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bioRxiv2021

HIV-1 Vpr drives a tissue residency-like phenotype during selective infection of resting memory T cells

Human immunodeficiency virus type 1 (HIV-1) replicates in CD4+ T cells leading to profound T cell loss, immunological dysfunction and AIDS. Determining how HIV-1 shapes the immunological niche in which it resides to create a permissive environment is central to informing efforts to limit pathogenesis, disturb viral reservoirs and achieve a cure. A key roadblock in understanding HIV-T cell interactions is the requirement to activate CD4+ T cells in vitro in order to make them permissive to infection. This dramatically alters T cell biology, obscuring native virus-host interactions. Here we show that HIV-1 cell-to-cell spread permits efficient and productive infection of resting CD4+ T cells without the need for prior activation. Infection is preferential for resting memory T cells, is observed with both CXCR4-tropic virus and CCR5-tropic transmitter-founder viruses and results in virus production and onward spreading infection. Strikingly, we find that HIV-1 infection of resting memory CD4+ T cells primes for induction of a tissue-resident memory (TRM)-like phenotype evidenced by upregulation of TRM markers CD69/CXCR6 alongside co-expression of CD49a, PD-1, CD101 as well as transcription factor Blimp-1. Furthermore, we reveal that HIV-1 initiates a transcriptional program that overlaps with the core TRM transcriptional signature. This reprograming depends on the HIV-1 accessory protein Vpr. We propose that HIV-1 infection drives a CD4+ TRM-phenotype potentially sequestering infected cells within tissues to support viral replication and persistence.

microbiology↗

bioRxiv2021

Benzofuran sulfonates and small self-lipid antigens activate type II NKT cells via CD1d

Natural Killer T (NKT) cells detect lipids presented by CD1d. Most studies focus on type I NKT cells that express semi-invariant {beta} T cell receptors (TCR) and recognise -galactosylceramides. However, CD1d also presents structurally distinct lipids to NKT cells expressing diverse TCRs (type II NKT cells) but our knowledge of the antigens for type II NKT cells is limited. An early study identified an NKT cell agonist, phenyl pentamethyldihydrobenzofuransulfonate (PPBF), which is notable for its similarity to common sulfa-drugs, but its mechanism of NKT-cell activation remained unknown. Here we demonstrate that a range of pentamethylbenzofuransulfonate (PBFs), including PPBF, activate polyclonal type II NKT cells from human donors. Whereas these sulfa drug-like molecules might have acted pharmacologically on cells, here we demonstrate direct contact between TCRs and PBF-treated CD1d complexes. Further, PBF-treated CD1d-tetramers identified type II NKT cell populations cells expressing {beta} and {gamma}{delta}TCRs, including those with variable and joining region gene usage (TRAV12-1-TRAJ6) that was conserved across donors. By trapping a CD1d-type II NKT TCR complex for direct mass spectrometric analysis, we detected molecules that allow binding of CD1d to TCRs, finding that both PBF and short-chain sphingomyelin lipids are present in these complexes. Furthermore, the combination of PPBF and short-chain sphingomyelin enhances CD1d tetramer staining of PPBF-reactive T cell lines over either molecule alone. This study demonstrates that non-lipidic small molecules, that resemble sulfa-drugs implicated in systemic hypersensitivity and drug allergy reactions, activate a polyclonal population of type II NKT cells in a CD1d-restricted manner. Significance StatementWhereas T cells are known to recognize peptide, vitamin B metabolite or lipid antigens, we identify several non-lipidic small molecules, pentamethylbenzofuransulfonates (PBFs), that activate a population of CD1d-restricted NKT cells. This represents a breakthrough in the field of NKT cell biology. This study also reveals a previously unknown population of PBF-reactive NKT cells in healthy individuals with stereotyped receptors that paves the way for future studies of the role of these cells in immunity, including sulfa-drug hypersensitivity.

immunology↗

bioRxiv2021

Genome-wide association study on 13,167 individuals identifies regulators of hematopoietic stem and progenitor cell levels in human blood

