Perturbation of the insomnia WDR90 GWAS locus pinpoints rs3752495 as a causal variant influencing distal expression of neighboring gene, PIG-Q

Although genome wide association studies (GWAS) have identified loci for sleep-related traits, they do not directly uncover the underlying causal variants and corresponding effector genes. The majority of such variants reside in non-coding regions and are therefore presumed to impact cis-regulatory elements. Our previously reported 'variant-to-gene mapping' effort in human induced pluripotent stem cell (iPSC)-derived neural progenitor cells (NPCs), combined with validation in both Drosophila and zebrafish, implicated PIG-Q as a functionally relevant gene at the insomnia 'WDR90' GWAS locus. However, importantly that effort did not characterize the corresponding underlying causal variant. Specifically, our previous 3D genomic datasets nominated a shortlist of three neighboring single nucleotide polymorphisms (SNPs) in strong linkage disequilibrium within an intronic enhancer region of WDR90 that contacted the open PIG-Q promoter. We sought to investigate the influence of these SNPs collectively and then individually on PIG-Q modulation to pinpoint the causal "regulatory" variant. Starting with gross level perturbation, deletion of the entire region in NPCs via CRISPR-Cas9 editing and subsequent RNA sequencing revealed expression changes in specific PIG-Q transcripts. Results from individual luciferase reporter assays for each SNP in iPSCs revealed that the region with the rs3752495 risk allele induced a ~2.5-fold increase in luciferase expression. Importantly, rs3752495 also exhibited an allele specific effect, with the risk allele increasing the luciferase expression by ~2-fold versus the non-risk allele. In conclusion, our variant-to-function approach and in vitro validation implicates rs3752495 as a causal insomnia variant embedded within WDR90 while modulating the expression of the distally located PIG-Q.

Perturbation of the insomnia WDR90 GWAS locus pinpoints rs3752495 as a causal variant influencing distal expression of neighboring gene, PIG-Q

Although genome wide association studies (GWAS) have been crucial for the identification of loci associated with sleep traits and disorders, the method itself does not directly uncover the underlying causal variants and corresponding effector genes. The overwhelming majority of such variants reside in non-coding regions and are therefore presumed to impact the activity of cis-regulatory elements, such as enhancers. Our previously reported 'variant-to-gene mapping' effort in human induced pluripotent stem cell (iPSC)-derived neural progenitor cells (NPCs), combined with validation in both Drosophila and zebrafish, implicated PIG-Q as a functionally relevant gene at the insomnia 'WDR90' locus. However, importantly that effort did not characterize the corresponding underlying causal variant at this GWAS signal. Specifically, our genome-wide ATAC-seq and high-resolution promoter-focused Capture C datasets generated in this cell setting brought our attention to a shortlist of three tightly neighboring single nucleotide polymorphisms (SNPs) in strong linkage disequilibrium in a candidate intronic enhancer region of WDR90 that contacted the open PIG-Q promoter. The objective of this study was to investigate the influence of the proxy SNPs collectively and then individually on PIG-Q modulation and to pinpoint the causal "regulatory" variant among the three SNPs. Starting at a gross level perturbation, deletion of the entire region harboring all three SNPs in human iPSC-derived neural progenitor cells via CRISPR-Cas9 editing and subsequent RNA sequencing revealed expression changes in specific PIG-Q transcripts. Results from more refined individual luciferase reporter assays for each of the three SNPs in iPSCs revealed that the intronic region with the rs3752495 risk allele induced a ~2.5-fold increase in luciferase expression (n=10). Importantly, rs3752495 also exhibited an allele specific effect, with the risk allele increasing the luciferase expression by ~2-fold compared to the non-risk allele. In conclusion, our variant-to-function approach and subsequent in vitro validation implicates rs3752495 as a causal insomnia risk variant embedded at the WDR90-PIG-Q locus.

Variant-to-gene mapping followed by cross-species genetic screening identifies GPI-anchor biosynthesis as a regulator of sleep

Genome-wide association studies (GWAS) in humans have identified loci robustly associated with several heritable diseases or traits, yet little is known about the functional roles of the underlying causal variants in regulating sleep duration or quality. We applied an ATAC-seq/promoter focused Capture C strategy in human iPSC-derived neural progenitors to carry out a "variant-to-gene" mapping campaign that identified 88 candidate sleep effector genes connected to relevant GWAS signals. To functionally validate the role of the implicated effector genes in sleep regulation, we performed a neuron-specific RNA interference screen in the fruit fly, Drosophila melanogaster, followed by validation in zebrafish. This approach identified a number of genes that regulate sleep including a critical role for glycosylphosphatidylinositol (GPI)-anchor biosynthesis. These results provide the first physical variant-to-gene mapping of human sleep genes followed by a model organism-based prioritization, revealing a conserved role for GPI-anchor biosynthesis in sleep regulation.

