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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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.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 1,729 records · Page 96Linked to original sources

bioRxiv2017

canvasXpress: A versatile interactive high-resolution scientific multi-panel visualization toolkit

To the Editor: CanvasXpress (https://canvasxpress.org) was developed as the core visualization component for bioinformatics and systems biology analysis at Bristol-Myers Squibb and further enhanced by scientists around the world and served as a key visualization engine for many popular bioinformatics tools1,2,3,4,5,6. It offers a rich set of interactive plots to display scientific and genomics data, such as oncoprint of cancer mutations, heatmap, 3D scatter, violin, radar, and profile plots (Figure 1, canvasXpress plots arranged by canvasDesigner https://baohongz.github.io/canvasDesigner). Recently, the reproducibility and usability of the package in real world bioinformatics and clinical use cases have been improved significantly witnessed by continuous add-on features and wide adoption of the toolkit in the scientific communities. Furthermore, It is the first noteworthy package harmonizing real time interactive exploring and analyzing of big data, full-fledged customizing of look-n-feel, and producing multi-panel publication-ready figures in PDF format simultaneously.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC=\"FIGDIR/small/186213_fig1.gif\" ALT=\"Figure 1\">\nView larger version (36K):\norg.highwire.dtl.DTLVardef@1d8392borg.highwire.dtl.DTLVardef@916a49org.highwire.dtl.DTLVardef@d90b05org.highwire.dtl.DTLVardef@162a8fc_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO Versatile plots generated by canvasXpress. A) Oncoprint of cancer mutations; B) Gene expression heatmap with comprehensive annotations; C) 3D scatter plot; D) Violin plot; E) Radar plot with annotations; F) Profile plot of gene expression.\n\nC_FIG

bioinformatics↗

bioRxiv2016

Cell-to-cell variability in the yeast pheromone response: Cytoplasmic microtubule functionstabilizes signal generation and promotes accurate fate choice

In a companion paper, we carried out a high-throughput screen to identify genes that suppressed cell-to-cell variability in signaling in yeast. Two genes affected cytoplasmic microtubules that can connect the nucleus to a signaling site on the membrane. Here, we show that microtubule perturbations that affected polymerization and depolymerization, membrane attachment, and force generation increased variability. For some perturbations, \"outlier\" cells drove the increased variability. Bypass experiments that activated the PRS ectopically at downstream points indicated that microtubule-dependent processes might stabilize the membrane-recruited scaffold protein Ste5. The variability caused by microtubule perturbations required the MAP kinase Fus3. Microtubule perturbations hindered stable scaffold formation and decreased the accuracy of a polarity-dependent fate choice. Our experiments suggest that membrane-attached microtubules stabilize signaling by scaffold-bound Fus3, and are consistent with a model in which signaling irregularities from changes in microtubule function are amplified by cross-stimulatory feedbacks among PRS proteins. The fact that microtubule perturbations also cause aberrant fate and polarity decisions during embryonic development and cancer initiation suggests that similar variation-reducing processes might also operate in metazoans.

systems biology↗

bioRxiv2017

Multimodal cell tracking from systemic administration to tumour growth by combining gold nanorods and reporter genes

Understanding the fate of exogenous cells after implantation is important for clinical applications. Preclinical studies allow imaging of cell location and survival. Labelling with nanoparticles enables high sensitivity detection, but cell division and cell death cause signal dilution and false positives. By contrast, genetic reporter signals are amplified by cell division. Here we characterise lentivirus-based bi-cistronic reporter gene vectors and silica-coated gold nanorods (GNRs) as synergistic tools for cell labelling and tracking. Co-expression of the bioluminescence reporter luciferase and the optoacoustic reporter near-infrared fluorescent protein iRFP720 enabled cell tracking over time in mice. Multispectral optoacoustic tomography (MSOT) showed immediate biodistribution of GNR-labelled cells after intracardiac injection and successive clearance of GNRs (day 1-15) with high resolution, while optoacoustic iRFP720 detection indicated tumour growth (day 10-40). This multimodal cell tracking approach could be applied widely for cancer and regenerative medicine research to monitor short- and long-term biodistribution, tumour formation and metastasis.

cell biology↗

bioRxiv2017

A class of GATA3 mutation reprograms the breast cancertranscriptional network through gain and loss of function

