Biology subjects

Joshi, T.

Publications and source records attributed to Joshi, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Aquaporin-4 Regulates Edema, Sustains Astrocyte Differentiation, and Constrains Immunosuppressive Remodeling in Glioblastoma

Vasogenic cerebral edema is a severe complication that affects most patients with glioblastoma (GBM). It leads to an increase in intracranial pressure, neurological deficits, and increased mortality rates. While there is considerable research on edema formation, the molecular and cellular mechanisms of edema resolution in GBM, particularly in response to dexamethasone or other anti-edema therapies, remain largely undefined. Our findings demonstrate that the water channel aquaporin-4 (AQP4), a key regulator of brain water homeostasis, is upregulated in human GBM compared to the normal brain. AQP4 expression correlates with peritumoral edema in GBM patients, with the classical (CL) GBM subtype exhibiting the highest AQP4 levels but the lowest edema content relative to the proneural (PN) and mesenchymal (MES) subtypes. Using the RCAS/tv-a system, we generated de novo GBM with defined driver mutations in Aqp4-proficient and -deficient mice. Loss of Aqp4 shortened survival and exacerbated edema, accompanied by reduced astrocytic coverage within the tumor core, but not at the tumor margin. Single-cell RNA-sequencing and spatial transcriptomics revealed that Aqp4 loss reprograms astrocytes toward an immature, progenitor-like state and alters their crosstalk with other cell types in the GBM microenvironment. Additionally, loss of Aqp4 skewed myeloid populations toward immunosuppressive phenotypes while reducing lymphoid infiltration. Treatment with anti-VEGFA antibody, an established anti-edema therapy, increased expression of Aqp4 and reduced vessel leakage, underscoring the role of AQP4 in the therapeutic modulation of brain water balance. Overall, this study highlights the important role of AQP4 in resolving edema and its critical function in maintaining astrocyte identity and shaping the immune landscape of GBM.

cancer biology↗

bioRxiv2026

The adaptive architecture of tRNA dependencies across physiological tumor environments

The genetic code is decoded by a highly redundant transfer RNA (tRNA) repertoire, yet whether this apparent redundancy serves a functional role beyond ensuring robust translation remains unclear. Here, we establish an atlas of tRNA dependencies through large-scale CRISPRi perturbation mapping across matched in vivo tumor growth and in vitro cell culture for 16 cancer cell lines spanning seven tissue types. During in vivo tumor growth, tRNA dependencies exhibited tissue organization at isodecoder resolution and were associated with codon demand at the isoacceptor level. Strikingly, these relationships were reorganized when cells were cultured in vitro, establishing environmental sensitivity of tRNA dependency--in contrast to protein components of the decoding machinery such as aminoacyl-tRNA synthetases (aaRSs), whose dependencies were largely preserved across environments. Despite pronounced context specificity, environmental alterations in tRNA dependency were dominated by a shared response across cancer cell lines, organized across isoacceptor and isodecoder levels. By disentangling stable cellular identity from environment-associated dependency states, we resolved a shared axis of isoacceptor dependency remodeling and identified specific tRNA isoacceptors associated with promoting or restraining adaptation to the tumor environment. We further connect this functional architecture to differential translation of codon-usage-biased programs associated with proliferation and tumor-microenvironmental stress. Together, our study reveals that tRNA redundancy does not imply functional equivalence, but instead forms a structured and environmentally plastic control layer linking coding information to translational output.

genomics↗

bioRxiv2026

RAP2.3 is required for MYB51 and SIGMA3 expression during the response of Arabidopsis thaliana to multifactorial stress combination

