Predictive Models of Recombination Rate Variation across the Drosophila melanogaster Genome
Andrew B. Adrian1,†, Johnny Cruz Corchado2,† and Josep M. Comeron1,2,*
In all eukaryotic species examined, meiotic recombination, and crossovers in particular, occur non‐randomly along chromosomes. The cause for this non-random distribution remains poorly understood but some specific DNA sequence motifs have been shown to be enriched near crossover hotspots in a number of species. We present analyses using machine learning algorithms to investigate whether DNA motif distribution across the genome can be used to predict crossover variation in Drosophila melanogaster, a species without hotspots. Our study exposes a combinatorial non-linear influence of motif presence able to account for a significant fraction of the genome-wide variation in crossover rates at all genomic scales investigated, from 20% at 5-kb to almost 70% at 2,500-kb scale. The models are particularly predictive for regions with the highest and lowest crossover rates and remain highly informative after removing sub-telomeric and -centromeric regions known to have strongly reduced crossover rates. Transcriptional activity during early meiosis and differences in motif use between autosomes and the X chromosome add to the predictive power of the models. Moreover, we show that population-specific differences in crossover rates can be partly explained by differences in motif presence. Our results suggest that crossover distribution in Drosophila is influenced by both meiosis-specific chromatin dynamics and very local constitutive open chromatin associated with DNA motifs that prevent nucleosome stabilization. These findings provide new information on the genetic factors influencing variation in recombination rates and a baseline to study epigenetic mechanisms responsible for plastic recombination as response to different biotic and abiotic conditions and stresses.
NPHP10 affects AIMP2 localization and alters its downstream target, p53
Bardet-Biedl Syndrome (BBS) is an autosomal recessive, pleiotropic disorder, with 21 genes currently identified as causative. One of these genes is serologically defined colon cancer antigen 8 (NPHP10 [MIM 613524]), a nephronophthisis-related ciliopathy gene (NPHP10 or BBS16). Patients with mutations in this gene exhibit retinal and renal abnormalities, obesity, and learning disabilities. Currently, little is known about the molecular functions of NPHP10 and how loss of NPHP10 function leads to the observed phenotypes. Our previous work identified strong interactors of NPHP10, consisting mainly of components of the multi-aminoacyl tRNA synthetase complex (MSC). More specifically, 8 out of 9 aminoacyl tRNA synthetases (ARS) as well as aminoacyl-tRNA-synthetase-complex interacting multifunctional protein 2 (AIMP2) interact with NPHP10. We also determined that among the MSC components, NPHP10 directly interacts with AIMP2. AIMP2 has a known non-canonical role in the apoptotic pathway via p53 activation. In response to DNA damage, a subset of AIMP2 localizes to the nucleus and binds to and prevents the ubiquitination of p53. This leads to an upregulation of apoptosis in response to DNA damage. Recently, we developed two NPHP10 knockout IMCD3 cell lines using CRISPR-mediated technology. Using these cell lines, we examined the effect of NPHP10 loss on AIMP2 localization in these cells. Immunofluorescence microscopy and cell fractionation with immunoblotting show that loss of NPHP10 leads to increased AIMP2 in the nucleus of cells. Additionally, we showed that overall p53 levels increased in knock-out cells. Further work focuses on how these changes affect downstream elements of p53 utilizing a luciferase reporter assay.
The g-Protocadherins interact with neuroligin-1 and inhibit its synaptogenic activity
Michael J. Molumby, Rachel M. Anderson, Dillan J. Newbold, Norah K. Koblesky, Andrew M. Garrett, Dietmar Schreiner, Jason J. Radley, Joshua A. Weiner
The a-, b-, and g-Protocadherins (g-Pcdhs) are cadherin superfamily adhesion molecules encoded by clustered gene families. The 22 g-Pcdhs are combinatorially expressed in the brain, and play critical roles in synaptogenesis, dendrite arborization and patterning, and the survival of subsets of neurons. The g-Pcdhs can interact promiscuously with each other, and with other clustered Pcdhs, in cis, but interact strictly homophilically in trans. Mice lacking the g-Pcdhs in the cerebral cortex exhibit severely reduced dendrite arborization (Garrett, et al., Neuron, 2012). Recently we demonstrated that g-Pcdhs promote dendrite arborization in vivo through local neuron-neuron and neuron-astrocyte homophilic interactions (Molumby et al., Cell Reports, 2016). Though -Pcdhs regulate the progression of spinal cord synaptogenesis (Garrett and Weiner, J. Neurosci., 2009), a role for these molecules in cortical dendritic spines and synapses has yet not been examined.
