Biology subjects

Sundaram, S.

Publications and source records attributed to Sundaram, S..

13 recordsLinked to original sources

bioRxiv2025

Evaluating the therapeutic efficacy of the US FDA-designated Orphan drug, uttroside B in impeding hepatocarcinogenesis via induction of immunogenic apoptosis, using a murine model of Aflatoxin B1-induced liver carcinogenesis

The sustained exposure to aflatoxin B1 (AFB1), a mycotoxin produced by Aspergillus sp., is one of the fundamental causes of hepatocellular carcinoma (HCC). We have previously documented the exceptional anti-HCC potential and pharmacological safety of uttroside B, a phytosaponin isolated in our lab (Utt-B). The current results indicate that Utt-B mitigates tumor development in mice that have been subjected to AFB1 exposure. Utt-B was found to be cytotoxic towards primary liver cancer cells cultured from mice bearing AFB1-induced liver tumors and the compound effectively prevented the formation of AfBO-DNA adducts in AFB1-induced liver tumors as well as primary liver cancer cells. In vitro studies revealed that treatment with Utt-B resulted in the induction of damage associated molecular patterns such as, ROS, HSP70 and inflammatory cytokines, IL-1{beta} and CXCL-10, suggesting the potential of Utt-B in triggering immunogenic cell death. Mechanistically, treatment with Utt-B enhances the antigen presentation potential, causes blockade of the major immune checkpoint molecules, namely, CTLA-4, PD-1, TIM-3, LAG-3 and TOX, and potentiates immunogenic apoptosis in the hepatic tumor microenvironment of mice pre-exposed to AFB1 via the activation of Zap70/Lck/GRZB signaling axis. Interestingly, it was also observed that Utt-B could abrogate the mutations induced by AFB1 in a concentration dependent manner. Taken together, the findings of the current study attest Utt-B as a propitious drug candidate against HCC.

cancer biology↗

bioRxiv2025

Uttroside B, a US FDA-designated Orphan drug, mitigates thedevelopment of hepatocellular carcinoma and its pulmonary metastasis via EGFR/ERK-mediated inhibition of SREBP-1 and STAT-3

Hepatocellular carcinoma (HCC) is a highly aggressive tumor with rapid propensity for extrahepatic metastasis, which critically limits the long-term clinical benefits of conventional chemotherapeutics and decreases the overall survival rate of patients. Our previous findings on the exceptional anti-HCC potential and pharmacological safety of uttroside B (Utt-B) have gained multiple international patents and the compound has been designated as an Orphan Drug against HCC by the US FDA. The current study substantiates the pharmacodynamics of Utt-B and is the first report to date on the anti-metastatic potential of the compound against HCC. Herein, we demonstrate the role of EGFR/ERK signaling axis and their downstream targets SREBP-1 and STAT-3, the key regulators of HCC development and the pulmonary metastasis, respectively, in orchestrating the anti-HCC and anti-metastatic potential of Utt-B. This is evidenced by the abrogation of the cytotoxic and pro-apoptotic effects of Utt-B upon pharmacological inhibition of this signaling axis. Orthotopic xenograft studies validated that Utt-B treatment restricted the development of tumors via the down-regulation of EGFR/ERK axis. Notably, Utt-B diminishes the migratory and invasive properties of liver cancer cells in vitro and impedes the pulmonary metastasis of HCC, in vivo. Taken together, the current findings attest to the exceptional therapeutic potential of Utt-B against primary and metastatic HCC and highlight its potential as a candidate drug to be evaluated in the clinics for the benefit of HCC patients having limited prognosis and therapeutic options.

cancer biology↗

bioRxiv2025

HO-3867 mediated modulation of Extracellular vesicles and Tumor microenvironment: A novel immunotherapeutic strategy for ovarian cancer