Expression of a constitutively active insulin receptor in Drosulfakinin (Dsk) neurons regulates metabolism and sleep in Drosophila

The ability of organisms to sense their nutritional environment and adjust their behavior accordingly is critical for survival. Insulin-like peptides (ilps) play major roles in controlling behavior and metabolism; however, the tissues and cells that insulin acts on to regulate these processes are not fully understood. In the fruit fly, Drosophila melanogaster, insulin signaling has been shown to function in the fat body to regulate lipid storage, but whether ilps act on the fly brain to regulate nutrient storage is not known. In this study, we manipulate insulin signaling in defined populations of neurons in Drosophila and measure glycogen and triglyceride storage. Expressing a constitutively active form of the insulin receptor (dInR) in the insulin-producing cells had no effect on glycogen or triglyceride levels. However, activating insulin signaling in the Drosulfakinin (Dsk)-producing neurons led to triglyceride accumulation and increased food consumption. The expression of ilp2, ilp3 and ilp5 was increased in flies with activated insulin signaling in the Dsk neurons, which along with the feeding phenotype, may cause the triglyceride storage phenotypes observed in these flies. In addition, expressing a constitutively active dInR in Dsk neurons resulted in decreased sleep in the fed state and less starvation-induced sleep suppression suggesting a role for insulin signaling in regulating nutrient-responsive behaviors. Together, these data support a role for insulin signaling in the Dsk-producing neurons for regulating behavior and maintaining metabolic homeostasis.

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Metabolism and behavior must be coordinately regulated for an animal to survive.

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Hormones act on the brain and peripheral tissues to control feeding and metabolism.

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Whether insulin acts on the Drosophila brain to maintain homeostasis is not known.

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Insulin signaling in Drosulfakinin (Dsk) neurons promotes triglyceride storage.

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Insulin pathway activation in Dsk neurons regulates sleep and feeding behavior.

0029 Developing a pipeline for translating genome-wide association signals to behavioral correlates of sleep dysfunction

Introduction

Insomnia is a pervasive sleep disorder affecting up to one-third of the adult U.S. population. An extensive amount of genetic association data from genome wide association studies (GWAS) has uncovered hundreds of loci associated with insomnia and other sleep traits, yet few of these targets have undergone full characterization and their contribution to sleep traits remain poorly understood. Additionally, GWAS does not necessarily determine the true effector gene(s) at a given locus, leading to frequent mischaracterization and misinterpretation of genotype-phenotype interactions.

Methods

Our group has developed a variant-to-gene mapping approach that integrates existing insomnia GWAS loci with a combination of ATAC-seq and promoter-focused Capture C-derived data in human induced pluripotent stem cell-derived neural progenitor cells. We identified candidate genes with accessible promoter regions that were contacted at high resolution by insomnia-associated SNPs residing in open chromatin. Target genes with known orthologs and available Drosophila RNAi lines were then subjected to deep phenotyping of sleep traits. Candidate genes producing greater than 20 percent change in sleep duration in Drosophila were then screened in a vertebrate zebrafish model using CRISPR/Cas9 mutagenesis in F0 larvae.

Results

This pipeline revealed fifteen genes producing robust sleep phenotypes with more than a 20 percent change in sleep duration in Drosophila. Of the candidate genes screened thus far in zebrafish, we found that disruption of pigq expression significantly (p<0.05) increased sleep duration in both zebrafish and Drosophila through regulation of sleep bout length and frequency, revealing a conserved, yet novel regulator of sleep duration. Additionally, CRISPR mutations in cbx1b and meis1b in zebrafish resulted in reduced sleep duration similar to results in Drosophila.

Conclusion

This pipeline uses cutting-edge genomic and behavioral approaches to perform high-throughput screening of existing GWAS-identified insomnia loci. This genotype-to-phenotype approach emphasizes the importance of behavioral validation following large cohort studies and narrowed the candidate gene list from more than 200 to fewer than 20 providing a more tractable set of gene targets for further molecular characterization. Cross-species validation also improves our understanding of the conservation of sleep characteristics throughout evolution.

