Biology subjects

Gandhi, R.

Publications and source records attributed to Gandhi, R..

At least 19 recordsLinked to original sources

bioRxiv2026

TGFB1-Engineered Induced Mesenchymal Stromal Cells Exhibit High Immunomodulatory Potency and Durably Reprogram Synovial Macrophages in Osteoarthritis

Clinical translation of mesenchymal stromal cell (MSC) therapies derived from primary tissue sources is limited by manufacturing inconsistencies driven by donor-to-donor variability, which reduces predictability of clinical response. Induced pluripotent stem cell (iPSC)-derived MSCs (iMSCs) offer a promising donor-independent, clonal alternative strategy that is also more amenable to engineering, but whether engineered iMSCs reproduce the potency attributes of primary MSCs remains unclear. Here, we benchmarked a doxycycline-inducible, hTERT-immortalized iMSC line engineered to overexpress TGFB1 (TGFB1-iMSCs), a key regulator of macrophage polarization, against multiple adipose tissue-derived MSC (MSC(AT)) donors across predefined immunomodulatory and angiogenic potency attributes. TGFB1-iMSCs were smaller and more circular with comparable or higher proliferative rates than primary MSC(AT) donors. Interestingly, they had a distinct angiogenic signature (EDIL3, EDN1, PDGFA), and nine differentially expressed microRNAs were predicted to target secretory trafficking and growth factor receptor signalling. Functionally, however, TGFB1-iMSCs secreted less VEGF and showed intermediate HUVEC tube formation, but matched or exceeded all primary MSC(AT) donors in a monocyte-macrophage transwell immunomodulatory assay. Notably, in a murine destabilization of the medial meniscus (DMM) model of post-traumatic osteoarthritis, a single intra-articular injection of TGFB1-iMSCs, but not MSC(AT), reduced total synovial macrophage numbers and lowered the MHCII/CD206 ratio at eight weeks, although it did not reduce cartilage degeneration, synovitis, or fibrosis. Together, these findings show that TGFB1-engineered iMSCs have a macrophage-directed potency profile distinct from that of primary MSC(AT). Immortalized iMSCs therefore provide a reproducible platform for mechanistically dissecting engineered MSC potency and its effects on the immune environment.

immunology↗

bioRxiv2026

Human knee osteoarthritis patient-specific cartilage-on-a-chip model captures donor differences to stressors and treatments

Knee Osteoarthritis (KOA) is a progressive whole-joint disease without approved disease modifying OA drugs (DMOADs). Effective treatments have been hindered by multiple layers of heterogeneity, including diverse disease etiology and patient-to-patient variability. Here, we present a scalable, KOA patient-derived (PD) cartilage-on-a-chip (CartChip) model integrating end-stage KOA cartilage tissue explants on a microengineered platform that, under mechanical overloading and hyperinflammatory stressors, mimics different KOA etiologies. These stressors drove distinct multivariable model features, including changes in a curated panel of anabolic and catabolic genes, extracellular matrix protein and soluble factors. Exploratory analysis of coordinated model readouts identified stressor-agnostic and -specific KOA disease signatures. Despite using KOA tissue, the model showed improvements to dexamethasone, a symptom-modifying, anti-inflammatory KOA treatment. The model responses to dexamethasone were dependent on both stressor and donor heterogeneity. Exploratory groupings of coordinated model readouts provided proof-of-concept for predicting categories of patient responsiveness to test therapeutics. Annotating patient data provided additional donor-dependent contexts for interpreting model responsiveness. PD-CartChip provides a powerful research platform to potentially surmount the donor and stressor heterogeneity barrier in developing DMOADs.

bioengineering↗

bioRxiv2026

Joint tissue explant model using psoriatic arthritis synovial fluid as a tool to capture patient-specific responses to treatments

