Biology subjects

Jadhav, V.

Publications and source records attributed to Jadhav, V..

17 recordsLinked to original sources

bioRxiv2026

Oncogenic transformation proceeds through a transient state of cellular plasticity constrained by lineage-specific barriers.

Normal tissues frequently harbor oncogenic mutations without progressing to cancer, but the cellular basis of this resistance remains poorly defined. We asked whether transformation requires selection of a rare, permissive state within normal-like cell populations. Dermal fibroblasts and mammary epithelial cells responded uniformly to combined HRAS-G12V expression and p53 disruption. Cellular barcoding revealed no loss or enrichment of clones during morphological transformation, arguing against clonal selection as the primary driver of neoplastic reprogramming. Instead, all transduced cells underwent an early, shared transcriptional transition characterized by loss of differentiation markers, induction of RAS-associated and inflammatory programs, activation of alternative-lineage signatures, increased single-cell entropy, and chromatin decondensation. These changes were transient: entropy and chromatin accessibility subsequently declined, and some cells moved toward the control transcriptional state, whereas others stabilized in altered states. The two lineages followed distinct trajectories. Fibroblasts showed greater initial transcriptional plasticity but subsequently reverted more strongly toward the normal state, whereas epithelial cells changed more gradually and continued to diverge from it, suggesting a stronger barrier to transformation in the mesenchymal lineage. Thus, oncogenic perturbation initiated reprogramming throughout the population but did not uniformly produce a stable transformed state. Together, these findings support a model in which normal-like cells tolerate oncogenic mutations not because most cells fail to respond, but because a p53-independent, cell-intrinsic barrier limits the stabilization of malignant transformation following a transient period of heightened plasticity. This framework may facilitate the identification of mechanisms that constrain tumor initiation.. Significance StatementLoss of TP53 and activation of oncogenic RAS are common drivers of human cancer and frequently coexist in the same tumor. Nevertheless, these alterations often fail to induce malignant transformation. To investigate why, we introduced both alterations into fibroblasts and epithelial cells and tracked their responses using clonal barcoding, single-cell transcriptomics, and phenotypic assays. Initially, cells uniformly reprogrammed their transcriptional and chromatin states without detectable clonal selection. They then diverged: some reacquired transcriptional profiles resembling those of the original normal cells, whereas others became transformed. Thus, normal cells resist transformation through an intrinsic barrier that operates despite p53 disruption. Because this transition is transient and reversible, it provides a tractable window for studying the earliest stages of cancer development.

cancer biology↗

bioRxiv2026

Tracing information propagation in fish schools with a conditioned escape response

Collective escape responses are widespread in animal groups, yet how threat-related information spreads from a few informed individuals to the collective remains poorly understood because the identities of the individuals who initially detect danger are rarely experimentally controlled. Here, we combined aversive conditioning, behavioural tracking, and computational modelling to investigate how escape information propagates through schools of Puntigrus tetrazona. We conditioned selected fish to associate a green light with an aversive stimulus. Subsequently, we tested the escape response of schools containing one informed and four naive fish to the green light. One informed fish was sufficient to trigger a collective escape response. Upon stimulus onset, conditioned fish accelerated and crossed the hurdle, after which naive fish sequentially increased their speed and followed. Temporal correlations in speed revealed a hierarchical leader-follower structure mostly aligned with hurdle-crossing order. Neither initial distance, viewing angle, nor relative orientation to informed fish predicted the order of the escape sequence. An agent-based model incorporating local alignment and distance regulation reproduced experimental observations and suggested that the informed individual likely remains partly attentive to its neighbours during escape. Overall, our work provides a general framework for experimentally dissecting information transfer in animal groups and identifying the behavioural mechanisms underlying collective escape dynamics.

animal behavior and cognition↗

bioRxiv2025

CCB79 is a primate-specific cilium initiation factor essential to maintain neural progenitor diversity in developing brain tissue.

