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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 1,009 records · Page 56Linked to original sources

Towards a Mechanical Model for anisotropic Glioma Spread using Darcy's law

The growth of a tumor within a finite domain (skull) generates mechanical forces that alter the physical interactions among cells. The relationship between these forces and the tumor architecture remains an open problem subjected to extensive research. Recently, it has been determined that those regions of high mechanical compression can accelerate and intensify the invasive capacity of the malignant cells, forming an irregular tumor whose full extent and edges are difficult to identify. In the present paper, we propose a one-dimensional mathematical model that describes the process of proliferation and diffusion of glioma cells taking into account the mechanical compression generated during its expansion. Supported on the mixture theory, we model the brain-tumor system as a multiphase mixture of cancer cells, healthy cells, biological fluids and extracellular matrix whose densities determine the mechanical loads generated during the volumetric growth. Our model provides a detailed understanding of the pressure distribution on the interface boundary between healthy and cancer cells. It validates the hypothesis that the conferred ability of cancer cells to proliferate depends strongly on the mechanical pressure sensed. Through the analysis of the mechanical pressure, we determine that the anisotropic loads promote cancer cells to grow preferentially in the directions of low mechanical compression.

bioengineering↗

The fluorescence-activating and absorption-shifting tag (FAST) enables live-cell fluorescence imaging of Methanococcus maripaludis

Live-cell fluorescence imaging in methanogenic archaea has been limited due to the strictly anoxic conditions required for growth and issues with autofluorescence associated with electron carriers in central metabolism. Here, we show that the fluorescence-activating and absorption-shifting tag (FAST) when complexed with the fluorogenic ligand 4-hydroxy-3-methylbenzylidene-rhodanine (HMBR) overcomes these issues and displays robust fluorescence in Methanococcus maripaludis. We also describe a mechanism to visualize cells under anoxic conditions using a fluorescence microscope. Derivatives of FAST were successfully applied for protein abundance analysis, subcellular localization, and determination of protein-protein interactions. FAST fusions to both formate dehydrogenase (Fdh) and F420-reducing hydrogenase (Fru) displayed increased fluorescence in cells grown on formate containing medium, consistent with previous studies suggesting increased abundance of these proteins in the absence of H2. Additionally, FAST fusions to both Fru and the ATPase associated with the archaellum (FlaI) showed membrane localization in single cells observed using anoxic fluorescence microscopy. Finally, a split reporter translationally fused to the alpha and beta subunits of Fdh reconstituted a functionally fluorescent molecule in vivo via bimolecular fluorescence complementation. Together, these observations demonstrate the utility of FAST as a tool for studying members of the methanogenic archaea. ImportanceMethanogenic archaea are important members of anaerobic microbial communities where they catalyze essential reactions in the degradation of organic matter. Developing additional tools for studying the cell biology of these organisms is essential to understanding them at a mechanistic level. Here, we show that FAST, in combination with the fluorogenic ligand HMBR, can be used to monitor protein dynamics in live cells of M. maripaludis. Application of FAST holds promise for future studies focused on the metabolism and physiology of methanogenic archaea.

microbiology↗

Dynamic mode decomposition for analysis and prediction of metabolic oscillations from time-lapse imaging of cellular autofluorescence

Metabolic oscillations are a common phenomenon in cell biology. They are based on non-linear coupling of biochemical reactions and can show rich dynamic behavior including sustained and damped oscillations, as found, for example, in glycolysis of yeast and other eukaryotic cells. Metabolic oscillations are often studied by time-lapse imaging of cellular autofluorescence based on the changing abundance of NAD(P)H, but the analysis of such experimental data is challenging. Here, we show that dynamic mode decomposition (DMD), a numerical algorithm for linear approximation and spectral analysis of non-linear dynamics, allows for dissecting glycolytic oscillations in simulations and experiments in a fully data-driven manner. By combining DMD with time-delay embedding the spatiotemporal dynamics of sustained and damped glycolytic oscillations can be learned. Together with a rigorous assessment of spurious eigenvalues, via residual DMD, this provides a unique spectrum for each scenario, allowing for high-fidelity time-series and image reconstruction as well as for phenotyping different starvation conditions. The ability of DMD to predict future time points depends on the delay embedding dimension and is comparable to that of long short-term memory (LSTM) neural networks. Together, our results demonstrate the potential of DMD for analysis of time-lapse microscopy of metabolic oscillations in living cells.

