Structural basis for self-discrimination by neoantigen-specific TCRs.

T cell receptors (TCR) are pivotal in mediating tumour cell cytolysis via recognition of mutation-derived tumour neoantigens (neoAgs) presented by major histocompatibility class-I (MHC-I). Understanding the factors governing the emergence of neoAg from somatic mutations is a major focus of current research. However, the structural and cellular determinants controlling TCR recognition of neoAgs remain poorly understood. This study describes the multi-level analysis of a model neoAg from the B16F10 murine melanoma, H2-Db/Hsf2 p.K72N68-76, as well as its cognate TCR 47BE7. Through cellular, molecular and structural studies we demonstrate that the p.K72N mutation enhances H2-Db binding, thereby improving cell surface presentation and stabilizing the TCR 47BE7 epitope. Furthermore, TCR 47BE7 exhibited high functional avidity and selectivity, attributable to a broad, stringent, binding interface enabling recognition of native B16F10 despite low antigen density. Our findings provide insight into the generation of anchor-residue modified neoAg, and emphasize the value of molecular and structural investigations of neoAg in diverse MHC-I contexts for advancing the understanding of neoAg immunogenicity.

Linking water use efficiency with water use strategy from leaves to communities.

Limitations and utility of three measures of water use characteristics were evaluated: water use efficiency (WUE), intrinsic WUE and marginal water cost of carbon gain ( ∂ E / ∂ A ) estimated, respectively, as ratios of assimilation (A) to transpiration (E), of A to stomatal conductance (gs ) and of sensitivities of E and A with variation in gs . Only the measure ∂ E / ∂ A estimates water use strategy in a way that integrates carbon gain relative to water use under varying environmental conditions across scales from leaves to communities. This insight provides updated and simplified ways of estimating ∂ E / ∂ A and adds depth to understanding ways that plants balance water expenditure against carbon gain, uniquely providing a mechanistic means of predicting water use characteristics under changing environmental scenarios.

Structural Basis for Self-Discrimination by Neoantigen-Specific TCRs.

Physical interactions between T cell receptors (TCRs) and mutation-derived tumour neoantigens (neoAg) presented by major histocompatibility class-I (MHC-I) enable sensitive and specific cytolysis of tumour cells. Adoptive transfer of neoAg-reactive T cells in patients is correlated with response to immunotherapy; however, the structural and cellular mechanisms of neoAg recognition remain poorly understood. We have identified multiple cognate neoAg:TCRs from B16F10, a common murine implantable tumour model of melanoma. We identified a high affinity TCR targeting H2-Db-restricted Hsf2K72N that conferred specific recognition of B16F10 in vitro and in vivo. Structural characterization of the peptide-MHC (pMHC) binary and pMHC:TCR ternary complexes yielded high-resolution crystal structures, revealing the formation of a solvent-exposed hydrophobic arch in H2-Db that enables multiple intermolecular contacts between pMHC and the TCR. These features of structural stability strikingly mimic that of a previously published influenza peptide-H2-Db complex and its corresponding TCR, suggesting that there are shared structural motifs between neoantigens and viral peptides that explain their shared immunogenicity.

Intravenous nanoparticle vaccination generates stem-like TCF1+ neoantigen-specific CD8+ T cells.

Personalized cancer vaccines are a promising approach for inducing T cell immunity to tumor neoantigens. Using a self-assembling nanoparticle vaccine that links neoantigen peptides to a Toll-like receptor 7/8 agonist (SNP-7/8a), we show how the route and dose alter the magnitude and quality of neoantigen-specific CD8+ T cells. Intravenous vaccination (SNP-IV) induced a higher proportion of TCF1+PD-1+CD8+ T cells as compared to subcutaneous immunization (SNP-SC). Single-cell RNA sequencing showed that SNP-IV induced stem-like genes (Tcf7, Slamf6, Xcl1) whereas SNP-SC enriched for effector genes (Gzmb, Klrg1, Cx3cr1). Stem-like cells generated by SNP-IV proliferated and differentiated into effector cells upon checkpoint blockade, leading to superior antitumor response as compared to SNP-SC in a therapeutic model. The duration of antigen presentation by dendritic cells controlled the magnitude and quality of CD8+ T cells. These data demonstrate how to optimize antitumor immunity by modulating vaccine parameters for specific generation of effector or stem-like CD8+ T cells.

