Cell Pairs Research Articles

Associations of neuro-glial network calcium activity with mice movements <i>in vivo</i>

Calcium imaging of nerve activity in the mouse hippocampus provides insights into cell-to-cell interactions [1]. Over time, fluctuations in cellular calcium levels encode distinct brain states during mouse brain imaging. Although synapses connect cells and transmit information, it is challenging to detect the spatiotemporal transmission pathway via calcium imaging of multiple cells due to the complexity of the spatial structure and imaging in a separate focal plane [2]. Reconstruction of the dynamic graph of connections between cells was proposed to overcome this problem. A dynamic graph comprises of individual graphs for each time point. A graph linked to a particular time t is composed of vertices representing cells and edges that depict the transmission of signals between cells at that moment. This paper puts forth 3 approaches for creating networks. The first method considers the overlapping time intervals of calcium events in individual cells [3]. The link is established between the cell with the earlier event and the cell with the later start of the event during the moments when the events occurred simultaneously in separate cells. Alternatively, time intervals between the start of events were taken into account. Potentially connected events that began no later than 2 s were linked, with the edge drawn from the cell depicting the earlier starting event to the second cell. The third technique involved linking sequentially occurring events in distinct cells. The edge is drawn from all active cells at the previous time step to newly activated cells at the subsequent time step. Data analysis is based on an experiment in which a mouse moved along a circular track while the fluorescence of neuronal calcium activity and the mouse’s position were recorded at a frequency of 20 frames per second [4]. A red dot was marked on the mouse’s head to track its position. The reconstructed dynamic graph was compared to the angular coordinate of the mouse on the ring to look for repeating patterns of activity. The racetrack was divided into 20 overlapping sectors, each spanning 36 degrees. The reconstructed networks were then assigned to sectors that aligned with the mouse’s angular position on the track. Next, we estimated the frequency of individual edge repetitions within each network group. Only edges that occurred at least three times were chosen for further analysis. We found repeated activations of various cell pairs that corresponded to clockwise and counterclockwise movement within the same sector. Furthermore, we identified the presence of alternating activation, where activity occurred in the first cell, then the second cell, and then again in the first cell. In addition, we identified complex sequences of 5–6 non-sequential activations, represented as a digraph without cycles, which is typical for single sectors.

A framework for scRNA-seq data clustering based on multi-view feature integration

Accurate and consistent estimation of cell-to-cell similarity is crucial for clustering single-cell RNA-seq (scRNA-seq) data. However, the high sparsity of scRNA-seq data often leads to suboptimal mining and decreased accuracy in identifying cell types. Moreover, using a larger number of features (genes) does not necessarily improve clustering accuracy due to redundant information. In this paper, we propose a framework, called scMVFI (single-cell Multi-View Feature Integration), which integrates linear and non-linear features of scRNA-seq data to address the disadvantage of zero-inflated noise caused by technical factors. By employing an autoencoder model for data reconstruction, scMVFI performs multi-view similarity estimation using subsets of features with different sampling rates to identify highly similar cell pairs. We evaluate the effectiveness of scMVFI using five real scRNA-seq datasets and three simulated datasets. The results demonstrate that scMVFI can effectively mitigate the impact of data “dropout” events compared to other methods. Moreover, the affinity networks constructed from both linear and non-linear perspectives can accurately capture sample relationships, thereby enhancing the identification of cell types when combined with existing clustering methods.

Abstract C163: KRAS alterations combined with TP53 mutations as novel synthetic lethal genomic lesions for PKMYT1 inhibition