bioinformatics↗

Studying stochastic systems biology of the cell with single-cell genomics data

Recent experimental developments in genome-wide RNA quantification hold considerable promise for systems biology. However, rigorously probing the biology of living cells requires a unified mathematical framework that accounts for single-molecule biological stochasticity in the context of technical variation associated with genomics assays. We review models for a variety of RNA transcription processes, as well as the encapsulation and library construction steps of microfluidics-based single-cell RNA sequencing, and present a framework to integrate these phenomena by the manipulation of generating functions. Finally, we use simulated scenarios and biological data to illustrate the implications and applications of the approach.

biophysics↗

Sequential Activation of Guide RNAs for Algorithmic Multiplexing of Cas9 Activities

SUMMARYGenetic manipulation of mammalian cells is instrumental to modern biomedical research but is currently limited by poor capabilities of sequentially controlling multiple manipulations in cells. Currently, either highly multiplexed manipulations can be delivered to populations of cells all at one time, or gene regulatory sequences can be engineered to conditionally activate a few manipulations within individual cells. Here, we provide proof-of-principle for a new system enabling multiple genetic manipulations to be executed as a preprogrammed cascade of events. The system leverages the programmability of the S. pyogenes Cas9 RNA-guided nuclease and is based on flexible arrangements of individual modules of activity. The basic module consists of an inactive single guide RNA (sgRNA) - like component that is converted to an active state through the effects of another sgRNA. Modules can be arranged to bring about an algorithmic program of genetic manipulations without the need for engineering cell type specific promoters or gene regulatory sequences. With the expanding diversity of available tools that utilize spCas9 to edit, repress or activate genes, this sgRNA-based system provides multiple levels for interfacing with host cell biology. In addition, ability of the system to progress through multiple modules from episomal plasmid DNA makes it suitable for applications sensitive to the presence of heterologous genomic DNA sequences and broadly applicable to biomedical research and mammalian cell engineering.Competing Interest StatementThe following competing interests are declared for RC, ART, HP, MSM, MR, and BJM as shareholders in Cellgorithmics, Inc., RC, HP, MSM, and BJM as cofounders of Cellgorithmics, Inc., and RC, HP, MSM, and BJM inventors on patent application number PCT/US2018/052211.View Full Text

synthetic biology↗

High efficiency transfection of thymic epithelial cell lines and primary thymic epithelial cells by Nucleofection.

Thymic epithelial cells (TECs) are required for the development and differentiation of T cells and are sufficient for the positive and negative selection of developing T cells. Although TECs play a critical role in T cell biology, simple, efficient and readily scalable methods for the transfection of TEC lines and primary TECs have not been described. We tested the efficiency of Nucleofection for the transfection of 4 different mouse thymic epithelial cell lines that had been derived from cortical or medullary epithelium. We also tested primary mouse thymic epithelial cells isolated from fetal and postnatal stages. We found that Nucleofection was highly efficient for the transfection of thymic epithelial cells, with transfection efficiencies of 30-70% for the cell lines and 15-35% for primary TECs with low amounts of cell death. Efficient transfection by Nucleofection can be performed with established cortical and medullary thymic epithelial cell lines as well as primary TECs isolated from E15.5 day fetal thymus or postnatal day 3 or 30 thymus tissue. The high efficiency of Nucleofection for TEC transfection will enable the use of TEC lines in high throughput transfection studies and simplifies the transfection of primary TECs for in vitro or in vivo analysis.

