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Correction to: https://doi.org/10.1038/s41423-021-00794-6; http://hdl.handle.net/10261/257710, In the version of this correspondence initially published, one of the SARS-CoV-2 variants used in Fig. 1B, which was originally described in the article as the SARS-CoV-2 variant ‘B.1.1.248.2 Gamma’, is actually the ‘P.2 Zeta’ SARS-CoV-2 variant of interest. The GISAID accession ID EPI_ISL_1831696 provided is correct, but it belongs to the Zeta variant. The results and conclusions are not affected by this unintentional inaccuracy.

Palatine tonsils are secondary lymphoid organs representing the first line of immunological defense against inhaled or ingested pathogens. Here, we present a comprehensive census of cell types forming the human tonsil by applying single-cell transcriptome, epigenome, proteome and adaptive immune repertoire sequencing as well as spatial transcriptomics, resulting in an atlas of >357,000 cells. We provide a glossary of 121 annotated cell types and states, and disentangle gene regulatory mechanisms that drive cells through specialized lineage trajectories. Exemplarily, we stratify multiple tonsil-resident myeloid slancyte subtypes, establish a distant BCL6 superenhancer as locally active in both follicle-associated T and B cells, and describe SIX5 as a potentially novel transcriptional regulator of plasma cell maturation. Further, our atlas is a reference map to understand alterations observed in disease. Here, we discover immune-phenotype plasticity in tumoral cells and microenvironment shifts of mantle cell lymphomas (MCL). To facilitate such reference-based analysis, we develop HCATonsilData and SLOcatoR, a computational framework that provides programmatic and modular access to our dataset; and allows the straightforward annotation of future single-cell profiles from secondary lymphoid organs.

The tumor immune microenvironment is a main contributor to cancer progression and a promising therapeutic target for oncology. However, immune microenvironments vary profoundly between patients, and biomarkers for prognosis and treatment response lack precision. A comprehensive compendium of tumor immune cells is required to pinpoint predictive cellular states and their spatial localization. We generated a single-cell tumor immune atlas, jointly analyzing published data sets of >500,000 cells from 217 patients and 13 cancer types, providing the basis for a patient stratification based on immune cell compositions. Projecting immune cells from external tumors onto the atlas facilitated an automated cell annotation system. To enable in situ mapping of immune populations for digital pathology, we applied SPOTlight, combining single-cell and spatial transcriptomics data and identifying colocalization patterns of immune, stromal, and cancer cells in tumor sections. We expect the tumor immune cell atlas, together with our versatile toolbox for precision oncology, to advance currently applied stratification approaches for prognosis and immunotherapy. This publication is part of a project (BCLLATLAS) that has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 810287). This work has received funding from the Ministerio de Ciencia, Innovación y Universidades (SAF2017-89109-P; AEI/FEDER, UE) and the Fundació La Marató de TV3 (201903-30-31-32).We further acknowledge funding from the St. Vincent’s Clinic Foundation (V.T.C.) and the National Health and Medical Research Council Investigator Grant (APP1175781, J.E.P.), the Fundación Asociación Española contra el Cáncer (AECC), FERO (EDM), Ramón Areces Foundation, Cellex Foundation, BBVA (CAIMI), the ISCIII, FIS (PI16/01278), Juan de la Cierva formación fellowship (C.R.-P.) and Sara Borrell fellowship (E.P.-R.). Core funding is from the ISCIII and the Generalitat de Catalunya. We acknowledge support of the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) to the EMBL partnership, the Centro de Excelencia Severo Ochoa, the CERCA Programme / Generalitat de Catalunya, the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) through the nstituto de Salud Carlos III and the Generalitat de Catalunya through Departament de Salut and Departament d’Empresa i Coneixement. We also acknowledge the cofinancing by the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) with funds from the European Regional Development Fund (ERDF) corresponding to the 2014–2020 Smart Growth Operating Program

OBJECTIVE Assessment of asymptomatic organ damage in the management of hypertension includes low (

