Cytotoxic T Lymphocytes Clones Research Articles

NF9 peptide specific cytotoxic T lymphocyte clone cross react to Y453F mutation of SARS-CoV-2 virus spike protein

The recognition by cytotoxic T cells (CTLs) is essential for the clearance of SARS-CoV-2 virus-infected cells. Several viral proteins have been described to be recognized by CTLs. Among them, the spike (S) protein is one of the immunogenic proteins. The S protein acts as a ligand for its receptors, and several mutants with different affinities for its cognate receptors have been reported, and certain mutations in the S protein, such as L452R and Y453F, have been found to inhibit the HLA-A24-restricted CTL response. In this study, we conducted a screening of candidate peptides derived from the S protein, specifically targeting those carrying the HLA-A24 binding motif. Among these peptides, we discovered that NF9 (NYNYLYRLF) represents an immunogenic epitope. CTL clones specific to the NF9 peptide were successfully established. These CTL clones exhibited the ability to recognize endogenously expressed NF9 peptide. Interestingly, the CTL clone demonstrated cross-reactivity with the Y453F peptide (NYNYLFRLF) but not with the L452R peptide (NYNYRYRLF). The CTL clone was able to identify the endogenously expressed Y453F mutant peptide. These findings imply that the NF9-specific CTL clone possesses the capability to recognize and respond to the Y453F mutant peptide.

Bone marrow-derived mesenchymal stromal cells obstruct AML-targeting CD8+ clonal effector and CAR T-cell function while promoting a senescence-associated phenotype

Bone marrow mesenchymal stromal cells (MSCs) have been described as potent regulators of T-cell function, though whether they could impede the effectiveness of immunotherapy against acute myeloid leukemia (AML) is still under investigation. We examine whether they could interfere with the activity of leukemia-specific clonal cytotoxic T-lymphocytes (CTLs) and chimeric antigen receptor (CAR) T cells, as well as whether the immunomodulatory properties of MSCs could be associated with the induction of T-cell senescence. Co-cultures of leukemia-associated Wilm’s tumor protein 1 (WT1) and tyrosine-protein kinase transmembrane receptor 1 (ROR1)-reactive CTLs and of CD123-redirected switchable CAR T cells were prepared in the presence of MSCs and assessed for cytotoxic potential, cytokine secretion, and expansion. T-cell senescence within functional memory sub-compartments was investigated for the senescence-associated phenotype CD28−CD57+ using unmodified peripheral blood mononuclear cells. We describe inhibition of expansion of AML-redirected switchable CAR T cells by MSCs via indoleamine 2,3-dioxygenase 1 (IDO-1) activity, as well as reduction of interferon gamma (IFNγ) and interleukin-2 (IL-2) release. In addition, MSCs interfered with the secretory potential of leukemia-associated WT1- and ROR1-targeting CTL clones, inhibiting the release of IFNγ, tumor necrosis factor alpha, and IL-2. Abrogated T cells were shown to retain their cytolytic activity. Moreover, we demonstrate induction of a CD28loCD27loCD57+KLRG1+ senescent T-cell phenotype by MSCs. In summary, we show that MSCs are potent modulators of anti-leukemic T cells, and targeting their modes of action would likely be beneficial in a combinatorial approach with AML-directed immunotherapy.

C-Met+ Cytotoxic T Lymphocytes Exhibit Enhanced Cytotoxicity in Mice and Humans In Vitro Tumor Models.

CD8+ cytotoxic T lymphocytes (CTLs) play a crucial role in anti-tumor immunity. In a previous study, we identified a subset of murine effector CTLs expressing the hepatocyte growth factor (HGF) receptor, c-Met (c-Met+ CTLs), that are endowed with enhanced cytolytic capacity. HGF directly inhibited the cytolytic function of c-Met+ CTLs, both in 2D in vitro assays and in vivo, leading to reduced T cell responses against metastatic melanoma. To further investigate the role of c-Met+ CTLs in a three-dimensional (3D) setting, we studied their function within B16 melanoma spheroids and examined the impact of cell-cell contact on the modulation of inhibitory checkpoint molecules' expression, such as KLRG1, PD-1, and CTLA-4. Additionally, we evaluated the cytolytic capacity of human CTL clones expressing c-Met (c-Met+) and compared it to c-Met- CTL clones. Our results indicated that, similar to their murine counterparts, c-Met+ human CTL clones exhibited increased cytolytic activity compared to c-Met- CTL clones, and this enhanced function was negatively regulated by the presence of HGF. Taken together, our findings highlight the potential of targeting the HGF/c-Met pathway to modulate CTL-mediated anti-tumor immunity. This research holds promise for developing strategies to enhance the effectiveness of CTL-based immunotherapies against cancer.

An epitope encoded by uORF of RNF10 elicits a therapeutic anti-tumor immune response

Tumor-specific antigens (TSAs) are crucial for tumor-specific immune response that reduces tumor burden and thus serve as important targets for immunotherapy. Identification of novel TSAs can provide new strategies for immunotherapies. In this study, we demonstrated that the upstream open reading frame (uORF) of RNF10 encodes an antigenic peptide (RNF10 uPeptide), capable of eliciting a Tcell-mediated anti-tumor immune response. We initially demonstrated the immunogenicity of the RNF10 uPeptide in a CT26 tumor mouse model, by showing that its epitope was specifically recognized by CD8+ Tcells. Vaccination of mice with the long form of the RNF10 uPeptide conferred strong anti-tumor activity. Next, we proved that the human RNF10 uORF could be translated. In addition, we predicted the binding of an RNF10 uPeptide epitope to HLA-A∗02:01 (HLA-A2). This HLA-A2-restricted epitope of the RNF10 uPeptide induced a potent specific human Tcell response. Finally, we showed that an HLA-A2-restricted cytotoxic Tcell (CTL) clone, derived from a pancreatic cancer patient, recognized the RNF10 uPeptide epitope (RLFGQQQRA) and lysed HLA-A2+ pancreatic carcinoma cells expressing the RNF10 uPeptide. These results indicate that the RNF10 uPeptide could be a promising target for pancreatic carcinoma immunotherapy.

