Association between copy number variations of HLA-DQA1 and ankylosing spondylitis in the Chinese Han population

Single Cell Transcriptome and Surface Epitope Analysis of Ankylosing Spondylitis Facilitates Disease Classification by Machine Learning

Ankylosing spondylitis (AS) is an immune-mediated inflammatory disorder that primarily affects the axial skeleton, especially the sacroiliac joints and spine. This results in chronic back pain and, in extreme cases, ankylosis of the spine. Despite its debilitating effects, the pathogenesis of AS remains to be further elucidated. This study used single cell CITE-seq technology to analyze peripheral blood mononuclear cells (PBMCs) in AS and in healthy controls. We identified a number of molecular features associated with AS. CD52 was found to be overexpressed in both RNA and surface protein expression across several cell types in patients with AS. CD16+ monocytes overexpressed TNFSF10 and IL-18Rα in AS, while CD8+ TEM cells and natural killer cells overexpressed genes linked with cytotoxicity, including GZMH, GZMB, and NKG7. Tregs underexpressed CD39 in AS, suggesting reduced functionality. We identified an overrepresented NK cell subset in AS that overexpressed CD16, CD161, and CD38, as well as cytotoxic genes and pathways. Finally, we developed machine learning models derived from CITE-seq data for the classification of AS and achieved an Area Under the Receiver Operating Characteristic (AUROC) curve of > 0.95. In summary, CITE-seq identification of AS-associated genes and surface proteins in specific cell subsets informs our understanding of pathogenesis and potential new therapeutic targets, while providing new approaches for diagnosis via machine learning.

CNV-MEANN: A Neural Network and Mind Evolutionary Algorithm-Based Detection of Copy Number Variations From Next-Generation Sequencing Data

Copy number variation (CNV), is defined as repetitions or deletions of genomic segments of 1 Kb to 5 Mb, and is a major trigger for human disease. The high-throughput and low-cost characteristics of next-generation sequencing technology provide the possibility of the detection of CNVs in the whole genome, and also greatly improve the clinical practicability of next-generation sequencing (NGS) testing. However, current methods for the detection of CNVs are easily affected by sequencing and mapping errors, and uneven distribution of reads. In this paper, we propose an improved approach, CNV-MEANN, for the detection of CNVs, involving changing the structure of the neural network used in the MFCNV method. This method has three differences relative to the MFCNV method: (1) it utilizes a new feature, mapping quality, to replace two features in MFCNV, (2) it considers the influence of the loss categories of CNV on disease prediction, and refines the output structure, and (3) it uses a mind evolutionary algorithm to optimize the backpropagation (neural network) neural network model, and calculates individual scores for each genome bin to predict CNVs. Using both simulated and real datasets, we tested the performance of CNV-MEANN and compared its performance with those of seven widely used CNV detection methods. Experimental results demonstrated that the CNV-MEANN approach outperformed other methods with respect to sensitivity, precision, and F1-score. The proposed method was able to detect many CNVs that other approaches could not, and it reduced the boundary bias. CNV-MEANN is expected to be an effective method for the analysis of changes in CNVs in the genome.

Evidence for sexual conflict over major histocompatibility complex diversity in a wild songbird

Sex differences in parasite load and immune responses are found across a wide range of animals, with females generally having lower parasite loads and stronger immune responses than males. Intrigued by these general patterns, we investigated if there was any sign of sex-specific selection on an essential component of adaptive immunity that is known to affect fitness, the major histocompatibility complex class I (MHC-I) genes, in a 20-year study of great reed warblers. Our analyses on fitness related to MHC-I diversity showed a highly significant interaction between MHC-I diversity and sex, where males with higher, and females with lower, MHC-I diversity were more successful in recruiting offspring. Importantly, mean MHC-I diversity did not differ between males and females, and consequently neither sex reached its MHC-I fitness optimum. Thus, there is an unresolved genetic sexual conflict over MHC-I diversity in great reed warblers. Selection from pathogens is known to maintain MHC diversity, but previous theory ignores that the immune environments are considerably different in males and females. Our results suggest that sexually antagonistic selection is an important, previously neglected, force in the evolution of vertebrate adaptive immunity, and have implications for evolutionary understanding of costs of immune responses and autoimmune diseases.

Copy number variations of the IL-22 gene are associated with ankylosing spondylitis: A case-control study in Chinese Han population

IL-22 provides a new insight into the mechanisms of autoimmunity, and copy number variations (CNVs) are associated with autoimmune diseases. This study aims to explore the association of IL-22 gene CNVs with ankylosing spondylitis (AS) susceptibility. The copy numbers of IL-22 gene (2 fragments: IL-22_1, IL-22_2) were examined by AccuCopy™ methods in a cohort of 649 AS patients and 628 controls. Association of IL-22 CNVs and AS susceptibility was analyzed, and AS risk was estimated by Odds Ratio (ORs) and 95% confidence intervals (CIs), and the Benjamini-Hochberg method was applied to regulate the false discovery rate (FDR). We found one copy of IL-22 gene was significantly associated with AS [OR=0.345, 95%CI (0.144, 0.827), P=0.013, PFDR=0.026] in the IL-22_2 fragment, and this association still exist after adjustment of age and sex [OR=0.344, 95%CI (0.143, 0.825), P=0.017, PFDR=0.034]. In the stratification analysis by gender, the statistical difference was detected in males in the IL-22_2 fragment [OR=0.306, 95%CI (0.121, 0.778), P=0.009, PFDR=0.018; adjusted OR=0.306, 95%CI (0.120, 0.777), P=0.013, PFDR=0.026]. We suggest that IL-22 CNVs are associated with AS and that lower copy number might be a protective factor for AS, especially in male patients.

