Analysis of Metacyclic Telomeres in Trypanosoma brucei

Trypanosoma brucei spp. are the agents responsible for African sleeping sickness in man and Nagana in cattle. The organisms have the ability to evade the host's immune system by antigenic variation of their surface coat. The surface coat of the infective forms is composed of a single molecular species, the variant surface glycoprotein (VSG). Each specific VSG is encoded by a separate gene, expression of which occurs in a loose hierarchical order. T. brucei has the coding capacity for approximately 10e3 VSG genes, which are found either in chromosomal clusters or at telomeric loci; it is only from the latter that the gene may be expressed. Telomeric expression sites (ESs) utilized during bloodstream infection are complex, typically between 40 - 60 Kb long, containing several non-VSG expression site associated genes (ESAGs) and preceded by a long barren region devoid of restriction sites. Transcription of telomeric ESs is insensitive to the toxin alpha-amanitin and transcription of a given ES appears to be mutually exclusive of other ESs in vivo. By virtue of their location, chromosomal internal VSG genes need to be transposed to a telomere for expression. The transposition event is duplicative and produces an expression linked copy of the gene. Telomeric VSG genes, however, can be expressed either by duplicative transposition or reciprocal recombination to an active ES, or by in situ activation. The metacyclic stage of the trypanosome life cycle is the first to express VSG genes. The metacyclic form utilizes a highly predictable subset of VSG genes (M-VSGs), comprising only 1-2% of the entire VSG gene repertoire, which appear to be expressed by a distinct and dominant mechanism to that employed during chronic bloodstream infection. Direct molecular analysis of M-VSG gene expression is precluded by the paucity of metacyclic forms in the salivary exudate of the tsetse fly vector and the transient nature of this developmental stage which cannot be cultured in vitro. M-VSG gene expression, however, is still extant in the host bloodstream in the first few days following fly bite. Analysis during this period is compounded by the polyclonal origin of the M-VSG genes expressed by individual organisms and instability of VSG expression. The work described in this thesis focuses on attempts to clone an M-VSG gene telomere and to gain insight into the predictability and stability of the M-VSG repertoire, by analysis of the telomere in a model trypanosome line which circumvents some of the problems associated with previous systems. Cloning and analysis of the BC telomeres for the M-VSG genes for GUTat 7.1 and ILTat 1.22 revealed that each had a remarkably small barren region and shared no sequence homology with ESs used in chronic bloodstream infection, apart from the 70 bp repeat sequence constituting the barren region 5'of the VSG gene. Transcriptional analysis of the ILTat 1.22 metacyclic ES, utilising the model line of trypanosomes expressing the gene in situ, revealed that the ES is extremely short in comparison to bloodstream ESs, extending no more than 3.5 - 4 Kb 5' of the VSG gene. One other region of the ILTat 1.22 BC and GUTat 7.1-2 BC telomeres appeared to be transcriptionally active. This comprised a genomic repetitive element which also was transcribed in procyclic tiypanosomes. The structural individuality of these telomeres was proposed as underlying the stability and physical distinction of the M- VSG repertoire. This hypothesis is supported by an epidemiological analysis of the ILTat 1.22 BC telomere over a 24 year period and spanning diverse epidemic foci of infection. Within Kenyan epidemic foci this telomere is present unaltered in all the stocks investigated over the the period examined and suggests that spread of the disease in East Africa is principally by mechanical transmission; this has important consequences for tackling the disease at source. Cloning and analysis of these telomeres now facilitates characterisation of metacyclic ES control elements and comparisons with other M-ES to be made

A genome-wide association study follow-up suggests a possible role for PPARG in systemic sclerosis susceptibility

Introduction: A recent genome-wide association study (GWAS) comprising a French cohort of systemic sclerosis (SSc) reported several non-HLA single-nucleotide polymorphisms (SNPs) showing a nominal association in the discovery phase. We aimed to identify previously overlooked susceptibility variants by using a follow-up strategy.<p></p> Methods: Sixty-six non-HLA SNPs showing a P value <10-4 in the discovery phase of the French SSc GWAS were analyzed in the first step of this study, performing a meta-analysis that combined data from the two published SSc GWASs. A total of 2,921 SSc patients and 6,963 healthy controls were included in this first phase. Two SNPs, PPARG rs310746 and CHRNA9 rs6832151, were selected for genotyping in the replication cohort (1,068 SSc patients and 6,762 healthy controls) based on the results of the first step. Genotyping was performed by using TaqMan SNP genotyping assays. Results: We observed nominal associations for both PPARG rs310746 (PMH = 1.90 × 10-6, OR, 1.28) and CHRNA9 rs6832151 (PMH = 4.30 × 10-6, OR, 1.17) genetic variants with SSc in the first step of our study. In the replication phase, we observed a trend of association for PPARG rs310746 (P value = 0.066; OR, 1.17). The combined overall Mantel-Haenszel meta-analysis of all the cohorts included in the present study revealed that PPARG rs310746 remained associated with SSc with a nominal non-genome-wide significant P value (PMH = 5.00 × 10-7; OR, 1.25). No evidence of association was observed for CHRNA9 rs6832151 either in the replication phase or in the overall pooled analysis.<p></p> Conclusion: Our results suggest a role of PPARG gene in the development of SSc

