年齡相關性黃斑變性（AMD）是發展國家高齡人群中不可逆盲的首要原因。在AMD患者中，即使在改變生活模式或進行治療后，其滲出性亞型仍導致超過80% 的病例出現嚴重視力喪失及法定盲。息肉狀脈絡膜血管病變 （PCV）是一種與滲出性AMD在臨床表型上存在相同之處的黃斑病變，它的典型病變被定性為眼底血管螢光造影時出現息肉狀的病灶。近年PCV被認為是滲出性AMD亞型中的一種，因為兩者共享相同的基因成份及環境因素。然而，PCV曾經被認為是與滲出性AMD截然不同的一種疾病，由於兩者的臨床表現並不一致。另外，PCV病人相對年輕，多為亞洲人，以及對光動力治療和抗血管內皮生長因子治療存在不同的反應。一個明確的鑒別診斷可以更好的輔助臨床醫生對患有這些疾病的老年病人進行管理，然而兩者是相同還是不同的疾病種類仍是一個具爭議性的議題。 / CFH 基因和ARMS2/HTRA1位點已被全基因組相關性研究及相關的分子學研究定位為AMD候選基因。鑒於FPR1基因的協調吞噬性白細胞激活及遷移的功能，它可能是一個新的AMD候選基因。本論文評估在滲出性AMD和PCV中FPR1作為一個新的疾病基因基因的可能，獲取滲出性AMD和PCV病人中的CFH，ARMS2，HTRA1和FPR1基因檔案，同時研究在ARMS2/HTRA1位點中基因型和疾病表型的關聯性，以此從基因學方面鑑別滲出性AMD與PCV。 / 本研究在滲出性AMD，PCV病例和對照人群中使用聚合酶鏈反應和直接測序法進行ARMS2， HTRA1， CFH 和FPR1基因篩查。本研究發現滲出性AMD和PCV之間存在不同的基因型分佈，關聯模式以及基因效應值。 / 在HTRA1的多態性中，rs11200638，rs2672598, rs1049331 和 rs2293870 在滲出性AMD和PCV之間表現出鑒別性關聯 （p < 0.001）。其中rs11200638 (p = 1.48×10⁻⁴) and rs2672598 (p = 2.27×10⁻³) 在滲出性AMD病人中相互校正后仍保持各自的顯著性，但rs2672598 未能在PCV病人中保持顯著性(p = 0.20)。並且本研究發現攜帶rs11200638和 rs2672598聯合基因型AA-CC 的病人更傾向是滲出性AMD病人，與PCV相比幾率高11.7倍。 / 在ARMS2中，有11個基因多態性與滲出性AMD和PCV存在顯著性的相關。在與rs11200638校正后，rs10490924保持和滲出性AMD的顯著相關性(p = 0.011)，但PCV中未能保持(p = 0.077)。同時，元分析結果顯示ARMS2 rs10490924和HTRA1 rs11200638不同人群的PCV中的等位基因相關性是一致的。 / 在FPR1中，rs78488639與滲出性AMD (p = 0.049, 比值比 (OR) = 2.05, 95% 信賴區間（CI）: 1.014.14)和PCV (p = 0.016, OR = 2.27, 95%CI: 1.154.47)的疾病風險存在顯著的相關性。多態性rs104229的G等位基因純合子和滲出性AMD存在顯著相關(p = 0.039, OR = 2.27, 95%CI: 1.084.74)，但在PCV中未發現相關性(p = 0.24)。多態性rs2070746 AMD (p = 0.021, OR = 0.57, 95%CI: 0.35 0.91)和rs867229 (p = 0.0091, OR = 0.54, 95%CI: 0.340.86) 的雜合子基因型與滲出性AMD相關，但在PCV中未發現相關性。與此同時，本研究在上述多態性中發現滲出性AMD和PCV之間不同的基因型分佈。 / 本研究發現在滲出性AMD和PCV病人中FPR1 rs78488639和CFH rs800292存在顯著的相互作用（ORs > 4）。兩個多態性之間的相互作用提高滲出性AMD和PCV的疾病風險，而不是僅對其中之一起作用。 / ARMS2 多態性 rs10490924 (A69S, 205G>T, pAMD = 1.01×10⁻²⁹ OR = 7.91, 95% CI: 4.93 - 12.67; pPCV = 8.25×10⁻⁷, OR = 3.51, 95% CI: 1.98 - 5.03), HTRA1 多態性rs11200638 (-625G>A, pAMD = 9.88×10⁻²⁸, OR = 6.95, 95% CI: 4.37 - 11.06; pPCV = 8.02×10⁻⁶, OR = 2.82, 95%CI: 1.77 - 4.47), CFH 多態性rs800292 (V62I, 184G>A, pAMD = 9.00×10⁻⁴ , OR = 0.58, 95% CI: 0.42 0.79; pPCV = 0.011, OR = 0.66, 95% CI: 0.49 0.90) and FPR1 多態性rs78488639 (L97M, 289C>A, pAMD = 0.049, OR = 2.05, 95% CI: 1.01 - 4.14; pPCV = 0.016, OR = 2.27, 95% CI: 1.15 - 4.47)代表各自基因的最強相關性。此外，元分析揭示了在不同種族人群PCV中的等位基因相關性顯著並且一致(ORtotal = 2.14, 95% CI: 1.97 2.33, ORtotal = 2.34, 95% CI: 1.98 2.76 and ORtotal = 0.49, 95% CI: 0.44 0.56)。表型-基因型分析發現ARMS2/HTRA1 的風險基因型和較差的治療反應呈正相關性(p = 0.04)。另外，本研究在滲出性AMD中發現HTRA1 rs11200638和吸煙的聯合作用。然而，在PCV中未觀察到次聯合作用，這可能提示兩者間存在不同的疾病機制。 / 本論文提出FPR1基因是一個新的滲出性AMD和PCV候選基因，揭示了ARMS2，HTRA1，CFH和FPR1在滲出性AMD和PCV間顯著並且一致的相關性， 提供鑒別兩者的基因學證據，闡明了ARMS2/HTRA1 的風險基因型和較差的治療反應之間的相關性以及顯示了吸煙在滲出性AMD和PCV之間的不同影響。然而，由於兩者間基因關聯的趨勢一致，目前尚未能清晰界定兩者的不同。因此，要進一步明確鑒別滲出性AMD和PCV，還需要進行不同種族的複製研究，以及更重要的是，尋找特定的PCV基因以鑒別兩個不同疾病。 / Age-related macular degeneration (AMD) is the leading cause of irreversible blindness for the elderly in developed countries. Its exudative subtype accounts for more than 80% of severe visual loss or legal blindness in AMD patients regardless of modified lifestyle and therapeutic treatments. Polypoidal choroidal vasculopathy (PCV) is a macular disorder characterized by typical polypoidal lesions on fundus angiograhpy and sharing similar phenotype with exudative AMD. PCV was suggested as a distinct disease from exudative AMD based on different clinical features in ophthalmic imaging. Furthermore, PCV patients tend to be younger and more prevalent in Asian, and have different responses to photo-dynamic therapy and anti-vascular endothelial growth factor treatments, compared to exudative AMD patients. Howerver, it has also been suggested that PCV could be a subtype of exudative AMD mainly because of their common genetic and environmental factors. Therefore, genetic differentiation between exudtive AMD and PCV might assist clinicans to determine the condition. / The complement factor H (CFH) gene, and age-related maculopathy susceptibility 2 (ARMS2)/high temperature requirement factor A1 (HTRA1) locus have been mapped for AMD by genome-wide association studies (GWAS) and subsequent molecular investigations. The formyl peptide receptor 1 (FPR1) gene, which mediates