Genetics and immunity in the era of single-cell genomics.

Recent developments in the field of single-cell genomics (SCG) are changing our understanding of how functional phenotypes of cell populations emerge from the behaviour of individual cells. Some of the applications of SCG include the discovery of new gene networks and novel cell subpopulations, fine mapping of transcription kinetics, and the relationships between cell clonality and their functional phenotypes. Immunology is one of the fields that is benefiting the most from such advancements, providing us with completely new insights into mammalian immunity. In this review, we start by covering new immunological insights originating from the use of single-cell genomic tools, specifically single-cell RNA-sequencing. Furthermore, we discuss how new genetic study designs are starting to explain inter-individual variation in the immune response. We conclude with a perspective on new multi-omics technologies capable of integrating several readouts from the same single cell and how such techniques might push our biological understanding of mammalian immunity to a new level

Are cells from a snowman realistic? Cryopreserved tissues as a source for single-cell RNA-sequencing experiments

A recently published study in Genome Biology shows that cells isolated from cryopreserved tissues are a reliable source of genetic material for single-cell RNA-sequencing experiments.Please see related Method article: http://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1171-9

The first observed stellar occultations by the irregular satellite Phoebe (Saturn IX) and improved rotational period

peer reviewedWe report six stellar occultations by Phoebe (Saturn IX), an irregular satellite of Saturn, obtained between mid-2017 and mid-2019. The 2017 July 6 event was the first stellar occultation by an irregular satellite ever observed. The occultation chords were compared to a 3D shape model of the satellite obtained from Cassini observations. The rotation period available in the literature led to a sub-observer point at the moment of the observed occultations where the chords could not fit the 3D model. A procedure was developed to identify the correct sub-observer longitude. It allowed us to obtain the rotation period with improved precision compared to the currently known value from literature. We show that the difference between the observed and the predicted sub-observer longitude suggests two possible solutions for the rotation period. By comparing these values with recently observed rotational light curves and single- chord stellar occultations, we can identify the best solution for Phoebe's rotational period as 9.27365 ± 0.00002 h. From the stellar occultations, we also obtained six geocentric astrometric positions in the ICRS as realized by the Gaia DR2 with uncertainties at the 1-mas level

The adhesion G protein-coupled receptor GPR56/ADGRG1 is an inhibitory receptor on human NK cells

Natural killer (NK) cells possess potent cytotoxic mechanisms that need to be tightly controlled. We here explored the regulation and function of GPR56/ADGRG1, an adhesion G protein-coupled receptor implicated in developmental processes and expressed distinctively in mature NK cells. Expression of GPR56 was triggered by Hobit, a homolog of Blimp-1, and declined upon cell activation. Through studying NK cells from polymicrogyria patients with disease-causing mutations in the ADGRG1 gene, encoding GPR56, and NK-92 cells ectopically expressing the receptor, we found that GPR56 negatively regulates immediate effector functions, including production of inflammatory cytokines and cytolytic proteins, degranulation, and target cell killing. GPR56 pursues this activity by associating with the tetraspanin CD81. We conclude that GPR56 inhibits natural cytotoxicity of human NK cells

The Human Lung Cell Atlas: A High-Resolution Reference Map of the Human Lung in Health and Disease.

Lung disease accounts for every sixth death globally. Profiling the molecular state of all lung cell types in health and disease is currently revolutionizing the identification of disease mechanisms and will aid the design of novel diagnostic and personalized therapeutic regimens. Recent progress in high-throughput techniques for single-cell genomic and transcriptomic analyses has opened up new possibilities to study individual cells within a tissue, classify these into cell types, and characterize variations in their molecular profiles as a function of genetics, environment, cell-cell interactions, developmental processes, aging, or disease. Integration of these cell state definitions with spatial information allows the in-depth molecular description of cellular neighborhoods and tissue microenvironments, including the tissue resident structural and immune cells, the tissue matrix, and the microbiome. The Human Cell Atlas consortium aims to characterize all cells in the healthy human body and has prioritized lung tissue as one of the flagship projects. Here, we present the rationale, the approach, and the expected impact of a Human Lung Cell Atlas.Supported by the Helmholtz Association and the German Center for Lung Research (DZL) (H.B.S.); the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement 753039 (L.M.S.); U.K. Medical Research Council grant G0900424 (E.L.R.); National Institutes of Health (NIH) grants ES013995, HL071643, and AG049665, and Veterans Administration grant BX000201 and Department of Defense grant PR141319 (G.R.S.B.); NIH grants HL135124 and AI135964 and Department of Defense grant PR141319 (A.V.M.); NIH grants R01HL141852, R01HL127349, UHHL3123886, U01HL122626, and UG3TR002445, and Department of Defence grant PR151124 (N.K.); and the Netherlands Lung Foundation grants 5.1.14.020 and 4.1.18.226 (M.C.N.)

Somatic mutations and single-cell transcriptomes reveal the root of malignant rhabdoid tumours.

