Biology subjects

Cheng, L.

Publications and source records attributed to Cheng, L..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

AutoZyme: An Autonomous Agentic Framework to Optimize Bioinformatics Software

Performance bottlenecks in widely used genomics and bioinformatics software present a substantial and growing burden as biological datasets continue to increase in size and number. Relieving these bottlenecks relies largely on expert manual optimization and therefore remains difficult to scale. Here we present AutoZyme, an agentic framework for scientific software optimization. Given a target function, AutoZyme builds benchmarks, identifies bottlenecks, and iteratively tests code changes, retaining only those that improve runtime while preserving output. We evaluated AutoZyme on 45 functions, improving runtime without substantial memory increases in over 95% of cases considered. Across 38 functions from Seurat, Scanpy and related packages in genomics and bioinformatics, AutoZyme reduced runtime by a median of 8.52-fold, with the largest reductions exceeding 676-fold. The optimized functions are distributed through AutoZyme-Library as drop-in replacements for existing analysis pipelines. We also release AutoZyme as a reusable framework for optimizing additional user-specified packages and functions.

bioinformatics↗

bioRxiv2026

DOC Release and Physiological Response of Zostera marina Under Light and Nutrient Gradients

The seagrass bed, known as an important blue carbon ecosystem, not only has robust carbon sequestration capacity, but also releases the fixed organic carbon into the water column in the form of dissolved organic carbon (DOC). Zostera marina is the main constructive species of the seagrass meadows of northern China, but the regulatory mechanism of its DOC release in response to environmental changes still remains unclear. Adult Z. marina was used as the experimental material in this research to investigate the effects of light intensity and nutrient concentration on its DOC release, and to observe its physiological responses. By using a total organic carbon (TOC) analyzer, dissolved oxygen monitoring, transmission electron microscopy (TEM), and transcriptome analysis, we explored how light and nutrients affect DOC release and the underlying physiological mechanisms in Z. marina. The results showed that both elevated light intensity and short-term nutrient enrichment promoted organic carbon release from Z. marina to the environment. Increased light enhanced the net primary productivity (NPP) of Z. marina, while the magnitude of DOC release increased more than NPP itself. Nutrient enrichment reduced NPP while raising the proportion of DOC released by Z. marina. Transcriptome analysis showed that nutrient enrichment significantly affected pathways, including flavonoid biosynthesis and fatty acid degradation. This study demonstrated that changes in light and nutrients can significantly influence DOC release and carbon allocation patterns in Z. marina, providing a theoretical basis for blue carbon accounting and ecological restoration evaluation in seagrass beds.

plant biology↗

bioRxiv2026

Arthritis-Associated Inflammation Remodels Colonic O-Glycosylation

The gut-joint axis describes how impaired intestinal epithelial function and increased gut permeability allow luminal factors to enter circulation. This can drive inflammation in Rheumatoid Arthritis, a chronic condition affecting the joint with systemic features. What mechanisms contribute to disease persistence are, as yet, incompletely understood. In health, extensively Oglycosylated intestinal mucins are central to epithelial protection and immune homeostasis; however, whether mucin glycosylation is altered during arthritis has not been addressed. Here, we investigated whether arthritisassociated inflammation alters mucin Oglycosylation, potentially compromising intestinal barrier function. Using a collageninduced arthritis mouse model, we combined epithelial transcriptomics, mass spectrometry-based glycomics, and imaging approaches to profile intestinal glycosylation. We identified distinct glycan remodeling in the colon, characterized by reduced fucosylation, while the ileum remained largely unaffected. In vitro studies using 3D human epithelial cultures further demonstrated that inflammatory cues, particularly from TNFactivated stromal cells, are sufficient to reduce epithelial fucosylation. Together, these findings identify a stromal-inflammatory mechanism that disrupts mucin glycosylation during arthritis. Loss of colonic fucosylation emerges as a novel element of inflammatory arthritis, providing an additional mechanistic link between intestinal inflammation and fibroblast-dependent modulation of the tissue microenvironment.

