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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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2025

The cytosolic PRMT5-CDK4 complex impairs cell cycle kinase signaling

Both, protein arginine methyltransferases (PRMTs) and protein kinases are critical regulators of cellular processes and frequently dysregulated in malignancy. To systematically study the crosstalk of the two regulatory enzyme classes, we used parallel yeast two-hybrid matrix screening and defined 45 interactions connecting 4 PRMTs and 20 human kinases. The PRMT-kinase network revealed a strong association between PRMTs and cell cycle/mitogen-activated kinases. Notably, the PRMT5-CDK4 emerged as the most prominent functional cell cycle link through integrative data analyses of different high-throughput datasets. Mechanistic cell biological studies confirmed that the PRMT5-CDK4 complex localizes exclusively in the cytosol, where its formation was enhanced during a G1/S cell cycle block. This PRMT5 interaction modulated the CDK4-CCND3 and CDK4-CDKN2A interaction dynamics, irrespective of PRMT5s methyltransferase activity. Phospho-proteomic profiling demonstrated that PRMT5 overexpression functionally phenocopies the signaling effects of pharmacological CDK4 inhibition with Palbociclib. The findings establish a non-enzymatic regulatory role for PRMT5, proposing it functions as an inhibitory modulator of CDK4-driven oncogenic signaling.

systems biology↗

bioRxiv2022

Uncovering the principles coordinating systems-level organelle biogenesis with cellular growth

Among the hallmark properties of the eukaryotic cell is its organization into specialized biochemical compartments known as organelles. Understanding how organelle biogenesis at systems-scale is coordinated with cellular growth rate and size is a major goal of quantitative cell biology. Here we map out the correlation structure of systems-level organelle biogenesis with cellular growth using "rainbow yeast", a strain of Saccharomyces cerevisiae that expresses fluorescent labels for 6 major organelles. By carrying out hyperspectral imaging of thousands of single rainbow yeast cells, we decomposed the systems-level organelle biogenesis program into specific modes that characterize the response to changes in nutrient availability. Upon chemical biological dissection of this response, our results suggest that systems-level organelle biogenesis represents the sum of distinct organelle modes excited by growth rate and cell size separately. The flexibility afforded by this regulatory architecture may underlie how eukaryotic cells leverage compartmentalization to independently tune cell sizes and growth rates and satisfy potentially incompatible environmental and developmental constraints.

systems biology↗

bioRxiv2022

Structure-based discovery of a novel small-molecule inhibitor of TEAD palmitoylation

The paralogous oncogenic transcriptional coactivators YAP and TAZ are the distal effectors of the Hippo signaling pathway, which play a critical role in cell proliferation, survival and cell fate specification. The core kinase cascade of the Hippo signaling pathway phosphorylates YAP/TAZ and restrict its activity by promoting cytoplasmic sequestration and degradation. Unphosphorylated YAP/TAZ translocates into the nucleus and associates with the TEA domain (TEAD1-4) transcription factors to regulate their target genes. They are frequently misregulated in most human cancers, where they contribute to multiple aspects of tumorigenesis including growth, metabolism, metastasis and chemo/immunotherapy resistance. Thus, they provide a critical point for therapeutic intervention. However, due to their intrinsically disordered structure, they are challenging to target directly. Since YAP/TAZ exerts oncogenic activity by associating with the TEAD1-4 transcription factors, to regulate target gene expression, YAP activity can be controlled indirectly by regulating TEAD1-4. Interestingly, TEADs undergo autopalmitoylation, which is essential for their stability and function. The palmitic acid occupies a hydrophobic pocket in TEAD1-4, and small-molecule inhibitors that bind to this site can render them unstable, and allosterically inhibit their interaction with YAP/TAZ and chromatin. Here we combined structure-based virtual ligand screening with biochemical and cell biological studies and identified a novel small-molecule that inhibits TEAD palmitoylation and stability. Further, it affects YAP-TEAD interaction and inhibits YAP transcriptional activity and impairs proliferation, colony formation and migration of breast and ovarian cancer cells.

