Biology subjects

Baroud, C.

Publications and source records attributed to Baroud, C..

10 recordsLinked to original sources

bioRxiv2025

SPEF1 mediates assembly of the central pair microtubule complexes in cilia of Tetrahymena.

SPEF1 is a conserved protein that reinforces the seam of central microtubules within the distal segment of motile cilia. We show that in Tetrahymena, loss of SPEF1 destabilized the central pair throughout the cilium length, producing gaps in the microtubule lattice, loss of proximal microtubule portions, and loss of lateral projections. While both central microtubules were affected, C1 suffered more damage than C2 and the defects were already apparent during ciliary assembly. Tetrahymena cells lacking SPEF1 had fewer cilia, which contained an excessively dense ciliary matrix and abnormal densities on the doublet microtubules. Although SPEF1 loss visibly affected only the central microtubules, it localized to all stable microtubules in the cell, both ciliary and non-ciliary. Within cilia, SPEF1 was enriched near the distal tip, but was also present throughout the middle segment, where it was more concentrated along the central than the outer doublet microtubules. In live cilia, SPEF1 particles were mostly stationary and turned over slowly, some diffused but none moved by IFT. We propose that SPEF1 acts as a stabilizer of central microtubules in both the middle and distal segment and its activity contributes to central microtubule assembly.

cell biology↗

bioRxiv2025

Extending digital biology: bacterial survival and morphological heterogeneity under antibiotic stress

The morphology of bacteria is modified by antibiotic stress while also serving to survive the antibiotic. However associating morphological descriptors with quantitative measurements of cell survival remains elusive. Here we present a workflow to generate morphological signatures for the progeny of individual cells for 168 different antibiotic conditions. The workflow uses stationary microfluidic droplets, to encapsulate and grow bacteria, and confocal microscopy to image the contents of each droplet. A custom image analysis pipeline is developed to interact with the images in order to label of the morphologies within a subset of the images and train a neural network. The network yields a multidimensional morphological signature for 82000 droplets, showing the co-existence of different morphologies even for the progeny of individual cells. The morphological signatures are different for varying antibiotic type and concentration, thus providing a way to distinguish antibiotics by their mode of action. By combining these morphological signatures with the digital detection of survival within droplets, this workflow can serve to understand the emergence of antibiotic resistance or to identify antimicrobial activity of unknown substances.

bioengineering↗

bioRxiv2024

Culture of pluripotent stem cells in microscale droplets modulates differentiation and tissue patterning towards organoids on chip

1The differentiation of pluripotent stem cells (PSCs) and their self-organization into organoids are influenced by cell-cell interactions mediated by contacts and secreted molecules. These interactions are enhanced in microfluidic droplets due to confinement and small culture volumes. However, a comprehensive study on the culture of PSCs within droplets and the impact of this microenvironment has yet to be conducted. In this study, we present a droplet platform for the 3D culture of PSCs at various stages of cellular commitment. We demonstrate PSC differentiation into the three germ layers and the feasibility of organoid formation within droplets. Our findings reveal that culturing PSCs in confined volumes regulates cell fate decisions, promoting tissue patterning in gastruloids through the sequential induction of growth and migration of distinct differentiated cell populations, and facilitating the self-organization of cardiac organoids. This technological approach provides unique insights into the intrinsic factors regulating tissue self-patterning in vitro. 2 Highlights and eTOC blurbO_ST_ABSHighlightsC_ST_ABSO_LIDroplet microfluidics allows expansion and supports the pluripotency of 3D aggregates of PSCs. C_LIO_LIDroplet microfluidics supports and regulates spontaneous differentiation into embryoid bodies. C_LIO_LIDroplet promotes tissue patterning in gastruloids through the sequential induction of growth and migration of mesoderm followed by ectoderm. C_LIO_LIPerfused microfluidic droplets support long term culture and derivation of organoids on chip. C_LI Vertti-Quintero et al. introduces a microfluidic droplet platform for the 3D culture of pluripotent stem cells (PSCs) at various differentiation stages. The format supports the long term 3D culture and the differentiation of PSCs -either spontaneous or directed-. This "microscale culture" can regulate PSCs fate decision, while promoting tissue pattering -as demonstrated in gastruloids polarization- and allowing self-organization towards cardioids formation.

