Biology subjects

Ouyang, J.

Publications and source records attributed to Ouyang, J..

14 recordsLinked to original sources

bioRxiv2026

PathPinpointR: Predicting the progression of sc-RNAseq samples through reference trajectories.

Single-cell RNA sequencing (scRNA-seq) has transformed our ability to analyse cellular heterogeneity, enabling detailed mapping of cellular progression. Trajectory inference tools construct trajectories from scRNA-seq data, facilitating the tracing of cellular progression through developmental pathways. PathPinpointR (PPR) is a lightweight and user-friendly R package developed to predict and compare the positions of scRNA-seq samples along reference biological trajectories, such as those created from large cell atlas projects. PPR utilises sets of switching-gene events from reference trajectories as indicators of cellular progression. By applying these positional indicators to query datasets, each cell can be accurately assigned a pseudo-time value, providing predictive insight into its position along a trajectory. This information can be used to stage cells within an established developmental process, or to evaluate how different patient samples compare when mapped onto reference disease or drug response trajectories. AvailabilityPathPinpointR is available at https://github.com/moi-taiga/PathPinpointR. Contacto.j.l.rackham@soton.ac.uk

bioinformatics↗

bioRxiv2025

Shared molecular consequences of epigenetic machinery disruption in neuronal progenitors

The Mendelian disorders of the epigenetic machinery (MDEMs) are an emerging cause of intellectual disability and growth abnormalities, which commonly disrupt hippocampal function. To investigate consequences of epigenetic machinery (EM) disruption during neurodevelopment, we systematically knocked out (KO) EM factors in neuronal progenitors isolated from the murine hippocampus and established a neurodifferentiation model to interrogate their functions. We then profiled gene expression and DNA methylation (DNAm) in the EM-KOs using RNA sequencing and Nanopore long-read DNA sequencing. While Dnmt1-KO induced extensive DNAm alterations, Kmt2a-KO had little effect on methylation. Nevertheless, the disruption of Kmt2a and Dnmt1 produced strikingly convergent transcriptional changes. Loss of either EM factor led to premature neuronal differentiation, partially explaining this convergence, and MYC appeared as a shared regulatory node linked to downregulation of cell-cycle programs in these cells. Extending our methylation analysis to 46 EM genes, we found that loss of DNA methyltransferases induced the strongest DNAm changes, whereas other EM-KOs had subtle or negligible effects. However, clustering of EM-KOs based on promoter DNAm levels revealed three distinct EM subgroups, of which two were enriched for interactions with the DNAm machinery. Allele-specific analysis of DNAm further identified a single differentially methylated region shared across the 46 EM-KOs, localized to the FVB allele over the Zic4 3UTR. Furthermore, Zic4 overexpression appears to maintain the neuronal progenitor state, suggesting functional relevance of this locus. Taken together, our results reveal both gene-specific and convergent effects across diverse EM-KOs and provide new insight into the molecular etiology of the MDEMs.

genomics↗

bioRxiv2025

Genomic Touchstone: Benchmarking Genomic Language Models in the Context of the Central Dogma

The emergence of genomic language models (gLMs) has revolutionized the analysis of genomic sequences, enabling robust capture of biologically meaningful patterns from DNA sequences for an improved understanding of human genome-wide regulatory programs, variant pathogenicity and therapeutic discovery. Given that DNA serves as the foundational blueprint within the central dogma, the ultimate evaluation of a gLM is its ability to generalize across this entire biological cascade. However, existing evaluations lack this holistic and consistent framework, leaving researchers uncertain about which model best translates sequence understanding into downstream biological prediction. Here we present Genomic Touchstone, a comprehensive benchmark designed to evaluate gLMs across 36 diverse tasks and 88 datasets structured along the central dogmas modalities of DNA, RNA, and protein, encompassing 5.34 billion base pairs of genomic sequences. We evaluate 34 representative models encompassing transformers and convolutional neural networks, as well as emerging efficient architectures such as Hyena and Mamba. Our analysis yield four key insights. First, gLMs achieve comparable or superior performance on RNA and protein tasks compared to models pretrained on these molecules. Second, transformer-based models continue to lead in overall performance, yet efficient sequence models show promising task-specific capabilities and deserve further exploration. Third, the scaling behavior of gLMs remains incompletely understood. While longer input sequences and more diverse pretraining data consistently improve performance, increases in model size do not always translate into better results. Fourth, pretraining strategies, including the choice of training objectives and the composition of pretraining corpora, exert substantial influence on downstream generalization across different genomic contexts. Genomic Touchstone establishes a unified evaluation framework tailored to human genomics. By spanning multiple molecular modalities and biological tasks, it offers a valuable foundation for guiding future gLM design and understanding model generalizability in complex biological contexts.

