Whole Exome Analysis of Individuals and Families with Chronic Recurrent Multifocal Osteomyelitis (CRMO)
Chronic recurrent multifocal osteomyelitis (CRMO) is a rare, autoinflammatory bone disease presenting in infancy and childhood. While CRMO is characterized by painful bone lesions, it is often comorbid with psoriasis or Crohn disease and many patients have close relatives with either of the more common disorders. Some syndromic cases of CRMO are caused by truncation mutations in the interleukin-1 receptor agonist (IL-1RA) gene and these children respond very well to treatment with recombinant IL-1RA. However, most cases are non-syndromic with an unknown genetic cause, although many patients respond to TNF-α blocking agents, implicating the pathway in the disease. Using whole exome sequencing paired with genetic analyses based on inheritance patterns in several affected families, I hope to determine a component of CRMO’s underlying genetics. Preliminary results implicate a shared pathway in the pathogenesis of the disease. I am currently sequencing a candidate gene in a large cohort of CRMO samples from our laboratory.
Effect of diet on genetically inherited seizure-like behavior in Drosophila
Hung-Lin Chen,1 Patrick Lansdon,1 Junko Kasuya,2 Toshihiro Kitamoto1,2
1Interdisciplinary Genetics Ph.D. Program and 2Department of Anesthesia
Nutritional therapies have the great potential to prevent or treat various neurological disorders, such as epilepsy, in an effective, natural, and economical manner. However, their exact therapeutic values have not been rigorously evaluated in most cases and the molecular mechanisms responsible for their beneficial effects remain elusive. The goal of this study is to unravel the fundamental molecular underpinnings of nutritional therapies for genetically inherited neurological dysfunctions using the fruit fly Drosophila melanogaster as a model organism. Shudderer (Shu) is a classical Drosophila mutant that is characterized by strong spontaneous jerking and twitching. Our molecular analysis revealed that Shu carries a gain-of-function mutation in the voltage-gated sodium channel gene, paralytic. Here we report that feeding Shu mutants a modified diet results in drastic improvement of their seizure-like phenotypes. Shu needs to be fed the “therapeutic” diet during the larval stage in order to receive a maximum benefit from the food, suggesting that the diet has a therapeutic effect on Shu by affecting development of the nervous system. These findings are significant because they provide an unprecedented opportunity to employ versatile experimental tools available for Drosophila and investigate the mechanisms underlying the diet-dependent improvement of inherited behavioral abnormalities under strictly controlled genetic and environmental conditions.
SPECIATION GENETICS IN DROSPHILA: INSIGHTS FROM GENES, GENOMES, AND TRANSCRIPTOMES (YEAR 3)
Speciation typically occurs when a single species splits into two populations in which gene flow is severely reduced. Over time, the two populations accumulate genetic differences that eventually produce two independent species. While hybridization between two species, and thus the potential for gene exchange, has traditionally been viewed as a reproductive mistake, recent studies suggest that it is not as rare as once believed. Previous studies suggest that although regions of the mitochondrial and nuclear genomes can be exchanged independently or together, the X chromosome often plays a large role in speciation and gene exchange is typically barred on the X. One way in which the X chromosome may play a large role in speciation is though X-linked trans-regulatory elements (TREs) effecting the expression of autosomal genes through interactions with autosomal cis-regulatory elements (CREs). Indeed, whole-genome analyses of gene expression in our lab indicate that X-linked genes are more differentially expressed between species while autosomal genes are preferentially misexpressed in hybrid males. Because there is only one copy of the X chromosome producing X-linked TREs in hybrid males, we hypothesize that the hemizygosity of the X chromosome leads to greater levels of autosomal misexpression in the heterogametic sex. To investigate the effects of the uni-parental origin of the X chromosome on autosomal misexpression, we will analyze whole-genome expression in attached-X stocks of Drosophila yakuba, D. santomea, and their hybrids wherein the X chromosomes are inherited in a uni-parental manner in females. It is my expectation that if the hemizygosity of the X chromosome contributes to autosomal misexpression in males, attached-X F1 hybrid females will mimic results from F1 hybrid males.
