Maneesh Kumar Misra

All Publications

• Editorial: HLA in personalized medicine. Frontiers in Genetics Misra, M. K., Mostafa, A., Charron, D. 2024; 15: 1480936

  View details for DOI 10.3389/fgene.2024.1480936

  View details for PubMedCentralID PMC11385277

• Next-generation sequencing identifies two novel HLA-DPB1 alleles: HLA-DPB1*1069:01 and DPB1*1072:01. HLA Misra, M. K., Brown, N. K., Marino, S. G. 2024; 103 (2): e15368

  Abstract

  Characterization of two novel HLA-DPB1 alleles: HLA-DPB1*1069:01, and DPB1*1072:01 containing non-synonymous nucleotide substitutions.

  View details for DOI 10.1111/tan.15368

  View details for PubMedID 38342772

• Identification of Candidate mRNA Genes and Their Potential MicroRNA Targets in Lung Cancer Induced by Smoking Tobacco. Frontiers in bioscience (Scholar edition) Mishra, A. K., Mumtaz, N., Misra, M. K. 2023; 15 (4): 13

  Abstract

  Smoking is considered the single highest risk factor for lung cancer and has been suggested to be associated with accelerated somatic mutations in respiratory mucosa that lead to the development of lung cancer. MicroRNAs serve as modulators in smoking-induced mRNA gene expression changes in the human airway epithelium and are linked to the development of lung cancer. The thermodynamics in the microRNA (miRNA)-mRNA interactions may be affected in tobacco smokers, consequently, leading to phenotypic variations in lung cancer patients. Therefore, this study aimed to investigate the impact of smoking tobacco on somatic mutations in mRNA genes and assess their potential impact on miRNA-mRNA interactions in lung cancers.The clinically significant pathogenic variants in mRNA genes in the dataset in lung cancer cases linked to smoking tobacco (n = 330) were obtained from the Cancer Atlas database (TCGA, http://cancergenome.nih.gov/) and used to assess the potential role of tobacco consumption in driving the genetic alterations in proto-oncogenes associated with lung cancer. The analysis of the miRNA interaction with the top five altered mRNA proto-oncogenes in lung cancer cases due to tobacco consumption was performed using the target prediction function in the miRDP program (Database version 5.2.3.1, https://mirdb.org/).We identified the top five mRNA proto-oncogenes enriched with simple somatic mutations (SSM) in lung cancer were TP53, EGFR, KRAS, FAT4, and KMT2D. Interestingly, we observed the highest incidence of SSM in the Tumor Protein p53 (TP53) gene at 63.64%. Similarly, the SSM incidence was 23.94% in the Epidermal Growth Factor Receptor (EGFR), 22.12% in the Kirsten Rat Sarcoma Viral Oncogene Homolog (KRAS), 18.48% in the FAT Atypical Cadherin 4 (FAT4), and 14.24% in the Lysine (K)-Specific Methyltransferase 2D (KMT2D) genes. Subsequently, we used a bioinformatics approach to assess the effect of miRNA-mRNA interactions in lung cancer among the top five SSM-enriched mRNA proto-oncogenes. Among the top 20 identified and selected miRNAs, we observed 18 unique microRNAs that bind specifically to TP53, KRAS, and FAT4 genes and 17 and 19 microRNAs that exclusively bind with the EGFR and KMT2D genes, respectively.Our study found that the top five SSM-enriched mRNA proto-oncogenes in lung cancers among tobacco smokers were TP53, EGFR, KRAS, FAT4, and KMT2D. Further, our results provide an important insight into the involvement of the intricate network of mRNA-miRNA interactions in the development of lung cancer.

  View details for DOI 10.31083/j.fbs1504013

  View details for PubMedID 38163953

• Exceptional diversity of KIR and HLA class I in Egypt. HLA Montero-Martin, G., Kichula, K. M., Misra, M. K., de Brito Vargas, L., Marin, W. M., Hollenbach, J. A., Fernandez-Vina, M. A., Elfishawi, S., Norman, P. J. 2023

  Abstract

  Genetically determined variation of killer cell immunoglobulin like receptors (KIR) and their HLA class I ligands affects multiple aspects of human health. Their extreme diversity is generated through complex interplay of natural selection for pathogen resistance and reproductive health, combined with demographic structure and dispersal. Despite significant importance to multiple health conditions of differential effect across populations, the nature and extent of immunogenetic diversity is under-studied for many geographic regions. Here, we describe the first high-resolution analysis of KIR and HLA class I combinatorial diversity in Northern Africa. Analysis of 125 healthy unrelated individuals from Cairo in Egypt yielded 186 KIR alleles arranged in 146 distinct centromeric and 79 distinct telomeric haplotypes. The most frequent haplotypes observed were KIR-A, encoding two inhibitory receptors specific for HLA-C, two that are specific for HLA-A and -B, and no activating receptors. Together with 141 alleles of HLA class I, 75 of which encode a KIR ligand, we identified a mean of six distinct interacting pairs of inhibitory KIR and HLA allotypes per individual. We additionally characterize 16 KIR alleles newly identified in the study population. Our findings place Egyptians as one of the most highly diverse populations worldwide, with important implications for transplant matching and studies of immune-mediated diseases.