Author Correction: A conserved dendritic-cell regulatory program limits antitumour immunity.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

A conserved dendritic-cell regulatory program limits antitumour immunity.

Checkpoint blockade therapies have improved cancer treatment, but such immunotherapy regimens fail in a large subset of patients. Conventional type 1 dendritic cells (DC1s) control the response to checkpoint blockade in preclinical models and are associated with better overall survival in patients with cancer, reflecting the specialized ability of these cells to prime the responses of CD8+ T cells1-3. Paradoxically, however, DC1s can be found in tumours that resist checkpoint blockade, suggesting that the functions of these cells may be altered in some lesions. Here, using single-cell RNA sequencing in human and mouse non-small-cell lung cancers, we identify a cluster of dendritic cells (DCs) that we name 'mature DCs enriched in immunoregulatory molecules' (mregDCs), owing to their coexpression of immunoregulatory genes (Cd274, Pdcd1lg2 and Cd200) and maturation genes (Cd40, Ccr7 and Il12b). We find that the mregDC program is expressed by canonical DC1s and DC2s upon uptake of tumour antigens. We further find that upregulation of the programmed death ligand 1 protein-a key checkpoint molecule-in mregDCs is induced by the receptor tyrosine kinase AXL, while upregulation of interleukin (IL)-12 depends strictly on interferon-γ and is controlled negatively by IL-4 signalling. Blocking IL-4 enhances IL-12 production by tumour-antigen-bearing mregDC1s, expands the pool of tumour-infiltrating effector T cells and reduces tumour burden. We have therefore uncovered a regulatory module associated with tumour-antigen uptake that reduces DC1 functionality in human and mouse cancers.

Mutation-derived Neoantigen-specific T-cell Responses in Multiple Myeloma.

PURPOSE: Somatic mutations in cancer cells can give rise to novel protein sequences that can be presented by antigen-presenting cells as neoantigens to the host immune system. Tumor neoantigens represent excellent targets for immunotherapy, due to their specific expression in cancer tissue. Despite the widespread use of immunomodulatory drugs and immunotherapies that recharge T and NK cells, there has been no direct evidence that neoantigen-specific T-cell responses are elicited in multiple myeloma. EXPERIMENTAL DESIGN: Using next-generation sequencing data we describe the landscape of neo-antigens in 184 patients with multiple myeloma and successfully validate neoantigen-specific T cells in patients with multiple myeloma and support the feasibility of neoantigen-based therapeutic vaccines for use in cancers with intermediate mutational loads such as multiple myeloma. RESULTS: In this study, we demonstrate an increase in neoantigen load in relapsed patients with multiple myeloma as compared with newly diagnosed patients with multiple myeloma. Moreover, we identify shared neoantigens across multiple patients in three multiple myeloma oncogenic driver genes (KRAS, NRAS, and IRF4). Next, we validate neoantigen T-cell response and clonal expansion in correlation with clinical response in relapsed patients with multiple myeloma. This is the first study to experimentally validate the immunogenicity of predicted neoantigens from next-generation sequencing in relapsed patients with multiple myeloma. CONCLUSIONS: Our findings demonstrate that somatic mutations in multiple myeloma can be immunogenic and induce neoantigen-specific T-cell activation that is associated with antitumor activity in vitro and clinical response in vivo. Our results provide the foundation for using neoantigen targeting strategies such as peptide vaccines in future trials for patients with multiple myeloma.

Immune Checkpoint Blockade Enhances Shared Neoantigen-Induced T-cell Immunity Directed against Mutated Calreticulin in Myeloproliferative Neoplasms.

