Biology subjects

Xing, M.

Publications and source records attributed to Xing, M..

8 recordsLinked to original sources

bioRxiv2026

Mass spectrometry imaging shows specific lipids signals linked to Cyp27b1 ablation in the MMTV PyMT breast cancer model

Bioactive vitamin D (1,25-dihydoxyvitamin D or 1,25(OH)2D) is synthesized from its inert circulating form 25-hydroxyvitamin D (25(OH)D) by the enzyme 1--hydroxylase in the kidneys and in other tissues including breast. Because breast cancer is associated with changes in intra-tumoral lipid composition and vitamin D is known to affect lipid metabolism, we investigated the potential role of tumor-produced 1,25(OH)2D on lipid profile expression during breast tumor progression. For that purpose, we used the MMTV-PyMT mouse model which mimics the four phases of tumor progression seen in human breast cancer (hyperplasia, adenoma/mammary intraepithelial neoplasia (MIN), early carcinoma and late carcinoma). In previous studies we showed that conditional ablation of the gene encoding 1--hydroxylase (Cyp27b1), specifically in the mammary epithelium of this MMTV-PyMT mouse model, resulted in enhanced spontaneous tumor initiation and progression. In the present study, we used mass spectrometry imaging to compare lipid composition in the mammary glands of Cyp27b1 ablated and non-ablated MMTV-PyMT mice. In non-ablated control animals, we observed changes to specific lipid signals linked to stages of tumor progression. In particular, several discriminatory lipid signals were significantly up regulated throughout tumor progression. In ablated mice, absence of Cyp27b1 in the mammary epithelium was accompanied by different lipid signals in hyperplastic lesions. Several lipid signals were exclusively detected in non-ablated tumors but absent in hyperplasia. Our findings suggest that the tumor-produced 1,25(OH)2D known to play a key role in mammary tumor progression is mechanistically related to early changes in lipid composition seen prior to the development of hyperplasia.

cancer biology↗

bioRxiv2026

Hierarchical refinements of cis-regulatory inputs improve scalable gene expression prediction

Deciphering the relationships between cis-regulatory elements (CREs) and target gene expression has long been a challenging problem in molecular biology. However, predicting gene expression from hundreds of candidate cis-regulatory elements (cCREs) requires models that scale to long, noisy inputs while retaining interpretable regulatory structure. Existing Transformer-based approaches typically attend over all nucleotides and all surrounding cCREs, diluting causal signals when hundreds of elements compete for limited model capacity. Here we introduce a two-stage selective framework (TSSF) that performs hierarchical refinements: nucleotide-level masking within each cCRE, followed by cCRE-level selection around each gene, implemented with information-bottleneck priors and a fully Transformer-based architecture. Across 70 human cell types and tissues, TSSF and lightweight variants improve expression prediction and enhancer-gene prioritization relative to strong baselines, including on cross-cell-line and cell-type-specific benchmarks. Prediction-stratified analysis motivates a distance-decay prior that aligns attention with long-range regulatory geometry, and chromatin-contact augmentation improves recovery of distal links. Motif analyses of high-confidence predictions recover proximal and distal regulatory programs, supporting mechanistic interpretability. TSSF offers a general strategy for scalable, interpretable modeling of high-dimensional regulatory inputs in genomics.

bioinformatics↗

bioRxiv2025

Influence of Macrocyclization Strategies on DNA-Encoded Cyclic Peptide Libraries

Discovery of cyclic peptide hits using DNA-encoded libraries (DELs) has recently been extensively researched, with significant efforts directed toward developing DEL-compatible macrocyclization methods. To investigate how different cyclic linkers influence DEL selection outcomes, we constructed eight distinct sub-libraries and screened them against two protein targets, MDM2 and GIT1, resulting in two representative yet contrasting scenarios. Validation studies for MDM2 revealed that structural similarity patterns observed across multiple sub-libraries could enhance confidence in the authenticity of identified hits. Notably, cmp-10 demonstrated potent inhibitory activity, exhibiting an inhibition constant of 11 nM. In contrast, selections against GIT1 produced discrete enrichment patterns. From these outcomes, two exemplary compounds were selected and validated through both on-DNA and off-DNA modes. cmp-17 was confirmed to bind specifically to the desired binding pocket, displaying a dissociation constant of 1.22 M. Furthermore, ITC experiments using mutant GIT1 proteins (GIT1L271A/L279A and GIT1L271L/L279L) provided additional insights into the mechanism by which cmp-17 disrupts the interaction between GIT1 and {beta}-Pix.