  View details for DOI 10.1111/tan.15177

  View details for PubMedID 37528739

• Spherotech-EDTA combined serum treatment reduces background more effectively as compared to One Lambda Adsorb Out™ and LIFECODES Serum Cleaner in Luminex-based solid-phase immunoassays for HLA antibody detection. HLA Misra, M. K., Weidner, J. G., Upchurch, R. L., Mankey, A. M., Fernandez-Viña, M. A., Marino, S. G. 2023

  Abstract

  Spherotech (SPT) microparticles capture non-specific binding materials present in test serum, and EDTA removes the so called" prozone effect". This study presents a novel approach of combined SPT-EDTA serum treatment prior to Luminex HLA antibody testing to remove high background, and prozone effect in a single step process, and compared the efficacy of SPT-EDTA serum pre-treatment with AdsorbOut (ADS) and Serum Cleaner (SC) to reduce background in solid phase immunoassays (SPI). A total of 21 serum samples with a history of elevated negative control (NC) values ≥500, and 20 samples with normal NC values were included to assess the potential adverse effects. A problem of high background was noted in 25% of our samples in SPI. We observed 80% effectiveness in reducing NC values <500 with SPT-EDTA serum pre-treatment compared to 72%, and 67% for ADS and SC-treated sera, respectively. Interestingly, we found a strong correlation in antibody-binding levels between SPT versus ADS; and ADS versus SC-treated sera for both phenotype and single antigen bead assays (p < 0.001). No adverse effect was noted on NC, positive control (PC) values, PC/NC ratios in the upfront use of SPT-EDTA as compared to EDTA alone. Our data revealed that combined SPT-EDTA treated sera is more effective than ADS, and SC in reducing high background in SPI. Taken together, SPT-EDTA serum treatment prior to Luminex HLA Ab testing is cost-effective, our laboratory saves nearly 30% of the annual total cost for Ab testing and improved test turnaround time by two business days.

  View details for DOI 10.1111/tan.15024

  View details for PubMedID 36961354

• A splice acceptor variant in HLA-DRA affects the conformation and cellular localization of the class II DR alpha-chain. Immunology Didonna, A., Damotte, V., Shams, H., Matsunaga, A., Caillier, S. J., Dandekar, R., Misra, M. K., Mofrad, M. R., Oksenberg, J. R., Hollenbach, J. A. 2021; 162 (2): 194-207

  Abstract

  Class II human leucocyte antigen (HLA) proteins are involved in the immune response by presenting pathogen-derived peptides to CD4+ T lymphocytes. At the molecular level, they are constituted by α/β-heterodimers on the surface of professional antigen-presenting cells. Here, we report that the acceptor variant (rs8084) in the HLA-DRA gene mediates the transcription of an alternative version of the α-chain lacking 25 amino acids in its extracellular domain. Molecular dynamics simulations suggest this isoform undergoes structural refolding which in turn affects its stability and cellular trafficking. The short HLA-DRA isoform cannot reach the cell surface, although it is still able to bind the corresponding β-chain. Conversely, it remains entrapped within the endoplasmic reticulum where it is targeted for degradation. Furthermore, we demonstrate that the short isoform can be transported to the cell membrane via interactions with the peptide-binding site of canonical HLA heterodimers. Altogether, our findings indicate that short HLA-DRA functions as a novel intact antigen for class II HLA molecules.

  View details for DOI 10.1111/imm.13273

  View details for PubMedID 32986852

  View details for PubMedCentralID PMC7808164

• Effective desensitization for a strong donor-specific HLA antibody in a case of HLA-mismatched allogeneic hematopoietic cell transplantation. HLA Misra, M. K., Xin, J. J., Brown, N. K., Weidner, J. G., Upchurch, R. L., Bishop, M. R., Wool, G. D., Artz, A. S., Marino, S. R. 2019; 94 (3): 307-311

  Abstract

  We describe a unique ABO compatible and 9/10 HLA-matched case of successful allogeneic hematopoietic cell transplantation (HCT) after effective desensitization of a strong anti-HLA-A24 donor-specific antibody (DSA) with mean fluorescence intensity of approximately 18 000. Due to absence of a suitable matched unrelated donor the patient sibling was considered the best available donor, and it was decided to desensitize patient prior to transplant. The strength of HLA-A24 DSA slowly decreased over the course of treatment, necessitating a total of 23 sessions of therapeutic plasma exchange in order to bring the DSA strength to undetectable levels, followed by a successful transplant. In summary, the outcome of this case shows effective application of desensitization treatment to remove strong DSA in HCT patients.

  View details for DOI 10.1111/tan.13627

  View details for PubMedID 31314169

• A specific amino acid motif of HLA-DRB1 mediates risk and interacts with smoking history in Parkinson's disease. Proceedings of the National Academy of Sciences of the United States of America Hollenbach, J. A., Norman, P. J., Creary, L. E., Damotte, V., Montero-Martin, G., Caillier, S., Anderson, K. M., Misra, M. K., Nemat-Gorgani, N., Osoegawa, K., Santaniello, A., Renschen, A., Marin, W. M., Dandekar, R., Parham, P., Tanner, C. M., Hauser, S. L., Fernandez-Vina, M., Oksenberg, J. R. 2019

  Abstract

  Parkinson's disease (PD) is a neurodegenerative disease in which genetic risk has been mapped to HLA, but precise allelic associations have been difficult to infer due to limitations in genotyping methodology. Mapping PD risk at highest possible resolution, we performed sequencing of 11 HLA genes in 1,597 PD cases and 1,606 controls. We found that susceptibility to PD can be explained by a specific combination of amino acids at positions 70-74 on the HLA-DRB1 molecule. Previously identified as the primary risk factor in rheumatoid arthritis and referred to as the "shared epitope" (SE), the residues Q/R-K/R-R-A-A at positions 70-74 in combination with valine at position 11 (11-V) is highly protective in PD, while risk is attributable to the identical epitope in the absence of 11-V. Notably, these effects are modified by history of cigarette smoking, with a strong protective effect mediated by a positive history of smoking in combination with the SE and 11-V (P = 10-4; odds ratio, 0.51; 95% confidence interval, 0.36-0.72) and risk attributable to never smoking in combination with the SE without 11-V (P = 0.01; odds ratio, 1.51; 95% confidence interval, 1.08-2.12). The association of specific combinations of amino acids that participate in critical peptide-binding pockets of the HLA class II molecule implicates antigen presentation in PD pathogenesis and provides further support for genetic control of neuroinflammation in disease. The interaction of HLA-DRB1 with smoking history in disease predisposition, along with predicted patterns of peptide binding to HLA, provide a molecular model that explains the unique epidemiology of smoking in PD.