Identifying the genes that regulate the accurate spatiotemporal diversity of neural progenitor cells (NPCs) helps to understand the mechanisms of human neocortex expansion. In primate brains, an additional intermediate progenitor layer, the outer subventricular zone (oSVZ), facilitates the expansion of the neocortex. Here, we identify an uncharacterized gene, KIAA0408, and show that its expression is enriched in intermediate progenitors. Removing KIAA0408 in human-induced pluripotent stem cell (iPSC)-derived brain organoids results in an impaired cortical organization characterized by abnormal cell fate and patterning defects, including the depletion of intermediate and ventral progenitors. Molecularly, KIAA0408 codes for a 79-kilodalton centriolar distal appendage protein (DAP) that controls cilium biogenesis (hereafter CCB79). CCB79 forms a complex with other DAP components and specifically localizes in the DAP at the onset of ciliogenesis, and its absence blocks ciliogenesis. Mechanistically, progenitors in 3D brain tissues are unable to form cilia, which induces aberrant hedgehog signaling and causes premature differentiation. Finally, human CCB79, rather than the mouse ortholog, rescues cilia defects, suggesting that CCB79 has undergone rapid evolution from rodents to primates to fine-tune ciliogenesis for proper brain development.

neuroscience↗

bioRxiv2024

Induction of pluripotent oncogenic stem cells from mouse fibroblasts

Natural biological agents that can transform normal somatic cells into cancer stem cells, have not been identified. We earlier reported that cell free chromatin particles (cfChPs) that circulate in blood of cancer patients can horizontally transfer themselves to healthy cells to induce dsDNA breaks and inflammation. Here we show that a single cell clone D5 developed from NIH3T3 mouse fibroblast cells treated with cfChPs isolated from sera of cancer patients exhibited upregulation of stemness related transcription factors and surface markers, and the ability to form spheroids in appropriate culture medium. Transcriptome analysis revealed upregulation of cancer related pathways including invasion, metastasis and stemness. Subcutaneous inoculation into SCID mice resulted in development of malignant tumors which expressed all three germline markers. Our results suggest the cfChPs that circulate in blood of cancer patients are oncogenic and can transform susceptible somatic cells into cancer stem cells with the potential to promote metastasis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/622204v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@4288org.highwire.dtl.DTLVardef@1102d4borg.highwire.dtl.DTLVardef@10daaf6org.highwire.dtl.DTLVardef@53084d_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

Image-Based Quantitative Single-Cell Method Showed Increase of Global Chromatin Accessibility in Tumor Compared to Normal Cells

The phenotypic plasticity of cancer cells has recently emerged as an important factor of treatment failure. The mechanisms of phenotypic plasticity are not fully understood. One of the hypotheses is that the degree of chromatin accessibility defines the easiness of cell transitions between different phenotypes. To test this, a method to compare overall chromatin accessibility between cells in a population or between cell populations is needed. We propose to measure the chromatin accessibility of a cell by total fluorescence signal from nuclei stained with DNA-binding fluorescent molecules. This method is based on the existing data that some small molecules bind nucleosome-free DNA more easily than nucleosomal DNA. Thus, nuclear fluorescence of these molecules is proportional to the amount of nucleosome-free DNA, serving as a measure of chromatin accessibility. We optimized the method using several DNA binding molecules and known chromatin modulating agents. Using a set of tumor and non-tumor cells of different origins we observed the tendency to the higher chromatin accessibility of tumor versus non-tumor cells. Chromatin accessibility was also increased upon oncogene-induced transformation of mouse and human cells.

cancer biology↗

bioRxiv2024

Collective responses of flocking sheep to a herding dog

Across taxa, group-living organisms exhibit collective escape responses to stimuli varying from mild stress to predatory pressures. How exactly does information flow among group members leading to a collective escape remains an open question. Here we study the collective responses of a flock of sheep to a shepherd dog in a driving task between well-defined target points. We collected highresolution spatio-temporal data from 14 sheep and the dog, using Ultra Wide Band tags attached to each individual. Through the time delay analysis of velocity correlations, we identify a hierarchy among sheep in terms of directional influence. Notably, the average spatial position of a sheep along the front-back axis of the groups velocity strongly correlates with its impact on the collective movement. Our findings demonstrate that, counter-intuitively, directional information on shorter time scales propagates from the front of the group towards the rear, and that the dog exhibits adaptive movement adjustments in response to the flocks dynamics. Furthermore, we show that a simple shepherding model can capture key features of the collective response of the sheep flocks. In conclusion, our study reveals novel insights on how directional information propagates in escaping animal groups.

