Biology subjects

Teng, J.

Publications and source records attributed to Teng, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Genetic regulation of circulating metabolome in cattle

The circulating metabolome is a vital intermediate layer linking genetics to complex phenotypes, yet existing genome-wide studies-even in humans-rarely capture dynamic physiological contexts or cellular regulatory mechanisms. Here, we present the Cattle Metabolome Atlas (https://cattlema.farmgtex.org/), a comprehensive resource of 3,436 plasma metabolites and 4,851 serum metabolites from 4,651 animals with matched sequence-level genotypes across highly dynamic parity and lactation stages. We mapped 728 plasma and 622 serum metabolite quantitative trait loci (mQTL), revealing widespread context-dependent regulatory architectures. Integrating these mQTL with the multi-tissue expression quantitative trait loci (eQTL) and single-cell atlas of 59 tissues demonstrates that 74-79% of mQTL colocalize with eQTL across 29 tissues, prioritizing the liver as the primary systemic hub and resolving metabolic programs at single-cell resolution. Furthermore, we charted 538 causal gene-tissue-metabolite-trait cascades across 11 complex traits in cattle. Finally, cross-species analyses demonstrate partial evolutionary conservation of genetic metabolism between cattle and humans, establishing this atlas as a powerful asset for cattle genetics and genomics, selective breeding, and comparative biology.

genetics↗

bioRxiv2026

Differential benefits for temporal intervals and line segments with feedback and relevance to new learning with transfer effects

Learning to accurately estimate temporal intervals and spatial magnitudes is important to everyday behavior, yet few studies have directly compared how learning unfolds across these domains. Theoretical models of temporal interval estimation provide conflicting accounts of how this learning process might occur and how it might differ from other entities like spatial line estimation. In the present study, participants completed temporal interval and line-length production tasks under feedback or no-feedback conditions during a training phase. They were then tested without feedback and subsequently presented with untrained temporal intervals and line lengths to examine whether learning generalized to novel magnitudes. We found that both temporal and spatial production exhibited similar learning trajectories, characterized by rapid initial improvements, followed by asymptotic performance. Despite similar learning trajectories, however, spatial production reached higher levels of accuracy and precision faster and in a more sustained manner than temporal production. Feedback facilitated learning in both domains, with improvements in precision emerging early during training and improvements in accuracy becoming evident during the subsequent test phase. These benefits persisted into the transfer phase, particularly for spatial production, indicating that feedback-supported learning generalized to untrained magnitudes. Transfer performance also reflected systematic biases in magnitude estimation, consistent with a central tendency effect, with shorter magnitudes tending to be overproduced and longer magnitudes underestimated. Together, these findings demonstrate that temporal and spatial magnitude learning share some common and some dissociable learning dynamics, providing new insight into the shared and distinct mechanisms underlying magnitude learning and highlighting the important role of feedback in promoting learning and transfer.

animal behavior and cognition↗

bioRxiv2026

Subclonal IDH1/2 Mutations as a Targetable Vulnerability in Vascular Tumors

Despite extensive sequencing, the genetic etiology of sporadic angiosarcoma remains poorly defined (1-3). Maffucci syndrome, characterized by vascular tumors and elevated cancer risk, is driven by mosaic gain-of-function mutations in IDH1/2 (4,5), though these have not been reported in sporadic angiosarcoma. We identify recurrent, low-variant allele frequency hotspot mutations in IDH1/2 in over half of sporadic angiosarcomas. Mutations were validated by Sanger sequencing and immunohistochemistry. Mutant IDH1 endothelial cells promote tumorigenesis through non-cell-autonomous mechanisms, secreting 2-hydroxyglutarate (2-HG) to increase growth factor and endothelial-to-mesenchymal transition gene expression, activate pAkt/pERK signaling, induce DNA methylation changes, and promote anchorage-independent growth, which are reversed by the mutant IDH1 inhibitor ivosidenib. Patients with mosaic IDH1 mutations show reduced serum 2-HG and marked tumor regression following ivosidenib treatment. The clinical efficacy of ivosidenib in vascular tumors with subclonal IDH1 mutations suggests that low VAF IDH1/2 mutations may be a targetable vulnerability in sporadic angiosarcoma. (6,7) Statement of SignificanceWe identify recurrent, low-VAF IDH1/2 mutations in angiosarcoma and provide evidence that these subclonal mutations promote tumorigenesis through non-cell-autonomous mechanisms. Vascular tumors driven by subclonal IDH1 mutations responded dramatically to ivosidenib, thus revealing a novel treatment for a subset of vascular tumors.