immunology↗

bioRxiv2026

Epistasis of two classical color genes, B and L-2, synergistically controls carotenoid accumulation in squash

Carotenoid accumulation underlies fruit color and nutritional quality in squash (Cucurbita pepo). One pair of dominant genes, B and L-2, have been long known to interact epistatically, substantially boosting carotenoid accumulation and producing intensely orange-fleshed fruit. However, their molecular identities and regulatory mechanism are unknown. Here, we show that B encodes a truncated H subunit of magnesium chelatase (CpCHLHB) and L-2 encodes a homolog of Arabidopsis Pseudo-Response Regulator 2 (CpAPRR2-A). Significantly, expression of phytoene synthase (CpPSY-A), which encodes the major rate-limiting enzyme in carotenoid biosynthesis, was dramatically upregulated in fruit of B/B L-2/L-2 plants compared with b/b L-2/L-2 or B/B l-2/l-2, showing that the B and L-2 interaction affects CpPSY-A transcription. A similar upregulation was also observed in Arabidopsis gun5 L-2 transgenic plants, where gun5 is a genetic mimic of the C. pepo B gene. The wild-type CpCHLHb physically interacted with CpAPRR2-A, attenuating the CpAPRR2-A-mediated activation of CpPSY-A. In contrast, the truncated CpCHLHB lost its ability to interact with CpAPRR2-A, enabling CpAPRR2-A to activate CpPSY-A and produce intensely orange fruit. These findings uncover the mechanism underlying the epistatic interaction through which B and L-2 act synergistically to boost carotenoid production, offering novel mechanistic insights and key targets for improving crop quality. One-sentence summarySynergistic epistasis between B and L-2 arises from loss of interaction between their encoded proteins, resulting in dramatically upregulating the key rate-limiting enzyme in carotenoid biosynthesis pathway to produce intensely orange-fleshed fruit in squash.

plant biology↗

bioRxiv2026

Dynamic dorsal body morphology encodes engineering design principles of fish propulsion and hydrodynamics

Understanding how biological shape and movement interact with surrounding fluids represents a fundamental challenge at the intersection of biology, physics, and engineering. Fish locomotion exemplifies this challenge: body morphology and swimming kinematics together determine the hydrodynamic forces and flow structures that enable efficient propulsion and maneuverability. Whereas biologists have long sought to connect morphological variation to swimming performance, traditional morphometric approaches provide limited insight into the fluid mechanical consequences of shape differences. Similarly, although computational fluid dynamics can reveal detailed flow physics, simulating hydrodynamics across diverse and dynamic morphologies remains prohibitively expensive for systematic investigation. To bridge this gap, we introduce a data-driven framework that connects fish body shape dynamics to hydro-dynamic performance through compact morphospace parameterization and reduced-order modeling. Using CFD simulations of 15 fish species from the Digital Life Project database (www.digitallife3d.org/3d-model), we generate hydrodynamic datasets capturing the shape-flow relationship. Principal Component Analysis (PCA) extracts four dominant shape parameters from dorsal body profiles, which are then integrated into an Inverse-Design with Dynamic Mode Decomposition (ID-DMD) framework to model the resulting fluid dynamics. The resulting modal analysis suggests that locomotion strategies emerge from specific shape-flow interactions. We further demonstrate the frameworks utility through single- and multi-objective shape optimization, showing how it enables efficient exploration of the morphology-hydrodynamics relationship. This approach offers a novel analysis and design tool for understanding how biological form and motion interact with fluid mechanics, with applications ranging from bio-inspired vehicle development to evolutionary biomechanics.

biophysics↗

bioRxiv2026

Neuronal EphB2 signaling drives persistent neuropathic pain following spinal cord injury