animal behavior and cognition↗

bioRxiv2024

Syngap1 regulates the synaptic drive and membrane excitability of Parvalbumin-positive interneurons in mouse auditory cortex

SYNGAP1 haploinsufficiency-related intellectual disability (SYNGAP1-ID) is characterized by moderate to severe ID, generalized epilepsy, autism spectrum disorder, sensory processing dysfunction and other behavioral abnormalities. While numerous studies have highlighted a role of Syngap1 in cortical excitatory neurons development, recent studies suggest that Syngap1 plays a role in GABAergic inhibitory neuron development as well. However, the molecular pathways by which Syngap1 acts on GABAergic neurons, and whether they are similar or different from the mechanisms underlying its effects in excitatory neurons, is unknown. Here, we examined whether, and how, embryonic-onset Syngap1 haploinsufficiency restricted to GABAergic interneurons derived from the medial ganglionic eminence (MGE) impacts their synaptic and intrinsic properties in adult primary auditory cortex (A1). We found that Syngap1 haploinsufficiency significantly affected the intrinsic properties, overall leading to increased firing threshold, and decreased excitatory synaptic drive of Parvalbumin (PV)+ neurons in adult Layer IV A1. Further, the AMPA component of thalamocortical evoked-EPSC was decreased in PV+ cells from mutant mice. Mutant somatostatin (SST)+ interneurons exhibited decreased spontaneous excitatory input and impaired evoked firing without alterations in firing threshold. Finally, we found that the selective blocking of voltage-gated D-type K+ currents was sufficient to rescue PV+ mutant cell-intrinsic properties to wild-type levels. Together, these data suggest that Syngap1 plays a specific role in the maturation of PV+ cell intrinsic properties and synaptic drive, and its haploinsufficiency may lead to reduced PV cell recruitment in the adult A1, which could in turn contribute to the auditory processing alterations found in SYNGAP1-ID preclinical models and patients.

neuroscience↗

bioRxiv2023

Metastases arise as new cancers from cells of target organs transformed by cell-free chromatin particles released from dying cancer cells

IntroductionBased on our earlier finding that cell-free chromatin particles (cfChPs) released from dying cancer cells are potentially oncogenic, we hypothesised that metastases arise as new cancers from the cells of target organs transformed by cfChPs released from dying cancer cells. MethodsWe fluorescently dually-labelled MDA-MB-231 human breast cancer cells and A-375 human melanoma cells in their DNA with BrdU and in their histones with CellLight(R) Histone 2BGFP. One hundred thousand dually-labelled cells were intravenously injected into SCID mice. In other experiments unlabelled cells were injected for detection of lung metastasis. Also intravenously injected were 700 ng of purified cfChPs isolated from radiation-killed MDA-MB-231 cells. ResultsWe observed that the fluorescently dually-labelled MDA-MB-231 and A-375 cells died upon reaching the lungs and released dually-labelled fluorescent chromatin particles that accumulated in the nuclei of lung cells at 48 h. Injection of unlabelled cfChPs led to the activation of 10 hallmarks of cancer and immune checkpoints in lung cells at 72 h, suggesting that the lung cells had rapidly transformed into incipient cancer cells. Fluorescent in situ hybridisation analysis of lung metastases that subsequently developed using mouse and human specific DNA probes revealed that the tumour cells contained both mouse and human DNA in almost equal proportions. Similarly, immune-fluorescence analysis using species specific mAbs revealed that the tumour cells co-expressed mouse and human specific proteins. Metaphase preparations and single-cell clones developed from cell cultures of lung metastases were found to contain chimeric chromosomes containing both mouse and human DNA, and the cells to co-express both human- and mouse-specific proteins. The Intravenously injected purified cfChPs isolated from radiation-killed MDA-MB-231 cells also induced lung metastasis which predominantly contained mouse DNA strongly suggesting that the metastatic tumours had arisen from the mouse lung cells. ConclusionThese results provide strong evidence that cfChPs released from dying cancer cells integrate into genomes of target lung cells to transform them into new cancers that masquerade as metastasis. They support our hypothesis that metastases arise from the cells of target organs and not from those of the primary tumour. These findings have implications for the principles of cancer therapy.