ObjectiveWe developed a patient- and joint-specific explant co-culture system to model active psoriatic arthritis (PsA) and capture donor-specific tissue responses to therapeutic interventions. MethodsBased on convergent joint pathology between end-stage osteoarthritis (OA) and PsA, OA cartilage-bone and synovium tissues from arthroplasty patients were exposed to synovial fluid (SF) obtained from PsA and OA patients. Histological outcomes (synovitis, proteoglycan distribution), curated gene expression, soluble mediators, and proteinase activity were assessed over 7-21-days. Model responses to dexamethasone (DEX) and the anti-tumor necrosis factor antibody adalimumab (ADA) were evaluated. ResultsPsA SF induced distinct inflammatory and tissue remodeling responses compared to OA SF and control conditions, including altered cartilage proteoglycan distribution, increased synovitis, and tissue-specific transcriptional changes. Multivariate analyses identified distinct osteochondral and synovial transcriptional responses to PsA SF, characterized by reduced osteochondral COL2A1 expression and increased synovial expression of inflammatory and matrix-remodeling genes, including MMP1 and CXCL8. DEX and ADA elicited donor-specific responses across histological, transcriptional, and protein readouts. Among multivariable model outputs, histologic synovitis scores emerged as the most clinically aligned parameter, demonstrating associations with baseline PsA donor disease activity, active joint counts, pain, high-sensitivity C-reactive protein (hsCRP), and radiographic scores. Synovitis score changes to DEX and ADA treatments also aligned with corresponding PsA SF donor clinical improvements to corticosteroid and TNF-modifying therapies. ConclusionThis osteochondral-synovial explant co-culture model captured donor-specific inflammatory and treatment-responsive features of PsA SF-induced pathology, thereby providing a clinically relevant ex vivo platform for studying patient-specific therapeutic responses in PsA.

immunology↗

bioRxiv2026

Contemporaneity of the past in stochastic intergenerational homeostasis

What recurring patterns of behaviors are hidden in the stochastic intergenerational dynamics of individual bacterial cells in different environments? Embracing the inherently stochastic nature of the homeostasis process, first we reconceptualize homeostasis as representing a "standing pattern of variation in trajectory space" of a naturally occurring adaptive complex system (rather than the simple "set-point" of a self-regulating apparatus), then delineate two mechanistically distinct potential routes to achieving homeostasis (either elastic, reflexive, memory-free adaptation or plastic, reflective, memoryful adaptation) and show that both schemes are simultaneously utilized during multigenerational stochastic growth and division of an individual cell. From experimental data we identify an intergenerational scaling law which directly yields the exact stochastic map governing stochastic intergenerational cell size homeostasis of individual bacterial cells. Its broad applicability across bacterial species, growth conditions, and microenvironments suggests that the organizational motif representing the nature of coupling of growth to division is effectively the same in all of these scenarios, despite apparent differences in actualization through molecular circuitry. The precise parameters characterizing the intergenerational scaling law vary from condition to condition and provide early hints of two tradeoffs: precision-speed and precision-energy.

biophysics↗

bioRxiv2026

Individualized and stereotypical seizure semiology in a porcine model of post-traumatic epilepsy.

Large-animal models of traumatic brain injury may yield translatable data on epileptogenesis, given their similarities in anatomy, brain size, and immune systems to humans. Adult male and female swine received bilateral cortical impact (N=16) or sham surgery (N=6) and were screened for convulsions via video-EEG for up to one year. Post-traumatic epilepsy (PTE) was defined as 2 seizures after 1-week post-injury. Nine out of sixteen pigs (56%) receiving bilateral cortical impact developed PTE, with an average 4.6 months ({+/-}3.4,SD) latent period. Seizures (N = 199) began focally, sometimes with motor onset including automatisms, before becoming generalized, with tonic-clonic or tonic convulsions. We defined a library differentiating peri-ictal behaviors (N = 31) from rhythmic/odd behaviors typical in healthy pigs (N = 12). Seizures had an average of 7.3 behaviors per seizure (max 26) lasting an average of 1.8 minutes (max 7.9). For seizures comprised of multiple convulsive episodes, the first convulsion had a greater number of peri-ictal behaviors than subsequent convulsions (P < 0.001). The array of peri-ictal behaviors displayed was pig-specific, with many behaviors consistently observed across seizures. The seizure frequency detected was 0.38/day. This large-brain model of PTE exhibits a variable period of epileptogenesis, a substantial rate of PTE, and an expansive repertoire of ictal behaviors. This first description of semiology in this species will serve as a guide for other porcine epilepsy models. Biofidelic models of PTE are expected to increase our understanding of the pathophysiology, enabling the identification and testing of therapeutics that translate into human patients. HighlightsO_LIThe average time from bilateral cortical impact to post-traumatic epilepsy in swine is 6 months, and is highly variable, ranging from 2 to 47 weeks post-TBI. C_LIO_LISwine with post-traumatic epilepsy display an array of specific behaviors around convulsions, distinct from pigs without post-traumatic epilepsy. C_LIO_LIThough the duration of convulsion was typically a few seconds, the entire seizure, with the associated peri-ictal behaviors, lasts up to 7.9 minutes. C_LIO_LIThe complexity of behaviors around convulsions tended to increase from early traumatic seizures to post-traumatic seizures. C_LIO_LIPeri-ictal behaviors observed around convulsions in an individual were often displayed prior to the first convulsion. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/708000v2_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@9523aborg.highwire.dtl.DTLVardef@158cfa6org.highwire.dtl.DTLVardef@1a8b499org.highwire.dtl.DTLVardef@e8c86f_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