Here, we provide evidence that the g-Pcdhs negatively regulate synapse formation and spine morphogenesis in forebrain neurons. Mice lacking all -Pcdhs in the cortex exhibit significantly increased spine density in vivo, while spine density is significantly decreased in mice overexpressing one of the 22 -Pcdh isoforms. We thus asked whether the -Pcdhs might be inhibitory in an artificial synapse co-culture assay. Indeed, we found that multiple g-Pcdhs can, when co-expressed in COS cells, strongly inhibit the ability of the synaptic cell adhesion molecule neuroligin-1 to promote presynaptic differentiation in contacting axons. The g-Pcdhs physically interact in cis with neuroligin-1 on dendrites of cultured neurons, and can co-immunoprecipitate neuroligin-1 both in vitro and in vivo. We present in vitro evidence that the interaction between -Pcdhs and neuroligin-1 disrupts the latter’s binding to its presynaptic partner neurexin1β. Additionally, we show that g-Pcdh overexpression in cultured hippocampal neurons suppresses the increase in spine density observed upon neuroligin-1 overexpression. This work suggests a potential new mechanism by which g-Pcdhs regulate the “choice” between dendrite arbor growth and formation and/or stabilization of dendritic spines and synapses in the developing brain.
Identification of a novel, de novo FGFR1 mutation in an individual with Hartsfield Syndrome
Harney, L.A., Bernabe, H., Nidey, N., Standley, J., Schnieders, M., Murray, J.C.
Mutations in FGFR1 have recently been associated with Hartsfield Syndrome, a disease with the rare combination of holoprocencephaly (HPE) and ectrodactyly (EEC). Here we report a novel, de novo mutation in FGFR1 in a previously unsolved clinical case of multiple congenital anomalies. The proband presented with bilateral cleft lip and palate, malformed auricles and bilateral EEC of his hands and feet at birth. He was later diagnosed with diabetes insipidus, spastic quadriplegia, developmental delay, and agenesis of the corpus callosum. Microarray analysis resulted in an unremarkable copy number variant profile. Although this exact combination of clinical features has not been reported in a patient to date, we noted phenotypic overlap with individuals with Hartsfield Syndrome. Sequencing of FGFR1 identified a novel and previously unreported de novo mutation in exon 11 (p.G487C), resulting in the diagnosis of Hartsfield Syndrome for this individual.
Drosophila vs The World: The Nkd EF-Hand Domain Modulates Divergent Wnt Signaling Outputs
Autumn N. Marsden, Sarah W. Derry, Trudi A. Westfall, Diane C. Slusarski
The Wnt signaling network plays critical roles in development and is implicated in human disease. Wnts comprise a complex signaling network that, upon ligand binding, activates the phosphoprotein Dishevelled (Dvl), leading to distinct outputs including polarized cell movement (known as planar cell polarity, Wnt/PCP) and stabilization of the transcription factor β-catenin (Wnt/β-catenin). The mechanisms that determine a specific output are not completely understood, especially because they share receptors and cellular effectors, such as Naked-cuticle (Nkd), a Dvl-interacting protein. The Nkd protein contains a myristoylation domain and an EF-hand, a putative calcium binding domain. Genetic evidence in Drosophila demonstrates that Nkd acts as a Wnt/β-catenin antagonist, while in contrast, Nkd modulates both branches of Wnt signaling in vertebrates. We hypothesize that the specialized role of Nkd in Drosophila is due to a disrupted EF-hand that cannot not bind calcium. Indeed, this change is unique to Drosophila and is not present in closely related insects. To test the role of the Nkd EF-hand in Wnt signal integration, we created Nkd with a neutralized EF-hand, as well as a Drosophila-like EF-hand, and manipulate Nkd activity in the zebrafish. Using a combination of biochemical and functional assays, we identified a requirement for the Nkd EF-hand in Wnt/PCP but not in Wnt/β-catenin transcriptional outputs. We demonstrate that the Drosophila-like Nkd antagonizes Wnt/β-catenin more robustly than zebrafish Nkd. The EF-hand of Nkd is similar to the EF-hand of a known calcium binding protein, Recoverin, a myristoyl-swtich protein that shuttles between the membrane and the cytoplasm depending on its calcium bound state. Consistently, we observe that NkdWT shows localization changes in the calcium fluxing DFCs versus calcium quiescent cells but not the mutant forms. The Nkd EF-hand may serve to interpret the physiology of a cell receiving multiple cues and provides mechanistic insight into Wnt signal integration in vivo.
