Fetal Alcohol Spectrum Disorders (FASDs), are caused by maternal alcohol consumption during pregnancy [3]. FASD encompasses a wide variety of cardiac and neural anomalies, while also associated with improper limb development, abnormal craniofacial features, problems within the central nervous system (CNS), and disabilities in learning and communication. Gene-regulating FASDs have not been well studied during the crucial phases of early embryonic development. Genes within the Wnt/Beta-catenin pathway control a vast amount of embryonic developmental processes. Among them is the Wnt7a gene, a significant downstream gene regulator which positively controls neural stem cell proliferation and cardiomyocyte differentiation on a large scale during early embryonic development. This project will serve to provide potential insight into the genes involved in FASD. We hypothesize that ethanol administration to early embryonic mice will suppress Wnt7a expression in the heart and brain, leading to FASD development. RNA-sequencing (RNA-Seq) and real-time quantitative PCR (qPCR) were used to measure Wnt7a gene expression within the early embryonic mouse heart and brain. After evaluation of RNA-Seq data and a comparative analysis using the 2-ΔΔCTmethod, it is evident Wnt7a is present in embryonic mouse age E10.5 heart and brain samples, and Wnt7a is suppressed at age E10.5 in embryonic mouse heart, but not brain, when induced with ethanol.

Excessive drinking during early pregnancy is associated with fetal developmental anomalies [1], particularly affecting heart formation, known as Congenital Heart Disease (CHD). This health concern is underscored by studies that indicate a high incidence of binge drinking among expectant mothers [1]. This research delves into alcohol's role in altering epigenetic patterns across the embryonic cardiac genome, seeking to isolate genes and their specific sites influenced by in utero alcohol exposure. The theory posits that ethanol-exposed embryonic mouse hearts will exhibit distinctive patterns of methylation in contrast to unexposed controls [2]. To investigate the proposed theory, ethanol was orally delivered to mouse models at a gestational stage critical for heart development, specifically embryonic day 9.5 (E9.5). Subsequently, at embryonic day 11.5 (E11.5)—a pivotal moment in cardiac morphogenesis—the mice were euthanized to harvest the embryonic hearts. The genomic material was then meticulously extracted from these hearts to enable a comprehensive analysis through whole-genome bisulfite sequencing (WGBS). Preliminary results revealed a marginal shift toward lower methylation levels without broad genomic changes in the ethanol treated samples [7]. Nonetheless, particular genes, like WNT7A gene, have been pinpointed for their suppressed activity following alcohol exposure, guiding further inquiries into aimed methylation changes and epigenetic variations that may illuminate the mechanisms by which maternal alcohol consumption prompts cardiac anomalies in CHD [7]

O desenvolvimento embrionário dos membros é um processo complexo e dinâmico. É controlado por diversos genes e diversos mecanismos morfogenéticos, muitos dos quais ainda não estão completamente elucidados. O objetivo deste estudo é identificar as alterações genéticas responsáveis por defeitos de membros em quatro famílias brasileiras. A família 1 apresenta três indivíduos com um espectro extremamente variável de displasia ectodérmica, ectrodactilia e fenda labiopalatina, características da síndrome EEC. O gene TP63 foi analisado por sequenciamento de Sanger e foi descoberta uma variante nunca descrita anteriormente, c.1037C>A (p.Ala346Gly), em heterozigose, segregando com o fenótipo. Mutações no gene TP63 já foram associadas com casos da síndrome EEC. Concluímos que a variante no gene TP63 é a responsável pelo quadro clínico de EEC na família. A família 2 incluiu cinco indivíduos afetados por polegar trifalângico. O fenótipo de um dos indivíduos é mais grave e se caracteriza por, além do polegar trifalângico, pela presença de braço direito grosseiramente curto e deformado com dedos hipoplásicos, pé direito malformado com metatarsos hipoplásicos e orelha direita pequena e protuberante. Estudos de mapeamento gênico com arrays de SNPs revelaram Lod scores sugestivos de ligação com 8 regiões cromossômicas distintas. O sequenciamento massivo em paralelo do exoma com a amostra de um dos afetados, seguida da seleção das