Biology subjects

Rulands, S.

Publications and source records attributed to Rulands, S..

17 recordsLinked to original sources

bioRxiv2026

Dynamical Regimes in Rejuvenation

Biological aging is accompanied by systematic changes in epigenetic modifications and chromatin organization. The reversal of the effects of aging, rejuvenation, is experimentally achieved by the transient induction of factors that modify these marks in cells and organisms. Here, we show that key features of rejuvenation experiments emerge from the biophysical interplay between dynamic epigenetic marks and the three-dimensional conformation of chromatin. Using a minimal field theory and molecular dynamics simulations, we show that the system responds in three distinct temporal regimes. The intermediary regime fulfills necessary conditions for successful rejuvenation. In this regime, the system spends time near a separatrix, allowing for high epigenetic plasticity, while memory retained in the chromatin conformation enables restoration of the original epigenetic correlations. Analysis of sequencing data further supports the predicted coupling between chromatin compaction and epigenetic correlations. Our results provide a physical explanation for how rejuvenation may remodel age-associated epigenetic states without irreversibly erasing cellular identity. We identify a general mechanism by which memory stored in a slow structural variable permits reversible remodeling of a faster internal state.

biophysics↗

bioRxiv2025

Genetic barcoding of individual cells links cancer evolutionary trajectories and prognostic outcomes

Intratumoural heterogeneity (ITH) reflects cancer progression, by integrating clonal dynamics, cell plasticity, and metastatic potential of malignant cells. Defining the origins and evolutionary trajectories of tumour cells is central to preventing tumour growth and dissemination, yet significant gaps in knowledge persist. Here, we used an original single cell resolution lineage tracing system to investigate how ITH underlies changes in tumour cell states, such as the acquisition of an epithelial-to-mesenchymal transition (EMT) phenotype and invasive capacity. By combining in vivo genetic barcoding with single-cell transcriptomics, we uncover two parallel evolutionary trajectories toward EMT: one associated with alveolar differentiation, and another characterized by gene regulatory programs activated during stress and tissue regeneration. Of interest, only the gene modules defining the regenerative trajectory were found to correlate with poor survival in breast cancer patients. Our results also provide a quantitative framework to measure cellular plasticity that enables the identification of highly plastic cells and their gene signatures, correlating with rapid changes in transcriptional state, EMT features and aggressive cancer. These findings deliver a comprehensive view of in vivo clonal evolution in breast cancer, uncovering the interplay between lineage plasticity and tumour progression with quantitative and robust statistical approaches.

cancer biology↗

bioRxiv2025

A temporal hierarchy determines epigenetic aging

Aging involves processes spanning orders of magnitude in time, from fast events that occur at the molecular scale to the slow decrease of physiological function. Whether and how fast molecular events lead to the slow progression of aging, and what ultimately sets the timescale of aging, is not understood. Here, by focusing on dynamic changes in DNA methylation, we show how aging phenomena on long timescales emerge from the kinetics of fast molecular processes, providing a bridge between temporal scales. By combining DNA methylation sequencing data across a range of timescales with a statistical modeling-based approach, we show that DNA methylation aging is governed by a three-fold hierarchy of processes that dominate on distinct timescales: individual stochastic events in which enzymes interact with the DNA and with each other (milliseconds); the convergence of molecular concentrations to steady states (days to months); and stochastic transitions between these steady states (years to decades). Our findings provide a unified picture of how DNA methylation aging arises across temporal scales.