Assessment of Whole-Exome Sequence Data in Attempted Suicide within a Bipolar Disorder Cohort
Suicidal behavior, which includes both attempted and completed suicide, is the source of tremendous cost and loss of life. Within the United States alone, suicidal behavior accounts for approximately 836,000 emergency room visits and over 41,000 deaths, ranking as the 10th leading cause of death overall and the 2nd leading cause of death for ages 10-34 as reported by the CDC. Efforts to better understand the biological basis and risk factors for suicidal behavior have included a large number of genetic studies due to a significant genetic component to this phenotype. Existing genetic studies have focused primarily on specific candidate genes and/or common variation and have left a significant proportion of the expected heritability of suicidal behavior unexplained. Our current work is focused on the investigation of the contribution of rare functional variation to the risk for suicidal behavior through the use of next-generation sequencing techniques. Specifically, we have performed a comprehensive analysis of 1,018 whole-exome sequences, divided into 387 individuals with bipolar disorder and a history of suicide attempt and 631 individuals with bipolar disorder and no past suicidal behavior. We performed analyses within ~490,000 single variants, across all covered genes, and within 3,621 pathways. No result from any of these analyses survived conservative Bonferroni correction, though several suggestive and potentially important findings were identified within the gene and pathway-based results. In addition, this study generated a large and highly novel dataset that will be of substantial value to future genetic investigations within suicidal behavior. This effort marks the first large-scale effort to identify the contribution of rare functional variation to suicidal behavior and provides the basis for expanded efforts to explain the biological basis of this devastating phenotype.
Genes involved in bone remodeling are mutated in chronic recurrent multifocal osteomyelitis (CRMO)
Chronic recurrent multifocal osteomyelitis (CRMO) is a rare, pediatric, autoinflammatory disease characterized by bone pain due to sterile osteomyelitis, and is often accompanied by psoriasis or inflammatory bowel disease. Via whole-exome sequencing, we detected a homozygous mutation in the filamin-binding domain of FBLIM1 in an affected child with consanguineous parents. Microarray analysis of bone marrow macrophages from the CRMO murine model determined that the Fblim1 ortholog is the most differentially expressed gene, further implicating it in disease pathogenesis. We sequenced FBLIM1 in 96 CRMO subjects and found a second proband with a novel frameshift mutation in exon 6 and a rare regulatory variant. In two other families, we detected a shared rare mutation in a related gene, PLCG2. FBLIM1 and PLCG2 are both directly involved in β-integrin activation, which was recently implicated in sterile inflammation via Bruton tyrosine kinase signaling. Additional work involves functional validation of the FBLIM1 and PLCG2 mutations, and pathway analysis of exomes from a cohort of individuals with CRMO. Our data suggest CRMO is a disorder of integrin activation and imbalanced bone remodeling.
TFAP2A drives melanocyte gene expression in parallel with MITF
Hannah E. Seberg, Eric Van Otterloo, Stacie K. Loftus, Greg Bonde, Ramakrishna Sompallae, Juan F. Santana, J. Robert Manak, William J. Pavan, Robert A. Cornell
Disruption of the transcription factor network governing melanocyte differentiation contributes to the pathogenesis of pigmentation disorders and melanoma. Transcription factor activator protein 2 alpha (TFAP2A) is expressed in melanoblasts, and mutations in this gene cause pigmentation phenotypes in humans, mice, and zebrafish. However, the the transcriptional targets of TFAP2A, and the extent to which they are shared with MITF, a master regulator of melanocyte biology and melanoma progression, have been unclear. To determine the position of TFAP2A in the melanocyte gene regulatory network, we conducted anti-TFAP2A ChIP-seq to create profiles of TFAP2A-bound loci in melan-a cells and human primary melanocytes. We then used microarray analysis in zebrafish and mouse immortalized melanocytes (melan-a cells) to profile genes that are downregulated in the absence of TFAP2A. Genes at the intersection of the microarray and ChIP-seq profiles are likely direct targets of TFAP2A. These include mc1r and several melanin synthesis or melanosome structural genes, most of which are also thought to be direct targets of MITF. Comparison of our TFAP2A ChIP-seq profile with a published MITF ChIP-seq profile showed that TFAP2A peaks overlap MITF peaks at a large fraction of promoters and enhancers. In reporter assays, deletion of TFAP2A binding sites decreased activity of a minimal TRPM1 promoter, similar to published results for deletion of MITF binding sites from this element. We also observed a genetic interaction between tfap2a and mitfa in zebrafish. The significance of these findings is, first, they show that TFAP2A and MITF work in parallel to promote gene expression in melanocytes. Second, they show that a widely-expressed transcription factor, TFAP2A, co-operates with a more tissue-restricted transcription factor, MITF, to directly regulate expression of lineage-specific melanocyte genes. Third, they suggest that the reduction of TFAP2A expression levels observed in advanced melanoma is a cause and not an effect of melanoma progression, as such a reduction would be expected to decrease the pro-differentiation effect mediated by TFAP2A.
