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Martinez-Ortiz W, Zhou MM. Could PROTACs Protect Us From COVID-19? Drug Discov Today 2020; 25:S1359-6446(20)30338-X. [PMID: 32889063 PMCID: PMC7462587 DOI: 10.1016/j.drudis.2020.08.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/25/2022]
Affiliation(s)
- Wilnelly Martinez-Ortiz
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ming-Ming Zhou
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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52
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Ryu HY, Ahn SH, Hochstrasser M. SUMO and cellular adaptive mechanisms. Exp Mol Med 2020; 52:931-939. [PMID: 32591648 PMCID: PMC7338444 DOI: 10.1038/s12276-020-0457-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/16/2020] [Accepted: 05/13/2020] [Indexed: 02/06/2023] Open
Abstract
The ubiquitin family member SUMO is a covalent regulator of proteins that functions in response to various stresses, and defects in SUMO-protein conjugation or deconjugation have been implicated in multiple diseases. The loss of the Ulp2 SUMO protease, which reverses SUMO-protein modifications, in the model eukaryote Saccharomyces cerevisiae is severely detrimental to cell fitness and has emerged as a useful model for studying how cells adapt to SUMO system dysfunction. Both short-term and long-term adaptive mechanisms are triggered depending on the length of time cells spend without this SUMO chain-cleaving enzyme. Such short-term adaptations include a highly specific multichromosome aneuploidy and large changes in ribosomal gene transcription. While aneuploid ulp2Δ cells survive, they suffer severe defects in growth and stress resistance. Over many generations, euploidy is restored, transcriptional programs are adjusted, and specific genetic changes that compensate for the loss of the SUMO protease are observed. These long-term adapted cells grow at normal rates with no detectable defects in stress resistance. In this review, we examine the connections between SUMO and cellular adaptive mechanisms more broadly. Cellular stress caused by disrupting attachment of the ubiquitous small ubiquitin-like modifier (SUMO) proteins, which are present in most organisms and regulate numerous DNA processes and stress responses by attaching to key proteins, results in some remarkable adaptations. Mark Hochstrasser at Yale University, New Haven, USA, and co-workers review how this “sumoylation” is reversed by protease enzymes, and how imbalances between sumoylation and desumoylation may be linked to diseases including cancer. When certain SUMO proteases are deliberately disrupted, the cells quickly become aneuploid, i.e., carry an abnormal number of chromosomes. These cells show severe growth defects, but over many generations they regain the normal number of chromosomes. They also undergo genetic changes that promote alternative mechanisms that compensate for losing the SUMO protease and facilitate the same efficient stress responses as the original cells.
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Affiliation(s)
- Hong-Yeoul Ryu
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, College of National Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea.,Brain Science and Engineering Institute, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Seong Hoon Ahn
- Department of Molecular and Life Science, College of Science and Convergence Technology, Hanyang University, Ansan, 15588, Republic of Korea
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
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53
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Cai L, Caraballo Galva LD, Peng Y, Luo X, Zhu W, Yao Y, Ji Y, He Y. Preclinical Studies of the Off-Target Reactivity of AFP 158-Specific TCR Engineered T Cells. Front Immunol 2020; 11:607. [PMID: 32395117 PMCID: PMC7196607 DOI: 10.3389/fimmu.2020.00607] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/17/2020] [Indexed: 01/27/2023] Open
Abstract
Autologous T cells engineered with T receptor genes (TCR) are being studied to treat cancers. We have recently identified a panel of mouse TCRs specific for the HLA-A0201/alpha fetoprotein epitope (AFP158) complex and have shown that human T cells engineered with these TCR genes (TCR-Ts) can eradicate hepatocellular carcinoma (HCC) xenografts in NSG mice. However, due to TCR’s promiscuity, their off-target cross-reactivity must be studied prior to conducting clinical trials. In this study, we conducted in vitro X-scan assay and in silico analysis to determine the off-target cross-reactivity of 3 AFP158-specific TCR-Ts. We found that the 3 AFP158-specific TCR-Ts could be cross-activated by ENPP1436 peptide and that the TCR3-Ts could also be activated by another off-target peptide, RCL1215. However, compared to AFP158, it requires 250 times more ENPP1436 and 10,000 times more RCL1215 peptides to achieve the same level of activation. The EC50 of ENPP1436 peptide for activating TCR-Ts is approximately 17–33 times higher than AFP158. Importantly, the ENPP1+ tumor cells did not activate TCR1-Ts and TCR2-Ts, and only weakly activated TCR3-Ts. The IFNγ produced by TCR3-Ts after ENPP1+ cell stimulation was >22x lower than that after HepG2 cells. And, all TCR-Ts did not kill ENPP1 + tumor cells. Furthermore, ectopic over-expression of ENPP1 protein in HLA-A2+ tumor cells did not activate TCR-Ts. In silico analysis showed that the ENPP1436 peptide affinity for HLA-A0201 was ranked 40 times lower than AFP158 and the chance of ENPP1436 peptide being processed and presented by HLA-A0201 was 100 times less likely than AFP158. In contrast, the two off-targets (Titin and MAGE-A3) that did cause severe toxicity in previous trials have the same or higher MHC-binding affinity and the same or higher chance of being processed and presented. In conclusion, our data shows that TCR-Ts can be activated by off-target ENPP1436 peptide. But, compared to target AFP158, it requires at least 250 times more ENPP1436 to achieve the same level of activation. Importantly, ENPP1436 peptide in human cells is not processed and presented to a sufficient level to activate the AFP158-specific TCR-Ts. Thus, these TCR-Ts, especially the TCR1-Ts and TCR2-Ts, will unlikely cause significant off-target toxicity.
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Affiliation(s)
- Lun Cai
- Georgia Cancer Center, Medical College of Georgia, Augusta, GA, United States
| | - Leidy D Caraballo Galva
- Georgia Cancer Center, Medical College of Georgia, Augusta, GA, United States.,The Graduate School, Augusta University, Augusta, GA, United States
| | - Yibing Peng
- Georgia Cancer Center, Medical College of Georgia, Augusta, GA, United States
| | - Xiaobing Luo
- Cellular Biomedicine Group (CBMG), Gaithersburg, MD, United States
| | - Wei Zhu
- Georgia Cancer Center, Medical College of Georgia, Augusta, GA, United States
| | - Yihong Yao
- Cellular Biomedicine Group (CBMG), Gaithersburg, MD, United States
| | - Yun Ji
- Cellular Biomedicine Group (CBMG), Gaithersburg, MD, United States
| | - Yukai He
- Georgia Cancer Center, Medical College of Georgia, Augusta, GA, United States.,The Graduate School, Augusta University, Augusta, GA, United States.,Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA, United States.,Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA, United States
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54
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Role for ribosome-associated quality control in sampling proteins for MHC class I-mediated antigen presentation. Proc Natl Acad Sci U S A 2020; 117:4099-4108. [PMID: 32047030 PMCID: PMC7049129 DOI: 10.1073/pnas.1914401117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Pathogens and tumors are detected by the immune system through the display of intracellular peptides on MHC-I complexes. These peptides are generated by the ubiquitin−proteasome system preferentially from newly synthesized polypeptides. Here we show that the ribosome-associated quality control (RQC) pathway, responsible for proteasomal degradation of polypeptide chains that stall during translation, mediates efficient antigen presentation of model proteins independent of their intrinsic folding properties. Immunopeptidome characterization of RQC-deficient cells shows that RQC contributes to the presentation of a wide variety of proteins, including proteins that may otherwise evade presentation due to efficient folding. By identifying endogenous substrates of the RQC pathway in human cells, our results also enable the analysis of common principles causing ribosome stalling under physiological conditions. Mammalian cells present a fingerprint of their proteome to the adaptive immune system through the display of endogenous peptides on MHC-I complexes. MHC-I−bound peptides originate from protein degradation by the proteasome, suggesting that stably folded, long-lived proteins could evade monitoring. Here, we investigate the role in antigen presentation of the ribosome-associated quality control (RQC) pathway for the degradation of nascent polypeptides that are encoded by defective messenger RNAs and undergo stalling at the ribosome during translation. We find that degradation of model proteins by RQC results in efficient MHC-I presentation, independent of their intrinsic folding properties. Quantitative profiling of MHC-I peptides in wild-type and RQC-deficient cells by mass spectrometry showed that RQC substantially contributes to the composition of the immunopeptidome. Our results also identify endogenous substrates of the RQC pathway in human cells and provide insight into common principles causing ribosome stalling under physiological conditions.
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55
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van den Bulk J, Verdegaal EME, Ruano D, Ijsselsteijn ME, Visser M, van der Breggen R, Duhen T, van der Ploeg M, de Vries NL, Oosting J, Peeters KCMJ, Weinberg AD, Farina-Sarasqueta A, van der Burg SH, de Miranda NFCC. Neoantigen-specific immunity in low mutation burden colorectal cancers of the consensus molecular subtype 4. Genome Med 2019; 11:87. [PMID: 31888734 PMCID: PMC6938004 DOI: 10.1186/s13073-019-0697-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 11/20/2019] [Indexed: 12/30/2022] Open
Abstract
Background The efficacy of checkpoint blockade immunotherapies in colorectal cancer is currently restricted to a minority of patients diagnosed with mismatch repair-deficient tumors having high mutation burden. However, this observation does not exclude the existence of neoantigen-specific T cells in colorectal cancers with low mutation burden and the exploitation of their anti-cancer potential for immunotherapy. Therefore, we investigated whether autologous neoantigen-specific T cell responses could also be observed in patients diagnosed with mismatch repair-proficient colorectal cancers. Methods Whole-exome and transcriptome sequencing were performed on cancer and normal tissues from seven colorectal cancer patients diagnosed with mismatch repair-proficient tumors to detect putative neoantigens. Corresponding neo-epitopes were synthesized and tested for recognition by in vitro expanded T cells that were isolated from tumor tissues (tumor-infiltrating lymphocytes) and from peripheral mononuclear blood cells stimulated with tumor material. Results Neoantigen-specific T cell reactivity was detected to several neo-epitopes in the tumor-infiltrating lymphocytes of three patients while their respective cancers expressed 15, 21, and 30 non-synonymous variants. Cell sorting of tumor-infiltrating lymphocytes based on the co-expression of CD39 and CD103 pinpointed the presence of neoantigen-specific T cells in the CD39+CD103+ T cell subset. Strikingly, the tumors containing neoantigen-reactive TIL were classified as consensus molecular subtype 4 (CMS4), which is associated with TGF-β pathway activation and worse clinical outcome. Conclusions We have detected neoantigen-targeted reactivity by autologous T cells in mismatch repair-proficient colorectal cancers of the CMS4 subtype. These findings warrant the development of specific immunotherapeutic strategies that selectively boost the activity of neoantigen-specific T cells and target the TGF-β pathway to reinforce T cell reactivity in this patient group.
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Affiliation(s)
| | | | - Dina Ruano
- Pathology, LUMC, Postbus 9600, 2300 RC, Leiden, The Netherlands
| | | | - Marten Visser
- Medical Oncology, Oncode Institute, LUMC, Leiden, The Netherlands
| | | | | | | | | | - Jan Oosting
- Pathology, LUMC, Postbus 9600, 2300 RC, Leiden, The Netherlands
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56
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Hardy MP, Vincent K, Perreault C. The Genomic Landscape of Antigenic Targets for T Cell-Based Leukemia Immunotherapy. Front Immunol 2019; 10:2934. [PMID: 31921187 PMCID: PMC6933603 DOI: 10.3389/fimmu.2019.02934] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/29/2019] [Indexed: 12/30/2022] Open
Abstract
Intensive fundamental and clinical research in cancer immunotherapy has led to the emergence and evolution of two parallel universes with surprisingly little interactions: the realm of hematologic malignancies and that of solid tumors. Treatment of hematologic cancers using allogeneic hematopoietic cell transplantation (AHCT) serendipitously led to the discovery that T cells specific for minor histocompatibility antigens (MiHAs) could cure hematopoietic cancers. Besides, studies based on treatment of solid tumor with ex vivo-expanded tumor infiltrating lymphocytes or immune checkpoint therapy demonstrated that anti-tumor responses could be achieved by targeting tumor-specific antigens (TSAs). It is our contention that much insight can be gained by sharing the tremendous amount of data generated in the two-abovementioned universes. Our perspective article has two specific goals. First, to discuss the value of methods currently used for MiHA and TSA discovery and to explain the key role of mass spectrometry analyses in this process. Second, to demonstrate the importance of broadening the scope of TSA discovery efforts beyond classic annotated protein-coding genomic sequences.