IntroductionOvarian cancer (OC) remains the most lethal gynecologic malignancy, with poor long-term survival, largely due to its diagnosis at advanced stages and its high rate of recurrence with resistance to platinum therapies. This study evaluates the therapeutic efficacy of HO-3867, a STAT3 inhibitor, and bevacizumab, an anti-VEGF antibody, alone and in combination in an immunocompetent (IC) syngeneic ovarian cancer progression model. MethodsThe ability of HO-3867 to induce macrophage polarization was assessed in RAW264.7 cells, while its impact on anti-tumor immunity was evaluated in splenocytes co-cultured with ID8 and OC ascites cells. Immune modulation, including cytokine induction, extracellular vesicle (EV) release, and endosomal sorting complex required for transport (ESCRT) protein expression, was analyzed in-vitro and using in-vivo OC model. The therapeutic effects of HO-3867 and bevacizumab were examined in vivo by measuring ascites volume, EV secretion levels, and immune cell populations via flow cytometry. ResultsOur results demonstrate that combination therapy significantly reduced ascites accumulation, and limited peritoneal disease spread in ovarian cancer mouse models. EV analysis revealed a decrease in total EVs and CD9+ subpopulations, which correlated with the associated ESCRT proteins involved in EV formation and secretion implicating EVs in tumor progression and immune modulation. Flow cytometry analysis of ascites immune cell populations showed that combination therapy reduced myeloid-derived suppressor cells (MDSCs) and their PD-L1 expression, while enhancing CD8+ T cell cytotoxicity via granzyme B secretion. Cytokine profiling revealed upregulation of IFN-{gamma} and downregulation of IL-6, IL-10 and CXCL-2 suggesting enhanced anti-tumor immune response. Furthermore, HO-3867 promoted macrophage polarization toward tumoricidal M1 phenotype and reduced MDSC expansion in-vitro, enhancing anti-tumor immunity. ConclusionHO-3867 and bevacizumab synergistically reprogram the tumor microenvironment, inhibit EV-mediated progression, and enhance antitumor immunity. These findings support its immunomodulatory potential in ovarian cancer ascites, offering a promising therapeutic strategy.

cancer biology↗

bioRxiv2025

Ectodysplasin overexpression reveals spatiotemporally dynamic tooth formation competency in stickleback and zebrafish

Organ initiation is often driven by extracellular signals that activate precursor cells competent to receive and respond to the signal, yet little is known about how dynamic competency is in space and time during development. Teeth are excellent organs to study organ initiation competency because they can be activated with the addition of a single signaling ligand, Ectodysplasin (Eda). Eda, a Tumor Necrosis Factor (TNF) ligand, is a critical regulator of ectodermal organ development, including teeth, acting through TNF receptors, like Edar, to activate NF-{kappa}B signaling in tooth precursor cells. While Eda is both necessary for normal tooth formation and sufficient for ectopic tooth formation, the spatial and temporal dynamics of competency for ectopic tooth initiation and maintenance remains unknown. To investigate the role of Eda in tooth specification, we generated transgenic sticklebacks and zebrafish with heat shock-inducible Eda overexpression. We find that stickleback Eda can drive de novo tooth formation in at least eight distinct oropharyngeal and cranial domains. Both zebrafish and stickleback exhibit maximal responsiveness to Eda overexpression during the critical window of pioneer tooth initiation, highlighting that the precursors of ectopic pharyngeal teeth likely follow a similar developmental trajectory as endogenous tooth precursors. Furthermore, we observe that some induced dental fields often undergo tooth regeneration to maintain themselves, allowing them to persist for months after the cessation of transgene activation. Finally, analysis of TNF receptor expression in sticklebacks reveals that ectopic tooth formation in the pharynx correlates with Edar and Troy expression, while in the region where teeth can form on the face, only Troy expression was detected, providing a possible molecular mechanism of competency involving spatially restricted receptor expression. These findings underscore the latent developmental potential, i.e. competency, of the vertebrate dentition and provide insights into organ competency during embryonic and post-embryonic development.

developmental biology↗

bioRxiv2024

Uttroside B, a US-FDA-Designated Orphan Drug Against Hepatocellular Carcinoma (HCC), Impedes Non-alcoholic Steatohepatitis (NASH) and NASH -Induced HCC

