Unraveling the genetics of arsenic toxicity with cellular morphology QTL

The health risks that arise from environmental exposures vary widely within and across human populations, and these differences are largely determined by genetic variation and gene-by-environment (gene-environment) interactions. However, risk assessment in laboratory mice typically involves isogenic strains and therefore, does not account for these known genetic effects. In this context, genetically heterogenous cell lines from laboratory mice are promising tools for population-based screening because they provide a way to introduce genetic variation in risk assessment without increasing animal use. Cell lines from genetic reference populations of laboratory mice offer genetic diversity, power for genetic mapping, and potentially, predictive value for in vivo experimentation in genetically matched individuals. To explore this further, we derived a panel of fibroblast lines from a genetic reference population of laboratory mice (the Diversity Outbred, DO). We then used high-content imaging to capture hundreds of cell morphology traits in cells exposed to the oxidative stress-inducing arsenic metabolite monomethylarsonous acid (MMAIII). We employed dose-response modeling to capture latent parameters of response and we then used these parameters to identify several hundred cell morphology quantitative trait loci (cmQTL). Response cmQTL encompass genes with established associations with cellular responses to arsenic exposure, including Abcc4 and Txnrd1, as well as novel gene candidates like Xrcc2. Moreover, baseline trait cmQTL highlight the influence of natural variation on fundamental aspects of nuclear morphology. We show that the natural variants influencing response include both coding and non-coding variation, and that cmQTL haplotypes can be used to predict response in orthogonal cell lines. Our study sheds light on the major molecular initiating events of oxidative stress that are under genetic regulation, including the NRF2-mediated antioxidant response, cellular detoxification pathways, DNA damage repair response, and cell death trajectories.

Cell morphology QTL reveal gene by environment interactions in a genetically diverse cell population

Genetically heterogenous cell lines from laboratory mice are promising tools for population-based screening as they offer power for genetic mapping, and potentially, predictive value for in vivo experimentation in genetically matched individuals. To explore this further, we derived a panel of fibroblast lines from a genetic reference population of laboratory mice (the Diversity Outbred, DO). We then used high-content imaging to capture hundreds of cell morphology traits in cells exposed to the oxidative stress-inducing arsenic metabolite monomethylarsonous acid (MMAIII). We employed dose-response modeling to capture latent parameters of response and we then used these parameters to identify several hundred cell morphology quantitative trait loci (cmQTL). Response cmQTL encompass genes with established associations with cellular responses to arsenic exposure, including Abcc4 and Txnrd1, as well as novel gene candidates like Xrcc2. Moreover, baseline trait cmQTL highlight the influence of natural variation on fundamental aspects of nuclear morphology. We show that the natural variants influencing response include both coding and non-coding variation, and that cmQTL haplotypes can be used to predict response in orthogonal cell lines. Our study sheds light on the major molecular initiating events of oxidative stress that are under genetic regulation, including the NRF2-mediated antioxidant response, cellular detoxification pathways, DNA damage repair response, and cell death trajectories.

"Stripe" transcription factors provide accessibility to co-binding partners in mammalian genomes

Regulatory elements activate promoters by recruiting transcription factors (TFs) to specific motifs. Notably, TF-DNA interactions often depend on cooperativity with colocalized partners, suggesting an underlying cis-regulatory syntax. To explore TF cooperativity in mammals, we analyze ∼500 mouse and human primary cells by combining an atlas of TF motifs, footprints, ChIP-seq, transcriptomes, and accessibility. We uncover two TF groups that colocalize with most expressed factors, forming stripes in hierarchical clustering maps. The first group includes lineage-determining factors that occupy DNA elements broadly, consistent with their key role in tissue-specific transcription. The second one, dubbed universal stripe factors (USFs), comprises ∼30 SP, KLF, EGR, and ZBTB family members that recognize overlapping GC-rich sequences in all tissues analyzed. Knockouts and single-molecule tracking reveal that USFs impart accessibility to colocalized partners and increase their residence time. Mammalian cells have thus evolved a TF superfamily with overlapping DNA binding that facilitate chromatin accessibility.

Interaction between Mas1 and AT1RA contributes to enhancement of skeletal muscle angiogenesis by angiotensin-(1-7) in Dahl salt-sensitive rats

The heptapeptide angiotensin-(1-7) (Ang-(1-7)) is protective in the cardiovascular system through its induction of vasodilator production and angiogenesis. Despite acting antagonistically to the effects of elevated, pathophysiological levels of angiotensin II (AngII), recent evidence has identified convergent and beneficial effects of low levels of both Ang-(1-7) and AngII. Previous work identified the AngII receptor type I (AT1R) as a component of the protein complex formed when Ang-(1-7) binds its receptor, Mas1. Importantly, pharmacological blockade of AT1R did not alter the effects of Ang-(1-7). Here, we use a novel mutation of AT1RA in the Dahl salt-sensitive (SS) rat to test the hypothesis that interaction between Mas1 and AT1R contributes to proangiogenic Ang-(1-7) signaling. In a model of hind limb angiogenesis induced by electrical stimulation, we find that the restoration of skeletal muscle angiogenesis in SS rats by Ang-(1-7) infusion is impaired in AT1RA knockout rats. Enhancement of endothelial cell (EC) tube formation capacity by Ang-(1-7) is similarly blunted in AT1RA mutant ECs. Transcriptional changes elicited by Ang-(1-7) in SS rat ECs are altered in AT1RA mutant ECs, and tandem mass spectrometry-based proteomics demonstrate that the protein complex formed upon binding of Ang-(1-7) to Mas1 is altered in AT1RA mutant ECs. Together, these data support the hypothesis that interaction between AT1R and Mas1 contributes to proangiogenic Ang-(1-7) signaling.

