Integrating single-cell transcriptomics with cellular phenotypes: cell morphology, Ca2+ imaging and electrophysiology.

I review recent technological advancements in coupling single-cell transcriptomics with cellular phenotypes including morphology, calcium signaling, and electrophysiology. Single-cell RNA sequencing (scRNAseq) has revolutionized cell type classifications by capturing the transcriptional diversity of cells. A new wave of methods to integrate scRNAseq and biophysical measurements is facilitating the linkage of transcriptomic data to cellular function, which provides physiological insight into cellular states. I briefly discuss critical factors of these phenotypical characterizations such as timescales, information content, and analytical tools. Dedicated sections focus on the integration with cell morphology, calcium imaging, and electrophysiology (patch-seq), emphasizing their complementary roles. I discuss their application in elucidating cellular states, refining cell type classifications, and uncovering functional differences in cell subtypes. To illustrate the practical applications and benefits of these methods, I highlight their use in tissues with excitable cell-types such as the brain, pancreatic islets, and the retina. The potential of combining functional phenotyping with spatial transcriptomics for a detailed mapping of cell phenotypes in situ is explored. Finally, I discuss open questions and future perspectives, emphasizing the need for a shift towards broader accessibility through increased throughput.

Ballistic long bone fracture pattern: an experimental study.

When dealing with badly preserved cadavers or skeletal human remains, the assessment of death circumstances remains challenging. When forensic evidence cannot be taken from the skin and soft tissue, the information may only be deduced from more resistant elements such as bone. Compared to cranial gunshot injuries, reliable data on ballistic long bone trauma remains scarce. This study aims to define ballistic fracture characteristics in human long bones. The shaft of 16 femurs and 13 humeri from body donors was perpendicularly shot with a 9-mm Luger full metal jacket bullet at an impact velocity of 360 m/s from a distance of 2 m. Some bones were embedded in Clear Ballistics Gel®, and some were shot without soft tissue simulant in order to better visualise the fracture propagation on the high-speed camera. The fractures were examined macroscopically and compared between the sample groups. We consistently found comminuted fractures with a stellate pattern. Fracture details were classified into entrance, exit and general characteristics. For some traits, we detected different occurrence values in the group comparison. The results indicate that some of the traits depend on bone properties such as shaft diameter, bone length and cortical thickness. The presence of ballistic gel also influenced some fracture traits, emphasising the relevance of soft tissue simulant in osseous gunshot experiments. This study revealed new insights in the detailed fracture pattern of human long bones. These may serve as guidelines for the identification and reconstruction of gunshot trauma in human long bones.

Endoscopic management of gastric neuroendocrine tumors: an analysis of 50 cases.

Of 50 cases gastric neuroendocrine tumors, in 30 (60%) endoscopic treatment, with relapse rate of 25%, perforation 3,6% and bleeding 7,1%.

Integrating genetics with single-cell multiomic measurements across disease states identifies mechanisms of beta cell dysfunction in type 2 diabetes.

Dysfunctional pancreatic islet beta cells are a hallmark of type 2 diabetes (T2D), but a comprehensive understanding of the underlying mechanisms, including gene dysregulation, is lacking. Here we integrate information from measurements of chromatin accessibility, gene expression and function in single beta cells with genetic association data to nominate disease-causal gene regulatory changes in T2D. Using machine learning on chromatin accessibility data from 34 nondiabetic, pre-T2D and T2D donors, we identify two transcriptionally and functionally distinct beta cell subtypes that undergo an abundance shift during T2D progression. Subtype-defining accessible chromatin is enriched for T2D risk variants, suggesting a causal contribution of subtype identity to T2D. Both beta cell subtypes exhibit activation of a stress-response transcriptional program and functional impairment in T2D, which is probably induced by the T2D-associated metabolic environment. Our findings demonstrate the power of multimodal single-cell measurements combined with machine learning for characterizing mechanisms of complex diseases.

Integration of single-cell multiomic measurements across disease states with genetics identifies mechanisms of beta cell dysfunction in type 2 diabetes.