cancer biology↗

bioRxiv2026

The enhanced multi-tissue atlas of regulatory effects in cattle

Cattle are integral to global food security, yet the molecular architecture of their complex traits remains poorly understood. Here, we present the Cattle Genotype-Tissue Expression (CattleGTEx) Phase 1 resource (https://cattlegtex.farmgtex.org/), a substantial expansion of the pilot study. By leveraging 12,422 RNA-seq profiles across 43 tissues and 82 breeds, we characterized 433,972 primary and 161,428 non-primary regulatory effects spanning seven molecular phenotypes. This high-resolution atlas resolves 75% of GWAS signals for 44 complex traits, significantly addressing the "missing regulation" in livestock. We propose a genetic regulatory model demonstrating how variants across multiple biological layers interact with specific biological contexts to shape phenotypic variation. Furthermore, CattleGTEx elucidates mechanisms underlying adaptive evolution between Bos taurus and Bos indicus, as well as artificial selection in dairy and beef breeds. Finally, by mapping evolutionary constraints on these regulatory effects, we demonstrate the translational value of this resource for prioritizing causal variants in human complex diseases. Together, Phase 1 of CattleGTEx provides a transformative framework for functional genomics, precision breeding, and comparative genetics.

genetics↗

bioRxiv2026

Context-dependent genetic regulation of gene expression in pigs

Production livestock provide a natural system for studying gene regulation under physiologically demanding conditions shaped by rapid growth, environmental exposure, and immune challenges. Using farm pigs from the PigGTEx resource as a model, we applied quantile regression to uncover latent, context-dependent genetic effects on gene expression across tissues. This approach identifies quantile-specific expression quantitative trait loci (eQTLs) that are not detected by standard linear regression and are enriched in distal regulatory elements and three-dimensional genome architectural features rather than promoter-proximal regions. Genes with quantile-dependent eQTLs are more intolerant to loss-of-function variants and exhibit stronger enrichment in GO functional categories, indicating their likely functional significance. Cross-species comparisons reveal substantial overlap between pig and human eGenes across tissues, indicating conservation of regulatory architecture. Notably, many quantile-specific eQTLs influence tail expression states and involve genes relevant to human disease. For example, we identify a cis-eQTL affecting the conserved transcriptional regulator BCL6B in pig blood that modulates enhancer activity and reduces expression at lower quantiles. In contrast, BCL6B is minimally expressed in resting human blood and lacks detectable cis-regulatory variation under baseline conditions, consistent with its reported induction during immune activation. These findings demonstrate that pig eQTL maps can reveal context-dependent regulatory variation at loci that remain silent or weakly variable in human cohorts.

bioinformatics↗

bioRxiv2026

FMR1 reduction alters cellular and circuit properties in human cortex

Transcriptional silencing of FMR1 results in Fragile X syndrome (FXS), the leading inherited cause of intellectual disability (ID) and autism. The Fmr1-/y mouse model has been used to identify FXS disease mechanisms, whereas mechanistic insights from human brain are lacking. By leveraging organotypic human cortical slices and viral tools to reduce FMR1 expression, we create a new model that captures cell type-specific transcriptomic changes similar to FXS patient cortex that are not seen in the Fmr1-/y mouse. Among these are ion channel subunit changes in deep layer pyramidal neurons, which are consistent with a robust hyperexcitability seen by whole-cell patch-clamp recordings, and increased synchronized activity revealed by 2-photon calcium imaging. Together, this work defines the impact of FMR1 reduction in human cortex and provides a new model for testing therapeutic interventions in FXS.