cell biology↗

bioRxiv2025

Collective Gene Expression Fluctuations Encode the Regulatory State of Cells

Gene expression is inherently stochastic, leading to substantial cell-to-cell variability in mRNA and protein abundances. Variability in the expression of individual genes has been associated both with impaired signal processing and with facilitation of stress responses and differentiation. Here, combining machine learning, theory, and analysis of scRNA-seq data across various organisms and tissues, we show that variability in gene expression can be coordinated cell-wide. We define a statistical score that quantifies this coordination in single-cell data and demonstrate that distinct coordination patterns reflect the regulatory state of cells. We further develop a physics-informed machine-learning framework that identifies and predicts such variability patterns. Coordinated gene-expression variability emerges as a hallmark of stem and progenitor cells and distinguishes intrinsic stochasticity from cell-population heterogeneity. Together, our results establish the structure of gene expression variability as a cellular-scale signature of cell identity and regulatory organization.

biophysics↗

bioRxiv2025

A transcriptional clock of the human pluripotency transition

Developmental timing differs strikingly between mammals. All embryonic and some placental lineages emerge from the pluripotent epiblast in a temporally defined sequence, lasting about two weeks in the human embryo, but only two days in mice. Moreover, the order of lineage segregation and gene expression differ between the species. We used human pluripotent stem cells to recapitulate this window of epiblast development in vitro. Simultaneous profiling of gene expression and chromatin accessibility in single cells revealed a robust, autonomous switch between cell states during this process. We reconstructed the integrative gene regulatory network (GRN) of transcription factors (TFs) and signalling molecules. Notably, this revealed a transcriptional cascade including temporally close positive and distant inhibitory connections. We suggest that this cascade acts as a transcriptional clock and governs the directionality, timing and intrinsic decisions during epiblast development. From individual gene interactions, we derived a mechanistic mathematical model of the transcriptional clock of pluripotency that closely reproduced gene expression dynamics and identified key regulatory connections. Moreover, our model revealed a bistable switch governing the transition, thus translating the GRN inference into an interpretable mechanism. Strikingly, the GRN model derived for humans predicted the acceleration of developmental timing in mice when initialised with mouse-specific expression patterns, yet still leading to a human-like expression state. Therefore, TF levels explain developmental timing, whereas the architecture of the network defines its trajectory. Together, our work provides novel conceptual insights into the intrinsic mechanisms of developmental transitions in the human embryo. HIGHLIGHTSO_LIThe human pluripotency transition is guided by an intrinsic developmental programme C_LIO_LIA cascade of transcription factors defines directionality and timing of the pluripotency transition through positive and negative interactions C_LIO_LITranscription factor levels explain developmental timing C_LIO_LIThe architecture of the gene regulatory network defines its trajectory C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/643129v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@1faf1aaorg.highwire.dtl.DTLVardef@10053borg.highwire.dtl.DTLVardef@1c76aacorg.highwire.dtl.DTLVardef@12c7b89_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2024

Collective dynamics of DNA methylation during ageing

Ageing is the decline of physiological function over time. Statistical models termed ageing clocks can predict chronological and biological age from the longitudinal time evolution of DNA methylation. Here, we show that DNA methylation ageing is also manifest in how pairs of genomic loci evolve with respect to each other with age. Using sequencing data from a range of tissues in mouse we show that genomic correlations in DNA methylation during ageing are characterised by an enrichment of correlations between sites that are roughly 500 bp apart. We trace the origin of this behaviour to collective dynamics in the boundaries of CpG islands. We derive a simple, biophysical model that explains the origin due to a tilt in the competition between methylating and demethylating processes and an ensuing wetting-like phenomenon. Using Chip-seq data, we argue for a molecular mechanism based on a PRC2-dependent dilution of H3K27me3 during ageing. Our work gives a new perspective on epigenetic ageing, highlighting the importance of correlative as opposed to longitudinal dynamics.