cancer biology↗

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↗

bioRxiv2019

Conserved function of ether lipids and sphingolipids in the early secretory pathway

Sphingolipids have been shown to play important roles in physiology and cell biology, but a systematic examination of their functions is lacking. We performed a genome-wide CRISPRi screen in sphingolipid-depleted cells and identified hypersensitive mutants in genes of membrane trafficking and lipid biosynthesis, including ether lipid synthesis. Systematic lipidomic analysis showed a coordinate regulation of ether lipids with sphingolipids, where depletion of one of these lipid types resulted in increases in the other, suggesting an adaptation and functional compensation. Biophysical experiments on model membranes show common properties of these structurally diverse lipids that also share a known function as GPI anchors in different kingdoms of life. Molecular dynamics simulations show a selective enrichment of ether phosphatidylcholine around p24 proteins, which are receptors for the export of GPI-anchored proteins and have been shown to bind a specific sphingomyelin species. Our results support a model of convergent evolution of proteins and lipids, based on their physico-chemical properties, to regulate GPI-anchored protein transport and maintain homeostasis in the early secretory pathway.

biochemistry↗

bioRxiv2022

Robust probabilistic modeling for single-cell multimodal mosaic integration and imputation

Recent advances in single-cell technologies enable joint profiling of multiple omics. These profiles can reveal the complex interplay of different regulatory layers in single cells; still, new challenges arise when integrating datasets with some features shared across experiments and others exclusive to a single source; combining information across these sources is called mosaic integration. The difficulties lie in imputing missing molecular layers to build a self-consistent atlas, finding a common latent space, and transferring learning to new data sources robustly. Existing mosaic integration approaches based on matrix factorization cannot efficiently adapt to nonlinear embeddings for the latent cell space and are not designed for accurate imputation of missing molecular layers. By contrast, we propose a probabilistic variational autoencoder model, scVAEIT, to integrate and impute multimodal datasets with mosaic measurements. A key advance is the use of a missing mask for learning the conditional distribution of unobserved modalities and features, which makes scVAEIT flexible to combine different panels of measurements from multimodal datasets accurately and in an end-to-end manner. Imputing the masked features serves as a supervised learning procedure while preventing overfitting by regularization. Focusing on gene expression, protein abundance, and chromatin accessibility, we validate that scVAEIT robustly imputes the missing modalities and features of cells biologically different from the training data. scVAEIT also adjusts for batch effects while maintaining the biological variation, which provides better latent representations for the integrated datasets. We demonstrate that scVAEIT significantly improves integration and imputation across unseen cell types, different technologies, and different tissues. Significance StatementSingle-cell multimodal assays provide an unprecedented opportunity for investigating heterogeneity of cell types and novel associations with disease and development. Although analyses of such multimodal datasets have the potential to provide new insights that cannot be inferred with a single modality, access typically requires the integration of multiple data sources. We propose a probabilistic variational autoencoder model for mosaic integration, which involves merging data sources that include features shared across datasets and features exclusive to a single data source. Our model is designed to provide a lower dimensional representation of the cells for visualization, clustering, and other downstream tasks; accurate imputation of missing features and observations; and transfer learning for robustly imputing new datasets when only partial measurements are available.

genetics↗

bioRxiv2025

Lack of mRNA Methylation in Schwann Cells Results in Demyelination and Regenerative Failure

