Spatial multiomics map of trophoblast development in early pregnancy.

The relationship between the human placenta-the extraembryonic organ made by the fetus, and the decidua-the mucosal layer of the uterus, is essential to nurture and protect the fetus during pregnancy. Extravillous trophoblast cells (EVTs) derived from placental villi infiltrate the decidua, transforming the maternal arteries into high-conductance vessels1. Defects in trophoblast invasion and arterial transformation established during early pregnancy underlie common pregnancy disorders such as pre-eclampsia2. Here we have generated a spatially resolved multiomics single-cell atlas of the entire human maternal-fetal interface including the myometrium, which enables us to resolve the full trajectory of trophoblast differentiation. We have used this cellular map to infer the possible transcription factors mediating EVT invasion and show that they are preserved in in vitro models of EVT differentiation from primary trophoblast organoids3,4 and trophoblast stem cells5. We define the transcriptomes of the final cell states of trophoblast invasion: placental bed giant cells (fused multinucleated EVTs) and endovascular EVTs (which form plugs inside the maternal arteries). We predict the cell-cell communication events contributing to trophoblast invasion and placental bed giant cell formation, and model the dual role of interstitial EVTs and endovascular EVTs in mediating arterial transformation during early pregnancy. Together, our data provide a comprehensive analysis of postimplantation trophoblast differentiation that can be used to inform the design of experimental models of the human placenta in early pregnancy.

Single-cell roadmap of human gonadal development.

Gonadal development is a complex process that involves sex determination followed by divergent maturation into either testes or ovaries1. Historically, limited tissue accessibility, a lack of reliable in vitro models and critical differences between humans and mice have hampered our knowledge of human gonadogenesis, despite its importance in gonadal conditions and infertility. Here, we generated a comprehensive map of first- and second-trimester human gonads using a combination of single-cell and spatial transcriptomics, chromatin accessibility assays and fluorescent microscopy. We extracted human-specific regulatory programmes that control the development of germline and somatic cell lineages by profiling equivalent developmental stages in mice. In both species, we define the somatic cell states present at the time of sex specification, including the bipotent early supporting population that, in males, upregulates the testis-determining factor SRY and sPAX8s, a gonadal lineage located at the gonadal-mesonephric interface. In females, we resolve the cellular and molecular events that give rise to the first and second waves of granulosa cells that compartmentalize the developing ovary to modulate germ cell differentiation. In males, we identify human SIGLEC15+ and TREM2+ fetal testicular macrophages, which signal to somatic cells outside and inside the developing testis cords, respectively. This study provides a comprehensive spatiotemporal map of human and mouse gonadal differentiation, which can guide in vitro gonadogenesis.

Psychometric properties of the Spanish version of the Type 2 Diabetes Stigma Assessment Scale (DSAS 2) in a Colombian population / Propiedades psicométricas de la versión en español del Type 2 Diabetes Stigma Assessment Scale (DSAS 2) en población colombiana

Introduction: The perception of stigma has been negatively associated with the metabolic control and quality of life in patients with type 2 diabetes. The Diabetes Stigma Assessment Scale 2 (DSAS 2) was designed to specifically measure the stigma associated with this type of diabetes. However, the psychometric properties of its Spanish version have not yet been addressed. Objective: To analyze the validity and reliability of the Spanish version of DSAS 2 in a Colombian population. Materials and methods: In total, 501 patients with type 2 diabetes from Barranquilla answered the Spanish version of DSAS 2, a questionnaire with sociodemographic and clinical indicators, as well as instruments to measure depression, self-efficacy, and stress. We performed a factor analysis (exploratory and confirmatory) to determine the internal structure of the DSAS 2 in Spanish and used the alpha coefficient (α) to evaluate its reliability. Additionally, we analyzed the relationship between the DSAS 2 scores and the other variables under study. Results: The three-factor structure (different treatment / judgment, guilt and shame) showed good fit to the data (RMSEA = 0.081, CFI = 0.959, TLI = 0.95) and good reliability (α = 0.76). Significant correlations of the scores of the DSAS 2 Spanish version were observed with self-efficacy (rs=-0.37, p<0.001), stress (rs =0.24 , p<0.001), and depression (rs=0.1, p=0.021). Besides, the scores showed variations associated with sociodemographic and clinical variables. Conclusions: The Spanish version showed certain differences compared with the original version of the DSAS2 but there was adequate evidence of its validity and reliability to be used in Colombia.