genomics↗

bioRxiv2024

Pre-cancerous Niche Remodelling Dictates Nascent Tumour Survival

Interactions between mutant cells and their environment play a key role in determining cancer susceptibility. However, our understanding of how the pre-cancer microenvironment contributes to early tumorigenesis remains limited. Here, we show that newly emerging tumours at their most incipient stages shape their microenvironment in a critical process that determines their survival. Analysis of nascent squamous tumours in the upper gastrointestinal tract of the mouse reveals that the stress response of early tumour cells instructs the underlying mesenchyme to form a supportive "pre-cancer niche", which dictates the long-term outcome of epithelial lesions. Stimulated fibroblasts beneath emerging tumours activate a wound healing response that triggers a dramatic remodelling of the underlying extracellular matrix, resulting in the formation of a fibronectin-rich stromal scaffold that promotes tumour growth. Functional heterotypic 3D culture assays and in vivo grafting experiments, combining carcinogen-free healthy epithelium and tumour-derived stroma, demonstrate that the pre-cancerous niche alone is sufficient to confer tumour properties to healthy epithelial cells. We propose a model where both mutations and the stromal response to genetic stress defines the likelihood of early tumours to survive and progress towards more advanced disease stages.

cancer biology↗

bioRxiv2024

Transcriptional landscapes underlying Notch-induced lineageconversion and plasticity of mammary basal cells

The mammary epithelium derives from multipotent mammary stem cells (MaSCs) that progressively restrict their potency and engage into lineage commitment during embryonic development. Although postnatal mammary progenitors are lineage-restricted and unipotent, several lines of evidence have documented their extensive plasticity and ability to reactivate multipotency in several non-physiological contexts. We have previously shown that ectopic Notch1 activation in committed mammary basal cells, which never experience Notch activity in homeostatic conditions, triggers a progressive cell fate switch from basal to luminal cell identity in both the pubertal and adult mouse mammary gland. Here, we tested the conservation of this mechanism in other glandular epithelia and found that constitutive Notch1 signaling also induces a basal-to-luminal cell fate switch in adult cells of the lacrimal gland, the salivary gland, and the prostate. Since cells do not undergo lineage transition synchronously and this switch is progressive in time, we performed single cell transcriptomic analysis by SMART-Seq on index-sorted mutant mammary cells at different stages of lineage conversion, to reveal the molecular pathways underlying the fate transition. Combining single cell transcriptomics analyses with assays in organoid cultures, we demonstrate that proliferation of basal mutant cells is indispensable to convert them into luminal progenitors. We thus reveal the molecular mechanisms and individual transcriptional landscapes controlling lineage conversion and cellular plasticity of unipotent committed mammary cells in vivo with spatial and temporal resolution. Given the strong implications of Notch signaling in cancer, these results also provide important insights into the mechanisms that drive cellular transformation.

developmental biology↗

bioRxiv2023

Self-propagating wave drives noncanonical antidurotaxis of skull bones in vivo

Cell motility is a key feature of tissue morphogenesis, and it is thought to be driven primarily by the active migration of individual cells or collectives. However, this model is unlikely to apply to cells lacking overt cytoskeletal, stable cell-cell or cell-cell adhesions, and molecular polarity, such as mesenchymal cells. Here, by combining a novel imaging pipeline with biophysical modeling, we discover that during skull morphogenesis, a self-generated collagen gradient expands a population of osteoblasts towards a softer matrix. Biomechanical measurements revealed a gradient of stiffness and collagen along which cells move and divide. The moving cells generate an osteogenic front that travels faster than individual tracked cells, indicating that expansion is also driven by cell differentiation. Through biophysical modeling and perturbation experiments, we found that mechanical feedback between stiffness and cell fate drives bone expansion and controls bone size. Our work provides a mechanism for coordinated motion that does not rely upon the cytoskeletal dynamics of cell migration. We term this self-propagating motion down a stiffness gradient, noncanonical antidurotaxis. Identification of alternative mechanisms of cellular motion will help in understanding how directed cellular motility arises in complex environments with inhomogeneous material properties.

biophysics↗

bioRxiv2023

Compartmentalization and synergy of osteoblasts drive bone formation in the regenerating fin

