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Joshi, S.

Publications and source records attributed to Joshi, S..

At least 37 records · Page 2Linked to original sources

A SIRT5-induced metabolic switch underlies chemoresistance and ATR checkpoint dependence in triple-negative breast cancer

Chemoresistance is the leading cause of poor prognosis in triple-negative breast cancer (TNBC), yet the underlying mechanisms remain unknown. To reveal metabolic drivers of de novo chemoresistance in TNBC, we analyzed pretreatment primary tumor biopsies, employing quantitative proteomics and metabolomics. Chemoresistant TNBCs exhibit hallmarks of oxidative phosphorylation (OXPHOS) and altered nucleotide metabolism linked to overexpression of the mitochondrial sirtuin, SIRT5. Through gain- and loss-of-function studies and stable isotope tracing, we demonstrate that SIRT5 induces a coordinated metabolic switch that redirects glycolysis to the pentose phosphate pathway, thereby augmenting nucleotide pools, while enhancing glutaminolysis to support OXPHOS. Mechanistically, SIRT5 enhances conversion of 6-phospho-D-gluconate to ribulose-5-phosphate through demalonylation of 6-phosphogluconate dehydrogenase (6-PGD), and coordinately activates oncogenic c-MYC to promote glutamine utilization and dependence. Concurrently, SIRT5-induced nucleotide deregulation induces replication stress and hypersensitivity to ATR checkpoint activation, and ATR inhibition synergistically reverses chemoresistance in TNBC. Thus, elevated SIRT5 orchestrates a coordinated metabolic switch to expand nucleotide pools and drive chemoresistance, while producing ATR checkpoint dependence that represents a metabolic vulnerability of SIRT5-overexpressing TNBC. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=182 HEIGHT=200 SRC="FIGDIR/small/716852v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@1c7a27corg.highwire.dtl.DTLVardef@17cb22borg.highwire.dtl.DTLVardef@1956670org.highwire.dtl.DTLVardef@1786dee_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

HORI-EN: Atomic-level energetic profiling and higher-order network identification in protein structures

MotivationCharacterizing atomic-level stability and cooperative interaction networks is essential for understanding protein function and evolution. However, existing tools often lack the precision to integrate detailed physicochemical energies with higher-order graph-theoretic analyses. ResultsWe present HORI-EN, an updated implementation to the HORI framework, featuring hybrid energetic scoring (Physicochemical + Knowledge-Based) and a Normalized Interaction Score (NIS) based on cumulative distribution functions. HORI-EN identifies higher-order cliques of interacting residues, revealing cooperative stabilization networks. Validation on the SKEMPI v2 dataset demonstrates that HORI-EN shows discriminative performance in identifying mutational hotspots, achieving an ROC-AUC of 0.780 on the full dataset and 0.844 on a clean benchmark. Enrichment analysis indicates a 3.1-fold increase in precision for the top 1% of predictions. Furthermore, analysis of the residue interaction network recovers 77.4% of non-contacting hotspots by identifying one-hop bridging interactions to the partner chain. Beyond hotspot prediction, HORI-EN distinguishes native structures from decoys and captures conserved energetic signatures in evolutionary case studies of serine proteases and lipases. Availability and ImplementationThe web server is freely available at https://caps.ncbs.res.in/HORI-EN and source code is available at https://github.com/thesixeyedknight/HoriPy. Contactmini@ncbs.res.in

bioinformatics↗

Single cell multiomics reveal clonal and functional dynamics of MDS stem/progenitor cells during hypomethylating therapy

Progressive somatic mutations in hematopoietic stem cells (HSCs) drive the development of myelodysplastic neoplasms (MDS). Hypomethylating agents such as azacitidine (AZA) can improve blood counts and reduce blasts, although responses are rarely durable. Determinants of AZA response are complex and incompletely understood, although accumulating evidence suggests that epigenetic rewiring of mutated HSCs underlies improved hematopoietic output. Using single cell multiomics on longitudinal bone marrow samples, we show that AZA responsiveness involves expansion of cells with transcriptomic profiles shared with hematopoietic stem and progenitor cells (HSPCs) from healthy donors. These regenerating cells are depleted of copy number variations and of TP53 mutations. We also identify patient-restricted cell populations, some of which recede through transcriptional restoration or AZA cytotoxicity, and others which expand, regardless of initial clinical response, and dominate at progression. Individual patients carried multiple patient-restricted populations which had unique surface immunophenotypes and were genetically distinct. Strikingly, sorted cells from in vivo progression clones that were AZA-refractive in patients regained AZA-sensitivity when cultured in vitro, suggesting that lack of AZA response at the cellular level can be modulated by cell-extrinsic factors in vivo. Overall, we find that AZA response involves partial hematopoietic regeneration via functional differentiation of mutated, but not cytogenetically abnormal HSPCs, and that persistence of AZA-refractive sub-populations contributes to eventual disease progression.

