Biology subjects

Han, Y.

Publications and source records attributed to Han, Y..

At least 109 records · Page 6Linked to original sources

bioRxiv2025

MLL1 complex is a critical regulator of fetal hemoglobin repression

Increasing fetal-type hemoglobin (HbF) expression in adult erythroid cells holds promise in the treatment of sickle cell disease (SCD) and {beta}-thalassemia. We have identified MLL1 complex as a critical regulator of fetal and embryonic hemoglobin repression. Knockdowns of MEN1 and KMT2A, encoding essential components of the complex, caused a significant downregulation of BCL11A expression and a substantial increase in {gamma}- and {varepsilon}-globin mRNA levels in HUDEP-2 cells. Significant binding of MEN1 and KMT2A were readily detected at the promoter and a critical enhancer of BCL11A in HUDEP-2 cells, suggesting that BCL11A is a direct transcriptional target of MLL1 complex. Consistent with these results, MEN1 or KMT2A knockdown in normal human CD34+ hematopoietic stem and progenitor cells (HSPCs) induced to undergo erythroid differentiation also significantly decreased their BCL11A expression and increased their {gamma}- and {varepsilon}-globin expression and the production of F cells in the culture. Treatment of these cells with MENIN inhibitors yielded similar results and promoted erythroid differentiation with minimal effects on their growth. These findings underscore a critical role of MLL1 complex in regulating fetal and embryonic hemoglobin expression and suggest that MENIN inhibitors could offer a promising therapeutic approach for sickle cell disease and {beta}-thalassemia.

developmental biology↗

bioRxiv2025

The bacterial chaperone CsgC inhibits functional amyloid CsgA formation by promoting the intrinsically disordered pre-nuclear state

E. coli assembles a functional amyloid called curli during biofilm formation. The major curlin subunit is the CsgA protein, which adopts a beta-sheet rich fold upon fibrillization. The chaperone-like protein CsgC inhibits CsgA amyloid formation. CsgA undergoes a 3-stage aggregation process: an initial lag phase where beta-rich nuclei form, an exponential elongation phase, and a plateau phase. It is currently not known if CsgC inhibits amyloid formation by inhibiting formation of a pre-fibril nucleus, or if CsgC inhibits a later stage of amyloid formation by blocking monomer addition. Here, CsgC homologs from C. youngae, C. davisae, and H. alvei were purified and characterized for their ability to interrogate CsgA amyloid formation. Each of the CsgC homologs prolonged the lag phase of E. coli CsgA amyloid formation similar to E. coli CsgC. Additionally, we found E. coli CsgC interacted transiently and weakly with a monomeric, pre-nucleus species of CsgA which delayed amyloid formation. A transient CsgC-CsgA heterodimer was observed using ion mobility-mass spectrometry. When CsgC was added to actively polymerizing CsgA, exponential growth commonly associated with nucleation-dependent amyloid formation was lost. Adding preformed CsgA seeds did not rescue exponential growth, indicating that CsgC also has inhibitory activity during fibril elongation. Indeed, CsgC interacted strongly with CsgA fibers, suggesting the interaction between CsgC and CsgA fibers can slow new fiber growth. CsgC displays unique inhibitory activity at multiple stages of amyloid formation. CsgC acts as an energy-independent chaperone that transiently interacts with prefibrillar CsgA and an amyloid fiber.

biochemistry↗

bioRxiv2025

CD34 serves as an intrinsic innate immune guardrail protecting stem cells from replicating retroviruses

Stem cells are highly resistant to viral infection compared to their differentiated progeny, and this resistance is associated with stem cell-specific restriction factors and intrinsic interferon stimulated genes (ISGs). In HIV infection, proviral DNA has been detected in certain bone marrow hematopoietic stem cells, yet widespread stem cell infection in vivo is restricted. Intriguingly, exposing bone marrow stem cells to HIV in vitro led to viral replication selectively only in the CD34- population, but not in the CD34+ cells. The mechanism dictating this CD34-based HIV restriction remained a mystery, especially since HIV has a capacity to antagonize restriction factors and ISGs. CD34 is a common marker of hematopoietic stem and progenitor cells. Here, we report the intrinsic antiviral properties of CD34. Expression of CD34 in HIV-1 producer cells results in the loss of progeny virion infectivity. Conversely, removal of CD34 using CRISPR/Cas9 knockout or stem cell differentiation cytokines promotes HIV-1 replication in stem cells. These results suggest that in addition to restriction factors and intrinsic ISGs, CD34 serves as a host innate protection preventing retrovirus replication in stem cells. Mechanistically, CD34 does not block viral entry, integration, and release. Instead, it becomes incorporated onto progeny virions, which inactivates virus infectivity. These findings offer new insights into innate immunity in stem cells, and highlight intriguing retrovirus-host interactions in evolution.