GATA3 is frequently mutated in breast cancer; these mutations are widely presumed to be loss of function. Here, we address molecular alterations downstream of a novel class of GATA3 mutations, revealing both gain and loss of function. Mutation of one allele of GATA3 led to loss of binding and decreased expression at a subset of genes, including Progesterone Receptor. At other loci, associated with epithelial to mesenchymal transition, gain of binding at a novel sequence motif correlated with increased gene expression. These results demonstrate that not all GATA3 mutations are equivalent and that these mutations impact breast cancer through gain and loss of function.

cell biology↗

bioRxiv2018

WDFY2 restrains matrix metalloprotease secretion and cell invasion by retention of VAMP3 in endosomal tubules

The endosomal FYVE- and WD40-domain-containing protein WDFY2 has been assigned a function as tumour suppressor, but its functional mechanism has remained elusive. Here we have used confocal, widefield and super-resolution fluorescence microscopy to show that WDFY2 localizes to the base of retromer-containing endosomal tubules by a mechanism that involves recognition of a specific pool of phosphatidylinositol 3-phosphate (PtdIns3P) by the WDFY2 FYVE domain. Affinity purification and mass spectrometry identified the v-SNARE VAMP3 as an interaction partner of WDFY2, and cellular knockout of WDFY2 caused a strong redistribution of VAMP3 into small vesicles near the plasma membrane. This was accompanied by increased secretion of the matrix metalloprotease MT1-MMP, enhanced degradation of extracellular matrix, and increased cell invasion. WDFY2 is frequently lost in metastatic cancers, most predominantly in ovarian and prostate cancer. We propose that WDFY2 acts as a tumor suppressor by serving as a gatekeeper for VAMP3 recycling.

cell biology↗

bioRxiv2016

microRNA-mRNA interaction identification in Wilms tumor using principalcomponent analysis based unsupervised feature extraction

Wilms tumor is one of lethal child renal cancers, for which no known disease causing mechanisms exist. In this paper, we tried to identify possible disease causing microRNA(miRNA)-mRNA pairs (interactions) by analyzing (partially matched) miRNA/mRNA gene expression profiles with the recently proposed principal component analysis based unsupervised feature extraction. It successfully identified multiple miRNA-mRNA pairs whose biological natures are convincing. Correlation coefficients between miRNA and mRNA expression in matched parts of profiles turned out to be significantly negative. Constructed miRNA-mRNA network will be a key to understand Wilms tumor causing mechanisms.

Bioinformatics↗

bioRxiv2017

Decoding directional genetic dependencies through orthogonal CRISPR/Cas screens

Genetic interaction studies are a powerful approach to identify functional interactions between genes. This approach can reveal networks of regulatory hubs and connect uncharacterised genes to well-studied pathways. However, this approach has previously been limited to simple gene inactivation studies. Here, we present an orthogonal CRISPR/Cas-mediated genetic interaction approach that allows the systematic activation of one gene while simultaneously knocking out a second gene in the same cell. We have developed this concept into a quantitative and scalable combinatorial screening platform that allows the parallel interrogation of hundreds of thousands of genetic interactions. We demonstrate that the established platform works robustly to uncover genetic interactions in human cancer cells and to interpret the direction of the flow of genetic information.

molecular biology↗

bioRxiv2017

Dual Phenotype Of MDA-MB-468 Cancer Cells Reveals Mutual Regulation Of Tensin3 And Adhesion Plasticity

Plasticity between adhesive and less-adhesive states is important for mammalian cell behaviour. To investigate adhesion plasticity, we have selected a stable isogenic subpopulation of MDA-MB-468 breast carcinoma cells which grows in suspension. These suspension cells are unable to re-adhere to various matrices or to contract three-dimensional collagen lattices. By transcriptome analysis, we identified the focal adhesion protein tensin3 (Tns3) as a determinant of adhesion plasticity. Tns3 is strongly reduced on mRNA and protein level in suspension cells. Furthermore, challenging breast cancer cells transiently with non-adherent conditions markedly reduces Tns3 expression, which is regained upon re-adhesion. Stable knockdown of Tns3 in parental cells results in defective adhesion, spreading and migration. Tns3 knockdown cells display impaired structure and dynamics of focal adhesion complexes as determined by immunostaining. Restoration of Tns3 expression in suspension cells partially rescues adhesion and focal contact composition. Our work identifies Tns3 as a critical focal adhesion component regulated by, and functionally contributing to, the switch between adhesive and non-adhesive states in MDA-MB-468 cancer cells.\n\nSummary statementWe identify the cell-matrix adapter protein tensin3 as a determinant of adhesion plasticity, using cancer cells selected for non-adherent growth. Tensin3 expression constitutes a feedback loop controlling adhesion and motility.

