OR39 De novo assembly of the major histocompatibility complex using single-molecule real-time sequencing of large contiguous DNA fragments captured by targeted region specific extraction

2015 ◽  
Vol 76 ◽  
pp. 32 ◽  
Author(s):  
Peter M. Clark ◽  
Mark Kunkel ◽  
Hilary Mehler ◽  
Dimitri Monos
Keyword(s):  
Major Histocompatibility Complex ◽  
Real Time ◽  
Single Molecule ◽  
De Novo Assembly ◽  
De Novo ◽  
Dna Fragments ◽  
Major Histocompatibility ◽  
Histocompatibility Complex

Expression of Major Histocompatibility Complex Class II Antigens in Porcine Leptospiral Nephritis

2009 ◽  
Vol 46 (5) ◽  
pp. 800-809 ◽  
Author(s):  
E. Radaelli ◽  
F. Del Piero ◽  
L. Aresu ◽  
F. Sciarrone ◽  
N. Vicari ◽  
...  
Keyword(s):  
Major Histocompatibility Complex ◽  
De Novo ◽  
Class Ii ◽  
Renal Tissue ◽  
Major Histocompatibility ◽  
Serum Samples ◽  
Histocompatibility Complex ◽  
Antigen Presenting ◽  
Renal Infection ◽  
Mhcii Expression

Class II major histocompatibility complex (MHCII) is required for the presentation of antigens to CD4 helper T cells. During nephritis, not only primary antigen presenting cells such as histiocytes and lymphocytes, but also cytokine-stimulated tubular epithelial cells express MHCII. Leptospirosis in fattening pigs is characterized by several degrees of nephritis, from absence of lesions to severe multifocal tubulo-interstitial inflammation. Renal tissue from 20 8-month-old pigs with spontaneous nephritis and 6 control pigs without renal lesions were investigated for leptospirosis by indirect immunohistochemistry (IHC) and polymerase chain reaction (PCR). IHC for MHCII also was performed on renal samples. Serum samples were tested for different serovars of Leptospira interrogans. Control pigs were free of interstitial nephritis and negative for leptospirosis by all tests. In pigs with nephritis, serology was positive for serovar Pomona in 19/20 pigs. In 16 of these 19 pigs, leptospiral renal infection was confirmed by PCR and/or indirect IHC. Nephritic lesions were classified histologically into perivascular lymphocytic (4 pigs), lymphofollicular (6 pigs), lymphohistiocytic (8 pigs), and neutrophilic (2 pigs) pattern. MHCII expression by histiocytes and lymphocytes was observed in all lesions. Prominent MHCII expression in regenerating tubular epithelium was observed in lymphofollicular and lymphohistiocytic nephritis. No tubular colocalization between leptospiral and MHCII antigen was observed. Results suggest that during leptospiral nephritis, MHCII contributes to the intensity of the inflammatory response. Furthermore de novo MHCII expression in regenerating tubules may play a role in the defence mechanism against leptospiral tubular colonization.

scholarly journals Differentiation-stage specific self-peptides bound by major histocompatibility complex class I molecules.

1993 ◽  
Vol 177 (3) ◽  
pp. 783-790 ◽  
Author(s):  
P E Harris ◽  
F Lupu ◽  
B Hong ◽  
E F Reed ◽  
N Suciu-Foca
Keyword(s):  
Major Histocompatibility Complex ◽  
Mhc Class I ◽  
High Performance ◽  
De Novo ◽  
Interleukin 1 ◽  
Class I ◽  
Major Histocompatibility ◽  
Histocompatibility Complex ◽  
Differentiation Stage ◽  
Mhc Class I Molecules

We have tested the hypothesis that phenotypic changes of development are accompanied by expression of differentiation-stage specific peptides bound to major histocompatibility complex (MHC) class I molecules. The U937 cell line, when cultured in the presence of phorbol myristate acetate (PMA), undergoes differentiation from monoblasts to macrophage-like cells. The high-performance liquid chromatography profile of peptides eluted from purified human histocompatibility leukocyte antigen class I molecules expressed by U937 treated with PMA differs from that obtained from control, untreated U937 cells. Chemical sequencing of eluted peptides identified a peptide derived from cytomegalovirus in both treated and untreated cells. PMA-treated, but not untreated cells, displayed an additional peptide derived from interleukin 1 beta. Hence, differentiation-induction of U937 is accompanied by the presentation of at least one differentiation-stage specific peptide. Our results indicate that, similar to viral infection, cellular development and transformation is accompanied by the de novo synthesis of proteins which are processed and presented on MHC class I molecules.

scholarly journals A Kmer-based paired-end read (KPR) de novo assembler and genotyper to genotype major histocompatibility complex class I (MHC-I) alleles for the dog

2020 ◽  
Author(s):  
Yuan Feng ◽  
William H. Hildebrand ◽  
Stephen M. Tompkins ◽  
Shaying Zhao
Keyword(s):  
Major Histocompatibility Complex ◽  
Major Histocompatibility Complex Class ◽  
De Novo ◽  
Class I ◽  
Complex Class ◽  
Rna Seq ◽  
Major Histocompatibility ◽  
Class I Mhc ◽  
Mhc I ◽  
Histocompatibility Complex