Introducción. El estigma se ha asociado negativamente al control metabólico y la calidad de vida de pacientes con diabetes de tipo 2. El cuestionario Diabetes Stigma Assesment Scale 2 (DSAS 2) fue diseñado para medir específicamente el estigma asociado en personas con este tipo de diabetes. Sin embargo, las propiedades psicométricas de su versión en español aún no han sido analizadas. Objetivo. Analizar la validez y confiabilidad de la versión en español del DSAS 2 en población colombiana. Materiales y métodos. Se solicitó a 501 pacientes con diabetes de tipo 2 en Barranquilla contestar la versión en español del DSAS 2, un cuestionario con indicadores sociodemográficos y clínicos, así como instrumentos de medición de la depresión, la autoeficacia y el estrés. Se hizo un análisis factorial (exploratorio y confirmatorio) para determinar la estructura interna del DSAS 2 en español y se usó el coeficiente alfa (α) para evaluar su confiabilidad. Además, se analizó la relación entre los puntajes del DSAS 2 y las otras variables estudiadas. Resultados. La estructura de tres factores (trato diferente-juicio, culpa y vergüenza) se ajustó adecuadamente a los datos (raíz del error cuadrático medio (RMSEA)=0,081, índice de ajuste comparativo (CIF)=0,959, índice de Tucker-Lewis (TLI)=0,95) y su confiabilidad fue buena (α=0,76). Se observaron correlaciones significativas del puntaje del DSAS 2 en español con la autoeficacia (rs=-0,37; p<0,001), el estrés (rs=0,24; p<0,001) y la presencia de síntomas depresivos (rs=0,1; p=0,021). Además, los puntajes de la escala mostraron variaciones asociadas a variables sociodemográficas y clínicas. Conclusiones. La versión en español presenta ciertas diferencias con la versión original del DSAS2, sin embargo, su validez y confiabilidad son suficientes y adecuadas para su uso en Colombia.

Propiedades psicométricas de la versión en español del Type 2 Diabetes Stigma Assessment Scale (DSAS 2) en población colombiana / Psychometric properties of the Spanish version of the Type 2 Diabetes Stigma Assessment Scale (DSAS 2) in a Colombian population

Introducción. El estigma se ha asociado negativamente al control metabólico y la calidad de vida de pacientes con diabetes de tipo 2. El cuestionario Diabetes Stigma Assesment Scale 2 (DSAS 2) fue diseñado para medir específicamente el estigma asociado en personas con este tipo de diabetes. Sin embargo, las propiedades psicométricas de su versión en español aún no han sido analizadas. Objetivo. Analizar la validez y confiabilidad de la versión en español del DSAS 2 en población colombiana. Materiales y métodos. Se solicitó a 501 pacientes con diabetes de tipo 2 en Barranquilla contestar la versión en español del DSAS 2, un cuestionario con indicadores sociodemográficos y clínicos, así como instrumentos de medición de la depresión, la autoeficacia y el estrés. Se hizo un análisis factorial (exploratorio y confirmatorio) para determinar la estructura interna del DSAS 2 en español y se usó el coeficiente alfa (α) para evaluar su confiabilidad. Además, se analizó la relación entre los puntajes del DSAS 2 y las otras variables estudiadas. Resultados. La estructura de tres factores (trato diferente-juicio, culpa y vergüenza) se ajustó adecuadamente a los datos (raíz del error cuadrático medio (RMSEA)=0,081, índice de ajuste comparativo (CIF)=0,959, índice de Tucker-Lewis (TLI)=0,95) y su confiabilidad fue buena (α=0,76). Se observaron correlaciones significativas del puntaje del DSAS 2 en español con la autoeficacia (rs=-0,37; p<0,001), el estrés (rs=0,24; p<0,001) y la presencia de síntomas depresivos (rs=0,1; p=0,021). Además, los puntajes de la escala mostraron variaciones asociadas a variables sociodemográficas y clínicas. Conclusiones. La versión en español presenta ciertas diferencias con la versión original del DSAS2, sin embargo, su validez y confiabilidad son suficientes y adecuadas para su uso en Colombia.