Abstract Background: Membrane-associated tyrosine- and threonine-specific Cdc2-inhibitory kinase (PKMYT1) is a cell cycle regulatory kinase that inhibits CDK1/CyclinB activity, delaying entry into mitosis in tumor cells experiencing replication stress (RS). RS is frequently induced by genetic alterations that drive premature transition from G1 to S phase, promoting genome instability and creating a synthetic lethal (SL) relationship between these specific alterations and PKMYT1 inhibition. This relationship has been demonstrated preclinically and clinically with CCNE1 amplification and FBXW7 mutations, common alterations in ovarian and colorectal cancers, respectively. Oncogenic KRAS gain of function (GOF) mutations, combined with TP53 alterations, are bona fide drivers of RS. Here we investigate the relationship between KRAS/TP53 alterations and PKMYT1 inhibition, mediated by the first-in-class, potent and selective PKMYT1 inhibitor lunresertib (RP-6306), alone or in combination with RS-inducing agents. Methods: KRAS/TP53 double mutant isogenic cell pairs, across relevant tumor origins, were genetically engineered to express multiple KRAS GOF mutant codons and alleles (G12D, G12C, G12V, G12R, G13D and Q61H). Cell cycle distribution perturbations and RS were evaluated. Sensitivity to lunresertib alone or in combination with chemotherapeutic or targeted agents was assessed by cell growth assays. In vitro findings were further evaluated in KRAS/TP53 double mutant patient-derived xenografts (PDX). Results: Lunresertib inhibited the growth of isogenic KRAS/TP53 double mutant cells, with up to a 12-fold EC50 shift compared to control parental cells. Combination of lunresertib with RS-inducing chemotherapeutic agents (eg. gemcitabine), or the ATR inhibitor camonsertib (RP-3500) led to synergistic cell growth inhibition in KRAS/TP53 mutant cells at significantly lower concentrations than in wild type lines. Mechanistically, KRAS/TP53 isogenic cells showed elongated S-phase and increased cyclin B1 levels, phenocopying the effects of CCNE1 amplification. Lunresertib induced premature mitosis and DNA damage in KRAS/TP53 mutant cells, sparing parental cell lines. PDX efficacy studies demonstrated robust combination benefit in pancreatic, lung and colorectal settings, with durable tumor regressions and complete responses observed. Conclusion: GOF KRAS mutations, when combined with TP53 alterations, show a strong SL relationship with PKMYT1 inhibition, alone or in combination with RS-inducing antitumor agents. Importantly, the SL phenotype was observed across multiple tumor indications and KRAS mutant codons/alleles, suggesting a potential broad scope of clinical utility beyond approved KRAS inhibitors. The mechanism is similar to CCNE1 amplification, characterized by enhanced G1/S transition driving heightened dependence on PKMYT1 to inhibit CDK1/CyclinB. Taken together, our data form rationale for the therapeutic evaluation of PKMYT1 inhibitors in KRAS/TP53 altered tumors and uncover a potential new patient selection biomarker for lunresertib. Citation Format: Marc L. Hyer, Jimmy Fourtounis, David Gallo, Vivek Bhaskaran, Rino Stocco, Rosie Kryczka, Sai Save, Helen Burston, Olivier Nicolas, Stephen Morris, Anne Roulston, Jordan T. F. Young, Michal Zimmermann, C. Gary Marshall, Artur Veloso, Elia Aguado-Fraile. KRAS alterations combined with TP53 mutations as novel synthetic lethal genomic lesions for PKMYT1 inhibition [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr C163.

Advancing CAR-T Therapy in Acute Lymphoblastic Leukemia: Multi-Omic Analyses of CD19-Directed CAR-T Cells Enabled By an Ex Vivo Co-Culture Platform