Understanding how hematopoietic stem and progenitor cells (HSPCs) are regulated is of central importance for the development of new therapies for blood disorders and stem cell transplantation. To date, HSPC regulation has been extensively studied in vitro and in animal models, but less is known about the mechanisms in vivo in humans. Here, in a genome-wide association study on 13,167 individuals, we identify 9 significant and 2 suggestive DNA sequence variants that influence HSPC (CD34+) levels in human blood. The identified loci associate with blood disorders, harbor known and novel HSPC genes, and affect gene expression in HSPCs. Interestingly, our strongest association maps to the PPM1H gene, encoding an evolutionarily conserved serine/threonine phosphatase never previously implicated in stem cell biology. PPM1H is expressed in HSPCs, and the allele that confers higher blood CD34+ cell levels downregulates PPM1H. By functional fine-mapping, we find that this downregulation is caused by the variant rs772557-A, which abrogates a MYB transcription factor binding site in PPM1H intron 1 that is active in specific HSPC subpopulations, including hematopoietic stem cells, and interacts with the promoter by chromatin looping. Furthermore, rs772557-A selectively increases HSPC subpopulations in which the MYB site is active, and PPM1H shRNA- knockdown increased CD34+ and CD34+90+ cell proportions in umbilical cord blood cultures. Our findings represent the first large-scale association study on a stem cell trait, illuminating HSPC regulation in vivo in humans, and identifying PPM1H as a novel inhibition target that can potentially be utilized clinically to facilitate stem cell harvesting for transplantation.

genomics↗

bioRxiv2022

The cryo-EM structure of the CENP-A nucleosome in complex with ggKNL2

Centromere protein A (CENP-A) nucleosome is an epigenetic marker that specifies centromere position. The Mis18 complex is a licensing factor for new CENP-A deposition via the CENP-A chaperone, Holliday junction recognition protein (HJURP) on the centromere chromatin. Chicken KINETOCHORE NULL2 (KNL2) (ggKNL2), a Mis18 complex component, has a CENP-C-like motif, and our previous study suggested that ggKNL2 directly binds to the CENP-A nucleosome to recruit HJURP/CENP-A to the centromere. However, the molecular basis for CENP-A nucleosome recognition by ggKNK2 remains unclear. Here, we present the cryo-EM structure of the chicken CENP-A nucleosome in complex with a ggKNL2 fragment containing a CENP-C-like motif. Chicken KNL2 distinguishes between CENP-A and histone H3 in the nucleosome using the CENP-C-like motif and its downstream region. Both the C-terminal tail and RG-loop of CENP-A are simultaneously recognized as CENP-A characteristics. The CENP-A nucleosome-ggKNL2 interaction is thus essential for CENP-A deposition. Furthermore, our structural, biochemical, and cell biology data indicate that ggKNL2 alters its binding partner at the centromere during chicken cell cycle progression.

biochemistry↗

bioRxiv2022

The two enantiomers of 2-hydroxyglutarate differentially regulate cytotoxic T cell function

2-hydroxyglutarate (2HG) is a by-product of the TCA cycle, and is readily detected in the tissues of healthy individuals. 2HG is found in two enantiomeric forms: S-2HG and R-2HG. Here, we investigate the differential roles of these two enantiomers in CD8+ T cell biology, where we found they had highly divergent effects on proliferation, differentiation, and T cell function. We show here an analysis of structural determinants that likely underlie these differential effects on specific a-ketoglutarate (aKG)-dependent enzymes. Treatment of CD8+ T cells with exogenous S-2HG, but not R-2HG, increased CD8+ T cell fitness in vivo, and enhanced anti-tumour activity. These data show that S-2HG and R-2HG should be considered as two distinct and important actors in the regulation of T cell function.

immunology↗

bioRxiv2023

Super-resolution histology of paraffin-embedded samples via photonic chip-based microscopy