Introduction: The perception of stigma has been negatively associated with the metabolic control and quality of life in patients with type 2 diabetes. The Diabetes Stigma Assessment Scale 2 (DSAS 2) was designed to specifically measure the stigma associated with this type of diabetes. However, the psychometric properties of its Spanish version have not yet been addressed. Objective: To analyze the validity and reliability of the Spanish version of DSAS 2 in a Colombian population. Materials and methods: In total, 501 patients with type 2 diabetes from Barranquilla answered the Spanish version of DSAS 2, a questionnaire with sociodemographic and clinical indicators, as well as instruments to measure depression, self-efficacy, and stress. We performed a factor analysis (exploratory and confirmatory) to determine the internal structure of the DSAS 2 in Spanish and used the alpha coefficient (α) to evaluate its reliability. Additionally, we analyzed the relationship between the DSAS 2 scores and the other variables under study. Results: The three-factor structure (different treatment / judgment, guilt and shame) showed good fit to the data (RMSEA = 0.081, CFI = 0.959, TLI = 0.95) and good reliability (α = 0.76). Significant correlations of the scores of the DSAS 2 Spanish version were observed with self-efficacy (rs=-0.37, p<0.001), stress (rs =0.24 , p<0.001), and depression (rs=0.1, p=0.021). Besides, the scores showed variations associated with sociodemographic and clinical variables. Conclusions: The Spanish version showed certain differences compared with the original version of the DSAS2 but there was adequate evidence of its validity and reliability to be used in Colombia.

Single-cell Atlas of common variable immunodeficiency shows germinal center-associated epigenetic dysregulation in B-cell responses.

Common variable immunodeficiency (CVID), the most prevalent symptomatic primary immunodeficiency, displays impaired terminal B-cell differentiation and defective antibody responses. Incomplete genetic penetrance and ample phenotypic expressivity in CVID suggest the participation of additional pathogenic mechanisms. Monozygotic (MZ) twins discordant for CVID are uniquely valuable for studying the contribution of epigenetics to the disease. Here, we generate a single-cell epigenomics and transcriptomics census of naïve-to-memory B cell differentiation in a CVID-discordant MZ twin pair. Our analysis identifies DNA methylation, chromatin accessibility and transcriptional defects in memory B-cells mirroring defective cell-cell communication upon activation. These findings are validated in a cohort of CVID patients and healthy donors. Our findings provide a comprehensive multi-omics map of alterations in naïve-to-memory B-cell transition in CVID and indicate links between the epigenome and immune cell cross-talk. Our resource, publicly available at the Human Cell Atlas, gives insight into future diagnosis and treatments of CVID patients.

Pathogenic variants in the human m6A reader YTHDC2 are associated with primary ovarian insufficiency.

Primary ovarian insufficiency (POI) affects 1% of women and carries significant medical and psychosocial sequelae. Approximately 10% of POI has a defined genetic cause, with most implicated genes relating to biological processes involved in early fetal ovary development and function. Recently, Ythdc2, an RNA helicase and N6-methyladenosine reader, has emerged as a regulator of meiosis in mice. Here, we describe homozygous pathogenic variants in YTHDC2 in 3 women with early-onset POI from 2 families: c. 2567C>G, p.P856R in the helicase-associated (HA2) domain and c.1129G>T, p.E377*. We demonstrated that YTHDC2 is expressed in the developing human fetal ovary and is upregulated in meiotic germ cells, together with related meiosis-associated factors. The p.P856R variant resulted in a less flexible protein that likely disrupted downstream conformational kinetics of the HA2 domain, whereas the p.E377* variant truncated the helicase core. Taken together, our results reveal that YTHDC2 is a key regulator of meiosis in humans and pathogenic variants within this gene are associated with POI.

Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro.

The endometrium, the mucosal lining of the uterus, undergoes dynamic changes throughout the menstrual cycle in response to ovarian hormones. We have generated dense single-cell and spatial reference maps of the human uterus and three-dimensional endometrial organoid cultures. We dissect the signaling pathways that determine cell fate of the epithelial lineages in the lumenal and glandular microenvironments. Our benchmark of the endometrial organoids reveals the pathways and cell states regulating differentiation of the secretory and ciliated lineages both in vivo and in vitro. In vitro downregulation of WNT or NOTCH pathways increases the differentiation efficiency along the secretory and ciliated lineages, respectively. We utilize our cellular maps to deconvolute bulk data from endometrial cancers and endometriotic lesions, illuminating the cell types dominating in each of these disorders. These mechanistic insights provide a platform for future development of treatments for common conditions including endometriosis and endometrial carcinoma.

A Cross-Sectional Analysis of the Stigma Surrounding Type 2 Diabetes in Colombia.