T-Cell Receptor Amino Acid Sequence Selected By Cytotoxic T Cells Specific to HTLV-1 in HLA-A02:01-Positive ATL Patients

Purpose: Adult T cell leukemia/lymphoma (ATL) is an aggressive peripheral malignancy of T cells caused by human T cell lymphotropic virus type-1 (HTLV-1). Its prognosis remains very poor. Tax is the most important regulatory protein for HTLV-1, which is associated with the proliferation of host cells. Tax has been considered as an important target antigen for CD8+cytotoxic T cells (CTLs). We aimed to reveal such a unique sequence of complementarity-determining region 3 (CDR3) of the T cell receptor (TCR)-α and-β chain of HLA-A*02:01-restricted Tax11-19-specific CTLs (Tax-CTL). Methods: We serially analyzed Tax-CTLs from ATL patients with HLA-A*02:01 who had received allogeneic hematopoietic cell transplantation (all-HCT), chemotherapies alone, or had not ever received any treatment. Tax-CTLs were defined as a living CD3+CD8+Tax-tetramer+cells. After sorting Tax-CTLs directly from an actual patient sample into a PCR tube, TCR-α and -β chains of individual CTL clones were determined by the next-generation sequence (NGS) method with SMARTer technology. In addition, we cultured and established individual Tax-CTL clones from a sorted single cell, and finally evaluated the cytotoxicity of Tax-CTLs by calcein-acetoxymethyl (AM)-based cytotoxicity assay. Results: Peripheral blood samples were obtained from 7 patients (Pt-1,-2,-3,-4,-5,-6 and -7). Pt-1 had received allo-HCT and the samples were available 270 days, 1 year, 3 years, 5 years and 7 years after allo-HCT. Samples before treatment were available in the other 5 patient (acute ATL Pt-2,-3, and -6; chronic ATL, Pt-4; HTLV-1 asymptomatic charrier, Pt-5), while the samples after treatment were available in 1 patient (acute ATL Pt-7). Tax-specific CTLs were detected in 0.03-0.58% of total peripheral blood mononuclear cells, and 144-1000 cells per sample (median; 250 cells) were sorted and analyzed for TCR determination. Of them, 2 to 30 Tax-specific CTL clones were identified for each patient. Tax-specific CTLs seemed oligoclonal, and their usage of BV and BJ genes were restricted in TCR-BV28(30.5%), -BV6-5(33.3%), and -BJ2-1(30.5%), while their usage of AV and AJ genes were restricted in TCR-AV12-2(54.5%) and -AJ24(24.2%) gene families. The length of amino acids (AA) in TCR-α and TCR-β CDR3 of all Tax-CTLs clones seemed to be symmetrically distributed, and the most frequently observed AA length was 13 in TCR-α, and 15 in TCR-β. The unique motifs of "DSWGK" in TCR-α and "LAGG" in TCR-β at CDR3 were observed in almost all ATL patients. The 'DSWGK' motif was observed in 0-81.7% (median; 55.5%), and the 'LAGG' motif was observed in 5.2%-80.3% (median; 48%). Pt-2 didn't have any clones with 'DSWGK' motif in TCR-α, whereas regarding 'LAGG' motif in TCR-β, all patients had it in this study. We established Tax11-19-specific CTL clones from a single cell of Pt-4, which showed killing activities against Tax-peptide-pulsed HLA-A2+ T2 cell lines. Conclusion: These methods and results can help us to better understand immunity against ATL, leading to future studies on the clinical application of adoptive T-cell therapies in the future.

STAT3 mutations in "gray-zone" cases of T-cell large granular lymphocytic leukemia associated with autoimmune rheumatic diseases.

A persistently increased T-cell large granular lymphocyte (T-LGL) count in the blood of more than 2 × 109/L for at least 6 months is necessary for a reliable diagnosis of T-LGL leukemia. In cases with LGL counts of approximately 0.5–2 × 109/L, a diagnosis of T-LGL leukemia can be made if clonal rearrangement of T-cell receptor (TCR) genes is present and if the patient shows typical manifestations of T-LGL leukemia, such as cytopenia, splenomegaly, or concomitant autoimmune disease. However, in cases with LGL counts of less than 0.5 × 109/L, the diagnosis of T-LGL leukemia is questionable (termed as “gray-zone” cases). Although mutations in signal transducer and activator of transcription 3 (STAT3) gene are the molecular hallmark of T-LGL leukemia, their diagnostic value in the “gray-zone” cases of T-LGL leukemia has not been evaluated – our study has been aimed to examine the prevalence of STAT3 mutations in these cases. Herein, we describe 25 patients with autoimmune rheumatic diseases, neutropenia, clonal rearrangement of TCR genes, and circulating LGL count of less than 0.5 × 109/L. Splenomegaly was observed in 19 (76%) patients. Mutations in the STAT3 were detected in 56% of patients using next-generation sequencing. Importantly, in 3 patients, no involvement of the blood and bone marrow by malignant LGLs was noted, but examination of splenic tissue revealed infiltration by clonal cytotoxic T-lymphocytes within the red pulp, with greater prominence in the cords. We suggest using the term “splenic variant of T-LGL leukemia” for such cases.

