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Das, J.

Publications and source records attributed to Das, J..

At least 19 recordsLinked to original sources

Reactivation of neural signatures of food during REM-like sleep in the high-level visual cortex of monkeys

Can we tell what animals are dreaming about from their brain activity? This fascinating question has been explored extensively using the rodent hippocampus, where place cells are sequentially reactivated during sleep, consistent with replay of paths explored while awake. However, dreams involve vivid visual experiences, and whether analogous replays occur in the visual cortex has not been explored, that too in primates. To address this gap, we performed wireless neural recordings from the high-level visual (IT) and motor regions (PMv, PFC) in two monkeys while they viewed food images on a screen while awake, and afterwards while they slept in their natural setting. Decoders trained on sleep/wake neural activity in each region were able to accurately predict the ongoing sleep/wake state, as well as upcoming transitions between states. Interestingly, decoders trained to categorize neural responses to food (but not faces/objects) showed increased probability during REM-like sleep compared to NREM or awake states. Thus, behaviorally relevant visual stimuli seen while awake are reactivated during REM-like sleep. In other words, these monkeys saw food, faces and objects while awake, and dreamt selectively about food while sleeping.

neuroscience↗

High-level visual and motor regions are doubly dissociated in controlled tasks but only at specific times during natural behaviors

Our knowledge of the neural basis of sensory and motor information processing comes largely from recording brain activity in controlled settings. This approach, while insightful, blinds us from understanding natural behaviors, which involve far richer visual inputs and far larger range of movements. The prevailing belief is that, during natural behaviors, movement information would modulate visual cortex, and visual inputs would modulate motor cortex. Alternatively, this mixing might only reflect correlations between sensory inputs and movements present during natural behavior. To resolve this issue, we performed wireless recordings from high-level visual (IT) and motor regions (PMv/PFC) in freely moving monkeys while they performed a natural task and a fixation task. In each task, we extracted visual and movement features and asked to what degree these features explained neural activity. In the fixation task, we found a striking double dissociation whereby visual (but not movement) features predicted neural activity in IT, whereas motor (but not visual) features predicted neural activity in PMv & PFC. This dissociation was far weaker in the natural task but present particularly at key events when the visual and motor features were less correlated. Thus, high-level sensory and motor regions in the brain are doubly dissociated under controlled conditions, and remain so at specific times during natural behavior.

neuroscience↗

Interpretable machine learning coupled to gene regulatory networks uncovers subcircuits underlying cell fate decisions

Gene regulatory networks (GRNs) model causal linkages that control cell fate decisions and differentiation transitions. Prioritizing regulatory subnetworks underlying cell state differences is of critical importance, but current methods including those reliant on topological metrics introduce circularity as the metrics prioritizing TFs are computed from the same networks whose assumptions they inherit. Separately, interpretable machine learning methods can identify latent factors (LFs) that discriminate cellular states with formal statistical guarantees but do not model regulatory linkages. Here, we present FOCAL (Factor-Outcome Coupling for Assessment of Linkages), a paradigm to prioritize regulatory subnetworks by coupling state-specific and dynamic GRNs with outcome-supervised LFs learned using interpretable machine learning without reference to network topology. This shifts GRN focus from macroscopic TF nodes to state-specific and dynamic TF-gene linkages. In B and T cells, FOCAL identified GIFs (GRNs coupled to Interpretable latent Factors), prioritized regulatory subnetworks underlying established states as well as transient regulatory episodes preceding them. By coupling LFs learnt from perturbation experiments of lineage-defining TFs, FOCAL identified transcriptional predisposition to alternative fates within progenitor cell populations before overt differentiation. This uncovered a novel NFATC2-IRF8 interplay in activated B cells, that was validated by in-vitro and in-vivo genetic perturbations. The two transcription factors act cooperatively to restrain extrafollicular plasmablast differentiation and promote germinal center B cell fate.

systems biology↗

FlowMap: Geometry Dynamics Consistent Embedding of RNA Velocity for Interpretable Cellular Trajectories