In nature, plants are subjected to multiple environmental stress factors simultaneously or sequentially. Recent studies revealed that when three or more stress factors impact a plant simultaneously (termed multifactorial stress combination; MFSC), plant survival declines, even if the intensity of each individual stress involved in the MFSC is low. We previously identified RAP2.3 as a key transcription factor (TF) required for Arabidopsis thaliana survival, specifically under a MFSC of salt+excess light+heat stress (i.e., S+EL+HS). Here we report that RAP2.3 is required for the expression of SIGMA3, a nuclear-encoded factor that directs plastid RNA polymerase to specific plastid promoters, and MYB51, a key stress response TF involved in glucosinolate metabolism and oxidative stress responses, specifically during a MFSC of S+EL+HS. Like rap2.3 mutants, myb51 and sig3 mutants display significantly low survival rate specifically under the MFSC of S+EL+HS. Based on MYB51 gene regulatory network analysis and characterization of jasmonic acid (JA) mutants, we further reveal that suppression of JA signaling could play an important role in promoting plant survival under conditions of S+EL+HS. Our findings uncover an additional layer of the response of plants to MFSC, as well as identify potential targets for breeding crops with enhanced tolerance to climate change.

plant biology↗

bioRxiv2026

Systemic hypoxia suppresses solid tumor growth

Local hypoxia is a hallmark of solid tumors and a negative prognostic factor in the progression and treatment of cancer. Here, we showed that systemic hypoxia, in contrast to localized tumor hypoxia, decreases tumor growth in vivo across multiple cancer types and preclinical models. The reduced tumor growth in systemic hypoxia was not explained by hypoglycemia, hypoinsulinemia, or HIF activation. Instead, metabolite profiling in tumors and tumor interstitial fluid revealed extensive perturbations in purine-related metabolites. Stable isotope tracing demonstrated that systemic hypoxia caused tumors to suppress de novo purine synthesis. Furthermore, tumors did not develop resistance to systemic hypoxia therapy, and when used in combination with chemotherapy or immunotherapy, systemic hypoxia dramatically suppressed tumor growth. Finally, we showed that systemic hypoxia can be achieved pharmacologically with the small molecule HypoxyStat. These findings challenge the long-held paradigm of hypoxia as a negative prognostic factor in cancer progression, and they suggest a potential therapeutic role for systemic hypoxia in suppressing solid tumor growth.

cancer biology↗

bioRxiv2025

Tonic interferons defend against respiratory viruses in primary human lung organoid-derived air-liquid interface cultures

Innate defences of the respiratory epithelium are the first barrier against incoming respiratory viruses. To understand the contribution of both basal (tonic) and induced interferon (IFN) to antiviral defences in a physiologically relevant system, we established air-liquid interface (ALI) cultures of primary human bronchial epithelium (HBE) and small airway epithelium (HSE). Via an organoid intermediate stage, the limited healthy donor material was expanded while preserving stemness and subsequently differentiated. Characterisation by spatial and transcriptomic analyses showed that the cellular diversity and architecture of our ALI cultures were comparable to native human lung epithelium. Upon infection with relevant human respiratory pathogens, such as Human Rhinovirus (HRV16) and human Coronaviruses (229E and NL63), only HRV16 induced a strong and early type I and III IFN response, leading to its eventual clearance from the cultures. Depletion of tonic type I/III IFNs using neutralising antibodies or scavengers reduced expression of levels of IFN-stimulated genes and increased infectious HRV production by [~]7-10-fold. Taken together, we present a method for generating primary lung epithelial cultures that retain their IFN status, demonstrate clearance of HRV by innate defences, and highlight the importance of tonic IFN in early antiviral defences. IMPORTANCEMild respiratory viral infections, for example, with human common cold coronaviruses or rhinoviruses, are a massive cause of human morbidity. The respiratory tract is the primary entry route for these viruses and also the contact site for initial innate immune defences. Here, we show that primary human lung epithelial cell-derived air-liquid interface cultures mimic the architecture and cell composition of native human lung epithelium, and retain both induced and tonic interferon (IFN) responses. Notably, our data show that the models innate immune defences are sufficient to clear human Rhinovirus (HRV) infections, which are characterised by rapid and robust IFN responses. Finally, depletion of tonic IFNs led to a marked increase in HRV infection. Thus, our research suggests that tonic low levels of IFNs contribute to the epithelial defence against viruses, maintaining the tissues immune readiness. Failure to maintain these tonic IFN levels increases the susceptibility towards infections.

microbiology↗

bioRxiv2025

United we stand: Plants that physically touch each other are more resilient to stress