cell biology↗

bioRxiv2018

Overdosage of balanced protein complexes reduces proliferation rate in aneuploid cells

Cells with complex aneuploidies, such as tumor cells, display a wide range of phenotypic abnormalities. However, molecular basis for this has been mainly studied in trisomic (2n+1) and disomic (n+1) cells. To determine how karyotype affects proliferation rate in cells with complex aneuploidies we generated forty 2n+x yeast strains in which each diploid cell has an extra 5 to 12 chromosomes and found that these strains exhibited abnormal cell-cycle progression. Proliferation rate was negatively correlated with the number of protein complexes in which all subunits were at the 3-copy level, but not with the number of imbalanced complexes made up of a mixture of 2-copy and 3-copy genes. Proteomics revealed that most 3-copy members of imbalanced complexes were expressed at only 2n protein levels whereas members of complexes in which all subunits are stoichiometrically balanced at 3 copies per cell had 3n protein levels. We identified individual protein complexes for which overdosage reduces proliferation rate, and found that deleting one copy of each member partially restored proliferation rate in cells with complex aneuploidies. Lastly, we validated this finding using orthogonal datasets from both yeast and from human cancers. Taken together, our study provides a novel explanation how aneuploidy affects phenotype.

systems biology↗

bioRxiv2018

Replication stress induces mitotic death through parallel pathways regulated by WAPL and telomere deprotection

Mitotic catastrophe is a broad descriptor encompassing unclear mechanisms of cell death. Here we investigate replication stress-driven mitotic catastrophe in human cells and identify that replication stress principally induces mitotic death signalled through two independent pathways. In p53-compromised cells we find that lethal replication stress confers WAPL-dependent centromere cohesion defects that maintain spindle assembly checkpoint-dependent mitotic arrest in the same cell cycle. Mitotic arrest then drives cohesion fatigue and triggers mitotic death through a primary pathway of BAX/BAK-dependent apoptosis. Simultaneously, a secondary mitotic death pathway is engaged through non-canonical telomere deprotection, regulated by TRF2, Aurora B and ATM. Additionally, we find that suppressing mitotic death promotes genome instability in replication stressed cells through diverse mechanisms depending upon how cell death is averted. These data demonstrate how replication stress-induced mitotic catastrophe signals cell death with implications for cancer treatment and genome instability.

molecular biology↗

bioRxiv2017

PI3K regulates intraepithelial cell positioning through Rho GTP-ases in the developing neural tube.

SUMMARY STATEMENTDuring neural tube development, PI3K pathway promotes cell survival and provides the apical-basal navigation clues that define the final location of neurons in the epithelium.\n\nSUMMARYPhosphatidylinositol 3-kinases (PI3Ks) are signal transducers of many biological processes. Class 1A PI3Ks are hetero dimers formed by a regulatory and a catalytic subunit. We have used the developing chicken neural tube (NT) to study the roles played by PI3K during the process of cell proliferation and differentiation. Notably, we have observed that in addition to its well characterized anti apoptotic activity, PI3K also plays a crucial role in intra epithelial cell positioning, and unlike its role in survival that mainly depends on AKT, the activity in cell positioning is mediated by Rho GTPase family members. Additionally, we have observed that activating mutations of PI3K that are remarkably frequent in many human cancers, cause an unrestrained basal migration of the neuroepithelial cells that end up breaking through the basal membrane invading the surrounding mesenchymal tissue. The mechanism described in this work contribute not only to acquire a greater knowledge of the intraepithelial cell positioning process, but also give new clues on how activating mutations of PI3K contribute to cell invasion during the first stages of tumour dissemination.

cell biology↗

bioRxiv2018

Quantitative solid-phase assay to measure deoxynucleoside triphosphate pools

Deoxyribonucleoside triphosphates (dNTPs) are the reduced nucleotides used as the building blocks and energy source for DNA replication and maintenance in all living systems. They are present in highly regulated amounts and ratios in the cell, and their balance has been implicated in the most important cell processes, from determining the fidelity of DNA replication to affecting cell fate. Furthermore, many cancer drugs target biosynthetic enzymes in dNTP metabolism, and mutations in genes directly or indirectly affecting these pathways are the cause of devastating diseases. The accurate and systematic measurement of these pools is key to understand the mechanisms behind these diseases and their treatment. We present a new method for measuring dNTP pools from biological samples, utilising the current state-of-the-art polymerase method, modified to a solid-phase setting and optimised for larger scale measurements.

