Into the multiverse: Advances in single-cell multiomic profiling

Single-cell transcriptomic approaches have revolutionised the study of complex biological systems, with the routine measurement of gene expression in thousands of cells enabling construction of whole-organism cell atlases. However, the transcriptome is just one layer amongst many that coordinate to define cell type and state and, ultimately, function. In parallel with the widespread uptake of single-cell RNA-seq (scRNA-seq), there has been a rapid emergence of methods that enable multiomic profiling of individual cells, enabling parallel measurement of intercellular heterogeneity in the genome, epigenome, transcriptome, and proteomes. Linking measurements from each of these layers has the potential to reveal regulatory and functional mechanisms underlying cell behaviour in healthy development and disease

Transcriptional dynamics of induced pluripotent stem cell differentiation into β cells reveals full endodermal commitment and homology with human islets.

Abstract Background aims Induced pluripotent stem cells (iPSCs) have the capacity to generate β cells in vitro, but the differentiation is incomplete and generates a variable percentage of off-target cells. Single-cell RNA sequencing offers the possibility of characterizing the transcriptional dynamics throughout differentiation and determining the identity of the final differentiation product. Methods Single-cell transcriptomics data were obtained from four stages across differentiation of iPSCs into β cells and from human donor islets. Results Clustering analysis revealed that iPSCs undertake a full endoderm commitment, and the obtained endocrine pancreatic cells have high homology with mature islets. The iPSC-derived β cells were devoid of pluripotent residual cells, and the differentiation was pancreas-specific, as it did not generate ectodermal or mesodermal cells. Pseudotime trajectory identified a dichotomic endocrine/non-endocrine cell fate and distinct subgroups in the endocrine branch. Conclusions Future efforts to produce β cells from iPSCs must aim not only to improve the resulting endocrine cell but also to avoid differentiation into non-pancreatic endoderm cells

Enhancing clinical potential of liquid biopsy through a multi-omic approach: A systematic review

In the last years, liquid biopsy gained increasing clinical relevance for detecting and monitoring several cancer types, being minimally invasive, highly informative and replicable over time. This revolutionary approach can be complementary and may, in the future, replace tissue biopsy, which is still considered the gold standard for cancer diagnosis. “Classical” tissue biopsy is invasive, often cannot provide sufficient bioptic material for advanced screening, and can provide isolated information about disease evolution and heterogeneity. Recent literature highlighted how liquid biopsy is informative of proteomic, genomic, epigenetic, and metabolic alterations. These biomarkers can be detected and investigated using single-omic and, recently, in combination through multi-omic approaches. This review will provide an overview of the most suitable techniques to thoroughly characterize tumor biomarkers and their potential clinical applications, highlighting the importance of an integrated multi-omic, multi-analyte approach. Personalized medical investigations will soon allow patients to receive predictable prognostic evaluations, early disease diagnosis, and subsequent ad hoc treatments

Stima della portata della fistola artero-venosa mediante termodiluizione nei pazienti in emodialisi cronica: esperienza monocentrica.

Purpose: Vascular access surveillance in hemodialysis is today an important challenge for nephrologist. Low blood flow is a risk factor for development of thrombosis of native fistula or graft. The aim of the study is to evaluate the correspondence between flow measurement by thermodilution and Color Doppler, and to identify flow rate values using the Blood temperature monitor (BTM) method in the case of stenosis. Methods: We evaluated 29 patients on chronic hemodialysis. The evaluation of blood flow with BTM were performed during the first hour of the hemodialysis session. All patients underwent a color doppler of vascular access within 10 days from the BTM measurements. Results: The mean vascular access flow calculated with BTM resulted 1142 ± 700 ml/min and there was a correlation with color doppler data 1199 ± 644 ml/min (p=0,0001 r=0,829). The flow of patients with hemodynamically significant stenosis was 332 ± 92 ml/min with a minimum value of 270 ml/min and a maximum value of 440 ml/min. Conclusion: the correspondence between thermodilution and color doppler support the implementation of intradialitic evaluation of the vascular access blood flow with the BTM method. Thermodilution allows to identify earlier patients with high risk of vascular access failure and the need for further diagnostic and therapeutic investigations

Neural precursor cells tune striatal connectivity through the release of IGFBPL1

The adult brain retains over life endogenous neural stem/precursor cells (eNPCs) within the subventricular zone (SVZ). Whether or not these cells exert physiological functions is still unclear. In the present work, we provide evidence that SVZ-eNPCs tune structural, electrophysiological, and behavioural aspects of striatal function via secretion of insulin-like growth factor binding protein-like 1 (IGFBPL1). In mice, selective ablation of SVZ-eNPCs or selective abrogation of IGFBPL1 determined an impairment of striatal medium spiny neuron morphology, a higher failure rate in GABAergic transmission mediated by fast-spiking interneurons, and striatum-related behavioural dysfunctions. We also found IGFBPL1 expression in the human SVZ, foetal and induced-pluripotent stem cell-derived NPCs. Finally, we found a significant correlation between SVZ damage, reduction of striatum volume, and impairment of information processing speed in neurological patients. Our results highlight the physiological role of adult SVZ-eNPCs in supporting cognitive functions by regulating striatal neuronal activity

Analyzing genomic and epigenetic profiles in single cells by hybrid transposase (scGET-seq)

Summary: scGET-seq simultaneously profiles euchromatin and heterochromatin. scGET-seq exploits the concurrent action of transposase Tn5 and its hybrid form TnH, which targets H3K9me3 domains. Here we present a step-by-step protocol to profile single cells by scGET-seq using a 10× Chromium Controller. We describe steps for transposomes preparation and validation. We detail nuclei preparation and transposition, followed by encapsulation, library preparation, sequencing, and data analysis.For complete details on the use and execution of this protocol, please refer to Tedesco et al. (2022)1 and de Pretis and Cittaro (2022).2 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics