Thesis (M. Phil.)--University of Hong Kong, 2010. / Includes bibliographical references (p. 167-183). Also available in print.

Biliary atresia (BA) is a rare and severe cholestatic disease in neonates characterized by an idiopathic inflammatory process affecting both intra- and extra-hepatic bile ducts, causing cholestasis and ultimately leading to obliteration of the biliary tract. Through a previous genome-wide-association-study (GWAS) on Han Chinese, we discovered association of the 10q24.2 region encompassing ADD3 and XPNPEP1 gene. But disease pathogenesis and genetic architecture of BA is still obscure. We mapped the 10q24.2 association locus with 107 single nucleotide polymorphisms (SNPs) on 339 Han Chinese patients and 401 matched controls, follow-up studies of the association signals were performed. We revealed the common risk haplotype encompassing 5 tagging-SNPs, capturing the risk-predisposing alleles in 10q24.2 [logistic regression p=5.32x10-11; odds ratio, OR:2.38; confidence interval, CI:(2.14-2.62)]. No deleterious rare variants (RVs) residing on the risk haplotype were found, dismissing the theory of “synthetic” association. Moreover, the BA-associated potential regulatory SNPs correlated ADD3 gene expression (linear regression p=0.0030). Remarkably, the risk haplotype frequency coincides with BA incidences in the general population, and, positive selection (favoring the derived alleles that arose from mutations) was evident at the ADD3 locus. Our finding suggested the complexity of BA genetic architecture and role of environmental effects in the disease. We then revisited BA GWAS dataset and annotated the association signals with expression quantitative trail loci (eQTL) information available on normal adult livers. We did not see excessive enrichment of BA associated SNPs in liver eQTLs. We speculate that the liver eQTLs currently available relate to adulthood liver function and are not necessarily involved in liver development, adaptation to oxidative stress, or inflammation changes seen in BA pathophysiology. To investigate whether rare alleles can predispose to BA, we called copy number variations (CNVs) from the GWAS Affymetrix gene chip 5.0. We obtained 86 BA private CNVs distributed among 131 BA patients were compared to the CNV profile of 11,943 database samples and 846 hypertension disease samples. Assuming that pathogenic CNVs interrupt dosage-sensitive genes, we prioritized the dosage-sensitive genes and the pathogenic CNVs by integrating multiple lines of evidence. Through gene set enrichment analysis we found that the ‘core’ genes affected by BA CNVs were members of the Calcium signaling pathway, which has been involved in the pathogenesis of polycystic liver and kidney diseases. Further we initiated the survey on rare coding variants in BA through Exome sequencing 23 BA liver genomes, while patients’ blood DNA and parental DNA would be examined in the validation stage to validate de novo mutations, including somatic mosaicism in liver. We found inherited deleterious mutations in polycystic liver and kidney disease genes in BA patients, and the role of these mutations in BA pathogenesis is being investigated. Functional validation of the BA variants identified in this study is compulsory given the overall obscurity of BA pathogenesis. Together, this study presents a comprehensive catalog of both common and rare variants implicated in BA. We hope that our findings will contribute to enriching the BA-associated genetic network. / published_or_final_version / Surgery / Doctoral / Doctor of Philosophy

No description available.

No description available.

published_or_final_version / Psychiatry / Master / Master of Philosophy

No description available.

