scholarly journals Acid Stripping after Infection Improves the Detection of Viral HLA Class I Natural Ligands Identified by Mass Spectrometry

2021 ◽  
Vol 22 (19) ◽  
pp. 10503
Author(s):  
Elena Lorente ◽  
Miguel Marcilla ◽  
Patricia G. de la Sota ◽  
Adriana Quijada-Freire ◽  
Carmen Mir ◽  
...  

Identification of a natural human leukocyte antigen (HLA) ligandome is a key element to understand the cellular immune response. Advanced high throughput mass spectrometry analyses identify a relevant, but not complete, fraction of the many tens of thousands of self-peptides generated by antigen processing in live cells. In infected cells, in addition to this complex HLA ligandome, a minority of peptides from degradation of the few proteins encoded by the viral genome are also bound to HLA class I molecules. In this study, the standard immunopeptidomics strategy was modified to include the classical acid stripping treatment after virus infection to enrich the HLA ligandome in virus ligands. Complexes of HLA-B*27:05-bound peptide pools were isolated from vaccinia virus (VACV)-infected cells treated with acid stripping after virus infection. The HLA class I ligandome was identified using high throughput mass spectrometry analyses, yielding 37 and 51 natural peptides processed and presented untreated and after acid stripping treatment VACV-infected human cells, respectively. Most of these virus ligands were identified in both conditions, but exclusive VACV ligands detected by mass spectrometry detected on acid stripping treatment doubled the number of those identified in the untreated VACV-infected condition. Theoretical binding affinity prediction of the VACV HLA-B*27:05 ligands and acute antiviral T cell response characterization in the HLA transgenic mice model showed no differences between HLA ligands identified under the two conditions: untreated and under acid stripping condition. These findings indicated that acid stripping treatment could be useful to identify HLA class I ligands from virus-infected cells.

2012 ◽  
Vol 287 (42) ◽  
pp. 34895-34903 ◽  
Author(s):  
Elena Lorente ◽  
Susana Infantes ◽  
David Abia ◽  
Eilon Barnea ◽  
Ilan Beer ◽  
...  

The transporter associated with antigen processing (TAP) enables the flow of viral peptides generated in the cytosol by the proteasome and other proteases to the endoplasmic reticulum, where they complex with nascent human leukocyte antigen (HLA) class I. Later, these peptide-HLA class I complexes can be recognized by CD8+ lymphocytes. Cancerous cells and infected cells in which TAP is blocked, as well as individuals with unusable TAP complexes, are able to present peptides on HLA class I by generating them through TAP-independent processing pathways. Here, we identify a physiologically processed HLA-E ligand derived from the D8L protein in TAP-deficient vaccinia virus-infected cells. This natural high affinity HLA-E class I ligand uses alternative interactions to the anchor motifs previously described to be presented on nonclassical HLA class I molecules. This octameric peptide was also presented on HLA-Cw1 with similar binding affinity on both classical and nonclassical class I molecules. In addition, this viral peptide inhibits HLA-E-mediated cytolysis by natural killer cells. Comparison between the amino acid sequences of the presenting HLA-E and HLA-Cw1 alleles revealed a shared structural motif in both HLA class molecules, which could be related to their observed similar cross-reactivity affinities. This motif consists of several residues located on the floor of the peptide-binding site. These data expand the role of HLA-E as an antigen-presenting molecule.


Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 2104-2104
Author(s):  
Alexander A. Perakis ◽  
Haley L. Peters ◽  
Jason Roszik ◽  
Mao Zhang ◽  
Anna Sergeeva ◽  
...  

Abstract Introduction Multiple myeloma (MM) remains incurable and accounts for 20% of deaths from hematologic malignancies. Immune modulating drugs and immunotherapy have been shown to be beneficial in MM patients, highlighting the importance of the immune system in MM. The success of these interventions relies on the unique ability of the immune system to specifically distinguish between MM and normal cells. One example involves the use of cytotoxic T-lymphocytes (CTL) that eliminate cancer cells by recognizing tumor specific antigens (TSA) that are presented on human leukocyte antigen (HLA) class I molecules on the tumor cells. TSA are presented on HLA class I via the canonical antigen-processing pathway, which causes the tumor cells to become targets for killing by CTL. On the other hand, exogenous antigens are typically presented on HLA class II molecules. Through cross-presentation, exogenous antigens are taken up and presented on HLA class I molecules. We have recently identified cross-presentation as a mechanism by which tumor cells, including MM, present exogenous antigens, leading to an expanded repertoire of possible tumor antigens that can be targeted. Here we demonstrate that targeting cross-presented antigens is a feasible immunotherapeutic strategy in MM. To this end, we used the anti-PR1/HLA-A2 antibody, 8F4, which effectively eliminates PR1/HLA-A2-expressing tumor cells, and identified novel cross-presented antigens. Experimental design NSG mice were sublethally irradiated with 200 Rad. After 24 hours, 2x106 U266 cells transduced with luciferase/GFP were IV injected. Engraftment was confirmed by measuring human IgE in the mouse serum by ELISA and bioluminescent imaging (BLI). Mice were treated with 8F4 (10 mg/kg), IgG isotype control (10 mg/kg) or PBS. Mice were sacrificed on week 9, bone marrow was harvested and analyzed by flow cytometry. To identify novel cross-presented antigens, polymorphonuclear cells (PMN) were isolated from HLA-A2- healthy donors. PMN were lysed and cultured with U266 cells for 24 hours at a 2:1 PMN:U266 cell ratio. U266 cells were lysed, incubated with anti-HLA-ABC antibody and protein-A/G-sepharose beads. Immunoprecipitated proteins were recovered by mild acid elution and peptides were discovered using tandem mass spectrometry. HLA-A2 specific peptides with strong predicted in silico binding were analyzed using the HLArestrictor 1.2 algorithm. Antigen processing machinery (APM) of primary patient samples were analyzed using western blots. Results 8F4 treated mice showed a 2 fold decrease in the percent of U266 in the bone marrow compared to isotype and untreated mice (P<0.05) (Figure 1). ELISA demonstrated approximately a 3-fold decrease in human IgE ng/mL in serum of mice treated with 8F4 (P<0.001). BLI quantification showed approximately a 0.5 fold decrease in total flux (p/s) in mice treated with 8F4 compared to isotype and untreated mice. In addition to illustrating the therapeutic potential of targeting PR1, we also sought to identify other cross-presented MM peptides. Initially, over 4x103 total peptides were discovered by mass spectrometry (Figure 2). Using our reality score indexing and bioinformatics we identified approximately 5x102 unique, high confidence, cross-presented peptides. Our top candidate peptides have predicted HLA-A2 binding affinities of <18 nM, ion scores >21, retention time >30.42 minutes, and are rank 1 for their spectral matches. Since we have demonstrated the capability of MM to cross-present antigens, we investigated whether the APM was dysregulated in MM patients. Patients show dysregulation in tapasin, LMP2/7, and calnexin by western blot analysis. Conclusion Collectively, our data demonstrate that the MM antigen repertoire is much larger than previously appreciated, and that there is a new catalogue of potential immunotherapeutic targets in MM derived from exogenous antigens. Disclosures Sergeeva: Astellas Pharma: Patents & Royalties. Molldrem:Astellas Pharma: Patents & Royalties.


Hepatology ◽  
1996 ◽  
Vol 23 (5) ◽  
pp. 1181-1188 ◽  
Author(s):  
K Kurokohchi ◽  
M Carrington ◽  
D L Mann ◽  
T B Simonis ◽  
M A Alexander-Miller ◽  
...  

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 4119-4119
Author(s):  
Daniel Johannes Kowalewski ◽  
Heiko Schuster ◽  
Claudia Berlin ◽  
Lothar Kanz ◽  
Helmut R Salih ◽  
...  