bioinformatics↗

bioRxiv2025

FASN Inactivation-induced Progranulin (GRN) Expression Promotes Lysosome-dependent Cell Death to Suppress Leukemogenesis

Cancer cells rely on lipogenesis in addition to exogenous lipid uptake, and fatty acid synthase (FASN) is aberrantly overexpressed in myeloid leukemia. However, the precise role of FASN in leukemogenesis in vivo remains elusive. Here, we demonstrated that FASN is essential for leukemogenesis. Ablation of FASN impeded leukemic cell growth, survival, clonogenicity in vitro, and the leukemic burden in vivo. Conditional knockout of FASN barely affected hematopoiesis but significantly attenuated the leukemic progression of MLL-AF9 transplants. By screening a library of platensimycin derivatives, we identified compound MS-C19 as a potent FASN inhibitor. Pharmacological targeting of FASN by MS-C19 suppressed leukemic cell growth and clonogenicity in clinical AML blasts. Mechanistically, both MS-C19 treatment and FASN deficiency triggered the activation of lysosomal and inflammatory gene expression. Loss of FASN led to lysosomal membrane permeabilization and subsequent lysosome-associated cell death, but not lysosome biogenesis. We further identified that GRN, a lysosomal and neuroinflammatory gene, was potently transcribed by TFEB upon FASN loss. Depletion of GRN significantly reversed the inhibitory effects caused by FASN knockdown. Our work demonstrates that FASN is a therapeutic target for myeloid leukemia, and inactivation of FASN by the lead compound MS-C19 provides an alternative approach for leukemic intervention. Key PointsO_LIGenetic ablation of FASN induces apoptosis, impedes leukemia cell growth, and improves the survival of leukemic xenografts. C_LIO_LITargeting FASN by the compound MS-C19, a derivative of the natural microbe antibiotic platensimycin, reduces the cell survival of leukemic cell lines, the clinical leukemic blasts, and MLL-AF9 transformed murine leukemic cells. C_LIO_LIFASN inhibition induces lysosome-dependent cell death that relies on Progranulin (GRN) expression. C_LI

cancer biology↗

bioRxiv2024

BrainSTEM: A multi-resolution fetal brain atlas to assess the fidelity of human midbrain cultures

Many midbrain dopaminergic neuron (mDA) differentiation protocols aimed at Parkinsons disease (PD) modeling and cell replacement therapy have been developed. However, comprehensive evaluations of the transcriptomic fidelity of these protocols at the single-cell level against a common in vivo reference have been lacking. To this end, we constructed an integrated human fetal whole-brain atlas and a midbrain subatlas to use as a standard of comparison. From the whole-brain atlas, we observed distinct brain-region-specific gene expression in most neural cell types, emphasizing the need to first evaluate in vitro protocols at the whole-brain level to identify midbrain-associated cells. These cells are then mapped to the midbrain subatlas for more refined neuronal subtype specification and trajectory analysis specific to the midbrain. We surveyed all publicly available single-cell datasets of human midbrain culture models and performed the two-tier mapping. Using this biologically-driven multi-resolution mapping strategy which we termed BrainSTEM (brain Single-cell Two tiEr Mapping), we confirmed the presence of multiple midbrain cell types ( on-target), but also a substantial proportion of cells associated with non-midbrain regions and subtypes ( off-target). This leads to an overall inflation of mDA presence, stemming from non-midbrain-associated cells, across all published protocols. BrainSTEM thus offers an unbiased framework for understanding the current state of midbrain models and aids the improvement of midbrain differentiation protocols for PD studies.

bioinformatics↗

bioRxiv2024

In-utero rescue of neurological dysfunction in a mouse model of Wiedemann-Steiner syndrome

