Biology subjects

Jain, T.

Publications and source records attributed to Jain, T..

10 recordsLinked to original sources

bioRxiv2026

Inhibition of mucin-type O-glycosylation impairs melanogenesis, melanoma growth, and metastatic capacity

Tumor-associated glycans are critical regulators of immune evasion in melanoma. Despite the success of immune checkpoint blockade, resistance and relapse remain a challenge, highlighting the need to therapeutically target additional immunosuppressive axes. One such axis involves Siglec-sialoglycan interactions that facilitate tumor immune evasion. The melanoma-associated antigen Pmel17/gp100 is a melanosomal glycoprotein overexpressed in tumor cells and essential for melanosomal architecture. Pmel17/gp100 forms amyloid fibrils within melanosomes, and its extensive O-glycosylation contributes to melanin biosynthesis and melanoma progression. We show that pharmacological inhibition of O-glycosylation using peracetyl N-thioglycolyl-D-galactosamine (Ac5GalNTGc, 1a) decreases Pmel17/gp100 glycosylation and melanin synthesis in B16F10 melanoma cells, induces tumor surface hyposialylation, diminishes Siglec-E engagement, and disrupts the Siglec-sialoglycan immune checkpoint. In C57BL/6J mice, 1a significantly delayed tumor growth, prolonged survival, and reduced lung metastases relative to controls. These findings identify O-glycosylation as a dual-mode therapeutic vulnerability, linking melanosome dysfunction to attenuation of Siglec-mediated immune evasion in melanoma. SummaryMucin-type O-glycans on melanoma cell surfaces and the melanosomal protein, Pmel17/gp100, regulate melanogenesis and melanoma metastasis. The O-glycosylation inhibitor, peracetyl N-thioglycolyl-D-galactosamine (Ac5GalNTGc, 1a), suppressed melanin synthesis and induced hyposialylation, thereby disrupting Siglec-mediated immune evasion and retarding tumor growth and metastasis.

cancer biology↗

bioRxiv2025

Sensitive Transcriptomics and Genotyping reveals function of genetic variants in immunity

Advancements in genomics have revolutionized human genetics by defining the genetic architecture of disease. However, identifying causal variants and their mechanisms of action remains a challenge in translating genetics into therapeutic interventions. Here, we developed Sensitive Transcriptomics And Genotyping by sequencing (STAG-seq), a high-throughput platform designed to define mechanistic genotype-phenotype relationships through simultaneous single-cell measurements of genomic DNA and RNA transcripts. Combined with base-editing, STAG-seq enables functionalization of variants in relevant cellular contexts. We demonstrate the applicability of this approach in several settings. First, we screened genetic perturbations to identify monoallelic and biallelic variant effects in primary human macrophages treated with innate immune stimuli. Next, we phenotyped clinically relevant missense variants associated with immunodeficiency and autoimmunity. Finally, we defined a noncoding variant in a pleiotropic autoimmunity locus that governs TNRC18 expression in primary T cells. STAG-seq thus enables variant phenotyping at scale to advance functional genomics and disease biology.

genomics↗

bioRxiv2025

Tissue Engineering Applications for Novel Integrated and Mobile Perfusion System

Perfusion offers unique benefits to tissue-engineered systems, enhancing oxygen and nutrient transport which improves tissue formation and growth. In this study, we present a novel and integrated portable perfusion system, termed the FluidON. Weighing <10 lbs, the system can maintain continuous flow in a standard incubation environment (37{degrees}C, 5% CO2), effectively functioning as a portable perfusion and culture chamber. To test the systems perfusion parameters, we measured the volumetric flow rate across a range of pressures and found that the system could achieve flow as low as 0.40{+/-} 0.19uL/s, which is similar to in vivo interstitial flow. Computational fluid dynamics revealed uniform flow distribution, laminar flow, and gentle circulation, helping ensure even fluid and nutrient distribution. To study the biocompatibility of the system, bioengineered tissue patches were created and perfused. Viability was assessed through flow cytometry. The system does not adversely affect cell health as the viability of perfused samples was found to be 40.99{+/-}6.22% alive after 24 hours (n=4), while that of the static control was 38.56{+/-}4.22% alive (n=4). To determine the effects of perfusion on spheroid spatial arrangement, perfused tissue patches were analyzed with light microscopy. It was discovered that perfusion promoted spheroid aggregation and cohesion, causing the distance from one spheroid to its nearest neighbor to decrease after 24 hours of perfusion. Perfusion was also found to improve the strength of hydrogels as the average hole area, caused by hydrolytic enzymes that degrade the hydrogel matrix, was smaller in perfused conditions compared to the control. Complemented by its ability to provide mobile perfusion and incubation, this novel integrated portable perfusion system holds promise for promoting tissue maturation, elevating tissue bioengineering studies.

