Association study of TAP and HLA-I gene combination with chronic hepatitis C virus infection in a Han population in China.

Host immune system genes play key roles in the progression of chronic hepatitis C virus (HCV) infection. Transporters associated with antigen processing (TAP) play an important role in the loading of viral peptides onto MHC class I molecules. This study aimed to investigate the association between TAP gene polymorphisms and chronic HCV in a Chinese Han population. A total of 232 chronic hepatitis C (CHC) patients and 362 healthy individuals were recruited from the Han population in Yunnan province in southwest China, and a TaqMan SNP genotyping assay was used to detect six single nucleotide polymorphisms (SNPs) of TAP1 and three SNPs of TAP2 genes. The association of the TAP gene with CHC was analysed at the allele, genotype, and haplotype levels. There were no significant differences in the allele and genotype frequencies of these SNPs in the TAP gene between CHC patients and controls after Bonferroni correction. A novel TAP1 allele (TAP1*unknown_1: rs41555220-rs41549617-rs1057141-rs1135216-rs1057149-rs41551515: G-G-A-G-G-G) was only present in the CHC group, and this allele significantly increased susceptibility to CHC (p = .005, odds ratio [OR] = 11.105. 95% confidence interval [CI]: 1.362-90.558). Homozygous TAP1*03:01/TAP1*03:01 was observed only in the CHC group that exhibited an obvious risk for CHC (p = .002, OR = 9.637, 95% CI: 1.153-80.574). And the haplotype TAP1*unknown_1-TAP2*01:01 was only present in the CHC group and indicated a significant risk for CHC (p = .002, OR = 9.498, 95% CI: 1.140-79.149). We observed significant interactions among HLA-A, -B,C, TAP1, and TAP2 alleles, and combination analysis revealed that the combination of TAP1*01:01-TAP2*01:01-HLA-B*35:01 was only present in the control group (2.2%) and resulted in significantly increased resistance to CHC (p = .002, OR = 0.096, 95% CI: 0.012-0.759). Whereas, the combination of TAP1*01:01-TAP2*01:01-HLA-C*07:02 and TAP1*03:01-TAP2*01:01-HLA-C*01:02 increased the susceptibility to CHC significantly (p = .001, OR = 2.016, 95% CI: 1.309-3.106 and p = .002, OR = 8.070, 95% CI: 1.018-63.997, respectively). Our results indicated that TAP and HLA-I may exert a combined effect on CHC susceptibility in the Chinese Han population.

Norovirus GII.17 Natural Infections in Rhesus Monkeys, China.

Noroviruses are a leading viral cause of acute gastroenteritis among humans. During the 2014-15 epidemic season, norovirus GII.17 was detected in rhesus monkeys in China. Genetic, structural, and challenge studies revealed virus mutations and verified the infections. Thus, cross-species transmission may occur, and monkeys may be a virus reservoir.

PU.1-Bim axis is involved in Trichostatin A-induced apoptosis in murine pro-B lymphoma FL5.12 cells.

Trichostatin A (TSA) is a well-known histone deacetylases (HDACs) inhibitor that has been reported to show potent anti-tumor capabilities in some types of cancer cell lines. However, detailed mechanism of TSA action on lymphoma remains to be described. In the present study, anti-proliferative effects of TSA were investigated using a murine pro-B lymphoma cell line FL5.12. MTT assay revealed that TSA potently inhibited the proliferation of FL5.12 cells in a time- and dose-dependent manner. Bright-field microscopy of FL5.12 cells showed apoptotic morphology at 24 h after TSA treatment. Consistently, TSA treatment led to DNA fragmentation and increased the protein levels of cleaved caspase 3 and PARP as revealed by western blot analysis. To explore the underlying mechanism of TSA-induced apoptosis of FL5.12 cells, we further analyzed the hematopoietic transcription factor Purine Rich Box-1 (PU.1) by western blot analysis. TSA treatment resulted in the inhibition of PU.1 in FL5.12 cells. In contrast, apoptotic protein Bim was induced by TSA, which was inversely correlated with the survival of FL5.12 cells. These results suggest the possible mechanism of TSA-induced apoptosis in murine pro-B lymphoma FL5.12 cells via the PU.1-Bim axis.

