Biology subjects

Chakrabarti, S.

Publications and source records attributed to Chakrabarti, S..

At least 19 recordsLinked to original sources

bioRxiv2026

A Donor T-Cell Receptor Structural Signature Determines Alloreactive Potential and Predicts Acute Graft-Versus-Host Disease

Acute graft-versus-host disease (GVHD) remains a lethal barrier to successful allogeneic hematopoietic cell transplantation, yet pre-transplant donor selection entirely ignores hypervariable T-cell receptor (TCR) architecture. Here, by characterizing over 64,000 alloreactive clonotypes, we demonstrate that human alloreactivity is dictated by a constrained, predictable baseline structural signature. Pathogenic, tissue-infiltrating alloreactive T cells exhibit significantly shortened CDR3{beta} regions, altered antigen-facing biophysical features, biased VJ gene usage and extensive inter-donor sharing originating from public anti-pathogen memory reservoirs. These potent clones natively cluster within the high-frequency fraction of the unstimulated baseline donor repertoire. We introduce R50, an assay-independent metric quantifying this clonal dominance, which independently predicted a six-fold increased risk of acute GVHD in a cross-institutional cohort. This scalable in silico platform shifts pre-transplant risk stratification from HLA typing and demographic surrogates to precision immune-receptor modeling.

immunology↗

bioRxiv2026

Early peripheral immune signaling precedes tau elevation and blood-brain barrier disruption in Alzheimer's disease

AbstractNeuroinflammation, along with amyloid beta (A{beta}) deposition, phospho-tau (ptau) accumulation, blood-brain barrier (BBB) disruption, and cognitive decline are recognized components of Alzheimers disease (AD). However, the timing and nature of peripheral immune changes across AD biological and clinical stages remain poorly understood. Here we performed mass cytometry profiling of whole blood and cerebrospinal fluid (CSF) immune cells from 351 human samples across two independent clinical cohorts spanning the AD continuum. We identify coordinated peripheral immune signaling signatures that emerge during preclinical stage of AD and precede significant elevation of plasma ptau217, CSF ptau181 and BBB disruption measured by dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI). AD-enriched immune features, including increased phospho-Akt signaling in nai ve T killer cells and phospho-PLC{gamma}2 signaling in granulocytes, were not observed in patients with Frontotemporal lobar degeneration or treatment-nai ve multiple sclerosis. Furthermore, these immune signaling states could be induced in healthy donor immune cells following exposure to plasma or CSF from individuals with AD, indicating that circulating factors can drive these peripheral immune alterations. Together, our findings demonstrate that dynamic peripheral immune state changes arise early in AD and precede canonical biomarker and vascular changes, highlighting immune signaling pathways as potential targets for early therapeutic intervention. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=187 HEIGHT=200 SRC="FIGDIR/small/716122v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@f5060corg.highwire.dtl.DTLVardef@600ba7org.highwire.dtl.DTLVardef@19d281dorg.highwire.dtl.DTLVardef@b4a36a_HPS_FORMAT_FIGEXP M_FIG Early peripheral immune signaling precedes tau elevation and blood-brain barrier disruption in Alzheimers disease. C_FIG

neuroscience↗

bioRxiv2026

Computational insights into the interaction between Topoisomerase I and Rpc82 subunit of RNA Polymerase III in Saccharomyces cereviseae

The process of DNA transcription leads to the generation of torsional stress, which must be resolved for smooth progression of the transcription machinery. In Saccharomyces cerevisiae, DNA topoisomerase I (Top1), a type IB topoisomerase, plays a critical role in relaxing supercoils and mitigating the topological strain associated with transcription. While several proteins from the transcription machinery have been reported to interact with yeast Top1, detailed characterization and functional relevance of these interactions have remained underexplored. This gap is partly due to the absence of a complete three-dimensional structure of the full-length enzyme, which hinders structure-based computational analyses of its interactome. In this study, we present a template-based model of full-length yeast Top1. Leveraging this model, we investigated its molecular interaction with Rpc82, a key subunit of RNA polymerase III enzyme, responsible for transcribing small non-coding RNAs such as tRNAs and 5S rRNA. Through molecular docking and molecular dynamics simulations, critical residues at the Top1-Rpc82 interface were identified that likely mediate their interaction. Our findings provide new insights into the structural basis of Top1s association with RNA polymerase III and its potential role in regulating Pol III-mediated transcription. The Top1 model developed here offers a valuable framework for future in silico studies aimed at elucidating the broader interactome and regulatory mechanisms of this essential enzyme.

