Biology subjects

Desai, B.

Publications and source records attributed to Desai, B..

17 recordsLinked to original sources

bioRxiv2026

Defining the Functional Consequence of the Human Ocular Microbiome

The ocular surface is one of the body's most environmentally exposed mucosal barriers, yet it is considered low biomass and harbors orders of magnitude fewer bacteria than microbe-rich sites like the gut. This has cast doubt on whether a functional core ocular microbiome exists at all. Having previously defined a protective gd T cell and IL-17 axis engaged by the murine commensal Corynebacterium mastitidis, we asked whether human-derived bacteria could do the same. Pairing sequencing and culturomics of healthy human conjunctiva from two geographically distinct cohorts, we define a stable core microbiome and identify Corynebacterium bovis as a consistent eye-resident commensal rather than a transient contaminant. In humans, C. bovis elicits a non-pathogenic response marked by IL-17 secretion by {gamma}{delta} T cells and circulating C. bovis-specific IgG, which suggests commensalism rather than pathology. Colonizing mice with human C. bovis strains from Pittsburgh or Miami reproduced this program and conferred protection against ocular infection with Staphylococcus aureus. Together, these findings identify C. bovis as a human-derived ocular commensal that can drive protective {gamma}{delta} T cell immunity, translating a mechanism previously defined only in mice into human relevance and a rational target against sight-threatening infection.

immunology↗

bioRxiv2026

Central Glucagon-Like Peptide-1 Agonism Ameliorates Colonic Inflammation in a Murine Model of Inflammatory Bowel Disease

Glucagon-like peptide-1 receptor agonists (GLP-1RAs) have revolutionized the treatment of obesity and type 2 diabetes (T2D). These drugs also have anti-inflammatory effects that have recently been extended to the treatment of inflammatory bowel disease (IBD). Whether the mechanism underlying this benefit involves a direct action on the intestine or instead is mediated via GLP-1Rs in the brain, however, is unknown. Based on evidence implicating the brain as the target for the anti-obesity and anti-inflammatory effects of GLP-1RAs, we sought to determine if central GLP-1R signaling is sufficient to explain its intestinal anti-inflammatory effects. To this end, we compared the efficacy of peripheral vs central administration of the GLP-1RA, semaglutide (SEMA), in diet-induced obese (DIO) mice with dextran sodium sulfate (DSS)-induced colitis. We report that compared to vehicle, both colitis severity and histopathological injury following DSS administration are reduced by peripheral administration of SEMA. We also report that this benefit is largely recapitulated by intracerebroventricular administration of SEMA at a low dose that, when administered peripherally, is below that needed to affect food intake and body weight. We conclude that in a mouse model of colitis, activation of GLP-1Rs in the brain is sufficient to explain the intestinal anti-inflammatory effect conferred by GLP-1R agonism.

neuroscience↗

bioRxiv2026

A reference-calibrated spatial-statistical framework for quantifying stroma-tumor cell spatial associations from histology and its geometric limits

Quantifying interactions in biological tissues requires determining whether an interaction exists, the distance over which it operates, and its strength. Existing spatial-statistical approaches can characterize spatial organization but often require interaction range or interaction models to be specified a priori, making them less suited to settings where these quantities are themselves unknown. Here, we present a practical framework that recovers the presence, range, and association strength of spatial bias toward a tissue structure directly from segmented histology. The framework combines four complementary statistics, the resource selection function, nearest-structure distance distributions, the cross J-function, and the radial distribution function, with specimen-specific reference states that preserve tissue stromal architecture while spanning a continuum of known spatial biases. Across controlled in silico tissues, we show that tissue stromal architecture imposes geometric limits on the range of recoverable interactions and that event fraction independently constrains statistical sensitivity. These spatial associations establish fundamental bounds on inference and demonstrate that spatial statistics must be interpreted relative to tissue-specific reference states rather than absolute scales. We apply the framework to proliferating tumor cells relative to CAF-rich stroma during tyrosine kinase inhibitor therapy in an ALK+ NSCLC model and identify a strong stroma-associated proliferation bias extending approximately 30-60 micrometers. The framework broadly applies to any histological setting where events and reference structures can be defined, providing a practical approach to quantify localized interactions directly from tissue stromal architecture.

