Polymorphism In Regulatory Region Research Articles

Polymorphisms in transcription factor binding sites and enhancer regions and pancreatic ductal adenocarcinoma risk

Genome-wide association studies (GWAS) are a powerful tool for detecting variants associated with complex traits and can help risk stratification and prevention strategies against pancreatic ductal adenocarcinoma (PDAC). However, the strict significance threshold commonly used makes it likely that many true risk loci are missed. Functional annotation of GWAS polymorphisms is a proven strategy to identify additional risk loci. We aimed to investigate single-nucleotide polymorphisms (SNP) in regulatory regions [transcription factor binding sites (TFBSs) and enhancers] that could change the expression profile of multiple genes they act upon and thereby modify PDAC risk. We analyzed a total of 12,636 PDAC cases and 43,443 controls from PanScan/PanC4 and the East Asian GWAS (discovery populations), and the PANDoRA consortium (replication population). We identified four associations that reached study-wide statistical significance in the overall meta-analysis: rs2472632(A) (enhancer variant, OR 1.10, 95%CI 1.06,1.13, p = 5.5 × 10−8), rs17358295(G) (enhancer variant, OR 1.16, 95%CI 1.10,1.22, p = 6.1 × 10−7), rs2232079(T) (TFBS variant, OR 0.88, 95%CI 0.83,0.93, p = 6.4 × 10−6) and rs10025845(A) (TFBS variant, OR 1.88, 95%CI 1.50,1.12, p = 1.32 × 10−5). The SNP with the most significant association, rs2472632, is located in an enhancer predicted to target the coiled-coil domain containing 34 oncogene. Our results provide new insights into genetic risk factors for PDAC by a focused analysis of polymorphisms in regulatory regions and demonstrating the usefulness of functional prioritization to identify loci associated with PDAC risk.

Role of the HLA-G regulatory region polymorphisms in idiopathic recurrent spontaneous abortions (RSA).

HLA-G polymorphisms have a functional impact on its expression and may cause a breakdown of maternal tolerance towards the semi-allogenic fetus, resulting in recurrent spontaneous abortions (RSA). This study reports on the association of HLA-G regulatory region polymorphisms with idiopathic RSA. Seventy-five couples with ≥2 spontaneous abortions were recruited in comparison to 75 healthy couples who had normal pregnancies. About 5mL of blood samples were collected from all the participants, and DNA was extracted. Screening of HLA-G 5'-upstream regulatory region (5'-URR) was done by direct sequencing in 50 each of RSA and healthy couples, respectively. The 14bp deletion/insertion polymorphism in the 3'-untranslated region (3'-UTR) was genotyped in 75 each of RSA and healthy couples, respectively, by PCR amplification of HLA-G exon 8. MedCalc, GraphPad Prism, Haploview, PLINK, and multifactor dimensionality reduction were used to analyze the data. HLA-G screening revealed the presence of -762C/T, -725C/G, -716T/G, -689A/G, -486C/A, and -477C/G single nucleotide polymorphisms (SNPs) in the 5'-URR. At positions -762 and -477, the frequency of CC homozygotes was significantly higher in controls compared to the patients. The 14bp deletion/insertion polymorphism in the 3'-UTR showed an association with RSA with the heterozygous genotype being significantly higher in RSA compared to controls. The study indicates a protective role of the CC genotypes of the two HLA-G 5'-URR polymorphisms, -762C/T and -477C/G, against RSA. It also suggests that women with the 14bp deletion/insertion genotype have a significantly higher risk of RSA.

Distinct patterning responses of wing and leg neuromuscular systems to different preaxial polydactylies.

The tetrapod limb has long served as a paradigm to study vertebrate pattern formation and evolutionary diversification. The distal part of the limb, the so-called autopod, is of particular interest in this regard, given the numerous modifications in both its morphology and behavioral motor output. While the underlying alterations in skeletal form have received considerable attention, much less is known about the accompanying changes in the neuromuscular system. However, modifications in the skeleton need to be properly integrated with both muscle and nerve patterns, to result in a fully functional limb. This task is further complicated by the distinct embryonic origins of the three main tissue types involved-skeleton, muscles and nerves-and, accordingly, how they are patterned and connected with one another during development. To evaluate the degree of regulative crosstalk in this complex limb patterning process, here we analyze the developing limb neuromuscular system of Silkie breed chicken. These animals display a preaxial polydactyly, due to a polymorphism in the limb regulatory region of the Sonic Hedgehog gene. Using lightsheet microscopy and 3D-reconstructions, we investigate the neuromuscular patterns of extra digits in Silkie wings and legs, and compare our results to Retinoic Acid-induced polydactylies. Contrary to previous findings, Silkie autopod muscle patterns do not adjust to alterations in the underlying skeletal topology, while nerves show partial responsiveness. We discuss the implications of tissue-specific sensitivities to global limb patterning cues for our understanding of the evolution of novel forms and functions in the distal tetrapod limb.