bioinformatics↗

bioRxiv2025

Epoxyazadiradione ameliorates Parkinson's disease by upregulating heat shock factor 1 and protein degradation pathways in mice.

Parkinsons disease (PD) is a major debilitating health concern for millions of the elderly population all over the world. This progressive neurodegenerative disorder also poses a severe mental and financial burden to caregivers and society. Despite a major thrust on research for therapy development, no significant progress has been made; only temporary management options are currently available. To this end, we have reported azadiradione (AZD), a triterpenoid that we isolated from neem seed extract using a cell-based assay. AZD showed high efficacy in ameliorating protein aggregation-induced pathology and symptoms in fruit flies and mice. Current evidence suggests that AZD functions through activating the transcriptional function of heat shock factor 1 (HSF1), a master regulator of protein quality control pathways, without modulating the cellular redox balance. To better understand the pharmacophore of AZD, a triterpenoid in its observed function, we have analysed various structural derivatives, focusing on their HSF1-activating function in vitro and their efficacies in ameliorating protein aggregation-induced toxicities in cell and mouse models. Our analyses, based on real-time PCR, immunoblots, fluorescent anisotropy, and a mouse model of MPTP-induced PD, highlighted Epoxy-azadiradione (Epoxy) as being as efficient as AZD in in vivo functional tests, albeit activating the promoter binding activity of HSF1 with at least two-fold higher efficacy in vitro. Notably, similar to AZD, Epoxy did not induce cellular redox imbalance. We also incorporated molecular docking analyses involving the published crystal structure of the DNA-binding domain of HSF1 bound to its DNA recognition element to study molecular dynamics-based energy estimation. The analysis revealed a higher energy stability of the epoxy-bound complexes, as indicated by a significant decrease in binding free energy ({Delta}G) estimated from an ensemble of intermediate docked complex structures.

pharmacology and toxicology↗

bioRxiv2025

Modular to cyclic TCA governs hematopoiesis in Drosophila

TCA cycle is well known for its role in bioenergetics and also a hub for metabolic exchange, here we identify a developmentally programmed, non-uniform TCA architecture that is required for hematopoietic state transitions in the Drosophila lymph gland. Early blood progenitors operate a modular TCA configuration, in which a CS/mAcon1-derived citrate node preserves progenitor identity, while a Gdh/Kdh mediated -ketoglutarate to succinyl-CoA branch, not succinate, supports proliferative potential. As cells exit the progenitor state and initiate lineage commitment, the cells undergo metabolic reorganization and engage a fully cyclic, Pdh- and Idh-dependent oxidative TCA cycle whose cataplerotic activity keeps the levels of TCA metabolites in check as their excess otherwise induces differentiation. Blocking these metabolic transitions disrupts progenitor homeostasis, compromises proliferative competency of transitional progenitors, and distorts balanced differentiation. These findings establish a developmentally regulated alternative to the traditional TCA cycle and reveals that appropriate engagement of modular versus cyclic TCA modes is required for orchestrating hematopoietic fate transitions. This work highlights TCA topology and not flux alone functions as a core determinant of stemness, proliferation, and lineage progression during hematopoiesis. Significance StatementHematopoietic development requires precise metabolic control to maintain progenitors while enabling their transition into differentiated lineages. We show that the Drosophila lymph gland achieves this through a developmentally programmed switch in TCA-cycle configuration where early progenitors rely on a modular TCA architecture that independently sustains identity and proliferation, whereas later stages require a fully cyclic, oxidative TCA mode to maintain homeostasis and balanced differentiation. Disrupting either phase perturbs hematopoietic organization, demonstrating that TCA topology itself regulates cell-state transitions. These findings reveal TCA architecture as the determinant of hematopoietic fate and provides a conceptual framework relevant to hematopoiesis and also stem cell biology.