Introdução: A atresia biliar (AB) é uma doença que se inicia na infância e caracteriza-se por obstrução das vias biliares extra-hepáticas, e por colangiopatia progressiva, de etiologia desconhecida. Seu tratamento consiste numa portoenterostomia, cujo sucesso é variável. Fatores como a idade na portoenterostomia e normalização de bilirrubinas séricas influenciam a sobrevida do paciente com seu próprio fígado. Nosso grupo estuda o envolvimento de uma arteriopatia na etiologia da AB. O fator de crescimento vascular endotelial (VEGF) e seus receptores VEGFR1 e VEGFR2 participam da angiogênese em situações de distúrbio vascular. Objetivo: Quantificar a expressão gênica de VEGFA e seus receptores, relacionando com variáveis moleculares, morfométricas e clínico-laboratoriais associadas com a gravidade da AB e o prognóstico pós-portoenterostomia. Métodos: Estudo de amostras de biópsias em cunha coletadas na laparotomia exploradora de pacientes com AB, na sua forma isolada IgM- para citomegalovírus (n= 32), comparando com lactentes com colestase intra-hepática (CIH, n= 09), pareados por idade. Uma amostra foi ultracongelada (análise molecular) e outra, parafinizada (análises histológica e imunoistoquímica). A expressão dos genes angiogênicos (VEGFA, VEGFR1 e VEGFR2), fibrogênico (MCP1, proteína quimiotática de monócitos) e de reação ductular (CK19, citoqueratina 19), além do gene normalizador, ribossomal 18S, foi medida por PCRq com sondas TaqMan®. As análises morfométricas, a partir de material parafinado, incluindo extensão de fibrose e reação ductular foram mensuradas através do programa Image Pro Plus 6.0. Variáveis clínico-laboratoriais foram prospectivamente coletadas no banco de dados da Unidade de Hepatologia Pediátrica do HCPA. Resultados: VEGFR2 foi menos expresso na AB em comparação com CIH (P <0,001), enquanto não houve diferença significante na expressão de VEGFR1 (P= 0,086) e apenas uma tendência de menor expressão do VEGFA (P= 0,060) no grupo AB. Quanto à expressão de VEGFA e VEGFR2, dois subgrupos de AB foram observados: um com expressão levemente superior ou igual à CIH e outro com expressão 3 vezes menor que a mediana do grupo CIH. Os subgrupos com menor expressão foram denominados loVEGFA e loVEGFR2. Na AB, a expressão do VEGFA teve correlação positiva com a de seus receptores VEGFR1 e VEGFR2 (rs=0,8; P<0,001 e rs=0,5; P=0,001). A expressão de VEGFR2 teve uma forte correlação negativa com a idade na portoenterostomia (rs=-0,6;P=0,001). As bilirrubinas séricas total e direta foram negativamente correlacionadas com VEGFA (rs=-0,5;P=0,007 e rs=-0,4;P=0,033) e VEGFR2 (rs=-0,5;P=0;004 e rs=-0,6;P=0,001). No subgrupo loVEGFR2 a expressão de CK19 estava diminuída, e a de MCP1 não se associou à expressão gênica das moléculas angiogênicas. Conclusões: Na AB há um subgrupo com diminuição na expressão de VEGFA e VEGFR2. A expressão de ambas as moléculas correlacionou-se ao comportamento das variáveis associadas a gravidade da doença e obstrução do fluxo biliar na portoenterostomia, incluindo bilirrubinas séricas e idade. O subgrupo de baixa expressão do VEGFR2 apresentou diminuição da massa de colangiócitos, segundo a expressão do CK 19, mas foi independente da expressão do marcador de fibrose, MCP1. / Background: Biliary atresia (BA) is a disease that begins in infancy and is characterized by complete obstruction of extrahepatic biliary ducts and a progressive cholangiopathy of undefined etiology. Treatment of BA consists of a portoenterostomy, whose success is variable. Factors such as age at portoenterostomy and post-operative normalization of serum bilirubin influence the native liver survival. Our group studies the role of an arteriopathy, and thus of hypoxia, in the etiology of BA. Expression of vascular endothelial growth factor (VEGF) A and its receptors, VEGFR1 and VEGFR2, induce angiogenesis in response to hypoxia. Aim: To assess gene expression of VEGFA and its receptors in BA, correlating with molecular, morphometric and clinical-laboratory variables associated with the disease severity and the post-portoenterostomy prognosis of BA. Methods: Liver biopsy specimens collected at exploratory laparotomy of age-matched patients with isolated, cytomegalovirus IgM-negative BA (n=32) and intrahepatic