Genetic polymorphisms of IL6 gene -174G>C and -597G>A are associated with the risk of COVID-19 severity.

Coronavirus disease-2019 (COVID-19) is pro-inflammatory disorder characterized by acute respiratory distress syndrome. Interleukin-6, a cytokine secreted by macrophages, which mediates an inflammatory response, is frequently increased and associated with the severity in COVID-19 patients. The differential expression of IL6 cytokine in COVID-19 patients may be associated with the presence of single nucleotide polymorphisms (SNPs) in regulatory region of cytokine genes. The aim of this study is to investigate the role of two promoter polymorphisms of the IL6 gene (-597G>A and -174G>C) with the severity of COVID-19. The study included 242 patients, out of which 97 patients with severe symptoms and 145 patients with mild symptoms of COVID-19. Genotyping of two selected SNPs, rs1800795 (-174G>C) and rs1800797 (-597G>A) of promoter region of IL6 gene, was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). In our study, individuals with GC genotypes of IL6 (-174G>C) polymorphism showed significantly higher risk of severity [adjusted odds (OR) 3.86, p<.001] but we did not observe any association of COVID-19 severity with rs1800797 (-597G>A) polymorphism. The COVID-19 severity was significantly higher in individuals having 'C' allele of IL6 (-174G>C) polymorphism (p=.014). Linkage disequilibrium between rs1800795 (-174G>C) and rs1800797 (-597G>A) showed that individuals having AC* haplotype significantly association with COVID-19 severity (p=.034). Our results suggest that 'C' allele of rs1800795 (-174G>C) polymorphism of IL6 may be the risk allele for severity of COVID-19 in North Indian population.

Investigation of the association between HLA-G polymorphisms and obesity

Background/Aim: Obesity is a global public health problem seen worldwide, with an increasing prevalence over time. Obesity is a multifactorial disease affected by both genetic and environmental factors. It is accompanied by many other diseases, the most important of which are immune system disorders. Induction of suppression of HLA-G molecule T and B lymphocytes is associated with natural killer cells and antigen-presenting cells. The HLA-G gene shows functional polymorphisms in regulatory regions. The HLA-G gene is slightly more conserved compared to other HLA genes, both in the same population and among different populations. The aim of this research is to determine the association of HLA-G gene polymorphisms (14 bp insertion/deletion 3 'UTR (rs66554220), rs41557518, and rs1063320) with obesity. Methods: Fifty normal (BMI ≤30) individuals having no obesity-related chronic disorder, and 50 obese (BMI≥ 30) individuals were included in the study. After DNA isolation, PCR and PCR-RFLP methods were used for genotyping. Results: The genotype frequencies of HLA-G polymorphisms (rs66554220, rs41557518, and rs1063320) in the normal and obese groups were compared, and as a result, no significant difference was found (P>0.05). Conclusion: No significant association was found between rs66554220, rs41557518, and rs1063320 polymorphisms and obesity.

199. Polymorphisms in Key Regulatory Regions of the bla operon Correlate with the Cefazolin Inoculum Effect in Methicillin-Susceptible Staphylococcus aureus (MSSA)

