Biology subjects

Deshpande, P.

Publications and source records attributed to Deshpande, P..

14 recordsLinked to original sources

bioRxiv2026

AI-Driven Generation of Cortisol-Binding Peptides for Non-Invasive Stress Detection

Cortisol is a primary biomarker of stress, released in sweat at concentrations that directly correlate with physiological stress levels. Detecting cortisol non-invasively offers significant potential for real-time stress monitoring and healthcare applications. Biosensors capable of binding cortisol can thus enable the development of novel diagnostic platforms for personalised health management. In our earlier work, a 38-mer peptide fragment derived from the protein 2V95 was identified as a functional binder to cortisol. In the present study, we applied generative artificial intelligence (AI) approaches to expand the sequence space and identify superior candidate peptides with improved binding affinity. By integrating sequence-based and structure-based AI models, we generated and screened a peptide library of nearly 10,000 sequences against cortisol, leading to the identification of high-affinity candidates for further evaluation.

bioengineering↗

bioRxiv2026

Unsupervised Identification of Cancer Attractor States through the Lens of Embryonic Origin and Cancer Hallmarks

BackgroundOncogenesis is a highly intricate process characterized by the transition of normal cells into aberrant biological attractor states. These states emerge from the non-random combinatorial interactions between inherent lineage-specific programs, governed by Gene Regulatory Networks (GRNs), and acquired somatic mutations. While the hallmarks of cancer provide a functional framework for transformation, current genomic models often fail to account for the topographical constraints of the cell of origin. We hypothesized that integrating embryological origin (EO) with hallmark-related mutations (HRM) enables the unsupervised identification of stable, pan-cancer attractor states. MethodsUtilizing the MSK-MET database (n=25,775), we annotated somatic variants across 15 hallmarks. We developed and compared two unsupervised clustering models using Jaccard-distanced t-SNE and K-means algorithms: one based solely on HRM profiles and another integrating EO with HRM (EO/HRM). Model robustness and attractor stability were evaluated via bootstrap resampling and five-fold cross-validation. ResultsHallmark-related mutations were identified in 95.5% of tumors. The EO/HRM model identified 11 distinct clusters and demonstrated superior stability (ARI: 0.74 vs. 0.70) and prognostic performance (C-index: 0.59 vs. 0.56) compared to the HRM-only model. These clusters represent stable functional basins, such as the TP53-driven minimalist attractor in Cluster C6 and the hyper-unstable attractor in Cluster C10. The clusters exhibited unique, organ-specific metastatic predilections independent of histological subtypes. Critically, we observed prognostic inversions, such as Cluster C0 representing a favorable attractor in lung adenocarcinoma but an aggressive state in prostate carcinoma, illustrating that attractor behavior is gated by the embryological landscape. ConclusionIntegrating embryological origin as a proxy for inherent cellular programming significantly enhances the identification of stable, prognostically relevant biological attractor states. This framework provides a novel strategy for functional risk stratification and the development of context-aware precision therapies aimed at destabilizing malignant attractors.

cancer biology↗

bioRxiv2026

Environmental Toxin Rotenone Drives LRRK2-Mediated Microtubule, Cilia and Proteostasis Disruption in Parkinson's Disease Model

Exposure to the environmental toxin rotenone increases risk for Parkinsons disease (PD). However, protein phosphorylation changes induced by rotenone in neural-derived cells have not been reported. We examined the effect of rotenone on the proteome and phosphoproteome of cortex-derived cultures from wild-type and Lrrk2-/- mouse brains. We also analyzed the phosphoproteome of the PD cadaver brain using a previously unanalyzed dataset. Rotenone alters phosphorylation at 904 sites, most of which are unchanged in Lrrk2-/- cultures. Common targets include proteins that control microtubule stability, vesicular transport, and protein clearance via the autophagosomal/lysosomal pathway. Analysis of phosphosites with known function indicate that rotenone activates histone deacetylase-1 and represses the pro-survival transcriptional regulators Mef2C and Mef2D, while inhibiting translation by phosphorylating Eif2b5. These effects do not occur in Lrrk2-/- cultures. This study shows that Lrrk2 is required the earliest rotenone-triggered phospho-signalling events.