cancer biology↗

Salient auditory stimuli evoke spatially segregated phasic and sustained neural responses in the human brain

Salient sensory stimuli are known to evoke neural activations across distributed brain regions. However, the temporal dynamics of these responses over sub-second timescales remain poorly understood, in part due to limitations in the temporal resolution of non-invasive neuroimaging methods. We examined the spatiotemporal dynamics of neural activations evoked by salient sensory stimuli (rare sounds) using 1,194 widely distributed intracranial electrodes in 5 neurosurgical patients. Salient stimuli preferentially activated 263 of 1,194 electrodes (22%), with responses segregating into two largely distinct spatiotemporal patterns: (1) phasic activation in sensorimotor regions, and (2) sustained activation within the salience network. Cross-correlation analysis revealed that phasic sensorimotor activation preceded sustained salience network activation on a trial-by-trial basis. These findings support an updated view of salience processing in the human brain, revealing that salient stimuli evoke two sequential stages of neural activation--phasic sensorimotor responses followed by sustained salience network activity--rather than simultaneous widespread activation.

neuroscience↗

Vascular dementia increases levels of methylenetetrahydro-folate reductase and cystathionine β-synthase in female patients and changes gene expression of acetylcholine and glutamate clathrin-sculpted transport vesicles

Vascular dementia (VaD) is a complex clinical syndrome arising from cerebrovascular disease, characterized by cognitive decline and functional impairment, and is projected to double in prevalence over the next three decades. Deficiencies in one-carbon (1C) metabolism are linked to the onset of VaD. Our previous work using mouse models has demonstrated that reduced dietary folic acid intake or genetic disruptions in 1C metabolism exacerbate outcomes in a model of VaD. However, the impact of VaD on one-carbon metabolism remains poorly understood. This study aims to provide a detailed molecular portrait of 1C metabolism within the context of VaD, shedding light on potential molecular mechanisms. In post-mortem medial prefrontal cortex tissue from VaD female and male patients and controls we measured protein expression of the folate receptor (FR) and 1C enzymes including methylenetetrahydrofolate reductase (MTHFR), thymidylate synthase (TS), choline acetyltransferase (ChAT), acetylcholinesterase (AChE), cystathionine {beta}-synthase (CBS) co-localized with NeuN. There was an interaction between VaD and gender for levels of FR. Both male and female VaD had increased levels of ChAT. Female VaD patients had higher levels of MTHFR and CBS when compared to males. VaD is a complex disease; the results of this study demonstrate that VaD impacts neuronal levels of 1C enzymes. Future studies should assess 1C in other cell types of the brain, as well as measure enzyme activity levels.

neuroscience↗

Glutamine-Dependent Biosynthetic Pathways Fuel Autoreactive T and B Cells in Foxp3 Deficiency-mediated Disease

Foxp3 deficiency causes a profound loss of immune tolerance, unleashing autoreactive T and B cells, lymphoproliferation, cytokine-driven inflammation, and autoantibody production. This autoimmune pathology is fueled by increased glutamine usage, but it remains unresolved whether glutamine is necessary to produce energy, or for biosynthetic pathways leading to inosine and asparagine production. Here, we demonstrate that glutamine utilization supports Foxp3-deficiency mediated disease independently of pathogenic Foxp3-deficient Treg cell energetic reprogramming. Mechanistically, glutamine biosynthetic pathways sustain conventional T cell activation and proinflammatory cytokine production preventing inosine accumulation and signaling, thus implicating adenosine pathway modulation in autoreactive T cell dysregulation. Conversely, autoreactive B cell activation and autoantibody production depend on glutamine-dependent asparagine synthesis, which we reveal as a targetable vulnerability for autoantibody formation. These findings highlight glutamine-driven biosynthetic processes as critical drivers of autoimmunity and reveal distinct metabolic vulnerabilities in autoreactive T and B cells that can be targeted for therapeutic intervention.