Schwann cells are essential for peripheral nerve myelination and regeneration. N6-methyladenosine (m6A) RNA methylation, regulated by methyltransferase-like 14 (Mettl14), is a critical post-transcriptional modification, but its role in Schwann cell biology remains unclear. Using a conditional knockout (cKO) mouse model, we investigated the impact of Mettl14-mediated m6A methylation on Schwann cells. Mice born with Schwann cell-specific genetic deletion of Mettl14 developed normally but starting in young adulthood exhibited progressive motor deficits, severe demyelination, and axonal degeneration, confirmed by behavioral assessments and histological analyses. Mettl14-deficient Schwann cells displayed impaired proliferation and mitochondrial dysfunction in vitro. Following sciatic nerve injury, Mettl14 cKO mice showed defective macrophage recruitment, slowed axonal degeneration, and impaired regeneration. These findings suggest that Mettl14-mediated m6A methylation is critical for Schwann cell maintenance but not development. Given that Mettl14 cKO mice developed a demyelinating polyneuropathy, it is possible that manipulation of m6A methylation in Schwann cells is a promising therapeutic strategy targeting peripheral nerve repair and myelination.

neuroscience↗

bioRxiv2018

Changes in endosymbiont complexity drive host-level compensatory adaptations in cicadas

For insects that depend on one or more bacterial endosymbionts for survival, it is critical that these bacteria are faithfully transmitted between insect generations. Cicadas harbor two essential bacterial endosymbionts, Sulcia muelleri and Hodgkinia cicadicola. In some cicada species, Hodgkinia has fragmented into multiple distinct cellular and genomic lineages that can differ in abundance by more than two orders of magnitude. This complexity presents a potential problem for the host cicada, because low-abundance-but-essential Hodgkinia lineages risk being lost during the symbiont transmission bottleneck from mother to egg. Here we show that all cicada eggs seem to receive the full complement of Hodgkinia lineages, and that in cicadas with more complex Hodgkinia this outcome is achieved by increasing the number of Hodgkinia cells transmitted by up to six-fold. We further show that cicada species with varying Hodgkinia complexity do not visibly alter their transmission mechanism at the resolution of cell biological structures. Together these data suggest that a major cicada adaptation to changes in endosymbiont complexity is an increase in the number of Hodgkinia cells transmitted to each egg. We hypothesize that the requirement to increase the symbiont titer is one of the costs associated with Hodgkinia fragmentation.

evolutionary biology↗

bioRxiv2026

LARP4 is a B cell-specific metabolic checkpoint for plasma cell differentiation and a therapeutic target in systemic lupus erythematosus

RNA-binding protein LARP4 plays an important role in T cell activation and differentiation, but its role in B cell biology and the pathogenesis of systemic lupus erythematosus (SLE) remains unclear. This study found that LARP4 was specifically highly expressed in B cells of SLE patients and was positively correlated with disease activity. By constructing T cell-specific and B cell-specific conditional knockout mice, we found that deletion of LARP4 in B cells, but not in T cells, significantly alleviated pristane-induced and Bm12-induced lupus nephritis. Further analysis showed that LARP4 deletion selectively inhibited B cell differentiation into plasma cells, but did not affect germinal center B cell formation. Integrated transcriptomic and metabolomics analyses revealed that this effect is due to reduced phosphatidic acid synthesis and decreased mTORC1 activity caused by mitochondrial oxidative phosphorylation dysfunction. Furthermore, we used LIPEP, a LARP4 inhibitory peptide that effectively mimicked the therapeutic effects of LARP4 gene knockout in the MRL/lpr spontaneous lupus model and outperformed cyclophosphamide in reducing glomerular immune complex deposition and improving extrarenal dermatitis. These results indicates that LARP4 is a key metabolic checkpoint regulating B cell differentiation into Plasma cells and suggest that it may be a potential therapeutic target for SLE.

