Louiselle, D. | bioRxiv Science

bioRxiv2025

A comprehensive bulk and single-cell transcriptional atlas of pediatric leukemias

Advancements in understanding the molecular factors driving pediatric leukemias have led to an ever-increasing volume and diversity of data being generated. Recent studies are moving beyond DNA-based profiling to incorporate transcriptional data, enhancing the characterization of these cancers and informing clinical decisions. However, many existing datasets focus on specific leukemia subtypes, limiting the extraction of broader clinically relevant insights. Here, we present a comprehensive dataset of bulk and single-cell transcriptional data from 69 pediatric leukemia patients, encompassing eight leukemias. This is one of the most diverse pediatric leukemia datasets published to date. Through comparative analysis and explainable machine learning, we demonstrate the utility of these datasets in improving pediatric leukemia characterization and supporting the integration of transcriptional data into clinical testing.

cancer biology↗

bioRxiv2022

Neonatal hyperoxia induces sex-dependent pulmonary cellular and transcriptomic changes in an experimental mouse model of bronchopulmonary dysplasia

Hyperoxia (HOX) disrupts lung development in mice and causes bronchopulmonary dysplasia (BPD) in neonates. To investigate sex-dependent molecular and cellular programming involved in HOX, we surveyed the mouse lung using single cell RNA sequencing (scRNA-seq), and validated our findings in human neonatal lung cells in vitro. HOX-induced inflammation in alveolar type (AT) 2 cells gave rise to damage associated transient progenitors (DATP). It also induced a new subpopulation of AT1 cells with reduced expression of growth factors normally secreted by AT1 cells, but increased mitochondrial gene expression. Female alveolar epithelial cells had less EMT and pulmonary fibrosis signaling in HOX. In the endothelium, expansion of Car4+ EC (Cap2) was seen in HOX along with an emergent subpopulation of Cap2 with repressed VEGF signaling. This regenerative response was increased in females exposed to HOX. Mesenchymal cells had inflammatory signatures in HOX, with a new distal interstitial fibroblast subcluster characterized by repressed lipid biosynthesis and a transcriptomic signature resembling myofibroblasts. HOX-induced gene expression signatures in human neonatal fibroblasts and alveolar epithelial cells in vitro resembled mouse scRNA-seq data. These findings suggest that neonatal exposure to HOX programs distinct sex-specific stem cell progenitor and cellular reparative responses that underpin lung remodeling in BPD.

developmental biology↗