  View details for PubMedID 30910980

• Structure-based selection of human metabolite binding P4 pocket of DRB1*15:01 and DRB1*15:03, with implications for multiple sclerosis. Genes and immunity Misra, M. K., Damotte, V., Hollenbach, J. A. 2019; 20 (1): 46-55

  Abstract

  Binding of small molecules in the human leukocyte antigen (HLA) peptide-binding groove may result in conformational changes of bound peptide and an altered immune response, but previous studies have not considered a potential role for endogenous metabolites. We performed virtual screening of the complete Human Metabolite Database (HMDB) for docking to the multiple sclerosis (MS) susceptible DRB1*15:01 allele and compared the results to the closely related yet non-susceptible DRB1*15:03 allele; and assessed the potential impact on binding of human myelin basic peptide (MBP). We observed higher energy scores for metabolite binding to DRB1*15:01 than DRB1*15:03. Structural comparison of docked metabolites with DRB1*15:01 and DRB1*15:03 complexed with MBP revealed that PhenylalanineMBP92 allows binding of metabolites in the P4 pocket of DRB1*15:01 but ValineMBP89 abrogates metabolite binding in the P1 pocket. We observed differences in the energy scores for binding of metabolites in the P4 pockets of DRB1*15:01 vs. DRB1*15:03 suggesting stronger binding to DRB1*15:01. Our study confirmed that specific, disease-associated human metabolites bind effectively with the most polymorphic P4 pocket of DRB1*15:01, the primary MS susceptible allele in most populations. Our results suggest that endogenous human metabolites bound in specific pockets of HLA may be immunomodulatory and implicated in autoimmune disease.

  View details for DOI 10.1038/s41435-017-0009-5

  View details for PubMedID 29362509

  View details for PubMedCentralID PMC6054566

• Report from the Killer-cell Immunoglobulin-like Receptors (KIR) component of the 17th International HLA and Immunogenetics Workshop. Human immunology Misra, M. K., Augusto, D. G., Martin, G. M., Nemat-Gorgani, N., Sauter, J., Hofmann, J. A., Traherne, J. A., Gonzalez-Quezada, B., Gorodezky, C., Bultitude, W. P., Marin, W., Vierra-Green, C., Anderson, K. M., Balas, A., Caro-Oleas, J. L., Cisneros, E., Colucci, F., Dandekar, R., Elfishawi, S. M., Fernandez-Vina, M. A., Fouda, M., Gonzalez-Fernandez, R., GroSSe, A., Herrero-Mata, M. J., Hollenbach, S. Q., Marsh, S. G., Mentzer, A., Middleton, D., Moffett, A., Moreno-Hidalgo, M. A., Mossallam, G. I., Nakimuli, A., Oksenberg, J. R., Oppenheimer, S. J., Parham, P., Petzl-Erler, M., Planelles, D., Sanchez-Garcia, F., Sanchez-Gordo, F., Schmidt, A. H., Trowsdale, J., Vargas, L. B., Vicario, J. L., Vilches, C., Norman, P. J., Hollenbach, J. A. 2018

  Abstract

  The goals of the KIR component of the 17th International HLA and Immunogenetics Workshop (IHIW) were to encourage and educate researchers to begin analyzing KIR at allelic resolution, and to survey the nature and extent of KIR allelic diversity across human populations. To represent worldwide diversity, we analyzed 1269 individuals from ten populations, focusing on the most polymorphic KIR genes, which express receptors having three immunoglobulin (Ig)-like domains (KIR3DL1/S1, KIR3DL2 and KIR3DL3). We identified 13 novel alleles of KIR3DL1/S1, 13 of KIR3DL2 and 18 of KIR3DL3. Previously identified alleles, corresponding to 33 alleles of KIR3DL1/S1, 38 of KIR3DL2, and 43 of KIR3DL3, represented over 90% of the observed allele frequencies for these genes. In total we observed 37 KIR3DL1/S1 allotypes, 40 for KIR3DL2 and 44 for KIR3DL3. As KIR allotype diversity can affect NK cell function, this demonstrates potential for high functional diversity worldwide. Allelic variation further diversifies KIR haplotypes. We determined KIR3DL3  KIR3DL1/S1  KIR3DL2 haplotypes from five of the studied populations, and observed multiple population-specific haplotypes in each. This included 234 distinct haplotypes in European Americans, 191 in Ugandans, 35 in Papuans, 95 in Egyptians and 86 in Spanish populations. For another 35 populations, encompassing 642,105 individuals we focused on KIR3DL2 and identified another 375 novel alleles, with approximately half of them observed in more than one individual. The KIR allelic level data gathered from this project represents the most comprehensive summary of global KIR allelic diversity to date, and continued analysis will improve understanding of KIR allelic polymorphism in global populations. Further, the wealth of new data gathered in the course of this workshop component highlights the value of collaborative, community-based efforts in immunogenetics research, exemplified by the IHIW.

