Yoon Shin Cho

Erythroid Cell-Specific α-Globin Gene Regulation by the CP2 Transcription Factor Family

ABSTRACT We previously demonstrated that ubiquitously expressed CP2c exerts potent erythroid-specific transactivation of α-globin through an unknown mechanism. This mechanism is reported here to involve specific CP2 splice variants and protein inhibitor of activated STAT1 (PIAS1). We identify a novel murine splice isoform of CP2, CP2b, which is identical to CP2a except that it has an additional 36 amino acids encoded by an extra exon. CP2b has an erythroid cell-specific transcriptional activation domain, which requires the extra exon and can form heteromeric complexes with other CP2 isoforms, but lacks the DNA binding activity found in CP2a and CP2c. Transcriptional activation of α-globin occurred following dimerization between CP2b and CP2c in erythroid K562 and MEL cells, but this dimerization did not activate the α-globin promoter in nonerythroid 293T cells, indicating that an additional erythroid factor is missing in 293T cells. PIAS1 was confirmed as a CP2 binding protein by the yeast two-hybrid screen, and expression of CP2b, CP2c, and PIAS1 in 293T cell induced α-globin promoter activation. These results show that ubiquitously expressed CP2b exerts potent erythroid cell-specific α-globin gene expression by complexing with CP2c and PIAS1.

Celastrol ameliorates cytokine toxicity and pro-inflammatory immune responses by suppressing NF-κB activation in RINm5F beta cells.

Upregulation of pro-inflammatory mediators contributes to β-cell destruction and enhanced infiltration of immune cells into pancreatic islets during development of type 1 diabetes mellitus. In this study, we examined the regulatory effects and the mechanisms of action of celastrol against cytotoxicity and pro-inflammatory immune responses in the RINm5F rat pancreatic β-cell line stimulated with a combination of interleukin-1 beta, tumor necrosis factor-alpha, and interferon-γ. Celastrol significantly restored cytokine-induced cell death and significantly inhibited cytokine-induced nitric oxide production. In addition, the protective effect of celastrol was correlated with a reduction in pro-inflammatory mediators, such as inducible nitric oxide synthase, cyclooxygenase-2, and CC chemokine ligand 2. Furthermore, celastrol significantly suppressed cytokine-induced signaling cascades leading to nuclear factor kappa B (NF-κB) activation, including IκB-kinase (IKK) activation, IκB degradation, p65 phosphorylation, and p65 DNA binding activity. These results suggest that celastrol may exert its cytoprotective activity by suppressing cytokine-induced expression of pro-inflammatory mediators by inhibiting activation of NF-κB in RINm5F cells. [BMB Reports 2015; 48(3): 172-177]

Replication of the Wellcome Trust genome-wide association study on essential hypertension in a Korean population

Essential hypertension has a high rate of morbidity and mortality, primarily because of the associated complications. The Wellcome Trust Case Control Consortium recently conducted a genome-wide association study and identified six single nucleotide polymorphisms (SNPs) associated with essential hypertension. The Family Blood Pressure Program later investigated these six SNPs in an attempt to reproduce the aforementioned associations, but only one such association was found. However, this replication study did not include any Asian patients. Therefore, we investigated the association of the six SNPs with hypertension using 7551 unrelated individuals from the Korean Association REsource, a genome-wide association study based on epidemiological cohorts in Korea. We carried out a logistic regression analysis for hypertension status, and a linear regression analysis with systolic blood pressure and diastolic blood pressure as quantitative traits. Even though two SNPs, rs6997709 and rs7961152, were associated with systolic and diastolic blood pressures, respectively, in the quantitative trait association test, no associations were found using a case–control association test. The Korean Association REsource data consisted of two community cohorts (the Ansung and Ansan areas in Korea). The SNP rs7961152 was found to be associated with hypertension risk (OR (odds ratio) =1.286, CI (confidence interval) 1.012–1.636, P=0.040), but only in the Ansan cohort. This study as well as the Family Blood Pressure Program study show that because of the complexity of the genetic architecture, an association study with a larger sample population may be necessary to identify genetic variants that affect hypertension.

Genotype instability during long-term subculture of lymphoblastoid cell lines.

Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines (LCLs) promise to address the challenge posed by the limited availability of primary cells needed as a source of genomic DNA for genetic studies. However, the genetic stability of LCLs following prolonged culture has never been rigorously investigated. To evaluate genotypic errors caused by EBV integration into human chromosomes, we isolated genomic DNA from human peripheral blood mononuclear cells and LCLs collected from 20 individuals and genotyped the DNA samples using the Affymetrix 500K SNP array set. Genotype concordance measurements between two sources of DNA from the same individual indicated that genotypic discordance is negligible in early-passage LCLs (<20 passages) but substantial in late-passage LCLs (>50 passages). Analysis of concordance on a chromosome-by-chromosome basis identified genomic regions with a high frequency of genotypic errors resulting from the loss of heterozygosity observed in late-passage LCLs. Our findings suggest that, although LCLs harvested during early stages of propagation are a reliable source of genomic DNA for genetic studies, investigations that involve genotyping of the entire genome should not use DNA from late-passage LCLs.