Speciation Genetics in Drosophila: Insights from Male and Female Transcriptomes
Population genetic models predict that the X chromosome will evolve at a faster rate than autosomes (i.e., faster-X evolution). The basis for faster-X evolution is that recessive genes located on the X chromosome can be exposed in males while these genes are hidden if located on the autosomes. Evaluations of protein-coding sequences have indeed shown mixed results with some studies showing an excess of divergence on the X chromosome compared to autosomes, particularly in genes expressed higher in males than in females (i.e., male-biased genes). In addition, whole-genome analyses of gene expression in Drosophila yakuba and D. santomea males indicate that X-linked genes are more differentially expressed between species (i.e., faster-X evolution of gene expression) than autosomal genes. This trend is once again strongest for male-biased genes. However, these studies utilized only males and were therefore limited in their expression profiles. Here, we investigate the whole-genome profiles of D. yakuba and D. santomea males and females to determine the relative rates of evolution for all gene classes. In addition, we explore the implications of sex chromosome inheritance on autosomal gene expression in the hybrids of these species.
THE ROLE OF ENDOGENOUS MICROBIOTA IN SEIZURE-LIKE BEHAVIOR OF SHUDDERER, A DROSOPHILA VOLTAGE-GATED SODIUM CHANNEL MUTANT
It is widely recognized that mutations in genes encoding voltage-gated sodium (Nav) channels contribute to the etiology underlying various seizure disorders. Shudderer (Shu), a gain-of-function mutant for the Drosophila Nav channel gene, exhibits neuronal hyperexcitability and seizure-like behavioral defects, including spontaneous jerking and heat-induced convulsion. Results of microarray analyses indicated that Shu mutants have an increased innate immune response and reduced insulin signaling. Because the endogenous gut microbiota has a substantial impact on the host immune system and insulin-mediated metabolic regulation, we hypothesized that the microbiome plays a role in Shu phenotypes. Intriguingly, removing the gut microbiota of Shu and wild-type (WT) flies using antibiotic-containing or sterile food significantly suppressed Shu behavioral phenotypes while having no effect on WT behavior. Culturing homogenized guts dissected from Shu and WT flies on MRS agar revealed drastic differences in the number of culturable bacteria. Further, we performed high-throughput sequencing of the bacterial 16S ribosomal RNA gene which revealed species-specific differences in the gut microbiome of Shu and WT flies. Because neurological disorders and changes in the microbiota can individually increase oxidative stress in an organism, we examined the antioxidant response in the guts of Shu and WT flies using a GFP reporter, (GST-D-GFP). GST-D-GFP expression was altered in Shu and WT flies fed antibiotics, suggesting a potential involvement of oxidative stress in the antibiotic-dependent rescue of seizure-like behavior. Additional experiments will determine ROS levels in Shu and WT flies and are expected to yield a better understanding of the role of the microbiome in the context of seizure disorders.
Mutation in regulatory protease, CAPN5, results in eye disease
Uveitis (intraocular inflammation) causes significant visual morbidity and blindness in all ages, yet it has proven refractive to current therapies, underscoring the critical need for new clinical approaches. Nevertheless, a major barrier to developing new medicines has been the lack of any specific molecular cause for the disease. To gain insight into the molecular mechanisms driving uveitis, we sought the disease-associated gene in kindreds with a Mendelian form—Autosomal Dominant Neovascular Inflammatory Vitreoretinopathy (ADNIV). Our studies showed the underlying cause of ADNIV was mutations in CAPN5 (calpain-5), making CAPN5 the first nonsyndromic uveitis gene discovered. This discovery provides an unprecedented starting point for investigating the substantial gap in our understanding of the molecular basis of ocular inflammation.