biochemistry↗

bioRxiv2024

Fibrillarin modulates fetal hemoglobin silencing

Decoding the molecular mechanisms underlying human fetal ({gamma}) globin gene silencing impacts therapeutic strategies for {beta}-thalassemia and sickle cell disease. Here, we identified a nucleolar protein, fibrillarin (FBL), which mediates the methylation of glutamine104 in histone H2A and functions as a repressor of the {gamma}-globin gene in cultured erythroid cells, including those from {beta}-thalassemia patients. Conditional Fbl depletion in adult {beta}-YAC transgenic mice or in {beta}IVS-2-654-thalassemic mice reactivated the human {gamma}-globin gene or murine embryonic globin expression, respectively, which corrects hematologic and pathologic defects in {beta}-thalassemic mice. We showed that FBL plays a dual role in activating BCL11A expression and repressing {gamma}-globin gene expression, which is dependent on its histone methyltransferase activity. Our study may provide an alternative strategy for therapeutic targeted treatment of {beta}-hemoglobinopathies.

molecular biology↗

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

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↗

bioRxiv2021

Integrative Epigenomic and High-Throughput Functional Enhancer Profiling Reveals Determinants of Enhancer Heterogeneity in Gastric Cancer

BackgroundEnhancers are distal cis-regulatory elements required for cell-specific gene expression and cell fate determination. In cancer, enhancer variation has been proposed as a major cause of inter-patient heterogeneity - however, most predicted enhancer regions remain to be functionally tested. ResultsAnalyzing 128 epigenomic histone modification profiles of primary GC samples, normal gastric tissues, and GC cell lines, we report a comprehensive catalog of 75,730 recurrent predicted enhancers, the majority of which are tumor-associated in vivo (>50,000) and associated with lower somatic mutation rates inferred by whole-genome sequencing. Applying Capture-based Self-Transcribing Active Regulatory Region sequencing (CapSTARR-seq) to the enhancer catalog, we observed significant correlations between CapSTARR-seq functional activity and H3K27ac/H3K4me1 levels. Super-enhancer regions exhibited increased CapSTARR-seq signals compared to regular enhancers even when decoupled from native chromatin contexture. We show that combining histone modification and CapSTARR-seq functional enhancer data improves the prediction of enhancer-promoter interactions and pinpointing of germline single nucleotide polymorphisms (SNPs), somatic copy number alterations (SCNAs), and trans-acting TFs involved in GC expression. Specifically, we identified cancer-relevant genes (e.g. ING1, ARL4C) whose expression between patients is influenced by enhancer differences in genomic copy number and germline SNPs, and HNF4 as a master trans-acting factor associated with GC enhancer heterogeneity. ConclusionsOur study indicates that combining histone modification and functional assay data may provide a more accurate metric to assess enhancer activity than either platform individually, and provides insights into the relative contribution of genetic (cis) and regulatory (trans) mechanisms to GC enhancer functional heterogeneity.

cancer biology↗

bioRxiv2020

Everyone Can Learn to Meditate: Characterizing a Personalized Connectomic State Space among Meditation Groups

Alterations in brain connectivity has been shown for many disease states and groups of people from different levels of cognitive training. To study dynamic functional connectivity, we propose a method for a personalized connectomic state space called Thought Chart. Experienced meditators are an interesting group of healthy subjects for brain connectivity analyses due to their demonstrated differences in resting state dynamics, and altered brain connectivity has been implicated as a potential factor in several psychiatric disorders. Three distinct techniques of meditation are explored: Isha Yoga, Himalayan Yoga, and Vipassana, as well as a meditation-naive group of individuals. All individuals participated in a breath awareness task, an autobiographical thinking task, and one of three different meditation practices according to their expertise, while being recorded by a 64-electrode electroencephalogram (EEG). The functional brain connectivity was estimated using weighted phase lag index (WPLI) and the connectivity dynamics were investigated using a within-individual formulation of Thought Chart, a previously proposed dimensionality reduction method which utilizes manifold learning to map out a state space of functional connectivity. Results showed that the two meditation tasks (breath awareness task and own form of meditation) in all groups were found to have consistently different functional connectivity patterns relative to those of the instructed mind-wandering (IMW) tasks in each individual, as measured using the Hausdorff distance in the state space. The specific meditation state was found to be most similar to the breath awareness state in all groups, as expected in these meditation traditions which all incorporate breath awareness training in their practice trajectory. The difference in connectivity was found to not be solely driven by specific frequency bands. These results demonstrate that the within-individual form of Thought Chart consistently and reliably separates similar tasks among healthy meditators and non-meditators during resting state-like EEG recordings. Unexpectedly, we found the dissimilarity between breath awareness/meditation and IMW, measured via Hausdorff distance, regardless of meditation experience or tradition, with no significant group differences.

neuroscience↗