  View details for PubMedID 30321631

• The immunogenetics of neurological disease. Immunology Misra, M. K., Damotte, V., Hollenbach, J. A. 2018; 153 (4): 399-414

  Abstract

  Genes encoding antigen-presenting molecules within the human major histocompatibility complex (MHC) account for the highest component of genetic risk for many neurological diseases, such as multiple sclerosis, neuromyelitis optica, Parkinson's disease, Alzheimer's disease, schizophrenia, myasthenia gravis and amyotrophic lateral sclerosis. Myriad genetic, immunological and environmental factors may contribute to an individual's susceptibility to neurological disease. Here, we review and discuss the decades long research on the influence of genetic variation at the MHC locus and the role of immunogenetic killer cell immunoglobulin-like receptor (KIR) loci in neurological diseases, including multiple sclerosis, neuromyelitis optica, Parkinson's disease, Alzheimer's disease, schizophrenia, myasthenia gravis and amyotrophic lateral sclerosis. The findings of immunogenetic association studies are consistent with a polygenic model of inheritance in the heterogeneous and multifactorial nature of complex traits in various neurological diseases. Future investigation is highly recommended to evaluate both coding and non-coding variation in immunogenetic loci using high-throughput high-resolution next-generation sequencing technologies in diverse ethnic groups to fully appreciate their role in neurological diseases.

  View details for DOI 10.1111/imm.12869

  View details for PubMedID 29159928

  View details for PubMedCentralID PMC5838423

• Co-stimulatory CD28 and transcription factor NFKB1 gene variants affect idiopathic recurrent miscarriages. Journal of human genetics Misra, M. K., Singh, B., Mishra, A., Agrawal, S. 2016; 61 (12): 1035-1041

  Abstract

  Co-stimulatory CD28 and transcription factor NFKB1 genes are considered as a crucial player in the determination of inflammatory responses; genetic variability in these may modulate the risk for idiopathic recurrent miscarriages (IRM). We investigated the association of functional variants of CD28 (rs3116496 T/C) and NFKB1 (rs28362491 ins/del and rs696 A/G) with IRM cases. We recruited 200 IRM women with a history of at least three consecutive pregnancy losses before 20th week of pregnancy and 300 fertile control women. Determination of CD28 (rs3116496 T/C) and NFKB1 (rs28362491 ins/del and rs696 A/G) gene variants were based on the polymerase chain reaction pursued by restriction fragment length polymorphism analysis and validated with Sanger sequencing. Single marker analysis and multifactor dimensionality reduction (MDR) model used to predict the IRM risk. We observed nearly three- to twofold increased risk in single marker analysis for minor homozygous genotypes of rs3116496 T/C, rs28362491 ins/del and rs696 A/G tag-SNPs in IRM cases, suggesting the risk association. In MDR analysis, we observed 10.5-fold augmented risk among IRM women in three-SNP model (rs3116496 T/C, rs28362491 ins/del and rs696 A/G). The eQTL mapping analyses was performed to strengthen the results of our study. The eQTL mapping analysis revealed that the variations in CD28 and NFKB1 gene content might affect the abundance of transcripts of CD28 and Family with sequence similarity 177 member A1 (FAM177A1) genes, respectively. These results suggest that CD28 and NFKB1 gene variants may be associated with increased risks to IRM.

  View details for DOI 10.1038/jhg.2016.100

  View details for PubMedID 27488439

• Association of functional genetic variants of CTLA4 with reduced serum CTLA4 protein levels and increased risk of idiopathic recurrent miscarriages. Fertility and sterility Misra, M. K., Mishra, A., Phadke, S. R., Agrawal, S. 2016; 106 (5): 1115-1123.e6

  Abstract

  To determine whether idiopathic recurrent miscarriages (IRM) are associated with the alteration in serum CTLA4 protein levels and to evaluate their correlation with CTLA4 tag single-nucleotide polymorphisms (SNPs).Retrospective case-control study.Tertiary-care referral hospital.Three hundred women with IRM (mean age: 28.6 ± 5.4 years) and 600 age-matched (mean age: 29.2 ± 6.8) control women.Detection of genetic variants of CTLA4 markers rs231775, rs5742909, rs11571317, rs16840252, rs4553808, and rs3087243 by polymerase chain reaction followed by restriction fragment length polymorphism analysis and validated through DNA sequencing, and CTLA4 serum levels measured by enzyme-linked immunosorbent assay.Serum CTLA4 levels, genotypes, and haplotype frequencies compared in IRM cases versus controls.We observed statistically significantly higher occurrence of minor allele homozygous of rs231775 and rs3087243 tag-SNPs in IRM cases, which suggests a risk association. A statistically significantly reduced level of CTLA4 protein was seen for mutant genotypes of rs231775 and rs3087243 tag-SNPs in women with IRM, revealing a risk association. Serum CTLA4 levels were statistically significantly reduced in women with IRM as compared with the control women. The mutant haplotype carriers of six studied tag-SNPs showed 2.34-fold higher frequencies in IRM cases. In silico analyses strengthened our observations and suggested that variation in CTLA4 gene content may influence the expression of this gene and directly or indirectly influence the function of other genes in the protein-protein interaction pathway.These results suggest an effect of CTLA4 gene variants, with reduced sCTLA4 secretion and an increased risk for IRM. Reduced CTLA4 secretion and specific CTLA4 variants may contribute to the pathogenesis of IRM.

