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HLA‐DQB2 is a gene of limited polymorphism, with unknown function that presents at least two transcript variants: v1, which encodes the full‐length beta‐chain, and v2, which lacks exon 4 and could give rise to a soluble protein. We previously showed a strong correlation between high v2 expression in preimplantation biopsies (PIB) of kidneys from young (18‐ to 49‐year olds) but not from old, deceased donors and 1‐year posttransplant low (estimated glomerular filtration rate < 45 ml/min/1.73 m2) graft function (GF). In this study, we aimed to investigate the impact of posttransplant soluble HLA‐DQB2 (sDQB2) serum levels, v1 expression in PIB, and recipient HLA‐DQB2 rs7453920 A/G polymorphism on GF. sDQB2 was evaluated by enzyme‐linked immunosorbent assay in sera from 114 recipients, collected at least 1 year (median 2.1 years) after transplantation. Higher sDQB2 levels were observed in recipients of kidneys from young, but not from old, donors that had a ≥30% decline in GF within 1 year after blood collection for sDQB2 determination. Among the 15 recipients of kidneys from young donors with sDQB2 ≥ 1.52 ng/ml, 40% presented a ≥30% decline in GF, whereas this occurred in none of the 43 recipients with lower sDQB2 levels (p = 0.007; OR: 36.5). Expression of HLA‐DQB2 variant 1, measured by reverse transcription‐polymerase chain reaction (RT‐PCR) in 92 PIB from young or old donors, did not significantly differ between transplants with high or low 4‐year GF. HLA‐DQB2 rs7453920 single nucleotide polymorphism (SNP) frequencies did not significantly differ between recipients with low or high 4‐year GF. We conclude that HLA‐DQB2 variant 1 expression in PIB and recipient rs7453920 SNP polymorphism are not associated with graft outcome. On the other hand, the association, in transplants of kidneys from young donors, between high posttransplant serum sDQB2 levels and decline in GF is a very interesting finding that deserves a validation study in a larger cohort. [ABSTRACT FROM AUTHOR]

Background: Accurate pre-transplant prediction of late graft function remains an unmet need in kidney transplantation. The aim of this study was to evaluate HLA genes expression levels in pre-implantation biopsies (PIB) of deceased donor kidneys as markers for long-term graft outcome. Methods: HLA genes expression analysis was initially performed using microarray data of 53 PIB, previously generated by our laboratory. The validation analysis was performed by real-time PCR in 116 PIB from an independent cohort. Results: The microarray data showed association between high expression levels of HLA class II genes, especially HLA-DQB1 and -DQB2, in kidneys from young (18 to 49-year-old) donors and poor (eGFR < 45 mL/min/1.73 m 2 ) 1- and 5-year graft function. A subsequent study in an independent cohort, in which only HLA-DQB2 expression was evaluated, validated the association between increased HLA-DQB2 expression in PIB of kidneys from young donors and poor 1-year graft function: expression levels ≥0.0025 relative units conferred an odds ratio of 22.5, with positive and negative predictive values of 71.4% and 90.0%, respectively. Conclusion: Heightened expression of HLA-DQB1 and -DQB2 in PIB are promising tools for pre-transplant risk assessment of poor late graft function in transplants with kidneys from 18 to 49-year-old donors. [ABSTRACT FROM AUTHOR]

