Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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RNA-seq of human blood samples from MiBLEND study on the effect of fruit and vegetable blends on gene expression

ABSTRACT: This study investigates the effects of fruit and vegetable (F&V) intake on biomarkers of chronic diseases in healthy human volunteers. The study uses a randomized crossover design with a total duration of 7 weeks. Each participant underwent a 2-week run-in period to standardize F&V intake at 50g per day, followed by two separate 2-week intervention phases, during which F&V intake was increased to 450g per day, with a 1-week washout period between interventions. Participants were randomized to receive two out of seven different nutrition interventions, each providing distinct combinations of F&V. Blood samples were collected at baseline and after each intervention phase. Whole blood was drawn into EDTA-coated tubes, and RNA was extracted using the Directzol RNA microprep kit (ZY-R2052, Zymo Research), following ribo-depletion of rRNA. RNA quality and concentration were checked using a Qubit Fluorometer and Bioanalyzer. Samples with RIN values greater than 7 were used for library preparation. Library preparation was performed using the NextFlex Rapid Directional RNA kit 2.0 with ribo-depletion, followed by sequencing on the Illumina platform (200-cycle S4 flow cells). Sequencing generated paired-end reads of 150bp from approximately 150 samples per flow cell. The resulting fastq files were processed, de-multiplexed, and reviewed for quality, and all samples from each participant were analyzed in batches. Data analysis focused on differential gene expression related to antioxidant capacity, inflammation, and DNA damage markers.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER:

PROVIDER: E-MTAB-14563 | biostudies-arrayexpress |

SECONDARY ACCESSION(S): ERP165523

REPOSITORIES: biostudies-arrayexpress

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Project description:Mutation of the adenomatous polyposis coli (APC gene), an early event in the adenoma-carcinoma sequence, is present in 70-80% of sporadic human colorectal adenomas and carcinomas. To test the hypothesis that mutation of the APC gene alters microbial interactions with host intestinal mucosa prior to the development of polyposis, culture-independent methods (targeted qPCR assays and Illumina sequencing of the 16S rRNA gene V1V2 hypervariable region) were used to compare the intestinal microbial composition of 30 six-week old C57BL/6 APCMin/+ and 30 congenic wild type (WT) mice. The results demonstrate that similar to 12-14 week old APCMin/+ mice with intestinal neoplasia, 6 week old APCMin/+ mice with no detectable neoplasia, exhibit an increased relative abundance of Bacteroidetes spp in the colon. Parallel mouse RNA sequence analysis, conducted on a subset of proximal colonic RNA samples (6 APCMin/+, 6 WT) revealed 130 differentially expressed genes (DEGs, fold change ? 2, FDR <0.05). Hierarchical clustering of the DEGs was carried out by using 1-r dissimilarity measurement, where r stands for the Pearson correlation, and Ward minimum variance linkage, in order to reduce the number of input variables. When the cluster centroids (medians) were included along with APC genotype as input variables, analysis of variance and covariance (ANCOVA) with stepwise variable selection, selected two of seven mouse gene clusters, in addition to APC genotype, as significantly associated (p = 0.011 and p = 0.004) with the increased relative abundance of Bacteroidetes spp. One of the two clusters includes several downregulated genes encoding immunoglobulin variable regions and non-protein coding RNAs. These results support the concept that mutation of the APC gene alters colonic-microbial interactions prior to polyposis. It remains to be determined whether interventions directed at ameliorating dysbiosis in APCMin/+mice, such as through probiotics, prebiotics or antibiotics, could reduce tumor formation. Comparing the differential gene expressions in proximal colonic mucosal samples from 6 six-week-old female Apc Min/+ and 6 six-week-old female WT mice

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RNA-seq of human blood samples from MiBLEND study on the effect of fruit and vegetable blends on gene expression

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