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Affiliation(s)
- Marie-Pierre Hardy
- Department of Immunobiology, Institute for Research in Immunology and Cancer, Montreal, QC, Canada
| | - Krystel Vincent
- Department of Immunobiology, Institute for Research in Immunology and Cancer, Montreal, QC, Canada
| | - Claude Perreault
- Department of Immunobiology, Institute for Research in Immunology and Cancer, Montreal, QC, Canada
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57
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Amon L, Lehmann CHK, Baranska A, Schoen J, Heger L, Dudziak D. Transcriptional control of dendritic cell development and functions. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2019; 349:55-151. [PMID: 31759434 DOI: 10.1016/bs.ircmb.2019.10.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Dendritic cells (DCs) are major regulators of adaptive immunity, as they are not only capable to induce efficient immune responses, but are also crucial to maintain peripheral tolerance and thereby inhibit autoimmune reactions. DCs bridge the innate and the adaptive immune system by presenting peptides of self and foreign antigens as peptide MHC complexes to T cells. These properties render DCs as interesting target cells for immunomodulatory therapies in cancer, but also autoimmune diseases. Several subsets of DCs with special properties and functions have been described. Recent achievements in understanding transcriptional programs on single cell level, together with the generation of new murine models targeting specific DC subsets, advanced our current understanding of DC development and function. Thus, DCs arise from precursor cells in the bone marrow with distinct progenitor cell populations splitting the monocyte populations and macrophage populations from the DC lineage, which upon lineage commitment can be separated into conventional cDC1, cDC2, and plasmacytoid DCs (pDCs). The DC populations harbor intrinsic programs enabling them to react for specific pathogens in dependency on the DC subset, and thereby orchestrate T cell immune responses. Similarities, but also varieties, between human and murine DC subpopulations are challenging, and will require further investigation of human specimens under consideration of the influence of the tissue micromilieu and DC subset localization in the future.
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Affiliation(s)
- Lukas Amon
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Christian H K Lehmann
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Anna Baranska
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Janina Schoen
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Lukas Heger
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Diana Dudziak
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany.
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58
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Tomkinson B. Tripeptidyl-peptidase II: Update on an oldie that still counts. Biochimie 2019; 166:27-37. [DOI: 10.1016/j.biochi.2019.05.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/14/2019] [Indexed: 12/30/2022]
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59
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IJsselsteijn ME, Sanz-Pamplona R, Hermitte F, de Miranda NF. Colorectal cancer: A paradigmatic model for cancer immunology and immunotherapy. Mol Aspects Med 2019; 69:123-129. [DOI: 10.1016/j.mam.2019.05.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 05/16/2019] [Accepted: 05/24/2019] [Indexed: 12/28/2022]
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60
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Brown LV, Gaffney EA, Wagg J, Coles MC. An in silico model of cytotoxic T-lymphocyte activation in the lymph node following short peptide vaccination. J R Soc Interface 2019. [PMID: 29540543 DOI: 10.1098/rsif.2018.0041] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Tumour immunotherapy is dependent upon activation and expansion of tumour-targetting immune cells, known as cytotoxic T-lymphocytes (CTLs). Cancer vaccines developed in the past have had limited success and the mechanisms resulting in failure are not well characterized. To elucidate these mechanisms, we developed a human-parametrized, in silico, agent-based model of vaccination-driven CTL activation within a clinical short-peptide vaccination context. The simulations predict a sharp transition in the probability of CTL activation, which occurs with variation in the separation rate (or off-rate) of tumour-specific immune response-inducing peptides (cognate antigen) from the major histocompatibility class I (MHC-I) receptors of dendritic cells (DCs) originally at the vaccination site. For peptides with MHC-I off-rates beyond this transition, it is predicted that no vaccination strategy will lead to successful expansion of CTLs. For slower off-rates, below the transition, the probability of CTL activation becomes sensitive to the numbers of DCs and T cells that interact subsequent to DC migration to the draining lymph node of the vaccination site. Thus, the off-rate is a key determinant of vaccine design.
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Affiliation(s)
- Liam V Brown
- Wolfson Centre For Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK
| | - Eamonn A Gaffney
- Wolfson Centre For Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK
| | - Jonathan Wagg
- Clinical Pharmacology, Roche Innovation Center Basel, Basel, Switzerland
| | - Mark C Coles
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
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61
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Lhuillier C, Rudqvist NP, Elemento O, Formenti SC, Demaria S. Radiation therapy and anti-tumor immunity: exposing immunogenic mutations to the immune system. Genome Med 2019; 11:40. [PMID: 31221199 PMCID: PMC6587285 DOI: 10.1186/s13073-019-0653-7] [Citation(s) in RCA: 164] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The expression of antigens that are recognized by self-reactive T cells is essential for immune-mediated tumor rejection by immune checkpoint blockade (ICB) therapy. Growing evidence suggests that mutation-associated neoantigens drive ICB responses in tumors with high mutational burden. In most patients, only a few of the mutations in the cancer exome that are predicted to be immunogenic are recognized by T cells. One factor that limits this recognition is the level of expression of the mutated gene product in cancer cells. Substantial preclinical data show that radiation can convert the irradiated tumor into a site for priming of tumor-specific T cells, that is, an in situ vaccine, and can induce responses in otherwise ICB-resistant tumors. Critical for radiation-elicited T-cell activation is the induction of viral mimicry, which is mediated by the accumulation of cytosolic DNA in the irradiated cells, with consequent activation of the cyclic GMP-AMP synthase (cGAS)/stimulator of interferon (IFN) genes (STING) pathway and downstream production of type I IFN and other pro-inflammatory cytokines. Recent data suggest that radiation can also enhance cancer cell antigenicity by upregulating the expression of a large number of genes that are involved in the response to DNA damage and cellular stress, thus potentially exposing immunogenic mutations to the immune system. Here, we discuss how the principles of antigen presentation favor the presentation of peptides that are derived from newly synthesized proteins in irradiated cells. These concepts support a model that incorporates the presence of immunogenic mutations in genes that are upregulated by radiation to predict which patients might benefit from treatment with combinations of radiotherapy and ICB.
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Affiliation(s)
- Claire Lhuillier
- Department of Radiation Oncology, Weill Cornell Medicine, Stich Radiation Oncology Center, 525 East 68th Street, New York, NY, 10065, USA
| | - Nils-Petter Rudqvist
- Department of Radiation Oncology, Weill Cornell Medicine, Stich Radiation Oncology Center, 525 East 68th Street, New York, NY, 10065, USA
| | - Olivier Elemento
- Department of Physiology and Biophysics, Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, 413 East 69th Street, New York, NY, 10021, USA.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA.,Institute for Computational Biomedicine, Weill Cornell Medical College, 1305 York Avenue, New York, NY, 10021, USA
| | - Silvia C Formenti
- Department of Radiation Oncology, Weill Cornell Medicine, Stich Radiation Oncology Center, 525 East 68th Street, New York, NY, 10065, USA.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Sandra Demaria
- Department of Radiation Oncology, Weill Cornell Medicine, Stich Radiation Oncology Center, 525 East 68th Street, New York, NY, 10065, USA. .,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA. .,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA.
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62
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Besser H, Yunger S, Merhavi-Shoham E, Cohen CJ, Louzoun Y. Level of neo-epitope predecessor and mutation type determine T cell activation of MHC binding peptides. J Immunother Cancer 2019; 7:135. [PMID: 31118084 PMCID: PMC6532181 DOI: 10.1186/s40425-019-0595-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 04/22/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Targeting epitopes derived from neo-antigens (or "neo-epitopes") represents a promising immunotherapy approach with limited off-target effects. However, most peptides predicted using MHC binding prediction algorithms do not induce a CD8 + T cell response, and there is a crucial need to refine the predictions to readily identify the best antigens that could mediate T-cell responses. Such a response requires a high enough number of epitopes bound to the target MHC. This number is correlated with both the peptide-MHC binding affinity and the number of peptides reaching the ER. Beyond this, the response may be affected by the properties of the neo-epitope mutated residues. METHODS Herein, we analyzed several experimental datasets from cancer patients to elaborate better predictive algorithms for T-cell reactivity to neo-epitopes. RESULTS Indeed, potent classifiers for epitopes derived from neo-antigens in melanoma and other tumors can be developed based on biochemical properties of the mutated residue, the antigen expression level and the peptide processing stage. Among MHC binding peptides, the present classifiers can remove half of the peptides falsely predicted to activate T cells while maintaining the absolute majority of reactive peptides. CONCLUSIONS The classifier properties further highlight the contribution of the quantity of peptides reaching the ER and the mutation type to CD8 + T cell responses. These classifiers were then validated on neo-antigens obtained from other datasets, confirming the validity of our prediction. Algorithm Availability: http://peptibase.cs.biu.ac.il/Tcell_predictor/ or by request from the authors as a standalone code.
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Affiliation(s)
- Hanan Besser
- The Leslie and Susan Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, 5290002, Ramat Gan, Israel
- Department of Mathematics, Bar-Ilan University, 5290002, Ramat Gan, Israel
| | - Sharon Yunger
- Ella Lemelbaum Institute for Immuno Oncology, Sheba Medical Center, Ramat Gan, Israel
| | - Efrat Merhavi-Shoham
- Ella Lemelbaum Institute for Immuno Oncology, Sheba Medical Center, Ramat Gan, Israel
| | - Cyrille J Cohen
- Laboratory of Tumor Immunology and Immunotherapy, Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel.
| | - Yoram Louzoun
- The Leslie and Susan Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, 5290002, Ramat Gan, Israel.
- Department of Mathematics, Bar-Ilan University, 5290002, Ramat Gan, Israel.
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63
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Hongo A, Kanaseki T, Tokita S, Kochin V, Miyamoto S, Hashino Y, Codd A, Kawai N, Nakatsugawa M, Hirohashi Y, Sato N, Torigoe T. Upstream Position of Proline Defines Peptide-HLA Class I Repertoire Formation and CD8 + T Cell Responses. THE JOURNAL OF IMMUNOLOGY 2019; 202:2849-2855. [PMID: 30936292 DOI: 10.4049/jimmunol.1900029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 03/08/2019] [Indexed: 02/02/2023]
Abstract
Cytotoxic CD8+ T lymphocytes (CTLs) recognize peptides displayed by HLA class I molecules on cell surfaces, monitoring pathological conditions such as cancer. Difficulty in predicting HLA class I ligands is attributed to the complexity of the Ag processing pathway across the cytosol and the endoplasmic reticulum. By means of HLA ligandome analysis using mass spectrometry, we collected natural HLA class I ligands on a large scale and analyzed the source-protein sequences flanking the ligands. This comprehensive analysis revealed that the frequency of proline at amino acid positions 1-3 upstream of the ligands was selectively decreased. The depleted proline signature was the strongest among all the upstream and downstream profiles. Experiments using live cells demonstrated that the presence of proline at upstream positions 1-3 attenuated CTL responses against a model epitope. Other experiments, in which N-terminal-flanking Ag precursors were confined in the endoplasmic reticulum, demonstrated an inability to remove upstream prolines regardless of their positions, suggesting a need for synergistic action across cellular compartments for making the proline signature. Our results highlight, to our knowledge, a unique role and position of proline for inhibiting downstream epitope presentation, which provides a rule for defining natural peptide-HLA class I repertoire formation and CTL responses.
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Affiliation(s)
- Ayumi Hongo
- Department of Pathology, Sapporo Medical University, Sapporo, Hokkaido 060-8556, Japan
| | - Takayuki Kanaseki
- Department of Pathology, Sapporo Medical University, Sapporo, Hokkaido 060-8556, Japan;
| | - Serina Tokita
- Department of Pathology, Sapporo Medical University, Sapporo, Hokkaido 060-8556, Japan
| | - Vitaly Kochin
- Department of Immunology, Nagoya University, Nagoya 466-8550, Japan
| | - Sho Miyamoto
- Department of Oral Surgery, Sapporo Medical University, Sapporo, Hokkaido 060-8556, Japan; and
| | - Yuiko Hashino
- Department of Pathology, Sapporo Medical University, Sapporo, Hokkaido 060-8556, Japan
| | - Amy Codd
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, Wales, United Kingdom
| | - Noriko Kawai
- Department of Pathology, Sapporo Medical University, Sapporo, Hokkaido 060-8556, Japan
| | - Munehide Nakatsugawa
- Department of Pathology, Sapporo Medical University, Sapporo, Hokkaido 060-8556, Japan
| | - Yoshihiko Hirohashi
- Department of Pathology, Sapporo Medical University, Sapporo, Hokkaido 060-8556, Japan
| | - Noriyuki Sato
- Department of Pathology, Sapporo Medical University, Sapporo, Hokkaido 060-8556, Japan
| | - Toshihiko Torigoe
- Department of Pathology, Sapporo Medical University, Sapporo, Hokkaido 060-8556, Japan
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van den Bulk J, Verdegaal EM, de Miranda NF. Cancer immunotherapy: broadening the scope of targetable tumours. Open Biol 2019; 8:rsob.180037. [PMID: 29875199 PMCID: PMC6030119 DOI: 10.1098/rsob.180037] [Citation(s) in RCA: 149] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/11/2018] [Indexed: 12/12/2022] Open
Abstract
Cancer immunotherapy has experienced remarkable advances in recent years. Striking clinical responses have been achieved for several types of solid cancers (e.g. melanoma, non-small cell lung cancer, bladder cancer and mismatch repair-deficient cancers) after treatment of patients with T-cell checkpoint blockade therapies. These have been shown to be particularly effective in the treatment of cancers with high mutation burden, which places tumour-mutated antigens (neo-antigens) centre stage as targets of tumour immunity and cancer immunotherapy. With current technologies, neo-antigens can be identified in a short period of time, which may support the development of complementary, personalized approaches that increase the number of tumours amenable to immunotherapeutic intervention. In addition to reviewing the state of the art in cancer immunotherapy, we discuss potential avenues that can bring the immunotherapy revolution to a broader patient group including cancers with low mutation burden.
