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Molecular mechanism of phosphopeptide neoantigen immunogenicity

Patskovsky, Yury; Natarajan, Aswin; Patskovska, Larysa; Nyovanie, Samantha; Joshi, Bishnu; Morin, Benjamin; Brittsan, Christine; Huber, Olivia; Gordon, Samuel; Michelet, Xavier; Schmitzberger, Florian; Stein, Robert B; Findeis, Mark A; Hurwitz, Andy; Van Dijk, Marc; Buell, Jennifer S; Underwood, Dennis; Krogsgaard, Michelle
Altered protein phosphorylation in cancer cells often leads to surface presentation of phosphopeptide neoantigens. However, their role in cancer immunogenicity remains unclear. Here we describe a mechanism by which an HLA-B*0702-specific acute myeloid leukemia phosphoneoantigen, pMLL747-755 (EPR(pS)PSHSM), is recognized by a cognate T cell receptor named TCR27, a candidate for cancer immunotherapy. We show that the replacement of phosphoserine P4 with serine or phosphomimetics does not affect pMHC conformation or peptide-MHC affinity but abrogates TCR27-dependent T cell activation and weakens binding between TCR27 and pMHC. Here we describe the crystal structures for TCR27 and cognate pMHC, map of the interface produced by nuclear magnetic resonance, and a ternary complex generated using information-driven protein docking. Our data show that non-covalent interactions between the epitope phosphate group and TCR27 are crucial for TCR specificity. This study supports development of new treatment options for cancer patients through target expansion and TCR optimization.
PMCID:10290117
PMID: 37353482
ISSN: 2041-1723
CID: 5538512

Structural Model of the Extracellular Assembly of the TCR-CD3 Complex

Natarajan, Aswin; Nadarajah, Vidushan; Felsovalyi, Klara; Wang, Wenjuan; Jeyachandran, Vivian R; Wasson, Riley A; Cardozo, Timothy; Bracken, Clay; Krogsgaard, Michelle
Antigen recognition of peptide-major histocompatibility complexes (pMHCs) by T cells, a key step in initiating adaptive immune responses, is performed by the T cell receptor (TCR) bound to CD3 heterodimers. However, the biophysical basis of the transmission of TCR-CD3 extracellular interaction into a productive intracellular signaling sequence remains incomplete. Here we used nuclear magnetic resonance (NMR) spectroscopy combined with mutational analysis and computational docking to derive a structural model of the extracellular TCR-CD3 assembly. In the inactivated state, CD3gammaepsilon interacts with the helix 3 and helix 4-F strand regions of the TCR Cbeta subunit, whereas CD3deltaepsilon interacts with the F and C strand regions of the TCR Calpha subunit in this model, placing the CD3 subunits on opposing sides of the TCR. This work identifies the molecular contacts between the TCR and CD3 subunits, identifying a physical basis for transmitting an activating signal through the complex.
PMCID:4902171
PMID: 26997265
ISSN: 2211-1247
CID: 2051952

T-cell receptor affinity and avidity defines antitumor response and autoimmunity in T-cell immunotherapy

Zhong, Shi; Malecek, Karolina; Johnson, Laura A; Yu, Zhiya; Vega-Saenz de Miera, Eleazar; Darvishian, Farbod; McGary, Katelyn; Huang, Kevin; Boyer, Josh; Corse, Emily; Shao, Yongzhao; Rosenberg, Steven A; Restifo, Nicholas P; Osman, Iman; Krogsgaard, Michelle
T cells expressing antigen-specific T-cell receptors (TCRs) can mediate effective tumor regression, but they often also are accompanied by autoimmune responses. To determine the TCR affinity threshold defining the optimal balance between effective antitumor activity and autoimmunity in vivo, we used a unique self-antigen system comprising seven human melanoma gp100(209-217)-specific TCRs spanning physiological affinities (1-100 muM). We found that in vitro and in vivo T-cell responses are determined by TCR affinity, except in one case that was compensated by substantial CD8 involvement. Strikingly, we found that T-cell antitumor activity and autoimmunity are closely coupled but plateau at a defined TCR affinity of 10 microM, likely due to diminished contribution of TCR affinity to avidity above the threshold. Together, these results suggest that a relatively low-affinity threshold is necessary for the immune system to avoid self-damage, given the close relationship between antitumor activity and autoimmunity. The low threshold, in turn, indicates that adoptive T-cell therapy treatment strategies using in vitro-generated high-affinity TCRs do not necessarily improve efficacy.
PMCID:3637771
PMID: 23576742
ISSN: 0027-8424
CID: 304932