systems biology↗

bioRxiv2025

Transient Dietary Changes Modulate Inflammatory Disease Trajectory in the Lean State

Obesity potently alters immune responses across various inflammatory contexts1-7. However, it is unclear whether a transient high-fat diet (HFD) can affect immune function despite minimal effects on body weight. Here, we demonstrate that a short-term HFD regimen significantly exacerbates disease severity in a model of experimental psoriasis, comparable to what is observed in obese mice on long-term HFD. We find that a critical 4-day window of HFD coinciding with disease onset is sufficient to overactivate the immune response, leading to worsened disease outcomes. Mechanistically, we identify the CD4+ T cell compartment as an essential mediator of HFD-induced disease severity. Within the compartment, we functionally validate that disease exacerbation is driven by increased differentiation of a pathogenic population of T helper 17 (TH17) cells8 expressing IL1R1 (interleukin-1 receptor, type I)9, which is triggered by localized activation of the NLRP3 (NOD-, LRR-, and pyrin domain-containing protein 3) inflammasome10. This brief window of HFD at disease onset leads to immune-dependent sensitization, as disease severity is increased upon a subsequent flare, despite complete recovery and under a low-fat diet (LFD) regimen. Our data indicate that transient dietary changes during the initial stages of an inflammatory event can rewire the immune milieu, profoundly influencing disease progression and inflammatory memory11. This phenomenon may have broad implications for conditions where obesity, and not diet itself, is considered the primary risk factor.

immunology↗

bioRxiv2025

Humanized Caffeine-Inducible Systems for Controlling Cellular Functions

Current cell therapies are limited by the lack of tools for controlling gene expression using humanized systems responsive to non-toxic stimuli. Starting from nanobodies that homodimerize in response to caffeine, we computationally designed inducible heterodimers and humanized the best-performing pairs. We used the resulting caffeine-inducible domains in engineered cytokine receptors for caffeine-inducible STAT3 signaling and in split transcription factors (caff-TFs) containing human-derived zinc-finger proteins. Heterodimerization of split transcription factors drastically enhanced their performance compared to homodimerization. We demonstrate that caff-TFs are compatible with lentiviral and retroviral delivery to Jurkat T-cells and enable inducible expression of therapeutic genes such as chimeric antigen receptors (CARs) in response to caffeine concentrations consistent with normal coffee consumption. By using the common, non-toxic molecule caffeine, and exclusively humanized protein components, these systems promise to be a safer alternative to existing systems and may be used in synthetic biology applications and for safer, more effective cell therapies.

synthetic biology↗

bioRxiv2025

Identifying JNK-regulated phosphoproteome markers of anxiety-like behaviour in mouse hippocampus

JNKs mediate neuronal damage in neurodegenerative disease and inhibitors of JNK1 have shown anxiolytic and anti-depressive effects in mice. Here, we analyze the phosphoproteomes of hippocampus and nucleus accumbens from DJNKI-1 (JNK inhibitor)-infused mice. We correlate phospho-site changes with anxiety-like behaviours in the elevated plus maze and light-dark test and identify unique changes in responder mice. Among the DJNKI-1 regulated phosphosites, several lie within GSK3 motifs and are exclusively down-regulated. Consistent with this, GSK3{beta} is inhibited and AKT activated. Importantly, we detect multilevel regulation of glucose metabolism enzymes including increased PDPK1-S241 phosphorylation, and a 5-fold increase in pyruvate dehydrogenase (PDHA1)-S-293 phosphorylation, signifying its inhibition. This suggests that JNK inhibitor drives a metabolic transformation to the neuronal Warburg response. This and a range of identified synaptic and cytoskeletal protein phosphosite changes are discussed in the context of JNK-regulated anxiety responses. The annotated hippocampal and nucleus accumbens phosphoproteomes described here will support a mechanistic understanding of the JNK pathway for future studies of brain disorders.

