AntiSplodge: a neural-network-based RNA-profile deconvolution pipeline designed for spatial transcriptomics

With the current surge of spatial transcriptomics (ST) studies, researchers are exploring the deep interactive cell-play directly in tissues, in situ. However, with the current technologies, measurements consist of mRNA transcript profiles of mixed origin. Recently, applications have been proposed to tackle the deconvolution process, to gain knowledge about which cell types (SC) are found within. This is usually done by incorporating metrics from single-cell (SC) RNA, from similar tissues. Yet, most existing tools are cumbersome, and we found them hard to integrate and properly utilize. Therefore, we present (AntiSplodge), a simple feed-forward neural-network-based pipeline designed to effective deconvolute ST profiles by utilizing synthetic ST profiles derived from real-life SC datasets. (AntiSplodge) is designed to be easy, fast and intuitive while still being lightweight. To demonstrate (AntiSplodge), we deconvolute the human heart and verify correctness across time points. We further deconvolute the mouse brain, where spot patterns correctly follow that of the underlying tissue. In particular, for the hippocampus from where the cells originate. Furthermore, (AntiSplodge) demonstrates top of the line performance when compared to current state-of-the-art tools. Software availability: https://github.com/HealthML/AntiSplodge/

Phrenologyand the Insanity Defence: Medical Jurisprudence in the McNaughtan Trial

This thesis argues that phrenology shaped the defence argument in the McNaughtan trial. The role of this now-discredited science exemplifies the negotiation of scientific, legal and lay knowledge in the early nineteenth century, at a time when science was challenging the primacy of lay understandings of insanity. Phrenological ideas allowed the defence to privilege medical opinion over lay opinion, and propose a model of the mind that could account for McNaughtan’s insanity. This was possible because the medical and professional communities accepted some elements of the science. They applied these principles when explaining and verifying insanity in a courtroom setting

Cells and gene expression programs in the adult human heart

Cardiovascular disease is the leading cause of death worldwide. Advanced insights into disease mechanisms and strategies to improve therapeutic opportunities require deeper understanding of the molecular processes of the normal heart. Knowledge of the full repertoire of cardiac cells and their gene expression profiles is a fundamental first step in this endeavor. Here, using large-scale single cell and nuclei transcriptomic profiling together with state-of-the-art analytical techniques, we characterise the adult human heart cellular landscape covering six anatomical cardiac regions (left and right atria and ventricles, apex and interventricular septum). Our results highlight the cellular heterogeneity of cardiomyocytes, pericytes and fibroblasts, revealing distinct subsets in the atria and ventricles indicative of diverse developmental origins and specialized properties. Further we define the complexity of the cardiac vascular network which includes clusters of arterial, capillary, venous, lymphatic endothelial cells and an atrial-enriched population. By comparing cardiac cells to skeletal muscle and kidney, we identify cardiac tissue resident macrophage subsets with transcriptional signatures indicative of both inflammatory and reparative phenotypes. Further, inference of cell-cell interactions highlight a macrophage-fibroblast-cardiomyocyte network that differs between atria and ventricles, and compared to skeletal muscle. We expect this reference human cardiac cell atlas to advance mechanistic studies of heart homeostasis and disease

Titin-truncating variants affect heart function in disease cohorts and the general population

Titin-truncating variants (TTNtv) commonly cause dilated cardiomyopathy (DCM). TTNtv are also encountered in ~1% of the general population, where they may be silent, perhaps reflecting allelic factors. To better understand TTNtv, we integrated TTN allelic series, cardiac imaging and genomic data in humans and studied rat models with disparate TTNtv. In patients with DCM, TTNtv throughout titin were significantly associated with DCM. Ribosomal profiling in rat showed the translational footprint of premature stop codons in Ttn, TTNtv-position-independent nonsense-mediated degradation of the mutant allele and a signature of perturbed cardiac metabolism. Heart physiology in rats with TTNtv was unremarkable at baseline but became impaired during cardiac stress. In healthy humans, machine-learning-based analysis of high-resolution cardiac imaging showed TTNtv to be associated with eccentric cardiac remodeling. These data show that TTNtv have molecular and physiological effects on the heart across species, with a continuum of expressivity in health and disease