Abstract Abstract 4119 Recurrent disease, selection for chemo resistant clones and inhibition of immune effector functions are limitations of chemotherapeutic treatment of cancer including CLL. This is even more since graft-versus-leukemia effects and remissions after donor lymphocyte infusions have been correlated to long-term CLL free survival. Clonotype analysis of such cases suggested clonally expanded CD8+ T cells that recognize tumor associated antigens (TAAs) presented on HLA (human leukocyte antigen) as mediators of the observed effects, thus making CLL an attractive target for peptide vaccine based immunotherapy. For this goal we established the approach of direct isolation and identification of naturally processed and presented HLA ligands from tissues of interest by affinity chromatography and mass spectrometry. Comparative, semi-quantitative analysis of the HLA ligandomes of malignant and benign samples provided the rationale for selection of potential targets. 42 CLL patients (ages 48–85; median 70 years) of different HLA types and disease stages (Binet A, 24 patients; Binet B, 11 patients; Binet C, 7 patients) were enrolled in this study. Furthermore we collected blood samples from 50 healthy volunteers. HLA class I ligands were isolated from CLL cells as well as benign B cells from healthy donors and unsorted healthy PBMC using a standard affinity chromatography protocol implementing the pan-HLA class I specific antibody W6/32. Liquid chromatography coupled mass spectrometry (LC-MS/MS) based peptide analysis was performed on an LTQ Orbitrap hybrid mass spectrometer followed by annotation of fragment spectra using the MASCOT search algorithm against the human proteome comprised in the SwissProt database. Spectral counting based analysis provided semi-quantitative information regarding the abundance of HLA ligands and their source proteins in the respective ligandomes. In addition, HLA quantification experiments on the cell surface of CLL cells and autologous healthy B cells were performed using a flow cytometric indirect immunofluorescence assay. For this interim analysis we completely analyzed the HLA ligandomes of 7 CLL patients and 10 healthy controls. In total, we identified more than 15.000 different HLA ligands representing more than 7300 different proteins. This comprised more than 6,500 different ligands from CLL cells representing a total of 4,149 source proteins. Comparative analysis of representation in the HLA ligandomes of CLL cells, healthy B cells and healthy PBMC identified 1741 different source proteins as being exclusively expressed in CLL. Semi-quantitative evaluation revealed 138 of these proteins as being highly expressed on CLL (e.g. SET proto-oncogene, Pim-1 Oncogene, Mucin 1). Flow cytomerty based quantification of surface HLA expression revealed similar amounts of HLA class I (p=0.23, unpaired t-test) and II (p=0.33, unpaired t-test) molecules on CLL cells and autologous benign B lymphocytes, with a trend to higher HLA expression on CLL cells. Taken together, the presented strategy enabled the identification of a vast array of both known and novel TAAs and their corresponding naturally processed and presented HLA ligands in CLL. It pinpointed highly overrepresented TAAs for further analysis and immunogenicity testing. Expansion of the dataset after analysis of all enrolled patients will provide an unprecedented in-depth characterization of the HLA ligandome of CLL for future immunotherapeutic approaches. Disclosures: No relevant conflicts of interest to declare.


Blood ◽  
2000 ◽  
Vol 95 (10) ◽  
pp. 3168-3175
Author(s):  
Cécile Gouttefangeas ◽  
Marianne Diehl ◽  
Wieland Keilholz ◽  
Rainer Frank Hörnlein ◽  
Stefan Stevanović ◽  
...  