Design and evaluation of a multi-epitope DNA vaccine against HPV16.

Cervical cancer, among the deadliest cancers affecting women globally, primarily arises from persistent infection with high-risk human papillomavirus (HPV). To effectively combat persistent infection and prevent the progression of precancerous lesions into malignancy, a therapeutic HPV vaccine is under development. This study utilized an immunoinformatics approach to predict epitopes of cytotoxic T lymphocytes (CTLs) and helper T lymphocytes (HTLs) using the E6 and E7 oncoproteins of the HPV16 strain as target antigens. Subsequently, through meticulous selection of T-cell epitopes and other necessary elements, a multi-epitope vaccine was constructed, exhibiting good immunogenic, physicochemical, and structural characteristics. Furthermore, in silico simulations showed that the vaccine not only interacted well with toll-like receptors (TLR2/TLR3/TLR4), but also induced a strong innate and adaptive immune response characterized by elevated Th1-type cytokines, such as interferon-gamma (IFN-γ) and interleukin-2 (IL2). Additionally, our study investigated the effects of different immunization intervals on immune responses, aiming to optimize a time-efficient immunization program. In animal model experiments, the vaccine exhibited robust immunogenic, therapeutic, and prophylactic effects. Administered thrice, it consistently induced the expansion of specific CD4 and CD8 T cells, resulting in substantial cytokines release and increased proliferation of memory T cell subsets in splenic cells. Overall, our findings support the potential of this multi-epitope vaccine in combating HPV16 infection and signify its candidacy for future HPV vaccine development.

Through the stringent selection of T-cell epitopes and other necessary elements, a novel multi-epitope vaccine targeting HPV 16 E6 and E7 oncoproteins was constructed using an immunoinformatics approach.The vaccine designed can induce both cellular and humoral immune responses, encompassing all the required immunogenic, physicochemical, and structural characteristics for an ideal vaccine design. Moreover, it offers decent worldwide coverage.In animal studies, the vaccine demonstrated strong immune responses, including expansion of CD4 and CD8 T cells, cytokine release, and enhanced memory T cell proliferation, resulting in long-term anti-tumor effects, inhibition of tumor growth, and prolonged survival in tumor-bearing mice.The immunological evaluation of the designed vaccine suggests its potential as a novel vaccine candidate against HPV 16.

[Distribution of HLA-G 14 bp insertion/deletion polymorphism and their associations with HLA-A alleles in four Chinese ethnic groups].

Recently, a 14 bp insertion/deletion polymorphism (+14 bp/-14 bp) in exon 8 of the human leucocyte antigen-G (HLA-G) gene has been widely recognized to associate with recurrent miscarriage, autoimmune diseases, hepatocellular carcinoma and other diseases. Our previous studies have shown the distribution characteristics of linguistic family for HLA-G 14 bp insertion/deletion in different ethnic groups. In the present study, we investigated the distribution of HLA-G 14 bp insertion/deletion polymorphism and their subsequent associations with HLA-A alleles in Tu, Yugu, Lisu and Nu ethnic populations based upon the HLA-A genotyping data. Our results showed that the frequencies of the 14 bp insertion/deletion polymorphism were diverse in these four populations while that in the same linguistic subfamily was similar. The significant difference in different linguistic subfamily except for Han and Mongolian language subfamily was identified. In addition, the 14 bp insertion was found to associate with HLA-A alleles in different ethnic populations.

[Association between Alu insertion polymorphisms and HLA class I alleles in Chinese Lisu and Nu ethnic populations].

OBJECTIVE: To investigate the frequencies of HLA-Alu repeat polymorphisms (AluMICB, AluTF, AluHJ, AluHG and AluHF) in Chinese Lisu and Nu ethnic populations. METHODS: The frequencies of HLA-Alu repeat polymorphisms in above populations were determined with polymerase chain reaction (PCR). The associations between HLA-Alu repeat polymorphisms and HLA-A, HLA-B and HLA-C alleles were also analyzed. Phylogenetic trees were constructed with genetic distance calculated from the frequencies of HLA-Alu repeat polymorphisms. RESULTS: Frequencies of AluTF*2 and AluHF*2 were different between the two populations (P< 0.05), while those of other three insertions were similar. The strength of association between HLA-Alus and HLA alleles were different (P< 0.05) in the two populations. Although AluMICB*2 were associated with HLA-B*56:01 in both populations, the association was stronger in Lisu population (74.0%) but moderate in Nu population (30.7%). HLA-Alus were associated with particular HLA subtypes, e.g., AluHG*2 with certain HLA-A*02 subtypes. By phylogenetic analysis, Lisu and Nu were clustered together with southern Chinese and Thai populations. CONCLUSION: The distribution of HLA-Alus and the strength of associations between HLA-Alus and HLA class I alleles have varied between the two populations. Study of this association may facilitate identification of origins, evolution, progenitor haplotypes and recombination within the HLA class I region.

