Biology subjects

Chandra, T.

Publications and source records attributed to Chandra, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Increased stress in early life epigenetically rewires pathways related to aging and longevity

Environmental conditions experienced early in life have profound consequences for vertebrate health, yet the molecular pathways linking developmental stress to aging and reduced lifespan remain poorly understood. Through a novel highly accurate epigenetic clock, developed from RRBS-based blood DNA methylation profiles, we show that experimental lifespan-reducing early-life stress rapidly accelerates epigenetic age in zebra finch chicks (Taeniopygia guttata). Corticosterone-treated 29-day-old chicks share differentially methylated loci with non-treated aged birds and cluster with 6-month-old birds. The transcriptional repressor ZBTB16 emerges as an epigenetically top age-correlated gene and is strongest affected by corticosterone. Elevated developmental corticosterone causes rapid epigenetic remodelling of metabolic pathways well-established in aging and longevity. Our results demonstrate epigenetic rewiring of the aging trajectory through conserved stress-survival mechanisms immediately following elevated early-life stress exposure.

developmental biology↗

bioRxiv2025

Loss of MITF activity leads to emergent cell states from the melanocyte stem cell lineage

How embryonic cells generate large clones of cells in the adult represents a fundamental question in biology. Here using melanocyte stem cells (McSCs) in the zebrafish as a model we explore the function of the master melanocyte transcription factor (MITF) in safeguarding McSCs in embryonic development and their potential to pigment large clones in the adult. MITF is well known is for its role in the specification of melanoblasts from the neural crest (NC) and their differentiation into melanocytes, yet little is known about how this activity shapes the stem cell lineages. Here, we use live imaging coupled with single-cell transcriptomics and lineage tracing to show that MITF (mitfa in zebrafish) protects the melanocyte stem cell (McSC) fate in zebrafish. Utilizing a temperature sensitive mitfavc7 mutant, we show that loss of Mitfa activity leads to a surprising premature and aberrant expansion of McSC progeny at the niche during embryogenesis, coupled with novel emergent transcriptional cell states. Linage tracing of McSCs from the embryonic to juvenile stages reveals Mitfa activity is subsequently required in regeneration by Schwann cell-like and melanocyte stem cell progenitors that serve as a reservoir for fast-responding pigment progenitors. Thus, the impact of Mitfa loss on the melanocyte lineage is cell-state and stage-specific. The emergent cell states resulting from mitfa loss may have important implications for understanding how reduced MITF activity contributes to human genetic disease and melanoma.

developmental biology↗

bioRxiv2025

Inference of clonal hematopoiesis using the collective behaviour of DNA methylation states

Clonal expansion occurs when descendants of a single progenitor cell come to dominate a tissue. We show that this process generates a predictable collective behaviour in DNA methylation landscapes: at CpG sites that faithfully transmit their allelic methylation status across cell divisions, methylation proportions shift toward discrete values (0%, 50%, or 100%) as clones expand. We demonstrate this phenomenon in clonal hematopoiesis, in which a hematopoietic stem cell acquires a fitness-conferring mutation that leads to clonal expansion. Exploiting these dynamics, we developed COMET (Clonal Observation from METhylation), which quantifies clonal burden from bulk methylation data without prior knowledge of driving mutations. Validation against targeted sequencing demonstrated robust prediction across mutation types, accurate longitudinal tracking, and detection of sequencing artifacts. Applied to 15,900 individuals, COMET-predicted clonal hematopoiesis replicated known genetic associations (TCL1A, NRIP1) and phenotypic relationships with smoking and chronic obstructive pulmonary disease. These findings reveal fundamental principles of how clonal dynamics manifest epigenetically and establish a mutation-agnostic approach for clonal burden assessment.

genetics↗

bioRxiv2025

Inflammasomes and DNA Damage Orchestrate Divergent Pyroptotic Fates in Neutrophils

