Biology subjects

Samanta, A.

Publications and source records attributed to Samanta, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Differential Impact of Isoflurane and Propofol on Apoptotic Regulation of Helper T cells

BackgroundAnesthetic agents administered during surgery are one of the key perioperative factors affecting immune modulation in cancer patients. This comparative study elucidated the mechanisms by which the volatile anesthetic, isoflurane and the intravenous anesthetic, propofol impacted apoptosis signaling in CD4+ helper T (Th) cells. MethodsFlow cytometry was used to analyze apoptosis, mitochondrial function and reactive oxygen species (ROS) generation, while Western blotting, ELISA and RT-qPCR were employed to study protein/gene expression in sorted CD4{square} Th cells from perioperative breast cancer female patients (anesthetized with isoflurane or propofol, n=15 per group) and Jurkat T cells. ResultsPatient-derived CD4{square} Th cells and Jurkat T cells exhibited that isoflurane at clinically relevant concentrations triggered apoptosis through mitochondrial depolarization, ROS generation, DNA damage, and activation of caspase-3/7. Specific use of caspase-3/7 inhibitor, Z-DEVD-FMK and antioxidant N-acetyl cysteine rescued isoflurane-induced apoptosis. Further, isoflurane relative to propofol, activated p38 mitogen-activated protein kinase (MAPK), and use of p38 inhibitor, SB203580 suppressed isoflurane-induced apoptosis. Collectively, these findings validated the involvement of the ROS-p38-caspase-3/7 axis in isoflurane-associated apoptosis signaling. On the other hand, propofol conserved mitochondrial integrity, reduced oxidative stress, and maintained higher proliferative capacity. Interestingly, isoflurane-associated apoptosis was transient, with postoperative recovery in patients and similar rescue from apoptosis was evident in Jurkat T cells within 24-48 h of drug removal. ConclusionsBy integrating analyses of patient-derived CD4+ Th cells with mechanistic validations in Jurkat T cells, this study identified the ROS-p38-caspase-3/7 signaling axis and the reversible nature of isoflurane-induced apoptosis.

cancer biology↗

bioRxiv2026

DNA Protonuclei as Programmable Nuclear Mimics Reveal Environmental Context on Protein Phase Separation

Understanding protein phase separation in cellular environments remains a major challenge, as ex vivo assays often fail to capture the influence of environmental context - such as crowding, multimodal interactions, and the dynamic properties of the cytosol or nucleus. Here, we introduce programmable DNA-based protonuclei (PN) as nucleus-inspired compartments to probe phase separation of the neurodegeneration-linked protein FUS. We show that FUS partitioning and condensate formation are highly sensitive to nucleic acid sequence, spatial confinement, and viscoelastic properties of the PN core. Notably, classical test-tube affinity assays fail to predict protein behavior within the crowded and multivalent PN environment. By tuning DNA crosslinking, we modulate condensate dynamics and suppress liquid-to-solid transitions of FUS - a hallmark of disease. These findings demonstrate that multivalent, confined environments fundamentally reshape protein-nucleic acid interactions and phase behavior. The PN platform complements test-tube assays and complex cellular settings and enables to dissect nuclear condensates under controllable conditions.

synthetic biology↗

bioRxiv2026

Gum Odina, a novel prebiotic, promotes the expression of sealing tight junction proteins in colon organoids developed from the C57BL/6 mice model