variantes presentes nas regiões com Lod scores sugestivos, revelou a presença da variante c.410dupG (p.Gly138Argfs∗43) no gene SALL4, a qual nunca havia sido descrita. Mutações no SALL4 que alteram a matriz de leitura já foram associadas com casos da síndrome de Okihiro, a qual é caracterizada por defeitos radiais de membros e anomalia oftalmológica de Duane. A segregação da variante entre os indivíduos afetados foi confirmada por sequenciamento de Sanger. Concluimos que esta variante é responsável pelo quadro clínico da família, a qual apresenta a síndrome de Okihiro, porém sem a anomalia de Duane. A análise de todos os casos descritos com variantes no gene SALL4 sugere que há uma correlação entre defeitos nos membros inferiores e o tamanho reduzido da proteína truncada SALL4. A família 3 apresenta três indivíduos afetados por sindactilia completa com polidactilia pré-axial nas mãos, classificada como sindactilia do tipo IV. O sequenciamento massivo em paralelo do exoma com as amostras de três indivíduos afetados e dois normais não revelou a presença de qualquer alteração genética candidata a explicar o quadro clínico. O estudo do array-CGH revelou uma duplicação de aproximadamente 97 kb no gene LMBR1 abrangendo a região de enhancer (ZRS) do gene SHH. Duplicações no ZRS já foram identificadas em casos de sindactilia do tipo IV. Concluímos que a duplicação no ZRS é responsável pelo quadro. A revisão da literatura sobre os casos com duplicação dessa região sugere uma correlação entre duplicações com tamanho ao redor de 97 kb e o fenótipo clássico de sindactilia do tipo IV. A família 4 apresenta seis indivíduos afetados por uma síndrome relativamente nova descrita por nossa equipe em 2008, a síndrome de Santos. Essa síndrome é caracterizada por aplasia/hipoplasia fibular e anoniquia/hipoplasia ungueal dentre outros defeitos de membros. O estudo de ligação com array de SNP e marcadores de microssatélites, com posterior cálculo de Lod score, indicou duas regiões no cromossomo 3 como candidatas a conter a alteração genética responsável pelo fenótipo. Análise dos genes presentes nessas regiões indicou o gene WNT7A como o principal candidato. Alterações neste gene já foram associadas com a síndrome de Fuhrmann e a AARRS (Al-Awadi⁄Raas-Rothschild syndrome), de herança recessiva, as quais apresentam fenótipos correlatos aos presentes na síndrome de Santos. O sequenciamento de Sanger deste gene revelou a presença da variante c.934G>A (p.Gly312Ser), não descrita, em homozigose em cinco dos seis indivíduos afetados da família. O sexto indivíduo afetado é heterozigoto e apresenta fenótipo muito menos grave. Não apresenta qualquer defeito fibular e ungueal, característicos da síndrome. Esse é o primeiro relato de um caso de defeitos de membros como resultado da presença de uma variante em heterozigose no gene WNT7A. O sequenciamento massivo em paralelo do exoma foi realizado com as amostras deste indivíduo e de um dos indivíduos afetados. Contudo, nenhuma outra variante se mostrou candidata a explicar o quadro clínico. Concluímos que a síndrome de Santos é o resultado desta mutação no gene WNT7A. Estudos funcionais in situ baseados na atividade da Luciferase estão em andamento para comprovar o efeito deletério desta variante / Limb development is a complex and dynamic process driven by many different genes and morphogenetic mechanisms. Many of them have not been properly clarified yet. The aim of this study is to identify genetic alterations responsible for limb defects in four Brazilian families. Family 1 includes three individuals affected by an extremely variable phenotype of ectrodactyly, ectodermal dysplasia and cleft lip/palate, and other clinical signs of EEC syndrome. The TP63 gene, associated with this condition, was analyzed through Sanger sequencing and a novel variant, c.1037C>A (p.Ala346Gly), was found; the variant segregated in heterozygous state with the EEC phenotype. Mutations in TP63 gene are already known to be associated with EEC syndrome. Due to the extremely variable phenotype presented by the individuals in the family, the possibility of the mutation c.1037C>G being related to acro-dermato-ungual-lacrimal-tooth (ADULT) syndrome and SHFM cannot be ruled out. Family 2 presents five individuals affected by preaxial polydactyly (triphalangeal thumbs). The phenotype of the proband is more severe, being characterized by triphalangeal thumb, with the following manifestations: grossly shortened and