PEI-Coated Microbubble Attachment to Neutrophils: Potential for Radiation Force Assisted Delivery into Tissue

Immunotherapies have advanced cancer treatment; however, their clinical efficacy remains limited for solid tumors due to challenges associated with effectively directing immune cells into the complex tumor microenvironment. Recent developments in Ultrasound Contrast Agent (UCA -- also known as "microbubble") technology have provided novel opportunities to enhance targeted therapeutic delivery. In this study, we introduce an innovative approach of leveraging microbubbles to enhance immune cell targeting by directly attaching microbubbles to immune cells, enabling the targeted delivery and localization of immune cells into solid tumors using radiation force ultrasound (US) application. To create novel microbubble-immune cell conjugates, we created polyethyleneimine (PEI) coated microbubbles and attached them to differentiated HL-60 (dHL-60) cells. These positively charged PEI microbubbles were formulated using azide-DBCO click chemistry between DBCO-labeled microbubbles and the azide functional groups on the PEI polymer. Following this step, we utilized electrostatic interactions to attach our positively charged PEI microbubbles to our negatively charged dHL-60 cells. We conducted viability experiments to assess the compatibility of these designs and verified that cell viability remained greater than 88% four hours after the conjugation process for different ratios of dHL-60 cells to PEI microbubbles. We used microfluidic chemotaxis platforms to quantify the microbubble-conjugated dHL-60 cell migratory behavior, examining parameters including migration velocity and percentage. Additionally, we investigated the impact of ultrasound power on primary human neutrophils to validate the functional responsiveness of these physiologically relevant immune cells. Here we demonstrated the possibility of ultrasound-responsive immune cell constructs as a targeted strategy without loss of function in migration capabilities. The novel PEI microbubble and immune cell conjugates reported in this work will be used to improve future immunotherapy techniques.

bioengineering↗

bioRxiv2025

Emergent simplicities in an individual cell's stochastic response to disruptive change

Here we seek and find recurring patterns of behaviors in the stochastic response of an individual bacterial cell to a disruptive change in growth conditions. Building on the known scaling law that a single timescale, a cellular unit of time, governs stochastic growth and division of individual bacterial cells under constant growth conditions, here we show using experimental data that a dynamic rescaling of the cellular unit of time captures the predominant effect of temporal variations in environmental conditions. Furthermore, we identify the instantaneous exponential growth rate as the scaling factor that scales the internal clocks of the cells to the laboratory time. Our results reveal the natural representation for these time-dependent dynamics. When recast in its terms the cell age distribution for suitable initial conditions evolves under time-invariant rules even as growth conditions remain dynamic! Through the experimental realization at different temperatures of otherwise identical disruptive changes, we not only substantiate the general applicability of the cellular frame of reference but also uncover more emergent simplicities. Motivated by this representation, when time and instantaneous growth rate are expressed in terms of their naturally dimensionless counterparts, remarkably consistent patterns are revealed. These include a unimodal-bimodal-unimodal transition in the shape of the instantaneous growth rate distribution as cells initially in homeostasis experience a disruptive change in nutrient quality and subsequently recover and attain a new homeostasis. The remarkable scaling of the pattern of responses across temperatures suggests that the organizational rules and processes governing the response to disruptive change in nutrient quality remain the same at different temperatures. While the progression of the response appears to proceed at different tempos at different temperatures, upon shifting from the laboratory to the cellular frame of reference these changes progress at the same pace even at different temperatures.

biophysics↗

bioRxiv2025

GPR97/ADGRG3 is activated by its tethered peptide agonist and not by steroids to induce neutrophil polarization and migration