Malignant rhabdoid tumour (MRT) is an often lethal childhood cancer that, like many paediatric tumours, is thought to arise from aberrant fetal development. The embryonic root and differentiation pathways underpinning MRT are not firmly established. Here, we study the origin of MRT by combining phylogenetic analyses and single-cell mRNA studies in patient-derived organoids. Comparison of somatic mutations shared between cancer and surrounding normal tissues places MRT in a lineage with neural crest-derived Schwann cells. Single-cell mRNA readouts of MRT differentiation, which we examine by reverting the genetic driver mutation underpinning MRT, SMARCB1 loss, suggest that cells are blocked en route to differentiating into mesenchyme. Quantitative transcriptional predictions indicate that combined HDAC and mTOR inhibition mimic MRT differentiation, which we confirm experimentally. Our study defines the developmental block of MRT and reveals potential differentiation therapies

Constraints on (2060) Chiron's size, shape, and surrounding material from the November 2018 and September 2019 stellar occultations

After the discovery of rings around the largest known Centaur object, (10199) Chariklo, we carried out observation campaigns of stellar occultations produced by the second-largest known Centaur object, (2060) Chiron, to better characterize its physical properties and presence of material on its surroundings. We predicted and successfully observed two stellar occultations by Chiron. These observations were used to constrain its size and shape by fitting elliptical limbs with equivalent surface radii in agreement with radiometric measurements. Constraints on the (2060) Chiron shape are reported for the first time. Assuming an equivalent radius of R$_{equiv}$ = 105$^{+6}_{-7}$ km, we obtained a semi-major axis of a = 126 $\pm$ 22 km. Considering Chiron's true rotational light curve amplitude and assuming it has a Jacobi equilibrium shape, we were able to derive a 3D shape with a semi-axis of a = 126 $\pm$ 22 km, b = 109 $\pm$ 19 km, and c = 68 $\pm$ 13 km, implying in a volume-equivalent radius of R$_{vol}$ = 98 $\pm$ 17 km, implying a density of 1119 $\pm$ 4 kg m$^{-3}$. We determined the physical properties of the 2011 secondary events around Chiron, which may then be directly compared with those of Chariklo rings, as the same method was used. Data obtained from SAAO in 2018 do not show unambiguous evidence of the proposed rings, mainly due to the large sampling time. Meanwhile, we discarded the possible presence of a permanent ring similar to (10199) Chariklo's C1R in optical depth and extension. Using the first multi-chord stellar occultation by (2060) Chiron and considering it to have a Jacobi equilibrium shape, we derived its 3D shape. New observations of a stellar occultation by (2060) Chiron are needed to further investigate the material's properties around Chiron, such as the occultation predicted for September 10, 2023

Refined physical parameters for Chariklo's body and rings from stellar occultations observed between 2013 and 2020