The origin and the function of HLA class I molecules present on the surface of human platelets are still unclear. In particular, it is controversial which fraction of these class I molecules represents integral membrane components derived from the megakaryocyte-platelet lineage versus soluble plasma HLA molecules acquired by adsorption. Results of the present study show that HLA-A2 ligands isolated from platelets possess the same peptide motif as described for HLA-A2-associated peptides obtained from nucleated cells. Sequencing of these platelet-derived peptides reveals that they originate mainly from ubiquitously expressed proteins also present in the megakaryocyte-platelet lineage. Moreover, one of these peptides derives from the GPIX protein, which is specifically expressed by platelets and their precursors. Platelet HLA molecules are unstable in vitro at 37°C, but can be partially stabilized by addition of exogenous β2-microglobulin and HLA class I binding peptide, suggesting that platelets cannot load HLA molecules with endogenous peptides. In in vitro experiments platelets were used to stimulate peripheral blood mononuclear cells. No allospecific cytotoxicity was observed after primary stimulation, or secondary restimulation, with allogenic resting or activated platelets, even in the presence of additional third-party helper activity. These data indicate that HLA class I molecules from platelets cannot directly induce allogenic CD8+ cytotoxic T-cell response in vitro.


2005 ◽  
Vol 79 (24) ◽  
pp. 15537-15546 ◽  
Author(s):  
Francesca Bettosini ◽  
Maria Teresa Fiorillo ◽  
Adriana Magnacca ◽  
Laura Leone ◽  
Maria Rosaria Torrisi ◽  
...  

ABSTRACT Cytotoxic T lymphocytes (CTLs) are the most powerful weapon of the immune system to eliminate cells infected by intracellular parasites or tumors. However, very often, escape mechanisms overcome CTL immune surveillance by impairing the classical HLA class I antigen-processing pathway. Here, we describe a strategy for CTL activation based on the ability of Tat to mediate transcellular delivery of viral proteins encompassing HLA class I-restricted epitopes. In this system, the recombinant protein TAT-NpFlu containing the transduction domain of Tat of human immunodeficiency virus type 1 fused to the amino acid region 301 to 498 of the nucleoprotein of influenza A virus is proven to sensitize different human cells to lysis by HLA-B27-restricted, Flu 383-391-specific CTL lines. The fusion protein is processed very effectively, since a comparable biological effect is obtained with an amount of protein between 1 and 2 orders of magnitude lower than that of the synthetic peptide. Interestingly, while part of TAT-NpFlu undergoes fast and productive cleavage, a large amount of it remains intact for up to 24 h. Confocal microscopy shows that TAT-NpFlu accumulates in the trans-Golgi network (TGN), where it starts to be detectable 1 h after transduction. Using TAT-NpFlu mutants and hybrid constructs, we demonstrate that enrichment in the TGN occurs only when the carboxy-terminal region of NpFlu (amino acids 400 to 498) is present. These data disclose an unconventional route for presentation of epitopes restricted for HLA class I molecules.


Blood ◽  
2002 ◽  
Vol 99 (5) ◽  
pp. 1723-1729 ◽  
Author(s):  
Massimo Vitale ◽  
Jacques Zimmer ◽  
Roberta Castriconi ◽  
Daniel Hanau ◽  
Lionel Donato ◽  
...  

Natural killer (NK) cells are characterized by the ability to kill cells that lack HLA class I molecules while sparing autologous normal (HLA class I+) cells. However, patients with transporter-associated antigen processing (TAP) deficiency, though displaying strong reductions of HLA class I surface expression, in most instances do not experience NK-mediated autoimmune phenomena. A possible mechanism by which TAP−/− NK cells avoid autoreactivity against autologous HLA class I–deficient cells could be based on either quantitative or qualitative defects of surface receptors involved in NK cell triggering. In this study we show that NK cells derived from 2 patients with TAP2−/− express normal levels of all known triggering receptors. As revealed by the analysis of polyclonal and clonal NK cells, these receptors display normal functional capabilities and allow the killing of a panel of NK-susceptible targets, including autologous B-LCLs. On the other hand, TAP2−/− NK cells were unable to kill either allogeneic (HLA class I+) or autologous (HLA class I− ) phytohemagglutinin (PHA) blasts even in the presence of anti-HLA class I monoclonal antibody. These data suggest that TAP2−/− NK cells express still unknown inhibitory receptor(s) capable of down-regulating the NK cell cytotoxicity on binding to surface ligand(s) expressed by T cell blasts. Functional analyses, both at the polyclonal and at the clonal level, are consistent with the concept that the putative inhibitory receptor is expressed by virtually all TAP2−/− NK cells, whereas it is present only in rare NK cells from healthy persons. Another possibility would be that TAP2−/− NK cells are missing a still unidentified triggering receptor involved in NK cell-mediated killing of PHA blasts.


Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 5223-5223
Author(s):  
Jens Bauer ◽  
Nora Zieger ◽  
Annika Nelde ◽  
Leon Bichmann ◽  
Helmut R. Salih ◽  
...  

Abstract In recent years, therapeutic approaches for acute myeloid leukemia (AML) have been improved, however the disease is still characterized by high relapse rates and a poor overall survival mainly in elderly patients aged 60 years and older. The standard therapy for these AML patients involves hypomethylating agents (HMAs) such as decitabine. With this, treatment remission can be achieved in some patients, however effective post-remission therapies are still overdue. Recent data suggests that HMAs induce gene expression of various cancer/testis antigens (CTAs), which could lead to the presentation of cancer/testis antigen-derived peptides on human leukocyte antigen (HLA) molecules. These CTA-derived peptides might serve as prime targets for tailored T cell-based immunotherapy approaches, which could represent an effective post-remission combination therapy. Here we present a mass spectrometry-based study, which longitudinally maps the HLA-presented immunopeptidome and in particular cancer/testis antigens of AML cells under in vitro decitabine treatment. To analyze the impact of decitabine on the presentation of HLA ligands we treated the AML cell lines U937 and MONO-MAC-6 as well as primary AML cells (n = 1) with decitabine for 48 h (t48) and 72 h (t72) in vitro. Upon flow cytometry-based quantification of HLA class I and II surface expression levels, no significant changes of HLA surface molecule levels under decitabine treatment compared to untreated controls were observed. Implementing label-free quantitation mass spectrometry, we then quantitatively assessed HLA class I ligand presentation under decitabine treatment. Only minor effects of decitabine on the whole HLA class I-restricted peptidome were observed: We detected a significant upregulation of 2.6 ± 0.9% of HLA class I ligands (fold change (FC) ≥ 4, p ≤ 0.01) after 48 h of decitabine treatment, whereas 9.6 ± 5.7% of the ligands were altered in their abundance over time without treatment. At t72 similar proportions of decitabine modulation were observed with 4.2 ± 2.7% of up-regulated HLA ligands. A total of 69 HLA class I ligands derived from 31 different CTAs were identified by mass spectrometric analysis, 9 of these ligands were presented exclusively under decitabine treatment. Furthermore, we showed that decitabine exposure caused a significantly increased presentation of 7/69 CTA-derived HLA ligands at least at one time point in the cell lines and the primary AML cells (FC ≥ 4, p ≤ 0.01). From the CTA cyclin A1, two HLA class I-presented peptides were significantly upregulated in U937 cells at t48 (FC 79.0 and 8.2) and t72 (FC 14.1 and 12.4). In primary AML cells, two peptides derived from JARID1B and KIAA0100 were significantly upregulated at either t48 (FC 21.8) or t72 (FC 6.6). In addition, we screened our dataset for HLA ligands derived from previously described decitabine-regulated genes and identified a HLA class I-presented peptide from DAZL, which was significantly upregulated in U937 cells at t72 under decitabine treatment (FC 57.2). Taken together, our results demonstrate a modulatory effect of the hypomethylating agent decitabine on the HLA ligandome of AML cells, enhancing the presentation of CTA-derived peptides on HLA class I molecules. The latter will be further evaluated for their eligibility as targets for tailored peptide-based immunotherapeutic approaches in AML patients undergoing HMA treatment. Disclosures Salih: Several patent applications: Patents & Royalties: e.g. EP3064507A1.


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