Identification of cytotoxic T cells and their T cell receptor sequences targeting COVID-19 using MHC class I-binding peptides

Since severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, COVID-19) was first reported in China in December 2019, various variants have been identified in different areas of the world such as United Kingdom (alpha), South Africa (beta and omicron), Brazil (gamma), and India (delta). Some of SARS-CoV-2 variants, each of which is characterized by a unique mutation(s) in spike protein, are concerned due to their high infectivity and the capability to escape from neutralizing antibodies elicited by vaccinations. To identify peptide epitopes that are derived from SARS-CoV-2 viral proteins and possibly induce CD8+ T cell immunity, we investigated SARS-CoV-2-derived peptides that are likely to bind to major histocompatibility complex (MHC) class I molecules. We identified a total of 15 peptides that bind to human leukocyte antigen (HLA)-A*24:02, HLA-A*02:01, or HLA-A*02:06, and possibly induce cytotoxic T lymphocytes (CTLs); thirteen of them corresponded to ORF1ab polyprotein, one peptide to spike protein and the remaining one to membrane glycoprotein. CD8+ T cells that recognize these peptides were detected in peripheral blood samples in three individuals recovered from COVID-19 as well as non-infected individuals. Since most of these peptides are commonly conserved among other coronaviruses including SARS-CoV and/or MERS-CoV, these might be useful to maintain T cell responses to coronaviruses that are pandemic at present and will become the future threat. We could define pairs of TRA and TRB sequences of nine CTL clones that recognize SARS-CoV-2-derived peptides. We might use these SARS-CoV-2-derived peptide-reactive TCR sequences for investigating the history of SARS-CoV-2 infection.

Heat Shock Protein 105 as an Immunotherapeutic Target for Patients With Cervical Cancer.

Heat shock protein 105 (HSP105) is overexpressed in various cancers, but not in normal tissues. We investigated the expression levels of HSP105 in cervical cancer and the efficacy of immunotherapy targeting HSP105. Previously, we established human leukocyte antigen-A*02:01 (HLA-A2) restricted HSP105 peptide-specific cytotoxic T lymphocyte (CTL) clones from a colorectal cancer patient vaccinated with an HSP105 peptide. Herein, we evaluated the expression of HSP105 in cervical cancer and cervical intraepithelial neoplasia. Moreover, we tested the effectiveness of an HLA-A2-restricted HSP105 peptide-specific CTL clone against cervical cancer cell lines. HSP105 was expressed in 95% (19/20) of examined cervical cancer tissues. Moreover, the HSP105 peptide-specific CTL clone recognized HSP105- and HLA-A*02:01-positive cervical cancer cell lines and also showed that cytotoxicity against the cervical cancer cell lines depends on HSP105 peptide and HLA class I restricted manners. HSP105 could be an effective target for immunotherapy in patients with cervical cancer.

GRIK2 is a target for bladder cancer stem-like cell-targeting immunotherapy.

Recent studies have revealed that treatment-resistant cancer stem-like cells (CSCs)/cancer-initiating cells (CICs) can be targeted by cytotoxic T lymphocytes (CTLs). CTLs recognize antigenic peptides derived from tumor-associated antigens; thus, the identification of tumor-associated antigens expressed by CSCs/CICs is essential. Human leucocyte antigen (HLA) ligandome analysis using mass spectrometry enables the analysis of naturally expressed antigenic peptides; however, HLA ligandome analysis requires a large number of cells and is challenging for CSCs/CICs. In this study, we established a novel bladder CSC/CIC model from a bladder cancer cell line (UM-UC-3 cells) using an ALDEFLUOR assay. CSCs/CICs were isolated as aldehyde dehydrogenase (ALDH)-high cells and several ALDHhigh clone cells were established. ALDHhigh clone cells were enriched with CSCs/CICs by sphere formation and tumorigenicity in immunodeficient mice. HLA ligandome analysis and cap analysis of gene expression using ALDHhigh clone cells revealed a distinctive antigenic peptide repertoire in bladder CSCs/CICs, and we found that a glutamate receptor, ionotropic, kainite 2 (GRIK2)-derived antigenic peptide (LMYDAVHVV) was specifically expressed by CSCs/CICs. A GRIK2 peptide-specific CTL clone recognized GRIK2-overexpressing UM-UC-3 cells and ALDHhigh clone cells, indicating that GRIK2 peptide can be a novel target for bladder CSC/CIC-targeting immunotherapy.

Differential Impact of Signaling Inhibitor Treatment Versus Standard Chemoimmunotherapy on Chronic Lymphocytic Leukemia T Cells: Clinical Implications