bioengineering↗

bioRxiv2025

Stress drives plasticity in leaf maturation transcriptional dynamics

Leaf development is dynamic, adapting to environmental stress to optimize resource use. For example, in response to drought, Arabidopsis restricts leaf growth to enhance water use efficiency. While this plastic response is well described at the physiological level, the underlying transcriptional changes that facilitate adjustments in leaf development in response to stress remain poorly described. By constructing a [~]1 million single-nuclei transcriptome atlas, we demonstrate that drought stress limits leaf growth by advancing transcriptional responses related to maturation and aging. Notably, we find that these transcriptional changes scale with environmental stress, and help explain how shoot size can decline proportionally with stress intensity. Leveraging these insights, we increased leaf growth under stress by cell-type targeted upregulation of FERRIC REDUCTION OXIDASE 6 in the mesophyll.

plant biology↗

bioRxiv2023

Sleep is required for neural network plasticity in the jellyfish Cassiopea

Sleep in animals plays roles that appear specific to the brain, including synaptic homeostasis [1], neurotransmitter regulation [2], cellular repair [3], memory consolidation [4], and neural plasticity [5,6]. Would any of these functions of sleep be relevant to an animal without a brain? The upside-down jellyfish Cassiopea xamachana, like other cnidarians, lacks a centralized nervous system, yet the animal sleeps [7]. By tracking the propensity of the radially spaced ganglia to initiate muscle contractions over several days we determined how neural activity changes between sleep and wake in a decentralized nervous system. Ganglia-network sleep/ wake activity patterns range from being highly specialized to a few ganglia, to being completely unspecialized. Ganglia specialization also changes over time, indicating a high degree of plasticity in the neural network. The ganglia that lead activity can persist or switch between sleep/wake transitions, signifying a level of local control of the behavioral state in a decentralized nervous system. Following sleep deprivation, ganglia usage becomes far more sleep specialized, demonstrating reduced network plasticity. Together, these findings identify a novel behavioral control system that is decentralized and yet displays temporal specialization and centralization, and show a role for sleep in maintaining neural network plasticity, revealing a conserved function of sleep in this brain-less animal.

neuroscience↗

bioRxiv2022

Wireless closed-loop smart bandage for chronic wound management and accelerated tissue regeneration

Chronic non-healing wounds represent a major source of morbidity for patients and a significant economic burden. Current wound care treatments are generally passive and are unable to adapt to changes in the wound environment in real time. By integrating multimodal sensors and adding stimulators in a bandage, real-time physiological monitoring is possible and provides an opportunity for active intervention into the complex wound environment. Here, we develop a battery-free flexible bioelectronic system consisting of wirelessly powered, closed-loop sensing and stimulation circuits with tissue-interfacing tough conducting hydrogel electrodes for robust signal transduction, on-demand adhesion, and detachment. Using multiple pre-clinical models, we demonstrate the capability of our wound care system to continuously monitor skin impedance and temperature, to trigger directional electrical stimulation. The accelerated wound closure was confirmed to be due to the activation of pro-regenerative genes linked to accelerated wound closure, increased neovascularization, and enhanced dermal recovery.

bioengineering↗

bioRxiv2021

Glycan engineering using synthetic ManNAc analogues enhances sialyl-Lewis-X expression and adhesion of leukocytes