[Detection and preliminary study of a family carrying a CCR5Δ32 deletional mutation].

OBJECTIVE: To investigate the frequencies of chemokine (C-C motif) receptor 5 gene (CCR5)Δ32 deletional mutation of in Han and Dai populations from Yunnan province. Immortalized cell lines were derived from a family carrying the CCR5Δ32 mutation. METHODS: Blood samples of 346 Han and 355 Dai individuals were collected for genotyping. The coding regions of CCR5 gene were amplified with PCR followed by agarose gel electrophoresis. Suspected mutations were verified with DNA sequencing. Immortalized cell lines were constructed by using Epstain Barr virus and cyclosporine A. The difference between the cell lines and original blood samples was verified with PCR. RESULTS: One ethnic Han individual was confirmed to be heterozygous for a deletional mutation by sequencing, which has led to discovery of a family with CCR5Δ32. Nine immortalized cell lines were established from this family, and no difference between the cell lines and original blood samples was detected by PCR. CONCLUSION: Together with previous reports, this study has indicated a significant difference in CCR5Δ32 among different ethnic groups in China. Established immortalized cell lines can also provide material for future research.

Diversity of killer cell immunoglobulin-like receptor genes in four ethnic groups in China.

Killer cell immunoglobulin-like receptors (KIRs) show extensive variation in terms of gene content and allelic polymorphisms among different populations. The aim of this study was to analyze the distribution of KIR genes in the Bulang, Nu, Yugu, and Zhuang ethnic groups, which belong to four different language families in China, and thus to provide basic KIR gene and genotype data for these Chinese ethnic groups. Genotyping of 16 KIR genes was performed in 425 unrelated individuals using the polymerase chain reaction-sequence-specific oligonucleotide probe method with the Luminex MultiAnalyte Profiling System. The four framework KIR genes were detected in all four ethnic groups. The activating KIR genes as well as the inhibitory KIR genes showed extreme diversity among these four populations. A total of 35 distinct KIR genotypes were identified, one of which was previously unknown. The four most common genotypes were identified in all four populations and comprised 66.1~91.1% of all the genotypes. The group A haplotype occurred more frequently than the group B haplotype in the Nu, Yugu, and Zhuang populations, as in other East Asian populations. In contrast, the group A and group B haplotypes occurred equally in the Bulang population. The results of the present study suggested that the KIR genes and genotypes are diverse in these four ethnic groups, and each ethnic group has its own characteristic KIR distribution. The findings with respect to KIR gene diversity in these four populations should provide relevant genomic diversity data for the future study of viral infections, autoimmune diseases, and reproductive fitness.

[Distribution of HLA-C genes and HLA C-B, A-C-B haplotypes in Jinuo, Maonan and Wa ethnic populations in southwest China].