The understanding of pyroptotic cell death and its mechanistic insights in neutrophils remains less explored and ambiguous. This study analyzes neutrophil pyroptotic responses under different conditions and dissects distinct pyroptosis-associated events, including IL-1{beta} release and cell death. We decipher the signalling pathways underlying these responses and distinguish them from other cell death mechanisms. Interestingly, we observe IL-1{beta} release and enhanced survival in neutrophils in response to LPS-primed ATP-treatment, in contrast to a combination of IL-1{beta} release with cell death in macrophages. While LPS-primed nigericin-treated neutrophils exhibit IL-1{beta} release and cell death, characterized by nuclear rounding, cell swelling/ ballooning, plasma membrane pore formation, and subsequent cell rupture, confirming the occurrence of pyroptotic cell death. While nigericin alone triggers cytokine uncoupled pyroptosis. Intriguingly, these phenomena do not induce under other death programs, including apoptosis, NETosis. This provides opportunity to unravel the regulation of these pyroptotic responses in neutrophils. Data observed reveal the role of NLRP3 and context-dependent caspase -1 & 11 in IL-1{beta} secretion. While, DNA damage and caspase-7 & 9 regulate pyroptotic death. Intriguingly, forced DNA damage by ATM kinase inhibitor mitigated inflammasome activation and IL-1{beta} release, while spur death. Furthermore, this study identifies perinuclear actomyosin forces driving nuclear rounding and pyroptotic death. Both murine neutrophils exposed to bacteria and human neutrophils treated with nigericin exhibit these pyroptotic processes, highlighting their broad relevance. This study depicts decision whether to secrete cytokines or undergo pyroptotic cell death emphasizing the regulatory role of DNA damage-cytoskeletal axis beyond inflammasome activation. Moreover, LPS and bacteria induced acute lung injury in mice displays nuclear rounding presenting pyroptotic neutrophils and enhanced NLRP3, Caspase-11 activation, and IL-1{beta} release. Together, this study defines intriguing crosstalk of NLRP3, caspases, DNA damage, and actomyosin forces that orchestrate divergent inflammatory fates, potentially leading to opportunities for targeted strategies for combating inflammation. HIGHLIGHTSO_LINeutrophils undergo pyroptotic cell death with nigericin and bacteria, but not with ATP. C_LIO_LILPS priming is essential for IL-1{beta} secretion, while dispensable for cell swelling/ballooning and death. C_LIO_LINLRP3 and Caspase 1/11 regulate IL-1{beta} secretion, while DNA damage and Caspase-7/9 control pyroptotic cell death. C_LIO_LIPerinuclear actomyosin signalling regulates nuclear rounding during pyroptotic cell death. C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=174 HEIGHT=200 SRC="FIGDIR/small/673694v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@102da3forg.highwire.dtl.DTLVardef@46838borg.highwire.dtl.DTLVardef@16648faorg.highwire.dtl.DTLVardef@413bc2_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

A DNA methylation-based clock for age estimates in the wood mouse (Apodemus sylvaticus)

Environmental stressors are expected to accelerate senescence but demonstrating this requires both a measure of senescence and knowledge of chronological age - data rarely available for most wild animals. Here, we constructed a DNA methylation-based epigenetic clock for the wood mouse (Apodemus sylvaticus) using known-aged laboratory individuals and applied it to a wild population of unknown ages. This represents one of the first demonstrations that a laboratory-trained epigenetic clock can be used to infer age structure in free-living animals. Multiple lines of evidence validated use of the clock in wild individuals: age estimates fell within expected ranges, recapitulated population demographic structure, and recovered predicted signatures of senescence, including an increase in infection probability with age. Moreover, wild mice given experimental food supplementation and parasite-removal drugs exhibited slower epigenetic ageing rates. Together, our findings demonstrate that epigenetic clocks can infer both chronological age and ageing rates in the wild, providing a powerful framework to identify the ecological and individual determinants of ageing.

