Novel insight into the genetic signatures of altitude adaptation related body composition in Tibetans.

Background: The Tibetan population residing in high-altitude (HA) regions has adapted to extreme hypoxic environments. However, there is limited understanding of the genetic basis of body compositions in Tibetan population adapted to HA. Methods: We performed a genome-wide association study (GWAS) to identify genetic variants associated with HA and HA-related body composition traits. A total of 755,731 single nucleotide polymorphisms (SNPs) were genotyped using the precision medicine diversity array from 996 Tibetan college students. T-tests and Pearson correlation analysis were used to estimate the association between body compositions and altitude. The mixed linear regression identified the SNPs significantly associated with HA and HA-related body compositions. LASSO regression was used to screen for important SNPs in HA and body compositions. Results: Significant differences were observed in lean body mass (LBW), muscle mass (MM), total body water (TBW), standard weight (SBW), basal metabolic rate (BMR), total protein (TP), and total inorganic salt (Is) in different altitudes stratification. We identified three SNPs in EPAS1 (rs1562453, rs7589621 and rs7583392) that were significantly associated with HA (p < 5 × 10-7). GWAS analysis of 7 HA-related body composition traits, we identified 14 SNPs for LBM, 11 SNPs for TBW, 15 SNPs for MM, 16 SNPs for SBW, 9 SNPs for BMR, 12 SNPs for TP, and 26 SNPs for Is (p < 5.0 × 10-5). Conclusion: These findings provide insight into the genetic basis of body composition in Tibetan college students adapted to HA, and lay the foundation for further investigation into the molecular mechanisms underlying HA adaptation.

Identification of Six Pathogenic Genes for Tibetan Familial Ventricular Septal Defect by Whole Exome Sequencing.

INTRODUCTION: Ventricular septal defect (VSD) is the most common congenital heart malformation in children. This study aimed to investigate potential pathogenic genes associated with Tibetan familial VSD. METHODS: Whole genomic DNA was extracted from eight Tibetan children with VSD and their healthy parents (a total of 16 individuals). Whole-exome sequencing was performed using the Illumina HiSeq platform. After filtration, detection, and annotation, single nucleotide variations and insertion-deletion markers were examined. Comparative evaluations using the Sorting Intolerant from Tolerant, PolyPhen V2, Mutation Taster, and Combined Annotation Dependent Depletion databases were conducted to predict harmful mutant genes associated with the etiology of Tibetan familial VSD. RESULTS: A total of six missense mutations in genetic disease-causing genes associated with the development of Tibetan familial VSD were identified: activin A receptor type II-like 1 (c.652 C > T: p.R218 W), ATPase cation transporting 13A2 (c.1363 C > T: p.R455 W), endoplasmic reticulum aminopeptidase 1 (c.481 G > A: p.G161 R), MRI1 (c.629 G > A: p.R210Q), tumor necrosis factor receptor-associated protein 1 (c.224 G > A: p.R75H), and FBN2 (c.2260 G > A: p.G754S). The Human Gene Mutation Database confirmed activin A receptor type II-like 1, MRI1, and tumor necrosis factor receptor-associated protein 1 as pathogenic mutations, while FBN2 was classified as a probable pathogenic mutation. CONCLUSIONS: This novel study directly screens genetic variations associated with Tibetan familial VSD using whole-exome sequencing, providing new insights into the pathogenesis of VSD.

NOTCH2, ATIC, MRI1, SLC6A13, ATP13A2 Genetic Variations are Associated with Ventricular Septal Defect in the Chinese Tibetan Population Through Whole-Exome Sequencing.

Background: Ventricular septal defect (VSD) is the most common congenital cardiac abnormality in children and the second most common in adults. This study aimed to explore the potentially causative genes in VSD patients in the Chinese Tibetan population, and to provide a theoretical basis for the genetic mechanism of VSD. Methods: Peripheral venous blood was collected from 20 VSD subjects, and whole-genome DNA was extracted. High-throughput sequencing was performed on qualified DNA samples using whole-exome sequencing (WES) technology. After filtering, detecting, and annotating qualified data, single nucleotide variations (SNVs) and insertion-deletion (InDel) markers were analyzed, and data processing software such as GATK, SIFT, Polyphen, and MutationTaster were used for comparative evaluation and prediction of pathogenic deleterious variants associated with VSD. Results: A total of 4793 variant loci, including 4168 SNVs, 557 InDels and 68 unknown loci and 2566 variant genes were obtained from 20 VSD subjects through bioinformatics analysis. According to the screening of the prediction software and database, the occurrence of VSD was predicted to be associated with five inherited pathogenic gene mutations, all of which were missense mutations, including NOTCH2 (c.1396C >A:p.Gln466Lys), ATIC (c.235C >T:p.Arg79Cys), MRI1 (c.629G >A:p.Arg210Gln), SLC6A13 (c.1138G >A:p.Gly380Arg), ATP13A2 (c.1363C >T:p.Arg455Trp). Conclusion: This study demonstrated that NOTCH2, ATIC, MRI1, SLC6A13, ATP13A2 gene variants were potentially associated with VSD in Chinese Tibetan population.

Hypoxia enhances IL-10-producing B cell generation through upregulating high-mobility group B1 on tumor cell-released autophagosomes.