Calcium-dependent Naked-Dishevelled Interaction Modulates Wnt Signalling Outputs
AN Marsden1,2, SW Derry1, TA Westfall1, DC Slusarski1
1Department of Biology, University of Iowa, Iowa City, IA 52242, 2Interdisciplinary Graduate Program in Genetics
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 is not completely understood, especially since they share receptors and cellular effectors. My project focuses on two such shared components that also bind each other, Dvl and Naked (Nkd). Previously we demonstrated that Nkd is required for zebrafish dorsal forerunner cell (DFC) migration, Kupffer’s vesicle formation and proper organ laterality. Moreover, we identified calcium fluxes in the DFCs and determined that the EF-hand motif in Nkd weakly binds calcium. Using a combination of biochemical and functional assays, we show calcium-induced conformational changes in the Nkd-Dvl complex and identify a requirement for the Nkd EF-hand in cell polarity but not in β-catenin transcriptional outputs. We predict that Nkd and Dvl form a cooperative calcium binding pocket, which allows for conformational changes or subcellular localization to direct Wnt/PCP output. We identified a region in Dvl that may coordinate ion binding. We have mutated this novel Dvl calcium binding site, and performed biochemical, genetic, and functional studies. To determine the impact upon Wnt signaling output, I utilize gene knockdown and rescue in the zebrafish DFCs, in a tissue that hosts converging Wnt signals. I also determined the subcellular localization of Nkd and Dvl components within the cells known to have calcium fluxes and cells that are quiescent. Our data suggests that calcium-induced secondary structure changes in the Nkd-Dvl complex serve to interpret the physiology of a cell receiving multiple cues and provides mechanistic insight into Wnt signal integration in vivo.
Abstract for Emily Beck
Cyto-nuclear co-intogression in the sister species Drosophila yakuba and D. santomea
Introgression, also called introgressive hybridization, is the effective exchange of genetic information between species through natural hybridization, and can occur when reproductive isolation is incomplete. Previous genetic analysis of the hybrid zone formed by Drosophila yakuba and its sister species D. santomea showed that the mitochondrial genome of the former species had introgressed into the latter and completely replaced its native form. Since mitochondrial proteins work intimately with nuclear-encoded proteins in the oxidative phosphorylation (Oxphos) pathway, we hypothesized that some nuclear genes in Oxphos co-introgressed along with the mitochondrial genome allowing for preservation of function. We analyzed nucleotide variation in the 12 nuclear genes that form cytochrome c oxidase (COX), an Oxphos enzyme complex composed of both nuclear- and mitochondrial-encoded proteins, in 33 Drosophila lines. Using maximum likelihood methods, we detected significant introgression from D. yakuba to D. santomea in only the three nuclear genes composing subunit V of this complex. The detection of introgression in the three proteins that work together in same subunit, interact with one another, and directly with the mitochondrial-encoded core strongly supports coordinated cyto-nuclear co-introgression to allow for optimal COX activity. We aim to investigate the nuclear genes of all the other subunits of Oxphos (88 genes total) for evidence of co-introgression.
Abstract for Fengxiao Bu
CFH-mutation related atypical hemolytic uremic syndrome may be modulated by Coagulation factor X
F. Bu1,2, N. Borsa2, W. Tollefson3, M. Schnieders3, H. Azaiez2, K. Wang4, C. Thomas2,5, C. Nester2,5, R. Smith1,2,5
1) Interdepartmental PhD Program in Genetics, University of Iowa, Iowa City, IA; 2) Molecular Otolaryngology and Renal Research Laboratories, University of Iowa, Iowa City, IA; 3) Department of Biochemistry, University of Iowa, Iowa City, IA, USA; 4) Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, IA; 5) Rare Renal Disease Clinic, Departments of Pediatrics and Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA,
Background: Atypical hemolytic uremic syndrome (aHUS) is a complement-related rare renal disorder characterized by microangiopathic hemolytic anemia, thrombocytopenia and acute renal failure. Mutations in CFH account for approximately 22% of aHUS cases. In familial cases, CFH-mutation penetrance ranges from 12.5% to 100% suggesting the involvement of other genetic factors/modifiers in the etiology of this disorder.
Methods: Five families carrying the same disease mutation – c.3644G>A, p.Arg1215Gln – in CFH were included in this study. Using targeted genomic enrichment and massively parallel sequencing, all coding exons of genes in complement and coagulation cascades were screened for coding variants. Data were analyzed using a customized local Galaxy pipeline. After filtering for quality and frequency, novel and rare variants were annotated based on computational algorithms and reported studies. For selected variants the predicted functional impact was confirmed in vitro.
Results: A known factor X deficiency variant (F10 c.424G>A, p.Glu142Lys) was identified in a three-generation pedigree. No carriers of both the F10 p.Glu142Lys variant and the CFH p.Arg1215Gln variant developed aHUS, although two persons carrying only the CFH p.Arg1215Gln variant developed disease in early childhood. Protein modeling shows that wild-type Glu142 hydrogen bonds with Cys129, while mutated Lys142 hydrogen bonds with Ser146, a shift that destabilizes an important intra-light-chain interaction between a two-stranded beta-sheet and a small alpha-helical secondary structure element. Consistent with this prediction, recombinant mutant factor X secretion was altered in HEK293 cells and its activity was reduced by 30%.