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65
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Abstract
This chapter focuses on the discovery of the Major Histocompatibility Complex (MHC) in mice (H-2) and in humans (HLA), and on the role played by the International HLA Workshops in the analysis and characterization of this complex genetic system. The early days of Tumour Immunology and the importance of the definition of Tumour Associated Transplantation Antigens (TATA) are also discussed. Today we know that tumour cells can be killed by T lymphocytes by recognizing tumour antigenic peptides presented by MHC molecules and they can also escape this recognition by losing the expression of MHC molecules. This important phenomenon has been profoundly studied for many years both in my lab in Granada and in other laboratories. The results of this research have important implications for the new generation of cancer immunotherapy that boosts T cell responses. A historical perspective of major discoveries is presented in this chapter, with the names of the scientists that have made a significant contribution to the enormous progress made in the field of Tumour Immunology.
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Affiliation(s)
- Federico Garrido
- Departamento de Analisis Clinicos e Inmunologia, Hospital Universitario Virgen de las Nieves, Facultad de Medicina, Universidad de Granada, Granada, Spain
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66
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Egui A, Lasso P, Pérez-Antón E, Thomas MC, López MC. Dynamics of T Cells Repertoire During Trypanosoma cruzi Infection and its Post-Treatment Modulation. Curr Med Chem 2018; 26:6519-6543. [PMID: 30381063 DOI: 10.2174/0929867325666181101111819] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 09/11/2018] [Accepted: 09/25/2018] [Indexed: 01/16/2023]
Abstract
Chagas disease courses with different clinical phases and has a variable clinical presentation and progression. The acute infection phase mostly exhibits a non-specific symptomatology. In the absence of treatment, the acute phase is followed by a chronic phase, which is initially asymptomatic. This chronic asymptomatic phase of the disease is characterized by a fragile balance between the host's immune response and the parasite replication. The loss of this balance is crucial for the progression of the sickness. The virulence and tropism of the T. cruzi infecting strain together to the inflammation processes in the cardiac tissue are the main factors for the establishment and severity of the cardiomyopathy. The efficacy of treatment in chronic Chagas disease patients is controversial. However, several studies carried out in chronic patients demonstrated that antiparasitic treatment reduces parasite load in the bloodstream and leads to an improvement in the immune response against the Trypanosoma cruzi parasite. The present review is mainly focused on the cellular patterns associated to the clinical status and the evolution of the disease in chronic patients, as well as the effectiveness of the treatment related to T. cruzi infection control. Therefore, an emphasis is placed on the dynamics of specific-antigens T cell subpopulations, their memory and activation phenotypes, their functionality and their contribution to pathogenesis or disease control, as well as their association with risk of congenital transmission of the parasite.
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Affiliation(s)
- Adriana Egui
- Instituto de Parasitologia y Biomedicina Lopez-Neyra, Consejo Superior de Investigaciones Científicas; Granada, Spain
| | - Paola Lasso
- Grupo de Inmunobiologia y Biologia Celular, Pontificia Universidad Javeriana; Bogota, Colombia
| | - Elena Pérez-Antón
- Instituto de Parasitologia y Biomedicina Lopez-Neyra, Consejo Superior de Investigaciones Científicas; Granada, Spain
| | - M Carmen Thomas
- Instituto de Parasitologia y Biomedicina Lopez-Neyra, Consejo Superior de Investigaciones Científicas; Granada, Spain
| | - Manuel Carlos López
- Instituto de Parasitologia y Biomedicina Lopez-Neyra, Consejo Superior de Investigaciones Científicas; Granada, Spain
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67
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Woon AP, Purcell AW. The use of proteomics to understand antiviral immunity. Semin Cell Dev Biol 2018; 84:22-29. [PMID: 30449533 DOI: 10.1016/j.semcdb.2017.12.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 11/27/2017] [Accepted: 12/06/2017] [Indexed: 01/01/2023]
Abstract
Viruses are intracellular pathogens that cause a vast array of diseases, which are often severe and typified by high morbidity and mortality rates. Viral infections continue to be a global health burden and effective vaccines and therapeutics are constantly sought to prevent and treat these infections. The development of such treatments generally relies on understanding the mechanisms that underpin efficient host antiviral immune responses. This review summarises recent developments in our understanding of antiviral adaptive immunity and in particular, highlights the use of mass spectrometry to elucidate viral antigens and their processing and presentation to T cells and other immune effectors. These processed peptides serve as potential vaccine candidates or may facilitate clinical monitoring, diagnosis and immunotherapy of infectious diseases.
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Affiliation(s)
- Amanda P Woon
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
| | - Anthony W Purcell
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
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68
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Chadha R, Kalminskii G, Tierney AJ, Knopf JD, Lazo de la Vega L, McElrath B, Kovarik ML. Effect of Loading Method on a Peptide Substrate Reporter in Intact Cells. Anal Chem 2018; 90:11344-11350. [PMID: 30175919 DOI: 10.1021/acs.analchem.8b02111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Studies of live cells often require loading of exogenous molecules through the cell membrane; however, effects of loading method on experimental results are poorly understood. Therefore, in this work, we compared three methods for loading a fluorescently labeled peptide into cells of the model organism Dictyostelium discoideum. We optimized loading by pinocytosis, electroporation, and myristoylation to maximize cell viability and characterized loading efficiency, localization, and uniformity. We also determined how the loading method affected measurements of enzyme activity on the peptide substrate reporter using capillary electrophoresis. Loading method had a strong effect on the stability and phosphorylation of the peptide. The half-life of the intact peptide in cells was 19 ± 2, 53 ± 15, and 12 ± 1 min, for pinocytosis, electroporation, and myristoylation, respectively. The peptide was phosphorylated only in cells loaded by electroporation. Fluorescence microscopy suggested that the differences between methods were likely due to differences in peptide localization.
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Affiliation(s)
- Rahuljeet Chadha
- Department of Chemistry , Trinity College , 300 Summit Street , Hartford , Connecticut 06106 , United States
| | - Grigorii Kalminskii
- Department of Chemistry , Trinity College , 300 Summit Street , Hartford , Connecticut 06106 , United States
| | - Allison J Tierney
- Department of Chemistry , Trinity College , 300 Summit Street , Hartford , Connecticut 06106 , United States
| | - Joshua D Knopf
- Department of Chemistry , Trinity College , 300 Summit Street , Hartford , Connecticut 06106 , United States
| | - Lorena Lazo de la Vega
- Department of Chemistry , Trinity College , 300 Summit Street , Hartford , Connecticut 06106 , United States
| | - Berjana McElrath
- Department of Chemistry , Trinity College , 300 Summit Street , Hartford , Connecticut 06106 , United States
| | - Michelle L Kovarik
- Department of Chemistry , Trinity College , 300 Summit Street , Hartford , Connecticut 06106 , United States
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69
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Solcia E, Necchi V, Sommi P, Ricci V. Proteasome-Rich PaCS as an Oncofetal UPS Structure Handling Cytosolic Polyubiquitinated Proteins. In Vivo Occurrence, in Vitro Induction, and Biological Role. Int J Mol Sci 2018; 19:ijms19092767. [PMID: 30223470 PMCID: PMC6164709 DOI: 10.3390/ijms19092767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 09/11/2018] [Indexed: 11/16/2022] Open
Abstract
In this article, we outline and discuss available information on the cellular site and mechanism of proteasome interaction with cytosolic polyubiquitinated proteins and heat-shock molecules. The particulate cytoplasmic structure (PaCS) formed by barrel-like particles, closely reproducing in vivo the high-resolution structure of 26S proteasome as isolated in vitro, has been detected in a variety of fetal and neoplastic cells, from living tissue or cultured cell lines. Specific trophic factors and interleukins were found to induce PaCS during in vitro differentiation of dendritic, natural killer (NK), or megakaryoblastic cells, apparently through activation of the MAPK-ERK pathway. Direct interaction of CagA bacterial oncoprotein with proteasome was shown inside the PaCSs of a Helicobacter pylori-infected gastric epithelium, a finding suggesting a role for PaCS in CagA-mediated gastric carcinogenesis. PaCS dissolution and autophagy were seen after withdrawal of inducing factors. PaCS-filled cell blebs and ectosomes were found in some cells and may represent a potential intercellular discharge and transport system of polyubiquitinated antigenic proteins. PaCS differs substantially from the inclusion bodies, sequestosomes, and aggresomes reported in proteinopathies like Huntington or Parkinson diseases, which usually lack PaCS. The latter seems more linked to conditions of increased cell proliferation/differentiation, implying an increased functional demand to the ubiquitin–proteasome system.
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Affiliation(s)
- Enrico Solcia
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy.
- Pathologic Anatomy Unit, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy.
| | - Vittorio Necchi
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy.
- Centro Grandi Strumenti, University of Pavia, 27100 Pavia, Italy.
| | - Patrizia Sommi
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy.
| | - Vittorio Ricci
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy.
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70
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van der Gracht AMF, de Geus MAR, Camps MGM, Ruckwardt TJ, Sarris AJC, Bremmers J, Maurits E, Pawlak JB, Posthoorn MM, Bonger KM, Filippov DV, Overkleeft HS, Robillard MS, Ossendorp F, van Kasteren SI. Chemical Control over T-Cell Activation in Vivo Using Deprotection of trans-Cyclooctene-Modified Epitopes. ACS Chem Biol 2018; 13:1569-1576. [PMID: 29733186 PMCID: PMC6006443 DOI: 10.1021/acschembio.8b00155] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
Activation
of a cytotoxic T-cell is a complex multistep process,
and tools to study the molecular events and their dynamics that result
in T-cell activation in situ and in vivo are scarce. Here, we report the design and use of conditional epitopes
for time-controlled T-cell activation in vivo. We
show that trans-cyclooctene-protected SIINFEKL (with
the lysine amine masked) is unable to elicit the T-cell response characteristic
for the free SIINFEKL epitope. Epitope uncaging by means of an inverse-electron
demand Diels–Alder (IEDDA) event restored T-cell activation
and provided temporal control of T-cell proliferation in vivo.
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Affiliation(s)
- Anouk M. F. van der Gracht
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Mark A. R. de Geus
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Marcel G. M. Camps
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Tracy J. Ruckwardt
- Vaccine Research Center, National Institute of Allergy and Infectious Disease, National Institute of Health, 40 Convent Drive, Building 40, Bethesda, Maryland 20814, United States
| | - Alexi J. C. Sarris
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Jessica Bremmers
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Elmer Maurits
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Joanna B. Pawlak
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Michelle M. Posthoorn
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Kimberly M. Bonger
- Department of Biomolecular Chemistry, Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Dmitri V. Filippov
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Herman S. Overkleeft
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Marc S. Robillard
- Tagworks Pharmaceuticals, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Ferry Ossendorp
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Sander I. van Kasteren
- Leiden Institute of Chemistry and The Institute for Chemical Immunology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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71
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Komov L, Kadosh DM, Barnea E, Milner E, Hendler A, Admon A. Cell Surface MHC Class I Expression Is Limited by the Availability of Peptide-Receptive "Empty" Molecules Rather than by the Supply of Peptide Ligands. Proteomics 2018; 18:e1700248. [PMID: 29707912 DOI: 10.1002/pmic.201700248] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 04/16/2018] [Indexed: 01/07/2023]
Abstract
While antigen processing and presentation (APP) by the major histocompatibility complex class I (MHC-I) molecules have been extensively studied, a question arises as to whether the level of MHC-I expression is limited by the supply of peptide-receptive (empty) MHC molecules, or by the availability of peptide ligands for loading. To this end, the effect of interferons (IFNs) on the MHC peptidomes of human breast cancer cells (MCF-7) were evaluated. Although all four HLA allotypes of the MCF-7 cells (HLA-A*02:01, B*18, B*44, and C*5) present peptides of similar lengths and C-termini, which should be processed similarly by the proteasome and by the APP chaperones, the IFNs induced differential modulation of the HLA-A, B, and C peptidomes. In addition, overexpression of recombinant soluble HLA-A*02:01, introduced to compete with the identical endogenous membrane-bound HLA-A*02:01 for peptides of the MCF-7 cells, did not alter the expression level or the presented peptidome of the membrane-bound HLA-A*02:01. Taken together, these results indicate that a surplus supply of peptides is available inside the ER for loading onto the MHC-I peptide-receptive molecules, and that cell surface MHC-I expression is likely limited by the availability of empty MHC molecules.