neuroscience↗

bioRxiv2026

Sex-specific Genetic Regulatory Effects in Chickens

Sexual dimorphism is a defining vertebrate feature, yet its sex-specific molecular architecture remains poorly understood. Here we established a sex-balanced, uniformly reared chicken cohort to map this landscape, integrating individual whole-genome sequencing with 7,969 bulk and 779,380 single nucleus transcriptomes across 32 tissues from 280 birds. We identified 495,098 independent expression quantitative trait loci for 20,194 genes, including 10,937 loci modulated by cell-type composition. Notably, 340 genes were regulated by 449 loci in a sex-dependent manner, significantly enrichment in endocrine tissues like adipose and the adrenal gland. Furthermore, we fine-mapped 1,219 structural variants, demonstrating their unique roles to tissue- and sex-specific expression beyond SNPs. Ultimately, we showed the utility of these regulatory effects in elucidating the molecular basis of metabolism and complex traits in both chickens and humans. This comprehensive atlas of regulatory effects provides profound insights into the genomic and molecular basis of sexual dimorphism in vertebrates.

genomics↗

bioRxiv2025

A multi-tissue atlas of genetic regulatory effects in sheep

Characterizing the impact of genomic variants on genome function and ultimately complex traits in livestock is essential for the development of sustainable precision agriculture and comparative genomics. Here, as part of the Farm animal Genotype-Tissue Expression (FarmGTEx) project, we present the pilot phase of the SheepGTEx resource through analyzing 6,761 RNA-sequencing samples of 51 primary tissues in a multi-breed population of sheep. We identify millions of regulatory variants associated with seven types of molecular phenotypes, and fine-map 322,468 primary and 114,017 non-primary effects, revealing a high degree of regulatory allelic heterogeneity. We systematically characterize the pleiotropic effects of these variants on molecular phenotypes, assess their context-specific regulatory patterns across tissues, breeds, sexes, and developmental stages, as well as explore their evolutionary constraints across mammals. Finally, we demonstrate the substantial potential of the SheepGTEx resource (https://sheepgtex.farmgtex.org), by providing examples of regulatory mechanisms underpinning 34 complex traits, population divergence between European and Asian breeds, and adaptive evolution in sheep over the past ten millennia.

genomics↗

bioRxiv2025

High-Fat Diet-Induced Obesity Impairs Endothelium-Dependent Relaxation via MLCK Activation: Reversal by ML-7 in Rabbits

ObjectiveObesity is an independent risk factor for CVD(cardiovascular diseases) and elevated cardiovascular mortality, though the precise mechanisms remain incompletely elucidated. Impaired endothelium-dependent relaxation is an early manifestation of cardiovascular diseases. This study investigated the impact of HFD(high-fat diet)-induced obesity on endothelium-dependent relaxation function and explored the potential role of MLCK(myosin light chain kinase) signaling. MethodsForty-five New Zealand White rabbits were randomized into three groups: a control group (normal diet), HFD(high-fat diet) group, and an ML-7 group (HFD plus the MLCK inhibitor ML-7). After 8 weeks of feeding, vascular endothelial function was assessed in vivo by measuring FMD(flow-mediated dilation). Serum lipids and blood glucose levels were determined. Endothelium-dependent vasodilation was evaluated ex vivo using aortic ring assays. The protein expression levels of MLCK and eNOS(endothelial nitric oxide synthase), as well as the phosphorylation level of MLC(myosin light chain), in rabbit arteries were analyzed by Western blot. ResultsHFD-fed rabbits developed obesity, dyslipidemia (elevated TC[total cholesterol], LDL-C[low-density lipoprotein cholesterol], and ox-LDL[oxidized low-density lipoprotein]), perirenal adipose tissue deposition, and significant endothelial dysfunction, evidenced by impaired endothelium-dependent relaxation function and morphological endothelial damage. Western blot analysis revealed upregulated MLCK and eNOS expression, along with increased phosphorylation of MLC in the arterial walls of obese rabbits, despite no significant change in NO(nitric oxide) levels compared to controls. Treatment with ML-7 ameliorated endothelium-dependent relaxation function impairment. Furthermore, the inherent limitations of FMD as a non-invasive technique in terms of accuracy and sensitivity for evaluating endothelium-dependent dilation. ConclusionsObesity-induced endothelial dysfunction arise from visceral fat accumulation, dyslipidemia, oxidative stress, and MLCK overexpression. Notably, MLCK inhibition via ML-7 restores vascular function, highlighting its therapeutic potential in obesity-related vascular injury.