Immunology↗

Wnt/β-catenin regulates alloreactive T cells for the treatment of hematological malignancies

Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is one of the most widely applied forms of adaptive immunotherapy. Both the detrimental graft-versus-host disease (GVHD) and the beneficial graft-versus-leukemia (GVL) effects occurring after allo-HSCT are largely mediated by alloantigen-reactive donor T cells in the graft. Separating GVHD from GVL effects is a formidable challenge, and a greater understanding of donor T cell biology is required to accomplish the uncoupling of GVHD from GVL. Here, we tested a novel mouse model of {beta}-catenin (Cat-Tg) in an allo-HSCT model. Our data show that T cells from Cat-Tg mice did not cause GVHD. Surprisingly, Cat-Tg T cells maintained the GVL effect. Donor T cells from Cat-Tg mice exhibited significantly lower inflammatory cytokine production and reduced donor T cell proliferation, while upregulating cytotoxic mediators that resulted in enhanced cytotoxicity. RNA sequencing data revealed changes in the expression of over 150 genes for CD4, and over 250 genes for CD8+T cells involved in essential aspects of immune response and GVHD pathophysiology. Transgenic over-expression of human {beta}-catenin primarily affects CD8+ T cell phenotype. Altogether, our data suggest that {beta}-catenin is a druggable target for developing therapeutic strategies to reduce GVHD while preserving the beneficial GVL effects following allo-HSCT treatment.

immunology↗

A comprehensive analysis of single-cell transcriptome network underlying gastric premalignant lesions and early gastric cancer

Intestinal-type gastric cancer is preceded by premalignant lesions including chronic atrophic gastritis (CAG) and intestinal metaplasia (IM), which are characterized as changes in cell types. In this study, for the first time, we systematically constructed a single-cell atlas for a total of 31,164 high-quality cells from gastric mucosa biopsies of patients spanning a cascade of gastric premalignant lesions and early gastric cancer (EGC) using single-cell RNA sequencing (scRNA-seq). Based on the atlas, we construct a network underlying the changes of cellular and molecular characteristics of gastric epithelial cells across different lesions. We found the conversion of gland mucous cells (GMCs) toward a more intestinal-like stem cell phenotype during metaplasia, and identified OR51E1 as a novel marker for early-malignant enteroendocrine cells. We also found that HES6 might mark a goblet cell subset that precede morphologically identifiable goblet cells in IM mucosa, potentially aiding the identification of metaplasia at the early stage. Finally, we identified a panel of EGC-related specific signature, with clinical implications for the precise diagnosis of EGC. Our study offers unparalleled insights into the human gastric cellulome in premalignant and early-malignant lesions and provides an important data resource that will facilitate studies in gastritis-induced tumourigenesis and gastric cell biology.\n\nSignificance StatementUnderstanding cellular characteristics in gastric premalignant and malignant lesions would help us better understand the gastric cancer (GC) pathogenesis. In this paper, for the first time, we systematically constructed a single-cell transcriptome network of human premalignant gastric mucosa and early GC (EGC) and derived novel findings from it. We identified OR51E1 as a novel marker for early-malignant enteroendocrine cells and a panel of genes as the EGC-specific signature, with clinical implications for the precise diagnosis of EGC. We also found HES6 might mark a goblet cell subset that precede morphologically identifiable goblet cells in IM mucosa, potentially aiding the identification of metaplasia at the early stage. Our study provided an unprecedented data resource that will facilitate studies underlying gastritis-induced tumorigenesis.

bioinformatics↗

Transcriptomic, epigenetic and metabolic characterization of the pluripotency continuum in rabbit preimplantation embryos

Despite the growing interest in the rabbit model for developmental and stem cell biology, the characterization of embryos at the molecular level is still poorly documented. We conducted a transcriptome analysis of rabbit pre-implantation embryos from E2.7 (morula stage) to E6.6 (early primitive streak stage) using bulk and single-cell RNA-sequencing. In parallel, we studied oxidative phosphorylation and glycolysis and analysed active and repressive epigenetic modifications during blastocyst formation and expansion. We generated a transcriptomic, epigenetic, and metabolic map of the pluripotency continuum in rabbit preimplantation embryos and identified novel markers of naive pluripotency that might be instrumental for deriving naive pluripotent stem cell lines. Although the rabbit is evolutionarily closer to mice than to primates, we found that the transcriptome of rabbit epiblast cells shares common features with that of humans and non-human primates. Summary StatementRabbit preimplantation embryos share characteristics with human and monkey embryos with respect to timing of early lineage segregation and expression of marker genes for naive and primed pluripotency.