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Affiliation(s)
- Liran Komov
- Department of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Dganit Melamed Kadosh
- Department of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Eilon Barnea
- Department of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Elena Milner
- Department of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Ayellet Hendler
- Department of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Arie Admon
- Department of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
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72
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Viral peptides-MHC interaction: Binding probability and distance from human peptides. J Immunol Methods 2018; 459:35-43. [PMID: 29800577 DOI: 10.1016/j.jim.2018.05.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 03/26/2018] [Accepted: 05/09/2018] [Indexed: 11/23/2022]
Abstract
Identification of peptides binding to MHC class I complex can play a crucial role in retrieving potential targets able to trigger an immune response. Affinity binding of viral peptides can be estimated through effective computational methods that in the most of cases are based on machine learning approach. Achieving a better insight into peptide features that impact on the affinity binding rate is a challenging issue. In the present work we focused on 9-mer peptides of Human immunodeficiency virus type 1 and Human herpes simplex virus 1, studying their binding to MHC class I. Viral 9-mers were partitioned into different classes, where each class is characterized by how far (in terms of mutation steps) the peptides belonging to that class are from human 9-mers. Viral 9-mers were partitioned in different classes, based on the number of mutation steps they are far from human 9-mers. We showed that the overall binding probability significantly differs among classes, and it typically increases as the distance, computed in terms of number of mutation steps from the human set of 9-mers, increases. The binding probability is particularly high when considering viral 9-mers that are far from all human 9-mers more than three mutation steps. A further evidence, providing significance to those special viral peptides and suggesting a potential role they can play, comes from the analysis of their distribution along viral genomes, as it revealed they are not randomly located, but they preferentially occur in specific genes.
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73
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Mpakali A, Maben Z, Stern LJ, Stratikos E. Molecular pathways for antigenic peptide generation by ER aminopeptidase 1. Mol Immunol 2018; 113:50-57. [PMID: 29678301 DOI: 10.1016/j.molimm.2018.03.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/11/2018] [Accepted: 03/29/2018] [Indexed: 10/17/2022]
Abstract
Endoplasmic Reticulum aminopeptidase 1 (ERAP1) is an intracellular enzyme that can generate or destroy potential peptide ligands for MHC class I molecules. ERAP1 activity influences the cell-surface immunopeptidome and epitope immunodominance patterns but in complex and poorly understood manners. Two main distinct pathways have been proposed to account for ERAP1's effects on the nature and quantity of MHCI-bound peptides: i) ERAP1 trims peptides in solution, generating the correct length for binding to MHCI or overtrimming peptides so that they are too short to bind, and ii) ERAP1 trims peptides while they are partially bound onto MHCI in manner that leaves the peptide amino terminus accessible. For both pathways, once an appropriate length peptide is generated it could bind conventionally to MHCI, competing with further trimming by ERAP1. The two pathways, although not necessarily mutually exclusive, provide distinct vantage points for understanding of the rules behind the generation of the immunopeptidome. Resolution of the mechanistic details of ERAP1-mediated antigenic peptide generation can have important consequences for pharmacological efforts to regulate the immunopeptidome for therapeutic applications, and for understanding association of ERAP1 alleles with susceptibility to autoimmune disease and cancer. We review current evidence in support of these two pathways and discuss their relative importance and potential complementarity.
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Affiliation(s)
| | - Zachary Maben
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Lawrence J Stern
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA.
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74
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Ji Y, Zhao J, Chu CC. Enhanced MHC-I antigen presentation from the delivery of ovalbumin by light-facilitated biodegradable poly(ester amide)s nanoparticles. J Mater Chem B 2018; 6:1930-1942. [PMID: 32254359 DOI: 10.1039/c7tb03233a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The generation of CD8 T cells is crucial in adaptive immunity against cancer and many infectious diseases. Vaccines aimed to stimulate CD8 T cell response typically become ineffective because the antigens are subject to sequestration in endocytic compartments, instead of being delivered cytosolically for MHC-I processing and presentation. In this study, a nano-carrier (Arg-Phe-PEA(AP) nanoparticles) for ovalbumin (OVA) was developed from arginine- and phenylalanine-based poly(ester amide)s, which further formed an electrostatic complex with AlPcS2a, a typical photosensitizer for photochemical internalization (PCI) strategies. The nanocarrier significantly enhanced the internalization efficiency by dendritic cells of both OVA and AlPcS2a. The photochemical interruption of endocytic compartments by the AlPcS2a photosensitizer complexed in the nanocarrier enabled the light-facilitated endosomal escape of OVA. MHC-I presentation and CD8 T cell response were elicited by OVA-loaded Arg-Phe-PEA(AP) nanoparticles when light irradiation was applied at 660 nm. The light-facilitated delivery of OVA was dependent on the light dose and the concentration of the photosensitizer, both in vitro and in vivo. The optimized stimulation of MHC-I response demonstrated the potency of this light-facilitated nano-platform for CD8 T cell-inducing vaccination.
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Affiliation(s)
- Ying Ji
- Department of Fiber Science and Apparel Design, Cornell University, Ithaca, New York 14853-4401, USA
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75
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Di Carluccio AR, Triffon CF, Chen W. Perpetual complexity: predicting human CD8 + T-cell responses to pathogenic peptides. Immunol Cell Biol 2018; 96:358-369. [PMID: 29424002 DOI: 10.1111/imcb.12019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 02/01/2018] [Accepted: 02/02/2018] [Indexed: 01/17/2023]
Abstract
The accurate prediction of human CD8+ T-cell epitopes has great potential clinical and translational implications in the context of infection, cancer and autoimmunity. Prediction algorithms have traditionally focused on calculated peptide affinity for the binding groove of MHC-I. However, over the years it has become increasingly clear that the ultimate T-cell recognition of MHC-I-bound peptides is governed by many contributing factors within the complex antigen presentation pathway. Recent advances in next-generation sequencing and immunnopeptidomics have increased the precision of HLA-I sub-allele classification, and have led to the discovery of peptide processing events and individual allele-specific binding preferences. Here, we review some of the discoveries that initiated the development of peptide prediction algorithms, and outline some of the current available online tools for CD8+ T-cell epitope prediction.
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Affiliation(s)
- Anthony R Di Carluccio
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Cristina F Triffon
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Weisan Chen
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
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76
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Choi BK, Kim SH, Kim YH, Kwon BS. Cancer immunotherapy using tumor antigen-reactive T cells. Immunotherapy 2018; 10:235-245. [DOI: 10.2217/imt-2017-0130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Studies over the last 30 years have shown the promise of cancer immunotherapy using T cells. In particular, since the report by Rosenberg and colleagues in 2002 that adoptive T-cell therapy (ACT) under lymphopenic conditions substantially increased response rates in melanoma patients, ACT has become a promising immunotherapeutic route to cancer treatment. Here we provide a brief history of ACT and review the characteristics of T-cell therapeutics that are specific to this approach. Since every T-cell treatment has its own unique properties in terms of number and type of target antigens, and number of epitopes and type of T cells, we review the main strategies for designing ACT: how Ag specificity is determined, how is it standardized and the need for lymphodepletion to induce epitope spreading. We also briefly consider the next generation of ACT.
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Affiliation(s)
- Beom K. Choi
- Biomedicine Production Branch, National Cancer Center, Goyang, Korea
| | - Seon-Hee Kim
- Immunotherapeutics Branch, Division of Convergence Technology, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang-si, Korea 10408
| | - Young H. Kim
- Biomedicine Production Branch, National Cancer Center, Goyang, Korea
- Eutilex, Suite 1401 Daeryung Technotown 17, Gasan Digital 1-ro 25, Geumcheon-gu, Seoul, Korea 08594
| | - Byoung S. Kwon
- Eutilex, Suite 1401 Daeryung Technotown 17, Gasan Digital 1-ro 25, Geumcheon-gu, Seoul, Korea 08594
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77
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Fayer EL, Gilliland WM, Ramsey JM, Allbritton NL, Waters ML. N-Gemini peptides: cytosolic protease resistance via N-terminal dimerization of unstructured peptides. Chem Commun (Camb) 2017; 54:204-207. [PMID: 29230440 DOI: 10.1039/c7cc06819k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein we describe a synthetically simple strategy for increasing the lifetime of unstructured peptides in cytosolic environment via dimerization at the N-terminus to block threading into the catalytic cleft of cytosolic proteases. We establish this approach with kinase substrates, allowing for phosphorylation in cells as a demonstration of protease resistance.
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Affiliation(s)
- Effrat L Fayer
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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78
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Eccleston RC, Coveney PV, Dalchau N. Host genotype and time dependent antigen presentation of viral peptides: predictions from theory. Sci Rep 2017; 7:14367. [PMID: 29084996 PMCID: PMC5662608 DOI: 10.1038/s41598-017-14415-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 10/11/2017] [Indexed: 01/20/2023] Open
Abstract
The rate of progression of HIV infected individuals to AIDS is known to vary with the genotype of the host, and is linked to their allele of human leukocyte antigen (HLA) proteins, which present protein degradation products at the cell surface to circulating T-cells. HLA alleles are associated with Gag-specific T-cell responses that are protective against progression of the disease. While Pol is the most conserved HIV sequence, its association with immune control is not as strong. To gain a more thorough quantitative understanding of the factors that contribute to immunodominance, we have constructed a model of the recognition of HIV infection by the MHC class I pathway. Our model predicts surface presentation of HIV peptides over time, demonstrates the importance of viral protein kinetics, and provides evidence of the importance of Gag peptides in the long-term control of HIV infection. Furthermore, short-term dynamics are also predicted, with simulation of virion-derived peptides suggesting that efficient processing of Gag can lead to a 50% probability of presentation within 3 hours post-infection, as observed experimentally. In conjunction with epitope prediction algorithms, this modelling approach could be used to refine experimental targets for potential T-cell vaccines, both for HIV and other viruses.
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Affiliation(s)
- R Charlotte Eccleston
- Centre for Computational Science, Department of Chemistry, University College London, London, WC1H 0AJ, UK.,CoMPLEX, University College London, London, WC1E 6BT, UK
| | - Peter V Coveney
- Centre for Computational Science, Department of Chemistry, University College London, London, WC1H 0AJ, UK.,CoMPLEX, University College London, London, WC1E 6BT, UK
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79
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Eccleston RC, Wan S, Dalchau N, Coveney PV. The Role of Multiscale Protein Dynamics in Antigen Presentation and T Lymphocyte Recognition. Front Immunol 2017; 8:797. [PMID: 28740497 PMCID: PMC5502259 DOI: 10.3389/fimmu.2017.00797] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 06/22/2017] [Indexed: 12/15/2022] Open
Abstract
T lymphocytes are stimulated when they recognize short peptides bound to class I proteins of the major histocompatibility complex (MHC) protein, as peptide-MHC complexes. Due to the diversity in T-cell receptor (TCR) molecules together with both the peptides and MHC proteins they bind to, it has been difficult to design vaccines and treatments based on these interactions. Machine learning has made some progress in trying to predict the immunogenicity of peptide sequences in the context of specific MHC class I alleles but, as such approaches cannot integrate temporal information and lack explanatory power, their scope will always be limited. Here, we advocate a mechanistic description of antigen presentation and TCR activation which is explanatory, predictive, and quantitative, drawing on modeling approaches that collectively span several length and time scales, being capable of furnishing reliable biological descriptions that are difficult for experimentalists to provide. It is a form of multiscale systems biology. We propose the use of chemical rate equations to describe the time evolution of the foreign and host proteins to explain how the original proteins end up being presented on the cell surface as peptide fragments, while we invoke molecular dynamics to describe the key binding processes on the molecular level, including those of peptide-MHC complexes with TCRs which lie at the heart of the immune response. On each level, complementary methods based on machine learning are available, and we discuss the relationship between these divergent approaches. The pursuit of predictive mechanistic modeling approaches requires experimentalists to adapt their work so as to acquire, store, and expose data that can be used to verify and validate such models.