genomics↗

bioRxiv2025

Clinical progression of clonal hematopoiesis is determined by a combination of mutation timing, fitness, and clonal structure

Clonal hematopoiesis (CH) is characterized by expanding blood cell clones carrying somatic mutations in healthy aged individuals and is associated with various age-related diseases and all-cause mortality. While CH mutations affect diverse genes associated with myeloid malignancies, their mechanisms of expansion and disease associations remain poorly understood. We investigate the relationship between clonal fitness and clinical outcomes by integrating data from three longitudinal aging cohorts (n=713, observations=2,341). We demonstrate pathway-specific fitness advantage and clonal composition influence clonal dynamics. Further, the timing of mutation acquisition is necessary to determine the extent of clonal expansion reached during the host individuals lifetime. We introduce MACS120, a metric combining mutation context, timing, and variant fitness to predict future clonal growth, outperforming traditional variant allele frequency measurements in predicting clinical outcomes. Our unified analytical framework enables standardized clonal dynamics inference across cohorts, advancing our ability to predict and potentially intervene in CH-related pathologies.

genetics↗

bioRxiv2024

Machine learning recognises senescence in glioblastoma and discovers senescence-inducing compounds

Senescence is a cell-intrinsic tumour suppressive response. A one-two-punch cancer treatment strategy aims to induce senescence in cancerous cells before removing them with a senolytic. It is important to accurately recognise senescent cells to investigate the feasibility of such a treatment strategy and identify compounds that induce senescence in cancer. We focus specifically on the terminal brain cancer glioblastoma, firstly identifying senescent glioblastoma cells with conventional stains, before training a machine learning model to distinguish senescent cells using only a DAPI nuclear stain. To demonstrate how our method can aid drug discovery, we apply our pipeline to existing glioblastoma high-throughput phenotypic drug screening imaging data to identify compounds that induce senescence in glioblastoma and verify these predictions experimentally. Author SummaryDamaged cells can enter a senescent cell state, in which they do not divide, but continue to interact with the environment around them. A novel potential cancer treatment strategy is to make tumor cells senescent, before removing senescent cancer cells with a targeted drug. To investigate this treatment strategy in the brain cancer glioblastoma, it is important to be able to accurately recognise senescent glioblastoma cells. As identifying senescent cells is challenging, we create a machine learning pipeline which can detect senescent glioblastoma cells in imaging data. We show that by applying our method to existing data we can discover compounds that induce senescence in glioblastoma. We verify our predictions by testing the compounds experimentally.

cell biology↗

bioRxiv2023

DNA methylation rates scale with maximum lifespan across mammals

DNA methylation rates have previously been found to broadly correlate with maximum lifespan in mammals, yet no precise relationship has been observed. We developed a statistically robust framework to compare methylation rates at conserved age-related sites across mammals. We found that methylation rates negatively scale with maximum lifespan in both blood and skin. The emergence of explicit scaling suggests that methylation rates are - or are linked to - an evolutionary constraint on maximum lifespan acting across diverse mammalian lineages.

genetics↗

bioRxiv2023

Modelling the dynamics of senescence spread

Cellular senescence is a cell surveillance mechanism that arrests the cell cycle in damaged cells. The senescent phenotype can spread from cell to cell through paracrine and juxtacrine signalling, but the dynamics of this process are not well understood. Although senescent cells are important in ageing, wound healing, and cancer, it is unclear how the spread of senescence is contained in senescent lesions. In the absence of the immune system, senescence could theoretically spread infinitely from one cell to another, but this contradicts experimental evidence. To investigate this issue, we developed both a minimal mathematical model and a stochastic simulation of senescence spread. Our results suggest that differences in the number of signalling molecules secreted between subtypes of senescent cells can limit the spread of senescence. We found that dynamic, timedependent paracrine signalling prevents the uncontrolled spread of senescence and we demonstrate how model parameters can be determined using Bayesian inference in a proposed experiment.