Single-cell RNA sequencing reveals how cells vary across states, but these measurements capture only static snapshots of dynamic biological processes. RNA velocity addresses this limitation by estimating how gene expression is changing over time, providing directional information about cell state transitions. However, current approaches treat cellular state and dynamics separately, leading to representations that violate fundamental geometric consistency and obscure biological interpretation. Here, we present FlowMap, a framework that jointly models cellular states and their dynamics within a unified geometric representation. FlowMap simultaneously reconstructs a smooth low-dimensional manifold of gene expression and constrains RNA velocity to follow its local geometry, producing coherent and denoised representations of cellular trajectories. Across simulated and real datasets, FlowMap recovers interpretable dynamical patterns, including continuous progressions, branching events, cyclic behaviors, and stable-like states. It highlights key genes and gene programs involved in development that play distinct roles in these dynamics, and extends naturally to spatial transcriptomics, where it captures spatially organized developmental processes. Together, FlowMap establishes a principled geometric framework for modeling cellular dynamics, bridging representation learning and dynamical inference in single-cell analysis.

bioinformatics↗

Inflammatory proteolysis generates pathogenic APOL1 fragments with distinct intracellular toxicities in podocytes derived from children with HIV associated nephropathy

APOL1 risk variants are the strongest genetic determinants of HIV-associated nephropathy (HIVAN), yet the mechanisms linking inflammation to APOL1-mediated podocyte injury remain poorly understood because authentic patient-derived human disease models are lacking. Using urine-derived podocytes established from children with HIVAN and endogenous APOL1 reporter cell lines derived from these cells, we identified a previously unrecognized pathway of inflammatory, cathepsin-dependent APOL1 proteolysis. Endogenous APOL1 cleavage was detected in patient-derived podocytes, whereas reporter cell lines enabled the identification and functional characterization of N-terminal and C-terminal APOL1 fragments with distinct intracellular localization and pathogenic functions. The nuclear N-terminal fragment activated inflammatory transcriptional programs and promoted podocyte injury, whereas the membrane-associated C-terminal fragment mediated membrane toxicity and remained susceptible to pharmacologic inhibition by inaxaplin. Cathepsin S directly cleaved APOL1 in vitro, linking inflammatory signaling to APOL1 fragmentation. These findings identify inflammatory APOL1 proteolysis as a mechanism that partitions APOL1 toxicity into distinct pathogenic programs and nominate APOL1 processing as a therapeutic target for HIV-associated and other APOL1-mediated kidney diseases.

cell biology↗

Mixed effects modeling of the synergy between immune checkpoint and thrombin inhibitors in a preclinical mouse model of colon cancer

Immune checkpoint blockade (ICB) therapy has revolutionized cancer treatment, though it is still effective in only about 20-40% of patients. To increase the efficacy of ICB therapy, combinations of ICB antibodies such as anti-PD1 and anticoagulants (e.g., thrombin inhibitors) have been studied in preclinical mouse models and clinical trials. We developed a Bliss-type analysis to quantify the synergy between anti-PD1 and dabigatran etexilate using published tumor growth data from a mouse model. We then developed a minimal mechanistic computational model to quantitatively study the synergy between anti-PD1 and the thrombin inhibitor dabigatran etexilate in a published study (Metelli et al.) of a preclinical mouse model of colon cancer. Our model included tumor cells, CD8+ T cells, and the pleiotropic cytokine TGF{beta}, whose production in platelets is influenced by thrombin, and described a potential mechanism of interplay among these components in the tumor microenvironment. We performed nonlinear mixed-effects modeling to capture mouse-to-mouse variation in tumor growth under different treatment conditions. The estimated parameter values pointed to several underlying mechanisms of synergy, including increased expansion of CD8+ T cells in the tumor microenvironment in the presence of anti-PD1 and dabigatran etexilate. These predictions can be further validated in future experiments. Thus, the combination of longitudinal tumor growth data, mechanistic population dynamics modeling, and nonlinear mixed-effects modeling can be used to study synergy between ICB and other drugs in controlling tumor growth.