Neuropathic pain after spinal cord injury reflects persistent hyperexcitability in the spinal cord dorsal horn, yet the molecular drivers sustaining this maladaptive state are unknown. Using an antibody microarray of dorsal horn tissue from mice six weeks after cervical contusion spinal cord injury, we found persistent upregulation of Eph-ephrin signaling, including increased EphB1, EphB2 and EphB3 expression and phosphorylation. Reversible chemogenetic inhibition of EphB kinase activity, using an EphB1/2/3 analog-sensitive knock-in mouse, selectively reversed established mechanical allodynia without affecting thermal hyperalgesia or motor function and also shifted dorsal horn signaling away from pain sensitization-associated pathways. Among EphB receptors, EphB2 showed the most consistent and robust injury-induced increase in expression within dorsal horn. Although EphB2 transcript levels increased in both dorsal horn neurons and astrocytes, conditional deletion of EphB2 only in dorsal horn neurons, but not in astrocytes, reversed established mechanical allodynia and reduced dorsal horn neuronal activation. These findings identify EphB signaling, and neuronal EphB2 in particular, as a mechanism that actively maintains pain hypersensitivity after spinal cord injury.

neuroscience↗

bioRxiv2026

Three-dimensional Virtual Adult Cardiomyocyte Transcriptomics

Obtaining transcriptomes of adult cardiomyocytes at single-cell resolution remains challenging due to their large size, elongated morphology, and frequent multinucleation. Although spatial transcriptomics preserves tissue architecture and captures gene expression in situ, current analytical frameworks largely rely on nuclear-based segmentation and are therefore poorly suited to adult cardiomyocytes. Furthermore, individual tissue sections capture only a fraction of a cardiomyocyte, preventing reconstruction of complete cell-level transcriptomes. Here we present three-dimensional virtual cardiomyocyte (3D-VirtualCM), a membrane-guided framework that integrates cell-contour similarity and optimal transport to reconstruct volumetric cardiomyocyte transcriptomes from consecutive spatial transcriptomic sections. Applying 3D-VirtualCM to infarcted adult mouse hearts, we generated a panoramic transcriptomic atlas spanning 100 m thickness at single-cell resolution. 3D-VirtualCM identified spatially and transcriptionally distinct cardiomyocyte populations within the infarct border zone, enabled high-throughput quantification of cardiomyocytes re-entering the cell cycle together with their associated molecular signatures, and revealed heterogeneous RNA distribution along the longitudinal axis of individual cardiomyocytes. By integrating three-dimensional cellular morphology with in situ transcriptomic data, 3D-VirtualCM provides a scalable approach for resolving cardiomyocyte states and spatial organization in physiological and pathological cardiac remodeling.

bioinformatics↗

bioRxiv2026

Engineering age-adaptive mRNA lipid nanoparticle cancer vaccines via reprogramming systemic gene expression

Lipid nanoparticle (LNP)-based mRNA vaccines have transformed cancer immunotherapy, yet their efficacy in older individuals, who represent the majority of cancer patients, remains poorly understood. Here, we uncover a critical and previously underappreciated barrier to mRNA LNP cancer vaccine performance in aged hosts: impaired systemic transgene expression. Using the SM-102 mRNA LNPs as a benchmark formulation, we show that while local immune activation and antigen presentation at the injection site and draining lymph nodes remain largely intact with age, transgene expression in peripheral organs, including the liver, lungs, and spleen, is markedly reduced. This deficit limits the magnitude and durability of CD8 and CD4 T cell responses and substantially compromises tumour control. Transcriptomic profiling further reveals that attenuated transgene expression parallels broad attenuation of antigen processing, presentation, and activation pathways in immune cells from aged animals, implicating impaired systemic mRNA translation as a central driver of the downstream immune defects and antitumour efficacy loss. Building on these insights, we identify a rationally selected LNP formulation that reestablishes distal antigen expression across age groups as an engineering strategy to revive T cell immunity, achieving full rescue of therapeutic efficacy in aged mice without additional intervention. Together, these findings establish systemic mRNA translation as a tuneable lever of vaccine performance and highlight that optimizing LNP formulations to sustain systemic transgene expression across age groups may enable next-generation, age-adaptive mRNA vaccines for cancer and other diseases of aging.

