Biology subjects

Krishnan, K.

Publications and source records attributed to Krishnan, K..

At least 19 recordsLinked to original sources

bioRxiv2026

SENgEAR: an interactive visualization platform for comparative analysis of senescence signatures and cellular communication

Single-cell and spatial transcriptomic datasets provide tremendous potential to identify the cellular states and communication networks associated with senescence. Annotating senescent cells in these datasets is hindered by the lack of universal markers for senescent cells and their context-dependent variability. To overcome this, several groups have developed gene signatures to annotate cells with distinct senotypes. However, comparing these signatures and their biological contexts to determine the specificity of senescence signatures remains complicated by the separate data platforms for signatures and datasets. We present SENgEAR, a no-code web platform for senescent cell annotation, visualization of cell-cell communication networks, and comparison of senescence signatures across studies, tissues, species, and data modalities. SENgEAR provides a unified framework to explore contextual signature specificity, cellular communication pathways, and senotype heterogeneity. We demonstrate the use of SENgEAR for applications spanning aging, fibrosis, and wound healing and its ability to interrelate these states.

bioinformatics↗

bioRxiv2026

Age and sex alter the immune response in a chronic fibrosis model via changes in T cell and macrophage phenotype

The foreign body response (FBR) is an immune mediated event that occurs with every material implant. The extent of the fibrosis is dependent on many factors including the biomaterial design, tissue location, and host factors such as age, sex, ancestry, diet. There are known clinical outcomes of implants dependent on age and sex, including increased fibrosis and implant failure in aged and female patients. As the population ages, there is a growing need to understand how aging affects the FBR, and how preclinical models can capture this to guide biomaterial design. Here, we investigated how chronic fibrosis in a murine model of the FBR is altered by two biological factors: age and sex. We investigated changes in fibrosis using a volumetric muscle loss (VML) injury model coupled with polycaprolactone (PCL) or polyethylene (PE) microparticle implants. Fibrosis was quantified through gene expression, microscopic analysis of histologic sections, and the corresponding immune response measured via gene expression and flow cytometry data. We found gene expression differences with immune pathways enriched in female mice, and microscopy revealed collagen birefringence area increased in young male mice. Both the innate and adaptive immune response were altered by age and sex via T cell and macrophage phenotype, and the effects of aging differed between sexes. These results reveal both variables contribute to discrepant outcomes in both fibrosis and the local immune response to synthetic material implants. This demonstrates a clear need to understand and account for the influence of biological factors in biomaterial design.

bioengineering↗

bioRxiv2026

Senescent cell networks link matrix remodeling and vascular dysfunction in human fibroids

Uterine fibroids (leiomyomas) are highly prevalent benign tumors defined by excessive extracellular matrix (ECM) deposition, altered vascular structure, and progressive tissue stiffening, yet the cellular programs that coordinate these features remain poorly understood. Cellular senescence has been implicated in fibroid biology, but whether senescence represents a uniform state or distinct, functionally specialized cell identities within fibroids is unknown. Here, we identify the distinct heterogeneous populations of senescent cells ("senotypes") present in human fibroids and characterize their role in shaping the fibroid microenvironment. Using single-cell RNA sequencing (scRNA-seq) integrated with a senescence gene signature and protein-level validation, we identify senescent cells (SnC) distributed across fibroblast, mural, and endothelial compartments, each exhibiting distinct transcriptional programs. SnC endothelial cells (ECs) are enriched in fibroids relative to matched myometrium and activate TEAD4-associated mechanosensing, angiogenic, and immune signaling pathways, despite being associated with impaired vessel maturation in situ. In parallel, SnC fibroblast and mural populations in fibroids upregulated SRF-associated cytoskeletal and ECM programs, accompanied by increased COL6A3 expression and collagen VI deposition, consistent with tissue stiffening. Ligand-receptor and spatial analyses reveal that these SnC populations function as interconnected signaling hubs, coordinating immune cell recruitment and stromal remodeling. Importantly, analysis of human fibroids treated with collagenase demonstrated a reduction in both ECM density and SnC burden, supporting a reinforcing relationship between matrix mechanics and senescence. Together, these findings establish senescence in fibroids as a heterogeneous, mechanically reinforced, and network-driven process that links vascular dysfunction, immune signaling, and fibrosis, highlighting distinct SnC states as potential translational targets for non-surgical therapies.

