Primary hyperparathyroidism (pHPT) is a pathology associated with one or multiple hyperfunctioning parathyroid glands.  The disease prevalence occurs in roughly 1-2% of the population primarily post-menopausal women.  The molecular pathology of the disease is poorly understood.  Elevated serum calcium levels in the setting of an inappropriately elevated parathyroid hormone level are indicative of the disease process.  The ultimate treatment of the disease is to remove the hyperfunctioning gland. The aim of this thesis was to examine potential genetic and epigenetic aberrations that are potentially disease causing. The methylation signature of normal and pathological parathyroid tissue has yet to be investigated.  DNA was bisulphite modified and analyzed using the Infinium HumanMethylation27 BeadChip. Distinct hierarchical clustering of genes with altered DNA methylation profiles in normal and pathologic parathyroid tissue was evident.  DNA hypermethylation of CDKN2B, CDKN2A, WT1, SFRP1, SFRP2, and SFRP4 known to be important in the development of parathyroid tumors were associated with reduced gene expression in both benign and malignant parathyroid tumors. Familial primary hyperparathyroidism (FPHPT) may occur due to an underlying germ-line mutation in the MEN1, CASR, or HRPT2/CDC73 genes.  Eighty-six young (≤45 years of age) patients with clinically non-syndromic PHPT underwent genetic analysis.  Eight of 86 (9.3%) young patients with clinically non-familial PHPT displayed deleterious germ-line mutations in the susceptibility genes (4 MEN1, 3 CASR, and 1 HRPT2/ CDC73). Accumulation of non-phosphorylated active β -catenin has been reported to commonly occur in parathyroid adenomas from patients with primary hyperparathyroidism (pHPT).  We assessed possible β-catenin stabilizing mutations in a large series of parathyroid adenomas. A total of one hundred and eighty sporadic parathyroid adenomas were examined for mutations in exon 3 of the CTNNB1gene. The mutation S33C (TCT >TGT) was detected by direct-DNA sequencing of PCR fragments in 1 out of 180 sporadic parathyroid adenomas (0.68 %). Eight matched tumor-constitutional DNA pairs from patients with sporadic parathyroid adenomas underwent whole-exome capture and high-throughput sequencing.  Four of eight tumors displayed a frame shift deletion or nonsense mutations within the MEN1 gene, which was accompanied by loss of heterozygosity of the remaining wild-type allele.  One tumor harbored a Y641N mutation of the histone methyltransferase EZH2 gene, previously linked to myeloid and lymphoid malignancy formation. Targeted sequencing in the additional 185 parathyroid adenomas revealed a high rate of MEN1 mutations (35%).