trafficking and activation of phagocytic leukocytes, is related to the AMD-associated inflammatory condition. This thesis aims to evaluate FPR1 as a novel disease gene for exudative AMD and PCV, to compare the genetic profiles of ARMS2, HTRA1, CFH, and FPR1 in exudative AMD and PCV, to investigate the correlation of ARMS2/HTRA1 genotypes with disease phenotypes, and to differentiate these two disorders throught the genomic compositions. / Case-control association studies were conducted on ARMS2, HTRA1, CFH and FPR1 in exudative AMD and PCV patients of our Hong Kong Chinese cohort using polymerase chain reaction and direct sequencing. We observed different genotypic distributions (p < 0.05), association patterns and effect sizes between these two diseases. / In HTRA1 polymorphisms, rs11200638, rs2672598, rs1049331 and rs2293870 showed differential associations between exudative AMD and PCV (p < 0.001). Both rs11200638 (p = 1.48×10⁻⁴) and rs2672598 (p = 2.27×10⁻³) remained significant after adjusting for each other in exudative AMD, whereas rs2672598 was not significantly associated with PCV (p = 0.20). The joint genotype AA-CC constructed by the risk alleles of these rs11200638 and rs2672598 were prone to exudative AMD, conferring an 11.7-fold higher risk (p = 4.00×10⁻³) when compared to PCV. / In ARMS2, 11 single nucleotide polymorphisms (SNPs) showed significant associations with both exudative AMD and PCV. After adjusting for rs11200638, ARMS2 rs10490924 remained significantly associated with exudative AMD (p = 0.011), but not with PCV (p = 0.077). / In FPR1, SNP rs78488639 significantly increased the risk to exudative AMD (p = 0.049, odds ratio (OR) = 2.05, 95% confidence interval (CI): 1.014.14) and PCV (p = 0.016, OR = 2.27, 95%CI: 1.154.47). The homozygous G allele of rs1042229 was associated with exudative AMD (p = 0.039, OR = 2.27, 95%CI: 1.084.74), but not with PCV (p = 0.24). The heterozygous genotypes of rs2070746 and rs867229 were associated with exudative AMD (p = 0.021, OR = 0.57, 95%CI: 0.35 0.91; p = 0.0091, OR = 0.54, 95%CI: 0.340.86, respectively), but not with PCV. / Significant interaction was identified between FPR1 rs78488639 and CFH rs800292, with joint ORs > 4 folds for both exudative AMD and PCV. Interactions between FPR1 rs78488639 with CFH rs800292 enhance risks to both AMD and PCV, not just one of them. / Overall, the ARMS2 rs10490924 (A69S, 205G>T, pAMD = 1.01×10⁻²⁹, OR = 7.91, 95% CI: 4.93 - 12.67; pPCV = 8.25×10⁻⁷, OR = 3.51, 95% CI: 1.98 - 5.03), HTRA1 rs11200638 (-625G>A, pAMD = 9.88×10⁻²⁸, OR = 6.95, 95% CI: 4.37 - 11.06; pPCV = 8.02×10⁻⁶, OR = 2.82, 95%CI: 1.77 - 4.47), CFH rs800292 (V62I, 184G>A, pAMD = 9.00×10⁻⁴ , OR = 0.58, 95% CI: 0.42 0.79; pPCV = 0.011, OR = 0.66, 95% CI: 0.49 0.90) and FPR1 rs78488639 (L97M, 289C>A, pAMD = 0.0487, OR = 2.05, 95% CI: 1.01 - 4.14; pPCV = 0.0161, OR = 2.27, 95% CI: 1.15 - 4.47) were responsible for the strongest association in each gene. Moreover, meta-analysis revealed a consistent and significant association of the ARMS2/HTRA1 locus with PCV in different ethnic cohorts (OR{U+209C}{U+2092}{U+209C}{U+2090}{U+2097} = 2.14, 95% CI: 1.97 2.33, OR{U+209C}{U+2092}{U+209C}{U+2090}{U+2097} = 2.34, 95% CI: 1.98 2.76 and {U+209C}{U+2092}{U+209C}{U+2090}{U+2097} = 0.49, 95% CI: 0.44 0.56, respectively). The phenotype-genotype analysis implicated a positive correlation between ARMS2/HTRA1 risk genotype and a worse response to treatment (p = 0.04) in our exudative AMD patients. In addition, joint effects between cigarette smoking and HTRA1 rs11200638 was found in exudative AMD group. However, this effect was not significant in PCV group, which might implicate a different disease mechanism. / This thesis attempts to dissect the genetic profiles of exudative AMD and PCV. Results in this thesis suggest FPR1 as a novel candidate gene for exudative AMD and PCV, reveal a significant and consistent association of ARMS2, HTRA1, CFH and FPR1 with both exudative AMD and PCV, provide evidences for genetic differentiation of these two disorders, demonstrate a significant correlation between ARMS2/HTRA1 genotypes and response to treatment, and indicate different influence of smoking in exudative AMD and PCV. However, definite differentiation between exudative AMD and PCV was limited because of the same trend of associations between these two disorders. Therefore, replication studies in other enthic populations are necessary, and identification of PCV-specific genes/polymorphisms could further differentiate PCV from exudative AMD. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Liang, Xiaoying. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2012. / Includes bibliographical references (leaves 124-143). / Abstract also in Chinese. / Title page --- p.i / Abstract --- p.iii / 摘要 --- p.vii / Acknowledgements --- p.xii / Table of Contents --- p.xiii / List of Figures --- p.xix / List of Tables --- p.xxi / Abbreviations --- p.xxiv / Publications --- p.xxvii / Conference Presentations --- p.xxviii / Chapter Chapter 1: --- Introduction / Chapter 1.1. --- Normal retinal architecture --- p.1 / Chapter 1.2. --- Age-related retinal changes --- p.3 / Chapter 1.3. --- Age-related macular degeneration (AMD) --- p.7 / Chapter 1.3.1. --- Classification, clinical manifestation and disease course --- p.7 / Chapter 1.3.2. --- Exudative AMD and therapeutic strategies --- p.9 / Chapter 1.3.3. --- Pathology of AMD --- p.10 / Chapter 1.3.4. --- Risk factors and associated pathogenesis --- p.12 / Chapter 1.3.4.1. --- Age --- p.12 / Chapter 1.3.4.2. --- Ethnicity --- p.13 / Chapter 1.3.4.3. --- Oxidative stress --- p.13 / Chapter 1.3.4.3.1. --- Reactive oxygen species and AMD --- p.14 / Chapter 1.3.4.3.2. --- Antioxidants --- p.15 / Chapter 1.3.4.3.3. --- Association of oxidation genes with AMD --- p.16 / Chapter 1.3.4.4. --- Inflammation --- p.16 / Chapter 1.3.4.4.1. --- Complement in AMD --- p.17 / Chapter 1.3.4.4.2. --- The potential role of formyl peptide receptor 1 (FPR1) in AMD --- p.19 / Chapter 1.3.4.5. --- Genetic predisposition --- p.19 / Chapter 1.3.4.5.1. --- Complement factor H --- p.21 / Chapter 1.3.4.5.2. --- The 10q26 locus --- p.22 / Chapter 1.3.4.5.3. --- Phenotype-genotype correlation --- p.23 / Chapter 1.4. --- Comparisons between exudative AMD and Polypoidal choroidal vasculopathy --- p.24 / Chapter 1.4.1. --- History --- p.25 / Chapter 1.4.2. --- Natural course --- p.26 / Chapter 1.4.3. --- Epidemiological factors --- p.27 / Chapter 1.4.3.1. --- Ethnicity --- p.27 / Chapter 1.4.3.2. --- Gender --- p.27 / Chapter 1.4.3.3. --- Age --- p.28 / Chapter 1.4.3.4. --- Risk factors --- p.28 / Chapter 1.4.4. --- Clinical manifestation and histopathological features --- p.29 / Chapter 1.4.5. --- Genetic determinants --- p.29 / Chapter 1.4.5.1. --- Genes with common associations --- p.30 / Chapter 1.4.5.2. --- Genes not have common association --- p.32 / Chapter 1.4.6. --- Response to treatments --- p.32 / Chapter 1.5. --- Objectives and research prospects --- p.33 / Chapter Chapter 2: --- Materials and Methods / Chapter 2.1. --- Polymorphism identification in ARMS2, HTRA1, FPR1 and CFH --- p.39 / Chapter 2.1.1. --- Study subjects --- p.39 / Chapter 2.1.1.1. --- Diagnostic features of AMD and PCV --- p.39 / Chapter 2.1.1.2. --- Control subjects --- p.40 / Chapter 2.1.2. --- Laboratory methods --- p.40 / Chapter 2.1.2.1. --- DNA extraction and quantification --- p.40 / Chapter 2.1.2.2. --- Genotyping --- p.41 / Chapter 2.1.2.2.1. --- Polymerase chain reaction (PCR) and agrose gel electrophoresis --- p.41 / Chapter 2.1.2.2.2. --- DNA sequencing --- p.42 / Chapter 2.1.3. --- Statistical analysis --- p.43 / Chapter 2.1.3.1. --- Genotypic association analysis --- p.43 / Chapter 2.1.3.2. --- Haplotype association analysis --- p.43 / Chapter 2.1.3.3. --- Logistic regression analysis --- p.44 / Chapter 2.1.3.4. --- Joint effect analysis --- p.44 / Chapter 2.1.3.5. --- Meta-analysis --- p.45 / Chapter 2.1.3.6. --- Statistical power calculation and sample size --- p.45 / Chapter 2.2. --- Phenotype-genotype correlation in ARMS2/HTRA1 locus --- p.46 / Chapter 2.2.1. --- Patient recruitment --- p.46 / Chapter 2.2.2. --- Genotyping --- p.46 / Chapter 2.2.3. --- Outcome measurement --- p.46 / Chapter 2.2.4. --- Statistical analysis --- p.47 / Chapter Chapter 3: --- Results / Chapter 3.1. --- The age and gender distribution in study subjects --- p.57 / Chapter 3.2. --- The HTRA1 sequencing in exudative AMD and PCV --- p.57 / Chapter 3.2.1. --- Polymorphism identification and genotypic association --- p.57 / Chapter 3.2.2. --- Haplotype structure and Haplotype-based association analysis --- p.59 / Chapter 3.2.3. --- Joint genotype analysis --- p.59 / Chapter 3.3. --- Differential association of exudative AMD and PCV with the ARMS2/HTRA1 locus --- p.60 / Chapter 3.3.1. --- Genotypic association --- p.60 / Chapter 3.3.2. --- Haplotype analysis --- p.62 / Chapter 3.3.3. --- Logistic regression --- p.63 / Chapter 3.3.4. --- Meta-analysis of ARMS2/HTRA1 association with PCV --- p.64 / Chapter 3.3.5. --- In-position OR plot --- p.64 / Chapter 3.4. --- FPR1 and CFH in exudative AMD and PCV --- p.65 / Chapter 3.4.1. --- Polymorphism identification and genotypic association --- p.65 / Chapter 3.4.2. --- Haplotype analysis of FPR1 --- p.66 / Chapter 3.4.3. --- The association of CFH rs800292 --- p.67 / Chapter 3.4.4. --- Joint effect analysis of the CFH and FPR1 genes --- p.67 / Chapter 3.4. --- Phenotype-genotype correlation in ARMS2/HTRA1 locus --- p.68 / Chapter 3.4.1. --- Distribution of age and bilaterality --- p.69 / Chapter 3.4.2. --- Greatest linear dimension of CNV lesion in exudative AMD --- p.69 / Chapter 3.4.3. --- Response to treatment in exudative AMD --- p.69 / Chapter 3.4.4. --- Recurrence in PCV --- p.70 / Chapter 3.4.5. --- Smoking status --- p.70 / Chapter Chapter 4: --- Discussion / Chapter 4.1. --- Age and gender distribution --- p.104 / Chapter 4.2. --- Genetic differentiation in ARMS2/HTRA1 locus --- p.S104 / Chapter 4.2.1. --- SNPs with common association --- p.106 / Chapter 4.2.2. --- SNPs with different association S --- p.106 / Chapter 4.2.3. --- Comparison with previous studies C --- p.107 / Chapter 4.2.4. --- Sample size S --- p.109 / Chapter 4.3. --- The FPR1 gene in exudative AMD and PCV --- p.110 / Chapter 4.4. --- Interaction between FPR1 and CFH --- p.112 / Chapter 4.5. --- Correlation between phenotypes and genotypes --- p.113 / Chapter 4.6. --- Common and rare variants for complex disease --- p.114 / Chapter 4.6.1. --- The debate of common disease common variant versus common disease rare variant --- p.115 / Chapter 4.6.2. --- Candidate gene screening versus geno-wide association study --- p.117 / Chapter 4.6.3. --- Common variants versus rare variants in 10q26 locus --- p.118 / Chapter 4.6.3.1. --- Common variants --- p.119 / Chapter 4.6.3.2. --- Rare variants --- p.120 / Chapter Chapter 5: --- Conclusions and future prospects --- p.122 / Chapter Chapter 6: --- References --- p.124

Tam, Oi Sin Pancy. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2007. / Includes bibliographical references (leaves 101-128). / Abstracts in English and Chinese. / Table of Contents / Title page --- p.i / Abstract --- p.iii / 摘要 --- p.vi / Acknowledgements --- p.viii / Table of Contents --- p.ix / List of Figures --- p.xiii / List of Tables --- p.xv / Abbreviations --- p.xvii / Publications related to the work of this thesis --- p.xx / Conference Presentations related to this thesis --- p.xxi / Chapter Chapter 1 --- Introduction / Chapter 1.1 --- AMD --- p.1 / Chapter 1.2 --- Epidemiology --- p.4 / Chapter 1.3 --- Classification --- p.5 / Chapter 1.3.1 --- Dry AMD --- p.6 / Chapter 1.3.2 --- Wet/Exudative AMD --- p.9 / Chapter 1.4 --- Etiology and risk factors of AMD --- p.10 / Chapter 1.4.1 --- Gender and Ethnicity --- p.10 / Chapter 1.4.2 --- Smoking and vascular factors --- p.11 / Chapter 1.4.3 --- Genetic Factor --- p.11 / Chapter 1.5 --- Molecular Genetics of AMD --- p.12 / Chapter 1.5.1 --- Linkage studies --- p.12 / Chapter 1.5.2 --- Candidate genes search --- p.15 / Chapter 1.5.3 --- Genome-Wide Association --- p.18 / Chapter 1.5.3.1 --- Complement Factor H --- p.20 / Chapter 1.5.3.2 --- LOC387715 --- p.22 / Chapter 1.6 --- Statistical Analysis --- p.23 / Chapter 1.6.1 --- Genotyping --- p.23 / Chapter 1.6.2 --- Quality Assessment