Multiple loci are associated with white blood cell phenotypes

White blood cell (WBC) count is a common clinical measure from complete blood count assays, and it varies widely among healthy individuals. Total WBC count and its constituent subtypes have been shown to be moderately heritable, with the heritability estimates varying across cell types. We studied 19,509 subjects from seven cohorts in a discovery analysis, and 11,823 subjects from ten cohorts for replication analyses, to determine genetic factors influencing variability within the normal hematological range for total WBC count and five WBC subtype measures. Cohort specific data was supplied by the CHARGE, HeamGen, and INGI consortia, as well as independent collaborative studies. We identified and replicated ten associations with total WBC count and five WBC subtypes at seven different genomic loci (total WBC count-6p21 in the HLA region, 17q21 near ORMDL3, and CSF3; neutrophil count-17q21; basophil count- 3p21 near RPN1 and C3orf27; lymphocyte count-6p21, 19p13 at EPS15L1; monocyte count-2q31 at ITGA4, 3q21, 8q24 an intergenic region, 9q31 near EDG2), including three previously reported associations and seven novel associations. To investigate functional relationships among variants contributing to variability in the six WBC traits, we utilized gene expression- and pathways-based analyses. We implemented gene-clustering algorithms to evaluate functional connectivity among implicated loci and showed functional relationships across cell types. Gene expression data from whole blood was utilized to show that significant biological consequences can be extracted from our genome-wide analyses, with effect estimates for significant loci from the meta-analyses being highly corellated with the proximal gene expression. In addition, collaborative efforts between the groups contributing to this study and related studies conducted by the COGENT and RIKEN groups allowed for the examination of effect homogeneity for genome-wide significant associations across populations of diverse ancestral backgrounds.     

Identification of six novel susceptibility loci for dyslipidemia using longitudinal exome-wide association studies in a Japanese population

Recent genome-wide association studies have identified various dyslipidemia-related genetic variants. However, most studies were conducted in a cross-sectional manner. We thus performed longitudinal exome-wide association studies of dyslipidemia in a Japanese population. We used ~244,000 genetic variants and clinical data of 6022 Japanese individuals who had undergone annual health checkups for several years. After quality control, the association of dyslipidemia-related phenotypes with 24,691 single nucleotide polymorphisms (SNPs) was tested using the generalized estimating equation model. In total, 82 SNPs were significantly (P < 2.03 × 10^?6) associated with dyslipidemia phenotypes. Of these SNPs, four (rs74416240 of TCHP, rs925368 of GIT2, rs7969300 of ATXN2, and rs12231744 of NAA25) and two (rs34902660 of SLC17A3 and rs1042127 of CDSN) were identified as novel genetic determinants of hypo-HDL- and hyper-LDL-cholesterolemia, respectively. A replication study using the cross-sectional data of 8310 Japanese individuals showed the association of the six identified SNPs with dyslipidemia-related traits.     

Quantitative trait loci for white blood cell numbers in swine

Differential white blood cell counts are essential diagnostic parameters in veterinary practice but knowledge on the genetic architecture controlling variability of leucocyte numbers and relationships is sparse, especially in swine. Total leucocyte numbers (Leu) and the differential leucocyte counts, i.e. the fractions of lymphocytes (Lym), polymorphonuclear leucocytes [neutrophils (Neu), eosinophils (Eos) and basophils (Bas)] and monocytes (Mon) were measured in 139 F₂ pigs from a Meishan/Pietrain family, before and after challenge with the protozoan pathogen Sarcocystis miescheriana for genome-wide quantitative trait loci (QTL) analysis. After infection, the pigs passed through three stages representing acute disease, reconvalescence and chronic disease. Nine genome-wide significant and 29 putative, single QTL controlling leucocyte traits were identified on 15 chromosomes. Because leucocyte traits varied with health and disease status, QTL influencing the leucocyte phenotypes showed specific health/disease patterns. Regions on SSC1, 8 and 12 contained QTL for baseline leucocyte traits. Other QTL regions reached control on leucocyte traits only at distinct stages of the disease model. Two-thirds of the QTL have not been described before. Single QTL explained up to 19% of the phenotypic variance in the F₂ animals. Related traits were partly under common genetic influence. Our analysis confirms that leucocyte trait variation is associated with multiple chromosomal regions.     

Genetic polymorphism of haptoglobin subtypes in a Japanese population

Haptoglobin (Hp) subtypes have been determined in the Japanese population by polyacrylamide gel isoelectric focusing followed by immunoblotting and by two-dimensional polyacrylamide gel electrophoresis. In the present study, neuraminidase-treated plasma samples were used for subtyping of Hp, without prior purification. These samples were obtained from 372 unrelated healthy donors. Allelic frequencies were: Hp*1F = 0.0014; Hp*1S+ = 0.2688; Hp*2FF = 0.0000; Hp*2FS = 0.7284, and Hp*2SS = 0.0014. The phenotypic distribution was in good accordance with the Hardy-Weinberg equilibrium.     

