Biology subjects

Sinha, D.

Publications and source records attributed to Sinha, D..

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

CTCF regulates wild-type and recombinant AAV gene expression by shaping viral chromatin

Adeno-Associated Viruses (AAVs) are powerful platforms for delivering therapeutic transgenes via recombinant AAV (rAAV) vectors. However, a limited understanding of the regulation of AAV gene expression has narrowed the ability to efficiently express therapeutic transgenes from rAAV vectors. Since rAAVs retain only the wtAAV inverted terminal repeats (ITR), we hypothesized that regulatory elements outside the ITR that govern wild-type AAV (wtAAV) gene expression can be used to modify rAAV genomes to enhance vector performance. Through in silico analysis, biochemical pulldowns, and high-throughput sequencing, we have identified that the host architectural protein CCCTC-binding Factor (CTCF) associates with the wtAAV type 2 (wtAAV2) genome but is absent from rAAV vectors. Global knockdown and site-specific deletion revealed that the CTCF binding element (CBE) on the wtAAV2 genome, located upstream of the viral P5 promoter, regulates expression of the viral Rep68/78 genes. We have re-engineered new rAAV vectors expressing a GFP reporter transgene to contain the wtAAV2-CBE upstream of the vector promoter. Our results show that CTCF binding dramatically increased rAAV transduction efficiency and GFP expression by up to four-fold across multiple cell types. This enhancement was independent of the AAV capsid serotype used for packaging rAAV vectors. CUT&RUN analysis revealed that this CBE was necessary and sufficient to regulate the chromatin landscape of wtAAV2 and rAAV2. Finally, we observed that CTCF-mediated chromatin remodeling of rAAV2 led to increased production of nascent RNA transcripts from the vector genome. Based on our findings, we propose that CTCF supports wtAAV2/rAAV gene expression by shaping the local chromatin landscape. SIMPLE ABSTRACTRecombinant Adeno-Associated Viruses (rAAV) gene therapy vectors have been engineered from wild-type AAV (wtAAV) by inserting the viral telomeres (that serve as replication and packaging signals) on either side of therapeutic transgenes. However, efficient expression of transgenes using current rAAV technologies require high doses, which can lead to sporadic toxic side effects. We hypothesized that uncharacterized regulatory elements in the wtAAV2 genome drive efficient viral gene expression and are absent from the current generation of rAAV vectors. Using in-silico analysis combined with biochemical pulldowns, high-throughput sequencing, and mutant viral systems, we have identified a novel cis-acting element bound by the cellular architectural protein CCCTC-binding Factor (CTCF). This CTCF binding element is necessary for wtAAV2 gene expression and is sufficient to enhance the rAAV vectors ability to express reporter transgenes. This CTCF-binding element regulates the chromatin landscape of the virus and its vectors. Our discovery that adding the 19-bp AAV2 CTCF-binding element enhances transgene expression without affecting vector production efficiency presents a promising new rAAV gene therapy platform that is likely to reduce clinical doses and minimize toxicity in therapeutic applications.

microbiology↗

bioRxiv2026

Calmodulin requires calcium to be a constitutive component of the spindle pole bodies in fission yeast

Although calmodulin is best known as a calcium sensor, it also possesses Ca2+-independent functions, exemplified by the surprising finding that the budding yeast cells remain viable using a calmodulin mutant that cant bind Ca2+ (Geiser et al., 1991). It remains unclear why Ca2+-calmodulin is required in other yeasts or vertebrates. Here, we determined whether such holo-calmodulin is an essential cytoskeletal protein in fission yeast. The S. pombe calmodulin Cam1 was an integral part of both the spindle pole body (SPB) and many actin structures at the equatorial division plane. Two mutants Cam1-2V and -3V, which bound Ca2+ poorly, reduced their localization at the SPBs by 90%. However, their presence in the actin structures remained unchanged. Replacing the endogenous cam1 with cam1-2V cut the number of the Cam1-interacting protein Pcp1 in the SPB by [~]70% and delayed mitosis. In contrast, the assembly and constriction of the cytokinetic ring, which depends on the Cam1-interacting myosins Myo1, Myo51 and Myo52, accelerated. The temperature-sensitive cam1-2V mutant was rescued by either over-expression of pcp1 or deletion of myo1. Thus, Cam1 depends on Ca2+ to promote the SPB assembly and to modulate the actomyosin ring constriction, suggesting holo-calmodulin as an essential cytoskeletal protein.