Fatty acid uptake and altered metabolism constitute hallmarks of metastasis1,2, yet evidence of the underlying biology, as well as whether all dietary fatty acids are prometastatic, is lacking. Here we show that dietary palmitic acid (PA), but not oleic acid or linoleic acid, promotes metastasis in oral carcinomas and melanoma in mice. Tumours from mice that were fed a short-term palm-oil-rich diet (PA), or tumour cells that were briefly exposed to PA in vitro, remained highly metastatic even after being serially transplanted (without further exposure to high levels of PA). This PA-induced prometastatic memory requires the fatty acid transporter CD36 and is associated with the stable deposition of histone H3 lysine 4 trimethylation by the methyltransferase Set1A (as part of the COMPASS complex (Set1A/COMPASS)). Bulk, single-cell and positional RNA-sequencing analyses indicate that genes with this prometastatic memory predominantly relate to a neural signature that stimulates intratumoural Schwann cells and innervation, two parameters that are strongly correlated with metastasis but are aetiologically poorly understood3,4. Mechanistically, tumour-associated Schwann cells secrete a specialized proregenerative extracellular matrix, the ablation of which inhibits metastasis initiation. Both the PA-induced memory of this proneural signature and its long-term boost in metastasis require the transcription factor EGR2 and the glial-cell-stimulating peptide galanin. In summary, we provide evidence that a dietary metabolite induces stable transcriptional and chromatin changes that lead to a long-term stimulation of metastasis, and that this is related to a proregenerative state of tumour-activated Schwann cells. Palmitic acid induces stable transcriptional and chromatin changes that lead to long-term stimulation of metastasis in orthotopic models of cancer through the secretion by tumour-associated Schwann cells of a specialized proregenerative extracellular matrix, the ablation of which inhibits metastasis initiation.

Antigen-presenting cells (APCs) may be resistant to SARS-CoV-2 infection but still contribute to viral pathogenesis. Lectins such as sialic acid-binding Ig-like lectin 1 (Siglec-1/CD169) mediate the attachment of viruses to APCs. Here, we show that APCs effectively capture SARS-CoV-2 within compartments via recognition of Siglec-1. This receptor interacts with sialylated gangliosides on membranes of SARS-CoV-2 variants, as previously shown for retroviruses or filoviruses [1]. Blockage of Siglec-1 on monocyte-derived dendritic cells (MDDCs) decreased SARS-CoV-2 viral transfer or trans-infection to bystander target cells. However, monocyte-derived macrophages (MDMs) capturing SARS-CoV-2 via Siglec-1 did not transmit infectious particles. The presence of pulmonary APCs co-expressing Siglec-1 and SARS-CoV-2 corroborated these findings in vivo., The research of the CBIG consortium (constituted by IRTA-CReSA, BSC, & IrsiCaixa) is supported by Grifols Pharmaceutical. The authors also acknowledge the crowdfunding initiative #Yomecorono (https://www.yomecorono.com). N.I.-U. is supported by the grant PID2020-117145RB-I00 from the Spanish Ministry of Science and Innovation. J.M.-P. is supported by the grant PID2019-109870RB-I00 from the Spanish Ministry of Science and Innovation and in part also by Grifols. The C.R. laboratory is funded by RTI2018-094445-B100 (MCIU/AEI/FEDER, UE). The NHP study was primarily supported by a YNPRC Coronavirus Pilot Research Project Program grant to M.Pa. under award P51 OD11132, Emergent Venture Fast grant program to M.Pa. under awards #2206 and #2144, and William and Lula Pitts Foundation (to M.Pa.). X.M.-T. is supported by the Spanish Ministry of Science and Innovation and the European Regional Development Fund under agreement BES-2017-082900.

The tumor immune microenvironment is a main contributor to cancer progression and a promising therapeutic target for oncology. However, immune microenvironments vary profoundly between patients and biomarkers for prognosis and treatment response lack precision. A comprehensive compendium of tumor immune cells is required to pinpoint predictive cellular states and their spatial localization. We generated a single-cell tumor immune atlas, jointly analyzing >500,000 cells from 217 patients and 13 cancer types, providing the basis for a patient stratification based on immune cell compositions. Projecting immune cells from external tumors onto the atlas facilitated an automated cell annotation system for a harmonized interpretation. To enable in situ mapping of immune populations for digital pathology, we applied SPOTlight, combining single-cell and spatial transcriptomics data and identifying striking spatial immune cell patterns in tumor sections. We expect the tumor immune cell atlas, together with our versatile toolbox for precision oncology, to advance currently applied stratification approaches for prognosis and immuno-therapy.