Studies by us and others have documented the clonal architecture of the T cell repertoire in chronic lymphocytic leukemia (CLL), with T cell clones which persist and expand over time in untreated patients, appear disease-specific and may be shared among different patients, thereby indicating selection by restricted antigens. Here, we investigated T cell repertoire dynamics in CLL after different types of treatment by employing high-throughput next-generation sequencing in order to comprehensively assess changes in relation to the type of treatment as well as the clinical response. We analyzed 42 pre- and 3-month post-treatment blood samples from 16 CLL patients who received (i) standard chemoimmunotherapy (FCR regimen, n=5), (ii) ibrutinib (IB, n=9), and/or (iii) rituximab-idelalisib (R-ID, n=7). At the post-treatment sampling, all patients who received FCR had achieved complete remission (CR), and all patients on IB or R-ID had achieved partial remission (PR). Two patients, one on IB and one on R-ID, who later achieved CR were analyzed at that timepoint, as well. We excluded patients who developed rituximab-related late-onset neutropenia after FCR, since it is known to be mediated by cytotoxic T-cell clones. Starting material was PB mononuclear cells. TRBV-TRBD-TRBJ gene rearrangements were RT-PCR amplified and subjected to paired-end NGS. Raw NGS reads were processed through a previously published, purpose-built bioinformatics pipeline designed for paired-read stitching, sequence curation, clonotype computation and repertoire analysis. Only productive TRBV-TRBD-TRBJ rearrangements were included in the analysis (n= 7,494,236, 85.3% of filtered-in sequences, median 178,063/sample). For repertoire analysis, clonotypes (i.e. TRB rearrangements with identical TRBV gene usage and amino acid complementarity-determining region 3 sequence) were considered (median 11,290 distinct clonotypes/sample). The TRBV gene repertoire remained relatively stable after treatment across all treatment groups. All cases displayed significant clonal T cell expansions both pre- and post-treatment (median cumulative frequency of the 10 most expanded T cell clonotypes/sample 30.3% versus 38.6%, respectively). However, differences were noted between the three treatment subgroups. More specifically, clonality (measured as the median cumulative frequency of the 10 most expanded clonotypes/sample) significantly increased after FCR (20.8% to 39.0%, p=0.03) and R-ID (33.0% to 41.1%, p=0.001), whereas it tended to decrease after IB (36.1% to 31.0%, p=0.34). Notably, achieving deeper clinical response (from PR to CR) correlated with a significant increase of clonality in the R-ID case (41.0% to 56.2%), but had no impact in this respect for the IB case (48.3% to 48.1%). The increased clonality in the R-ID case culminated from further expansion of 5 major clonotypes which also dominated the pre-treatment repertoire, suggesting that they may correspond to T-cell clones with anti-tumor properties activated by treatment. Overall, FCR resulted in reconstitution of the T-cell repertoire (median of 2/10 most frequent T-cell clones pre-treatment remained significantly expanded post-treatment), whereas pre-treatment major clones persisted after both IB and R-ID (8/10 and 7/10, respectively). In conclusion, NGS immunoprofiling in CLL documents the differential impact of various treatments on T cells. Particularly, chemoimmunotherapy increases T cell clonality likely through an ablative mechanism, in contrast to signaling inhibitors which retain T cell clones that may have developed in response to tumor antigens and possibly activate them, at least as indicated for the R-ID case, with obvious clinical implications. DisclosuresAgathangelidis:Gilead Sciences: Research Funding. Stavroyianni:Gilead Sciences: Honoraria; Takeda: Honoraria; Janssen Pharmaceuticals: Honoraria. Stamatopoulos:Janssen Pharmaceuticals: Honoraria, Research Funding; Novartis SA: Research Funding; Gilead: Consultancy, Honoraria, Research Funding; Abbvie: Honoraria, Research Funding.

Quantitative Assessment of TCR Repertoire and Allo-Reactivity of Human Acute Gvhd Tissue-Infiltrating T Cells

Abstract Introduction: Due to difficulty in isolating T cells from human tissues, the diversity of allo-reactive T cells that are infiltrating human acute GVHD (aGVHD) tissues remains largely uninvestigated. Here, we report the analysis of comprehensive T cell repertoire and allo-reactivity of human aGVHD tissue-infiltrating T cells. Patients and Methods: Skin (n = 7), stomach (n = 3) and colon (n = 2) biopsy samples and blood samples (n = 8) were obtained from eight post-transplant patients when the patients were supposed to develop aGVHD and prior to the fist-line treatment of aGVHD. Total RNA was extracted from tissue and blood samples, and T cell receptor (TCR)-β gene deep sequencing was performed (~100000 reads for each sample). To estimate the TCR-β repertoire diversity, inverse Simpson's diversity index (1/Ds) were calculated. T cells were isolated from tissues and cloned by limiting dilution. This study was approved by the ethics committees of Nagoya University. Results: In the skin of patient #1, the relative abundance of the most and second most frequent clonotypes were 74.9% and 22.8%, respectively, suggesting that only two T cell clones accounted for approximately 98% of GVHD skin-infiltrating T cells. Two T cell clones, termed clones A and B, were isolated from the skin of patient #1. Both clones lysed patient peripheral blood mononuclear cells, but failed to lyse donor cells. Thus, clones A and B were allo-reactive cytotoxic T lymphocytes (CTLs). The IFN-γ production of clone B was significantly increased when stimulated by COS cells transfected with HLA-DRB1*14:54 cDNA, suggesting that the clone B recognized the mismatched patient's HLA-DRB1*14:54 molecule. To confirm the relative abundance of clones A and B in his skin, the TCR-β usage and CDR3 were determined. Surprisingly, clones A and B were the most and second most frequent skin-infiltrating T cell clones. Taken together, these data suggested that a limited allo-reactive CTL clones were involved in GVHD development of patient #1. In all samples, the mean 1/Ds of skin, stomach, colon and all tissues were 9.4 (range, 1.2-21.3), 7.5 (1.9-14.9), 3.3 (1.0-5.5) and 7.9 (1.0-21.3), respectively, while that of all blood samples was 247 (18.8-888.7) (P 10% frequency) clonotypes in a certain tissue were detected in other tissue(s) of the same patient at an extremely low frequency ( 10% frequency) clonotypes in the skin of a certain patient were detected in those of other patients with an extremely low frequency ( Conclusion: In humans, a limited allo-reactive CTL clones, which differ from tissue to tissue and from patient to patient, may induce aGVHD. The degree of skewing of tissue-infiltrating T cell repertoire may be predictive of GVHD outcome. Download : Download high-res image (62KB) Download : Download full-size image Disclosures Kiyoi: Nippon Boehringer Ingelheim Co., Ltd.: Research Funding; Astellas Pharma Inc.: Consultancy, Research Funding; FUJIFILM Corporation: Patents & Royalties, Research Funding; Eisai Co., Ltd.: Research Funding; Meiji Seika Pharma Co.,Ltd.: Research Funding; Nippon Shinyaku Co., Ltd.: Research Funding; Sumitomo Dainippon Pharma Co., Ltd.: Research Funding; JCR Pharmaceuticals Co.,Ltd.: Research Funding; Novartis Pharma K.K.: Research Funding; MSD K.K.: Research Funding; ONO Pharmaceutical Co., Ltd.: Research Funding; Phizer Japan Inc.: Honoraria, Research Funding; Chugai Pharmaceutical Co., Ltd.: Research Funding; Bristol-Myers Squibb: Honoraria, Research Funding; Kyowa Hakko Kirin Co., Ltd.: Research Funding; Zenyaku Kogyo Co., Ltd.: Research Funding; Celgene Corporation: Consultancy, Research Funding; Takeda Pharmaceutical Co., Ltd.: Research Funding.

