An empirical likelihood ratio test robust to individual heterogeneity for differential expression analysis of RNA-seq.

The individual sample heterogeneity is one of the biggest obstacles in biomarker identification for complex diseases such as cancers. Current statistical models to identify differentially expressed genes between disease and control groups often overlook the substantial human sample heterogeneity. Meanwhile, traditional nonparametric tests lose detailed data information and sacrifice the analysis power, although they are distribution free and robust to heterogeneity. Here, we propose an empirical likelihood ratio test with a mean-variance relationship constraint (ELTSeq) for the differential expression analysis of RNA sequencing (RNA-seq). As a distribution-free nonparametric model, ELTSeq handles individual heterogeneity by estimating an empirical probability for each observation without making any assumption about read-count distribution. It also incorporates a constraint for the read-count overdispersion, which is widely observed in RNA-seq data. ELTSeq demonstrates a significant improvement over existing methods such as edgeR, DESeq, t-tests, Wilcoxon tests and the classic empirical likelihood-ratio test when handling heterogeneous groups. It will significantly advance the transcriptomics studies of cancers and other complex disease.

Association of METS-IR index with prevalence of gallbladder stones and the age at the first gallbladder stone surgery in US adults: A cross-sectional study.

Objective: The purpose of this study was to assess the correlation between the metabolic score for insulin resistance (METS-IR) index and gallbladder stoneprevalence in US adults, as well as the age at first gallbladder stone surgery. Methods: A logistic regression analysis, subgroup analysis, and dose-response curve were computed for participants in the 2017-2018 National Health and Nutrition Examination Survey (NHANES) to assess the relationship between the METS-IR index and gallbladder stone prevalence and age at first surgery for gallbladder stones. Results: This study ultimately included 9452 participants aged >20 years, of whom 534 self-reported a history of gallbladder stones, and after adjusting for all confounders, each unit increase in METS-IR index was associated with a 3.3% increase in gallbladder stone prevalence (OR= 1.033, 95% CI: 1.0258, 1.0403) along with an earlier age at first gallbladder stone surgery 0.26 years (ß= -0.26, 95% CI: -0.35, -0.17), stratified analysis showed that increased METS-IR index was associated with increased prevalence of gallbladder stones in all subgroups, and the dose-response curve showed a positive linear correlation between METS-IR index and prevalence of gallbladder stones, while a negative linear correlation was observed between increased METS-IR index and age at first gallbladder stone There was a negative linear correlation between age at surgery. Conclusion: The METS-IR index has been positively associated with gallbladder stone prevalence, thereby contributing to age at first surgery for gallbladder stones. However, the causal relationship between the METS-IR and gallbladder stones cannot be concluded.

MiR-590 Suppresses Proliferation and Induces Apoptosis in Pancreatic Cancer by Targeting High Mobility Group A2.

BACKGROUND: Pancreatic ductal adenocarcinoma is a common malignancy with high morbidity. MicroRNAs have been demonstrated to be critical posttranscriptional regulators in tumorigenesis. This study aimed to investigate the effect of microRNA-590 on the proliferation and apoptosis of pancreatic ductal adenocarcinoma. MATERIAL AND METHODS: The expression of microRNA-590 and high mobility group AT-hook 2 were examined in clinical pancreatic ductal adenocarcinoma tissues. Pancreatic ductal adenocarcinoma cell line Capan-2 was employed and transfected with microRNA-590 mimics or inhibitor. The correlation between microRNA-590 and high mobility group AT-hook 2 was verified by luciferase reporter assay. Cell viability and apoptosis were detected by MTT and flow cytometry assay. The protein level of high mobility group AT-hook 2, AKT, p-AKT, mTOR, and phosphorylated mTOR were analyzed by Western blotting. RESULTS: MicroRNA-590 was found to be negatively correlated with the expression of high mobility group AT-hook 2 in pancreatic ductal adenocarcinoma tissues. Further studies identified high mobility group AT-hook 2 as a direct target of microRNA-590. Moreover, overexpression of microRNA-590 downregulated expression of high mobility group AT-hook 2, reduced cell viability, and promoted cell apoptosis, while knockdown of miR-590 led to an inverse result. MicroRNA-590 also suppressed the phosphorylation of AKT and mTOR without altering total AKT and mTOR levels. CONCLUSION: Our study indicated that microRNA-590 negatively regulates the expression of high mobility group AT-hook 2 in clinical specimens and in vitro. MicroRNA-590 can inhibit cell proliferation and induce cell apoptosis in pancreatic ductal adenocarcinoma cells. This regulatory effect of microRNA-590 may be associated with AKT signaling pathway. Therefore, microRNA-590 has the potential to be used as a biomarker for predicting the progression of pancreatic ductal adenocarcinoma.

miR-410 acts as an oncogene in colorectal cancer cells by targeting dickkopf-related protein 1 via the Wnt/ß-catenin signaling pathway.

Colorectal cancer (CRC) is a common malignancy with high morbidity. MicroRNAs (miRNAs or miRs) have been demonstrated to be critical post-transcriptional regulators in tumorigenesis. The current study aimed to investigate the effect of miR-410 on the proliferation and metastasis of CRC. The expression of miR-410 was examined in CRC cell lines. SW-480 and HCT-116 CRC cell lines were employed and transfected with miR-410 inhibitor or miR-410 mimics. The association between miR-410 and dickkopf-related protein 1 (DKK-1) was verified by luciferase reporter assay. Cell viability and apoptosis were detected by Cell Counting Kit-8 (CCK-8) and flow cytometry assay. Cell migration and invasion capacity were determined by Transwell assay. The protein level of DKK1, ß-catenin and phosphorylated glycogen synthase kinase-3ß (pGSK-3ß) were analyzed by western blotting. miR-410 was revealed to be upregulated in CRC cell lines. Further studies identified DKK-1 as a direct target of miR-410. In addition, knockdown of miR-410 promoted the expression of DKK, inhibited CRC cell proliferation, migration and invasion capacity, and induced cell apoptosis, while overexpression of miR-410 reversed these results. miR-410 silencing also decreased ß-catenin and pGSK-3ß levels. The current study indicated that miR-410 negatively regulates the expression of DKK-1 in vitro. miR-410 promotes malignancy phenotypes in CRC cell lines. This regulatory effect of miR-410 may be associated with the Wnt/ß-catenin signaling pathway. Therefore, miR-410 could be used as a biomarker for predicting the progression of CRC.