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The inducible T‐cell costimulator (ICOS) may play an important role in adaptive immunity by regulating the interaction between T cells and antigen‐presenting cells. Disruption of this molecule can lead to autoimmune diseases, in particular systemic lupus erythematosus (SLE). In this study, we aimed to explore the possible association between ICOS gene polymorphisms and SLE as well as their influence on disease susceptibility and clinical outcomes. A further objective was to assess the potential impact of these polymorphisms on RNA expression. A case–control study, including 151 patients with SLE, and 291 unrelated healthy controls (HC) matched in gender, and geographical origin, was performed to genotype two polymorphisms located in the ICOS gene: rs11889031 (−693 G/A) and rs10932029 (IVS1 + 173 T/C); using the polymerase chain reaction (PCR)‐restriction fragment length polymorphism method. The different genotypes were validated by direct sequencing. The expression level of ICOS mRNA was assessed by quantitative PCR in peripheral blood mononuclear cells of SLE patients and HC. The results were analysed using Shesis and spss.20. Our results revealed a significant association between ICOS gene rs11889031 > CC genotype and SLE disease (codominant genetic model 1, (C/C vs. C/T), p =.001, odds ratio [OR] = 2.18 IC [1.36–3.49]); codominant genetic model 2, (C/C vs. T/T) p =.007, OR = 15.29 IC [1.97–118.5]); dominant genetic model, (C/C vs. C/T + T/T) p =.0001, OR = 2.44 IC [1.53–3.9]). Besides, there was a marginal association between rs11889031 > TT genotype and T allele with a protective role from SLE (recessive genetic model, p =.016, OR = 0.08 IC [0.01–0.63] and p = 7.6904E − 05, OR = 0.43 IC = [0.28–0.66], respectively). Moreover, statistical analysis indicated that the rs11889031 > CC genotype was linked with clinical and serological manifestations of SLE, including blood pressure, and anti‐SSA antibodies production in SLE patients. However, the ICOS gene rs10932029 polymorphism was not associated with susceptibility to SLE. On the other side, we did not note any effect of the two selected polymorphisms on the level of ICOS mRNA gene expression. The study showed a significant predisposing association of the ICOS rs11889031 > CC genotype with SLE, in contrast to a protective effect of rs11889031 > TT genotype in Tunisian patients. Our results suggest that ICOS rs11889031 may act as a risk factor for SLE and could be used as a genetic susceptibility biomarker. [ABSTRACT FROM AUTHOR]

Background: Soil salinity drastically reduced wheat growth and production in Pakistan. It is a need of an hour to identify the best suitable salt tolerance or resistant wheat varieties which shows good growth under salinity affected areas. In presented study, two wheat varieties Johar (salt tolerant) and Sarsabaz (salt sensitive) were examined under NaCl stress conditions. Methods: Antioxidant enzyme activities were investigated in 10-days old wheat seedlings under 200 mM NaCl stress in hydroponic conditions. To investigate the various growth parameters, antioxidant enzyme activities such as superoxide dismutase (SOD: EC 1.15.1.1), catalase (CAT: EC 1.11.1.6) and ascorbate peroxidase (APX: EC 1.11.1.11) were monitored and studied. Besides this various growth parameters such as length of the roots, shoots, as well as Physiological parameters likes lipid peroxidation by malondialdehyde (MDA), hydrogen peroxide (H2O2), and proline contents and antioxidant enzyme activities were estimated. The effect of salinity was also observed on gene transcription level and eventually expression level. Results: Shoot and root length were decreased in Sarsabaz variety while it showed opposite trend in johar at 200 mM salt concentration. The concentration of proline showed a noticeable rise in salt dependency. Higher concentrations of Proline in Johar were observed as compared to Sarsabaz. SOD showed the increase in activity for antioxidant enzymes. Significant increase of SOD levels were observed in shoot tissues as compared to root tissues. The results indicated that the shoots were more susceptible to salt stress. Activity of APX showed similar affects in both varieties. The production of CAT enzyme in the shoot and root tissues of both varieties showed substantial growth under increased salt stress. Furthermore, NaCl stress has increased the expression of certain genes coding for antioxidant enzymes such as catalase, superoxide dismutase, and peroxidase. Maximum expression of all the antioxidant enzyme coding genes were observed in Johar (tolerant) at 48 h exposure to salt. In contrast the expression of the all mentioned genes in Sarsabaz variety were found maximum at early hours (24 h) and gradually decreased at 48 h. Conclusion: The study showed that the selected salt tolerant wheat variety Johar is significantly resistant to 200 mM NaCl salt level as compared to Sarsabaz. [ABSTRACT FROM AUTHOR]

The highly polymorphic human major histocompatibility complex (MHC) also known as the human leukocyte antigen (HLA) encodes class I and II genes that are the cornerstone of the adaptive immune system. Their unique diversity (>25,000 alleles) might affect the outcome of any transplant, infection, and susceptibility to autoimmune diseases. The recent rapid development of new next-generation sequencing (NGS) methods provides the opportunity to study the influence/correlation of this high level of HLA diversity on allele expression levels in health and disease. Here, we describe the NGS capture RNA-Seq method that we developed for genotyping all 12 classical HLA loci (HLA-A, HLA-B, HLA-C, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQB1, HLA-DRA, HLA-DRB1, HLA-DRB3, HLA-DRB4, and HLA-DRB5) and assessing their allelic imbalance by quantifying their allele RNA levels. This is a target enrichment method where total RNA is converted to a sequencing-ready complementary DNA (cDNA) library and hybridized to a complex pool of RNA-specific HLA biotinylated oligonucleotide capture probes, prior to NGS. This method was applied to 161 peripheral blood mononuclear cells and 48 umbilical cord blood cells of healthy donors. The differential allelic expression of 10 HLA loci (except for HLA-DRA and HLA-DPA1) showed strong significant differences (P < 2.1 × 10−15). The results were corroborated by independent methods. This newly developed NGS method could be applied to a wide range of biological and medical questions including graft rejections and HLA-related diseases.

The highly polymorphic human major histocompatibility complex (MHC) also known as the human leukocyte antigen (HLA) encodes class I and II genes that are the cornerstone of the adaptive immune system. Their unique diversity (>25,000 alleles) might affect the outcome of any transplant, infection, and susceptibility to autoimmune diseases. The recent rapid development of new next-generation sequencing (NGS) methods provides the opportunity to study the influence/correlation of this high level of HLA diversity on allele expression levels in health and disease. Here, we describe the NGS capture RNA-Seq method that we developed for genotyping all 12 classical HLA loci (HLA-A, HLA-B, HLA-C, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQB1, HLA-DRA, HLA-DRB1, HLA-DRB3, HLA-DRB4 , and HLA-DRB5) and assessing their allelic imbalance by quantifying their allele RNA levels. This is a target enrichment method where total RNA is converted to a sequencing-ready complementary DNA (cDNA) library and hybridized to a complex pool of RNA-specific HLA biotinylated oligonucleotide capture probes, prior to NGS. This method was applied to 161 peripheral blood mononuclear cells and 48 umbilical cord blood cells of healthy donors. The differential allelic expression of 10 HLA loci (except for HLA-DRA and HLA-DPA1) showed strong significant differences (P < 2.1 × 10−15). The results were corroborated by independent methods. This newly developed NGS method could be applied to a wide range of biological and medical questions including graft rejections and HLA-related diseases. [ABSTRACT FROM AUTHOR]