developmental biology↗

Endogenous RALF peptide function is required for powdery mildew host colonization

The receptor kinase FERONIA (FER) is a susceptibility factor for biotrophic powdery mildew fungal pathogens in Arabidopsis thaliana, but the underlying molecular mechanisms remain largely unknown. FER is required for the perception of endogenous RAPID ALKALINIZATION FACTOR (RALF) peptides to control various aspects of plant growth, development and immunity. RALFs are perceived by FER-LORELEI-LIKE GPI-ANCHORED PROTEIN (LLG) heterocomplexes to induce cellular responses and bind to LEUCINE-RICH REPEAT EXTENSIN (LRX) proteins as structural components of the cell wall. Combining genetics, cell biology and biochemistry, we found that FERs endogenous RALF ligands are necessary for full colonization success of the powdery mildew species Erysiphe cruciferarum. We reveal that LLGs and LRXs are also powdery mildew susceptibility factors. We show that cell wall remodeling and apoplastic pH homeostasis, hallmark features of RALF function, support powdery mildew reproductive success. Moreover, we provide data that RALF-dependent powdery mildew pathogenesis is partially independent of FER. Powdery mildew fungi likely do not produce RALF peptide mimics, suggesting their reliance on endogenous RALFs for successful host colonization. We propose that powdery mildew fungi require RALF-mediated modulation of apoplastic pH and pectin re-modelling for successful host colonization, highlighting a new susceptibility mechanism by obligate biotrophic fungi.

plant biology↗

Genome expansions and regulatory contact entanglement help preserve ancestral metazoan synteny

Chromosomes constitute deeply conserved evolutionary units in many metazoan genomes, with chromosomal fusions and fissions, accompanied by sub-chromosomal rearrangements, rewiring three dimensional genome architecture. How chromatin loops and compartments that define distal regulatory interactions within chromosomes impose functional constraints that affect this long-term evolutionary process (and vice-versa) is an emerging research topic. Genome expansions, especially through transposable element (TE) activity, test these constraints by increasing the genomic distances over which regulatory interactions must function and were thus suggested to be the drivers of chromosomal rearrangements. To study dynamics and stability of such distal interactions in the light of genome expansions, we focus on the cnidarian Hydra vulgaris, which, based on its simple and well-understood biology as well as one of the largest genomes among cnidarians, is particularly suited to test how chromatin loop and genome architecture respond to genome expansion. We investigate genome architecture using Micro-C, single-cell Hi-C (Dip-C), and DNA FISH, and perform comparative analysis using available genomic and epigenomic data. Contrary to prior expectations, our analysis of whole-genome data and particular loci (e.g., Wnt) suggests a scenario where genome expansion did not only result in chromatin loops often reaching several megabases in hydra, but also led to regulatory contact mixing and entanglement, introducing additional constraints to maintain ancestral genomic architecture. Generalizing these findings across hundreds of metazoan genomes, we show a new mechanistic role for genome expansion in yielding entangled long-range regulatory configurations that, in turn, decelerate chromosomal rearrangements, thus maintaining (and not breaking) ancestral regulatory states and synteny. Significance statementSome of the largest and most repetitive animal genomes retain a surprisingly high level of deeply conserved metazoan synteny. As repetitive regions are often associated with chromosomal rearrangements, it has been enigmatic why syntenic retention is so frequently observed. In this study, using hydra as a model system for both stem cell biology and an evolutionary history rich in transposable-element driven genome expansion, a multi-level conformational landscape dissection reveals a multitude of long-range regulatory states. We show that mixing of multiple such regulatory links accompanied by genomic expansion is associated with maintained ancestral synteny, thus pointing to the counter-intuitive role of genome expansions as "fossilization" agents across metazoan genomes.