Fluorescence-based super-resolution optical microscopy (SRM) techniques allow the visualization of biological structures beyond the diffraction limit of conventional microscopes. Despite its successful adoption in cell biology, the integration of SRM into the field of histology has been deferred due to several obstacles. These include limited imaging throughput, high cost, and the need for complex sample preparation. Additionally, the refractive index heterogeneity and high labeling density of commonly available formalin-fixed paraffin-embedded (FFPE) tissue samples pose major challenges to applying existing super-resolution microscopy methods. Here, we demonstrate that photonic chip-based microscopy alleviates several of these challenges and opens avenues for super-resolution imaging of FFPE tissue sections. By illuminating samples through a high refractive-index waveguide material, the photonic chip-based platform enables ultra-thin optical sectioning via evanescent field excitation, which reduces signal scattering and enhances both the signal-to-noise ratio and the contrast. Furthermore, the photonic chip provides decoupled illumination and collection light paths, allowing for total internal reflection fluorescence (TIRF) imaging over large and scalable fields of view. By exploiting the spatiotemporal signal emission via MUSICAL, a fluorescence fluctuation-based super-resolution microscopy (FF-SRM) algorithm, we demonstrate the versatility of this novel microscopy method in achieving superior contrast super-resolution images of diverse FFPE tissue sections derived from human colon, prostate, and placenta. The photonic chip is compatible with routine histological workflows and allows multimodal analysis such as correlative light-electron microscopy (CLEM), offering a promising tool for the adoption of super-resolution imaging of FFPE sections in both research and clinical settings.

pathology↗

bioRxiv2017

A physical model of cell metabolism

Cell metabolism is characterized by three fundamental energy demands to sustain cell maintenance, to trigger aerobic fermentation and to achieve maximum metabolic rate. Here we report a physical model of cell metabolism that explains the origin of these three energy scales. Our key hypothesis is that the maintenance energy demand is rooted on the energy expended by molecular motors to fluidize the cytoplasm and counteract molecular crowding. Using this model and independent parameter estimates we make predictions for the three energy scales that are in quantitative agreement with experimental values. The model also recapitulates the dependencies of cell growth with extracellular osmolarity and temperature. This theory brings together biophysics and cell biology in a tractable model that can be applied to understand key principles of cell metabolism.

biophysics↗

bioRxiv2018

Baculovirus AC102 is a nucleocapsid protein that is crucial for nuclear actin polymerization and nucleocapsid morphogensis

The baculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV), the type species of alphabaculoviruses, is an enveloped DNA virus that infects lepidopteran insects and is commonly known as a vector for protein expression and cell transduction. AcMNPV belongs to a diverse group of viral and bacterial pathogens that target the host cell actin cytoskeleton during infection. AcMNPV is unusual, however, in that it absolutely requires actin translocation into the nucleus early in infection, and actin polymerization within the nucleus late in infection coincident with viral replication. Of the six viral factors that are sufficient, when coexpressed, to induce the nuclear localization of actin, only AC102 is essential for viral replication and the nuclear accumulation of actin. We therefore sought to better understand the role of AC102 in actin mobilization in the nucleus early and late in infection. Although AC102 was thought to function early in infection, we found that AC102 is predominantly expressed as a late protein. In addition, we observed that AC102 is required for F-actin assembly in the nucleus during late infection, as well as for proper formation of viral replication structures and nucleocapsid morphogenesis. Finally, we found that AC102 is a nucleocapsid protein and a newly recognized member of a complex consisting of the viral proteins EC27, C42, and the actin polymerization protein P78/83. Taken together, our findings suggest that AC102 is necessary for nucleocapsid morphogenesis and actin assembly during late infection through its role as a component of the P78/83-C42-EC27-AC102 protein complex.\n\nIMPORTANCEThe baculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is an important biotechnological tool for protein expression and cell transduction, and related nucleopolyhedroviruses are also employed as environmentally benign insecticides. One impact of our work is to better understand the fundamental mechanisms through which AcMNPV exploits the cellular machinery of the host for replication, which may aid in the development of improved baculovirus-based research and industrial tools. Moreover, AcMNPVs ability to mobilize the host actin cytoskeleton within the cells nucleus during infection makes it a powerful cell biological tool. It is becoming increasingly clear that actin plays important roles in the cells nucleus, yet the regulation and function of nuclear actin is poorly understood. Our work to better understand how AcMNPV relocalizes and polymerizes actin within the nucleus may reveal fundamental mechanisms that govern nuclear actin regulation and function, even in the absence of viral infection.

