Variations in HLA-B cell surface expression, half-life and extracellular antigen receptivity

Yarzabek, Brogan; Zaitouna, Anita; Olson, Edwin; Silva, Gayathri N.; Geng, Jie; Geretz, Aviva; Thomas, Rasmi; Krishnakumar, Sujatha; Ramón, Daniel; Raghavan, Malini

doi:10.7554/elife.34961

Cited by 42 publications

(67 citation statements)

References 61 publications

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“…Mass spectrometric analyses of eluted peptides identified 3774 peptides that were assigned to bind HLA-A*02:01, HLA-B*40:01 or HLA-C*03:04 based on peptide affinity prediction (Figure 2D). Sequence logos corresponding to the 9-mer peptides for HLA-A*02:01, HLA-B*40:01 and HLA-C*03:04 were in concordance with literature (Figure 2E)(16, 24, 25). Thus, PAKC is well-suited for high-resolution peptide elution studies which further benefit from the fact that PAKC is made on a single genetic and proteomic background.…”

Section: Resultssupporting

confidence: 88%

PAKC: A novel Panel of HLA class I Antigen presentation machinery Knockout Cells from the same genetic origin

Waard

Verkerk

Jongsma

et al. 2020

Preprint

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With the emergence of immunotherapies, the understanding of functional HLA class I antigen presentation to T cells is more relevant than ever. Current knowledge on antigen presentation is based on decades of research in a wide variety of cell types with varying antigen presentation machinery (APM) expression patterns, proteomes and HLA haplotypes. This diversity complicates the establishment of individual APM contributions to antigen generation, selection and presentation. Therefore, we generated a novel Panel of APM Knockout Cell lines (PAKC) from the same genetic origin. After CRISPR/Cas9 genome-editing of ten individual APM components in a human cell line, we derived clonal cell lines and confirmed their knockout status and phenotype. We then show how PAKC will accelerate research on the functional interplay between APM components and their role in antigen generation and presentation. This will lead to improved understanding of peptide-specific T cell responses in infection, cancer and autoimmunity.Key pointsWe generated a panel of cell lines to study HLA class I antigen presentationWe show how this will spark research in infection, tumor biology and autoimmunity

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Section: Resultssupporting

confidence: 88%

PAKC: A novel Panel of HLA class I Antigen presentation machinery Knockout Cells from the same genetic origin

Waard

Verkerk

Jongsma

et al. 2020

Preprint

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“…cross-reactive with some HLA-A (Bw4) and HLA-C (Bw6) allotypes (57). As previously reported, we identified a donor that was heterozygous for Bw4 (B*51:01) and Bw6 (B*07:02) with no cross-reactive HLA-A alleles and minimal cross-reactivity from HLA-C, allowing us to reliably measure expression of two HLA-B alleles (SI Appendix, Fig.…”

Section: Cma Reverses Nef-mediated Down-regulation Of Hla-b In Primarymentioning

confidence: 76%

“…As previously reported, we identified a donor that was heterozygous for Bw4 (B*51:01) and Bw6 (B*07:02) with no cross-reactive HLA-A alleles and minimal cross-reactivity from HLA-C, allowing us to reliably measure expression of two HLA-B alleles (SI Appendix, Fig. S12A) (57). We observed significant downmodulation of both HLA-B*51:01 and HLA-B*07:02 in cells infected with ΔGPE, which was consistently counteracted by CMA ( Fig.…”

Section: Cma Reverses Nef-mediated Down-regulation Of Hla-b In Primarymentioning

confidence: 94%

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Concanamycin A counteracts HIV-1 Nef to enhance immune clearance of infected primary cells by cytotoxic T lymphocytes

Painter

Zimmerman

Merlino

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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Nef is an HIV-encoded accessory protein that enhances pathogenicity by down-regulating major histocompatibility class I (MHC-I) expression to evade killing by cytotoxic T lymphocytes (CTLs). A potent Nef inhibitor that restores MHC-I is needed to promote immune-mediated clearance of HIV-infected cells. We discovered that the plecomacrolide family of natural products restored MHC-I to the surface of Nef-expressing primary cells with variable potency. Concanamycin A (CMA) counteracted Nef at subnanomolar concentrations that did not interfere with lysosomal acidification or degradation and were nontoxic in primary cell cultures. CMA specifically reversed Nef-mediated down-regulation of MHC-I, but not CD4, and cells treated with CMA showed reduced formation of the Nef:MHC-I:AP-1 complex required for MHC-I down-regulation. CMA restored expression of diverse allotypes of MHC-I in Nef-expressing cells and inhibited Nef alleles from divergent clades of HIV and simian immunodeficiency virus, including from primary patient isolates. Lastly, we found that restoration of MHC-I in HIV-infected cells was accompanied by enhanced CTL-mediated clearance of infected cells comparable to genetic deletion of Nef. Thus, we propose CMA as a lead compound for therapeutic inhibition of Nef to enhance immune-mediated clearance of HIV-infected cells.

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“…HLA Genotyping and KIR Expression. HLA genotyping was performed as described previously (43). The presence of KIR3DL1 was assessed by 4% agarose gel electrophoresis following PCR-sequence-specific priming (44) with primers 5′-CCCTGGTGAAATCAGGAGAGAG-3′ and 5′-TGTAGGTCCCTGCAAGGGCAA-3′.…”

Section: Methods Studymentioning

confidence: 99%

CD8αα homodimers function as a coreceptor for KIR3DL1

Geng

Raghavan

2019

Proc. Natl. Acad. Sci. U.S.A.

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Cluster of differentiation 8 (CD8) is a cell surface glycoprotein, which is expressed as 2 forms, αα homodimer or αβ heterodimer. Peptide-loaded major histocompatibility complex class I (pMHC-I) molecules are major ligands for both forms of CD8. CD8αβ is a coreceptor for the T cell receptor (TCR) and binds to the same cognate pMHC-I as the TCR, thus enabling or augmenting T cell responses. The function of CD8αα homodimers is largely unknown. While CD8αβ heterodimer is expressed exclusively on CD8+ T cells, the CD8αα homodimer is present in subsets of T cells and human natural killer (NK) cells. Here, we report that the CD8αα homodimer functions as a coreceptor for KIR3DL1, an inhibitory receptor of NK cells that is specific for certain MHC-I allotypes. CD8αα enhances binding of pMHC-I to KIR3DL1, increases KIR3DL1 clustering at the immunological synapse, and augments KIR3DL1-mediated inhibition of NK cell activation. Additionally, interactions between pMHC-I and CD8αα homodimers regulate KIR3DL1+ NK cell education. Together, these findings reveal another dimension to the modulation of NK cell activity.

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Variations in HLA-B cell surface expression, half-life and extracellular antigen receptivity

Cited by 42 publications

References 61 publications

PAKC: A novel Panel of HLA class I Antigen presentation machinery Knockout Cells from the same genetic origin

PAKC: A novel Panel of HLA class I Antigen presentation machinery Knockout Cells from the same genetic origin

Concanamycin A counteracts HIV-1 Nef to enhance immune clearance of infected primary cells by cytotoxic T lymphocytes

CD8αα homodimers function as a coreceptor for KIR3DL1

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