evolutionary biology↗

Genetic tools for the stable overexpression of circular RNAs

Circular RNAs (circRNAs) are a class of non-coding RNAs that feature a covalently closed ring structure formed through backsplicing. circRNAs are broadly expressed and contribute to biological processes through a variety of functions. Standard gain-of-function and loss-of-function approaches to study gene functions have significant limitations when studying circRNAs. Overexpression studies in particular suffer from the lack of efficient genetic tools. While mammalian expression plasmids enable transient overexpression of circRNAs in cultured cells, most cell biological studies require long-term ectopic expression. Here we report the development and characterization of genetic tools enabling stable circRNA overexpression in vitro and in vivo. We demonstrated that circRNA expression constructs can be delivered to cultured cells via transposons, whereas lentiviral vectors have limited utility for the delivery of circRNA constructs. We further showed that circRNA transposons can be supplied to mouse livers via hydrodynamic tail vein injection, resulting in ectopic circRNA expression in a hepatocellular carcinoma mouse model. Furthermore, we generated genetically engineered mice harboring circRNA expression constructs. We demonstrate that this approach enables constitutive, global circRNA overexpression as well as inducible circRNA expression directed specifically to melanocytes in a melanoma mouse model. Overall, these tools expand the genetic toolkit available for the functional characterization of circRNAs of interest.

molecular biology↗

BMI-1 Modulation and Trafficking During M Phase in Diffuse Intrinsic Pontine Glioma

BMI-1 (B cell-specific Moloney murine leukemia virus integration site 1) has been implicated in both normal and cancer cell biology. While the canonical function of BMI-1 involves epigenetic repression, novel extra-nuclear functions have been recently reported. In the present study, we demonstrate that the phosphorylation of BMI-1 in diffuse intrinsic pontine glioma (DIPG) cells occurs in M phase and that triggers simultaneous translocation of the phosphorylated BMI-1 to the cytoplasm. This translocation is mediated by the RanGTP-dependent transporter CRM1, also known as exportin. Furthermore, we uncovered a previously unidentified nuclear export signal (NES) in BMI-1 protein, suggesting an active transport type of modified BMI-1 mediated by CRM1. These findings associate BMI-1 phosphorylation with its trafficking in M phase. Collectively, this study sheds light on the molecular mechanisms underlying BMI-1 functions in DIPG, thereby potentially paving the way for the development of targeted therapeutic strategies related to M phase progression.

cancer biology↗

NF-κB c-REL-OTUD4 axis regulates B-cell receptor in B-cell lymphoma

The B-cell receptor (BCR) is essential for B-cell development and a crucial clinical target in immuno-oncology. However, therapeutic success against the BCR and downstream signaling pathways is hampered by enhanced NF-{kappa}B activation as a resistance mechanism. Using a multiomic approach, we discover the c-REL proto-oncogenic subunit of the NF-{kappa}B family as a key transcription factor regulating BCR subunit levels in B-cell lymphoma. Subsequent ChIP- seq, cell biology experiments, and patient data analysis reveal that OTUD4 is a critical deubiquitinase for inhibiting proteasomal degradation of c-REL and for stabilizing a multi-loop positive feedback of NF-{kappa}B to the BCR pathway. Remarkably, OTUD4 downregulation destabilizes c-REL and BCR levels and inhibits cell growth of B cell lymphoma. Thus, we shed light on the malignant potential of c-REL abundance, identify a positive feedback from c-REL to upstream BCR and present OTUD4 as a vulnerability to synergistically target NF-{kappa}B and BCR pathways in B-cell lymphoid malignancies.

cancer biology↗

Optical regulation of endogenous RhoA reveals switching of cellular responses by signal amplitude

