Biology subjects

Zong, C.

Publications and source records attributed to Zong, C..

17 recordsLinked to original sources

bioRxiv2026

Intra-Complex Differential Transcription Strategies for Scaffold versus Effector Proteins

Scaffold-organized multi-protein complexes are major drivers of cellular regulatory pathways, but how the expression of their constituent genes is coordinated to support efficient assembly and cell-to-cell homeostasis remains poorly understood. Using snapTotal-seq data, this study addresses this issue at the transcription level through comparative analyses of stochastic transcription bursting - a major driver of expression level and primary source of its intrinsic cell-to-cell noise. We compared scaffold proteins and their effector partners in major regulatory multi-protein complexes: TNRC6A/B/C (in the miRISC complex) and CNOT1/2 (in the CCR4-NOT complex) in mRNA regulation; and AXIN1, APC, KSR2, AKAPs, DLG1, PATJ, HOMER1/2, and SQSTM1 in signal transduction. Our analyses reveal a shared strategy: compared to genes for active effector partner proteins and the general transcriptome, genes for structural scaffold proteins consistently utilize more frequent and smaller-sized bursting to achieve the fine tuning of a homeostatic expression level. This finding establishes a fundamental link between a proteins physical role within a regulatory complex and the transcriptional bursting kinetics of its gene.

Systems Biology↗

bioRxiv2026

Do drugs with biliary toxicity cause cholangiocarcinoma?

AO_SCPLOWBSTRACTC_SCPLOWMany commonly used therapeutic drugs cause biliary toxicity, but it is unclear if they are directly responsible for the increasing incidence of cholangiocarcinoma (CCA). We tested experimentally and analyzed through a cohort approach whether drugs, such as the commonly used antibiotic Augmentin, which is a poster-child of biliary toxicity, are causally linked to CCA development. Using sophisticated analytical tools in cholangiocytes, including single extracellular vesicle (EV) analysis, we found no evidence that Augmentin increases the cholangiocyte malignancy marker YAP1 or phospho-YAP1. Furthermore, we analyzed the CCA incidence in our healthcare system and determined it to be 0.0932% (Augmentin group) and 0.0799% (amoxicillin control group). Although the Augmentin group showed a numerically higher CCA incidence, the association did not reach statistical significance (RR = 1.1669, 95% CI 0.6200-2.1961; Fishers exact test, P = 0.7493). Similarly, we found no evidence for cholangiocarcinoma development with other commonly used drugs, including chlorpromazine, floxuridine, 5-fluorouracil, flucloxacillin and terbinafine. We conclude that there is no direct causal relationship between clinical Augmentin doses and CCA development.

cancer biology↗

bioRxiv2026

SigFormer: an Attention-Based Framework for Robust Single-Sample Mutational Signature Decomposition

Somatic mutational signatures imprint the history of exogenous exposures and endogenous processes on the genome, offering critical insights into pathologic etiology and disease risk. However, accurate signature decomposition at the single-sample level is still challenging when mutation burden is low, sampling noise is high, and candidate catalogs are large and redundant. Here, we present SigFormer, a set-conditioned transformer framework designed to facilitate robust somatic mutation analysis without reliance on large cohorts. By leveraging a cross-attention mechanism between customized reference input and sample mutation profile, SigFormer improves exposure recovery and detection accuracy compared with likelihood-driven refitting (MuSiCal) with the largest performance gains in high-noise and overcomplete settings. On PCAWG genomes, SigFormer preserves major tissue-level structure while sensitively and accurately capturing cooccurrence of low-abundance signatures but without the need for tumor-type-specific gating. In low-burden normal-tissue datasets spanning clonal expansion and microdissection studies, SigFormer maintains the high accuracy and recovers stable tissue-dependent patterns of SBS1/SBS5/SBS40a, pointing to underlying tissue-specific mutagenic heterogeneity in normal tissues. Finally, SigFormer quantifies an explicit unattributable residual component when the catalogue is incomplete, preventing forced allocation into flexible flat signatures and providing a useful signal for downstream analyses.

bioinformatics↗

bioRxiv2025

Benchmarking of duplex sequencing approaches to reveal somatic mutation landscapes

