Biology subjects

Guibentif, C.

Publications and source records attributed to Guibentif, C..

9 recordsLinked to original sources

bioRxiv2026

Resolving thyroid lineage cell trajectories merging into a dual endocrine gland in mammals

The thyroid has a remarkable evolution, first appearing in invertebrate chordates as an integral exocrine constituent of the pharyngeal endostyle that is transformed into an endocrine gland during metamorphosis in basal vertebrates. In mammals, the thyroid acquires a second endocrine cell type, calcitonin-producing C-cells, which for long were inferred a neural crest origin, shuttled to the embryonic thyroid by the ultimobranchial bodies. However, recent lineage tracing experiments firmly establish these neuroendocrine cells also derive from foregut endoderm. Key questions remaining unanswered are how thyroid primordia independently develop and, unlike in all non-mammalian vertebrates, merge into a dual endocrine organ. Here, by leveraging a single-cell transcriptome atlas derived from mouse pharyngeal endoderm and its subsequent cell fates, we characterize the global gene expression profile of thyroid- and ultimobranchial-derived progenitor cells and identify comprehensive gene regulatory networks of lineage-specific transcription factors and novel target genes predicted to differentially regulate cell proliferation, plasticity and differentiation during development. Spatiotemporal analyses reveal C-cell precursors are triggered to undergo epithelial-mesenchymal transition (EMT) and cell-autonomously down-regulate collagen IV and degrade laminin that delineates the ultimobranchial body epithelium. However, the EMT program is not fully deployed until both cell lineages are mixed and propagate conjointly thus forming the typical thyroid histoarchitecture of follicles and parafollicular C-cells, every follicle/C-cell unit being enveloped by a renewed basement membrane. Mixed-type thyroid carcinoma recapitulates a synchronous lineage growth pattern but only the neuroendocrine tumor cells are able to escape the compound follicle boundaries and become invasive adopting a C-cell precursor-like migratory phenotype.

developmental biology↗

bioRxiv2023

Systematic characterisation of perturbations in complex developing cell populations reveals mechanisms underpinning development and disease

Perturbation studies using gene knockouts have become a key tool for understanding the roles of regulatory genes in development and disease. Here we systematically characterise the knockout effects of the key developmental regulators T and Mixl1 in chimeric mouse embryos during gastrulation and organogenesis. We present a comprehensive and effective suite of statistical tools for systematic characterisation of effects at the level of differential abundance of cell types, lineage development, and gene dysregulation. Applying our computational approach to a novel chimera data set with Mixl1 knockout reveals a disruption in Epicardium development in the absence of Mixl1, characterized by lack of upregulation of the key transcription factor Tbx18 and the Wnt regulator Sfrp5, and by dysregulation of the recently identified juxta-cardiac field. Finally, we demonstrate the wider utility of our framework by applying it to published acute myeloid leukemia (AML) patient data, and show how different responses to therapy are reflected in changes in gene expression along the myeloid trajectory between healthy and AML patients.

genomics↗

bioRxiv2023

Tracking Early Mammalian Organogenesis - Prediction and Validation of Differentiation Trajectories at Whole Organism Scale

Early organogenesis represents a key step in animal development, where pluripotent cells divide and diversify to initiate formation of all major organs. Here, we used scRNA-Seq to profile over 300,000 single cell transcriptomes sampled in 6 hour intervals from mouse embryos between E8.5 and E9.5. Combining this dataset with our previous E6.5 to E8.5 atlas resulted in a densely sampled time course of over 400,000 cells from early gastrulation to organogenesis. Computational lineage reconstruction at full organismal scale identified complex waves of blood and endothelial development, including a new molecular programme for somite-derived endothelium. To assess developmental fates across the primitive streak, we dissected the E7.5 primitive streak into four adjacent regions, performed scRNA- Seq and predicted cell fates computationally. We next defined early developmental state/fate relationships experimentally by a combination of orthotopic grafting, microscopic analysis of graft contribution as well as scRNA-Seq to transcriptionally determine cell fates of the grafted primitive streak regions after 24h of in vitro embryo culture. Experimentally determined fate outcomes were in good agreement with the fates predicted computationally, thus demonstrating how classical grafting experiments can be revisited to establish high-resolution cell state/fate relationships. Such interdisciplinary approaches will benefit future studies in both developmental biology as well as guide the in vitro production of cells for organ regeneration and repair.

