Biology subjects

Buchner, D. A.

Publications and source records attributed to Buchner, D. A..

6 recordsLinked to original sources

bioRxiv2024

Cell-state dependent regulation of PPARγ signaling by ZBTB9 in adipocytes

Adipocytes play a critical role in metabolic homeostasis. Peroxisome proliferator-activated receptor-{gamma} (PPAR{gamma}) is a nuclear hormone receptor that is a master regulator of adipocyte differentiation and function. ZBTB9 was predicted to interact with PPAR{gamma} based on large-scale protein interaction experiments. In addition, GWAS studies in the type 2 diabetes (T2D) Knowledge Portal revealed associations between Zbtb9 and both BMI and T2D risk. Here we show that ZBTB9 positively regulates PPAR{gamma} activity in mature adipocytes. Surprisingly Zbtb9 knockdown (KD) also increased adipogenesis in 3T3-L1 cells and human preadipocytes. E2F activity was increased and E2F downstream target genes were upregulated in Zbtb9-KD preadipocytes. Accordingly, RB phosphorylation, which regulates E2F activity, was enhanced in Zbtb9-KD preadipocytes. Critically, an E2F1 inhibitor blocked the effects of Zbtb9 deficiency on adipogenic gene expression and lipid accumulation. Collectively, these results demonstrate that Zbtb9 inhibits adipogenesis as a negative regulator of Pparg expression via altered RB-E2F1 signaling. Our findings reveal complex cell-state dependent roles of ZBTB9 in adipocytes, identifying a new molecule that regulates adipogenesis and adipocyte biology as both a positive and negative regulator of PPAR{gamma} signaling depending on the cellular context, and thus may be important in the pathogenesis and treatment of obesity and T2D.

cell biology↗

bioRxiv2023

Molecular regulation of PPARγ/RXRα signaling by the novel cofactor ZFP407

Cofactors interacting with PPAR{gamma} can regulate adipogenesis and adipocyte metabolism by modulating the transcriptional activity and selectivity of PPAR{gamma} signaling. ZFP407 was previously demonstrated to regulate PPAR{gamma} target genes such as GLUT4, and its overexpression improved glucose homeostasis in mice. Here, using a series of molecular assays, including protein-interaction studies, mutagenesis, and ChIP-seq, ZFP407 was found to interact with the PPAR{gamma}/RXR protein complex in the nucleus of adipocytes. Consistent with this observation, ZFP407 DNA binding sites significantly overlapped with PPAR{gamma} sites, with more than half of ZFP407 binding sites overlapping with PPAR{gamma} DNA binding sites. Transcription factor binding motifs enriched in these overlapping sites included GFY-Staf, ELF1, ETS, ELK1, and ELK4, which regulate key functions within adipocytes. Site-directed mutagenesis of frequent PPAR{gamma} phosphorylation or SUMOylation sites did not prevent its regulation by ZFP407, while mutagenesis of ZFP407 regions necessary for RXR and PPAR{gamma} binding abrogated any impact of ZFP407 on PPAR{gamma} activity. These data suggest that ZFP407 controls the activity of PPAR{gamma}, but does so independently of post-translational modifications, likely by direct binding, establishing ZFP407 as a newly identified PPAR{gamma} cofactor. In addition, ZFP407 was also found to bind to DNA in regions that did not overlap with PPAR{gamma}. These DNA binding sites were more significantly enriched for the transcription factor binding motifs of GFY and ZNF143, which may contribute to the non-PPAR{gamma} dependent functions of ZFP407 in adipocytes and other cell types.

molecular biology↗

bioRxiv2022

Omnigenic epistasis regulates complex trait heritability

A better understanding of genetic architecture will help translate genetic data into improved precision-based medicine and clinical care. Towards this end, we explored the use of sex-stratified analyses for several traits in the Hybrid Mouse Diversity Panel (HMDP) and UK Biobank to better determine trait polygenicity and identify contributing loci. This was accomplished by comparing the direction of allelic effects in males and females in sex-stratified analyses under the hypothesis that loci that are not associated with a trait should have equal chances of trending in the same direction of effect. Instead, we found that even for most alleles that do not meet nominal levels of statistical significance, the direction of effect in the two sexes was highly concordant. Results were consistent with hundreds of loci regulating each mouse trait and thousands of loci regulating each human trait, including traits for which no statistically significant loci were identified using conventional approaches. We also found evidence of likely spurious widespread epistasis. Collectively, these findings demonstrate the importance of stratifying by sex to discover novel associating loci, suggest a new method for identifying biologically rather than statistically significant associations, and caution that widespread marginal effects can lead to phantom epistasis.