neuroscience↗

bioRxiv2025

JNK regulates GABAAR expression at the cell surface via the receptor clustering protein GIT1 (ArfGAP1)

GABAA-type receptors (GABAARs) mediate fast and tonic inhibition and are essential for maintaining excitatory/inhibitory balance in neural circuits. Disrupted GABAergic signaling leads to maladaptive changes associated with neuropsychiatric disorders, yet the mechanisms that regulate GABAAR surface availability remain incompletely understood. We previously identified that the stress-activated kinase JNK1 drives anxiety-like behaviours in mice suggesting a potential link between stress signalling and GABAergic regulation. Here, we show that genetic deletion or inhibition of JNK1 increases surface expression of {beta}3-containing GABAARs at extrasynaptic sites and at excitatory synapses where they may participate in shunting inhibition. We identify the signalling scaffold GIT1 as a direct JNK1 substrate, phosphorylated at S371, and find that GIT1 accumulates in dendritic spines in Jnk1-/- neurons or following JNK inhibition, whereas the phosphomimetic GIT1-S371D is excluded. Moreover, GIT1 is required for JNK-dependent regulation of {beta}3-GABAAR trafficking. Accordingly, neurons from Jnk1-/- mice exhibit increased spontaneous inhibitory postsynaptic potentials and enhanced tonic inhibition. These results reveal a JNK1-GIT1 signalling axis that suppresses GABAAR stability and inhibitory tone, providing a mechanism by which the stress-activated JNK pathway modulates synaptic and extrasynaptic inhibition.

neuroscience↗

bioRxiv2024

Multispecies relations shape bird-feeding practices

While humans often feed birds in their backyards, there is growing awareness that this has positive and negative effects on local biodiversity. Whether the observed species assemblage shapes human activities has, however, rarely been investigated. We analyzed 15,088 open-ended answers from 9,473 Finnish respondents about why they have increased or reduced feeding birds. They mentioned 58 avian and non-avian species linked to changed practices. The main reasons for change were 1) respondents relation to non-human species, 2) respondents relation to other humans and 3) relations between non-human species. Most taxa and reasons could lead to both increase or decrease in feeding, although the direction was context-dependent. We suggest that bird-feeding is an interactive process where the species community strongly affects feeding practices, which in turn can affect community composition. Recognising this process is crucial for understanding the effects of bird-feeding on both humans and nature and providing more nuanced guidance.

scientific communication and education↗

bioRxiv2024

Screening of glucose binding proteins for the development of biosensors

Selecting suitable glucose-binding proteins (GBPs) is vital for biosensor development for medical diagnostics and quality control in the food industry. Biosensors offer advantages such as high specificity, selectivity, fast response time, continuous measurement, and cost-effectiveness. The current work utilized a combination of molecular docking, molecular dynamics (MD) simulations, and free energy calculations to develop a high-throughput bioinformatics pipeline to select GBP candidates from an extensive protein database (37,325 proteins). Using molecular docking, GBPs with good binding affinity to glucose (1,447 candidates) were virtually screened from the Protein Data Bank. MD simulations ascertained the binding dynamics of a few selected candidates. Further, steered MD (Brownian dynamics fluctuation-dissipation-theorem) was used to estimate binding free energies of the ligand-protein complex. Correlations between ligand-binding parameters obtained from longer MD simulations and binding parameters interpreted from significantly faster docking simulations were investigated. The correlation plots suggested that a combination of threshold values of the following three docking parameters: docking binding energy, binding cavity depth, and the number of hydrogen bonds between the ligand and binding site residues can be used to predict candidate GBPs reliably. Thus, a high-throughput and accurate protein selection process based on relatively faster docking simulations was proposed to screen GBPs for glucose biosensing.

bioinformatics↗

bioRxiv2024

Modified histone peptides uniquely tune the material properties of HP1α condensates.