CAPN5 is a calcium-activated, intracellular protease expressed at photoreceptor synapses. Similar to the function of other calpains, we believe that proteolysis by CAPN5 is a tightly controlled, post-translational regulatory mechanism that deploys protein fragments with altered activity. Although it is a member of a relatively large, well-studied family, little is known regarding the CAPN5 natural substrates. One exception to this is CAPN5 autoproteolysis, which uncovers one natural substrate of CAPN5: CAPN5 itself. We aim to identify the sequences in CAPN5 that are the targets of autoproteolysis and also to determine the CAPN5 cleavage site in a substrate we recently identified, platelet-derived growth factor B (PDGFB). PDGFB was previously identified as a protein cleaved into an active angiogenic form by an unknown protease, and PDGFB is active in a number of similar eye diseases, including AMD, PVR and diabetic retinopathy. The insight gained from these studies may eventually be used to design therapies for a variety of previously untreatable eye diseases.
Functional Characterization of Epilepsy Related Genes in Zebrafish
TD Fuller1,2, TA Westfall1, DC Slusarski1
1Department of Biology, University of Iowa, Iowa City, IA 52242, 2Interdisciplinary Graduate Program in Genetics
Statement of Purpose: Epilepsy is a chronic condition of recurrent seizures which affects approximately one percent of the general population. Though several causative genes have already been identified, these account for only a small percentage of all the genetically caused cases of epilepsy. Further, even when genes are identified, we lack tractable animal models to rapidly translate these findings into mechanistic insights and ultimately new anti-epileptic therapies. For this reason, the zebrafish is increasingly being used as a model of epilepsy due to its high genetic and physiologic homology to humans and its seizure-like behavior in response to various pharmacological and genetic manipulations. Using High throughput sequencing, a significant number of gene variants are being identified, yet their role in the disease state remain unknown. My project utilizes the zebrafish and focuses on characterizing the functional role of 15 genes in the NIH Undiagnosed Diseases Program for which mutations have been associated with epilepsy, and for which zebrafish orthologues have been identified. Methods: I isolated the zebrafish orthologues and characterized gene expression patterns by RTPCR and whole mount in situ hybridization techniques. We previously demonstrated that knockdown of Prickle (PK), a gene associated with human epilepsy, sensitizes zebrafish to seizure-inducing drugs through the use of larval motility assays. To facilitate high-throughput in vivo screens, I adapted this approach and developed a code to rapidly and efficiently analyze the generated data sets. This allowed for the characterization of the 15 candidate genes in the context of seizure sensitization. Results: Of the fifteen candidates, I found five: syne1b, sms, ccdc89, wscd1, and nid2a, to result in seizure sensitization when knocked down in the zebrafish. I show that each of these genes is expressed in specific regions in the brain during critical times of neuronal development. Further, I find genes expressed in the retina result in axon defects when knocked down.
The Conserved and Unique Determinants of Crossover Events
Meiotic recombination promotes genetic diversity and allows for the continuous adaptation of natural populations to ever changing environments. Mechanistically, recombination relies heavily on protein-protein and protein-DNA interactions. The goal of my project is to find out how genetic incompatibilities through failed interactions disrupt the tight control of recombination localization across the genome in interspecific hybrids. To this end, I am currently generating high-resolution recombination maps in two closely related species of fruit flies, Drosophila yakuba and D. santomea, and their hybrids. Our findings will have a positive impact in our understanding of the role of protein interactions in recombination control, will illuminate the pervasiveness of sexual reproduction and recombination in nature, and will enable the development of new theoretical models on the maintenance of genetic variation.
Genetic therapeutic strategies for the Bardet-Biedl Syndrome (BBS) M390R mutation
Bardet-Beidl Syndrome (BBS) is a pleiotropic ciliopathy that causes a variety of phenotypes in humans and animal models, including blindness and male infertility. BBS is considered a model disease for ciliopathies in general, which affect approximately 1 in 1000 people worldwide. There are no current efficient non-surgical treatments for ciliopathies, illustrating a critical need for new therapeutic strategies. The most common cause of BBS is the M390R mutation in Bardet-Biedl Syndrome 1 (BBS1) gene, an essential component of the BBsome that is required for basal body function and primary ciliogenesis. This mutation leads to photoreceptor degeneration and dysfunctional flagella in sperm. My objective is to use gene replacement and editing techniques to restore male fertility and prevent retinal degeneration in a Bbs1M390R/M390R mouse model. I hypothesize that these phenotypes are amenable to correction by gene therapy and gene correction. Here, I will test this hypothesis by using BBS1 gene therapy and correction as a strategy to preserve photoreceptors in a mouse model. First, I will elucidate the mechanism by which BBS1 overexpression in the retina causes toxicity. I hypothesize that overexpression of BBS1 leads to homodimerization and subsequent inability to incorporate into the BBsome, thereby affecting ciliary function. I will deliver adeno-associated viruses (AAVs) expressing BBS1 driven by the BBS1 promoter to the Bbs1M390R/M390R mice postnatally, and subsequently test photoreceptor preservation by electroretinogram (ERG) and immunohistology. I will also use CRISPR/Cas9 mediated homologous recombination to correct the M390R mutation in vitro and in vivo. In addition to Cas9, I will employ Cpf1, a Cas9-like class 2 CRISPR endonuclease, to simultaneously knock out dysfunctional BBS1 and introduce functional BBS1 cDNA driven by the BBS1 promoter. By correcting the germline in vivo, all downstream progeny should effectively be corrected. While most studies using gene editing techniques are completed ex vivo, my approach will show the level of correction that can occur in vivo using various novel methods. These techniques may be applied to other degenerative genetic diseases.