cancer biology↗

bioRxiv2026

Bridging Biomedical Atlas Ecosystem: Cross-Atlas Alignment And Scalable Tissue Specimen Registration

Over the last five years, over 13,000 tissue datasets with 200+ million cells from 20 consortia have been spatially registered into the Human Reference Atlas (HRA) common coordinate framework (CCF). The shared 3D spatial and semantic reference system enables exploration of datasets in the context of all other data across organs, assay types, and spatial scales. However, manual registration of individual samples remains resource intensive, posing feasibility challenges exacerbated by the proliferation of samples, assays, and atlasing efforts. This paper presents two approaches to scale up HRA construction: (1) projecting data across biomedical reference atlas systems and (2) using millitomes to bulk register tissue blocks into a reference organ. Both methods use the AutoMated Alignment and Projection (AMAP) pipeline to align 3D mesh models using point cloud registration. We demonstrate the evolving HRA-aligned atlas ecosystem for 6 models from the SPARC Program (heart), Gut Cell Atlas (large intestine), 500-subject consensus kidneys, and the Julich Brain Atlas. Additionally, we used AMAP to project 7 millitome models across 5 organs onto the HRA ecosystem, integrating 300+ tissue extraction sites. AMAP enables scalable tissue registration of data across atlas ecosystems enabling the construction of detailed reference maps of the human body.

bioinformatics↗

bioRxiv2026

Pharmacokinetic Acceleration via CYP3A4 Hyperactivation as a Clinically Actionable Mechanism of Targeted Therapy Resistance in NSCLC

Resistance of cancers to targeted therapies is traditionally framed as a tumor-intrinsic phenomenon, mediated by tumor cell-intrinsic or microenvironmental mechanisms. Here, we identify a tumor-extrinsic, systemic resistance mechanism resulting from hyperactivation of the hepatic cytochrome P450 enzyme, CYP3A4. This tumor-extrinsic resistance mechanism can function independently of, or in tandem with, tumor-intrinsic resistance. Focusing on experimental mouse models of targetable lung cancer, we find that xenobiotic-mediated induction of CYP3A4 results in accelerated drug metabolism and a drastic reduction in systemic and tumor-drug exposure in vivo. CYP3A4 activation can be triggered by chemically unrelated xenobiotics, leading to resistance to a wide range of targeted therapies, including ALK, EGFR, and KRASG12C inhibitors. Retrospective analysis of clinical cohorts suggests that variability in CYP3A4 activity might be a major contributor to variability in clinical outcomes. While higher CYP3A4 activity leads to sub-therapeutic tumor drug exposure and shorter progression-free survival, reduced drug metabolism is expected to result in supratherapeutic exposure and increased systemic toxicity. To address the consequences of abnormal CYP3A4 activity, we utilized mathematical modeling to demonstrate that drug concentrations can be restored through the optimization of dosing amounts and intervals. Further, we show that tumor sensitivity to targeted therapies can be rescued through pharmacological inhibition of CYP3A4. Our findings establish systemic metabolic variability as a bona fide resistance and toxicity driver, providing a translational framework for personalized dosing to maximize both safety and efficacy.

cancer biology↗

bioRxiv2025

Mismatch negativity develops in adolescence and independently of microglia

Higher brain functions and cognition undergo a critical period of development during adolescence, when psychiatric disorders such as schizophrenia typically onset. Understanding how developmental processes during adolescence interact with schizophrenia pathophysiology and risk remains a central goal in psychiatry. Here we show that a well-established biomarker of schizophrenia, mismatch negativity, matures during adolescence in mouse primary visual cortex, along with a strengthening of fronto-visual functional connectivity. Because microglia are implicated in schizophrenia risk and disease states, we further investigated what role microglia may play in the development of mismatch responses under physiological conditions. We found that microglial depletion with PLX5622 in adolescence arrests the development of resting oscillations in frontal areas, but does not affect the development of deviance detection, other signatures of visual context processing, or prefrontal-visual functional connectivity. Our findings suggest (a) a key component of mismatch negativity develops in adolescence, a period of vulnerability to schizophrenia, and (b) the development underlying this component does not require robust microglia activity, clarifying the developmental role of microglia in higher order visual processing.