Thesis (PhD)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: Schizophrenia is a debilitating disorder that occurs the world over. Although antipsychotics are largely effective in treating the positive symptoms of schizophrenia, the outcomes are non-optimal in many patients. As antipsychotic treatment response has been shown to be heritable, it is expected that the implementation of antipsychotic pharmacogenomics should aid in the optimization of antipsychotic treatments, however to date clinically applicable results are limited. Therefore this study utilized exome sequencing in a cohort of well characterized first episode schizophrenia patients to identify the genetic factors contributing to antipsychotic treatment response. The utility of exome sequencing for antipsychotic pharmacogenomic applications in the African context was assessed through examination of the literature and publically available data. Thereafter, a cohort of 104 well characterized South African first episode schizophrenia patients who were treated with flupenthixol decanoate for twelve months was collected. From this cohort, subsets of patients on extreme ends of the treatment response spectrum were identified for exome sequencing. Thereafter a bioinformatics pipeline was used to call and annotate variants. These variants and those that have previously been associated with antipsychotic response, along with a panel of ancestry informative markers, were prioritized for genotyping in the entire cohort of patients. After genotyping of the 393 variants, statistical analyses were performed to identify associations with treatment response outcomes. Examination of the literature revealed a need for exome sequencing in Africa. However, critical analyses of next generation sequencing data demonstrated that complex regions of the genome may not be well suited to these technologies. Thus, it may be necessary to combine exome sequencing with knowledge obtained from past research, as was done in this study to identify the genetic factors contributing to antipsychotic treatment response. Using this strategy, the current study highlighted the potential role that rare variants play in antipsychotic treatment response and additionally detected 11 variants that were significantly associated with antipsychotic treatment response outcomes (P=2.19x10-5). Nine of these variants were predicted to alter the function of the genes in which they occurred; of which eight were novel with regards to antipsychotic treatment response. The remaining two variants have been associated with antipsychotic treatment outcomes in previous GWAS. Examination of the function of the genes in which the variants occurred revealed that the variants associated with (i) positive symptom improvement were involved in the folate metabolism pathway and (ii) negative and general pathological symptoms improvement had potential links to neuronal development and migration. To our knowledge this study is the first to utilize exome sequencing for antipsychotic pharmacogenomic purposes. The ability of this study to identify significant associations, even after correction for multiple testing, has highlighted the importance of combining genomic technologies with well characterized cohorts. The results generated from this study have served both to replicate results from previous antipsychotic pharmacogenetic studies and to identify novel genes and pathways involved in antipsychotic response. These results should aid in improving our understanding of the biological underpinnings of antipsychotic treatment response and may ultimately aid in the optimization of these treatments. / AFRIKAANSE OPSOMMING: Skisofrenie is ‘n siekte wat wêreldwyd voorkom en lei tot erge funksionele inkorting. Alhoewel antipsigotiese medikasie redelik effektief is in die behandeling van die positiewe simptome van skisofrenie, is die funksionele uitkomste in baie pasiënte nie optimaal nie. Die reaksie op antipsigotiese behandeling blyk oorerflik te wees. Die verwagting is dus dat die implementering van antipsigotiese farmakogenomika met die optimalisering van antipsigotiese behandeling sal help. Tot dusver het die resultate van farmakogenomika studies egter beperkte kliniese toepassings opgelewer. Hierdie studie het dus eksoomvolgordebepaling in 'n groep van goed-karakteriseerde eerste-episode skisofrenie pasiënte gebruik om die genetiese faktore wat bydra tot die antipsigotiese behandelings-reaksies te identifiseer. Die gebruik van eksoom-volgordebepaling vir antipsigotiese farmakogenomika in die Afrikakonteks is deur die ondersoek van literatuur en openbaar-beskikbare data geëvalueer. Daarna is 'n groep van 104 goed-gekarakteriseerde Suid-Afrikaanse eerste-episode skisofrenie pasiënte, wat met flupenthixol dekanoaat vir twaalf maande behandel is, versamel. Uit hierdie groep is subgroepe van pasiënte op die teenoorgestelde eindpunte van die behandelings-reaksiespektrum vir eksoom-volgordebepaling geïdentifiseer. Hierna is 'n bioinformatika pyplyn gebruik om variante te identifiseer en te annoteer. Hierdie variante, asook variante wat voorheen met antipsigotiese reaksie geassosieer is, is saam met 'n paneel van afkoms-informatiewe merkers vir genotipering in die hele groep pasiënte geprioritiseer vir genotipering. Na genotipering van die 393 variante, is statistiese analises uitgevoer om assosiasies met behandelings-reaksie uitkomste te identifiseer. ‘n Ondersoek van die literatuur het getoon dat daar 'n behoefte vir eksoomvolgordebepaling in Afrika is. ‘n Kritiese analise van volgende-generasie volgordebepalings data het egter getoon dat komplekse dele van die genoom nie geskik is vir die gebruik van hierdie tegnologie nie. Om die genetiese faktore wat bydra tot suksesvolle antipsigotiese behandeling te identifiseer, mag dit nodig wees om eksoom-volgordebepaling te kombineer met bevindings verkry uit vorige navorsing, soos gedoen in hierdie studie. In die huidige studie het die gebruik van hierdie strategie die potensiële rol van skaars variante in antipsigotiese behandelings-reaksies beklemtoon en ‘n bykomende 11 variante is geïdentifiseer wat beduidend met antipsigotiese behandelingsrespons geassosieer is (P=2.19x10-5). Daar is voorspel dat nege van hierdie variante die funksie van die gene waarin hulle voorkom sal verander en agt van hierdie variante is vir die eerste keer met antipsigotiese behandelingsrespons geassosieer. Die oorblywende twee variante is met antipsigotiese behandelingsrespons in vorige GWAS geassosieer. ‘n Ondersoek na die funksie van die gene waarin die variasies voorgekom het, toon dat die variante wat geassosieer is met (i) verbetering van positiewe simptome ‘n rol speel in folaatmetabolisme, terwyl variante wat geassosieer is met (ii) die verbetering in negatiewe en algemene patologiese simptome potensiële skakels met neuron ontwikkeling en migrasie het. Na ons wete is hierdie die eerste studie wat eksoom-volgordebepaling vir antipsigotiese farmakogenomika doeleindes gebruik. Die vermoë van hierdie studie om beduidende assosiasies te identifiseer, selfs na korreksie vir veelvoudige toetse, onderstreep die belangrikheid van die kombinering van genomiese tegnologie met goed-gekarakteriseerde pasiënte. Die bevindinge van hierdie studie het nie net die resultate van vorige antipsigotiese farmakogenetiese studies bevestig nie, maar ook nuwe gene en variante wat betrokke is in antipsigotiese reaksie geïdentifiseer. Hierdie resultate sal hopelik ons begrip van die onderliggende biologiese faktore wat antipsigotiese behandelingsrespons beïnvloed verbeter en uiteindelik ook met die optimalisering van behandeling help.

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. There are two syndromic forms of CRMO, Majeed syndrome and DIRA, for which the genetic cause is known. However, for the majority of cases, the genetic basis is unknown. Via whole-exome sequencing and linkage analysis, we determined the most likely causative mutations in four families. While the mutations are in three different genes – FBLIM1, PLCG2 and PIP; all three genes are involved in Fcγ signaling and osteoclast activation. In a large cohort of 61 individuals with CRMO, we performed gene and pathway based association analysis using the 1000 genomes participants of European ancestry as controls. One gene from the family-based analyses, ANO6, was significantly enriched for rare variants in our cohort of cases. ANO6 is involved in P2RX7- mediated inflammasome activation and in the regulation of bone mineralization. While no pathways were enriched for rare variants in the CRMO cohort after genome-wide correction, four pathways were significantly enriched for rare variants in the control samples, indicating a protective effect of the variants. The second most significant pathway, activation of chaperone genes by XBP1s, is relevant to CRMO pathogenesis as XBP1s is a transcription factor that attenuates ER stress, and regulates the expression of genes involved in RANKL signaling and bone remodeling. An association analysis using a larger set of cases followed by functional validation of candidate genes is necessary to confidently declare the mutations isolated in the work presented here to be pathogenic. Our preliminary findings suggest that mutations in genes involved in both the inflammatory response and bone remodeling underlie the pathogenesis of CRMO.

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第21254号 / 医博第4372号 / 新制||医||1029(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 山田 亮, 教授 Shohab YOUSSEFIAN, 教授 小杉 眞司 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

No description available.

Craniosynostosis is a disorder characterized by the premature fusing of cranial sutures in an infant. Premature closure of these sutures can lead to detrimental consequences on the development of a child. The two broad categories of craniosynostosis are classified as syndromic and nonsyndromic. Nonsyndromic craniosynostosis involves only the fusion of one or more sutures, whereas syndromic craniosynostosis involves other abnormalities throughout the body of the affected individual. Two of the families analyzed in this study were of the syndromic nature, and known FGFR mutations were discovered. However, phenotypical features documented in association with these mutations differed from our individuals. Two families affected with nonsyndromic sagittal synostosis were also analyzed. Within one of these families, three candidate mutations were identified as possible disease causing mutations. These mutations were found in the genes ITGAV, SLC30A9, and BAMBI. Here we analyze the function of these proteins and determine the significance of the role they may play in nonsyndromic craniosynostosis.

Skeletal dysplasias and dysostoses are a genotypically and phenotypically diverse group of disorders that affect the growth, development and maintenance of cartilage and bone. General disorders of bone affecting bones and cartilage throughout the body have been referred to as skeletal dysplasias, whereas defects that selectively affect certain bones or bone groups are called skeletal dysostoses. Despite this distinction, modern molecular techniques are showing that this division is somewhat superficial, given the similarity in their underlying causes. Although the rate of disease gene discovery has grown substantially since the advent of next-generation sequencing technologies, most of the disorders have unknown molecular defects. Skeletal dysostoses are rarely observed, occurring at such low incidence levels that no comprehensive study has ascertained their frequency. The effects range from mild growth inhibition to complete absence of entire bone groups. The axial skeleton is most often involved in skeletal dysostoses with common symptoms including poorly formed cranial bones, mandible, ribs and vertebrae. Several important signaling pathways control the migration and formation of mesodermal cells, which eventually differentiate into many elements of the vertebral column. The importance of these pathways, namely the T-box transcription factors, Wnt, Notch, and Smad pathways are integrally involved in the very early stages of vertebral development. Currently, the most cost-effective method of pathogenic gene discovery for rare genetic diseases is exome sequencing. Utilizing this technology, as well as SNP arrays for identity-by-descent loci mapping, two independent skeletal dysostosis cases with similar phenotypes were studied to determine pathogenic candidate genes. Next-generation sequencing and identity-by-descent analysis revealed a possible candidate gene, PM20D2, in one proband. The gene includes peptidase dimerization, peptidase M20/M25/M40, and N-myristolylation domains based on predicted functional analysis. It is implicated in various metabolic activities, having hydrolase, protein binding, and metallopeptidase molecular functions. Further investigation into this gene, as well as further studies of these probands is needed to understand the role, if any, the defect plays in the disease.