Altered function and gene regulation of pancreatic islet beta cells is a hallmark of type 2 diabetes (T2D), but a comprehensive understanding of mechanisms driving T2D is still missing. Here we integrate information from measurements of chromatin activity, gene expression and function in single beta cells with genetic association data to identify disease-causal gene regulatory changes in T2D. Using machine learning on chromatin accessibility data from 34 non-diabetic, pre-T2D and T2D donors, we robustly identify two transcriptionally and functionally distinct beta cell subtypes that undergo an abundance shift in T2D. Subtype-defining active chromatin is enriched for T2D risk variants, suggesting a causal contribution of subtype identity to T2D. Both subtypes exhibit activation of a stress-response transcriptional program and functional impairment in T2D, which is likely induced by the T2D-associated metabolic environment. Our findings demonstrate the power of multimodal single-cell measurements combined with machine learning for identifying mechanisms of complex diseases.

Documento de consenso de la Sociedad Española de Endoscopia Digestiva sobre SpyGlass-DS / SEED Consensus Document on SpyGlass-DS

La colangiopancreatografía retrógrada endoscópica (CPRE) es la técnica de elección para el tratamiento de la patología biliopancreática. Sin embargo, las imágenes fluoroscópicas no siempre permiten un diagnóstico adecuado. Por otra parte, algunos cálculos de gran tamaño no se pueden extraer con los métodos habituales. En estas situaciones, la colangioscopia ha mostrado ser una herramienta fundamental para el diagnóstico de las estenosis biliares y el tratamiento de los cálculos de gran tamaño. Además, su papel en la patología pancreática está en creciente aumento. El desarrollo de un colangioscopio de un único operador y desechable ha permitido expandir la técnica entre buena parte de los hospitales que realizan CPRE. Por este motivo, la Sociedad Española de Endoscopia Digestiva ha desarrollado este documento de consenso sobre la utilización del colangioscopio Spyglass-DS. El documento ha sido elaborado por un grupo de endoscopistas expertos en colangioscopia, revisando la evidencia científica de las principales indicaciones actuales de la colangiopancreatoscopia.(AU)

Endoscopic retrograde cholangiopancreatography (ERCP) is the technique of choice for the treatment of biliopancreatic pathology. However, fluoroscopic imaging does not always allow an adequate diagnosis. On the other hand, some large stones cannot be removed by the usual methods. In these situations, cholangioscopy has proven to be an essential tool for the diagnosis of biliary strictures and the treatment of large stones. Its role in pancreatic pathology is also increasing. The development of a single-operator, disposable cholangioscope has made it possible to expand the technique to a large number of hospitals that perform ERCP. For this reason, the Spanish Society of Digestive Endoscopy has developed this consensus document on the use of the Spyglass-DS cholangioscope. The document has been prepared by a group of endoscopists with expertise in cholangioscopy, reviewing the scientific evidence on the main current indications for cholangiopancreatoscopy.(AU)

SEED Consensus Document on SpyGlass-DS. / Documento de consenso de la Sociedad Española de Endoscopia Digestiva sobre SpyGlass-DS.

Endoscopic retrograde cholangiopancreatography (ERCP) is the technique of choice for the treatment of biliopancreatic pathology. However, fluoroscopic imaging does not always allow an adequate diagnosis. On the other hand, some large stones cannot be removed by the usual methods. In these situations, cholangioscopy has proven to be an essential tool for the diagnosis of biliary strictures and the treatment of large stones. Its role in pancreatic pathology is also increasing. The development of a single-operator, disposable cholangioscope has made it possible to expand the technique to a large number of hospitals that perform ERCP. For this reason, the Spanish Society of Digestive Endoscopy has developed this consensus document on the use of the Spyglass-DS cholangioscope. The document has been prepared by a group of endoscopists with expertise in cholangioscopy, reviewing the scientific evidence on the main current indications for cholangiopancreatoscopy.

A simple score to predict early severe infections in patients with newly diagnosed multiple myeloma.

Infections remain a common complication in patients with multiple myeloma (MM) and are associated with morbidity and mortality. A risk score to predict the probability of early severe infection could help to identify the patients that would benefit from preventive measures. We undertook a post hoc analysis of infections in four clinical trials from the Spanish Myeloma Group, involving a total of 1347 patients (847 transplant candidates). Regarding the GEM2010 > 65 trial, antibiotic prophylaxis was mandatory, so we excluded it from the final analysis. The incidence of severe infection episodes within the first 6 months was 13.8%, and majority of the patients experiencing the first episode before 4 months (11.1%). 1.2% of patients died because of infections within the first 6 months (1% before 4 months). Variables associated with increased risk of severe infection in the first 4 months included serum albumin ≤30 g/L, ECOG > 1, male sex, and non-IgA type MM. A simple risk score with these variables facilitated the identification of three risk groups with different probabilities of severe infection within the first 4 months: low-risk (score 0-2) 8.2%; intermediate-risk (score 3) 19.2%; and high-risk (score 4) 28.3%. Patients with intermediate/high risk could be candidates for prophylactic antibiotic therapies.