Maintaining gut-microbiome homeostasis is the biggest issue worldwide as per public health concerns. Gut probiotics not only inhibit pathogen invasion in the systemic circulation but also help us metabolize complex food. Therefore, for decades, gut dysbiosis has been proven to be the gateway to several diseases, leading to comorbidity and even mortality. Prebiotics are natural products, mainly nondigestible food ingredients, that help the selective growth of probiotic bacteria in the gut. This study focuses on the novel Gum-Odina (GO) prebiotic and its efficacy on gut microbial metabolite modulation and maintaining gut barrier integrity. Gut wall enterocytes are integrated by a series of tight junctional (TJ) proteins. This study explains the effect of GO prebiotic-modulated gut metabolites on tight-junctional (TJ) protein expression in a murine colon Organoid model. Fecal microbiota from a colitis patient were used to inoculate the SHIME gut simulator, comprising a colitis control run and a Gum-Odina-supplemented run to enrich commensal bacteria selectively. Metabolites from both groups were then applied to healthy colon organoids. According to the mRNA expression analysis, tight junctional sealing proteins such as Zonula occludens, or ZO-1, Occludin, Claudin-1, 4, and 5 were significantly upregulated in the colon organoids upon Gum-Odina administration, whereas no change in the Junctional Adhesion Molecule-A or JAM-A was observed. Downregulation of sealing TJ proteins is the Hallmark of Leaky gut, which was successfully reversed using the Gum-Odina supplement. Hence, Gum-Odina prebiotics have a promising capability to reduce colitis-induced gut permeability and can be considered to be a therapeutic agent in the future.

cell biology↗

bioRxiv2025

Preclinical evaluation of antisense oligonucleotide therapy in a mouse model of HNRNPH2-related neurodevelopmental disorder

Mutations in HNRNPH2 cause an X-linked disorder characterized by developmental delay, intellectual disability, motor and gait disturbances, and seizures. Murine models that reproduce key clinical features of HNRNPH2-related neurodevelopmental disorder suggest that it may result from a toxic gain of function of the mutant protein or a complex loss of normal HNRNPH2 function with impaired compensation by its homolog, HNRNPH1. In this study, we tested gapmer antisense oligonucleotides (ASOs) that target murine Hnrnph2 in a non-allele-specific manner. The lead ASO reduced Hnrnph2 mRNA and protein levels while inducing compensatory upregulation of Hnrnph1 in both WT and Hnrnph2 mutant mouse brains. A single intracerebroventricular injection of the Hnrnph2 ASO into neonatal mutant Hnrnph2 mice rescued molecular and audiogenic seizure phenotypes and improved motor and cognitive functions. ASO treatment at the juvenile stage also rescued audiogenic seizures and motor deficits. In contrast, Hnrnph2 ASO administration did not improve survival, body weight, or hydrocephalus. In human iPSC-derived neurons, a human-specific HNRNPH2 research ASO reduced HNRNPH2 and upregulated HNRNPH1 mRNA levels. Mechanistically, we demonstrate that HNRNPH1 expression is regulated by alternative splicing and that HNRNPH2 modulates this process. These findings provide preclinical proof of concept for HNRNPH2 ASO therapy and offer insights into its underlying molecular mechanism. One Sentence SummaryASO-mediated Hnrnph2 knockdown induces Hnrnph1 upregulation and rescues phenotypes in a mouse model of HNRNPH2-related neurodevelopmental disorder.

animal behavior and cognition↗

bioRxiv2025

SEASONAL PM2.5 DIFFERENTIALLY REGULATES JAK2/STAT3 SIGNALING IN RURAL AND URBAN COHORTS

Ambient particulate matter (PM2.5) is a major environmental carcinogen linked to lung cancer, yet its molecular insights on asymptomatic non-smokers remains unclear. This study examined the effect of seasonal fluctuations of PM2.5 on oxidative stress and pro-oncogenic signaling in rural (RU) and urban (UR) cohorts from West Bengal, India. Environmental monitoring revealed higher PM2.5 and associated benzo[]pyrene in UR, during winter, induced oxidative stress (elevated ROS, 8-OHdG), reduced antioxidants (SOD, catalase, GPx), and promoted airway inflammation. Transcriptomic and bioinformatic analyses identified activation of IL-6/EGFR-driven JAK2/STAT3 signaling and its crosstalk with Ras/Raf/MAPK, leading to increased expression of downstream effectors (BCL-2, MCL-1, c-MYC, cyclin D1) and repression of tumor suppressors (BAX, p21). Notably, downregulation of JAK/STAT inhibitors PIAS2 and SOCS2 suggested persistent activation of oncogenic signaling. Linear mixed-effects models linked winter PM2.5 surges to oxidative stress, inflammation, and altered JAK2/STAT3 signaling, while regression models showed stronger responses in UR. Risk modeling predicted significantly higher lung cancer mortality in UR, underscoring the role of seasonal PM2.5 surges in JAK2/STAT3-driven carcinogenic susceptibility and the urgent need for targeted interventions.