cancer biology↗

bioRxiv2023

In vivo expansion of gene-targeted hepatocytes through transient inhibition of an essential gene

Homology Directed Repair (HDR)-based genome editing is an approach that could permanently correct a broad range of genetic diseases. However, its utility is limited by inefficient and imprecise DNA repair mechanisms in terminally differentiated tissues. Here, we tested "Repair Drive", a novel method for improving targeted gene insertion in the liver by selectively expanding correctly repaired hepatocytes in vivo. Our system consists of transient conditioning of the liver by knocking down an essential gene, and delivery of an untargetable version of the essential gene in cis with a therapeutic transgene. We show that Repair Drive dramatically increases the percentage of correctly targeted hepatocytes, up to 25%. This resulted in a five-fold increased expression of a therapeutic transgene. Repair Drive was well-tolerated and did not induce toxicity or tumorigenesis in long term follow up. This approach will broaden the range of liver diseases that can be treated with somatic genome editing.

genetics↗

bioRxiv2023

Leadership and information transfer in groups escaping a (simulated) threat in the wild

Collective motion in many species is believed to be driven by predation, which is considered a crucial evolutionary force. However, there are limited studies on how information about predators spreads through a group, particularly in natural settings. Here, using high-resolution drone-based recordings, we analyze the collective escape dynamics of a group living species - blackbuck (Antilope cervicara), an Indian antelope - under the conditions of a simulated threat in their natural grassland habitat. Our analysis reveals that, in response to the simulated threat, group cohesion first increases, followed by a simultaneous increase in median speed and polarization. We also observe the emergence of a temporary leader-follower relationship during the collective escape. Interestingly, we found that the distance of individuals from the "predator" affected only their response time, not their influence on the group movement. The individuals furthest from the threat were the least likely to initiate movement and were uncoordinated with the groups speed. Additionally, we discovered that the most influential individuals during the collective escape were the least likely to occupy front positions during group movement. Instead, our results indicate that individuals at the rear "push" individuals at the front during collective escape events. This contrasts with the typical notion of individuals at the front determining group movement and those at the back trying to catch up.

animal behavior and cognition↗

bioRxiv2023

Cell-free chromatin particles activate immune checkpoints in human T cells: Implications for cancer therapy

Immune checkpoint blockade is an exciting breakthrough in cancer therapy, but how immune checkpoints are activated is unknown. We have earlier reported that cell-free chromatin particles (cfChPs) that circulate in the blood, or those that are released locally from dying cells, are readily internalized by healthy cells with biological consequences. Here we show that treatment of human lymphocytes with cfChPs isolated from sera of cancer patients led to marked activation of immune checkpoints viz. PD-1, CTLA-4, LAG-3, NKG2A, and TIM-3. Concurrently activated were stress-related markers cJun, cFos, JunB, FosB, NF[Kcy]B, and EGR1. The above immune checkpoints were also activated when lymphocytes were treated with cfChPs released from dying HeLa cells; the latter could be abrogated by three cfChPs deactivating agents. These results suggest that immune checkpoints are activated by lymphocytes as stress response to cfChPs. Simultaneous downregulation of multiple immune checkpoints may herald a new approach to immunotherapy of cancer. Statement of SignificanceWe show that cell-free chromatin particles (cfChPs) that circulate in the blood of cancer patients, or those released from dying cancer cells, simultaneously activate five immune checkpoints as a stress response by human lymphocytes. Activation of checkpoints was abrogated by cfChPs deactivating agents suggesting a novel approach to cancer treatment.