Conclusion: We have identified a variant in F10, p.Glu142Lys, that may modify CFH-related aHUS perhaps protecting CFH-mutation carriers from developing the phenotype.This finding may explain some instances of incomplete penetrance and offer new therapeutic targets to treat this life-threating disease.
|6/12/2014||Jennifer Teitle: The Versatile PhD||106 BBE|
|6/26/2014||Emily Beck||106 BBE|
|7/10/2014||Danielle Herrig||106 BBE|
|7/24/2014||Igor and Patricia (Genetics Alumni)||106 BBE|
|8/7/2014||Hung-Lin Chen||106 BBE|
The Role of Maternal Wnts and Frizzleds in Dorso-Ventral Axis Specification
Elucidating the molecular mechanisms that transform a symmetric egg into a more complex embryonic body has interested developmental biologists for some time. The asymmetric distribution of determinants within the oocyte is critical to normal developmental processes such as dorsal axis determination and cell migration. In Xenopus laevis in particular, maternal mRNAs involved in the patterning of the secondary body axis are localized to the oocyte vegetal cortex, and upon sperm entry, are subsequently translocated to the future dorsal side. This process, called cortical rotation, is required for the asymmetric activation of the Wnt/β-Catenin signaling pathway on the dorsal side of the blastula. β-catenin, a down-stream wnt effector, regulates the transcriptional activation of dorsal-specific genes at the midblastula transition. Support for the role for β-Catenin signaling in the specification of the dorso-ventral (D/V) axis was garnered from maternal mRNA depletion studies in Xenopus. Recent evidence has suggested that secreted Wnt ligands Wnt11 and Wnt5a may act together in axis formation. However, the function of other maternally expressed Wnts and their cognate receptors (frizzleds) remains uncharacterized. We propose that one or more uncharacterized wnts/fzds act in D/V axis specification. Preliminary analysis of the developmental expression patterns of all wnts and frizzleds (fzds) present in frog, found that wnts 1, 2, 5a, 5b, and 10b and fzds 1, 3, 4, 5, 6, and 7 are expressed in the oocyte, suggestive of a role in D/V patterning. Moreover, maternal fzd1-depleted embryos exhibit a ventralization phenotype and partial defects in dorsal-specific gene expression, while fzd4-depleted embryos exhibit a dorsalization phenotype and an expansion of dorsal specific markers. Further characterization of the genetic factors involved in D/V axis specification could advance the understanding of the pervasive Wnt signaling pathway and provide mechanistic insights into developmental defects.
Long-Range Chromatin Interactions in Fetal and Adult Hematopoietic Stem Cells
HSCs in fetal liver undergo rapid self-renewal divisions, which lead to a massive increase in cell number of the HSC pool. In contrast, the adult bone marrow HSCs have lower self-renewal capacity. Fetal and adult HSCs display differences in their differentiated cell output. Fetal HSCs have erythro-myeloid lineage output while adult HSCs have balanced lineage output. These differences of biological properties between fetal and adult HSCs correlate with distinct gene expression in HSCs. The transcription factor Sox17 is required for the maintenance of fetal, but not adult, HSCs. Ezh2, a core component of polycomb repressive complex 2 (PRC2), is essential for fetal, but not adult, HSCs. In contrast, Bmi1, Gfi1, Etv6, and C/EBPα are required for restriction of self-renewal in adult HSCs. Several studies have shown that the expression of Sox17 is controlled by long-range chromatin interaction. SUZ12, a PRC2 subunit, can occupy the promoter region of Sox17 and repress its expression in ES cells. In addition, the expression of Sox17 is controlled by polycomb protein and H3K27me3 during pancreatic differentiation. The transcription factor SMAD2/3 can bind to the promoter region of Sox17 and is associated with H3K27me3 depletion to activate gene expression. Ezh2 and Bmi1, aother two polycomb proteins, are also involved into HSCs regulation. It is clear that polycomb proteins are key factors of long-range chromatin interaction. In addition, the expression of Gfi1 is regulated by five regulatory regions with Scl/Tal1, Gata2, PU.1, Erg, Meis1, and Runx1 as upstream regulators. These indicate that long-range chromatin interaction is essential to the expression of key regulators in fetal and adult HSCs. We currently use 3C-based technologies to identify the long-range chromatin interactions in both fetal liver and bone marrow HSCs.