  View details for DOI 10.1016/j.fertnstert.2016.06.011

  View details for PubMedID 27351445

• Association of functional genetic variants of transcription factor Forkhead Box P3 and Nuclear Factor-κB with end-stage renal disease and renal allograft outcome. Gene Misra, M. K., Mishra, A., Pandey, S. K., Kapoor, R., Sharma, R. K., Agrawal, S. 2016; 581 (1): 57-65

  Abstract

  The transcription factor FOXP3 and NF-κB regulates the expression of various genes that play an important role in the regulation of renal inflammation. We investigated the association of FOXP3 (rs2232365, rs3761548, rs5902434 and rs2294021) and NF-κB1 (rs28362491 and rs696) gene variants in susceptibility and prognosis of end stage renal disease (ESRD) and renal allograft outcome.We genotyped four common polymorphisms of FOXP3 and two-tag SNPs of NF-κB1 genes in 350 ESRD cases and 350 controls. Single marker analysis and SNP-SNP interaction model (one to six way combinations) was used for determination of clinical outcome of ESRD and acute rejection episode (ARE).We observed significantly higher occurrence of mutant genotypes of tag-SNPs of FOXP3 namely; rs2232365 and rs3761548 along with NF-kB1 namely; rs28362491 and rs696 in ESRD and ARE cases, suggested a risk association for ESRD and ARE. Interestingly, multifactor dimension reduction analysis suggested an increased risks of nearly 6-folds for ESRD and 23-folds for ARE cases under the six factors model which consists of tag-SNPs of FOXP3 (rs2232365, rs3761548, rs5902434 and rs2294021) and NF-kB1 (rs28362491 and rs696). Kaplan-Meier survival analysis showed the lowest overall survival for mutant genotypes compared with wild and heterozygous genotypes of rs2232365 and rs3761548 tag SNPs of FOXP3 as well as NF-kB1 tag-SNPs rs28362491 and rs696 in renal allograft recipients. The crude and adjusted hazard ratios in univariate and multivariate Cox regression models showed almost 2-folds to 3-folds risk for overall survival against mutant genotypes of tag-SNPs of FOXP3 (rs2232365 and rs3761548) and NF-kB1 (rs28362491 and rs696) genes.These results suggest that variants of transcription factor FOXP3 and NF-kB1 might be associated with increased risk to the clinical outcome of ESRD and renal allograft survival.

  View details for DOI 10.1016/j.gene.2016.01.028

  View details for PubMedID 26794449

• Non-Classical Human Leukocyte Antigen-G Allelic Diversity Among North Indians ANTHROPOLOGY Prakash, S., Misra, M. K., Agrawal, . 2016; 2 (1): 1-9

  View details for DOI 10.17140/ANTPOJ-2-106

• Genetic associations of killer immunoglobulin like receptors and class I human leukocyte antigens on childhood acute lymphoblastic leukemia among north Indians. Human immunology Misra, M. K., Prakash, S., Moulik, N. R., Kumar, A., Agrawal, S. 2016; 77 (1): 41-46

  Abstract

  Molecular interactions between KIRs and their cognate HLA class-I ligands, play a central role in the regulation of natural killer (NK) cell responses in malignancies. We aimed to determine the role of KIR genes and their HLA ligands in genetic predisposition of childhood acute lymphoblastic leukemia (ALL).Genotyping of 16 KIR genes, along with HLA class-I groups C1/C2 and Bw4 super-type ligands, was carried-out in 137 childhood ALL cases and 274 healthy controls.We observed an increased incidence of activating KIRs namely; 2DS2 (OR=2.23, p=<0.001), 2DS3 (OR=1.74, p=0.011), 3DS1 (OR=2.22, p=<0.001), 2DS5 (OR=2.10, p=0.001), 2DS1 (OR=4.42, p=<0.001) and 2DS4 (OR=2.88, p=<0.001) genes in childhood ALL cases compared to controls. Frequency of BB genotype that possess 2-6 activating KIR genes was predominant in cases compared to controls (OR=2.55, p=<0.001). KIR-receptor/HLA-ligand combinations analysis revealed a moderate risk of almost 2-fold for activating KIR-ligand combinations namely; KIR2DS1-HLAC2, KIR2DS2-HLAC1 and KIR3DS1-HLABw4 in childhood ALL cases.Our data suggests the role for KIR genes and their HLA ligands in aetiology of childhood ALL.

  View details for DOI 10.1016/j.humimm.2015.10.009

  View details for PubMedID 26472014

• Genetic variation in Micro-RNA genes of host genome affects clinical manifestation of symptomatic Human Cytomegalovirus infection. Human immunology Misra, M. K., Mishra, A., Pandey, S. K., Kapoor, R., Sharma, R. K., Agrawal, S. 2015; 76 (10): 765-9

  Abstract

  Micro-RNAs are implicated in various physiological and pathologic processes. In this study, we tested whether Micro-RNA gene variants of host-genome affect clinical manifestation of symptomatic HCMV infection.HCMV infection was detected by fluorescent PCR and immuno-histochemistry. The detection of genetic variants of four studied Micro-RNA tag-SNPs was done through PCR-RFLP assay and validated with DNA sequencing.We observed an increased risk ranged from 3-folds to 5-folds among symptomatic HCMV cases for mutant genotype of rs2910164 (crude OR=3.11, p=0.009 and adjusted OR=3.25, p=0.007), rs11614913 (crude OR=3.20, p=0.006 and adjusted OR=3.48, p=0.004) and rs3746444 (crude OR=4.91, p=0.002 and adjusted OR=5.28, p=0.002) tag-SNPs. Interestingly, all the tag-SNPs that were significant after multiple comparisons at a FDR of 5% in symptomatic HCMV cases remained significant even after bootstrap analysis, providing internal validation to these results. Multifactor Dimensionality Reduction (MDR) analysis revealed 5-folds increased risk for symptomatic HCMV cases under the four-factor model (rs2910164, rs2292832, rs11614913 and rs3746444).These results suggest that Micro-RNA gene variants of host-genome may affect clinical manifestation of symptomatic HCMV infection.