bioengineering↗

bioRxiv2023

Cancer-on-a-chip model shows that the adenomatous polyposis coli mutation impairs T cell engagement and killing of cancer spheroids

Evaluating the ability of cytotoxic T lymphocytes (CTLs) to eliminate tumor cells is crucial, for instance to predict the efficiency of cell therapy in personalized medicine. However, the destruction of a tumor by CTLs involves CTL migration in the extra-tumoral environment, accumulation on the tumor, antigen recognition, and cooperation in killing the cancer cells. Therefore, identifying the limiting steps in this complex process requires spatio-temporal measurements of different cellular events over long periods. Here, we use a cancer-on-a-chip platform to evaluate the impact of adenomatous polyposis coli (APC) mutation on CTL migration and cytotoxicity against 3D tumor spheroids. The APC mutated CTLs are found to have a reduced ability to destroy tumor spheroids compared with control cells, even though APC mutants migrate in the extra-tumoral space and accumulate on the spheroids as efficiently as control cells. Once in contact with the tumor however, mutated CTLs display reduced engagement with the cancer cells, as measured by a new metric that distinguishes different modes of CTL migration. Realigning the CTL trajectories around localized killing cascades reveals that all CTLs transition to high engagement in the two hours preceding the cascades, which confirms that the low engagement is the cause of reduced cytotoxicity. Beyond the study of APC mutations, this platform offers a robust way to compare cytotoxic cell efficiency of even closely related cell types, by relying on a multiscale cytometry approach to disentangle complex interactions and to identify the steps that limit the tumor destruction.

bioengineering↗

bioRxiv2023

Spatiotemporal dynamics of cytokines expression dictate fetal liver hematopoiesis.

During embryogenesis, yolk-sac and intra-embryonic-derived hematopoietic progenitors, comprising the precursors of adult hematopoietic stem cells, converge into the fetal liver. With a new staining strategy, we defined all non-hematopoietic components of the fetal liver and found that hepatoblasts are the major producers of hematopoietic growth factors. We identified mesothelial cells, a novel component of the stromal compartment, producing Kit ligand, a major hematopoietic cytokine. A high-definition imaging dataset analyzed using a deep-learning based pipeline allowed the unambiguous identification of hematopoietic and stromal populations, and enabled determining a neighboring network composition, at the single cell resolution. Throughout active hematopoiesis, progenitors preferentially associate with hepatoblasts, but not with stellate or endothelial cells. We found that, unlike yolk sac-derived progenitors, intra-embryonic progenitors respond to a chemokine gradient created by CXCL12-producing stellate cells. These results revealed that FL hematopoiesis is a spatiotemporal dynamic process, defined by an environment characterized by low cytokine concentrations.

developmental biology↗

bioRxiv2023

Measuring single-cell susceptibility to antibiotics within monoclonal bacterial populations

Given the emergence of antimicrobial drug resistance, it is critical to understand the heterogeneity of response to an antibiotic within a population of cells. Since the drug can exert a selection pressure that leads to the emergence of resistant phenotypes. To date, neither bulk nor single-cell methods are able to link the heterogeneity of single-cell susceptibility to the population-scale response to antibiotics. Here we present a platform that measures the ability of individual E. coli cells to form small colonies at different ciprofloxacin concentrations, by using anchored microfluidic drops and an image and data analysis pipelines. The microfluidic results are benchmarked against classical microbiology measurements of antibiotic susceptibility, showing an agreement between the pooled microfluidic chip and replated bulk measurements. Further, the experimental likelihood of a single cell to form a colony is used to provide a probabilistic antibiotic susceptibility curve. In addition to the probabilistic viewpoint, the microfluidic format enables the characterization of morphological features over time for a large number of individual cells. This pipeline can be used to compare the response of different bacterial strains to antibiotics with different action mechanisms.

bioengineering↗

bioRxiv2022

Apical size and deltaA expression predict adult neural stem cell decisions along lineage progression