immunology↗

GRAYU: Graph-based Database integrating Ayurvedic formulations, medicinal plants, phytochemicals and diseases

The translation of Indias extensive traditional knowledge on indigenous medicinal plants into modern therapeutic solutions is contingent upon a systematic framework. While traditional Indian medicine offers a rich source of therapeutic leads, this knowledge is often not structured for modern computational analysis, creating a barrier to systematic drug discovery. To this end, we present GRAYU, a curated and comprehensive online database that integrates data across multiple categories, connecting 1039 traditional formulations to 12,949 indigenous plants, 129,542 phytochemicals, and 13,480 indicated diseases. It also provides insights into 1,382,362 plant-phytochemical, 116,824 plant-disease, 2,405 plant-formulation, and 4,087 formulation-disease associations. Case studies on phytochemical analogs, sustainable plant substitution, and disease-network pharmacology showcased the potential of integrative graphs to decode shared molecular signatures and therapeutic networks across traditional Ayurvedic formulations. GRAYU represents a user-friendly resource for researchers to investigate complex bio-associations and formulate novel therapeutic hypotheses, with insights from traditional Indian medicine. GRAYU is available at https://caps.ncbs.res.in/GRAYU/.

bioinformatics↗

Hyper-migratory CAR T cells alleviate ovarian cancer metastatic burden and improve prognosis

Cellular immunotherapy has shown remarkable efficacy in hematological malignancies but remains limited by infiltration issues in solid tumors, leading to poor treatment efficacy. We have recently shown that mesothelin-targeting CAR T cells co-transduced with cytokine-binding synthetic velocity receptors (VRs, referred to as CAR TV cells) demonstrate increased motility, improved infiltration in solid primary tumors, and lead to a better anti-tumor effect compared to CAR T cells that do not express VRs. However, it is metastasis that causes the vast majority of cancer related deaths and is difficult to target clinically, indicating an urgent unmet need. We show that these CAR T cells engineered to be hyper-migratory using VRs are highly effective against liver metastasis of ovarian cancer along different stages of the metastatic cascade. Mesothelin-targeting CAR TV cells expressing synthetic or native receptors responsive to the cytokine Interleukin-5 improved the survival of mice bearing an extremely high or terminal level of metastatic burden compared to CAR T cells that did not express VRs. Against newly established metastatic lesions and lesions undergoing metastatic outgrowth, CAR TV cells showed a robust anti-cancer effect resulting in an improved prognosis compared to control CAR T cells. Histopathological assessments showed a substantial reduction of metastasis number and lesion size with CAR TV treatment, concomitant with increased immune cell infiltration in the metastatic regions. Our work demonstrates the efficacy of high-motility CAR T cells in a metastatic setting and extends their scope to the treatment of metastasis of solid tumors.

bioengineering↗

3D multi-omic mapping of whole nondiseased human fallopian tubes at cellular resolution reveals a large incidence of ovarian cancer precursors

Uncovering the spatial and molecular landscape of precancerous lesions is essential for developing meaningful cancer prevention and early detection strategies. High-Grade Serous Carcinoma (HGSC), the most lethal gynecologic malignancy, often originates from Serous Tubal Intraepithelial Carcinomas (STICs) in the fallopian tubes, yet their minute size and our historical reliance on standard 2D histology contribute to their underreporting. Here, we present a spatially resolved, multi-omics framework that integrates whole-organ 3D imaging at cellular resolution with targeted proteomic, metabolomic, and transcriptomic profiling to detect and characterize microscopic tubal lesions. Using this platform, we identified a total of 99 STICs and their presumed precursors that harbor TP53 mutations in morphologically unremarkable tubal epithelium in all five specimens obtained from cancer-free organ donors with average-risk of developing ovarian cancer. Although these lesions comprised only 0.2% of the epithelial compartment, they displayed geographic diversity, immune exclusion, metabolic rewiring, and DNA copy number changes among lesions and normal fallopian tube epithelium discovered alterations in STIC-associated genes and the pathways they control. In sum, this platform provides a comprehensive 3D atlas of early neoplastic transformation, yielding mechanistic insights into tumor initiation and informing clinical screening strategies for detecting cancer precursors in whole organs at cellular resolution.

