Biology subjects

Chakravarti, S.

Publications and source records attributed to Chakravarti, S..

11 recordsLinked to original sources

bioRxiv2026

Dual inhibition of p38α MAPK and Casein kinase δ/ϵ as a novel treatment strategy for AR-independent and taxane-resistant advanced prostate cancer

Prostate cancer (PCa) is the most commonly diagnosed cancer and the second leading cause of cancer death among US men. Metastatic castration-resistant PCa (mCRPC) is a clinically advanced form of PCa, often associated with increased aggressiveness, metastatic potential, morbidity, and a higher risk of developing resistance to taxanes (TX), the first-line chemotherapy for mCRPC. Furthermore, cancer stemness and epithelial to mesenchymal trans-differentiation (EMT) potentially contribute to aggressiveness and the development of drug resistance in mCRPC. Here, we applied our drug development pipeline, secDrug, which utilizes a pharmacogenomics data-driven computational algorithm, to demonstrate that TAK-715 - a dual inhibitor of p38 MAPK and Casein kinase {delta}/{epsilon}, is a promising treatment for these advanced/lethal variants of PCa. Using in vitro cytotoxicity assays followed by cell-based functional assays in a panel of mCRPC cell lines representing TX-sensitive mCRPC, clonally derived TX-resistant lines, and a highly aggressive metastatic variant of mCRPC, we demonstrated the efficacy of TAK-715 treatment as a single agent and in combination with TX, including cancer stem-like cells. Further, we showed that the apoptotic effects of TAK-715 occur via a mitochondrial-mediated pathway. Bulk tumor RNA sequencing followed by pathway analysis identified genes associated with mitochondrial dysfunction and cell cycle arrest as the top molecular networks associated with TAK-715 single-treatment. HES1, a gene associated with nodal metastasis and PCa progression, was the top differentially expressed gene. Single-cell transcriptomics analysis revealed that TAK-715 treatment erodes the subclonal populations responsible for cancer stemness, metastasis, and drug resistance. The clinical significance of these findings was validated in silico using multiple patient datasets. Our results suggest that TAK-715 treatment has the potential to decrease oncogenic progression and cancer stem cell-like activity in drug-resistant, aggressive, and stem-like mCRPC cells.

cancer biology↗

bioRxiv2026

Extracellular matrix proteoglycans lumican and biglycan promote innate immune signals and viral clearance in HSV-1 infections of mouse corneas

The extracellular matrix (ECM) regulates innate immunity, but its role in HSV-1 keratitis is unclear. Here, we identify the ECM proteoglycans lumican (Lum) and biglycan (Bgn) as key regulators of early antiviral defense in the cornea. Lum-/- and BgnKO mice showed impaired viral clearance, increased corneal opacity, and worse keratitis than wild-type controls. These defects were associated with reduced early recruitment of neutrophils, monocytes, and plasmacytoid dendritic cells, and blunted induction of pro-inflammatory cytokines, chemokines, and type I interferons. In infected wild-type corneas, Lum and Bgn were upregulated, including in the basal epithelium, where Ccl2 emerged as an early epithelial response that was diminished in knockout mice. In human corneal epithelial cells, recombinant LUM or BGN enhanced HSV-1-induced CCL2 secretion, and human corneal organoids recapitulated epithelial viral tropism and CCL2 induction. Together, these findings identify Lum and Bgn as regulators of epithelial-innate immune crosstalk that promote early antiviral immunity during corneal HSV-1 infection.

immunology↗

bioRxiv2026

B7-H3-targeted natural killer cells effectively kill atypical teratoid / rhabdoid tumors and extend survival in orthotopic xenografts

BackgroundAtypical teratoid/rhabdoid tumors (AT/RTs) are the most common malignant CNS tumor in infants, and patients suffer from low survival rates and treatment-related morbidities. These tumors frequently overexpress the pan-cancer antigen B7-H3 (CD276), which can be targeted with immunotherapy. We hypothesized that adding a B7-H3-targeting cytotoxic chimeric antigen receptor (CAR) to NK cells can enhance killing against AT/RTs. MethodsWe designed a library of variable affinity B7-H3-targeted CARs, which were transduced into primary healthy donor-derived NK cells. We verified B7-H3 expression in a panel of AT/RT cell lines and further engineered luciferase and nuclear GFP-expressing AT/RT (CHLA-04, CHLA-06, BT12, BT37) as well as a CHLA-06-derived B7-H3 knockout. We tested CAR-NK cell functionality using in vitro co-culture cytotoxicity assays. We delivered anti-B7-H3 CAR-NK cells intratumorally or intracerebroventricularly (ICV) to AT/RT orthotopic xenografts and monitored for tumor growth and animal survival. ResultsB7-H3-targeted CAR-NK cells demonstrated target-specific cytotoxicity when compared to unmodified NK cells. Knockout of B7-H3 in target cells abolished the increased CAR-mediated target killing. When delivered intratumorally to CHLA-06 orthotopic xenograft-bearing mice, anti-B7-H3 CAR-NK cells eliminated tumor cells and prolonged survival. When CAR-NK cells were delivered ICV against a CNS disseminated tumor model of BT12, treated mice had significantly improved survival. ConclusionsAnti-B7-H3 CAR-NK cells effectively kill AT/RTs in multiple pre-clinical in vitro and in vivo models in an antigen-specific manner. Evidence of efficacy in translationally relevant models provides support for using B7-H3-targeting CAR-NK cells in high-risk AT/RT patients.

