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.

A T cell receptor targeting a recurrent driver mutation in FLT3 mediates elimination of primary human acute myeloid leukemia in vivo.

Acute myeloid leukemia (AML), the most frequent leukemia in adults, is driven by recurrent somatically acquired genetic lesions in a restricted number of genes. Treatment with tyrosine kinase inhibitors has demonstrated that targeting of prevalent FMS-related receptor tyrosine kinase 3 (FLT3) gain-of-function mutations can provide significant survival benefits for patients, although the efficacy of FLT3 inhibitors in eliminating FLT3-mutated clones is variable. We identified a T cell receptor (TCR) reactive to the recurrent D835Y driver mutation in the FLT3 tyrosine kinase domain (TCRFLT3D/Y). TCRFLT3D/Y-redirected T cells selectively eliminated primary human AML cells harboring the FLT3D835Y mutation in vitro and in vivo. TCRFLT3D/Y cells rejected both CD34+ and CD34- AML in mice engrafted with primary leukemia from patients, reaching minimal residual disease-negative levels, and eliminated primary CD34+ AML leukemia-propagating cells in vivo. Thus, T cells targeting a single shared mutation can provide efficient immunotherapy toward selective elimination of clonally involved primary AML cells in vivo.

Fundamental immune-oncogenicity trade-offs define driver mutation fitness.

Missense driver mutations in cancer are concentrated in a few hotspots1. Various mechanisms have been proposed to explain this skew, including biased mutational processes2, phenotypic differences3-6 and immunoediting of neoantigens7,8; however, to our knowledge, no existing model weighs the relative contribution of these features to tumour evolution. We propose a unified theoretical 'free fitness' framework that parsimoniously integrates multimodal genomic, epigenetic, transcriptomic and proteomic data into a biophysical model of the rate-limiting processes underlying the fitness advantage conferred on cancer cells by driver gene mutations. Focusing on TP53, the most mutated gene in cancer1, we present an inference of mutant p53 concentration and demonstrate that TP53 hotspot mutations optimally solve an evolutionary trade-off between oncogenic potential and neoantigen immunogenicity. Our model anticipates patient survival in The Cancer Genome Atlas and patients with lung cancer treated with immunotherapy as well as the age of tumour onset in germline carriers of TP53 variants. The predicted differential immunogenicity between hotspot mutations was validated experimentally in patients with cancer and in a unique large dataset of healthy individuals. Our data indicate that immune selective pressure on TP53 mutations has a smaller role in non-cancerous lesions than in tumours, suggesting that targeted immunotherapy may offer an early prophylactic opportunity for the former. Determining the relative contribution of immunogenicity and oncogenic function to the selective advantage of hotspot mutations thus has important implications for both precision immunotherapies and our understanding of tumour evolution.

Neoantigen-specific CD8 T cell responses in the peripheral blood following PD-L1 blockade might predict therapy outcome in metastatic urothelial carcinoma.

CD8+ T cell reactivity towards tumor mutation-derived neoantigens is widely believed to facilitate the antitumor immunity induced by immune checkpoint blockade (ICB). Here we show that broadening in the number of neoantigen-reactive CD8+ T cell (NART) populations between pre-treatment to 3-weeks post-treatment distinguishes patients with controlled disease compared to patients with progressive disease in metastatic urothelial carcinoma (mUC) treated with PD-L1-blockade. The longitudinal analysis of peripheral CD8+ T cell recognition of patient-specific neopeptide libraries consisting of DNA barcode-labelled pMHC multimers in a cohort of 24 patients from the clinical trial NCT02108652 also shows that peripheral NARTs derived from patients with disease control are characterised by a PD1+ Ki67+ effector phenotype and increased CD39 levels compared to bystander bulk- and virus-antigen reactive CD8+ T cells. The study provides insights into NART characteristics following ICB and suggests that early-stage NART expansion and activation are associated with response to ICB in patients with mUC.