cell biology↗

bioRxiv2026

Gut-derived metabolic reprogramming drives immune aging and tissue degeneration

Aging is characterized by changes in gut microbiome, metabolic imbalance and chronic inflammation, yet how these processes integrate to drive tissue degeneration remains poorly defined. Using age-related macular degeneration (AMD) as a model of tissue aging, we identify a diet-induced metabolic-immune axis that promotes systemic and retinal degeneration. In mice, a high-fat, cholesterol-enriched (HFC) diet induced perturbations in the gut structural integrity and microbiome repertoire, as well as systemic metabolic aging signatures, prominently marked by reduced circulating histidine. Plasma histidine levels were similarly decreased in AMD patients and inversely correlated with body mass index (BMI) in control donors. These diet-induced gut microbiome changes and subsequent metabolic alterations promoted peripheral innate immune reprogramming, with expansion of inflammatory neutrophils and monocytes that infiltrated the outer retina in a mouse model. Mechanistically, the gut-derived IGF1R/AKT2 signaling acts as a central regulator of global epigenetic remodeling and systemic immune aging under high-fat conditions in C. elegans. In a mouse model with an age-dependent dry AMD-like pathology, distinct retinal pigment epithelium (RPE) subpopulations exhibited downregulation of the histidine transporter SLC7A5, linking metabolic stress to activation of MIF/CD74-dependent inflammatory signaling between RPE and infiltrating immune cells. Histidine supplementation or AKT2 phospho-state modulation attenuated systemic immune activation and rescued retinal degeneration. These findings identify histidine-axis dysregulation as a mechanistic bridge between diet-induced microbiome changes, metabolic stress, immune aging, and retinal degeneration.

cell biology↗

bioRxiv2026

Protein import-driven mitochondrial hyperactivation dictates angiogenesis independently of HIF-1α

Angiogenesis is essential for sustained neoplastic progression, yet its initiation has largely been framed through hypoxia-dependent HIF signalling. In OXPHOS driven tumours, how mitochondrial function contributes to angiogenic induction remains poorly understood. Here, we uncover a non-canonical mechanism linking tumour cell mitochondrial hyperactivity to a pro-angiogenic response. Mitochondrial function critically depends on the import of nuclear-encoded proteins, largely mediated by TIM23 translocase. We found Timm44, the central scaffold of this translocase, to be broadly upregulated across angiogenesis-dependent malignancies. Using gain-of-function system that recapitulate tumour-associated Timm44 amplification, we enhanced mitochondrial protein import capacity, thereby remodelling mitochondrial gene expression and driving hyperactivation of the electron transport chain, particularly Complex I. This hyperactive mitochondrial state generated a signalling-competent ROS-enrich environment that induces VEGFA expression independently of HIF-1 stabilization, via a redox-licensed TRX-ASK1-p38MAPK-SP1 axis, thereby promoting endothelial sprouting and proliferation. These findings define protein import-driven mitochondrial hyperfunction as an alternative driver of tumour angiogenesis, extending current paradigms beyond classical hypoxia-dependent mechanisms and highlighting new therapeutic vulnerabilities.

