YALE CENTER FOR MENDELIAN DISORDERS
Gunel Murat
Yale Universitycity: New Haven country: United States (us)
Grant 1U54HG006504-01 from National Human Genome Research Institute
Abstract: The identification of mutations causing Mendelian diseases has revolutionized the understanding of diseases of every organ system. While over 3,000 such diseases have been solved at the molecular level, with 21,000 genes in the human genome and about 15% embryonic lethal loci, it is clear that many remain to be discovered. This includes both described and presently undescribed human traits that contribute to both health and disease. With the spectacular 6-log drop in the cost of DNA sequencing over the last 12 years, it has become apparent that selectively sequencing all of the genes in the genome, which comprise only ~1 % of the human genome represents a very cost-effective means for discovering the basis of new Mendelian diseases. We have pioneered the development of the exome sequencing method as well as the tools for analysis, and have shown that both are scalable, with current cost under $1,500 per exome and expected to be under $1,000 in the near future. We have demonstrated the utility of this approach with the identification of a range of disease genes that were previously intractable due to difficulties in gene mapping owing to high locus heterogeneity, de novo mutations, or small one-of-a-kind families. These considerations motivate new efforts to efficiently solve substantially all Mendelian traits using these technologies. To this end we have established the Yale Center for Mendelian Disorders which will ascertain and acquire samples from patients and families with known or suspected Mendelian diseases, sequence exomes to high coverage sufficient to call 95% of all variants with high specificity and use new analytic approaches we have devised to identify new Mendelian trait genes. We will make all sequences available to the research community as allowed and will establish a Web interface to enable physicians and investigators to submit research samples and retrieve annotated results. These studies will rapidly expand our understanding of the genes and pathways underlying human disease. Sequencing all of the genes in the genome is a new method for discovering gene mutations that cause specific human diseases. The discovery of the inherited basis for those diseases that are caused by a single mutation provides a foundation for the understanding of human health and disease and identifies specific biochemical pathways that might be altered for health benefit, as well as new tools for early diagnosis
Project start date: 2011-12-05
Project end date: 2015-11-30
Budget start date: 5-DEC-2011
Budget end date: 30-NOV-2012
1U54HG006504-01 (2012): $1050000
Sponsored Links Excellgen http://Excellgen.com
Grants awarded to Gunel Murat
MOLECULAR GENETIC PATHOGENESIS OF INTRACRANIAL ANEURYSMS
Gunel Murat, Faculty/ Professor
Yale Universitycity: New Haven country: United States (us)
Grant 5R01NS057756-05 from National Institute Of Neurological Disorders And Stroke
Abstract: Stroke represents a major public health problem in the US, affecting nearly 700,000 individuals annually. Among the different types of stroke, subarachnoid hemorrhage (SAH), most commonly due to intracranial aneurysm (IA), carries the highest mortality rate. Lifetime prevalence estimates of IA range from 0.2%-9.9% (mean 5.5%). Despite this common prevalence, little is known regarding the pathophysiology of IA. While environmental factors are thought to play a role, there is also considerable support for a genetic contribution. In order to dissect the molecular genetics of IA and to clone disease causing transcripts, we have taken an outlier approach and searched nationally and internationally for extended IA kindreds. Over the past 10 years, we have screened over 3200 IA patients and identified 168 IA families, with a total of more than 450 affected individuals. Since the original submission, we have obtained additional samples from 18 Utah kindreds and identified over 250 independent Finnish IA index cases. We are now in the process of collecting these samples. Critically, eight of the already families are sufficiently large to support genome-wide significance independently. We have now completed genome-wide linkage analysis on four of these families (IAs 20, 100, 101 and 112) and have identified IA loci on chromosomes 1p, 6p, 11 q and 14q with lod scores > 3. Importantly, the 11q and 14q loci have been shown likely to contain IA genes in previous sib pair linkage studies. In addition, we have identified multiple additional families that show suggestive linkages to each of these regions. Since the original application, we have also completed the first stage of genome wide linkage analysis of 5 extended Utah kindreds showing that two of them share a conserved haplotype linking and significantly narrowing the 11q locus. We are now confirming these preliminary results in our second stage analysis using STS markers. Our preliminary analysis of the remaining 3 extended Utah kindreds further confirm the presence of additional IA susceptibility loci throughout the genome.We propose to use this unique set of IA kindreds to fine map these loci and perform mutational analysis of coding and non-coding regions of candidate genes located within these intervals by using all families that link to a particular locus in order to identify IA disease genes. Once specific transcripts are cloned, we will be able to examine the pathophysiology of IA, which ultimately may lead to novel therapeutic approaches