OBJECTIVE: To investigate the distribution of human leukocyte antigen(HLA) class I genes and haplotypes in Jinuo, Maonan and Wa ethnic populations in southwest China. METHODS: Polymerase chain reaction-sequence specific oligonucleotide (PCR-SSO) typing by Luminex was performed to genotype the HLA-C alleles in unrelated healthy individuals in the three populations. HLA C-B, A-C-B haplotypes were computed by combining the previous HLA-A and -B genotyping data using Pypop7.0 software. RESULTS: Eighteen HLA-C genes were identified in the three populations, with 17, 13 and 15 HLA-C genes in Jinuo, Maonan and Wa populations respectively. The alleles with frequency of more than 10% from high to low were C*08:01, C*01:02, C*03:04 and C*07:02 in the Jinuo, C*03:04, C*01:02, C*07:02 and C*08:01 in the Maonan, and C*12:03, C*08:01, C*07:02 and C*04:01 in the Wa. The predominant HLA A-C-B haplotypes were A*02:07-C*01:02-B*46:01, A*11:01-C*08:01-B*15:02 and A*11:01-C*03:04-B*13:01 in the Jinuo, A*11:01-C*03:04-B*13:01, A*02:07-C*01:02-B*46:01, A*11:01-C*08:01-B*15:02 and A*02:03-C*07:02-B*38:02 in the Maonan, and A*11:01-C*08:01-B*15:02, A*11:01-C*12:03-B*15:32 and A*11:01-C*04:01-B*35:01 in the Wa, respectively. CONCLUSION: There were different characteristics in the distributions of HLA-C genes and HLA C-B, A-C-B haplotypes in the Jinuo, Maonan and Wa populations. However, haplotypes C*08:01-B*15:02 and A*11:01-C*08:01-B*15:02 with high frequencies were common in the three populations, which might be the common ancient haplotypes of southern Chinese population. The study of HLA genes and haplotypes in these populations may be of significance in the study of population genetics, transplantation and disease association.

[Association between diversity of hypoxia at different altitude and the polymorphism of EPAS1 gene].

OBJECTIVE: To study the selection effect of endothelial PAS domain protein 1 (EPAS1) gene induced by high altitude hypoxia environment. METHODS: Fourteen single nucleotide polymorphism sites (SNPs) of the EPAS1 gene were genotyped using PCR-restriction fragment length polymorphism (PCR-RFLP) in three Tibetan groups (58 samples from Tibetan living in an altitude of about 3700 meters above sea level, 47 from Qinghai province, about 3100 meters above sea level, 43 from Yunnan province, about 2500 meters above sea level), and Han of Shandong (47 samples, about 50 meters above sea level). RESULTS: There were significant differences of most SNP allelic, genotypic and haplotypic frequencies when comparing Han of Shandong, Tibetan of Yunnan with Tibetan of Tibetan and Qinghai. But no difference between Han of Shandong and Tibetan of Yunnan was found. CONCLUSION: The EPAS1 gene might be under hypoxic selection induced by high altitude.

[Polymorphic Alu insertions and their associations with HLA I alleles in Yugu and Zhuang ethnic populations].

Many studies have show that the structurally polymorphic Alu insertion within HLA class I region are useful tools for investigating the origin, evolution and recombination of HLA class I progenitor haplotypes and gene diversity in different ethnic populations. In the present study, we determined the frequencies of HLA-Alus (i.e., AluMICB, AluTF, AluHJ, AluHG, and AluHF) in Zhuang and Yugu ethnic populations at first. Then, combined with HLA genotyping data, we studied associations between HLA-Alus and HLA-A alleles in Zhuang, Yugu, Bulang, Dai, and Hani ethnic populations. Our results showed that (1) the frequencies of five HLA-Alus were 1.5%~35.8% and 9.2%~34.8% in Zhuang and Yugu, respectively; and (2) the results of association between HLA-A alleles and HLA-Alu showed strong association between AluHG insertion and HLA-A 02 subtypes in all populations, association between AluHJ insertion and HLA-A 2402 in all populations, and association between AluHJ insertion and HLA-A 1101, -A 2407 in Bulang. The present study suggested that the distribution of HLA-Alus as well as the associations between HLA-Alus and HLA class I alleles are variable in different ethnic populations. HLA Alus alone or together with the HLA class I alleles are informative genetic markers for the identification of HLA class I allele and variation of haplotype lineages in different populations.

Identification of HLA-B*55:117N in an individual from Zhuang population of China.

The novel HLA-B*55:117N allele identified in an individual of Zhuang ethnic population of China.

Haplotypic Associations and Differentiation of MHC Class II Polymorphic Alu Insertions at Five Loci With HLA-DRB1 Alleles in 12 Minority Ethnic Populations in China.