BackgroundThe cefazolin inoculum effect (CzIE), defined as Cz minimum inhibitory concentration ≥ 16 µg/ml at high inoculum (HI-MIC), has been associated with poor clinical outcomes in patients with MSSA bacteremia or osteomyelitis. The CzIE is correlated with the presence of the blaZ gene, one of the components of the bla operon encoding the BlaZ β-lactamase (type A, B, C or D). Other portions of the bla operon include blaR and blaI (encoding the antibiotic sensor and transcriptional repressor, respectively) and the intergenic region with operator and promoter sequences (Figure 1). In BlaR, residue 293 mediates signal transduction, and the Z and R dyads in the intergenic region are the DNA-binding sites for BlaI (Figure 2). Previous experiments have shown that the regulatory portions of the bla operon play a key role in the CzIE. Here, we investigated the association between the CzIE and specific variations in the regulatory sequences of the bla operon. Figure 1. Functioning of the bla operon and the production of the staphylococcal β-lactamase BlaZ. Figure 2. Structure and key regions of the intergenic region of the bla operon, incluiding the promoter and the BlaI DNA-binding regions (Z and R dyads). MethodsA total of 437 MSSA containing blaZ were evaluated for the CzIE using broth microdilution at high inoculum. Using whole genome sequencing, the sequences of the bla operons were classified into cassettes based on unique changes in predicted amino acid sequences of BlaZ, BlaR and BlaI paired with specific nucleotide alterations in the intergenic region. The bla operon sequence of S. aureus ATCC29213 was used as reference (cassette 0).ResultsAmong 437 MSSA isolates, 46% exhibited the CzIE. We identified 55 unique bla cassettes. The bla cassettes were phylogenetically grouped in 7 clusters (Figure 3) which grouped cassettes with different BlaZ types and variations in the Z dyad, the -35 box, residue 293 of BlaR, and the blaI ribosomal binding site. Each cluster had an association to the CzIE and distinct Cz HI-MICs. The combination of: a BlaZ type A, C or D, an adenine in the position -66 of blaZ (-35 box of blaZ), a cytosine in the position -22 of blaZ(Z dyad), and either an arginine or a serine in position 293 of BlaR was a very strong predictor of the CzIE (Figure 4). Figure 3. Phylogenetical organization of bla operon cassettes into clusters, their association with polymorphisms in key regulatory regions and the CzIE. GM Cz-MIC: Geometric mean of the Cefazolin MIC at high Inoculum. Figure 4. Variations of the bla operon, their association with the CzIE, their GM (Geometric Mean) of the Cefazolin MIC and the MIC distribution of the strains with each specific combination of polymorphisms. ConclusionSpecific variations in regulatory portions of the bla operon, which are likely to influence BlaZ expression, are highly associated with the CzIE, supporting the notion that regulation of blaZ is the key factor responsible for the CzIE in MSSA. Disclosures Lorena Diaz, PhD , Nothing to disclose William R. Miller, MD , Entasis Therapeutics (Scientific Research Study Investigator)Merck (Grant/Research Support) William R. Miller, MD , Entasis (Individual(s) Involved: Self): Scientific Research Study Investigator; Merck (Individual(s) Involved: Self): Grant/Research Support Cesar A. Arias, M.D., MSc, Ph.D., FIDSA, Entasis Therapeutics (Grant/Research Support)MeMed Diagnostics (Grant/Research Support)Merk (Grant/Research Support)

Association between ADRB2 regulatory region polymorphisms and susceptibility to childhood asthma.

To study the association of β2-drenergic receptor (ADRB2) regulatory region single nucleotides polymorphism (SNP)/haplotypes at rs11168070, rs17108803, rs2053044, rs12654778, rs11959427, and rs2895795 loci with childhood asthma. A total of 143 children with asthma who attended the hospital from October 2016 to October 2020 were enrolled as the asthma group, among whom 61 children had mild symptoms (mild group) and 82 children had moderate-to-severe symptoms (moderate-to-severe group). A total of 137 healthy children were enrolled as the control group. Peripheral venous blood samples were collected from the two groups. The SNaPshot SNP technique was used to analyze the SNP and haplotypes of the ADRB2 regulatory region at rs11168070, rs17108803, rs2053044, rs12654778, rs11959427, and rs2895795 loci in all children. The asthma group and the control group were compared in terms of the association of ADRB2 regulatory region SNP and haplotypes at the above six loci with susceptibility to asthma and severity of asthma. Polymorphisms were observed in the ADRB2 regulation region at the above six loci in both the asthma group and the control group, with significant differences between the two groups in the distribution of genotype and allele frequencies at rs2895795 (-1429T /A), rs2053044(-1023G/A), and rs12654778 (-654G/A) loci (P<0.05). Linkage disequilibrium of SNP was observed at the six loci of the ADRB2 regulatory region.The haplotypes of TATGCT, TATGGC, and AGTGCT were associated with susceptibility to childhood asthma, among which TATGCT and TATGGC were risk factors for childhood asthma (OR=1.792 and 1.946 respectively, P<0.05), while AGTGCT was a protective factor (OR=0.523, P<0.05). SNP/haplotype of the ADRB2 regulatory region is associated with the susceptibility to childhood asthma. The haplotypes of TATGCT and TATGGC formed by such SNP/haplotype are risk factors for childhood asthma, while AGTGCT is a protective factor.