developmental biology↗

bioRxiv2023

Defective ribosome assembly impairs leukemia stem cell function in a murine model of acute myeloid leukemia

Despite the advanced understanding of disease mechanisms, the current therapeutic regimen fails to cure most patients with acute myeloid leukemia (AML). In the present study, we address the role of protein synthesis control in AML leukemia stem cell (LSC) function and leukemia propagation. We apply a murine model of mixed-lineage leukemia-rearranged AML to demonstrate that LSCs are characterized by high global protein synthesis rate. Using a genetic model that permits inducible and graded regulation of ribosomal subunit joining, we show that defective ribosome assembly leads to a significant survival advantage by selectively eradicating LSCs but not normal hematopoietic stem and progenitor cells. Finally, transcriptomic and proteomic analyses identify a rare subset of LSCs with immature stem cell signature and high ribosome content that promotes the resistance to defective ribosome assembly. Collectively, our study unveils a critical requirement of high protein synthesis rate for LSC function and highlights ribosome assembly as a therapeutic target in AML.

cancer biology↗

bioRxiv2022

Rabbit Development as a Model for Single Cell Comparative Genomics

Biomedical research relies heavily on the use of model organisms to gain insight into human health and development. Traditionally, the mouse has been the favored vertebrate model, due to its experimental and genetic tractability. Non-rodent embryological studies however highlight that many aspects of early mouse development, including the egg-cylinder topology of the embryo and its method of implantation, diverge from other mammals, thus complicating inferences about human development. In this study, we constructed a morphological and molecular atlas of rabbit development, which like the human embryo, develops as a flat-bilaminar disc. We report transcriptional and chromatin accessibility profiles of almost 180,000 single cells and high-resolution histology sections from embryos spanning gastrulation, implantation, amniogenesis, and early organogenesis. Using a novel computational pipeline, we compare the transcriptional landscape of rabbit and mouse at the scale of the entire organism, revealing that extra-embryonic tissues, as well as gut and PGC cell types, are highly divergent between species. Focusing on these extra-embryonic tissues, which are highly accessible in the rabbit, we characterize the gene regulatory programs underlying trophoblast differentiation and identify novel signaling interactions involving the yolk sac mesothelium during hematopoiesis. Finally, we demonstrate how the combination of both rabbit and mouse atlases can be leveraged to extract new biological insights from sparse macaque and human data. The datasets and analysis pipelines reported here set a framework for a broader cross-species approach to decipher early mammalian development, and are readily adaptable to deploy single cell comparative genomics more broadly across biomedical research.

developmental biology↗

bioRxiv2022

Detection of latent Epstein-Barr virus gene expression in single-cell sequencing of peripheral blood mononuclear cells

Epstein-Barr virus (EBV) DNA is regularly found in the blood of patients with EBV associated diseases and occasionally in healthy individuals. However, EBV infected primary B-lymphocytes have not yet been detected using scRNA seq. Here, we screened the viral transcriptome in single cell RNA sequencing datasets from peripheral blood to identify virus infected cells. Whereas EBV RNA was detected in an immunocompromised patient, EBV associated nasopharyngeal carcinoma and multiple sclerosis samples did not display any levels of circulating EBV RNA. We further screened whole-blood samples from a cohort of immunosuppressed patients for viral transcripts using a custom enhanced RT-qPCR panel and detected latency programs dominated by noncoding RNAs (EBERs and RPMS1). To explore the interplay between the EBV and the host-cell transcriptome profile, we used enriched B-lymphocytes from a splenectomy patient with 30% EBER positivity estimated by in situ hybridization and performed 5 single-cell RNA sequencing with paired VDJ profiling. The EBV expression pattern of the patients B-lymphocytes confirmed the RT-qPCR assay with RPMS1 and LMP-1/BNLF2a/b significantly dominating the sequenced EBV polyadenylated RNA. A comparison between the expression profile of EBV positive B-lymphocytes and healthy controls B-lymphocytes revealed the upregulation in genes involved in cell population proliferation when infected with EBV. This is further supported by a measurable polyclonal expansion in the patient, as compared to a control, emphasizing EBVs role in a host-cells tendency for cellular expansion. However, when contrasting to cells that have undergone malignant transformation, the primary EBV infected cells display a rather dissimilar expression profile, even to cells that are supposed to simulate primary EBV infection (I.e. Lymphoblastoid Cell Lines). This implies that during primary infection of EBV, the host-cell enters a state of premalignancy rather than a complete oncogenic transformation at the initial time of infection