Identification of a novel population of human cord blood cells with hema-topoietic and chondrocytic potential

With the exception of mature erythrocytes, cells within the human hematopoietic system are characterized by the cell surface expression of the pan-leukocyte receptor CD45. Here, we identify a novel subset among mononuclear cord blood cells depleted of lineage commitment markers (Lin-) that are devoid of CD45 expression. Surprisingly, functional examination of Lin-CD45- ceils also lacking cell surface CD34 revealed they were capable of multipotential hematopoietic progenitor capacity. Co-culture with mouse embryonic limb bud cells demonstrated that Lin^-CD45^-CD34^- cells were capable of contributing to cartilage nodules and differentiating into human chondrocytes. BMP-4, a mesodermal factor known to promote chondrogenesis, significantly augmented Lin^-CD45^-CD34^-differentiation into chondrocytes. Moreover, unlike CD34~ human hematopoietic stem cells, Lin^-CD45^-CD34^- cells were unable to proliferate or survive in liquid cultures, whereas single Lin^-CD45^-CD34^- cells were able to chimerize the inner cell mass (1CM) of murine blastocysts and proliferate in this embryonic environment. Our study identifies a novel population of Lin-CD45-CD34^- cells capable of commitment into both hematopoietic and chondrocytic lineages, suggesting that human cord blood may provide a more ubiquitous source of tissue with broader developmental potential than previously appreciated.     

与宁夏人群强直性脊柱炎关联的新基因淋巴毒素-α(LTA)的识别

淋巴毒素-α(Lymphotoxin-alpha,LTA)基因与系统性红斑狼疮、银屑病及类风湿性关节炎的遗传性有关,但目前还未有关于LTA基因与强直性脊柱炎(Ankylosing spondylitis,AS)关联的报道。文章采用病例-对照设计,在宁夏人群中对人类白细胞抗原(Human leukocyte antigen,HLA)的Ⅲ类基因约58 kb区域进行了高密度标志的基因组扫描,在33个SNPs及其单倍型中,仅定位于LTA基因中的SNPs组成的TCC单倍型的分布在病例-对照间比较有统计学意义(P=0.0005)。在宁夏群体(病例组:300,对照组:385)中发现,LTA基因中的rs909253 T/C多态性在AS患者中出现的频率显著高于正常对照(28.5%vs 19.7%,P=2×10-6)。结果表明LTA基因变异和AS易感性之间存在相关性,由此识别LTA基因可能与宁夏人群AS关联。     

Identification of quantitative trait loci associated with self-compatibility in a Prunus species

Self-compatibility in Rosaceous fruit species is based on a single-locus qualitative trait. However, the evidence observed in different species has indicated the presence of modifier genes outside the S locus affecting the expression of self-compatibility/self-incompatibility. The study of a progeny obtained from the cross of the almond genotypes ‘Vivot’× ‘Blanquerna’ has allowed the construction of a genetic map based on microsatellite markers and the identification for the first time in the Rosaceae family of two additional loci located outside the S locus and affecting the expression of self-compatibility/self-incompatibility. A quantitative trait locus (QTL) was located relatively close to the S locus, on linkage group 6 (G6), whereas the second one was located on G8. These QTLs appear to be involved in conferring self-compatibility to genotypes not possessing the S _f allele. These results are consistent with almond being a self-incompatible species with a genetic background of pseudo-self-compatibility controlled by modifier genes. The effect of the S _f allele and the two QTLs may contribute to explain the wide range of fruit sets observed when self-pollinating different almond genotypes.     

Identification of genetic loci associated with ear-emergence in bread wheat

A doubled haploid population constructed from a cross between the South Australian wheat cultivars ‘Trident’ and ‘Molineux’ was grown under winter field conditions, under field conditions over summer and under artificial light both with and without vernalisation. The duration from planting to ear-emergence was recorded and QTL associated with heading date were detected using a previously constructed genetic linkage map. Associations were shown with chromosomal regions syntenous to previously identified photoperiod (Ppd-B1) and vernalisation (Vrn-A1) sensitive loci. Additional QTL associated with time to heading were also identified on chromosomes 1A, 2A, 2B, 6D, 7A and 7B. Comparisons between the genetic associations observed under the different growing conditions allowed the majority of these loci to be classified as having either photoperiod-sensitive, vernalisation-sensitive or earliness per se actions. The identification of a photoperiod-sensitive QTL on chromosome 1A provides evidence for a wheat gene possibly homoeologous to Ppd-H2 previously identified on chromosome 1H of barley. The occurrence of a putative major gene for photoperiod sensitivity observed on chromosome 7A is presented. The combined additive effects at these loci accounted for more than half the phenotypic variance in the duration from planting to ear-emergence in this population. The possible role of these loci on the adaptation of wheat in Australia is discussed.     