A regulatory variant of tryptophan hydroxylase gene modulates transcription activity and biases growth rate in the Pacific oyster, Crassostrea gigas

Growth is an important trait with significant impact on economic value of cultured organisms. Identification of critical genes and nucleotide variations associated with growth is an important step toward molecular breeding of growth-related traits. In this study, we showed that tryptophan hydroxylase (TPH), the rate-limiting enzyme of serotonin (5-HT) biosynthesis, played an indispensable role in growth regulation in the Pacific oyster, Crassostrea gigas. We identified the C. gigas TPH (CgTPH) and performed comparative analyses of its expression and nucleotide variations between selectively bred fast-growing Pacific oysters (“Haida No. 1”) and wild oysters. Expression profiling and RNA localization showed that CgTPH was specifically expressed in the nerve-rich tissues. Notably, expression level of CgTPH was significantly higher in fast-growing “Haida No.1” than wild oysters. Association and haplotype analysis of single nucleotide polymorphisms (SNPs) in upstream regulatory region of CgTPH revealed four SNPs (located at −904, −522, −272, −262 bp) and two haplotypes (CCCC and TCTC) that were significantly associated with growth rate of C. gigas. Luciferase reporter assay identified the core transcription regulatory element located at −403 ~ −179 bp, in which the SNP -272C/T was critical for transcription activity of CgTPH. Further analysis revealed that the different transcription activity was due to the distinct binding efficiency with two transcription factors, FoxO and CUX. Together, we showed that a critical SNP in the regulatory region of CgTPH leading to differential transcription regulation by FoxO and CUX, which would affect 5-HT synthesis and growth in C. gigas. This work is of great significance for elucidating the role of 5-HT system in regulation of growth in mollusks and provides a marker for molecular breeding of growth with other production and performance traits in C. gigas.

Vascular endothelial growth factor (VEGF-2578 C > A) gene polymorphism as a genetic biomarker for breast cancer: A case control study

Breast cancer (BC) is one of the most frequently diagnosed cancers among Saudi women. Vascular endothelial growth factor (VEGF) is a key mediator of breast cancer angiogenesis. Hence, the present study was aimed to investigate the genetic association of VEGF (-2578 C > A, rs699947) polymorphism with BC among Saudi women. The present study includes 104 BC cases and 100 controls. Polymorphic analysis was carried out adopting polymerase chain reaction with restriction fragment length polymorphism (PCR-RFLP) method. The homozygous variant (AA) (RR = 3.96, EF = 0.583, p = 0.005) and allele A (RR = 1.56, EF = 0.206, p = 0.03) of VEGF (-2578C > A) gene were significantly (p < 0.05) higher in the BC cases when compared to the controls. The recessive genotypes' combination (CC + CA) has shown a strong association (p = 0.003) with BC. Further, AA genotype has shown a strong association (p = 0.009) with BC in patients >40 years of age. AA genotype was significantly (p = 0.023) associated with advanced (T4) stage and high histologic tumor grades II (p = 0.015) and III (p = 0.006) of BC patients as well. Therefore, the homozygous variant and allele A of VEGF (−2578 C > A) gene polymorphism could be an associative genetic risk factor for BC in Saudi population. Regulatory region polymorphism in VEGF may help better to predict the risk of the BC at an early stage and will be assistive in the development of new diagnostic markers and treatment strategies.

