Simultaneous analysis of pMHC binding and reactivity unveils virus-specific CD8 T cell immunity to a concise epitope set

CD8 T cells provide immunity to virus infection through recognition of epitopes presented by peptide major histocompatibility complexes (pMHCs). To establish a concise panel of widely recognized T cell epitopes from common viruses, we combined analysis of TCR down-regulation upon stimulation with epitope-specific enumeration based on barcode-labeled pMHC multimers. We assess CD8 T cell binding and reactivity for 929 previously reported epitopes in the context of 1 of 25 HLA alleles representing 29 viruses. The prevalence and magnitude of CD8 T cell responses were evaluated in 48 donors and reported along with 137 frequently recognized virus epitopes, many of which were underrepresented in the public domain. Eighty-four percent of epitope-specific CD8 T cell populations demonstrated reactivity to peptide stimulation, which was associated with effector and long-term memory phenotypes. Conversely, nonreactive T cell populations were associated primarily with naive phenotypes. Our analysis provides a reference map of epitopes for characterizing CD8 T cell responses toward common human virus infections.

IMPROVE: a feature model to predict neoepitope immunogenicity through broad-scale validation of T-cell recognition

Background

Mutation-derived neoantigens are critical targets for tumor rejection in cancer immunotherapy, and better tools for neoepitope identification and prediction are needed to improve neoepitope targeting strategies. Computational tools have enabled the identification of patient-specific neoantigen candidates from sequencing data, but limited data availability has hindered their capacity to predict which of the many neoepitopes will most likely give rise to T cell recognition.

Method

To address this, we make use of experimentally validated T cell recognition towards 17,500 neoepitope candidates, with 467 being T cell recognized, across 70 cancer patients undergoing immunotherapy.

Results

We evaluated 27 neoepitope characteristics, and created a random forest model, IMPROVE, to predict neoepitope immunogenicity. The presence of hydrophobic and aromatic residues in the peptide binding core were the most important features for predicting neoepitope immunogenicity.

Conclusion

Overall, IMPROVE was found to significantly advance the identification of neoepitopes compared to other current methods.

Ex vivo modulation of intact tumor fragments with anti-PD-1 and anti-CTLA-4 influences the expansion and specificity of tumor-infiltrating lymphocytes

Checkpoint inhibition (CPI) therapy and adoptive cell therapy with autologous tumor-infiltrating lymphocytes (TIL-based ACT) are the two most effective immunotherapies for the treatment of metastatic melanoma. While CPI has been the dominating therapy in the past decade, TIL-based ACT is beneficial for individuals even after progression on previous immunotherapies. Given that notable differences in response have been made when used as a subsequent treatment, we investigated how the qualities of TILs changed when the ex vivo microenvironment of intact tumor fragments were modulated with checkpoint inhibitors targeting programmed death receptor 1 (PD-1) and cytotoxic T-lymphocyte-associated protein 4 (CTLA-4). Initially, we show that unmodified TILs from CPI-resistant individuals can be produced, are overwhelmingly terminally differentiated, and are capable of responding to tumor. We then investigate these properties in ex vivo checkpoint modulated TILs finding that that they retain these qualities. Lastly, we confirmed the specificity of the TILs to the highest responding tumor antigens, and identified this reactivity resides largely in CD39⁺CD69⁺ terminally differentiated populations. Overall, we found that anti-PD-1 will alter the proliferative capacity while anti-CTLA4 will influence breadth of antigen specificity.

Neoantigen-reactive CD8+ T cells affect clinical outcome of adoptive transfer with tumor-infiltrating lymphocytes in melanoma

BACKGROUND

Neoantigen-driven recognition and T cell-mediated killing contribute to tumor clearance following adoptive cell therapy (ACT) with Tumor-Infiltrating Lymphocytes (TILs). Yet, how diversity, frequency, and persistence of expanded neoepitope-specific CD8+ T cells derived from TIL infusion products affect patient outcome is not fully determined.

METHODS

Using barcoded pMHC multimers, we provide a comprehensive mapping of CD8+ T cells recognizing neoepitopes in TIL infusion products and blood samples from 26 metastatic mela-noma patients who received ACT.

RESULTS

We identified 106 neoepitopes within TIL infusion products corresponding to 1.8% of all predicted neoepitopes. We observed neoepitope-specific recognition to be virtually devoid in TIL infusion products given to patients with progressive disease outcome. Moreover, we found that the frequency of neoepitope-specific CD8+ T cells in TIL infusion products correlated with in-creased survival, and that detection of engrafted CD8+ T cells in post-treatment (i.e. originating from the TIL infusion product) were unique to responders of TIL-ACT. Finally, we found that a transcriptional signature for lymphocyte activity within the tumor microenvironment was associated with a higher frequency of neoepitope-specific CD8+ T cells in the infusion product.

CONCLUSIONS

These data support previous case studies of neoepitope-specific CD8+ T cells in melanoma, and indicate that successful TIL-ACT is associated with an expansion of neoepitope-specific CD8+ T cells.

FUNDING

NEYE Foundation; European Research Council; Lundbeck Foundation Fellowship; Carlsberg Foundation.

