Splicing across adipocyte differentiation is highly dynamic and impacted by metabolic phenotype

Adipose tissue dysfunction underlies many of the metabolic complications associated with obesity. A better understanding of the gene regulation differences present in metabolically unhealthy adipose tissue can provide insights into the mechanisms underlying adipose tissue dysfunction. Here, we used RNA-seq data collected from a differentiation time course of lean, obese, and obese with type 2 diabetes (T2D) individuals to characterize the role of alterative splicing in adipocyte differentiation and function. We found that splicing was highly dynamic across adipocyte differentiation in all three cohorts, and that the dynamics of splicing were significantly impacted by metabolic phenotype. We also found that there was very little overlap between genes that were differentially spliced in adipocyte differentiation and those that were differentially expressed, positioning alternative splicing as a largely independent gene regulatory mechanism whose impact would be missed when looking at gene expression changes alone. To assess the impact of alternative splicing across adipocyte differentiation on genetic risk for metabolic diseases, we integrated the differential splicing results generated here with genome-wide association study results for body mass index and T2D, and found that variants associated with T2D were enriched in regions that were differentially spliced in early differentiation. These findings provide insight into the role of alternative splicing in adipocyte differentiation and can serve as a resource to guide future variant-to-function studies.

Establishment of human induced trophoblast stem-like cells from term villous cytotrophoblasts

Human trophoblast stem cells (hTSC) can be isolated from first trimester placenta but not from term placenta. Here we demonstrate that villous cytotrophoblasts (vCTB) from term placenta can be reprogrammed into induced trophoblastic stem-like cells (iTSC) by introducing sets of transcription factors. The iTSCs express TSC markers such as GATA3, TEAD4 and ELF5, and are multipotent, validated by their differentiation into both extravillous trophoblasts (EVT) and syncytiotrophoblasts (STB) in vitro and in vivo. The iTSC can be passaged indefinitely in vitro without slowing of growth. The transcriptome profile of these cells closely resembles the profile of hTSC isolated from first trimester placentae but different from the term placental vCTB from which they originated. The ability to reprogram cells from term placenta into iTSC will allow study of early gestation events which impact placental function later in gestation, including preeclampsia and spontaneous preterm birth.

Abstract 439: Trajectory Analysis of Left Ventricular Dimensions From Biobank Data Uncovers Novel Genetic Associations

Background: Approximately 6 million adults in the United States have heart failure. The progression of heart failure is variable arising from differences in sex, age, genetic background including ancestry, and medication response. Many population-based genetic studies of heart failure have been cross-sectional in nature, failing to gain additional power from longitudinal analyses. As heart failure is known to change over time, using longitudinal data trajectories as a quantitative trait will increase power in genome wide association studies (GWAS).

Methods: We used the electronic health record in a racially and ethnically diverse medical biobank from a single, metropolitan US center. We used whole genome data from 896 unrelated participants analyzed, including 494 who had at least 1 electrocardiogram and 324 who had more than 1 echocardiogram (average of 3 observations per person). A mixture model based semiparametric latent growth curve model was used to cluster outcome measures used for genome-wide analyses.

Results: GWAS on the trajectory probability of QTc interval identified significant associations with variants in regulatory regions proximal to the WLS gene, which encodes Wntless, a Wnt ligand secretion mediator. WLS was previously associated with QTc and myocardial infarction, thus confirming the power of the method. GWAS on the trajectory probability of left ventricular diameter (LVIDd) identified significant associations with variants in regulatory regions near MYO10 , which encodes unconventional Myosin-10. MYO10 was previously associated with obesity and metabolic syndrome.

Conclusions: This is the first study to show an association with variants in or near MYO10 and left ventricular dimension changes over time. Further, we found that using trajectory probabilities can provide increased power to find novel associations with longitudinal data. This reduces the need for larger cohorts, and increases yield from smaller, well-phenotyped cohorts, such as those found in biobanks. This approach should be useful in the study of rare diseases and underrepresented populations.

TCF7L2 (Transcription Factor 7-Like 2) Regulation of GATA6 (GATA-Binding Protein 6)-Dependent and -Independent Vascular Smooth Muscle Cell Plasticity and Intimal Hyperplasia

Supplemental Digital Content is available in the text.

Objective—

TCF7L2 (transcription factor 7-like 2) is a Wnt-regulated transcription factor that maintains stemness and promotes proliferation in embryonic tissues and adult stem cells. Mice with a coronary artery disease–linked mutation in Wnt-coreceptor LRP6 (LDL receptor-related protein 6) exhibit vascular smooth muscle cell dedifferentiation and obstructive coronary artery disease, which are paradoxically associated with reduced TCF7L2 expression. We conducted a comprehensive study to explore the role of TCF7L2 in vascular smooth muscle cell differentiation and protection against intimal hyperplasia.