cancer biology↗

bioRxiv2025

A non-canonical AKT1-TERT pathway coordinates autophagy and ERphagy

The retinal pigment epithelium (RPE) sustains lifelong proteostasis under chronic stress, yet how post-mitotic cells activate autophagy when canonical kinase pathways suppress it remains unresolved. Here we demonstrate that AKT1, conventionally regarded as an autophagy suppressor, drives autophagy through a non-canonical transcriptional mechanism triggered by isoform imbalance. In RPE and age-related macular degeneration (AMD) models, AKT2 hyperactivation destabilizes mTORC2 and engages S6K-mediated IRS-1 inhibition, creating a feedforward autophagic arrest. Compensatory AKT1 activation via mTORC2 phosphorylates telomerase reverse transcriptase (TERT) at Serine 824, driving nuclear translocation that is independent of telomere maintenance. In the nucleus, TERT assembles with FOXO3 and MYC into a tripartite transcriptional complex that occupies the EIF2AK3 promoter, enabling PERK transcriptional activation. This activity converts the unfolded protein response from pro-apoptotic to cytoprotective: PERK-ATF4 signaling drives biogenesis of core autophagy machinery while simultaneously inducing selective ERphagy through the receptors TEX264 and CCPG1, which prevents pathological PERK clustering and preserves tubular ER architecture in diseased RPE. Using C. elegans phosphorylation-deficient mutants, mouse models and AMD patient induced pluripotent stem cell-derived retinal pigment epithelium (iPSC-RPE), we establish that AKT1-mediated TERT phosphorylation is an evolutionarily conserved prerequisite for FOXO/DAF-16 nuclear function and lysosomal homeostasis in post-mitotic cells. Pharmacologic targeting of AKT2 with a first-in-class dual-pocket allosteric inhibitor selectively enhances AKT1 compensation, restoring macroautophagic and ERphagy flux across disease models. These findings reveal a kinase-to-transcription axis that reprograms organelle quality control and identify the AKT1-TERT-PERK-ATF4 pathway as a therapeutic target in proteostasis-driven disease.

cell biology↗

bioRxiv2025

Unveiling Differential Epigenetic Regulation of ABC Transporter Genes in Wild and Domestic Rice in Response to Heavy Metal Stress

Plants are continually subjected to heavy metal (HM) stress, which impairs critical physiological and metabolic processes. ATP-binding cassette (ABC) transporters play an important role in heavy metal detoxification, their epigenetic regulation under heavy metal stress remains poorly understood. Epigenetic changes, such as DNA methylation (5mC) and N6-methyladenine (6mA), are emerging as important regulators of stress-responsive genes. We studied the epigenetic regulation of ABC transporter genes in three Oryza species Oryza sativa indica, Oryza rufipogon, and Oryza glaberrima by analysing promoter methylation patterns. Our data show that 5mC is abundant in CHG motifs, whereas 6mA is mostly found at AHCA motifs, indicating sequence-specific methylation preferences across different rice species. Notably, indica rice exhibited higher promoter methylation levels compared to O. rufipogon and O. glaberrima, suggesting a potential link between increased DNA methylation and reduced ABC transporter expression, which may contribute to heightened HM sensitivity in cultivated rice. Phylogenetic analysis further highlighted species-specific variations in methylation patterns, supporting the role of epigenetics in shaping HM stress adaptation. These results provide new insights into the regulatory mechanisms governing heavy metal tolerance in rice and open avenues for epigenetic-based crop improvement strategies.

plant biology↗

bioRxiv2025

OpEnHiMR: Optimization based Ensemble Model for Prediction of Histone Modification in Rice

Histone modifications are central to gene regulation, yet their systematic identification in plants remains limited due to the complexity of epigenomic landscapes. We present OpEnHiMR, an optimization-based ensemble learning framework for multiclass prediction of three key histone modifications, H3K4me3, H3K27me3, and H3K9ac, in rice. The framework integrates Support Vector Machines, Random Forest, and Gradient Boosting models, optimized via Ant Colony Optimization to maximize performance. Biologically meaningful features, including mononucleotide binary encoding, nucleotide chemical properties, GC content, and k-mer frequencies, were used for training after rigorous data curation and redundancy removal. OpEnHiMR achieved a classification accuracy of 77.54%, outperforming individual models and ensuring improved recall, specificity, and Matthews correlation coefficient. Model interpretability was enhanced using SHAP analysis, which highlighted critical sequence features influencing prediction outcomes. To promote community-wide adoption, a user-friendly webserver (https://dipro-sinha.shinyapps.io/OpEnHiMR/) and R package (https://cran.r-project.org/web/packages/OpEnHiMR/index.html) were developed. OpEnHiMR thus provides a scalable, accurate, and interpretable tool for histone modification prediction in plants, advancing epigenomics research and supporting data-driven crop improvement strategies.

bioinformatics↗

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

Prevenying vision loss in a mouse model of Leber Congenital Amaurosis by engineered tRNA