genetics↗

bioRxiv2020

Revealing heritability missed by single locus analyses by examining epistasis in mouse chromosome substitution strains

The genetic contribution of additive versus non-additive (epistatic) effects in the regulation of complex traits is unclear. While genome-wide association studies typically ignore gene-gene interactions, in part because of the lack of statistical power for detecting them, mouse chromosome substitution strains (CSSs) represent an alternate and powerful model for detecting epistasis given their limited allelic variation. Therefore, we utilized CSSs to identify and map both additive and epistatic loci that regulate a range of hematologic- and metabolism-related traits, as well as hepatic gene expression. Quantitative trait loci (QTLs) were identified using a CSS-based backcross strategy involving the segregation of variants on the A/J-derived substituted chromosomes 4 and 6 on an otherwise C57BL/6J genetic background. In the liver transcriptomes of offspring from this cross, we identified and mapped additive QTLs regulating the hepatic expression of 768 genes, and epistatic QTL pairs for 519 genes. Similarly, we identified additive QTLs for fat pad weight, platelets, and the percentage of granulocytes in blood, as well as epistatic QTL pairs controlling the percentage of lymphocytes in blood and red cell distribution width. The variance attributed to the epistatic QTL pairs was approximately equal to that of the additive QTLs; however, the SNPs in the epistatic QTL pairs that accounted for the largest variances were undetected in our single locus association analyses. These findings highlight the need to account for epistasis in association studies, and more broadly demonstrate the importance of identifying genetic interactions to understand the complete genetic architecture of complex traits.

genetics↗

bioRxiv2018

Mutations In PIK3C2A Cause Syndromic Short Stature, Skeletal Abnormalities, and Cataracts Associated With Ciliary Dysfunction

PIK3C2A is a class II member of the phosphoinositide 3-kinase (PI3K) family that catalyzes the phosphorylation of phosphatidylinositol (PI) into PI(3)P and the phosphorylation of PI(4)P into PI(3,4)P2. We identified homozygous loss-of-function mutations in PIK3C2A in children from three independent consanguineous families with short stature, coarse facial features, cataracts with secondary glaucoma, multiple skeletal abnormalities, neurological manifestations, among other findings. Cellular studies of patient-derived fibroblasts found that they lacked PIK3C2A protein, had impaired cilia formation and function, and demonstrated reduced proliferative capacity. Collectively, the genetic and molecular data implicate mutations in PIK3C2A in a new Mendelian disorder of PI metabolism, thereby shedding light on the critical role of a class II PI3K in growth, vision, skeletal formation and neurological development. This discovery expands what is known about disorders of PI metabolism and helps unravel the role of PIK3C2A and class II PI3Ks in health and disease.

genetics↗

bioRxiv2017

Widespread Inter-Chromosomal Epistasis Regulates Glucose Homeostasis And Gene Expression

The relative contributions of additive versus non-additive interactions in the regulation of complex traits remains controversial. This may be in part because large-scale epistasis has traditionally been difficult to detect in complex, multi-cellular organisms. We hypothesized that it would be easier to detect interactions using mouse chromosome substitution strains that simultaneously incorporate allelic variation in many genes on a controlled genetic background. Analyzing metabolic traits and gene expression levels in the offspring of a series of crosses between mouse chromosome substitution strains demonstrated that inter-chromosomal epistasis was a dominant feature of these complex traits. Epistasis typically accounted for a larger proportion of the heritable effects than those due solely to additive effects. These epistatic interactions typically resulted in trait values returning to the levels of the parental CSS host strain. Due to the large epistatic effects, analyses that did not account for interactions consistently underestimated the true effect sizes due to allelic variation or failed to detect the loci controlling trait variation. These studies demonstrate that epistatic interactions are a common feature of complex traits and thus identifying these interactions is key to understanding their genetic regulation.

genetics↗