microbiology↗

bioRxiv2022

StabMap: Mosaic single cell data integration using non-overlapping features

Currently available single cell -omics technologies capture many unique features with different biological information content. Data integration aims to place cells, captured with different technologies, onto a common embedding to facilitate downstream analytical tasks. Current horizontal data integration techniques use a set of common features, thereby ignoring non-overlapping features and losing information. Here we introduce StabMap, a mosaic data integration technique that stabilises mapping of single cell data by exploiting the non-overlapping features. StabMap is a flexible approach that first infers a mosaic data topology, then projects all cells onto supervised or unsupervised reference coordinates by traversing shortest paths along the topology. We show that StabMap performs well in various simulation contexts, facilitates disjoint mosaic data integration, and enables the use of novel spatial gene expression features for mapping dissociated single cell data onto a spatial transcriptomic reference.

bioinformatics↗

bioRxiv2020

Coordinated Changes in Gene Expression Kinetics Underlie both Mouse and Human Erythroid Maturation

BackgroundSingle cell technologies are transforming biomedical research, including the recent demonstration that unspliced pre-mRNA present in single cell RNA-Seq permits prediction of future expression states. Here we applied this RNA velocity concept to an extended timecourse dataset covering mouse gastrulation and early organogenesis. ResultsIntriguingly, RNA velocity correctly identified epiblast cells as the starting point, but several trajectory predictions at later stages were inconsistent with both real time ordering and existing knowledge. The most striking discrepancy concerned red blood cell maturation, with velocity-inferred trajectories opposing the true differentiation path. Investigating the underlying causes revealed a group of genes with a coordinated step-change in transcription, thus violating the assumptions behind current velocity analysis suites, which do not accommodate time-dependent changes in expression dynamics. Using scRNA-Seq analysis of chimeric mouse embryos lacking the major erythroid regulator Gata1, we show that genes with the step-changes in expression dynamics during erythroid differentiation fail to be up-regulated in the mutant cells, thus underscoring the coordination of modulating transcription rate along a differentiation trajectory. In addition to the expected block in erythroid maturation, the Gata1- chimera dataset revealed induction of PU.1 and expansion of megakaryocyte progenitors. Finally, we show that erythropoiesis in human fetal liver is similarly characterized by a coordinated step-change in gene expression. ConclusionsBy identifying a limitation of the current velocity framework coupled with in vivo analysis of mutant cells, we reveal a coordinated step-change in gene expression kinetics during erythropoiesis, with likely implications for many other differentiation processes.

developmental biology↗

bioRxiv2020

Highly multiplexed spatially resolved gene expression profiling of mouse organogenesis

Transcriptional and epigenetic profiling of single-cells has advanced our knowledge of the molecular bases of gastrulation and early organogenesis. However, current approaches rely on dissociating cells from tissues, thereby losing the crucial spatial context that is necessary for understanding cell and tissue interactions during development. Here, we apply an image-based single-cell transcriptomics method, seqFISH, to simultaneously and precisely detect mRNA molecules for 387 selected target genes in 8-12 somite stage mouse embryo tissue sections. By integrating spatial context and highly multiplexed transcriptional measurements with two single-cell transcriptome atlases we accurately characterize cell types across the embryo and demonstrate how spatially-resolved expression of genes not profiled by seqFISH can be imputed. We use this high-resolution spatial map to characterize fundamental steps in the patterning of the midbrain-hindbrain boundary and the developing gut tube. Our spatial atlas uncovers axes of resolution that are not apparent from single-cell RNA sequencing data - for example, in the gut tube we observe early dorsal-ventral separation of esophageal and tracheal progenitor populations. In sum, by computationally integrating high-resolution spatially-resolved gene expression maps with single-cell genomics data, we provide a powerful new approach for studying how and when cell fate decisions are made during early mammalian development.

developmental biology↗