immunology↗

bioRxiv2025

Automated Image-Based Profiling of Pluripotent Stem Cell Colonies

Quantitative image analysis is essential for advancing stem cell biology, developmental studies, and drug discovery, yet most workflows still rely on manual or semi-quantitative scoring that is slow, subjective, and poorly scalable. A major challenge is converting complex colony morphologies into reproducible, high-dimensional datasets. To address this gap, we developed ColonyQuant, an open-source platform that integrates automated colony segmentation, alkaline phosphatase (AP) intensity quantification, morphometric profiling, and statistical classification into a single workflow. ColonyQuant computes per-colony functional readouts alongside comprehensive shape descriptors, capturing both staining intensity and structural features in a unified framework. Applied to embryonic stem cells (ESCs) treated with a selective KDM4 histone-demethylase inhibitor, ColonyQuant revealed dose-dependent reductions in colony area and integrated AP signal, together with systematic remodeling of morphometric metrics. Multivariate analyses robustly stratified treatment groups and identified intensity and solidity as principal features capturing dose-dependent colony responses. By transforming subjective scoring into objective, scalable, and biologically interpretable phenotyping, ColonyQuant provides a reproducible platform for stem cell research and high-content screening.

developmental biology↗

bioRxiv2020

Protein-bound molybdenum cofactor is bioavailable and rescues molybdenum cofactor-deficient C. elegans

The molybdenum cofactor (Moco) is a 520 dalton prosthetic group that is synthesized in all domains of life. In animals, four oxidases (among them sulfite oxidase) use Moco as a prosthetic group. Moco is essential in animals; humans with mutations in genes that encode Moco-biosynthetic enzymes display lethal neurological and developmental defects. Moco supplementation seems a logical therapy, however the instability of Moco has precluded biochemical and cell biological studies of Moco transport and bioavailability. The nematode Caenorhabditis elegans can take up Moco from its bacterial diet and transport it to cells and tissues that express Moco-requiring enzymes, suggesting a system for Moco uptake and distribution. Here we show that protein-bound Moco is the stable, bioavailable species of Moco taken up by C. elegans from its diet and is an effective dietary supplement, rescuing a C. elegans model of Moco deficiency. We demonstrate that diverse Moco:protein complexes are stable and bioavailable, suggesting a new strategy for the production and delivery of therapeutically active Moco to treat human Moco deficiency.

developmental biology↗

bioRxiv2019

The human proteome co-regulation map reveals functional relationships between proteins

The annotation of protein function is a longstanding challenge of cell biology that suffers from the sheer magnitude of the task. Here we present ProteomeHD, which documents the response of 10,323 human proteins to 294 biological perturbations, measured by isotope-labelling mass spectrometry. Using this data matrix and robust machine learning we create a co-regulation map of the cell that reflects functional associations between human proteins. The map identifies a functional context for many uncharacterized proteins, including microproteins that are difficult to study with traditional methods. Co-regulation also captures relationships between proteins which do not physically interact or co-localize. For example, co-regulation of the peroxisomal membrane protein PEX11{beta} with mitochondrial respiration factors led us to discover a novel organelle interface between peroxisomes and mitochondria in mammalian cells. The co-regulation map can be explored at www.proteomeHD.net.

systems biology↗

bioRxiv2024

Niche cytoskeletal architecture is required for proper stem cell signaling and oriented division in the Drosophila testis

Stem cells are critical to repair and regenerate tissues, and often reside in a niche that controls their behavior. The Drosophila testis niche has been a paradigm for niche-stem cell interactions and is used here to address the cell biological features that maintain niche structure and function during its steady-state operation. We report enrichment of the Myosin II (MyoII) and a key regulator of acto-myosin contractility (AMC), Rho Kinase (ROK), within the niche cell cortex at the interface with germline stem cells (GSCs). Compromising MyoII and ROK disrupts niche architecture, suggesting that AMC in niche cells is important to maintain the reproducible structure of this niche. Furthermore, defects in niche architecture cause changes in stem cell function. Our data suggest that the niche signals less robustly to adjacent germ cells, yet the disrupted structure permits increased numbers of cells to respond to the signal. Finally, compromising Myo II in niche cells leads to an increase in mis-oriented centrosomes in GSCs as well as defects in the centrosome orientation checkpoint. Ultimately, this work identifies a critical role for AMC-dependent maintenance of niche structure to ensure a proper complement of stem cells with correct execution of stem cell divisions. Summary statementActomyosin contractility regulated niche architecture is critical for proper signaling and oriented division of germline stem cells.