developmental biology↗

bioRxiv2025

Drosophila blood cells bridge distant injury and gut homeostasis through Upd3-mediated inter-organ signaling

Inter-organ communication is a central feature of host defence and tissue repair. In Drosophila, hemocytes secrete the cytokine-like ligand Unpaired 3 (Upd3, an IL-6 homolog) to activate JAK/STAT signaling in the gut, yet why this axis is essential for survival after injury has remained unclear. Here we show that loss of hemocyte activation by reactive oxygen species (ROS) and the consequent failure to produce Upd3 leads to adherens junction disruption, intestinal barrier dysfunction, and increased lethality following clean injury. Hemocyte-derived Upd3 drives sustained STAT activation in the gut epithelium, promoting enterocyte turnover and survival after injury. Chronic STAT activity further modulates intestinal stem cell fate and differentiation, indicating that hemocyte-gut signaling shapes long-term epithelial homeostasis. Notably, hemocytes home to the gut after distant wounding, where their localized presence enhances resistance to enteric infection. Taken together, these findings reveal that Drosophila blood cells bridge distant injury and gut homeostasis through Upd3-mediated inter-organ signaling that links wound sensing to epithelial integrity and host survival.

immunology↗

bioRxiv2025

Ultrasensitive proteomics uncovers nociceptor diversity and novel pain targets

The richness of our somatosensory experience is reflected in the functional diversity of somatic sensory neurons. Single-cell sequencing (scRNA) of sensory neurons has revealed a molecular basis for such diversity1-3. However, sensory neuron diversity has yet to be captured at the level of the proteome. Here, we combined electrophysiology with deep visual proteomics (DVP)4 to quantify over 6,000 proteins from phenotypically-defined sensory neurons and identified novel proteomic markers of sensory neuron subtypes. Comparative analysis revealed both concordance and meaningful divergence between transcriptomes and proteomes. We further show that up to 3,000 proteins can be quantified from one-fourth of a single neuron, demonstrating subset-specific protein signatures. In culture, nociceptive neurons can be acutely sensitized to mechanical stimuli by nerve growth factor (NGF) which normally drives inflammatory pain in vivo5. Indeed, overnight exposure of peptidergic nociceptors to NGF and a protein kinase C (PKC) activator produced functional sensitization associated with proteome changes. Functional knockdown experiments identified the up-regulated B3GNT2 enzyme as a potential effector of nociceptor sensitization. In summary, we present a high-resolution proteomic resource linking molecular identity to function, enabling the discovery of novel mechanisms underlying somatic sensation and pain sensitization.

systems biology↗

bioRxiv2025

Cell cycle-dependent variation in endocytosis drives phenotypic diversity in M. tuberculosis

Cell-to-cell heterogeneity is a hallmark of biology, yet how host variability shapes intracellular pathogen phenotypes is unclear. Using single cell approaches and redox-sensitive Mycobacterium tuberculosis reporters, we reveal that interphase-driven shifts in endocytic capacity create distinct intracellular niches. Bacilli residing in high-endocytic G2 cells adopt more oxidized redox states, whereas those in low-endocytic G1 cells remain reduced, generating phenotypic diversity within a single infected population. Experimental manipulation of host cell cycle stage reprograms endocytic capacity and intrabacterial redox, establishing a causal link between host state and pathogen diversification. Notably, the finding that the cell cycle regulates endocytic capacity constitutes a fundamental cell-biological discovery with broad implications. This variability persists in post-differentiated macrophages, indicating that proliferative history imprints functional diversity onto innate immune cells. Together, these results identify interphase-regulated endocytosis as a host-intrinsic mechanism that shapes Mycobacterium tuberculosis phenotypes and suggest new host-directed avenues to influence infection trajectories and persistence.

