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Genes and Immunity

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https://www.readbyqxmd.com/read/29307888/high-resolution-hla-analysis-reveals-independent-class-i-haplotypes-and-amino-acid-motifs-protective-for-multiple-sclerosis
#1
Steven J Mack, Julia Udell, Franziska Cohen, Kazutoyo Osoegawa, Sharon K Hawbecker, David A Noonan, Martha B Ladner, Damian Goodridge, Elizabeth A Trachtenberg, Jorge R Oksenberg, Henry A Erlich
We investigated association between HLA class I and class II alleles and haplotypes, and KIR loci and their HLA class I ligands, with multiple sclerosis (MS) in 419 European American MS patients and 412 ethnically matched controls, using next-generation sequencing. The DRB1*15:01~DQB1*06:02 haplotype was highly predisposing (odds ratio (OR) = 3.98; 95% confidence interval (CI) = 3-5.31; p-value (p) = 2.22E-16), as was DRB1*03:01~DQB1*02:01 (OR = 1.63; CI = 1.19-2.24; p = 1.41E-03). Hardy-Weinberg (HW) analysis in MS patients revealed a significant DRB1*03:01~DQB1*02:01 homozyote excess (15 observed; 8...
January 8, 2018: Genes and Immunity
https://www.readbyqxmd.com/read/29307887/critical-amino-acid-variations-in-hla-dqb1-molecules-confers-susceptibility-to-autoimmune-thyroid-disease-in-south-india
#2
S Ramgopal, C Rathika, R Padma Malini, V Murali, K Arun, K Balakrishnan
The HLA-DQB1* region exhibits complex associations with autoimmune thyroid disease (AITD). AITD patients (Hashimoto's thyroiditis, HT = 180; Graves' disease, GD = 55) and age/sex matched controls (n = 235) were genotyped for DQB1* alleles by PCR-SSP. Alleles DQB1*02:02, *06:03, *06:09, *03:02, and *03:03 showed an increased risk and *02:01, *05:02, and *06:02 showed a protection toward AITD. Multiple sequence alignment was used to find out the amino acid variations within the peptide-binding pockets of susceptible and/or protective DQB1* alleles...
January 8, 2018: Genes and Immunity
https://www.readbyqxmd.com/read/29305595/frequency-analysis-of-the-g-7081t-g-a-and-g-10872t-g-polymorphisms-in-the-fcgr3a-gene-cd16a-using-nested-pcr-and-their-functional-specific-effects
#3
Camilo Andrés Pérez-Romero, Isaura Pilar Sánchez, Laura Naranjo-Piedrahita, Julio Cesar Orrego-Arango, Carlos Enrique Muskus-López, Winston Rojas-Montoya, Jose Luis Franco Restrepo, Claudia Milena Trujillo-Vargas
Polymorphic variants p.66L>R/H (g.7081T>G/A; rs10127939) and p.176F>V (g.10872T>G; rs396991) in FCGR3A (CD16A) have been associated with defects in cytotoxic function of natural killer (NK) cells in humans. Genotyping of these variants in genomic DNA has been ambiguous because of high degree of homology between FCGR3A and FCGR3B. We designed a strategy to genotype these polymorphisms and to evaluate their effects on NK cells' cytotoxic activity. One hundred and fifteen individuals from different geographical regions of Colombia were included...
January 5, 2018: Genes and Immunity
https://www.readbyqxmd.com/read/29302052/the-act1-d10n-missense-variant-impairs-cd40-signaling-in-human-b-cells
#4
Ning Yu, Sylviane Lambert, Joshua Bornstein, Rajan P Nair, Charlotta Enerbäck, James T Elder
The TRAF3IP2 gene resides within one of at least 63 psoriasis susceptibility loci and encodes Act1, an adapter protein involved in IL-17 receptor and CD40 signaling pathways. TRAF3IP2 is distinctive (among <10% of candidate susceptibility genes) in that a strongly disease-associated variant encodes a missense SNP predicted to be functionally relevant (SNP rs33980500 C/T encoding Act1 pD10N). As assessed by flow cytometry, Act1 protein was expressed at the highest levels in monocytes, with lower levels in T-cells and B-cells...