physiology↗

bioRxiv2025

An atlas of cell type specific regulatory effects in cattle

Understanding the genetic and molecular architecture of complex traits and artificial selection is crucial for advancing sustainable precision breeding in cattle and other livestock. Yet, how genetic variation affects cellular gene expression remains elusive in cattle. Here, by integrating 8,866 bulk RNA-seq samples and 999,192 single cells of 81 cell types in 22 bovine tissues, we presented a comprehensive atlas of regulatory variants at the cell type resolution in cattle. By colocalizing with bulk-tissue expression quantitative trait loci (beQTL), we detected 57,043 novel cell-type stratified eQTL and cell-type/state interaction eQTL in 18,153 genes, which also exhibited a stronger tissue/cell-type specificity than beQTL. By examining genome-wide associations (GWAS) of 44 complex traits, these cell-resolved eQTL were colocalized with 505 (24%) additional GWAS loci compared to beQTL. Through integrating this resource with selection signatures between dairy and beef cattle, we provided tissue/cell-specific regulatory insights into cattle breeding. Overall, the current atlas of cell-type-specific regulatory variants will serve as an invaluable resource for cattle genomics and selective breeding.

genetics↗

bioRxiv2024

OmiGA: A Toolkit for Ultra-efficient Molecular Trait Analysis in Complex Populations

Molecular quantitative trait loci (molQTL) mapping is one of the most popular approaches to systematically characterize functional impacts of genomic variants, leading to advanced understanding of the regulatory mechanisms underpinning complex traits and diseases. However, when applied to high-throughput molecular phenotypes, the existing molQTL mapping tools often implement simple linear models, overlooking complex inter-individual relatedness, leading to false positives and insufficient statistical power. Here, we introduce the Omics Genetic Analysis toolkit (OmiGA), an ultra-efficient linear mixed model (LMM) based toolkit, for molQTL mapping in populations with complex relatedness. Both computational simulations and real data analyses demonstrated that OmiGA outperformed the existing popular tools regarding molQTL discovery power, fine mapping of causal variants, colocalization of molQTL and trait associations, and computational efficiency. In summary, we recommend OmiGA for molQTL mapping in populations with complex relatedness, for example, those in the Farm animal Genotype-Tissue Expression (FarmGTEx) project and family-based molQTL studies in humans.

bioinformatics↗

bioRxiv2024

Autoimmune mechanisms elucidated through muscle acetylcholine receptor structures

Skeletal muscle contraction is mediated by acetylcholine (ACh) binding to its ionotropic receptors (AChRs) at neuromuscular junctions. In myasthenia gravis (MG), autoantibodies target AChRs, disrupting neurotransmission and causing muscle weakness. Despite available treatments, patient responses vary, suggesting pathogenic heterogeneity. Current information on molecular mechanisms of autoantibodies is limited due to the absence of structures of an intact human muscle AChR. Here, we overcome challenges in receptor purification and present high-resolution cryo-EM structures of the human adult AChR in different functional states. Using a panel of six MG patient-derived monoclonal antibodies, we mapped distinct epitopes involved in diverse pathogenic mechanisms, including receptor blockade, internalization, and complement activation. Electrophysiological and binding assays further defined how these autoantibodies impair AChR function. These findings provide critical insights into MG immunopathology, revealing previously unrecognized antibody epitope diversity and mechanisms of receptor inhibition, offering a foundation for personalized therapies targeting antibody-mediated autoimmune disorders. HighlightsO_LIHuman adult muscle AChR receptor structures in resting and desensitized states C_LIO_LIEpitope mapping for mechanistically distinct pathogenic MG autoantibodies C_LIO_LIStructural and functional elucidation of different inhibition mechanisms in MG C_LI