cancer biology↗

bioRxiv2025

Oxidative-stress related increase in keratoconus tear MDA and GPX3 while NRF2-antioxidant functions decrease in stromal cells

Keratoconus (KC) is a common eye disease where the cornea undergoes degenerative thinning and steepening. The absence of biomarkers for early diagnosis prior to the onset of overt corneal phenotypes and the lack of curative treatments rooted in a fundamental understanding of KC biology remain significant challenges. To address these issues, we investigated the role of unresolved oxidative stress in KC pathogenesis. Malondialdehyde (MDA) a lipid peroxidation byproduct that accumulates during oxidative stress was significantly elevated in the tears of KC patients compared to unaffected controls and positively correlated with maximal keratometry (Kmax), a measure of KC severity. Similarly, the secreted antioxidant glutathione peroxidase 3 (GPX3), was significantly increased in patient tears, and strongly correlated with Kmax. In a cell culture model of oxidative stress, KC corneal stromal cells displayed increased apoptosis and suboptimal activation of NRF2, a transcription factor master regulator of antioxidant genes. Conversely, inhibition of NRF2 in donor stromal cells elicited KC-like cellular phenotype, whereas sulforaphane, an NRF2 booster restored antioxidant gene expression and the deposition of cornea-typical collagens. Our study identified cellular antioxidant signaling dysregulations in keratoconus where sulforaphane treatment may be restorative. Consistent increases in patient tear MDA and GPX3 present these as promising biomarkers for KC diagnosis and severity predictions.

cell biology↗

bioRxiv2024

Paracrine regulations of IFN-γ secreting CD4+ T cells by lumican and biglycan are protective in allergic contact dermatitis

The extracellular matrix (ECM) is known to regulate innate immune cells but its role in T cell functions is poorly understood. Here, we show a protective role for ECM proteoglycans, lumican and biglycan in hapten-induced contact dermatitis that is achieved through limiting proinflammatory CD4+T cells. Lumican and biglycan-null mice develop significant inflammation with greater numbers of CD4+T cells in hapten-challenged ear pinnae, while their draining lymph nodes show increased T-bet-STAT1 signaling, Th1 commitment, and IFN-{gamma} secreting CD4+T cell proliferation. Wild type mouse lymph node fibroblastic reticular cells secrete lumican, biglycan and decorin, a related proteoglycan, while none are expressed by naive or activated T cells. In vitro, lumican and biglycan co-localize with LFA-1 on T cell surfaces, and all three proteoglycans suppress LFA-1 mediated T cell activation. Overall, this study elucidates a novel paracrine regulation of Th1 cells by ECM proteoglycans to limit inflammation and tissue damage.

immunology↗

bioRxiv2024

Evaluating the Effects of Aircraft Noise on Hearing and Physiological Indicators: A Study of Military Personnel Using iTRAQ Proteomics and Cognitive Assessments

BackgroundNoise pollution poses a significant public health risk, with prolonged exposure to high levels of noise linked to various adverse outcomes such as annoyance, sleep disturbances, cognitive impairment, hypertension, and cardiovascular diseases. Noise-induced hearing loss (NIHL) is a prominent concern in noisy occupational settings. MethodThis study investigated NIHL among 621 male Air Force soldiers aged 18-45, exposed to intense aircraft noise. Auditory assessments included pure-tone audiometry (125 Hz to 8 kHz) to categorize hearing into normal, mild, moderate, and severe impairment. Distortion product otoacoustic emissions (DPOAE) and auditory brainstem response (ABR) were used to evaluate cochlear and auditory nerve function. Heart rate variability (HRV) provided insights into autonomic responses. Cognitive functions were assessed through computerized tests, and blood plasma was analyzed for cardiac biomarkers, oxidative stress indicators, inflammatory markers, and neurotransmitters. Proteomic analysis used iTRAQ labeling, MudPIT, and MALDI-TOF/TOF mass spectrometry for protein quantification and identification, with validation through ELISA. ResultsThe audiometric tests revealed varying degrees of hearing impairment, with significant threshold differences at 2000, 3000, 4000, and 6000 Hz, especially pronounced at 6000 Hz. The right ear showed greater impairment, and a characteristic high-frequency notch was observed, consistent with noise exposure. Proteomic analysis indicated that NIHL is associated with oxidative stress and systemic inflammation, with differential protein expression related to hearing, coagulation, and inflammation. ConclusionThis study highlights the severe impact of aircraft noise on hearing and systemic health, demonstrating correlations between hearing impairment and biochemical markers. It emphasizes the role of oxidative stress and inflammation in NIHL development and underscores the need for effective noise management and protective measures in noisy work environments.