Keywords: 11q; 14q; Affect; Autosomal Dominant Polycystic Kidney; base; Candidate Disease Gene; Chromosomes; Code; Collaborations; Collection; Data; Databases; Diagnosis; Disease; DNA; Environmental Risk Factor; Extended Family; Family; Family member; Finland; founder mutation; Functional disorder; Functional RNA; Future; gene cloning; gene discovery; Gene Mutation; Genes; Genetic; genetic linkage analysis; genetic pedigree; Genome; genome-wide; genome-wide linkage; Genomics; Genotype; Goals; Haplotypes; Hemorrhage; Hereditary Disease; Hypertension; indexing; Individual; Intracranial Aneurysm; Japanese Population; kindred; Lead; Letters; Link; Location; Lod Score; Maps; Meleagris gallopavo; Methods; Microsatellite Repeats; Molecular Genetics; Mortality Vital Statistics; Mutation; Mutation Analysis; neurosurgery; novel; novel therapeutic intervention; Nucleic Acid Regulatory Sequences; outcome forecast; Participant; Pathogenesis; Patients; Pattern; Play; Predisposition; Prevalence; Process; public health medicine (field); Recording of previous events; Recruitment Activity; Reporting; Resources; Review Literature; Risk; Role; Rupture; sample collection; Sampling; Screening procedure; Smoking; Staging; statistics; stroke; Subarachnoid Hemorrhage; Suggestion; Susceptibility Gene; Techniques; Testing; Therapeutic Intervention; Transcript; Turkey bird; United States; Universities; Update; Utah
Project start date: 2007-03-01
Project end date: 2012-02-29
Budget start date: 1-MAR-2011
Budget end date: 29-FEB-2012
5R01NS057756-05 (2011): $325828
5R01NS057756-04 (2010): $358412
MOLECULAR VARIANTS THAT DETERMINE GENETIC SUSCEPTIBILITY TO INTRACRANIAL ANEURYSM
Gunel Murat, Faculty/ Professor
Yale Universitycity: New Haven country: United States (us)
Grant 5R01NS067023-03 from National Institute Of Neurological Disorders And Stroke
Abstract: Intracranial aneurysms (IA) affect ~2% of the population and cause 500,000 hemorrhagic strokes annually in relatively young patients (median age 50), resulting in death and severe neurological impairment. The pathogenesis of aneurysm formation and rupture is unknown, and pre-morbid identification is essential to prevent catastrophic hemorrhage. We have recently completed a multistage genome-wide association study (GWAS) with over 2,100 IA patients and 8,000 controls and identified common SNPs on chromosomes 2, 8 and 9 that surpass stringent thresholds and replicate association with IA (odds ratios 1.24 - 1.36). In this initial study, we also found evidence for several other IA susceptibility loci showing P values less than10-4, carrying modest odds ratios (OR<1.25) and likely contributing to IA risk in a cumulative fashion. In order to increase our power to detect and confirm these loci, we have recruited over 5,100 new cases and 22,000 controls bringing the total number of cases and controls over 7,300 and 30,500. The major emphasis of this proposal is to take our GWAS results to the next stage by identifying the causative alleles in each locus so that the IA genes can be confirmed. Discovery of these genes will lead in future applications to hypothesis driven research aimed at understanding the function of these transcripts and gaining mechanistic insight into IA pathophysiology. Our effort in this application can be divided into three conceptually distinct but complementary efforts 1) we will characterize the specific functional variation at each locus accounting for the common variant findings, identified through our prior GWAS; 2) we will evaluate the potential contribution of both rare and common structural variation to IA, and 3) we will seek to identify evidence for additional variants contributing to IA. The end result of these analyses will be a comprehensive view of the genetic architecture of this disorder focusing on common alleles that will serve as the launching point for biological studies of IA and begin creating an opportunity to identify genetically at-risk individuals prior to any morbid events such as IA rupture. Intracranial aneurysms (IA) affect ~2% of the population and cause 500,000 hemorrhagic strokes annually in relatively young patients (median age 50), resulting in death and severe neurological impairment. The pathogenesis of aneurysm formation and rupture is unknown, and there is evidence to suggest that genetic factors play a role both in formation and rupture. We have recently completed a large scale genetics project that included DNA samples from 2,100 IA patients and 8,000 controls and identified 3 chromosomal regions that carry aneurysm genes. We now propose to do follow-up studies to identify these aneurysm genes and continue to search for additional ones