Functional polymorphisms and transcriptional analysis in the 5\u2032 region of the human serotonin receptor 1B gene (HTR1B) and their associations with psychiatric disorders

BackgroundThe 5-hydroxytryptamine 1B receptor (5-HT1B) plays an essential role in the serotonin (5-HT) system and is widely involved in a variety of brain activities. HTR1B is the gene encoding 5-HT1B. Genome-wide association studies have shown that HTR1B polymorphisms are closely related to multiple mental and behavioral disorders; however, the functional mechanisms underlying these associations are unknown. This study investigated the effect of several HTR1B haplotypes on regulation of gene expression in vitro and the functional sequences in the 5′ regulatory region of HTR1B to determine their potential association with mental and behavioral disorders.MethodsSix haplotypes consisting of rs4140535, rs1778258, rs17273700, rs1228814, rs11568817, and rs130058 and several truncated fragments of the 5′ regulatory region of HTR1B were transfected into SK-N-SH and HEK-293 cells. The relative fluorescence intensities of the different haplotypes and truncated fragments were detected using a dual-luciferase reporter assay system.ResultsCompared to the major haplotype T-G-T-C-T-A, the relative fluorescence intensities of haplotypes C-A-T-C-T-A, C-G-T-C-T-A, C-G-C-A-G-T, and C-G-T-A-T-A were significantly lower, and that of haplotype C-G-C-A-G-A was significantly higher. Furthermore, the effects of the rs4140535T allele, the rs17273700C-rs11568817G linkage combination, and the rs1228814A allele made their relative fluorescence intensities significantly higher than their counterparts at each locus. Conversely, the rs1778258A and rs130058T alleles decreased the relative fluorescence intensities. In addition, we found that regions from − 1587 to − 1371 bp (TSS, + 1), − 1149 to − 894 bp, − 39 to + 130 bp, + 130 to + 341 bp, and + 341 to + 505 bp upregulated gene expression. In contrast, regions − 603 to − 316 bp and + 130 to + 341 bp downregulated gene expression. Region + 341 to + 505 bp played a decisive role in gene transcription.ConclusionsHTR1B 5′ regulatory region polymorphisms have regulatory effects on gene expression and potential correlate with several pathology and physiology conditions. This study suggests that a crucial sequence for transcription is located in region + 341 ~ + 505 bp. Regions − 1587 to − 1371 bp, − 1149 to − 894 bp, − 603 to − 316 bp, − 39 to + 130 bp, and + 130 to + 341 bp contain functional sequences that can promote or suppress the HTR1B gene expression.

Genetic Polymorphisms in Transforming Growth Factor-β, Interferon-γ and Interleukin-6 Genes and Susceptibility to Behcet's Disease in Saudi Population.

BackgroundBehcet’s disease (BD) is a complex, inflammatory, immune-mediated multi-systemic disease of unknown etiology. Cytokines play major roles in the pathophysiology of BD, and its production may be affected by polymorphism in cytokine genes. Hence, the present study was planned to investigate any possible association between the polymorphism in TGF-β, IFN-γ, and IL-6 genes and BD in the Saudi population.Materials and MethodsThe present study includes 79 BD cases and 117 age-matched controls. Polymerase chain reaction with restriction fragment length polymorphism (PCR-RFLP) and amplification refractory mutation systems (ARMS) PCR methods were used for polymorphic analysis.ResultsThe heterozygous (CT) and (CT+TT) combined genotypes of TGF-β (509-C/T), heterozygous (AT), variant (TT), and (AT+TT) combined genotypes of IFN-γ (874-A/T) were significantly (P<0.05) associated with BD in the Saudi population. No significant differences were observed for IL-6 (174-G/C) genotypes and alleles between BD cases and controls. Gender does not reflect any significant genotypic and allelic association with males and females.ConclusionCT genotype of TGF-β, and AT and TT genotypes of IFN-γ could be associative genetic risk factors for BD in Saudis. Regulatory region polymorphism in cytokines gene can increase inflammation and deregulated immune response, which could be risk factor for BD.

244-OR: Single Nuclei Chromatin and Transcriptome Profiling across Human and Rat Skeletal Muscle Identifies Regulatory Elements, Genes, and Cell Types Associated with Diabetes GWAS Signals