The maintenance of neural stem cells (NSCs) in the adult brain depends on their activation frequency and division mode. We use long-term intravital imaging of NSCs in the zebrafish adult telencephalon to link activation and division mode with predictive cellular and molecular parameters. We reveal that apical surface area and expression of the Notch ligand DeltaA predict NSC activation frequency, while deltaA expression marks NSC commitment to neurogenesis. We also find that deltaA-negative NSCs constitute the bona fide self-renewing NSC pool and systematically engage in asymmetric divisions generating a self-renewing deltaAneg and a neurogenic deltaApos NSC. Finally, modulation of Notch signaling during imaging indicates that the prediction of activation frequency by apical size, and the asymmetric divisions of deltaAneg NSCs, are functionally independent of Notch. These results provide dynamic qualitative and quantitative readouts of NSC lineage progression in vivo and support a hierarchical organization of NSCs in differently fated sub-populations.

neuroscience↗

bioRxiv2022

Griottes: a generalist tool for network generation from segmented tissue images

Microscopy techniques and image segmentation algorithms have improved dramatically this decade, leading to an ever increasing amount of biological images and a greater reliance on imaging to investigate biological questions. This has created a need for methods to extract the relevant information on the behaviors of cells and their interactions, while reducing the amount of computing power required to organize this information. This task can be performed by using a network representation in which the cells and their properties are encoded in the nodes, while the neighborhood interactions are encoded by the links. Here we introduce Griottes, an open-source tool to build the "network twin" of 2D and 3D tissues from segmented microscopy images. We show how the library can provide a wide range of biologically relevant metrics on individual cells and their neighborhoods, with the objective of providing multi-scale biological insights. The librarys capacities are demonstrated on different image and data types. This library is provided as an open-source tool that can be integrated into common image analysis workflows to increase their capacities.

bioinformatics↗

bioRxiv2021

A Multiscale Immuno-Oncology on-Chip System (MIOCS) establishes that collective T cell behaviors govern tumor regression

T cell-based tumor immunotherapies such as CAR T cells or immune checkpoint inhibitors harness the cytotoxic potential of T cells to promote tumor regression. However, patient response to immunotherapy remains heterogeneous, highlighting the need to better understand the rules governing a successful T cell attack. Here, we develop a microfluidic-based method to track the outcome of T cell activity on many individual cancer spheroids simultaneously, with a high spatiotemporal resolution. By combining these parallel measurements of T cell behaviors and tumor fate with probabilistic modeling, we establish that the first recruited T cells initiate a positive feedback loop leading to an accelerated effector accumulation on the spheroid. We also provide evidence that cooperation between T cells on the spheroid during the killing phase facilitates tumor destruction. We propose that tumor destruction does not simply reflect the sum of individual T cell activities but relies instead on collective behaviors promoting both T cell accumulation and function. The possibility to track many replicates of immune-tumor interactions with such a level of detail should help delineate the mechanisms and efficacy of various immunotherapeutic strategies.

biophysics↗

bioRxiv2018

Studying 3D cell cultures in a microfluidic droplet array under multiple time-resolved conditions

The relevance of traditional cell cultures to cellular behavior in vivo is limited, since the two-dimensional (2D) format does not appropriately reproduce the microenvironment that regulates cell functions. In this context, spheroids are an appealing 3D cell culture format to complement standard techniques, by combining a high level of biological relevance with simple production protocols. However the methods for spheroid manipulation are still labor intensive, which severely limits the complexity of operations that can be performed on statistically relevant numbers of individual spheroids. Here we show how to apply hundreds of different conditions on spheroids in a single microfluidic chip, where each spheroid is produced and immobilized in an anchored droplet. By using asymmetric anchor shapes, a second drop can be merged with the spheroid-containing drop at a later time. This time-delayed merging uniquely enables two classes of applications that we demonstrate: (1) the initiation of cell-cell interactions on demand, either for building micro-tissues within the device or for observing antagonistic cell-cell interactions with applications in immuno-therapy or host-pathogen interactions, (2) a detailed dose-response curve obtained by exposing an array of hepatocyte-like spheroids to droplets containing a wide range of acetaminophen concentrations. The integrated microfluidic format allows time-resolved measurements of the response of hundreds of spheroids with a single-cell resolution. The data shows an internally regulated evolution of each spheroid, in addition to a heterogeneity of the responses to the drug that the single-cell analysis correlates with the initial presence and location of dead cells within each spheroid.

bioengineering↗