immunology↗

bioRxiv2025

A genome-scale drug discovery pipeline uncovers new therapeutic targets and a unique p97 allosteric binding site in Schistosoma mansoni

Schistosomes are parasitic flatworms that infect more than 200 million people globally. However, there is a shortage of molecular tools that enable the discovery of potential drug targets within schistosomes. Thus, praziquantel has remained the frontline treatment for schistosomiasis despite known liabilities. Here, we have conducted a genome-wide study in S. mansoni using the human druggable genome as a bioinformatic template to identify essential genes within schistosomes bearing similarity to catalogued drug targets. Then, we assessed these candidate targets in silico using a set of unbiased criteria to determine which possess ideal characteristics for a ready-made drug discovery campaign. Following this prioritization, we pursued a parasite p97 ortholog as a bona-fide drug target for the development of therapeutics to treat schistosomiasis. From this effort, we identified a covalent inhibitor series that kills schistosomes through an on-target killing mechanism by disrupting the ubiquitin proteasome system. Fascinatingly, these inhibitors induce a conformational change in the conserved D2 domain P-loop of schistosome p97 upon modification of Cys519. This conformational change reveals an allosteric binding site adjacent to the D2 domain active site reminiscent of the DFG flip in protein kinases. This allosteric binding site can potentially be utilized to generate new classes of species-selective p97 inhibitors. Furthermore, these studies provide a resource for the development of alternative therapeutics for schistosomiasis and a workflow to identify potential drug targets in similar systems with few available molecular tools. Significance StatementSchistosomes cause widespread infections in humans, leading to severe chronic illnesses in endemic regions. There is no vaccine for schistosomiasis, and there has been limited success using the current standard-of-care treatment, praziquantel. Therefore, it is essential to identify drug targets within these parasites. Here, we identify potential drug targets in schistosomes bearing similarity to established human therapeutic targets, evaluate their essentiality for parasite survival, then prioritize them using an unbiased set of criteria to uncover high-value targets for the treatment of schistosomiasis. We investigated one candidate as a proof-of concept, a p97 ortholog, to discover newly characterized inhibitors of the parasite enzyme. This study demonstrates that this workflow can lead to the identification of small molecules that kill schistosomes.

microbiology↗

bioRxiv2025

Extending Prot2Token: Aligning Protein Language Models for Unified and Diverse Protein Prediction Tasks

AO_SCPLOWBSTRACTC_SCPLOWComprehensive protein function and property prediction remains a major challenge due to the vast diversity of sequences, structural variations, and limited labeled data. Existing models are often specialized to be task-specific, requiring independent training, which limits scalability. To address this, we extend Prot2Token, a unified autoregressive framework that focuses on the post-training alignment of pre-trained protein language models (PLMs), to new applications. Our approach enables next-token prediction across new applications of proteinprediction tasks, including protein-protein structure similarity, 3D structure prediction, mutation stability, post-translational modifications (PTMs), substratekinase phosphorylation sites, protein-protein affinity, and protein-ion binding sites. We introduce a self-supervised pre-training stage for the decoder, enhancing model initialization and improving downstream predictions. By integrating a causal autoregressive transformer with a pre-trained ESM-2 encoder, our model effectively aligns diverse protein tasks within a single framework. Additionally, we discuss the opportunities and limitations of this approach, providing insights for future research in optimizing PLMs as a general tool for broader biological applications. Code is available on GitHub Repository.

bioinformatics↗

bioRxiv2025

Effects of Pesticide Exposure on Neuroinflammation and Microglial Gene Expression: Relevance to Mechanisms of Alzheimer's Disease Risk