Premature termination codons (PTCs) are associated with rare genetic disorders. Inducing targeted read-through of these nonsense mutations presents a potential therapeutic strategy for modifying disease outcomes. We previously reported that one such PTC, W53X, in the KCNJ13 gene causes blindness and Leber congenital amaurosis type-16 (LCA-16) due to loss of function of the inwardly rectifying potassium channel 7.1 (Kir7.1). Here, we present the proof of concept of a therapeutic approach based on anticodon-engineered transfer RNA (ACE-tRNA). The ACE-tRNA encodes the amino acid tryptophan (Trp) and suppresses the W53X PTC, restoring full-length protein expression. We used helper-dependent adenovirus (HDAd) to deliver the ACE-tRNATrp.UAG (tRNATrp.UAG) and rescue Kir7.1 function and physiology in patient-specific human induced pluripotent stem cell-derived retinal pigment epithelium (hiPSC-RPE) cells. Furthermore, in a W53X mouse model of LCA16, HDAd delivery of tRNATrp.UAG resulted in durable restoration of vision as measured by retinography. This study provides the first example of the therapeutic application of ACE-tRNA for treating an inherited form of blindness.

physiology↗

bioRxiv2025

Genome-Wide CRISPR Screening Identifies Cellular Factors Controlling Nonviral Genome Editing Efficiency

After administering genome editors, their efficiency is limited by a multi-step process involving cellular uptake, trafficking, and nuclear import of the vector and its payload. These processes vary widely across cell types and differ depending on the nature and structure of the vector, whether it is a lipid nanoparticle or a different synthetic material. We developed a novel genome-wide CRISPR screening strategy to better understand these limitations within human cells to identify genes modulating cellular uptake, payload delivery, and gene editing efficiency. Our screen interrogates the cellular processes controlling genome editing by Cas-based nuclease and base editing strategies in human cells. We designed a genome-wide screen targeting 19,114 genes in HEK293 cells, and we identified six genes whose knockout increased nonviral editing efficiency in human cells by up to five-fold. Further validation through arrayed knockouts of the top hits from our screen boosted the editing efficiency from 5% to 50% when Cas9 was delivered via lipid-based nanoparticles. By designing the guides to target the screen library cassette, we could accurately track the library sgRNA identity and the editing outcome on the same amplicon via short-read sequencing, enabling the identification of rare outcomes via computationally sorting edited from unedited cells within a heterogenous pool of >200M cells. In patient-derived human retinal pigment epithelium cells derived from pluripotent stem cells, BET1L, GJB2, and MS4A13 gene knockouts increased targeted genome editing by over five-fold. We anticipate that this high-throughput screening approach will facilitate the systematic engineering of novel nonviral genome editing delivery methods, where the identified novel gene hits can be further used to increase editing efficiency for other therapeutically relevant cell types.

genomics↗

bioRxiv2025

Cigarette smoke and biological age induce degenerative heterogeneity in retinalpigment epithelium

Environmental exposure such as cigarette smoke induces epigenetic changes that can induce degenerative heterogeneity and accelerate aging. In early age-related macular degeneration (AMD), the leading worldwide cause of blindness among the elderly, retinal pigment epithelial (RPE) cell heterogeneity is a key change. Since smoking is the strongest environmental risk factor for AMD, we hypothesized that cigarette smoke induces degenerative RPE heterogeneity through epigenetic changes that are distinct from aging, and that with aging, the RPE becomes vulnerable to cigarette smoke insult. We administered cigarette smoke condensate (CSC) intravitreally to young and aged mice and performed snRNA-seq and snATAC-seq on the RPE/choroid. This analysis identified separate cell clusters corresponding to healthy and abnormal, dedifferentiated RPE in both aged vehicle-treated and young CSC-treated mice. The dedifferentiated RPE were characterized by a global decrease in chromatin accessibility and decreased expression of genes in functional categories that were linked to hallmarks of aging. Notably, young, dedifferentiated RPE also exhibited a compensatory upregulation of hallmarks of aging-related genes, specifically those related to mitochondrial function and proteostasis. In contrast, aged dedifferentiated RPE did not express these compensatory changes, and did not survive CSC treatment, as experimentally verified with TUNEL labeling. These changes are relevant to early AMD because we identified through scRNA-seq, similar dedifferentiated and healthy macular RPE clusters in a donor who smoked and another with early AMD, but not from a nonsmoker. Degenerative cellular heterogeneity can include an abnormal cluster that jeopardizes cell survival and may represent an additional hallmark of ocular aging.