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Affiliation(s)
- R Charlotte Eccleston
- Centre for Computational Science, Department of Chemistry, University College London, London, United Kingdom
| | - Shunzhou Wan
- Centre for Computational Science, Department of Chemistry, University College London, London, United Kingdom
| | | | - Peter V Coveney
- Centre for Computational Science, Department of Chemistry, University College London, London, United Kingdom
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80
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Abstract
Autophagy, a self-eating machinery, has been reported as an adaptive response to maintain metabolic homeostasis when cancer cells encounter stress. It has been appreciated that autophagy acts as a double-edge sword to decide the fate of cancer cells upon stress factors, molecular subtypes, and microenvironmental conditions. Currently, the majority of evidence support that autophagy in cancer cells is a vital mechanism bringing on resistance to current and prospective treatments, yet whether autophagy affects the anticancer immune response remains unclear and controversial. Accumulated studies have demonstrated that triggering autophagy is able to facilitate anticancer immunity due to an increase in immunogenicity, whereas other studies suggested that autophagy is likely to disarm anticancer immunity mediated by cytotoxic T cells and nature killer (NK) cells. Hence, this contradiction needs to be elucidated. In this review, we discuss the role of autophagy in cancer cells per se and in cancer microenvironment as well as its dual regulatory roles in immune surveillance through modulating presentation of tumor antigens, development of immune cells, and expression of immune checkpoints. We further focus on emerging roles of autophagy induced by current treatments and its impact on anticancer immune response, and illustrate the pros and cons of utilizing autophagy in cancer immunotherapy based on preclinical references.
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81
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Li H, Chen C, Yao H, Li X, Yang N, Qiao J, Xu K, Zeng L. Identification of Suitable Reference Genes for mRNA Studies in Bone Marrow in a Mouse Model of Hematopoietic Stem Cell Transplantation. Transplant Proc 2017; 48:2826-2832. [PMID: 27788825 DOI: 10.1016/j.transproceed.2016.07.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 07/14/2016] [Indexed: 11/24/2022]
Abstract
BACKGROUND Bone marrow micro-environment changes during hematopoietic stem cell transplantation (HSCT) with subsequent alteration of genes expression. Quantitative polymerase chain reaction (q-PCR) is a reliable and reproducible technique for the analysis of gene expression. To obtain more accurate results, it is essential to find a reference during HSCT. However, which gene is suitable during HSCT remains unclear. This study aimed to identify suitable reference genes for mRNA studies in bone marrow after HSCT. METHODS C57BL/6 mice were treated with either total body irradiation (group T) or busulfan/cyclophosphamide (BU/CY) (group B) followed by infusion of bone marrow cells. Normal mice without treatments were served as a control. All samples (group T + group B + control) were defined as group G. On days 7, 14, and 21 after transplantation, transcription levels of 7 candidate genes, ACTB, B2M, GAPDH, HMBS, HPRT, SDHA, and YWHAZ, in bone marrow cells were measured by use of real-time quantitative PCR. The expression stability of these 7 candidate reference genes were analyzed by 2 statistical software programs, GeNorm and NormFinder. RESULTS Our results showed that ACTB displayed the highest expression in group G, with lowest expression of PSDHA in group T and HPRT in groups B and G. Analysis of expression stability by use of GeNorm or NormFinder demonstrated that expression of B2M in bone marrow were much more stable during HSCT, compared with other candidate genes including commonly used reference genes GAPDH and ACTB. CONCLUSIONS ACTB could be used as a suitable reference gene for mRNA studies in bone marrow after HSCT.
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Affiliation(s)
- H Li
- Department of Clinical Laboratory, the Affiliated Hospital of Xuzhou Medical College, Xuzhou, China
| | - C Chen
- Blood Diseases Institute, Xuzhou Medical College, Xuzhou, China; Key Laboratory of Bone Marrow Stem Cell, Jiangsu Province, Xuzhou, China
| | - H Yao
- Blood Diseases Institute, Xuzhou Medical College, Xuzhou, China; Key Laboratory of Bone Marrow Stem Cell, Jiangsu Province, Xuzhou, China
| | - X Li
- Blood Diseases Institute, Xuzhou Medical College, Xuzhou, China; Key Laboratory of Bone Marrow Stem Cell, Jiangsu Province, Xuzhou, China
| | - N Yang
- Blood Diseases Institute, Xuzhou Medical College, Xuzhou, China; Key Laboratory of Bone Marrow Stem Cell, Jiangsu Province, Xuzhou, China
| | - J Qiao
- Blood Diseases Institute, Xuzhou Medical College, Xuzhou, China; Key Laboratory of Bone Marrow Stem Cell, Jiangsu Province, Xuzhou, China; Department of Hematology, the Affiliated Hospital of Xuzhou Medical College, Xuzhou, China
| | - K Xu
- Blood Diseases Institute, Xuzhou Medical College, Xuzhou, China; Key Laboratory of Bone Marrow Stem Cell, Jiangsu Province, Xuzhou, China; Department of Hematology, the Affiliated Hospital of Xuzhou Medical College, Xuzhou, China.
| | - L Zeng
- Blood Diseases Institute, Xuzhou Medical College, Xuzhou, China; Key Laboratory of Bone Marrow Stem Cell, Jiangsu Province, Xuzhou, China; Department of Hematology, the Affiliated Hospital of Xuzhou Medical College, Xuzhou, China.
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82
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van Hateren A, Bailey A, Elliott T. Recent advances in Major Histocompatibility Complex (MHC) class I antigen presentation: Plastic MHC molecules and TAPBPR-mediated quality control. F1000Res 2017; 6:158. [PMID: 28299193 PMCID: PMC5321123 DOI: 10.12688/f1000research.10474.1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/13/2017] [Indexed: 01/25/2023] Open
Abstract
We have known since the late 1980s that the function of classical major histocompatibility complex (MHC) class I molecules is to bind peptides and display them at the cell surface to cytotoxic T cells. Recognition by these sentinels of the immune system can lead to the destruction of the presenting cell, thus protecting the host from pathogens and cancer. Classical MHC class I molecules (MHC I hereafter) are co-dominantly expressed, polygenic, and exceptionally polymorphic and have significant sequence diversity. Thus, in most species, there are many different MHC I allotypes expressed, each with different peptide-binding specificity, which can have a dramatic effect on disease outcome. Although MHC allotypes vary in their primary sequence, they share common tertiary and quaternary structures. Here, we review the evidence that, despite this commonality, polymorphic amino acid differences between allotypes alter the ability of MHC I molecules to change shape (that is, their conformational plasticity). We discuss how the peptide loading co-factor tapasin might modify this plasticity to augment peptide loading. Lastly, we consider recent findings concerning the functions of the non-classical MHC I molecule HLA-E as well as the tapasin-related protein TAPBPR (transporter associated with antigen presentation binding protein-related), which has been shown to act as a second quality-control stage in MHC I antigen presentation.
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Affiliation(s)
- Andy van Hateren
- Institute for Life Sciences and Cancer Sciences Unit, University of Southampton, Southampton, UK
| | - Alistair Bailey
- Institute for Life Sciences and Cancer Sciences Unit, University of Southampton, Southampton, UK
| | - Tim Elliott
- Institute for Life Sciences and Cancer Sciences Unit, University of Southampton, Southampton, UK
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83
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Thomas C, Tampé R. Proofreading of Peptide-MHC Complexes through Dynamic Multivalent Interactions. Front Immunol 2017; 8:65. [PMID: 28228754 PMCID: PMC5296336 DOI: 10.3389/fimmu.2017.00065] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 01/16/2017] [Indexed: 11/18/2022] Open
Abstract
The adaptive immune system is able to detect and destroy cells that are malignantly transformed or infected by intracellular pathogens. Specific immune responses against these cells are elicited by antigenic peptides that are presented on major histocompatibility complex class I (MHC I) molecules and recognized by cytotoxic T lymphocytes at the cell surface. Since these MHC I-presented peptides are generated in the cytosol by proteasomal protein degradation, they can be metaphorically described as a window providing immune cells with insights into the state of the cellular proteome. A crucial element of MHC I antigen presentation is the peptide-loading complex (PLC), a multisubunit machinery, which contains as key constituents the transporter associated with antigen processing (TAP) and the MHC I-specific chaperone tapasin (Tsn). While TAP recognizes and shuttles the cytosolic antigenic peptides into the endoplasmic reticulum (ER), Tsn samples peptides in the ER for their ability to form stable complexes with MHC I, a process called peptide proofreading or peptide editing. Through its selection of peptides that improve MHC I stability, Tsn contributes to the hierarchy of immunodominant peptide epitopes. Despite the fact that it concerns a key event in adaptive immunity, insights into the catalytic mechanism of peptide proofreading carried out by Tsn have only lately been gained via biochemical, biophysical, and structural studies. Furthermore, a Tsn homolog called TAP-binding protein-related (TAPBPR) has only recently been demonstrated to function as a second MHC I-specific chaperone and peptide proofreader. Although TAPBPR is PLC-independent and has a distinct allomorph specificity, it is likely to share a common catalytic mechanism with Tsn. This review focuses on the current knowledge of the multivalent protein–protein interactions and the concomitant dynamic molecular processes underlying peptide-proofreading catalysis. We do not only derive a model that highlights the common mechanistic principles shared by the MHC I editors Tsn and TAPBPR, and the MHC II editor HLA-DM, but also illustrate the distinct quality control strategies employed by these chaperones to sample epitopes. Unraveling the mechanistic underpinnings of catalyzed peptide proofreading will be crucial for a thorough understanding of many aspects of immune recognition, from infection control and tumor immunity to autoimmune diseases and transplant rejection.
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Affiliation(s)
- Christoph Thomas
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt , Frankfurt am Main , Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt , Frankfurt am Main , Germany
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84
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Interspecies comparison of peptide substrate reporter metabolism using compartment-based modeling. Anal Bioanal Chem 2016; 409:1173-1183. [PMID: 27900431 DOI: 10.1007/s00216-016-0085-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/07/2016] [Indexed: 01/03/2023]
Abstract
Peptide substrate reporters are fluorescently labeled peptides that can be acted upon by one or more enzymes of interest. Peptide substrates are readily synthesized and more easily separated than full-length protein substrates; however, they are often more rapidly degraded by peptidases. As a result, peptide reporters must be made resistant to proteolysis in order to study enzymes in intact cells and lysates. This is typically achieved by optimizing the reporter sequence in a single cell type or model organism, but studies of reporter stability in a variety of organisms are needed to establish the robustness and broader utility of these molecular tools. We measured peptidase activity toward a peptide substrate reporter for protein kinase B (Akt) in E. coli, D. discoideum, and S. cerevisiae using capillary electrophoresis with laser-induced fluorescence (CE-LIF). Using compartment-based modeling, we determined individual rate constants for all potential peptidase reactions and explored how these rate constants differed between species. We found the reporter to be stable in D. discoideum (t 1/2 = 82-103 min) and S. cerevisiae (t 1/2 = 279-314 min), but less stable in E. coli (t 1/2 = 21-44 min). These data suggest that the reporter is sufficiently stable to be used for kinase assays in eukaryotic cell types while also demonstrating the potential utility of compartment-based models in peptide substrate reporter design. Graphical abstract Cell lysates from several evolutionarily divergent species were incubated with a peptide substrate reporter, and compartment-based modeling was used to determine key steps in the metabolism of the reporter in each cell type.
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85
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Combinational Immunotherapy with Allo-DRibble Vaccines and Anti-OX40 Co-Stimulation Leads to Generation of Cross-Reactive Effector T Cells and Tumor Regression. Sci Rep 2016; 6:37558. [PMID: 27874054 PMCID: PMC5118714 DOI: 10.1038/srep37558] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 11/01/2016] [Indexed: 11/13/2022] Open
Abstract
It is well-known that vaccines comprising of irradiated whole tumor cells or tumor-derived heat shock proteins can generate tumor-specific immune responses. In contrast, we showed recently that vaccines composed of autophagosomes (DRibbles) derived from syngeneic sarcomas could induce cross-reactive T-cell responses and cross-protection against the tumor. This unusual property of DRibbles was related to the selective recruitment of defective ribosomal products (DRiPs) and other short-lived proteins (SLiPs) into autophagosomes via sequestosome (SQSTM1, p62) mediated association of ubiquitinated SLiPs to the autophagy gene product LC3. Here, we extend our observations to mammary carcinomas from mice of different genetic background. We demonstrated that combined of intranodal administration of autologous or allogeneic DRibbles together with anti-OX40 antibody led to robust proliferation, expansion, and differentiation of memory and effector T cells. We also showed that SLiPs is an excellent source of antigen for cross-priming of CD8+ T-cells that recognize shared tumor antigens in the context of host MHC class I molecules. Thus, our results provide a strong basis for novel clinical trials that combine allogeneic “off-the-shelf” DRibble vaccines together with antibodies against co-stimulatory molecules.