Background: Acute Lymphoblastic Leukemia (ALL) has witnessed remarkable progress in the treatment of patients with Chimeric Antigen Receptor T-cell (CAR-T) therapies, leading to high response rates and durable remissions. However, challenges persist for patients who do not respond to CAR-T treatment, experience relapse, or encounter adverse events such as cytokine release syndrome. Overcoming these challenges necessitates a deeper understanding of mechanisms and the development of advanced technologies and assays. This study focuses on harnessing the potential of an innovative microfluidic platform for high-throughput cell-based assays, enabling multi-omics and functional analysis using a minimal amount of primary patient cells. By utilizing this platform, we aim to gain insight into the dynamics of primary patient material by evaluating responses to aid in selection of promising CAR-T enhancements or combination therapies designed to overcome mechanisms of CAR-T failure or relapse to improve clinical outcomes. Methods: For the cytotoxicity assay, we utilized autologous or allogeneic pairs of CD19-directed CAR-T cells and T-cell negative fractions from ALL patients' blood apheresis samples, containing CD19-expressing cancer cells. A negative control was established using untransduced T-cells. To ensure high cell viability and purity, the cells underwent careful processing and were labeled with long-lived dyes for tracking. Multiple cell suspensions with precise Effector to Target to Negative Fraction ratios were prepared. Only a few thousand cells from each coculture suspension were seeded in microfluidic culture chambers, which required no fluidic control system. Experiments were conducted for up to 96 hours with media replacement every 24 hours. At each endpoint, media was collected for cytokine quantification, and cells were stained for live/dead counting as well as quantification of intracellular or surface marker expression by imaging. After image acquisition, cells were collected for RNA extraction and gene expression analysis. Results: Results demonstrated that the developed co-culture platform allows precise control over culture conditions, ensuring culture of accurate ratios of highly complex cell populations. The viability of primary cells in the device guaranteed functional relevance of the cytotoxicity assays for up to a 96-hour timepoint. Strong CAR-T-mediated cell killing was observed, with a dose-dependent effect depending on the co-culture's relative CAR-T content. Less than 50% cell survival was observed in cocultures with Effector to Target ratio 1:1, as compared to the untransduced T-cell control. Furthermore, strong CAR-T activation was observed with over 60% of CART expressing CD25 and CD69 surface markers, as measured by imaging. A multi-color staining panel allowed for precise monitoring of changes over time within the assay of immune cell populations, including cancer cells, monocytes/macrophages, and NK cells, among others. Cytokine analysis revealed an increased secretion of IL-2, TNFa, IFNg, and Granzyme B in coculture with CAR-T cells compared to untransduced T-cells, with a dose-dependent effect based on the CAR-T cell ratio. Finally, RNA isolated from remaining cells at the end of the assay was of high quality with yields sufficient to enable transcriptome analysis for each treatment condition. Discussion: This study contributes to the development of innovative multiplexed high throughput strategies for in vitro functionality assessments in cell therapy, including combination studies and deeper mechanistic understandings. The platform's ability to generate fully integrated, multi-omics readings from complex allogeneic and autologous cocultures of CAR-T and patient cells offers a new frontier in early discovery and translational cancer research. This opens new possibilities for drug discovery, drug screening, and disease modeling, ultimately advancing our understanding of complex biological processes and accelerating therapeutic development. Future directions include exploring mechanisms of resistance and sensitivity, including donor-specific effector cell functionality, combination studies, impacts of immunosuppressive cell types, patient heterogeneity of target antigen expression or other co-stimulatory molecules, and evaluation of product potency or fitness of incoming apheresis material.

Bexarotene drives the self-renewing proliferation of adult neural stem cells, promotes neuron-glial fate shift, and regulates late neuronal differentiation.

Treatment with bexarotene, a selective retinoid X receptor (RXR) agonist, significantly improves behavioral dysfunctions in various neurodegenerative animal models. Additionally, it activates neurodevelopmental and plasticity pathways in the brains of adult mice. Our objective was to investigate the impact of RXR activation by bexarotene on adult neural stem cells (aNSC) and their cell lineages. To achieve this, we treated NSCs isolated from the subventricular zone (SVZ) of adult rat brains from the proliferative stage to the differentiated status. The results showed that bexarotene-treated aNSC exhibited increased BrdU incorporation, SOX2+ dividing cell pairs, and cell migration from neurospheres, revealing that the treatment promotes self-renewing proliferation and cell motility in SVZ-aNCS. Furthermore, bexarotene induced a cell fate shift characterized by a significant increase in GFAP+/S100B+ differentiated astrocytes, which uncovers the participation of activated-RXR in astrogenesis. In the neuronal lineage, the fate shift was counteracted by bexarotene-induced enhancement of NeuN+ nuclei together with neurite network outgrowth, indicating that the RXR agonist stimulates SVZ-aNCS neuronal differentiation at later stages. These findings establish new connections between RXR activation, astro- and neurogenesis in the adult brain, and contribute to the development of therapeutic strategies targeting nuclear receptors for neural repair.

Determinants of electrical propagation and propagation block in Arrhythmogenic Cardiomyopathy

Gap junction and ion channel remodeling occur early in Arrhythmogenic Cardiomyopathy (ACM), but their pathogenic consequences have not been elucidated. Here, we identified the arrhythmogenic substrate, consisting of propagation slowing and conduction block, in ACM models expressing two different desmosomal gene variants. Neonatal rat ventricular myocytes were transduced to express variants in genes encoding desmosomal proteins plakoglobin or plakophilin-2. Studies were performed in engineered cells and anisotropic tissues to quantify changes in conduction velocity, formation of unidirectional propagation, cell–cell electrical coupling, and ion currents. Conduction velocity decreased by 71% and 63% in the two ACM models. SB216763, an inhibitor of glycogen synthase kinase-3 beta, restored conduction velocity to near normal levels. Compared to control, both ACM models showed greater propensity for unidirectional conduction block, which increased further at greater stimulation frequencies. Cell–cell electrical conductance measured in cell pairs was reduced by 86% and 87% in the two ACM models. Computer modeling showed close correspondence between simulated and experimentally determined changes in conduction velocity. The simulation identified that reduced cell–cell electrical coupling was the dominant factor leading to slow conduction, while the combination of reduced cell–cell electrical coupling, reduced sodium current and inward rectifier potassium current explained the development of unidirectional block. Expression of two different ACM variants markedly reduced cell–cell electrical coupling and conduction velocity, and greatly increased the likelihood of developing unidirectional block – both key features of arrhythmogenesis. This study provides the first quantitative analysis of cellular electrophysiological changes leading to the substrate of reentrant arrhythmias in early stage ACM.