cell biology↗

bioRxiv2025

Mechanically-gated currents in mouse sensory neurons lacking PIEZO2

Touch sensation starts with the opening of mechanically-gated activated ion channels at neuroglial endings of mechanoreceptors in the skin. The function of around half of low threshold mechanoreceptors is dependent on the presence of the mechanically gated ion channel PIEZO2. It has been reported that particularly rapidly-adapting mechanosensitive currents (RA-currents) in the cell bodies of acutely cultured sensory neurons are dependent on PIEZO2. Here we re-examined this question by making a quantitative study of mechanically-gated currents activated by substrate deflection in sensory neurons lacking PIEZO2. We characterized mechanically-gated currents from embryonic and post-natal sensory neurons, taken from global Piezo2-/- or Piezo2 conditional knockouts (Piezo2cko), respectively. Surprisingly in both models, Piezo2 gene deletion was not associated with any significant reduction in the sensitivity or incidence of mechanosensitive currents compared to wild type controls. There was, however, a moderate reduction in the incidence of RA-currents with very fast activation and inactivation kinetics in both embryonic Piezo2-/- and juvenile Piezo2cKO mice. These results show that PIEZO2 channels are not the only mechanosensitive channels mediating RA-currents in sensory neurons. Furthermore, our data suggest that the phenotypes associated with Piezo2 loss of function alleles may sometimes be due to secondary effects of gene deletion, for example, by changing the developmental trajectory of sensory neurons. Emphasis should be put on the diversity of mechanosensitive ion channel function in sensory neurons which needs to be further elucidated. SignificanceThe mechanosensitive ion channel PIEZO2 has been proposed to be the major mechanically-gated ion channel for the transduction of touch. We used patch-clamp electrophysiology to measure mechanically gated currents in sensory neurons lacking PIEZO2 channels using two distinct genetic strategies. Piezo2 gene deletion was associated with a moderate reduction in the frequency of very rapidly inactivating mechanosensitive currents in early post-natal sensory neurons. No significant reduction in the sensitivity or incidence of mechanosensitive currents was observed. These data challenge the idea that PIEZO2 channels are the main transducers of force in sensory neurons, at least via substrate deflection. Other interpretations of loss of function phenotypes, including the possibility that early loss of PIEZO2 could alter developmental trajectories of sensory neurons to impair mechanoreceptor function, should be considered.

neuroscience↗

bioRxiv2025

Reproducibility of Scientific Claims in Drosophila Immunity: A Retrospective Analysis of 400 Publications

Drosophila immunity has been the focus of intense study and has impacted other research fields including innate immunity and agriculturally or epidemiologically relevant investigations of insect pests and vectors. Unsurprisingly for such a large body of work, some published results were later found to be irreplicable. Although some results have been contradicted in the literature, many have no published follow-up, either due to a lack of research or low motivation to publish negative or contradictory results. We have addressed this by performing a reproducibility project that analyses the conceptual replicability of claims from articles published on Drosophila immunity before 2011. To assess replicability, we extracted claims from 400 articles on the Drosophila immune response to bacteria and fungi and performed preliminary verification by comparing these claims to other published literature in the field. Using alternative approaches, we also experimentally tested some unchallenged claims, with no published follow-up. The intent of this analysis was to centralize evidence on insights and findings to improve clarity for scientists that may base research programs on these data. Although the aim of the ReproSci project is to assess the replicability of claims made in articles published in the field of Drosophila immunity, it is in no way an assessment of the scientific value of the research. All our data are published on a publicly available website associated with this article (https://ReproSci.epfl.ch/) that encourages community participation. This article provides a short summary of claims that were found to have contradictory evidence, which may help the community to assess past findings on Drosophila immunity and improve clarity going forward. Statistical analysis of this reproducibility study and metascience insights obtained from this approach are discussed in a companion article.

genetics↗

bioRxiv2025

A retrospective analysis of 400 publications reveals patterns of irreproducibility across an entire life sciences research field