BackgroundAlzheimers disease (AD) is characterized by the presence of amyloid-{beta} plaques, neurofibrillary tangles, and neuroinflammation. Previously, we reported serum levels of dichlorodiphenyldichloroethylene (DDE), the primary metabolite of the pesticide dichlorodiphenyltrichloroethane (DDT), were significantly higher in AD patients compared to age-matched controls and that DDT exposure worsened AD pathology in animal models. ObjectiveHere, we investigated the effect of DDT on neuroinflammation in primary mouse microglia (PMG) and C57BL/6J mice. MethodsEffects of DDT on inflammation and disease-associated microglia were determined in primary mouse microglia and C57BL/6J mice. ResultsPMG exposed to DDT (0.5-5.0 {micro}M) elicited a [~]2-3-fold increase in Il-1b mRNA levels, with similar concentration-dependent upregulation in Il-6, Nos2, and Tnfa. These effects were blocked by the sodium channel antagonist tetrodotoxin, demonstrating the role of DDT-microglial sodium channel interactions in mediating this response. Additionally, NOS2 protein levels increased by [~]1.5-2-fold, while TNFa was elevated by 2-4-fold. C57BL/6J male and female mice exposed to DDT (30 mg/kg) demonstrated significantly increased mRNA levels of Nos2, Il-1b, and Il-6 in the frontal cortex (1.5-2.3-fold), and Nos2, Il-1b, and Tnfa (1.5-1.8-fold) in the hippocampus. Furthermore, microglial homeostatic genes, Cx3cr1, P2ry12, and Tmem119, were downregulated, while stage 1 disease-associated microglia genes were upregulated both in vitro and in vivo. Notably, Apoe and Trem2 were only upregulated in the frontal cortex and hippocampus of females. ConclusionThese data indicate that DDT increases neuroinflammation, which may result from direct actions of DDT on microglia, providing a novel pathway by which DDT may contribute to AD risk.

neuroscience↗

bioRxiv2025

Developing Foundation Models for Predicting Viral Animal Host Range in Intelligent Surveillance

Emerging human infectious viruses originating from animals continue to pose a persistent threat to global public health. Understanding the host range of animal viruses is crucial for identifying potential spillover pathways and mitigating the risk of future pandemics. Here, we present VirHRanger, a prediction method that integrates foundation models trained on viral genome and protein sequences, alongside genomic and protein compositional traits, viral phylogeny, and protein-protein interactions. To systematically predict the animal host range, VirHRanger incorporates host taxonomy-aware neural networks trained on a comprehensive collection of animal-virus associations spanning mammals, birds, and arthropods. Within a dataset of 4,006 virus species spanning 99 viral families, our model achieved robust performance with a micro-averaged AUROC of 0.938 across all host categories, demonstrating its effectiveness in capturing generalizable host signals from viral genetic data. On a dataset of 315 novel viruses, which are associated with key reservoir animal hosts and insect vectors, VirHRanger notably outperformed the homology-based method, exhibiting a strong generalizability to novel viruses. Furthermore, VirHRanger identified host range variations among closely related viruses within the Coronaviridae family and successfully predicted the ability of SARS-CoV-2 to infect humans and other animal hosts. These findings highlight the potential of VirHRanger to transform sequencing data into timely insights for disease control during the early stages of zoonotic outbreaks.

bioinformatics↗

bioRxiv2025

Glycosylphosphatidylinositol biosynthesis restricts coronavirus infection via the regulation of LY6E

Coronaviruses, including SARS-CoV-2, rely on host factors for their replication and pathogenesis, while hosts deploy defense mechanisms to counteract viral infections. Although numerous host proviral factors have been identified, the landscape of host restriction factors and their underlying mechanisms remain less explored. Here, we conducted genome-wide CRISPR knockout screens using three distinct coronaviruses--SARS-CoV-2, HCoV-OC43 (a common cold human virus from the genus Betacoronavirus) and porcine epidemic diarrhea virus (Alphacoronavirus) to identify conserved host restriction factors. We identified glycosylphosphatidylinositol (GPI) biosynthesis as the pan-coronavirus host factor that restrict viral entry by disrupting spike protein-mediated membrane fusion at both endosomal and plasma membranes. GPI biosynthesis generates GPI moieties that covalently anchor proteins (GPI-anchored proteins [GPI-APs]) to the cell membrane, playing essential roles in various cellular processes. Through focused CRISPR knockout screens targeting 193 GPI-APs, we identified LY6E as the key downstream effector mediating the antiviral activity of the GPI biosynthesis pathway. These findings reveal a novel role for GPI biosynthesis as a conserved host defense mechanism against coronaviruses and highlight LY6E as a critical antiviral effector. This study provides new insights into virus-host interactions and the development of host-directed antiviral therapies.

microbiology↗

bioRxiv2025

Leopard Cats Occupied Human Settlements in China for 3,500 years before the Arrival of Domestic cats in 600-900 CE around the Tang Dynasty