The purpose of this study was to investigate possible markers for predicting delayed graft function (DGF). To this end we analyzed, in pre-implantation biopsies (PIB) and in first-day post-Tx peripheral blood mononuclear cells (PBMC), the expression of five genes ( ACSL4 , CUBN , DEFB1 , FABP3 , GK ) through real-time TaqMan PCR assays. These genes were selected from a large scale gene expression study in PIB. DEFB1 , FABP3 and GK expression levels in PIB were lower in cases with DGF and, in a multivariate analysis which included these genes and clinical variables, only FABP3 expression remained independently associated with DGF. FABP3 expression lower than −1.32 units of relative expression conferred an odds ratio for DGF of 41.1. Compared to the PBMC of recipients without DGF, recipients with prolonged DGF (pDGF) had lower ACSL4 and higher DEFB1 expression levels. In a multivariate analysis, including PBMC gene expression levels of ACSL4 , DEFB1 and TLR4 (data from a previous study with the same patients) and clinical variables, only TLR4 remained independently associated with pDGF. In summary, this study revealed FABP3 expression in PIB as a marker for DGF and disclosed new genes possibly involved in the pathogenesis of DGF. [ABSTRACT FROM AUTHOR]

Highlights from the article: We have previously showed that decreased FABP3 expression, in preimplantation kidney biopsies (PIB), was associated with delayed graft function (DGF) (Mourão et al., 2016). In a multivariate analysis, including clinical variables related to DGF, as well as FABP3 expression, only TMEM52B expression (p = 0.010) and donor last creatinine (DCr) (p = 0.001) remained independently associated with DGF.

The purpose of this single center retrospective study was to investigate the relationship between HLA and ABO polymorphisms and COVID‐19 susceptibility and severity in kidney transplant recipients. It included 720 recipients who had COVID‐19 and 1680 controls composed by recipients in follow‐up who did not contact the transplantation center for COVID‐19 symptoms, up to the moment of their inclusion in the study. HLA‐A, ‐B, and ‐DRB1 allele groups and ABO frequencies were compared between recipients with COVID‐19 (all cases, or separately mild/moderate and severe disease) and controls. The HLA association study was conducted in two case–control series and only associations that showed a p‐value <0.05 in both series were considered. No HLA association regarding COVID‐19 occurrence or severity met this criterion. Homozygosity at HLA‐A locus was associated with COVID‐19 susceptibility (odds ratio 1.4) but not severity. Blood groups A and O were associated with susceptibility and resistance to COVID‐19, respectively. COVID‐19 severity was associated only with older age and cardiac disease, in a multivariate analysis. We conclude that an influence of HLA on COVID‐19 susceptibility is supported by the association with homozygosity at HLA‐A locus but that there is no evidence for a role of any particular HLA‐A, ‐B, or ‐DRB1 polymorphism. Thus, we suggest that what matters is the overall capability of an individual's HLA molecules to present SARS‐CoV‐2 peptides to T cells, a factor that might have a great influence on the breadth of the immune response. [ABSTRACT FROM AUTHOR]

Aim The aim of this study was to investigate the expression of HLA genes in pre-implantation kidney biopsies (PIB) in relation to graft function after kidney transplantation (Tx) from deceased donors. Methods The analyses were performed using the expression data of PIB from our previous microarray study (paper in submission). Herein we analyzed the expression of HLA class I (A, B, C) and class II (DRA, DQA1, DQB1, DQA2, DQB2, DPA1, DPB1) genes in relation to delayed graft function (DGF) occurrence (27 cases with and 27 without) and graft dysfunction (estimated creatinine clearance ⩽ 45 mL/min) at 1 year (y) post-Tx (10 cases with and 41 cases without graft dysfunction). Finally, the genes were tested in an independent data set from the literature. Results No differences in expression levels of any HLA gene were observed in cases with or without DGF. HLA-B and HLA-C were not differentially expressed between kidneys that presented deteriorated or stable renal function at 1y. On the other hand, kidneys that presented deteriorated function at 1y post-Tx had significantly higher expression of HLA-A ( p = 0.02), -DRA ( p = 0.003), -DQA1 ( p = 0.002), -DQB1 ( p = 0.00002), HLA-DQA2 ( p = 0.0008), -DQB2 ( p = 0.00005), -DPA1 ( p = 0.02), -DPB1 ( p = 0.0006). All these genes, with the exception of HLA-DQA2, were represented in the microarray study performed by Park et al, 2010, in biopsies collected at 1y post-Tx and were also associated with poor outcome, represented by biopsies with interstitial fibrosis/tubular atrophy (IF/TA) and inflammation. Conclusion The association between increased expression of HLA genes in PIB and poor renal function at 1y post-Tx is consistent with the assumption that heightened expression of HLA genes contributes to increase allograft immunogenicity and consequently lowers long-term graft function and survival. Interestingly, among the genes with increased expression were the HLA-DQA2 and -DQB2 genes, whose normal expression pattern has not yet been determined. [ABSTRACT FROM AUTHOR]