immunology↗

bioRxiv2023

Therapeutic interventions on human xenografts promote systemic dissemination of oncogenes

We generated xenografts of human cancer cells in mice, and using immuno-FISH analysis detected multiple co-localizing signals of human DNA and eight human oncoproteins in brain cells. Signals increased dramatically five days after treatment with chemotherapy, localized radiotherapy or surgery, which could be minimized by concurrent treatment with cell-free chromatin deactivating agents. These results suggest that therapeutic interventions may potentially encourage metastatic spread which is preventable by deactivating cell-free chromatin.

cancer biology↗

bioRxiv2022

RNAi-mediated rheostat for dynamic control of AAV-delivered transgenes

Adeno-associated virus (AAV)-based gene therapy could be facilitated by the development of molecular switches to control the magnitude and timing of expression of therapeutic transgenes. RNA interference (RNAi)-based approaches hold unique potential as a clinically proven modality to pharmacologically regulate AAV gene dosage in a sequence-specific manner. We present a generalizable RNAi-based rheostat wherein AAV transgene expression is silenced using the clinically validated modality of chemically modified short interfering RNA (siRNA) conjugates or vectorized co-expression of short hairpin RNA (shRNA). For transgene induction, we employ REVERSIR technology, a synthetic high-affinity oligonucleotide complementary to the siRNA or shRNA guide strand to reverse RNAi activity and rapidly recover transgene expression. For potential clinical development, we report potent and specific siRNA sequences that may allow selective regulation of transgenes while minimizing unintended off-target effects. Our results establish a conceptual framework for RNAi-based regulatory switches with potential for infrequent dosing in clinical settings to dynamically modulate expression of virally-delivered gene therapies.

genomics↗

bioRxiv2022

A pro-oxidant combination of resveratrol and copper down-regulates multiple biological hallmarks of ageing and neurodegeneration

Several hundred billion to a trillion cells die in the body every day, and cell-free chromatin particles (cfChPs) that are released from them enter into the extracellular compartments of the body, including into the circulation. We have earlier reported that cfChPs can readily enter into healthy cells to damage their DNA, activate apoptotic pathways and induce inflammatory cytokines. We hypothesized that repeated lifelong assault on healthy cells by cfChPs is the underlying cause of ageing, and that the ageing process could be retarded by deactivating cfChPs. The latter can be effected by oxygen radicals that are generated upon admixing the nutraceuticals resveratrol (R) and copper (Cu). Using confocal microscopy and antibodies against DNA and histone we detected copious presence of extra-cellular cfChPs in brain of ageing mice, and observed that these were deactivated / eradicated following prolong oral administration of small quantities of R-Cu. Deactivation / eradication of cfChPs was associated with down-regulation of several biological hallmarks of ageing in brain cells which included reduction in: 1) telomere attrition, 2) amyloid deposition, 3) DNA damage, 4) apoptosis, 5) inflammation, 6) senescence, 7) aneuploidy and 8) mitochondrial dysfunction. At a systemic level, R- Cu treatment led to significant reduction in blood levels of glucose, cholesterol and C-reactive protein. These results suggest that cfChPs may be global instigators of ageing and neurodegeneration, and that therapeutic use of R-Cu may help to retard the process of ageing.

neuroscience↗

bioRxiv2022

Robust and durable prophylactic protection conferred by RNA interference in preclinical models of SARS-CoV-2

RNA interference is a natural antiviral mechanism that could be harnessed to combat SARS-CoV-2 infection by targeting and destroying the viral genome. We screened lipophilic small-interfering RNA (siRNA) conjugates targeting highly conserved regions of the SARS-CoV-2 genome and identified leads targeting outside of the spike-encoding region capable of achieving [≥]3-log viral reduction. Serial passaging studies demonstrated that a two-siRNA combination prevented development of resistance compared to a single-siRNA approach. A two-siRNA combination delivered intranasally protected Syrian hamsters from weight loss and lung pathology by viral infection upon prophylactic administration but not following onset of infection. Together, the data support potential utility of RNAi as a prophylactic approach to limit SARS-CoV-2 infection that may help combat emergent variants, complement existing interventions, or protect populations where vaccines are less effective. Most importantly, this strategy has implications for developing medicines that may be valuable in protecting against future coronavirus pandemics.