Somatic frameshift mutations in the calreticulin (CALR) gene are key drivers of cellular transformation in myeloproliferative neoplasms (MPN). All patients carrying these mutations (CALR + MPN) share an identical sequence in the C-terminus of the mutated CALR protein (mut-CALR), with the potential for utility as a shared neoantigen. Here, we demonstrate that although a subset of patients with CALR + MPN develop specific T-cell responses against the mut-CALR C-terminus, PD-1 or CTLA4 expression abrogates the full complement of responses. Significantly, blockade of PD-1 and CLTA4 ex vivo by mAbs and of PD-1 in vivo by pembrolizumab administration restores mut-CALR-specific T-cell immunity in some patients with CALR + MPN. Moreover, mut-CALR elicits antigen-specific responses from both CD4+ and CD8+ T cells, confirming its broad applicability as an immunogen. Collectively, these results establish mut-CALR as a shared, MPN-specific neoantigen and inform the design of novel immunotherapies targeting mut-CALR. SIGNIFICANCE: Current treatment modalities for MPN are not effective in eliminating malignant cells. Here, we show that mutations in the CALR gene, which drive transformation in MPN, elicit T-cell responses that can be further enhanced by checkpoint blockade, suggesting immunotherapies could be employed to eliminate CALR + malignant cells in MPN.This article is highlighted in the In This Issue feature, p. 1143.

Losses, inefficiencies and waste in the global food system.

Losses at every stage in the food system influence the extent to which nutritional requirements of a growing global population can be sustainably met. Inefficiencies and losses in agricultural production and consumer behaviour all play a role. This paper aims to understand better the magnitude of different losses and to provide insights into how these influence overall food system efficiency. We take a systems view from primary production of agricultural biomass through to human food requirements and consumption. Quantities and losses over ten stages are calculated and compared in terms of dry mass, wet mass, protein and energy. The comparison reveals significant differences between these measurements, and the potential for wet mass figures used in previous studies to be misleading. The results suggest that due to cumulative losses, the proportion of global agricultural dry biomass consumed as food is just 6% (9.0% for energy and 7.6% for protein), and 24.8% of harvest biomass (31.9% for energy and 27.8% for protein). The highest rates of loss are associated with livestock production, although the largest absolute losses of biomass occur prior to harvest. Losses of harvested crops were also found to be substantial, with 44.0% of crop dry matter (36.9% of energy and 50.1% of protein) lost prior to human consumption. If human over-consumption, defined as food consumption in excess of nutritional requirements, is included as an additional inefficiency, 48.4% of harvested crops were found to be lost (53.2% of energy and 42.3% of protein). Over-eating was found to be at least as large a contributor to food system losses as consumer food waste. The findings suggest that influencing consumer behaviour, e.g. to eat less animal products, or to reduce per capita consumption closer to nutrient requirements, offer substantial potential to improve food security for the rising global population in a sustainable manner.

Dendritic Cell Strategies for Eliciting Mutation-Derived Tumor Antigen Responses in Patients.

Dendritic cells (DCs) are equipped for sensing danger signals and capturing, processing, and presenting antigens to naive or effector cells and are critical in inducing humoral and adaptive immunity. Successful vaccinations are those that activate DCs to elicit both cellular and humoral responses, as well as long-lasting memory response against the target of interest. Recently, it has become apparent that tumor cells can provide new sources of antigens through nonsynonymous mutations or frame-shift mutations, leading to potentially hundreds of mutation-derived tumor antigens (MTAs) or neoantigens. T cells recognizing MTA have been detected in cancer patients and can even lead to tumor regression. Designing MTA-specific vaccination strategies will have to take into account the adjuvant activity of DC subsets and the best formulation to elicit an effective immune response. We discuss the potential of human DCs to prime MTA-specific responses.

Patterns of crop cover under future climates.

We study changes in crop cover under future climate and socio-economic projections. This study is not only organised around the global and regional adaptation or vulnerability to climate change but also includes the influence of projected changes in socio-economic, technological and biophysical drivers, especially regional gross domestic product. The climatic data are obtained from simulations of RCP4.5 and 8.5 by four global circulation models/earth system models from 2000 to 2100. We use Random Forest, an empirical statistical model, to project the future crop cover. Our results show that, at the global scale, increases and decreases in crop cover cancel each other out. Crop cover in the Northern Hemisphere is projected to be impacted more by future climate than the in Southern Hemisphere because of the disparity in the warming rate and precipitation patterns between the two Hemispheres. We found that crop cover in temperate regions is projected to decrease more than in tropical regions. We identified regions of concern and opportunities for climate change adaptation and investment.