bioinformatics↗

Detection of multiple per- and polyfluoroalkyl substances (PFAS) using a biological brain-based gas sensor

Per- and polyfluoroalkyl substances (PFAS) are man-made compounds that bioaccumulate in environments. Current PFAS detection technologies encounter difficulty in detecting trace concentrations and require complex data processing, limiting their on-site applicability. By leveraging biological chemical sensing systems (insect olfaction) we can detect broad ranges of PFAS. Insects advanced combinatorial coding mechanism at the level of olfactory sensory neurons enables highly sensitive and specific odor detection. Here, we harness the locust olfactory system to differentiate several PFAS. In-vivo extracellular neural recordings displayed unique odor-evoked responses for multiple PFAS at environmental concentrations. Using population neuronal response, we classified multiple PFAS with an average 87% accuracy. Machine learning algorithms incorporated separate training and testing datasets, reaching a 61% accuracy. Overall, our study demonstrates the first biological olfaction based broad PFAS detection system. Structured AbstractO_ST_ABSIntroductionC_ST_ABSPer- and polyfluoroalkyl substances (PFAS) pose a significant environmental threat due to their widespread presence in consumer waste and resistance to degradation. These "forever chemicals" persist in various ecosystems and exhibit bio accumulative behavior. Increased human exposure to PFAS has been linked to numerous health issues. Despite their growing relevance, current detection methods often lack the sensitivity and efficiency needed for comprehensive environmental monitoring and are unable to simultaneously detect multiple PFAS at environmental concentrations. RationaleThe locust (Schistocerca americana) possesses a highly developed olfactory system that has been extensively studied and is accessible for physiological recordings across multiple brain regions. Utilizing olfactory receptor neurons and combinatorial coding strategies, locusts can generate distinct neural fingerprints for trillions of odorants across a wide range of concentrations. Through spatiotemporal neural coding at the antennal lobe (AL) neurons, they can detect chemicals at parts per trillion levels, functioning as a biological chemical sensor with exceptional sensitivity and broad specificity. In this study, we aimed to directly harness the locusts olfactory neural circuitry to develop a next-generation, brain-based cyborg sensor capable of (1) simultaneously identifying multiple PFAS and (2) determining their concentration ranges, addressing key limitations of existing detection technologies with the integration of machine learning algorithms. ResultsIn-vivo extracellular neural recordings from the locust AL revealed that individual neurons exhibited distinct response profiles to different PFAS and their varying concentrations, indicating that neuronal activity if modulated by both chemical identity and concentration. By incorporating both spatial and temporal dimensions of neural activity, the recorded neuronal populations produced unique and reproducible response patterns corresponding to specific PFAS and concentration levels. Using this approach, the cyborg sensor demonstrated an overall detection accuracy of 87% across a panel of seven PFAS, with high sensitivity and specificity for both individual analytes and broader chemical groupings. Notably, classification of PFAS concentration ranges down to parts per trillion achieved 84% accuracy, with PFOS concentrations reaching 100% detection rate. A machine learning algorithm trained on high concentration data and tested on low concentration data achieved a 61% accuracy. These results underscore the potential of biologically integrated cyborg sensors for real-time, high-resolution environmental monitoring of several PFAS. ConclusionThis study demonstrates, for the first time, the locust olfactory neural network harnessed as a highly effective cyborg sensor for detecting and classifying various PFAS across concentration ranges. This sensor can accurately distinguish between multiple PFAS and controls with high sensitivity and specificity. Through combinatorial coding and spatiotemporal neural dynamics, the locust neural computation encodes distinct activity patterns in response to PFAS and their concentrations. These neural signatures serve as unique "fingerprints" for individual PFAS and concentrations, enabling precise identification. In-vivo electrophysiological recordings revealed clear, compound-specific differences in neural activity, with high classification accuracy. Real-time and machine learning analysis further addressed key limitations of conventional PFAS sensors. This novel approach represents a significant step toward the development of compact, real-time, brain-based PFAS detection sensor capable of discriminating multiple compounds and concentrations simultaneously.