cholestasis (IHC, n=9) were evaluated. A sample was ultrafrozen (for molecular analysis) and the other was paraffin-embedded (for histological and morphometric analyzes). The expression of genes involved in angiogenic (VEGFA, VEGFR1 and VEGFR2), biliary fibrosis (MCP1 - monocyte chemotaxis protein 1) and cholangiocyte phenotype (CK19 – cytokeratin 19), was measured by TaqMan® probes with qPCR, using ribosomal 18S as the normalizing gene. Extents of fibrosis and ductular reaction were morphometrically assessed using the Image Pro Plus 6.0. Clinical-laboratory variables were collected from the database of the Pediatric Hepatology Unit of Hospital de Clínicas de Porto Alegre. Results: VEGFR2 was less expressed in BA compared with IHC (P <0.001), whereas there was no significant difference in the expression of VEGFR1 (P=0.086) and only a trend of a lower expression of VEGFA (P=0.060) in the BA group. Regarding VEGFA and VEGFR2, two subgroups of BA were defined: low expression, with values 3 times lower than the median of the IHC group, and high expression. In BA, VEGFA expression was positively correlated with that of VEGFR1 and VEGFR2 (rs=0.8, P<0.001; rs=0.58, P=0.001). The expression of VEGFR2 had a strong negative correlation with age at portoenterostomy (rs=-0.6, P=0.001). Total and direct reacting bilirubins were both negatively correlated with VEGFA expression (rs=-0.5, P=0.007; rs=-0.4,P=0.033) and VEGFR2 (rs=-0.5,P=0.004; rs=-0.6,P=0.001). In the low VEGFR2 expression (loVEGFR2) subset, gene expression of CK19, marker of cholangiocyte phenotype, was decreased. MCP1, marker of fibrosis, was not associated with he expression of the angiogenic factors. Conclusion: In BA there is a subset of patients with decreased expression of VEGFA and VEGFR2. The expression of these molecules is correlated with variables associated to disease severity and bile flow obstruction at portoenterostomy, including age and serum bilirubin levels. The loVEGFR2 expression is associated with a decreased cholangiocyte mass as evaluated by CK19 expression, and is independent of the expression of the fibrosis marker MCP1.

Introdução: A atresia biliar (AB) é uma doença que se inicia na infância e caracteriza-se por obstrução das vias biliares extra-hepáticas, e por colangiopatia progressiva, de etiologia desconhecida. Seu tratamento consiste numa portoenterostomia, cujo sucesso é variável. Fatores como a idade na portoenterostomia e normalização de bilirrubinas séricas influenciam a sobrevida do paciente com seu próprio fígado. Nosso grupo estuda o envolvimento de uma arteriopatia na etiologia da AB. O fator de crescimento vascular endotelial (VEGF) e seus receptores VEGFR1 e VEGFR2 participam da angiogênese em situações de distúrbio vascular. Objetivo: Quantificar a expressão gênica de VEGFA e seus receptores, relacionando com variáveis moleculares, morfométricas e clínico-laboratoriais associadas com a gravidade da AB e o prognóstico pós-portoenterostomia. Métodos: Estudo de amostras de biópsias em cunha coletadas na laparotomia exploradora de pacientes com AB, na sua forma isolada IgM- para citomegalovírus (n= 32), comparando com lactentes com colestase intra-hepática (CIH, n= 09), pareados por idade. Uma amostra foi ultracongelada (análise molecular) e outra, parafinizada (análises histológica e imunoistoquímica). A expressão dos genes angiogênicos (VEGFA, VEGFR1 e VEGFR2), fibrogênico (MCP1, proteína quimiotática de monócitos) e de reação ductular (CK19, citoqueratina 19), além do gene normalizador, ribossomal 18S, foi medida por PCRq com sondas TaqMan®. As análises morfométricas, a partir de material parafinado, incluindo extensão de fibrose e reação ductular foram mensuradas através do programa Image Pro Plus 6.0. Variáveis clínico-laboratoriais foram prospectivamente coletadas no banco de dados da Unidade de Hepatologia Pediátrica do HCPA. Resultados: VEGFR2 foi menos expresso na AB em comparação com CIH (P <0,001), enquanto não houve diferença significante na expressão de VEGFR1 (P= 0,086) e apenas uma tendência de menor expressão do VEGFA (P= 0,060) no grupo AB. Quanto à expressão de VEGFA e VEGFR2, dois subgrupos de AB foram observados: um com expressão levemente superior ou igual à CIH e outro com expressão 