developmental biology↗

bioRxiv2024

Evolutionary analysis of paired box gene family and biological function exploration of Lr.Pax7 in lamprey (Lethenteron reissneri)

The Pax(paired box)gene family comprises highly conserved transcription factors that play a crucial regulatory role in embryonic development, tissue morphogenesis, and cell differentiation. The gene family comprises of nine members, namely Pax1 to Pax9, each exhibiting distinct functionalities and expression patterns. Among the members of the Pax family, Pax7 is particularly involved in key regulatory functions related to skeletal muscle development and satellite cell biology in vertebrates. However, the precise role of Pax7 and its downstream targets in jawless vertebrates such as lamprey remains relatively understudied. Therefore, investigating the expression and function of lampreys Pax genes holds significant value as a model organism for understanding developmental processes, evolution, and interactions with other vertebrates. In this study, we identified Pax7 in Lethentero reissneri and multiple bioinformatics analyses suggested that it may represent the ancestral gene of the Pax7 shared among higher vertebrates. To further elucidate the function and regulatory mechanism of Pax7, we performed transcriptome sequencing analysis after silencing Lr.Pax7 expression which revealed alterations in metabolic processes along with associated genes(Plcy,Jagged2,Hes,Myod,Frizzled2,etc) involved in various immune pathways(Notch, Wnt, IL-17, TNF, etc), myogenesis process, adipocyte formation process consistent with those observed in higher vertebrates. Comparative studies between lamprey and high vertebrates could provide valuable insight into understanding the functional role of Pax7 and its downstream targets across diverse biological process as well as disease states.

evolutionary biology↗

bioRxiv2025

Tahoe-x1: Scaling Perturbation-Trained Single-CellFoundation Models to 3 Billion Parameters

Foundation models have transformed natural language processing and computer vision, yet their potential in single-cell biology--particularly for complex diseases such as cancer-- remains underexplored. We present Tahoe-x1 (Tx1), a family of perturbation-trained single-cell foundation models with up to 3 billion parameters. Tx1 is pretrained on large-scale single-cell transcriptomic datasets, including the Tahoe-100M perturbation compendium, and fine-tuned for cancer-relevant tasks. Through architectural optimizations, data loader refinements, and efficient training strategies, Tx1 achieves 3-30x higher compute efficiency than prior implementations of cell-state models. Tx1 jointly learns representations of genes, cells, and compounds using a masked-expression generative objective that incorporates a drug token, enabling flexible adaptation to diverse downstream applications. We evaluate Tx1 across four key disease-relevant benchmarks: (1) prediction of overall and context-specific gene essentiality, (2) identification of genes contributing to the hallmarks of cancer, (3) cell-type classification, and (4) prediction of perturbation responses in held-out cellular contexts. Tx1 achieves state-of-the-art performance across all tasks. We release pretrained checkpoints, training code, and evaluation workflows to accelerate the development of perturbation-trained single-cell foundation models for applications in precision oncology and beyond. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=52 SRC="FIGDIR/small/683759v1_ufig1.gif" ALT="Figure 1"> View larger version (13K): org.highwire.dtl.DTLVardef@aa33d5org.highwire.dtl.DTLVardef@310a38org.highwire.dtl.DTLVardef@195f204org.highwire.dtl.DTLVardef@143f7e3_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2024

Differentially expressed growth factors and cytokines drive phenotypic changes in transmissible cancers