January 5, 2018: Genes and Immunity
https://www.readbyqxmd.com/read/29282355/low-expression-of-a-ddm7-ldm7-hybrid-mutant-d-ldm7-in-the-novel-haplotype-h-2nc-identified-in-atopic-dermatitis-model-nc-nga-mice
#5
Kozo Ohkusu-Tsukada, Tadashi Yamashita, Teruyo Tsukada, Kimimasa Takahashi
Environmental factors and the major histocompatibility complex (MHC) are involved in the pathogenesis of atopic dermatitis (AD). However, MHC type (H2 haplotype) of AD model mice NC/Nga is poorly understood. Alloreactive CD8+ or CD4+ T cells in NC/Nga strongly responded to each antigen-presenting cells (A/J: H-2a, C57BL/6: H-2b, BALB/c: H-2d, or C3H/HeJ: H-2k), suggesting that NC/Nga has other H2 haplotype. Polymorphic microsatellite (CA)n repeats in TNF-α gene differ based on the H2 haplotype at present. NC/Nga's (CA)n repeats (n = 19) were different from other examined strains, A/J (n = 14), BALB/c (n = 14), C3H/HeJ (n = 16), and C57BL/6 (n = 20)...
December 22, 2017: Genes and Immunity
https://www.readbyqxmd.com/read/29238036/identification-of-additional-ehmt2-variant-associated-with-the-risk-of-chronic-hepatitis-b-by-gwas-follow-up-study
#6
Joong-Gon Shin, Hyun Sub Cheong, Jason Yongha Kim, Jeong-Hoon Lee, Su Jong Yu, Jung-Hwan Yoon, Jae Youn Cheong, Sung Won Cho, Neung Hwa Park, Suhg Namgoong, Lyoung Hyo Kim, Yoon Jun Kim, Hyoung Doo Shin
Chronic hepatitis B (CHB) is a precursor to liver cirrhosis and hepatocellular carcinoma, caused by a Hepatitis B viral infection. Genome-wide association studies (GWASs) have been conducted to find genes associated with CHB risk. In previous GWAS, EHMT2 was identified as one of the susceptibility genes for CHB. To further characterize this association and discover possible causal variants, we conducted an additional association study. A total of 11 EHMT2 single-nucleotide polymorphisms (SNP) were selected and genotyped in 3902 subjects (1046 CHB patients and 2856 controls)...
December 14, 2017: Genes and Immunity
https://www.readbyqxmd.com/read/29217828/frequently-used-bioinformatics-tools-overestimate-the-damaging-effect-of-allelic-variants
#7
Line Lykke Andersen, Ewa Terczyńska-Dyla, Nanna Mørk, Carsten Scavenius, Jan J Enghild, Klara Höning, Veit Hornung, Mette Christiansen, Trine H Mogensen, Rune Hartmann
We selected two sets of naturally occurring human missense allelic variants within innate immune genes. The first set represented eleven non-synonymous variants in six different genes involved in interferon (IFN) induction, present in a cohort of patients suffering from herpes simplex encephalitis (HSE) and the second set represented sixteen allelic variants of the IFNLR1 gene. We recreated the variants in vitro and tested their effect on protein function in a HEK293T cell based assay. We then used an array of 14 available bioinformatics tools to predict the effect of these variants upon protein function...