3 vezes menor que a mediana do grupo CIH. Os subgrupos com menor expressão foram denominados loVEGFA e loVEGFR2. Na AB, a expressão do VEGFA teve correlação positiva com a de seus receptores VEGFR1 e VEGFR2 (rs=0,8; P<0,001 e rs=0,5; P=0,001). A expressão de VEGFR2 teve uma forte correlação negativa com a idade na portoenterostomia (rs=-0,6;P=0,001). As bilirrubinas séricas total e direta foram negativamente correlacionadas com VEGFA (rs=-0,5;P=0,007 e rs=-0,4;P=0,033) e VEGFR2 (rs=-0,5;P=0;004 e rs=-0,6;P=0,001). No subgrupo loVEGFR2 a expressão de CK19 estava diminuída, e a de MCP1 não se associou à expressão gênica das moléculas angiogênicas. Conclusões: Na AB há um subgrupo com diminuição na expressão de VEGFA e VEGFR2. A expressão de ambas as moléculas correlacionou-se ao comportamento das variáveis associadas a gravidade da doença e obstrução do fluxo biliar na portoenterostomia, incluindo bilirrubinas séricas e idade. O subgrupo de baixa expressão do VEGFR2 apresentou diminuição da massa de colangiócitos, segundo a expressão do CK 19, mas foi independente da expressão do marcador de fibrose, MCP1. / Background: Biliary atresia (BA) is a disease that begins in infancy and is characterized by complete obstruction of extrahepatic biliary ducts and a progressive cholangiopathy of undefined etiology. Treatment of BA consists of a portoenterostomy, whose success is variable. Factors such as age at portoenterostomy and post-operative normalization of serum bilirubin influence the native liver survival. Our group studies the role of an arteriopathy, and thus of hypoxia, in the etiology of BA. Expression of vascular endothelial growth factor (VEGF) A and its receptors, VEGFR1 and VEGFR2, induce angiogenesis in response to hypoxia. Aim: To assess gene expression of VEGFA and its receptors in BA, correlating with molecular, morphometric and clinical-laboratory variables associated with the disease severity and the post-portoenterostomy prognosis of BA. Methods: Liver biopsy specimens collected at exploratory laparotomy of age-matched patients with isolated, cytomegalovirus IgM-negative BA (n=32) and intrahepatic cholestasis (IHC, n=9) were evaluated. A sample was ultrafrozen (for molecular analysis) and the other was paraffin-embedded (for histological and morphometric analyzes). The expression of genes involved in angiogenic (VEGFA, VEGFR1 and VEGFR2), biliary fibrosis (MCP1 - monocyte chemotaxis protein 1) and cholangiocyte phenotype (CK19 – cytokeratin 19), was measured by TaqMan® probes with qPCR, using ribosomal 18S as the normalizing gene. Extents of fibrosis and ductular reaction were morphometrically assessed using the Image Pro Plus 6.0. Clinical-laboratory variables were collected from the database of the Pediatric Hepatology Unit of Hospital de Clínicas de Porto Alegre. Results: VEGFR2 was less expressed in BA compared with IHC (P <0.001), whereas there was no significant difference in the expression of VEGFR1 (P=0.086) and only a trend of a lower expression of VEGFA (P=0.060) in the BA group. Regarding VEGFA and VEGFR2, two subgroups of BA were defined: low expression, with values 3 times lower than the median of the IHC group, and high expression. In BA, VEGFA expression was positively correlated with that of VEGFR1 and VEGFR2 (rs=0.8, P<0.001; rs=0.58, P=0.001). The expression of VEGFR2 had a strong negative correlation with age at portoenterostomy (rs=-0.6, P=0.001). Total and direct reacting bilirubins were both negatively correlated with VEGFA expression (rs=-0.5, P=0.007; rs=-0.4,P=0.033) and VEGFR2 (rs=-0.5,P=0.004; rs=-0.6,P=0.001). In the low VEGFR2 expression (loVEGFR2) subset, gene expression of CK19, marker of cholangiocyte phenotype, was decreased. MCP1, marker of fibrosis, was not associated with he expression of the angiogenic factors. Conclusion: In BA there is a subset of patients with decreased expression of VEGFA and VEGFR2. The expression of these molecules is correlated with variables associated to disease severity and bile flow obstruction at portoenterostomy, including age and serum bilirubin levels. The loVEGFR2 expression is associated with a decreased cholangiocyte mass as evaluated by CK19 expression, and is independent of the expression of the fibrosis marker MCP1.