neuroscience↗

bioRxiv2024

An endothelial SOX18-mevalonate pathway axis enables repurposing of statins for infantile hemangioma

Infantile hemangioma (IH) is the most common tumor in children and a paradigm for pathological vasculogenesis, angiogenesis and regression. Propranolol is the mainstay of treatment for IH. It inhibits hemangioma vessel formation via a {beta}-adrenergic receptor independent off-target effect of its R(+) enantiomer on the endothelial specific transcription factor sex-determining region Y (SRY) box transcription factor 18 (SOX18). Transcriptomic profiling of patient-derived hemangioma stem cells uncovered the mevalonate pathway (MVP) as a target of R(+) propranolol. Loss of SOX18 function confirmed R(+) propranolol mode of action on the MVP. Functional validation in preclinical IH models revealed that statins - targeting the MVP - are potent inhibitors of hemangioma vessel formation. We propose a novel SOX18-MVP-axis as a central regulator of IH pathogenesis and suggest statin repurposing to treat IH. Our findings reveal novel pleiotropic effects of beta-blockers and statins acting on the SOX18-MVP axis to disable an endothelial specific program in IH, which may impact other scenarios involving pathological vasculogenesis and angiogenesis. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=135 SRC="FIGDIR/small/577829v2_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@f02b2corg.highwire.dtl.DTLVardef@1a2790forg.highwire.dtl.DTLVardef@1ba0318org.highwire.dtl.DTLVardef@1213522_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2023

Parallel Molecular Data Storage by Printing Epigenetic Bits on DNA

DNA storage has shown potential to transcend current silicon-based data storage technologies in storage density, lifetime and energy consumption. However, writing large-scale data directly into DNA sequences by de novo synthesis remains uneconomical in time and cost. Inspired by the natural genomic modifications, in this work, we report an alternative, parallel strategy that enables the writing of arbitrary data on DNA using premade nucleic acids. With epigenetic modifications as information bits, our system employed DNA self-assembly guided enzymatic methylation to perform movable-type printing on universal DNA templates. By programming with a finite set of 700 DNA movable types and 5 templates, we achieved the synthesis-free writing of [~]270000 bits on an automated platform with 350 bits written per reaction. The data encoded in complex epigenetic patterns were retrieved high-throughput by nanopore sequencing, and algorithms were developed to finely resolve 240 modification patterns per sequencing reaction. Our framework presents a new modality of DNA-based data storage that is parallel, programmable, stable and scalable. Such a modality opens up avenues towards practical data storage and dual-mode data functions in biomolecular systems.

biochemistry↗

bioRxiv2023

CEP44 is required for maintaining centriole duplication and spindle integrity

In animal cells, the centrosome, consisting of two centrioles, duplicates only once per cell cycle for bipolar spindle formation. Defective centriole duplication results in abnormal spindle formation and chromosome missegregation, which is closely linked to tumor growth. However, the molecular mechanisms licensing only one centriole duplication cycle within a cell cycle are less well known. Here we found that CEP44 is negatively correlated with breast carcinoma. CEP44, jointly with CEP57 and CEP57L1, maintains centriole engagement in the interphase to ensure centriole duplication once per cell cycle. Depletion of CEP44 leads to centriole overduplication because of premature centriole disengagement, and multipolar spindle formation. Additionally, CEP44 is phosphorylated by Aurora A at the G2/M phase to facilitate spindle localization and maintain spindle integrity. Collectively, our results show the function of CEP44 in spindle formation by preventing centriole overduplication and maintaining spindle integrity, and CEP44 may serve as a potential marker for breast carcinoma prognosis.