Specific Increase in Potency via Structure-Based Design of a TCR

Malecek, Karolina; Grigoryan, Arsen; Zhong, Shi; Gu, Wei Jun; Johnson, Laura A; Rosenberg, Steven A; Cardozo, Timothy; Krogsgaard, Michelle
Adoptive immunotherapy with Ag-specific T lymphocytes is a powerful strategy for cancer treatment. However, most tumor Ags are nonreactive "self" proteins, which presents an immunotherapy design challenge. Recent studies have shown that tumor-specific TCRs can be transduced into normal PBLs, which persist after transfer in approximately 30% of patients and effectively destroy tumor cells in vivo. Although encouraging, the limited clinical responses underscore the need for enrichment of T cells with desirable antitumor capabilities prior to patient transfer. In this study, we used structure-based design to predict point mutations of a TCR (DMF5) that enhance its binding affinity for an agonist tumor Ag-MHC (peptide-MHC [pMHC]), Mart-1 (27L)-HLA-A2, which elicits full T cell activation to trigger immune responses. We analyzed the effects of selected TCR point mutations on T cell activation potency and analyzed cross-reactivity with related Ags. Our results showed that the mutated TCRs had improved T cell activation potency while retaining a high degree of specificity. Such affinity-optimized TCRs have demonstrated to be very specific for Mart-1 (27L), the epitope for which they were structurally designed. Although of somewhat limited clinical relevance, these studies open the possibility for future structural-based studies that could potentially be used in adoptive immunotherapy to treat melanoma while avoiding adverse autoimmunity-derived effects.
PMCID:4205480
PMID: 25070852
ISSN: 0022-1767
CID: 1089952

Quantitative analysis of T cell receptor complex interaction sites using genetically encoded photo-cross-linkers

Wang, Wenjuan; Li, Tianqi; Felsovalyi, Klara; Chen, Chunlai; Cardozo, Timothy; Krogsgaard, Michelle
The T cell receptor (TCR)-cluster of differentiation 3 (CD3) signaling complex plays an important role in initiation of adaptive immune responses, but weak interactions have obstructed delineation of the individual TCR-CD3 subunit interactions during T cell signaling. Here, we demonstrate that unnatural amino acids (UAA) can be used to photo-cross-link subunits of TCR-CD3 on the cell surface. Incorporating UAA in mammalian cells is usually a low efficiency process. In addition, TCR-CD3 is composed of eight subunits and both TCR and CD3 chains are required for expression on the cell surface. Photo-cross-linking of UAAs for studying protein complexes such as TCR-CD3 is challenging due to the difficulty of transfecting and expressing multisubunit protein complexes in cells combined with the low efficiency of UAA incorporation. Here, we demonstrate that by systematic optimization, we can incorporate UAA in TCR-CD3 with high efficiency. Accordingly, the incorporated UAA can be used for site-specific photo-cross-linking experiments to pinpoint protein interaction sites, as well as to confirm interaction sites identified by X-ray crystallography. We systemically compared two different photo-cross-linkers-p-azido-phenylalanine (pAzpa) and H-p-Bz-Phe-OH (pBpa)-for their ability to map protein subunit interactions in the 2B4 TCR. pAzpa was found to have higher cross-linking efficiency, indicating that optimization of the selection of the most optimal cross-linker is important for correct identification of protein-protein interactions. This method is therefore suitable for studying interaction sites of large, dynamic heteromeric protein complexes associated with various cellular membrane systems.
PMCID:4168801
PMID: 25061810
ISSN: 1554-8929
CID: 1252232

Strength of PD-1 signaling differentially affects T-cell effector functions

Wei, Fang; Zhong, Shi; Ma, Zhengyu; Kong, Hong; Medvec, Andrew; Ahmed, Rafi; Freeman, Gordon J; Krogsgaard, Michelle; Riley, James L
High surface expression of programmed death 1 (PD-1) is associated with T-cell exhaustion; however, the relationship between PD-1 expression and T-cell dysfunction has not been delineated. We developed a model to study PD-1 signaling in primary human T cells to study how PD-1 expression affected T-cell function. By determining the number of T-cell receptor/peptide-MHC complexes needed to initiate a Ca2+ flux, we found that PD-1 ligation dramatically shifts the dose-response curve, making T cells much less sensitive to T-cell receptor-generated signals. Importantly, other T-cell functions were differentially sensitive to PD-1 expression. We observed that high levels of PD-1 expression were required to inhibit macrophage inflammatory protein 1 beta production, lower levels were required to block cytotoxicity and IFN-gamma production, and very low levels of PD-1 expression could inhibit TNF-alpha and IL-2 production as well as T-cell expansion. These findings provide insight into the role of PD-1 expression in enforcing T-cell exhaustion and the therapeutic potential of PD-1 blockade.
PMCID:3703988
PMID: 23610399
ISSN: 0027-8424
CID: 377372

Hybrid and vaccine-induced immunity against SAR-CoV-2 in MS patients on different disease-modifying therapies

Kister, Ilya; Curtin, Ryan; Pei, Jinglan; Perdomo, Katherine; Bacon, Tamar E; Voloshyna, Iryna; Kim, Joseph; Tardio, Ethan; Velmurugu, Yogambigai; Nyovanie, Samantha; Valeria Calderon, Andrea; Dibba, Fatoumatta; Stanzin, Igda; Samanovic, Marie I; Raut, Pranil; Raposo, Catarina; Priest, Jessica; Cabatingan, Mark; Winger, Ryan C; Mulligan, Mark J; Patskovsky, Yury; Silverman, Gregg J; Krogsgaard, Michelle
OBJECTIVE:To compare "hybrid immunity" (prior COVID-19 infection plus vaccination) and post-vaccination immunity to SARS CoV-2 in MS patients on different disease-modifying therapies (DMTs) and to assess the impact of vaccine product and race/ethnicity on post-vaccination immune responses. METHODS:Consecutive MS patients from NYU MS Care Center (New York, NY), aged 18-60, who completed primary COVID-19 vaccination series ≥6 weeks previously were evaluated for SARS CoV-2-specific antibody responses with electro-chemiluminescence and multiepitope bead-based immunoassays and, in a subset, live virus immunofluorescence-based microneutralization assay. SARS CoV-2-specific cellular responses were assessed with cellular stimulation TruCulture IFNγ and IL-2 assay and, in a subset, with IFNγ and IL-2 ELISpot assays. Multivariate analyses examined associations between immunologic responses and prior COVID-19 infection while controlling for age, sex, DMT at vaccination, time-to-vaccine, and vaccine product. RESULTS:Between 6/01/2021 and 11/11/2021, 370 MS patients were recruited (mean age 40.6 years; 76% female; 53% non-White; 22% with prior infection; common DMT classes: ocrelizumab 40%; natalizumab 15%, sphingosine-1-phosphate receptor modulators 13%; and no DMT 8%). Vaccine-to-collection time was 18.7 (±7.7) weeks and 95% of patients received mRNA vaccines. In multivariate analyses, patients with laboratory-confirmed prior COVID-19 infection had significantly increased antibody and cellular post-vaccination responses compared to those without prior infection. Vaccine product and DMT class were independent predictors of antibody and cellular responses, while race/ethnicity was not. INTERPRETATION/CONCLUSIONS:Prior COVID-19 infection is associated with enhanced antibody and cellular post-vaccine responses independent of DMT class and vaccine type. There were no differences in immune responses across race/ethnic groups.
PMID: 36165097
ISSN: 2328-9503
CID: 5334142

Kinase Insert Domain Receptor Q472H Pathogenic Germline Variant Impacts Melanoma Tumor Growth and Patient Treatment Outcomes