LINCing prostaglandin signaling and the regulation of collective cell migration.
Emily Toombs, Tina Tootle
Collective cell migration – the coordinated movement of tightly or loosely associated cells – is important for development and tumor invasion. Many signals are involved in collective cell migration including mechanotransduction, or the transfer of physical force into electrical or chemical signals. While there are many ways in which cells can respond to force, a key mechanism important for cellular migration is the direct connection of the cytoskeleton to the nucleoskeleton via the Linker of Nucleoskeleton and Cytoskeleton (LINC) complex. Alterations in the LINC complex affect nuclear shape, nuclear position, and transcription; however, not much is known about its regulation. Another mechanism regulating cell migration is prostaglandin (PG) signaling. PGs are short-range lipid signals that are implicated in many processes, but, at the same time, little is known about their downstream targets. Our lab has shown that PGs have a large affect on actin remodeling via regulating actin binding proteins. Importantly, actin binding proteins play key roles in mechanotransduction; however, PG signaling has not been previously implicated in regulating mechanotransduction. Using the robust genetic model system of Drosophila, and the well characterized process of oogenesis or follicle development, we present the first evidence that PGs regulate the LINC Complex during the collective and invasive cell migration of the border cells. We hypothesize that PG signaling regulates perinuclear Fascin to control LINC complex function. This hypothesis is based on our prior studies that revealed PG signaling regulates Fascin, an actin bundling protein widely implicated in cell migration. This regulation occurs, in part, by PGs modulating the localization of Fascin, including Fascin’s new perinuclear localization. In both PG synthesis and LINC complex mutant follicles Fascin’s localization to the nuclear periphery is lost. Furthermore, our collaborators have found that in cancer cells, Fascin interacts directly with the LINC Complex. Here we present that loss of PGs or the LINC complex results in delayed and aberrant border cell migration; importantly, Fascin is highly expressed in the border cells. We have identified several tools and approaches that will allow us to quantitatively assess the connection between PG signaling and the LINC complex, as well as the role of Fascin in LINC complex regulation. This research is expected to provide the mechanistic insight into how PGs regulate cellular migration by controlling actin binding proteins to modulate the LINC complex, and, therefore, affect mechanotransduction. These findings will improve our understanding of the functions of PGs, Fascin, and the LINC complex both developmentally and during tumor progression.
Defining the Mediator CDK8 Module in Cardiac Stress
The Mediator complex plays key roles in regulating the transcription of nearly all RNA PolII transcribed genes. Mediator is comprised of four modules: the head, middle, tail (collectively known as the core Mediator), and the CDK8 module which is known to transiently interact with the core Mediator. Classically, it was believed that the composition of Mediator was largely invariant and that the CDK8 module was largely repressive in function. However, recent evidence suggests that during development and cellular differentiation, the composition of core Mediator and CDK8-Mediator changes. This compositional change may account for the large scale transcriptional reprogramming observed in differentiated cells. One component of the CDK8 module is Med13. Cardiac Med13 has been previously shown to regulate cardiac and whole body metabolism, with cardiac expression of Med13 being inversely proportional to susceptibility to metabolic syndromes. In murine cardiomyocytes, the expression of most CDK8 module proteins (including MED13) is decreased following birth. However, recent findings suggest that in cardiomyocytes isolated from mice exposed to cardiac stress, the expression of the CDK8 module proteins is increased. This change in expression may result in a change in composition of CDK8-Mediator, resulting in a modified transcriptome in the cardiomyocytes exposed to cardiac stress. This research aims to define the composition of the CDK8 module as well as components of core Mediator during disease progression and in CDK8 submodule mutants as a means of elucidating the etiology of cardiovascular disease.