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86
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Pawlak JB, Hos BJ, van de Graaff MJ, Megantari OA, Meeuwenoord N, Overkleeft HS, Filippov DV, Ossendorp F, van Kasteren SI. The Optimization of Bioorthogonal Epitope Ligation within MHC-I Complexes. ACS Chem Biol 2016; 11:3172-3178. [PMID: 27704768 DOI: 10.1021/acschembio.6b00498] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Antigen recognition followed by the activation of cytotoxic T-cells (CTLs) is a key step in adaptive immunity, resulting in clearance of viruses and cancers. The repertoire of peptides that have the ability to bind to the major histocompatibility type-I (MHC-I) is enormous, but the approaches available for studying the diversity of the peptide repertoire on a cell are limited. Here, we explore the use of bioorthogonal chemistry to quantify specific peptide-MHC-I complexes (pMHC-I) on cells. We show that modifying epitope peptides with bioorthogonal groups in surface accessible positions allows wild-type-like MHC-I binding and bioorthogonal ligation using fluorogenic chromophores in combination with a Cu(I)-catalyzed Huisgen cycloaddition reaction. We expect that this approach will make a powerful addition to the antigen presentation toolkit as for the first time it allows quantification of antigenic peptides for which no detection tools exist.
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Affiliation(s)
- Joanna B. Pawlak
- Leiden
Institute of Chemistry and The Institute for Chemical Immunology, Leiden University Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Brett J. Hos
- Department
of Immunohematology and Blood Transfusion, Leiden University Medical Center and The Institute for Chemical Immunology, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Michel J. van de Graaff
- Leiden
Institute of Chemistry and The Institute for Chemical Immunology, Leiden University Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Otty A. Megantari
- Leiden
Institute of Chemistry and The Institute for Chemical Immunology, Leiden University Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Nico Meeuwenoord
- Leiden
Institute of Chemistry and The Institute for Chemical Immunology, Leiden University Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Herman S. Overkleeft
- Leiden
Institute of Chemistry and The Institute for Chemical Immunology, Leiden University Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Dmitri V. Filippov
- Leiden
Institute of Chemistry and The Institute for Chemical Immunology, Leiden University Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Ferry Ossendorp
- Department
of Immunohematology and Blood Transfusion, Leiden University Medical Center and The Institute for Chemical Immunology, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Sander I. van Kasteren
- Leiden
Institute of Chemistry and The Institute for Chemical Immunology, Leiden University Einsteinweg 55, 2333 CC Leiden, The Netherlands
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87
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Pearson H, Daouda T, Granados DP, Durette C, Bonneil E, Courcelles M, Rodenbrock A, Laverdure JP, Côté C, Mader S, Lemieux S, Thibault P, Perreault C. MHC class I-associated peptides derive from selective regions of the human genome. J Clin Invest 2016; 126:4690-4701. [PMID: 27841757 DOI: 10.1172/jci88590] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 09/30/2016] [Indexed: 12/24/2022] Open
Abstract
MHC class I-associated peptides (MAPs) define the immune self for CD8+ T lymphocytes and are key targets of cancer immunosurveillance. Here, the goals of our work were to determine whether the entire set of protein-coding genes could generate MAPs and whether specific features influence the ability of discrete genes to generate MAPs. Using proteogenomics, we have identified 25,270 MAPs isolated from the B lymphocytes of 18 individuals who collectively expressed 27 high-frequency HLA-A,B allotypes. The entire MAP repertoire presented by these 27 allotypes covered only 10% of the exomic sequences expressed in B lymphocytes. Indeed, 41% of expressed protein-coding genes generated no MAPs, while 59% of genes generated up to 64 MAPs, often derived from adjacent regions and presented by different allotypes. We next identified several features of transcripts and proteins associated with efficient MAP production. From these data, we built a logistic regression model that predicts with good accuracy whether a gene generates MAPs. Our results show preferential selection of MAPs from a limited repertoire of proteins with distinctive features. The notion that the MHC class I immunopeptidome presents only a small fraction of the protein-coding genome for monitoring by the immune system has profound implications in autoimmunity and cancer immunology.
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88
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Rock KL, Reits E, Neefjes J. Present Yourself! By MHC Class I and MHC Class II Molecules. Trends Immunol 2016; 37:724-737. [PMID: 27614798 DOI: 10.1016/j.it.2016.08.010] [Citation(s) in RCA: 463] [Impact Index Per Article: 57.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 08/09/2016] [Accepted: 08/15/2016] [Indexed: 12/01/2022]
Abstract
Since the discovery of MHC molecules, it has taken 40 years to arrive at a coherent picture of how MHC class I and MHC class II molecules really work. This is a story of the proteases and MHC-like chaperones that support the MHC class I and II molecules in presenting peptides to the immune system. We now understand that the MHC system shapes both the repertoire of presented peptides and the subsequent T cell response, with important implications ranging from transplant rejection to tumor immunotherapies. Here we present an illustrated review of the ins and outs of MHC class I and MHC class II antigen presentation.
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Affiliation(s)
- Kenneth L Rock
- Department of Pathology, UMass Medical School, Worcester, MA, USA
| | - Eric Reits
- Department of Cell Biology and Histology, Amsterdam Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Jacques Neefjes
- Department of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands; Department of Chemical Immunology, Leiden University Medical Center, Leiden, The Netherlands.
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89
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Dhanik A, R. Kirshner J, MacDonald D, Thurston G, C. Lin H, J. Murphy A, Zhang W. In-silico discovery of cancer-specific peptide-HLA complexes for targeted therapy. BMC Bioinformatics 2016; 17:286. [PMID: 27439771 PMCID: PMC4955262 DOI: 10.1186/s12859-016-1150-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 07/13/2016] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Major Histocompatibility Complex (MHC) or Human Leukocyte Antigen (HLA) Class I molecules bind to peptide fragments of proteins degraded inside the cell and display them on the cell surface. We are interested in peptide-HLA complexes involving peptides that are derived from proteins specifically expressed in cancer cells. Such complexes have been shown to provide an effective means of precisely targeting cancer cells by engineered T-cells and antibodies, which would be an improvement over current chemotherapeutic agents that indiscriminately kill proliferating cells. An important concern with the targeting of peptide-HLA complexes is off-target toxicity that could occur due to the presence of complexes similar to the target complex in cells from essential, normal tissues. RESULTS We developed a novel computational strategy for identifying potential peptide-HLA cancer targets and evaluating the likelihood of off-target toxicity associated with these targets. Our strategy combines sequence-based and structure-based approaches in a unique way to predict potential off-targets. The focus of our work is on the complexes involving the most frequent HLA class I allele HLA-A*02:01. Using our strategy, we predicted the off-target toxicity observed in past clinical trials. We employed it to perform a first-ever comprehensive exploration of the human peptidome to identify cancer-specific targets utilizing gene expression data from TCGA (The Cancer Genome Atlas) and GTEx (Gene Tissue Expression), and structural data from PDB (Protein Data Bank). We have thus identified a list of 627 peptide-HLA complexes across various TCGA cancer types. CONCLUSION Peptide-HLA complexes identified using our novel strategy could enable discovery of cancer-specific targets for engineered T-cells or antibody based therapy with minimal off-target toxicity.
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Affiliation(s)
- Ankur Dhanik
- Regeneron Pharmaceuticals Inc, Old Saw Mill River Road, Tarrytown, NY USA
| | | | - Douglas MacDonald
- Regeneron Pharmaceuticals Inc, Old Saw Mill River Road, Tarrytown, NY USA
| | - Gavin Thurston
- Regeneron Pharmaceuticals Inc, Old Saw Mill River Road, Tarrytown, NY USA
| | - Hsin C. Lin
- Regeneron Pharmaceuticals Inc, Old Saw Mill River Road, Tarrytown, NY USA
| | - Andrew J. Murphy
- Regeneron Pharmaceuticals Inc, Old Saw Mill River Road, Tarrytown, NY USA
| | - Wen Zhang
- Regeneron Pharmaceuticals Inc, Old Saw Mill River Road, Tarrytown, NY USA
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90
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Kammerl IE, Meiners S. Proteasome function shapes innate and adaptive immune responses. Am J Physiol Lung Cell Mol Physiol 2016; 311:L328-36. [PMID: 27343191 DOI: 10.1152/ajplung.00156.2016] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 06/17/2016] [Indexed: 11/22/2022] Open
Abstract
The proteasome system degrades more than 80% of intracellular proteins into small peptides. Accordingly, the proteasome is involved in many essential cellular functions, such as protein quality control, transcription, immune responses, cell signaling, and apoptosis. Moreover, degradation products are loaded onto major histocompatibility class I molecules to communicate the intracellular protein composition to the immune system. The standard 20S proteasome core complex contains three distinct catalytic active sites that are exchanged upon stimulation with inflammatory cytokines to form the so-called immunoproteasome. Immunoproteasomes are constitutively expressed in immune cells and have different proteolytic activities compared with standard proteasomes. They are rapidly induced in parenchymal cells upon intracellular pathogen infection and are crucial for priming effective CD8(+) T-cell-mediated immune responses against infected cells. Beyond shaping these adaptive immune reactions, immunoproteasomes also regulate the function of immune cells by degradation of inflammatory and immune mediators. Accordingly, they emerge as novel regulators of innate immune responses. The recently unraveled impairment of immunoproteasome function by environmental challenges and by genetic variations of immunoproteasome genes might represent a currently underestimated risk factor for the development and progression of lung diseases. In particular, immunoproteasome dysfunction will dampen resolution of infections, thereby promoting exacerbations, may foster autoimmunity in chronic lung diseases, and possibly contributes to immune evasion of tumor cells. Novel pharmacological tools, such as site-specific inhibitors of the immunoproteasome, as well as activity-based probes, however, hold promises as innovative therapeutic drugs for respiratory diseases and biomarker profiling, respectively.
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Affiliation(s)
- Ilona E Kammerl
- Comprehensive Pneumology Center, University Hospital, Ludwig-Maximilians University and Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Silke Meiners
- Comprehensive Pneumology Center, University Hospital, Ludwig-Maximilians University and Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
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91
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Page DB, Hulett TW, Hilton TL, Hu HM, Urba WJ, Fox BA. Glimpse into the future: harnessing autophagy to promote anti-tumor immunity with the DRibbles vaccine. J Immunother Cancer 2016; 4:25. [PMID: 27190627 PMCID: PMC4869314 DOI: 10.1186/s40425-016-0130-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/05/2016] [Indexed: 12/01/2022] Open
Abstract
Because the benefits of immune checkpoint blockade may be restricted to tumors with pre-existing immune recognition, novel therapies that facilitate de novo immune activation are needed. DRibbles is a novel multi-valent vaccine that is created by disrupting degradation of intracellular proteins by the ubiquitin proteasome system. The DRibbles vaccine is comprised of autophagosome vesicles that are enriched with defective ribosomal products and short-lived proteins, known tumor-associated antigens, mediators of innate immunity, and surface markers that encourage phagocytosis and cross-presentation by antigen presenting cells. Here we summarize the rationale and preclinical development of DRibbles, translational evidence in support of DRibbles as a therapeutic strategy in humans, as well as recent developments and expected future directions of the DRibbles vaccine in the clinic.
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Affiliation(s)
- David B Page
- Earle A. Chiles Research Institute / Providence Portland Cancer Center, 4805 N.E. Glisan St., North Tower, Suite 2N87, Portland, OR 97213 USA
| | - Tyler W Hulett
- Earle A. Chiles Research Institute / Providence Portland Cancer Center, 4805 N.E. Glisan St., North Tower, Suite 2N87, Portland, OR 97213 USA.,Oregon Health & Science University, Portland, OR USA
| | | | | | - Walter J Urba
- Earle A. Chiles Research Institute / Providence Portland Cancer Center, 4805 N.E. Glisan St., North Tower, Suite 2N87, Portland, OR 97213 USA
| | - Bernard A Fox
- Earle A. Chiles Research Institute / Providence Portland Cancer Center, 4805 N.E. Glisan St., North Tower, Suite 2N87, Portland, OR 97213 USA.,UbiVac, Inc., Portland, OR USA.,Oregon Health & Science University, Portland, OR USA
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92
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Kaabinejadian S, McMurtrey CP, Kim S, Jain R, Bardet W, Schafer FB, Davenport JL, Martin AD, Diamond MS, Weidanz JA, Hansen TH, Hildebrand WH. Immunodominant West Nile Virus T Cell Epitopes Are Fewer in Number and Fashionably Late. THE JOURNAL OF IMMUNOLOGY 2016; 196:4263-73. [PMID: 27183642 DOI: 10.4049/jimmunol.1501821] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 03/20/2016] [Indexed: 12/23/2022]
Abstract
Class I HLA molecules mark infected cells for immune targeting by presenting pathogen-encoded peptides on the cell surface. Characterization of viral peptides unique to infected cells is important for understanding CD8(+) T cell responses and for the development of T cell-based immunotherapies. Having previously reported a series of West Nile virus (WNV) epitopes that are naturally presented by HLA-A*02:01, in this study we generated TCR mimic (TCRm) mAbs to three of these peptide/HLA complexes-the immunodominant SVG9 (E protein), the subdominant SLF9 (NS4B protein), and the immunorecessive YTM9 (NS3 protein)-and used these TCRm mAbs to stain WNV-infected cell lines and primary APCs. TCRm staining of WNV-infected cells demonstrated that the immunorecessive YTM9 appeared several hours earlier and at 5- to 10-fold greater density than the more immunogenic SLF9 and SVG9 ligands, respectively. Moreover, staining following inhibition of the TAP demonstrated that all three viral ligands were presented in a TAP-dependent manner despite originating from different cellular compartments. To our knowledge, this study represents the first use of TCRm mAbs to define the kinetics and magnitude of HLA presentation for a series of epitopes encoded by one virus, and the results depict a pattern whereby individual epitopes differ considerably in abundance and availability. The observations that immunodominant ligands can be found at lower levels and at later time points after infection suggest that a reevaluation of the factors that combine to shape T cell reactivity may be warranted.
