Gene-level association analysis of systemic sclerosis: A comparison of African-Americans and White populations

All authors: Olga Y. Gorlova , Yafang Li, Ivan Gorlov, Jun Ying, Wei V. Chen, Shervin Assassi, John D. Reveille, Frank C. Arnett, Xiaodong Zhou, Lara Bossini-Castillo, Elena Lopez-Isac, Marialbert Acosta-Herrera, Peter K. Gregersen, Annette T. Lee, Virginia D. Steen, Barri J. Fessler, Dinesh Khanna, Elena Schiopu, Richard M. Silver, Jerry A. Molitor, Daniel E. Furst, Suzanne Kafaja, Robert W. Simms, Robert A. Lafyatis, Patricia Carreira, Carmen Pilar Simeon, Ivan Castellvi, Emma Beltran, Norberto Ortego, Christopher I. Amos, Javier Martin, Maureen D. Mayes.Data Availability Statement: Genetic data is available from dbGaP repository (https://www.ncbi. nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_ id=phs000357.v1.p1).Gene-level analysis of ImmunoChip or genome-wide association studies (GWAS) data has not been previously reported for systemic sclerosis (SSc, scleroderma). The objective of this study was to analyze genetic susceptibility loci in SSc at the gene level and to determine if the detected associations were shared in African-American and White populations, using data from ImmunoChip and GWAS genotyping studies. The White sample included 1833 cases and 3466 controls (956 cases and 2741 controls from the US and 877 cases and 725 controls from Spain) and the African American sample, 291 cases and 260 controls. In both Whites and African Americans, we performed a gene-level analysis that integrates association statistics in a gene possibly harboring multiple SNPs with weak effect on disease risk, using Versatile Gene-based Association Study (VEGAS) software. The SNP-level analysis was performed using PLINK v.1.07. We identified 4 novel candidate genes (STAT1, FCGR2C, NIPSNAP3B, and SCT) significantly associated and 4 genes (SERBP1, PINX1, TMEM175 and EXOC2) suggestively associated with SSc in the gene level analysis in White patients. As an exploratory analysis we compared the results on Whites with those from African Americans. Of previously established susceptibility genes identified in Whites, only TNFAIP3 was significant at the nominal level (p = 6.13x10-3) in African Americans in the gene-level analysis of the ImmunoChip data. Among the top suggestive novel genes identified in Whites based on the ImmunoChip data, FCGR2C and PINX1 were only nominally significant in African Americans (p = 0.016 and p = 0.028, respectively), while among the top novel genes identified in the gene-level analysis in African Americans, UNC5C (p = 5.57x10-4) and CLEC16A (p = 0.0463) were also nominally significant in Whites. We also present the gene-level analysis of SSc clinical and autoantibody phenotypes among Whites. Our findings need to be validated by independent studies, particularly due to the limited sample size of African Americans.Funding was provided to MDM by the National Institutes of Health (NIH) the National Institute of Arthritis, Musculoskeletal and Skin Diseases (NIAMS https://www.niams.nih.gov/) Centers of Research Translation (CORT) P50-AR054144, NIH grant N01-AR-02251 and R01-AR-055258, and the Department of Defense (DD) Congressionally Directed Medical Research Program (http://cdmrp.army.mil/) W81XWH-07-1-011 and WX81XWH-13-1-0452 for the collection, analysis and interpretation of the data

Genotype and allele distribution for <i>TYK2</i> polymorphisms in seropositive and seronegative individuals.

<p>Genotype and allele distribution for <i>TYK2</i> polymorphisms in seropositive and seronegative individuals.</p

Genotype and allele distribution for <i>TYK2</i> polymorphisms in chronic Chagas cardiomyopathy (CCC) and asymptomatic individuals.

