Biology subjects

Postiglione, L.

Publications and source records attributed to Postiglione, L..

7 recordsLinked to original sources

bioRxiv2025

Inheritance entropy quantifies epigenetic regulation of cell-cycle exit in human bone marrow stromal cells

Human bone marrow stromal cells (BMSC) include skeletal stem cells with ground-breaking the-rapeutic potential. However, BMSC colonies have very heterogeneous in vivo behaviour, due to their different potency; this unpredictability is the greatest hurdle to the development of skeletal regeneration therapies. Colony-level heterogeneity urges a fundamental question: how is it possible that one colony as a collective unit behaves differently from another one? If cell-to-cell variability were just an uncorrelated random process, a million cells in a transplant-bound colony would be enough to yield statistical homogeneity, hence washing out any colony-level traits. A possible answer is that the differences between two originating cells are transmitted to their progenies and collectively persist through an hereditary mechanism. But non-genetic inheritance remains an elusive notion, both at the experimental and at the theoretical level. Here, we prove that heterogeneity in the lineage topology of BMSC clonal colonies is determined by heritable traits that regulate cell-cycle exit. The cornerstone of this result is the definition of a novel entropy of the colony, which measures the hereditary ramifications in the distribution of inactive cells across different branches of the proliferation tree. We measure the entropy in 32 clonal colonies, obtained from single-cell lineage tracing experiments, and show that in the greatest majority of clones this entropy is decisively smaller than that of the corresponding non-hereditary lineage. This result indicates that hereditary epigenetic factors play a major role in determining cycle exit of bone marrow stromal cells.

biophysics↗

bioRxiv2025

Topology, Kinetics and Inheritance in Clonal Colonies of Bone Marrow Stromal Cells

Bone marrow stromal cells (BMSC) - which include skeletal stem cells - are a promising tool in regenerative medicine. However, their heterogeneous and unpredictable in vivo behaviour remains a critical barrier preventing the development of standardized therapeutic approaches for skeletal tissue regeneration. Several studies have attempted to identify in vitro features that could correlate with the in vivo differentiation properties, yet the mechanisms ruling BMSC heterogeneity remain poorly understood. Here, using time-lapse imaging, we lineage-trace 32 single-cell-derived BMSC colonies through seven generations. We observe significant inter-colony and intra-colony heterogeneity in lineage topology (determined by the number of senescent or apoptotic cells) and in replicative kinetics (measured from proliferating cells only). Interestingly, topology and kinetics result strongly correlated, suggesting the existence of regulatory factors linking the non-dividing/apoptotic subpopulations with proliferating cells. Furthermore, BMSCs display highly synchronized cell cycles during early generations, indicating stage-specific regulatory mechanisms through which cells influence each other. By employing a non-interacting population growth model, we demonstrate that the observed synchronisation cannot be explained by an uncorrelated branching process; instead, cell-to-cell correlation of division times must exist. Our findings reveal fundamental mechanisms governing BMSC heterogeneity and growth dynamics that may inform strategies to control their regenerative potential.

biophysics↗

bioRxiv2020

ChipSeg: an automatic tool to segment bacteria and mammalian cells cultured in microfluidic devices

Extracting quantitative measurements from time-lapse images is necessary in external feedback control applications, where segmentation results are used to inform control algorithms. While such image segmentation applications have been previously reported, there is in the literature a lack of open-source and documented code for the community. We describe ChipSeg, a computational tool to segment bacterial and mammalian cells cultured in microfluidic devices and imaged by time-lapse microscopy. The method is based on thresholding and uses the same core functions for both cell types. It allows to segment individual cells in high cell-density microfluidic devices, to quantify fluorescence protein expression over a time-lapse experiment and to track individual cells. ChipSeg enables robust segmentation in external feedback control experiments and can be easily customised for other experimental settings and research aims.

synthetic biology↗

bioRxiv2020

Cheetah: a computational toolkit for cybergenetic control

Advances in microscopy, microfluidics and optogenetics enable single-cell monitoring and environmental regulation and offer the means to control cellular phenotypes. The development of such systems is challenging and often results in bespoke setups that hinder reproducibility. To address this, we introduce Cheetah - a flexible computational toolkit that simplifies the integration of real-time microscopy analysis with algorithms for cellular control. Central to the platform is an image segmentation system based on the versatile U-Net convolutional neural network. This is supplemented with functionality to robustly count, characterise and control cells over time. We demonstrate Cheetahs core capabilities by analysing long-term bacterial and mammalian cell growth and by dynamically controlling protein expression in mammalian cells. In all cases, Cheetahs segmentation accuracy exceeds that of a commonly used thresholding-based method, allowing for more accurate control signals to be generated. Availability of this easy-to-use platform will make control engineering techniques more accessible and offer new ways to probe and manipulate living cells.

synthetic biology↗

bioRxiv2020

In vivo Feedback Control of an Antithetic Molecular-Titration Motif in Escherichia coli using Microfluidics

We study both in silico and in vivo the real-time feedback control of a molecular titration motif that has been earmarked as a fundamental component of antithetic and multicellular feedback control schemes in E. coli. We show that an external feedback control strategy can successfully regulate the average fluorescence output of a bacterial cell population to a desired constant level in real-time. We also provide in silico evidence that the same strategy can be used to track a time-varying reference signal where the set-point is switched to a different value halfway through the experiment. We use the experimental data to refine and parameterize an in silico model of the motif that can be used as an error computation module in future embedded or multicellular control experiments.

synthetic biology↗

bioRxiv2019

Towards automated control of embryonic stem cell pluripotency

Mouse embryonic stem cells (mESCs) have been shown to exist in three distinct pluripotent states (ground, naive and primed pluripotent states), depending on culture conditions. External feedback control strategies have been, so far, mainly used to automatically regulate gene expression in bacteria and yeast. Here, we exploit a microfluidics/microscopy platform and segmentation and external feedback control algorithms for the automatic regulation of pluripotency phenotypes in mESCs. We show feasibility of automatically controlling, in living mESCs, levels of an endogenous pluripotency gene, Rex1, through a fluorescent reporter, used as control output, and drugs commonly used to modulate pluripotency (i.e. MEK kinase and Gsk3{beta} inhibitors) as control inputs. Our results will ultimately aid in the derivation of superior protocols for pluripotency maintenance and differentiation of mouse and human stem cells.

developmental biology↗

bioRxiv2018

A tunable dual-input system for on-demand dynamic geneexpression regulation.

Cellular systems have evolved numerous mechanisms to finely control signalling pathway activation and properly respond to changing environmental stimuli. This is underpinned by dynamic spatiotemporal patterns of gene expression. Indeed, in addition to gene transcription and translation regulation, modulation of protein levels, dynamics and localization are also essential checkpoints that govern cell functions. The introduction of tetracycline-inducible promoters has allowed gene expression control using orthogonal small molecules, facilitating rapid and reversible manipulation to study gene function in biological systems. However, differing protein stabilities means this solely transcriptional regulation is insufficient to allow precise ON-OFF dynamics, thus hindering generation of temporal profiles of protein levels seen in vivo. We developed an improved Tet-On based system augmented with conditional destabilising elements at the post-translational level that permits simultaneous control of gene expression and protein stability. Integrating these properties to control expression of a fluorescent protein in mouse Embryonic Stem Cells (mESCs), we found that adding protein stability control allows faster response times to changes in small molecules, fully tunable and enhanced dynamic range, and vastly improved microfluidic-based in-silico feedback control of gene expression. Finally, we highlight the effectiveness of our dual-input system to finely modulate levels of signalling pathway components in stem cells.

synthetic biology↗