pharmacology and toxicology↗

Real-time electrochemical protein monitoring using molecular pendulum sensors

Continuous monitoring of proteins in complex biological fluids is essential for advancing personalized medicine, yet existing biosensors are often limited by instability, single-use designs, and insufficient sensitivity. Here, we describe a detailed protocol for the fabrication and operation of molecular pendulum (MP) electrochemical sensors integrated with an active-reset mechanism to enable real-time, reversible, and ultrasensitive protein detection. The protocol is described in two parts. First, we describe the microfabrication of gold microelectrodes and their nanostructured modification, followed by assembly of DNA-based pendulum probes with redox reporters and affinity receptors that translate binding into kinetic electron-transfer shifts. Second, we detail the sensing and active-reset approach, which detects the target analyte and applies tunable oscillatory potentials to accelerate its dissociation, regenerate sensor surfaces, and extend operational lifetime. The protocol includes detailed guidance on device fabrication, surface functionalization, sensing and reset cycles, and data analysis. When implemented, MP sensors with active-reset achieve pg/ml sensitivity, rapid equilibration, and robust performance across biofluids and in situ models, enabling continuous protein monitoring over extended periods. This combined technology represents a biosensing platform with significant potential, opening new avenues for wearable and implantable molecular monitoring, early disease detection, and personalized therapeutic guidance.

bioengineering↗

SHERLOC: An interpretable deep learning model for longitudinal circulating tumor DNA data in survival analysis

Longitudinal circulating tumor DNA (ctDNA) measurements offer a noninvasive means to monitor treatment response, but clinical trial data present substantial methodological challenges due to high-dimensional short longitudinal ctDNA sequences and limited sample sizes. We introduce SHERLOC, a deep learning framework specifically designed for survival analysis using longitudinal on-treatment ctDNA data, which integrates shared temporal representations of gene-level variant allele frequencies, feature-specific temporal trajectories of panel-level ctDNA biomarkers, and survival-aware genomic representations pre-trained on a large pan-cancer tissue-biopsy dataset (MSK-CHORD), within an interpretable Cox proportional hazards framework. Benchmarked against diverse statistical, ensemble, and deep learning approaches in a non-small-cell lung cancer cohort from the phase III IMpower150 trial, SHERLOC consistently achieved superior survival discrimination and calibration, while remaining interpretable and robust to reductions in the number of available longitudinal liquid biopsy time points per patient. The resulting ctDNA-based risk score provided prognostic information both independent of and complementary to standard radiographic response assessments, and enabled patient stratification within homogeneous RECIST response groups--highlighting its potential as an early, non-invasive decision-support tool to guide treatment adaptation and patient management.

cancer biology↗

Pleiotropic antimalarial activities and immunomodulation exhibited by Himalayan Buransh (Rhododendron arboreum) in human and rodent malaria models

Emerging drug resistance against the malaria parasite is worrisome and necessitates the development of novel antimalarials. Himalayan Buransh (Rhododendron arboreum) is a well-known medicinal plant found in the northern states of India. In this study, we observed the pleiotropic antimalarial activities and immunomodulation exhibited by the aqueous extract of Buransh flower (AEBF). AEBF demonstrated significant IC50 values (16-29 {micro}g/ml) against the asexual stages of various P. falciparum strains (3D7, Dd2-chloroquine-resistant and C580Y-artemisinin resistant). The oral administration of AEBF (200 mg/kg) in mice, suppressed [~]80% P. berghei parasitemia, improved mean survival time (MST-23.5 days) and prevented splenomegaly. Notably, the combination of AEBF and artesunate not only cleared primary infection, but also conferred sustained immunity. This immunomodulatory effect, driven by protective IFN-{gamma} resulted in reduced parasitemia during a homologous challenge without the need for further treatment. It is important to highlight the malaria transmission blocking activity of AEBF, resulting in reduced sexual stage male gametocyte exflagellation. Furthermore, the virtual drug screening of selected bioactive constituents from Buransh flower demonstrated potent binding against multiple P. falciparum proteins, suggested a pleiotropic mode of action. Altogether, our results corroborated the first ever evidence of the multistage antimalarial potential of Buransh flower, supported by in vitro cell studies, in vivo rodent malaria model and in silico docking analyses. Based on our studys findings and the traditional use of Buransh juice as a medicinal beverage in Uttarakhand, India, we propose exploring it as an adjunct therapy for drug-resistant malaria, subject to further clinical validation.

pathology↗

Breast cancer stem cells mediated CD8+ T cell exhaustion among different molecular subtypes of breast cancer regulated via NOTCH1/RBPJ/PD-L1 axis