Plants use sophisticated signaling networks to communicate with each other. While this process is thought to support the overall health and resilience of plant communities, it could also reflect eavesdropping between plants used for competition. Here we reveal that plants that physically touch each other aboveground are more resilient to excess light stress, and that this phenomenon is dependent on the ability of plants to exchange aboveground electric and H2O2 signals with each other. Using a mutant that is unable to transfer Ca2+/reactive oxygen species (ROS) signals but can transfer electric signals (hpca1), as a mediator/connector between different plants, we further separate electric from Ca2+/ROS plant-to-plant signals and transcriptional landscapes, and show that the transfer of Ca2+/ROS signals, as well as the function of several Ca2+/ROS-dependent transcripts, is required for excess light stress acclimation. Our study reveals that plants that live together and physically touch each other establish an aboveground community-wide signaling network that enhances their collective resilience to stress. TeaserPlants that physically touch and exchange aboveground signals with each other are more resilient to excess light stress.

plant biology↗

bioRxiv2025

Enhanced cell aggregation in the Chlamydomonas reinhardtii rbo1 mutant in response to multifactorial stress combination

Global change factors associated with climate change and increased pollution are subjecting plants, microbes, and different ecosystems to conditions of multifactorial stress combination (MFSC). While recent studies centered on the effects of MFSC on different plants and ecosystems, much less is known about how these conditions impact unicellular organisms. Here, we report on the physiological and proteomic responses of wild type and respiratory burst oxidase homolog 1 (rbo1) mutant cells of Chlamydomonas reinhardtii to a MFSC of 5 different abiotic stresses. While several similarities were found between plant and C. reinhardtii responses to MFSC, our work revealed that MFSC induces aggregation in the unicellular organism C. reinhardtii. We further show that MFSC induced aggregation is enhanced in the rbo1 mutant and can be triggered by H2O2. As aggregation typically leads to reduced growth, respiration and/or photosynthesis, enhanced aggregation of unicellular organisms in different ecosystems subjected to MFSC could explain part of the negative impacts of MFSC on the services they provide. Our findings shed new light on the response of unicellular organisms to MFSC and suggest that one of the main drivers leading to multicellularity during evolution was early conditions of MFSC under an oxygenated environment.

plant biology↗

bioRxiv2025

bHLH35 mediates specificity in plant responses to multiple stress conditions

How biological systems respond to stress is a fundamental question in biology, primarily addressed using the reductionist approach of applying one stress condition at a time. In nature, however, organisms experience a multitude of stresses, simultaneously or sequentially, questioning the validity of the reductionist approach for predicting plant responses to stress under natural conditions. Here, we reveal that in the flowering plant Arabidopsis thaliana, the transcriptional regulator bHLH35 is required for plant survival under a specific set of stress conditions that includes a combination of salinity, excess light, and heat, occurring simultaneously (but not for each of these stresses applied individually or in any other combination). Under these conditions, bHLH35 interacts with NAC069 and binds the promoter of LBD31, also specifically required for survival under the 3-stress combination. Our findings uncover a high degree of specificity in the response of organisms to stress, a specificity that would not have been revealed using the reductionist approach, and one that should be taken into consideration when developing agronomically important crops with heightened resilience to climate change.

plant biology↗

bioRxiv2025

Transcriptomic and physiological responses of soybean plants subjected to a combination of water deficit and heat stress under field conditions

Water deficit, heat stress, and a combination of water deficit and heat stress are highly disruptive to crop yield worldwide. Unfortunately, the frequency and intensity of these conditions is gradually increasing due to climate change. Previous studies of water deficit and heat stress combination were primarily conducted under controlled growth conditions, revealing that the combination of water deficit and heat stress resulted in the activation of unique stress responses and acclimation pathways. However, whether similar responses to stress combination occur in the field remained largely unknown. Here we report on a two-year field study in which the transcriptomic and physiological responses of vegetative and reproductive tissues of soybean (Glycine max) to water deficit, heat treatment and their combination were studied. Our findings reveal that the transcriptomic responses of soybeans grown in the field are different from those grown under controlled growth chamber conditions. These differences were especially noticeable in plants subjected to the heat or water deficit treatments, and less in plants subjected to the stress combination. In addition, we report that differential transpiration between leaves and pods, that was originally discovered in plants grown under controlled growth conditions, occurs in field grown soybeans in response to heat stress, as well as heat stress combined with water deficit. We hope that the transcriptomic datasets generated by our study will contribute to future studies of crop responses to different stresses in the field, as well as highlight the need for more omics studies of plants grown under field conditions.