Study questionTo which degree does maternal age affect the transcriptome of human oocytes at the germinal vesicle (GV) stage or at metaphase II after maturation in vitro (IVM-MII)?Summary answerWhile the oocytes’ transcriptome is predominantly determined by maturation stage, transcript levels of genes related to chromosome segregation, mitochondria and RNA processing are affected by age after in vitro maturation of denuded oocytes.What is known alreadyFemale fertility is inversely correlated with maternal age due to both a depletion of the oocyte pool and a reduction in oocyte developmental competence. Few studies have addressed the effect of maternal age on the human mature oocyte (MII) transcriptome, which is established during oocyte growth and maturation, and the pathways involved remain unclear. Here, we characterize and compare the transcriptomes of a large cohort of fully grown GV and IVM-MII oocytes from women of varying reproductive age.Study design, size, durationIn this prospective molecular study, 37 women were recruited from May 2018 to June 2019. The mean age was 28.8 years (SD=7.7, range 18-43). A total of 72 oocytes were included in the study at GV stage after ovarian stimulation, and analyzed as GV (n=40) and in vitro matured oocytes (IVM-MII; n=32).Participants/materials, setting, methodsDenuded oocytes were included either as GV at the time of ovum pick-up or as IVM-MII after in vitro maturation for 30 hours in G2™ medium, and processed for transcriptomic analysis by single-cell RNA-seq using the Smart-seq2 technology. Cluster and maturation stage marker analysis were performed using the Seurat R package. Genes with an average fold change greater than 2 and a p-value < 0.01 were considered maturation stage markers. A Pearson correlation test was used to identify genes whose expression levels changed progressively with age. Those genes presenting a correlation value (R) >= |0.3| and a p-value < 0.05 were considered significant.Main results and the role of chanceFirst, by exploration of the RNA-seq data using tSNE dimensionality reduction, we identified two clusters of cells reflecting the oocyte maturation stage (GV and IVM-MII) with 4,445 and 324 putative marker genes, respectively. Next we identified genes, for which RNA levels either progressively increased or decreased with age. This analysis was performed independently for GV and IVM-MII oocytes. Our results indicate that the transcriptome is more affected by age in IVM-MII oocytes (1,219 genes) than in GV oocytes (596 genes). In particular, we found that genes involved in chromosome segregation and RNA splicing significantly increase in transcript levels with age, while genes related to mitochondrial activity present lower transcript levels with age. Gene regulatory network analysis revealed potential upstream master regulator functions for genes whose transcript levels present positive (GPBP1, RLF, SON, TTF1) or negative (BNC1, THRB) correlation with age.Limitations, reasons for cautionIVM-MII oocytes used in this study were obtained after in vitro maturation of denuded GV oocytes, therefore, their transcriptome might not be fully representative of in vivo matured MII oocytes.The Smart-seq2 methodology used in this study detects polyadenylated transcripts only and we could therefore not assess non-polyadenylated transcripts.Wider implications of the findingsOur analysis suggests that advanced maternal age does not globally affect the oocyte transcriptome at GV or IVM-MII stages. Nonetheless, hundreds of genes displayed altered transcript levels with age, particularly in IVM-MII oocytes. Especially affected by age were genes related to chromosome segregation and mitochondrial function, pathways known to be involved in oocyte ageing. Our study thereby suggests that misregulation of chromosome segregation and mitochondrial pathways also at the RNA-level might contribute to the age-related quality decline in human oocytes.Study funding/competing interest(s)This study was funded by the AXA research fund, the European commission, intramural funding of Clinica EUGIN, the Spanish Ministry of Science, Innovation and Universities, the Catalan Agència de Gestió d’Ajuts Universitaris i de Recerca (AGAUR) and by contributions of the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) to the EMBL partnership and to the “Centro de Excelencia Severo Ochoa”.The authors have no conflict of interest to declare.