bioengineering↗

bioRxiv2026

Identification of the Phytophthora PAMP Pep-13 Receptor Using Diploid Potato Inbred Lines

Plants employ cell surface receptors to recognize pathogen-associated molecular patterns (PAMPs) and activate pattern-triggered immunity, a crucial defense mechanism against invading pathogens. Pep-13 is a PAMP derived from a class of conserved cell wall transglutaminases present in Phytophthora species, and its receptor PERU (Pep-13 receptor unit), was reported recently. In our parallel study, we observed distinct responses to Pep-13 between two diploid potato inbred lines: E4-63 recognizes Pep-13, whereas A6-10 does not. Genetic analysis demonstrated that Pep-13 recognition in E4-63 is controlled by a single genetic locus, tentatively designated TGER (Transglutaminase elicitor response). Through bulked segregant analysis sequencing, followed by complementation assays, we found that the TGERa gene in E4-63 is essential for Pep-13 recognition. Sequence alignment revealed that TGERa shares 99.91% amino acid sequence identity with PERU, indicating that TGERa and PERU are allelic variants of the same gene (PERU/TGERa). TGERb, a highly homologous gene of TGERa, was identified in the E4-63 genome; notably, TGERa, but not TGERb, can recognize Pep-13. We further demonstrated that TGERb exhibits defects in ligand binding. Additionally, we found that the TGERa allele in A6-10 is a weak allele with reduced expression levels, presumably resulting from a 3 kb DNA fragment insertion in its first intron. Heterologous introduction of TGERa into Nicotiana benthamiana and tomato significantly enhanced their resistance to Phytophthora infestans. Collectively, our findings confirm that PERU/TGERa functions as the Pep-13 receptor in potato and provide a valuable molecular target for improving Phytophthora resistance in plants.

plant biology↗

bioRxiv2026

MetaSAG: A Tool for Multi-level Exploration and Taxonomic Analysis of Microbial Single-Amplified Genomes

Microbial single-amplified genome (SAG) sequencing technologies have elevated microbial research resolution to the single-cell level. However, neither upstream data processing nor downstream analysis has been fully developed, greatly limiting the research in strain level. Herein, we developed MetaSAG (Multi-level Exploration and Taxonomic Analysis of microbial Single-Amplified Genomes), which enables accurate and rapid taxonomic classification of microbial SAGs. MetaSAG outperforms existing method in species classification certainty, computational efficiency, and sensitivity of low abundance species identification. In addition, MetaSAG enables species-level functional analysis, as well as strain-level evolutionary analysis. With the help of MetaSAG, we discovered the parasitic relationship between phages and bacteria, identifying multiple susceptible bacteria and a broad spectrum of phages. Furthermore, we developed MetaK-Lytic (k-mer-based meta-learning framework to predict phage lytic ability) to achieve accurate prediction of phage lytic activity based on 31-mer short sequences, which is well adapted to the characteristics of incomplete SAG sequences. Overall, we offer a comprehensive integrated tool that can parse microbial SAG data from raw data to the strain level to decipher the functional ecology of microbial dark matter, with broad implications for microbial ecology and phage therapy (https://github.com/liangcheng-hrbmu/MetaSAG). Significance StatementThis work provides a comprehensive framework for high-resolution SAG data analysis. The developed pipeline improves taxonomic annotation sensitivity and speed. Strain-level tracking enables dynamic evolutionary and functional insights, while single-cell bacterial-virus network reconstruction reveals precise interaction patterns. The novel annotation-free short sequence-based MetaK-Lytic facilitates functional prediction of uncharacterized phage sequences. Integrated into the MetaSAG platform, these tools deliver a streamlined, multi-level solution for interpreting SAG data, advancing studies in microbial ecology, evolution, and virology.

microbiology↗

bioRxiv2026

Phyllosphere and rhizosphere microbiomes empower Nicotiana tobacum complex traits dissection and prediction