cell biology↗

bioRxiv2023

Evolution is All You Need in Promoter Design and Optimization

Predicting the strength of promoters and guiding their directed evolution is a crucial task in synthetic biology. This approach significantly reduces the experimental costs in conventional promoter engineering. Previous studies employing machine learning or deep learning methods have shown some success in this task, but their outcomes were not satisfactory enough, primarily due to the neglect of evolutionary information. In this paper, we introduce the Chaos-Attention net for Promoter Evolution (CAPE) to address the limitations of existing methods. We comprehensively extract evolutionary information within promoters using chaos game representation and process the overall information with DenseNet and Transformer. Our model achieves state-of-the-art results on two kinds of distinct tasks. The incorporation of evolutionary information enhances the models accuracy, with transfer learning further extending its adaptability. Furthermore, experimental results confirm CAPEs efficacy in simulating in silico directed evolution of promoters, marking a significant advancement in predictive modeling for prokaryotic promoter strength. Our paper also presents a user-friendly website for the practical implementation of in silico directed evolution on promoters.

synthetic biology↗

bioRxiv2023

Integrating large-scale meta-GWAS and PigGTEx resources to decipher the genetic basis of complex traits in pig.

Understanding the molecular and cellular mechanisms that underlie complex traits in pigs is crucial for enhancing their genetic improvement program and unleashing their substantial potentials in human biomedicine research. Here, we conducted a meta-GWAS analysis for 232 complex traits with 28.3 million imputed whole-genome sequence variants in 70,328 individuals from 14 pig breeds. We identified a total of 6,878 genomic regions associated with 139 complex traits. By integrating with the Pig Genotype-Tissue Expression (PigGTEx) resource, we systemically explored the biological context and regulatory circuits through which these trait-associated variants act and finally prioritized 16,664 variant-gene-tissue-trait circuits. For instance, rs344053754 regulates the expression of UGT2B31 in the liver by affecting the activity of regulatory elements and ultimately influences litter weight at weaning. Furthermore, we investigated the conservation of genetic and regulatory mechanisms underlying 136 human traits and 232 pig traits. Overall, our multi-breed meta-GWAS in pigs provides invaluable resources and novel insights for understanding the regulatory and evolutionary mechanisms of complex traits in both pigs and humans.

genetics↗

bioRxiv2023

The ChickenGTEx pilot analysis: a reference of regulatory variants across 28 chicken tissues

Chicken is a valuable model for understanding fundamental biology, vertebrate evolution and diseases, as well as a major source of nutrient-dense and lean-protein-enriched food globally. Although it is the first non-mammalian amniote genome to be sequenced, the chicken genome still lacks a systematic characterization of functional impacts of genetic variants. Here, through integrating 7,015 RNA-Seq and 2,869 whole-genome sequence data, the Chicken Genotype- Tissue Expression (ChickenGTEx) project presents the pilot reference of regulatory variants in 28 chicken tissue transcriptomes, including millions of regulatory effects on primary expression (including protein-coding genes, lncRNA and exon) and post-transcriptional modifications (alternative splicing and 3 untranslated region alternative polyadenylation). We explored the tissue-sharing and context-specificity of these regulatory variants, their underlying molecular mechanisms of action, and their utility in interpreting adaptation and genome-wide associations of 108 chicken complex traits. Finally, we illustrated shared and lineage-specific features of gene regulation between chickens and mammals, and demonstrated how the ChickenGTEx resource can further assist with translating genetic findings across species. One-Sentence SummaryThe ChickenGTEx provides a multi-tissue reference of regulatory variants for chicken genetics and genomics, functional genomics, precision breeding, veterinary medicine, vertebrate evolution and even human biomedicine.

genetics↗