The challenges of research data management in cardiovascular science: a DGK and DZHK position paper-executive summary

The sharing and documentation of cardiovascular research data are essential for efficient use and reuse of data, thereby aiding scientific transparency, accelerating the progress of cardiovascular research and healthcare, and contributing to the reproducibility of research results. However, challenges remain. This position paper, written on behalf of and approved by the German Cardiac Society and German Centre for Cardiovascular Research, summarizes our current understanding of the challenges in cardiovascular research data management (RDM). These challenges include lack of time, awareness, incentives, and funding for implementing effective RDM; lack of standardization in RDM processes; a need to better identify meaningful and actionable data among the increasing volume and complexity of data being acquired; and a lack of understanding of the legal aspects of data sharing. While several tools exist to increase the degree to which data are findable, accessible, interoperable, and reusable (FAIR), more work is needed to lower the threshold for effective RDM not just in cardiovascular research but in all biomedical research, with data sharing and reuse being factored in at every stage of the scientific process. A culture of open science with FAIR research data should be fostered through education and training of early-career and established research professionals. Ultimately, FAIR RDM requires permanent, long-term effort at all levels. If outcomes can be shown to be superior and to promote better (and better value) science, modern RDM will make a positive difference to cardiovascular science and practice. The full position paper is available in the supplementary materials

Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells

The COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, creates an urgent need for identifying molecular mechanisms that mediate viral entry, propagation, and tissue pathology. Cell membrane bound angiotensin-converting enzyme 2 (ACE2) and associated proteases, transmembrane protease serine 2 (TMPRSS2) and Cathepsin L (CTSL), were previously identified as mediators of SARS-CoV2 cellular entry. Here, we assess the cell type-specific RNA expression of ACE2, TMPRSS2, and CTSL through an integrated analysis of 107 single-cell and single-nucleus RNA-Seq studies, including 22 lung and airways datasets (16 unpublished), and 85 datasets from other diverse organs. Joint expression of ACE2 and the accessory proteases identifies specific subsets of respiratory epithelial cells as putative targets of viral infection in the nasal passages, airways, and alveoli. Cells that co-express ACE2 and proteases are also identified in cells from other organs, some of which have been associated with COVID-19 transmission or pathology, including gut enterocytes, corneal epithelial cells, cardiomyocytes, heart pericytes, olfactory sustentacular cells, and renal epithelial cells. Performing the first meta-analyses of scRNA-seq studies, we analyzed 1,176,683 cells from 282 nasal, airway, and lung parenchyma samples from 164 donors spanning fetal, childhood, adult, and elderly age groups, associate increased levels of ACE2, TMPRSS2, and CTSL in specific cell types with increasing age, male gender, and smoking, all of which are epidemiologically linked to COVID-19 susceptibility and outcomes. Notably, there was a particularly low expression of ACE2 in the few young pediatric samples in the analysis. Further analysis reveals a gene expression program shared by ACE2(+)TMPRSS2(+) cells in nasal, lung and gut tissues, including genes that may mediate viral entry, subtend key immune functions, and mediate epithelial-macrophage cross-talk. Amongst these are IL6, its receptor and co-receptor, IL1R, TNF response pathways, and complement genes. Cell type specificity in the lung and airways and smoking effects were conserved in mice. Our analyses suggest that differences in the cell type-specific expression of mediators of SARS-CoV-2 viral entry may be responsible for aspects of COVID-19 epidemiology and clinical course, and point to putative molecular pathways involved in disease susceptibility and pathogenesis

Supplements to: A naturalistic cohort study of first-episode schizophrenia spectrum disorder: a description of the early phase of illness in the PSYSCAN cohort