cancer biology↗

bioRxiv2025

Bacteriophage-Mimetic DNA Origami Needle for Targeted Membrane Penetration and Cytosolic Cargo Delivery

Inspired by the natural ability of bacteriophages to deliver genetic material directly into host cells, we employed a bottom-up approach to construct a multifunctional synthetic DNA origami needle-like structure. This origami is functionalized with trastuzumab antibodies, cholesterol, protective polymers, and two dyes, which together enable selective targeting and insertion into SKBR3 cancer cells. A disulfide-linked dye payload was attached to the apex of the needle, allowing controlled release in the cytoplasm triggered by the high intracellular glutathione concentration. Real-time tracking of the payload confirmed both successful targeting of the origami structure and subsequent direct cytosolic delivery. By mimicking fundamental mechanisms of bacteriophages, we propose that this artificial needle structure can serve as a prototypical device for the targeted delivery of small-molecule drugs directly into the cytosol.

biochemistry↗

bioRxiv2024

Small Extracellular Vesicles by Nucleus Pulposus Cells Maintain Niche and Cell Homeostasis via Receptor Shuffling and Metabolic Enzyme Supplements

BackgroundSmall extracellular vesicles (sEV) are a conserved mean of communication across the domains of life and lately gained more interest in mammalian non-cancerous work as non-cellular, biological therapeutic with encouraging results in recent studies of chronic degenerative diseases. The nucleus pulposus (NP) is the avascular and aneural center of an intervertebral disc (IVD), home to unique niche conditions and affected in IVD degeneration. We investigated the proteome of autologous and mesenchymal stem cell (MSC) sEVs for their potential to contribute to cell and tissue homeostasis in this niche. MethodsWe aimed to identify characteristics of NP sEVs via mass spectrometric proteome and functional enrichment analysis. We explored the proteome profile of sEVs generated by autologous parent cell lines from bovine coccygeal IVD and adipose tissue, with a focus on NP cells, using adult and fetal donors. We compared these findings to published sEV databases and MSC sEV data. FindingsWe propose several mechanisms associated with NP sEVs: 1. Membrane receptor trafficking to modify signal responses promoting niche homeostasis. 2. Cell homeostasis via proteasome delivery; 3. Redox and energy homeostasis via metabolic enzymes delivery. 4. Immunomodulation beyond an association with a serum protein corona. ConclusionThe proteome signature of sEVs generated by NP parent cells is similar to previously published sEV data, yet with a focus on supplementing anaerobic metabolism and redox balance while contributing to the maintenance of an aneural and avascular microniche.

cell biology↗

bioRxiv2024

Differential Contributions of CA3 and Entorhinal Cortex Inputs to Ripple Patterns in the Hippocampus Under Cannabidiol

Cannabidiol (CBD), increasingly recognized for its potential to treat insomnia, notably extends NonREM sleep phases and modifies sleep-associated ripple dynamics. Utilizing a threshold-based approach, our study differentiated distinct ripple types in rats, clarifying the contributions of intra-hippocampal (CA3) and cortical (mEC) regions to these events. The findings reveal that CBD primarily influences the CA3s input to the CA1, resulting in an increased occurrence of short ripples predominantly induced by cortical (mEC) activity and a corresponding decrease in long, intra-hippocampal sharp-wave-ripples. This study highlights the critical interplay between the CA3 and entorhinal cortex dynamics in shaping the characteristics of hippocampal ripples under the influence of CBD.

neuroscience↗

bioRxiv2024

The TD drive - A parametric, open-source implant for multi-area electrophysiological recordings in behaving and sleeping rats