Most adhesion G protein coupled receptors (AGPCRs) are activated by intramolecular binding of a tethered-peptide agonist (TA). Shear force-induced dissociation of the AGPCR N-terminal fragment (NTF) and C-terminal fragment (CTF) exposes the TA. The decrypted TA binds rapidly to its orthosteric site within the CTF to stabilize the active state of the AGPCR. Corticosteroids were previously proposed to be agonists for GPR97/ADGRG3. Later, other steroids and androgens were purported to be selective agonists of additional AGPCRs. Here, we demonstrate that GPR97/ADGRG3 is activated by dissociation of its NTF/CTF and follows the TA mechanism. TA peptidomimetics and the ADGRG subfamily partial agonist 3-acetoxydihydrodeoxygeduin (3--DOG), but not corticoids, stimulated GPR97/ADGRG3 in cell-based luciferase reporter assays and receptor/G protein reconstitution assays. GPR97 was defined as a promiscuous AGPCR that couples to G13, Gs and Gi, but not Gq. GPR97 is highly expressed in human polymorphonuclear neutrophils (hPMNs). Neutrophils undergo actin polymerization-induced cell shape changes and polarization and migrate upon activation. We found that GPR97 activation via TA peptidomimetics or 3--DOG robustly stimulated hPMN and mouse bone-marrow neutrophil (mBMN) polarization. Furthermore, GPR97 TA peptidomimetics and 3--DOG, but not beclomethasone, induced hPMN and mBMN chemotaxis. Together, our results demonstrate that GPR97/ADGRG3 utilizes a tethered agonist mechanism to activate G protein signaling and induce neutrophil polarization and migration. One Sentence SummaryGPR97/ADGRG3 tethered agonism regulates G protein signaling in neutrophils.

pharmacology and toxicology↗

bioRxiv2025

Mesenchymal Stromal Cells Immunosuppress Osteoarthritis Synovial Fluid Tolerized Monocytes via IL-6

BackgroundMesenchymal stromal cell (MSC) interactions with monocytes/macrophages are central to their therapeutic effects in knee osteoarthritis (KOA); however, mechanisms of these interactions are not fully understood. HypothesisWe hypothesize that MSC soluble factors, particularly interleukin-6 (IL-6) and C-C motif chemokine ligand (CCL2) modulate monocytes in KOA environment. MethodsUsing healthy donor CD14+ monocytes exposed to KOA synovial fluid (SF) in the presence or absence of marrow-derived MSC(M) directly or conditioned medium (CM), we evaluated cell surface markers and signaling via signal transducer and activator of transcription (STAT3), nuclear factor kappa-light-chain-enhancer of activated B (NF-{kappa}B) and c-Jun Terminal Kinase (JNK); functional responses were measured by secretion of tumor necrosis factor (TNF) and IL-1, and by phagocytosis of pHrodo Red E-coli. ResultsCD14+ monocytes demonstrated a mixed phenotype in KOA SF with increased CD163, CD206 and unchanged HLA-DR, CD86 marker expression. This was accompanied by activated STAT3, JNK and NF-{kappa}B signaling. TNF and IL-1 secreted levels were unchanged, but phagocytosis was impaired, indicative of a net dysfunctional repair phenotype and functionality. CD14+ monocytes in KOA SF were hyporesponsive to additional lipopolysaccharide re-challenge, based on TNF and IL-1 secretion. Addition of MSC(M) to KOA SF programmed CD14+ monocytes resolved the dysfunctional phenotype and functionality, with significant increases in CD163, CD206; significant reductions in HLA-DR and CD86 expression; this was accompanied by significantly increased activated STAT3, and decreased activated JNK and NF-{kappa}B. TNF and IL-1 secretion were also significantly reduced, and phagocytic capacity restored. Blocking IL-6, or to a lesser extent, CCL2, partially abrogated MSC(M) soluble factor effects. MSC(M) experienced apoptosis in KOA SF; however, apoptotic bodies did not fully recapitulate MSC(M) soluble factor effects. ConclusionIL-6, CCL2, other soluble factors and apoptotic bodies from MSC(M) secretome mitigate the dysfunctional effects of KOA SF on CD14+ monocytes resulting in immunosuppressed phenotype and functionality.