  View details for DOI 10.1016/j.humimm.2015.09.035

  View details for PubMedID 26429309

• The transcription factor Forkhead Box P3 gene variants affect idiopathic recurrent pregnancy loss. Placenta Saxena, D., Misra, M. K., Parveen, F., Phadke, S. R., Agrawal, S. 2015; 36 (2): 226-31

  Abstract

  Forkhead Box P3 (FOXP3) is an essential transcription factor for the induction and development of Tregs. It plays an important role in regulation and suppression of immune responses. We tested whether FOXP3 gene variants are associated with idiopathic recurrent miscarriages (IRM).We included 200 women with at least three unexplained spontaneous abortions before twentieth week of gestation and 300 healthy parous women. The detection of genetic variants of rs2232365, and rs5902434 SNPs were carried-out by using polymerase chain reaction (PCR) with sequence-specific primers, while rs3761548 and rs2294021 SNPs were genotyped by PCR followed by RFLP analysis. The logistic odds ratios (ORs) of idiopathic RM risk were estimated with a 95% confidence interval (CI) after maternal age adjustment. Multifactor dimension reduction (MDR) analysis was used to evaluate the potential SNP ∼ SNP interactions.Single marker analysis revealed an increased risk ranged from almost 3-fold-2-fold for rs2232365, rs3761548, rs5902434 and rs2294021 SNPs in IRM cases. The mutant haplotype carriers of rs2232365, rs3761548, rs5902434 and rs2294021 SNPs showed an increased risk of 2.5-fold for IRM cases. Linkage disequilibrium analysis revealed moderate LD between rs2232365, rs3761548, rs5902434 and rs2294021 SNPs. The MDR analysis revealed 6-fold increased risk for IRM cases in four factor models of rs2232365, rs3761548, rs5902434 and rs2294021 SNPs. The maximum testing accuracy, highest cross validation consistency and greater significance was observed in four SNP model.These results suggest that variants of FOXP3 SNPs namely; rs2232365, rs3761548, rs5902434 and rs2294021 may be associated with idiopathic RM.

  View details for DOI 10.1016/j.placenta.2014.11.014

  View details for PubMedID 25499308

• Implication of HLA-G 5' upstream regulatory region polymorphisms in idiopathic recurrent spontaneous abortions. Reproductive biomedicine online Agrawal, D., Prakash, S., Misra, M. K., Phadke, S. R., Agrawal, S. 2015; 30 (1): 82-91

  Abstract

  The effect of HLA-G 5'-upstream regulatory region (URR) single nucleotide polymorphisms (SNP) in idiopathic recurrent spontaneous abortion (RSA) was evaluated. Parental genotype combination analysis and HLA-G expression at transcriptional level was evaluated for 5'URR SNP, which have shown increased risk for idiopathic RSA. If a fetus were aneuploid, attributing causation to a HLA-G 5'-URR SNP would be illogical; therefore couples with abnormal parental karyotypes and also those with abortus material that revealed chromosomal abnormalities were excluded. One hundred women who had experienced idiopathic RSA, along with their respective male partners and 100 pairs of control couples, were studied. HLA-G 5'-URR SNP were evaluated through sequencing. Quantitative polymerase chain reaction was used for HLA-G expression analysis. An increased risk for idiopathic RSA cases among women carriers of mutant genotypes of -1179G>A(rs1233335), -725C>G/T(rs915670) and -486A>C(rs114252012) SNP. The parental genotype combination analysis revealed a 3.5-fold increased risk for -1179G>A and 4.3-fold increased risk for -725C>G/T SNP among carriers of mutant parental genotypes in couples who have experienced idiopathic RSA. Down-regulation in HLA-G expression was seen at transcriptional level for -1179G>A and -725C>G/T SNPs in cases of idiopathic RSA. Transmission of a mutant allele from single carrier parents may, therefore, affect pregnancy outcome.

  View details for DOI 10.1016/j.rbmo.2014.09.015

  View details for PubMedID 25457193

• Cytotoxic T-lymphocyte antigen 4 gene polymorphism influences the incidence of symptomatic human cytomegalovirus infection after renal transplantation. Pharmacogenetics and genomics Misra, M. K., Pandey, S. K., Kapoor, R., Sharma, R. K., Agrawal, S. 2015; 25 (1): 19-29

  Abstract

  The role of CTLA4 gene polymorphisms in T-cell-mediated immunity in association with human cytomegalovirus (HCMV) infection after transplantation is poorly understood. In the present study, we have made an attempt to investigate the impact of CTLA4 single nucleotide polymorphisms (SNPs) (rs231775, rs5742909, rs11571317, rs16840252, rs4553808, rs3087243) and dinucleotide (AT)n repeat polymorphism on the incidence of symptomatic HCMV infection (disease) among 270 renal allograft recipients.Genotyping of CTLA4 SNPs was performed by a PCR, followed by a restriction fragment length polymorphism assay. The detection of the dinucleotide (AT)n repeat polymorphism was carried out by PCR-polyacrylamide gel electrophoresis.An almost three-fold increased risk was observed for the incidence of symptomatic HCMV infection in mutant genotype carriers of rs231775 and rs3087243 SNPs under additive and recessive models, respectively. The mutant haplotype carriers of six studied SNPs (rs231775, rs5742909, rs11571317, rs16840252, rs4553808 and rs3087243) showed an almost two-fold higher risk for symptomatic HCMV cases, whereas wild-type haplotype combinations of these six SNPs showed a protective effect. Subsequently, no correlation was observed in the promoter region SNPs of CTLA4, namely, rs5742909, rs11571317, rs16840252 and rs4553808 in symptomatic HCMV cases at the genotypic/allelic level. Survival analysis showed that the mutant genotypes of rs231775 and rs3087243 SNPs were associated with the lowest HCMV disease-free survival compared with heterozygous and wild genotypes. The crude and adjusted hazard ratios showed an almost three-fold and 2.5-fold increased risk in univariate and multivariate Cox regression models, respectively, for HCMV disease-free survival against mutant genotypes of rs231775 and rs3087243 SNPs. CTLA4 dinucleotide (AT)n repeat analysis showed that the smaller allele (102 bp) was associated with a protective effect, whereas the longer (110 and 116 bp) alleles showed a susceptible effect for symptomatic HCMV cases.These results suggested that CTLA4 variants might be involved in the clinical manifestation of HCMV diseases.