The earliest cats in human settlements in China were not domestic cats (Felis catus), but native leopard cats (Prionailurus bengalensis). To trace when and how domestic cats arrived in East Asia, we analyzed 22 feline bones from 14 sites across China spanning 5,000 years. Nuclear and mitochondrial genomes revealed that leopard cats began occupying anthropogenic scenes around 5,400 years ago and last appeared in 150 CE. Following several centuries gap of archeological feline remains, the first known domestic cat (706-883 CE) in China was identified in Shaanxi during the Tang Dynasty. Genomic analysis suggested a white or partially white coat and a link to a contemporaneous domestic cat from Kazakhstan, indicating a likely dispersal route via the Silk Road. The two felids once independently occupied ancient anthropogenic environments in China but followed divergent paths and reached different destinations in human-animal interactions.

evolutionary biology↗

bioRxiv2025

KIDINS220 and InsP8 safeguard the stepwise regulation of phosphate exporter XPR1

XPR1 is emerging as the only known inorganic phosphate (Pi) exporter in humans, critical for Pi homeostasis, with its activity stimulated by inositol pyrophosphate InsP8 and regulated by neuronal scaffold protein KIDINS220. Our structural studies reveal InsP8 specifically activates XPR1 in a stepwise manner, involving profound SPX domain movements. Each XPR1 subunit functions with four gating states, in which Pi permeates a constriction site via a "knock-kiss-kick" process. In contrast, KIDINS220 delicately stabilizes XPR1 in a closed conformation through multiple mechanisms, one of which involves trapping the XPR1 1 helix--critical for InsP8 binding--within an interaction hub. InsP8 serves as a key to release KIDINS220s restraint, reinforcing a "key-to-locks" mechanism to safeguard the stepwise activation. Additionally, our study provides direct structural insights into XPR1-associated neuronal disorders and highlights the evolutionary conservation and divergence among XPR1 orthologues, offering a comprehensive understanding of Pi homeostasis across species.

molecular biology↗

bioRxiv2025

Clinical and Taxonomic Characterization of a Novel Urinary Tract Pathogen Providencia lanzhouensis

BackgroundThe genus Providencia includes species of ecological and clinical significance, with some acting as opportunistic pathogens in hospital-acquired infections such as urinary tract infection (UTI). However, overlapping phenotypic traits and genetic similarities pose challenges for accurate species characterization. This study exemplifies this challenge by identifying a novel Providencia isolate through genomic analysis. ResultsIn this study, strain PAZ2 was isolated from the urine sample of a hospitalized patient in Lanzhou, Gansu Province, China. Initial mass spectrometry analysis identified the strain as Providencia alcalifaciens. It exhibits a resistance profile against antibiotics including ampicillin, tetracycline, tigecycline, polymyxin B, colistin, trimethoprim-sulfamethoxazole, and ciprofloxacin. However, whole-genome sequence analysis indicated that this strain is a novel species with an average nucleotide identity (ANI) values ranging from 79.92% to 94.73% and digital DNA-DNA hybridization (dDDH) values between 21.2% and 57.6% when compared with all known Providencia species. Furthermore, strain PAZ2 exhibited unique biochemical properties that differentiated it from all previously described species within the genus. ConclusionsGenomic and biochemical evidence supports PAZ2 as a novel Providencia species, which we named Providencia lanzhouensis sp. nov. This finding enhances the taxonomy of Providencia and underscores its clinical relevance, notably in UTIs and other nosocomial infections. Accurate identification is crucial for guiding effective treatment and preventing misdiagnosis. Further studies should investigate its pathogenicity, antimicrobial resistance, and epidemiology to inform infection control measures.

microbiology↗

bioRxiv2025

The single amino acid change of R516K enables efficient generation of vesicular stomatitis virus-based Crimean-Congo hemorrhagic fever reporter virus

Crimean-Congo hemorrhagic fever virus (CCHFV) is a medically important tick-borne virus, causing severe hemorrhagic diseases in humans. There is no approved vaccines and therapeutics for CCHFV infection. The study of CCHFV authentic virus requires biosafety level 3 facilities, hindering the research and development of antivirals. Here we report the generation of a recombinant vesicular stomatitis virus (VSV) bearing both CCHFV glycoprotein precursor (GPC) and EGFP reporter (rVSV-CCHFV-GFP). We also find that the acquisition of an unexpected single R516K mutation in the GPC protein enables the packaging of high-titer pseudotyped particles. The replication-competent rVSV-CCHFV-GFP reporter virus resembles the entry properties of authentic virus and allows for rapid assessment of susceptible cell lines, neutralizing antibodies, and host entry factors such as heparan sulfate in fluorescence-based assays. This study provides valuable strategy for packaging of high-titer CCHFV pseudovirus, and the tool generated here can be served for the identification and evaluation of countermeasures against the cell entry of CCHFV.