immunology↗

bioRxiv2025

Responders vs. non-responders to mesenchymal stromal cells in knee osteoarthritis patients: mechanistic correlates of donor cell attributes and patient features

Mesenchymal stromal cell (MSC) injection has afforded heterogenous outcomes in knee osteoarthritis (KOA). Herein, a framework that dually correlates KOA patient responsiveness to baseline autologous bone marrow-derived MSC(M) donor batch attributes and baseline clinical and biomarker features is provided. Using clinical trial data, we demonstrated that MSC(M) with increased immunomodulatory potency are more efficacious. Multivariable MSC(M) genes correlated strongly with responder status and to 12- and 24-month improvements in Knee Injury and Osteoarthritis Outcome Scores. Responder MSC(M) donor batches had unique microRNA expression and ability to polarize CD14+ monocytes in vitro. KOA Responders had lower baseline physical activity and trended toward more severe baseline KOA. Baseline local but not systemic biomarkers showed trending correlations to patient responsiveness. 42% of KOA patients were Responders at 24 months, emphasizing durability of single MSC(M) injections. Together, our analytical methodology defines critical quality attributes of potent MSC(M) donor batches and identifies putative KOA patient theratypes to MSC treatments. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=159 HEIGHT=200 SRC="FIGDIR/small/665028v4_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@18bbb07org.highwire.dtl.DTLVardef@a406e8org.highwire.dtl.DTLVardef@c18c8corg.highwire.dtl.DTLVardef@f2731c_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

A cell atlas of human and mouse synovium from early and advanced stages of knee osteoarthritis: BHLHE40 regulates fibroblast activation

Osteoarthritis (OA) is a destructive joint disease affecting multiple tissues, including synovium. Previous studies have identified some distinct fibroblast subtypes within synovium; however, the characterization of fibroblast subsets during distinct stages of knee (K)OA disease, and their contributions to the endogenous mechanisms that drive synovial fibrosis during KOA, are not well characterized. Here we profile synovium from early- (KL I) and advanced- (KL III/IV) stages of radiographic KOA. First, bulk-RNA sequencing of early- and advanced-staged KOA synovial tissue revealed transcriptomic differences between the two disease stages. Using single-nuclei RNA sequencing (snRNA-seq) and flow cytometry, we identified distinct fibroblast subsets and uncovered an endotypic shift in fibroblast subsets during KOA pathogenesis, transitioning from DPP4+ in early-stage to ITGB8+ in advanced-stages. SnRNA-seq of synovium from mice with experimental KOA revealed analogous populations of Dpp4+ and Itgb8+ fibroblasts in tissue from early and advanced model stages. Human advanced-stage KOA synovial tissue had stronger expression of matrisome-annotated genes compared to early-stage tissue. BHLHE40, a crucial transcriptional regulator of ECM related genes, was identified as upregulated in ITGB8+ fibroblasts compared to DPP4+ fibroblasts. Using primary human OA fibroblasts in vitro, and conditional knock out mice in vivo, we found that fibroblast-intrinsic loss of BHLHE40 increased fibrosis-related gene expression, enhanced fibroblast activation and induced severe synovial fibrosis in vivo. In contrast, overexpression of BHLHE40 in vitro was able to suppress TGF-{beta}-induced fibroblast activation. Overall, this study provides a comprehensive cellular atlas of KOA synovium and has identified BHLHE40 as a crucial regulator of fibroblast-mediated synovial fibrosis.

molecular biology↗

bioRxiv2024

Identification of Ephrin type-B receptor 4 as a critical mediator of tissue fibrosis

Pulmonary fibrosis (PF) is a pathology associated with interstitial lung diseases (ILDs), including idiopathic pulmonary fibrosis (IPF). Fibrosis promotes continual secretion of extracellular matrix (ECM), producing non-functional scar tissue and causing organ failure. This study investigated the tyrosine kinase receptor Ephrin type-B receptor 4 (EphB4) as a mediator of PF. To this end, we generated mice with conditional Col1a2-driven deletion of Ephb4 and used a preclinical mouse model of PF, total and single nuclei RNA (snRNA) sequencing, NanoString, previously published single cell data, computational analysis, and functional assays of mouse and human healthy control and IPF lung fibroblasts. Col1a2-CreERT-driven Ephb4 deletion, or EphB4 inhibition via NVP-BHG712, markedly protected against bleomycin-induced PF. Total RNA-sequencing of fibroblasts isolated from Ephb4-deficient fibrotic mouse lungs exhibited reduced expression of ECM, ER Cargo, and protein trafficking-related genes. NVP-BHG712 reduced expression of these identified genes in mouse lung fibroblasts under fibrotic conditions in vitro. SnRNA sequencing of mouse lungs treated with NVP-BHG712 identified transcriptomic changes of ECM genes in specific fibroblast subpopulations. RNA sequencing, computational, and functional assays using mouse and human IPF fibroblasts identified elastin as a key mediator involved in EphB4 signaling. Combined, our data show that EphB4 is a crucial mediator of PF.