BackgroundBreast cancer stem cells (BCSCs) contribute significantly to breast cancer (BC) mortality among women globally. It underpins tumor heterogeneity in BC by driving variations in stemness potential and altering immune microenvironment. However, how BCSCs, subpopulations of breast cancer cells from distinct molecular subtypes differentially modulate CD8 T-cell exhaustion and immune dysfunction remain unclear. MethodsWe conducted our study from patients with BC of four subtypes. MACS sorted (Lin-CD44+CD24-) BCSCs were prepared for mammosphere formation assay from mastectomies samples. Flow-cytometry was used to analyze breast cancer stem cells (BCSCs). Immunofluorescence, immunohistochemistry, Real Time and Reverse Transcriptase PCR array, Chromatin-immunoprecipitation assay, Transwell, ELISA, Western blotting, Cloning, Transfection, Knockdown, chromatin immunoprecipitation approaches were used to investigate the underlying mechanisms. ResultsHere, we report that BCSCs actively participate in tumor progression by modulating effector CD8 T-cells. Triple-negative breast cancer (TNBC), being the subtype with the most adverse outcomes, sustains the enrichment of stem cell regulating transcription factors like NANOG, OCT4 and SOX2 compared to HER2, Luminal B, and Luminal A subtypes. Tumor from TNBC patients exhibited an exhausted phenotype within CD8 T-cell infiltrates with PD1high TIM3high LAG3 high IFN{gamma}low signature. BCSCs induced increased proportion of exhausted CD8 T-cells, predominantly in the TNBC subtype. Cell-surface Notch1 expression was upregulated in BCSCs across all molecular BC subtypes, with the highest elevation observed in TNBC. Knockdown or inhibition of Notch1 downregulated stemness-associated genes and diminished CSC-mediated induction of CD8 T-cell exhaustion. Cumulatively, these findings suggest that assessment of high Notch1 and Nanog frequency within BCSCs can guide Notch1-targeted therapies and may formulate for new combinatorial treatment strategies to improve patient outcomes. Additionally, therapeutic targeting of BCSC-intrinsic NOTCH1-NANOG/NOTCH1-PD-L1 axis could represent an effective strategy to reduce stemness programs and alter BCSC-driven CD8 T-cell exhaustion, majorly in aggressive subtypes such as TNBC. ConclusionsBCSCs aggressiveness is perpetuated through Notch1-mediated axis. Targeting Notch1 would reduce stemness (majorly NANOG), survival, as well as prevent CD8 T-cell exhaustion (upregulating PD-1, TIM3, LAG3), thereby weakening tumor progression.

cancer biology↗

T cell-specific loss of IRF1 results in defective CD8 T cell activation and antitumor immunity

Interferon regulatory factor 1 (IRF1) has long been recognized as a tumor suppressor; however, recent studies have revealed context-specific and sometimes opposing roles in cancer progression. Here, we describe a T cell-specific mechanism underlying the antitumor activity of IRF1. Unlike germline Irf1-deficient mice, T cell-specific loss of IRF1 does not lead to a deficiency in cytotoxic CD8 T cells. Nevertheless, tumor burden remains elevated in these mice, associated with reduced CD8 T cell infiltration driven by impaired activation and proliferation in the absence of IRF1. Transcriptomic analysis of activated Irf1-deficient T cells identified NFATc1 as a key gene significantly downregulated upon IRF1 loss. Analysis of human melanoma datasets further corroborated this finding, highlighting a previously unappreciated role for IRF1 in regulating T cell activation and antitumor immunity.

immunology↗

High cRel-expressing germinal center B cells favor precursor plasma cell generation

Germinal centers (GCs) are the site of antibody affinity maturation by the process of somatic hypermutation (SHM) and produce long-lived plasma cells (PCs). GC B cells circulate between two distinct zones: the light zone (LZ) and the dark zone (DZ). It has been demonstrated that the transcription factor NF{kappa}B cRel is required for B cell proliferation and GC B cell maintenance. cRel-deleted GC B cells show reduced SHM and affinity maturation. In contrast, transgenic overexpression of cRel does not affect SHM and results in little or no increase in affinity maturation. Therefore, the function of cRel in regulating SHM and GC B cell-derived PC generation remains unknown. To understand the function of cRel in GC B cell selection, we have used cRel fluorescence reporter mice, which provide insight into cRel function in GC B cells at the level of natural expression variation. We found that about 6-9% of LZ cells increased cRel expression compared to DZ cells, and high cRel-expressing LZ cells showed increased SHM and increased expression of IRF4 and cyclin D2, though cMyc expression remained similar. Combining single-cell RNA-Seq and flow cytometry, we revealed that high cRel-expressing LZ cells are enriched for precursor PCs (pre-PCs), not precursor memory B cells (pre-MBCs). Our findings provide insight into the physiologic function of cRel in regulating GC B cell output.