plant biology↗

bioRxiv2025

Integrative analysis of plant responses to a combination of water deficit, heat stress and eCO2 reveals a role for OST1 and SLAH3 in regulating stomatal responses

The frequency, intensity and duration of global change factors and/or environmental stressors, such as droughts, heat waves, floods, and pollution, are increasing due to anthropogenic activities, subjecting plants to compound conditions of Global Change Factor combination (GCFc), or stress combination. These can have contrasting or additive effects on plant physiological performance and impact different ecosystems and agro-ecosystems worldwide. Using an integrative physiological, genetic, hormonal, and transcriptomic analysis, we studied the response of Arabidopsis thaliana (L.) Heynh to a combination of water deficit (WD), heat stress (HS) and/or elevated levels of CO2 (eCO2). Our findings reveal high specificity in plant responses to GCFc. We further reveal that stomatal aperture regulation under conditions of GCFc is controlled by a blend of unique and shared regulators, that together determine the specific aperture size under each different set of GCFc conditions. Under a combination of WD, HS, and eCO2 (WD+HS+eCO2), for example, stomatal closure required the function of nitric oxide, OPEN STOMATA 1 and the S-type anion channel SLAH3, but not the S-type anion channel SLAC1, or many other regulators typically found to control stomatal aperture under less complex conditions, including HS+WD. Our findings highlight the complexity of plant physiological and molecular responses to conditions of stress combination and open the way for future studies of plant responses to stress combination, crucial to our understanding of how GCFc impacts different ecosystems and agro-ecosystems worldwide. In addition, our study provides an initial definition for a stomatal hierarchical stress code that could apply to future studies.

plant biology↗

bioRxiv2025

Discovery of a tRNA-regulatory transcription factor that suppresses breast cancer metastasis

Transfer RNAs (tRNAs), once viewed as static adaptors in translation, are now recognized as dynamic regulators of gene expression. While recent studies have illuminated roles for tRNA stability, the upstream mechanisms governing tRNA transcription remain poorly understood. To address this gap, we generated the EXpression atlas of tRNA (EXTRNA), a high-resolution tRNA expression dataset spanning 24 cell lines across 9 human tissues. EXTRNA revealed both tissue-type-specific expression programs ("tRNAomes") and unexpected intra-tissue heterogeneity across breast cancer samples. Integrating EXTRNA with computational network analysis and data from other publicly available datasets, we identified Zinc Finger ZZ-Type And EF-Hand Domain Containing 1 (ZZEF1) as the first sequence-specific transcription factor of a particular tRNA. ZZEF1 promoted tRNA-LysUUU transcription by partnering with the ATP-dependent chromatin remodeler Chromodomain Helicase DNA Binding Protein 6 (CHD6), enhancing chromatin accessibility at tRNA-Lys-TTT-3 loci. ZZEF1 deficiency reduced tRNA-LysUUU abundance, decreased the translational efficiency of AAR codon-enriched mRNAs--including the tumor suppressor Serine/Threonine Kinase 3 (STK3)--and promoted metastatic progression in breast cancer in vivo. Together, our findings establish a previously unrecognized mechanism for RNA polymerase III-mediated tRNA transcription and define a regulatory circuit linking chromatin remodeling, codon-specific translation, and tumor suppression. More broadly, this work introduces a framework for dissecting the regulatory logic of the tRNAome and highlights tRNA expression control as a promising avenue for therapeutic intervention.

genomics↗

bioRxiv2025

Titin as a mechanical damper: Balancing Stability and longevity through inter-domain linker design