microbiology↗

bioRxiv2018

Humoral immune response to adenovirus induce tolerogenic bystander dendritic cells that promote generation of regulatory T cells

Following repeated encounters with adenoviruses most of us develop robust humoral and cellular immune responses that are thought to act together to combat ongoing and subsequent infections. Yet in spite of robust immune responses, adenoviruses establish subclinical persistent infections that can last for decades. While adenovirus persistence pose minimal risk in B-cell compromised individuals, if T-cell immunity is severely compromised, reactivation of latent adenoviruses can be life threatening. This dichotomy led us to ask how anti-adenovirus antibodies influence adenovirus-specific T-cell immunity. Using primary human blood cells, transcriptome and secretome profiling, and pharmacological, biochemical, genetic, molecular, and cell biological approaches, we initially found that healthy adults harbor adenovirus-specific regulatory T cells (Tregs). As peripherally induced Tregs are generated by tolerogenic dendritic cells (DCs), we then addressed how tolerogenic DCs could be created. Here, we demonstrate that DCs that take up immunoglobulin-complexed (IC)-adenoviruses create an environment that causes bystander DCs to become tolerogenic. These adenovirus antigen-loaded tolerogenic DCs can drive naive T cells to mature into adenovirus-specific Tregs. Our results may provide ways to improve antiviral therapy and/or pre-screening high-risk individuals undergoing immunosuppression.\n\nAuthor summaryWhile numerous studies have addressed the cellular and humoral response to primary virus encounters, relatively little is known about the interplay between persistent infections, neutralizing antibodies, antigen-presenting cells, and the T-cell response. Our studies suggests that if adenovirus-antibody complexes are taken up by professional antigen-presenting cells (dendritic cells), the DCs generate an environment that causes bystander dendritic cells to become tolerogenic. These tolerogenic dendritic cells favors the creation of adenovirus-specific regulatory T cells. While this pathway likely favors pathogen survival, there may be advantages for the host also.

microbiology↗

bioRxiv2026

IFN gamma-induced IRF1 synergizes with TLR7 signals to tune the IRF4-IRF8 axis and drive pathogenic effector B cell fate

Interferon regulatory factor 1 (IRF1), a transcription factor encoded within the 5q31 locus harboring systemic lupus erythematosus (SLE) associated variants, promotes inflammatory responses by T and myeloid cells. Although IFN{gamma}-activated B cells also express IRF1, its role in B cell biology and SLE is unclear. Here, we use a mouse SLE model, single-cell multiomics, and human B cells to show that IRF1 intrinsically regulates Irf4 gene chromatin accessibility and expression in B cells to control the balance between the antibody secreting cell (ASC) lineage commitment factor, IRF4, and the B cell identity factor, IRF8. We demonstrate that IRF1, through its integration of IFN{gamma} and TLR7 induced transcriptional programs, tips B cells toward a terminal effector inflammatory AC fate at the expense of preserving more stem-like, resting and regulatory B cells that do not elicit autoantibody-associated pathology in SLE. Thus, IRF1 serves as a central node controlling B cell-driven autoimmune disease.

immunology↗

bioRxiv2026

A latent space thermodynamic model of cell differentiation

Inferring the governing dynamics of differentiation that capture cell state evolution remains a central challenge in single-cell biology. We present Latent Space Dynamics (LSD), a thermodynamics-inspired framework that models cell differentiation as evolution on a learned Waddington landscape in latent space. LSD jointly infers a low-dimensional cell state, a differentiable potential function governing developmental flow, and a local entropy term that quantifies cellular plasticity. Using a neural ordinary differential equation, LSD reconstructs continuous differentiation trajectories from time-ordered single-cell data. Across diverse developmental systems, LSD accurately recovers lineage hierarchies, predicts fate commitment for unseen cell types, and outperforms existing trajectory inference approaches in directional accuracy. Moreover, in silico gene perturbations reveal how individual regulators reshape the landscape, and entropy provides a quantitative measure of plasticity in development and cancer.

bioinformatics↗

bioRxiv2026

Improving Generalizability in Whole-Cell Antibiotic Discovery Through Active Learning