Type 2 diabetes is a global epidemic, and many people feel stigmatized for having this disease. The stigma is a relevant barrier to diabetes management. However, evidence in this regard is scarce in Latin America. This study aimed to analyze the level of stigma surrounding type 2 diabetes in the Colombian population and its relationships with sociodemographic, clinical, psychosocial variables and behaviors related to management of the disease (self-management behaviors). This cross-sectional study included 501 Colombian adults with type 2 diabetes. We estimated the relation between stigma and selected variables through linear regression models. Additionally, we analyzed the mediator role of psychosocial variables in the relationship between stigma and self-management behaviors through structural equation models. A total of 16.4% of patients showed concerning levels of stigma. The time elapsed since diagnosis (ß = -0.23) and socioeconomic status (ß = -0.13) were significant predictors of the level of stigma. Stigma was negatively correlated with self-efficacy (ß = -0.36), self-esteem (ß = -0.37), and relationship with health care provider (ß = -0.46), and positively correlated with stress (ß = 0.23). Self-efficacy, self-esteem, and the relationships with health care providers had a mediation role in the relationship between stigma and self-management behaviors. These variables would be part of the mechanisms through which the perception of stigma harms self-management behaviors. The stigma of type 2 diabetes is frequent in the Colombian population and negatively associated with important aspects of disease management.

El estigma asociado a la diabetes: elementos conceptuales, mecanismos involucrados y desafíos / Diabetes Surrounding Stigma: Conceptual Issues, Mechanisms Involved and Challenges

RESUMEN La diabetes es una epidemia a nivel mundial. Los factores psicosociales han sido reconocidos como un elemento importante en el manejo y control de la enfermedad. El estigma asociado a la diabetes ha emergido recientemente como un nuevo factor psicosocial que afecta negativamente la salud de los pacientes con diabetes. Sin embargo, la evidencia reciente en torno a este fenómeno aún no ha sido sintetizada. Esta revisión narrativa de literatura aborda: (i) elementos conceptuales y epidemiológicos que contribuyen a la comprensión del fenómeno y su magnitud; (ii) los factores psicosociales, conductuales y fisiológicos involucrados en la relación entre el estigma asociado a la diabetes y los resultados en salud en pacientes con la enfermedad; (iii) desafíos y posibles áreas de investigación.

ABSTRACT Diabetes is a worldwide epidemic. Psychosocial factors have been recognized as an essential element in the management and control of this disease. The diabetes surrounding stigma has recently emerged as a new psychosocial factor that negatively affects patient's health. However, the recent evidence regarding this phenomenon has not been summarized. This narrative literature review address: (i) conceptual and epidemiological elements that contribute to understanding this phenomenon and its magnitude; (ii) the psychosocial, behavioral, and physiological factors involved in the relationship between diabetes stigma and health outcomes in patients with the disease; (iii) challenges and possible research areas.

The functional landscape of the human phosphoproteome.

Protein phosphorylation is a key post-translational modification regulating protein function in almost all cellular processes. Although tens of thousands of phosphorylation sites have been identified in human cells, approaches to determine the functional importance of each phosphosite are lacking. Here, we manually curated 112 datasets of phospho-enriched proteins, generated from 104 different human cell types or tissues. We re-analyzed the 6,801 proteomics experiments that passed our quality control criteria, creating a reference phosphoproteome containing 119,809 human phosphosites. To prioritize functional sites, we used machine learning to identify 59 features indicative of proteomic, structural, regulatory or evolutionary relevance and integrate them into a single functional score. Our approach identifies regulatory phosphosites across different molecular mechanisms, processes and diseases, and reveals genetic susceptibilities at a genomic scale. Several regulatory phosphosites were experimentally validated, including identifying a role in neuronal differentiation for phosphosites in SMARCC2, a member of the SWI/SNF chromatin-remodeling complex.

Benchmark and integration of resources for the estimation of human transcription factor activities.