Predictive RNA profiles for early and very early spontaneous preterm birth.

BACKGROUND: Spontaneous preterm birth remains the main driver of childhood morbidity and mortality. Because of an incomplete understanding of the molecular pathways that result in spontaneous preterm birth, accurate predictive markers and target therapeutics remain elusive. OBJECTIVE: This study sought to determine if a cell-free RNA profile could reveal a molecular signature in maternal blood months before the onset of spontaneous preterm birth. STUDY DESIGN: Maternal samples (n=242) were obtained from a prospective cohort of individuals with a singleton pregnancy across 4 clinical sites at 12-24 weeks (nested case-control; n=46 spontaneous preterm birth <35 weeks and n=194 term controls). Plasma was processed via a next-generation sequencing pipeline for cell-free RNA using the Mirvie RNA platform. Transcripts that were differentially expressed in next-generation sequencing cases and controls were identified. Enriched pathways were identified in the Reactome database using overrepresentation analysis. RESULTS: Twenty five transcripts associated with an increased risk of spontaneous preterm birth were identified. A logistic regression model was developed using these transcripts to predict spontaneous preterm birth with an area under the curve =0.80 (95% confidence interval, 0.72-0.87) (sensitivity=0.76, specificity=0.72). The gene discovery and model were validated through leave-one-out cross-validation. A unique set of 39 genes was identified from cases of very early spontaneous preterm birth (<25 weeks, n=14 cases with time to delivery of 2.5±1.8 weeks); a logistic regression classifier on the basis of these genes yielded an area under the curve=0.76 (95% confidence interval, 0.63-0.87) in leave-one-out cross validation. Pathway analysis for the transcripts associated with spontaneous preterm birth revealed enrichment of genes related to collagen or the extracellular matrix in those who ultimately had a spontaneous preterm birth at <35 weeks. Enrichment for genes in insulin-like growth factor transport and amino acid metabolism pathways were associated with spontaneous preterm birth at <25 weeks. CONCLUSION: Second trimester cell-free RNA profiles in maternal blood provide a noninvasive window to future occurrence of spontaneous preterm birth. The systemic finding of changes in collagen and extracellular matrix pathways may serve to identify individuals at risk for premature cervical remodeling, with growth factor and metabolic pathways implicated more often in very early spontaneous preterm birth. The use of cell-free RNA profiles has the potential to accurately identify those at risk for spontaneous preterm birth by revealing the underlying pathophysiology, creating an opportunity for more targeted therapeutics and effective interventions.

Heterogenous impairment of α cell function in type 2 diabetes is linked to cell maturation state.

In diabetes, glucagon secretion from pancreatic α cells is dysregulated. The underlying mechanisms, and whether dysfunction occurs uniformly among cells, remain unclear. We examined α cells from human donors and mice using electrophysiological, transcriptomic, and computational approaches. Rising glucose suppresses α cell exocytosis by reducing P/Q-type Ca2+ channel activity, and this is disrupted in type 2 diabetes (T2D). Upon high-fat feeding of mice, α cells shift toward a "ß cell-like" electrophysiological profile in concert with indications of impaired identity. In human α cells we identified links between cell membrane properties and cell surface signaling receptors, mitochondrial respiratory chain complex assembly, and cell maturation. Cell-type classification using machine learning of electrophysiology data demonstrated a heterogenous loss of "electrophysiologic identity" in α cells from donors with type 2 diabetes. Indeed, a subset of α cells with impaired exocytosis is defined by an enrichment in progenitor and lineage markers and upregulation of an immature transcriptomic phenotype, suggesting important links between α cell maturation state and dysfunction.

RNA profiles reveal signatures of future health and disease in pregnancy.

