Genetic Characteristics of Lithuanian and Latvian Patients with Inflammatory Bowel Disease ; Uždegiminėmis žarnyno ligomis sergančių Lietuvos ir Latvijos ligonių genetinės ypatybės

Thinkpad Sl510

Sujets

• Biology
• Crohn's disease
• Single-nucleotide polymorphism
• Ulcerative colitis

Informations

• Publié par: kaunas_university_of_medicine
• Publié le: 01 janvier 2011
• Nombre de lectures: 71
• Langue: English
• Poids de l'ouvrage: 2 Mo

Extrait

LITHUANIAN UNIVERSITY OF HEALTH SCIENCES






Jurgita Šventoraitytė



GENETIC CHARACTERISTICS
OF LITHUANIAN AND LATVIAN
PATIENTS WITH INFLAMMATORY
BOWEL DISEASE


Doctoral Dissertation
Biomedical Sciences, Biology (01 B)










Kaunas, 2011 Dissertation has been prepared at Lithuanian University of Health Sciences
during the period of 2006–2010.



Scientific Supervisor
Prof. Dr. Neringa Paužienė (Lithuanian University of Health Sciences,
Biomedical Sciences, Biology – 01 B)


Consultants:
Prof. Habil. Dr. Limas Kupčinskas (Lithuanian University of Health
Sciences, Biomedical Sciences, Medicine – 07 B)
Prof. Dr. rer. nat. Andre Franke (Christian-Albrechts University in Kiel,
Biomedical Sciences, Biology – 01 B)

CONTENT

ABBREVIATIONS ............................................................................................. 5
INTRODUCTION ............................... 7
Aim and objectives of the study ....................................... 9
Originality of the study..................... 9
1. LITERATURE REVIEW ........................................... 11
1.1. Inflammatory bowel disease 11
1.1.1. Clinical aspects of Crohn‟s disease .............................................. 11
1.1.2. Clinicacts of ulcerative colitis ............. 13
1.1.3. Epidemiology ................................................ 14
1.1.4. Pathogenesis ................. 16
1.2. Genetic mapping in complex human diseases ..................................... 20
1.2.1. Genome-wide linkage studies ....................................................... 20
1.2.2. Genome-wide association studies ................. 22
1.3. Epistasis in determining susceptibility to complex human diseases ... 26
1.4. Genetic aspects of inflammatory bowel disease .................................. 28
1.4.1. Genetic epidemiology ................................... 28
1.4.2. Inflammatory bowel disease genetic studies 29
2. MATERIALS AND METHODS ............................... 40
2.1. Patients ................................................................ 40
2.2. Sample preparation .............................................. 42
2.2.1. DNA extraction from blood .......................................................... 42
2.2.2. Plate design ................... 46
2.2.3. Whole genome amplification ........................ 46
2.2.4. Agarose gel electrophoresis .......................... 49
2.3. Genotyping ................................................................ 50
2.3.1. SNP selection ................ 50
2.3.2. SNPlex™ ...................... 50
®2.3.3. TaqMan ....................... 60
2.4. Statistical analysis ............................................................................... 63
2.4.1. Pre-hoc analysis ............ 63
2.4.2. Quality control measures .............................................................. 64
2.4.3. Association analysis ...................................... 65
2.4.4. SNP-SNP epistasis analysis .......................... 67
2.4.5. In sicilo prediction of gene interactive network ........................... 68
2.4.6. Genetic risk profile analysis ......................................................... 69
3 3. RESULTS ..................................................................................................... 71
3.1. Genotyping success rate and heterogeneity ........ 71
3.2. Single marker case-control association analysis 71
3.2.1. Association analysis in Crohn‟s disease ...... 71
3.2.2. lysis in ulcerative colitis ..................................... 73
3.3. Genetic association with disease phenotype ....... 76
3.3.1. Assoch Crohn‟s disease phenotype .............................. 77
3.3.2. iation with ulcerative colitis phenotype ............................. 80
3.4. SNP-SNP epistasis .............................................................................. 82
3.4.1. In sicilo prediction of PTPN22 and C13orf31 interactive
network.........................................................................................84
3.5. Genetic risk profile ............. 85
3.5.1. Genetic risk profile for ulcerative colitis ..................................... 85
3.5.2. Genetic rfile for Crohn‟s disease ...... 89
4. DISCUSSION ............................................................................................... 93
CONCLUSIONS ............................. 108
REFERENCES ................................ 110
LIST OF PUBLICATIONS ............................................ 131
ACKNOWLEDGEMENT .............................................. 133
APPENDIX ..................................... 134