Two novel susceptibility loci for type 2 diabetes mellitus identified by longitudinal exome-wide association studies in a Japanese population

Recent genome-wide association studies identified genetic variants that confer susceptibility to type 2 diabetes mellitus (T2DM). However, few longitudinal genome-wide association studies of this metabolic disorder have been reported to date. Therefore, we performed a longitudinal exome-wide association study of T2DM, using 24,579 single nucleotide polymorphisms (SNPs) and repeated measurements from 6022 Japanese individuals. The generalized estimating equation model was applied to test relations of SNPs to three T2DM-related parameters: prevalence of T2DM, fasting plasma glucose level, and blood glycosylated hemoglobin content. Three SNPs that passed quality control were significantly (P < 2.26 × 10^? 7) associated with two of the three T2DM-related parameters in additive and recessive models. Of the three SNPs, rs6414624 in EVC and rs78338345 in GGA3 were novel susceptibility loci for T2DM. In the present study, the SNP of GGA3 was predicted to be a genetic variant whose minor allele frequency has recently increased in East Asia.     

Identification of novel dendritic cell subset markers in human blood

Human dendritic cells (DC) are key regulators of innate and adaptive immunity that can be divided in at least three major subpopulations: plasmacytoid DC (pDC), myeloid type 1 DC (mDC1) and myeloid type 2 DC (mDC2) exhibiting different functions. However, research, diagnostic and cell therapeutic studies on human DC subsets are limited because only few DC subset markers have been identified so far. Especially mDC2 representing the rarest blood DC subset are difficult to be separated from mDC1 and pDC due to a paucity of mDC2 markers. We have combined multiparameter flow cytometry analysis of human blood DC subsets with systematic expression analysis of 332 surface antigens in magnetic bead-enriched blood DC samples. The initial analysis revealed eight novel putative DC subset markers CD26, CD85a, CD109, CD172a, CD200, CD200R, CD275 and CD301 that were subsequently tested in bulk peripheral blood mononuclear cell (PBMC) samples from healthy blood donors. Secondary analysis of PBMC samples confirmed three novel DC subset markers CD26 (dipeptidyl peptidase IV), CD85a (Leukocyte immunoglobulin-like receptor B3) and CD275 (inducible costimulator ligand). CD85a is specifically expressed in mDC1 and CD26 and CD275 represent novel mDC2 markers. These markers will facilitate human DC subset discrimination and additionally provide insight into potentially novel DC subset-specific functions.     

Identification of HLA-B44 subtypes associated with extended MHC haplotypes

The HLA class I antigen B44 is found in each of two different extended major histocompatibility haplotypes (allele combinations of HLA-B, HLA-DR, and complement genes BF, C2, C4A, and C4B in linkage disequilibrium). Using isoelectric focusing, two variants of HLA-B44 were identified. The basic variant was found in all cell lines with the extended haplotype HLA-B44, DR7, FC31, and the acidic variant in all cell lines with the extended haplotype HLA-B44, DR4, SC30. The occurrence of each antigen variant with a unique extended haplotype explains previous observations concerning the nonrandom association of B44 variants with DR antigens.     

Genetic variants associated with the white blood cell count in 13,923 subjects in the eMERGE Network

White blood cell count (WBC) is unique among identified inflammatory predictors of chronic disease in that it is routinely measured in asymptomatic patients in the course of routine patient care. We led a genome-wide association analysis to identify variants associated with WBC levels in 13,923 subjects in the electronic Medical Records and Genomics (eMERGE) Network. We identified two regions of interest that were each unique to subjects of genetically determined ancestry to the African continent (AA) or to the European continent (EA). WBC varies among different ancestry groups. Despite being ancestry specific, these regions were identifiable in the combined analysis. In AA subjects, the region surrounding the Duffy antigen/chemokine receptor gene (DARC) on 1q21 exhibited significant association (p value?=?6.71e-55). These results validate the previously reported association between WBC and of the regulatory variant rs2814778 in the promoter region, which causes the Duffy negative phenotype (Fy-/-). A second missense variant (rs12075) is responsible for the two principal antigens, Fya and Fyb of the Duffy blood group system. The two variants, consisting of four alleles, act in concert to produce five antigens and subsequent phenotypes. We were able to identify the marginal and novel interaction effects of these two variants on WBC. In the EA subjects, we identified significantly associated SNPs tagging three separate genes in the 17q21 region: (1) GSDMA, (2) MED24, and (3) PSMD3. Variants in this region have been reported to be associated with WBC, neutrophil count, and inflammatory diseases including asthma and Crohn's disease.     