Computational Pipeline for the PGV-001 Neoantigen Vaccine Trial.

This paper describes the sequencing protocol and computational pipeline for the PGV-001 personalized vaccine trial. PGV-001 is a therapeutic peptide vaccine targeting neoantigens identified from patient tumor samples. Peptides are selected by a computational pipeline that identifies mutations from tumor/normal exome sequencing and ranks mutant sequences by a combination of predicted Class I MHC affinity and abundance estimated from tumor RNA. The personalized genomic vaccine (PGV) pipeline is modular and consists of independently usable tools and software libraries. We hope that the functionality of these tools may extend beyond the specifics of the PGV-001 trial and enable other research groups in their own neoantigen investigations.

TGFß receptor 1: an immune susceptibility gene in HPV-associated cancer.

Only a minority of those exposed to human papillomavirus (HPV) develop HPV-related cervical and oropharyngeal cancer. Because host immunity affects infection and progression to cancer, we tested the hypothesis that genetic variation in immune-related genes is a determinant of susceptibility to oropharyngeal cancer and other HPV-associated cancers by performing a multitier integrative computational analysis with oropharyngeal cancer data from a head and neck cancer genome-wide association study (GWAS). Independent analyses, including single-gene, gene-interconnectivity, protein-protein interaction, gene expression, and pathway analysis, identified immune genes and pathways significantly associated with oropharyngeal cancer. TGFßR1, which intersected all tiers of analysis and thus selected for validation, replicated significantly in the head and neck cancer GWAS limited to HPV-seropositive cases and an independent cervical cancer GWAS. The TGFßR1 containing p38-MAPK pathway was significantly associated with oropharyngeal cancer and cervical cancer, and TGFßR1 was overexpressed in oropharyngeal cancer, cervical cancer, and HPV(+) head and neck cancer tumors. These concordant analyses implicate TGFßR1 signaling as a process dysregulated across HPV-related cancers. This study demonstrates that genetic variation in immune-related genes is associated with susceptibility to oropharyngeal cancer and implicates TGFßR1/TGFß signaling in the development of both oropharyngeal cancer and cervical cancer. Better understanding of the immunogenetic basis of susceptibility to HPV-associated cancers may provide insight into host/virus interactions and immune processes dysregulated in the minority of HPV-exposed individuals who progress to cancer.

Counseling the patient with potentially HPV-related newly diagnosed head and neck cancer.

The recent emergence of a clinically distinct subset of head and neck cancers (HNC) caused by infection with the human papillomavirus (HPV) necessitates critical reevaluation of the existing counseling paradigm for patients with newly diagnosed HNC. Herein we propose a structural framework for patient counseling in which HPV testing is incorporated and the impact of HPV-status is discussed in the context of multiple medical and psychosocial domains. We strive to maintain a balance between making recommendations based on the best available scientific evidence and acknowledgment of uncertainty for both patients and providers. We anticipate that both the standard-of-care diagnostic workup and treatment, and counseling guidelines for these patients will change rapidly in the years ahead, as data from ongoing and planned prospective clinical trials become available.

An introduction to flux measurements in difficult conditions.

The origins of the aerodynamic techniques now widely used at sites around the world to measure continuous biosphere-atmosphere exchange of carbon and energy are briefly reviewed. A survey of the current state of this approach concludes that the technique often fails when standard analysis routines are applied to data from single towers in complex flows. In the daytime, problems are signaled by failure to close the surface energy balance because turbulent energy fluxes are routinely underestimated. Complex flows are more prevalent at night when they lead to failure to measure all the respired CO2. At such times, the aerodynamic methodology is commonly supplemented by biological models. A set of papers from a workshop on "Flux Measurements in Difficult Conditions" held at the National Center for Atmospheric Research (NCAR) in January 2006 are introduced next. Two papers review the causes and magnitude of these flow-based problems. Four papers describe intensive field experiments that detail the mechanisms that cause problematic complex flows. These experiments show, inter alia, that the technique of replacing nighttime eddy flux measurements by biological models can also be systematically biased. Finally, two model studies are used both to illustrate the physics behind these complex flows and to motivate an approach to systematic correction of single-tower results.