of Genetic Data --- p.24 / Chapter 1.6.3 --- Association Analysis --- p.26 / Chapter 1.6.4 --- Population Stratification --- p.26 / Chapter 1.6.5 --- Haplotype Analysis of Multiple SNPs --- p.26 / Chapter 1.6.6 --- Population Attributable Risk --- p.27 / Chapter 1.6.7 --- Interaction analysis --- p.28 / Chapter 1.7 --- Objectives --- p.28 / Chapter Chapter 2 --- Materials and Method --- p.30 / Chapter 2.1. --- Materials --- p.30 / Chapter 2.1.1. --- Proteins --- p.30 / Chapter 2.1.2. --- Chemicals --- p.30 / Chapter 2.1.3. --- Solutions and Buffers --- p.31 / Chapter 2.1.4. --- Reagents and Kits --- p.31 / Chapter 2.1.5. --- Apparatus --- p.32 / Chapter 2.1.6. --- Softwares --- p.32 / Chapter 2.2. --- Methods --- p.32 / Chapter 2.2.1. --- Study Subjects --- p.33 / Chapter 2.2.2. --- AMD atients --- p.33 / Chapter 2.2.3. --- Control Subjects --- p.34 / Chapter 2.2.4. --- DNA Extraction and Quantification --- p.34 / Chapter 2.2.5. --- Whole genome wide SNP scanning --- p.34 / Chapter 2.2.6. --- HTRA1 Genotyping --- p.38 / Chapter 2.2.6.1. --- Serial Polymerase Chain Reactions --- p.38 / Chapter 2.2.6.2. --- Cycle sequencing --- p.40 / Chapter 2.3. --- Statistical analysis --- p.40 / Chapter 2.3.1. --- Hardy-Weinberg Equilibrium Test --- p.40 / Chapter 2.3.2. --- Association Analysis: Linkage disequilibrium --- p.42 / Chapter 2.3.3. --- Haplotype Analysis --- p.43 / Chapter 2.3.4. --- Interaction Analysis --- p.43 / Chapter Chapter 3 --- Results --- p.46 / Chapter 3.1. --- Genome-wide Association Study of Exudative AMD --- p.46 / Chapter 3.1.1. --- Genotyping and Association Analysis --- p.46 / Chapter 3.1.2. --- Haplotype Analysis --- p.50 / Chapter 3.2. --- HTRA1 Genotyping --- p.57 / Chapter 3.2.1. --- Association Analysis --- p.57 / Chapter 3.2.2. --- Haplotype Analysis --- p.68 / Chapter 3.2.3. --- rsl 1200638 - Smoking Interaction --- p.68 / Chapter 3.2.4. --- rsl 1200638 - rs800292 Interaction --- p.74 / Chapter Chapter 4 --- Discussion --- p.79 / Chapter 4.1. --- Genome-wide Association Study of Exudative AMD --- p.79 / Chapter 4.1.1. --- Limitations and Concerns of Genome-Wide Association Study --- p.84 / Chapter 4.2. --- HTRA1 Genotyping --- p.85 / Chapter 4.2.1 --- Association and Haplotype Analysis --- p.85 / Chapter 4.2.2. --- HTRA1 --- p.87 / Chapter 4.2.3. --- Gene-Environment Interaction --- p.93 / Chapter 4.2.4. --- Gene-Gene Ineraction --- p.94 / Conclusions and Future Aspects --- p.97 / Electronic-Database Information --- p.100 / References --- p.101

An estimated 170.38 million elderly adults suffer from some stage of age-related macular degeneration (AMD) worldwide, a vision defect that damages the macula, the central region of the retina required for sharp vision, such as reading, driving, and recognizing faces. Genetic factors strongly modify one's risk for developing AMD, and most of these genetic changes are found in genes of the alternative complement cascade, a component of the immune system. The lack of effective AMD prevention calls for the identification of druggable molecules and pathways. In my research, I use microarrays and RNA sequencing to investigate the events occurring in early AMD, the reasons for macular susceptibility to AMD, and the events triggering aberrant blood vessel growth in late AMD. First, I found that genes associated with endothelial cells tend to be expressed at lower levels in human donors eyes affected by early AMD than in control eyes, concordant with previous studies indicating loss of choriocapillaris in early AMD. Second, I found that molecular signals across regions of the retina, retinal pigment epithelium, and choroid generally mirror the distribution of cell types in these regions. Third, I found that damage to cultured primate chorioretinal endothelial cells by the end product of complement activation, membrane attack complex, produces an environment conducive to choroidal neovascularization, a symptom of late-stage AMD. I propose a model that bridges genetic variants in the complement cascade genes with blood vessel loss in early AMD and the pathological growth of blood vessels in late AMD.