Wiedemann-Steiner syndrome (WDSTS) is a rare genetic cause of intellectual disability primarily caused by heterozygous loss of function variants in the gene encoding the histone methyltransferase KMT2A. Prior studies have shown successful postnatal amelioration of disease phenotypes for Rett, Rubinstein-Taybi and Kabuki syndromes, related Mendelian disorders of the epigenetic machinery. To explore whether the neurological phenotype in WDSTS is treatable in-utero, we created a novel mouse model carrying a loss of function variant in between two loxP sites. Kmt2a+/LSL mice demonstrate core features of WDSTS including growth retardation, craniofacial abnormalities, and hypertrichosis as well as hippocampal memory defects. The neurological phenotypes show rescue upon restoration of KMT2A in-utero following breeding to a nestin-Cre. Together, our data provide a novel mouse model to explore the therapeutic window in WDSTS. Our work suggests that WDSTS has a window of opportunity extending at least until the mid-point of in-utero development, making WDSTS an ideal candidate for future therapeutic strategies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/604339v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@1b913caorg.highwire.dtl.DTLVardef@1c23ce3org.highwire.dtl.DTLVardef@12b8a25org.highwire.dtl.DTLVardef@17a9a4e_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG

genetics↗

bioRxiv2024

Caspase-8-mediated CYLD cleavage boots LPS-induced endotoxic shock.

Caspase-8, a pivotal protease intricately involved in various cellular signaling pathways related to cell death and inflammation, has been identified as a contributor to cytokine production during septic shock. However, the mechanisms governing this regulatory role remain enigmatic. In this study, we uncovered that mice harboring a specific mutation in CYLD at its D215 position (CyldD215A/D215A mutant mice), rendering CYLD resistant to caspase8 cleavage, exhibited marked protection against lethal endotoxic shock. Moreover, the removal of Cyld in Caspase8-/-Mlkl-/- mice restored their sensitivity to endotoxic shock, indicating Caspase8 promotes LPS-induced endotoxic shock by cleaving its substrate CYLD and maintaining CYLD stability confers resistance to endotoxic shock. Mechanistically, CYLD was found to catalyze the removal of LUBAC-mediated M1-linked ubiquitination of NF-kB p65 at K301/K303, thereby suppressing the nuclear translocation and activation of p65 for subsequent cytokines production. Notably, the cleaved N-terminal fragment of CYLD (named CP25) is secreted in a TRIF/Caspase8-dependent manner. Moreover, CP25 can be detected in the serum of septic mice, and its levels show a strong correlation with corresponding serum IL-1{beta}, suggesting its potential utility as an inflammatory biomarker. Overall, these findings highlight the significance of CYLD cleavage as a promising therapeutic target and diagnostic marker for endotoxic shock.

immunology↗

bioRxiv2023

Hormonal plasticity to food restriction is heritable

Theoretical and empirical studies agree that populations harbor extensive among-individual variation in phenotypic plasticity, but the mechanisms generating and maintaining this variation are often unknown. Endocrine systems that exhibit plastic changes in response to environmental variation may be subject to natural selection, but their evolution requires heritable variation. It is currently unknown if endocrine plasticity to environmental challenges is heritable. We tested whether glucocorticoid responsiveness to food restriction is heritable in house sparrows, Passer domesticus, by subjecting individuals to a standardized dietary restriction and selecting individuals according to their hormonal responsiveness to the treatments: into high plastic, low plastic, and control groups and let them reproduce. Using a cross-foster design, we compared the parental and the F1 generation to partition the heritability of glucocorticoid responsiveness into genetic and environmental sources of variation. We found moderate heritability (h2>20%) of glucocorticoid plasticity in response to food availability in both restricted and adequate food conditions. Environmental variance played a larger role under restricted than adequate food conditions, whereas residual variance was much higher under adequate food conditions. Our findings provide empirical evidence for the existence of heritable individual variation in glucocorticoid plasticity that selection can act upon, especially in rapidly changing environments.

evolutionary biology↗

bioRxiv2023

Excessive apoptosis of naïve T cells resulting hyperactivation as a cause of mammalian aging

In mammals, the most remarkable T cell variations with aging are the shrinking of naive T cell pool and enlargement of memory T cell pool, which are partially caused by thymic involution. However, it remains an enigma whether these T-cell-related changes are consequences or causes of mammalian aging. In this study, we find that the T-cell specific Rip1 KO mice present similar age-related T cell changes and exhibit signs of accelerated aging, including inflammation, multiple age-related diseases and a shorter lifespan. Mechanistically, T cells lacking RIP1 displayed excessive apoptosis, leading to T cell compensatory proliferation, hyperactivation, increased inflammation, and ultimately premature death. Consistent with this, blocking apoptosis by co-deletion of Fadd in Rip1 deficient T cells significantly recovered the lymphopenia and imbalance between naive and memory T cell, substantially restored ageing-related phenotypes, and prolonged life span in T-cell specific Rip1 KO mice. These results suggest that changes in T cells play a causal role in mammalian aging. Therefore, replenishing or blocking apoptosis of naive T cells could offer new therapeutic approaches for aging and age-related diseases.