Characterizing the NPHP10 Mouse
Nephronophthisis (NPHP) is a recessive kidney disorder that is the leading cause of early onset, end-stage renal failure. Localization to the ciliary-centrosomal complex of many proteins mutated in cystic kidney disease provided a coalescing mechanism for NPHP-related ciliopathies (NPHP-RC). Aside from renal failure and kidney cysts, the two other main phenotypes are retinal and cerebellar degeneration. One such disease with NPHP-RC phenotypes is Bardet-Biedl Syndrome (BBS), with cardinal phenotypes of retinal degeneration, renal abnormalities, obesity, polydactyl, and learning disabilities. An NPHP gene associated with BBS is serologically defined colon cancer antigen 8 (SDCCAG8), later defined as NPHP10. BBS patients with NPHP10 mutations exhibit retinal and renal abnormalities, obesity, and learning disabilities. An NPHP10 knockout (KO) mouse model has been generated using a Sleeping Beauty transposon insertion and these KO mice die shortly after birth. Current work focuses on characterizing the phenotypes of this mouse and determining if death is due to a gross morphological defect or a severe signaling pathway defect.
Global View of Enhancer-Promoter Interactome in Human Cells
Enhancer mapping has been greatly facilitated by various genomic marks associated with it. However, little is available in our toolbox to link enhancers with their target promoters, hampering mechanistic understanding of enhancer-promoter (EP) interaction. We develop and characterize multiple genomic features for distinguishing true EP pairs from non-interacting pairs. We integrate these features into a probabilistic predictor for EP interactions. Multiple validation experiments demonstrate a significant improvement over state-of-the-art approaches. Systematic analyses of EP interactions across eleven cell types reveal several global features of EP interactions: 1) about 60% of EP interactions are tissue-specific; 2) promoters controlled by multiple enhancers have higher tissue specificity but the regulating enhancers are less conserved; 3) cohesin plays a role in mediating tissue-specific EP interactions via chromatin looping in a CTCF independent manner. Our approach presents a systematic and effective strategy to decipher the mechanisms underlying EP communication.
Insult by complement: Laying the MAC down on monkey choroidal endothelial cells
Age-related macular degeneration (AMD) is the most common cause of irreversible blindness among elderly adults in developed countries. Mounting evidence points to complement activation in the choriocapillaris as the earliest pathological change in AMD. We hypothesized that formation of the membrane attack complex (MAC), the final stage of complement activation, alters gene expression in primate choroidal endothelial cells, creating an environment conducive to AMD. To test this hypothesis, we challenged RF/6A cells with normal and heat-inactivated human serum and assessed the cellular response using immunohistochemistry and RNA-Seq. MAC treated cells showed altered gene expression in several pathways, including some implicated in AMD.
Identification of novel exomic regions for targeted exome analysis using RNA-sequencing
Heritable retinal degenerative diseases are rare and exhibit great genetic heterogeneity. Consequently, identification of disease-causing variants in a patient’s exome may prove challenging, particularly when one or more of the true variants lie outside of the profiled regions in targeted exome sequencing. Presented is a method using RNA-seq in healthy tissues for identifying such regions towards the purpose of constructing augmented exome capture kits for disease variant identification. Results from this method in a patient cohort demonstrate its utility in identifying genetic variants causative of retinal dystrophies.
A novel post-synaptic signaling system involved in synaptic homeostasis at the Drosophila neuromuscular junction
Forms of homeostatic neuroplasticity stabilize synaptic outputs in spite of challenges to synaptic function. Aberrant synaptic activity may underlie a number of neurological disorders including epilepsy. As such, it is important to develop an understanding of the mechanisms that stabilize neuronal function. We utilize the Drosophila neuromuscular junction (NMJ) as a model synapse for studying homeostatic plasticity. At the NMJ, impaired postsynaptic glutamate receptor activity is offset by an increase in presynaptic glutamate release, allowing muscle depolarization to be maintained at wild-type levels. However, our understanding of the signaling systems that drive this process is minimal.
In a recent screen, we uncovered that C-terminal Src kinase (Csk) and the fibroblast growth factor Heartless (Htl) are required for synaptic homeostasis. Examination of loss-of-function Csk and Htl mutant alleles confirmed these result. Both Csk and Htl are known to regulate the activity of Src family kinases (SFKs). As such, we examined the roles of Src64B and Src42A, the SFK homologs in Drosophila, at the NMJ. This analysis has revealed a role for both Src64B and Src42A in homeostatic compensation, and led us to analyze downstream targets of SFK signaling. One potential target of SFK signaling at the NMJ is Fasciclin II (FasII), a homolog of mammalian neural cell adhesion molecule (NCAM) that forms trans-synaptic complexes. We have shown that misexpression of FasII at the NMJ blocks homeostatic compensation and that Csk, Src64B, and Htl mutant NMJs have altered FasII localization. This has led us to a model in which a signaling system consisting of Csk, SFKs, and Htl regulates synaptic homeostasis, perhaps through FasII.