TCR-engaging scaffolds selectively expand antigen-specific T-cells with a favorable phenotype for adoptive cell therapy

Background Adoptive cell therapy (ACT) has shown promising results for the treatment of cancer and viral infections. Successful ACT relies on ex vivo expansion of large numbers of desired T-cells with strong cytotoxic capacity and in vivo persistence, which constitutes the greatest challenge to current ACT strategies. Here, in this study, we present a novel technology for ex vivo expansion of antigen-specific T-cells; artificial antigen-presenting scaffolds (Ag-scaffolds) consisting of a dextran-polysaccharide backbone, decorated with combinations of peptide-Major Histocompatibility Complex (pMHC), cytokines and co-stimulatory molecules, enabling coordinated stimulation of antigen-specific T-cells.Methods The capacity of Ag-scaffolds to expand antigen-specific T-cells was explored in ex vivo cultures with peripheral blood mononuclear cells from healthy donors and patients with metastatic melanoma. The resulting T-cell products were assessed for phenotypic and functional characteristics.Results We identified an optimal Ag-scaffold for expansion of T-cells for ACT, carrying pMHC and interleukin-2 (IL-2) and IL-21, with which we efficiently expanded both virus-specific and tumor-specific CD8+ T cells from peripheral blood of healthy donors and patients, respectively. The resulting T-cell products were characterized by a high frequency of antigen-specific cells with high self-renewal capacity, low exhaustion, a multifunctional cytokine profile upon antigen-challenge and superior tumor killing capacity. This demonstrates that the coordinated stimuli provided by an optimized stoichiometry of TCR engaging (pMHC) and stimulatory (cytokine) moieties is essential to obtain desired T-cell characteristics. To generate an ‘off-the-shelf’ multitargeting Ag-scaffold product of relevance to patients with metastatic melanoma, we identified the 30 most frequently recognized shared HLA-A0201-restricted melanoma epitopes in a cohort of 87 patients. By combining these in an Ag-scaffold product, we were able to expand tumor-specific T-cells from 60–70% of patients with melanoma, yielding a multitargeted T-cell product with up to 25% specific and phenotypically and functionally improved T cells.Conclusions Taken together, the Ag-scaffold represents a promising new technology for selective expansion of antigen-specific CD8+ T cells directly from blood, yielding a highly specific and functionally enhanced T-cell product for ACT

Late Quaternary dynamics of Arctic biota from ancient environmental genomics

During the last glacial–interglacial cycle, Arctic biotas experienced substantial climatic changes, yet the nature, extent and rate of their responses are not fully understood1,2,3,4,5,6,7,8. Here we report a large-scale environmental DNA metagenomic study of ancient plant and mammal communities, analysing 535 permafrost and lake sediment samples from across the Arctic spanning the past 50,000 years. Furthermore, we present 1,541 contemporary plant genome assemblies that were generated as reference sequences. Our study provides several insights into the long-term dynamics of the Arctic biota at the circumpolar and regional scales. Our key findings include: (1) a relatively homogeneous steppe–tundra flora dominated the Arctic during the Last Glacial Maximum, followed by regional divergence of vegetation during the Holocene epoch; (2) certain grazing animals consistently co-occurred in space and time; (3) humans appear to have been a minor factor in driving animal distributions; (4) higher effective precipitation, as well as an increase in the proportion of wetland plants, show negative effects on animal diversity; (5) the persistence of the steppe–tundra vegetation in northern Siberia enabled the late survival of several now-extinct megafauna species, including the woolly mammoth until 3.9 ± 0.2 thousand years ago (ka) and the woolly rhinoceros until 9.8 ± 0.2 ka; and (6) phylogenetic analysis of mammoth environmental DNA reveals a previously unsampled mitochondrial lineage. Our findings highlight the power of ancient environmental metagenomics analyses to advance understanding of population histories and long-term ecological dynamics

Late Quaternary dynamics of Arctic biota from ancient environmental genomics.