As common features of human solid tumors, hypoxia and nutrient starvation play multifaceted roles in cancer progress. However, the mechanisms are far from clear. Our previous work has indicated that tumor cell-released autophagosomes (TRAPs) are sufficient to suppress anti-tumor immune response in mouse by inducing IL-10-producing B cells through high-mobility group B1 (HMGB1). Here, we hypothesized that hypoxia or starvation might exert immunosuppressive effect through upregulating HMGB1 on TRAPs. We found that HMGB1 on TRAPs from human hepatocellular carcinoma cell line HepG2 played a significant role in IL-10-producing B cell induction. HMGB1 in tumor cells was upregulated under hypoxia and starvation, but only hypoxia significantly enhanced the level of HMGB1 present on the surfaces of TRAPs. Moreover, hypoxic TRAPs induced more IL-10-producing B cells with suppressive activities on CD4+ and CD8+ T cells. The finding indicates the role of TRAPs as a messenger of hypoxic response to enhance immunosuppression in tumor microenvironment.

Association of IL4, IL6, and IL10 polymorphisms with pulmonary tuberculosis in a Tibetan Chinese population.

BACKGROUND: Pulmonary tuberculosis (PTB) is an infectious disease with a high incidence worldwide. Genes encoding cytokines IL4, IL6, and IL10 are highly polymorphic and can influence the susceptibility to PTB. RESULTS: We found correlations between one SNP in IL6 (rs2069837 p = 6.63E-11), seven SNPs in IL10 (rs1554286 p = 6.87E-20, rs1518111 p = 6.11E-11, rs3021094 p = 6.75E-29, rs3790622 p = 2.40E-06, rs3024490 p = 6.73E-11, rs1800872 p = 6.18E-11, rs1800871 p = 6.73E-11) and incidences of PTB. The SNPs rs2069837, rs1554286, rs1518111, rs3024490, rs1800872, and rs1800871 increased PTB risk by 1.95-fold, 2.34-fold, 1.84-fold, 1.84-fold, 1.84-fold and 1.84-fold, respectively. The SNPs rs3021094 and rs3790622 decreased PTB risk by 0.33-fold and 0.38-fold, respectively. We also found two linkage disequilibrium blocks in the studied IL SNPs. The IL4 haplotype TCCCGGA (OR = 1.33, p = 0.014) increased PTB risk, the IL10 haplotypes ATGGATA (OR = 0.39, p = 4.84E-06) provided a protective effect and decreased PTB risk. MATERIALS AND METHODS: For this study, we recruited 467 subjects with PTB and 503 healthy subjects from a Tibetan population living in Lhasa and nearby, China. Association analyses of sixteen single-nucleotide polymorphisms (SNPs) in IL4, IL6, and IL10 were performed. CONCLUSIONS: Our findings demonstrate an association between polymorphisms in IL6 and IL10 and risk of PTB.

Tumor-released autophagosomes induce IL-10-producing B cells with suppressive activity on T lymphocytes via TLR2-MyD88-NF-κB signal pathway.

Recent studies have shown that tumor cells can release autophagosomes, which transport a broad array of biologically active molecules with potential modulatory effects on immune cell functions. In this study, we aimed to investigate the role of tumor cells-released autophagosomes (i.e. TRAP) in regulating B cell differentiation and function. TRAPs from murine tumor cell lines were found to induce splenic B cells to differentiate into IL-10-producing regulatory B cells (Bregs) with a distinct phenotype of CD1d(+) CD5(+), which could potently inhibit CD8(+) and CD4(+) T cell responses in IL-10-depedent manner both in vitro and in vivo. Notably, adoptive transfer of TRAP-induced Bregs abrogated the immune response and antitumor effect induced by OVA-loaded DC vaccinations in E.G7-OVA-bearing mouse model. Mechanistic studies revealed that membrane-bound high-mobility group B1 (HMGB1) on the intact TRAPs was crucial for inducing Breg differentiation via the activation of TLR2-MyD88-NF-κB signal pathway in B cells. Moreover, TRAPs enriched from malignant effusions of cancer patients could induce human B cells to differentiate into IL-10-producing B cells with immunoregulatory functions, the frequency of which were positively correlated with the HMGB1 levels on TRAPs. Together, our findings have demonstrated that TRAPs promote the generation of IL-10(+) Bregs, which may contribute to the suppression of antitumor immunity.

Macrophages enhance tumor-derived autophagosomes (DRibbles)-induced B cells activation by TLR4/MyD88 and CD40/CD40L.

Our previous studies have showed that tumor-derived autophagosomes (termed "DRibbles") induce B cell activation, resulting in antibody production and cytokine secretion. Unexpectedly, we found that unfractionated splenocytes produced a higher level of antibody and cytokine than that of purified B cells. In the current study, we investigated the role of accessory cells in DRibbles-induced B cell activation. We found that cognate macrophages, but not T cells, significantly enhanced the B cell activities. Such an enhancement required cell-cell contact. Furthermore, DRibbles stimulation up-regulated CD40L expression on macrophages, resulting in increased level of CD40 expressed on B cells. The accessory role of macrophages in DRibbles-activated B cells is critically dependent on the CD40/CD40L interaction. In addition, the effects of macrophages were found to be largely dependent on TLR4 and MyD88 signaling pathway. Finally, our results showed that macrophages were able to enhance the antigen presentation function of B cells for specific T cell stimulation. Thus, these results suggest that macrophages play an important accessory role for DRibbles-induced B cell immune function.