Association of a non-synonymous functional variant of the ITGAM gene with systemic sclerosis.

Systemic sclerosis (SSc) is a chronic fibrotic autoimmune disease of complex aetiology which shares genetic similarities with systemic lupus erythematosus (SLE).1 2 One of the novel risk loci that have been recently associated with SLE is the integrin α M (ITGAM) gene, which encodes the α subunit of the αMβ2-integrin.3 4 The most likely causal polymorphism that best explains this association is a non-synonymous single-nucleotide polymorphism (SNP) at the exon 3, rs1143679, which changes the 77th amino acid residue arginine to histidine (R77H). This functional SNP represents one of the highest associated signals with SLE and is predicted to alter the structure and function of the integrin.4 5 To determine whether ITGAM rs1143679 is also associated with SSc susceptibility and clinical manifestations, we genotyped a total of 3735 SSc patients and 3930 matched healthy individuals from seven independent European cohorts of Caucasian origin (Spain, Germany, The Netherlands, Italy, Norway, Sweden and UK) using a predesigned TaqMan® assay (ID: C___2847895_1_) in an ABI 7900HT (both from Applied Biosystems, Foster City, California, USA). Case …Peer Reviewe

Retinal Vascular Fractal Dimension, Childhood IQ, and Cognitive Ability in Old Age: The Lothian Birth Cohort Study 1936

<div><p>Purpose</p><p>Cerebral microvascular disease is associated with dementia. Differences in the topography of the retinal vascular network may be a marker for cerebrovascular disease. The association between cerebral microvascular state and non-pathological cognitive ageing is less clear, particularly because studies are rarely able to adjust for pre-morbid cognitive ability level. We measured retinal vascular fractal dimension (<i>D</i>_<i>f</i>) as a potential marker of cerebral microvascular disease. We examined the extent to which it contributes to differences in non-pathological cognitive ability in old age, after adjusting for childhood mental ability.</p><p>Methods</p><p>Participants from the Lothian Birth Cohort 1936 Study (LBC1936) had cognitive ability assessments and retinal photographs taken of both eyes aged around 73 years (<i>n</i> = 648). IQ scores were available from childhood. Retinal vascular <i>D</i>_<i>f</i> was calculated with monofractal and multifractal analysis, performed on custom-written software. Multiple regression models were applied to determine associations between retinal vascular <i>D</i>_<i>f</i> and general cognitive ability (<i>g</i>), processing speed, and memory.</p><p>Results</p><p>Only three out of 24 comparisons (two eyes × four <i>D</i>_<i>f</i> parameters × three cognitive measures) were found to be significant. This is little more than would be expected by chance. No single association was verified by an equivalent association in the contralateral eye.</p><p>Conclusions</p><p>The results show little evidence that fractal measures of retinal vascular differences are associated with non-pathological cognitive ageing.</p></div

Confirmation of CCR6 as a risk factor for anti-topoisomerase I antibodies in systemic sclerosis

Item does not contain fulltextOBJECTIVES: The current knowledge of the influence of systemic sclerosis (SSc) risk loci in the clinical sub-phenotypes is still limited. The main limitation lies in the low frequency of some sub-phenotypes which could be solved by replication studies in independent cohorts and meta-analysis between studies. In this regard, CCR6 gene variants have been recently associated with anti-topoisomerase I positive (ATA+) production in SSc patients in a candidate gene study. This gene has been proposed to have a critical role in IL-17-driven autoimmunity in human diseases. METHODS: In order to confirm the association between CCR6 and ATA+ SSc patients, we performed an independent replication study in populations of European ancestry. We studied two CCR6 genetic variants (rs968334 and rs3093024) in a total of 901 ATA+ SSc cases, 3,258 ATA- SSc cases and 7,865 healthy controls and compared allelic frequencies for those SNPs in ATA+ SSc with healthy controls and also with ATA- SSc patients. RESULTS: The comparison performed between ATA+ SSc patients and healthy controls showed significant association with SNP rs968334 (p=4.88 x 10-2, OR=1.11). When we compared ATA+ SSc cases with ATA- SSc, both SNPs, rs3093024 and rs968334, showed significant associations (p=2.89 x 10-2, OR=1.13; p=1.69 x 10-2, OR=1.15). Finally, in order to increase even more sample size and statistical power, we meta-analysed our study with the previous reported and found a significant association between SNP rs3093024 and ATA+ SSc patients (p=1.00 x 10-4, OR=1.16) comparing with healthy controls. CONCLUSIONS: Our work confirms the association of CCR6 gene and ATA+ SSc patients