Keywords: 9p21; Accounting; Affect; Age; Alleles; Aneurysm; Aortic Aneurysm; Architecture; Asians; base; Biological; Biology; Brain hemorrhage; case control; Caucasians; Caucasoid Race; Cause of Death; cerebral artery; Cerebral hemisphere hemorrhage; Cessation of life; Chromosomes, Human, Pair 2; Clinical; Code; cohort; Collection; Control Groups; Copy Number Polymorphism; cost; Data; Data Analyses; database of Genotypes and Phenotypes; Databases; Deposition; Detection; Diagnosis; Disease; DNA; Europe; European; Event; Family; Finland; follow-up; Frequencies (time pattern); Functional disorder; Functional RNA; Future; Gender; gene discovery; Gene Expression Profile; Gene Frequency; General Population; Genes; Genetic; Genetic Polymorphism; Genetic Predisposition to Disease; Genome; genome wide association study; genome-wide; Genotype; German population; Germany; Hand; Hemorrhage; Hypertension; Impairment; Individual; insight; interest; Intracranial Aneurysm; Intracranial Hemorrhages; Investigation; Japan; Lead; Left; Lesion; Life; Maps; Measures; Meta-Analysis; Methods; Minor; Molecular; Molecular Biology; Morbidity - disease rate; Mortality Vital Statistics; Mutation; Myocardial Infarction; Natural History; Nature; Netherlands; Neurologic; novel; Odds Ratio; Operative Surgical Procedures; outcome forecast; Pathogenesis; Patients; Pattern; Phase; Play; Population; Population Control; Positioning Attribute; Predisposition; prevent; Probability; proband; public health relevance; Publishing; Recording of previous events; Recruitment Activity; Recurrence; repaired; Reporting; Research; Research Methodology; Research Personnel; Resources; Risk; Role; Rupture; Sample Size; Sampling; Siblings; Smoking; SNP genotyping; Staging; Stratification; stroke; Subgroup; Survivors; Testing; Time; Transcript; United States National Institutes of Health; Variant; young adult
Relevance: Intracranial aneurysms (IA) affect ~2% of the population and cause 500,000 hemorrhagic strokes annually in relatively young patients (median age 50), resulting in death and severe neurological impairment. The pathogenesis of aneurysm formation and rupture is unknown, and there is evidence to suggest that genetic factors play a role both in formation and rupture. We have recently completed a large scale genetics project that included DNA samples from 2,100 IA patients and 8,000 controls and identified 3 chromosomal regions that carry aneurysm genes. We now propose to do follow-up studies to identify these aneurysm genes and continue to search for additional ones
Project start date: 2009-09-30
Project end date: 2014-07-31
Budget start date: 1-AUG-2011
Budget end date: 31-JUL-2012
PFA/PA: PA-07-070
5R01NS067023-03 (2011): $643035
FUNCTIONAL GENOMICS OF THE CAVERNOUS MALFORMATION GENE
Gunel Murat, Faculty/ Professor
Yale Universitycity: New Haven country: United States (us)
Grant 5R01NS046521-07 from National Institute Of Neurological Disorders And Stroke
Abstract: Cerebral cavernous malformations (CCM), characterized by dilated sinusoidal vascular spaces lined by a single layer of endothelium, affect the central nervous system and may lead to neurological problems including bleeding and seizures. Mutations in the three genes, CCM1 (KRIT1, Krev1/Rap1a Interaction Trapped 1), CCM2 (OSM, malcavernin) and CCM3 (PDCD10, Programmed Cell Death Protein 10) have been shown to cause CCM. While recent in vitro studies have begun to illuminate the nature of CCM signaling, an in vivo, mechanistic understanding of CCM pathophysiology is lacking. Based on our recent data from in vitro cell culture studies, in vivo data from our mouse conditional knock-out of Ccm3 in neural cells, and intriguing observations in animal models from various groups, we hypothesize that CCM3 is a negative modulator of Akt signaling via interactions with PP2A, and CCM lesions are the consequence of altered expression of Akt and its downstream effectors. We further hypothesize that CCM3 signaling mediates an interaction between neural and endothelial cells and alteration of this interaction caused by neural CCM3 loss, results in a vascular phenotype. We propose to test these hypotheses using in vitro and in vivo approaches aimed at elaborating this novel Ccm3 signaling pathway and to investigate its potential influence on the interactions among various cell types within the neurovascular unit in CCM lesion development. We will perform studies aimed at clarifying