The ReproSci project retrospectively analyzed the conceptual replicability of 1006 claims from 400 papers published between 1959 and 2011 in the field of Drosophila immunity. This project attempts to provide a comprehensive assessment, 14 years later, of the replicability of nearly all publications across an entire scientific community in experimental life sciences. We found that 61% of claims were verified, while only 7% were directly challenged (not replicable), a replicability rate higher than previous assessments. Notably, 24% of claims had never been independently tested and remain unchallenged. We performed experimental validations of a selection of 45 unchallenged claim, that revealed that a significant fraction (38/45) of them is in fact non-replicable. We also found that high-impact journals and top-ranked institutions are more likely to publish challenged claims. In line with the reproducibility crisis narrative, the rates of both challenged and unchallenged claims increased over time, especially as the field gained popularity. We characterized the uneven distribution of irreplicability among first and last authors. Surprisingly, irreplicability rates were similar between PhD students and postdocs, and did not decrease with experience or publication count. However, group leaders, who had prior experience as first authors in another Drosophila immunity team, had lower irreplicability rates, underscoring the importance of early-career training. Finally, authors with a more exploratory, short-term engagement with the field exhibited slightly higher rates of challenged claims and a markedly higher proportion of unchallenged ones. While limited by its reliance on published literature, this systematic, field-wide retrospective study offers meaningful perspective into the ongoing discussion on reproducibility in experimental life sciences.

scientific communication and education↗

bioRxiv2025

Lead optimization against drug-resistant Leishmania donovani infection: Semi-synthetic derivatives of ethyl linoleate isolated from Indian edible mushroom Meripilus giganteus.

Visceral leishmaniasis, the most severe form, affects thousands of people annually. Current drugs in practice fail to provide an absolute cure. Globally, treatment relies on a single dose of liposomal amphotericin B, which requires a costly setup and cold chain to maintain. Natural molecules remain the vital sources of therapeutic ingredients in modern medicine. Meripilus giganteus is traditionally consumed by the people of the North-eastern regions of the Himalayas, India. In this study, we planned for the stepwise bioactivity-guided isolation of natural molecules from M. giganteus and to synthesize more potential therapeutic derivatives against the drug-resistant Leishmania infection. HPLC chromatogram of ethyl acetate extract obtained from M. giganteus revealed the presence of ethyl linoleate as the most active anti-leishmanial molecule. Several derivatives of ethyl linoleate were synthesized and evaluated against Leishmania promastigotes. Among them, a single epoxygenated variant of ethyl linoleate, ethyl (Z)-8-(3-(oct-2-en-1-yl) oxiran-2-yl) octanoate (EL3), showed promising anti-leishmanial activity against both drug-sensitive and drug-resistant Leishmania donovani. The lead derivative disrupts the biosynthesis of trypanothione from glutathione and spermidine, making the parasite vulnerable to the oxidative burst inside the host. Interestingly, the lead derivative was found to be more efficient against the drug-resistant L. donovani, in vivo. Besides this, it has almost no toxicity towards host cells. Considering the urgency for new drug development, we propose this novel semi-synthetic derivative as a potent therapeutic lead.

immunology↗

bioRxiv2025

SIRT1-IDR-Driven Temporal Gating of Sequential Transcription-Factor Recruitment Coordinates Fasting Adaptation

Precise temporal control of gene expression is critical for metabolic adaptation, yet how transcriptional regulators coordinate dynamic responses to nutrient stress remains poorly understood. Here, we identify the intrinsically disordered region (IDR) of SIRT1, encoded by exon-2 (E2), as a key determinant of transcriptional timing during fasting. Using global and conditional SIRT1{Delta}E2 mouse model, which mimics an endogenous transcript variant, we demonstrate that loss of the N-terminal IDR disrupts the hierarchical engagement of transcription factors (TFs), leading to premature and exaggerated activation of gluconeogenic genes. Mechanistically, the IDR acts as a "conformational timer," competitively gating SIRT1 interactions with CREB, FOXO1, and PPAR to ensure sequential TF recruitment and resolution. Absence of this regulatory module resulted in "runaway" CREB activity, aberrant hepatic glucose output, and impaired fasting-refeeding transitions, linking IDR-driven temporal control to systemic metabolic homeostasis. Our findings reveal a paradigm wherein IDRs in upstream metabolic sensors orchestrate transcriptional handovers, offering a molecular basis for the dynamic rewiring of gene networks during physiological transitions. This work expands the functional repertoire of disordered regions beyond TFs, positioning them as critical nodes in nutrient-responsive transcriptional circuits and potential targets for metabolic disorders.