biochemistry↗

bioRxiv2018

Nucleo-cytoplasmic trafficking regulates nuclear surface area during nuclear organogenesis

Throughout development, nuclei must be assembled following every cell division to establish a functional organelle from compact, mitotic chromatin. During nuclear organogenesis, chromatin expands to establish a nucleus of a given size seperate from the cytoplasm. Determining how nuclear organogenesis is regulated is particularly significant in the context of certain cancers in which scaling relationships between cell and nuclear sizes are not maintained. Controlling cell size in vitro using a microfluidics approach, we determined that neither nuclear volume nor surface area scale directly with cell size. Looking to explain differential nuclear scaling relationships, we developed a simple mechano-chemical mathematical model. In simulating biological perturbations in silico, our model predicted crucial roles for nucleo-cytoplasmic trafficking in regulating nuclear expansion and in restricting the recruitment of a potential nuclear surface area factor. In mammalian tissue culture, inhibiting nuclear export increased nuclear expansion rates and reduced the amount of nuclear lamin, a candidate surface area factor, being recruited to assembling nuclei, supporting our models predictions. Targeting the principal nuclear export component in the Drosophila syncytial embryo, Embargoed, we show that nuclear expansion rates are also increased in this developmental context, consistent with our model. Using the MS2-reporter system in fly embryos, we demonstrate a role for nuclear export in regulating transcription activation timing and dynamics, suggesting that regulating nuclear assembly is crucial for downstream nuclear function. Taken together, we propose a simple model through which nuclear organogenesis is achieved and demonstrate a role for nuclear export in regulating nuclear assembly.

cell biology↗

bioRxiv2018

Integrative pathway enrichment analysis of multivariate omics data

Multi-omics datasets quantify complementary aspects of molecular biology and thus pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple omics datasets using a statistical data fusion approach, rationalizes contributing evidence and highlights associated genes. We demonstrate its utility by analyzing coding and non-coding mutations from 2,583 whole cancer genomes, revealing frequently mutated hallmark pathways and a long tail of known and putative cancer driver genes. We also studied prognostic molecular pathways in breast cancer subtypes by integrating genomic and transcriptomic features of tumors and tumor-adjacent cells and found significant associations with immune response processes and anti-apoptotic signaling pathways. ActivePathways is a versatile method that improves systems-level understanding of cellular organization in health and disease through integration of multiple molecular datasets and pathway annotations.

bioinformatics↗

bioRxiv2015

The genomic basis of electrotaxis in Dictyostelium discoideum: Electric field sensitive amino acids are dynamically encoded en masse for the streaming-stage proteome

Electrotaxis plays a critical role in developmental cell migration, axon growth cone guidance, epithelial wound healing, tissue regeneration, and the degree of invasiveness characterizing different cancer cell lines. During electrotaxis in a direct current electric field (EF), a cell migrates preferentially either towards the anode or cathode depending on the cell-type. However, the types and ranges of mechanisms coupling trans-cellular electric fields to cellular EF-sensitive signaling systems are largely unknown. To address this cell biological phenomenon, I use transcriptomic data from a developmental genetic model in which multicellular social aggregation is induced by starvation of amoeboid cells. I find that the developmental proteome expressed during the streaming aggregation stage is measurably and substantially enriched in charged and highly polar amino acids relative to the proteomes of either the unicellular amoeboid or the multicellular fruiting body. This large-scale coding augmentation of EF-sensitive amino acid residues in thousands of streaming-specific proteins is accompanied by a proportional coding decrease in the number of small, uncharged amino acid residues. I also confirm an expected coding increase of biosynthetically costly amino acids in the proteome of the satiated feeding-stage amoeboid. These findings suggest that electrotactic capability is encoded broadly in the genetically regulated deployment of a developmental proteome with augmented EF-sensitivity. These results signify that extreme, nonuniform, evolutionary constraints can be exerted on the amino acid composition of an organisms proteome.

