this study, we explored the relationship between PSMC6 expression in the HCC and clinical prognosis, immune infiltration, and drug sensitivity. METHODS: We analyzed RNA expression data of patients with HCC from The Cancer Genome Atlas (TCGA) and GEO databases to explore the value of PSMC6 mRNA expression in clinical prognosis. Quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) and western blotting were employed to validate PSMC6 expression at the mRNA and protein levels. We then investigated cell viability and migratory ability by CCK8 and transwell assay, respectively. Results: The expression of PSMC6 in HCC tumor tissues was significantly higher than that in normal tissues (p < 0.001). PSMC6 expression was closely correlated with immune cell infiltration. Twelve sensitive drugs were screened in the PSMC6 high-expression group, and further experiments confirmed that the mRNA and protein expression levels of PSMC6 in HCC cells were upregulated. PSMC6 knockdown by Small interfering RNA significantly reduced HCC cancer cell viability and invasion . CONCLUSION: PSMC6 may be used as a novel prognostic marker, which and can help be used to formulate personalized treatments for HCC patients.

show abstract

A replication study of genome-wide CNV association for hepatic biomarkers identifies nine genes associated with liver function

Cited by 6 publications

References 33 publications

Milk Fat Globule Membrane Attenuates Acute Colitis and Secondary Liver Injury by Improving the Mucus Barrier and Regulating the Gut Microbiota

Milk Fat Globule Membrane Attenuates Acute Colitis and Secondary Liver Injury by Improving the Mucus Barrier and Regulating the Gut Microbiota

VCS: Tool for Visualizing Copy Number Variation and Single Nucleotide Polymorphism

PSMC6 as a Potential Novel Prognostic and Diagnostic Marker in Hepatocellular Carcinoma Associated with Immune Infiltration and Drug Sensitivity

Contact Info

Product

Resources

About