Ana Castro’s Abstract
The role of the anti-sigma factor RsiV in lysozyme sensing and stress response
A Castro1, Jessica Hastie1, Craig Ellermeier1
Microbiology Department, College of Medicine, University of Iowa
Bacteria respond to changes in their environment by altering gene expression. Understanding the mechanism by which information is transmitted from outside the cells across the membrane is critical, as it will provide insight into how cells regulate resistance mechanisms. The goal is to gain insight into stress response mechanisms that may contribute to microbial survival in rapidly changing conditions. Extra cytoplasmic function (ECF) s factors are a subset of s factors that allow many organisms to sense and respond to changes in the environment. Most ECF s factors are held in an inactive state by an anti-s factor that prevents the ECF s from interacting with RNA polymerase. Certain envelope stresses in bacteria include the regulated intramembrane proteolysis (RIP), a mechanisms which results in the sequential cleavage of membrane-bound proteins, including s factors. In Bacillus subtilis, the ECF s factor, sV, belongs to the ECF30 subfamily of ECF s factors, members which are primarily found in firmicutes.sV is activated specifically by lysozyme, a critical component of the host innate immune system. sV induces resistance to lysozyme in organisms such as Clostridium difficile. In the absence of lysozyme sV is inhibited by the anti-s factor RsiV. In response to lysozyme, RsiV is cleaved by signal peptidase at site-1 leading to the release and activation of sV. We have shown that RIP dependent mechanism of sV activation is dependent on the anti-s, RsiV, binding to the inducing signal, lysozyme. My project involves using B. subtilis as a model to determine RsiV factors that allow signal peptidase cleavage in the presence of lysozyme. We will determine how σV is important for pathogenesis and virulence in B. subtilis. The objective of this project is to determine the mechanisms by which RsiV binding to lysozyme allow for signal peptidase cleavage at site-1 in the extracellular domain.
Joseph Giacalone’s Abstract
Disease modeling using patient-specific photoreceptor precursor cells
Induced pluripotent stem cell (iPSC)-derived photoreceptor precursor cells can be used to study biological processes and have the potential to restore vision to patients with retinal degenerative diseases like retinitis pigmentosa. Biopsies were obtained from patients with inherited retinal degeneration and fibroblast lines were established. Patient-specific iPSCs were then generated, clonally expanded and validated. Post-mitotic photoreceptor precursor cells were generated using a stepwise 3D differentiation protocol. This method will serve as a platform for studying RPGR-associated XLRP.
Matt Strub’s Abstract
Genomic Signature-Based Approaches to Drug Repositioning for ΔF508-CFTR Rescue
Cystic fibrosis (CF) is a lethal autosomal recessive disease caused by mutations in the CF transmembrane conductance regulator (CFTR) gene. The most common CFTR mutation, termed ΔF508, is a 3 base deletion resulting in the loss of a phenylalanine residue. This causes protein misfolding, resulting in proteosomal degradation. However, if CFTR-ΔF508 is allowed to traffick to the cell membrane, anion channel function may be partially restored. The McCray Lab previously reported that transfection with a miR-138 mimic or siRNA knockdown of SIN3A in primary cultures of CF airway epithelia increases CFTR mRNA and protein levels, and partially restores cAMP-stimulated Cl– conductance. The Connectivity Map (CMAP) is a catalog of gene expression profiles from cultured human cells treated with a variety of bioactive chemical compounds and has pattern-matching software to mine data. A CMAP query using previously generated gene expression signatures identified 27 candidate small molecules that mimicked miR-138 and DsiRNA SIN3A treatments. Our lab reported the identification of 4 small molecules that partially restored CFTR-ΔF508 function in primary CF airway epithelia, highlighting the utility of a genomic signature approach in drug discovery. Currently, the NIH is greatly expanding the CMAP dataset into the Library of Integrated Network-based Cellular Signatures (LINCS). Here we query the LINCS database using a meta-analysis of rescue signatures to identify candidate compounds for rescue of CFTR-ΔF508 function.