neuroscience↗

bioRxiv2025

Evolutionary antifragile therapy

A population of cells within a tumor can be described as antifragile (the opposite of fragile) if they derive a benefit from fluctuations or perturbations in environmental conditions induced by treatment. We hypothesized that treatment fluctuations may either promote (antifragile tumor) or inhibit (fragile tumor) the evolution of treatment resistance to targeted therapies. Analysis of the convexity of dose response curves provides a direct prediction of response to prescribed fluctuations in treatment. Theory predicts that continuous treatment protocols (i.e. zero prescribed fluctuations in treatment) will outperform uneven protocols when dose response is convex. We apply this theory to predict in vivo response to targeted therapy and validate these predictions by experimentally testing high/low intermittent dosing (uneven dosing) and continuous dosing (even dosing) schedules. Convexity (and its inverse, concavity) explains two phenomena: dose response is a convex (fragile) function but resistance onset rate is a concave (antifragile) function. Thus, we design, propose, and validate alternative treatment schedules which maximize response while maintaining prolonged sensitivity to treatment. These analyses provide supporting evidence that fluctuations alter the evolutionary trajectory of tumors in response to targeted therapy, even without altering the cumulative dose. This insight is used to design alternative, switching treatment protocols to limit the evolution of resistance, a process which we call evolutionary antifragile therapy.

cancer biology↗

bioRxiv2024

Trastuzumab deruxtecan combination strongly enhances responses and overcomes sotorasib resistance in KRASG12C-mutant NSCLC

IntroductionRecent advances in the treatment of KRAS-mutant non-small cell lung cancer (NSCLC) have led to the development of KRASG12C inhibitors, such as sotorasib and adagrasib. However, resistance and disease progression remain significant challenges. In this study, we investigated the therapeutic potential of combining trastuzumab deruxtecan (T-DXd), an anti-HER2 antibody-drug conjugate, with sotorasib in KRASG12C-mutant NSCLC, while also evaluating HER2 expression in NSCLC samples. MethodsThe HER2 expression dependence of xenograft responses to sotorasib, T-DXd, and their combination was evaluated in therapy-naive and sotorasib-treated tumors by immunohistochemistry (IHC). Also, we analyzed 191 clinical (pre- or on-treatment) and rapid autopsy (post-treatment) samples from 31 patients with driver-positive and driver-negative advanced stage NSCLC, assessing HER2 expression using interpretation guidelines developed for breast cancer (BC) and gastroesophageal adenocarcinoma (GEA). ResultsIn the majority of preclinical models, including sotorasib-resistant tumors, the sotorasib-T-DXd combination induced stronger and more durable responses compared to monotherapies. The strong effect of the combination therapy was likely attributable to sotorasib-induced adaptive HER2 upregulation; stronger HER2 expression in sotorasib-treated tumors was linked with stronger responses. Although HER2 expression was higher in samples from patients with KRASG12C-mutant NSCLC compared to NSCLC with other driver mutations or no drivers, the difference was not statistically significant. HER2 IHC score discrepancy was also observed between BC and GEA interpretation guidelines. ConclusionsOur results support the potential clinical utility of the sotorasib-T-DXd combination, including tumors with intrinsic and acquired resistance to sotorasib monotherapy. Since the strengths of the responses depend on HER2 expression levels, successful clinical implementation necessitates optimizing patient selection. Our results highlight the complexities of accurate HER2 interpretation in NSCLC and highlight the need for standardized testing methods.

cancer biology↗

bioRxiv2024

Constitutive expression of CX3CR1-BAC-Cre introduces minimal off-target effects in microglia

CX3CR1-Cre mouse lines have produced important advancements in our understanding of microglial biology. Recent studies have demonstrated the adverse effects of tamoxifen-induced CX3CR1-Cre expression during development, which include changes in microglial density, phenotype, and DNA damage, as well as anxiety-like behavior. However, the unintended effects of constitutive CX3CR1-BAC-Cre expression remain unexplored. Here, we characterized the effects of CX3CR1-BAC-Cre expression on microglia in CX3CR1-BAC-Cre+/- and CX3CR1-BAC-Cre-/-male and female littermates during early postnatal development and adulthood in multiple brain regions. Additionally, we performed anxiety-like behavior tests to assess changes caused by Cre expression. We found that CX3CR1-BAC-Cre expression causes subtle region- and sex-specific changes in microglial density, volume, and morphology during development, but these changes normalized by adulthood in all brain regions except the hippocampus. No behavioral effects were found. Our findings suggest that the constitutive-Cre model might be less detrimental than the inducible model, and highlight the need for proper controls.