The prediction of transcription factor (TF) activities from the gene expression of their targets (i.e., TF regulon) is becoming a widely used approach to characterize the functional status of transcriptional regulatory circuits. Several strategies and data sets have been proposed to link the target genes likely regulated by a TF, each one providing a different level of evidence. The most established ones are (1) manually curated repositories, (2) interactions derived from ChIP-seq binding data, (3) in silico prediction of TF binding on gene promoters, and (4) reverse-engineered regulons from large gene expression data sets. However, it is not known how these different sources of regulons affect the TF activity estimations and, thereby, downstream analysis and interpretation. Here we compared the accuracy and biases of these strategies to define human TF regulons by means of their ability to predict changes in TF activities in three reference benchmark data sets. We assembled a collection of TF-target interactions for 1541 human TFs and evaluated how different molecular and regulatory properties of the TFs, such as the DNA-binding domain, specificities, or mode of interaction with the chromatin, affect the predictions of TF activity. We assessed their coverage and found little overlap on the regulons derived from each strategy and better performance by literature-curated information followed by ChIP-seq data. We provide an integrated resource of all TF-target interactions derived through these strategies, with confidence scores, as a resource for enhanced prediction of TF activities.

Functional linkage of gene fusions to cancer cell fitness assessed by pharmacological and CRISPR-Cas9 screening.

Many gene fusions are reported in tumours and for most their role remains unknown. As fusions are used for diagnostic and prognostic purposes, and are targets for treatment, it is crucial to assess their function in cancer. To systematically investigate the role of fusions in tumour cell fitness, we utilized RNA-sequencing data from 1011 human cancer cell lines to functionally link 8354 fusion events with genomic data, sensitivity to >350 anti-cancer drugs and CRISPR-Cas9 loss-of-fitness effects. Established clinically-relevant fusions were identified. Overall, detection of functional fusions was rare, including those involving cancer driver genes, suggesting that many fusions are dispensable for tumour fitness. Therapeutically actionable fusions involving RAF1, BRD4 and ROS1 were verified in new histologies. In addition, recurrent YAP1-MAML2 fusions were identified as activators of Hippo-pathway signaling in multiple cancer types. Our approach discriminates functional fusions, identifying new drivers of carcinogenesis and fusions that could have clinical implications.

The modular network structure of the mutational landscape of Acute Myeloid Leukemia.

Acute myeloid leukemia (AML) is associated with the sequential accumulation of acquired genetic alterations. Although at diagnosis cytogenetic alterations are frequent in AML, roughly 50% of patients present an apparently normal karyotype (NK), leading to a highly heterogeneous prognosis. Due to this significant heterogeneity, it has been suggested that different molecular mechanisms may trigger the disease with diverse prognostic implications. We performed whole-exome sequencing (WES) of tumor-normal matched samples of de novo AML-NK patients lacking mutations in NPM1, CEBPA or FLT3-ITD to identify new gene mutations with potential prognostic and therapeutic relevance to patients with AML. Novel candidate-genes, together with others previously described, were targeted resequenced in an independent cohort of 100 de novo AML patients classified in the cytogenetic intermediate-risk (IR) category. A mean of 4.89 mutations per sample were detected in 73 genes, 35 of which were mutated in more than one patient. After a network enrichment analysis, we defined a single in silico model and established a set of seed-genes that may trigger leukemogenesis in patients with normal karyotype. The high heterogeneity of gene mutations observed in AML patients suggested that a specific alteration could not be as essential as the interaction of deregulated pathways.

Pathway-based dissection of the genomic heterogeneity of cancer hallmarks' acquisition with SLAPenrich.

Cancer hallmarks are evolutionary traits required by a tumour to develop. While extensively characterised, the way these traits are achieved through the accumulation of somatic mutations in key biological pathways is not fully understood. To shed light on this subject, we characterised the landscape of pathway alterations associated with somatic mutations observed in 4,415 patients across ten cancer types, using 374 orthogonal pathway gene-sets mapped onto canonical cancer hallmarks. Towards this end, we developed SLAPenrich: a computational method based on population-level statistics, freely available as an open source R package. Assembling the identified pathway alterations into sets of hallmark signatures allowed us to connect somatic mutations to clinically interpretable cancer mechanisms. Further, we explored the heterogeneity of these signatures, in terms of ratio of altered pathways associated with each individual hallmark, assuming that this is reflective of the extent of selective advantage provided to the cancer type under consideration. Our analysis revealed the predominance of certain hallmarks in specific cancer types, thus suggesting different evolutionary trajectories across cancer lineages. Finally, although many pathway alteration enrichments are guided by somatic mutations in frequently altered high-confidence cancer genes, excluding these driver mutations preserves the hallmark heterogeneity signatures, thus the detected hallmarks' predominance across cancer types. As a consequence, we propose the hallmark signatures as a ground truth to characterise tails of infrequent genomic alterations and identify potential novel cancer driver genes and networks.