Maternal morbidity and mortality continue to rise, and pre-eclampsia is a major driver of this burden1. Yet the ability to assess underlying pathophysiology before clinical presentation to enable identification of pregnancies at risk remains elusive. Here we demonstrate the ability of plasma cell-free RNA (cfRNA) to reveal patterns of normal pregnancy progression and determine the risk of developing pre-eclampsia months before clinical presentation. Our results centre on comprehensive transcriptome data from eight independent prospectively collected cohorts comprising 1,840 racially diverse pregnancies and retrospective analysis of 2,539 banked plasma samples. The pre-eclampsia data include 524 samples (72 cases and 452 non-cases) from two diverse independent cohorts collected 14.5 weeks (s.d., 4.5 weeks) before delivery. We show that cfRNA signatures from a single blood draw can track pregnancy progression at the placental, maternal and fetal levels and can robustly predict pre-eclampsia, with a sensitivity of 75% and a positive predictive value of 32.3% (s.d., 3%), which is superior to the state-of-the-art method2. cfRNA signatures of normal pregnancy progression and pre-eclampsia are independent of clinical factors, such as maternal age, body mass index and race, which cumulatively account for less than 1% of model variance. Further, the cfRNA signature for pre-eclampsia contains gene features linked to biological processes implicated in the underlying pathophysiology of pre-eclampsia.

Combinatorial transcription factor profiles predict mature and functional human islet α and ß cells.

Islet-enriched transcription factors (TFs) exert broad control over cellular processes in pancreatic α and ß cells, and changes in their expression are associated with developmental state and diabetes. However, the implications of heterogeneity in TF expression across islet cell populations are not well understood. To define this TF heterogeneity and its consequences for cellular function, we profiled more than 40,000 cells from normal human islets by single-cell RNA-Seq and stratified α and ß cells based on combinatorial TF expression. Subpopulations of islet cells coexpressing ARX/MAFB (α cells) and MAFA/MAFB (ß cells) exhibited greater expression of key genes related to glucose sensing and hormone secretion relative to subpopulations expressing only one or neither TF. Moreover, all subpopulations were identified in native pancreatic tissue from multiple donors. By Patch-Seq, MAFA/MAFB-coexpressing ß cells showed enhanced electrophysiological activity. Thus, these results indicate that combinatorial TF expression in islet α and ß cells predicts highly functional, mature subpopulations.

A New Hypothesis for Type 1 Diabetes Risk: The At-Risk Allele at rs3842753 Associates With Increased Beta-Cell INS Messenger RNA in a Meta-Analysis of Single-Cell RNA-Sequencing Data.

OBJECTIVES: Type 1 diabetes is characterized by the autoimmune destruction of insulin-secreting beta cells. Genetic variants upstream at the insulin (INS) locus contribute to ∼10% of type 1 diabetes heritable risk. Previous studies showed an association between rs3842753 C/C genotype and type 1 diabetes susceptibility, but the molecular mechanisms remain unclear. To date, no large-scale studies have looked at the effect of genetic variation at rs3842753 on INS mRNA at the single-cell level. METHODS: We aligned all human islet single-cell RNA sequencing data sets available to us in year 2020 to the reference genome GRCh38.98 and genotyped rs3842753, integrating 2,315 ß cells and 1,223 ß-like cells from 13 A/A protected donors, 23 A/C heterozygous donors and 35 C/C at-risk donors, including adults without diabetes and with type 2 diabetes. RESULTS: INS expression mean and variance were significantly higher in single ß cells from females compared with males. On comparing across ß cells and ß-like cells, we found that rs3842753 C‒containing cells (either homozygous or heterozygous) had the highest INS expression. We also found that ß cells with the rs3842753 C allele had significantly higher endoplasmic reticulum stress marker gene expression compared with the A/A homozygous genotype. CONCLUSIONS: These findings support the emerging concept that inherited risk of type 1 diabetes may be associated with inborn, persistent elevated insulin production, which may lead to ß-cell endoplasmic reticulum stress and fragility.

Microplastics from headwaters to tap water: occurrence and removal in a drinking water treatment plant in Barcelona Metropolitan area (Catalonia, NE Spain).