neuroscience↗

bioRxiv2024

Cancer-associated fibroblasts confer ALK inhibitor resistance in EML4-ALK-driven lung cancer via concurrent integrin and MET signaling

Cancer-associated fibroblasts (CAFs) are associated with tumor progression and modulate drug sensitivity of cancer cells. However, the underlying mechanisms are often incompletely understood and crosstalk between tumor cells and CAFs involves soluble secreted as well as adhesion proteins. Interrogating a panel of non-small cell lung cancer (NSCLC) cell lines driven by EML4-ALK fusions, we observed substantial CAF-mediated drug resistance to clinical ALK tyrosine kinase inhibitors (TKIs). Array-based cytokine profiling of fibroblast-derived conditioned- media identified HGF-MET signaling as a major contributor to CAF-mediated paracrine resistance that can be overcome by MET TKIs. However, Cell Type specific labeling using Amino acid Precursors (CTAP)-based expression and phosphoproteomics in direct coculture also highlighted a critical role for the fibronectin-integrin pathway. Flow cytometry analysis confirmed activation of integrin {beta}1 (ITGB1) in lung cancer cells by CAF coculture. Treatment with pharmacological inhibitors, cancer cell-specific silencing or CRISPR-Cas9-mediated knockout of ITGB1 overcame adhesion protein-mediated resistance. Concurrent targeting of MET and integrin signaling effectively abrogated CAF-mediated resistance of EML4-ALK-driven NSCLC cells to ALK TKIs in vitro. Consistently, combination of the ALK TKI alectinib with the MET TKI capmatinib and/or the integrin inhibitor cilengitide was significantly more efficacious than single agent treatment in suppressing tumor growth using an in vivo EML4-ALK-dependent allograft mouse model of NSCLC. In summary, these findings emphasize the complexity of resistance-associated crosstalk between CAFs and cancer cells, which can involve multiple concurrent signaling pathways, and illustrate how comprehensive elucidation of paracrine and juxtacrine resistance mechanisms can inform on more effective therapeutic approaches.

cancer biology↗

bioRxiv2024

Peristromal niches protect lung cancers from targeted therapies through a combined effect of multiple molecular mediators

Targeted therapies directed against oncogenic signaling addictions, such as inhibitors of ALK in ALK+ NSCLC often induce strong and durable clinical responses. However, they are not curative in metastatic cancers, as some tumor cells persist through therapy, eventually developing resistance. Therapy sensitivity can reflect not only cell-intrinsic mechanisms but also inputs from stromal microenvironment. Yet, the contribution of tumor stroma to therapeutic responses in vivo remains poorly defined. To address this gap of knowledge, we assessed the contribution of stroma-mediated resistance to therapeutic responses to the frontline ALK inhibitor alectinib in xenograft models of ALK+ NSCLC. We found that stroma-proximal tumor cells are partially protected against cytostatic effects of alectinib. This effect is observed not only in remission, but also during relapse, indicating the strong contribution of stroma-mediated resistance to both persistence and resistance. This therapy-protective effect of the stromal niche reflects a combined action of multiple mechanisms, including growth factors and extracellular matrix components. Consequently, despite improving alectinib responses, suppression of any individual resistance mechanism was insufficient to fully overcome the protective effect of stroma. Focusing on shared collateral sensitivity of persisters offered a superior therapeutic benefit, especially when using an antibody-drug conjugate with bystander effect to limit therapeutic escape. These findings indicate that stroma-mediated resistance might be the major contributor to both residual and progressing disease and highlight the limitation of focusing on suppressing a single resistance mechanism at a time.

cancer biology↗

bioRxiv2024

Evolutionary double-bind treatment using radiotherapy and NK cell-based immunotherapy in prostate cancer