Abstract A14: Neoepitope-specific CD8+ T cells in adoptive T-cell transfer

Adoptive T-cell therapy (ACT) relies on expansion of tumor-infiltrating lymphocytes and infusion into patients following lymphodepletion, which have yielded complete responders in up to 25% of treated patients suffering from metastatic melanoma. However, a large proportion of patients have no clinical benefit (50-60%). Previous studies have found that clinical outcome correlates with tumor mutational and putative neoantigen load. Furthermore, expression of core antigen-presentation pathways including MHC class I genes in tumors correlates with clinical benefit. Based on these findings, we hypothesize that the presence of neoepitope-specific CD8+ T cells within the infusion product of ACT is a key determinant of clinical benefit. We apply in silico prediction of neoepitopes along with DNA-barcoded dextran multimer libraries to screen for personal neoepitope-specific CD8+ T cells. We show persistence of neoepitope-specific CD8+ T cells within patient peripheral blood for up to 24 months after therapy. Furthermore, we show an almost complete lack of neoepitope-specific CD8+ T cells within the infusion products of patients with progressive disease. However, patients with stable disease and long-term responses only have a modest increase in the number of targeted neoepitopes, as wells as the total frequency of neoepitope-specific CD8+ T cells. For future experimentation, we therefore aim to include more patients as well as study the phenotypical differences within the pool neoepitope-specific CD8+ T cells, the ultimate goal being a better understanding of what parameters from neoepitope-specific CD8+ T cells correlate with clinical efficacy of ACT.

Citation Format: Nikolaj Pagh Kristensen, Christina Heeke, Siri A. Tvingsholm, Anne-Mette Bjerregaard, Arianna Draghi, Amalie Kai Bentzen, Rikke Andersen, Marco Donia, Inge Marie Svane, Sine Reker Hadrup. Neoepitope-specific CD8+ T cells in adoptive T-cell transfer [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2019 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(3 Suppl):Abstract nr A14.

Global network of computational biology communities: ISCB's Regional Student Groups breaking barriers

Regional Student Groups (RSGs) of the International Society for Computational Biology Student Council (ISCB-SC) have been instrumental to connect computational biologists globally and to create more awareness about bioinformatics education. This article highlights the initiatives carried out by the RSGs both nationally and internationally to strengthen the present and future of the bioinformatics community. Moreover, we discuss the future directions the organization will take and the challenges to advance further in the ISCB-SC main mission: "Nurture the new generation of computational biologists".

CD8+ T cells from patients with narcolepsy and healthy controls recognize hypocretin neuron-specific antigens

Narcolepsy Type 1 (NT1) is a neurological sleep disorder, characterized by the loss of hypocretin/orexin signaling in the brain. Genetic, epidemiological and experimental data support the hypothesis that NT1 is a T-cell-mediated autoimmune disease targeting the hypocretin producing neurons. While autoreactive CD4+ T cells have been detected in patients, CD8+ T cells have only been examined to a minor extent. Here we detect CD8+ T cells specific toward narcolepsy-relevant peptides presented primarily by NT1-associated HLA types in the blood of 20 patients with NT1 as well as in 52 healthy controls, using peptide-MHC-I multimers labeled with DNA barcodes. In healthy controls carrying the disease-predisposing HLA-DQB1*06:02 allele, the frequency of autoreactive CD8+ T cells was lower as compared with both NT1 patients and HLA-DQB1*06:02-negative healthy individuals. These findings suggest that a certain level of CD8+ T-cell reactivity combined with HLA-DQB1*06:02 expression is important for NT1 development.

Human P2Y11 Expression Level Affects Human P2X7 Receptor-Mediated Cell Death

Adenosine triphosphate (ATP) is known to induce cell death in T lymphocytes at high extracellular concentrations. CD4⁺ and CD8⁺ T lymphocytes have a differential response to ATP, which in mice is due to differences in the P2X7 receptor expression levels. By contrast, we observed that the difference in human CD4⁺ and CD8⁺ T lymphocyte response toward the synthetic ATP-analog BzATP is not explained by a difference in human P2X7 receptor expression. Rather, the BzATP-induced human P2X7 receptor response in naïve and immune-activated lymphocyte subtypes correlated with the expression of another ATP-binding receptor: the human P2Y₁₁ receptor. In a recombinant expression system, the coexpression of the human P2Y₁₁ receptor counteracted BzATP-induced human P2X7 receptor-driven lactate dehydrogenase release (a marker of cell death) and pore formation independent of calcium signaling. A mutated non-signaling human P2Y₁₁ receptor had a similar human P2X7 receptor-inhibitory effect on pore formation, thus demonstrating that the human P2X7 receptor interference was not caused by human P2Y₁₁ receptor signaling. In conclusion, we demonstrate an important species difference in the ATP-mediated cell death between mice and human cells and show that in human T lymphocytes, the expression of the human P2Y₁₁ receptor correlates with human P2X7 receptor-driven cell death following BzATP stimulation.