pathology↗

bioRxiv2024

Cell and Transcriptomic Diversity of Infrapatellar Fat Pad during Knee Osteoarthritis

ObjectivesIn this study, we employ a multi-omic approach to identify major cell types and subsets, and their transcriptomic profiles within the infrapatellar fat pad (IFP), and to determine differences in the IFP based on knee osteoarthritis (KOA), sex, and obesity status. MethodsSingle-nucleus RNA sequencing of 82,924 nuclei from 21 IFPs (n=6 healthy control and n=15 KOA donors), spatial transcriptomics and bioinformatic analysis were used to identify contributions of the IFP to KOA. We mapped cell subclusters from other white adipose tissues using publicly available literature. The diversity of fibroblasts within the IFP was investigated by bioinformatic analyses, comparing by KOA, sex, and obesity status. Metabolomics was used to further explore differences in fibroblasts by obesity status. ResultsWe identified multiple subclusters of fibroblasts, macrophages, adipocytes, and endothelial cells with unique transcriptomic profiles. Using spatial transcriptomics, we resolved distributions of cell types and their transcriptomic profiles, and computationally identified putative cell-cell communication networks. Furthermore, we identified transcriptomic differences in fibroblasts from KOA versus healthy control donor IFPs, female versus male KOA-IFPs, and obese versus normal body mass index (BMI) KOA-IFPs. Finally, using metabolomics, we defined differences in metabolite levels in supernatants of naive, profibrotic- and proinflammatory stimuli-treated fibroblasts from obese compared to normal BMI KOA-IFP. ConclusionsOverall, by employing a multi-omic approach, this study provides the first comprehensive map of cellular and transcriptomic diversity of human IFP and identifies IFP fibroblasts as a key cell type contributing to transcriptomic and metabolic differences related to KOA disease, sex, or obesity.

cell biology↗

bioRxiv2024

Incomplete remyelination via endogenous or therapeutically enhanced oligodendrogenesis is sufficient to recover visual cortical function

Myelin loss induces deficits in action potential propagation that result in neural dysfunction and contribute to the pathophysiology of neurodegenerative diseases, injury conditions, and aging. Because remyelination is often incomplete, better understanding endogenous remyelination and developing remyelination therapies that seek to restore neural function are clinical imperatives. Here, we used in vivo two-photon microscopy and electrophysiology to study the dynamics of endogenous and therapeutic-induced cortical remyelination and functional recovery after cuprizone-mediated demyelination in mice. We focused on the visual pathway, which is uniquely positioned to provide insights into structure-function relationships during de/remyelination. We show that endogenous remyelination is driven by recent oligodendrocyte loss and is highly efficacious following mild demyelination, but fails to restore the oligodendrocyte population when high rates of oligodendrocyte loss occur too quickly. Testing a novel thyromimetic compared to clemastine fumarate, we find it better enhances oligodendrocyte gain during remyelination and hastens recovery of neuronal function. Surprisingly, its therapeutic benefit was temporally restricted, and it acted exclusively following moderate to severe demyelination to eliminate endogenous remyelination deficits. However, complete remyelination is unnecessary as partial oligodendrocyte restoration was sufficient to recover visual neuronal function. These findings advance our understanding of remyelination and its impact on functional recovery to inform future therapeutic strategies.

neuroscience↗

bioRxiv2023

Non-Markovian memory and emergent simplicities in the stochastic and plastic adaptation of individual cells to dynamic environments