Suppl. Figure 1. Percentage of FES patients in symptomatic remission throughout the study.Suppl. Figure 2. Percentage of FES patients in functional remission throughout the study.Suppl. Figure 3. Clustered boxplot displaying the mean depression scores per time point (measured using the Hamilton Depression Rating Scale) in the subgroup meeting criteria for a depressive episode at baseline (assessed through the SCID-I) versus the subgroup without a depressive episode at baseline.Suppl. Table 1. Baseline demographics and clinical characteristics of study completers and drop-outs.Suppl. Table 2. Number of patients in symptomatic and functional remission throughout the period of follow-up.Suppl. Table 3. Generalized linear mixed models: pairwise contrasts for symptomatic and functional remission.Suppl. Table 4. Linear mixed models: estimated marginal means for PANSS, GAF, SOFAS, CGI, GF-S, GF-R and HAM-D.Suppl. Table 5. Linear mixed models: estimates of fixed effect time on PANSS, GAF, SOFAS, CGI, GF-S, GF-R and HAM-D.Suppl. Table 6. Number of patients admitted to the hospital since the previous visit due to psychotic symptoms and due to psychiatric reasons in general.Suppl. Table 7. Substances used at least once in the past three months (WHO-ASSIST).Suppl. Table 8. Number of patients reporting daily or almost daily substance use in the past three months, separated per time point and substance category (WHO-ASSIST).Suppl. Table 9. Number of patients reporting daily or almost daily substance use in the past three months, separated for the group of symptomatic remitters and non-remitters at month 12.Suppl. Table 10. Baseline demographics and clinical characteristics of symptomatic remitters and non-remitters at month 12.Suppl. Table 11. Summary of sociodemographics and baseline clinical characteristics of FES participants, separated per country.Suppl. Table 12. Number of FES patients in symptomatic remission throughout the period of follow-up, separated per country.Suppl. Table 13. Number of FES patients in functional remission throughout the period of follow-up, separated per country.Suppl. Table 14. Number of FES patients admitted to the hospital for psychiatric reasons throughout the period of follow-up, separated per country.Suppl. Table 15. Number of FES patients admitted to the hospital for psychosis throughout the period of follow-up, separated per country.Suppl. Table 16. Number of FES patients using antipsychotic medication throughout the period of follow-up, separated per country.Suppl. Table 17. Overview of subjects not meeting eligibility criteria.Suppl. Table 18. Number of patients in symptomatic and functional remission throughout the period of follow-up when using alternative definitions.Suppl. Table 19. Generalized linear mixed models: pairwise contrasts for symptomatic and functional remission when using alternative definitions.Peer reviewe

A naturalistic cohort study of first-episode schizophrenia spectrum disorder: A description of the early phase of illness in the PSYSCAN cohort

[Background] We examined the course of illness over a 12-month period in a large, international multi-center cohort of people with a first-episode schizophrenia spectrum disorder (FES) in a naturalistic, prospective study (PSYSCAN).[Method] Patients with a first episode of schizophrenia, schizoaffective disorder (depressive type) or schizophreniform disorder were recruited at 16 institutions in Europe, Israel and Australia. Participants (N = 304) received clinical treatment as usual throughout the study.[Results] The mean age of the cohort was 24.3 years (SD = 5.6), and 67 % were male. At baseline, participants presented with a range of intensities of psychotic symptoms, 80 % were taking antipsychotic medication, 68 % were receiving psychological treatment, with 46.5 % in symptomatic remission. The mean duration of untreated psychosis was 6.2 months (SD = 17.0). After one year, 67 % were in symptomatic remission and 61 % were in functional remission, but 31 % had been readmitted to hospital at some time after baseline. In the cohort as a whole, depressive symptoms remained stable over the follow-up period. In patients with a current depressive episode at baseline, depressive symptoms slightly improved. Alcohol, tobacco and cannabis were the most commonly used substances, with daily users of cannabis ranging between 9 and 11 % throughout the follow-up period.[Conclusions] This study provides valuable insight into the early course of a broad range of clinical and functional aspects of illness in FES patients in routine clinical practice.PSYSCAN was supported as part of the European Funding 7th Framework Programme (grant number 603196).Peer reviewe