December 4, 2017: Genes and Immunity
https://www.readbyqxmd.com/read/28835680/transcriptome-analysis-of-ankylosing-spondylitis-patients-before-and-after-tnf-%C3%AE-inhibitor-therapy-reveals-the-pathways-affected
#8
X B Wang, J J Ellis, D J Pennisi, X Song, J Batra, K Hollis, L A Bradbury, Z Li, T J Kenna, M A Brown
Tumor necrosis factor-α (TNF-α) inhibitors are highly effective in suppressing inflammation in ankylosing spondylitis (AS) patients, and operate by suppression of TFN-α and downstream immunological pathways. To determine the mechanisms of action of TNF-α inhibitors in AS patients, we used transcriptomic and bioinformatic approaches on peripheral blood mononuclear cells from AS patients pre and post treatment. We found 656 differentially expressed genes, including the genome-wide significant AS-associated genes, IL6R, NOTCH1, IL10, CXCR2 and TNFRSF1A...
September 2017: Genes and Immunity
https://www.readbyqxmd.com/read/28794505/differential-transcriptome-of-tolerogenic-versus-inflammatory-dendritic-cells-points-to-modulated-t1d-genetic-risk-and-enriched-immune-regulation
#9
T Nikolic, N J C Woittiez, A van der Slik, S Laban, A Joosten, C Gysemans, C Mathieu, J J Zwaginga, B Koeleman, B O Roep
Tolerogenic dendritic cells (tolDCs) are assessed as immunomodulatory adjuvants to regulate autoimmunity. The underlying gene expression endorsing their regulatory features remains ill-defined. Using deep mRNA sequencing, we compared transcriptomes of 1,25-dihydroxyvitaminD3/dexametasone-modulated tolDCs with that of non-modulated mature inflammatory DCs (mDCs). Differentially expressed genes controlled cellular interactions, metabolic pathways and endorse tolDCs with the capacity to regulate cell activation through nutrient and signal deprivation, collectively gearing tolDCs into tolerogenic immune regulators...
September 2017: Genes and Immunity
https://www.readbyqxmd.com/read/28794504/promoter-hypermethylation-of-bcl11b-gene-correlates-with-downregulation-of-gene-transcription-in-ankylosing-spondylitis-patients
#10
J Karami, M Mahmoudi, A Amirzargar, M Gharshasbi, A Jamshidi, S Aslani, M H Nicknam
Methylation of DNA is one of the important regulatory mechanisms of gene transcription. B-cell chronic lymphocytic leukemia/lymphoma 11B (BCL11B) plays a key role in the development, proliferation, differentiation, and survival of T cells. The aim of this study was to evaluate promoter methylation of BCL11B gene and its mRNA level in peripheral blood mononuclear cells (PBMCs) of ankylosing spondylitis (AS) patients in relation to healthy controls and evaluate their correlation with diseases clinical indices...
September 2017: Genes and Immunity
https://www.readbyqxmd.com/read/28794503/inflammatory-genes-tnf%C3%AE-and-il6-display-no-signs-of-increased-h3k4me3-in-circulating-monocytes-from-untreated-rheumatoid-arthritis-patients
#11
T C Messemaker, H M M Mikkers, T W Huizinga, R E M Toes, A H M van der Helm-van Mil, F Kurreeman
Innate immune cells, such as monocytes, can adopt a long-lasting pro-inflammatory phenotype, a phenomenon called 'trained immunity'. In trained immunity, increased cytokine levels of genes, like interleukin (IL)-6 and tumor necrosis factor (TNF)-α, are observed, which are associated with increased histone 3 lysine 4 trimethylation (H3K4me3) in the promoter region. As systemic IL6 and TNFα levels are increased in rheumatoid arthritis (RA) patients and monocytes are known to be the primary producers of TNFα and IL6, we hypothesized that 'trained immunity' signals may be observed at these genes in monocytes from RA patients...