Abstract: Lymphotoxin alpha (LTA) is a member of the TNF cytokine superfamily, produced principally by lymphocytes. It plays an important role in immune and inflammatory responses. Many TNF superfamily members have functionally important isoforms generated by alternative splicing but alternative splicing of LTA has never been studied. The known LTA protein is encoded by a transcript containing four exons. Here we report seven new LTA splice variants, three of them evolutionary conserved. We demonstrate their presence in cytoplasmic RNA suggesting that they could be translated into new LTA isoforms. We observed that their expression is differentially regulated upon activation of peripheral blood mononuclear cells and lymphocyte subpopulations (CD4+, CD8+, and CD19+). Our data suggest that the new LTA splice variants might play a role in the regulation of the immune response. [Copyright &y& Elsevier]

Various single nucleotide polymorphisms (SNPs) have been investigated regarding association with gene expression levels or human diseases. Although different SNPs within one gene are frequently analyzed individually, it is highly probable that in the majority of the cases, a precise combination of SNP alleles, i.e., haplotype, determines a functional trait. Methods commonly used for haplotype determination, involving studies in families, cloning, or somatic cell hybrids, are expensive and time-consuming. We herein suggest a novel and simple strategy for haplotype determination, involving selective haplotype depletion with a restriction enzyme, followed by sequencing. We studied 11 LTA gene polymorphisms in 102 Brazilian individuals, and we applied this novel methodology for haplotyping 67 out of 70 LTA heterozygous individuals. We concluded that the method is rapid and efficient, and, as it includes only simple and widespread-used techniques, it could be used in most of the laboratories without further investment in equipments. The wider usage of haplotyping could be important to clarify contradictory results frequently observed among studies that focus on a single SNP. [ABSTRACT FROM AUTHOR]

Background: Gene covariation networks are commonly used to study biological processes. The inference of gene covariation networks from observational data can be challenging, especially considering the large number of players involved and the small number of biological replicates available for analysis. Results: We propose a new statistical method for estimating the number of erroneous edges in reconstructed networks that strongly enhances commonly used inference approaches. This method is based on a special relationship between sign of correlation (positive/negative) and directionality (up/down) of gene regulation, and allows for the identification and removal of approximately half of all erroneous edges. Using the mathematical model of Bayesian networks and positive correlation inequalities we establish a mathematical foundation for our method. Analyzing existing biological datasets, we find a strong correlation between the results of our method and false discovery rate (FDR). Furthermore, simulation analysis demonstrates that our method provides a more accurate estimate of network error than FDR. Conclusions: Thus, our study provides a new robust approach for improving reconstruction of covariation networks. [ABSTRACT FROM AUTHOR]

Background: DAPfinder and DAPview are novel BRB-ArrayTools plug-ins to construct gene coexpression networks and identify significant differences in pairwise gene-gene coexpression between two phenotypes. Results: Each significant difference in gene-gene association represents a Differentially Associated Pair (DAP). Our tools include several choices of filtering methods, gene-gene association metrics, statistical testing methods and multiple comparison adjustments. Network results are easily displayed in Cytoscape. Analyses of glioma experiments and microarray simulations demonstrate the utility of these tools. Conclusions: DAPfinder is a new friendly-user tool for reconstruction and comparison of biological networks. [ABSTRACT FROM AUTHOR]