4 ABBREVIATIONS


AoD assay-on-Demand
ARPC actin-related protein 2/3 complex
ASO allele-specific oligo
ATG16L1 autophagy-related protein 16-like 1
BSN bassoon (presynaptic cytomatrix protein)
BTNL2 butyrophilin-like 2
C13orf31 chromosome 13 open reading frame 31
CARD caspase recruitment domain
CCR6 CC chemokine receptor 6
CD Crohn‟s disease
CI confidence interval
Csk C-terminal src kinase
ECM1 extracellular matrix protein 1
gDNA genomic deoxyribonucleic acid
GWAS genome wide association studies
HLA human leukocyte antigen
HWE Hardy Weinberg equilibrium
IBD inflammatory bowel disease
ICOSLG inducible T-cell co-stimulator ligand
IFN-γ interferon-γ
IL interleukin
IL23R interleukin 23 receptor
IRGM immunity-related GTPase family, M
JAK2 Janus kinase 2
LD linkage disequilibrium
LOD logarithm of odds
LR likehood ratio
LSO locus-specific oligo
MAF minor allele frequency
MST1 macrophage stimulating 1
NELL1 nel-like 1
NKX2-3 NK2 transcription factor-related locus 3
NOD2 nucleotide-binding oligomerization domain containing 2
5 NPV negative predictive value
OR odds ratio
ORMDL3 orosomucoid1-like 3
OTUD3 OTU domain containing 3
PCR polymerase chain reaction
PLA2G2E phospholipase A2, group IIE
PPV positive predictive value
PTGER4 prostaglandin receptor EP4 gene
PTPN protein tyrosine phosphatase non-receptor
RNF186 ring finger protein 186
S100Z S100 calcium binding protein Z
SD standart deviation
SLC22A4 solute carrier family 22, member 4
SNP single nucleotide polymorphism
STAT3 signal transducer and activator of transcription 3
TCR T cell receptor
TE Tris-ethylenediaminetetraacetic acid
TNFSF15 tumor necrosis factor (ligand) superfamily, member 15
TNF-α tumour necctor α
UC ulcerative colitis
WGA whole genome amplification
WTCCC Wellcome Trust Case Control Consortium

DNA base nomenclature

A Adenine
C Cytosine
G Guanine
T Thymine

6 INTRODUCTION

The gastrointestinal tract is a barrier organ that constitutes one of the largest
sites of exposure to the outside environment. The intestinal mucosal surface,
which consists of a single-layered epithelium, is continuously exposed to a
diverse admixture of commensal bacteria comprised of 500 to 1000 species
11 12(reaching up to 10 –10 cells per milliliter or gram of luminal contents) [1, 2],
as well as to an enormous antigenic load through dietary and environmental
factors [3]. The normal response to penetration of epithelium by antigens as
well as commensal and pathogenic microbes is controlled by immune system
mediated self-limiting inflammation [3]. Dysregulation of the fine-tuned
immune response, leading to chronic inflammation of the gastrointestinal tract
and loss of epithelial integrity, results in inflammatory bowel disease (IBD) [4].
The two clinically defined conditions of IBD (OMIM 601458) – Crohn‟s
disease (CD; OMIM 266600) and ulcerative colitis (UC; OMIM 191390) – are
chronic remittent and progressive immune-mediated inflammatory disorders.
They are characterized by episodes of recurring abdominal pain, diarrhea, rectal
bleeding and malnutrition [5]. IBD represents an important public health
problem. It tends to afflict young people and has a protracted and relapsing
clinical course, affecting patients working abilities, education, social life, and
quality of life [6, 7]. These disorders also increase the risk of colon cancer [8].
Although mortality is low, morbidity associated with IBD is substantial [9]. The
incidence of the diseases is reported to be the highest in the industrialized
Western countries, with prevalence rates in North America and Europe ranging
from 21 to 246 per 100,000 inhabitants for UC and 8 to 214 per 100,000
inhabitants for CD [10]. Until recently, only few data was available on the
epidemiology of IBD in the developing countries. The recent data from this
region indicated low, but gradually rising incidence of IBD [11, 12].
The precise etiologic and pathogenetic mechanisms underlying the
pathogenesis of CD and UC remain uncertain. However, the presently available
data support the hypothesis of a complex interplay between genetic factors in a
fraction of the population and the rather drastic change in environmental