Biology subjects

Stapleton, D. S.

Publications and source records attributed to Stapleton, D. S..

6 recordsLinked to original sources

bioRxiv2026

Distinct genetic architecture of gene and isoform level QTL in the Diversity Outbred (DO) mouse population

Genetic association studies of mRNA abundance phenotypes link regulatory gene loci to mRNA abundance (quantitative trait loci; QTL). Here, we used liver RNA-seq data from a large cohort of the Diversity Outbred (DO) mouse population to map QTL for gene abundance (eQTL), isoform abundance (isoQTL), isoform ratios (irQTL), and splicing (sQTL). QTL studies using this heterogeneous mouse population have been limited to gene-level abundance of mRNAs and have not focused on mRNA isoforms or splicing. We show for the first time that genetic effects on expression are distinct from splicing in the DO mouse population. Using allele-effect patterns from local QTL for protein-coding gene-isoform pairs, we show that genetic variation drives allele-specific isoform usage, generating isoforms whose genetic signals diverge from their aggregated gene-level effects. We conducted pathway enrichment on distal eQTL and isoQTL hotspots and uncovered pathways not detected with eQTL. We then applied a composite mediation approach at these distal hotspots that compares gene-gene, isoform-isoform, and isoform-gene mediator models. By contrasting these causal models of transcriptional regulation, we identified unique associations between mRNA isoforms. We identified candidate genes at irQTL and sQTL hotspots that regulate mRNAs primarily through isoform usage and splicing, including Alkbh1 and Dicer1. For these driver genes, we nominated novel candidate targets through mediation analysis and pathway associations with known RNA-binding targets. We integrated our QTL data with human genetic data, prioritizing effector genes in loci associated with metabolically relevant traits. Our data also suggest that sex and diet influence eQTL and isoQTL distinctly and primarily through distal-acting gene loci. Overall, our findings highlight distinctive genetic effects on transcriptional and post-transcriptional mechanisms of gene regulation.

genetics↗

bioRxiv2023

Lipidomic QTL in Diversity Outbred mice identifies a novel function for α/β hydrolase domain 2 (Abhd2) as an enzyme that metabolizes phosphatidylcholine and cardiolipin

We and others have previously shown that genetic association can be used to make causal connections between gene loci and small molecules measured by mass spectrometry in the bloodstream and in tissues. We identified a locus on mouse chromosome 7 where several phospholipids in liver showed strong genetic association to distinct gene loci. In this study, we integrated gene expression data with genetic association data to identify a single gene at the chromosome 7 locus as the driver of the phospholipid phenotypes. The gene encodes /{beta}-hydrolase domain 2 (Abhd2), one of 23 members of the ABHD gene family. We validated this observation by measuring lipids in a mouse with a whole-body deletion of Abhd2. The Abhd2KO mice had a significant increase in liver levels of phosphatidylcholine and phosphatidylethanolamine. Unexpectedly, we also found a decrease in two key mitochondrial lipids, cardiolipin and phosphatidylglycerol, in male Abhd2KO mice. These data suggest that Abhd2 plays a role in the synthesis, turnover, or remodeling of liver phospholipids.

genetics↗

bioRxiv2022

Genetic variation in mouse islet Ca2+ oscillations reveals novel regulators of islet function

Insufficient insulin secretion to meet metabolic demand results in diabetes. The intracellular flux of Ca2+ into {beta}-cells triggers insulin release. Since genetics strongly influences variation in islet secretory responses, we surveyed islet Ca2+ dynamics in eight genetically diverse mouse strains. We found high strain variation in response to four conditions: 1) 8 mM glucose; 2) 8 mM glucose plus amino acids; 3) 8 mM glucose, amino acids, plus 10 nM GIP; and 4) 2 mM glucose. These stimuli interrogate {beta}-cell function, -cell to {beta}-cell signaling, and incretin responses. We then correlated components of the Ca2+ waveforms to islet protein abundances in the same strains used for the Ca2+ measurements. To focus on proteins relevant to human islet function, we identified human orthologues of correlated mouse proteins that are proximal to glycemic-associated SNPs in human GWAS. Several orthologues have previously been shown to regulate insulin secretion (e.g. ABCC8, PCSK1, and GCK), supporting our mouse-to-human integration as a discovery platform. By integrating these data, we nominated novel regulators of islet Ca2+ oscillations and insulin secretion with potential relevance for human islet function. We also provide a resource for identifying appropriate mouse strains in which to study these regulators.

biochemistry↗

bioRxiv2021

Systems genetics uncovers microbe-lipid-host connections in the murine gut

The molecular bases of how host genetic variation impact gut microbiome remain largely unknown. Here, we used a genetically diverse mouse population and systems genetics strategies to identify interactions between molecular phenotypes, including microbial functions, intestinal transcripts and cecal lipids that influence microbe-host dynamics. Quantitative trait loci (QTL) analysis identified genomic regions associated with variations in bacterial taxa, bacterial functions, including motility, sporulation and lipopolysaccharide production, and levels of bacterial- and host-derived lipids. We found overlapping QTL for the abundance of Akkermansia muciniphila and cecal levels of ornithine lipids (OL). Follow-up studies revealed that A. muciniphila is a major source of these lipids in the gut, provided evidence that OL have immunomodulatory effects and identified intestinal transcripts co-regulated with these traits. Collectively, these results suggest that OL are key players in A. muciniphila-host interactions and support the role of host genetics as a determinant of responses to gut microbes.

genetics↗

bioRxiv2021

INFIMA leverages multi-omics model organism data to identify effector genes of human GWAS variants

Genome-wide association studies have revealed many non-coding variants associated with complex traits. However, model organism studies have largely remained as an untapped resource for unveiling the effector genes of non-coding variants. We develop INFIMA, Integrative Fine-Mapping, to pinpoint causal SNPs for Diversity Outbred (DO) mice eQTL by integrating founder mice multi-omics data including ATAC-seq, RNA-seq, footprinting, and in silico mutation analysis. We demonstrate INFIMAs superior performance compared to alternatives with human and mouse chromatin conformation capture datasets. We apply INFIMA to identify novel effector genes for GWAS variants associated with diabetes. The results of the application are available at http://www.statlab.wisc.edu/shiny/INFIMA/

bioinformatics↗

bioRxiv2019

Genetic determinants of gut microbiota composition and bile acid profiles in mice

The microbial communities that inhabit the distal gut of humans and other mammals exhibit large inter-individual variation. While host genetics is a known factor that influences gut microbiota composition, the mechanisms underlying this variation remain largely unknown. Bile acids (BAs) are hormones that are produced by the host and chemically modified by gut bacteria. BAs serve as environmental cues and nutrients to microbes, but they can also have antibacterial effects. We hypothesized that host genetic variation in BA metabolism and homeostasis influence gut microbiota composition. To address this, we used the Diversity Outbred (DO) stock, a population of genetically distinct mice derived from eight founder strains. We characterized the fecal microbiota composition and plasma and cecal BA profiles from 400 DO mice maintained on a high-fat high-sucrose diet for [~]22 weeks. Using quantitative trait locus (QTL) analysis, we identified several genomic regions associated with variations in both bacterial and BA profiles. Notably, we found overlapping QTL for Turicibacter sp. and plasma cholic acid, which mapped to a locus containing the gene for the ileal bile acid transporter, Slc10a2. Mediation analysis and subsequent follow-up validation experiments suggest that differences in Slc10a2 gene expression associated with the different strains influences levels of both traits and revealed novel interactions between Turicibacter and BAs. This work illustrates how systems genetics can be utilized to generate testable hypotheses and provide insight into host-microbe interactions.\n\nAuthor summaryInter-individual variation in the composition of the intestinal microbiota can in part be attributed to host genetics. However, the specific genes and genetic variants underlying differences in the microbiota remain largely unknown. To address this, we profiled the fecal microbiota composition of 400 genetically distinct mice, for which genotypic data is available. We identified many loci of the mouse genome associated with changes in abundance of bacterial taxa. One of these loci is also associated with changes in the abundance of plasma bile acids--metabolites generated by the host that influence both microbiota composition and host physiology. Follow up validation experiments provide mechanistic insights linking host genetic differences, with changes in ileum gene expression, bile acid-bacteria interactions and bile acid homeostasis. Together, this work demonstrates how genetic approaches can be used to generate testable hypothesis to yield novel insight into how host genetics shape gut microbiota composition.

systems biology↗