Machine learning (ML) has accelerated molecular discovery, yet training models to generalize to out-of-distribution (OOD) chemical spaces remains fundamentally constrained by the high cost of experimental validation. In antibiotic discovery, where whole-cell phenotypic high throughput screening (HTS) is resource-intensive, iterative ML-guided compound selection - or Active Learning (AL) - offers a pathway to efficiently navigate available chemical spaces. However, the algorithmic tradeoffs between prioritizing compound novelty (exploration), predicted bioactivity (exploitation), and their impact on OOD generalizability remain unresolved for noisy, whole-cell biological systems. In this work, we systematically evaluate three AL strategies for whole-cell bacterial bioactivity and benchmark their effects on model accuracy, hit rate, and OOD performance. Using retrospective simulations on Mycobacterium tuberculosis HTS data, we identify an optimal AL strategy that balances predicted hit/non-hit novelty with overall hit rate. We then integrate the strategy in a closed-loop Borrelia burgdorferi antibiotic discovery HTS campaign. The AL-guided approach successfully increased the experimental screening hit rate five-fold (from a 0.2% rate within investigator-selected plates to 1.0%). Further, when the trained model was applied in prospective in silico selection of highly diverse compounds across multiple bacterial species, the AL-trained whole-cell inhibition predictor demonstrates 53-fold enrichment over investigator-directed screening (11.0% experimental validation of predicted hits). Of these, 100% demonstrated the intended narrow spectrum activity for Borrelia burgdorferi. These results demonstrate that calibrated AL strategies can overcome data acquisition bottlenecks and train generalizable property predictors able to extrapolate to OOD molecules.

bioinformatics↗

bioRxiv2026

An expanded LPS translocon mediates surface lipoprotein export in the Bacteroidota

Cell surface lipoproteins (SLPs) play crucial roles in the pathogenesis and cell biology of gram-negative bacteria, yet the route by which they reach the cell surface has remained unknown except in special cases. Here we show that in Bacteroidota bacteria, a phylum that includes prominent human commensals and anaerobic pathogens, SLP export is carried out by the outer membrane lipopolysaccharide (LPS) translocon. Isolation and structural characterisation of LPS translocon complexes from two Bacteroidota species reveals that they are massively enlarged and elaborated relative to the Escherichia coli paradigm with up to eight additional subunits located within, and on either side of, the outer membrane. We establish a role for the universally conserved core LptD subunit and four of the additional Bacteroidota-specific subunits in SLP export. Expansion of the LPS translocon in the Bacteroidota may allow export of the unusually complex SLPs found in this phylum. Our discoveries raise the possibility that SLP export is a conserved second function of the LPS transport pathway across gram-negative bacteria.

microbiology↗

bioRxiv2026

Mapping the regulatory wiring of endothelial cell differentiation reveals a critical role for Hippo mechanosignaling

At each step of development, stem cells encounter a branching decision to differentiate into one type of cell or another. This decision is executed through the action of competing gene programs that specify different cellular identities. Consequently, creating a comprehensive map of the gene programs that drive each branching step of human cell differentiation remains a long-sought goal of developmental and stem cell biology. Here, we introduce a framework combining genome-wide CRISPR screens, single-cell readouts, and gene program inference to systematically discover and characterize regulators of cell differentiation. This framework includes a method for CRISPR perturbations paired with single-cell RNA-seq called circular capture Perturb-seq (CC-Perturb-seq), which improves gRNA detection from split-pool combinatorial indexing protocols and enables perturbing many candidate regulators to map their effects on gene programs. We applied this framework to map how human pluripotent stem cells differentiate into arterial endothelial cells (ECs), and identified 174 regulators that promote or inhibit EC differentiation. By tracking gene programs across three stages of differentiation, we resolved when and how regulators divert cells toward alternative fates. This map revealed an unexpected requirement for the Hippo mechanosignaling pathway in EC specification. During lateral mesoderm differentiation, Hippo mechanosignaling was required to activate ETV2, the master transcriptional regulator of endothelial identity. Inhibiting Hippo blocked ETV2 even in the presence of VEGF and diverted progenitors to a mesenchymal fate in vitro. Likewise, Hippo signaling was required for maximal etv2 expression in developing zebrafish embryos. Conversely, pharmacologically activating the Hippo pathway increased the purity of both arterial and venous EC differentiation in vitro. Our framework thus identifies novel regulators of endothelial cell differentiation, improves stem-cell differentiation protocols via manipulation of mechanosignaling, and provides a generalizable platform for mapping the regulatory wiring of human development.