IntroductionNon-alcoholic steatohepatitis (NASH) is characterized by excessive accumulation of fat, accompanied by inflammation and liver injury. NASH can lead to chronic conditions like fibrosis and cirrhosis, and has an elevated risk of progressing to hepatocellular carcinoma (HCC). Currently there are no FDA-approved drugs for the treatment of NASH. ObjectivesOur discovery of Uttroside B (Utt-B), a phytosaponin isolated from Solanum nigrum Linn., which exhibits remarkable anti-HCC potential, has gained global recognition and is currently a US-FDA-designated orphan drug against HCC. The present study highlights Utt-B as an anti-NASH molecule, by utilizing a High-Fat-Diet murine model, and as an inhibitor to the progression of NASH to HCC, using a streptozotocin-induced steatohepatitis-derived HCC animal model, thereby warranting its further validation as a propitious candidate drug molecule against NASH and NASH-induced HCC. MethodsHigh fat diet-induced NASH and streptozotocin-induced steatohepatitis-derived HCC were developed in C57BL/6 mice. Utt-B was administered intraperitoneally. q-PCR, immunoblotting and staining techniques such as Haematoxylin and eosin, Oil Red O, Sirius Red and Massons Trichrome, were performed to assess the therapeutic potency of Utt-B against NASH. Nanostring n-Counter analysis was conducted to verify the anti-fibrotic potential of Utt-B in NASH-induced HCC mouse model. ResultsUtt-B ameliorates the pathological features such as, steatosis, hepatocyte ballooning and inflammation associated with NASH. Utt-B up-regulates the expression of autophagy markers ATG7, Beclin-1 and LC-III and down-regulates the expression of -SMA, the indicator protein for the activation of hepatic stellate cells. Utt-B hinders the development of fibrosis and halts the progression of NASH to HCC in NASH-induced HCC mouse model. ConclusionOur investigation reveals that Utt-B effectively alleviates NASH and abrogates its progression to HCC. As no treatment options are currently available against NASH, our findings are very relevant and strengthen the prospect of developing Utt-B as a potent drug for the treatment of NASH and NASH-induced HCC. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/622394v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@1d637dcorg.highwire.dtl.DTLVardef@ed6b34org.highwire.dtl.DTLVardef@1195acaorg.highwire.dtl.DTLVardef@197b072_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

Nonlinear EEG Analysis for Distinguishing Mind Wandering and Focused Attention: A Machine Learning Approach

This study uses nonlinear analysis techniques to distinguish between mind wandering (MW) and focused attention (FA) states using EEG data. EEG recordings from 21 sessions were segmented into intervals of 2, 3, 5, 6, 10, and 15 seconds, and seven nonlinear features were extracted to capture the brains dynamic complexity. Machine learning models, including gradient boosting trees, were applied to classify MW and FA states, with the highest accuracy of 75% achieved using 5-second segments. Frequency-related features, particularly mean frequency and global frequency, were the most important in distinguishing between MW and FA. These findings emphasize the role of nonlinear EEG analysis in understanding the chaotic brain patterns underlying cognitive states. Future work should focus on temporal dynamics and personalized models to improve classification accuracy, with potential applications in cognitive enhancement and mental health.

bioinformatics↗

bioRxiv2024

Three-dimensional flow assessment of microvascular beds with interstitial space

The health and function of microvascular beds are dramatically impacted by the mechanical forces that they experience due to fluid flow. These fluid flow-generated forces are challenging to measure directly and are typically calculated from experimental flow data. However, current computational fluid dynamics (CFD) models either employ truncated 2D models or overlook the presence of extraluminal flows within the interstitial space between vessels that result from the permeability of the endothelium lining the vessels, which are crucial components affecting flow dynamics. To address this, we present a bottom-up modeling approach that assesses fluid flow in 3D-engineered vessel networks featuring an endothelial lining and interstitial space. Using image processing algorithms to segment 3D confocal image stacks from engineered capillary networks, we reconstructed a 3D computational model of the networks. We incorporated vascular permeability and matrix porosity values to model the contributions of the endothelial lining and interstitial spaces to the flow dynamics in the networks. Simulations suggest that including the endothelial monolayer and the interstitium significantly affects the predicted flow magnitude in the vessels and flow profiles in the interstitium. To demonstrate the importance of these factors, we showed experimentally and computationally that while cytokine (IL-1{beta}) treatment did not affect the network architecture, it significantly increased vessel permeability and resulted in a dramatic decrease in wall shear stresses and flow velocities intraluminally within the networks. In conclusion, this framework offers a robust methodology for studying flow dynamics in 3D in vitro vessel networks, enhancing our understanding of vascular physiology and pathology. TRANSLATIONAL IMPACT STATEMENTThis study introduces a new approach to modeling and flow assessment in 3D microvascular beds and surrounding interstitial spaces. Modeling interstitial space and endothelial monolayer thickness is essential for capturing fluid leakage from the microvascular network into the interstitial space and vice versa when the endothelial monolayer permeability is significantly affected in pathological conditions. Our approach to modeling 3D vascular networks can be used in vivo and in clinical settings to understand flow in tissue microvasculature and its surroundings under disease and healthy conditions.

bioengineering↗

bioRxiv2022

Computationally restoring the potency of a clinical antibody against SARS-CoV-2 Omicron subvariants