physiology↗

bioRxiv2025

Spatiotemporal Single-Cell Analysis Reveals T Cell Clonal Dynamics and Phenotypic Plasticity in Human Graft-versus-Host Disease

Allogeneic hematopoietic cell transplantation (alloHCT) is curative for various hematologic diseases but often leads to acute graft-versus-host disease (GVHD), a potentially life-threatening complication. We leverage GVHD as a uniquely tractable disease model to dissect complex T-cell-mediated pathology in 27 alloHCT recipients. We integrate pre-transplant identification of alloreactive T-cells with longitudinal tracking across blood and gut, using mixed lymphocyte reaction-based clonal "fingerprinting", TCR clonotyping, single-cell RNA/TCR sequencing, and spatial transcriptomics. Using DecompTCR, a novel computational tool for longitudinal TCR analysis, we uncover clonal expansion programs linked to GVHD severity and TCR features. Multi-omics profiling of gut biopsies reveals enrichment and clonal expansion of CD8 effector and ZNF683(Hobit) resident memory T-cells, cytolytic remodeling of regulatory and unconventional T-cells, and localization of CD8 effector T-cells near intestinal stem cells in crypt loss regions. This framework defines dynamic immune circuit rewiring and phenotypic plasticity with implications for biomarkers and therapies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC="FIGDIR/small/655962v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@178b77dorg.highwire.dtl.DTLVardef@569226org.highwire.dtl.DTLVardef@1951281org.highwire.dtl.DTLVardef@1f1e046_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIPersistent expansion of diverse alloreactive T cell clones is a hallmark of severe GVHD C_LIO_LIDecompTCR reveals dynamic clonal expansion programs linked to GVHD severity and clinical outcome C_LIO_LICD8+ T cell clones exhibit phenotypic plasticity in vivo across intestinal tissue compartments in GVHD C_LIO_LIHigh-resolution spatial profiling shows CD8+ effector T cells localize near intestinal stem cell niches and drive epithelial injury in GVHD C_LI

systems biology↗

bioRxiv2025

UPF1 shuttles between nucleus and cytoplasm independently of its RNA binding and ATPase activities

The ATP-dependent RNA helicase Up-frameshift 1 (UPF1) is an essential protein in mammalian cells and a key factor in nonsense-mediated mRNA decay (NMD), a translation-dependent mRNA surveillance process. UPF1 is mainly cytoplasmic at steady state but accumulates in the nucleus after inhibiting CRM1-mediated nuclear export by Leptomycin B (LMB), indicating that UPF1 shuttles between the nucleus and the cytoplasm. Consistent with its dual localization, there is evidence for nuclear functions of UPF1, for instance in DNA replication, DNA damage response, and telomere maintenance. However, whether any of UPF1s biochemical activities are required for its nuclear-cytoplasmic shuttling remains unclear. To investigate this, we examined two UPF1 mutants: the well-described ATPase-deficient UPF1-DE (D636A/E637A) and a newly generated RNA-binding mutant UPF1-NKR (N524A/K547A/R843A). Biochemical assays confirmed that the UPF1-NKR mutant cannot bind RNA or hydrolyze ATP in vitro but retains interaction with UPF2, UPF3B, and SMG6. Overexpression of UPF1-NKR exerted a dominant-negative eaect on endogenous UPF1 and inhibited NMD. Subcellular localization studies revealed that UPF1-DE accumulates in cytoplasmic granules (P-bodies), even in the presence of LMB, whereas UPF1-NKR shuttles normally. This indicates that UPF1s shuttling does not require its RNA-binding or ATPase activities. Notably, the UPF1-DE.NKR double mutant restored nuclear-cytoplasmic shuttling and prevented accumulation in P-bodies, suggesting that the shuttling defect of UPF1-DE arises from its tight binding to RNA. Overall, our findings demonstrate that UPF1s shuttling is independent of its ATPase and RNA-binding activities, with RNA binding itself being a key determinant of its cytoplasmic retention.