genomics↗

bioRxiv2025

Actin network heterogeneity tunes activator-inhibitor dynamics at the cell cortex

Biological systems can display diverse patterns of self-organization, even when built on conserved networks of interaction between molecular species. In these cases, reaction-diffusion equations provide a valuable tool to learn how new dynamics could emerge from quantitative tuning of parameters. Bringing these models into quantitative correspondence with biological data remains an outstanding challenge, especially when the data manifest heterogeneities that are difficult to account for mathematically. One particular example occurs in cell biology, where the membrane-bound regulatory protein RhoA interacts with the filamentous actin cortex in an activator-inhibitor loop. Though this core biochemical circuit is conserved across multiple cell types in different organisms, it produces different patterns of RhoA activity in different contexts, from traveling waves in starfish to transient pulses in C. elegans. To understand how this variation emerges, we develop an activator-inhibitor model that accounts explicitly for actin assembly and heterogeneity. By fitting the model to summary statistics of experimental data, subject to known parameter constraints, we show that F-actin assembly dynamics tune the spatiotemporal patterns of RhoA activity. A minimal representation of these dynamics reveals how directional transport (via polymerization) combines with stochasticity in F-actin number and orientation to produce the observed patterns. This work sheds light on how phenotypic diversity arises from heterogeneity and anisotropy, with important implications for the next generation of activator-inhibitor models. SignificanceTo divide, move, and polarize, cells must self-organize their constituent proteins into large-scale patterns with varied spatiotemporal character. The design principles of this process remain poorly understood, primarily because quantitatively matching mathematical models to experimental data is difficult. Here we consider pattern formation from two constituents on the cell cortex: the regulatory protein RhoA and actin filaments. Using a mathematical model, constrained quantitatively by data from multiple organisms, we show how diversity in RhoA activity can arise from intra- and inter-organismal changes in actin filament architecture and assembly dynamics. Our results reveal general principles for pattern formation at the cortex, and our combination of data analysis, modeling, and parameter inference provides a broadly-applicable, interdisciplinary methodology to unravel mechanisms of self-organization.

cell biology↗

bioRxiv2023

Apoptosis-coupled senescence causes cancer cell senotherapy

Although new generations of anti-cancer modalities have been accumulated involving immuno-oncology cancers remain prevailing. This implies the current understanding of cancer cell biology is far from satisfactory. Curation of cancers is extremely rare. We hypothesized what could be the easiest Achilles Hill of cancer cells such that simple administration can jab cancer cells to be knocked out. Of conspicuous differences between cancer cells and normal cells, for example, metabolism, hypoxia, anaerobic glycolysis, uncontrolled cell proliferation, etc. exist. What could be the easiest and the most reliable anti-cancer modalities? We discovered one was cancer cell senescence (CCS) because cancer cells are the most presenescent (old) cells. We utilized a synthetic polyphenol designated as ONG41008. ONG41008 was able to induce massive senescence of pathologic myofibroblasts (pMFBs) and a vast majority of representative human cancer cells as well as a line of primary NSCLCs. All these cells turned out to be senescence-associated beta-galactosidase (SAbGAL) positive to different degrees, which does not mean real senescence is occurring in these cells. ONG41008 did not harm normal cells and elicited massive senescence in pMFBs without apoptosis. However, ONG41008 caused massive senescence as well as apoptosis in cancer cells. In other words, ONG41008 was capable of sensing intracellular molecular environments between normal cells, cancer cells, and pMFBs. This molecular recognition capability prompted us to explore how ONG4008 behaved on A549 (a human lung adenocarcinoma), PANC1(malignant human ductal adenocarcinoma), and mdr+PC3 (multidrug-resistant human prostate cancer). TP53, p21, and p16 were induced and/or nuclear relocated, suggesting that ONG41008 was recognized by these cells. ONG41008 drove A549 and PANC1 at G2/M phase arrest during 48 hrs, resulting in massive mitotic collapse. All cells died. Moreover, the cisplatin-resistant mdr+PC3 was also eliminated by ONG41008. An array of common components of apoptosis were activated, and especially, induction of Mcl1 was especially notable. These senolytics features were reported to oncogene-induced-senescence (OIS), in which the expression of over two activated oncogenes in the embryonic fibroblasts caused massive senescence and cell death as well. And the signature expression of Mcl1, an anti-apoptotic protein (a long form), was notable but two kinds of short forms are pro-apoptotic proteins. OIS was conducted in vitro cell culture models and whether or not the presence of OIS counterpart in vivo remains to be delineated. Taken together, we discovered a synthetic polyphenol referred to as ONG41008 was both senogenic and senolytic and its senescent impacts may make the cell cycles of the ONG41008-treated cancer cells immensely arrested at the G2/M phase, leading to mitotic slippage and cell death. This interesting observation may be able to create an idealistic anti-cancer modality, specifically killing cancer cells, but normal cells remain unharmed.