  View details for DOI 10.1097/FPC.0000000000000102

  View details for PubMedID 25356901

• Platelet-specific collagen receptor glycoprotein VI gene variants affect recurrent pregnancy loss. Fertility and sterility Siddesh, A., Parveen, F., Misra, M. K., Phadke, S. R., Agrawal, S. 2014; 102 (4): 1078-1084.e3

  Abstract

  To determine whether platelet-specific collagen receptor glycoprotein VI (GP6) gene variants are associated with recurrent miscarriages (RM).Genetic association study.Tertiary care referral hospital.A total of 200 women with at least three unexplained spontaneous abortions before 20 weeks of gestation and 300 healthy parous women.Determination of variants of GP6 single-nucleotide polymorphisms (SNPs) namely; rs1671153, rs1654410, rs1654419, and rs1613662 was based on polymerase chain reaction-restriction fragment-length polymorphism.Genotypes and haplotypes frequencies were compared in RM case subjects versus control subjects.We observed significantly higher occurrence of rare alleles of SNPs in GP6, namely, rs1671153, rs1654410, rs1654419, and rs1613662, among RM cases, revealing risk association for fetal losses. The synergistic effects of haplotype combinations were also evaluated and showed that four haplotypes G-T-G-G, T-C-A-A, G-C-G-A, and G-T-A-A were more prevalent among RM cases, revealing increased risk for fetal losses. In silico analysis revealed that GP6 has an impact on biologic pathways and significant influence in collagen binding. Gene-gene interaction network analysis revealed that GP6 consisted of a total of 25 interactions with 13 genes in the human genome.These results suggest that variants of GP6 SNPs, namely, rs1671153, rs1654410, rs1654419, and rs1613662, may be associated with risk of recurrent miscarriage. In silico analyses demonstrated the influence of GP6 in biologic pathways, molecular function, including collagen binding, and gene-gene interaction in the human genome.

  View details for DOI 10.1016/j.fertnstert.2014.07.002

  View details for PubMedID 25086789

• Genetic variants of MicroRNA-related genes in susceptibility and prognosis of end-stage renal disease and renal allograft outcome among north Indians. Pharmacogenetics and genomics Misra, M. K., Pandey, S. K., Kapoor, R., Sharma, R. K., Agrawal, S. 2014; 24 (9): 442-50

  Abstract

  MicroRNAs are important molecules of the innate and adaptive immune system, which may play an important role in maintaining normal immune homeostasis. The aim of this study was to investigate the impact of MIR146A C>G (rs2910164), MIR149 T>C (rs2292832), MIR196A2 T>C (rs11614913), and MIR499A A>G (rs3746444) single nucleotide polymorphisms (SNPs) among end-stage renal disease (ESRD) and acute allograft rejection (AR) cases.Genotyping of MicroRNA SNPs was performed using a PCR, followed by restriction fragment length polymorphism in 350 ESRD patients and 350 age-matched, sex-matched, and ethnically matched controls.We observed an increased risk of almost two-fold for ESRD and three-fold for AR cases under univariate and multivariate models for mutant genotypes of rs2910164, rs11614913, and rs3746444 SNPs. Subsequently, no susceptible/protective effect was observed for rs2292832 SNP with ESRD and AR cases. Interestingly, all the SNPs that were significant after multiple comparisons in ESRD and AR cases remained significant in the bootstrap analysis, providing internal validation to our initial observations. Survival analysis showed that the mutant genotypes of rs2910164, rs11614913, and rs3746444 SNPs were associated with the lowest overall survival compared with heterozygous and wild genotypes among renal allograft recipients. The crude and adjusted hazard ratios in univariate and multivariate Cox regression models showed an almost two-fold increased risk for overall survival against mutant genotypes of rs2910164, rs11614913, and rs3746444 SNPs in renal allograft recipients.These results suggest that the variants of MicroRNA SNPs, namely, rs2910164, rs11614913, and rs3746444, might be involved in susceptibility to ESRD and AR.

  View details for DOI 10.1097/FPC.0000000000000074

  View details for PubMedID 24978643

• HLA-G gene expression influenced at allelic level in association with end stage renal disease and acute allograft rejection. Human immunology Misra, M. K., Pandey, S. K., Kapoor, R., Sharma, R. K., Kapoor, R., Prakash, S., Agrawal, S. 2014; 75 (8): 833-9

  Abstract

  Human leukocyte antigen (HLA)-G is a non-classical major-histocompatibility complex class-I molecule associated with immunosuppressive function. We have evaluated the impact of HLA-G allele associated with untranslated-region (UTR)-haplotype in end stage renal disease (ESRD) and acute allograft rejection (AR) cases. The mRNA levels of different HLA-G isoforms were evaluated in ESRD and AR cases. Subsequently, the total HLA-G mRNA levels and protein concentration were evaluated against its UTR-haplotype among ESRD and AR cases.Sequence based typing of the promoter region was carried-out to evaluate the impact of HLA-G haplotype in 350 ESRD cases and 300 controls. HLA-G gene expression was evaluated at the transcriptional level using semi-quantitative and quantitative PCR, whereas protein concentration was determined by ELISA among both cases and control.Increased risk was observed for G*01:01:01:03, G*01:01:02, G*01:06 and G*01:05:N haplotypes while G*01:01:01:01 and G*01:04:01 haplotypes showed a protective effect in ESRD and AR cases. Higher level of soluble HLA-G isoforms (G5 and G6) was observed among ESRD cases. Reduced levels of soluble isoform (G5) and increased levels of membrane bound (G1 and G3) isoforms were found among AR cases, revealing risk association. Decreased HLA-G expression was observed at both mRNA and protein level for G*01:01:01:03 and G*01:05:N haplotypes in ESRD and AR cases.These results suggest that the variation in the expression profile of membrane bound and soluble isoforms may modulate the risk for ESRD and AR. UTR-haplotypes appear to be involved in different HLA-G expression patterns at transcriptional and translational levels.