bioengineering↗

Lactate receptor, HCAR1, in neonatal hypoxic-ischemic encephalopathy

IntroductionHydroxycarboxylic acid receptor 1 (HCAR1) is a G-protein coupled receptor for lactate that is expressed in the brain and plays a role in neuronal excitability, angiogenesis, and repair after injury. Hypoxic-ischemic encephalopathy (HIE) is the most common cause of brain injury and seizures in term neonates. The goal of this study was to describe HCAR1 expression and function in the neonatal brain and further understand its role in HIE. MethodsHCAR1 expression was measured using qRT-PCR in developing mice (postnatal day (p)10, 20, 30, 50). Electrophysiology was used to measure neuronal properties and spontaneous excitatory postsynaptic currents (sEPSC) in hippocampal principal neurons from HCAR1 knockout and wildtype mice when exposed to lactate. Then, p10 HCAR1 knockout and wildtype mice were exposed to hypoxia-ischemia (HI) and placed on electroencephalography (EEG) to compare seizure burden. HCAR1 expression after neonatal HI was measured with PCR. ResultsHCAR1 is expressed at p10 at similar levels to adults (n=6/group; 1-way ANOVA, p<0.0004). Lactate decreases amplitudes and sEPSC frequency in wildtype (p<0.0001, p<0.001) but not HCAR1 knockout mice (p<0.26, p=0.91). After HI, HCAR1 knockout mice have higher seizure burden (2318s in WT vs. 6497s in KO (p=0.04)) and behavioral seizure scores (4 in WT vs. 6 in KO (p<0.001)) than wildtypes. HCAR1 expression increased 24h post-HI but drops to below baseline at 48h post-HI. (n=3/group; p=0.02). ConclusionHCAR1 is expressed on neurons in the developing mouse brain. Lactate decreases neuronal excitability via HCAR1. HCAR1 is upregulated post-HI and mice lacking HCAR1 exhibit worse neonatal HI seizures. HighlightsO_LIHCAR1, a G-protein coupled, lactate receptor is expressed in the developing mouse brain C_LIO_LIHCAR1 is expressed on neurons in the neonatal mouse hippocampus C_LIO_LIHCAR1 is upregulated 24 hours after neonatal hypoxia-ischemia C_LIO_LIMice lacking HCAR1, exhibit worse neonatal hypoxic-ischemic seizures C_LI

neuroscience↗

METTL13 Promotes Pre-Leukemic Transformation and the Development of Pediatric Leukemia

Post-transcriptional RNA modifications, such as N6-methyladenosine (m6A) methylation and adenosine to inosine (A-to-I) editing, are critical regulators of hematopoietic stem cell (HSC) self-renewal and differentiation, yet their precise contributions to malignant transformation are not fully elucidated. In this study, we uncovered the epitranscriptomic landscape caused by knockdown of genes from the methyltransferase (METTL)-family in hematopoietic stem and progenitor cells (HSPCs). We identified both converging and distinct roles of METTL3 and METTL14, known members of the m6A writer complex, as well as orphan gene METTL13. Notably, METTL13 was uniquely upregulated by adenosine deaminase acting on RNA 1 (ADAR1) overexpression, while other METTL genes were downregulated. Knockdown of METTL13 altered the expression of multiple genes involved in oncogenic development in HSPCs. Furthermore, METTL13 was associated with a high-risk profile in pediatric T-cell acute lymphoblastic leukemia (T-ALL), and functional studies confirmed that METTL13 is required for T-ALL cell proliferation and survival both in vitro and in vivo. Collectively, our results indicate a previously unrecognized, oncogenic role for METTL13 in pre-leukemic transformation and T-ALL pathogenesis. SignificanceIn this study we uncovered a novel regulatory link between ADAR1 and the METTL-family of RNA methyltransferases in hematopoietic stem cells. Overexpression of ADAR1 uniquely upregulated METTL13 while suppressing other METTL genes. Loss of orphan gene METTL13 affected proliferation, apoptosis and p53 signaling in hematopoietic stem cells. Furthermore, loss of METTL13 suppressed cell proliferation and survival in pediatric T-cell acute lymphoblastic leukemia. Our findings suggest a potential role for METTL13 in pre-leukemia transformation and oncogenic development.

