Dietary Intake Regulates the Circulating Inflammatory Monocyte Pool.
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ABSTRACT:
SUBMITTER: Jordan S
PROVIDER: S-EPMC7357241 | biostudies-literature | 2019 Aug
REPOSITORIES: biostudies-literature
Publications
Dietary Intake Regulates the Circulating Inflammatory Monocyte Pool.
Jordan Stefan S Tung Navpreet N Casanova-Acebes Maria M Chang Christie C Cantoni Claudia C Zhang Dachuan D Wirtz Theresa H TH Naik Shruti S Rose Samuel A SA Brocker Chad N CN Gainullina Anastasiia A Hornburg Daniel D Horng Sam S Maier Barbara B BB Cravedi Paolo P LeRoith Derek D Gonzalez Frank J FJ Meissner Felix F Ochando Jordi J Rahman Adeeb A Chipuk Jerry E JE Artyomov Maxim N MN Frenette Paul S PS Piccio Laura L Berres Marie-Luise ML Gallagher Emily J EJ Merad Miriam M
Cell 20190801 5
Caloric restriction is known to improve inflammatory and autoimmune diseases. However, the mechanisms by which reduced caloric intake modulates inflammation are poorly understood. Here we show that short-term fasting reduced monocyte metabolic and inflammatory activity and drastically reduced the number of circulating monocytes. Regulation of peripheral monocyte numbers was dependent on dietary glucose and protein levels. Specifically, we found that activation of the low-energy sensor 5'-AMP-act ...[more]
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Quality control checks for raw data FASTQ files were done by using FASTQC (a quality control tool for high throughput sequence data; http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Paired-end reads were mapped to the Mus musculus genome (GRCm38) using Bowtie 2-2.1.0, TopHat-2.0.10, and Samtools-0.1.19; uniquely mapped reads for each gene were counted against the GTF file of GRCm38 provided by Ensembl (release 83) using HTSeq-0.6.1p1 using the strand = reverse; after read count data were obtained from the TopHat-HTSeq pipeline, counts per million (CPM) value for each gene was calculated by using the R package ‘edgeR’ (version 3.12.0, R version 3.2.2) to normalize the count data by the size of the library of each sample. Genes with the CPM value ≥ 1 in at least one of the 24 diets group were retained (Anders et al., 2013). Generalized Linear Modelling (GLM) was applied by R (version 3.2.2). The GLM model used here was: ~p+f+p:f, which regresses gene expression (CPM) against the protein (p) and fat contents (f) of diets, as well as their interaction (p:f). However, when the effect of the interaction was not significant (p value ≥ 0.05), the interaction term was dropped and a revised model (~p+f) was utilized. Results: With TopHat-HTSeq pipeline, reads of each sample were mapped to 46,078 genes. In hypothalamus there were 15,371 genes with the counts per million (CPM) value ≥ 1 in at least one of the 24 diets group; in white adipose tissue there were 18,202 genes with the CPM value ≥ 1 in at least one of the 24 diets group. No major changes in hypothalamic gene expression levels were found in relation to different dietary protein levels at fixed fat contents, however hypothalamic gene expression showed increase in expression of genes in reward pathways in relation to dietary fat, while Agrp and Npy were both downregulated in relation to dietary fat levels. 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