microbiology↗

bioRxiv2024

PSGL-1 excludes HIV Env from virion surface through spatial hindrance involving structural folding of the decameric repeats (DR)

P-selectin glycoprotein ligand-1 (PSGL-1), a mucin-like surface glycoprotein, is primarily expressed on lymphoid and myeloid cells. PSGL-1 has recently been identified as an HIV restriction factor, blocking HIV infectivity mainly through virion incorporation that sterically hinders virion attachment to target cells. PSGL-1 also inhibits HIV Env incorporation into virions. However, the molecular mechanisms of PSGL-1-mediated Env exclusion remained unclear. Here, we investigated the role of PSGL-1s extracellular (EC) and intracellular (IC) domains in Env exclusion. We demonstrate that both EC and IC are important for Env exclusion; when EC was deleted, PSGL-1 completely lost its ability to inhibit Env incorporation, whereas when IC was deleted, PSGL-1 partially lost this activity. In addition, when the decameric repeats (DR) were deleted from EC, PSGL-1 also lost its ability to inhibit Env incorporation. Sequential DR deletion mutagenesis further demonstrated that a minimum of 9 DRs is necessary for Env exclusion. Molecular modeling of the DR structure revealed that PSGL-1 mutants with 7 or fewer DRs pose as an extended "rod-like" structure, whereas those with 9 or more DRs collapse into a "coil-like" structure that spatially excludes Env. Our studies suggest a model in which Env exclusion involves Gag-mediated PSGL-1 targeting to the virion assembly site where DR-mediated spatial exclusion blocks Env incorporation.

microbiology↗

bioRxiv2024

Afadin Sorts Different Retinal Neuron Types into Accurate Cellular Layers

Neurons use cell-adhesion molecules (CAMs) to interact with other neurons and the extracellular environment: the combination of CAMs specifies migration patterns, neuronal morphologies, and synaptic connections across diverse neuron types. Yet little is known regarding the intracellular signaling cascade mediating the CAM recognitions at the cell surface across different neuron types. In this study, we investigated the neural developmental role of Afadin1-4, a cytosolic adapter protein that connects multiple CAM families to intracellular F-actin. We introduced the conditional Afadin mutant5 to an embryonic retinal Cre, Six3-Cre6-8. We reported that the mutants lead to the scrambled retinal neuron distribution, including Bipolar Cells (BCs), Amacrine Cells (ACs), and retinal ganglion cells (RGCs), across three cellular layers of the retina. This scrambled pattern was first reported here at neuron-type resolution. Importantly, the mutants do not display deficits for BCs, ACs, or RGCs in terms of neural fate specifications or survival. Additionally, the displayed RGC types still maintain synaptic partners with putative AC types, indicating that other molecular determinants instruct synaptic choices independent of Afadin. Lastly, there is a significant decline in visual function and mis-targeting of RGC axons to incorrect zones of the superior colliculus, one of the major retinorecipient areas. Collectively, our study uncovers a unique cellular role of Afadin in sorting retinal neuron types into proper cellular layers as the structural basis for orderly visual processing.

neuroscience↗

bioRxiv2024

A universal single-cell transcriptomics atlas of human lung decodes multiple pulmonary diseases

Human lung is a complex organ susceptible to various diseases. Single-cell transcriptomic studies provide rich data to targeting specific research questions. Here, we present uniLUNG, the largest lung transcriptomic cell atlas, comprising over 10 million cells across 20 disease states and healthy controls. We ensembled a universal hierarchical annotation framework and conducted a full benchmarking of data integration to define a standardized nomenclature and marker genes for lung cell types. Using uniLUNG, we identified Lym-monocyte and T-like B cells, new cell types in specific lung diseases, confirming their existence by comparing with external single-cell atlases. Additionally, we discovered the NSCLC-like SCLC subpopulation, a transitional malignant cell population associated with the transition from NSCLC to SCLC, which was validated and further characterized in spatial dimensions, revealing its complex role in tumour progression. Overall, uniLUNG represents a comprehensive range of human lung cell diversity, providing valuable data resources and a reliable foundation for lung single-cell research. HIGHLIGHTSO_LIThe largest scRNA atlas for human lung covers 10 million cells from 20 lung states. C_LIO_LIA four-level universal cell annotation framework encompasses 120 lung cell types. C_LIO_LIComprehensive benchmarking on 18 strategies guides data integration. C_LIO_LISpecific distribution of Lym-monocytes and T-like B cells in specific lung diseases. C_LIO_LIThe NSCLC-like SCLC subpopulation in transitional events of malignant cells from NSCLC to SCLC. C_LI

bioinformatics↗

bioRxiv2024

I2SIM: Boosting High-Fidelity Isotropic Super-Resolution with Image Interference and Spatial-Spectrum Optimization