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

BACKGROUNDNeoantigen-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.METHODSUsing barcoded pMHC multimers, we provide a comprehensive mapping of CD8+ T cells recognizing neoepitopes in TIL infusion products and blood samples from 26 metastatic melanoma patients who received ACT.RESULTSWe 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 increased survival and that neoepitope-specific CD8+ T cells shared with the infusion product in posttreatment blood samples 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.CONCLUSIONSThese 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.FUNDINGNEYE Foundation; European Research Council; Lundbeck Foundation Fellowship; Carlsberg Foundation.

Tracking evolution of myoglobin stability in cetaceans using experimentally calibrated computational methods that account for generic protein relaxation.

The evolution of cetaceans (whales, dolphins, and porpoises) from land to water is one of the most spectacular events in mammal evolution. It has been suggested that selection for higher myoglobin stability (∆G of folding) allowed whales to conquer the deep-diving niche. The stability of multi-site protein variants, including ancient proteins, is however hard to describe theoretically. From a compilation of experimental ∆∆G vs. ∆G we first find that protein substitutions are subject to large generic protein relaxation effects. Using this discovery, we develop a simple two-parameter model that predicts multi-site ∆∆G as accurately as standard methods do for single-site mutations and reproduces trends in contemporary myoglobin stabilities. We then apply this new method to the study of the evolution of Mb stability in cetaceans: With both methods the main change in stability (about 1kcal/mol) occurred very early, and stability was later relaxed in dolphins and porpoises, but was further increased in the sperm whales. This suggests that single proteins can affect whole organism evolution and indicates a role of Mb stability in the evolution of cetaceans. Transition to the deep-diving niche probably occurred already in the ancestor of contemporary baleen and toothed whales. In summary, we have discovered generic stability relaxation effects in proteins that, when incorporated into a simple model, improves the description of multi-site protein variants.

[Increased post-stroke risk of suicide]. / Der er øget risiko for selvmord efter apopleksi.

The purpose of this work is to illustrate a possible cohesion between stroke and subsequent risk of suicide, presenting a review of the literature covering the past 26 years. 80% of the primary studies find that the risk of suicide increases post-stroke. The first five years post-stroke is the most risky period of time. Furthermore, the risk appears to be greatest among patients below the age 60 years. Recommended is attention towards these specific risks. Some of the literature show limitations due to the lack of consideration of confounders such as depression and sociodemographic data.

Polarity-Driven Quasi-3-Fold Composition Symmetry of Self-Catalyzed III-V-V Ternary Core-Shell Nanowires.

A quasi-3-fold composition symmetry has for the first time been observed in self-catalyzed III-V-V core-shell nanowires. In GaAsP nanowires, phosphorus-rich sheets on radial {110} planes originating at the corners of the hexagonal core were observed. In a cross section, they appear as six radial P-rich bands that originate at the six outer corners of the hexagonal core, with three of them higher in P content along ⟨112⟩A direction and others along ⟨112⟩B, forming a quasi-3-fold composition symmetry. We propose that these P-rich bands are caused by a curvature-induced high surface chemical potential at the small corner facets, which drives As adatoms away more efficiently than P adatoms. Moreover, their polarity related P content difference can be explained by the different adatom bonding energies at these polar corner facets. These results provide important information on the further development of shell growth in the self-catalyzed core-shell NW structure and, hence, device structure for multicomponent material systems.

Self-catalyzed ternary core-shell GaAsP nanowire arrays grown on patterned Si substrates by molecular beam epitaxy.

The growth of self-catalyzed ternary core-shell GaAsP nanowire (NW) arrays on SiO2 patterned Si(111) substrates has been demonstrated by using solid-source molecular beam epitaxy. A high-temperature deoxidization step up to ∼ 900 °C prior to NW growth was used to remove the native oxide and/or SiO2 residue from the patterned holes. To initiate the growth of GaAsP NW arrays, the Ga predeposition used for assisting the formation of Ga droplets in the patterned holes, was shown to be another essential step. The effects of the patterned-hole size on the NW morphology were also studied and explained using a simple growth model. A lattice-matched radial GaAsP core-shell NW structure has subsequently been developed with room-temperature photoluminescence emission around 740 nm. These results open up new perspectives for integrating position-controlled III-V NW photonic and electronic structures on a Si platform.

