Biology subjects

Cadinu, P.

Publications and source records attributed to Cadinu, P..

6 recordsLinked to original sources

bioRxiv2026

Early hematopoietic fate decisions are independent of bone marrow niche

Hematopoietic stem cells (HSCs) reside in specialized bone marrow microenvironments, termed niches, which regulate self-renewal and differentiation through local support programs. Although multiple anatomically distinct niches with unique cellular compositions have been described, it remains unclear to what degree these niches differentially shape HSC fate. In parallel, hematopoietic output is modulated with age, yet it remains unclear if this shift in HSC fate is driven by niche-specific modifications. To address these questions, we applied Multiplexed Error Robust Fluorescence in situ Hybridization to jointly define the cellular and spatial organization of the femoral marrow in young and aged mice. We find that while HSC niches are anatomically and compositionally distinct, stem cell lineage priming is not strongly associated with niche identity consistent with our demonstration that fate-shaping signals are provided redundantly across niches. Moreover, we find that while aging remodels the cellular composition of the marrow, reshapes cellular expression, and alters hematopoietic differentiation, HSC niches are preserved, and HSC fate remains niche agnostic. Together these findings separate anatomical niche identity from early HSC fate decisions and are consistent with a model in which hematopoietic support is distributed across different niche locations rather than partitioned among discrete sites.

immunology↗

bioRxiv2026

RNA-aware tissue preservation workflows for high-quality spatial transcriptomics

Image-based transcriptomic approaches can define, discover, and chart cell types and states within an array of tissues. However, measurement quality depends on RNA integrity, and the modern tissue preservation toolbox was not designed to protect this highly labile molecule. Here we leverage MERFISH to show that tissue-dependent differences in endogenous RNase activity can shape spatial transcriptomics data quality for different preservation methods and that RNase-activity-guided protocol optimization can improve data quality. In parallel, we introduce an RNA-aware pan-tissue preservation approach, Rapid Inhibition and Permanent Inactivation of Nucleases (RIPIN), that rapidly stabilizes samples with a broad-spectrum RNase inhibitor while permitting slow, chemical inactivation. RIPIN produces high-quality MERFISH measurements in all profiled human and mouse tissues, is compatible with clinical workflows, and is easily integrated with frozen or paraffin sectioning. By highlighting how RNA integrity can be lost during tissue processing, our work may inspire the next generation of RNA-aware histology methods.

genomics↗

bioRxiv2025

An image-based transcriptomics atlas reveals the regional and microbiota-dependent molecular, cellular, and spatial structure of the murine gut

The gastrointestinal environment is home to a massive diversity of diet-, host-, and microbiota-derived small molecules, collectively sensed by a remarkable variety of cells. To explore the cellular and spatial organization of sensation, we used MERFISH to profile receptor expression across 2.1 million cells in multiple regions of the murine gut under specific-pathogen-free (SPF) and germ-free (GF) conditions. This atlas revealed expected and novel cell types--including a candidate murine homolog of human BEST4 enterocytes--demonstrated cell-type regional specialization, discovered extensive location-dependent spatial fine-tuning in mucosal cell expression, and suggested cell-type specific mediators of the effects of microbiota-derived small molecules. In addition, this atlas revealed that, aside from immune cell abundance, many aspects of the murine gut are host-intrinsic and modified only modestly in the absence of a microbiota. Collectively, this atlas provides a valuable resource for understanding the cellular and spatial organization underlying small molecule sensation in the gut.

genomics↗

bioRxiv2025

Protocol Optimization Improves the Performance of Multiplexed RNA Imaging

Spatial transcriptomics has emerged as a powerful tool to define the cellular structure of diverse tissues. One such method is multiplexed error robust fluorescence in situ hybridization (MERFISH). MERFISH identifies RNAs with error tolerant optical barcodes generated through sequential rounds of single-molecule fluorescence in situ hybridization (smFISH). MERFISH performance depends on a variety of protocol choices, yet their effect on performance has yet to be systematically examined. Here we explore a variety of properties to identify optimal choices for probe design, hybridization, buffer storage, and buffer composition. In each case, we introduce protocol modifications that can improve performance, and we show that, collectively, these modified protocols can improve MERFISH quality in both cell culture and tissue samples. As RNA FISH-based methods are used in many different contexts, we anticipate that the optimization experiments we present here may provide empirical design guidance for a broad range of methods.

genomics↗

bioRxiv2023

Charting the cellular biogeography in colitis reveals fibroblast trajectories and coordinated spatial remodeling

Gut inflammation involves contributions from immune and non-immune cells, whose interactions are shaped by the spatial organization of the healthy gut and its remodeling during inflammation. The crosstalk between fibroblasts and immune cells is an important axis in this process, but our understanding has been challenged by incomplete cell-type definition and biogeography. To address this challenge, we used MERFISH to profile the expression of 940 genes in 1.35 million cells imaged across the onset and recovery from a mouse colitis model. We identified diverse cell populations; charted their spatial organization; and revealed their polarization or recruitment in inflammation. We found a staged progression of inflammation-associated tissue neighborhoods defined, in part, by multiple inflammation-associated fibroblasts, with unique expression profiles, spatial localization, cell-cell interactions, and healthy fibroblast origins. Similar signatures in ulcerative colitis suggest conserved human processes. Broadly, we provide a framework for understanding inflammation-induced remodeling in the gut and other tissues.

immunology↗

bioRxiv2020

Visualising G-quadruplex DNA dynamics in live cells by fluorescence lifetime imaging microscopy

Guanine rich regions of oligonucleotides fold into quadruple-stranded structures called G-quadruplexes (G4). Increasing evidence suggests that these G4 structures form in vivo and play a crucial role in cellular processes. However, their direct observation in live cells remains a challenge. Here we demonstrate that a fluorescent probe (DAOTA-M2) in conjunction with Fluorescence Lifetime Imaging Microscopy (FLIM) can identify G4 within nuclei of live and fixed cells. We present a new FLIM-based cellular assay to study the interaction of non-fluorescent small molecules with G4 and apply it to a wide range of drug candidates. We also demonstrate that DAOTA-M2 can be used to study G4 stability in live cells. Reduction of FancJ and RTEL1 expression in mammalian cells increases the DAOTA-M2 lifetime and therefore suggests an increased number of G4 in these cells, implying that FancJ and RTEL1 play a role in resolving G4 structures in cellulo.

biophysics↗