Abstract P160: A Genome-spanning Map of Chromatin Structure Near the Renin Proximal Promoter

Chromatin conformation capture technologies (3C, 4C-seq) allow mapping of the three dimensional spatial structure of the genome. Physical proximity mapping, which captures these 3 dimensional interactions, fills an important gap in our understanding of enhancer-gene relationship by linking possible regulatory regions to specific genes that may be distant from the enhancer by thousands or millions of base pairs or even located on different chromosomes. The goal of the current study was to expand our understanding of renin regulation by identifying regions containing potential regulatory elements of renin more than a few kilobases from the renin proximal promoter, using 4C-seq technology, in isolated SS/JrHrdMcwi cardiac microvascular endothelial cells. Three replicates of ten million cells were fixed, digested with EcoRI, ligated, and then decrosslinked. Secondary digestion with NlaIII followed by a second ligation captured an unknown sequence surrounded by the sequence of the renin promoter. A sequencing library was prepared using primers specific to the renin promoter to identify the captured sequences. Sequence reads were mapped to rat genome (Rn 5) divided into fragments cut by EcoRI. Reads were verified to contain the renin proximal promoter sequence and a uniquely mapped captured sequence. The read counts were binarized and Z-scores were calculated based on a windowed average reads relative to background, and Z-scores corresponding to FDR < 0.01 were considered significant. We found 62 loci spanning the genome in contact with the renin proximal promoter. Clusters of interactions were found on Chr13 at 39.6-40.5Mpb and at 53.9-56.3Mbp where the Renin gene is located. Additional contacting loci were found on all chromosomes except X. Quantitative PCR in newly isolated endothelial cells processed as 3C samples (fixed, digested, ligated, decrosslinked) were used to test 9 of the interactions, of which 8 were validated. These loci are enriched with genes whose expression is correlated with renin (53 of 268 genes, p = 7x10 -10 ) in humans, rats and mice. The present study generated a genome-wide map of segments physically interacting with the renin proximal promoter producing the first such map for a gene that is essential for cardiovascular physiology.

Abstract 11: Characterizing Gender-Specific Differences in Angiogenesis and Protection from Hypertension: Congenic Lines Lead to Identification of Btg2 as a Candidate Gene

Whole and partial chromosome introgression from the Brown Norway (BN) rat into the Dahl Salt Sensitive (SS) rat is a valuable tool for identifying genes and pathways associated with disease phenotypes in the SS rat. We have created two congenic lines with BN substitutions differing by 22.9 Kbp. The congenic regions differ by one gene, Btg2 , and have 35 sequence variants, three of which occur in Btg2 . We have characterized angiogenesis and development of hypertension in these new strains, and since Btg2 is known to be modulated by estradiol, we measured both phenotypes in males and females. Mean arterial pressure (MAP) was measured by telemetry after three weeks of 8% NaCl diet. Angiogenesis was measured by electrical stimulation of one hindlimb (Tibialis anterior, TA, and Extensor digitorum longus, EDL) with the contralateral leg acting as control. Renal damage was assessed by 24-h protein/albumin excretion after two weeks on 8% NaCl diet. Btg2 expression was determined by QRT-PCR on renal cortex and medulla as well as stimulated and unstimulated TA muscle. Males from both lines had the same MAP following three weeks of 8% NaCl diet (Btg2 BN : 187±5 mmHg, Btg2 SS : 185±3). Females with Btg2 BN had significantly higher MAP (180±6 mmHg) than Btg2 SS females (153±7 mmHg). Angiogenesis in response to electrical stimulation was observed in Btg2 BN males (TA=20.0±4.5% increase in vessel density, EDL=15.8±5.8%), but not in Btg2 SS males (TA= 5.1±2.2%, EDL=4.4±2.7%). Females of both strains had angiogenesis (Btg2 BN : TA=9.8±6%, EDL=8.5±1.2%; Btg2 SS : TA=12.7±2.4%, EDL=12.1±4.1%). Btg2 BN females had significantly higher protein excretion than SS and Btg2 SS was significantly lower; males had no significant differences. Btg2 mRNA expression in male skeletal muscle displayed a 2-fold increase (stimulated to unstimulated) in Btg2 BN and a 3.5-fold increase in Btg2 SS . Males had no differences in expression in renal cortex or medulla, but females had significant differences in cortex (Btg2 BN : 1.8±0.2 fold change, Btg2 SS : 0.4±.01). These data suggest Btg2 expression may contribute to the development of hypertension and inhibited angiogenic response in SS rats, with gender-specific differences in the expression of this gene.