Intricate interactions between multiple brain areas underlie most functions attributed to the brain. The process of learning, as well as formation and consolidation of memories are two examples that rely heavily on functional connectivity across the brain. In addition, investigating hemispheric similarities and/or differences goes hand in hand with these multi-area interactions. Electrophysiological studies trying to further elucidate these complex processes thus depend on recording brain activity at multiple locations simultaneously and often in a bilateral fashion. Presented here is a 3D-printable implant for rats, named TD drive, capable of symmetric, bilateral wire electrode recordings, currently in up to ten distributed brain areas simultaneously. The open-source design was created employing parametric design principles, allowing prospective users to easily adapt the drive design to their needs by simply adjusting high-level parameters, such as anterior-posterior and medio-lateral coordinates of the recording electrode locations. The implant design was validated in n = 20 Lister Hooded rats that performed different tasks. The implant was compatible with tethered sleep recordings and open field recordings (Object Exploration) as well as wireless recording in a large maze (HexMaze 9x5 m) using two different commercial recording systems and headstages. In sum, presented here is the adaptable design and assembly of a new electrophysiological implant facilitating fast preparation and implantation.

neuroscience↗

bioRxiv2023

G6PD deficiency mediated impairment of iNOS and lysosomal acidification affecting phagocytotic clearance in microglia in response to SARS-CoV-2

The glucose-6-phosphate dehydrogenase (G6PD) deficiency is X-linked and is the most common enzymatic deficiency disorder globally. It is a crucial enzyme for the pentose phosphate pathway and produces NADPH, which plays a vital role in the regulation of oxidative stress of many cell types. The deficiency of G6PD causes hemolytic anemia, diabetes, cardiovascular and neurological disorders. Notably, the patient with G6PD deficiency was severely affected by SARS-CoV-2 and showed prolonged COVID-19 symptoms, neurological impacts, and high mortality. However, the mechanism of COVID-19 severity in G6PD deficient patients is still ambiguous. Here, using a CRISPR-edited G6PD deficient human microglia cell culture model, we observed a significant reduction in NADPH and an increase in basal reactive oxygen species (ROS) in microglia. Interestingly, the deficiency of the G6PD-NAPDH axis impairs induced nitric oxide synthase (iNOS) mediated nitric oxide (NO) production which plays a fundamental role in inhibiting viral replication. Surprisingly, we also observed that the deficiency of the G6PD-NADPH axis reduced lysosomal acidification, which further abrogates the lysosomal clearance of viral particles. Thus, impairment of NO production and lysosomal acidification as well as redox dysregulation in G6PD deficient microglia altered innate immune response, promoting the severity of SARS-CoV-2 pathogenesis.

cell biology↗

bioRxiv2023

CBD lengthens sleep, shortens ripples and leads to intact simple but worse cumulative memory

Cannabidiol (CBD) is on the rise as over-the-counter medication to treat sleep disturbances, anxiety, pain and epilepsy due to its action on the excitatory/inhibitory balance in the brain. However, it remains unclear if CBD also leads to adverse effects via changes of sleep macro- and microarchitecture. To investigate the effect of CBD on sleep and sleep-related memory consolidation, we performed two experiments using the Object Space Task testing both simple and cumulative memory in rats. We show that oral CBD administration extended the sleep period but changed the properties of NonREM sleep oscillations (delta, spindle, ripples). Specifically, CBD also led to less long (>100ms) ripples and consequently worse cumulative memory consolidation. In contrast, simple memories were not affected. In sum, we can confirm the beneficial effect of CBD on sleep, however, this comes with changes in NonREM oscillations that negatively impact memory consolidation.

neuroscience↗

bioRxiv2023

Hypothalamic Protein Profiling from Mice Subjected to Social Defeat Stress

The Hypothalmic-pituitary axis also known as the HPA axis is central to stress response. It also acts as the relay centre between the body and the brain. We analysed hypothalamic proteome from mice subjected to chronic social defeat paradigm using iTRAQ based quantitative proteomics in identify changes associated with stress response. We identified greater than 2000 proteins processing our samples analysed through Q-Exactive (Thermo) and Orbitrap Velos (Thermo) at 5% FDR. Analysis of data procured from the runs showed that the proteins whose levels were affected belonged primarily to mitochondrial and metabolic processes, translation, complement pathway among others. We also found increased levels of fibrinogen, myelin basic protein (MBP) and neurofilaments (NEFL, NEFM, NEFH) in the hypothalamus from socially defeated mice. Interestingly these proteins are found upregulated in blood and CSF of subjects exposed to trauma and stress. Since hypothalamus is in direct contact of blood and CSF, their utility as biomarkers in depression holds an impressive probability and should be validated in clinical samples.