Copy Number Variation of HLA-DQA1 and APOBEC3A/3B Contribute to the Susceptibility of Systemic Sclerosis in the Chinese Han Population

OBJECTIVE

Systemic sclerosis (SSc) is a systemic connective tissue disease caused by a genetic aberrant. The involvement of the copy number variations (CNV) in the pathogenesis of SSc is unclear. We tried to identify some CNV that are involved with the susceptibility to SSc.

METHODS

A genome-wide CNV screening was performed in 20 patients with SSc. Five SSc-associated common CNV that included HLA-DRB5, HLA-DQA1, IRGM, CDC42EP3, and APOBEC3A/3B were identified from the screening and were then validated in 365 patients with SSc and 369 matched healthy controls.

RESULTS

Three hundred forty-four CNV (140 gains and 204 losses) and 2 CNV hotspots (6q21.3 and 22q11.2) were found in the SSc genomes (covering 24.2 megabases), suggesting that CNV were ubiquitous in the SSc genome and played important roles in the pathogenesis of SSc. The high copy number of HLA-DQA1 was a significantly protective factor for SSc (OR 0.07, p = 2.99 × 10(-17)), while the high copy number of APOBEC3A/B was a significant risk factor (OR 3.45, p = 6.4 × 10(-18)), adjusted with sex and age. The risk prediction model based on genetic factors in logistic regression showed moderate prediction ability, with area under the curve = 0.80 (95% CI 0.77-0.83), which demonstrated that APOBEC3A/B and HLA-DQA1 were powerful biomarkers for SSc risk evaluation and contributed to the susceptibility to SSc.

CONCLUSION

CNV of HLA-DQA1 and APOBEC3A/B contribute to the susceptibility to SSc in a Chinese Han population.

Interleukin-10 gene polymorphisms are associated with Behcet's disease but not with Vogt-Koyanagi-Harada syndrome in the Chinese Han population

PURPOSE

This study aimed to investigate the association of interleukin (IL)-10 gene polymorphisms with Behcet's disease (BD) and Vogt-Koyanagi-Harada (VKH) syndrome in the Chinese Han population.

METHODS

A two-stage association study was performed on 718 BD patients, 300 VKH patients, and 1,753 controls. Genotyping of the IL-10 gene was performed for six single nucleotide polymorphisms (SNPs), including rs1800871, rs1800872, rs1800896, rs3021094, rs3790622, and rs1554286 using PCR-restricted fragment length polymorphism or TaqMan SNP assays. Real-time PCR was performed to test the IL-10 mRNA expression of the associated polymorphisms.

RESULTS

The first-stage result showed significantly increased frequencies of the rs1800871 T allele, rs1800872 A allele, and rs1554286 T allele in BD patients compared with controls (Pcorrected (Pcorr)=1.82×10(-5), OR=1.837; Pcorr=6.1×10(-5), OR=1.780; Pcorr=3.15×10(-5), OR=1.794, respectively). There was no association of the tested six SNPs with VKH syndrome. A second-stage study was therefore performed in BD patients to validate the result of the first stage, showing a significantly increased frequency of the rs1800871 T allele (Second stage, Pcorr=5.59×10(-5), OR=1.493; Combined data, Pcorr=3.65×10(-11), OR=1.632). Compared to the controls, an increased frequency of the rs1800871 T allele was observed in BD patients with extraocular findings, including genital ulcers, skin lesions, and a positive pathergy test. No difference was found among the mRNA expressions of IL-10 in the peripheral blood mononuclear cells (PBMCs) of controls with different genotypes of rs1800871 after stimulation of lipopolysaccharide (LPS) or anti-CD3/CD28 antibodies.

CONCLUSIONS

The findings showed that IL-10 is a risk gene for BD but not for VKH syndrome.

An update on the contribution of the MHC to AS susceptibility

The 40-year-old association of HLA-B27 with ankylosing spondylitis is one of the best examples of disease association with a hereditary marker. Genomewide association and family studies suggest that other important major histocompatibility complex (MHC) influences are operative in ankylosing spondylitis (AS) susceptibility. HLA-B27 positive hepatitis C individuals are immunologically more efficient in combating viral infections such as HIV-1, hepatitis C, and influenza and less efficient in combating against certain bacteria (and perhaps other organisms) capable of surviving intracellularly. A recent representative population survey of the frequency of HLA-B27 in the USA found a lower frequency of HLA-B27 in older US adults, perhaps reflecting this. Other HLA class I and class II alleles have been implicated in AS susceptibility, the most consistent being HLA-B*40/B60 (B*40:01) but also B14, B15, A*0201, DRB1*04:04, and certain DPA1 and DPB1 alleles. Non-HLA MHC alleles have also been implicated, although many such studies have been inconsistent, likely due to power issues related to the low number of HLA-B27-negative AS patients examined. The best evidence is for major histocompatibility complex class I chain-related gene A (MICA) whose recognition by intestinal epithelial T cells expressing different V-delta-1 gamma/delta TCR further implicates the gut in AS pathogenesis. The HLA class I and class II and other non-HLA allelic associations underscore the importance of T cells in AS pathogenesis.