immunology↗

bioRxiv2022

LKB1 loss rewires JNK-induced apoptotic protein dynamics through NUAKs and sensitizes KRAS-mutant NSCLC to combined KRASG12C + MCL-1 blockade

The efficacy of molecularly targeted anti-cancer therapies may be limited by the presence of co-occurring mutations within a tumor1-3. Conversely, these alterations may confer collateral vulnerabilities that can be leveraged for the development of novel therapeutic approaches. KRAS-mutant lung cancers are distinguished by recurrent inactivating mutations in the tumor suppressor STK11/LKB14 that facilitate tumorigenesis by modulating energy balance5, 6, enhancing metastatic potential7,8 and enabling immune evasion9,10. However, whether LKB1 plays a role in modulating cellular responses to therapeutic stress is largely unknown. Here we show that LKB1 suppresses JNK-dependent stress signaling in KRAS-mutant lung cancer cells upon acute loss of oncogenic signaling. In LKB1-deficient KRAS-mutant cells, inhibition of KRAS or its downstream effector MEK leads to hyperactivation of JNK due to loss of NUAK-mediated PP1B phosphatase activity. JNK-mediated inhibitory phosphorylation of BCL-XL rewires apoptotic dependencies, rendering LKB1-deficient cells vulnerable to MCL-1 inhibition. These results uncover a previously unknown role for LKB1 in regulating stress signaling and the mitochondrial apoptotic response of cancer cells independent of its tumor suppressor activity mediated by AMPK11-13 and SIK14,15 kinases. Additionally, our study reveals a therapy-induced vulnerability in LKB1-deficient KRAS-mutant lung cancer cells that could be exploited as a genotype-informed strategy to improve the efficacy of KRAS-targeted therapies.

cancer biology↗

bioRxiv2019

ProGeo-neo: a Customized Proteogenomic Workflow for Neoantigen Prediction and Selection

Neoantigens can be differentially recognized by T cell receptor (TCR) as these sequences are derived from mutant proteins and are unique to the tumor. The discovery of neoantigens is the first key step for tumor-specific antigen (TSA) based immunotherapy. Based on high-throughput tumor genomic analysis, each missense mutation can potentially give rise to multiple neopeptides, resulting in a vast total number, but only a small percentage of these peptides may achieve immune-dominant status with a given major histocompatibility complex (MHC) class I allele. Specific identification of immunogenic candidate neoantigens is consequently a major challenge. Currently almost all neoantigen prediction tools are based on genomics data. Here we report the construction of proteogenomics prediction of neoantigen (ProGeo-neo) pipeline, which incorporates the following modules: mining tumor specific antigens from next-generation sequencing genomic and mRNA expression data, predicting the binding mutant peptides to class I MHC molecules by latest netMHCpan (v.4.0), verifying MHC-peptides by MaxQuant with mass spectrometry proteomics data searched against customized protein database, and checking potential immunogenicity of T-cell-recognization by additional screening methods. ProGeo-neo pipeline achieves proteogenomics strategy and the neopeptides identified were of much higher quality as compared to those identified using genomic data only. The pipeline was constructed based on the genomics and proteomics data of Jurkat leukemia cell line but is generally applicable to other solid cancer research. With massively parallel sequencing and proteomics profiling increasing, this proteogenomics workflow should be useful for neoantigen oriented research and immunotherapy.

bioinformatics↗

bioRxiv2019

Dependence of fluorodeoxyglucose (FDG) uptake on cell cycle and dry mass: a single-cell study using a multi-modal radiography platform