In collaboration with the Broad Institute, we used previously generated gene sets to iteratively query the Library of Integrated Network-based Cellular Signatures (LINCS). 125 candidate small molecules were selected for further testing. Functional screens performed in CFBE (ΔF508/ΔF508) cells identified 7/125 compounds that partially rescued ΔF508 function, as assessed by cAMP-activated Cl– conductance. Additional experiments performed to assess their activity in primary human CF epithelial cells confirmed the ability of these seven compounds to partially rescue ΔF508 function. Interestingly, some of these compounds showed significant cooperativity when administered with C18. We then obtained 70 congeners, derivatives, or related compounds of the seven validated LINCS hits and identified 18/70 compounds that increased cAMP-activated chloride conductance by at least 50% compared to a DMSO control. We also tested compounds in the presence of C18 and identified four compounds that increased conductance by at least 40% compared to a C18 control.
We recently used a meta-analytic approach to analyze multiple rescue signatures and relevant pathways to create a prioritized candidate drug list for functional screens. Transcriptomic profiles of RNAi (siRNA knockdown of SIN3A, SYVN1, and NEDD8, and miR-138 overexpression) and temperature (27°C for 24 hours, 40°C for 24 hours, and 27°C for 24 hours followed by 40°C for 24 hours) treatments were used to represent a rescue signature. Profiles of primary cells (both human and pig) from CF and healthy donors were used to represent a disease signature. The rescue and disease signatures were then analyzed together to create representative lists of up- and down-regulated genes. Meanwhile, gene sets were extracted from relevant curated pathways related to CFTR trafficking (from Thomson Reuters MetaCore). Gene sets from both strategies were then scored against all drug profiles contained in the CMAP and LINCS databases. The rescue signature- and disease signature-based scores were combined to form an overall score that was used to identify and prioritize candidate molecules. We have tested 115 compounds from the resulting meta-analysis-based candidate drug list and 36 compounds have been shown to increase cAMP-activated chloride conductance by at least 30% compared to DMSO. Additionally, 21 compounds in the presence of C18 increased conductance by at least 30% compared to a C18 control. Further analysis of preliminary hits will include validation in primary cells. We also have the ability to test the most efficacious drugs in our ΔF508/ΔF508 porcine model. Lastly, we are performing chemogenomic enrichment analysis using the results of all tested compounds to elucidate possible classification, structural, or transcriptomic similarities between efficacious drugs. Such analysis may help us to identify and prioritize additional candidates.
Tricia Braun’s Abstract
Genome-wide DNA methylation analysis of glucocorticoid treatment in human Blood and saliva and the correlation of DNA methylation between peripheral tissues and brain
Patricia Braun1, Yasunori Nagahama2, Marie Hafner1, Lauren O’Sullivan1, Melissa McKane1, Tanner D. Gardiner1, Andrew Grossbach2, Matthew A Howard III2, Hiroto Kawasaki2, James B. Potash1, Gen Shinozaki1
1Department of Psychiatry, University of Iowa Carver College of Medicine
2Department of Neurosurgery, University of Iowa Carver College of Medicine
Glucocorticoids help regulate the stress response, and an imbalance of glucocorticoids has been implicated in depression. Within mouse models, candidate genes have been shown to be differentially methylated in response to glucocorticoid treatment. Using the Infinium HumanMethylation 450K Array, which covers over 450,000 CpGs, we performed preliminary studies on genome-wide DNA methylation (DNAm) changes that occur within saliva samples from 10 subjects and blood samples from 6 subjects before and after treatment with dexamethasone, a corticosteroid, in the context of neurosurgery. Within saliva samples, average DNAm differences of >10% were observed for 84 CpGs. One CpG in a long intergenic non-coding RNA (LINC00871) attained near genome-wide level of significance (average DNAm: pre-dexamethasone 49%, post-dexamethasone 38%; p=5×10-7). Within blood samples, over 200 CpGs had >20% difference; however, none were statistically significant. These findings provide initial evidence for an influence of glucocorticoids on DNAm within humans. To understand the relevance DNAm in saliva and blood to brain DNAm, we also examined the correlation of DNAm between peripheral tissues and brain tissues. This is an essential issue for not only our analysis, but for the field more broadly. We obtained saliva, blood, and live brain tissue samples from 13 patients undergoing neurosurgery and analyzed genome-wide DNAm with the 450K Array. Blood and saliva showed a high degree of correlation for DNAm (r2=0.97), and saliva DNAm was revealed to be more similar to brain DNAm (r2=0.84) than blood (r2=0.81; p<1×10-4). As we have ongoing access to samples from neurosurgery patients, we will expand these studies to understand the extent to which peripheral tissues can be used as surrogate tissues for DNAm in the brain. Furthermore, we will collect samples from oral surgery patients given a higher dosage of glucocorticoids to more fully ascertain the global effects of glucocorticoids on DNAm.