Biology subjects

Tomei, S.

Publications and source records attributed to Tomei, S..

4 recordsLinked to original sources

bioRxiv2025

The hidden predictors of human haematopoietic clonal fate

Human haematopoietic stem and progenitor cells (HSPCs) exhibit heterogeneous lineage output, but the molecular programs underlying clonal fate remain poorly defined. To address this, we developed a human haematopoietic organoid supporting differentiation into 15 lineages and used it to track barcoded HSPC clones over time. By integrating single-cell transcriptomes, surface phenotypes, and clonal fate, we applied machine learning to identify clonal fate modules - gene and marker signatures predictive of lineage commitment. This approach uncovered hidden transcriptional and surface correlates of multipotency, including CD200, which marked a subset of HSCs with broad output capacity, which we leveraged to increase manufactured type 1 dendritic cell purity for immunotherapy applications. Our study provides a framework for decoding clonal fate decisions in human HSPCs and identifies molecular features that distinguish truly multipotent clones, advancing strategies for stem cell purification and therapeutic engineering.

cell biology↗

bioRxiv2023

Human monoclonal antibodies reveal subdominant gonococcal and meningococcal cross-protective antigens

Gonococcus (Gc), a bacterium resistant to most antibiotics causing more than 80 million cases of gonorrhea annually, is a WHO high priority pathogen. Recently, vaccine development prospects were boosted by reports that licensed meningococcus serogroup B (MenB) vaccines provided partial protection against Gc infection. To determine antigens responsible for cross-protection, memory B cells from 4CMenB vaccinated volunteers were single-cell sorted to identify antibodies that kill Gc in a bactericidal assay. Nine different antibodies, all deriving from the IGHV4-34 germline carrying unusually long HCDR3s, recognized the PorB protein, four recognized the lipooligosaccharide (LOS), and four unknown antigens. One of the PorB antibodies, tested in vivo, provided protection from Gc infection. The identification of PorB and LOS as key antigens of gonococcal and meningococcal immunity provides a mechanistic explanation of the cross-protection observed in the clinic and shows that isolating human monoclonal antibodies from vaccinees can be instrumental for bacterial antigen discovery.

immunology↗

bioRxiv2022

The decision to develop into αβ or γδ T cells is pre-programmed in distinct subpopulations of DN1 thymocytes

The {beta} and {gamma}{delta} T cell lineages are both are thought to differentiate in the thymus from common uncommitted progenitors. The earliest stage of T cell development is known as known as CD4-CD8- double negative 1 (DN1). These thymocytes have previously been revealed to be a heterogenous mixture of cells, which of only the CD117+ fraction have been proposed to be true T cell progenitors that progress to the DN2 and DN3 thymocyte stages, at which point the development of the {beta} and {gamma}{delta} T cell lineages diverge. However, recently, it has been shown that at least some {gamma}{delta} T cells are actually derived from a subset of CD117- DN thymocytes. Along with other ambiguities, this suggests that T cell development may not be as straightforward as previously thought. To better understand early T cell development, particularly the heterogeneity of DN1 thymocytes, we performed single cell RNA sequence (scRNAseq) of mouse DN and {gamma}{delta} thymocytes and show that the various DN stages are indeed comprised of transcriptionally diverse subpopulations of cells. We also show that multiple subpopulations of DN1 thymocytes exhibit preferential development towards the {gamma}{delta} lineage. Furthermore, specific {gamma}{delta}-primed DN1 subpopulations preferentially develop into IL-17 or IFN{gamma}-producing {gamma}{delta} T cells. We show that DN1 subpopulations that only give rise to IL-17-producing {gamma}{delta} T cells already express many of the transcription factors associated with type 17 immune cell differentiation, while the DN1 subpopulations that can give rise to IFN{gamma}-producing {gamma}{delta} T cell already express transcription factors associated with type 1 immune cell differentiation.

immunology↗

bioRxiv2020

The clonal and molecular aetiology of emergency dendritic cell development

Extrinsic regulation of single haematopoietic stem and progenitor cell (HSPC) fate is crucial for immune cell development. Here, we examine the aetiology of Flt3 ligand (Flt3L)-mediated emergency development of type 1 conventional dendritic cells (cDC1s), which results in enhanced immunity against infections and cancer. Using cellular barcoding, we demonstrate a predominant role of enhanced clonal expansion and moderate contribution via recruitment of additional cDC1-generating HSPCs. The selective cDC1 expansion occurs primarily via multi-/oligo-potent clones, without compromising output to other lineages. To understand the molecular hallmarks early during a Flt3L response, we develop Divi-Seq to simultaneously profile cell division history, surface phenotype and transcriptional state of single HSPCs. We discover that Flt3L-responsive HSPCs maintain a proliferative early progenitor-like state, which leads to selective emergence of CD11c+cKit+ transitional precursors with high cellular output to cDC1s. These findings inform the mechanistic action of Flt3L in natural immunity and immunotherapy at a clonal level.

immunology↗