the nature of Ccm3 interactions with the Akt signaling pathway. We will comprehensively study the Emx1-Cre;Ccm3lox/lox mouse model that we have recently generated. Unlike other conditional Ccm3 knockouts, these mice survive long term and develop vascular pathology. The vascular pathology is characterized by dilated vessels throughout the brain and isolated lesions that are reminiscent of human CCM disease. We will take advantage of our findings to gain insight into CCM3 function and signaling. In addition, we propose to cross inducible VE-cadherin-CreER and GFAP-CreER to Ccm3lox/lox mice to study cell autonomous effects of CCM3 in endothelial cells and postnatal astrocytes. The proposed experiments are focused on identifying the molecular pathways relevant to CCM disease and on studying these pathways in vivo with a long-term goal of defining new and more effective therapies. Mutations in the gene Programmed Cell Death Protein 10 (PDCD10) cause Cerebral Cavernous Malformation 3 (CCM3), a vascular disorder mainly affecting the brain. The root causes of CCM are largely unknown. To study these causes, we propose to use a mouse model, Emx1-Cre;Ccm3lox/lox that we recently developed which leads, in part, to the same of abnormalities seen in humans suffering from CCM. These mice develop spontaneous vascular lesions identical to those in human CCM. By using a variety of assays, we plan to identify the molecular mechanisms that lead to the vascular pathology. We also propose to develop new models with inducible Cre lines that will allow us to modulate CCC3 expression in astrocytes or endothelial cells at postnatal stages to study cell specific effects of CCM3. A deeper understanding of the causes of CCM pathology at the cellular and molecular level in vivo will set the stage for efforts to define new and more effective therapies for this potentially debilitating and sometimes fatal disorder
Keywords: Accounting; Actins; Adult; Affect; Age; aged; Animal Model; Apoptosis; Astrocytes; base; Biological Assay; Biology; Birth; Blood Vessels; Brain; Brain hemorrhage; cadherin 5; Caenorhabditis elegans; Cavernous Malformation; CCM1 gene; Cell Communication; Cell Culture Techniques; Cell Cycle; Cell Line; Cell Proliferation; cell type; Cells; Cerebellum; Cerebral Cavernous Malformations 1; Cerebrum; Clinical; Collaborations; Complex; Critiques; Data; Development; Diffuse; Disease; Dorsal; effective therapy; Elements; Embryo; Endothelial Cells; Endothelium; expression vector; Functional disorder; functional genomics; Gene Expression Profile; Genes; Genetic; Glial Fibrillary Acidic Protein; Goals; Hemorrhage; Homologous Gene; Human; In Vitro; in vivo; Individual; insight; Knock-out; Knockout Mice; Lead; Lesion; Link; Long-Term Survivors; loss of function mutation; Maintenance; malformation; Measures; Mediating; mitogen-activated protein kinase p38; MLLT7 gene; Modeling; Molecular; Morphology; mouse model; Mus; mutant; Mutant Strains Mice; Mutation; Nature; neonate; nerve stem cell; nestin protein; Neuraxis; Neurobiology; Neurologic; Neurons; neurovascular unit; Nitric Oxide Synthase; novel; Nuclear; Organism; Pathology; Pathway interactions; Phenotype; Phosphoric Monoester Hydrolases; Plant Roots; Population; postnatal; Prevalence; professor; programs; Protein Phosphatase 2A Regulatory Subunit PR53; Proteins; Proto-Oncogene Proteins c-akt; public health relevance; Publishing; Reagent; relating to nervous system; research study; Resistance; Seizures; Series; Signal Pathway; Signal Transduction; Small Interfering RNA; Staging; Symptoms; System; Testing; Time; Tissues; transcription factor; Vascular Diseases; Work
Relevance: Mutations in the gene Programmed Cell Death Protein 10 (PDCD10) cause Cerebral Cavernous Malformation 3 (CCM3), a vascular disorder mainly affecting the brain. The root causes of CCM are largely unknown. To study these causes, we propose to use a mouse model, Emx1-Cre;Ccm3lox/lox that we recently developed which leads, in part, to the same of abnormalities seen in humans suffering from CCM. These mice develop spontaneous vascular lesions identical to those in human CCM. By using a variety of assays, we plan to identify the molecular mechanisms that lead to the vascular pathology. We also propose to develop new models with inducible Cre lines that will allow us to modulate CCC3 expression in astrocytes or endothelial cells at postnatal stages to study cell specific effects of CCM3. A deeper understanding of the causes of CCM pathology at the cellular and molecular level in vivo will set the stage for efforts to define new and more effective therapies for this potentially debilitating and sometimes fatal disorder
Project start date: 2003-07-01
Project end date: 2014-08-31
Budget start date: 1-SEP-2011
Budget end date: 31-AUG-2012
PFA/PA: PA-07-070
5R01NS046521-07 (2011): $572096
5R01NS046521-04 (2007): $322651
5R01NS046521-03 (2006): $332288