Skeletal muscle is the largest organ, by weight (&amp;gt;40%), in the human body; insulin resistance in this and other peripheral tissues is a hallmark of type 2 diabetes (T2D). Recent genome wide association study (GWAS) results show significant enrichment for fasting insulin single nucleotide polymorphisms (SNPs) in skeletal muscle tissue chromatin-defined regulatory regions. The next steps towards mechanistic translation are identification of causal variants, the target genes these variants regulate, and the specific cell populations in which they function. To accomplish this, we optimized and performed single-nuclei resolution chromatin (snATAC-seq) and transcriptome (snRNA-seq) profiling across human and rat frozen skeletal muscle, collectively measuring ’omic profiles on 38,386 nuclei. We used integrative non-negative matrix factorization for data fusion across ’omics modalities and species, revealing seven distinct clusters that range in abundance from 58% to 2.1% of all nuclei. The clusters are consistent across independent human and rat samples and across ’omic modalities. We find heterogeneity in fasting insulin GWAS enrichment across snATAC peaks for the muscle cell types (2/7 significantly enriched), one of which is mesenchymal stem cells (∼4% of nuclei). We use genetically fine-mapped SNPs from the largest T2D GWAS and find the highest posterior probability 99% credible set SNP (rs702634) out of three at the ARL15 locus resides in a muscle mesenchymal stem cell-specific snATAC peak. We are nearly finished snRNA+snATAC profiling across 400 additional samples, which will enable muscle cell-specific e/chromQTL analyses and GWAS colocalization reports for the ADA meeting. This work represents a unique resource for the genetic signature of skeletal muscle biology at unprecedented epigenomic, transcriptomic, and cellular scales. Disclosure S. Parker: None. Funding American Diabetes Association (1-14-INI-07 to S.P.); National Institutes of Health (R01DK117960)

Transcriptional activity of FIGLA, NEUROG2, and EGR1 transcription factors associated with polymorphisms in the proximal regulatory region of GPR54 gene in cattle

Activity of transcription factors affect synthesis of G-protein coupled receptor 54 (GPR54), an important factor in regulation of initiation of puberty. Expression of the GPR54 gene in cattle is associated with polymorphisms in the proximal regulatory region (PRR) of the GPR54 gene. Transcription resulting in production of GPR54 mRNA transcript occurs as a result of transcription factor (TF) interactions in the PRR. Polymorphisms in the PRR may be associated with extent of activity of these TFs. Folliculogenesis-specific BHLH TF (FIGLA), neurogenin 2 (NEUROG2), and early growth response 1 (EGR1) are important in modulation of ovarian follicle development and neurons synthesizing GnRH, thus, regulating biosynthesis of luteinizing hormone. The aim of this study, therefore, was to assess the transcription-activating potential of binding sites for FIGLA, NEUROG2, and EGR1 TFs in the GPR54 promoter of cattle. Two luciferase-based promoters, ATC and CCT, which contain three single nucleotide polymorphisms (SNPs), A/C-794, T/C-663, and C/T-601, in the GPR54 PRR, were analyzed to evaluate gene expression and activation of different promoters by FIGLA, NEUROG2, and EGR1. The FIGLA induced GPR54 transcription through the CCT, whereas NEUROG2 and EGR1 induced GPR54 transcription through the ATC promoter-binding site. The CCT-activating effects of FIGLA were greater (2.56-fold) than the ATC-activating effects (P < 0.05). The ATC-activating effects of NEUROG2 and EGR1 were markedly greater (12.91- and 8.41-fold; P < 0.01) than CCT-activating effects. The polymorphisms, CCT and ATC, of the cattle GPR54 affect the activity of transcription factors, therefore, have an important effect on production of GPR54 mRNA transcript.

Profiles of Local and Systemic Inflammation in the Outcome of Treatment of Human Cutaneous Leishmaniasis Caused by Leishmania (Viannia).

The immune mechanisms that contribute to the efficacy of treatment of cutaneous leishmaniasis (CL) are not fully understood. The aim of this study was to define immune correlates of the outcome of treatment of CL caused by Leishmania (Viannia) species during standard of care treatment with pentavalent antimonials. We conducted a comparative expression profiling of immune response genes in peripheral blood mononuclear cells (PBMCs) and lesion biopsy specimens obtained from CL patients before and at the end of treatment (EoT) with meglumine antimoniate. The ex vivo response of PBMCs to L (V) panamensis partially reflected that of lesion microenvironments. Significant downregulation of gene expression profiles consistent with local innate immune responses (monocyte and neutrophil activation and chemoattractant molecules) was observed at EoT in biopsy specimens of patients who cured (n = 8), compared to those from patients with treatment failure (n = 8). Among differentially expressed genes, pretreatment expression of CCL2 was significantly predictive of the therapeutic response (receiver operating characteristic [ROC] curve, area under the curve [AUC] = 0.82, P = 0.02). Polymorphisms in regulatory regions of the CCL2 promoter were analyzed in a pilot cohort of DNA samples from CL patients (cures, n = 20, and treatment failure, n = 20), showing putative association of polymorphisms rs13900(C/T) and rs2857656(G/C) with treatment outcome. Our data indicate that dampening gene expression profiles of monocyte and neutrophil activation characterize clinical cure after treatment of CL, supporting participation of parasite-sustained inflammation or deregulated innate immune responses in treatment failure.