Loss of p53 Impairs Death Receptor Expression and Confers Resistance to CD19-Directed CAR T-Cell Therapy in B-Cell Precursor Acute Lymphoblastic Leukemia

Background In recent years, new therapy strategies such as the antibody-drug conjugate inotuzumab ozogamicin, the bi-specific T-cell engager blinatumomab, and chimeric antigen receptor (CAR) T-cells have been introduced to salvage relapsed precursor B acute lymphoblastic leukemia (ALL). However, recent evidence indicates that these new therapies are ineffective in TP53-aberrant ALL, although the mechanism remains unclear. TP53 is the most frequently mutated gene in cancer, but in ALL, mutations or deletions affecting TP53 are rare, with an incidence of only 3% at diagnosis. However, at relapse, TP53 aberrations are found in approximately 12% of the patients and predict a very poor outcome. Consequently, relapsed TP53 deleted ALL is now classified as ‘very high risk’. Since p53-mediated apoptosis is an endpoint for many (cytotoxic) drugs, loss of p53 function induces therapy resistance to classical chemotherapeutics. Hence, there is a clear clinical need for more effective strategies to treat TP53 aberrant relapsed ALL. Methods Using CRISPR/Cas9, we introduced frameshift mutations in the TP53 gene to generate isogenic wild type and knockout models in TP53 WT ALL cell lines Nalm6 and RCH-ACV. Additionally, we prepared CD19-directed CAR T-cells with a 4-1BB co-stimulatory domain from three healthy donors by isolating, transducing, and expanding CD4+ and CD8+ T-cells separately. With flow cytometry, we assessed survival of p53 WT and p53 KO leukemic cells in the presence of CD4+ and CD8+ CAR T-cells at a 1:1 CD4:CD8 ratio. Moreover, we performed mRNA profiling by qRT-PCR and cell membrane profiling by flow cytometry to determine how loss of p53 affects CAR T mediated killing. Initial findings in cell lines were then validated in patient-derived xenografts. Results We observed that loss of p53 led to up to a 35% decrease in killing by overnight CAR T treatment in both cell line models (Figure 1A). Although loss of p53 has been linked to reduced cell surface expression of CD19 (Pan et al., 2020, Leukemia), no changes in CD19 expression were observed in response to p53 loss. In search for an explanation for the diminished killing, we performed mRNA profiling and found a reduced expression of death receptors CD95/Fas and DR5/TRAILR2 in p53-deficient cells, which was confirmed at the protein level with flow cytometry (Figure 1B). Indeed, CRISPR/Cas9 mediated loss of CD95/Fas expression in p53 wild type cells reduced CAR T mediated cell killing, consistent with a key role for CD95/Fas in T-cell mediated killing. Conversely, treatment of p53 proficient cells with MDM2 inhibitors induced expression of CD95/Fas and DR5/TRAILR2 (Figure 1B), which translated into enhanced killing of target cells. Most of these observations have already been recapitulated in a diagnosis-relapse pair of patient-derived cells in which the diagnosis was p53wild typeand the relapse was p53 deficient (Figure 1A-B). We observed lower baseline mRNA expression of CD95/Fas and DR5/TRAILR2 in p53-deficient cells, accompanied by a 50% reduction in killing relative to the p53 wild type controls. Conversely, MDM2 inhibition increased death receptor expression only in p53-proficient cells. The ongoing experiments validating enhanced killing after MDM2 inhibition in patient-derived cells will be presented during the meeting. Conclusions Loss of p53 impairs expression of CD95/Fas and DR5/TRAILR2, thereby protecting ALL cells from CAR T induced cell death. In addition, our results indicate that the p53-controlled expression of these receptors may be exploited to increase the efficacy of CAR T-cell therapy in p53-proficient patients.