Evolution-informed therapies exploit ecological and evolutionary consequences of drug resistance to inhibit the expansion of treatment-resistant populations and prolong time to progression. One strategy, termed an evolutionary double-bind, uses an initial therapy to elicit a specific adaptive response by the cancer cells, which is then selectively targeted by a follow-on therapy. Here we examine the combination of radiation therapy and immunotherapy as a quantifiable double-bind strategy. Radiotherapy (RT) induces lethal double-strand DNA breaks, but cancer cells can adapt by upregulating DNA damage response pathways. While this evolutionary strategy increases resistance to DNA damaging agents, it also results in enhanced expression of natural killer (NK) cell ligands potentially increasing vulnerability to an immune response. Using a radiation-resistant human prostate carcinoma cell line (22Rv1), we demonstrate that RT-resistant cells upregulate NK cell ligands, including major histocompatibility complex class I chain-related protein A/B (MICA/B), and poliovirus receptors (PVR1, PVRL2) with a 2-fold increase in sensitivity to NK cell mediated killing. We investigated this potential evolutionary double bind through in vitro studies and evolution-based mathematical models. Radiotherapy alone slowed overall growth but strongly selected for RT-resistant cells. NK cell therapy alone suppressed the RT-resistant population but with a surviving population of radiation-sensitive cells. These dynamics were framed mathematically, and model simulation predicted optimal tumour control would be achieved through initial RT rapidly followed by NK-based immunotherapy. Subsequent experiments confirmed the model prediction. We conclude that radiotherapy and NK cell-based immunotherapy produces an evolutionary double bind that can be exploited in heterogenous tumours to limit RT resistance.

cancer biology↗

bioRxiv2020

Understanding the Evolutionary Games in NSCLC Microenvironment

While initially highly successful, targeted therapies eventually fail as populations of tumor cells evolve mechanisms of resistance, leading to resumption of tumor growth. Historically, cell-intrinsic mutational changes have been the major focus of experimental and clinical studies to decipher origins of therapy resistance. While the importance of these mutational changes is undeniable, a growing body of evidence suggests that non-cell autonomous interactions between sub-populations of tumor cells, as well as with non-tumor cells within tumor microenvironment, might have a profound impact on both short term sensitivity of cancer cells to therapies, as well as on the evolutionary dynamics of emergent resistance. In contrast to well established tools to interrogate the functional impact of cell-intrinsic mutational changes, methodologies to understand non-cell autonomous interactions are largely lacking. Evolutionary Game Theory (EGT) is one of the main frameworks to understand the dynamics that drive frequency changes in interacting competing populations with different phenotypic strategies. However, despite a few notable exceptions, the use of EGT to understand evolutionary dynamics in the context of evolving tumors has been largely confined to theoretical studies. In order to apply EGT towards advancing our understanding of evolving tumor populations, we decided to focus on the context of the emergence of resistance to targeted therapies, directed against EML4-ALK fusion gene in lung cancers, as clinical responses to ALK inhibitors represent a poster child of limitations, posed by evolving resistance. To this end, we have examined competitive dynamics between differentially labelled therapy-naive tumor cells, cells with cell-intrinsic resistance mechanisms, and cells with cell-extrinsic resistance, mediated by paracrine action of hepatocyte growth factor (HGF), within in vitro game assays in the presence or absence of front-line ALK inhibitor alectinib. We found that producers of HGF were the fittest in every pairwise game, while also supporting the proliferation of therapy-naive cells. Both selective advantage of these producer cells and their impact on total population growth was a linearly increasing function of the initial frequency of producers until eventually reaching a plateau. Resistant cells did not significantly interact with the other two phenotypes. These results provide insights on reconciling selection driven emergence of subpopulations with cell non-cell autonomous resistance mechanisms, with lack of evidence of clonal dominance of these subpopulations. Further, our studies elucidate mechanisms for co-existence of multiple resistance strategies within evolving tumors. This manuscript serves as a technical report and will be followed up with a research paper in a different journal.

cancer biology↗

bioRxiv2020

Neuronal Hyperexcitability is a DLK-dependent Trigger of HSV-1 Reactivation that can be Induced by IL-1