The analysis of polymorphic variations in the human major histocompatibility complex (MHC) class II genomic region on the short-arm of chromosome 6 is a scientific enquiry to better understand the diversity in population structure and the effects of evolutionary processes such as recombination, mutation, genetic drift, demographic history, and natural selection. In order to investigate associations between the polymorphisms of HLA-DRB1 gene and recent Alu insertions (POALINs) in the HLA class II region, we genotyped HLA-DRB1 and five Alu loci (AluDPB2, AluDQA2, AluDQA1, AluDRB1, AluORF10), and determined their allele frequencies and haplotypic associations in 12 minority ethnic populations in China. There were 42 different HLA-DRB1 alleles for ethnic Chinese ranging from 12 alleles in the Jinuo to 28 in the Yugur with only DRB1∗08:03, DRB1∗09:01, DRB1∗12:02, DRB1∗14:01, DRB1∗15:01, and DRB1∗15:02 present in all ethnic groups. The POALINs varied in frequency between 0.279 and 0.514 for AluDPB2, 0 and 0.127 for AluDQA2, 0.777 and 0.995 for AluDQA1, 0.1 and 0.455 for AluDRB1 and 0.084 and 0.368 for AluORF10. By comparing the data of the five-loci POALIN in 13 Chinese ethnic populations (including Han-Yunnan published data) against Japanese and Caucasian published data, marked differences were observed between the populations at the allelic or haplotypic levels. Five POALIN loci were in significant linkage disequilibrium with HLA-DRB1 in different populations and AluDQA1 had the highest percentage association with most of the HLA-DRB1 alleles, whereas the nearby AluDRB1 indel was strongly haplotypic for only DRB1∗01, DRB1∗10, DRB1∗15 and DRB1∗16. There were 30 five-locus POALIN haplotypes inferred in all populations with H5 (no Alu insertions except for AluDQA1) and H21 (only AluDPB2 and AluDQA1 insertions) as the two predominant haplotypes. Neighbor joining trees and principal component analyses of the Alu and HLA-DRB1 polymorphisms showed that genetic diversity of these genomic markers is associated strongly with the population characteristics of language family, migration and sociality. This comparative study of HLA-DRB1 alleles and multilocus, lineage POALIN frequencies of Chinese ethnic populations confirmed that POALINs whether investigated alone or together with the HLA class II alleles are informative genetic and evolutionary markers for the identification of allele and haplotype lineages and genetic variations within the same and/or different populations.

[Study of nine single nucleotide polymorphism loci of human HIF1A gene in three Tibetan groups].

OBJECTIVE: To investigate the effect of hypoxia environment induced by altitude on hypoxia inducible factor 1α (HIF1A) gene. METHODS: Nine single nucleotide polymorphism (SNP) loci of the HIF1A gene from three Tibetan groups (Tibet, Qinghai Province and Yunnan Province) were genotyped using PCR-restriction fragment length polymorphism (PCR-RFLP) method. RESULTS: For non-synonymous mutation SNP site, there was no significant difference among the three Tibetan groups, except for SNP rs11549465 between Tibet Tibetan and Yunnan Tibetan, as well as between Qinghai Tibetan and Yunnan Tibetan. Frequencies of genotypes and alleles in rs4899056, rs1957757, rs10873142 and rs3783752 had significant differences between Tibet Tibetan and Yunnan Tibetan, and between Qinghai Tibetan and Yunnan Tibetan (all P<0.05). We also observed that the difference was negatively correlated with the altitude. CONCLUSION: The results suggested that the HIF1A gene might be under hypoxic selection induced by high altitude in the three groups.

[Analysis of the 14 bp insertion/deletion polymorphism in human leukocyte antigen-G gene in Chinese Dai and Han ethnic groups in Yunnan Province].

A 14 bp insertion/deletion polymorphism (+14 bp/-14 bp) in exon 8 of HLA-G gene has been investigated extensively because this polymorphism was associated with HLA-G mRNA stability and could influence HLA-G mRNA expression. In the present study, we genotyped 14 bp insertion/deletion polymorphisms in the HLA-G gene in Dai and Han populations in Yunnan Province. The frequencies of +14 bp in Dai and Han were 31.97% and 40.87%, respectively. The frequency of +14 bp/+14 bp in Dai was lower (8.20%) than that of Han (17.31%). Nevertheless, the frequency of +14 bp/-14 bp was similar in both populations (47.54% in Dai and 47.11% in Han). When compared with other populations, the frequency of 14 bp insertion/deletion of Han was similar to others, whereas the Dai showed significant difference from others and presented it's specific characteristic. We assumed that the distribution characteristic of 14 bp insertion/deletion in Dai might be the results of random genetic drift, but the role of natural selection cannot be excluded.