September 2017: Genes and Immunity
https://www.readbyqxmd.com/read/28769070/il6r-haplotype-rs4845625-t-rs4537545-c-is-a-risk-factor-for-simultaneously-high-crp-ldl-and-apob-levels
#12
A A Arguinano, E Naderi, N C Ndiaye, M Stathopoulou, S Dadé, B Alizadeh, S Visvikis-Siest
Interleukin 6 receptor (IL-6R), mediating IL-6's biological functions, plays an important role in different diseases such as diabetes, obesity and cardio-vascular diseases. In this study, we investigated the effects of two single nucleotide polymorphisms (SNPs), within the IL-6R loci, previously associated with C-reactive protein (CRP) and coronary heart diseases risk, and with controversial effects on lipids traits: SNP rs4845625 and SNP rs4537545. The results showed that both investigated SNPs were antagonistically related with CRP levels; the minor rs4845625*T allele was associated with increased CRP levels (P-value=0...
September 2017: Genes and Immunity
https://www.readbyqxmd.com/read/28769069/autosomal-recessive-agammaglobulinemia-due-to-defect-in-%C3%AE-heavy-chain-caused-by-a-novel-mutation-in-the-ighm-gene
#13
P Silva, A Justicia, A Regueiro, S Fariña, J M Couselo, L Loidi
Agammaglobulinemia is a primary immunodeficiency disorder characterized by profoundly low or absent serum antibodies and low or absent circulating B cells. The most common form is X-linked agammaglobulinemia (XLA) caused by mutations in BTK gene. The remaining cases, clinically similar to XLA, are autosomal recessive agammaglobulinemia (ARA). Nearly 30% of ARA cases present mutations in the μ heavy constant region gene IGHM. Here, we present a 7-month-old patient, born from non-consanguineous parents, who is affected by ARA due to defect in the μ heavy chain...
September 2017: Genes and Immunity
https://www.readbyqxmd.com/read/28747736/association-of-ubash3a-gene-polymorphism-and-atopic-dermatitis-in-the-chinese-han-population
#14
Y Li, H Cheng, F-L Xiao, B Liang, F-S Zhou, P Li, X-D Zheng, L-D Sun, S Yang, X-J Zhang
Genome-wide association studies have revealed a large number of genetic-risk loci for many autoimmune diseases. One clear finding emerging from the published genetic studies of autoimmunity is that different autoimmune diseases share susceptibility loci. Recent evidence has demonstrated that UBASH3A gene was associated with multiple autoimmune diseases. The aim of this study was to explore the association between UBASH3A single-nucleotide polymorphisms (SNPs) and atopic dermatitis (AD) in a Chinese Han population...
September 2017: Genes and Immunity
https://www.readbyqxmd.com/read/28703132/association-of-a-functional-tnf-variant-with-plasmodium-falciparum-parasitaemia-in-a-congolese-population
#15
T N Nguyen, S Baaklini, F Koukouikila-Koussounda, M Ndounga, M Torres, L Pradel, F Ntoumi, P Rihet
Several studies have provided evidence of both helpful and harmful effects of TNF on the outcome of Plasmodium falciparum malaria infection. Several TNF polymorphisms that are located within non-coding regions have been associated with parasitaemia, mild malaria or severe malaria. We investigated the association of TNF1304 (rs3093664), TNF-308 (rs1800629), TNF-238 (rs361525) and TNF-244 (rs673) with mild malaria and symptomatic maximum parasitaemia in a population-based design (n=310). We obtained nominal evidence for an association between symptomatic maximum parasitaemia and TNF-308, TNF-238, and TNF-244 on the one hand, and between the number of mild malaria attacks and TNF-244 on the other hand...
September 2017: Genes and Immunity
https://www.readbyqxmd.com/read/28703131/egfr-rs11506105-and-ifnl3-snps-but-not-rs8099917-are-strongly-associated-with-treatment-responses-in-iranian-patients-with-chronic-hepatitis-c
#16
M Asnavandi, M Zargar, F Vaziri, F R Jamnani, S Gharibzadeh, A Fateh, S D Siadat
Interferon lambda 3 (IFNL3) and epidermal growth factor receptor (EGFR) single nucleotide polymorphisms (SNPs) may play a key role in the spontaneous clearance of hepatitis C virus (HCV) and treatment responses. The aim of this study was to evaluate the effect of IFNL3 SNPs and EGFR rs11506105 on treatment outcomes in patients with chronic HCV (CHC). IFNL3 SNPs and EGFR rs11506105 were genotyped by PCR-restriction fragment length polymorphism and PCR-sequencing, respectively, in 235 naïve patients with CHC infection...