Novel technologies for genome analysis have provided almost unlimited opportunities to uncover structural gene variants behind human disorders. Whole exome sequencing (WES) is especially useful for understanding rare Mendelian conditions, because it reduces the requirements for a priori clinical data, and can be applied on a small number of patients. However, supporting functional data on the effect of specific gene variants are often required to power these findings. A variety of methods and biological model systems exists for this purpose. Among those, induced pluripotent stem cells (iPSCs), which are capable of self-renewal and differentiation, stand out as an alternative to animal models. In papers I and II we took advantage of WES to identify gene variants underlying autosomal recessive pure hair and nail ectodermal dysplasia (AR PHNED) as well as autosomal dominant familial visceral myopathy (FVM). We identified a homozygous variant c.821T>C (p.Phe274Ser) in the KRT74 gene as the causative mutation in AR PHNED, supported by the fact that Keratin-74 was undetectable in hair follicles of an affected family member. In a family segregating FVM we found a heterozygous tandem base substitution c.806_807delinsAA (p.(Gly269Glu)) in the ACTG2 gene in the affected members. This novel variant is associated with a broad range of visceral symptoms and a variable age of onset. In Paper III we explored the similarity between clonally derived iPSC lines originating from a single parental fibroblast line and we highlighted the necessity to use lines originating from various donors in disease modeling because of biological variation. Paper IV focused on how the genomic integrity of iPSCs is affected by the choice of reprogramming methods. We described several novel cytogenetic rearrangements in iPSCs and we identified a chromosome 5q duplication as a candidate aberration for growth advantage. In summary, this doctoral thesis brings novel findings on unreported disease-causing variants, as supported by extensive genetic analysis and functional data. A novel molecular mechanism behind AR PHNED is presented and the phenotypic spectrum associated with FVM is expanded. In addition, the thesis brings novel understanding of benefits and limitations of the iPSC technology to be considered for disease modeling.

