Integrated multi-dimensional analysis highlights DHCR7 mutations involving in cholesterol biosynthesis and contributing therapy of gastric cancer.

BACKGROUND: Genetic background plays an important role in the occurrence and development of gastric cancer (GC). With the application of genome-wide association study (GWAS), an increasing number of tumor susceptibility genes in gastric cancer have been discovered. While little of them can be further applicated in clinical diagnosis and treatment due to the lack of in-depth analysis. METHODS: A GWAS of peripheral blood leukocytes from GC patients was performed to identify and obtain genetic background data. In combination with a clinical investigation, key SNP mutations and mutated genes were screened. Via in vitro and in vivo experiments, the function of the mutated gene was verified in GC. Via a combination of molecular function studies and amino acid network analysis, co-mutations were discovered and further identified as potential therapeutic targets. RESULTS: At the genetic level, the G allele of rs104886038 in DHCR7 was a protective factor identified by the GWAS. Clinical investigation showed that patients with the rs104886038 A/G genotype, age ≥ 60, smoking ≥ 10 cigarettes/day, heavy drinking and H. pylori infection were independent risk factors for GC, with odds ratios of 12.33 (95% CI, 2.10 ~ 72.54), 20.42 (95% CI, 2.46 ~ 169.83), and 11.39 (95% CI, 1.82 ~ 71.21), respectively. Then molecular function studies indicated that DHCR7 regulated cell proliferation, migration, and invasion as well as apoptosis resistance via cellular cholesterol biosynthesis pathway. Further amino acid network analysis based on the predicted structure of DHCR7 and experimental verification indicated that rs104886035 and rs104886038 co-mutation reduced the stability of DHCR7 and induced its degradation. DHCR7 mutation suppressed the malignant behaviour of GC cells and induced apoptosis via inhibition on cell cholesterol biosynthesis. CONCLUSION: In this work, we provided a comprehensive multi-dimensional analysis strategy which can be applied to in-depth exploration of GWAS data. DHCR7 and its mutation sites identified by this strategy are potential theratic targets of GC via inhibition of cholesterol biosynthesis.

ELOVLs Predict Distinct Prognosis Value and Immunotherapy Efficacy In Patients With Hepatocellular Carcinoma.

Background: Hepatocellular carcinoma (HCC) is a primary malignancy of the liver with high prevalence worldwide and poor prognosis. It has been verified that elongation of very-long-chain fatty acids gene family (ELOVLs), a group of genes that responsible for elongation of saturated and polyunsaturated fatty acids, participate in the pathogenesis and development of multiplex disease including cancers. However, the functions and prognosis of ELOVLs in HCC are still indistinguishable. Methods: First, we searched the mRNA expression and survival data of ELOVLs in patients with HCC via the data of The Cancer Genome Atlas (TCGA). The prognosis value of ELOVLs on HCC was assessed by Kaplan-Meier plotter and Cox regression analysis. reverse transcription quantitative- polymerase chain reaction (RT-qPCR), Western blot (WB), and immunohistochemistry were applied to assess the specific mRNA and protein expression of ELOVLs in HCC clinical specimens of our cohort. Then, the functional enrichment of ELOVL1 especially the pathways relating to the immune was conducted utilizing the Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA) analysis. Additionally, TIMER, CIBERSOR, and tumor immune dysfunction and exclusion (TIDE) were employed to evaluate the relationship between ELOVL1 and immune responses. Last, the correlation of ELOVL1 with genome heterogeneity [microsatellite instability (MSI), tumor mutational burden (TMB), mutant-allele tumor heterogeneity (MATH), homologous recombination deficiency (HRD), purity, ploidy, loss of heterozygosity (LOH), and neoantigens] and mutational landscape were also evaluated basing on the date in TCGA. Results: Significant expression alteration was observed in ELOVLs family at the pan-cancer level. In liver cancer, ELOVL1 and ELOVL3 were strongly associated with poor prognosis of HCC by survival analysis and differential expression analysis. Immunohistochemistry microarray, WB, and RT-qPCR confirmed that ELOVL1 but not ELOVL3 played an important role in HCC. Mechanistically, functional network analysis revealed that ELOVL1 might be involved in the immune response. ELOVL1 could affect immune cell infiltration and immune checkpoint markers such as PD-1 and CTLA4 in HCC. Meanwhile, high expression of ELOVL1 would be insensitive to immunotherapy. Correlation analysis of immunotherapy markers showed that ELOVL1 has been associated with MSI, TMB, and oncogene mutations such as TP53. Conclusion: ELOVLs play distinct prognostic value in HCC. ELOVL1 could predict the poor prognosis and might be a potential indicator of immunotherapy efficacy in HCC patients.

Identification and validation of immune related core transcription factors GTF2I in NAFLD.