September 2017: Genes and Immunity
https://www.readbyqxmd.com/read/28621304/epigenetic-and-gene-expression-analysis-of-ankylosing-spondylitis-associated-loci-implicate-immune-cells-and-the-gut-in-the-disease-pathogenesis
#17
Z Li, K Haynes, D J Pennisi, L K Anderson, X Song, G P Thomas, T Kenna, P Leo, M A Brown
Ankylosing spondylitis (AS) is a common immune-mediated arthropathy primarily affecting the spine and pelvis. Most AS patients have subclinical intestinal inflammation, suggesting the gut microbiome and the immune response play a role in pathogenesis. Susceptibility to AS is primarily genetic, and at least 114 susceptibility variants have been identified to date. We applied bioinformatic methods utilizing epigenetic and gene and protein expression data to identify the cell types through which AS-associated variants operate...
September 2017: Genes and Immunity
https://www.readbyqxmd.com/read/28569259/revealing-complete-complex-kir-haplotypes-phased-by-long-read-sequencing-technology
#18
D Roe, C Vierra-Green, C-W Pyo, K Eng, R Hall, R Kuang, S Spellman, S Ranade, D E Geraghty, M Maiers
The killer cell immunoglobulin-like receptor (KIR) region of human chromosome 19 contains up to 16 genes for natural killer (NK) cell receptors that recognize human leukocyte antigen (HLA)/peptide complexes and other ligands. The KIR proteins fulfill functional roles in infections, pregnancy, autoimmune diseases and transplantation. However, their characterization remains a constant challenge. Not only are the genes highly homologous due to their recent evolution by tandem duplications, but the region is structurally dynamic due to frequent transposon-mediated recombination...
September 2017: Genes and Immunity
https://www.readbyqxmd.com/read/28539651/an-orthologous-non-mhc-locus-in-rats-and-mice-is-linked-to-cd4-and-cd8-t-cell-proportion
#19
D Franckaert, R Collin, J Dooley, R H Wallis, P Poussier, A Liston, E E Hillhouse, S Lesage
CD4+ and CD8+ T cells have a central role in the immune system due to their ability to protect against infection and cancer development without targeting self. Consequently, changes in CD4+ and CD8+ T-cell homeostasis can be indicative of an array of serious illnesses, ranging from viral infections to autoimmune diseases. In addition to environmental influences, there is evidence for a genetic component regulating the proportion of CD4+ and CD8+ T cells in lymphoid organs. Indeed, identifying the genetic determinants defining the frequency of the T-cell subsets is critical as it may reveal a targetable genetic pathway to modulate CD4+ and CD8+ T-cell numbers, which could be of clinical relevance for multiple disease settings...
September 2017: Genes and Immunity
https://www.readbyqxmd.com/read/28490805/a-skint6-allele-potentially-contributes-to-mouse-lupus
#20
Z Xu, J Xu, J Ju, L Morel
Our previous study uncovered that the overlapping region of murine lupus susceptibility Sle2c1rec1a and Sle2c1rec1d subloci is strongly associated with lymphadenopathy and systemic autoimmunity. In order to identify the specific candidate gene, we generated a novel shorter recombinant, named as Sle2c1re1d1 (rec1d1), from Sle2c1rec1d sublocus (rec1d). The rec1d1 interval corresponds precisely to the overlapping region of Sle2c1rec1a and Sle2c1rec1d subloci. Functionally, this rec1d1 sublocus showed a strong epistatic interaction with lpr, similar to that seen with Sle2c1rec1a or...
September 2017: Genes and Immunity
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