Recapitulation of the association of the Val66Met polymorphism of BDNF gene with BMI in Koreans.

Recent evidence suggests that brain‐derived neurotrophic factor (BDNF) regulates food intake and the control of body weight. A common polymorphism in human BDNF, Val66Met (single‐nucleotide polymorphism database (dbSNP) no. rs6265), impairs intracellular trafficking, resulting in the reduced secretion of BDNF. Several European studies have indicated that Val66Met is associated with BMI. In this study, we examined the association of the Val66Met polymorphism with BMI in Koreans (n = 20,270) from three independent epidemiological cohorts. All three studies observed a consistent association of this polymorphism with BMI, and their combined analysis demonstrated a robust correlation (β = −0.17 ± 0.03 and P = 5.6 × 10−8). We also examined the effect of smoking on the link between Val66Met and BMI. The association of Val66Met with BMI was statistically significant only in the smoking group, reflecting a possible interaction between smoking and the BDNF polymorphism for BMI. Thus, we have confirmed BDNF as a genetic risk factor for BMI in an Asian population and hypothesize that the Val66Met mutation influences individual differences in BMI. In addition, smoking might interact with BDNF Val66Met to modulate BMI.

Association of polymorphisms in the Interleukin 23 receptor gene with osteonecrosis of femoral head in Korean population

Osteonecrosis of the femoral head (ONFH) is known as death of the cellular portion of the femoral head due to an interruption in the vascular supply. The underlying pathophysiology regarding bone cell death remains uncertain. Recently, several studies have shown that autoimmune disorders were related to the development of osteonecrosis. This study investigated the genetic effects of Interleukin 23 receptor (IL23R) polymorphisms regarding the risk of ONFH. Ten SNPs were selected and genotyped in 443 ONFH patients and 273 control subjects in order to perform the genetic association analysis. It was found that polymorphisms of the IL23R gene (rs4655686, rs1569922 and rs7539625) were significantly associated with an increased risk of ONFH (P values; 0.0198-0.0447, OR; 1.30-1.49). Particularly, a stratified analysis based on etiology (alcohol, steroid or idiopathic) showed that the associations between these polymorphisms and ONFH were most significant in idiopathic ONFH patients (P values; 0.0001-0.0150, OR; 1.45-2.17). These results suggest that IL23R polymorphisms may play an important role in the development of ONFH.

Polymorphisms in the Annexin gene family and the risk of osteonecrosis of the femoral head in the Korean population

OBJECTIVE The pathogenesis of osteonecrosis of the femoral head (ONFH) probably reflects multiple etiologies. Recent studies have explored associations between genetic mutations and/or polymorphisms and ONFH. Annexins (ANXs) have been implicated in many physiological functions, including blood coagulation, inflammation, apoptosis, as well as Ca(2+) homeostasis in bone cells, all of which may be associated with ONFH. The aim of this study was to evaluate the possible association of AnnexinA (ANXA) family gene polymorphisms with ONFH. METHODS 52 SNPs from three genes of the ANXA family were selected from public databases and genotyped in 443 ONFH patients and 273 control subjects using the Affymetrix Targeted Genotyping 3 K Chip array. The association analysis of genotyped SNPs and haplotypes was performed with ONFH. RESULTS Among the polymorphisms tested of the ANXA family gene, the rs9324679, rs9324677, rs10037814, and rs11960458 SNPs of the ANXA6 gene were significantly associated with the risk of ONFH in all alternative analysis models (p range; 0.0007-0.049, odds ratio (OR); 0.63-1.72). Further analysis stratified by pathological etiology showed that these SNPs were also associated with the risk of ONFH in at least one subgroup (p range; 0.0017-0.049). Haplotype association analysis showed that several haplotypes were significantly associated with a risk of ONFH, with p values ranging between 0.0005 and 0.049 (OR range; 0.44-1.76). CONCLUSIONS These findings indicate that the polymorphisms of ANXA6 are associated with ONFH. Thus, these polymorphisms may be useful genetic markers to identify high-risk individuals.