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Affiliation(s)
- Saghar Kaabinejadian
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - Curtis P McMurtrey
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - Sojung Kim
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110
| | - Rinki Jain
- Center for Immunotherapeutic Research, Texas Tech University Health Sciences Center School of Pharmacy, Abilene, TX 79601; Department of Immunotherapeutics and Biotechnology, Texas Tech University Health Sciences Center School of Pharmacy, Abilene, TX 79601; Receptor Logic, Inc., Abilene, TX 79601
| | - Wilfried Bardet
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - Fredda B Schafer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | | | | | - Michael S Diamond
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110; Department of Medicine, Washington University School of Medicine, St Louis, MO 63110; and Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO 63110
| | - Jon A Weidanz
- Center for Immunotherapeutic Research, Texas Tech University Health Sciences Center School of Pharmacy, Abilene, TX 79601; Department of Immunotherapeutics and Biotechnology, Texas Tech University Health Sciences Center School of Pharmacy, Abilene, TX 79601; Receptor Logic, Inc., Abilene, TX 79601
| | - Ted H Hansen
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110
| | - William H Hildebrand
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104;
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93
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Kowalewski DJ, Walz S, Backert L, Schuster H, Kohlbacher O, Weisel K, Rittig SM, Kanz L, Salih HR, Rammensee HG, Stevanović S, Stickel JS. Carfilzomib alters the HLA-presented peptidome of myeloma cells and impairs presentation of peptides with aromatic C-termini. Blood Cancer J 2016; 6:e411. [PMID: 27058226 PMCID: PMC4855252 DOI: 10.1038/bcj.2016.14] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 02/02/2016] [Indexed: 02/03/2023] Open
Abstract
Recent studies suggest that multiple myeloma is an immunogenic disease, which might be effectively targeted by antigen-specific T-cell immunotherapy. As standard of care in myeloma includes proteasome inhibitor therapy, it is of great importance to characterize the effects of this treatment on HLA-restricted antigen presentation and implement only robustly presented targets for immunotherapeutic intervention. Here, we present a study that longitudinally and semi-quantitatively maps the effects of the proteasome inhibitor carfilzomib on HLA-restricted antigen presentation. The relative presentation levels of 4780 different HLA ligands were quantified in an in vitro model employing carfilzomib treatment of MM.1S and U266 myeloma cells, which revealed significant modulation of a substantial fraction of the HLA-presented peptidome. Strikingly, we detected selective down-modulation of HLA ligands with aromatic C-terminal anchor amino acids. This particularly manifested as a marked reduction in the presentation of HLA ligands through the HLA allotypes A*23:01 and A*24:02 on MM.1S cells. These findings implicate that carfilzomib mediates a direct, peptide motif-specific inhibitory effect on HLA ligand processing and presentation. As a substantial proportion of HLA allotypes present peptides with aromatic C-termini, our results may have broad implications for the implementation of antigen-specific treatment approaches in patients undergoing carfilzomib treatment.
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Affiliation(s)
- D J Kowalewski
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - S Walz
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,Department of Hematology and Oncology, University of Tübingen, Tübingen, Germany
| | - L Backert
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,Applied Bioinformatics, Department of Computer Science, Center for Bioinformatics, University of Tübingen, Tübingen, Germany
| | - H Schuster
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - O Kohlbacher
- Applied Bioinformatics, Department of Computer Science, Center for Bioinformatics, University of Tübingen, Tübingen, Germany.,Quantitative Biology Center, University of Tübingen, Tübingen, Germany.,Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - K Weisel
- Department of Hematology and Oncology, University of Tübingen, Tübingen, Germany
| | - S M Rittig
- Department of Hematology and Oncology, University of Tübingen, Tübingen, Germany
| | - L Kanz
- Department of Hematology and Oncology, University of Tübingen, Tübingen, Germany
| | - H R Salih
- Department of Hematology and Oncology, University of Tübingen, Tübingen, Germany.,Clinical Cooperation Unit Translational Immunology, German Cancer Consortium (DKTK), DKFZ Partner Site, Tübingen, Germany
| | - H-G Rammensee
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ Partner Site, Tübingen, Germany
| | - S Stevanović
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ Partner Site, Tübingen, Germany
| | - J S Stickel
- Department of Hematology and Oncology, University of Tübingen, Tübingen, Germany
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94
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Rodriguez GM, Bobbala D, Serrano D, Mayhue M, Champagne A, Saucier C, Steimle V, Kufer TA, Menendez A, Ramanathan S, Ilangumaran S. NLRC5 elicits antitumor immunity by enhancing processing and presentation of tumor antigens to CD8(+) T lymphocytes. Oncoimmunology 2016; 5:e1151593. [PMID: 27471621 PMCID: PMC4938303 DOI: 10.1080/2162402x.2016.1151593] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 01/18/2016] [Accepted: 02/01/2016] [Indexed: 11/10/2022] Open
Abstract
Cancers can escape immunesurveillance by diminishing the expression of MHC class-I molecules (MHC-I) and components of the antigen-processing machinery (APM). Developing new approaches to reverse these defects could boost the efforts to restore antitumor immunity. Recent studies have shown that the expression of MHC-I and antigen-processing molecules is transcriptionally regulated by NOD-like receptor CARD domain containing 5 (NLRC5). To investigate whether NLRC5 could be used to improve tumor immunogenicity, we established stable lines of B16-F10 melanoma cells expressing NLRC5 (B16-5), the T cell co-stimulatory molecule CD80 (B16-CD80) or both (B16-5/80). Cells harboring NLRC5 constitutively expressed MHC-I and LMP2, LMP7 and TAP1 genes of the APM. The B16-5 cells efficiently presented the melanoma antigenic peptide gp10025–33 to Pmel-1 TCR transgenic CD8+ T cells and induced their proliferation. In the presence of CD80, B16-5 cells stimulated Pmel-1 cells even without the addition of gp100 peptide, indicating that NLRC5 facilitated the processing and presentation of endogenous tumor antigen. Upon subcutaneous implantation, B16-5 cells showed markedly reduced tumor growth in C57BL/6 hosts but not in immunodeficient hosts, indicating that the NLRC5-expressing tumor cells elicited antitumor immunity. Following intravenous injection, B16-5 and B16-5/80 cells formed fewer lung tumor foci compared to control cells. In mice depleted of CD8+ T cells, B16-5 cells formed large subcutaneous and lung tumors. Finally, immunization with irradiated B16-5 cells conferred protection against challenge by parental B16 cells. Collectively, our findings indicate that NLRC5 could be exploited to restore tumor immunogenicity and to stimulate protective antitumor immunity.
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Affiliation(s)
| | | | | | | | - Audrey Champagne
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke , Sherbrooke, Quebec, Canada
| | - Caroline Saucier
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada; CRCHUS, Sherbrooke, Québec, Canada
| | - Viktor Steimle
- Department of Biology, Faculty of Sciences, Université de Sherbrooke , Sherbrooke, Quebec, Canada
| | - Thomas A Kufer
- Department of Immunology, Institute of Nutritional Medicine, University of Hohenheim , Stuttgart, Germany
| | - Alfredo Menendez
- CRCHUS, Sherbrooke, Québec, Canada; Department of Microbiology and Infectious diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Sheela Ramanathan
- Immunology division, Department of Pediatrics; CRCHUS, Sherbrooke, Québec, Canada
| | - Subburaj Ilangumaran
- Immunology division, Department of Pediatrics; CRCHUS, Sherbrooke, Québec, Canada
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95
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Lasso P, Beltrán L, Guzmán F, Rosas F, Thomas MC, López MC, González JM, Cuéllar A, Puerta CJ. Promiscuous Recognition of a Trypanosoma cruzi CD8+ T Cell Epitope among HLA-A2, HLA-A24 and HLA-A1 Supertypes in Chagasic Patients. PLoS One 2016; 11:e0150996. [PMID: 26974162 PMCID: PMC4790940 DOI: 10.1371/journal.pone.0150996] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 02/21/2016] [Indexed: 01/20/2023] Open
Abstract
Background TcTLE is a nonamer peptide from Trypanosoma cruzi KMP-11 protein that is conserved among different parasite strains and that is presented by different HLA-A molecules from the A2 supertype. Because peptides presented by several major histocompatibility complex (MHC) supertypes are potential targets for immunotherapy, the aim of this study was to determine whether MHC molecules other than the A2 supertype present the TcTLE peptide. Methodology/Principal Findings From 36 HLA-A2-negative chagasic patients, the HLA-A genotypes of twenty-eight patients with CD8+ T cells that recognized the TcTLE peptide using tetramer (twenty) or functional (eight) assays, were determined. SSP-PCR was used to identify the A locus and the allelic variants. Flow cytometry was used to analyze the frequency of TcTLE-specific CD8+ T cells, and their functional activity (IFN-γ, TNFα, IL-2, perforin, granzyme and CD107a/b production) was induced by exposure to the TcTLE peptide. All patients tested had TcTLE-specific CD8+ T cells with frequencies ranging from 0.07–0.37%. Interestingly, seven of the twenty-eight patients had HLA-A homozygous alleles: A*24 (5 patients), A*23 (1 patient) and A*01 (1 patient), which belong to the A24 and A1 supertypes. In the remaining 21 patients with HLA-A heterozygous alleles, the most prominent alleles were A24 and A68. The most common allele sub-type was A*2402 (sixteen patients), which belongs to the A24 supertype, followed by A*6802 (six patients) from the A2 supertype. Additionally, the A*3002/A*3201 alleles from the A1 supertype were detected in one patient. All patients presented CD8+ T cells producing at least one cytokine after TcTLE peptide stimulation. Conclusion/Significance These results show that TcTLE is a promiscuous peptide that is presented by the A24 and A1 supertypes, in addition to the A2 supertype, suggesting its potential as a target for immunotherapy.