Biomolecular condensates have emerged as a powerful new paradigm in cell biology with broad implications to human health and disease, particularly in the nucleus where phase separation is thought to underly elements of chromatin organization and regulation. Specifically, it has been recently reported that phase separation of heterochromatin protein 1alpha (HP1) with DNA contributes to the formation of condensed chromatin states. HP1 localization to heterochromatic regions is mediated by its binding to specific repressive marks on the tail of histone H3, such as trimethylated lysine 9 on histone H3 (H3K9me3). However, whether epigenetic marks play an active role in modulating the material properties of HP1 and dictating emergent functions of its condensates, remains only partially understood. Here, we leverage a reductionist system, comprised of modified and unmodified histone H3 peptides, HP1 and DNA to examine the contribution of specific epigenetic marks to phase behavior of HP1. We show that the presence of histone peptides bearing the repressive H3K9me3 is compatible with HP1 condensates, while peptides containing unmodified residues or bearing the transcriptional activation mark H3K4me3 are incompatible with HP1 phase separation. In addition, inspired by the decreased ratio of nuclear H3K9me3 to HP1 detected in cells exposed to uniaxial strain, using fluorescence microscopy and rheological approaches we demonstrate that H3K9me3 histone peptides modulate the dynamics and network properties of HP1 condensates in a concentration dependent manner. These data suggest that HP1-DNA condensates are viscoelastic materials, whose properties may provide an explanation for the dynamic behavior of heterochromatin in cells in response to mechanostimulation. Statement of significanceThe organization of genomic information in eukaryotic cells necessitates compartmentalization into functional domains allowing for the expression of cell identity-specific genes, while repressing genes related to alternative fates. Heterochromatin hosts these transcriptionally silent regions of the genome - which ensure the stability of cell identity -and is characterized by repressive histone marks (H3K9m3) and other specialized proteins (HP1a), recently shown to phase separate with DNA. We show that HP1a forms condensates with DNA which persist in the presence of H3K9me3 peptides. The viscoelastic nature of these condensates depend on H3K9me3:HP1 ratios, which are modulated by mechanical strain in cells. Thus, phase separation may explain the dynamic behavior of heterochromatin in cells, in response to mechanostimulation.

biophysics↗

bioRxiv2023

Multiomic single-cell sequencing defines tissue-specific responses in Stevens-Johnson Syndrome and Toxic epidermal necrolysis.

Stevens-Johnson syndrome and toxic epidermal necrolysis (SJS/TEN) is a rare but life-threatening cutaneous drug reaction mediated by human leukocyte antigen (HLA) class I-restricted CD8+ T-cells. To obtain an unbiased assessment of SJS/TEN cellular immunopathogenesis, we performed single-cell (sc) transcriptome, surface proteome, and TCR sequencing on unaffected skin, affected skin, and blister fluid from 17 SJS/TEN patients. From 119,784 total cells, we identified 16 scRNA-defined subsets, confirmed by subset-defining surface protein expression. Keratinocytes upregulated HLA and IFN-response genes in the affected skin. Cytotoxic CD8+ T-cell subpopulations of expanded and unexpanded TCR{beta} clonotypes were shared in affected skin and blister fluid but absent or unexpanded in SJS/TEN unaffected skin. SJS/TEN blister fluid is a rich reservoir of oligoclonal CD8+ T-cells with an effector phenotype driving SJS/TEN pathogenesis. This multiomic database will act as the basis to define antigen-reactivity, HLA restriction, and signatures of drug-antigen-reactive T-cell clonotypes at a tissue level.

immunology↗

bioRxiv2022

Regulators of proteostasis are translationally repressed in fibroblasts from sporadic and LRRK2-G2019S Parkinson's patients