Herpes Simplex Virus (HSV) establishes a latent infection in neurons and periodically reactivates to cause disease. The neuronal stimuli that trigger HSV reactivation have not been fully elucidated. Here we demonstrate that HSV reactivation can be induced by neuronal hyperexcitability. Neuronal stimulation-induced reactivation was dependent on voltage-gated ion and hyperpolarization-activated cyclic nucleotide-gated (HCN) channels, demonstrating that neuronal activity is required for reactivation. Hyperexcitability-induced reactivation was dependent on the neuronal pathway of DLK/JNK activation and progressed via an initial wave of viral gene expression that was independent of histone demethylase activity and linked to histone phosphorylation. IL-1{beta} induces neuronal hyperexcitability and is released under conditions of stress and fever; both known triggers of clinical HSV reactivation. IL-1{beta} induced histone phosphorylation in sympathetic neurons, and importantly HSV reactivation, which was dependent on DLK and neuronal excitability. Thus, HSV co-opts an innate immune pathway resulting from IL-1 stimulation of neurons to induce reactivation.

microbiology↗

bioRxiv2020

Anti-tumor effects of an Id antagonist with no acquired resistance

Id proteins are helix-loop-helix (HLH) transcriptional regulators frequently overexpressed in cancer. Id proteins inhibit basic HLH transcription factors through protein-protein interactions, often inhibiting differentiation and sustaining proliferation. We recently identified a small-molecule, AGX51, which targets Id proteins for degradation and impairs ocular neovascularization in mouse models. Here we show that AGX51 treatment of cancer cell lines impaired cell growth and viability that results from a dramatic increase in ROS production upon Id degradation. In mouse models, AGX51 treatment suppressed breast cancer colonization in the lung, regressed the growth of paclitaxel-resistant breast tumors when combined with paclitaxel and reduced tumor burden in a model of sporadic colorectal neoplasia. Furthermore, in cells and mice, we failed to observe acquired resistance to AGX51 likely the result of the immutability of the binding pocket and efficient degradation of the Id proteins. Thus, AGX51 is a first-in-class compound that antagonizes Id proteins, shows strong anti-tumor effects and may be further developed for the management of multiple cancers.

cancer biology↗

bioRxiv2019

The Pipeline for Digital Analysis of IHC Images from NSCLC Xenograft Tissues

Multiple small molecule inhibitors and immunotherapy advances have shown success by prolonging patients survival in NSCLC but patient with metastasis or advanced stage of cancer often experiences relapse. Cancer associated fibroblast (CAFs), a major cellular component of tumor microenvironment plays key role in shaping solid tumors. In-vitro studies have reported that CAFs can blunt the effect of targeted therapies in tumor cells. The current study focuses on evaluating the impact of stromal protection by analyzing immunohistochemistry (IHC) images from xenograft experiment. The study investigates if the HGF-driven CAF mediated stromal protection in cancer cell contributes to the development of resistance to Alectinib. We utilized QuPath, a digital software to automatize the readout of proliferation rate of tumor cells and evaluate the impact of stromal protection.

cancer biology↗

bioRxiv2018

Resistance to ALK targeting therapies as a gradual Darwinian adaptation to inhibitor specific selective pressures

Despite high initial efficacy, therapies that target oncogenic kinases eventually fail in advanced, metastatic cancers. This failure in initially responsive tumors is the direct result of the evolution of drug resistance under therapy-imposed selective pressures. In contrast to the massive body of experimental research on the molecular mechanisms of resistance, understanding of its evolutionary origins and dynamics remains fragmented. Using a combination of experimental studies and mathematical modeling, we sought to dissect the evolution of resistance to different clinical ALK inhibitors in an experimental model of ALK positive NSCLC. We found that resistance can originate from heterogeneous, weakly resistant, sub-populations with variable sensitivity to different ALK inhibitors. Instead of the commonly assumed stochastic single hit (epi) mutational transition, or drug-induced reprogramming, we found evidence of a hybrid scenario, of gradual, multifactorial development through acquisition of multiple cooperating genetic and epigenetic adaptive changes, amplified by selection. Additionally, we found that intermediate resistance phenotypes might present unique, temporally restricted collateral sensitivities, absent in therapy naive or fully resistant cells, suggesting new opportunities for therapeutic interference.

cancer biology↗