cell biology↗

bioRxiv2026

Distinct fibroblast and perivascular senotypes define spatial niches that regulate fibrosis

Fibrotic conditions contribute to significant global morbidity and mortality. Yet the underlying processes that orchestrate fibrosis remain poorly understood due to the cellular and spatial complexity of the stromal, immune, and vascular compartments that regulate fibrotic disease progression. Senescent cells (SnCs) have been implicated in fibrosis, but their roles are unclear, as evidence indicates that they serve both pathogenic and reparative functions. Here, we show that fibrosis-associated SnCs contain functionally divergent senotypes that are organized into distinct spatial niches. Using integrated single-cell and spatial transcriptomics analyses and hierarchical factorization in a murine fibrosis model, we identify fibroblast and perivascular SnC subpopulations that upregulate diverse programs related to extracellular matrix (ECM) production, immune signaling, and vascular remodeling. Fibroblast senotypes localize to discrete microenvironments with distinct tissue architectures, including niches associated with fibrotic signaling, immune activity, and cartilage development. Perivascular SnCs occupy interfaces between fibrotic signaling and immune-active niches and upregulate vascular and fibrotic remodeling pathways. Depletion of pericyte-lineage SnCs increases vascular maturation and fibrotic ECM deposition, providing mechanistic validation of the beneficial role these SnCs play in vascular remodeling and fibrosis modulation. In addition, using a new web-based infrastructure to query our senotype gene signatures in public datasets, we demonstrate that these senotypes are conserved across different murine and human fibrotic conditions. These findings establish senescence as a spatially organized regulator of fibrosis and identify perivascular senescence as a link between vascular remodeling and fibrotic outcomes.

bioengineering↗

bioRxiv2026

Control of wildtype zebrafish optomotor response with a photoswitchable drug

For animals to interact effectively with their environment, the brain must integrate sensory information and generate appropriate motor responses. Multiple neuronal circuits contribute to this process, and identifying their roles remains a central focus in neuroscience. The recently developed photoswitchable compound Carbadiazocine controls neuronal firing across species. It modulates larval zebrafish locomotion and alleviates neuropathic pain in rodents in a reversible, light-induced manner. Given its effects on both motor and somatosensory circuits, we investigated the impact of Carbadiazocine on sensorimotor behaviors. We focused on the optomotor response in zebrafish larvae and assessed its potential as a tool for circuit perturbation and behavioral analysis, for the first time combined with photopharmacology. We performed experiments in head-fixed and free-swimming larvae to assess their capacity to detect and follow the direction of optic flow, as well as to characterize swimming speed patterns and individual tail bout properties following administration of the two Carbadiazocine photoisomers. In both paradigms, treatment with the pre-illuminated compound led to a decrease in accuracy in responding to optic flow (correct turning percentage dropping from [~]95 % to [~]80 % in head-fixed experiments and correctness decreasing from [~]65 % to [~]20 % in free-swimming experiments). Speed analysis revealed an increased number and duration of fast movements with a decrease in number and duration of slow movements, even during periods without visual stimulation. Tail bout analysis further showed an increase in 15-30 Hz bout frequencies, corresponding to incomplete, irregular tail movements. All these effects were absent when the dark-relaxed compound was administered. Together, these findings deepen our understanding of sensorimotor transformations and lay the foundations to probe native neuronal circuits underlying behavior in diverse animal species using a wide dynamic range of photostimulation patterns.

animal behavior and cognition↗

bioRxiv2026

Tissue Injury and Biomaterial Treatment Modulate Tumor Growth and Response to Immunotherapy