Causal identification of single-cell experimental perturbation effects with CINEMA-OT

Recent advancements in single-cell technologies allow characterization of experimental perturbations at single-cell resolution. While methods have been developed to analyze such experiments, the application of a strict causal framework has not yet been explored for the inference of treatment effects at the single-cell level. Here we present a causal-inference-based approach to single-cell perturbation analysis, termed CINEMA-OT (causal independent effect module attribution + optimal transport). CINEMA-OT separates confounding sources of variation from perturbation effects to obtain an optimal transport matching that reflects counterfactual cell pairs. These cell pairs represent causal perturbation responses permitting a number of novel analyses, such as individual treatment-effect analysis, response clustering, attribution analysis, and synergy analysis. We benchmark CINEMA-OT on an array of treatment-effect estimation tasks for several simulated and real datasets and show that it outperforms other single-cell perturbation analysis methods. Finally, we perform CINEMA-OT analysis of two newly generated datasets: (1) rhinovirus and cigarette-smoke-exposed airway organoids, and (2) combinatorial cytokine stimulation of immune cells. In these experiments, CINEMA-OT reveals potential mechanisms by which cigarette-smoke exposure dulls the airway antiviral response, as well as the logic that governs chemokine secretion and peripheral immune cell recruitment.

Vinculin is essential for sustaining normal levels of endogenous forces at cell-cell contacts

Transmission of cell-generated (i.e., endogenous) tension at cell-cell contacts is crucial for tissue shape changes during morphogenesis and adult tissue repair in tissues such as epithelia. E-cadherin-based adhesions at cell-cell contacts are the primary means by which endogenous tension is transmitted between cells. The E-cadherin-β-catenin-α-catenin complex mechanically couples to the actin cytoskeleton (and thereby the cell’s contractile machinery) both directly and indirectly. However, the key adhesion constituents required for substantial endogenous force transmission at these adhesions in cell-cell contacts are unclear. Due to the role of α-catenin as a mechanotransducer that recruits vinculin at cell-cell contacts, we expected α-catenin to be essential for sustaining normal levels of force transmission. Instead, using the traction force imbalance method to determine the inter-cellular force at a single cell-cell contact between cell pairs, we found that it is vinculin that is essential for sustaining normal levels of endogenous force transmission, with absence of vinculin decreasing the inter-cellular tension by over 50%. Our results constrain the potential mechanical pathways of force transmission at cell-cell contacts and suggest that vinculin can transmit forces at E-cadherin adhesions independent of α-catenin, possibly through β-catenin. Furthermore, we tested the ability of lateral cell-cell contacts to withstand external stretch and found that both vinculin and α-catenin are essential to maintain cell-cell contact stability under external forces.

Engineering Electrode Rinse Solution Fluidics for Carbon-Based Reverse Electrodialysis Devices.

Natural salinity gradients are a promising source of so-called "blue energy", a renewable energy source that utilizes the free energy of mixing for power generation. One promising blue energy technology that converts these salinity gradients directly into electricity is reverse electrodialysis (RED). Used at its full potential, it could provide a substantial portion of the world's electricity consumption. Previous theoretical and experimental works have been done on optimizing RED devices, with the latter often focusing on precious and expensive metal electrodes. However, in order to rationally design and apply RED devices, we need to investigate all related transport phenomena─especially the fluidics of salinity gradient mixing and the redox electrolyte at various concentrations, which can have complex intertwined effects─in a fully functioning and scalable system. Here, guided by fundamental electrochemical and fluid dynamics theories, we work with an iron-based redox electrolyte with carbon electrodes in a RED device with tunable microfluidic environments and study the fundamental effects of electrolyte concentration and flow rate on the potential-driven redox activity and power output. We focus on optimizing the net power output, which is the difference between the gross power output generated by the RED device and the pumping power input, needed for salinity gradient mixing and redox electrolyte reactions. We find through this holistic approach that the electrolyte concentration in the electrode rinse solution is crucial for increasing the electrical current, while the pumping power input depends nonlinearly on the membrane separation distance. Finally, from this understanding, we designed a five cell-pair (CP) RED device that achieved a net power density of 224 mW m-2 CP-1, a 60% improvement compared to the nonoptimized case. This study highlights the importance of the electrode rinse solution fluidics and composition when rationally designing RED devices based on scalable carbon-based electrodes.