Cardiovascular prevention is of particular interest in persons with asymptomatic peripheral arterial disease. We aimed to quantify its association with mortality and cardiovascular outcomes, compared to other indicators of high risk. We performed a retrospective cohort study using the Database of the Catalan primary care system (SIDIAPQ), for 2006&ndash, 2015, including 35&ndash, 85-year-old patients with an ankle&ndash, brachial index (ABI) measurement, classified according to the presence of diabetes, cardiovascular disease, and low ABI (&lt, 0.9). We calculated the incidences and hazard ratios (HRs) for all-cause mortality, acute myocardial infarction, and ischemic stroke. During a median follow-up of 5.9 years, we analyzed 58,118 persons. The mean (SD) age was 66.6 (10.7) years and 53.4% were men. Compared to the reference group with no diabetes, no previous cardiovascular disease, and normal ankle&ndash, brachial index, the HR for all-cause mortality was 1.42 (1.25&ndash, 1.63) in the group with low ABI, 1.35 (1.26&ndash, 1.45) in those with diabetes, 1.50 (1.34&ndash, 1.69) in those with previous cardiovascular disease, and 1.84 (1.68&ndash, 2.01) in those with low ABI and diabetes. In conclusion, participants with low ABI showed increased mortality, acute myocardial infarction, and ischemic stroke incidence in all the subgroups. Patients with low ankle&ndash, brachial index plus diabetes presented increased mortality, acute myocardial infarction, and ischemic stroke risk, all at rates similar to those with previous cardiovascular disease.

Resumen Introduccion y objetivos El indice vascular corazon-tobillo (CAVI) evalua la rigidez arterial. El objetivo es describir la distribucion del CAVI en una poblacion mediterranea, determinar la proporcion de CAVI ≥ 9 segun las categorias de riesgo coronario, y evaluar la asociacion del CAVI con los factores de riesgo cardiovascular y estilos de vida clasicos. Metodos Estudio transversal en la provincia de Girona. El CAVI se ha medido utilizando el VaSera VS-1500. Resultados Se incluyo a 2.613 individuos. La prevalencia de CAVI ≥ 9 fue del 46,8% en varones y el 36,0% en mujeres y aumento significativamente con el riesgo coronario: del 21,1 y el 24,8%, respectivamente, en el grupo con bajo riesgo al 76,7 y el 61,9% en el de alto riesgo. El CAVI aumento con la edad en ambos sexos y resulto superior en varones. En estos, el CAVI ≥ 9 se asocio con hipertension (OR = 2,70; IC95%, 1,90-3,87), diabetes (OR = 2,38; IC95%, 1,52-3,78), indice de masa corporal (IMC) ≤ 25 a Conclusiones El CAVI aumenta con la edad y es mayor en varones que en mujeres, y se asocia con factores de riesgo clasicos y con el riesgo coronario. Podria ser un buen biomarcador predictivo, aunque hacen falta estudios que evaluen su relevancia en la estratificacion del riesgo cardiovascular.

Background and aims The main aim of this study is to describe the differences in the cardio-ankle vascular index (CAVI) in individuals with metabolic cardiovascular risk factors or a previous history of vascular diseases (WCVRF) compared to healthy individuals (free of risk factors and previous history of vascular diseases; FCVRF) in a general Mediterranean population. The secondary aim is to describe the proportion of CAVI≥9 depending on the cardiovascular risk category in both CVRF groups by sex. Methods The study is a descriptive analysis of 2613 participants randomly selected in the Girona province (Catalonia, Spain). Results CAVI mean differences between sexes and age categories in both CVRF groups followed the same pattern, the FCVRF group (men 25.2%; women 14.4%) in turn had a lower prevalence of CAVI≥9 than the WCVRF group (men 57.9%; women 51.8%). The percentage of men and women with CAVI≥9 with low risk was 13.9% and 11.3% in the FCVRF group, and 31.8% and 42.0% in the WCVRF group; with moderate risk, it was 55.8% and 10.0% in the FCVRF group and 60.3% and 49.0% in the WCVRF group. Conclusions In both sexes, FCVRF groups had a lower prevalence of CAVI≥9 as well as lower mean CAVI scores, across all 10 year-age categories from 40 to 69 years, than WCVRF groups. Moreover, CAVI≥9 was frequent in individuals with low and moderate coronary risk in the WCVRF group but also in the FCVRF group. These results suggest that CAVI assessment to detect asymptomatic arteriosclerosis could be a useful tool to improve cardiovascular risk stratification.