molecular biology↗

bioRxiv2025

Molecular mechanisms of recruitment, function and regulation of UPF1 in histone mRNA decay

Animal replication-dependent histone mRNAs end in a conserved stem loop (SL) instead of the canonical poly(A) tail present in all other eukaryotic mRNAs. Degradation of the histone SL at the end of the S-phase is initiated by the stem-loop binding protein SLBP and its interplay with the RNA helicase UPF1 and the exoribonuclease 3hExo. We report direct interactions between SLBP and UPF1 and show that the unstructured SLBP N-terminus wraps around the UPF1 helicase core, contacting it at multiple sites. Although binding of SLBP to UPF1 impedes unwinding activity, it is critical for efficient histone mRNA decay in cells, as unwinding of the SL facilitates degradation by 3hExo. Here we show that the UPF1-activator, UPF2, binds 3hExo, and that UPF2-mediated activation of UPF1 overrides the inhibitory effect of SLBP. Our results highlight the intricate network of UPF1-centric protein-protein and protein/RNA interactions that fine-tunes its unwinding activity and orchestrates timely and efficient degradation of histone mRNA.

biochemistry↗

bioRxiv2025

Identifying memory gene expression from single sample scRNA-seq data using power law signatures

Genes with expression levels that fluctuate on time scales longer than cell division times are associated with cancer drug tolerance. However, current methods for identifying such memory genes rely on variants of the Luria-Delbruck experiment and require either multiple replicates or lineage information, limiting their use to model systems or in-vitro settings. We develop a new conceptual approach using recent results in Random Matrix Theory to demonstrate that the existence of memory genes results in a power-law signature in the cell covariance matrix eigenspectrum. Utilizing this theoretical framework, we develop Power-Seek, an algorithm to discover memory genes from a single time point scRNA-seq dataset. Without using prior information on lineages or cell-cycle times, Power-Seek correctly identifies memory genes in a melanoma cell line. Our results open up the possibility of identifying expression states driving drug tolerance in real-world scenarios, as we demonstrate using data from a human breast cancer tissue sample.

biophysics↗

bioRxiv2024

Inheritable cell-states shape drug-persister correlations and population dynamics in cancer cells

Drug tolerant persisters (DTPs) drive cancer therapy resistance by temporarily evading drug action, allowing multiple routes to eventual permanent resistance. Despite clear evidence for DTPs, the timing of their emergence, proliferative nature, and how their population dynamics arise from measured single-cell kinetics remain poorly understood. Here we use time-lapse microscopy data from two cancer cell lines, integrating single-cell and population measurements, to develop a quantitative description of drug persistence. Contrary to the expectation that increasing levels of genotoxic stress should lead to slower times to division and faster times to death, we observe minor changes in the single-cell intermitotic and death time distributions upon increasing cisplatin concentration. Yet, population decay rates increase 3-fold, suggesting a surprising independence of the overall dynamics from the measured birth and death rates. To explain this phenomenon, we argue that the observed lineage correlations and concentration-dependent decay rates imply cell-state dependent fate choices made both pre and post-cisplatin as opposed to just post-drug birth/death rate-based competitive fate choices. We demonstrate that these cell-states, present in the ancestors of DTP and sensitive cells, exhibit no difference in cycling speed and are inherited across 2-3 cellular generations. A stochastic model implementing these rules simultaneously recapitulates the observed decay rates and cell-fate correlations, also explaining how pre-drug fate decisions are consistent with barcoding experiments where barcode diversity remains unchanged after drug administration. Our results provide a powerful perspective on drug tolerance based on general arguments, without requiring knowledge of the underlying molecular architecture of the heterogeneous cell states.

cancer biology↗