AbstractThe major histocompatibility complex class I (MHC-I) genes are highly polymorphic among individuals. MHC-I genotyping is required for determining the antigen-binding specificity of each MHC-I molecule in an individual. Numerous tools have been developed for human MHC-I genotyping using deep sequencing data such as RNA-seq; however they do not work for the dog, due to very limited information for canine alleles. To address this issue, we developed a Kmer-based paired-end read (KPR) de novo assembler and genotyper, which first assemble paired-end RNA-seq reads mapped to the MHC-I regions into contigs de novo and then genotype each contig. Our KPR tools are validated by Sanger sequencing, simulation and published genotype data. Applying our KPR tools on the published RNA-seq data of 158 tumor and 64 normal samples from 158 dogs, we have achieved a genotyping success rate of 86%, which includes 133 tumor and 57 normal samples from 142 dogs. We have identified 39 known alleles and 83 new alleles of high confidence in these dogs, yielding a more comprehensive MHC-I allele diversity landscape for the dog.

scholarly journals Prevention of nephritis in major histocompatibility complex class II-deficient MRL-lpr mice.

1994 ◽  
Vol 179 (4) ◽  
pp. 1137-1143 ◽  
Author(s):  
A M Jevnikar ◽  
M J Grusby ◽  
L H Glimcher
Keyword(s):  
T Cells ◽  
Major Histocompatibility Complex ◽  
Mhc Class Ii ◽  
De Novo ◽  
Class Ii ◽  
Systemic Lupus Erythematosis ◽  
Major Histocompatibility ◽  
Mhc Molecules ◽  
Histocompatibility Complex

MRL-lpr mice develop aggressive autoimmune kidney disease associated with increased or de novo renal expression of major histocompatibility complex (MHC) class II molecules and a massive systemic expansion of CD4-CD- double negative (DN) T cells. Whereas non-MHC linked genes can have a profound effect on the development of nephritis, lymphadenopathy, and anti-DNA antibody production in MRL-lpr mice, the role of MHC molecules has not been unequivocally established. To study the role of MHC class II in this murine model of systemic lupus erythematosis, class II-deficient MRL-lpr mice (MRL-lpr -/-) were created. MRL-lpr -/- mice developed lymphadenopathy but not autoimmune renal disease or autoantibodies. This study demonstrates that class II expression is critical for the development of autoaggressive CD4+ T cells involved in autoimmune nephritis and clearly dissociates DN T cell expansion from autoimmune disease initiation.

scholarly journals A diploid assembly-based benchmark for variants in the major histocompatibility complex

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Chen-Shan Chin ◽  
Justin Wagner ◽  
Qiandong Zeng ◽  
Erik Garrison ◽  
Shilpa Garg ◽  
...  
Keyword(s):  
Major Histocompatibility Complex ◽  
Performance Assessment ◽  
Reference Genome ◽  
De Novo ◽  
Major Histocompatibility ◽  
Structural Variants ◽  
Histocompatibility Complex ◽  
Human Genomes ◽  
Long Reads ◽  
Complex Variation

Abstract Most human genomes are characterized by aligning individual reads to the reference genome, but accurate long reads and linked reads now enable us to construct accurate, phased de novo assemblies. We focus on a medically important, highly variable, 5 million base-pair (bp) region where diploid assembly is particularly useful - the Major Histocompatibility Complex (MHC). Here, we develop a human genome benchmark derived from a diploid assembly for the openly-consented Genome in a Bottle sample HG002. We assemble a single contig for each haplotype, align them to the reference, call phased small and structural variants, and define a small variant benchmark for the MHC, covering 94% of the MHC and 22368 variants smaller than 50 bp, 49% more variants than a mapping-based benchmark. This benchmark reliably identifies errors in mapping-based callsets, and enables performance assessment in regions with much denser, complex variation than regions covered by previous benchmarks.

scholarly journals Destabilizing single chain major histocompatibility complex class I protein for repurposed enterokinase proteolysis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Jackwee Lim
Keyword(s):  
Major Histocompatibility Complex ◽  
Major Histocompatibility Complex Class ◽  
De Novo ◽  
Class I ◽  
Complex Class ◽  
Major Histocompatibility ◽  
Single Chain ◽  
Mhc I ◽  
Histocompatibility Complex ◽  
Protein Instability

Abstract The lack of a high throughput assay for screening stabilizing peptides prior to building a library of peptide-major histocompatibility complex class I (pMHC-I) molecules has motivated the continual use of in silico tools without biophysical characterization. Here, based on de novo protein fragmentation, the EASY MHC-I (EZ MHC-I) assay favors peptide antigen screening to an unheralded hands-on time of seconds per peptide due to the empty single chain MHC-I protein instability. Unlike tedious traditional labeling- and antibody-based MHC-I assays, repurposed enterokinase directly fragments the unstable single MHC-I chain protein unless rescued by a stabilizing peptide under luminal condition. Herein, the principle behind EZ MHC-I assay not only characterizes the overlooked stability as a known better indicator of immunogenicity than classical affinity but also the novel use of enterokinase from the duodenum to target destabilized MHC-I protein not bearing the standard Asp-Asp-Asp-Asp-Lys motif, which may protend to other protein instability-based assays.

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