Biology subjects

Yao, L.

Publications and source records attributed to Yao, L..

3 recordsLinked to original sources

bioRxiv2018

Increased H. pylori stool shedding and EPIYA-D cagA alleles are associated with gastric cancer in an East Asian hospital

BackgroundHelicobacter pylori infection induces chronic inflammation and tissue damage in the stomach, increasing risk for gastric cancer. Paradoxically, these tissue alterations may promote loss of H. pylori infection during cancer progression. H. pyloris role in cancer progression beyond initiation is unclear. Geographic variation in gastric cancer risk has been attributed to variation in carriage and type of the H. pylori oncogene cagA.\n\nMethodsTo investigate possible differences in H. pylori load in the stomach and shedding in stool, H. pylori load and cagA genotype were assessed using droplet digital PCR assays on gastric mucosa and stool samples from 49 urea breath test-positive individuals, including 25 gastric cancer and 24 non-cancer subjects at Henan Cancer Hospital, Henan, China.\n\nResultsQuantitation of H. pylori DNA indicated similar gastric loads among cancer and non-cancer cases, but the gastric cancer group had a median H. pylori load in the stool that was six times higher than that of the non-cancer subjects. While the cagA gene was uniformly present among study subjects, only 70% had the East Asian cagA allele, which was significantly associated with gastric cancer (Fishers Exact Test, p = 0.03).\n\nConclusionH. pylori persists in a subset of gastric cancer cases and thus may contribute to cancer progression. In this East Asian population with a high prevalence of the cagA gene, the East Asian allele could still provide a marker for gastric cancer risk.\n\nImpactThis study contributes to our understanding of H. pylori dynamics in the context of pathological changes.

microbiology↗

bioRxiv2017

Enhancer Linking by Methylation/Expression Relationships with the R package ELMER version 2

MotivationDNA methylation has been used to identify functional changes at transcriptional enhancers and other cis-regulatory modules (CRMs) in tumors and other disease tissues. Our R/Bioconductor package ELMER (Enhancer Linking by Methylation/Expression Relationships) provides a systematic approach that reconstructs altered gene regulatory networks (GRNs) by combining enhancer methylation and gene expression data derived from the same sample set.\n\nResultsWe present a completely revised version 2 of ELMER that provides numerous new features including an optional web-based interface and a new Supervised Analysis mode to use pre-defined sample groupings. We show that this approach can identify GRNs associated with many new Master Regulators including KLF5 in breast cancer.\n\nAvailabilityELMER v.2 is available as an R/Bioconductor package at http://bioconductor.org/packages/ELMER/

bioinformatics↗

bioRxiv2017

The effect of dietary ginseng polysaccharide supplementation on the immune responses involved in porcine milk-derived esRNAs

Ginseng and its polysaccharides (GPS) have been well known as an immune modulator. This study was conducted to investigate the effects of dietary supplemental GPS on the immune responses involved in sows milk-derived exosomal shuttle RNAs (esRNAs) using RNA-Seq and miRNA-Seq. Of the 213 identified miRNA types, a total of 26 conserved miRNAs were differently expressed in response to GPS supplementation, including 10 up-regulated and 16 down-regulated miRNAs in GPS feeding group. In addition, exosomal transcriptome analysis identified 14,696 protein-coding genes in sows milk exosomes, and 283 genes with 204 and 79 candidates showing up and down-regulation were significantly responded to GPS supplementation. Integrated analysis of each differently expressed miRNA with significantly expressed genes further revealed the presence of 51 highly conserved miRNA-gene interactions that were annotated to be related to immunoregulatory functions. This work provided an important advance in the functional identification of dietary GPS supplementation and more fundamental information about how GPS promoted the immune response and healthy growth of the infant from mothers at molecular levels.

genomics↗