A genome wide association study identifies a lncRna as risk factor for pathological inflammatory responses in leprosy

Submitted by Sandra Infurna ([email protected]) on 2018-02-08T11:09:47Z No. of bitstreams: 1 milton_moraes_etal_IOC_2017.pdf: 3018090 bytes, checksum: 4f1884a5b459722255f6434f0d7dfe23 (MD5)Approved for entry into archive by Sandra Infurna ([email protected]) on 2018-02-08T11:28:23Z (GMT) No. of bitstreams: 1 milton_moraes_etal_IOC_2017.pdf: 3018090 bytes, checksum: 4f1884a5b459722255f6434f0d7dfe23 (MD5)Made available in DSpace on 2018-02-08T11:28:23Z (GMT). No. of bitstreams: 1 milton_moraes_etal_IOC_2017.pdf: 3018090 bytes, checksum: 4f1884a5b459722255f6434f0d7dfe23 (MD5) Previous issue date: 2017Research Institute of the McGill University Health Centre. Program in Infectious Diseases and Immunity in Global Health. Montreal, Quebec, canada / McGill University. The McGill International TB Centre, Departments of Human Genetics and Medicine. Montreal, Quebec, Canada.Research Institute of the McGill University Health Centre. Program in Infectious Diseases and Immunity in Global Health. Montreal, Quebec, canada / McGill University. The McGill International TB Centre, Departments of Human Genetics and Medicine. Montreal, Quebec, Canada.Institut National de la Santé et de la Recherche Médicale. Laboratory of Human Genetics of Infectious Diseases. Necker Branch. Paris, France / University Paris Descartes. Imagine Institute. Paris, France / Rockefeller University. Giles Laboratory of Human Genetics of Infectious Diseases. Rockefeller Branch. New York, USA.Research Institute of the McGill University Health Centre. Program in Infectious Diseases and Immunity in Global Health. Montreal, Quebec, canada / McGill University. The McGill International TB Centre, Departments of Human Genetics and Medicine. Montreal, Quebec, Canada.Hospital for Dermato-Venerology. Ho Chi Minh City, Vietnam.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Hanseníase. Rio de Janeiro, RJ. Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Hanseníase. Rio de Janeiro, RJ. Brasil.Universidade Federal de Goiás. Instituto de Saúde Pública e Patologia Tropical. Goiânia, GO, BrasilInstituto Lauro de Souza Lima. Bauru, SP. Brasil.Instituto Lauro de Souza Lima. Bauru, SP. Brasil.Hospital for Dermato-Venerology. Ho Chi Minh City, Vietnam.Institut National de la Santé et de la Recherche Médicale. Laboratory of Human Genetics of Infectious Diseases. Necker Branch. Paris, France / University Paris Descartes. Imagine Institute. Paris, France / Rockefeller University. Giles Laboratory of Human Genetics of Infectious Diseases. Rockefeller Branch. New York, USA.Institut National de la Santé et de la Recherche Médicale. Laboratory of Human Genetics of Infectious Diseases. Necker Branch. Paris, France / University Paris Descartes. Imagine Institute. Paris, France / Rockefeller University. Giles Laboratory of Human Genetics of Infectious Diseases. Rockefeller Branch. New York, USA.Research Institute of the McGill University Health Centre. Program in Infectious Diseases and Immunity in Global Health. Montreal, Quebec, canada / McGill University. The McGill International TB Centre, Departments of Human Genetics and Medicine. Montreal, Quebec, Canada.Leprosy Type-1 Reactions (T1Rs) are pathological inflammatory responses that afflict a sub-group of leprosy patients and result in peripheral nerve damage. Here, we employed a family-based GWAS in 221 families with 229 T1R-affect offspring with stepwise replication to identify risk factors for T1R. We discovered, replicated and validated T1R-specific associations with SNPs located in chromosome region 10p21.2. Combined analysis across the three independent samples resulted in strong evidence of association of rs1875147 with T1R (p = 4.5x10-8; OR = 1.54, 95% CI = 1.32-1.80). The T1R-risk locus was restricted to a lncRNA-encoding genomic interval with rs1875147 being an eQTL for the lncRNA. Since a genetic overlap between leprosy and inflammatory bowel disease (IBD) has been detected, we evaluated if the shared genetic control could be traced to the T1R endophenotype. Employing the results of a recent IBD GWAS meta-analysis we found that 10.6% of IBD SNPs available in our dataset shared a common risk-allele with T1R (p = 2.4x10-4). This finding points to a substantial overlap in the genetic control of clinically diverse inflammatory disorders

Study design to identify genetic variants associated with T1R in three independent samples.