Acknowledgements: Acknowledgements: We thank D. H. Mann for his detailed and constructive comments; and T. Ager, J. Austin, T. B. Brand, A. Cooper, S. Funder, M. T. P. Gilbert, T. Jørgensen, N. J. Korsgaard, S. Liu, M. Meldgaard, P. V. S. Olsen, M. L. Siggaard-Andersen, J. Stenderup, S. A. Woodroffe and staff at the GeoGenetics Sequencing Core and National Park Service-Western Arctic National Parklands for help and support. E.W. and D.J.M. thank the staff at St. John’s College, Cambridge, for providing a stimulating environment for scientific discussion of the project. E.W. thanks Illumina for collaboration. The Lundbeck Foundation GeoGenetics Centre is supported by the Carlsberg Foundation (CF18-0024), the Lundbeck Foundation (R302-2018-2155), the Novo Nordisk Foundation (NNF18SA0035006), the Wellcome Trust (UNS69906) and GRF EXC CRS Chair (44113220)—Cluster of Excellence. The PhyloNorway plant genome database is part of the Norwegian Barcode of Life Network (https://www.norbol.org) funded by the Research Council of Norway (226134/F50), the Norwegian Biodiversity Information Centre (14-14, 70184209) and The Arctic University Museum of Norway. Metabarcoding sequencing was funded by the Central Public-Interest Scientific Institution Basal Research Fund, CAFS (2017B001 and 2020A001). B.D.S. is supported by the Wellcome Trust programme in Mathematical Genomics and Medicine (WT220023); F.R. by a Villum Fonden Young Investigator award (no. 00025300); D.J.M. by the Quest Archaeological Research Fund; P.M. by the Swedish Research Council (VR); R.D. by the Wellcome Trust (WT207492); and A.R. by a Marie Skłodowska-Curie Actions Individual Fellowship (MSCA-IF, 703542) and the Research Council of Norway (KLIMAFORSK, 294929). L.O. has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (no. 681605); I.G.A. and Y.L. from the ERC under the European Union’s Horizon 2020 research and innovation programme (no. 819192). J.I.S. and J.M. are supported by the Research Council of Norway. P.B.H. and N.R.E. acknowledge NERC funding (grant NE/P015093/1). D.W.B. was supported by a Marie Skłodowska-Curie Actions Incoming International Fellowship (MCIIF-40974). T.S.K. is funded by a Carlsberg Foundation Young Researcher Fellowship (CF19-0712).During the last glacial-interglacial cycle, Arctic biotas experienced substantial climatic changes, yet the nature, extent and rate of their responses are not fully understood1-8. Here we report a large-scale environmental DNA metagenomic study of ancient plant and mammal communities, analysing 535 permafrost and lake sediment samples from across the Arctic spanning the past 50,000 years. Furthermore, we present 1,541 contemporary plant genome assemblies that were generated as reference sequences. Our study provides several insights into the long-term dynamics of the Arctic biota at the circumpolar and regional scales. Our key findings include: (1) a relatively homogeneous steppe-tundra flora dominated the Arctic during the Last Glacial Maximum, followed by regional divergence of vegetation during the Holocene epoch; (2) certain grazing animals consistently co-occurred in space and time; (3) humans appear to have been a minor factor in driving animal distributions; (4) higher effective precipitation, as well as an increase in the proportion of wetland plants, show negative effects on animal diversity; (5) the persistence of the steppe-tundra vegetation in northern Siberia enabled the late survival of several now-extinct megafauna species, including the woolly mammoth until 3.9 ± 0.2 thousand years ago (ka) and the woolly rhinoceros until 9.8 ± 0.2 ka; and (6) phylogenetic analysis of mammoth environmental DNA reveals a previously unsampled mitochondrial lineage. Our findings highlight the power of ancient environmental metagenomics analyses to advance understanding of population histories and long-term ecological dynamics

Supporting data for: Late Quaternary dynamics of Arctic biota revealed by ancient environmental metagenomics

[Dataset abstract] This dataset contains the assembled genome contigs (whole genome level) of the PhyloNorway plant database used in Wang et al. 2021 Late Quaternary Dynamics of Arctic Biota Revealed by Ancient Environmental Metagenomics. Methods for generating this database can be found in the paper. The 7 fasta files are the database. The PhyloNorway_com_acc2TaxaID.txt supplies a NCBI format acc2TaxaID file matching accession ID to NCBI TaxaID. Additional information about the database can be found in Alsos et al. 2020.</span