Biology subjects

Geng, F.

Publications and source records attributed to Geng, F..

8 recordsLinked to original sources

bioRxiv2026

Piezo1 links cytoskeletal remodeling to differential YAP and β-catenin signaling in response to mechanical cues

Mechanical cues from the extracellular matrix regulate cancer cell behavior, but how these inputs are translated into distinct nuclear signaling responses remains incompletely understood. This study examined whether Piezo1, a mechanosensitive ion channel, contributes to cytoskeletal remodeling and differential regulation of YAP and {beta}-catenin localization in breast cancer cells exposed to defined mechanical cues. MDA-MB-231 breast cancer cells were cultured on substrates of defined stiffness and analyzed after Piezo1 knockdown or pharmacological modulation of Piezo1, Src signaling, myosin II activity, and actin polymerization. Nuclear localization of YAP and {beta}-catenin was assessed by immunofluorescence imaging, cytoskeletal organization was evaluated using filamentous and globular actin staining, protein phosphorylation was analyzed by capillary electrophoresis-based immunoblotting, and cell migration was assessed using a wound-healing assay. Piezo1 knockdown reduced YAP nuclear localization and increased {beta}-catenin nuclear localization, while Piezo1 activation partially reversed these localization changes. Piezo1 knockdown also disrupted filamentous actin organization, and pharmacological disruption of actin polymerization produced similar effects on YAP and {beta}-catenin localization. Piezo1 knockdown selectively reduced YAP tyrosine phosphorylation without altering canonical Hippo-associated YAP serine phosphorylation, and inhibition of Src signaling produced effects similar to Piezo1 knockdown. Functionally, Piezo1 knockdown impaired stiffness-dependent cell migration. These findings support a role for Piezo1 in linking extracellular mechanical cues to cytoskeletal organization and differential regulation of YAP and {beta}-catenin localization in breast cancer cells. This work provides a framework for understanding how mechanosensitive ion-channel signaling may contribute to context-dependent nuclear signaling responses during cancer cell mechanotransduction.

cell biology↗

bioRxiv2023

ERas-Null Mice Generated Directly from Embryonic Stem Cells in a Lipid-rich Medium Enable the Discovery of A Novel Role in Craniofacial Development

Generating mice entirely from embryonic stem cells (ESCs) via tetraploid complementation, termed all-ESC mice, is considered the gold standard for pluripotency testing. In this study, we examined the effects of our newly reported lipid-rich 2i/LIF medium (2iLA) on ESCs for genetic engineering. As a proof of principle, we targeted the ERas gene using the 2iLA medium, since ERas-null mice displayed no noticeable phenotype in a previously developed mouse model through chimeras. We demonstrated that the 2iLA medium effectively supports the creation of both male and female ERas-null all-ESC mice, emphasizing the advantages of this culture medium. Unexpectedly, we observed that ERas-null all-ESC mice produced with the 2iLA medium exhibited a non-Mendelian lethal craniofacial anomaly, which can be mitigated by using the lipid-free 2i/LIF medium. Our findings not only highlight the potential of the 2iLA medium for gene targeting but also reveal a novel lipid-associated role of the ERas gene in craniofacial development. Our system offers a unique alternative for studying developmental gene functions unachievable with traditional methods and provides a novel platform for the rapid construction of mouse models. Graphic AbstractAll-ESC pups from wild-type (WT) ESCs cultured in lipid-rich 2iLA medium are normal. In contrast, both male and female ERas-null isogenic all-ESC pups produced from ESCs in 2iLA medium display a non-Mendelian craniofacial anomaly. This phenotype is alleviated when the ESCs are grown in a lipid-free 2iL medium. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=195 SRC="FIGDIR/small/565209v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@c2dd48org.highwire.dtl.DTLVardef@14dbd07org.highwire.dtl.DTLVardef@b54a86org.highwire.dtl.DTLVardef@2fcdd5_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2023

Transcriptional Activation of Regenerative Hematopoiesis via Vascular Niche Sensing

Transition between activation and quiescence programs in hematopoietic stem and progenitor cells (HSC/HSPCs) is perceived to be governed intrinsically and by microenvironmental co-adaptation. However, HSC programs dictating both transition and adaptability, remain poorly defined. Single cell multiome analysis divulging differential transcriptional activity between distinct HSPC states, indicated for the exclusive absence of Fli-1 motif from quiescent HSCs. We reveal that Fli-1 activity is essential for HSCs during regenerative hematopoiesis. Fli-1 directs activation programs while manipulating cellular sensory and output machineries, enabling HSPCs co-adoptability with a stimulated vascular niche. During regenerative conditions, Fli-1 presets and enables propagation of niche-derived Notch1 signaling. Constitutively induced Notch1 signaling is sufficient to recuperate functional HSC impairments in the absence of Fli-1. Applying FLI-1 modified-mRNA transduction into lethargic adult human mobilized HSPCs, enables their vigorous niche-mediated expansion along with superior engraftment capacities. Thus, decryption of stem cell activation programs offers valuable insights for immune regenerative medicine.