Identification of genetic loci associated with abdominal visceral adiposity in Korean populations

Abdominal obesity is characterized by accumulation of subcutaneous and visceral fat in the abdomen and has been reported to be largely responsible for many metabolic and vascular diseases. Although substantial effort has been dedicated to identification of genetic factors associated with abdominal obesity, as measured by the waist-hip ratio and waist circumference, only a few studies have explored associations with visceral fat accumulation in the abdomen. Furthermore, genetic studies of abdominal visceral adiposity conducted in Asian ethnic groups are rare. To gain insight into the genetic basis for visceral adiposity in Asian subjects, we conducted genome-wide association analysis for a pool of 1594 Korean subjects. Abdominal visceral fat area was estimated by computed tomography. After adjustment for age, linear association analysis identified three loci showing suggestive evidence of association (P?<?5?×?10^?6) in ASIC2, SLC35F3, and 5q14.2. Stratification by sex revealed one female-specific locus (rs17104731) located near LINC01519 with a genome-wide significant association for visceral adiposity (P?=?4.66?×?10^?8). Since visceral fat has been suggested to influence metabolic traits, we analyzed associations of the loci identified in this study with metabolic indicators, such as glucose, insulin, and lipid levels, and markers of kidney function. A locus (rs6699737) in SLC35F3 showed a nominal association (P?<?5?×?10^?2) with alanine transaminase, aspartate transaminase, and fasting plasma insulin. In addition, the linear association test using genetic risk score demonstrated that visceral adiposity loci detected in this study had a cumulative effect on abdominal visceral fat area, waist-hip-ratio, total cholesterol, and low density lipoprotein cholesterol. In summary, this study reports new loci associated with visceral adiposity and provides evidence supporting involvement of these loci in several metabolic traits in Korean populations.     

Spontaneous establishment of a novel Japanese macaque cell line with epithelial cell phenotypes

A novel macaque cell line (J3K) with epithelial phenotypes was spontaneously established from a kidney specimen of a Japanese macaque (Macaca fuscata). Its population doubling level reached more than 500, and it was regarded as an established permanent cell line. J3K cells have transformed cell phenotypes such as loss of contact inhibition and anchorage-independent cell growth. Unlike other monkey adherent cell lines, J3K had no SV40 large T antigen. After establishment, cells have constantly expressed telomerase activity, whereas telomere length has been maintained. No mutations in the coding regions of the p53 complementary deoxyribonucleic acid were detected in the late-passaged cells. J3K, a novel transformed epithelial cell line, will be useful material for the comparative study of human and other primate cellular aging as well as cancer cell biology.     

Oscillations in a white blood cell production model with multiple differentiation stages

Journal of Mathematical Biology - In this work we prove occurrence of a super-critical Hopf bifurcation in a model of white blood cell formation structured by three maturation stages. We provide an...     

Mutagenesis strategies for identifying novel loci associated with disease phenotypes

The systematic identification of the function of all the genes in the mammalian genome is one of the major scientific challenges for the 21st century. A comprehensive insight into mammalian gene function will illuminate our understanding of the genetic bases of disease. Mouse mutagenesis is a powerful tool for the study of mammalian gene function. Most recently, a number of approaches employing the chemical mutagen ethylnitrosourea (ENU) have been utilised by mouse geneticists to deliver a substantial new collection of mouse disease models. The growing mouse mutant archive provides a powerful resource for the identification of novel genes involved with human genetic disease.     

Polymorphisms at newly identified lipid-associated loci are associated with blood lipids and cardiovascular disease in an Asian Malay population

We conducted a cross-sectional study of Malay participants aged 40-80 years (n = 2,932) to examine the associations between polymorphisms at newly identified, lipid-associated loci with blood lipid levels and prevalent cardiovascular disease (CVD) in a Malay population in Asia. A polymorphism adjacent to the TRIB1 locus (rs17321515) was associated with elevated total cholesterol and LDL-cholesterol (LDL-C) after adjustment for age and sex (both P values <0.007) and with increased risk of coronary heart disease and CVD [odds ratio (OR) 1.23, 95% confidence interval (95% CI) 1.03-1.46; and OR 1.2, 95% CI 1.02-1.42, respectively] under an additive model of inheritance. In addition, using recessive models of inheritance, polymorphisms on chromosome 19 adjacent to the CILP2 and PBX4 loci (rs16996148) and on chromosome 1 at the GALNT2 locus (rs4846914) were associated with elevated HDL-C (P = 0.005) and lower LDL-C (P = 0.048), respectively. Although novel, the former is consistent with the association between this polymorphism and lower blood triglycerides observed in the initial studies conducted in populations of European ancestry. Neither showed statistically significant association with CVD. These observations should form the basis of further investigation to identify the causative polymorphisms at this locus, and also to understand the mechanistic roles that this protein may play in lipoprotein metabolism in Asians and other populations.