Global proteogenomic analysis of human MHC class I-associated peptides derived from non-canonical reading frames (original) (raw)
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The MHC class I peptide repertoire is molded by the transcriptome
Journal of Experimental Medicine, 2008
Under steady-state conditions, major histocompatibility complex (MHC) I molecules are associated with self-peptides that are collectively referred to as the MHC class I peptide (MIP) repertoire. Very little is known about the genesis and molecular composition of the MIP repertoire. We developed a novel high-throughput mass spectrometry approach that yields an accurate definition of the nature and relative abundance of unlabeled peptides presented by MHC I molecules. We identified 189 and 196 MHC I–associated peptides from normal and neoplastic mouse thymocytes, respectively. By integrating our peptidomic data with global profiling of the transcriptome, we reached two conclusions. The MIP repertoire of primary mouse thymocytes is biased toward peptides derived from highly abundant transcripts and is enriched in peptides derived from cyclins/cyclin-dependent kinases and helicases. Furthermore, we found that ∼25% of MHC I–associated peptides were differentially expressed on normal vers...
Impact of genomic polymorphisms on the repertoire of human MHC class I-associated peptides
Nature Communications, 2014
For decades, the global impact of genomic polymorphisms on the repertoire of peptides presented by major histocompatibility complex (MHC) has remained a matter of speculation. Here we present a novel approach that enables high-throughput discovery of polymorphic MHC class I-associated peptides (MIPs), which play a major role in allorecognition. On the basis of comprehensive analyses of the genomic landscape of MIPs eluted from B lymphoblasts of two MHC-identical siblings, we show that 0.5% of non-synonymous single nucleotide variations are represented in the MIP repertoire. The 34 polymorphic MIPs found in our subjects are encoded by bi-allelic loci with dominant and recessive alleles. Our analyses show that, at the population level, 12% of the MIP-coding exome is polymorphic. Our method provides fundamental insights into the relationship between the genomic self and the immune self and accelerates the discovery of polymorphic MIPs (also known as minor histocompatibility antigens).
Proceedings of the National Academy of Sciences, 2011
The MHC class I antigen presentation pathway allows the immune system to distinguish between self and nonself. Despite extensive research on the processing of antigenic peptides, little is known about their origin. Here, we show that mRNAs carrying premature stop codons that prevent the production of full-length proteins via the nonsense-mediated decay pathway still produce a majority of peptide substrates for the MHC class I pathway by a noncanonical mRNA translation process. Blocking the interaction of the translation initiation factor eIF4E with the cap structure suppresses the synthesis of full-length proteins but has only a limited effect on the production of antigenic peptides. These results reveal an essential cell biological function for a class of translation products derived during the pioneer round of mRNA translation and will have important implications for understanding how the immune system detects cells harboring pathogens and generates tolerance.
Molecular Biology and Evolution, 2012
The immune genes of the major histocompatibility complex (MHC) are characterized by extraordinarily high levels of nucleotide and haplotype diversity. This variation is maintained by pathogen-mediated balancing selection that is operating on the peptide-binding region (PBR). Several recent studies have found, however, that some populations possess large clusters of alleles that are translated into virtually identical proteins. Here, we address the question of how this nucleotide polymorphism is maintained with little or no functional variation for selection to operate on. We investigate circa 750-850 bp of MHC class II DAB genes in four wild populations of the guppy Poecilia reticulata. By sequencing an extended region, we uncovered 40.9% more sequences (alleles), which would have been missed if we had amplified the exon 2 alone. We found evidence of several gene conversion events that may have homogenized sequence variation. This reduces the visible copy number variation (CNV) and can result in a systematic underestimation of the CNV in studies of the MHC and perhaps other multigene families. We then focus on a single cluster, which comprises 27 (of a total of 66) sequences. These sequences are virtually identical and show no signal of selection. We use microsatellites to reconstruct the populations' demography and employ simulations to examine whether so many similar nucleotide sequences can be maintained in the populations. Simulations show that this variation does not behave neutrally. We propose that selection operates outside the PBR, for example, on linked immune genes or on the ''sheltered load'' that is thought to be associated to the MHC. Future studies on the MHC would benefit from extending the amplicon size to include polymorphisms outside the exon with the PBR. This may capture otherwise cryptic haplotype variation and CNV, and it may help detect other regions in the MHC that are under selection.