Genetic architecture of quantitative traits in beef cattle revealed by genome wide association studies of imputed whole genome sequence variants: I: feed efficiency and component traits

BackgroundGenome wide association studies (GWAS) on residual feed intake (RFI) and its component traits including daily dry matter intake (DMI), average daily gain (ADG), and metabolic body weight (MWT) were conducted in a population of 7573 animals from multiple beef cattle breeds based on 7,853,211 imputed whole genome sequence variants. The GWAS results were used to elucidate genetic architectures of the feed efficiency related traits in beef cattle.ResultsThe DNA variant allele substitution effects approximated a bell-shaped distribution for all the traits while the distribution of additive genetic variances explained by single DNA variants followed a scaled inverse chi-squared distribution to a greater extent. With a threshold of P-value < 1.00E-05, 16, 72, 88, and 116 lead DNA variants on multiple chromosomes were significantly associated with RFI, DMI, ADG, and MWT, respectively. In addition, lead DNA variants with potentially large pleiotropic effects on DMI, ADG, and MWT were found on chromosomes 6, 14 and 20. On average, missense, 3’UTR, 5’UTR, and other regulatory region variants exhibited larger allele substitution effects in comparison to other functional classes. Intergenic and intron variants captured smaller proportions of additive genetic variance per DNA variant. Instead 3’UTR and synonymous variants explained a greater amount of genetic variance per DNA variant for all the traits examined while missense, 5’UTR and other regulatory region variants accounted for relatively more additive genetic variance per sequence variant for RFI and ADG, respectively. In total, 25 to 27 enriched cellular and molecular functions were identified with lipid metabolism and carbohydrate metabolism being the most significant for the feed efficiency traits.ConclusionsRFI is controlled by many DNA variants with relatively small effects whereas DMI, ADG, and MWT are influenced by a few DNA variants with large effects and many DNA variants with small effects. Nucleotide polymorphisms in regulatory region and synonymous functional classes play a more important role per sequence variant in determining variation of the feed efficiency traits. The genetic architecture as revealed by the GWAS of the imputed 7,853,211 DNA variants will improve our understanding on the genetic control of feed efficiency traits in beef cattle.

Patent Highlights December 2018–January 2019

Patent Highlights December 2018–January 2019

Allelic variations in genes belonging to glutathione system increase proliferative retinopathy risk in type 1 diabetes individuals

AimsGiven the participation of oxidative stress in the pathogenesis of diabetic complications, we evaluated, in type 1 diabetes (T1D) individuals, the association between diabetic retinopathy (DR) and functional single nucleotide polymorphisms (SNPs) in regulatory regions of two genes belonging to the antioxidant glutathione (GSH) system: rs17883901 in GCLC and rs713041 in GPX4. MethodsA cross-sectional case-control study included 288 individuals (61% women, 34[±11] years old, diabetes duration of 22[±9] years, mean [±SD]) sorted according to DR stages: absence of DR (ADR), non-proliferative DR (NPDR) and proliferative DR (PDR). SNPs were genotyped by real-time PCR using fluorescent labelled probes. Logistic regression models with adjustment for confounding covariates were employed. ResultsThe presence of at least one T-allele of rs17883901 in GCLC was an independent risk factor for PDR (OR 4.13, 95% CI 1.38–13.66, p = 0.014) in a polytomous regression model (PDR versus ADR). The presence of at least one T-allele of rs713041 in GPX4 conferred protection against PDR (OR 0.30, 95% CI 0.11–0.80, p = 0.017) in female T1D individuals. ConclusionThe functional SNPs rs17883901 and rs713041 modulate the risk for PDR in the studied population of T1D individuals, widening the spectrum of candidate genes for this complication.

Expression polymorphism at the ARPC4 locus links the actin cytoskeleton with quantitative disease resistance to Sclerotinia sclerotiorum in Arabidopsis thaliana.