The COVID-19 pandemic underscored the promise of monoclonal antibody-based prophylactic and therapeutic drugs1-3, but also revealed how quickly viral escape can curtail effective options4, 5. With the emergence of the SARS-CoV-2 Omicron variant in late 2021, many clinically used antibody drug products lost potency, including EvusheldTM and its constituent, cilgavimab4, 6. Cilgavimab, like its progenitor COV2-2130, is a class 3 antibody that is compatible with other antibodies in combination4 and is challenging to replace with existing approaches. Rapidly modifying such high-value antibodies with a known clinical profile to restore efficacy against emerging variants is a compelling mitigation strategy. We sought to redesign COV2-2130 to rescue in vivo efficacy against Omicron BA.1 and BA.1.1 strains while maintaining efficacy against the contemporaneously dominant Delta variant. Here we show that our computationally redesigned antibody, 2130-1-0114-112, achieves this objective, simultaneously increases neutralization potency against Delta and many variants of concern that subsequently emerged, and provides protection in vivo against the strains tested, WA1/2020, BA.1.1, and BA.5. Deep mutational scanning of tens of thousands pseudovirus variants reveals 2130-1-0114-112 improves broad potency without incurring additional escape liabilities. Our results suggest that computational approaches can optimize an antibody to target multiple escape variants, while simultaneously enriching potency. Because our approach is computationally driven, not requiring experimental iterations or pre-existing binding data, it could enable rapid response strategies to address escape variants or pre-emptively mitigate escape vulnerabilities.

microbiology↗

bioRxiv2022

Modulation of tooth regeneration through opposing responses to Wnt and BMP signals in teleosts

Most vertebrate species undergo tooth replacement throughout adult life. This process is marked by the shedding of existing teeth and the regeneration of tooth organs. However, little is known about the genetic circuitry regulating tooth replacement. Here we tested whether fish orthologs of genes known to regulate mammalian hair regeneration have effects on tooth replacement. Using two fish species that demonstrate distinct modes of tooth regeneration, threespine stickleback (Gasterosteus aculeatus) and zebrafish (Danio rerio), we found that transgenic overexpression of four different genes changed tooth replacement rates in direction predicted by a hair regeneration model: Wnt10a and Grem2a increased tooth replacement rate, while Bmp6 and Dkk2 strongly inhibited tooth formation. Thus, similar to known roles in hair regeneration, Wnt and BMP signals promote and inhibit regeneration, respectively. Regulation of total tooth number was separable from regulation of replacement rates. RNA-seq on stickleback dental tissue showed that Bmp6 overexpression resulted in an upregulation of Wnt inhibitors. Together these data support a model where different epithelial organs like teeth and hair share genetic circuitry driving organ regeneration.

developmental biology↗

bioRxiv2022

Augmented efficacy of uttroside B over sorafenib in a murine model of human hepatocellular carcinoma

BackgroundWe previously reported the potency of S. nigrum-derived uttroside B (Utt-B). Recently Utt-B is flagged as an orphan drug against hepatocellular carcinoma (HCC) by the US FDA. The current study aims to validate the enhanced in vivo efficacy of Utt-B over sorafenib, the first-line treatment option against HCC. MethodsHuman liver cancer cell line, HepG2 was employed as an HCC model and the comparison between Utt-B vs sorafenib therapeutic efficacies against HCC in vivo were evaluated in NOD.CB17-Prkdcscid/J mice that bear HepG2-induced HCC xenografts. ResultsOur data indicate that Utt-B is a more potent anti-HCC drug than sorafenib, in vivo. Apart from the superior therapeutic benefit over sorafenib, Utt-B is pharmacologically safer in vivo, and owing to this virtue, the drug-induced side effects are largely alleviated in the context of HCC chemotherapy. ConclusionsOur data demonstrate the superior therapeutic index of Utt-B over sorafenib against HCC. Clinical studies in HCC patients utilizing Utt-B, which now holds the US FDA approval as an orphan drug, is an essential step to promote this drug from bench to bedside.

cancer biology↗

bioRxiv2021

SARS-COV-2 Omicron variant predicted to exhibit higher affinity to ACE-2 receptor and lower affinity to a larger range of neutralizing antibodies, using a rapid assessment platform