Nowadays, the presence of microplastics in drinking water is of concern worldwide due to potential impacts on human health. This paper has examined the presence of microplastics along the Llobregat river basin (Catalonia, Spain) and studied their behaviour and elimination along the drinking water treatment plant (DWTP). Due to different water composition, different sampling and sample preparation protocols were used to determine microplastics from river water and in the DWTP. Identification of microplastics of size range from 20 µm to 5 mm was performed by fourier-transform infrared spectroscopy (FTIR). Microplastics were detected in 5 out of 7 points along the Llobregat basin, with concentrations ranging between non-detected and 3.60 microplastics/L. In the intake of the DWTP, the mean concentration was 0.96 ± 0.46 microplastics/L (n=5), with a predominance of polyester (PES) and polypropylene (PP) and at the outlet the mean concentration was of 0.06 ± 0.04 microplastics/L with an overall removal efficiency of 93 ± 5%. Sand filtration was identified as the key stage in microplastic removal (78 ± 9%). Furthermore, the results showed that ultrafiltration/reverse osmosis (advanced treatment) is more effective for microplastic removal than ozonation/carbon filtration stage (upgraded conventional treatment). In addition, a preliminary migration test of the different materials used in the DWTP has been performed to identify potential sources of microplastics in each treatment step.

Patch-Seq Links Single-Cell Transcriptomes to Human Islet Dysfunction in Diabetes.

Impaired function of pancreatic islet cells is a major cause of metabolic dysregulation and disease in humans. Despite this, it remains challenging to directly link physiological dysfunction in islet cells to precise changes in gene expression. Here we show that single-cell RNA sequencing combined with electrophysiological measurements of exocytosis and channel activity (patch-seq) can be used to link endocrine physiology and transcriptomes at the single-cell level. We collected 1,369 patch-seq cells from the pancreata of 34 human donors with and without diabetes. An analysis of function and gene expression networks identified a gene set associated with functional heterogeneity in ß cells that can be used to predict electrophysiology. We also report transcriptional programs underlying dysfunction in type 2 diabetes and extend this approach to cryopreserved cells from donors with type 1 diabetes, generating a valuable resource for understanding islet cell heterogeneity in health and disease.

Molecular and genetic regulation of pig pancreatic islet cell development.

Reliance on rodents for understanding pancreatic genetics, development and islet function could limit progress in developing interventions for human diseases such as diabetes mellitus. Similarities of pancreas morphology and function suggest that porcine and human pancreas developmental biology may have useful homologies. However, little is known about pig pancreas development. To fill this knowledge gap, we investigated fetal and neonatal pig pancreas at multiple, crucial developmental stages using modern experimental approaches. Purification of islet ß-, α- and δ-cells followed by transcriptome analysis (RNA-seq) and immunohistology identified cell- and stage-specific regulation, and revealed that pig and human islet cells share characteristic features that are not observed in mice. Morphometric analysis also revealed endocrine cell allocation and architectural similarities between pig and human islets. Our analysis unveiled scores of signaling pathways linked to native islet ß-cell functional maturation, including evidence of fetal α-cell GLP-1 production and signaling to ß-cells. Thus, the findings and resources detailed here show how pig pancreatic islet studies complement other systems for understanding the developmental programs that generate functional islet cells, and that are relevant to human pancreatic diseases.

Interferencias de las alucinaciones auditivas verbales recurrentes sobre el rendimiento en una tarea de shadowing (sombreado) en la esquizofrenia / No disponible

No disponible

Pomalidomide-dexamethasone for treatment of soft-tissue plasmacytomas in patients with relapsed / refractory multiple myeloma.

OBJECTIVE: The presence of plasmacytomas (Ps) in patients with multiple myeloma (MM) is associated with a poor outcome, both in patients treated conventionally and in patients treated with novel agents. Two types of plasmacytomas have being recognized: paraskeletal plasmacytomas (PPs) and extramedullary plasmacytomas (EMPs), being the incidence of EMPs lower but with worse prognosis. Our aim has been to analyze the efficacy of the pomalidomide-dexamethasone combination in this patient profile. METHOD: In the present study, the efficacy of pomalidomide and dexamethasone in 21 patients from nine hospitals of Catalonia (Spain), with relapsed or refractory MM and Ps, was analyzed. For this purpose, we describe the evolution of paraprotein in serum and urine and the size of plasmacytomas during treatment with pomalidomide-dexamethasone. RESULTS: While 34% of the patients achieved a paraprotein response, only two patients with PPs (9%) responded (RC and PR). There were no responses among patients with EMPs. The median progression-free survival from the start of treatment with pomalidomide/dexamethasone was only 1.7 months and the median overall survival of 4.5 months. CONCLUSION: In conclusion, pomalidomide and dexamethasone has limited efficacy in patients with advanced MM and soft-tissue plasmacytomas.