Isogenic pairs of induced-pluripotent stem-derived endothelial cells identify DYRK1A/PPARG/EGR1 pathway is responsible for Down syndrome-associated pulmonary hypertension.

Down syndrome (DS) is the most prevalent chromosomal disorder associated with a higher incidence of pulmonary arterial hypertension (PAH). The dysfunction of vascular endothelial cells (ECs) is known to cause pulmonary arterial remodeling in PAH, although the physiological characteristics of ECs harboring trisomy 21 (T21) are still unknown. In this study, we analyzed the human vascular ECs by utilizing the isogenic pairs of T21-induced pluripotent stem cells (iPSCs) and corrected disomy 21 (cDi21)-iPSCs. In T21-iPSC-derived ECs, apoptosis and mitochondrial reactive oxygen species (mROS) were significantly increased, and angiogenesis and oxygen consumption rate (OCR) were significantly impaired as compared with cDi21-iPSC-derived ECs. The RNA-sequencing identified that EGR1 on chromosome 5 was significantly upregulated in T21-ECs. Both EGR1 suppression by siRNA and pharmacological inhibitor could recover the apoptosis, mROS, angiogenesis, and OCR in T21-ECs. Alternately, the study also revealed that DYRK1A was responsible to increase EGR1 expression via PPARG suppression, and that chemical inhibition of DYRK1A could restore the apoptosis, mROS, angiogenesis, and OCR in T21-ECs. Finally, we demonstrated that EGR1 was significantly upregulated in the pulmonary arterial ECs from lung specimens of a patient with DS and PAH. In conclusion, DYRK1A/PPARG/EGR1 pathway could play a central role for the pulmonary EC functions and thus be associated with the pathogenesis of PAH in DS.

Measurement of Trogocytosis: Quantitative Analyses Validated with Rigorous Controls.

Trogocytosis is a process in which receptors on acceptor cells remove and internalize cognate ligands from donor cells. Trogocytosis has a profound and negative impact on mAb-based cancer immunotherapy, as seen in the treatment of chronic lymphocytic leukemia (CLL) with CD20 mAbs, such as rituximab (RTX) and ofatumumab (OFA). Our clinical observations of RTX/OFA-mediated loss of the CD20 target from circulating CLL cells have been replicated in our in vitro studies. Here we describe flow cytometry and fluorescence microscopy experiments, which demonstrate that acceptor cells, such as monocytes/macrophages that express FcγR, remove and internalize both antigen and donor cell-bound cognate IgG mAbs for several different mAb-donor cell pairs. Fluorescent mAbs and portions of the plasma cell membrane are transferred from donor cells to acceptor cells, which include the THP-1 monocytic cell line as well as freshly isolated monocytes. We describe rigorous controls to validate the reactions and eliminate dissociation or internalization as alternative mechanisms. Trogocytosis is likely to contribute to neutropenia, thrombocytopenia, and liver damage associated with use of antibody-drug conjugates. The methods we have described should allow for examination of strategies focused on blocking trogocytosis and its adverse effects. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Trogocytosis of mAb-opsonized donor cells mediated by adherent THP-1 cells Alternate Protocol: Application of fluorescence microscopy to examine THP-1 cell-mediated trogocytosis Support Protocol 1: Alexa labeling of mAbs and determination of F/P ratios Support Protocol 2: Standard washing procedure Support Protocol 3: Labeling and opsonization of cells Basic Protocol 2: Trogocytosis mediated by human monocytes as acceptor cells Support Protocol 4: Isolation of human monocytes Basic Protocol 3: Trogocytosis mediated by THP-1 cells in solution Support Protocol 5: Retinoic acid treatment of THP-1 cells Support Protocol 6: Culturing of SCC-25, BT-474, MOLT-4 and THP-1 cell lines.