animal behavior and cognition↗

bioRxiv2022

Learning Fast and Slow: Increased cortical plasticity leads to memory interference and enhanced hippocampal-cortical interactions

Our brain is continuously challenged by daily experiences. Thus, how to avoid systematic erasing of previously encoded memories? While it has been proposed that a dual-learning system with "slow" learning in the cortex and "fast" learning in the hippocampus could protect previous knowledge from interference, this has never been observed in the living organism. Here, we report that increasing plasticity via the viral-induced overexpression of RGS14414 in the prelimbic cortex leads to better one-trial memory, but that this comes at the price of increased interference in semantic-like memory. Indeed, electrophysiological recordings showed that this manipulation also resulted in shorter NonREM-sleep bouts, smaller delta-waves and decreased neuronal firing rates. In contrast, hippocampal-cortical interactions in form of theta coherence during wake and REM-sleep as well as oscillatory coupling during NonREM-sleep were enhanced. Thus, we provide the first experimental evidence for the long-standing and unproven fundamental idea that high thresholds for plasticity in the cortex protects preexisting memories and modulating these thresholds affects both memory encoding and consolidation mechanisms.

neuroscience↗

bioRxiv2022

Defensive and offensive behaviors in social interaction settings in a Kleefstra syndrome mouse model

Kleefstra syndrome in humans is characterized by general delay in development, intellectual disability and autistic features. The mouse model of this disease (Ehmt1+/-) expresses anxiety, autistic-like traits, and aberrant social interactions with non-cagemates. To investigate how Ehmt1+/- mice behave with unfamiliar conspecifics, we allowed adult, male animals to freely interact for 10 minutes in a neutral, novel environment within a host-visitor setting. In 17 out of 74 trials there were defensive and offensive behaviors. Our key finding was that Ehmt1+/- mice displayed defensive postures, attacking and biting; in contrast, wild-type (WT) interacting with other WT did not enact such behaviors. Further, if there was a fight between an Ehmt1+/- and a WT mouse, it was always the Ehmt1+/- who initiated these behaviors.

neuroscience↗

bioRxiv2021

Analyzing the interaction of human ACE2 and RBD of spike protein of SARS-CoV-2 in perspective of Omicron variant

The newly identified Omicron (B.1.1.529) variant of Severe Acute Respiratory Syndrome Voronavirus 2 (SARS-CoV-2) has steered concerns across the world due to the possession of large number of mutations leading to high infectivity and vaccine escape potential. The Omicron variant houses 32 mutations in S protein alone. The viral infectivity is determined mainly by the ability of spike (S) protein receptor binding domain (RBD) to bind to the human Angiotensin I Converting Enzyme 2 (hACE2) receptor. In this paper, the interaction of the RBDs of SARS-CoV-2 variants with hACE2 was analyzed by using protein-protein docking and compared with the novel Omicron variant. Our findings reveal that the Omicron RBD interacts strongly with hACE2 receptor via unique amino acid residues as compared to the Wuhan and many other variants. However, the interacting residues of RBD are found to be the same in Lamda (C.37) variant. These unique binding of Omicron RBD with hACE2 suggests an increased potential of infectivity and vaccine evasion potential of the new variant. The evolutionary drive of the SARS-CoV-2 may not be exclusively driven by RBD variants but surely provides for the platform for emergence of new variants.

bioinformatics↗

bioRxiv2021

Spindle - slow oscillation coupling correlates with memory performance and connectivity changes in a hippocampal network after sleep