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Affiliation(s)
- Paola Lasso
- Laboratorio de Parasitología Molecular, Pontificia Universidad Javeriana, Bogotá, Colombia
- Grupo de Inmunobiología y Biología Celular, Pontificia Universidad Javeriana, Bogotá, Colombia
- Instituto de Parasitología y Biomedicina López-Neyra, CSIC, PTS-Granada, Granada, España
| | - Lina Beltrán
- Laboratorio de Parasitología Molecular, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Fanny Guzmán
- Núcleo de Biotecnología Curauma (NBC), Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Fernando Rosas
- Instituto de Arritmias Joseph Brugada, Fundación Clínica Abood Shaio, Bogotá, Colombia
| | - M. Carmen Thomas
- Instituto de Parasitología y Biomedicina López-Neyra, CSIC, PTS-Granada, Granada, España
| | - Manuel Carlos López
- Instituto de Parasitología y Biomedicina López-Neyra, CSIC, PTS-Granada, Granada, España
| | - John Mario González
- Grupo de Ciencias Básicas Médicas, Facultad de Medicina, Universidad de los Andes, Bogotá, Colombia
| | - Adriana Cuéllar
- Grupo de Inmunobiología y Biología Celular, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Concepción J. Puerta
- Laboratorio de Parasitología Molecular, Pontificia Universidad Javeriana, Bogotá, Colombia
- * E-mail:
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96
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Hjálmsdóttir Á, Bühler C, Vonwil V, Roveri M, Håkerud M, Wäckerle-Men Y, Gander B, Johansen P. Cytosolic Delivery of Liposomal Vaccines by Means of the Concomitant Photosensitization of Phagosomes. Mol Pharm 2016; 13:320-9. [PMID: 26704885 DOI: 10.1021/acs.molpharmaceut.5b00394] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
One of the greatest pharmaceutical challenges in vaccinology is the delivery of antigens to the cytosol of antigen-presenting cells (APCs) in order to allow for the stimulation of major histocompatibility complex (MHC) class I-restricted CD8(+) T-cell responses, which may act on intracellular infections or cancer. Recently, we described a novel method for cytotoxic T-lymphocyte (CTL) vaccination by combining antigens with a photosensitizer and light for cytosolic antigen delivery. The goal of the current project was to test this immunization method with particle-based formulations. Liposomes were prepared from dipalmitoylphosphatidylcholine and cholesterol, and the antigen ovalbumin (OVA) or the photosensitizer tetraphenyl chlorine disulfonate (TPCS2a) was separately encapsulated. C57BL/6 mice were immunized intradermally with OVA liposomes or a combination of OVA and TPCS2a liposomes, and light was applied the next day for activation of the photosensitizer resulting in cytosolic release of antigen from phagosomes. Immune responses were tested both after a prime only regime and after a prime-boost scheme with a repeat immunization 2 weeks post priming. Antigen-specific CD8(+) T-cell responses and antibody responses were analyzed ex vivo by flow cytometry and ELISA methods. The physicochemical stability of liposomes upon storage and light exposure was analyzed in vitro. Immunization with both TPCS2a- and OVA-containing liposomes greatly improved CD8(+) T-cell responses as compared to immunization without TPCS2a and as measured by proliferation in vivo and cytokine secretion ex vivo. In contrast, OVA-specific antibody responses (IgG1 and IgG2c) were reduced after immunization with TPCS2a-containing liposomes. The liposomal formulation protected the photosensitizer from light-induced inactivation during storage. In conclusion, the photosensitizer TPCS2a was successfully formulated in liposomes and enabled a shift from MHC class II to MHC class I antigen processing and presentation for stimulation of strong CD8(+) T-cell responses. Therefore, photosensitive particulate vaccines may have the potential to add to current vaccine practice a new method of vaccination that, as opposed to current vaccines, can stimulate strong CD8(+) T-cell responses.
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Affiliation(s)
- Ásdís Hjálmsdóttir
- Department of Dermatology, University of Zurich , Gloriastrasse 31, 8091 Zurich, Switzerland
| | - Céline Bühler
- Institute of Pharmaceutical Sciences, ETH Zurich , Vladimir-Prelog-Weg 1-5/10, 8093 Zurich, Switzerland
| | - Vera Vonwil
- Institute of Pharmaceutical Sciences, ETH Zurich , Vladimir-Prelog-Weg 1-5/10, 8093 Zurich, Switzerland
| | - Maurizio Roveri
- Institute of Pharmaceutical Sciences, ETH Zurich , Vladimir-Prelog-Weg 1-5/10, 8093 Zurich, Switzerland
| | - Monika Håkerud
- Department of Dermatology, University of Zurich , Gloriastrasse 31, 8091 Zurich, Switzerland.,Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital , Montebello, 0310 Oslo, Norway
| | - Ying Wäckerle-Men
- Department of Dermatology, University of Zurich , Gloriastrasse 31, 8091 Zurich, Switzerland
| | - Bruno Gander
- Institute of Pharmaceutical Sciences, ETH Zurich , Vladimir-Prelog-Weg 1-5/10, 8093 Zurich, Switzerland
| | - Pål Johansen
- Department of Dermatology, University of Zurich , Gloriastrasse 31, 8091 Zurich, Switzerland
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97
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Global proteogenomic analysis of human MHC class I-associated peptides derived from non-canonical reading frames. Nat Commun 2016; 7:10238. [PMID: 26728094 PMCID: PMC4728431 DOI: 10.1038/ncomms10238] [Citation(s) in RCA: 174] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 11/16/2015] [Indexed: 12/21/2022] Open
Abstract
In view of recent reports documenting pervasive translation outside of canonical protein-coding sequences, we wished to determine the proportion of major histocompatibility complex (MHC) class I-associated peptides (MAPs) derived from non-canonical reading frames. Here we perform proteogenomic analyses of MAPs eluted from human B cells using high-throughput mass spectrometry to probe the six-frame translation of the B-cell transcriptome. We report that ∼10% of MAPs originate from allegedly noncoding genomic sequences or exonic out-of-frame translation. The biogenesis and properties of these ‘cryptic MAPs' differ from those of conventional MAPs. Cryptic MAPs come from very short proteins with atypical C termini, and are coded by transcripts bearing long 3′UTRs enriched in destabilizing elements. Relative to conventional MAPs, cryptic MAPs display different MHC class I-binding preferences and harbour more genomic polymorphisms, some of which are immunogenic. Cryptic MAPs increase the complexity of the MAP repertoire and enhance the scope of CD8 T-cell immunosurveillance. Cryptic translation of the 'non-coding' genome is increasingly recognised, however its biological significance remains unclear. Laumont et al. employ proteogenomic techniques to map the human immunoproteome, and find that approximately 10% of MHC class I-associated peptides are cryptic.
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98
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Ternette N, Yang H, Partridge T, Llano A, Cedeño S, Fischer R, Charles PD, Dudek NL, Mothe B, Crespo M, Fischer WM, Korber BTM, Nielsen M, Borrow P, Purcell AW, Brander C, Dorrell L, Kessler BM, Hanke T. Defining the HLA class I-associated viral antigen repertoire from HIV-1-infected human cells. Eur J Immunol 2015; 46:60-9. [PMID: 26467324 PMCID: PMC4737398 DOI: 10.1002/eji.201545890] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 08/27/2015] [Accepted: 10/08/2015] [Indexed: 11/16/2022]
Abstract
Recognition and eradication of infected cells by cytotoxic T lymphocytes is a key defense mechanism against intracellular pathogens. High‐throughput definition of HLA class I‐associated immunopeptidomes by mass spectrometry is an increasingly important analytical tool to advance our understanding of the induction of T‐cell responses against pathogens such as HIV‐1. We utilized a liquid chromatography tandem mass spectrometry workflow including de novo‐assisted database searching to define the HLA class I‐associated immunopeptidome of HIV‐1‐infected human cells. We here report for the first time the identification of 75 HIV‐1‐derived peptides bound to HLA class I complexes that were purified directly from HIV‐1‐infected human primary CD4+ T cells and the C8166 human T‐cell line. Importantly, one‐third of eluted HIV‐1 peptides had not been previously known to be presented by HLA class I. Over 82% of the identified sequences originated from viral protein regions for which T‐cell responses have previously been reported but for which the precise HLA class I‐binding sequences have not yet been defined. These results validate and expand the current knowledge of virus‐specific antigenic peptide presentation during HIV‐1 infection and provide novel targets for T‐cell vaccine development.
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Affiliation(s)
- Nicola Ternette
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Hongbing Yang
- NIHR Oxford Biomedical Research Centre, Oxford, UK.,Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Thomas Partridge
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Anuska Llano
- HIVACAT, Irsicaixa AIDS Research Institute, Autonomous University of Barcelona, Badalona, Spain
| | - Samandhy Cedeño
- HIVACAT, Irsicaixa AIDS Research Institute, Autonomous University of Barcelona, Badalona, Spain
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Philip D Charles
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nadine L Dudek
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Beatriz Mothe
- HIVACAT, Irsicaixa AIDS Research Institute, Autonomous University of Barcelona, Badalona, Spain.,Lluita contra la Sida' Foundation, Hospital Germans Trias i Pujol, Badalona, Spain.,Universitat de Vic - Universitat Central de Catalunya, Vic, Spain
| | - Manuel Crespo
- HIV Unit, Hospital de la Vall d'Hebrón, Barcelona, Spain
| | - William M Fischer
- Group T-6, Theoretical Biology, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Bette T M Korber
- Group T-6, Theoretical Biology, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Morten Nielsen
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Persephone Borrow
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Christian Brander
- HIVACAT, Irsicaixa AIDS Research Institute, Autonomous University of Barcelona, Badalona, Spain.,Universitat de Vic - Universitat Central de Catalunya, Vic, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Lucy Dorrell
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,NIHR Oxford Biomedical Research Centre, Oxford, UK.,Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tomáš Hanke
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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99
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Marino F, Bern M, Mommen GP, Leney AC, van Gaans-van den Brink JA, Bonvin AM, Becker C, van Els CA, Heck AJR. Extended O-GlcNAc on HLA Class-I-Bound Peptides. J Am Chem Soc 2015; 137:10922-10925. [PMID: 26280087 PMCID: PMC4603548 DOI: 10.1021/jacs.5b06586] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report unexpected mass spectrometric observations of glycosylated human leukocyte antigen (HLA) class I-bound peptides. Complemented by molecular modeling, in vitro enzymatic assays, and oxonium ion patterns, we propose that the observed O-linked glycans carrying up to five monosaccharides are extended O-GlcNAc's rather than GalNAc-initiated O-glycans. A cytosolic O-GlcNAc modification is normally terminal and does not extend to produce a polysaccharide, but O-GlcNAc on an HLA peptide presents a special case because the loaded HLA class I complex traffics through the endoplasmic reticulum and Golgi apparatus on its way to the cell membrane and is hence exposed to glycosyltransferases. We also report for the first time natural HLA class I presentation of O- and N-linked glycopeptides derived from membrane proteins. HLA class I peptides with centrally located oligosaccharides have been shown to be immunogenic and may thus be important targets for immune surveillance.
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Affiliation(s)
- Fabio Marino
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | | | - Geert P.M. Mommen
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Institute for Translational Vaccinology, Bilthoven, Netherlands
| | - Aneika C. Leney
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | | | - Alexandre M.J.J. Bonvin
- Computational Structural Biology, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | | | - Cécile A.C.M. van Els
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, The Netherlands
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
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100
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Wei J, Gibbs JS, Hickman HD, Cush SS, Bennink JR, Yewdell JW. Ubiquitous Autofragmentation of Fluorescent Proteins Creates Abundant Defective Ribosomal Products (DRiPs) for Immunosurveillance. J Biol Chem 2015; 290:16431-9. [PMID: 25971973 PMCID: PMC4481239 DOI: 10.1074/jbc.m115.658062] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/12/2015] [Indexed: 11/06/2022] Open
Abstract
Green fluorescent protein (GFP) and other fluorescent proteins are essential tools for biological research. When fused to peptides or proteins as a reporter, GFP enables localization and quantitation of gene products in otherwise unmanipulated live cells or organisms. We previously reported that a sizable fraction of nascent GFP is post-translationally converted into a 20-kDa Triton X-100-insoluble proteasome substrate (Qian, S. B., Princiotta, M. F., Bennink, J. R., and Yewdell, J. W. (2006) J. Biol. Chem. 281, 392-400; Dolan, B. P., Li, L., Veltri, C. A., Ireland, C. M., Bennink, J. R., and Yewdell, J. W. (2011) J. Immunol. 186, 2065-2072). Here, we show that a similarly sized fragment is generated by all GFP and red fluorescent protein family members we examined. We demonstrate that fragmentation is a by-product of GFP chromophore rearrangement. A non-rearranging GFP mutant fails to fragment and generates diminished levels of K(b)-SIINFEKL complexes when SIINFEKL is genetically fused to either the C- or N-terminal domains of GFP fusion proteins. Instructively, another fragmenting GFP mutant that cannot create the functional chromophore but still generates fragments also demonstrates diminished K(b)-SIINFEKL generation. However, the mutant and wild-type fragments differ fundamentally in that wild-type fragments are rapidly liberated from the intact molecule and degraded quickly, accounting for increased K(b)-SIINFEKL generation. In the fragmenting mutant, the fragments are generated slowly and remain associated, likely in a native conformation based on their original structural description (Barondeau, D. P., Kassmann, C. J., Tainer, J. A., and Getzoff, E. D. (2006) J. Am. Chem. Soc. 128, 4685-4693). The wild-type GFP fragments represent the first biochemically defined natural defective ribosomal products to contribute peptides for immunosurveillance, enabling quantitation of peptide generation efficiency from this source of defective ribosomal products. More broadly, given the wide use of fluorescent proteins, their ubiquitous and abundant fragmentation must be considered when interpreting experiments using these extremely useful probes.
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Affiliation(s)
- Jiajie Wei
- From the Laboratory of Viral Diseases, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - James S Gibbs
- From the Laboratory of Viral Diseases, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Heather D Hickman
- From the Laboratory of Viral Diseases, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Stephanie S Cush
- From the Laboratory of Viral Diseases, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Jack R Bennink
- From the Laboratory of Viral Diseases, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Jonathan W Yewdell
- From the Laboratory of Viral Diseases, NIAID, National Institutes of Health, Bethesda, Maryland 20892
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