immunology↗

SIV infection disrupts the spatial cellular and communication networks of pulmonary granulomas during SIV/Mtb co-infection

Tuberculosis (TB) caused by Mycobacterium tuberculosis (Mtb) is the leading infectious cause of death globally. Despite wide use of antiretroviral therapy (ART) by people living with HIV, the risk of TB remains increased. To understand immune interactions within lung granulomas, we compared spatial transcriptomics of Mtb and simian immunodeficiency virus (SIV) in co-infected macaques with or without ART as a model for HIV/Mtb co-infection. Spatially differentiated transcriptional profiles were observed in Mtb-only granulomas, with myeloid cells enriched in metabolic/antimicrobial pathways within the inner ring and T cell costimulatory/activation pathways enriched in the outer ring. These spatially distinct patterns were lost in SIV/Mtb granulomas with higher enrichment in type I IFN pathways compared to Mtb-only granulomas. SIV/ART/Mtb granulomas had an intermediate transcriptional pattern without restoration to Mtb-only granulomas, despite a lack of viral replication. Cell-cell communication was reduced among SIV/Mtb co-infected groups. These data suggest that HIV disrupts spatially organized immune functions of granulomas, which are not fully restored by ART.

immunology↗

Gut-derived metabolic reprogramming drives immune aging and tissue degeneration

Aging is characterized by changes in gut microbiome, metabolic imbalance and chronic inflammation, yet how these processes integrate to drive tissue degeneration remains poorly defined. Using age-related macular degeneration (AMD) as a model of tissue aging, we identify a diet-induced metabolic-immune axis that promotes systemic and retinal degeneration. In mice, a high-fat, cholesterol-enriched (HFC) diet induced perturbations in the gut structural integrity and microbiome repertoire, as well as systemic metabolic aging signatures, prominently marked by reduced circulating histidine. Plasma histidine levels were similarly decreased in AMD patients and inversely correlated with body mass index (BMI) in control donors. These diet-induced gut microbiome changes and subsequent metabolic alterations promoted peripheral innate immune reprogramming, with expansion of inflammatory neutrophils and monocytes that infiltrated the outer retina in a mouse model. Mechanistically, the gut-derived IGF1R/AKT2 signaling acts as a central regulator of global epigenetic remodeling and systemic immune aging under high-fat conditions in C. elegans. In a mouse model with an age-dependent dry AMD-like pathology, distinct retinal pigment epithelium (RPE) subpopulations exhibited downregulation of the histidine transporter SLC7A5, linking metabolic stress to activation of MIF/CD74-dependent inflammatory signaling between RPE and infiltrating immune cells. Histidine supplementation or AKT2 phospho-state modulation attenuated systemic immune activation and rescued retinal degeneration. These findings identify histidine-axis dysregulation as a mechanistic bridge between diet-induced microbiome changes, metabolic stress, immune aging, and retinal degeneration.

cell biology↗

Natural behavior elicits reliable neural signatures in high-level sensory and motor regions of freely moving monkeys

Natural behaviors are challenging to study because they involve large variations in sensory inputs and motor outputs across trials. Even the simple act of eating can involve seeing food from many angles and reaching for it differently each time. The prevailing view is that natural behaviors are more noisy compared to controlled tasks, and involve mixing of sensorimotor information. Alternatively, natural behaviors might elicit reliable neural signatures in high-level visual and motor regions which contain invariant representations, and involve correlated sensory and motor information that leads to apparent mixing. Here, we provide evidence for the latter possibility through wireless recordings in freely moving monkeys performing natural tasks as well as controlled screen tasks. During natural interactions with food, neural activity was decodable with striking fidelity, equivalent to that of food images. Key events during these interactions elicited distinct and reliable neural signatures that reflected the encoding priorities of each region. Visual and motor regions were clearly dissociated in screen tasks, but were dissociated only at specific events in the natural task. Neurons active while seeing food were reactivated during sleep. Taken together, our results reveal that reliable neural signatures in high-level sensory and motor regions form the neural substrates for natural behaviors.

