Biology subjects

Tosti, L.

Publications and source records attributed to Tosti, L..

5 recordsLinked to original sources

bioRxiv2025

Latent plasticity of the human pancreas across development, health, and disease.

The pancreas plays a central role in major human diseases, yet our understanding of its cellular diversity and plasticity remains incomplete. Here, we present a single-cell multiomics atlas of the human pancreas, profiling over four million cells and nuclei from 57 donors across fetal development, adult homeostasis, and type 2 diabetes (T2D). Integrating sc/snRNA-seq, snATAC-seq, VASA-seq, spatial transcriptomics (Xenium), and multiplexed proteomics (CODEX), we resolve gene expression, chromatin accessibility, and spatial organization at high resolution. We identify transcriptionally plastic centroacinar-like cells (pCACs) in adults with fetal-like features, delineate endocrine and exocrine lineage trajectories during development, and uncover HNF1A-defined beta cell epigenetic states. In T2D, we observe shifts in beta cell subtypes and altered regulatory programs. Glucose perturbation of healthy islets reveals cell-type-specific adaptation and stress responses. This atlas provides a foundational framework to understand pancreas biology and the role of cellular plasticity in regeneration and disease.

genomics↗

bioRxiv2024

Epigenomic profiling of active regulatory elements by enrichment of unmodified CpG dinucleotides

Current approaches for the study of DNA methylation and other modified bases focus on the modified fraction of the genome and are particularly well-suited to the detection of DNA hypermethylation. However, the study of hypomethylation (loss of DNA methylation), which is typically associated with markers of active chromatin, has been largely overlooked, in part, due to the lack of a suitable methodology. We present an enrichment-based and bisulfite-free approach for epigenomic profiling named "Active-Seq" (Azide Click Tagging for In Vitro Epigenomic sequencing) that achieves genome-wide profiling of DNA, by enriching for non-modified CpG sites using a mutated methyltransferase enzyme. We show that the genomic regions enriched by Active-Seq overlap with promoters, enhancers and partially methylated domains, all of which have had their methylation status linked to the development and progression of diseases. Active-Seq is a fast epigenetic profiling platform with a simple and streamlined workflow, performed in tandem with sequencing library preparation. The enzymatic chemistry is non-damaging toward the DNA which is critical for working with low concentration DNA input and will facilitate the future development of multiomics assays. We demonstrate robust and reproducible performance of Active-Seq using low DNA input in cell lines, liquid biopsies (cell-free DNA, cfDNA) and formalin-fixed paraffin embedded (FFPE) tissue.

genomics↗

bioRxiv2022

Transcriptionally defined morphological subtypes of pancreatic ductal adenocarcinoma

Tumour heterogeneity remains a major obstacle to effective and precise therapy for pancreatic ductal adenocarcinoma (PDAC), the most common pancreatic cancer. Several transcriptional subtypes of PDAC with differential prognosis have been described, but they co-occur within tumours and are difficult to distinguish in routine clinical workflows. To investigate the relationship between transcriptional PDAC subtypes, local tissue morphology and the tumour microenvironment, we employed in situ sequencing to profile single cells in their spatial tissue context. We identify five transcriptional subtypes of PDAC cells occurring in three distinct morphological patterns, including secretory tumour cell monolayers, invasive tumour cells with high expression of cell adhesion molecules CEACAM5 and CEACAM6, and spatially distributed tumour cells associated with inflammatory-type fibroblasts. Analysis of bulk RNA-sequencing datasets of the TCGA-PAAD and PACA-AU cohorts according to these spatio-transcriptional subtypes confirmed their prognostic significance. Our results thus indicate an automatable substratification based on spatially-resolved transcriptomics of PDAC and identify distinct subtypes of classical PDAC, representing most cases of this devastating malignancy.

cancer biology↗

bioRxiv2019

Single nucleus RNA sequencing maps acinar cell states in a human pancreas cell atlas

Molecular evidence of cellular heterogeneity in the human exocrine pancreas has not been established, due to the local concentration of hydrolytic enzymes that can rapidly degrade cells and RNA upon resection. Here we innovated single-nucleus RNA sequencing protocols, and profiled more than 120,000 cells from adult and neonatal human donors to create the first comprehensive atlas of human pancreas cells, including epithelial and non-epithelial constituents. Adult and neonatal pancreata shared common features, including the presence of previously undetected acinar subtypes, but also showed marked differences in the composition of the endocrine, endothelial, and immune compartments. Spatial cartography, including cell proximity mapping through in situ sequencing, revealed dynamic developmental cell topographies in the endocrine and exocrine pancreas. Our human pancreas cell atlas can be interrogated to understand pancreatic cell biology, and provides a crucial reference set for future comparisons with diseased tissue samples to map the cellular foundations of pancreatic diseases.

genomics↗

bioRxiv2017

Mapping transcription factor occupancy using minimal numbers of cells in vitro and in vivo

The identification of transcription factor (TF) binding sites in the genome is critical to understanding gene regulatory networks (GRNs). While ChIP-seq is commonly used to identify TF targets, it requires specific ChIP-grade antibodies and high cell numbers, often limiting its applicability. DNA adenine methyltransferase identification (DamID), developed and widely used in Drosophila, is a distinct technology to investigate protein-DNA interactions. Unlike ChIP-seq, it does not require antibodies, precipitation steps or chemical protein-DNA crosslinking, but to date it has been seldom used in mammalian cells due to technical impediments. Here we describe an optimised DamID method coupled with next generation sequencing (DamID-seq) in mouse cells, and demonstrate the identification of the binding sites of two TFs, OCT4 and SOX2, in as few as 1,000 embryonic stem cells (ESCs) and neural stem cells (NSCs), respectively. Furthermore, we have applied this technique in vivo for the first time in mammals. Oct4 DamID-seq in the gastrulating mouse embryo at 7.5 days post coitum (dpc) successfully identified multiple Oct4 binding sites proximal to genes involved in embryo development, neural tube formation, mesoderm-cardiac tissue development, consistent with the pivotal role of this TF in post-implantation embryo. This technology paves the way to unprecedented investigations of TF-DNA interactions and GRNs in specific cell types with limited availability in mammals including in vivo samples.

genomics↗