A clinically applicable and scalable method to regenerate T-cells from iPSCs for off-the-shelf T-cell immunotherapy

Clinical successes demonstrated by chimeric antigen receptor T-cell immunotherapy have facilitated further development of T-cell immunotherapy against wide variety of diseases. One approach is the development of “off-the-shelf” T-cell sources. Technologies to generate T-cells from pluripotent stem cells (PSCs) may offer platforms to produce “off-the-shelf” and synthetic allogeneic T-cells. However, low differentiation efficiency and poor scalability of current methods may compromise their utilities. Here we show improved differentiation efficiency of T-cells from induced PSCs (iPSCs) derived from an antigen-specific cytotoxic T-cell clone, or from T-cell receptor (TCR)-transduced iPSCs, as starting materials. We additionally describe feeder-free differentiation culture systems that span from iPSC maintenance to T-cell proliferation phases, enabling large-scale regenerated T-cell production. Moreover, simultaneous addition of SDF1α and a p38 inhibitor during T-cell differentiation enhances T-cell commitment. The regenerated T-cells show TCR-dependent functions in vitro and are capable of in vivo anti-tumor activity. This system provides a platform to generate a large number of regenerated T-cells for clinical application and investigate human T-cell differentiation and biology.

CD4+ Cytotoxic T-Cell Clones Specific for bcr-abl b3a2 Fusion Peptide Augment Colony Formation by Chronic Myelogenous Leukemia Cells in a b3a2-Specific and HLA-DR–Restricted Manner

AbstractAlthough it is well known that CD8+cytotoxic T lymphocytes (CTLs) play an important role in the suppression of cancer cell growth, the significance of CD4+ CTLs in resistance to cancer is obscure. In an attempt to elucidate the role of CD4+ CTLs in immunosurveillance of chronic myelogenous leukemia (CML), we examined the immunologic functions of bcr-abl b3a2 fusion peptide-specific CD4+ CTL clones. Seven CD4+ T-cell clones that responded to stimulation with b3a2 peptide, but not with b2a2 peptide or physiological counterparts bcr b3b4 and abl 1A-a2 peptides, were established from two healthy individuals. Restriction elements of these clones were HLA-DRB1*0901. These CD4+ T-cell clones exhibited b3a2 peptide-specific and HLA-DRB1*0901-restricted cytotoxicity and produced interleukin-3 (IL-3), IL-4, IL-10, interferon-γ, tumor necrosis factor–α, and granulocyte-macrophage colony-stimulating factor in response to bcr-abl peptide stimulation, indicating they were Th0 clones. The numbers of HLA-DRB1*0901-positive b3a2, but not those of b2a2-positive or HLA-DRB1*0901-negative CML cell colonies increased when CML cells were cultured with b3a2-specific CD4+ CTL clones. These data suggest that bcr-abl–specific CD4+ CTLs recognize CML cells in an antigen-specific and HLA-DR–restricted manner, and that they do not inhibit, but in fact augment, CML cell growth.© 1998 by The American Society of Hematology.