neuroscience↗

Dynamic tracking of social variables in simultaneous brain recordings of socially interacting monkeys

Primates are deeply social, but understanding the neural basis has been challenging since it has previously only been possible to record from single monkeys interacting with a social partner. Here, we performed simultaneous wireless neural recordings from two macaque monkeys interacting socially in a natural, unconstrained setting. Neural activity in each monkey encoded key social variables such as allogrooming state, partner identity and joint movements. Interestingly, neurons in the high-level visual cortex of each monkey continuously tracked a social favor signal, i.e. net duration of allogrooming given versus received, providing a neural basis for grooming reciprocity. In each monkey, neural activity was predicted better by his partners joints and neural activity, particularly while giving compared to receiving grooming. Thus, the receiver of grooming drove the social interaction, not the groomer. Taken together, our findings elucidate the rich and dynamic neural basis of primate social interactions in an ecologically valid setting.

neuroscience↗

Proteomic Remodeling of the Cochlea During Chronic Suppurative Otitis Media Reveals Immune-Driven Injury Pathways

Chronic suppurative otitis media (CSOM) is a persistent middle ear infection in which chronic inflammation drives irreversible sensorineural hearing loss (SNHL), yet the molecular mechanisms linking middle ear chronic infection to cochlear injury remain poorly defined. Using a murine model of CSOM induced by Pseudomonas aeruginosa (PA) persisters, a quantitative proteomic profiling of cochlear tissue was performed at seven days post-infection. Mass spectrometry revealed over 250 proteins that were significantly altered, indicating broad immune activation, oxidative stress, and disruption of ion homeostasis. Among the top candidates, HSPA5, MPO, and ATP2A2 were strongly associated with inflammatory stress and cellular injury pathways. These findings identify immunometabolic remodeling and macrophage-driven inflammation as central mechanisms linking chronic middle ear infection to cochlear injury.

immunology↗

Modelling mental disorders in zebrafish. Neurexins severely modulate anxiety, social behaviours and aggression.

Can we reproduce mental disorders in zebrafish? To explore this question, we manipulated the neurexin gene family. Neurexin (nrxn) genes encode synaptic cell-adhesion molecules that have been repetitively associated with neurodevelopmental and mental disorders. While the zebrafish animal model offers tremendous advantages for dissecting neural development/function, no robust nrxn zebrafish models are currently available. In this study, we generated the first collection of zebrafish knockout lines for each nrxn gene, with mutations ranging from transmembrane domain- to full genomic locus-deletions. Surprisingly, all homozygous lines developed normally, presenting no gross neurodevelopmental or obvious early behavioural abnormalities. However, this absence of early phenotypes translated into profound, paralog-specific behavioural alterations emerging during juvenile-to-adult stages. All neurexin knockouts affected mating behaviour, complicating the generation and maintenance of homozygous lines. Except for this shared behavioural alteration, nrxn1, but not nrxn2 or nrxn3, led to marked changes in social behaviour and aggression. In contrast, nrxn2 mutants exhibited severe anxiety-like behaviours, including bottom-dwelling and repetitive freezing/seizure events. Strikingly, nrxn1 full-locus deletion mutants showed opposing behaviour, spending most of their time near the surface. The two also displayed opposite responses to open/closed field transitions; confinement alleviated nrxn2 anxiety but enhanced nrxn1 surface-dwelling. Meanwhile, nrxn3 mutants behaved normally in all our initial tests. In summary, our study introduces a complete set of zebrafish mutants covering the whole nrxn gene family, presenting striking juvenile/adult behavioural alterations despite the absence of noticeable early defects; echoing the delayed onset of human psychiatric disorders such as schizophrenia. This work demonstrates the value of zebrafish to study mental disorders and unlock a novel platform to unravel the pathogenic contribution of neurexin and associated subtle neurodevelopmental changes/timing that drive the emergence of mental illnesses.

neuroscience↗