  View details for DOI 10.1016/j.humimm.2014.06.005

  View details for PubMedID 24929145

• Association of CTLA-4 gene polymorphism with end-stage renal disease and renal allograft outcome. Journal of interferon & cytokine research : the official journal of the International Society for Interferon and Cytokine Research Misra, M. K., Kapoor, R., Pandey, S. K., Sharma, R. K., Agrawal, S. 2014; 34 (3): 148-61

  Abstract

  Cytotoxic T-lymphocyte antigen 4 (CTLA-4) is upregulated in effector-T-cells after activation that may alter signal transduction and subsequently cytokine production. The present study was designed to investigate the impact of CTLA-4+49 A>G (rs231775), -318 C>T (rs5742909), -658 C>T (rs11571317), -1147 C>T (rs16840252), -1661 A>G (rs4553808), +6230 A>G (rs3087243) SNPs, and microsatellite (AT)n repeat polymorphism among end-stage renal disease (ESRD), acute allograft rejection (AR), and delayed graft function (DGF) cases. In this regard, 350 ESRD patients and 350 controls were included. Polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis method was used for genotyping of CTLA-4 SNPs, while PCR-polyacrylamide gel electrophoresis method was adopted for studying CTLA4 (AT)n polymorphism. The mutant genotype GG of CTLA-4+49A>G,+6230 A>G, and longer alleles of (AT)n repeats polymorphisms were risk associated with ESRD, AR, and DGF cases. The distribution of haplotype+49G:+6230G and GCTTGG (constructed by using 6 studied SNPs) showed risk association for ESRD, DGF, and AR cases. Further, linkage analysis demonstrated strong to moderate linkage disequilibrium in our study populations. The meta-analysis also revealed risk associations for AR cases against GG genotype of CTLA-4+49A>G SNP, while CTLA-4 -318C>T polymorphism showed no correlation against TT genotype among AR cases. Subsequently, no correlation was established against the CTLA-4 -318C>T, -658 C>T, -1147 C>T, and -1661 A>G SNPs in the promoter region. Survival analysis revealed risk associations against GG genotype of CTLA-4+49A>G, +6230 A>G SNP's with overall survival (OS), and higher hazard for the OS. These results suggested that CTLA-4 variants might be involved in susceptibility to ESRD, AR, and DGF.

  View details for DOI 10.1089/jir.2013.0069

  View details for PubMedID 24313821

• Wireless Technology in Health prospective MISHRA, A., Misra, M. K. LAP LAMBERT ACADEMIC PUBLISHING, GERMANY. 2014
• Association of HLA-G promoter and 14-bp insertion-deletion variants with acute allograft rejection and end-stage renal disease. Tissue antigens Misra, M. K., Prakash, S., Kapoor, R., Pandey, S. K., Sharma, R. K., Agrawal, S. 2013; 82 (5): 317-26

  Abstract

  The aim of this study was to investigate the HLA-G 14-bp insertion/deletion (I/D) polymorphism among end-stage renal disease (ESRD) patients. Cytomegalovirus (CMV) infection, acute allograft rejection (AR) and overall survival after renal transplantation was investigated in 300 ESRD patients and 302 age, sex and ethnicity-matched controls. Sequencing was performed to evaluate the impact of HLA-G promoter region single-nucleotide polymorphisms (SNPs) whereas semi-quantitative PCR method was used to determine the probable HLA-G expression pattern among ESRD and AR cases. Further, soluble human leukocyte antigen (HLA)-G (sHLA-G) expression levels were compared in AR vs non-AR cases in the light of HLA-G 14-bp I/D polymorphism. Increased risk was found for 14-bp D/D (deletion-DD) genotype and 14-bp D allele [DD: odds ratio (OR) = 1.46, 95% confidence interval (CI) = 1.03-2.06, P value = 0.0358; D: OR = 1.29, 95% CI = 1.03-1.62, P value = 0.0277], respectively for ESRD and CMV infection (DD: OR = 2.70, 95% CI = 1.45-5.05, P value = 0.0021; D: OR = 1.94, 95% CI = 1.22-3.08, P value = 0.0052). Nearly fourfold (OR = 3.62, 95%CI = 1.61-8.14, p = 0.0039) risk was observed for 14-bp I/I (insertion-II) genotype for AR. Survival analysis showed increased overall survival (OS) (AR or death) for 14-bp D/D genotype. HLA-G promoter region sequencing was carried out among 60 ESRD patients and 100 normal controls which showed increased risk for -964 G>A, -725 C>G/T and -486 A>C SNPs. -964 G>A and -725 C>G/T SNPs showed risk association for AR patients. High level of HLA-G transcripts was observed among non-AR patients. Further soluble HLA-G (sHLA-G) showed increased levels in ESRD patients (mean ± SEM; 62.16 ± 2.43 U/ml) as compared to controls (mean ± SEM; 21.06 ± 3.89 U/ml) (P = <0.0001). The 14-bp I/I, 14-bp I/D and 14-bp D/D genotypes showed significantly higher levels of sHLA-G among non-AR as compared to AR patients.

  View details for DOI 10.1111/tan.12210

  View details for PubMedID 24131018