Understanding how plant-associated microbiomes interact with host genome variation to influence agronomic traits is essential for advancing microbiomeassisted crop improvement. In this study, we characterized the phyllosphere and rhizosphere microbiomes of 164 diverse Nicotiana tabacum accessions using 16S rRNA sequencing and integrated these data with host genomic variation and 22 agronomic traits. The two microbiomes exhibited distinct taxonomic structures, diversity patterns, and predicted metabolic functions. Microbiome genomewide association studies identified extensive host genetic control over microbial abundance, including 49 shared genomic loci that explained nearly half of the heritable variation in both microbiomes. Microbiomewide association studies revealed biologically meaningful associations between specific ASVs and agronomic traits. However, network analysis demonstrated that microbial subcommunities, rather than individual taxa, contributed substantially to phenotypic variation. Then, colocalization analysis further identified genetic variants jointly influencing microbial abundance and metabolite traits, highlighting potential host-microbe-trait causal links. Incorporating microbiome data into genomic selection models, we successfully improved prediction accuracy for several traits, especially plant architecture and flowering. Together, this work provides a comprehensive populationlevel framework linking host genetics, microbiome composition, and agronomic traits in tobacco, offering new insights for microbiomeinformed breeding strategies.

plant biology↗

bioRxiv2026

Phase response curve and RNA-sequencing demonstrate spiders' sensitivity to light and pinpoint candidate light-responsive genes

Spiders can maintain a wide range of free-running periods while still being entrained to a 24-hour day. To investigate the underlying mechanism of this entrainment, we constructed the phase-response curve (PRC) for the orb weaver, Metazygia wittfeldae, by subjecting the spiders to one-hour light pulses at various times throughout the circadian day. The resulting type 0 PRC showed high amplitude (> 6 hour) phase advance and delays when the light pulse was applied during circadian time (CT) 16-18, with a break point of advances to delays at CT 17. We then investigated the genetic mechanism of the phase response to light by splitting M. wittfeldae adult females entrained to 12 hours light:12 hours dark (LD 12:12) into two groups. One group received a 1-hour light pulse 5 hours after lights off (CT17), and one group did not. We then sacrificed spiders for RNA isolations 1 and 10 hours after the light pulse. We identified numerous genes that were downregulated by the light pulse 1 hour after the pulse relative to no pulse group. Intriguingly, many of these genes had a flipped pattern of expression 9 hours later - the pulse group had higher expression than the no pulse group. This pattern is consistent with the shifted phase of locomotor activity expected after the light pulse application. We also identified clock gene homologs in M. wittfeldae that had distinct expression patterns from other arthropods.

animal behavior and cognition↗

bioRxiv2026

Pan-genome and multi-omics analyses reveal the genomic basis of symbiotic evolution in the mycoheterotrophic medicinal orchid Gastrodia elata

Mycoheterotrophy represents an extreme evolutionary strategy in which plants abandon photosynthesis and become obligately dependent on fungal partners for carbon and nutrients. Gastrodia elata, a medicinal orchid forming long-term symbioses with Armillaria and Mycena, provides a compelling system to investigate the genomic basis of obligate plant-fungus mutualism. Here, we generate a chromosome-level genome assembly (1.09 Gb) of a dark-red G. elata accession and construct a pan-genome from 12 Gastrodia accessions to dissect the evolutionary consequences of mycoheterotrophy. Phylogenomic analyses reveal pervasive hybridization across cultivated germplasm and demonstrate that tuber morphology more accurately reflects intraspecific relationships than stem color, challenging the traditional color-based taxonomy. Comparative genomic analyses reveal a pronounced degeneration of photosynthetic capacity. We detect no intact nuclear-encoded rbcS loci, which would preclude assembly of the Rubisco holoenzyme and thus canonical Calvin-Benson carbon fixation. Notably, a subset of photosynthesis-related genes is retained and transcriptionally active, suggesting their co-option into non-photosynthetic regulatory roles. Despite millions of years of intimate association with fungal partners, we detect no evidence of fungal-derived horizontal gene transfer based on a multi-step phylogenomic validation pipeline, indicating that G. elata-fungus mutualism is sustained through metabolic exchange rather than genetic integration. We further identify the Gastrodia antifungal protein (GAFP) gene family as a key molecular innovation underlying symbiotic homeostasis. The recently derived Class 1 GAFP lineage exhibits distinct domain architecture, tandem expansion, and elevated expression, consistent with enhanced regulation of fungal overgrowth. Finally, we delineate a specialized nutrient-acquisition framework adapted to obligate heterotrophy, in which fungal trehalose hydrolysis supplies hexose carbon via an expanded sugar transporter protein (STP) repertoire, while organic nitrogen is assimilated through amino acid and oligopeptide transporters coupled with urease-mediated conversion, compensating for the loss of nitrate uptake and reduction pathways. Together, these results establish a pan-genomic blueprint for symbiotic adaptation and reductive genome evolution in G. elata.