Immunotherapies have transformed cancer care; however, tumor intrinsic and extrinsic factors contribute to high variability in therapeutic responses. While tissue injuries can impact cancer recurrence and metastatic spread, little is known about their potential to effect immune checkpoint blockade (ICB) response. In this study, we reveal that distal traumatic muscle injury accelerated progression and impaired adjuvant ICB response of multiple murine tumors. This injury-induced accelerated tumor growth coincided with decreased intra-tumoral density and effector phenotype of tumor-reactive CD8+ T cells and relied on communication through a shared draining lymph node. Enhancing injury repair using a biological scaffold abrogated the injury-induced accelerated tumor growth in an interleukin-4-dependent manner and improved ICB response. In a retrospective cohort analysis of breast cancer patients undergoing ICB treatment, biological scaffold implantation following mastectomy was associated with increased overall survival. This work suggests that injury-driven immune dysfunction may contribute to cancer progression and ICB resistance, but enhancing wound healing with pro-regenerative biomaterials may offer a viable strategy for mitigating adverse cancer outcomes, particularly in the setting of adjuvant and neoadjuvant ICB.

cancer biology↗

bioRxiv2026

Immune checkpoint inhibitors amplify type 2 immune mediated repair bypro-regenerative scaffolds

Extracellular matrix (ECM) scaffolds induce type 2 immunity to promote repair. Here, we show that immune cells recruited to ECM-treated murine muscle injuries and clinical soft tissue defects express immune checkpoints. Specifically, TH2 cells and regulatory T cells (Tregs) increase LAG3 expression, while macrophages express PDL2. TCR analysis and a triple-reporter strain for interleukin (IL)-13 and Treg fate-mapping suggest that Tregs in ECM-treated wounds transition into TH2-like exTregs that express LAG3. Immune checkpoint inhibition (ICI) significantly stimulated type 2 immunity in ECM-treated wounds, including increased TH2 cells, Treg transition to TH2-like exTregs, and pro-regenerative macrophages. Moreover, ICI enhanced muscle repair and reduced fibrosis in ECM-treated wounds. Collectively, these findings show Treg/TH2 plasticity in wound healing and introduce a novel ICI application to enhance immune-mediated regeneration.

bioengineering↗

bioRxiv2026

From Latent Manifolds to Functional Probes: An Interpretable, Kinome-Scale Generative Machine Learning Framework for Family-Targeted Kinase Inhibitor Design

The design of selective kinase inhibitors remains a formidable challenge due to the high structural conservation of the ATP-binding site across the kinome. While modern generative AI has enabled rapid exploration of chemical space, many advanced models operate as black boxes, obscuring the chemical rationale behind design choices and limiting interpretability. To explore these bottlenecks, we present a modular, generative framework for de novo design of SRC kinase inhibitors, integrating ChemVAE-based latent space modeling, a chemically interpretable Kinase Inhibition Likelihood (KIL) scoring function, Bayesian optimization, and cluster-guided local neighborhood sampling. The results demonstrate that kinase inhibitors spontaneously organize into a coherent, low-dimensional manifold in latent space, with SRC acting as a structural "hub" that enables rational scaffold transformation. Our local neighborhood sampling-based approach successfully converts inhibitors from other kinase families (notably LCK) into novel SRC-like chemotypes, with LCK-derived molecules accounting for [~]40% of high-similarity outputs. Critically, we expose a fundamental representation gap: despite aromatic ring count being a top KIL feature, SMILES-based generation systematically fails to access multi-ring pharmacophores characteristic of clinical kinase inhibitors. This limitation cannot be overcome by scoring refinement alone, demanding topology-aware representations. Our framework also demonstrates that unbiased exploration paired with cluster-guided sampling outperforms active-biased optimization, which traps search in narrow local optima. By exposing representational gaps and showcasing scaffold-aware navigation of latent space, this study argues for hybrid systems that combine the diagnostic transparency of interpretable machine learning frameworks with the generative power of modern architectures.

bioinformatics↗

bioRxiv2026

Regulatory T cells clonally expand and contribute to stromal cell function in fibrotic response to synthetic implants