4308 DEEP-PRIMED IL-15 SUPERAGONIST IMPROVES ANTIVIRAL EFFICACY OF HIV-SPECIFIC CD8+ T-CELLS IN HUMANIZED MOUSE MODEL

OBJECTIVES/GOALS: HIV-specific CD8+ T-cells play a critical role in partially controlling viral replication in infected-individuals, but ultimately fail to eliminate infection. Enhancing these T-cell responses through lymphocyte engineering approaches has the potential as a novel therapy capable of achieving durable control or eradication of infection. METHODS/STUDY POPULATION: IL-15 Superagonist (IL-15SA) potently supports the in vivo persistence and antiviral activity of adoptively transferred CD8+ T-cells. The Deep-PrimingTM technology platform, developed by Torque, allows for loading of immunomodulators onto the surface of T-cells via electrostatic ‘nanogels’, which slowly release to deliver sustained autocrine immune stimulation without the harmful effects of systemic exposure. Here, we investigate the impact of IL-15SA Deep-Priming on HIV-specific CD8+ T-cells in a humanized mouse model of HIV infection. Humanized mice were generated by engrafting NOD-scid-IL2Rgnull mice with memory CD4+ T-cells isolated from an ARV-suppressed HIV+ donor. An autologous HIV-specific Cytotoxic T-Lymphocyte (CTL) clone was isolated, and killing potential confirmed. Four weeks post humanization, mice were infected with HIV and received an infusion of unmodified HIV-Specific CTLs, or IL-15SA Deep-Primed HIV-specific CTLs (CTL-DP). T-cell numbers and plasma viral loads were quantified weekly by flow cytometry and qRT-PCR. RESULTS/ANTICIPATED RESULTS: Mice receiving unmodified CTLs trended toward reduced viral loads compared to the No Treatment condition, while mice receiving CTL-DP saw significant, 2-Log10 reductions in VL (p < 0.01). At 41 days post-infection 100% (5/5) of the No Treatment, 66.7% (4/6) of the CTL treatment, and 16.7% (1/6) of CTL-DP treatment mice had detectable viremia. IL-15SA Deep-Priming increased CTL expansion and persistence in peripheral blood which correlated with improved CD4+T-cell preservation. DISCUSSION/SIGNIFICANCE OF IMPACT: Here we demonstrate the first in vivo analysis of IL-15SA Deep-Priming of HIV-Specific CTLs. These data suggest that Deep-Priming of patient T-cells can enhance in vivo function and persistence, leading to improved viral suppression; a significant advancement in the field of HIV cure research. CONFLICT OF INTEREST DESCRIPTION: Austin Boesch, Thomas Andresen, and Douglas Jones are employees of Torque. Darrell Irvine is a co-founder of Torque and Chairman of Torque’s Scientific Advisory Board.

Development of a Unique T Cell Receptor Gene-Transferred Tax-Redirected T Cell Immunotherapy for Adult T Cell Leukemia.

Adult T cell leukemia/lymphoma (ATL) is an aggressive peripheral T cell neoplasm caused by infection with human T cell lymphotropic virus type-1 (HTLV-1). Its prognosis remains extremely poor. Tax, the most important regulatory protein for HTLV-1, is associated with the aggressive proliferation of host cells and is also a major target antigen for CD8+ cytotoxic T cells (CTLs). Based on our previous findings that Tax-specific CTLs with a T cell receptor (TCR) containing a unique amino-acid sequence motif exhibit strong HLA-A*24:02-restricted, Tax301-309-specific activity against HTLV-1, we aimed to develop a Tax-redirected T cell immunotherapy for ATL. TCR-ɑ/β genes were cloned from a previously established CTL clone and transduced into peripheral blood mononuclear cells (PBMCs) of healthy volunteers using a retroviral siTCR vector. Then the cytotoxic efficacy against HTLV-1-infected T cells or primary ATL cells was assessed both in vitro and in vivo. The redirected CTLs (Tax-siCTLs) produced a large amount of cytokines and showed strong killing activity against ATL/HTLV-1-infected T cells in vitro, although they did not have universal activity against ATL cells. Next, in a xenograft mouse model using an HTLV-1-infected T cell line (MT-2), in all mice treated with Tax-siCTLs, the tumor rapidly diminished and finally disappeared without normal tissue damage, although all mice that were untreated or treated with non-gene-modified PBMCs died because of tumor progression. Our findings confirm that Tax-siCTLs can exert strong anti-ATL/HTLV-1 effects without a significant reaction against normal cells and have the potential to be a novel immunotherapy for ATL patients.

Abstract B78: Co-potentiation of human T cells to identify subdominant tumor neoantigens from melanoma patients responding to immune checkpoint blockade

Abstract Malignant melanoma is the most aggressive form of skin cancer, accounting for 10,000 deaths annually. Largely resistant to conventional cytotoxic chemotherapy and radiation, immune checkpoint blockade (ICB) therapies have revolutionized patient care, accounting for partial or complete responses in up to 70% of patients. An important aspect of cancer elimination is activation of the cytotoxic T lymphocyte (CTL) response. Recent data suggest that ICB mediated broadening of the peripheral blood CTL repertoire correlates with good clinical outcomes. Thus, recent studies in cancer immunotherapy have focused on targeting tumor neoantigens (tNeoAg) with cancer vaccines for use in combination with ICB. Computational algorithm-driven predictions of immunogenic tNeoAgs yield vast numbers of potential peptide targets, only a fraction of which may be immunogenic in patients. This likely contributed to the modest success of cancer vaccines targeting predicted, high-avidity tNeoAgs, emphasizing the importance of identifying true tumor rejection antigens, including sub-dominant antigens, outside the scope of predictive models. In addition to promoting T cell-mediated tumor rejection, ICB often comes at the expense of treatment-induced immune-related adverse effects (irAE) that frequently require discontinuation of treatment. Modulation of ICB towards antitumor immunity and away from autoimmunity may dramatically improve the therapeutic index of modern cancer therapy. This appears feasible considering the clinical observation that antitumor efficacy does not correlate with type/severity of irAE, suggesting that the mechanisms of both processes, though likely related (CTL mediated), may not be identical. We aim to identify and separate non-cross-reacting antigenic targets mediating tumor rejection from those mediating irAEs to enable therapeutic interventions that maximize the efficacy of ICB, expanding tumor-specific CTLs with vaccines while minimizing irAEs through desensitization. We have access to samples from responding/nonresponding melanoma patients subjected to ICB with varying degrees of irAEs. We have designed an experimental approach that combines established mass spectrometry and sequencing techniques to identify peptides and matching TCR clones with a novel strategy that targets the TCR-associated CD3 complex to allow inclusion of subdominant antigens in our studies. T-cell “co-potentiation” is achieved when anti-CD3 monovalent Fabs induce a conformational change in the CD3 complex that sustains the T-cell response to weak antigenic stimulation. We have successfully used anti-human CD3 Fabs to co-potentiate in vitro the activation and subsequent response to weak peptide-HLA/TCR interactions of human T cells found in PBMCs isolated from healthy donors. Our preliminary data suggest T-cell co-potentiation may allow identification of ICB-induced CTL clones specific for subdominant tNeoAgs and irAE targets in patients with melanoma undergoing active immunotherapy. Citation Format: Laura Elsbernd, Alfreda Nelson, Hien Huynh, Michele Hoffmann, Christopher Parks, Wendy Nevala, Shari Sutor, Larry Pease, Adam Schrum, Diana Gil, Svetomir N. Markovic. Co-potentiation of human T cells to identify subdominant tumor neoantigens from melanoma patients responding to immune checkpoint blockade [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2018 Nov 27-30; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(4 Suppl):Abstract nr B78.