Confirmation of CCR6 as a risk factor for anti-topoisomerase I antibodies in systemic sclerosis

The current knowledge of the influence of systemic sclerosis (SSc) risk loci in the clinical sub-phenotypes is still limited. The main limitation lies in the low frequency of some sub-phenotypes which could be solved by replication studies in independent cohorts and meta-analysis between studies. In this regard, CCR6 gene variants have been recently associated with anti-topoisomerase I positive (ATA+) production in SSc patients in a candidate gene study. This gene has been proposed to have a critical role in IL-17-driven autoimmunity in human diseases

A genome wide association study follow-up suggests a possible role of PPARG in systemic esclerosis susceptiblity

Introduction A recent genome-wide association study (GWAS) comprising a French cohort of systemic sclerosis (SSc) reported several non-HLA single-nucleotide polymorphisms (SNPs) showing a nominal association in the discovery phase. We aimed to identify previously overlooked susceptibility variants by using a follow-up strategy. Methods Sixty-six non-HLA SNPs showing a P value <10-4 in the discovery phase of the French SSc GWAS were analyzed in the first step of this study, performing a meta-analysis that combined data from the two published SSc GWASs. A total of 2,921 SSc patients and 6,963 healthy controls were included in this first phase. Two SNPs, PPARG rs310746 and CHRNA9 rs6832151, were selected for genotyping in the replication cohort (1,068 SSc patients and 6,762 healthy controls) based on the results of the first step. Genotyping was performed by using TaqMan SNP genotyping assays. Results We observed nominal associations for both PPARG rs310746 (PMH = 1.90 × 10-6, OR, 1.28) and CHRNA9 rs6832151 (PMH = 4.30 × 10-6, OR, 1.17) genetic variants with SSc in the first step of our study. In the replication phase, we observed a trend of association for PPARG rs310746 (P value = 0.066; OR, 1.17). The combined overall Mantel-Haenszel meta-analysis of all the cohorts included in the present study revealed that PPARG rs310746 remained associated with SSc with a nominal non-genome-wide significant P value (PMH = 5.00 × 10-7; OR, 1.25). No evidence of association was observed for CHRNA9 rs6832151 either in the replication phase or in the overall pooled analysis

Confirmation of association of the macrophage migration inhibitory factor gene with systemic sclerosis in a large European population

Contains fulltext : 96758.pdf (publisher's version ) (Closed access)Objectives. The aim of this study was to confirm the implication of macrophage migration inhibitory factor (MIF) gene in SSc susceptibility or clinical phenotypes in a large European population. Methods. A total of 3800 SSc patients and 4282 healthy controls of white Caucasian ancestry from eight different European countries were included in the study. The MIF -173 single nucleotide polymorphism (SNP) was selected as genetic marker and genotyped using Taqman 5' allelic discrimination assay. Results. The MIF -173 SNP showed association with SSc [P = 0.04, odds ratio (OR) = 1.10, 95% CI 1.00, 1.19]. Analysis of the MIF -173 polymorphism according to SSc clinical phenotype revealed that the frequency of the -173*C allele was significantly higher in the dcSSc group compared with controls (P = 5.30E-03, OR = 1.21, 95% CI 1.07, 1.38). Conversely, the frequency of the MIF -173*C allele was significantly underrepresented in the lcSSc group compared with dcSSc patients, supporting previous findings [(P = 0.04, OR = 0.86, 95% CI 0.75, 0.99); meta-analysis including previous results (P = 0.005, OR = 0.83, 95% CI 0.73, 0.94)]. Conclusion. Our results confirm the role of MIF -173 promoter polymorphism in SSc, and provide evidence of a strong association with the dcSSc subgroup of patients. Hence, the MIF -173 variant is confirmed as a promising clinical phenotype genetic marker