Zebrafish faithfully regenerate their fins after amputation which includes restoration of bone tissue and a component of cell plasticity. It is currently unclear how different cell populations of the regenerate divide labor to allow for efficient regenerate growth and proper patterning. Here, we studied lineage relationships of FACS-enriched epidermal, blastemal and bone forming fin regenerate cells by single cell (sc) RNA sequencing, lineage tracing, targeted osteoblast ablation and electron microscopy to show that the majority of osteoblasts in the outgrowing regenerate derive from osterix+ osteoblasts, while mmp9+ cells give rise to a limited cell number at the fin segment joints. A third population of distal blastema cells contributes to distal osteoblast progenitors, suggesting compartmentalization during appendage regeneration. Fin elongation and bone formation are carried out by distinct regenerate cell populations, and these variably depend on Fgf signaling. Ablation of osterix+ osteoblasts irreversibly impairs patterning of segment joints, and prevents bone matrix formation in the proximal regenerate. The resulting reduced regenerate length is partially compensated for by the distal regenerate which shows increased Wnt signaling activity. Surprisingly, ablation of joint cells does not abolish the formation of segment joints. Our study characterizes rare fin regenerate cell populations, indicates intricate osteoblast-blastema lineage relationships, inherent detection and compensation of impaired regeneration, and demonstrates zonation of the elongating regenerate. Furthermore, it sheds light on the variable dependence of bone formation on growth factor signaling.

developmental biology↗

bioRxiv2023

Single cell DNA methylation ageing in mouse blood

Ageing is the accumulation of changes and overall decline of the function of cells, organs and organisms over time. At the molecular and cellular level, the concept of biological age has been established and biomarkers of biological age have been identified, notably epigenetic DNA-methylation based clocks. With the emergence of single-cell DNA methylation profiling methods, the possibility to study biological age of individual cells has been proposed, and a first proof-of-concept study, based on limited single cell datasets mostly from early developmental origin, indicated the feasibility and relevance of this approach to better understand organismal changes and cellular ageing heterogeneity. Here we generated a large single-cell DNA methylation and matched transcriptome dataset from mouse peripheral blood samples, spanning a broad range of ages (10-101 weeks of age). We observed that the number of genes expressed increased at older ages, but gene specific changes were small. We next developed a robust single cell DNA methylation age predictor (scEpiAge), which can accurately predict age in a broad range of publicly available datasets, including very sparse data and it also predicts age in single cells. Interestingly, the DNA methylation age distribution is wider than technically expected in 19% of single cells, suggesting that epigenetic age heterogeneity is present in vivo and may relate to functional differences between cells. In addition, we observe differences in epigenetic ageing between the major blood cell types. Our work provides a foundation for better single-cell and sparse data epigenetic age predictors and highlights the significance of cellular heterogeneity during ageing. Highlights- Model to estimate DNA methylation age in single cells - Large multi-omics dataset of single cells from murine blood - Epigenetic age deviations from chronological age are greater than technical expected from technical variability - Number of genes expressed increases with chronological and epigenetic age

cell biology↗

bioRxiv2022

Metabolic enhancement of mammalian developmental pausing

The quest to model and modulate embryonic development became a recent cornerstone of stem cell and developmental biology. Mammalian developmental timing is adjustable in vivo by preserving preimplantation embryos in a dormant state called diapause. Inhibition of the growth regulator mTOR (mTORi) pauses mouse development in vitro, yet constraints to pause duration are unrecognized. By comparing the response of embryonic and extraembryonic stem cells to mTORi-induced pausing, we identified lipid usage as a bottleneck to developmental pausing. Enhancing fatty acid oxidation (FAO) boosts embryo longevity, while blocking it reduces the pausing capacity. Genomic and metabolic analyses of single embryos point toward a deeper dormant state in FAO-enhanced pausing and reveal a link between lipid metabolism and embryo morphology. Our results lift a constraint on in vitro embryo survival and suggest that lipid metabolism may be a critical metabolic transition relevant for longevity and stem cell function across tissues. One-Sentence SummaryFacilitating fatty acid oxidation by carnitine supplementation enhances mTOR inhibition-mediated developmental pausing.