Biophysics↗

bioRxiv2017

DNA Damage Checkpoint Dynamics Drive Cell Cycle Phase Transitions

DNA damage checkpoints are cellular mechanisms that protect the integrity of the genome during cell cycle progression. In response to genotoxic stress, these checkpoints halt cell cycle progression until the damage is repaired, allowing cells enough time to recover from damage before resuming normal proliferation. Here, we investigate the temporal dynamics of DNA damage checkpoints in individual proliferating cells by observing cell cycle phase transitions following acute DNA damage. We find that in gap phases (G1 and G2), DNA damage triggers an abrupt halt to cell cycle progression in which the duration of arrest correlates with the severity of damage. However, cells that have already progressed beyond a proposed \"commitment point\" within a given cell cycle phase readily transition to the next phase, revealing a relaxation of checkpoint stringency during later stages of certain cell cycle phases. In contrast to G1 and G2, cell cycle progression in S phase is significantly less sensitive to DNA damage. Instead of exhibiting a complete halt, we find that increasing DNA damage doses leads to decreased rates of S-phase progression followed by arrest in the subsequent G2. Moreover, these phase-specific differences in DNA damage checkpoint dynamics are associated with corresponding differences in the proportions of irreversibly arrested cells. Thus, the precise timing of DNA damage determines the sensitivity, rate of cell cycle progression, and functional outcomes for damaged cells. These findings should inform our understanding of cell fate decisions after treatment with common cancer therapeutics such as genotoxins or spindle poisons, which often target cells in a specific cell cycle phase.

systems biology↗

bioRxiv2017

Variable sensitivity to DNA damaging chemotherapeutic modulated by cell type-dependent bimodal p53 dynamics

Mechanisms that determine drug sensitivity of distinct cancer types is poorly understood for most cytotoxic chemotherapy. In this study, we elucidated a new resistance mechanism to DNA damaging chemotherapeutic through modulation of p53 dynamics. While both sensitive and resistant cancer cell lines activated similar p53 oscillation followed by cell-cycle arrest in response to low dose of DNA damaging drug, they switched in a bimodal manner to monotonic or single pulse dynamics at high drug dose. Cell lines with monotonically increasing p53 underwent rapid and extensive drug-induced apoptosis, while those exhibiting a single p53 pulse mostly survived. By combining single cell imaging with computational modeling, we characterized a regulatory module involving ATM, p53, Mdm2 and Wip1, which generates bimodal p53 dynamics through coupled feed-forward and feedback, and we found that basal expression of ATM determined the differential modular output between drug sensitive and resistant lines. Moreover, we showed combinatorial inhibition of Mdm2 and Wip1 was an effective strategy to alter p53 dynamics in resistant cancer cells and sensitize their apoptotic response. Our results point to p53 pulsing as a potentially druggable mechanism that mediates resistance to cytotoxic chemotherapy.

systems biology↗

bioRxiv2017

Direct in vivo mapping of functional suppressors in glioblastoma genome

Glioblastoma (GBM) is one of the deadliest cancers, with limited effective treatments and single-digit five-year survival 1-7. A causative understanding of genetic factors that regulate GBM formation is of central importance 8-19. However, a global, quantitative and functional understanding of gliomagenesis in the native brain environment has been lacking due to multiple challenges. Here, we developed an adeno-associated virus (AAV) mediated autochthonous CRISPR screen and directly mapped functional suppressors in the GBM genome. Stereotaxic delivery of an AAV library targeting significantly mutated genes into fully immunocompetent conditional Cas9 mice robustly led to gliomagenesis, resulting in tumors that recapitulate features of human GBM. Targeted capture sequencing revealed deep mutational profiles with diverse patterns across mice, uncovering in vivo roles of previously uncharacterized factors in GBM such as immune regulator B2m, zinc finger protein Zc3h13, transcription repressor Cic, epigenetic regulators Mll2/3 and Arid1b, alongside canonical tumor suppressors Nf1 and Pten. Comparative cancer genomics showed that the mutation frequencies across all genes tested in mice significantly correlate with those in human from two independent patient cohorts. Co-mutation analysis identified frequently co-occurring driver combinations, which were validated using AAV minipools, such as Mll2, B2m-Nf1, Mll3-Nf1 and Zc3h13-Rb1. Distinct from Nf1-oncotype tumors, Rb1-oncotype tumors exhibit undifferentiated histopathology phenotype and aberrant activation of developmental reprogramming signatures such as Homeobox gene clusters. The secondary addition of Zc3h13 or Pten mutations drastically altered the gene expression profiles of Rb1 mutants and rendered them more resistant to the GBM chemotherapeutic temozolomide. Our study provides a systematic functional landscape of GBM suppressors directly in vivo, opening new paths for high-throughput molecular mapping and cancer phenotyping.

systems biology↗