pharmacology and toxicology↗

bioRxiv2021

Effect of Human Mesenchymal Stem Cells on Freund's adjuvant-induced Rheumatoid Arthritis in Sprague Dawley Rats

IntroductionMesenchymal stem cells (MSC) therapy is a new approach to treat RA. Studies evaluating anti-inflammatory effects of MSCs per RA severity are scarce. Our primary objective was to evaluate anti-inflammatory effects, change in cytokine levels and cartilage regeneration of two different MSC preparations delivered through two different routes of administration in three RA stages: mild, moderate and severe. MethodsHuman-derived umbilical cord tissue MSCs (hUCT-MSCs) and human bone marrow-derived MSCs (hBM-MSCs) delivered via intra-plantar and intravenous routes were tested in Freunds adjuvant-induced arthritis in rats. Arthritis severity was based on the arthritis score (<3=mild, 3=moderate and 4=severe). Assessments included changes in arthritis scoring, paw swelling, haematology parameters, biomarkers (TNF and IL-10) and histopathology analysis. ResultsMSC treatment significantly reduced arthritis scores in all treatment groups. IL-10 levels increased 30 days after treatment with (IP)hUCT-MSCs (P=0.0241), (IV)hUCT-MSCs (P=0.0095) and (IP)hBM-MSCs (P=0.0002). TNF- levels reduced compared to positive control at 30 days: (IP)hUCT-MSCs (P=0.0060), (IV)hUCT-MSCs (P=0.0003), (IP)hBM-MSCs (P=0.0005), (IV)hBM-MSCs (P<0.0001) and continued through 30-60 days. Microscopic examination showed regenerative changes in animal joints treated with both intra-plantar or intravenous MSCs. Arthritis scores reduced in all RA severity groups while benefits (changes in IL-10 and TNF-alpha) were more pronounced in moderate and severe RA. Haematology parameters remained similar among all animal groups at baseline, 30 days and 60 days indicating safety of MSCs. ConclusionTreatment with hUCT MSCs and hBM MSCs were safe, well-tolerated and effectively reduced joint inflammation, synovial cellularity and pro-inflammatory cytokine levels in CFA-induced RA rat model.

cell biology↗

bioRxiv2020

Inhibition of mTOR during a postnatal sensitive window rescues deficits in GABAergic PV cell connectivity and social behavior caused by loss of TSC1.

Mutations in regulators of the Mechanistic Target Of Rapamycin Complex 1 (mTORC1), such as Tsc1/2, lead to neurodevelopmental disorders associated with autism, intellectual disabilities and epilepsy. Whereas the effects of mTORC1 signaling dysfunction within diverse cell types are likely critical for the onset of the diverse neurological symptoms associated with mutations in mTORC1 regulators, they are not well understood. In particular, the effects of mTORC1 dys-regulation in specific types of inhibitory interneurons are unclear. Here, we showed that Tsc1 haploinsufficiency in parvalbumin (PV)-positive GABAergic interneurons either in cortical organotypic cultures or in vivo caused a premature increase in their perisomatic innervations, followed by a striking loss in adult mice. This effects were accompanied by alterations of AMPK-dependent autophagy in pre-adolescent but not adult mice. PV cell-restricted Tsc1 mutant mice showed deficits in social behavior. Treatment with the mTOR inhibitor Rapamycin restricted to the third postnatal week was sufficient to permanently rescue deficits in both PV cell innervation and social behavior in adult conditional haploinsufficient mice. All together, these findings identify a novel role of Tsc1-mTORC1 signaling in the regulation of the developmental time course and maintenance of cortical PV cell connectivity and provide a mechanistic basis for the targeted rescue of autism-related behaviors in disorders associated with deregulated mTORC1 signaling.

neuroscience↗