Distribution of HLA-A, HLA-B, HLA-C, and HLA-DRB1 alleles and haplotypes in Jingpo minority in Yunnan province of China.

HLA-A, HLA-B, HLA-C, and HLA-DRB1 allele frequencies and estimated haplotype frequencies from 105 unrelated healthy Jingpo ethnic subjects who living in Dehong Dai-Jingpo Autonomous Prefectures, Yunnan Province, southwest China has been reported. HLA genes were genotyped by SSOP typing method using Luminex Multi-Analyte Profiling system. Jingpo ethnic nationality belongs to southern group of East Asians, but with its specific HLA alleles and haplotypes characteristic.

Alcohol-related disorders in Beijing, China: prevalence, socio-demographic correlates, and unmet need for treatment.

BACKGROUND: The study aimed to determine the prevalence of alcohol use, episodic heavy drinking, and alcohol dependence and their socio-demographic correlates in Beijing, China. methods: A total of 5,926 subjects were randomly selected in Beijing and interviewed using the Composite International Diagnostic Interview (CIDI 1.0). Data on basic socio-demographic and current major medical conditions were also collected. RESULTS: The 12-month prevalence of alcohol use and episodic heavy drinking were 32.5 and 13.8%, respectively. The 12-month and lifetime prevalence of alcohol dependence were 1.7 and 4.3%, respectively. Age above 24 years, male sex, being married and employed, low education level (junior high school, primary school or illiterate), rural residence, and having comorbid psychiatric disorders were all significantly associated with a higher likelihood of alcohol-related disorders. Only 2.4% of the subjects with alcohol dependence were receiving treatment, and a mere 1.4% had sought treatment from mental health professionals. CONCLUSIONS: Nationwide surveys are urgently needed to further explore the prevalence of alcohol-related disorders in China.

Lifetime prevalence of suicidal ideation, suicide plans and attempts in rural and urban regions of Beijing, China.

OBJECTIVE: There has been no large-scale survey of suicide-related behaviours including suicidal ideations, plans and attempts in China involving both rural and urban areas and using standardized assessment tools. The aim of the present study was to determine the lifetime prevalence of suicide-related behaviour and its relationship with sociodemographic factors and psychiatric disorders in the rural and urban regions of Beijing, China. METHODS: A total of 5926 subjects were randomly selected in Beijing and interviewed using the Composite International Diagnostic Interview. Basic sociodemographic and clinical data and data on suicide-related behaviour were also collected. RESULTS: The overall lifetime prevalence estimates of suicidal ideation, plans and attempts were 2.3%, 1.4%, and 1.0%, respectively; the corresponding figures were 2.8%, 1.6%, and 1.3% in the rural sample, and 1.8%, 1.3%, and 0.9% in the urban sample. Age (>25 years), female sex, unmarried status, lower education level, lower (RMB2000 month(-1)) monthly income and presence of major medical disorders were significantly associated with increased risk of suicide-related behaviour. 36.2% of subjects with suicide-related behavior consulted a medical practitioner and 20.7% consulted a psychiatrist. CONCLUSIONS: The prevalence of lifetime suicide-related behaviour in Beijing is lower than in Western countries, but the low percentage of subjects treated for suicide-related behaviour indicates a major public health problem that should be addressed. National surveys are needed to further explore the prevalence of suicide-related behaviour in China.

[Establishment of immortalized cell lines and genetic stability evaluation for a family with spinocerebellar ataxia type 2].

OBJECTIVE: Immortalized cell lines of spinocerebellar ataxia type 2 (SCA2) with Parkinson disease symptoms were established in order to provide experimental material for future study. METHODS: The immortalized cell lines were constructed by using Epstein Barr virus and cyclosporine A. Microsatellite markers were detected to see whether there is any change between the cell lines and the original blood samples, and the genetic stability of the cell lines were evaluated. RESULTS: Twenty-five immortalized cell lines were established successfully from the family and the microsatellite markers were unchanged. CONCLUSION: The karyotypes of the immortal cell lines were normal and the cell lines were genetically stable.