genomics↗

bioRxiv2026

Engaging Unstabilized Alkyl Radicals with Pyridoxal Radical Biocatalysis: Enantiodivergent Synthesis of Aliphatic Non-Canonical Amino Acids

Harnessing transient, unstabilized alkyl radical intermediates for the enantioselective construction of valueadded chemical entities remains a fundamental challenge in biocatalysis. Through the repurposing and directed evolution of pyridoxal phosphate (PLP)-dependent tryptophan synthases, we advanced an open-shell enzyme platform capable of intercepting transient alkyl radicals for the efficient and enantioselective synthesis of aliphatic non-canonical amino acids. Engineering an orthogonal pair of radical PLP enzymes allowed unstabilized alkyl radicals, generated from diverse aliphatic organoboronates, to undergo dehydroxylative C(sp3)-C(sp3) coupling with a common L-serine donor, affording either L- or D-amino acids with excellent enantiopurity in an enzyme-controlled fashion. Mechanistic and computational investigations employing radical clock substrates and unusual radical-mediated rearrangement processes revealed that the radical intermediates generated in this system exhibit unexpectedly long lifetimes, highlighting the power of this dual enzyme-photocatalyst platform to engage unactivated alkyl radicals. Collectively, these findings delineate a potentially general strategy for generating and utilizing unstabilized alkyl radicals and underscore the synthetic potential of radical pyridoxal biocatalysts for stereodivergent amino acid construction.

biochemistry↗

bioRxiv2026

Carbon dioxide sequestration into biomineral armor by ants

Over geologic time, Earths climate has been shaped by the capture and conversion of atmospheric carbon dioxide (CO2) into stable carbonate minerals, including dolomite [CaMg(CO3)2]. Accelerating natural carbon mineralization offers significant potential for mitigating anthropogenic climate change. Using stable carbon isotope tracking, nano-scale secondary ion mass spectroscopy, and 13C SSNMR, we show that, paralleling global biosphere-level processes, Sericomyrmex amabilis fungus-farming ants rapidly convert CO2 in their nest chambers into a biomineral layer covering their exoskeletons. We further reveal that biogenic carbon mineralization by these ants produces partially ordered dolomite. This rapid sequestration of CO2 into defensive armor in ants provides a fascinating natural example of mediation of potentially toxic accumulation of atmospheric CO2 that could inform human efforts to mitigate climate change.

ecology↗

bioRxiv2026

A Glycosylation-Dependent Checkpoint Restrains Intestinal Intra-Epithelial Lymphocyte Activation