<p>In all samples T1R-affected subjects were matched with T1R-free subjects according to their clinical sub-type of leprosy. For the discovery phase, two sets of families with leprosy-affected offspring (T1R-free or T1R-affected) were selected from our records of Vietnamese leprosy families. A transmission disequilibrium test (TDT) was used to evaluate the non-random transmission of alleles from parents to offspring in the T1R-affected and T1R-free families independently. Next, a formal heterogeneity test was used to contrast the associations in the two family sets and to identify specific associations with the T1R-affected subset. Odds ratios were estimated by conditional logistic regression using the un-transmitted allele as a pseudosib control and compared to the actual offspring case in a matched case-control design. Subsequently, we recruited independent leprosy cases from Vietnam and Brazil for replication and validation of associations in the discovery phase. In these population-based case-control designs T1R-affected were compared with T1R-free subjects using a logistic procedure with adjustment for age at leprosy diagnosis and gender.</p

Enrichment of shared risk-alleles associated with T1R leprosy and IBD phenotypes.

<p>GWAS loci for (A) Inflammatory Bowel Disease [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006637#pgen.1006637.ref024" target="_blank">24</a>], (B) Schizophrenia [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006637#pgen.1006637.ref025" target="_blank">25</a>], (C) Human height [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006637#pgen.1006637.ref026" target="_blank">26</a>] and (D) Human blood metabolites [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006637#pgen.1006637.ref027" target="_blank">27</a>] are represented by a single SNP with the strongest evidence for association. The count of SNPs is given below each central blue pie (panels A—D) for each disease. The light blue pie slices indicate the numbers of SNPs that were not available for comparisons with the leprosy families. The proportions of shared SNPs with T1R-free leprosy (left light green pie) and T1R leprosy (right light orange pie) are indicated as pies for each of the GWAS sets (panel A—D). The pies in panel E represents the totality of SNPs tested in the present study for T1R-free and T1R-affected families. The yellow slices indicate the proportion of SNPs with nominal evidence for association with T1R-free leprosy or T1R/leprosy. The darker shade of yellow represent the proportion of SNPs that are significantly heterogeneous between T1R free and affected leprosy patients. The hypergeometric test used as baseline the proportion of nominally associated GWAS SNPs to estimate the significance of enrichment of the T1R/leprosy and T1R-free leprosy GWAS SNPs among the four selected disease phenotypes.</p

Variants associated with T1R across geographically separated and ethnically distinct populations.

<p>Variants associated with T1R across geographically separated and ethnically distinct populations.</p

Variants on chromosome 10 are preferentially associated with T1R.

<p>(A) Manhattan plot of the TDT results for the T1R-affected families in the discovery phase. Genetic variants represented by dots are plotted according to their chromosomal position on the x-axis against the negative log <i>p</i> values on the y-axis. The blue horizontal line indicates suggestive association (<i>p</i> = 1.0x10^-06), and the red horizontal line represents significant association (<i>p</i> = 5.0x10^-08). (B) Quantiles-Quantiles plots of genotyped and imputed variants for T1R-affected families in the discovery phase. Variants were plotted according to the observed <i>p</i> values on the y-axis and the expected <i>p</i> values on the x-axis. The 95% confidence interval dispersion is presented by grey shades. The slight deflation of the Q-Q plot is likely due to the sample size employed. (C) Visualization of a 220 kb region on chromosome region 10p21.2. Evidence of association for SNPs located in the interval is plotted for the T1R-free families and the T1R-affected families. The negative log of the <i>p</i>-value on the left y-axis is plotted against the chromosomal SNP position on the x-axis. The recombination rate in centimorgan per mega base is displayed on the right y-axis. The solid horizontal line indicates the suggestive association (<i>p</i> = 1.0 x 10⁻⁰⁶) while the doted horizontal line represents nominal association (<i>p</i> = 0.05). The diamond plot at the bottom of panel C indicates the <i>r</i>² linkage disequilibrium for variants nominally associated with T1R in 763 leprosy unaffected parents from both T1R-affected and T1R-free families. Highlighted in red are the leading SNPs in seven LD bins (<i>r</i>² > 0.9). (D) Evidence for association of seven tag SNPs for the SNPs associated with T1R in the Chromosome10p21.2 region is shown for the discovery phase only (red dots) and for the combined analysis of all three samples (orange lozenges). The negative log of the <i>p</i>-value is indicated on the left y-axis. The recombination rate in centimorgan per mega base is displayed on the right y-axis and indicated by a blue line. The blue horizontal line indicates suggestive association (<i>p</i> = 1.0x10^-06), and the red horizontal line represents significant association (<i>p</i> = 5.0x10^-08). The genomic locations of RefSeq or ENSEMBL genes are given at the bottom.</p