Introdução: A atresia biliar (AB) é uma doença que se inicia na infância e caracteriza-se por obstrução das vias biliares extra-hepáticas, e por colangiopatia progressiva, de etiologia desconhecida. Seu tratamento consiste numa portoenterostomia, cujo sucesso é variável. Fatores como a idade na portoenterostomia e normalização de bilirrubinas séricas influenciam a sobrevida do paciente com seu próprio fígado. Nosso grupo estuda o envolvimento de uma arteriopatia na etiologia da AB. O fator de crescimento vascular endotelial (VEGF) e seus receptores VEGFR1 e VEGFR2 participam da angiogênese em situações de distúrbio vascular. Objetivo: Quantificar a expressão gênica de VEGFA e seus receptores, relacionando com variáveis moleculares, morfométricas e clínico-laboratoriais associadas com a gravidade da AB e o prognóstico pós-portoenterostomia. Métodos: Estudo de amostras de biópsias em cunha coletadas na laparotomia exploradora de pacientes com AB, na sua forma isolada IgM- para citomegalovírus (n= 32), comparando com lactentes com colestase intra-hepática (CIH, n= 09), pareados por idade. Uma amostra foi ultracongelada (análise molecular) e outra, parafinizada (análises histológica e imunoistoquímica). A expressão dos genes angiogênicos (VEGFA, VEGFR1 e VEGFR2), fibrogênico (MCP1, proteína quimiotática de monócitos) e de reação ductular (CK19, citoqueratina 19), além do gene normalizador, ribossomal 18S, foi medida por PCRq com sondas TaqMan®. As análises morfométricas, a partir de material parafinado, incluindo extensão de fibrose e reação ductular foram mensuradas através do programa Image Pro Plus 6.0. Variáveis clínico-laboratoriais foram prospectivamente coletadas no banco de dados da Unidade de Hepatologia Pediátrica do HCPA. Resultados: VEGFR2 foi menos expresso na AB em comparação com CIH (P <0,001), enquanto não houve diferença significante na expressão de VEGFR1 (P= 0,086) e apenas uma tendência de menor expressão do VEGFA (P= 0,060) no grupo AB. Quanto à expressão de VEGFA e VEGFR2, dois subgrupos de AB foram observados: um com expressão levemente superior ou igual à CIH e outro com expressão 3 vezes menor que a mediana do grupo CIH. Os subgrupos com menor expressão foram denominados loVEGFA e loVEGFR2. Na AB, a expressão do VEGFA teve correlação positiva com a de seus receptores VEGFR1 e VEGFR2 (rs=0,8; P<0,001 e rs=0,5; P=0,001). A expressão de VEGFR2 teve uma forte correlação negativa com a idade na portoenterostomia (rs=-0,6;P=0,001). As bilirrubinas séricas total e direta foram negativamente correlacionadas com VEGFA (rs=-0,5;P=0,007 e rs=-0,4;P=0,033) e VEGFR2 (rs=-0,5;P=0;004 e rs=-0,6;P=0,001). No subgrupo loVEGFR2 a expressão de CK19 estava diminuída, e a de MCP1 não se associou à expressão gênica das moléculas angiogênicas. Conclusões: Na AB há um subgrupo com diminuição na expressão de VEGFA e VEGFR2. A expressão de ambas as moléculas correlacionou-se ao comportamento das variáveis associadas a gravidade da doença e obstrução do fluxo biliar na portoenterostomia, incluindo bilirrubinas séricas e idade. O subgrupo de baixa expressão do VEGFR2 apresentou diminuição da massa de colangiócitos, segundo a expressão do CK 19, mas foi independente da expressão do marcador de fibrose, MCP1. / Background: Biliary atresia (BA) is a disease that begins in infancy and is characterized by complete obstruction of extrahepatic biliary ducts and a progressive cholangiopathy of undefined etiology. Treatment of BA consists of a portoenterostomy, whose success is variable. Factors such as age at portoenterostomy and post-operative normalization of serum bilirubin influence the native liver survival. Our group studies the role of an arteriopathy, and thus of hypoxia, in the etiology of BA. Expression of vascular endothelial growth factor (VEGF) A and its receptors, VEGFR1 and VEGFR2, induce angiogenesis in response to hypoxia. Aim: To assess gene expression of VEGFA and its receptors in BA, correlating with molecular, morphometric and clinical-laboratory variables associated with the disease severity and the post-portoenterostomy prognosis