cancer biology↗

bioRxiv2019

Genetic design automation for autonomous formation of multicellular shapes from a single cell progenitor

AO_SCPLOWBSTRACTC_SCPLOWMulti-cellular organisms originate from a single cell, ultimately giving rise to mature organisms of heterogeneous cell type composition in complex structures. Recent work in the areas of stem cell biology and tissue engineering have laid major groundwork in the ability to convert certain types of cells into other types, but there has been limited progress in the ability to control the morphology of cellular masses as they grow. Contemporary approaches to this problem have included the use of artificial scaffolds, 3D bioprinting, and complex media formulations, however, there are no existing approaches to controlling this process purely through genetics and from a single-cell starting point. Here we describe a computer-aided design approach for designing recombinase-based genetic circuits for controlling the formation of multi-cellular masses into arbitrary shapes in human cells.

synthetic biology↗

bioRxiv2020

Model for Deformation of Cells from External Electric Fields at or Near Resonant Frequencies

This paper presents a numerical model to investigate the deformation of biological cells by applying external electric fields operating at or near cell resonant frequencies. Cells are represented as pseudo solids with high viscosity suspended in liquid media. The electric field source is an atmospheric plasma jet developed inhouse, for which the emitted energy distribution has been measured. Viscoelastic response is resolved in the entire cell structure by solving a deformation matrix assuming an isotropic material with a prescribed modulus of elasticity. To investigate cell deformation at resonant frequencies, one mode of natural cell oscillation is considered in which the cell membrane is made to radially move about its eigenfrequency. An electromagnetic wave source interacts with the cell and induces oscillation and viscoelastic response. The source carries energy in the form of a distribution function which couples a range of oscillating frequencies with electric field amplitude. Results show that cell response may be increased by the external electric field operating at or near resonance. In the elastic regime, response increases until a steady threshold value, and the structure moves as a damped oscillator. Generally, this response is a function of both frequency and magnitude of the source, with a maximum effect found at resonance. To understand the full effect of the source energy spectrum, the system is solved by considering five frequency-amplitude couplings. Results show that the total solution is a nonlinear combination of the individual solutions. Additionally, sources with different signal phases are simulated to determine the effect of initial conditions on the evolution of the system, and the result suggests that there may be multiple solutions within the same order of magnitude for elastic response and velocity. Cell rupture from electric stress may occur during application given a high energy source. SignificanceCold atmospheric plasma jets (CAPJs) have been widely researched for their potential applications in cancer therapy. Existing research has focused mainly on the ability of CAPJs to deliver a mixture of reactive species which can be absorbed by cancer cells and induce cell death. The objective of our study is to investigate the mechanical effect of CAPJ electromagnetic (EM) waves on interacting cells. By coupling the EM waves associated with plasma frequency and cell viscoelastic response, we have developed a numerical tool to investigate cell damage either by mechanical or thermal loads. This work is motivated by the promise of EM waves to function as a sensitizing agent for cancer cells in preparation for chemotherapy.

biophysics↗