Background: Nonalcoholic fatty liver disease (NAFLD) is the most common liver disease worldwide that endangers human health. Transcription factors (TFs) have gradually become hot spots for drug development in NAFLD for their impacts on metabolism. However, the specific TFs that regulate immune response in the development of NAFLD is not clear. This study aimed to investigate the TFs involved in the immune response of NAFLD and provide novel targets for drug development. Methods: Microarray data were obtained from liver samples from 26 normal volunteers and 109 NAFLD patients using the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were analyzed by limma package. Differentially expressed transcription factors (DETFs) were obtained on DEGs combined with Cistrome Cancer database. Immune signatures and pathways hallmark were identified by ssGSSEA and GSVA. The co-regulation network was constructed by the above results. Further, quantitative Real-time Polymerase Chain Reaction (qRT-PCR), Western blot (WB) and Immunohistochemistry (IHC) were used to validate the relationship between GTF2I and NAFLD. CIBERSORT analysis was performed to identify cell types to explore the relationship between differential expression of GTF2I and immune cell surface markers. Results: A total of 617 DEGs and six DETFs (ESR1, CHD2, GTF2I, EGR1, HCFC1, SP2) were obtained by differential analysis. Immune signatures and pathway hallmarks were identified by ssGSSEA and GSVA. GTF2I and CHD2 were screened through the co-regulatory networks of DEGs, DETFs, immune signatures and pathway hallmarks. Furthermore, qRT-PCR, WB and IHC indicated that GTF2I but not CHD2 was significantly upregulated in NAFLD. Finally, in silico, our data confirmed that GTF2I has a wide impact on the immune profile by negatively regulating the expression of the chemokine receptor family (227/261, count of significance). Conclusion: GTF2I plays a role in NAFLD by negatively regulating the chemokine receptor family, which affects the immune profile. This study may provide a potential target for the diagnosis or therapy of NAFLD.

A clinical and laboratory-based nomogram for predicting nonalcoholic fatty liver disease in non-diabetic adults: a cross-sectional study.

BACKGROUND: Although the close relationship between nonalcoholic fatty liver disease (NAFLD) and insulin resistance has been clarified and there is a five-fold higher prevalence of NAFLD in patients with diabetes compared to that in patients without diabetes, this is not a reason to focus only on the incidence of NAFLD in people with diabetes because people who are insulin resistant are not necessarily diagnosed with diabetes, which leads to the overlook of NAFLD in non-diabetic population. Actually, we are obligated to pay more attention to the non-diabetic population for early detection and intervention of NAFLD. There is a lack of a convenient tool for predicting NAFLD in non-diabetic adults, and thus we aim to develop and validate a novel clinical nomogram to predict NAFLD among non-diabetic population to save more medical resources and make less missed diagnosis. METHODS: Researchers initially enrolled 20,944 patients and excluded those with history of drinking, known medication usage, viral hepatitis, known liver disease, missing covariant data, age <18 years, and impaired fasting blood glucose, leaving 14,251 adults participating in the baseline analysis, who were randomly divided in a ratio of 3:1 into a training dataset with 10,689 participants and a validation dataset with 3,562 participants, using the classification and regression training (caret) package in R software v. 4.0.3. Variables for prediction were selected by multivariable logistic regression analysis, the LASSO method, and clinical experience. Based on these, we constructed a prediction model. Performance of this model was validated by the area under the receiver operator characteristic curve, calibration curve, and decision curve analysis. RESULTS: We used 6 variables to construct the prediction model: body mass index (BMI), aspartate aminotransferase (AST), triglyceride (TG), high-density lipoprotein cholesterol (HDL-C), hemoglobin A1c (HbA1c), and diastolic blood pressure (DBP). In the training and validation datasets, the AUROC value of this prediction was 0.891 [95% confidence interval (CI): 0.884 to 0.899] and 0.902 (95% CI: 0.890 to 0.914), respectively. The calibration plots and the decision curve analysis (DCA) demonstrated that the accuracy of this model was good, with high clinical practicability. CONCLUSIONS: The nomogram could screen non-diabetic adults for NAFLD and may aid clinical decision-making.

The adiposity indicators in relation to diabetes among adults in China: a cross-sectional study from China Health and Nutrition Survey.

BACKGROUND: Diabetes is a metabolic disease which has been confirmed to be involved with abnormal or excessive body fat accumulation. There is still a lack of nationwide research in China to discuss the relationship between adiposity indicators included body mass index (BMI), waist circumference (WC), visceral adiposity index, waist-height ratio, waist-to-hip ratio (WHR) and diabetes. The question of which one is the best indicator of obesity to predict diabetes in China remains to be unclear. METHODS: Data were collected from the China Health and Nutrition Survey (CHNS) in 2009, including 7,930 participants aged over 18 years old for cross-sectional analysis. Information about height, weight, WC, hip circumference, smoking status, alcohol consumption, physical activity, energy intake and blood samples were analyzed. Binary logistic regression models were used to explore the association of WC, BMI, WHR, waist-to-height ration (WHtR) and visceral adipose index (VAI) with the prevalence of diabetes in the 2009 CHNS respectively. Predictive potential of five adiposity indicators was validated by the area under the receiver operator characteristic curve (AUROC). The optimal cut-off points were determined by Youden's index, which was used to estimate the performance of adiposity indicators. RESULTS: The study shows patients in the highest quartile were more likely to have diabetes than those in the lowest quartile of WC (OR: 4.237, 95% CI: 3.265-5.499), BMI (OR: 3.312, 95% CI: 2.601-4.218), WHR (OR: 3.199, 95% CI: 2.493-4.104), WHtR (OR: 3.760, 95% CI: 2.891-4.890), VAI (OR: 4.347, 95% CI: 3.411-5.541). The area under the receiver operator characteristic curve of WC, BMI, WHR, WHtR and VAI for diabetes was 0.700, 0.663, 0.668, and 0.697 and 0.694, respectively. The optimal cut-offs regarding diabetes in Chinese are WHtR ≥0.520 for men and VAI ≥1.878 for women. CONCLUSIONS: Our findings indicate that WC, WHtR, BMI, WHR and VAI are all independent risk factors for diabetes among Chinese adults. WHtR is the most accurate indicator for diabetes in men, while VAI for women.