deformed forearm, markedly hypoplastic and appendicular thumb and malformed right foot with hypoplastic metatarsals. Linkage studies by SNP-array pointed to suggestive Lod score values in 8 distinct chromosomal regions. Whole exome sequencing with the sample from one affected individual revealed a novel frameshift variant, c.410dupG (p.Gly138Argfs∗43) in the SALL4 gene. Frameshift mutations in the SALL4 were already associated to Okihiro syndrome, which is characterized by radial limb defects and Duane anomaly. The segregation of the variant among the affected individuals was confirmed by Sanger sequencing. We concluded that this variant is the cause of the clinical signs in the family, which was classified as presenting Okihiro syndrome without Duane anomaly. The review of all clinical cases reported with SALL4 variants indicates a possible correlation between the foot malformation and the reduced size of the SALL4 protein. Family 3 has affected individuals with complete hand syndactyly associated to pre-axial polydactyly (syndactyly type IV). Whole exome sequencing was performed with the samples collected from the three affected individuals and two non-affected ones and no pathogenic variant was detected in genes related to limb development segregating with the phenotype. Through array-CGH, nevertheless, a duplication of about 97 kb including the enhancer (ZRS) of the SHH gene was detected. Duplications in ZRS region were already reported in Syndactyly type IV. We concluded that the 97-kb duplication is the cause of the syndactyly type IV in the family. A review of reported cases (including ours) suggested a possible correlation between the duplication with 97 kb size and the classic phenotype of syndactyly type IV. Family 4 has six individuals affected by a new syndrome (Santos syndrome) described by members of our group in 2008, a condition characterized by fibular agenesis/hipoplasia and ungual hypoplasia⁄anonychia, among other limb defects. Linkage study by SNP-array and microsatellite markers was performed and Lod score calculation pointed to two candidate regions on chromosome 3. Search for candidate genes revealed the WNT7A as the best candidate. Mutations in WNT7A gene, in homozygous state, are known to cause two other limb defect syndromes, Fuhrmann syndrome and AARRS (Al-Awadi/Raas-Rothschild syndrome), both presenting similar phenotypes to Santos syndrome. Sanger sequencing showed a novel variant, in homozygous state, c.934G>A (p.Gly312Ser) in the WNT7A gene in five out of six affected individuals. One affected individual, much less severely affected than his relatives, carries the mutation in heterozygous state. He does not present fibular or ungual malformations, characteristic signals of the syndrome; instead, he is the carrier of a complex polydactyly in his left hand. This is the first report about a heterozygous variant in WNT7A gene resulting in limb defect. Whole exome sequencing was performed with the samples from two affected individuals. However, no other variant in candidate gene to explain the limb defects was detected. We concluded that Santos syndrome is caused by a mutation in the WNT7A gene. Functional assays, based on Luciferase activity, are in execution to test the deleterious effect of the c.934G>A variant in the WNT7A gene

A idade da mutação e a ancestralidade local de segmentos cromossômicos que contém mutações associadas a doenças autossômicas recessivas em populações miscigenadas brasileiras continuam desconhecidas. Adicionalmente, a determinação dos níveis de endogamia continua grosseiramente estimados por abordagem genealógica e nada se sabe sobre a linhagem materna das famílias com indivíduos com doenças autossômicas recessivas. A tese está dividida em dois estudos. O primeiro visou calcular os níveis de endogamia pela abordagem de grandes regiões em homozigose, estimar a idade da mutação e inferir a ancestralidade local para determinar a origem de cada segmento cromossômico contendo mutações em KLC2, IMPA1, MED25 e WNT7A. Foram genotipadas amostras de 19 pacientes com doenças autossômicas recessivas. Os dados genotipados passaram por distintos procedimentos de filtragem para estimar os níveis de endocruzamento por abordagem molecular, para calcular a idade das mutações por meio de haplótipos, para inferir a ancestralidade global utilizando ADMIXTURE e Análise de Componentes Principais, e de forma refinada foi inferida a ancestralidade local pelo software RFMix