<p>Muscular dystrophy is a devastating disease for which no cures or preventative treatments are currently available. There has been great progress in the identification of genetic mutations that cause some forms of muscle disease; however, genetic heterogeneity is the rule rather than the exception. Molecular diagnosis of these disorders is challenging because the large number of known causative genes makes exhaustive clinical testing very expensive and the similarity of clinical presentation makes selection of likely candidate genes difficult. The Duke Limb-Girdle Muscular Dystrophy (LGMD) group strives to identify the mutations causing disease in affected members of families with molecularly undiagnosed, dominantly inherited forms of muscular dystrophy while potentially identifying and characterizing genes and mutations that have not been previously shown to be involved in muscle disease pathogenesis.</p><p>One strategy to identify disease-causing mutations in families with many affected individuals is to perform linkage analysis to identify a region of the genome that is likely to contain the disease-causing variant followed by candidate gene sequencing within the peak to isolate the mutation. Linkage analysis was performed for a family with a molecularly undiagnosed form of scapuloperoneal muscular dystrophy. Three suggestive linkage regions were identified on chromosomes 3, 4, and 14 respectively. Each affected individual in the family carried a heterozygous deletion of a lysine residue at position 1784 in exon 37 of MYH7, which maps to one of the linked loci. Other groups have also identified this variant in individuals with similar symptoms. The deletion of the lysine residue is likely the causative mutation in this family.</p><p>An alternate strategy for mutation identification is exome capture and sequencing. This approach may be used to screen genes that are known to be involved in muscle disease pathogenesis while potentially identifying candidate disease-causing variants in genes that have not previously been shown to be involved in the disease. This strategy was evaluated through the analysis of exome sequencing data obtained from multiple affected family members in two families with different muscle disease symptoms. Variant filtration and Sanger sequencing follow-up were performed to identify those variants located in genes known to be involved in skeletal and/or cardiac muscle disease that fit the expected inheritance patterns in each family and are rarely identified in the general population, and likely functional. The mutation, desmin IVS3+3 A>G, was identified in the first family, and the mutation, filamin C p.W2710X, was identified in the second family. These mutations segregated with affection status in the complete families. They have been identified in other individuals with similar phenotypes and were found to affect the proteins by functional analyses. Therefore, the mutations likely caused disease in affected members of these two families as well.</p><p>For families in which initial analysis of exome sequencing data does not reveal a likely disease-causing variant in genes in which mutations are known to cause skeletal muscle disease, it is necessary to determine whether the exome sequencing data provided deep, high-quality coverage at each base in their coding and splicing regions. Coverage variability in genes known to be involved in skeletal and/or cardiac muscle disease was examined for eleven example exomes. After duplicate removal, the mean coverage per exome ranged from 42X to 84X, and 85.7%-92.8% of the expected capture region was covered at ¡Ý10X as calculated with the command GATK ¨CDepthOfCoverage. Depth and quality of coverage were examined in the coding and splicing regions of 102 genes that are known to be involved in skeletal and/or cardiac muscle disease; they were found to vary across different exome captures. Some regions were not well covered in any of the exomes sequenced. The results indicate that while many causative genes are well-covered, gaps exist which may interfere with the identification of some disease-causing mutations. In some cases, these gaps may be filled by increasing overall coverage.</p><p>The initial screen indicated that mutations in known disease genes may be frequent in the Duke LGMD families, so the use of a single exome in a family to screen genes that are known to be involved in muscle disease was attempted. Exome sequence analysis was performed for single affected individuals from seven families with multiple affected family members. For each exome, the candidate set was restricted to variants found within the coding and splicing regions of 102 skeletal and/or cardiac muscle disease genes. Strict filters were applied to identify extremely rare, high quality variants located within those genes, and Sanger sequencing follow-up was performed to determine which variants segregated with affection status in the complete family. In five of the seven families, potential disease-causing variants were found in a heterozygous state in all affected individuals. When possible, functional testing of these alleles, preferably in an in vivo model, would be beneficial to assist in determining whether each allele is likely to be pathogenic.</p><p>The described work utilized linkage analysis followed by candidate gene sequencing as well as exome capture and sequencing to attempt to isolate the mutations responsible for muscular dystrophy in affected family members. While linkage analysis may continue to be important to identify regions of the genome that are identical by descent in extended families, the use of next generation sequencing technologies to isolate mutations that cause rare, highly penetrant disorders in smaller families can be effective. However, it is necessary to examine the depth and quality of coverage within the consensus coding and splicing regions of genes in which mutations are known to cause a similar phenotype to that found in a family of interest. In the future, functional follow-up will be important to assist in the interpretation of variants of unknown significance.</p> / Dissertation

Body mass varies considerably between different mammals and this variation is largely accounted for by a difference in total cell number rather than individual cell size. Insights into mechanisms regulating growth can therefore be gained by understanding what governs total cell number at any one point. In addition, control of cell proliferation and programmed cell death is fundamental to other areas of research such as cancer and stem cell research. Microcephalic Primordial Dwarfism (MPD) is a group of rare Mendelian human disorders in which there is an extreme global failure of growth with affected individuals often only reaching a height of around one metre in adulthood. To date, all identified disease genes follow an autosomal recessive mode of inheritance and encode key regulators of the cell cycle, where mutations impact on overall cell number and result in a substantially reduced body size. MPD therefore provides a valuable model for examining genetic and cellular mechanisms that impact on growth. The overall aims of this thesis were to identify novel disease causing genes, as well as provide further characterisation of known disease causing genes, through the analysis of whole exome sequencing (WES) within a large cohort of MPD patients. Following the design and implementation of an analytical bioinformatics pipeline, deleterious mutations were identified in multiple disease genes including LIG4 and XRCC4. Both genes encode components of the non-homologous end joining machinery, a DNA repair mechanism not previously implicated in MPD. Additionally, the pathogenicity of novel mutations in subunits of a protein complex involved in chromosome segregation was assessed using patient-derived cells. These findings demonstrate WES can be successfully implemented to identify known and novel disease causing genes within a large heterogeneous cohort of patients, expanding the phenotype of known disorders and improving diagnosis as well as providing novel insights into intrinsic cellular mechanisms critical to growth.