Fibrosis plays a key role in both chronic disease progression and failure of synthetic biomaterial implants. However, the contribution of adaptive immunity to fibrotic development remains incompletely understood, particularly for regulatory T cells (Tregs). Here, we used single-cell multiomic profiling, integrating transcriptomics with T cell receptor (TCR) sequencing, to map Treg heterogeneity and clonal dynamics in a synthetic material-induced model of fibrosis. We uncovered progressive Treg clonal expansion accompanied by TCR activation signatures and an increasingly immunosuppressive phenotype along a continuous transcriptional trajectory. These Tregs suppressed immune responses and influenced extracellular matrix and vascular gene expression. Cell-cell communication inference predicted Treg-driven activation of pro-fibrotic and vasculogenic transcriptional programs in fibroblasts and endothelial cells, including Sox-family transcription factors. Functional Treg depletion increased inflammation and significantly reduced neovascularization. Together, these findings identify Treg functions in the fibro-vascular niche through stromal cell modulation, highlighting immune-stromal interactions as an important axis in fibrosis.

immunology↗

bioRxiv2025

γδ17 T cell-stromal networks modulate matrix composition and vascularity in foreign body response

Immune-stromal crosstalk governs tissue fibrosis, which is marked by dysregulated extracellular matrix (ECM) production and aberrant vasculature. Here, we investigate how {gamma}{delta} T cell interactions with stromal cells shape fibrosis in the foreign body response. During the acute reaction, type-1 ({gamma}{delta}IFN{gamma}) and type-17 ({gamma}{delta}17) effector subsets accumulated at the implant. While {gamma}{delta}IFN{gamma} decreased as fibrosis progressed, activated {gamma}{delta}17 persisted as dominant interleukin-17 producers. The {gamma}{delta}17 increased with aging and high-fat diet, both factors associated with chronic inflammation and fibrosis. Co-culture with {gamma}{delta}17 stimulated fibroblast expression of collagen genes and intercellular communication inference linked {gamma}{delta} T cell ligands to activation of ECM remodeling and vascular development programs in fibroblasts and endothelial cells. Finally, genetic deletion of {gamma}{delta} T cells altered expression of ECM components and increased vessel size within the fibrotic matrix. Altogether, our findings implicate {gamma}{delta} T cells in regulating stromal behavior to modulate composition and vascularity of fibrotic tissues.

immunology↗

bioRxiv2025

Differential cell signaling testing for cell-cell communication inference from single-cell data by dominoSignal

Algorithms for ligand-receptor network inference have emerged as commonly used tools to estimate cell-cell communication from reference single-cell data. Many studies employ these algorithms to compare signaling between conditions and lack methods to statistically identify signals that are significantly different. We previously developed the cell communication inference algorithm Domino, which considers ligand and receptor gene expression in association with downstream transcription factor activity scoring. We developed the dominoSignal software to innovate upon Domino and extend its functionality to test statistically differential cellular signaling. This new functionality includes compilation of active signals as linkages from multiple subjects in a single-cell data set and testing condition-dependent signaling linkage. The software is applicable for analysis of single-cell data sets with multiple subjects as biological replicates as well as with bootstrapped replicates from data sets with few or pooled subjects. We use simulation studies to benchmark the number of subjects in compared groups and cells within an annotated cell type sufficient to accurately identify differential linkages. We demonstrate the application of the Differential Cell Signaling Test (DCST) in the dominoSignal software to investigate consequences of cancer cell phenotypes and immunotherapy on cell-cell communication in tumor microenvironments. These applications in cancer studies demonstrate the ability of differential cell signaling analysis to infer changes to cell communication networks from therapeutic or experimental perturbations, which is broadly applicable across biological systems.

bioinformatics↗

bioRxiv2025

Murine gut microbiota dysbiosis via enteric infection modulates the foreign body response to a distal biomaterial implant