<p>Genotype and allele distribution for <i>TYK2</i> polymorphisms in chronic Chagas cardiomyopathy (CCC) and asymptomatic individuals.</p

Lung Transcriptomics during Protective Ventilatory Support in Sepsis-Induced Acute Lung Injury

<div><p>Acute lung injury (ALI) is a severe inflammatory process of the lung. The only proven life-saving support is mechanical ventilation (MV) using low tidal volumes (LVT) plus moderate to high levels of positive end-expiratory pressure (PEEP). However, it is currently unknown how they exert the protective effects. To identify the molecular mechanisms modulated by protective MV, this study reports transcriptomic analyses based on microarray and microRNA sequencing in lung tissues from a clinically relevant animal model of sepsis-induced ALI. Sepsis was induced by cecal ligation and puncture (CLP) in male Sprague-Dawley rats. At 24 hours post-CLP, septic animals were randomized to three ventilatory strategies: spontaneous breathing, LVT (6 ml/kg) plus 10 cmH₂O PEEP and high tidal volume (HVT, 20 ml/kg) plus 2 cmH₂O PEEP. Healthy, non-septic, non-ventilated animals served as controls. After 4 hours of ventilation, lung samples were obtained for histological examination and gene expression analysis using microarray and microRNA sequencing. Validations were assessed using parallel analyses on existing publicly available genome-wide association study findings and transcriptomic human data. The catalogue of deregulated processes differed among experimental groups. The ‘response to microorganisms’ was the most prominent biological process in septic, non-ventilated and in HVT animals. Unexpectedly, the ‘neuron projection morphogenesis’ process was one of the most significantly deregulated in LVT. Further support for the key role of the latter process was obtained by microRNA studies, as four species targeting many of its genes (Mir-27a, Mir-103, Mir-17-5p and Mir-130a) were found deregulated. Additional analyses revealed '<i>VEGF</i> signaling' as a central underlying response mechanism to all the septic groups (spontaneously breathing or mechanically ventilated). Based on this data, we conclude that a co-deregulation of '<i>VEGF</i> signaling' along with 'neuron projection morphogenesis', which have been never anticipated in ALI pathogenesis, promotes lung-protective effects of LVT with high levels of PEEP.</p></div

Biological processes associated with significantly deregulated genes compared to the non-septic controls in each experimental group (<i>x</i>-axis).

<p>The enrichment score (left <i>y</i>-axis), a log transformation of the geometric mean of all the enrichment <i>p</i>-value, indicates the processes that play major roles in each group. The right <i>y</i>-axis reflects a transformation of the FDR to globally correct the enrichment <i>p</i>-value for the pathways included within each biological process. Whiskers represent their lower and upper FDR values. The horizontal discontinuous line represents the transformed value for a FDR = 0.05.</p

Plot illustrating the statistical power calculations for the study assuming four (two animals per group; dashed lines) and five samples (groups with two and three animals; solid lines), and a mean FC of 1.7, 2 and 2.5.

<p>Plot illustrating the statistical power calculations for the study assuming four (two animals per group; dashed lines) and five samples (groups with two and three animals; solid lines), and a mean FC of 1.7, 2 and 2.5.</p

Overlapping miRNAs among GSEA and sRNA-seq analyses.

<p>^aEnrichment score, reflecting the degree to which a gene set is overrepresented in the SHVT group after 10⁴ permutations.</p><p>^bNominal <i>p</i>-value.</p><p>^cIn bold, overlapping and significant miRNA species among analyses.</p><p>Overlapping miRNAs among GSEA and sRNA-seq analyses.</p

Venn diagram illustrating the distribution of statistically significant changes in gene expression and their overlap among experimental groups.

<p>SS: Sepsis spontaneous breathing, SLVT: septic with low tidal volume MV, SHVT: septic with high tidal volume MV. All the comparisons were made against the non-septic controls (NA).</p

Protein interaction network analysis.

<p>^aSS: Sepsis spontaneous breathing; SLTV: septic with low tidal volume mechanical ventilation; SHVT: septic with high tidal volume mechanical ventilation.</p><p>^bNetwork interconnectivity score indicating the pathways/processes that have functional association with the defined gene set.</p><p>^cAdjusted <i>p</i>-value for multiple testing using a False Discovery Rate.</p><p>Protein interaction network analysis.</p

Additional file 6: of A vascular endothelial growth factor receptor gene variant is associated with susceptibility to acute respiratory distress syndrome

Table 4. ARDS susceptibility association results in the discovery and replication studies. Summary of association results for the three SNPs associated with ARDS susceptibility in the discovery and replication studies. (DOC 40 kb