Rapid assessment of whether a pandemic pathogen may have increased transmissibility or be capable of evading existing vaccines and therapeutics is critical to mounting an effective public health response. Over the period of seven days, we utilized rapid computational prediction methods to evaluate potential public health implications of the emerging SARS-CoV-2 Omicron variant. Specifically, we modeled the structure of the Omicron variant, examined its interface with human angiotensin converting enzyme 2 (ACE-2) and evaluated the change in binding affinity between Omicron, ACE-2 and publicly known neutralizing antibodies. We also compared the Omicron variant to known Variants of Concern (VoC). Seven of the 15 Omicron mutations occurring in the spike protein receptor binding domain (RBD) occur at the ACE-2 cell receptor interface, and therefore may play a critical role in enhancing binding to ACE-2. Our estimates of Omicron RBD-ACE-2 binding affinities indicate that at least two of RBD mutations, Q493R and N501Y, contribute to enhanced ACE-2 binding, nearly doubling delta-delta-G (ddG) free energies calculated for other VoCs. Binding affinity estimates also were calculated for 55 known neutralizing SARS-CoV-2 antibodies. Analysis of the results showed that Omicron substantially degrades binding for more than half of these neutralizing SARS-CoV-2 antibodies, and for roughly 10 times as many of the antibodies than the currently dominant Delta variant. This early study lends support to use of rapid computational risk assessments to inform public health decision-making while awaiting detailed experimental characterization and confirmation.

bioinformatics↗

bioRxiv2020

Distinct tooth regeneration systems deploy a conserved battery of genes

BackgroundVertebrate teeth exhibit a wide range of regenerative systems. Many species, including most mammals, reptiles, and amphibians, form replacement teeth at a histologically distinct location called the successional dental lamina, while other species do not employ such a system. Notably, a lamina-less tooth replacement condition is found in a paraphyletic array of ray-finned fishes, such as stickleback, trout, cod, medaka, and bichir. Furthermore, the position, renewal potential, and latency times appear to vary drastically across different vertebrate tooth regeneration systems. The progenitor cells underlying tooth regeneration thus present highly divergent arrangements and potentials. Given the spectrum of regeneration systems present in vertebrates, it is unclear if morphologically divergent tooth regeneration systems deploy an overlapping battery of genes in their naive dental tissues. ResultsIn the present work, we aimed to determine whether or not tooth progenitor epithelia could be composed of a conserved cell type between vertebrate dentitions with divergent regeneration systems. To address this question, we compared the tooth regeneration processes in two ray-finned fishes: zebrafish (Danio rerio) and threespine stickleback (Gasterosteus aculeatus). These two teleost species diverged approximately 250 million years ago, and demonstrate some stark differences in dental morphology and regeneration. Here we find that the successional dental lamina in zebrafish sharply upregulates Wnt signaling and Lef1 expression during early morphogenesis stages of tooth development. Additionally, the naive zebrafish successional dental lamina expresses a battery of nine genes (Bmpr1a, Bmp6, CD34, Gli1, Igfbp5a, Lgr4, Lgr6, Nfatc1, and Pitx2). We also find that, despite the absence of a histologically distinct successional dental lamina in stickleback tooth fields, new tooth germs also sharply upregulate Wnt signaling and Lef1 expression, and additionally express the same battery of nine genes in the basalmost endodermal cell layer from which replacement tooth epithelia arise. Thus, two fish systems that either have an organized successional dental lamina (zebrafish) or lack a morphologically distinct successional dental lamina (sticklebacks) deploy similar genetic programs during tooth regeneration. ConclusionsWe propose that the expression domains described here delineate a highly conserved "successional dental epithelium" (SDE). Furthermore, a set of orthologous genes is known to mark hair follicle epithelial stem cells in mice, suggesting that regenerative systems in other epithelial appendages may utilize a related epithelial progenitor cell type, despite the highly derived nature of the resulting functional organs.

developmental biology↗

bioRxiv2019

The Golgi Glycoprotein MGAT4D Protects Testicular Germ Cells From Mild Heat Stress

Male germ cells are sensitive to heat stress and testes must be maintained outside the body for optimal fertility. However, no germ cell intrinsic mechanism that protects from heat has been reported. Here, we identify the germ cell specific Golgi glycoprotein MGAT4D as a protector of male germ cells from heat stress. Mgat4d is highly expressed in spermatocytes and spermatids. Unexpectedly, when the Mgat4d gene was inactivated globally or conditionally in spermatogonia, or mis-expressed in spermatogonia, spermatocytes or spermatids, neither spermatogenesis nor fertility were affected. On the other hand, when males were subjected to mild heat stress of the testis (43{degrees}C for 25 min), germ cells with inactivated Mgat4d were markedly more sensitive to the effects of heat stress, and transgenic mice expressing Mgat4d were partially protected from heat stress. Germ cells lacking Mgat4d generally mounted a similar heat shock response to control germ cells, but could not maintain that response. Several pathways activated by heat stress in wild type were induced to a lesser extent in Mgat4d[-/-] heat-stressed germ cells (NF{kappa}B response, TNF and TGF{beta} signaling, Hif1 and Myc genes). Thus, the Golgi glycoprotein MGAT4D is a novel, intrinsic protector of male germ cells from heat stress.

developmental biology↗