The gut microbiota influences systemic immunity and the function of distal tissues, including the brain, liver, skin, lung, and muscle. However, the role of the gut microbiota in the foreign body response (FBR) and fibrosis around medical implants is largely unexplored. To investigate this connection, we perturbed the homeostasis of the murine gut microbiota via enterotoxigenic Bacteroides fragilis (ETBF) infection and implanted the synthetic polymer polycaprolactone (PCL) into a distal muscle injury. ETBF infection in mice led to increased neutrophil and {gamma}{delta} T cell infiltration into the PCL implant site. ETBF infection alone promoted systemic inflammation and increased levels of neutrophils in the blood, spleen, and bone marrow. At the PCL implant site, we found significant changes in the transcriptome of sorted fibroblasts but did not observe gross ETBF- induced differences in the fibrosis levels after 6 weeks. These results demonstrate the ability of the gut microbiota to mediate long-distance effects such as immune and stromal responses to a distal biomaterial implant. Significance StatementThe foreign body response to implants leads to chronic inflammation and fibrosis that can be highly variable in the general patient population. Here, we demonstrate that gut dysbiosis via enteric infection promoted systemic inflammation and increased immune cell recruitment to an anatomically distant implant site. These results implicate the gut microbiota as a potential source of variability in the clinical biomaterial response and illustrate that the local tissue environment can be influenced by host factors that modulate systemic interactions.

bioengineering↗

bioRxiv2024

Sleep Disruption Improves Performance in Simple Olfactory and Visual Decision-Making Tasks

Sleep disruption drastically impacts cognitive functions including decision-making and attention across many different species. In this study, we leveraged the small size and conserved vertebrate brain structure of larval zebrafish to investigate how sleep disruption modulates visual-and olfactory-decision-making. Strikingly, sleep disruption improved performance in both paradigms. Specifically, sleep disruption lengthens reaction times and increases correct decisions in a visual motion discrimination task, an effect that we attribute to longer integration periods in disrupted animals. Using a drift diffusion model, we predict specific circuit changes underlying these effects. Additionally, we demonstrate that sleep disruption heightens odor sensitivity in an olfactory decision-making task, likely mediated by cortisol. Our findings lay essential groundwork for investigating the brain circuit changes that arise from sleep disruption across species.

neuroscience↗

bioRxiv2024

Cultured Bacteria Isolated from Primary Sclerosing Cholangitis Patient Bile Induce Inflammation and Cell Death

BackgroundPrimary sclerosing cholangitis (PSC) is a chronic liver disease characterized by inflammation and progressive fibrosis of the biliary tree. The pathogenesis of PSC remains poorly understood, and there are no effective therapeutic options. Previous studies have observed associations between changes in the colonic and biliary microbiome and PSC. We aimed to determine whether bacterial isolates cultured from PSC patient bile induced disease-associated phenotypes in cells. MethodsBile was collected from PSC patients (n=10) by endoscopic retrograde cholangiography and from non-PSC controls (n=3) undergoing cholecystectomies. Biliary bacteria were cultured anaerobically, and 50 colonies per sample were identified by 16S rRNA sequencing. The effects of supernatants from seven PSC-associated bacterial strains on cellular phenotypes were characterized using human colonic (Caco-2), hepatic (HepG2), and biliary (EGI-1) cells. ResultsNo bacteria were isolated from non-PSC controls, while bacteria were cultured from most PSC patients. The PSC bile microbiomes exhibited reduced diversity compared to the gut or oral cavity, with one or two bacterial strains predominating. Overall, PSC-associated bacteria produced factors that were cytotoxic to hepatic and biliary cells. Enterococcus faecalis, and to a lesser extent Veillonella parvula, induced epithelial permeability, while Escherichia coli, Fusobacterium necrophorum, and Klebsiella pneumoniae induced inflammatory cytokines in biliary cells. ConclusionsOur data suggest that bacteria cultured from PSC bile induce cellular changes that may contribute to PSC disease pathogenesis. Enterococcus may promote intestinal permeability, facilitating bacterial migration to the biliary tree. Once there, Escherichia, Fusobacterium and Klebsiella, may cause inflammation and damage in biliary and liver cells.