Approach and Results—

Using multiple mouse models, we demonstrate here that TCF7L2 promotes differentiation and inhibits proliferation of vascular smooth muscle cells. TCF7L2 accomplishes these effects by stabilization of GATA6 (GATA-binding protein 6) and upregulation of SM-MHC (smooth muscle cell myosin heavy chain) and cell cycle inhibitors. Accordingly, TCF7L2 haploinsufficient mice exhibited increased susceptibility to injury-induced hyperplasia, while mice overexpressing TCF7L2 were protected against injury-induced intimal hyperplasia compared with wild-type littermates. Consequently, the overexpression of TCF7L2 in LRP6 mutant mice rescued the injury-induced intimal hyperplasia.

Conclusions—

Our novel findings imply cell type-specific functional role of TCF7L2 and provide critical insight into mechanisms underlying the pathogenesis of intimal hyperplasia.

A novel mechanism of inherited TBG deficiency: mutation in a liver-specific enhancer

CONTEXT

T4-binding globulin (TBG), a protein secreted by the liver, is the main thyroid hormone (TH) transporter in human serum. TBG deficiency is characterized by reduced serum TH levels, but normal free TH and TSH and absent clinical manifestations. The inherited form of TBG deficiency is usually due to a mutation in the TBG gene located on the X-chromosome.

OBJECTIVE

Among the 75 families with X-chromosome-linked TBG deficiency identified in our laboratory, no mutations in the TBG gene were found in four families. The aim of the study was to identify the mechanism of TBG deficiency in these four families using biochemical and genetic studies.

DESIGN

Observational cohort, prospective.

SETTING

University research center.

PATIENTS

Four families with inherited TBG deficiency and no mutations in the TBG gene.

INTERVENTION

Clinical evaluation, thyroid function tests, and targeted resequencing of 1 Mb of the X-chromosome.

RESULTS

Next-generation sequencing identified a novel G to A variant 20 kb downstream of the TBG gene in all four families. In silico analysis predicted that the variant resides within a liver-specific enhancer. In vitro studies confirmed the enhancer activity of a 2.2-kb fragment of genomic DNA containing the novel variant and showed that the mutation reduces the activity of this enhancer. The affected subjects share a haplotype of 8 Mb surrounding the mutation, and the most recent common ancestor among the four families was estimated to be 19.5 generations ago (95% confidence intervals, 10.4-37).

CONCLUSIONS

To our knowledge, the present study is the first report of an inherited endocrine disorder caused by a mutation in an enhancer region.

TCF7L2 is a master regulator of insulin production and processing

Genome-wide association studies have revealed >60 loci associated with type 2 diabetes (T2D), but the underlying causal variants and functional mechanisms remain largely elusive. Although variants in TCF7L2 confer the strongest risk of T2D among common variants by presumed effects on islet function, the molecular mechanisms are not yet well understood. Using RNA-sequencing, we have identified a TCF7L2-regulated transcriptional network responsible for its effect on insulin secretion in rodent and human pancreatic islets. ISL1 is a primary target of TCF7L2 and regulates proinsulin production and processing via MAFA, PDX1, NKX6.1, PCSK1, PCSK2 and SLC30A8, thereby providing evidence for a coordinated regulation of insulin production and processing. The risk T-allele of rs7903146 was associated with increased TCF7L2 expression, and decreased insulin content and secretion. Using gene expression profiles of 66 human pancreatic islets donors’, we also show that the identified TCF7L2-ISL1 transcriptional network is regulated in a genotype-dependent manner. Taken together, these results demonstrate that not only synthesis of proinsulin is regulated by TCF7L2 but also processing and possibly clearance of proinsulin and insulin. These multiple targets in key pathways may explain why TCF7L2 has emerged as the gene showing one of the strongest associations with T2D.

Insights into the organization of dorsal spinal cord pathways from an evolutionarily conserved raldh2 intronic enhancer

Comparative studies of the tetrapod raldh2 (aldh1a2) gene, which encodes a retinoic acid (RA) synthesis enzyme, have led to the identification of a dorsal spinal cord enhancer. Enhancer activity is directed dorsally to the roof plate and dorsal-most (dI1) interneurons through predicted Tcf- and Cdx-homeodomain binding sites and is repressed ventrally via predicted Tgif homeobox and ventral Lim-homeodomain binding sites. Raldh2 and Math1/Cath1 expression in mouse and chicken highlights a novel, transient, endogenous Raldh2 expression domain in dI1 interneurons, which give rise to ascending circuits and intraspinal commissural interneurons, suggesting roles for RA in the ontogeny of spinocerebellar and intraspinal proprioceptive circuits. Consistent with expression of raldh2 in the dorsal interneurons of tetrapods, we also found that raldh2 is expressed in dorsal interneurons throughout the agnathan spinal cord, suggesting ancestral roles for RA signaling in the ontogenesis of intraspinal proprioception.