neuroscience↗

bioRxiv2025

Attenuated adenosine mediated immune-dampening increases natural killer cell activity in early age-related macular degeneration

Non-exudative age-related macular degeneration (AMD) involves retinal pigment epithelium (RPE) dysfunction and has been linked to altered intraocular immunity. Our investigation focuses on immune cell subsets and inflammation-associated factors in the eyes with early and intermediate AMD. We observed elevated levels of activated natural killer (NK) cells and interferon-{gamma}, concurrent with reduced myeloid-derived suppressor cells (MDSCs) and adenosine in AMD eyes. Aqueous humor from AMD patients had diminished ability to dampen NK cell activation, an effect rescued by adenosine supplementation. The Cryba1 cKO mouse model recapitulated these immune alterations, and single-cell RNA-sequencing identified NK cell-related genes and NK cell-RPE interactions. Co-culture of activated NK cells with RPE cells induced barrier dysfunction and Gasdermin-E driven pyroptosis providing a functional link relevant to AMD. These findings suggest a double-hit model where elevated immune activation and loss of immune dampening mechanisms drive AMD progression. Resetting the intraocular immune balance may be a promising therapeutic strategy for managing early and intermediate AMD. O_FIG O_LINKSMALLFIG WIDTH=198 HEIGHT=200 SRC="FIGDIR/small/634301v2_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1516bfaorg.highwire.dtl.DTLVardef@87f505org.highwire.dtl.DTLVardef@1e725caorg.highwire.dtl.DTLVardef@622717_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO Illustra tion of pro posed mechanism underlying NK cell-RPE interaction in early AMD pathogenesis. Dysregulated NK cell communicate s with stressed RPE in early AMD immunopathology. Aberrant AMD aqueous humor and retina shows increased NK cells and NK effector molecules like IFN{gamma} with reduced MDSC and adenosine in human subjects, don or eye and animal model. Activated NK cells interaction with RPE causes dysfunction and pyroptotic cell death via Gasdermin-E pathway in AMD.. Created with BioRender.com C_FIG

immunology↗

bioRxiv2024

Intra-cluster receptor density (IRD) dictates TNFR1 clusters' signaling efficacy

Tumor Necrosis Factor Receptor 1 (TNFR1) signaling regulates cell fate in inflammation, immune responses, and tumorigenesis. While TNF--mediated TNFR1 pathways are well known, the role of receptor clustering remains unclear. Utilizing homo-FRET using fluorescence anisotropy, we show that intra-cluster receptor density (IRD) governs TNFR1 signaling outcomes. Soluble TNF- (sTNF-) increases IRD at cluster cores but decreases it at rims via receptor reorganization. Reducing IRD through membrane tension, zafirlukast, actin depolymerization, or cholesterol depletion suppresses sTNF- signaling, whereas increasing IRD by lowering membrane tension or exposing cells in a 3D gel-like microenvironment triggers ligand-independent activation. These findings reveal IRD as a key regulator of receptor signaling, with potential relevance across related receptor families and innovative strategies in modulating TNFR1 signaling. TeaserIntra-cluster receptor density (IRD) is critical for TNFR1 signal modulation, with higher IRD activating and lower IRD impairing the TNFR1 signaling.

biophysics↗

bioRxiv2024

βA3/A1-crystallin is an epigenetic regulator of histone deacetylase 3 (HDAC3) in the retinal pigmented epithelial (RPE) cells

Introductory paragraphThe retinal pigmented epithelial (RPE) cells maintain retinal homeostasis, and alterations in their function contribute to non-exudative age-related macular degeneration (AMD)1,2. Here, we explore the intricate relationship between RPE cells, epigenetic modifications, and the development of AMD. Importantly, the study reveals a substantial decrease in histone deacetylase 3 (HDAC3) activity and elevated histone acetylation in the RPE of human AMD donor eyes. To investigate epigenetic mechanisms in AMD development, we used a mouse model with RPE-specific Cryba1 knockout3-5, revealing that the loss of {beta}A3/A1-crystallin selectively reduces HDAC3 activity, resulting in increased histone acetylation. {beta}A3/A1-crystallin activates HDAC3 by facilitating its interaction with the casein kinase II (CK2) and phosphorylating HDAC3, as well as by regulating intracellular InsP6 (phytic acid) levels, required for activating HDAC3. These findings highlight a novel function of {beta}A3/A1-crystallin as an epigenetic regulator of HDAC3 in the RPE cells and provide insights into potential therapeutic strategies in non-exudative AMD.