Defective Interferon Gamma Production by Tumor-Specific CD8+ T Cells Is Associated With 5'Methylcytosine-Guanine Hypermethylation of Interferon Gamma Promoter.

Interferon gamma (IFNγ) supports effector responses of CD8+ cytotoxic T lymphocytes (CTLs) and is a surrogate marker for detection of antigen-specific T cells. Here, we show that tumor-specific CTL clones have impaired IFNγ expression and production upon activation. Assessment of the relationship between IFNγ production and the 5′methylcytosine-guanine (CpG) dinucleotide methylation of the IFNγ promoter using bisulfite treatment has shown that IFNγ− CTL clones accumulates CpG hypermethylation within the promoter at key transcription factor binding sites (−186 and −54), known to be vital for transcription. We confirmed these findings using ex vivo isolated and short-term expanded bulk tumor-specific CTL lines from four cancer patients and demonstrated that IFNγ methylation inversely correlates with transcription, protein level, and cytotoxicity. Altogether, we propose that a sizeable portion of human tumor-specific CTLs are deficient in IFNγ response, contributed by CpG hypermethylation of the IFNγ promoter. Our findings have important implications for immunotherapy strategies and for methods to detect human antigen-specific T cells.

Skewed Repertoire Reconstitution and Gene Expression of HLA-A2402 CMV-CTLs after Allogeneic HCT

<h3>Background</h3> Cellular immunity is important for the control of Cytomegalovirus (CMV) reactivation after allogeneic hematopoietic cell transplantation (HCT). However, the actual <i>in vivo</i> dynamics of CMV-specific cytotoxic T-cell (CMV-CTL) clones are still unclear. Thus, we investigated the T-cell receptor (TCR)-beta repertoire and gene expressions of HLA-A*2402-restricted CMV-CTLs in allo-HCT, using next-generation sequence methods (NGS). <h3>Patients</h3> The clone repertoire and dynamics of HLA-A*2402-restricted CMV-CTL were analyzed in 20 cases (30-1000 cells in each). First, we focused on the clone diversity in the group who had never experienced CMV reactivation after HCT from CMV-positive donors (the transferred-immunity group without CMV reactivation, n=7 cases). Next, we focused on the group who received HCT from CMV-negative donors (the naively-introduced immunity group after CMV reactivation, n=13 cases). Patients who received HCT from CMV-positive donors but experienced CMV reactivation were excluded, since there might simultaneously exist the transferred and introduced immunities. <h3>Results</h3> First, we focused on the clone diversity in the transferred immunity group (n = 7) and identified 78 clones. The top 2 clones in each case at one month after HCT exclusively accounted for >75% (range: 78-100%) of CMV-CTLs in all cases (Fig.1). In addition, these top 2 clones were also dominant in their corresponding donors (n = 3), suggesting that the transferred CMV immunity from donors would play a critical role for the prevention of CMV reactivation. Next, looking at the naively-introduced immunity group (n = 13) where 139 clones were identified, the similar skewed CMV-CTL repertoire reconstitution was also observed, and the top 2 clones accounted for >75% in 10 of the 13 cases (range: 61-100%) at 3 months after HCT (Fig.1). Focusing on the diversity of CMV-CTLs in the late phase after HCT (range: 6 -24 months, n=16), some novel clones appeared and became one of dominant clones in several cases, but the top 1 dominant clones at the early phase in each case stayed at top in 13 of the 16 cases. TRBV7 and BJ1-2 were frequently used in their CDR3 of CMV-CTLs (Fig. 2). In terms of specific amino acid sequences of CDR3 of TCR-ƒÀ, no common motif was found through all cases. However, [TSG, Q(G)GG, DPG, and NQG] motifs were frequently observed 3 months after HCT in the naively-introduced group, while [G(Q)GG or DPG] was observed even among the different cases of the transferred-immunity group. Single-cell RNA sequences demonstrated relatively uniform population in terms of gene expression even if different CMV-CTL clones existed in a patient (Fig.3). <h3>Conclusion</h3> <i>In vivo</i> clone-monitoring and gene expression of CMV-CTLs using NGS could provide an insight into the mechanism of immunological reconstitution following HCT.

High Frequency Production of T Cell-Derived iPSC Clones Capable of Generating Potent Cytotoxic T Cells

Current adoptive T cell therapies conducted in an autologous setting are costly, time-consuming, and depend on the quality of the patient’s T cells, and thus it would be highly beneficial to develop an allogeneic strategy. To this aim, we have developed a method by which cytotoxic T lymphocytes (CTLs) are regenerated from induced pluripotent stem cells that are originally derived from T cells (T-iPSCs). In order to assess the feasibility of this strategy, we investigated the frequency of usable T-iPSC clones in terms of their T cell-generating capability and T cell receptor (TCR) affinity. We first established eight clones of T-iPSCs bearing different MART-1-specific TCRs from a healthy volunteer. Whereas all clones were able to give rise to mature CTLs, cell yield varied greatly, and five clones were considered to be usable. TCR affinity in the regenerated CTLs showed a large variance among the eight clones, but functional avidities measured by cytotoxic activity were almost equivalent among three selected clones representing high, medium, and low TCR affinity. In a total of 50 alloreactivity tests using five CTL clones versus ten target cells, alloreactivity was seen in only three cases. These findings collectively support the feasibility of this T-iPSC strategy.