High glucose uptake by cancer compared to normal tissues has long been utilized in fluorodeoxyglucose-based positron emission tomography (FDG-PET) as a contrast mechanism. The FDG uptake rate has been further related to the proliferative potential of cancer, specifically the proliferation index (PI) - the proportion of cells in S, G2 or M phases. The underlying hypothesis was that the cells preparing for cell division would consume more energy and metabolites as building blocks for biosynthesis. Despite the wide clinical use, mixed reports exist in the literature on the relationship between FDG uptake and PI. This may be due to the large variation in cancer types or methods adopted for the measurements. Of note, the existing methods can only measure the average properties of a tumor mass or cell population with highly-heterogeneous constituents. In this study, we have built a multi-modal live-cell radiography system and measured the [18F]FDG uptake by single HeLa cells together with their dry mass and cell cycle phase. The results show that HeLa cells take up twice more [18F]FDG in S, G2 or M phases than in G1 phase, which confirms the association between FDG uptake and PI at a single-cell level. Importantly, we show that [18F]FDG uptake and cell dry mass have a positive correlation in HeLa cells, which suggests that high [18F]FDG uptake in S, G2 or M phases can be largely attributed to increased dry mass, rather than the activities preparing for cell division. This interpretation is consistent with recent observations that the energy required for the preparation of cell division is much smaller than that for maintaining house-keeping proteins.

biophysics↗

bioRxiv2019

The great tit HapMap project: a continental-scale analysis of genomic variation in a songbird

A major aim of evolutionary biology is to understand why patterns of genomic diversity vary among populations and species. Large-scale genomic studies of widespread species are useful for studying how the environment and demographic history shape patterns of genomic divergence, and with the continually decreasing cost of sequencing and genotyping, such studies are now becoming feasible. Here, we carry out one of the most geographically comprehensive surveys of genomic variation in a wild vertebrate to date; the great tit (Parus major) HapMap project. We screened ca 500,000 SNP markers across 647 individuals from 29 populations, spanning almost the entire geographic range of the European great tit subspecies. We found that genome-wide variation was consistent with a recent colonisation across Europe from a single refugium in South-East Europe, with bottlenecks and reduced genetic diversity in island populations. Differentiation across the genome was highly heterogeneous, with clear "islands of differentiation" even among populations with very low levels of genome-wide differentiation. Low local recombination rate in the genome was a strong predictor of high local genomic differentiation (FST), especially in island and peripheral mainland populations, suggesting that the interplay between genetic drift and recombination is a key driver of highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, most likely as a result of recent directional selection at the range edges of this species. Haplotype-based measures of selection were also related to recombination rate, albeit less strongly, and highlighted population-specific sweeps that likely resulted from positive selection. These regions under positive selection contained candidate genes associated with morphology, thermal adaptation and colouration, providing promising avenues for future investigation. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into evolution.

evolutionary biology↗

bioRxiv2018

Effects of sublethal concentrations and application concentration of SYP-9625 on Tetranychus cinnabarinus (Boisduval) and its natural enemy, Neoseiulus californicus (McGregor)

ObjectiveExploring the effects of acaricides on predatory mites is crucial for the combination of biological and chemical control of pests. In this study, sublethal effects of the new acaricide SYP-9625 on Tetranychus cinnabarinus (Boisduval), effects of application concentration of SYP-9625 on the predatory mite Neoseiulus californicus (McGregor) and functional responses of N. californicus were assessed. The aim of the present study was to evaluate and explore the application of new acaricide SYP-9625 with natural enemy N. californicus.\n\nMethodAll the experiments were under laboratory conditions [25 {+/-} 1 {degrees}C, 16:8 (L:D) h and 75 {+/-} 5% RH] and based on an age-stage, two-sex life table. The sublethal concentrations against T. cinnabarinus, including LC10 (0.375 g/mL) and LC30 (0.841 g/mL) and the application concentration (100 g/mL) of SYP-9625, were used to evaluate effects on population parameters of N. californicus.\n\nResultT. cinnabarinus females treated with LC30 exhibited significantly reduced net reproductive rates (R0=11.02) of offspring compared to females treated with LC10 (R0=14.96) and untreated females (>R0=32.74). However, the intrinsic rate of increase (rm) and finite rate of increase ({lambda}) of N. californicus indicated that the application concentration of SYP-9625 had no significant negative effect on treated N. californicus eggs (rm=0.277,{lambda} =1.319) compared to the control (rm=0.292,{lambda} =1.338). Additionally, the sublethal concentrations against T. cinnabarinus including LC10 and LC30 showed a dose-dependent mechanism on the predatory mite. SYP-9625 also stimulated the predatory capacity of N. californicus against immobile stages such as eggs and larvae.\n\nConclusionIt is demonstrated that sublethal concentrations of SYP-9625 can inhibit population growth of T. cinnabarinus. And the sublethal concentrations and application concentration had little effect on the population growth of N. californicus. The two advantages showed great commercial potential of this new acaricide. Therefore, N. californicus can manage T. cinnabarinus populations effectively with appropriate SYP-9625 concentrations.

zoology↗