After experiences are encoded, post-encoding reactivations during sleep have been proposed to mediate long-term memory consolidation. Spindle-slow oscillation coupling during NREM sleep is a candidate mechanism through which a hippocampal-cortical dialogue may strengthen a newly formed memory engram. Here, we investigated the role of fast spindle- and slow spindle-slow oscillation coupling in the consolidation of spatial memory in humans with a virtual water maze task involving allocentric and egocentric learning strategies. Furthermore, we analyzed how resting-state functional connectivity evolved across learning, consolidation, and retrieval of this task using a data-driven approach. Our results show task-related connectivity changes in the executive control network, the default mode network, and the hippocampal network at post-task rest. The hippocampal network could further be divided into two subnetworks of which only one showed modulation by sleep. Decreased functional connectivity in this subnetwork was associated with higher spindle-slow oscillation coupling power, which was also related to better memory performance at test. Overall, this study contributes to a more holistic understanding of the functional resting-state networks and the mechanisms during sleep associated to spatial memory consolidation.

neuroscience↗

bioRxiv2020

Sleep leads to system-wide neural changes independent of allo- and egocentric spatial training in humans and rats

Sleep is important for memory consolidation, especially the process of systems consolidation should occur during sleep. While a significant amount of research has been done in regards to the effect of sleep on behavior and certain mechanisms during sleep, until now evidence is lacking that sleep leads to consolidation across the system. Here, we investigated the role of sleep in consolidation of spatial memory in the watermaze in both rats and humans using allocentric and egocentric based training. Combining behavior with immediate early gene expression analysis in rodents and functional MR imaging in humans, elucidated similar behavioral and neural effects in both species. Rats and humans showed a benefit of sleep on behavior. Interestingly, sleep led to systems-wide retrieval network in both species in both training conditions. Thus, we provide cross-species evidence for memory consolidation on the system-level occurring during sleep. Significance StatementProcesses occurring during sleep such as memory reactivations are proposed to lead to consolidation from the initial hippocampal memory representation to long-lasting cortical representations, this is known as systems consolidation. By combining behavioral measurements in the watermaze with immediate early gene expression analysis in rats and function magnetic resonance imaging in humans, we could show a benefit of sleep on behavioral memory performance. And, sleep lead to systems-wide changes in the retrieval network. These results are the first direct evidence supporting the role of sleep for systems-wide memory consolidation in both rats and humans.

neuroscience↗

bioRxiv2020

A biomimetic liver model recapitulating bio-physical properties and tumour stroma interactions in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is a primary liver tumor developing in the wake of chronic liver disease. Chronic liver disease and inflammation leads to a fibrotic environment actively supporting and driving hepatocarcinogenesis. Insight into hepatocarcinogenesis in terms of the interplay between the tumor stroma micro-environment and tumor cells is thus of considerable importance. Three-dimensional (3D) cell culture models are proposed as the missing link between current in vitro 2D cell culture models and in vivo animal models. Our aim was to design a novel 3D biomimetic HCC model with accompanying fibrotic stromal compartment and vasculature. Physiologically relevant hydrogels such as collagen and fibrinogen were incorporated to mimicking the bio-physical properties of the tumor ECM. In our model LX2 and HepG2 cells embedded in a hydrogel matrix were seeded onto the inverted insert membrane of a Transwell system. HUVEC cells were then seeded onto the opposite side of the membrane. Three formulations consisting of ECM-hydrogels embedded with cells were prepared and the bio-physical properties determined by rheology. Cell viability was determined by the AlamarBlue(R) assay over 21-days. The effect of the chemotherapeutic drug doxorubicin was evaluated in both a 2D co-culture and our 3D model for a period of 72h. We show that this model is viable for 25-days and gives rise to metastatic tumor nodules after 17 days in culture. Rheology results show that bio-physical properties of a fibrotic, cirrhotic and HCC liver can be successfully mimicked. Overall, results indicate that this 3D model is more representative of the in vivo situation compared to traditional 2D cultures. Our 3D tumor model showed a decreased response to chemotherapeutics, mimicking drug resistance typically seen in HCC patients. This model could in future provide a valuable new platform to study multifocal HCC or to identify mechanisms that contribute to early stages of metastasis. SUMMARYA protocol for a novel 3D biomimetic HCC model with accompanying fibrotic stromal compartment and vasculature, to study endocrine and paracrine signaling in liver cancer. The model uses physiological relevant hydrogels in ratios mimicking the bio-physical properties of the stromal extracellular matrix, which is an active mediator of cellular interactions, tumor growth and metastasis.

cancer biology↗