systems biology↗

bioRxiv2023

Probabilistic inference of epigenetic age acceleration from cellular dynamics

The emergence of epigenetic predictors was a pivotal moment in geroscience, propelling the measurement and concept of biological ageing into a quantitative era. However, while current epigenetic clocks have shown strong predictive power, they do not reflect the underlying biological mechanisms driving methylation changes with age. Consequently, biological interpretation of their estimates is limited. Furthermore, our findings suggest that clocks trained on chronological age are confounded by non-age-related phenomena. To address these limitations, we developed a probabilistic model that describes methylation transitions at the cellular level. Our approach reveals two measurable components, acceleration and bias, that directly relate to perturbations of the underlying cellular dynamics. Acceleration is the proportional increase in the speed of methylation transitions across CpG sites, whereas bias is the degree of global change in methylation affecting all CpG sites uniformly. Using data from 7,028 participants from the Generation Scotland study, we found the age acceleration parameter to be associated with physiological traits known to impact healthy ageing. Furthermore, a genome-wide association study of age acceleration identified four genomic loci previously linked with ageing.

cell biology↗

bioRxiv2023

Salmonella Typhimurium effector SseI regulates host peroxisomal dynamics to acquire lysosomal cholesterol for better intracellular growth

Intracellular Salmonella resides and multiplies in cholesterol-rich specialized compartment called Salmonella-containing vacuoles (SCVs) and avoids fusion with acidic lysosomes. Given, lysosomes are primary organelle that redistributes LDL derived cholesterol to other organelles; we questioned how lysosomal cholesterol can be transported to SCV. We demonstrate here that peroxisomes are recruited to SCVs in human primary macrophages, epithelial cells and functions as pro-bacterial organelles. Further, this interaction is assisted by SseI, a Salmonella effector protein containing mammalian peroxisome targeting sequence. SseI localizes to peroxisome, interacts and activates a host Ras GTPase, ARF-1 on the peroxisome membrane. Activation of ARF-1 leads to recruitment of phosphatidylinsolitol-5- phosphate-4 kinase to generate phosphatidylinsolitol-4-5-bisphosphate on peroxisomes. Accordingly, the{Delta} sseI strain showed reduced virulence in cell lines and during mice infection. Taken together, our work identified a fascinating mechanism by which a pathogen targets host organelles via its secretory effectors and exploits host metabolic intermediates for its intracellular proliferation.

cell biology↗

bioRxiv2023

Region-Based Epigenetic Clock Design Improves RRBS-Based Age Prediction

Recent studies suggest that epigenetic rejuvenation can be achieved using drugs that mimic calorie restriction and techniques such as reprogramming induced rejuvenation. To effectively test rejuvenation in vivo, mouse models are the safest alternative. However, we have found that the recent epigenetic clocks developed for mouse reduced-representation bisulphite sequencing (RRBS) data have significantly poor performance when applied to external datasets. We show that the sites captured and the coverage of key CpGs required for age prediction vary greatly between datasets, which likely contributes to the lack of transferability in RRBS clocks. To mitigate these coverage issues in RRBS-based age prediction, we present two novel design strategies that use average methylation over large regions rather than individual CpGs, whereby regions are defined by sliding windows (e.g. 5 kb), or density-based clustering of CpGs. We observe improved correlation and error in our regional blood clocks (RegBCs) compared to published individual-CpG-based techniques when applied to external datasets. The RegBCs are also more robust when applied to low coverage data and detect a negative age acceleration in mice undergoing calorie restriction. Our RegBCs offer a proof of principle that age prediction of RRBS datasets can be improved by accounting for multiple CpGs over a region, which negates the lack of read depth currently hindering individual-CpG-based approaches.

bioinformatics↗

bioRxiv2022

Single cell analysis of senescent epithelia reveals targetable mechanisms promoting fibrosis