How protein signaling networks respond to different input strengths is an important but poorly understood problem in cell biology. For example, the small GTPase RhoA regulates both focal adhesion (FA) growth or disassembly, but whether RhoA serves as a switch selecting between cellular outcomes, or if outcomes are simply modulated by additional factors in the cell, is not clear. Here, we develop a photoswitchable RhoA guanine exchange factor, psRhoGEF, to precisely control endogenous RhoA activity. We also develop a FRET-based biosensor to allow visualization of RhoA activity together with psRhoGEF control. Using these new optical tools, we discover that low levels of RhoA activation preferentially induce FA disassembly in a Src-dependent manner, while high levels induce both FA growth and disassembly in a ROCK-dependent manner. Thus, rheostatic control of RhoA activation with photoswitchable RhoGEF reveals that cells can use signal amplitude to produce multiple responses to a single biochemical signal.

bioengineering↗

Topological Constraints on Noise Propagation in Gene Regulatory Networks

Gene expression, the production of protein from DNA and mRNA in the biological cell, is inherently stochastic. Cells with identical DNA exhibit fluctuations or noise in gene expression. This noise propagates over gene regulatory networks (GRNs), which encode gene-gene interactions. The propagated extrinsic noise interacts and combines with intrinsic noise to affect biological decisions. Consequently, it is essential to understand how GRN topology affects total noise. Recently, uncertainty principles were established for noise propagation over GRN. In particular, in ring GRNs, exactly one node can have noise reduction below the intrinsic limit. We establish necessary and sufficient conditions for noise reduction in ring GRN. Specifically, for two- and three-node rings, an odd number of negative regulations is necessary for noise reduction. Further, sufficiency is ensured if sensitivities to input for feedforward and feedback regulations are bounded from below and above, respectively. These constraints are valid even if the ring GRN are regulated by an upstream gene. Finally, we use graph theory to decompose noise propagation in a general directed network over its strongly connected components. The combination of graph theory and stochastic processes may be a general framework for studying noise propagation.

systems biology↗

Development of a PC12 cell-based assay for in vitro screening of catechol-O-methyltransferase inhibitors

The male rat adrenal pheochromocytoma cell-originated PC12 cell line can synthesize and release catecholamine neurotransmitters, and it has been widely used as a model system in cell biology and toxicology research. Catechol-O-methyltransferase (COMT) is involved in the inactivation of the catecholamine neurotransmitters, and it is particularly important for theregulation of dopamine. In this study, we explored the feasibility of using PC12 cells as an in vitro drug screening platform to compare the activity of multiple COMT inhibitors. Incubation of PC12 cells with tolcapone, a highly potent and selective COMT inhibitor, increased the concentrations of dopamine and its metabolite 3,4-dihydroxyphenylacetic acid (DOPAC) while reducing the metabolites 3-methoxytyramine (3-MT) and homovanillic acid (HVA) in the cell culture medium. LIBD-3, a novel, non-nitrocatechol COMT inhibitor produced similar effects compared to tolcapone. LIBD-4, a less potent inhibitor, exhibited the expected right-shift in functional inhibition in the assay. These results match the known in vivo effects of COMT inhibition in rodents. Together, these data support the continued use of PC12 cells as an in vitro screen that bridges cell-free enzyme assays and more costly in vivo assays.

neuroscience↗

Benchmarking scRNA-seq Copy Number Inference: A Comprehensive Evaluation and Practitioner Guide

Accurately inferring copy number variation (CNV) from scRNA-seq data is critical for identifying malignant cells, reconstructing tumor subclonal architecture, and uncovering the genomic drivers that dictate cancer cell biology. However, the performance of existing tools varies significantly, and current benchmarks lack the breadth of datasets and methods necessary to provide definitive guidance. We present a comprehensive benchmark of 12 CNV inference methods across 28 real datasets (>100,000 cells) and diverse synthetic datasets. By evaluating methods based on malignant cell classification accuracy, CNV inference accuracy, scalability, and robustness, we establish a definitive practitioners guideline: allele-aware methods like Numbat excel when high-quality allelic inference can be achieved, whereas expression-centric tools such as Clonalscope, CopyKAT, inferCNV, and SCEVAN remain reliable when raw sequencing data are unavailable. Our study provides both a practical decision-making framework for researchers and a public repository of standardized CNV profiles to catalyze further methodological innovation.

cancer biology↗