In recent years, microarray technology has revealed the widespread presence of submicroscopic deletions and duplications throughout the human genome termed copy number variants (CNVs). CNVs have a profound effect on gene expression and are an important source of normal genetic variation. In addition, a small proportion of CNVs contribute to genetically simple and complex disease. This thesis focuses on the identification of pathogenic CNVs contributing to the etiology of diseases with "missing heritability" using a well-planned study design individually tailored to each disease cohort to optimize CNV detection and interpretation. We performed a genome-wide analysis for CNVs in five disease cohorts with genetic etiology: autism, age-related macular degeneration (AMD), glaucoma, clubfoot, and Bardet-Biedl syndrome (BBS). Our results indicate that CNVs likely account for a proportion of cases for each disease cohort reported in this thesis. Approximately 20% of our cohort of individuals with autism from trio pedigrees harbors a CNV known to confer risk to develop autism and we identified other novel and rare variants that may play a role in autism pathogenesis. We also characterized a duplication of 2p25.3 identified in two male half-siblings with autism and determined that their mother was somatic mosaic for the duplication. Our work provides evidence that this novel CNV disrupting the genes PXDN and MYT1L are the autism-causing mutation in this pedigree. A comparative cases experimental design was used in the study of AMD and glaucoma. While no common "risk CNVs" were identified for either eye disorder, we did identify several rare overlapping CNVs disrupting genes known to play a role in the eye that may confer risk to disease in a small proportion of individuals. In a fourth genetically complex disease, clubfoot, we identified a duplication of 17q23.2 disrupting the genes TBX4, NACA2, and BRIP1 that segregates with the autosomal dominant clubfoot phenotype in a large pedigree with 16 affected individuals. In addition, the duplication is within the linkage interval identified for this family. We also applied microarray technology to analyze the genomes of individuals with BBS, an autosomal recessive disorder, for the presence of CNVs in known BBS genes as well as CNVs that elucidate novel candidate genes for BBS. From 34 BBS patients with an unidentified mutation, we observed one CNV, a heterozygous deletion of BBS10, unmasking a BBS10 frameshift mutation. A promising BBS candidate gene also emerged from our studies, implicated by an intragenic deletion of the gene MARK3 predicted to result in a frameshift and premature truncation of the protein. Functional studies utilizing antisense morpholino gene knockdown in the zebrafish provide additional evidence that MARK3 is a BBS gene as knockdown of zebrafish mark3 results in a Kupffer's Vesicle defect and a melanosome transport delay, two cardinal BBS phenotypes in the zebrafish. In addition to identifying CNVs involved in disease, the work outlined in this thesis provides valuable insight into the study design and interpretation of a genome-wide analysis of CNV. This includes the appropriate use of controls and publicly available control databases, methods for enriching for CNVs in a patient cohort to maximize efficiency and discovery, and the importance of analyzing all patient cohorts with heritable disease for the presence of CNVs disrupting known disease genes and CNVs that implicate novel genetic candidates. As the reliability and resolution of CNV detection continue to improve, allowing detection of > 1,000 CNVs in each individual genome, it becomes more important than ever to have a well-defined study design for both the detection and interpretation of CNVs.

There have been several techniques developed in recent years to develop computer models of a variety of disease behaviors. Agent-based modeling is a discrete-based modeling approach used agents to represent individual cells that mechanically interact and secrete, consume or react to soluble products. It has become a powerful modeling approach, widely used by computational researchers. In this research, we utilized agent-based modeling to study and explore disease development, particularly in two applications, breast cancer and bioengineering experiments. We further proposed an error-minimization search approach and used it to estimate cellular parameters from multicellular in vitro data. In this dissertation, in the first study, we developed a 2D agent-based model that attempted to emulate the in vivo structure of breast cancer. The model was applied to describe the progression from DCIS into DCI. This model confirms that the interaction between tumor cells and the surrounding stroma in the duct plays a critical role in tumor growth and metastasis. This interaction depends on many mechanical and chemical factors that work with each other to produce tumor invasion of the surrounding tissue. In the second study, an in silico model was developed and applied to understanding the underlying mechanism of vascular-endothelial growth factor (VEGF) auto-regulation in REP and emulate the in vitro experiments as part of bioengineering research. This model may provide a system with robust predictive modeling and visualization that could enable discovery of the molecular mechanisms involved in age-related macular degeneration (AMD) progression and provide routers to the development of effective treatments. In the third and final study, a searching approach was applied to estimate cellular parameters from spatiotemporal data produced from bioengineered multicellular in vitro experiments. We applied a search method to an integrated cellular and multicellular model of retinal pigment epithelial cells to estimate the auto-regulation parameters of VEGF.