Parkinsons disease (PD) is characterized by heterogeneous motor and non-motor symptoms. The majority of PD cases are sporadic, whereas the leucine-rich repeat kinase 2 (LRRK2) G2019S mutation is the most common monogenic cause of familial PD and symptomatically indistinguishable from the sporadic form. Deficits in protein synthesis have been reported in PD. However, it is not known which proteins are affected or if there are synthesis differences between patients with sporadic and LRRK2 G2019S PD. Here we used non-canonical amino acid labeling and mass-spectrometry based proteomics to perform a quantitative comparison of nascent proteins in fibroblasts from sporadic and G2019S mutation PD patients compared to healthy individuals. We found that several proteins were under-represented among nascent proteins in cells from PD patients. Among these were regulators endo-lysosomal sorting, mRNA processing and translation itself. We further validated which of these proteins were dysregulated at the static proteome level using targeted proteomics. Key downregulated proteins included the autophagy regulator ATG9A and translational stability regulator YTHDF3. Notably, 68% of the identified proteins were downregulated in both sporadic and LRRK2-G2019S forms of PD. We identify translational repression of key regulators of proteostasis in patient fibroblasts that are common to both sporadic and LRRK2-G2019S PD.

neuroscience↗

bioRxiv2021

Novel newt regeneration genes regulate Wingless signaling to restore patterning in Drosophila eye

A fundamental process of regeneration, which varies among animals, recruits conserved signaling pathways to restore missing parts. Only a few animals like newts can repeatedly regenerate lost body parts throughout their lifespan that can be attributed to strategic regulation of conserved signaling pathways by newts regeneration tool-kit genes. Here we report use of genetically tractable Drosophila eye model to demonstrate the regeneration potential of a group of unique protein(s) from newt (Notophthalmus viridescens), which when ectopically expressed can significantly rescue missing photoreceptor cells in a Drosophila eye mutant. These newt proteins with signal peptides motifs exhibit non-cell-autonomous rescue properties and their regeneration potential even extends into later stages of fly development. Ectopic expression of these newt genes can rescue eye mutant phenotype by promoting cell proliferation and blocking cell death. These novel newt genes downregulate evolutionarily conserved Wingless (Wg)/Wnt signaling pathway to promote rescue. Modulation of Wg/Wnt signaling levels by using antagonists or agonists of Wg/Wnt signaling pathway in eye mutant background where newt gene(s) is ectopically expressed suggests that Wg signaling acts downstream of newt genes. Our data highlights the regeneration potential of novel newt proteins that regulate conserved pathways to trigger a robust regeneration response in Drosophila model with weak regeneration capability.

developmental biology↗

bioRxiv2020

Protein synthesis is suppressed in sporadic and familial Parkinson's Disease by LRRK2

Gain of function LRRK2-G2019S is the most common mutation associated with both familial and sporadic Parkinsons disease. It is expected therefore that understanding the cellular function of LRRK2 will provide much needed insight on the pathological mechanism of sporadic Parkinsons, which is the most common form. Here we show that constitutive LRRK2 activity represses nascent protein synthesis in rodent neurons. Specifically, enzymatic inhibition of LRRK2, gene silencing or gene knockout of Lrrk2 increase translation. In the rotenone model of Parkinsons, LRRK2 activity increases, leading to repression of translation and dopaminergic neuron atrophy both of which are prevented by LRRK2 inhibition. This is accompanied by altered phosphorylation of eIF2-S52({uparrow}), eIF2s2-S2({downarrow}) and eEF2-T57({uparrow}) in striatum/substantia nigra in a direction that signifies inhibition of protein synthesis. Significantly, LRRK2 is activated and translation is 40% reduced in Parkinsons patient fibroblasts (G2019S and sporadic) and LRRK2 inhibition restores normal translation. In contrast, translation is unchanged in cells from multiple system atrophy patients, implying disease specificity. These findings suggest that LRRK2-dependent repression of translation may be a proximal function of LRRK2 in Parkinsons pathology.

neuroscience↗