Ploidy Determination in Banana Hybrids through Stomatal Studies and Chloroplast Count

Stomata are probably a viable taxonomy distinguishing feature. The study of stomata characteristics of synthetic banana hybrids and their parentage has been carried out. Ploidy determination is essential in banana breeding programs to understand the genetic makeup of hybrid plants. The purpose of this study was to determine the ploidy level of hybrids in contrast with the properties of plant stomata in synthetic banana hybrids with those of their parent plants. Therefore, by examining components such as stomata location, number of epidermal cells, number of stomata cells, stomata length, width, area, intensity and density, as well as chloroplast count, it is possible to compare and contrast the traits of synthetic banana hybrids and their parentage which have different genomes. The entire mount approach was used to make an incision for the purpose of observing stomata. By characterising the stomata traits of the synthetic hybrids and their parentage, the results were then descriptively and qualitatively assessed. Three different locations on the abaxial of the leaf were taken for the determination. The samples were collected from close to the petiole (R1), middle (R2), and distal end (R3), stomata were observed using the replica method. Results showed that more number of stomata was observed in R2of leaf abaxial. The chloroplast count in pairs of stomatal guard cells from the accessions was also measured. The chloroplast density was determined in pairs of stomatal guard cells from the accessions. Based on morphological descriptions, it was observed that 16.66% of the accessions were diploid, 50% were triploid and 33.33% were tetraploid. When considering the chloroplast count, the accessions were categorized into groups, certain accessions classified as tetraploids, others as triploids, and diploids.

3D numerical simulation of the separation zone at the channel-pipe junction.

At the confluence zone, the separation zone affects the flow, pollutant transport, and damages the bed and sidewalls of the channel. In this research, the geometric characteristics of the separation zone and the tailwater effect at the 90° channel-pipe junction are investigated using experiments and numerical simulations. These characteristics are different from the previous study in the channel or river junctions. (1) The separation zone is not attached to the sidewall of the channel. The shape of the separation zone is close to an ellipse but there is depression at the inside of the separation zone. (2) There is a pair of helical cells with opposite flow directions near the sidewall, which affects the shape of the separation zone and results in the differences. (3) The volume of the separation zone is proportional to the discharge ratio and the water-surface height. Furthermore, it's found that the momentum ratio is the basic reason affecting the volume of the separation zone. (4) The tailwater effect is affected by the discharge ratio and the water-surface height. And there is a significant positive correlation between the volume of separation zone and tailwater effect.

Spatiotemporal cell junction assembly in human iPSC-CM models of arrhythmogenic cardiomyopathy.

Arrhythmogenic cardiomyopathy (ACM) is an inherited cardiac disorder that causes life-threatening arrhythmias and myocardial dysfunction. Pathogenic variants in Plakophilin-2 (PKP2), a desmosome component within specialized cardiac cell junctions, cause the majority of ACM cases. However, the molecular mechanisms by which PKP2 variants induce disease phenotypes remain unclear. Here we built bioengineered platforms using genetically modified human induced pluripotent stem cell-derived cardiomyocytes to model the early spatiotemporal process of cardiomyocyte junction assembly invitro. Heterozygosity for truncating variant PKP2R413X reduced Wnt/β-catenin signaling, impaired myofibrillogenesis, delayed mechanical coupling, and reduced calcium wave velocity inengineered tissues. These abnormalities were ameliorated by SB216763, which activated Wnt/β-catenin signaling, improved cytoskeletalorganization, restored cell junction integrity in cell pairs, and improved calcium wave velocity in engineered tissues.Together, these findings highlight the therapeutic potential of modulating Wnt/β-catenin signaling in a human model of ACM.

Three-dimensional acoustic asymmetric focusing by mode-conversion structure

Acoustic asymmetric focusing (AAF) has attracted widespread attention owing to its great potential in medical ultrasound. The recent development of acoustic metamaterials and metasurfaces has provided various concepts to achieve AAF systems. Generally, the previously demonstrated AAF lenses were limited to one-dimensional structures, leading to difficulties in practical applications. The realization of AAF in three-dimensional (3D) space based on a two-dimensional (2D) device still remains a challenge. Here, we experimentally and numerically study a 2D AAF lens based on mode converters composed of two pairs of phased unit cells I and II and a step waveguide. Based on the phase profile of sound focusing and the step waveguide of mode converters, we experimentally design and demonstrate a type of 2D AAF lens and observe acoustic focusing and asymmetric transmission simultaneously in 3D space under the excitation of the zero-order wave. Both the phenomena arise from the phase modulation of the lens and the cutoff frequency of the first-order wave for the step waveguide, respectively. The fractional bandwidth (the ratio of the bandwidth to the center frequency) of the lens can reach about 0.14. The proposed 2D AAF lens, as well as its associated mode converter, paves the way for the asymmetric manipulation of sound in 3D space that has potential applications in practical sound devices.