Sialyl-Lewis-X (sLeX/CD15s) epitopes regulate cell adhesion via interactions with selectins. High levels of sLeX are associated with chronic inflammation. Intense efforts have been devoted for the development of sLeX mimetics for the prevention of atherosclerosis. By contrast, low levels of sLeX are associated with leukocyte adhesion deficiency (LAD) disorders. In this context, we employed metabolic glycan engineering to alter the fine structures of sialoglycans. Treatment of HL-60 (human acute myeloid leukemia) cells with peracetyl N-cyclobutanoyl-D-mannosamine (Ac4ManNCb) resulted in a four-fold increase in both sLeX levels and adhesion to E-selectin-Fc chimera. Enhanced sLeX levels on CD162/PSGL-1, CD43, and CD44 were observed through immunoprecipitation. Molecular dynamics (MD) simulations on interactions with E-selectin revealed dramatic differentials in the conformational dynamics of sLeX-Cb compared to sLeX, highlighting the significance of remote N-acyl side chains of sialic acids in facilitating bio-active conformations. These results provide opportunities for pharmacological interventions in both LAD and chronic inflammation. Table of Contents O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=83 SRC="FIGDIR/small/473788v2_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@172ab54org.highwire.dtl.DTLVardef@14e45acorg.highwire.dtl.DTLVardef@1c05c65org.highwire.dtl.DTLVardef@1f2056e_HPS_FORMAT_FIGEXP M_FIG C_FIG Remote substituents on the tetrasaccharide sialyl-Lewis X (sLeX / CD15s) influence ensembles of bio-active conformations and alter biological outcomes. Treatment with peracetyl N-cyclobutanoyl-D-mannosamine (Ac4ManNCb) results in four-fold enhancement in the expression of sialyl-Lewis-X (sLeX / CD15s) and adhesion to E-selectin (CD62E). Molecular dynamics simulations show that the sLeX-Cb prefers a flatter bio-active conformation (gray) compared to wild-type sLeX (cyan). Institute and/or researcher Twitter usernames: @NImmunology @Gops_GlycoIndia

biochemistry↗

bioRxiv2021

Cyclic Microchip Assay for Measurement of Hundreds of Functional Proteins in Single Neurons

Proteins are responsible for nearly all cell functions throughout cellular life. To date, the molecular functions of hundreds of proteins have been studied as they are critical to cellular processes. Those proteins are varied dramatically at different statuses and differential stages of the cells even in the same tissue. The existing single-cell tools can only analyze dozens of proteins and thus have not been able to fully characterize a cell yet. Herein, we present a single-cell cyclic multiplex in situ tagging (CycMIST) technology that affords the comprehensive functional proteome profiling of single cells. It permits multiple, separate rounds of multiplex assays of the same single cells on a microchip where each round detects 40-50 proteins. A decoding process is followed to assign protein identities and quantify protein detection signals. We demonstrate the technology on a neuron cell line by detecting 182 proteins that includes surface makers, neuron function proteins, neurodegeneration markers, signaling pathway proteins and transcription factors. Further study on 5XFAD mouse, an Alzheimers Disease (AD) model, cells validate the utility of our technology which reveals the deep heterogeneity of brain cells. Through comparison with control mouse cells, the differentially expressed proteins in the AD mouse model have been detected. The single-cell CycMIST technology can potentially analyze the entire functional proteome spectrum, and thus it may offer new insights into cell machinery and advance many fields including systems biology, drug discovery, molecular diagnostics, and clinical studies.

bioengineering↗

bioRxiv2020

Cocculus hirsutus -derived phytopharmaceutical drug has potent anti-dengue activity