Genome-Wide Association Analyses on Blood Pressure Using Three Different Phenotype Definitions

Hypertension is the most prevalent disease worldwide and is itself a risk factor for cerebral, cardiac, and renal diseases. The inconsistency of candidate genes suggested by previous genomewide association studies (GWASs) may be due to not only differences in study design and genetic or environmental background but also the difference in the power of analysis between continuous traits and discrete traits. We analyzed 352,228 single nucleotide polymorphisms (SNPs) in 8842 unrelated Koreans obtained from Ansan and Ansung cohorts. We performed a series of GWA analyses using three different phenotype models; young hypertensive cases (278 subjects) versus elderly normotensive controls (680 subjects); the upper 25% (2211 hypertensive cases) versus the lower 25% of the SBP distribution (2211 hypotensive controls); and finally SBP and DBP as continuous traits (8842 subjects). The numbers of young hypertensive cases and elderly normotensive controls were not large enough to achieve genomewide significance. The model comparing the upper 25% subjects to the lower 25% of subjects showed a power that was approximate to that of QTL analysis. Two neighboring SNPs of the ATP2B1 gene, rs17249754 (SBP, p=; DBP, p=) and rs7136259 (SBP, p=; DBP, p=), were associated with both SBP and DBP. Interestingly, a SNP of the RPL6 gene, rs11066280, revealed a significant genomewide association with SBP in men only (p=), and four SNPs located near the MAN2A1 gene showed a strong association with DBP only in elderly men aged 60-70 years (e.g., rs6421827, p=). However, we did not observe any gene variant attaining genomewide significance consistently in the three phenotype models except for the ATP2B1 gene variants. In general, the association signal with blood pressure was stronger in women than in men. Genes identified in GWASs are expected to open the way for prevention, early diagnosis, and personalized treatment of hypertension.

Genome-wide Association Study Identification of a New Genetic Locus with Susceptibility to Osteoporotic Fracture in the Korean Population

Abstract Osteoporotic fracture (OF), along with bone mineral den-sity (BMD), is an important diagnostic parameter and a clinical predictive risk factor in the assessment of osteo-porosis in the elderly population. However, a genome- wide association study (GWAS) on OF has not yet been clarified sufficiently. To identify OF-associated genetic variants and candidate genes, we conducted a GWAS in a population-based cohort (Korean Association Resource [KARE], n=1,427 [case: 288 and control: 1139]) and per-formed a de novo replication study in hospital-based in-dividuals (Asan and Catholic Medical Center [ACMC], n=1,082 [case: 272 and control: 810]). In a combined meta-analysis, a newly identified genetic locus in an in-tergenic region at 10p11.2 (near genes FZD8 and ANKRD30A) showed the most significant association (odd ratio [OR] = 2.00, 95% confidence interval [CI] = 1.47∼2.74, p=1.27×10 −5 ) in the same direction. We provide the first evidence for a common genetic variant influencing OF and genetic information for further inves-tigation in bone metabolism.Keywords: genomewide association study, meta-analy-sis, osteoporotic fracture, intergenic

Identification of Causal and/or Rare Genetic Variants for Complex Traits by Targeted Resequencing in Population-based Cohorts

Genome-wide association studies (GWASs) have greatly contributed to the identification of common variants responsible for numerous complex traits. There are, however, unavoidable limitations in detecting causal and/or rare variants for traits in this approach, which depends on an LD-based tagging SNP microarray chip. In an effort to detect potential casual and/or rare variants for complex traits, such as type 2 diabetes (T2D) and triglycerides (TGs), we conducted a targeted resequencing of loci identified by the Korea Association REsource (KARE) GWAS. The target regions for resequencing comprised whole exons, exon-intron boundaries, and regulatory regions of genes that appeared within 1 Mb of the GWA signal boundary. From 124 individuals selected in population-based cohorts, a total of 0.7 Mb target regions were captured by the NimbleGen sequence capture 385K array. Subsequent sequencing, carried out by the Roche 454 Genome Sequencer FLX, generated about 110,000 sequence reads per individual. Mapping of sequence reads to the human reference genome was performed using the SSAHA2 program. An average of 62.2% of total reads was mapped to targets with an average 22X-fold coverage. A total of 5,983 SNPs (average 846 SNPs per individual) were called and annotated by GATK software, with 96.5% accuracy that was estimated by comparison with Affymetrix 5.0 genotyped data in identical individuals. About 51% of total SNPs were singletons that can be considered possible rare variants in the population. Among SNPs that appeared in exons, which occupies about 20% of total SNPs, 304 nonsynonymous singletons were tested with Polyphen to predict the protein damage caused by mutation. In total, we were able to detect 9 and 6 potentially functional rare SNPs for T2D and triglycerides, respectively, evoking a further step of replication genotyping in independent populations to prove their bona fide relevance to traits.