developmental biology↗

bioRxiv2021

Inference of emergent spatio-temporal processes from single-cell sequencing reveals feedback between de novo DNA methylation and chromatin condensates

Recent breakthroughs in single-cell genomics allow probing molecular states of cells with unprecedented detail along the sequence of the DNA. Biological function relies, however, on emergent processes in the three-dimensional space of the nucleus, such as droplet formation through phase separation. Here, we use single-cell multi-omics sequencing to develop a theoretical framework to rigorously map epigenome profiling along the DNA sequence onto a description of the emergent spatial dynamics in the nucleus. Drawing on scNMT-seq multi-omics sequencing in vitro and in vivo we exemplify our approach in the context of exit from pluripotency and global de novo methylation of the genome. We show how DNA methylation patterns of the embryonic genome are established through the interplay between spatially correlated DNA methylation and topological changes to the DNA. This feedback leads to the predicted formation of 30-40nm sized condensates of methylated DNA and determines genome-scale DNA methylation rates. We verify these findings with orthogonal single cell multi-omics data that combine the methylome with HiC measurements. Notably, this scale of chromatin organization has recently been described by super-resolution microscopy. Using this framework, we identify local methylation correlations in gene bodies that precede transcriptional changes at the exit from pluripotency. Our work provides a general framework of how mechanistic insights into emergent processes underlying cell fate decisions can be gained by the combination of single-cell multi-omics and methods from theoretical physics that have not been applied in the context of genomics before. HighlightsO_LIWe develop methodology to infer collective spatio-temporal processes in the physical space of the nucleus from single-cell methylome sequencing experiments. C_LIO_LIWe show that DNA methylation relies on a feedback between de novo methylation and nanoscale changes in DNA topology, leading to the formation of methylation condensates. C_LIO_LIChromatin condensates at this scale have recently been described by high-resolution microscopy but have remained without mechanistic explanation. C_LIO_LIUsing this framework, we identify changes in the distribution of DNA methylation marks in gene bodies that precede gene silencing at the exit from pluripotency. C_LI

genomics↗

bioRxiv2020

Specialisation and plasticity in a primitively social insect

Biological systems not only have the remarkable capacity to build and maintain complex spatio-temporal structures in noisy environments, they can also rapidly break up and rebuild such structures. How such systems can simultaneously achieve both robust specialisation and plasticity is poorly understood. Here we use primitive societies of Polistes wasps as a model system where we experimentally perturb the social structure by removing the queen and follow the re-establishment of the social steady state over time. We combine a unique experimental strategy correlating time-resolved measurements across vastly different scales with a theoretical approach. We show that Polistes integrates antagonistic processes on multiple scales to distinguish between extrinsic and intrinsic perturbations and thereby achieve both robust specialisation and rapid plasticity. The long-term stability of the social structure relies on dynamic DNA methylation which controls transcriptional noise. Such dynamics provide a general principle of how both specialization and plasticity can be achieved in biological systems. One Sentence SummaryA primitive social insect simultaneously achieves specialisation and plasticity by integrating antagonistic dynamics on different scales. HighlightsO_LIWe employ a unique experimental approach correlating dynamics of societies, individuals, and epigenetic gene regulation C_LIO_LIA social insect simultaneously achieves specialisation and plasticity by integrating antagonistic processes on different spatial scales C_LIO_LIRegulation of population-level noise by DNA methylation ensures long-term stability of phenotypic specialisation C_LI

biophysics↗

bioRxiv2019

Lineage hierarchies and stochasticity ensure the long-term maintenance of adult neural stem cells