Protective effects of gastrodin pretreatment on mouse hepatic ischemia-reperfusion occurring through antioxidant and anti-apoptotic mechanisms.

Hepatic ischemia-reperfusion injury (HIRI) often occurs following surgical procedures such as liver resection and transplantation. However, despite its clinical prominence, to the best of our knowledge, there remain no effective strategies to treat HIRI. Therefore, the aim of present study was to identify therapeutic agents that can exert beneficial effects against HIRI. The present study found that following hepatic IR modeling in mice, gastrodin (Gas) pretreatment improved the IR outcomes in terms of the serum biochemical indexes (alanine transaminase and aspartate transaminase), tissue biochemical indexes (superoxide dismutase, malondialdehyde and reduced glutathione content) and tissue pathology (H&E staining). In addition, compared with those in the IR + vehicle group, the IR + Gas group showed upregulated expression levels of nuclear erythroid 2-related factor 2, heme oxygenase 1 and Bcl-2 as detected by western blotting and reverse transcription-quantitative PCR. The mRNA and protein expression levels of Bax and caspase-3 were downregulated in the IR + Gas group compared with the IR + vehicle group. Concurrently, no significant differences were observed in the parameters between the Sham + vehicle and the Sham + Gas groups, indicating that Gas pretreatment may not cause liver damage. In conclusion, the findings of the present study revealed that Gas pretreatment exerted a protective effect in HIRI through both antioxidant and anti-apoptotic mechanisms.

Characterization of Grain Quality and Starch Fine Structure of Two Japonica Rice (Oryza Sativa) Cultivars with Good Sensory Properties at Different Temperatures during the Filling Stage.

Temperature during the growing season is a critical factor affecting grain quality. High temperatures at grain filling affect kernel development, resulting in reduced yield, increased chalkiness, reduced amylose content, and poor milling quality. Here, we investigated the grain quality and starch structure of two japonica rice cultivars with good sensory properties grown at different temperatures during the filling stage under natural field conditions. Compared to those grown under normal conditions, rice grains grown under hot conditions showed significantly reduced eating and cooking qualities, including a higher percentage of grains with chalkiness, lower protein and amylose contents, and higher pasting properties. Under hot conditions, rice starch contained reduced long-chain amylose (MW 10(7.1) to 10(7.4)) and significantly fewer short-chain amylopectin (DP 5-12) but more intermediate- (DP 13-34) and long- (DP 45-60) chain amylopectin than under normal conditions, as well as higher crystallinity and gelatinization properties.

SPE HG-AAS method for the determination of inorganic arsenic in rice--results from method validation studies and a survey on rice products.

The present paper describes the development, validation and application of a method for inorganic arsenic (iAs) determination in rice samples. The separation of iAs from organoarsenic compounds was done by off-line solid-phase extraction (SPE) followed by hydride generation atomic absorption spectrometry (HG-AAS) detection. This approach was earlier developed for seafood samples (Rasmussen et al., Anal Bioanal Chem 403:2825-2834, 2012) and has in the present work been tailored for rice products and further optimised for a higher sample throughput and a lower detection limit. Water bath heating (90 °C, 60 min) of samples with dilute HNO3 and H2O2 solubilised and oxidised all iAs to arsenate (As(V)). Loading of buffered sample extracts (pH 6 ± 1) followed by selective elution of arsenate from a strong anion exchange SPE cartridge enabled the selective iAs quantification by HG-AAS, measuring total arsenic (As) in the SPE eluate. The in-house validation gave mean recoveries of 101-106% for spiked rice samples and in two reference samples. The limit of detection was 0.02 mg kg(-1), and repeatability and intra-laboratory reproducibility were less than 6 and 9%, respectively. The SPE HG-AAS method produced similar results compared to parallel high-performance liquid chromatography coupled to inductively coupled plasma mass spectrometry (ICP-MS) analysis. The SPE separation step was tested collaboratively, where the laboratories (N = 10) used either HG-AAS or ICP-MS for iAs determination in a wholemeal rice powder. The trial gave satisfactory results (HorRat value of 1.6) and did not reveal significant difference (t test, p > 0.05) between HG-AAS and ICP-MS quantification. The iAs concentration in 36 rice samples purchased on the Danish retail market varied (0.03-0.60 mg kg(-1)), with the highest concentration found in a red rice sample.