N-terminal tagging of human P2X7 receptor disturbs calcium influx and dye uptake

The P2X7 receptor is a frequently studied member of the purinergic receptor family signalling via channel opening and membrane pore formation. Fluorescent imaging is an important molecular method for studying cellular receptor expression and localization. Fusion of receptors to fluorescent proteins might cause major functional changes and requires careful functional evaluation such as has been done for the rat P2X7 receptor. This study examines fusion constructs of the human P2X7 receptor. We assessed surface expression, channel opening with calcium influx, and pore formation using YO-PRO-1 dye uptake in response to BzATP stimulation in transfected cells. We found that tagging at the N-terminal of the human P2X7 receptor with the enhanced green fluorescent protein (eGFP) disturbed channel opening and pore formation despite intact surface expression. A triple hemagglutinin (3HA) fused to the N-terminal also disrupted pore formation but not channel opening showing that even a small tag alters the normal function of the receptor. Together, this suggests that in contrast to what has been observed for the rat P2X7 receptor, the human P2X7 receptor contains N-terminal motifs important for signalling that prevent the construction of a functionally active fusion protein.

The Australian moth family Lophocoronidae and the basal phylogeny of the Lepidoptera – Glossata

The endemic Australian primitive moth family Lophocoronidae is reviewed. The family was previously known from three species represented by male 'museum' specimens only. The family now consists of one genus, Lophocorona Common, with six species of which three (L. robinsoni, L. commoni and L. flavicosta) are here described as new. L. robinsoni differs markedly from the remaining species in wing pattern and phenology, but all species have very similar male genitalia. Females of two species (L. robinsoni and L. commoni) are described. All species and parts of their male genitalia are illustrated; a key to all species is given. All new distribution records are listed and the known Australian range of the family now extends from east of Perth to south of Sydney. Lophocoronid structure is surveyed, including information on aspects of the soft anatomy of L. pediasia Common: cephalic, spiracular, abdominal base and male genital musculature, male internal genitalia, alimentary canal, gross structure of the central nervous system (CNS) and thoracic aorta. The most significant findings include the following: extrinsic labral muscles are absent; the relatively well-developed mandibles have no musculature, hence the (unknown) lophocoronid pupa must be adecticous; there is no intrinsic proboscis musculature; the posterolateral comer of the laterocervicale covers the anepisternal tooth; an anterior pronotal plate is present; the mesobasistemum is markedly produced anteriorly; wingsurface scales are largely hollow; a sizeable metapostphragma is present; the female has a piercing oviscapt similar to that of Eriocraniidae and Acanthopteroctetidae; a stomodaeal crop is well developed, extending into the abdomen, and followed by a narrow tubular portion in front of the mesenteron; there are four malpighian tubules, each opening into the gut; the deutocerebral lobes meet in front of the posterionnost pharyngeal sucking pump dilator (forming a 'deutocerebral loop'); the abdominal nerve cord has five ganglionic masses and thick connective tissue on top; the metathoracic aorta touches the dorsal pulsatile diaphragm. Six basal clades are recognised within the Lepidoptera-Glossata: (1) Eriocraniidae, (2) Acanthopteroctetidae (including Catapterix), (3) Lophocoronidae, (4) Neopseustidae, (5) Exoporia and (6) Heteroneura. Putative autapomorphies are listed and discussed for each. Several structural traits are compared throughout the six clades, and 47 potentially phylogenetically informative characters are identified (Appendices 1 and 2). Analysis of these characters with Hennig86, by using a hypothetical ancestor (reconstructed on the basis of character state distribution within the non-glossatan moth grade), yields a single shortest tree: Eriocraniidae + (Acanthopteroctetidae + (Lophocoronidae + (Neopseustidae + (Exoporia + Heteroneura)))). This tree is compared with a number of competing trees; it is concluded to be the most biologically meaningful one. The formal classification of the Glossata is discussed. The Acanthopteroctetidae are assigned to a superfamily of their own. Redundant taxon names above familygroup (Dacnonypha, Lophocoronina and Neopseustina) are discarded. The new name Coelolepida is introduced for the high-rank taxon comprising all Glossata except the Eriocraniidae; it is characterised primarily by the acquisition of hollow wing-surface scales and an apomorphic configuration of the first thoracic spiracle. Some ecological and conservation-related implications of the new insights in glossatan phylogeny are outlined.

Revision of the genus Ogygioses (Palaeosetidae)

The systematics and external morphology of the oriental genus Ogygioses are reviewed. Monophyly of the genus is demonstrated by the two segmented labial palpi, loss of the jugal lobe in the forewing, stalking of the forewing R4 with the base of R2 + 3 and a specialised scale arrangement on the forewing base. Sculpturing of the egg chorion differs from that of other Exoporia in exhibiting elongate tubercles regularly dispersed over the surface. The genus is retained tentatively in the Paleosetidae on the basis of the loss of all tibia1 spurs, including the epiphysis, and the extreme reduction of the maxillae. Four species are recognised: O. caliginosa Issiki & Stringer, O. eurata Issiki & Stringer, O. issikii Davis, sp. nov., from Taiwan, and O luangensis Kristensen, sp. nov., from Thailand. Adults are diurnal with the males forming hovering groups, or leks, similar to some species of Hepialidae.