Intraepithelial lymphocytes (IELs) are abundant in the intestinal epithelium, where they maintain barrier integrity and provide immune defense. Because of their potent cytotoxic and effector potential, IEL activity must be tightly controlled to prevent tissue damage. However, the mechanisms that calibrate IEL responsiveness remain unclear. Here, we identify glucosaminyl (N-acetyl) transferase 2 (Gcnt2) as a key restrainer of both natural and induced gut IEL. Among T cells, Gcnt2 is uniquely enriched in the intestine and partly dependent on retinoic acid signaling. GCNT2-mediated branched glycosylation marks IELs with signatures of tissue adaptation and reduced TCR responsiveness. Genetic ablation of Gcnt2 enhanced IEL degranulation, cytokine production, and cytotoxicity upon stimulation, improving bacterial clearance and limiting infection-induced disease, while aggravating the pathological consequences of strong T cell activation. Mechanistically, GCNT2-mediated glycosylation of CD45 reduced its phosphatase activity, thereby dampening TCR signaling and effector responses. Together, these findings reveal GCNT2 as a glycosylation-dependent checkpoint that fine-tunes IEL effector functions, uncovering a novel mechanism by which the intestinal immune system balances responsiveness and tolerance. SummaryGCNT2-mediated I-branching glycosylation of CD45 restrains IEL activation.

immunology↗

bioRxiv2025

NIPBL-mediated 3D genome folding translates enhancer priming into gene activation and safeguards lineage fidelity during embryonic transitions

Precise gene control by complex regulatory landscapes is fundamental to embryo development, yet the instructive role of 3D genome architecture remains controversial. While acute cohesin depletion completely disrupts genome folding, it yields modest transcriptional impacts, but these findings are often confounded by cohesins essential roles in cell division and proliferation. Here, we resolve this discrepancy by decoupling architectural functions from cell-cycle roles using an acute NIPBL degron system. By integrating single-gene imaging with single-cell and bulk multi-omics during mouse pluripotency transitions and germ-layer specification, we show that NIPBL-mediated cohesin function is required for proper de novo activation of lineage-specifying genes. Mechanistically, NIPBL translates epigenetic priming into transcriptional outputs by physically bringing distal enhancers and target promoters into proximity. We further uncover a dual regulatory role: an acute requirement for establishing new enhancer-promoter interactions during cell state transitions and a long-term role in safeguarding transcriptional fidelity by preventing ectopic gene de-repression. Our findings demonstrate that NIPBL/cohesin-orchestrated genome folding facilitates the faithful execution of developmental gene expression programs. HighlightsO_LIAcute NIPBL depletion decouples the architectural functions of cohesin from its essential roles in chromosome segregation and cell cycle progression. C_LIO_LINIPBL-mediated loop extrusion is required to translate the epigenetic priming of distal enhancers into de novo gene activation during embryonic state transitions. C_LIO_LINIPBL is a "rate-limiting physical relay" required to bring distal enhancers and target promoters into proximity to initiate transcription. C_LIO_LI3D genome architecture serves a dual role: enabling acute enhancer-promoter communication and safeguarding long-term lineage fidelity by preventing ectopic gene de-repression. C_LI

genetics↗

bioRxiv2025

Genome editing for treatment of JAK2 V617F-driven myeloproliferative neoplasms

JAK2 V617F is a common haematological driver mutation and underlies most cases of myeloproliferative neoplasms (MPNs). Reducing variant allele frequency (VAF) is an important treatment goal, but no current treatment modalities fully and specifically inhibit mutant signalling. Thus, the consequences of V617F inactivation are unclear, including whether selective inhibition of V617F signalling will eradicate mutant cells due to oncogene addiction. Here, we describe an allele-selective CRISPR-Cas genome editing strategy that achieves selective and efficient JAK2 V617F inactivation in patient stem and progenitor cells. We show that JAK2 V617F heterozygous cells are not oncogene addicted and maintain viability and differentiation potential upon loss of their mutant allele. In contrast, homozygous mutant cells are eradicated upon deletion of both mutant alleles. Across in vitro, organoid, xenotransplantation and single-cell assays, selective deletion of V617F alleles reverts MPN hallmarks including erythroid clonogenicity, inflammatory gene expression signatures, as well as myelofibrosis and splenomegaly phenotypes in an in vivo xenograft model. Collectively, our results show that is it possible to revert heterozygous JAK2 V617F mutant cells to a normal phenotype and suggest that ex vivo genome editing of stem and progenitor cells may be a viable treatment option to achieve rapid and deep reductions in VAF.

cancer biology↗