A New Cancer Therapy with a Resonance Nuclear Reaction between 15n-5-ALA and Proton Beam: iPDT

A super-aged society, the prime example of which is Japan, is being flooded with increasing in numerous numbers of aged cancer patients, who often take anti-coagulant medicines to prevent the attacks of ischemic heart diseases and/ or strokes. Since they have diseases with bleeding tendency induced by the medicines, it’s hard for them to receive surgical operations. Thus, low invasive cancer treatments without bleedings are abundantly desired. In this study, the applicant will establish a new proton therapy, in which a resonance nuclear reaction (RNR) induced by collision of a proton with a stable nitrogen isotope (15N), can be a clue to injure cancer-cells specifically. The LET of the product ions (12C6+, 4He2+) of the 15N RNR is above 50 times in comparison with the LET of proton. To establish the cancer-specific 15N delivery, 15N-aminolevulinic acid (15N-ALA) will be used. This reagent has been already used and obtained regulatory approvals as a diagnostic medicine for the location of the glioblastoma in Japan.In this study, a pair of rat gastric epithelial cells, one is normal cell, and another is cancerous characteristics cells were used, 15N-ALA treated porphyrin fluorescent intensity of these cells will be compared with 14N-ALA treatment. The cells will be irradiated with a proton beam generated by an electrostatic accelerator and 4.43 MeV gamma-rays will be measured to demonstrate the amount of 15N collected specifically in the tumour cells. Such quantitative analysis of 15N in the tumour cells can be a new pre-diagnosis of iPDT.

Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions

The execution of cognitive functions requires coordinated circuit activity across different brain areas that involves the associated firing of neuronal assemblies. Here, we tested the circuit mechanism behind assembly interactions between the hippocampus and the medial prefrontal cortex (mPFC) of adult rats by recording neuronal populations during a rule-switching task. We identified functionally coupled CA1-mPFC cells that synchronized their activity beyond that expected from common spatial coding or oscillatory firing. When such cell pairs fired together, the mPFC cell strongly phase locked to CA1 theta oscillations and maintained consistent theta firing phases, independent of the theta timing of their CA1 counterpart. These functionally connected CA1-mPFC cells formed interconnected assemblies. While firing together with their CA1 assembly partners, mPFC cells fired along specific theta sequences. Our results suggest that upregulated theta oscillatory firing of mPFC cells can signal transient interactions with specific CA1 assemblies, thus enabling distributed computations.

Topological properties and shape of proliferative and nonproliferative cell monolayers.

During embryonic development, structures with complex geometry can emerge from planar epithelial monolayers; studying these shape transitions is of key importance for revealing the biophysical laws involved in the morphogenesis of biological systems. Here, using the example of normal proliferative monkey kidney (COS) cell monolayers, we investigate global and local topological characteristics of this model system in dependence on its shape. The obtained distributions of cells by their valence demonstrate a difference between the spherical and planar monolayers. In addition, in both spherical and planar monolayers, the probability of observing a pair of neighboring cells with certain valences depends on the topological charge of the pair. The zero topological charge of the cell pair can increase the probability for the cells to be the nearest neighbors. We then test and confirm that analogous relationships take place in a more ordered spherical system with a larger fraction of 6-valent cells, namely, in the nonproliferative epithelium (follicular system) of ascidian species oocytes. However, unlike spherical COS cell monolayers, ascidian monolayers are prone to nonrandom agglomeration of 6-valent cells and have linear topological defects called scars and pleats. The reasons for this difference in morphology are discussed. The morphological peculiarities found are compared with predictions of the widely used vertex model of epithelium.

Quantitative Analysis of the Coordinated Movement of Cells in a Freely Moving Cell Population

Coordinated movement of self-propelled agents has been well studied in collectives or swarms that display directional movement. Self-propelled agents also develop stable spatial patterns in which the agents do not necessarily exhibit directional collective movement. However, quantitative measures that are required to analyze the local and temporal coordinated movements during pattern formation processes have not been well established. Here, we study the coordinated movement of individual pairs of two different types of cells in a freely moving cell population. We introduced three criteria to evaluate coordinated movement in live imaging data obtained from the abdomen of the fruit fly, Drosophila melanogaster, at the pupal stage. All three criteria were able to reasonably identify coordinated movement. Our analysis indicates that the combined usage of these criteria can improve the evaluation of whether a pair of cells exhibits coordinated movement or not by excluding false positives. Quantitative approaches to identifying coordinated movement in a population of freely moving agents constitute a key foundational methodology to study pattern formations by self-propelled agents.