Titin, a giant protein ([~]3-4 MDa), functions as a molecular-spring to regulate muscle elasticity. More than 90% of Titin is composed of domains that absorb mechanical energy and undergo stochastic unfolding-refolding under tension ([~]tens of pN). These domains are connected in tandem by interdomain linkers (IDLs), which constitute less than 10% of the total mass. Despite their small genomic footprint, bioinformatics mapping suggests that IDLs have an outsized impact on protein mechanics, potentially contributing to disease pathology. Using magnetic tweezers, here we examine how linkers influence mechano-response of domains to constant and oscillatory forces. We found that short linkers limit interdomain movement and promote first-order cooperative folding transitions of domains. In contrast, long flexible linkers induce creep-like deformations interspersed with sharp, stepwise transitions. Surprisingly, linkers that improve domain-stability resist unfolding under constant pulling forces, but lose power retention faster under oscillatory forces. Our findings reveal a trade-off between mechanical stability and energy retention in titin, a key muscle protein. These insights offer new design principles for mechano-responsive protein engineering. TeaserTiny linkers fine-tune how bulky domains in titin respond to force.

biophysics↗

bioRxiv2024

Multiplexed mosaic tumor models reveal natural phenotypic variations in drug response within and between populations

Many agents that show promise in preclinical cancer models lack efficacy in patients due to patient heterogeneity that is not captured in traditional assays. To address this problem, we have developed GENEVA, a platform that measures the molecular and phenotypic consequences of drug perturbations within diverse populations of cancer cells at single-cell resolution, both in vitro and in vivo. Here, we apply GENEVA to study the KRAS G12C inhibitors, recapitulating known properties of these drugs and uncovering a previously unknown role for mitochondrial activation in cell death induced by KRAS inhibition. We demonstrate that this finding can be leveraged for the development of combination therapies with greater efficacy. Finally, we show that the application of GENEVA with in vivo mouse models revealed epithelial to mesenchymal transition (EMT) as a key mechanism for resistance to KRAS G12C inhibition.

cancer biology↗

bioRxiv2024

Spatial multi-omics defines a shared infiltrative signature in glioblastoma at the resection margin

Glioblastoma (GBM) remains an untreatable disease. Understanding GBMs infiltrative biology at the resection margin is limited, despite causing disease recurrence and progression. To address this, we generated a high-throughput single-nucleus (sn)RNA-seq and snATAC-seq multi-omic dataset from six tumors with distinct genomic drivers and combined it with spatial transcriptomics to characterize the unique molecular phenotype of GBM near the margin. By contrasting GBM-specific biology in matching "Core" vs. "Margin" dissections, we define unique, shared "GBM infiltration" and chromatin accessibility signatures near the margin. We prioritize EGFR as a top differentially expressed and accessible "Margin" marker across GBM subtypes, show its dynamic expression along a core-to-margin infiltration trajectory, and validate its role in migration through CRISPR/Cas9 deletion in two patient-derived models. ChIP-seq studies furthermore corroborate preferential TEAD1 binding at EGFRs accessible regulatory elements. This validated multi-omic dataset enables further studies into tumor and microenvironment biology in the context of residual GBM disease.

cancer biology↗

bioRxiv2024

G2PDeep-v2: a web-based deep-learning framework for phenotype prediction and biomarker discovery using multi-omics data

The G2PDeep-v2 server is a web-based platform powered by deep learning, for phenotype prediction and markers discovery from multi-omics data in any organisms including humans, plants, animals, and viruses. The server provides multiple services for researchers to create deep-learning models through an interactive interface and train these models using an automated hyperparameter tuning algorithm on high-performance computing resources. Users can visualize the results of phenotype and markers predictions and perform Gene Set Enrichment Analysis for the significant markers to provide insights into the molecular mechanisms underlying complex diseases and other biological processes. The G2PDeep-v2 server is publicly available at https://g2pdeep.org/.

bioinformatics↗

bioRxiv2024

Anti-EGFR aptamer exhibits direct anti-cancer effects in NSCLC cells harboring EGFR L858R mutations