combinando os dados de nossas amostras com os dados do projeto 1000 genomas (one thousand genome project - 1KGP) e projeto de diversidade genômica Simons (Simons genomic diversity project - SGDP). Os resultados apresentados não diferiram bastante do esperado para populações endogâmicas e miscigenadas do nordeste brasileiro de acordo com a literatura. A mutação em KLC2 mostrou-se mais antiga em relação às demais. Em um segundo estudo, para os indivíduos com mutação em KLC2 prosseguimos com a inferência dos haplogrupos de DNA mitocondrial para determinar a origem da linhagem materna das famílias. Onze pacientes com mutação em KLC2 foram escolhidos para sequenciamento de Sanger da região controle do DNA mitocondrial para determinação da matrilinhagem. Foi encontrado um possível haplogrupo fundador que pode corroborar narrativas históricas de entrada de mães sefarditas no litoral do Nordeste junto com os holandeses. Ambos trabalhos apresentam como novidade a contribuição para identificar a origem e entender como essas doenças são mantidas e dispersas em populações do Brasil e do mundo. Em especial, a matrilinhagem exibiu evidências de ligação entre as mães de famílias com indivíduos com mutação em KLC2 e mães de judeus sefarditas portugueses / The mutation age and local ancestry of chromosomal segments harbouring mutations associated with autosomal recessive (AR) disorders in Brazilian admixed populations remain unknown; additionally, inbreeding levels for these affected individuals continue to be roughly estimated by genealogical approach, and the maternal lineage of the families with affected individuals is unknown. The thesis is divided into two studies. The first one aimed to calculate inbreeding levels by runs of homozygosity approach, estimating the age of the mutation and inferring the local ancestry to determine the origin of each chromosomal segment containing mutations in KLC2, IMPA1, MED25 e WNT7A. Samples from 19 patients with autosomal recessive diseases were genotyped. The genotyped data underwent different filtering procedures to estimate the inbreeding levels by molecular approach, to calculate the age of the mutations by means of haplotypes, to infer the global ancestry using ADMIXTURE and Principal Component Analysis, and to infer refined the local ancestry by the RFMix software combining the data from our samples with the one thousand genome project (1KGP) and the Simons genomic diversity project (SGDP). The results presented did not differ significantly from those expected for inbred and admixed populations of the Brazil Northeast according to the literature. The mutation in KLC2 was older in relation to the others. In a second study, for individuals with a KLC2 mutation, we proceeded with the inference of mitochondrial DNA haplogroups to determine the origin of the families\' maternal lineage. Eleven patients with mutation in KLC2 were chosen for Sanger sequencing of the mitochondrial DNA control region for determination of matrilineage. It was found a possible founding haplogroup that can corroborate historical narratives of Sephardic mothers\' influx along the coast of the Northeast with the Dutch. Both papers present as a novelty the identification of the origin and the understanding of how these diseases are maintained and dispersed in populations of Brazil and the world. In particular, the matrilineage exhibited an evidence of kinship among mothers of families with individuals with mutation in KLC2 and mothers of portuguese Sephardic jews

京都大学 / 0048 / 新制・課程博士 / 博士(生命科学) / 甲第22133号 / 生博第420号 / 新制||生||55(附属図書館) / 京都大学大学院生命科学研究科高次生命科学専攻 / (主査)教授 渡邊 直樹, 教授 千坂 修, 教授 原田 浩 / 学位規則第4条第1項該当 / Doctor of Philosophy in Life Sciences / Kyoto University / DFAM

Muscle stem cells self-renew to maintain the long-term capacity for skeletal muscles to regenerate. However, the homeostatic regulation of muscle stem cell self-renewal is poorly understood. By utilizing high-throughput screening and transcriptomic approaches, we identify the critical function of dystrophin, the epidermal growth factor receptor (EGFR), and fibronectin in the establishment of cell polarity and in determining symmetric and asymmetric modes of muscle stem cell self-renewal. These findings reveal an orchestrated network of paracrine signaling that regulate muscle stem cell homeostasis during regeneration and have profound implications for the pathogenesis and development of therapies for Duchenne muscular dystrophy.