Progressive fibrosis and maladaptive organ repair result in significant morbidity and millions of premature deaths annually. Senescent cells accumulate with ageing and after injury and are implicated in organ fibrosis, but the mechanisms by which senescence influences repair are poorly understood. Using two murine models of injury and repair we show that obstructive injury generates senescent epithelia which persist after resolution of the original injury, promote ongoing fibrosis and impede adaptive repair. Depletion of senescent cells with ABT263 reduces fibrosis in reversed ureteric obstruction and after renal ischaemia-reperfusion injury. We validate these findings in humans, showing that senescence and fibrosis persist after relieved renal obstruction. We next characterise senescent epithelia in murine renal injury using single cell RNA-Seq. We extend our classification to human kidney and liver disease and identify conserved pro-fibrotic proteins which we validate in vitro and in human disease. We demonstrate that one such molecule, Protein Disulfide Isomerase Family A Member 3 (PDIA3), is essential for TGF-beta mediated fibroblast activation. Inhibition of PDIA3 in vivo significantly reduces kidney fibrosis during ongoing renal injury and as such represents a new potential therapeutic pathway. Analysis of the signalling pathways of senescent epithelia connects senescence to organ fibrosis, permitting rational design of anti-fibrotic therapies.

cell biology↗

bioRxiv2021

Tfap2b specifies an embryonic melanocyte stem cell population that retains adult multi-fate potential

Melanocytes, our pigment producing cells, are replenished from multiple stem cell niches in adult tissues. Although pigmentation traits are known risk-factors for melanoma, we know little about melanocyte stem cell (McSC) populations other than hair follicle McSCs, and lack key lineage markers with which to identify McSCs and study their function. Here, we discover that Tfap2b, and a select set of its target genes, specifies an McSC population at the dorsal root ganglia in zebrafish. Functionally, Tfap2b is required for only a few late-stage embryonic melanocytes, and instead is essential for McSC-dependent melanocyte regeneration. Fate- mapping data reveal that tfap2b-expressing McSCs have multi-fate potential, and are the cell-of- origin for large patches of adult melanocytes, and two other pigment cell types, iridophores and xanthophores. Hence, Tfap2b confers McSC identity in early development, thereby distinguishing McSCs from other neural crest and pigment cell lineages, and retains multi-fate potential in the adult zebrafish. HighlightsO_LITfap2b and its target genes specify McSCs with mixed pigment cell identities C_LIO_LIFunctional dependence on Tfap2b for melanocyte regeneration from the McSC C_LIO_LItfap2b specifies ErbB-dependent McSCs at the stem cell niche C_LIO_LIFate mapping reveals Tfap2b-McSCs have multi-fate potential for adult pigment cells C_LI

developmental biology↗

bioRxiv2021

Longitudinal dynamics of clonal hematopoiesis identifies gene-specific fitness effects

The prevalence of clonal haematopoiesis of indeterminate potential (CHIP) in healthy individuals increases rapidly from age 60 onwards and has been associated with increased risk for malignancy, heart disease and ischemic stroke. CHIP is driven by somatic mutations in stem cells that are also drivers of myeloid malignancies. Since mutations in stem cells often drive leukaemia, we hypothesised that stem cell fitness substantially contributes to transformation from CHIP to leukaemia. Stem cell fitness is defined as the proliferative advantage over cells carrying no or only neutral mutations. It is currently unknown whether mutations in different CHIP genes lead to distinct fitness advantages that could form the basis for patient stratification. We set out to quantify the fitness effects of CHIP drivers over a 12 year timespan in older age, using longitudinal error-corrected sequencing data. We developed a new method based on drift-induced fluctuation (DIF) filtering to extract fitness effects from longitudinal data, and thus quantify the growth potential of variants within each individual. Our approach discriminates naturally drifting populations of cells and faster growing clones, while taking into account individual mutational context. We show that gene-specific fitness differences can outweigh inter-individual variation and therefore could form the basis for personalised clinical management.