Age-related macular degeneration (AMD) is a chronic, irreversible disease that robs individuals of vision, quality of life, and independence. It is the leading cause of blindness in industrialized countries. Sleep-disordered breathing (SDB) is a condition characterized by repeated episodes of apnea and/or hypopnea, insomnia, short sleep duration, and/or sleep disturbances (snoring, gasping, etc.). Because SDB has been shown to cause chronic hypoxia resulting in oxidative stress on the retina, it has been proposed that SDB may be associated with AMD. Based on the life course theory of chronic disease, this quantitative, cross-sectional study used data from the 2005-2008 National Health and Nutrition Examination Survey to study whether there was an association between SDB and AMD, including neovascular AMD and geographic atrophy in adults 40 years and older. Descriptive statistics and logistic regression analyses were used. The results suggest that AMD is associated with diagnosed sleep disorders, including sleep apnea and insomnia, as well as sleep apnea symptoms of gasping snoring, snorting, and stopping breathing. The findings of this study highlight the importance of diagnostic screening and therapeutic intervention to treat SDB. Early diagnosis and therapy for SDB could address not only the comorbidities associated with SDB, but could also prevent or slow the progression of AMD. In turn, this would yield lower rates of vision loss, reduced comorbidities associated with vision loss, and reduced impact of AMD on the health care system and social and financial costs to society.

La formation de néo-vaisseaux sanguins est un processus impliqué dans de nombreuses pathologies, telles que le développement de carcinomes cutanés et la néo-vascularisation choroïdienne caractéristique de la forme exsudative de la dégénérescence maculaire liée à lâge (DMLA). Dans ces deux cas, lactivation du réseau vasculaire est un facteur de mauvais pronostic. Lanalogie entre ces deux pathologies est renforcée par le développement récent dapproches thérapeutiques anti-angiogènes. Ces approches ciblent principalement le VEGF et les molécules associées. Malgré lefficacité de ces molécules sur la pathologie ciblée, leur administration systémique engendre des effets secondaires non négligeables. Notre travail a pour but détudier limplication dautres acteurs moléculaires dans ces pathologies, en vue de développer des stratégies thérapeutiques alternatives ou complémentaires. Parmi les principales molécules impliquées lors de langiogenèse, les protéases et leurs inhibiteurs sont des cibles potentielles pour le développement de nouveaux traitements. Il était initialement admis que les protéases (MMPs, protéases à sérine) sont des facteurs pro-angiogènes et leurs inhibiteurs (TIMPs, PAI-1) des facteurs anti-angiogènes. Dans ce contexte, lhypothèse thérapeutique évidente était dinhiber les protéases et de protéger ou dactiver leurs inhibiteurs. Cependant, lorsque nous avons entamé ce travail, ce concept a été remis en question. En effet, un niveau élevé de PAI-1 a été détecté dans de nombreux cancers et représente un facteur de mauvais pronostic. Par ailleurs, les inhibiteurs des MMPs nont présenté aucun effet lors dessais cliniques, certains stimulant même la croissance tumorale. Il est important de noter que ces premiers inhibiteurs étaient des inhibiteurs à large spectre bloquant laction non seulement des MMPs, mais aussi des membres de familles proches. Une détection fine des rôles joués par les MMPs et linhibiteur PAI-1 sest avérée indispensable. Nous avons, dès lors, focalisé notre travail sur deux thèmes : létude de PAI-1 et létude du rôle individuel de quelques MMPs. Il a précédemment été démontré que linhibiteur PAI-1 exerce un rôle pro-angiogène lors du développement de carcinomes cutanés et de néo-vascularisation choroïdienne. PAI-1 exerce donc un effet paradoxal et complexe sur langiogenèse. Bien que le rôle de PAI-1 au cours de langiogenèse bourgeonnante était bien documenté, son implication au cours de la vasculogenèse nétait pas connue. Nos résultats démontrent que le développement des carcinomes cutanés nécessite la migration des cellules stromales adjacentes aux cellules tumorales. Par contre, la néo-vascularisation choroïdienne, également dépendante de PAI-1, requiert le recrutement des cellules issues de la moelle osseuse. Publications 1 et 2. La seconde partie de notre travail est consacrée aux métalloprotéinases matricielles. Nos résultats montrent les rôles opposés ou synergiques des MMPs. Les MMP-2 et -9 sont des protéases pro-angiogènes agissant de concert au cours de linvasion des carcinomes. A lopposé, la MMP-19 exerce une fonction anti-angiogène et nos travaux suggèrent que cette MMP contribuerait à la stabilité des vaisseaux matures et au maintien physiologique des tissus, son expression étant diminuée lors de linvasion tumorale. Publications 3, 4 et 5.