Do individual bacterial cells retain memories of the history of environmental conditions experienced in previous generations? Here we directly address this question through a synthesis of physics theory and high-precision experiments on statistically identical, non-interacting individual bacterial cells, which grow and divide with intrinsic stochasticity in precisely controlled conditions. From these data, we extract "emergent simplicities" in the seemingly complex interplay between history dependence, persistence, and transience in the stochastic memories of the dynamic environments experienced by individuals over multiple generations. First, we find that the instantaneous single-cell growth rate is the key physiologically relevant quantity where intergenerational memory is stored. In contrast, the cell size dynamics are memory free, or Markovian, over intergenerational timescales. Next, we find that the effect of experiencing dynamic environments can be captured quantitatively by recal-ibrating the cellular unit of time by the measured mean instantaneous growth rate; the dynamically rescaled cell age distributions undergo a scaling collapse. Moreover, in a given condition, an individual bacterial cell retains history-dependent, or non-Markovian, memory of its growth rate over tens of generations. We derive from first principles a physically-motivated metric to quantify the degree of non-Markovianity. Furthermore, when conditions change, the instantaneous single-cell growth distribution becomes bimodal, as the bacteriums memory of past environment encountered is reset stochastically and plastically, prior to achieving a new homeostasis.

biophysics↗

bioRxiv2022

Bacterial Strategies for Damage Management

Organisms are able to partition resources adaptively between growth and repair. The precise nature of optimal partitioning and how this emerges from cellular dynamics including insurmountable trade-offs remains an open question. We construct a mathematical framework to estimate optimal partitioning and the corresponding maximal growth rate constrained by empirical scaling laws. We model a biosynthesis tradeoff governing the partitioning of the ribosome economy between replicating functional proteins and replicating the ribosome pool, and also an energy tradeoff arising from the finite energy budget of the cell. Through exact analytic calculations we predict limits on the range of values partitioning ratios take while sustaining growth. We calculate how partitioning and cellular composition scale with protein and ribosome degradation rates and organism size. These results reveal different classes of optimizing strategies corresponding to phenotypically distinct bacterial lifestyles. We summarize these findings in a quadrant-based taxonomy including: a "greedy" strategy maximally prioritizing growth, a "prudent" strategy maximally prioritizing the management of damaged pools, and "strategically limited" intermediates.

biophysics↗

bioRxiv2022

Immunokinetic Model for COVID-19 Patients

In this paper, we develop a fractional-order differential model for the dynamics of immune responses to SARS-CoV-2 viral load in one host. In the model, a fractional-order derivative is incorporated to represent the effects of temporal long-run memory on immune cells and tissues for any age group of patients. The population of cytotoxic T-cells (CD8+), natural killer (NK) cells and infected viruses are unknown in this model. Some interesting sufficient conditions that ensure the asymptotic stability of the steady states are obtained. This model indicates some complex phenomena in COVID-19 such as "immune exhaustion" and "Long COVID". Sensitivity analysis is also investigated for model parameters to determine the parameters that are effective in determining of the long COVID duration, disease control and future treatment as well as vaccine design. The model is verified with clinical and experimental data of 5 patients with COVID-19.

bioengineering↗

bioRxiv2020

HIV-specific T-cell responses reflect substantive in vivo interactions with infected cells despite long-term therapy

Antiretroviral therapies (ART) durably suppress HIV replication to undetectable levels - however, infection persists in the form of long-lived reservoirs of infected cells with integrated proviruses, that re-seed systemic replication if ART is interrupted. A central tenet of our current understanding of this persistence is that infected cells are shielded from immune recognition and elimination through a lack of antigen expression from proviruses. Efforts to cure HIV infection have therefore focused on reactivating latent proviruses to enable immune-mediated clearance, but these have yet to succeed in driving reductions in viral reservoirs. Here, we revisited the question of whether HIV reservoirs are predominately immunologically silent from a new angle, by querying the dynamics of HIV-specific T-cell responses over long-term ART for evidence of ongoing recognition of HIV-infected cells. We show that T-cell responses to autologous reservoir viruses persist over years, and that the maintenance of HIV-Nef-specific responses was uniquely associated with residual frequencies of infected cells. These responses disproportionately exhibited a cytotoxic, effector functional profile, indicative of recent in vivo recognition of HIV-infected cells. These results indicate substantial visibility of the HIV reservoir to T-cells on stable ART, presenting both opportunities and challenges for the development of therapeutic approaches to curing HIV infection.

immunology↗