cancer biology↗

VISIBLE: An imaging-driven system for sampling, biofabrication, and manipulation of complex biological models

Complex in vitro models (CIVMs), including organoids, spheroids, and bioprinted constructs, have emerged as powerful platforms for recapitulating human tissue architecture and function. However, their inherent heterogeneity and dynamic nature pose significant challenges for standardization, reproducibility, and real-time manipulation. Here, we present VISIBLE (Versatile Imaging-Based Interactive Sampling and Bioprinting System), a modular, imaging-guided platform that integrates real-time monitoring with automated manipulation and 3D bioprinting that addresses these challenges. VISIBLE employs a dual-axis system comprising independently controlled tool-heads and microscope stages, enabling precise spatiotemporal interventions within live cultures. We demonstrate the system capabilities across a range of applications, including morphology- and function-based sampling of organoids and neurospheres, interactive 3D bioprinting, serial scratch assays, and real-time cell-cell interaction studies. Furthermore, we illustrate the system utility in translational contexts through the selective sampling and implantation of patient-derived xenograft organoids. VISIBLE supports long-term culture within an integrated incubation environment and accommodates interchangeable tool-heads for scalable, high-throughput workflows. By enabling closed-loop, feedback-controlled experimentation, VISIBLE addresses some of the critical limitations in existing CIVM platforms and offers a new versatile solution for a wide range of biomedical research applications. This work represents a significant step toward the development of autonomous experimental systems for complex tissue modelling and preclinical investigation.

bioengineering↗

Multimodal profiling unveils a reversible basal-like breast cancer cell state resistant to AKT inhibition

The PI3K/AKT/mTOR pathway is central to cell metabolism and growth. However, pharmacological inhibition of the pathway is not uniformly effective across cancer types, or even within a single cancer model. In this study, we leverage oblique plane microscopy of triple negative breast cancer organoids, as well as lineage tracing to uncover a source of heterogeneity. Non-genetic resistance to AKT inhibition is associated with basal cell features of normal breast epithelium and the master transcription factor of basal cell state, {Delta}Np63, is sufficient to confer resistance. Cells can transition between states within four weeks and therefore, AKT inhibition only delays tumour growth, with tumours rich in KRT14+ cells resulting. Thus, under selection, triple negative breast cancer exploits a repertoire of cell states inherent to the breast.

cancer biology↗

Drug screen reveals new potent host-targeted antivirals against Mpox virus

Mpox virus (MPXV), a re-emerging zoonotic threat, has caused outbreaks in non-endemic regions through respiratory, sexual, and close-contact transmission. The increased transmissibility of Clade IIb fueled the 2022 global outbreak, with 2024 Clade Ib spread in the Democratic Republic of Congo further escalating concern. Both outbreaks were declared public health emergencies by the WHO. Although tecovirimat (TPOXX) has been used off-label for Mpox, its limited effectiveness highlights the critical need for newer antivirals for MPXV. We conducted high- throughput antiviral drug screening using a host-directed kinase inhibitor library composed of 2,750 compounds against 2022 Clade IIb MPXV. Our primary screen identified 138 compounds preventing MPXV cytopathic effects, including multiple inhibitors of EGFR, PI3K-mTOR, and Ras/Raf, as well as apoptosis and autophagy regulators. Secondary and tertiary screenings yielded a shortlist of potent, nontoxic antiviral compounds that inhibited MPXV replication. Three selected compounds, IRAK4-IN-6, SM-7368, and KRAS inhibitor-10, reduced MPXV-induced cell death in primary human epidermal keratinocytes. IRAK4-IN-6 and SM-7368 were also found to modulate NF-{kappa}B and STING signaling. Furthermore, these compounds were found effective in reducing skin lesions and viral burden in a mouse model of MPXV skin infection. Together, our study reveals new classes of antiviral compounds against MPXV, offering promising candidates for future clinical development.

microbiology↗

CODAvision: best practices and a user-friendly interface for rapid, customizable segmentation of medical images