Ibrahim, Milad; Illa-Bochaca, Irineu; Fa"™ak, Faisal; Monson, Kelsey R.; Ferguson, Robert; Lyu, Chen; Vega-Saenz de Miera, Eleazar; Johannet, Paul; Chou, Margaret; Mastroianni, Justin; Darvishian, Farbod; Kirchhoff, Tomas; Zhong, Judy; Krogsgaard, Michelle; Osman, Iman
Background: We previously reported a higher incidence of a pathogenic germline variant in the kinase insert domain receptor (KDR) in melanoma patients compared to the general population. Here, we dissect the impact of this genotype on melanoma tumor growth kinetics, tumor phenotype, and response to treatment with immune checkpoint inhibitors (ICIs) or targeted therapy. Methods: The KDR genotype was determined and the associations between the KDR Q472H variant (KDR-Var), angiogenesis, tumor immunophenotype, and response to MAPK inhibition or ICI treatment were examined. Melanoma B16 cell lines were transfected with KDR-Var or KDR wild type (KDR-WT), and the differences in tumor kinetics were evaluated. We also examined the impact of KDR-Var on the response of melanoma cells to a combination of VEGFR inhibition with MAPKi. Results: We identified the KDR-Var genotype in 81/489 (37%) patients, and it was associated with a more angiogenic (p = 0.003) and immune-suppressive tumor phenotype. KDR-Var was also associated with decreased PFS to MAPKi (p = 0.022) and a trend with worse PFS to anti-PD1 therapy (p = 0.06). KDR-Var B16 murine models had increased average tumor volume (p = 0.0027) and decreased CD45 tumor-infiltrating lymphocytes (p = 0.0282). The anti-VEGFR treatment Lenvatinib reduced the tumor size of KDR-Var murine tumors (p = 0.0159), and KDR-Var cells showed synergistic cytotoxicity to the combination of dabrafenib and lenvatinib. Conclusions: Our data demonstrate a role of germline KDR-Var in modulating melanoma behavior, including response to treatment. Our data also suggest that anti-angiogenic therapy might be beneficial in patients harboring this genotype, which needs to be tested in clinical trials.
SCOPUS:85182244291
ISSN: 2072-6694
CID: 5629852

Perspectives in Melanoma: meeting report from the Melanoma Bridge (December 1st-3rd, 2022-Naples, Italy)

Ascierto, Paolo A; Agarwala, Sanjiv S; Warner, Allison Betof; Ernstoff, Marc S; Fox, Bernard A; Gajewski, Thomas F; Galon, Jérôme; Garbe, Claus; Gastman, Brian R; Gershenwald, Jeffrey E; Kalinski, Pawel; Krogsgaard, Michelle; Leidner, Rom S; Lo, Roger S; Menzies, Alexander M; Michielin, Olivier; Poulikakos, Poulikos I; Weber, Jeffrey S; Caracò, Corrado; Osman, Iman; Puzanov, Igor; Thurin, Magdalena
Outcomes for patients with melanoma have improved over the past decade with the clinical development and approval of immunotherapies targeting immune checkpoint receptors such as programmed death-1 (PD-1), programmed death ligand 1 (PD-L1) or cytotoxic T lymphocyte antigen-4 (CTLA-4). Combinations of these checkpoint therapies with other agents are now being explored to improve outcomes and enhance benefit-risk profiles of treatment. Alternative inhibitory receptors have been identified that may be targeted for anti-tumor immune therapy, such as lymphocyte-activation gene-3 (LAG-3), as have several potential target oncogenes for molecularly targeted therapy, such as tyrosine kinase inhibitors. Unfortunately, many patients still progress and acquire resistance to immunotherapy and molecularly targeted therapies. To bypass resistance, combination treatment with immunotherapies and single or multiple TKIs have been shown to improve prognosis compared to monotherapy. The number of new combinations treatment under development for melanoma provides options for the number of patients to achieve a therapeutic benefit. Many diagnostic and prognostic assays have begun to show clinical applicability providing additional tools to optimize and individualize treatments. However, the question on the optimal algorithm of first- and later-line therapies and the search for biomarkers to guide these decisions are still under investigation. This year, the Melanoma Bridge Congress (Dec 1st-3rd, 2022, Naples, Italy) addressed the latest advances in melanoma research, focusing on themes of paramount importance for melanoma prevention, diagnosis and treatment. This included sessions dedicated to systems biology on immunotherapy, immunogenicity and gene expression profiling, biomarkers, and combination treatment strategies.
PMCID:10375730
PMID: 37507765
ISSN: 1479-5876
CID: 5594222

Author Correction: Molecular mechanism of phosphopeptide neoantigen immunogenicity

Patskovsky, Yury; Natarajan, Aswin; Patskovska, Larysa; Nyovanie, Samantha; Joshi, Bishnu; Morin, Benjamin; Brittsan, Christine; Huber, Olivia; Gordon, Samuel; Michelet, Xavier; Schmitzberger, Florian; Stein, Robert B; Findeis, Mark A; Hurwitz, Andy; Van Dijk, Marc; Chantzoura, Eleni; Yague, Alvaro S; Pollack Smith, Daniel; Buell, Jennifer S; Underwood, Dennis; Krogsgaard, Michelle
PMID: 37500629
ISSN: 2041-1723
CID: 5618892