Support (If Any)

NIH grants R01 HL143790, P01 HL094307, T32 HL07953

A screen for sleep and starvation resistance identifies a wake-promoting role for the auxiliary channel unc79

The regulation of sleep and metabolism are highly interconnected, and dysregulation of sleep is linked to metabolic diseases that include obesity, diabetes, and heart disease. Furthermore, both acute and long-term changes in diet potently impact sleep duration and quality. To identify novel factors that modulate interactions between sleep and metabolic state, we performed a genetic screen for their roles in regulating sleep duration, starvation resistance, and starvation-dependent modulation of sleep. This screen identified a number of genes with potential roles in regulating sleep, metabolism, or both processes. One such gene encodes the auxiliary ion channel UNC79, which was implicated in both the regulation of sleep and starvation resistance. Genetic knockdown or mutation of unc79 results in flies with increased sleep duration, as well as increased starvation resistance. Previous findings have shown that unc79 is required in pacemaker for 24-hours circadian rhythms. Here, we find that unc79 functions in the mushroom body, but not pacemaker neurons, to regulate sleep duration and starvation resistance. Together, these findings reveal spatially localized separable functions of unc79 in the regulation of circadian behavior, sleep, and metabolic function.

Ir56d-dependent fatty acid responses in Drosophila uncover taste discrimination between different classes of fatty acids

Chemosensory systems are critical for evaluating the caloric value and potential toxicity of food. While animals can discriminate between thousands of odors, much less is known about the discriminative capabilities of taste systems. Fats and sugars represent calorically potent and attractive food sources that contribute to hedonic feeding. Despite the differences in nutritional value between fats and sugars, the ability of the taste system to discriminate between different rewarding tastants is thought to be limited. In Drosophila, taste neurons expressing the ionotropic receptor 56d (IR56d) are required for reflexive behavioral responses to the medium-chain fatty acid, hexanoic acid. Here, we tested whether flies can discriminate between different classes of fatty acids using an aversive memory assay. Our results indicate that flies are able to discriminate medium-chain fatty acids from both short- and long-chain fatty acids, but not from other medium-chain fatty acids. While IR56d neurons are broadly responsive to short-, medium-, and long-chain fatty acids, genetic deletion of IR56d selectively disrupts response to medium-chain fatty acids. Further, IR56d+ GR64f+ neurons are necessary for proboscis extension response (PER) to medium-chain fatty acids, but both IR56d and GR64f neurons are dispensable for PER to short- and long-chain fatty acids, indicating the involvement of one or more other classes of neurons. Together, these findings reveal that IR56d is selectively required for medium-chain fatty acid taste, and discrimination of fatty acids occurs through differential receptor activation in shared populations of neurons. Our study uncovers a capacity for the taste system to encode tastant identity within a taste category.

Regional differences in cardiovascular mortality in Minnesota

Cardiovascular disease is the leading cause of death in the United States. Initial results from our health survey in the Red River Valley of Minnesota suggested elevated cardiovascular mortality in men and women in younger age groups there compared with the rest of the state. Similarly, earlier published longitudinal studies of cardiovascular mortality in Minnesota revealed increased cardiovascular mortality in counties west of a diagonal line drawn through the tip of the arrowhead region (northeast Minnesota) to the southwest corner of the state. In this study we examined cardiovascular mortality by geographic region with respect to economic factors, residence patterns, and ethnic group. Since these regions vary in geology and major land use, environmental factors were considered as well. Our present data show a significant elevation in cardiovascular mortality from 1987-1997 in men and women aged 25-59 in northwest and northeast Minnesota counties compared with central-metro counties. In contrast, south-central Minnesota shows a rate of cardiovascular mortality for that age group similar to that seen in the central-metro region. The increase in cardiovascular deaths from myocardial infarct in the younger groups in the more rural, less affluent areas of northwest Minnesota is nearly two times higher than in the central-metro counties. Genetic factors may play a role in the increased mortality recorded for northeast Minnesota. Environmental contaminants such as pesticides are additional considerations. Finally, our data suggest the need to address long-standing regional cardiovascular mortality differences and rural health care access in Minnesota.

Altered kinetics of contraction of mouse atrial myocytes expressing ventricular myosin regulatory light chain

To investigate the role of myosin regulatory light chain isoforms as a determinant of the kinetics of cardiac contraction, unloaded shortening velocity was determined by the slack-test method in skinned wild-type murine atrial cells and transgenic cells expressing ventricular regulatory light chain (MLC2v). Transgenic mice were generated using a 4.5-kb fragment of the murine alpha-myosin heavy chain promoter to drive high levels of MLC2v expression in the atrium. Velocity of unloaded shortening was determined at 15 degrees C in maximally activating Ca2+ solution (pCa 4.5) containing (in mmol/l) 7 EGTA, 1 free Mg2+, 4 MgATP, 14.5 creatine phosphate, and 20 imidazole (ionic strength 180 mmol/l, pH 7.0). Compared with the wild type (n = 10), the unloaded shortening velocity of MLC2v-expressing transgenic murine atrial cells (n = 10) was significantly greater (3.88 +/- 1.19 vs. 2.51 +/- 1.08 muscle lengths/s, P < 0.05). These results provide evidence that myosin light chain 2 regulates cross-bridge cycling rate. The faster rate of cycling in the presence of MLC2v suggests that the MLC2v isoform may contribute to the greater power-generating capabilities of the ventricle compared with the atrium.