Evaluation of P4504a Genes for Hypertension and Renal Disease Using Chromosome 5 Congenic Strains of Dahl S Rats

53

P4504A1 and 4A2 genes are differentially expressed in the kidney and cosegregate with blood pressure in an F 2 cross of Dahl S and Lewis rats; however, it is unclear whether this pathway plays a causal or secondary role in the development of hypertension. The present study examined whether transfer of overlapping segments of chromosome 5 from D5Rat84 to D5Rat34 that excludes (4A- strain) or includes all four P4504A genes(4A+ strain),or just the 4A3 and 4A8 genes (4A3,8+ strain), of a Lewis rat alters blood pressure, proteinuria, and renal injury in 12 week old congenic strains of Dahl S rats fed a high salt diet (8% NaCl) for 3 weeks. MAP measured in conscious rats using a chronic catheter averaged 188 ± 3 mm Hg in male Dahl S rats (n=24), 190 ± 3 mm Hg in the 4A- congenic strain (n=24), 169 ± 4 mm Hg in the 4A+ congenic strain (n=30), and 172 ± 3 mm Hg in the 4A3,8+ strain (n=33). Transfer of the P4504A region also significantly reduced proteinuria, renal hypertrophy, and the degree of glomerular and tubulointerstitial injury. Protein excretion averaged 246 ± 22 mg/day in male Dahl S rats and 255 ± 25 mg/day, 129 ± 8 mg/day, and 169 ± 12 mg/day in the 4A-, 4A+, and 4A3,8+ strains, respectively. The antihypertensive and renoprotective effects of transfer of the P4504A region were associated with signficant increases in the expression of P4504A mRNA, P4504A protein levels, and the renal formation of 20-HETE. Interestingly, transfer of the P4504A region had no effect on blood pressure in female rats of the 4A+ or 4A3,8+ congenic strains, but it still reduced the degree of proteinuria and renal injury. These studies exclude the P4504A1 and 4A2 loci as the causal genes in this region in the development of hypertension in Dahl S rats. However, they indicate that the P4504A3 and 4A8 genes still lie in the interval between D5Rat108 and D5Rat54 that contains a locus that reduces blood pressure, is renoprotective, and alters the expression of P4504A genes in Dahl S rats.

On the functions of the yeast COX10 and COX11 gene products

COX10 and COX11 are nuclear genes of Saccharomyces cerevisiae whose products are localized in mitochondria and are required for the synthesis of cytochrome oxidase. Genes homologous to COX10 are present in at least four different bacterial cytochrome oxidase operons. The bacterial gene, termed cyoE, has recently been proposed to code for a farnesyl transferase that converts protoheme to heme O (Saiki et al. (1992), Biochem. Biophys. Res. Commun. 189, 1491-1497). In this communication we report that the COX10 protein, like the product of cyoE is needed for heme A synthesis. Analyses of the heme constituents in a cox11 mutant indicate the absence of heme A and presence of a novel heme with chromatographic properties indistinguishable from those of heme O. This evidence suggests that the COX11 protein may be another heme A biosynthetic enzyme involved in forming the formyl group at position 8 of the porphyrin ring.

Ablation of tumor and inflammatory tissue with absolute ethanol

Absolute ethanol was used to ablate tumors, inflammatory lesions, and end-stage nephrosclerotic kidneys in 38 patients. Thirty patients had various types of renal tumors, and 3 had chronic end-stage renal failure with malignant hypertension. One patient had a fibrosarcoma of the right leg and one had a metastasis in the humerus from a renal carcinoma. A large adrenal carcinoma was treated with absolute ethanol in a patient who had liver metastases that were ablated one year after the first procedure. An additional patient had metastatic liver disease from a non-functioning adrenal carcinoma. The remaining patient had an extensive hypervascular inflammatory lesion (tuberculosis and aspergilloma) of the right upper pulmonary lobe. In addition to ethanol, coils were introduced in one patient and Gelfoam in another. The amount of ethanol used ranged from 5 to 50 ml. Twenty-two patients suffered from considerable transient pain during ethanol injection, but sedation was necessary in only 3 of them. Skin necrosis appeared in 2 patients requiring plastic reconstruction in one of them. Two patients died within 5 days of the procedure unrelated to the ablation. Two patients presented upper gastrointestinal bleeding within 2 days of the ethanol injection and one of these died in acute renal failure. One patient suffered from left colonic infarction after left renal tumor ablation, but survived for several months. Absolute ethanol was a useful and efficient sclerosing agent causing extensive tumor destruction and marked reduction of the vascularity in tumor and inflammatory lesions, but caused an 18 per cent complication rate.

Transfer RNA genes in the cap-oxil region of yeast mitochondrial DNA

A cytoplasmic "petite" (rho-) clone of Saccharomyces cerevisiae has been isolated and found through DNA sequencing to contain the genes for cysteine, histidine, leucine, glutamine, lysine, arginine, and glycine tRNAs. This clone, designated DS502, has a tandemly repeated 3.5 kb segment of the wild type genome from 0.7 to 5.6 units. All the tRNA genes are transcribed from the same strand of DNA in the direction cap to oxil. The mitochondrial DNA segment of DS502 fills a sequence gap that existed between the histidine and lysine tRNAs. The new sequence data has made it possible to assign accurate map positions to all the tRNA genes in the cap-oxil span of the yeast mitochondrial genome. A detailed restriction map of the region from 0 to 17 map units along with the locations of 16 tRNA genes have been determined. The secondary structures of the leucine and glutamine tRNAs have been deduced from their gene sequences. The leucine tRNA exhibits 64% sequence homology to an E. coli leucine tRNA.