Quantitative disease resistance (QDR) is a form of plant immunity widespread in nature, and the only one active against broad host range fungal pathogens. The genetic determinants of QDR are complex and largely unknown, and are thought to rely partly on genes controlling plant morphology and development. We used genome-wide association mapping in Arabidopsis thaliana to identify ARPC4 as associated with QDR against the necrotrophic fungal pathogen Sclerotinia sclerotiorum. Mutants impaired in ARPC4 showed enhanced susceptibility to S.sclerotiorum, defects in the structure of the actin filaments and in their responsiveness to S.sclerotiorum. Disruption of ARPC4 also alters callose deposition and the expression of defense-related genes upon S.sclerotiorum infection. Analysis of ARPC4 diversity in A.thaliana identified one haplotype (ARPC4R ) showing a c. 1kbp insertion in ARPC4 regulatory region and associated with higher level of QDR. Accessions from the ARPC4R haplotype showed enhanced ARPC4 expression upon S.sclerotiorum challenge, indicating that polymorphisms in ARPC4 regulatory region are associated with enhanced QDR. This work identifies a novel actor of plant QDR against a fungal pathogen and provides a prime example of genetic mechanisms leading to the recruitment of cell morphology processes in plant immunity.

Effect of cytomegalovirus infection and leukocyte immunoglobulin like receptor B1 polymorphisms on receptor expression in peripheral blood mononuclear cells.

Leukocyte immunoglobulin like receptor B1 (LILRB1) plays a significant role in a number of infectious, autoimmune, cardiovascular, and oncologic disorders. LILRB1 expression varies between individuals and may be associated with polymorphisms on the regulatory region of the LILRB1 gene, as well as to previous cytomegalovirus infection. In this study, the contribution of these two factors to LILRB1 expression in peripheral blood mononuclear cells of healthy young adults was analyzed. LILRB1 expression in NK cells, T cells, B cells and monocytes was significantly stronger in individuals who had had cytomegalovirus infection than in those who had not (P < 0.001, P < 0.001, P < 0.01, and P < 0.001, respectively). Overall, no differences in LILRB1 expression were observed between individuals with and without GAA haplotypes of the LILRB1 regulatory region. However, when analyzed according to cytomegalovirus infection status, significant differences in LILRB1+ NK cells were observed. A higher proportion of LILRB1+ cells was found in GAA+ than in GAA- individuals who had not been infected (P < 0.01), whereas GAA- individuals had a larger proportion of LILRB1+ cells than GAA+ individuals who were cytomegalovirus positive (P < 0.01). In conclusion, cytomegalovirus infection has a major effect on LILRB1 expression in NK and other mononuclear cells and polymorphisms in the LILRB1 regulatory region appear to have a modulatory influence over this effect.

Intragenus (Homo) variation in a chemokine receptor gene (CCR5).

Humans have a comparatively higher rate of more polymorphisms in regulatory regions of the primate CCR5 gene, an immune system gene with both general and specific functions. This has been interpreted as allowing flexibility and diversity of gene expression in response to varying disease loads. A broad expression repertoire is useful to humans—the only globally distributed primate—due to our unique adaptive pattern that increased pathogen exposure and disease loads (e.g., sedentism, subsistence practices). The main objective of the study was to determine if the previously observed human pattern of increased variation extended to other members of our genus, Homo. The data for this study are mined from the published genomes of extinct hominins (four Neandertals and two Denisovans), an ancient human (Ust’-Ishim), and modern humans (1000 Genomes). An average of 15 polymorphisms per individual were found in human populations (with a total of 262 polymorphisms). There were 94 polymorphisms identified across extinct Homo (an average of 13 per individual) with 41 previously observed in modern humans and 53 novel polymorphisms (32 in Denisova and 21 in Neandertal). Neither the frequency nor distribution of polymorphisms across gene regions exhibit significant differences within the genus Homo. Thus, humans are not unique with regards to the increased frequency of regulatory polymorphisms and the evolution of variation patterns across CCR5 gene appears to have originated within the genus. A broader evolutionary perspective on regulatory flexibility may be that it provided an advantage during the transition to confrontational foraging (and later hunting) that altered human-environment interaction as well as during migration to Eurasia and encounters with novel pathogens.