cell biology↗

bioRxiv2020

Super-robust data storage in DNA by de Bruijn graph-based decoding

DNA data storage is a rapidly developing technology with great potential due to its high density, long-term durability, and low maintenance cost. The major technical challenges include various errors, such as the strand breaks, rearrangements, and indels that frequently arise during DNA synthesis, amplification, sequencing, and preservation. Through a de novo assembly strategy, we developed an algorithm based on the de Bruijn graph and greedy path search (DBGPS) to address these issues. DBGPS shows distinct advantages in handling DNA breaks, rearrangements, and indels. The robustness of DBGPS is demonstrated by accelerated aging, multiple independent data retrievals, deep error-prone PCR, and large data scale simulations. Remarkably, 6.8 MB of data can be retrieved accurately from a seriously corrupted sample that has been treated at 70 {degrees}C for 70 days. With DBGPS, we were able to achieve a logical density of 1.30 bits/cycle and a physical density of 295 PB/g. One-Sentence SummaryA de Bruijn graph-based de novo assembly algorithm for DNA data storage enables fast and robust data readouts even with DNA samples that have been severely corrupted.

bioinformatics↗

bioRxiv2020

Ribosomes act as cryosensors in plants

Cold temperatures are a threat to temperate plants, and Arabidopsis thaliana has acquired an adaptive gene expression network controlled by CBF transcription factors. The CBFs are sufficient to enable plants to survive otherwise lethal subzero temperatures. Constitutive CBF expression causes delayed flowering and stunted growth, and plants have evolved the ability to restrict CBF expression to occur only in the cold. This allows plants to anticipate likely freezing events and selectively deploy cold tolerance. The mechanism by which cold stress is sensed is however unknown. Here we show that protein translation rates in plants are proportional to temperature, and reduced translation rates trigger a rise in intracellular free calcium that activates the CAMTA transcription factors, and these directly activate cold-induced gene expression.

plant biology↗

bioRxiv2020

Generation of clonal male and female mice through CRISPR/Cas9-mediated Y chromosome deletion in embryonic stem cells

Mice derived entirely from embryonic stem (ES) cells can be generated in one step through tetraploid complementation. Although XY male ES cell lines are commonly used in this system, occasionally, monosomic XO female all-ES mice are produced through spontaneous Y chromosome loss. Here, we describe an efficient method to obtain monosomic XO ES cells by CRISPR/Cas9-mediated deletion of the Y chromosome allowing generation of clonal male and female mice by tetraploid complementation. The monosomic XO female mice are viable and are able to produce normal male and female offspring. Direct generation of clonal male and female mice from the same mutant ES cells significantly accelerates the production of complex genetically modified mouse models by circumventing multiple rounds of outbreeding.Competing Interest StatementThe authors have declared no competing interest.View Full Text

developmental biology↗

bioRxiv2019

Phytochromes measure photoperiod in Brachypodium

Daylength is a key seasonal cue for animals and plants. In cereals, photoperiodic responses are a major adaptive trait, and alleles of clock genes such as PHOTOPERIOD DEPENDENT1 (PPD1) and EARLY FLOWERING3 (ELF3) have been selected for in breeding barley and wheat for more northern latitudes (Faure et al., 2012; Turner, Beales, Faure, Dunford, & Laurie, 2005). How monocot plants sense photoperiod and integrate this information into growth and development is not well understood. We show that in Brachypodium distachyon, phytochrome C (phyC) acts as a molecular timer, directly communicating information to the circadian clock protein ELF3. In this way, ELF3 levels integrate night length information. ELF3 is a central regulator of photoperiodism in Brachypodium, and elf3 mutants display a constitutive long day transcriptome. Conversely, conditions that result in higher levels of ELF3 suppress long day responses. We are able to show that these effects are direct, as ELF3 and phyC occur in a common complex, and they associate with the promoters of a number of conserved regulators of photoperiodism, including PPD1. Consistent with observations in barley, we are able to show that PPD1 overexpression accelerates flowering in SD and is necessary for rapid flowering in response to LD. These findings provide a conceptual framework for understanding observations in the photoperiodic responses of key crops, including wheat, barley and rice.

plant biology↗

bioRxiv2017

Handling Multiplicity in Neuroimaging through Bayesian Lenses with Hierarchical Modeling

Here we address the current issues of inefficiency and over-penalization in the massively univariate approach followed by the correction for multiple testing, and propose a more efficient model that pools and shares information among brain regions. Using Bayesian multilevel (BML) modeling, we control two types of error that are more relevant than the conventional false positive rate (FPR): incorrect sign (type S) and incorrect magnitude (type M). BML also aims to achieve two goals: 1) improving modeling efficiency by having one integrative model and thereby dissolving the multiple testing issue, and 2) turning the focus of conventional null hypothesis significant testing (NHST) on FPR into quality control by calibrating type S errors while maintaining a reasonable level of inference efficiency The performance and validity of this approach are demonstrated through an application at the region of interest (ROI) level, with all the regions on an equal footing: unlike the current approaches under NHST, small regions are not disadvantaged simply because of their physical size. In addition, compared to the massively univariate approach, BML may simultaneously achieve increased spatial specificity and inference efficiency, and promote results reporting in totality and transparency. The benefits of BML are illustrated in performance and quality checking using an experimental dataset. The methodology also avoids the current practice of sharp and arbitrary thresholding in the p-value funnel to which the multidimensional data are reduced. The BML approach with its auxiliary tools is available as part of the AFNI suite for general use.

neuroscience↗