Non-small cell lung cancer (NSCLC) adenocarcinoma (LUAD) is a leading cause of death worldwide. Activating mutations in the tyrosine kinase domain of the oncogene epidermal growth factor receptor (EGFR) are responsible for [~]10-50% of all LUAD cases. Although EGFR tyrosine kinase inhibitors (TKIs) have been effective in prolonging NSCLC patient survival and quality of life, acquired resistance mechanisms and disease progression are inevitable. Contemporary second- and third-line treatments, such as immunotherapy, remain ineffective for these patients, presenting a clear and unmet need for alternative or adjuvant therapeutics for the treatment of mutant EGFR positive NSCLC. Here we show that an anti-EGFR aptamer (EGFRapt) decreases viability of NSCLC cell lines harboring the L858R {+/-} T790M mutation in EGFR but not cell lines harboring wild-type or exon 19 deletions. In a humanized xenograft mouse model of NSCLC, EGFRapt decreased tumor burden compared to controls when delivered intratumorally over multiple doses. To elucidate the mechanism by which EGFRapt exerts these effects, we monitored cellular processes associated with kinase-dependent and kinase-independent mechanisms and found that the anti-cancer effects of EGFRapt are cell line dependent, inhibiting cellular proliferation in one cell line and inducing cell death in another. Post hoc transcriptomics analysis supported these findings and provided additional mechanistic insights. Overall, these data establish that EGFRapt has direct anti-cancer activity in mutant EGFR positive NSCLC via targetable mechanisms that are independent of existing approaches, and they provide a foundation for further development of nucleic acid-based therapies that target EGFR.

cancer biology↗

bioRxiv2023

Integrative phenotypic-transcriptomic analysis of soybean plants subjected to multifactorial stress combination

Global warming, climate change, and industrial pollution are altering our environment subjecting crops to an increasing number and complexity of abiotic stress conditions, concurrently or sequentially. Recent studies revealed that a combination of 3 or more stresses simultaneously impacting a plant (termed multifactorial stress combination; MFSC) can cause a drastic decline in plant growth and survival, even if the level of each stress involved in the MFSC has a negligible effect on plants. However, the impacts of MFSC on crops are largely unknown. We subjected soybean plants to a MFSC of up to five different stresses (water deficit, salinity, low phosphate, acidity, and cadmium), in an increasing level of complexity, and conducted integrative transcriptomic-phenotypic analysis of reproductive and vegetative tissues. We reveal that MFSC has a negative cumulative effect on soybean yield, that each set of MFSC condition elicits a unique transcriptomic response (that is different between flowers and leaves), and that selected genes expressed in leaves or flowers are linked to the effects of MFSC on different vegetative, physiological, and/or reproductive parameters. We further reveal that the transcriptomic response of soybean and Arabidopsis to MFSC shares common features associated with reactive oxygen and iron/copper signaling/metabolism. Our study provides unique phenotypic and transcriptomic datasets for dissecting the mechanistic effects of MFSC on the vegetative, physiological, and reproductive processes of a crop plant.

plant biology↗

bioRxiv2023

Single-cell and spatial transcriptomics identify a macrophage population associated with skeletal muscle fibrosis

The monocytic/macrophage system is essential for skeletal muscle homeostasis, but its dysregulation contributes to the pathogenesis of muscle degenerative disorders. Despite our increasing knowledge of the role of macrophages in degenerative disease, it still remains unclear how macrophages contribute to muscle fibrosis. Here, we used single-cell transcriptomics to determine the molecular attributes of dystrophic and healthy muscle macrophages. We identified six novel clusters. Unexpectedly, none corresponded to traditional definitions of M1 or M2 macrophage activation. Rather, the predominant macrophage signature in dystrophic muscle was characterized by high expression of fibrotic factors, galectin-3 and spp1. Spatial transcriptomics and computational inferences of intercellular communication indicated that spp1 regulates stromal progenitor and macrophage interactions during muscular dystrophy. Galectin-3+ macrophages were chronically activated in dystrophic muscle and adoptive transfer assays showed that the galectin-3+ phenotype was the dominant molecular program induced within the dystrophic milieu. Histological examination of human muscle biopsies revealed that galectin-3+ macrophages were also elevated in multiple myopathies. These studies advance our understanding of macrophages in muscular dystrophy by defining the transcriptional programs induced in muscle macrophages, and reveal spp1 as a major regulator of macrophage and stromal progenitor interactions.

immunology↗