Intra-Tumoral CD8+ T-Cells in Follicular Lymphoma Contain Large Clonal Expansions That Are Amenable to Dual-Checkpoint Blockade

Introduction. Intra-tumoral T-cell infiltration is associated with R-CHOP responsiveness in aggressive B-cell lymphoma (Keane, Lancet Haem 2015). These patients also have a broad (i.e. diverse) intra-tumoral T-cell receptor (TCR) repertoire with a ~20% superior survival compared to those with a narrow (i.e. clonal) repertoire after R-CHOP therapy. Here, the major contributor to the TCR clonal expansion were CD8+ T cells (Keane, CCR 2017). Paradoxically, our recent results in Follicular Lymphoma (FL) (Tobin, JCO in press) found that clonal T-cell expansions were markedly enriched in those patients that experienced progression of disease within 24 months (POD24). Given that FL is a histological subtype associated with a tumor microenvironment distinct from DLBCL including numerous CD4+ T-follicular helper cells (TFH), we now expand upon these findings by comparing TCR repertoires across histological subtypes. We then established whether the TCR repertoire in FL is related to differential TCR clonal expansions between different T-cell subsets and immune checkpoints. Finally, the overlap between tissue and blood TCR repertoires was investigated. Methods. Firstly, unbiased, high-throughput TCRβ sequencing (ImmunoSEQ, Adaptive Biotechnologies) was compared in 164 FFPE tissues (12 healthy nodes, 40 FL, 88 DLBCL, and as a comparator tumor known to be sensitive to checkpoint blockade and to have a high neoantigen burden, 24 melanoma tissues). Next, to determine the contribution of individual T-cell subsets to overall clonality, a further 21 fresh de-aggregated/cryopreserved FL tumor samples were FACS sorted into four T-cell groupings: CD8+ cytotoxic T-lymphocytes (CTLs), CD4+ TFH, CD4+ regulatory T-cells (TREGs) and 'other' (non-TFH/TREG) CD4+ T-cells. Flow cytometry quantified the expression of the checkpoints LAG3, TIM3 and PD1. Then, 5 FL paired tissue/blood samples were tested for shared TCR clones. Results. FL exhibited strikingly reduced TCR repertoire clonality (higher diversity) compared to DLBCL, melanoma and healthy lymph nodes (Fig 1A). Analysis of de-aggregated sorted nodal T-cells revealed a more complex TCR repertoire. The outcome measure was median clonality index (CIx ranging from '0' or minimal, to '1' or maximal clonality). Large T-cell clones in FL (CIx=0.12) predominantly resided within the CTL subset (34% all T-cells). By contrast, there was marked T-cell diversity in TFH (CIx=0.04; 27% all T-cells), TREG (CIx=0.02; 7% all T-cells) and 'other' CD4+ T-cells (CIx=0.02; 32% all T-cells) (Fig 1B). The CTL population had a bimodal expression for PD1 (+51%/-49%), a marker in FL that has been shown to remain functionally active unless co-expressed with LAG3 and/or TIM3 (Yang, Oncotarget 2017). These dual-checkpoint expressing CTLs have reduced capacity to produce cytokines or lytic granules (i.e. they are 'exhausted'). Notably, 54% of the PD1+ CTLs co-expressed either LAG3 or TIM3. Put together, these results are consistent with expanded CTL clones that are frequently functionally exhausted. In contrast, TFH, TREG and 'other' CD4+ T-cells had a low expression of LAG3 and TIM3, although PD1 was frequently found (as expected, particularly in the TFH cells). Finally, in paired tissue/blood samples, there was weak overlap between the circulating and intra-tumoral TCR repertoire in CTLs and TFH T-cells. Conclusion. Although FL has a markedly less clonal TCR repertoire compared to DLBCL, melanoma and even healthy nodes, this result is misleading. Detailed analysis on sorted intra-tumoral T-cell subsets in FL revealed large clonal expansions in CTLs, with approximately half of these classified as functionally exhausted (dual-positive for PD1 and LAG3 and/or TIM3), a state potentially amenable to reversal by dual-checkpoint blockade. The explanation for TCR repertoire diversity lies in CD4+ T-cells (representing approximately two-thirds of T-cells, including the large TFH subset). T-cells in blood did not reflect FL tissue T-cell clones, further highlighting the need for sorted intra-tumoral nodal tissues to accurately assess TCR repertoires in FL. Further characterization of the neo-antigenic targets that CTL clones potentially recognize is required. These results have implications for therapeutic vaccine design and selective recruitment of patients for immune checkpoint blockade. Disclosures Keane: MSD: Consultancy; Gilead: Consultancy; Celgene: Consultancy; Roche: Consultancy, Other: Travel Grant; BMS: Research Funding. Gandhi:Roche: Honoraria, Other: Travel Support; Janssen: Membership on an entity's Board of Directors or advisory committees, Research Funding; Merck: Membership on an entity's Board of Directors or advisory committees; Amgen: Honoraria; Bristol Myers Squibb: Membership on an entity's Board of Directors or advisory committees, Research Funding; Celgene: Membership on an entity's Board of Directors or advisory committees, Research Funding; Gilead: Honoraria, Research Funding.