molecular biology↗

bioRxiv2024

Regulatory T cells and IFN-γ-producing Th1 cells play a critical role in the pathogenesis of Sjögren's Syndrome

ObjectivesSjogrens Disease (SjD) is an autoimmune disorder characterized by progressive dysfunction, inflammation and destruction of salivary and lacrimal glands, and by extraglandular manifestations. Its etiology and pathophysiology remain incompletely understood, though a role for autoreactive B cells has been considered key. Here, we investigated the role of effector and regulatory T cells in the pathogenesis of SjD. MethodsHistological analysis, RNA-sequencing and flow cytometry were conducted on glands, lungs, eyes and lymphoid tissues of mice with regulatory T cell-specific deletion of stromal interaction proteins (STIM) 1 and 2 (Stim1/2Foxp3), which play key roles in calcium signaling and T cell function. The pathogenicity of T cells from Stim1/2Foxp3mice was investigated through adoptively transfer into lymphopenic host mice. Additionally, single-cell transcriptomic analysis was performed on peripheral blood mononuclear cells (PBMCs) of patients with SjD and control subjects. ResultsStim1/2Foxp3 mice develop a severe SjD-like disorder including salivary gland (SG) and lacrimal gland (LG) inflammation and dysfunction, autoantibodies and extraglandular symptoms. SG inflammation in Stim1/2Foxp3 mice is characterized by T and B cell infiltration, and transcriptionally by a Th1 immune response that correlates strongly with the dysregulation observed in patients with SjD. Adoptive transfer of effector T cells from Stim1/2Foxp3 mice demonstrates that the SjD-like disease is driven by interferon (IFN)-{gamma} producing autoreactive CD4+ T cells independently of B cells and autoantiboodies. scRNA-seq analysis identifies increased Th1 responses and attenuated memory Treg function in PBMCs of patients with SjD. ConclusionsWe report a more accurate mouse model of SjD while providing evidence for a critical role of Treg cells and IFN-{gamma} producing Th1 cells in the pathogenesis of SjD, which may be effective targets for therapy.

immunology↗

bioRxiv2023

Single-cell analysis reveals lasting immunological consequences of influenza infection and respiratory immunisation in the pig lung

The pig is a natural host for influenza viruses and integrally involved in virus evolution through interspecies transmissions between humans and swine. Swine have many physiological, anatomical, and immunological similarities to humans, and are an excellent model for human influenza. Here, we employed single RNA-sequencing (scRNA-seq) and flow cytometry to characterize the major leucocyte subsets in bronchoalveolar lavage (BAL), twenty-one days after H1N1pdm09 infection or respiratory immunization with an adenoviral vector vaccine expressing haemagglutinin and nucleoprotein with or without IL-1{beta}. Mapping scRNA-seq clusters from BAL onto those previously described in peripheral blood facilitated annotation and highlighted differences between tissue resident and circulating immune cells. ScRNA-seq data and functional assays revealed lasting impacts of immune challenge on BAL populations. First, mucosal administration of IL-1{beta} reduced the number of functionally active Treg. Second, influenza infection upregulated IFI6 in BAL cells, decreasing their susceptibility to virus replication in vitro. Our data provides a reference map of porcine BAL cells and reveals lasting immunological consequences of influenza infection and respiratory immunisation in a highly relevant large animal model for respiratory virus infection. Author SummaryPigs and humans have a similar anatomy and physiology. In humans, cells from lung-washes are used to study immune responses and it was shown that these cells are crucial in protection against respiratory diseases such as influenza and COVID-19. To better understand lung immunity, we compared genes expressed in cells of pig lung-wash to white blood cells, providing an atlas for future studies of immunity in the lung. We also tested a vaccine given to the lung containing IL-1{beta}, a strong immune activator that protects mice against influenza virus infection. However, although IL-1{beta} increased pig immune responses it did not protect pigs against infection. We also showed that the number of immune cells that dampen immune responses (regulatory T cells) is reduced. In addition, we demonstrated increased expression of a protein, IFI6, 21 days after infection showing that while immune cells in the lung have common properties, the invading organisms influence them significantly. Our study elucidates why some vaccines fail despite inducing powerful immune responses, emphasizes the need for caution when applying results from small animals like mice to humans, and indicates the importance of the pig as a model to study disease in humans and livestock.