Fetal Alcohol Spectrum Disorders (FASDs) refer to a set of development abnormalities affecting a fetus that can result from prenatal alcohol exposure (PAE). Studies performed by the National Institute of Health estimate that the pervasiveness of FASDs may number as high as 1 to 5 per 100 school children. Congenital heart defects (CHDs) are a subset of these abnormalities and have been observed to occur in 38% of children with FASDs. While there is an association between PAE and CHDs, the exact molecular mechanism as to how it occurs remains unclear. A 2022 RNA sequencing study points to the Wnt7a gene as one of several others to have its mRNA expression significantly decrease in the heart in response to PAE at a critical developmental time point. This gene codes for the Wnt7a protein that can play a role in activating the Wnt signaling pathways. This critical pathway plays a role in cell differentiation, cell proliferation, morphogenesis, embryonic development, and adult tissue homeostasis. While mRNA expression in response to alcohol has been studied, the change in protein expression of Wnt7a is yet to be determined. This thesis serves to demonstrate assay techniques and antibodies that can be used to reliably detect Wnt7a protein. We hypothesize that Wnt7a protein expression can be reliably detected in Human Embryonic Kidney 293 (HEK 293) cells through Western blot and immunofluorescence assays when the protein is overexpressed. Fluorescent, and more effectively, chemiluminescent western blot procedures produced a positive signal for detection of Wnt7a protein at the expected 40-42 kDA molecular weight range. Through Immunofluorescence, the ii Wnt7a+ HEK cells were confirmed to express the protein through Alexa Fluor probing of an anti-Wnt7a antibody, and the DYK HEK cells failed to produce a signal for expression of the protein as expected. The methods and techniques used in this study can be used to detect Wnt7a protein in embryonic hearts and determine how much it is affected by alcohol exposure. This serves toward the larger goal of identifying Wnt7a as a potential biomarker for helping to diagnose alcohol-induced CHDs. Additionally, these future directions can help direct attention to this gene as a useful therapeutic target for preventing and treating CHD formation.