A step closer to membrane protein multiplexed nanoarrays using biotin-doped polypyrrole.

Whether for fundamental biological research or for diagnostic and drug discovery applications, protein micro- and nanoarrays are attractive technologies because of their low sample consumption, high-throughput, and multiplexing capabilities. However, the arraying platforms developed so far are still not able to handle membrane proteins, and specific methods to selectively immobilize these hydrophobic and fragile molecules are needed to understand their function and structural complexity. Here we integrate two technologies, electropolymerization and amphipols, to demonstrate the electrically addressable functionalization of micro- and nanosurfaces with membrane proteins. Gold surfaces are selectively modified by electrogeneration of a polymeric film in the presence of biotin, where avidin conjugates can then be selectively immobilized. The method is successfully applied to the preparation of protein-multiplexed arrays by sequential electropolymerization and biomolecular functionalization steps. The surface density of the proteins bound to the electrodes can be easily tuned by adjusting the amount of biotin deposited during electropolymerization. Amphipols are specially designed amphipathic polymers that provide a straightforward method to stabilize and add functionalities to membrane proteins. Exploiting the strong affinity of biotin for streptavidin, we anchor distinct membrane proteins onto different electrodes via a biotin-tagged amphipol. Antibody-recognition events demonstrate that the proteins are stably immobilized and that the electrodeposition of polypyrrole films bearing biotin units is compatible with the protein-binding activity. Since polypyrrole films show good conductivity properties, the platform described here is particularly well suited to prepare electronically transduced bionanosensors.

Self-catalyzed GaAsP nanowires grown on silicon substrates by solid-source molecular beam epitaxy.

We realize the growth of self-catalyzed GaAsP nanowires (NWs) on silicon (111) substrates using solid-source molecular beam epitaxy. By optimizing the V/III and P/As flux ratios, as well as the Ga flux, high-crystal-quality GaAsP NWs have been demonstrated with almost pure zinc-blende phase. Comparing the growth of GaAsP NWs with that of the conventional GaAs NWs indicates that the incorporation of P has significant effects on catalyst nucleation energy, and hence the nanowire morphology and crystal quality. In addition, the incorporation ratio of P/As between vapor-liquid-solid NW growth and the vapor-solid thin film growth has been compared, and the difference between these two growth modes is explained through growth kinetics. The vapor-solid epitaxial growth of radial GaAsP shell on core GaAsP NWs is further demonstrated with room-temperature emission at ~710 nm. These results give valuable new information into the NW nucleation mechanisms and open up new perspectives for integrating III-V nanowire photovoltaics and visible light emitters on a silicon platform by using self-catalyzed GaAsP core-shell nanowires.

Surface-passivated GaAsP single-nanowire solar cells exceeding 10% efficiency grown on silicon.

Continued development of high-efficiency multi-junction solar cells requires growth of lattice-mismatched materials. Today, the need for lattice matching both restricts the bandgap combinations available for multi-junctions solar cells and prohibits monolithic integration of high-efficiency III-V materials with low-cost silicon solar cells. The use of III-V nanowires is the only known method for circumventing this lattice-matching constraint, and therefore it is necessary to develop growth of nanowires with bandgaps >1.4 eV. Here we present the first gold-free gallium arsenide phosphide nanowires grown on silicon by means of direct epitaxial growth. We demonstrate that their bandgap can be controlled during growth and fabricate core-shell nanowire solar cells. We further demonstrate that surface passivation is of crucial importance to reach high efficiencies, and present a record efficiency of 10.2% for a core-shell single-nanowire solar cell.