ObjectiveWe sought to compare the association of categorized ankle–brachial index (ABI) with mortality and complications of diabetes in persons with no symptoms of peripheral arterial disease (PAD) and in primary cardiovascular disease prevention.Research design and methodsThis is a retrospective cohort study of persons with type 2 diabetes aged 35–85 years, from 2006 to 2011. Data were obtained from the Sistema d'Informació per al Desenvolupament de la Investigació en Atenció Primària (SIDIAPQ). Participants had an ABI measurement that was classified into six categories. For each category of ABI, we assessed the incidence of mortality; macrovascular complications of diabetes: acute myocardial infarction (AMI), ischemic stroke, and a composite of these two; and microvascular complications of this metabolic condition: nephropathy, retinopathy, and neuropathy. We also estimated the HRs for these outcomes by ABI category using Cox proportional hazards models.ResultsData from 34 689 persons with type 2 diabetes were included. The mean age was 66.2; 51.5% were men; and the median follow-up was 6.0 years. The outcome with the highest incidence was nephropathy, with 24.4 cases per 1000 person-years in the reference category of 1.1≤ABI≤1.3. The incidences in this category for mortality and AMI were 15.4 and 4.1, respectively. In the Cox models, low ABI was associated with increased risk and was significant from ABI lower than 0.9; below this level, the risk kept increasing steeply. High ABI (over 1.3) was also associated with significant increased risk for most outcomes.ConclusionsThe studied categories of ABI were associated with different risks of type 2 diabetes complications in persons asymptomatic for PAD, who were in primary cardiovascular prevention. These findings could be useful to optimize preventive interventions according to the ABI category in this population.

To assess whether statin treatment is associated with a reduction in atherosclerotic cardiovascular disease (CVD) and mortality in old and very old adults with and without diabetes. Design Retrospective cohort study. Setting Database of the Catalan primary care system (SIDIAP), Spain, 2006-15. Participants 46 864 people aged 75 years or more without clinically recognised atherosclerotic CVD. Participants were stratified by presence of type 2 diabetes mellitus and as statin non-users or new users. Main outcome measures Incidences of atherosclerotic CVD and all cause mortality compared using Cox proportional hazards modelling, adjusted by the propensity score of statin treatment. The relation of age with the effect of statins was assessed using both a categorical approach, stratifying the analysis by old (75-84 years) and very old (≥85 years) age groups, and a continuous analysis, using an additive Cox proportional hazard model. Results The cohort included 46 864 participants (mean age 77 years; 63% women; median follow-up 5.6 years). In participants without diabetes, the hazard ratios for statin use in 75-84 year olds were 0.94 (95% confidence interval 0.86 to 1.04) for atherosclerotic CVD and 0.98 (0.91 to 1.05) for all cause mortality, and in those aged 85 and older were 0.93 (0.82 to 1.06) and 0.97 (0.90 to 1.05), respectively. In participants with diabetes, the hazard ratio of statin use in 75-84 year olds was 0.76 (0.65 to 0.89) for atherosclerotic CVD and 0.84 (0.75 to 0.94) for all cause mortality, and in those aged 85 and older were 0.82 (0.53 to 1.26) and 1.05 (0.86 to 1.28), respectively. Similarly, effect analysis of age in a continuous scale, using splines, corroborated the lack of beneficial statins effect for atherosclerotic CVD and all cause mortality in participants without diabetes older than 74 years. In participants with diabetes, statins showed a protective effect against atherosclerotic CVD and all cause mortality; this effect was substantially reduced beyond the age of 85 years and disappeared in nonagenarians. Conclusions In participants older than 74 years without type 2 diabetes, statin treatment was not associated with a reduction in atherosclerotic CVD or in all cause mortality, even when the incidence of atherosclerotic CVD was statistically significantly higher than the risk thresholds proposed for statin use. In the presence of diabetes, statin use was statistically significantly associated with reductions in the incidence of atherosclerotic CVD and in all cause mortality. This effect decreased after age 85 years and disappeared in nonagenarians