<p>Pancreatic endocrine tumors (PETs) may cause typical syndromes of hormone excess, or appear clinically non-functioning without hormonal symptoms. PETs occur sporadically, in association with the multiple endocrine neoplasia type 1 (MEN1) syndrome, or rarely the von Hippel-Lindau syndrome. Molecular genetic investigations may reveal pathways important for tumor development, and be of clinical use.</p><p>The aim of this thesis was to investigate regulation of different genes involved in cell proliferation, and relate findings to signs of malignancy in PETs.</p><p>The MEN1 gene on chromosome 11q13 was mutated in three out of eleven sporadic malignant PETs. Two nonsense mutations, causing truncation of the protein, and one missense mutation were found.</p><p>Relation of allelic loss at 11q13 and 3p25 to malignant behavior was observed in sporadic PETs. Allelic loss at 18q21 was found in a subset of sporadic and MEN1-associated PETs, and mutation analysis of Smad4 excluded a tumor suppressor gene function.</p><p>In PETs with allelic loss on chromosome 3p25, mutation analysis of WNT7A and HDAC11 excluded function as tumor suppressor genes.</p><p>Menin, encoded by the MEN1 gene, was reported to regulate expression of the cyclin-dependent kinase inhibitors CDKN2C/p18, CDKN1B/p27, and CDKN2B/p15 in mouse pancreatic islet tumor models. Here, the mRNA expression of these genes was not related to MEN1 gene mutations in human PETs.</p><p>Cyclin-dependent kinase 4 (CDK4) and the protooncogene c-Myc were found to be overexpressed regardless of MEN1 gene mutational status of the PETs. The CDK4 gene was neither amplified nor mutated. Targeting of CDK4 may present an alternative to traditional chemotherapy of PETs in the future.</p>

Pancreatic endocrine tumors (PETs) may cause typical syndromes of hormone excess, or appear clinically non-functioning without hormonal symptoms. PETs occur sporadically, in association with the multiple endocrine neoplasia type 1 (MEN1) syndrome, or rarely the von Hippel-Lindau syndrome. Molecular genetic investigations may reveal pathways important for tumor development, and be of clinical use. The aim of this thesis was to investigate regulation of different genes involved in cell proliferation, and relate findings to signs of malignancy in PETs. The MEN1 gene on chromosome 11q13 was mutated in three out of eleven sporadic malignant PETs. Two nonsense mutations, causing truncation of the protein, and one missense mutation were found. Relation of allelic loss at 11q13 and 3p25 to malignant behavior was observed in sporadic PETs. Allelic loss at 18q21 was found in a subset of sporadic and MEN1-associated PETs, and mutation analysis of Smad4 excluded a tumor suppressor gene function. In PETs with allelic loss on chromosome 3p25, mutation analysis of WNT7A and HDAC11 excluded function as tumor suppressor genes. Menin, encoded by the MEN1 gene, was reported to regulate expression of the cyclin-dependent kinase inhibitors CDKN2C/p18, CDKN1B/p27, and CDKN2B/p15 in mouse pancreatic islet tumor models. Here, the mRNA expression of these genes was not related to MEN1 gene mutations in human PETs. Cyclin-dependent kinase 4 (CDK4) and the protooncogene c-Myc were found to be overexpressed regardless of MEN1 gene mutational status of the PETs. The CDK4 gene was neither amplified nor mutated. Targeting of CDK4 may present an alternative to traditional chemotherapy of PETs in the future.

Duchenne Muscular Dystrophy (DMD) is a disorder caused by loss-of-function mutations in dystrophin, a critical protein that maintains muscle fiber integrity. Our lab discovered that dystrophin-deficient skeletal muscle stem cells, also known as satellite cells, cannot generate enough myogenic progenitors for proper muscle regeneration. Previously, we demonstrated that WNT7A, a protein expressed during muscle regeneration, stimulates symmetric division of satellite cells, and gives rise to two daughter satellite cells. Conversely, epidermal growth factor (EGF) induces asymmetric division, which generates one daughter satellite cell and one committed precursor cell. We aimed to investigate these satellite cell division mechanisms following WNT7A or EGF treatment in a human model using healthy and DMD-patient derived hiPSCs differentiated into the myogenic lineage. The presence of satellite-like cells was confirmed in both lines by their characteristic expression of PAX7 and other myogenic markers. Intriguingly, DMD-patient hiPSCs precociously differentiated compared to healthy control human induced pluripotent stem cells (hiPSCs). More notably, WNT7A treatment had a potent effect on the DMD differentiated cells. High content analysis revealed an expansion of the satellite-like cell pool as observed by a higher number of PAX7+ cells within the total population and gene expression analysis demonstrated a significant increase in global PAX7 expression. In contrast, EGF treatment reduced the number of PAX7+ cells and increased the proportion of MYOG+ cells within the myogenic population, indicating an increase in myogenic progenitors. Taken together, WNT7A and EGF can alter the myogenic differentiation program of healthy and DMD-patient derived hiPSCs by modulating the satellite-like cell division dynamics.