cell biology↗

bioRxiv2024

The dynamic crosstalk between cytoskeletal filaments regulates the cytoplasmic mechanics across the apicobasal axis

The cytoplasm exhibits viscoelastic properties, displaying both solid and liquid-like behavior, and can actively regulate its mechanical attributes. The cytoskeleton is a major regulator among the numerous factors influencing cytoplasmic mechanics. We explore the interdependence of various cytoskeletal filaments and the impact of their density on cytoplasmic viscoelasticity. The heterogeneous distribution of these filaments give rise to polarised mechanical properties of the cytoplasm along the apicobasal axis. Actin filament (F-actin) disassembly softens the basal cytoplasm while stiffening the mid-cytoplasm due to increased vimentin filament assembly. Disruption of microtubules (MT) or depletion of vimentin softens both the basal and mid-cytoplasm. Cyto D treatment results in localised increase of vimentin assembly in the mid cytoplasm which is dependent on the cytolinker plectin. Nocodazole treatment has a negligible effect on F-actin distribution but significantly alters vimentins spatial arrangement. We demonstrate that Cyto D treatment upregulates vimentin expression via ROS-mediated activation of NF-{kappa}B. This manuscript investigates how different cytoskeletal filaments influence the rheological characteristics of various cytoplasmic regions.

cell biology↗

bioRxiv2024

MICROMANIPULATION OF LIVE MICRODISSECTED TISSUES WITH A LOW-COST INTEGRATED ROBOTIC PLATFORM

The scarcity of human biopsies available for drug testing is a paramount challenge for developing new therapeutics, disease models, and personalized treatments. Microtechnologies that combine the microscale manipulation of tissues and fluids offer the exciting possibility of miniaturizing both disease models and drug testing workflows on scarce human biopsies. Unfortunately, these technologies presently require microfluidic devices or robotic dispensers that are not widely accessible. We have rapidly-prototyped an inexpensive platform based on an off-the-shelf robot that can microfluidically manipulate live microtissues into/out of culture plates without using complicated accessories such as microscopes or pneumatic controllers. The robot integrates complex functions with a simple, cost-effective and compact construction, allowing placement inside a tissue culture hood for sterile workflows. We demonstrated a proof-of-concept cancer drug evaluation workflow of potential clinical utility using patient tumor biopsies with multiple drugs on 384-well plates. Our user-friendly, low-cost platform promises to make drug testing of microtissues broadly accessible to pharmaceutical, clinical, and biological laboratories. TeaserA low-cost robot for handling microtissues and catalyzing their use in cancer drug evaluation and personalized oncology.

bioengineering↗

bioRxiv2024

An essential mechanosensitive channel Pkd2 modulates the assembly of type II myosin and actin filaments in the cytokinetic contractile ring

Cytokinesis, the last step in cell division, separate daughter cells through the force produced by an actomyosin contractile ring assembled at the equatorial plane. In fission yeast cells, the ring helps recruit a mechanosensitive ion channel Pkd2 to the cleavage furrow, whose activation by membrane tension promotes calcium influx and daughter cell separation. However, it is unclear how the activities of Pkd2 may affect the actomyosin ring. Here, through both microscopic and genetic analyses of a hypomorphic mutant of the essential pkd2 gene, we examine its potential role in assembling and constricting the contractile ring. The pkd2-81KD mutation significantly increased the number of type II myosin heavy chain Myo2 (+20%), its regulatory light chain Rlc1 (+37%) and actin (+20%) molecules in the ring, compared to the wild type. Consistent with a regulatory role of Pkd2 in the ring assembly, we identified a strong negative genetic interaction between pkd2-81KD and the temperature-sensitive mutant myo2-E1. The pkd2-81KD myo2-E1 cells often failed to assemble a complete contractile ring. We conclude that Pkd2 modulates the recruitment of type II myosin and actin to the contractile ring, suggesting a novel calcium- dependent mechanism regulating the actin cytoskeletal structures during cytokinesis.

cell biology↗