The cellular basis and extent of neural stem cell (NSC) self-renewal in adult vertebrates, and their heterogeneity, remain controversial. To explore the functional behavior and dynamics of individual NSCs within brain germinal pools, we combined genetic lineage tracing, quantitative clonal analysis, intravital imaging and global population assessments in the adult zebrafish telencephalon. We show that adult neurogenesis is organized in a hierarchy where a subpopulation of reservoir NSCs with longterm self-renewal potential generate a pool of operational NSCs taking stochastic fates biased towards neuronal differentiation. To fuel the long-term growth of the adult germinal niche, we provide evidence for the existence of an additional, upstream, progenitor population that supports the continuous generation of new reservoir NSCs, contributing to their overall expansion. Hence, the dynamics of vertebrate neurogenesis relies on a hierarchical organization where growth, self-renewal and neurogenic functions are segregated between different NSC types.

neuroscience↗

bioRxiv2018

Lgr5+ stem/progenitor cells reside at the apex of the embryonic hepatoblast pool

AbstractDuring mouse embryogenesis, progenitors within the liver known as hepatoblasts give rise to adult hepatocyte and cholangiocyte cells. Hepatoblasts, which are specified at E8.5-E9.0, have been regarded as a homogeneous population of progenitors, which initiate differentiation into hepatocytes and cholangiocytes from E13.5 onwards. Recently, sub-populations of transcriptionally different hepatoblasts have been identified as already present at E11.5 by single cell RNAseq (scRNAseq) analysis. However, whether these transcriptional differences result from functionally heterogeneous hepatoblast populations is unknown. Here we show that the hepatoblast pool is not only transcriptionally but also functionally heterogeneous and that a sub-population of E9.5-E10.0 hepatoblasts exhibits a previously unidentified early commitment to cholangiocyte fate. Importantly, we also identify a sub-population of bona-fide E9.5 hepatoblasts which express the adult stem cell marker Lgr5 and contribute to liver development by generating both hepatocyte and cholangiocyte progeny that persist for the life-span of the mouse. Using a combination of lineage tracing and scRNAseq, we show that Lgr5 marks E9.5-E10.0 bi-potent liver progenitors residing at the apex of a hierarchy of the hepatoblast population. Notably, isolated Lgr5+ hepatoblasts can be clonally expanded in vitro into embryonic liver organoids, which can commit to hepatocyte or cholangiocyte fates dependent upon the culture conditions. Our study represents the first functional demonstration of heterogeneity within E9.5 hepatoblasts and identifies Lgr5 as a marker for a sub-population of truly bi-potent liver progenitors.\n\nSummary StatementLgr5 positive bi-potential hepatoblasts contribute to liver development and reside at the apex of an embryonic liver progenitor pool.

developmental biology↗

bioRxiv2018

Genome-scale oscillations in DNA methylation during exit from pluripotency

Pluripotency is accompanied by the erasure of parental epigenetic memory with naive pluripotent cells exhibiting global DNA hypomethylation both in vitro and in vivo. Exit from pluripotency and priming for differentiation into somatic lineages is associated with genome-wide de novo DNA methylation. We show that during this phase, coexpression of enzymes required for DNA methylation turnover, DNMT3s and TETs, promotes cell-to-cell variability in this epigenetic mark. Using a combination of single-cell sequencing and quantitative biophysical modelling, we show that this variability is associated with coherent, genome-scale, oscillations in DNA methylation with an amplitude dependent on CpG density. Analysis of parallel single-cell transcriptional and epigenetic profiling provides evidence for oscillatory dynamics both in vitro and in vivo. These observations provide fresh insights into the emergence of epigenetic heterogeneity during early embryo development, indicating that dynamic changes in DNA methylation might influence early cell fate decisions.\n\nHighlightsO_LICo-expression of DNMT3s and TETs drive genome-scale oscillations of DNA methylation\nC_LIO_LIOscillation amplitude is greatest at a CpG density characteristic of enhancers\nC_LIO_LICell synchronisation reveals oscillation period and link with primary transcripts\nC_LIO_LIMultiomic single-cell profiling provides evidence for oscillatory dynamics in vivo\nC_LI

genomics↗