BackgroundDengue is a serious public health concern worldwide, with ~3 billion people at risk of contracting dengue virus (DENV) infections. Currently, no effective vaccine or drug is available for the prevention or treatment of dengue, which leaves only anti-mosquito strategies to combat this disease. The present study was initiated to determine the in-vitro and in vivo protective effects of a plant-derived phytopharmaceutical drug for the treatment of dengue. Methodology/Principal FindingsIn our previous report, we had identified methanolic extract of the aerial parts of Cissampelos pareira to exhibit in vitro and in vivo anti-dengue activity against all the four DENV serotypes. In the current study, we have identified another Indian medicinal plant, Cocculus hirsutus, which has a more potent anti-dengue activity than C. pareira. The activity has been evaluated through flow-cytometry-based virus inhibition assay. Interestingly, the stem of C. hirsutus was found to be more potent than the aerial part irrespective of the extraction solvent used viz., denatured spirit, hydro-alcohol (50:50) and water. Hence, the aqueous extract of stem of C. hirsutus (AQCH) was further advanced for investigations because of greater regulatory acceptance. The AQCH exhibited dose-dependent inhibition of release of DENV and its secretory antigen, NS1. Five chemical markers viz. Sinococuline, 20-Hydroxyecdysone, Makisterone-A, Magnoflorine and Coniferyl alcohol were identified as the major chemical ingredients of the AQCH extract. These chemicals were subsequently used for extract standardisation. Importantly, AQCH completely protected AG129 mice at 25 mg/kg/dose body weight when fed 4 times a day post-infection with a lethal dose of DENV-2 S221 strain. Because of its potential as an effective phytopharmaceutical drug against dengue, AQCH, has been formulated into tablets for further pre-clinical and clinical developments. Conclusions/SignificanceWe provide evidence of the pan anti-dengue potential of C. hirsutus-based phytopharmaceutical drug as determined through in vitro and in vivo experiments. We have also characterized five chemical entities in the drug substance, which provides means for standardization of drug substance and drug product. Based on these findings, a program to develop a safe and effective C. hirsutus-derived phytopharmaceutical drug for the treatment of dengue has been initiated. Author summaryThere is an urgent need to develop a safe and effective drug against dengue, which is a rapidly expanding mosquito-borne viral disease. Half of the worlds population has been estimated to be at risk of contracting this disease and the situation remains grim due to lack of an approved drug. We aimed to develop an ethnopharmacological drug against dengue by exploring traditional Indian medicinal science, Ayurveda. This led us to identify a creeper, Cocculus hirsutus, as a more potent anti-dengue plant than Cissampelos pareira, reported in our earlier published study. The stem part of C. hirsutus was found to be more efficacious in inhibiting the propagation of dengue viruses (DENVs) in cell culture than its aerial part. Hence, we chose to advance aqueous extract of stem of C. hirsutus (AQCH) for further studies. Importantly, AQCH also protected immune-compromised mice from lethal DENV infection, which is suggestive of its potential clinical relevance. We have identified five chemical marker compounds in AQCH to gauge the quality and consistency of extract preparation and its formulation into stable tablets. Based on the findings of this study, we have undertaken the development of a safe and effective C. hirsutus-derived phytopharmaceutical drug for the treatment of dengue.

microbiology↗

bioRxiv2019

CD49f is a novel marker to purify functional human iPSC-derived astrocytes

Astrocytes play a central role in the central nervous system (CNS), maintaining brain homeostasis, providing metabolic support to neurons, regulating connectivity of neural circuits, and controlling blood flow as an integral part of the blood-brain barrier. They have been increasingly implicated in the mechanisms of neurodegenerative diseases, prompting a greater need for methods that enable their study. The advent of human induced pluripotent stem cell (iPSC) technology has made it possible to generate patient-specific astrocytes and CNS cells using protocols developed by our team and others as valuable disease models. Yet isolating astrocytes from primary specimens or from in vitro mixed cultures for downstream analyses has remained challenging. To address this need, we performed a screen for surface markers that allow FACS sorting of astrocytes. Here we demonstrate that CD49f is an effective marker for sorting functional human astrocytes. We sorted CD49f+ cells from a protocol we previously developed that generates a complex culture of oligodendrocytes, neurons and astrocytes from iPSCs. CD49f+-purified cells express all canonical astrocyte markers and perform characteristic functions, such as neuronal support and glutamate uptake. Of particular relevance to neurodegenerative diseases, CD49f+ astrocytes can be stimulated to take on an A1 neurotoxic phenotype, in which they secrete pro-inflammatory cytokines and show an impaired ability to support neuronal maturation. This study establishes a novel marker for isolating functional astrocytes from complex CNS cell populations, strengthening the use of iPSC-astrocytes for the study of their regulation and dysregulation in neurodegenerative diseases.

neuroscience↗