microbiology↗

bioRxiv2024

Changing air density affects flight costs in low-flying birds

Regional patterns in wind underpin the low-cost migratory flyways of billions of birds and insects1-3, but how large-scale changes in temperature affect flight is unknown. Flight costs should increase with rising temperatures, because lift decreases as density decreases, whereas weight remains unchanged. The effects of air density on flight costs are well-established in the context of high-altitude movements and migration4-7. Here, we examine the impact of air density on low-flying birds, in relation to seasonal, regional and global changes in temperature. Using multi-sensor loggers, we find that air density was the most important predictor of wingbeat frequency in red-tailed tropicbirds (Phaethon rubricauda) breeding year-round in Mauritius. Lower air densities in the Austral summer were associated with a small but significant increase in mean wingbeat frequency, which translated to an estimated 1-2% increase in flight costs. The variation in flight costs increased by an order of magnitude when considered in space, rather than time, with flight costs varying by [≥] 10 % across the tropicbirds range. Changes in air density can therefore be an important determinant of flight costs even when birds are operating close to sea-level. Indeed, mapping air density at sea-level revealed that global temperature gradients cause effective altitude to vary by >2 km when considered as seasonal averages. This "invisible topography" at sea-level could have influenced the biogeography of flight morphologies and life-history traits.

zoology↗

bioRxiv2024

Protein Sequence Domain Annotation using Language Models

Protein domain annotation underlies large-scale functional inference and is commonly performed by scanning sequences against libraries of profile hidden Markov models (profile HMMs). We describe PSALM, a protein domain annotation method that combines (i) a pretrained protein language model (ESM-2) with (ii) a per-residue domain-state classifier and (iii) a structured probabilistic decoder that produces a single, non-overlapping set of domain calls with explicit boundaries and scores. On a benchmark of 89M protein sequences with 107M annotated domains, PSALM attains a domain-detection sensitivity-specificity tradeoff comparable to HMMER. We characterize sequence and residue-level coverage on UniProtKB, observing higher coverage for HMMER at stringent expected false positive counts (E-values) and higher coverage for PSALM at relaxed E-values. We release code for data processing, training, and inference, along with the model weights and datasets used for training, validation, and benchmarking.

bioinformatics↗

bioRxiv2023

Genome-Wide Profiling of tRNA Using an Unexplored Reverse Transcriptase with High Processivity

Monitoring the dynamic changes of cellular tRNA pools is challenging, due to the extensive post-transcriptional modifications of individual species. The most critical component in tRNAseq is a processive reverse transcriptase (RT) that can read through each modification with high efficiency. Here we show that the recently developed group-II intron RT Induro has the processivity and efficiency necessary to profile tRNA dynamics. Using our Induro-tRNAseq, simpler and more comprehensive than the best methods to date, we show that Induro progressively increases readthrough of tRNA over time and that the mechanism of increase is selective removal of RT stops, without altering the misincorporation frequency. We provide a parallel dataset of the misincorporation profile of Induro relative to the related TGIRT RT to facilitate the prediction of non-annotated modifications. We report an unexpected modification profile among human proline isoacceptors, absent from mouse and lower eukaryotes, that indicates new biology of decoding proline codons.

genomics↗

bioRxiv2023

Multidimensional analysis of a social behavior identifies regression and phenotypic heterogeneity in a female mouse model for Rett syndrome

Regression is a key feature of neurodevelopmental disorders such as Autism Spectrum Disorder, Fragile X Syndrome and Rett syndrome (RTT). RTT is caused by mutations in the X-linked gene Methyl CpG-Binding Protein 2 (MECP2). It is characterized by an early period of typical development with subsequent regression of previously acquired motor and speech skills in girls. The syndromic phenotypes are individualistic and dynamic over time. Thus far, it has been difficult to capture these dynamics and syndromic heterogeneity in the preclinical Mecp2-heterozygous female mouse model (Het). The emergence of computational neuroethology tools allow for robust analysis of complex and dynamic behaviors to model endophenotypes in pre-clinical models. Towards this first step, we utilized DeepLabCut, a marker-less pose estimation software to quantify trajectory kinematics, and multidimensional analysis to characterize behavioral heterogeneity in Het over trials in the previously benchmarked, ethologically relevant social cognition task of pup retrieval. We report the identification of two distinct phenotypes of adult Het: Het that display a delay in efficiency in early days and then improve over days like wild-type mice, and Het that regress and perform worse in later days. Furthermore, regression is dependent on age, behavioral context, and is identifiable in early days of retrieval. Together, the novel identification of two populations of Het suggest differential effects on neural circuitry and opens new directions of exploration to investigate the underlying molecular and cellular mechanisms, and better design experimental therapeutics.

neuroscience↗