Effects of total replacement of atrial myosin light chain-2 with the ventricular isoform in atrial myocytes of transgenic mice

BACKGROUND

In contrast to their well-known and critical role in excitation-contraction coupling of vascular smooth muscle, the effects of the myosin light chains on cardiomyocyte mechanics are poorly understood. Accordingly, we designed the present experiment to define the cardiac chamber-specific functional effects of the ventricular isoform of the regulatory myosin light chain (MLC2v).

METHODS AND RESULTS

Postnatal transgenic cardiac-specific overexpression of MLC2v was achieved by use of the alpha-myosin heavy chain promoter. Enzymatically disaggregated atrial and ventricular mouse myocytes were field-stimulated at multiple frequencies, and mechanical properties and calcium kinetics were studied by use of video edge detection and FURA 2-AM, respectively. MLC2v overexpression resulted in complete replacement of the atrial with the ventricular isoform of the regulatory myosin light chain at the steady-state mRNA and protein levels in the atria of transgenic mice. Mechanical properties of transgenic atrial myocytes were enhanced to the level of ventricular myocytes of control animals in association with modest decreases in the amplitude of the calcium transient.

CONCLUSIONS

MLC2v modulates chamber-specific contractility by enhanced calcium sensitivity and/or improved cross-bridge cycling of the thin and thick filaments of the cardiomyocyte.

Transgenic remodeling of the contractile apparatus in the mammalian heart

The structure-function relationships of the sarcomeric proteins in the mammalian cardiac compartment remain ill-defined because of the lack of a suitable model in which they can be readily manipulated or exchanged in vivo. To establish the validity of the transgenic paradigm for remodeling the mammalian heart, the murine alpha -cardiac myosin heavy chain gene promoter was used to express a ventricular myosin light chain-2 transgene (MLC2v) in both the atria and ventricles of the adult animal. Expression resulted in high levels of the transgene's transcript in both compartments. In the ventricle, the transgene was expressed against the background expression of the normal isoform. In the atrium, the transgene's expression would be ectopic, in that normally, MLC2v expression is restricted to the ventricle. Ectopic expression of the transgene in the atria resulted in a complete replacement of the atrial myosin light chain-2 protein isoform, although the endogenous isoform's steady state transcript levels were unchanged. In contrast, ventricular expression of the transgene had no effect at the protein level, despite an eightfold increase in MLC2v transcript levels. The data show that sarcomeric protein stoichiometry is maintained rigorously via posttransciptional regulation and that protein replacement can be achieved through a single transgenic manipulation.

Structural and developmental analysis of two linked myosin heavy chain genes

We have identified at the molecular level two murine myosin heavy chain (MHC) genes which encode adult skeletal isoforms. As is the case for the murine cardiac MHC genes, the genes are closely linked, head to tail. To identify the isoform encoded by each gene, we located and sequenced the 3' termini and assessed the genes' temporal and tissue-specific expression patterns using probes specific for the 3' untranslated regions. These analyses indicate that the myosin encoded by the gene located 5' in the linked pair is the murine 2A isoform. The isoform encoded by the 3'-most gene of the linked pair appears to encode an additional isoform that is expressed in a number of adult skeletal muscles. The pattern of expression of the 3'-most gene indicates that it is tightly controlled developmentally. Transcripts from this gene, when compared to those from the MHC2A and beta-MHC genes, are the predominant MHC transcripts found in the diaphragm, tongue, soleus, and masseter, indicating that it encodes a major skeletal MHC isoform.

AMTEC: a cooperative effort in medical technology education

A committee in the St. Louis Metropolitan area has been established to promote communication and cooperation among the area's existing hospital-based programs in medical technology. Area Medical Technology Education Coordinators (AMTEC) was established three years ago primarily to facilitate the administrative functions of medical technology education and to serve as an instrument for the exchange of ideas. Its primary undertaking has been the central processing of applications to the area programs, as an aid in the admission process. In addition, a continuing education program sponsored by the committee has been established, and various "curriculum sharing" activities have been sponsored for the students enrolled in the schools. Future plans for the committee include sponsoring an on-going evaluation process of graduates by employers, and establishing a criterion-referenced question pool. The authors describe the experiences of the committee to date and plans for the implementation of future goals.