Spatial resolution is crucial for imaging subcellular structures. The advent of three-dimensional structured illumination microscopy (3D-SIM) greatly benefits the biology community, providing a powerful tool for imaging organelles with a two-fold resolution enhancement in all three dimensions. However, the axial resolution of 3D-SIM is limited to around 300 nm, which is inferior to its lateral resolution. Here, a novel method called image interference SIM (I2SIM) is reported, which utilizes two oppositely positioned objectives to detect fluorescence emission interference under three-beam excitation. By incorporating spectral modulation and spatial domain Frobenius-Hessian optimization, I2SIM achieves an axial resolution approximately twice that of 3D-SIM, reaching around 130 nm. Furthermore, the potential of I2SIM for imaging subcellular structures is demonstrated on various biological samples, including microtubules, actin filaments, and mitochondrial outer membranes. The enhanced optical sectioning capability can be utilized to resolve axial structures that are challenging to discern using ordinary 3D-SIM.

biophysics↗

bioRxiv2024

Oncogenic RAS Induces a Distinctive Form of Non-Canonical Autophagy Mediated by the P38-ULK1-PI4KB Axis

Cancer cells with RAS mutations exhibit enhanced autophagy, essential for their proliferation and survival, making it a potential target for therapeutic intervention. However, the regulatory differences between RAS-induced autophagy and physiological autophagy remain poorly understood, complicating the development of cancer-specific anti-autophagy treatments. In this study, we identified a form of non-canonical autophagy induced by oncogenic KRAS expression, termed RAS-induced non-canonical autophagy via ATG8ylation (RINCAA). RINCAA involves distinct autophagic factors compared to those in starvation-induced autophagy and incorporates non-autophagic components, resulting in the formation of non-canonical autophagosomes with multivesicular/multilaminar structures labeled by ATG8 family proteins (e.g., LC3 and GABARAP). We have designated these structures as RAS-induced multivesicular/multilaminar bodies of ATG8ylation (RIMMBA). A notable feature of RINCAA is the substitution of the class III PI3K in canonical autophagy for PI4KB. We identified a regulatory P38-ULK1-PI4KB-WIPI2 signaling cascade governing this process, where ULK1 phosphorylation at S317, S479, S556, and S758 activates PI4KB. This activation involves PI4KB phosphorylation at S256 and T263, initiating PI4P production, ATG8ylation, and non-canonical autophagy. Importantly, elevated PI4KB phosphorylation at S256 and T263 was observed in RAS-mutated cancer cells and colorectal cancer specimens. Inhibition of PI4KB S256 and T263 phosphorylation led to a reduction in RINCAA activity and tumor growth in both xenograft and KPC models of pancreatic cancer, suggesting that ULK1-mediated PI4KB-Peptide-1 phosphorylation could represent a promising therapeutic target for RAS-mutated cancers.

cell biology↗

bioRxiv2024

Morphological map of under- and over-expression of genes in human cells

Cell Painting images offer valuable insights into a cells state and enable many biological applications, but publicly available arrayed datasets only include hundreds of genes perturbed. The JUMP (Joint Undertaking in Morphological Profiling) Cell Painting Consortium perturbed roughly 75% of the protein-coding genome in human U-2 OS cells, generating a rich resource of single-cell images and extracted features. These profiles capture the phenotypic impacts of perturbing 15,243 human genes, including overexpressing 12,609 genes (using open reading frames, ORFs) and knocking out 7,975 genes (using CRISPR-Cas9). We mitigated technical artifacts by rigorously evaluating data processing options and validated the datasets robustness and biological relevance. Analysis of phenotypic profiles revealed novel gene clusters and functional relationships, including those associated with mitochondrial function, cancer, and neural processes. The JUMP Cell Painting genetic dataset is a valuable resource for exploring gene relationships and uncovering novel functions.

bioinformatics↗