Context. The Centaur (10199) Chariklo has the first ring system discovered around a small object. It was first observed using stellar occultation in 2013. Stellar occultations allow sizes and shapes to be determined with kilometre accuracy, and provide the characteristics of the occulting object and its vicinity. Aims. Using stellar occultations observed between 2017 and 2020, our aim is to constrain the physical parameters of Chariklo and its rings. We also determine the structure of the rings, and obtain precise astrometrical positions of Chariklo. Methods. We predicted and organised several observational campaigns of stellar occultations by Chariklo. Occultation light curves were measured from the datasets, from which ingress and egress times, and the ring widths and opacity values were obtained. These measurements, combined with results from previous works, allow us to obtain significant constraints on Chariklo's shape and ring structure. Results. We characterise Chariklo's ring system (C1R and C2R), and obtain radii and pole orientations that are consistent with, but more accurate than, results from previous occultations. We confirm the detection of W-shaped structures within C1R and an evident variation in radial width. The observed width ranges between 4.8 and 9.1 km with a mean value of 6.5 km. One dual observation (visible and red) does not reveal any differences in the C1R opacity profiles, indicating a ring particle size larger than a few microns. The C1R ring eccentricity is found to be smaller than 0.022 (3σ), and its width variations may indicate an eccentricity higher than ~0.005. We fit a tri-axial shape to Chariklo's detections over 11 occultations, and determine that Chariklo is consistent with an ellipsoid with semi-axes of 143.8-1.5+1.4, 135.2-2.8+1.4, and 99.1-2.7+5.4 km. Ultimately, we provided seven astrometric positions at a milliarcsecond accuracy level, based on Gaia EDR3, and use it to improve Chariklo's ephemeris.Fil: Morgado, B.E.. Centre National de la Recherche Scientifique. Observatoire de Paris; Francia. Ministério de Ciencia, Tecnologia e Innovacao. Observatorio Nacional; BrasilFil: Sicardy, Bruno. Centre National de la Recherche Scientifique. Observatoire de Paris; FranciaFil: Braga Ribas, Felipe. Ministério de Ciencia, Tecnologia e Innovacao. Observatorio Nacional; Brasil. Centre National de la Recherche Scientifique. Observatoire de Paris; Francia. Universidade Tecnologia Federal do Parana; BrasilFil: Desmars, Josselin. Centre National de la Recherche Scientifique. Observatoire de Paris; FranciaFil: Gomes Júnior, Altair Ramos. Universidade de Sao Paulo; BrasilFil: Bérard, D.. Centre National de la Recherche Scientifique. Observatoire de Paris; FranciaFil: Leiva, Rodrigo. Universidad de Chile; Chile. Centre National de la Recherche Scientifique. Observatoire de Paris; FranciaFil: Vieira Martins, Roberto. Ministério de Ciencia, Tecnologia e Innovacao. Observatorio Nacional; Brasil. Universidade Federal do Rio de Janeiro; BrasilFil: Benedetti Rossi, G.. Centre National de la Recherche Scientifique. Observatoire de Paris; Francia. Universidade Federal de Sao Paulo; BrasilFil: Santos Sanz, Pablo. Ministério de Ciencia, Tecnologia e Innovacao. Observatorio Nacional; BrasilFil: Camargo, Julio Ignacio Bueno. Ministério de Ciencia, Tecnologia e Innovacao. Observatorio Nacional; BrasilFil: Duffard, R.. Universidade Federal do Rio de Janeiro; BrasilFil: Rommel, F.L.. Ministério de Ciencia, Tecnologia e Innovacao. Observatorio Nacional; BrasilFil: Assafin, M.. Centre National de la Recherche Scientifique. Observatoire de Paris; FranciaFil: Boufleur, R.C.. Universidad Nacional de Córdoba; ArgentinaFil: Colas, F.. Ministério de Ciencia, Tecnologia e Innovacao. Observatorio Nacional; BrasilFil: Kretlow, Mike. Ministério de Ciencia, Tecnologia e Innovacao. Observatorio Nacional; BrasilFil: Beisker, W.. University of North Carolina; Estados UnidosFil: Sfair, Rafael. Centre National de la Recherche Scientifique. Observatoire de Paris; FranciaFil: Snodgrass, Colin. University of Edinburgh; Reino UnidoFil: Morales, N.. Pontificia Universidad Católica de Chile; Chile. Universidad Católica de Chile; ChileFil: Fernández Valenzuela, E.. Pontificia Universidad Católica de Chile; Chile. Universidad Católica de Chile; ChileFil: Amaral, L.S.. Massachusetts Institute of Technology; Estados UnidosFil: Amarante, A.. Ministério de Ciencia, Tecnologia e Innovacao. Observatorio Nacional; BrasilFil: Artola, R.A.. Centre National de la Recherche Scientifique. Observatoire de Paris; FranciaFil: Backes, M.. Universidad Nacional de Córdoba; ArgentinaFil: Bath, K. L.. University of North Carolina; Estados UnidosFil: Bouley, S.. University of St. Andrews; Reino UnidoFil: Garcia Lambas, Diego Rodolfo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Astronomía Teórica y Experimental. Universidad Nacional de Córdoba. Observatorio Astronómico de Córdoba. Instituto de Astronomía Teórica y Experimental; ArgentinaFil: Schneiter, Ernesto Matías. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Departamento de Ingeniería Económica y Legal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Astronomía Teórica y Experimental. Universidad Nacional de Córdoba. Observatorio Astronómico de Córdoba. Instituto de Astronomía Teórica y Experimental; Argentin

Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors.

Messenger RNA encodes cellular function and phenotype. In the context of human cancer, it defines the identities of malignant cells and the diversity of tumor tissue. We studied 72,501 single-cell transcriptomes of human renal tumors and normal tissue from fetal, pediatric, and adult kidneys. We matched childhood Wilms tumor with specific fetal cell types, thus providing evidence for the hypothesis that Wilms tumor cells are aberrant fetal cells. In adult renal cell carcinoma, we identified a canonical cancer transcriptome that matched a little-known subtype of proximal convoluted tubular cell. Analyses of the tumor composition defined cancer-associated normal cells and delineated a complex vascular endothelial growth factor (VEGF) signaling circuit. Our findings reveal the precise cellular identities and compositions of human kidney tumors

Single cell derived mRNA signals across human kidney tumors.

Funder: Department of HealthTumor cells may share some patterns of gene expression with their cell of origin, providing clues into the differentiation state and origin of cancer. Here, we study the differentiation state and cellular origin of 1300 childhood and adult kidney tumors. Using single cell mRNA reference maps of normal tissues, we quantify reference "cellular signals" in each tumor. Quantifying global differentiation, we find that childhood tumors exhibit fetal cellular signals, replacing the presumption of "fetalness" with a quantitative measure of immaturity. By contrast, in adult cancers our assessment refutes the suggestion of dedifferentiation towards a fetal state in most cases. We find an intimate connection between developmental mesenchymal populations and childhood renal tumors. We demonstrate the diagnostic potential of our approach with a case study of a cryptic renal tumor. Our findings provide a cellular definition of human renal tumors through an approach that is broadly applicable to human cancer