Image-based machine learning tools have emerged as powerful resources for analyzing medical images, with deep learning-based semantic segmentation commonly utilized to enable spatial quantification of structures in images. However, customization and training of segmentation algorithms requires advanced programming skills and intricate workflows, limiting their accessibility to many investigators. Here, we present a protocol and software for automatic segmentation of medical images guided by a graphical user interface (GUI) using the CODAvision algorithm. This workflow simplifies the process of semantic segmentation of microanatomical structures by enabling users to train highly customizable deep learning models without extensive coding expertise. The protocol outlines best practices for creating robust training datasets, configuring model parameters, and optimizing performance across diverse biomedical image modalities. CODAvision enhances the usability of the CODA algorithm (Nature Methods, 2022) by streamlining parameter configuration, model training, and performance evaluation, automatically generating quantitative results and comprehensive reports. We expand beyond the original implementation of CODA to serial histology by demonstrating robust performance across numerous medical image modalities and diverse biological questions. We provide sample results in data types including histology, magnetic resonance imaging (MRI), and computed tomography (CT). We demonstrate the diverse use of this tool in applications including quantification of metastatic burden in in vivo models and deconvolution of spot-based spatial transcriptomics datasets. This protocol is designed for researchers with interest in rapid design of highly customizable semantic segmentation algorithms and a basic understanding of programming and anatomy.

bioinformatics↗

Integration of nuclear morphology and 3D imaging to profile cellular neighborhoods

Nuclear morphology is an indicator of cellular function and disease states, as changes in nuclear size, shape, and texture often reflect underlying disease-related genetic, epigenetic, and microenvironmental alterations. For disease diagnosis, nuclear segmentation performed in 2D hematoxylin and eosin (H&E)-stained tissue sections has long represented the gold standard. However, recent advances in three-dimensional (3D) histology, which provide a more biologically accurate representation of the spatial heterogeneity of human microanatomy, has led to improved understandings of disease pathology. Yet challenges remain in the development of scalable and computationally efficient pipelines for extracting and interpreting nuclear features in 3D space. 2D histology neglects crucial spatial information, such as 3D connectivity, morphology, and rare events missed by sparser sampling. Here, through extension of the CODA platform, we integrate 3D imaging with nuclear segmentation to analyze nuclear morphological features in human tissue. Analysis of 3D tissue microenvironments uncovered critical changes in 3D morphometric heterogeneity. Additionally, it enables the spatial characterization of immune cell distribution in relation to tissue structures, such as variations in leukocyte density near pancreatic ducts and blood vessels of different sizes. This approach provides a more comprehensive understanding of tissue and nuclear structures, revealing spatial patterns and interactions that are critical for disease progression.

bioinformatics↗

GenDiS3 database: census on prevalence of protein domain superfamilies of known structure in the entire sequence database

Despite the vast amount of sequence data available, a significant disparity exists between the number of protein sequences identified and the relatively few structures that have been resolved. This disparity highlights the challenge in structural biology to bridge the gap between sequence information and three-dimensional structural data, and the necessity for robust databases capable of linking distant homologues to known structures. Studies have indicated that there is a limited number of structural folds, despite the vast diversity of proteins. Hence, computational tools can enhance our ability to classify protein sequences, much before their structures are determined or their functions characterised, thereby bridging the gap between sequence and structural data. GenDiS is a repository with information on Genomic Distribution of protein domain superfamilies, involving a one-time computational exercise to search for trusted homologues of protein domains of known structures against the vast sequence database. We have updated this database employing advanced bioinformatics tools, including DELTA-BLAST for initial detection of hits and HMMSCAN for validation, significantly improving the accuracy of domain identification. Using these tools, over 151 million sequence homologues for 2060 superfamilies (SCOPe) were identified and 116 million out of them were validated as true positives. Through a case study on glycolysis-related enzymes, variations in domain architectures of these enzymes are explored, revealing evolutionary changes and functional diversity amongst these essential proteins. We present another case, LoG gene, where there one can tune-in and find significant mutations across the evolutionary lineage. The GenDiS database, GenDiS3, and the associated tools made available at https://caps.ncbs.res.in/gendis3/, offer a powerful resource for researchers in functional annotation and evolutionary studies. Database URL: https://caps.ncbs.res.in/gendis3/

bioinformatics↗