of BA. Methods: Liver biopsy specimens collected at exploratory laparotomy of age-matched patients with isolated, cytomegalovirus IgM-negative BA (n=32) and intrahepatic cholestasis (IHC, n=9) were evaluated. A sample was ultrafrozen (for molecular analysis) and the other was paraffin-embedded (for histological and morphometric analyzes). The expression of genes involved in angiogenic (VEGFA, VEGFR1 and VEGFR2), biliary fibrosis (MCP1 - monocyte chemotaxis protein 1) and cholangiocyte phenotype (CK19 – cytokeratin 19), was measured by TaqMan® probes with qPCR, using ribosomal 18S as the normalizing gene. Extents of fibrosis and ductular reaction were morphometrically assessed using the Image Pro Plus 6.0. Clinical-laboratory variables were collected from the database of the Pediatric Hepatology Unit of Hospital de Clínicas de Porto Alegre. Results: VEGFR2 was less expressed in BA compared with IHC (P <0.001), whereas there was no significant difference in the expression of VEGFR1 (P=0.086) and only a trend of a lower expression of VEGFA (P=0.060) in the BA group. Regarding VEGFA and VEGFR2, two subgroups of BA were defined: low expression, with values 3 times lower than the median of the IHC group, and high expression. In BA, VEGFA expression was positively correlated with that of VEGFR1 and VEGFR2 (rs=0.8, P<0.001; rs=0.58, P=0.001). The expression of VEGFR2 had a strong negative correlation with age at portoenterostomy (rs=-0.6, P=0.001). Total and direct reacting bilirubins were both negatively correlated with VEGFA expression (rs=-0.5, P=0.007; rs=-0.4,P=0.033) and VEGFR2 (rs=-0.5,P=0.004; rs=-0.6,P=0.001). In the low VEGFR2 expression (loVEGFR2) subset, gene expression of CK19, marker of cholangiocyte phenotype, was decreased. MCP1, marker of fibrosis, was not associated with he expression of the angiogenic factors. Conclusion: In BA there is a subset of patients with decreased expression of VEGFA and VEGFR2. The expression of these molecules is correlated with variables associated to disease severity and bile flow obstruction at portoenterostomy, including age and serum bilirubin levels. The loVEGFR2 expression is associated with a decreased cholangiocyte mass as evaluated by CK19 expression, and is independent of the expression of the fibrosis marker MCP1.

The differentiation, in an infant with cholestasis, between extrahepatic biliary atresia (EHBA) and the neonatal hepatitis syndrome (NHS) is important in that laparotomy is always indicated in EHBA but is undesirable in NHS. This differentiation is particularly difficult in those infants with complete cholestasis. Hepatobiliary scintigraphy is a commonly used investigation in infants with obstructive jaundice. The scintigraphic demonstration of excretion into the gut excludes extrahepatic obstruction, however, absence of excretion may be due to EHBA, severe cholestasis with patent extrahepatic bile ducts or poor uptake of the agent, and is therefore not diagnostic. This study has examined the quantitative measurement of the hepatic uptake of p-butyl IDA and Sn colloid, and an estimation of liver shape, in a group of patients with complete cholestasis in whom conventional scan interpretation, based on excretion into the-gut, would not be useful. The scans were recorded as dynamic studies and the resultant time-activity curves were subjected to curve fitting to calculate a rate constant for uptake of radiopharmaceutical. Liver shape was determined from the anterior static image of the colloid scan. The results show a significant difference between the EHBA and the NHS patients in the rate of uptake of p-butyl IDA, in the ratio of the rate of uptake of p-butyl IDA/the rate of uptake of colloid and in the measurements used to express liver shape. Using this method of scan interpretation, a diagnostic accuracy of 85% was achieved in this study of patients who clinically, and on scan, had no evidence of bile flow. Hepatic scintigraphy is therefore a useful investigation in the diagnostic work-up of infants presenting with obstructive jaundice even when bile flow is completely absent.