immunology↗

bioRxiv2023

3D modeling of CpG DNA binding with matrix lumican shows leucine-rich repeat motif involvement as in TLR9- CpG DNA interactions

Lumican is an extracellular matrix proteoglycan, known to regulate toll-like receptor (TLR) signaling in innate immune cells. In experimental settings, lumican suppresses TLR9 signaling by binding to, and sequestering its synthetic ligand, CpG-DNA, in non-signal permissive endosomes. However, the molecular details of lumican interactions with CpG-DNA are obscure. Here, the 3-D structure of the 22 base-long CpG-DNA (CpG ODN_2395) bound to lumican or TLR9 were modeled using homology modeling and docking methods. Some of the TLR9-CpG ODN_2395 features predicted by our model are consistent with the previously reported TLR9-CpG DNA crystal structure, substantiating our current analysis. Our modeling indicated a smaller buried surface area for lumican-CpG ODN_2395 (1803 A2) compared to that of TLR9-CpG ODN_2395 (2094 A2), implying a potentially lower binding strength for lumican and CpG-DNA than TLR9 and CpG-DNA. The docking analysis identified 32 amino acids in lumican LRR1-11 interacting with CpG ODN_2395, primarily through hydrogen bonding, salt-bridges and hydrophobic interactions. Our study provides molecular insights into lumican and CpG-DNA interactions that may lead to molecular targets for modulating TLR9 mediated inflammation and autoimmunity.

immunology↗

bioRxiv2022

Integrating pharmacogenomics data-driven prediction with bulk and single-cell RNAseq to demonstrate the efficacy of an NAMPT inhibitor against aggressive, taxane-resistant, and stem-like cells in lethal prostate cancer

Metastatic prostate cancer is the second leading cause of cancer deaths in US men. Resistance to standard medical castration and secondary taxane-based chemotherapy is nearly universal. Further, presence of cancer stem-like cells (EMT/epithelial to mesenchymal transdifferentiation) and neuroendocrine PCa (NEPC) subtypes significantly contribute to aggressive/advanced/lethal variants of PCa (AVPC). In this study, first we used single-cell RNA sequencing (scRNAseq) analysis to demonstrate that ARlow PCa cells in metastatic prostate cancer, including castration-sensitive tumors, harbored signatures of EMT, and cancer stemness. Next, we introduced a novel pharmacogenomics data-driven computational approach and identified several potential agents that can be re-purposed as novel secondary drugs ("secDrugs") to treat advance variants of Prostate cancer. Using scRNAseq as a biomarker-based drug screen, we demonstrated that a majority of the single-cell subclones in mCRPC and mCSPC cell lines also showed significantly high expression of the NAMPT pathway genes, indicating that the secDrug FK866, which targets NAMPT, is potentially effective against drug-resistant and stem-cell-like subpopulation cluster. Next, we showed significant in vitro cytotoxicity of FK866 as single-agent and in combination with the taxanes or Enzalutamide against models of clinically-advanced PCa. We performed bulk- and single-cell RNAseq to identify several pathways underlining FK866 mechanism of action and found that in addition to NAMPT inhibition, FK866 regulates tumor metastasis, cell migration, invasion, DNA repair machinery, redox homeostasis, autophagy, as well as cancer stemness-related genes HES1 and CD44. Further, we performed a microfluidic chip-based cell migration assay that demonstrated that FK866 reduces cancer cell invasion and motility, indicating abrogation of metastasis. Finally, using multiple PCa patient datasets, we showed that FK866 is potentially capable of reversing expression of several genes associated with biochemical recurrence and inter-ethnic differences, including IFITM3 and LTB4R. Thus, using FK866 as a proof-of-concept drug, we introduced a novel, universally applicable preclinical drug development pipeline to circumvent subclonal aggressiveness, drug resistance, and stemness in lethal PCa.

molecular biology↗

bioRxiv2021

Single cell RNA-seq identifies developing corneal cell fates in the human cornea organoid

The cornea is a protective and refractive barrier in the eye crucial for vision. Understanding the human cornea in health, disease and cell-based treatments can be greatly advanced with cornea organoids developed in culture from induced pluripotent stem cells. While a limited number of studies have investigated the single-cell transcriptomic composition of the human cornea, its organoids have not been examined similarly. Here we elucidated the transcriptomic cell fate map of 4 month-old human cornea organoids and the central cornea from three donors. The organoids harbor cell clusters representing corneal epithelium, stroma and endothelium with sub populations that capture signatures of early developmental states. Unlike the adult cornea where the largest cell population is stromal, the organoids develop almost equal proportion of the three major cell types. These corneal organoids offer a three-dimensional platform to model corneal diseases and integrated responses of the different cell types to treatments. TeaserTranscriptomic Map of Cornea Organoid and Human Cornea

developmental biology↗