The Tasmanian devil is threatened by two deadly transmissible Schwann cell cancers. A vaccine to protect Tasmanian devils from both devil facial tumour 1 (DFT1) and devil facial tumour 2 (DFT2), and improved understanding of the cancer cell biology, could support improved conservation actions. Previous transcriptomic analysis has implicated phenotypic cellular plasticity as a potential immune escape and survival mechanism of DFT1 cells. This phenotypic plasticity facilitates transition from a myelinating Schwann cell to a repair Schwann cell phenotype that exhibits mesenchymal characteristics. Here, we have identified cytokines and growth factors differentially expressed across DFT cell phenotypes and investigated their role in driving phenotypic plasticity and oncogenic properties of DFT cells. Our results show that NRG1, IL16, TGF{beta}1, TGF{beta}2 and PDGFAA/AB proteins have significant and distinct effects on the proliferation rate, migratory capacity and/or morphology of DFT cells. Specifically, PDGFR signalling, induced by PDGFAA/AB, was a strong enhancer of cell proliferation and migration, while TGF{beta}1 and TGF{beta}2 induced epithelial-mesenchymal transition (EMT)-like changes, inhibited proliferation and increased migratory capacity. These findings suggest complex interactions between cytokine signalling, phenotypic plasticity, growth and survival of DFTs. Signalling pathways implicated in the propagation of DFT are potential targets for therapeutic intervention and vaccine development for Tasmanian devil conservation.

cancer biology↗

bioRxiv2026

Toolbox for fluorescent labelling of Pseudomonas aeruginosa across scales: from single cells to bacterial communities and host infection models

Fluorescence microscopy is central to the study of bacterial cell biology, multicellular behaviours, and host-pathogen interactions. Bright, robust and photostable labelling is required for bacterial identification, sorting and quantitative analysis, driving continuous development of state-of-the-art labelling tools. Here, we developed a multicolor fluorescent cell labelling toolkit for Gram-negative bacteria carrying the attTn7 site, using the opportunistic human pathogen Pseudomonas aeruginosa as a model. Cell labelling is achieved by constitutive chromosomal expression of genes encoding a choice of four novel fluorescent proteins, mNeonGreen, mJuniper, mLychee and mScarlet-I3, codon-optimised for P. aeruginosa. These reporters provide bright, stable fluorescence with minimal photobleaching and excellent spectral separation during long-term imaging of single cells, macrocolonies and biofilms. Chromosomal expression of mNeonGreen yielded brighter and more homogeneous labelling than expression of the same construct from a plasmid. Importantly, dual-color labelling of macrocolonies uncovered previously unrecognised phenomena of collective motility when two isogenic swarming populations interact. Finally, we demonstrate the applicability of our constructs in biologically relevant host-pathogen contexts by imaging both live and fixed P. aeruginosa-infected human airway epithelial cells. This versatile cell labelling platform enables reliable bacterial identification, segmentation, tracking, and quantitative fluorescence imaging across spatial and temporal scales, and is readily adaptable to most other Gram-negative bacteria as the attTn7 integration site is well conserved.

microbiology↗

bioRxiv2022

Chemoenzymatic fluorescence labeling of intercellularly contacting cells using lipidated sortase A

Methods to label intercellular contact attract particular attention due to their potential in cell biological and medical applications through analysis of intercellular communications. In this study, a simple and versatile method for chemoenzymatically labeling the intercellularly contacting cell was developed by using a cell-surface anchoring reagent of poly(ethylene glycol)(PEG)-lipid conjugate. The surfaces of each cell in cell pairs of interest were efficiently decorated with sortase A (SrtA) and triglycine peptide that were lipidated with PEG-lipid, respectively. In the mixture of the two cell populations, the triglycine-modified cells were enzymatically labeled with a fluorescent labeling reagent by contacting with the SrtA-modified cells both on the substrate and in cell suspensions. Such selective labeling of the contacting cells was confirmed by confocal microscopy and flow cytometry. The results show a proof of principle that the present method is a promising tool for selective visualization and quantification of the intercellularly contacting cells among cell mixtures in cell-cell communication analysis.

biochemistry↗