cell biology↗

bioRxiv2020

Methylation-Based Age Estimation in a Wild Mouse

The age structure of populations, or the ageing rate of individuals, impacts aspects of ecology, epidemiology and conservation. Yet for many wild organisms, age is an inaccessible trait. In many cases measuring age or ageing rates in the wild requires molecular biomarkers of age. Epigenetic clocks based on DNA methylation have been shown to accurately estimate the age of humans and laboratory mice, but they also show variable ticking rates that are associated with mortality risk above and beyond that predicted by chronological age. Thus, epigenetic clocks are proving to be useful markers of both chronological and biological age, and they are beginning to be applied to wild mammals and birds. We have acquired strong evidence that an accurate clock is possible for the wood mouse Apodemus sylvaticus by adapting epigenetic information from the laboratory mouse (Mus musculus). Apodemus sylvaticus is a well-studied, common small mammal in the UK and Europe, which is amenable to large-scale experimental perturbations and longitudinal sampling of individuals across their lives. These features of the wood mouse system offer opportunities to disentangle causal relationships between ageing rates and environmental stress. Our wood mouse epigenetic clock is PCR-based, and so requires only tiny amounts of tissue accessible through non-destructive sampling. We quantified methylation using Oxford Nanopore sequencing technology and present a new bioinformatics pipeline for data analysis. We thus describe a new and generalizable system that should enable ecologists and other field biologists to go from small tissue samples to an epigenetic clock for their study animal, which will enable investigations of ageing in the wild which where previously inaccessible.

genetics↗

bioRxiv2020

Kidney single-cell atlas reveals myeloid heterogeneity in progression and regression of kidney disease.

The kidney has a limited capacity to repair following injury, however, the endogenous reparative pathways are not well understood. Here we employ integrated droplet- and plate-based scRNA-seq in the murine reversible unilateral ureteric obstruction model to dissect the transcriptomic landscape at the single cell level during renal injury and resolution of fibrosis. We generate a comprehensive catalogue of the changes induced during injury and repair, revealing significant myeloid cell heterogeneity, which would not have been identifiable by conventional flow cytometry. We identify new markers for the myeloid populations within the kidney as well as identification of novel subsets including an Arg1+ monocyte population specific to early injury and a Mmp12+ macrophage subset exclusive to repair. Finally, using paired blood exchange to track circulating immune cells, we confirm that monocytes are recruited to the kidney early after injury and are the source of Ccr2+ macrophages that accumulate in late injury. Our data demonstrate the utility of complementary technologies to identify novel myeloid subtypes that may represent therapeutic targets to inhibit progression or promote regression of kidney disease.

immunology↗

bioRxiv2019

G2M splits mouse embryonic stem cells into naïve and formative pluripotency states

Embryonic stem cells (ESCs) express heterogeneous levels of pluripotency and developmental transcription factors (TFs) and their cell cycle is unsynchronised when grown in the presence of serum. Here, we asked whether the cell cycle and developmental heterogeneities of ESCs are coordinated by determining the state identities of G1- and G2M-enriched mouse ESCs (mESCs) at single cell resolution. We found that G2M cells were not all the same and demonstrate their split into the naive and formative (intermediate) pluripotency states marked by high or low Esrrb expression, respectively. The naive G2M sub-state resembles ground state pluripotency of the LIF/2i cultured mESCs. The naive and formative G2M sub-states exist in the pre- and post-implantation stages of the mouse embryo, respectively, verifying developmental distinction. Moreover, the G2M sub-states partially match between the mouse and human ESCs, suggesting higher similarity of transcriptional control between these species in G2M. Our findings propose a model whereby G2M separates mESCs into naive and formative pluripotency states. This concept of G2M-diverted pluripotency states provides new framework for understanding the mechanisms of pluripotency maintenance and lineage specification in vitro and in vivo, and the development of more efficient and clinically relevant reprogramming strategies.

developmental biology↗