Current anti-VEGF biologics, such as bevacizumab and VEGF trap, have been successfully used as therapeutic agents for cancer and age-related macular degeneration (AMD). Since these strategies target VEGF systemically, their toxicity profile, including proteinuria and thromboembolic events, and need for frequent eye injections in AMD treatment, prevail. Therefore, the aim of this PhD thesis was to generate novel anti-VEGF biologics that inhibit VEGF activity specifically at the desired target site. Two classes of biologics were engineered that simultaneously bind VEGF and either: 1) the extracellular matrix (ECM) or 2) target-site specific antigens. The first subgroup, “sticky-traps”, is composed of VEGF trap linked to a sequence of hydrophobic amino acids, with affinity for heparin sulfate proteoglycans of the ECM. The second subgroup, “lassos”, is composed of a C-terminus positioned form of VEGF trap linked to single-chain variable domain antibodies specific for either HER2 (HER2/V lasso) or fibronectin extra domain B (EDB; EDB/V lasso), expressed on breast cancer cell surfaces or in the vascular bed of solid tumours, respectively. ii Using a novel transgenic method, piggyBac transposons, biologics were expressed in transgenic cancer cell lines in a doxycycline inducible manner. They were shown to inhibit VEGF activity and also retain the native function of their constituent domains. Specifically, the sticky-traps adhered to the ECM and the HER2/V lasso inhibited the proliferation of HER2 positive cancer cell lines. Sticky-traps as well as lassos were able to inhibit or delay tumour growth of A-673, Pc-3, SKOV-3 and HT-29 xenografts. In contrast to soluble VEGF trap, sticky-traps were retained at the tumour site and were undetectable in the circulation. Moreover, sticky-traps, in contrast to VEGF trap, did not delay wound healing and regression of trachea blood vessels. Furthermore, transgenic studies indicated that HER2/V lasso is more effective compared to anti-HER2 Ab and VEGF trap used alone or in combination. These novel classes of antiangiogenic molecules could be advantageous in a clinical setting. Using the principles established in my PhD thesis work, similar dual function biologics can be designed for inhibition of other molecules with disease relevance.

Current anti-VEGF biologics, such as bevacizumab and VEGF trap, have been successfully used as therapeutic agents for cancer and age-related macular degeneration (AMD). Since these strategies target VEGF systemically, their toxicity profile, including proteinuria and thromboembolic events, and need for frequent eye injections in AMD treatment, prevail. Therefore, the aim of this PhD thesis was to generate novel anti-VEGF biologics that inhibit VEGF activity specifically at the desired target site. Two classes of biologics were engineered that simultaneously bind VEGF and either: 1) the extracellular matrix (ECM) or 2) target-site specific antigens. The first subgroup, “sticky-traps”, is composed of VEGF trap linked to a sequence of hydrophobic amino acids, with affinity for heparin sulfate proteoglycans of the ECM. The second subgroup, “lassos”, is composed of a C-terminus positioned form of VEGF trap linked to single-chain variable domain antibodies specific for either HER2 (HER2/V lasso) or fibronectin extra domain B (EDB; EDB/V lasso), expressed on breast cancer cell surfaces or in the vascular bed of solid tumours, respectively. ii Using a novel transgenic method, piggyBac transposons, biologics were expressed in transgenic cancer cell lines in a doxycycline inducible manner. They were shown to inhibit VEGF activity and also retain the native function of their constituent domains. Specifically, the sticky-traps adhered to the ECM and the HER2/V lasso inhibited the proliferation of HER2 positive cancer cell lines. Sticky-traps as well as lassos were able to inhibit or delay tumour growth of A-673, Pc-3, SKOV-3 and HT-29 xenografts. In contrast to soluble VEGF trap, sticky-traps were retained at the tumour site and were undetectable in the circulation. Moreover, sticky-traps, in contrast to VEGF trap, did not delay wound healing and regression of trachea blood vessels. Furthermore, transgenic studies indicated that HER2/V lasso is more effective compared to anti-HER2 Ab and VEGF trap used alone or in combination. These novel classes of antiangiogenic molecules could be advantageous in a clinical setting. Using the principles established in my PhD thesis work, similar dual function biologics can be designed for inhibition of other molecules with disease relevance.

Eine lokale Aktivierung des Komplementsystems im RPE ist ein pathogener Faktor der AMD. Neben der Wirkung von angiogenen Faktoren wie VEGF könnte eine Aktivierung des Blutgerinnungssystems im RPE dazu beitragen, dass sich aus einer trockenen eine feuchte AMD entwickelt. Dies könnte auf mehreren Ebenen geschehen: Gerinnungsfaktoren könnten die Expression der Komplementfaktoren und der angiogenen Faktoren regulieren sowie Wirkungen auf die Proliferation und Migration der RPE-Zellen besitzen. Eine Stimulierung der Proliferation und Migration der RPE-Zellen trägt zur Ausbildung von CNV-Membranen bei. Es ist aber bis jetzt nichts darüber bekannt, ob RPE-Zellen Faktoren des Blutgerinnungssystems exprimieren und ob z.B. Thrombin (als zentrale Protease des Blutgerinnungssystems) die Genexpression von Komplementfaktoren und von VEGF im RPE beeinflusst. Die Ziele der vorliegenden Dissertation waren daher: ● Nachweis der mRNA-Expression von Blutgerinnungs- und Komplementfaktoren im RPE; ● Nachweis der Wirkung von Thrombin auf die Expression von VEGF und von Komplementfaktoren, sowie auf die Proliferation und Migration der RPE-Zellen; und ● Nachweis der Wirkung der Komplementfaktoren C5a und C9 auf die Sekretion von VEGF und die Proliferation und Migration der RPE-Zellen.