Immunology, 1999
In the present study, the genetic mechanisms responsible for generation of antibodies recognizing the dominant epitope within a synthetic peptide PS1CT3 were examined. PS1CT3 is a peptide model antigen containing residues 28–42 of the large protein of the surface antigen of hepatitis B virus as B epitope (designated PS1), and the known T-helper-cell epitope derived from the circumsporozoite protein of the malaria parasite Plasmodium falciparum (designated CT3). To characterize the repertoire generated, the immunoglobulin heavy chain variable regions from IgM and IgG monoclonal antibodies against PS1CT3 were sequenced. Although all IgG monoclonal antibodies were directed against the immunodominant epitope, the genetic elements used were diverse. Comparison of the sequence of germ line precursor IgM to a mature IgG revealed that during maturation of the primary IgM response only the heavy chain fragment of the antibody molecule underwent somatic mutation.
Allelic variants of the human MHC class I chain-related B gene (MICB)
Immunogenetics, 1997
AbstractmThe human major histocompatibility complex (MHC) is located within a 4 megabase segment on chromosome 6p21.3. Recently, a highly divergent MHC class I chain-related gene family, MIC was identified within the class I region. The MICA and MICB genes in this family have unique patterns of tissue expression. The MICA gene is highly polymorphic, with more than 20 alleles identified to date. To elucidate the extent of MICB allelic variations, we sequenced exons 2 (a1), 3 (a2), 4 (a3), and 5 (transmembrane) as well as introns 2 and 4 of this gene in 46
Human antibody immune responses are personalized by selective removal of MHC-II peptide epitopes
2021
Human antibody responses are established by the generation of combinatorial sequence diversity in antibody variable domains, followed by iterative rounds of mutation and selection via T cell recognition of antigen peptides presented on MHC-II. Here, we report that MHC-II peptide epitope deletion from B cell receptors (BCRs) correlates with antibody development in vivo. Large-scale antibody sequence analysis and experimental validation of peptide binding revealed that MHC-II epitope removal from BCRs is linked to genetic signatures of T cell help, and donor-specific antibody repertoire modeling demonstrated that somatic hypermutation selectively targets the personalized MHC-II epitopes in antibody variable regions. Mining of class-switched sequences and serum proteomic data revealed that MHC-II epitope deletion is associated with antibody class switching and long-term secretion into serum. These data suggest that the MHC-II peptide epitope content of a BCR is an important determinant...
Journal of Experimental Medicine, 1990
Multiple different genetic defects can lead to the loss of constitutive class II MHC (la) expression in B cells (1). Somatic cell hybridization between spontaneous or experimentally selected human Ia-mutant B cell lines have divided the class II MHC expression mutants into at least three complementation groups . The defect in one such Ia mutant cell line, RJ 2.2.5, has been postulated to be in a positive transacting factor that is active across species, because it is complemented by a locus, a1r-1, that maps to mouse chromosome 16 (2). Class II Ea and DQ(3 upstream cis-active DNA elements transfected into RJ 2.2.5 cells do not act as transcriptional elements (3, 4). Nevertheless, these DNA motifs appear to bind nuclear factors in RJ 2.2.5 indistinguishable from those in the wild-type parent Raji. Thus, the absence of a positive transacting factor in RJ 2.2.5 could not be correlated with the absence of a DNA binding activity for a class fI gene.
MHC I–associated peptides preferentially derive from transcripts bearing miRNA response elements
Blood, 2012
MHC I–associated peptides (MIPs) play an essential role in normal homeostasis and diverse pathologic conditions. MIPs derive mainly from defective ribosomal products (DRiPs), a subset of nascent proteins that fail to achieve a proper conformation and the physical nature of which remains elusive. In the present study, we used high-throughput proteomic and transcriptomic methods to unravel the structure and biogenesis of MIPs presented by HLA-A and HLA-B molecules on human EBV-infected B lymphocytes from 4 patients. We found that although HLA-different subjects present distinctive MIPs derived from different proteins, these MIPs originate from proteins that are functionally interconnected and implicated in similar biologic pathways. Secondly, the MIP repertoire of human B cells showed no bias toward conserved versus polymorphic genomic sequences, were derived preferentially from abundant transcripts, and conveyed to the cell surface a cell-type–specific signature. Finally, we discover...