Detecting somatic mutations in normal tissues is challenging due to sequencing errors and the low allele fractions of post-zygotic variants. Duplex sequencing greatly reduces errors and can detect mutations at any allele fraction, but systematic, cross-platform comparisons are lacking. We present a comprehensive benchmarking of six duplex sequencing technologies used by the SMaHT Network: CODEC, CompDuplex-seq, HiDEF-seq, NanoSeq, ppmSeq, and VISTA-seq. We evaluated their performance using cord blood DNA, a tumor-normal cell line mixture, and homogenates from six human tissues. Each method shows distinct profiles in genomic footprint, sensitivity, and cost. Despite differences in library construction and sequencing platforms, estimates of mutation rates and mutational signatures are highly concordant. Integration with ultra-deep whole-genome sequencing shows that duplex approaches sensitively capture mutations and signatures beyond embryonic or clonally expanded variants. These results provide a foundation for selecting duplex methods and interpreting their data, enabling scalable single-molecule analyses of somatic mutation landscapes. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/692823v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@123b221org.highwire.dtl.DTLVardef@83ba0aorg.highwire.dtl.DTLVardef@2b0ab0org.highwire.dtl.DTLVardef@1cae35e_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2025

Expanding the Genome in a Bottle Truth Set: Detection and Validation of Novel Low-frequency Variants Using High-accuracy NanoSeq

HighlightsO_LINanoSeq-MBN achieves near-genome, Poisson-like coverage with minimal trinucleotide bias. C_LIO_LIExpands the GIAB truth set by up to 160k de novo variants. C_LIO_LIAdds a somatic layer to GIAB, enabling benchmarking and calibration of rare variants. C_LIO_LIHigh-CADD exonic and splice variants highlight value for surveillance and clinical triage. C_LI Somatic mutations record tissue molecular history and inform risk, prognosis, and therapy, yet their variant allele fractions often fall below the reliable detection limit of conventional short-read sequencing. In contrast, duplex sequencing technology featured by NanoSeq applies the principle of single molecule detection and thereby overcomes the limitation. However, the original NanoSeq protocol relies on the restriction enzyme-based genome fragmentation, which constrained its genome coverage to 30-40%. To enable whole-genome discovery with duplex-level fidelity, we pursued two complementary approaches to optimize the NanoSeq protocol: (i) a restriction-enzyme strategy densifies accessible sites using orthogonal 4-bp cutters; and (ii) a workflow using sonication followed by mung bean nuclease with T4 polynucleotide kinase, Klenow fragment and dATP/ddBTP mixture (NanoSeq-MBN) to blunt and repair/A-tailing DNA, while minimizing repair artifacts. We systematically benchmarked their performance using Genome in a Bottle (GIAB) gold-standard sample mixtures. As a result, NanoSeq-MBN achieved near genome-wide, Poissonlike coverage with minimal trinucleotide-context bias and ultra-high accuracy. Beyond variants already present in the GIAB truth set, NanoSeq-MBN identified approximately 120,000-160,000 de novo mutations per sample missing in the truth set, Notably, over 98% had orthogonal support in reanalyzed GIAB bulk Illumina HiSeq libraries. These novel variants extended GIAB from germline benchmarking to rare-variant discovery and calibration of subclonal detection. Functional annotation revealed enrichment of high Combined Annotation Dependent Depletion (CADD) scores mutations in exonic and splice-related regions. Variants intersecting ClinVar entries and OMIM genes highlighted potential for surveillance and clinical triage. Collectively, these results add a somatic layer to GIAB, enabling calibration of burdens and mutational signatures in lymphoblastoid lines and provide reference material for rare-variant assays. The NanoSeq-MBN workflow offers a path to whole-genome, high-fidelity discovery of ultra-rare somatic variation with relevance to clinical assay validation.

molecular biology↗

bioRxiv2025

Timing the onset of homologous recombination deficiency before cancer diagnosis

Mutations in BRCA1 and BRCA2 genes, whether inherited or somatically acquired, cause homologous recombination deficiency (HRD) in tumor cells. The timing of HRD onset in the emerging tumor lineage is unknown. Here, we present HRDTimer, an algorithm to infer the onset of HRD-driven mutagenesis prior to cancer diagnosis. We estimate that HRD arises at 34% of SBS1-based molecular time---corresponding to a median of 8.3 years (IQR 7.1--10.4) prior to diagnosis in triple-negative breast cancers, and 15.0 years (IQR 12.0--20.6) in ER-positive breast cancers. Bulk sequencing reveals accelerated SBS1 accumulation following neoplastic transformation compared to normal tissue, influencing the estimated age of HRD onset. Single-cell duplex sequencing confirms SBS1 acceleration in tumors and further shows that non-tumor cells largely lack the HRD signature, indicating that HRD is rare in pre-malignant cells, even in BRCA1/2 mutation carriers. Together, our analysis pinpoints the onset of HRD before diagnosis, defining a window for detection and potential interception.

genomics↗

bioRxiv2025

Shaker it OFF: Biophysical Characterization of an Inactivating Potassium Conductance Mediating Object Segmentation in a Collision-Detecting Neuron

Homologous ion channels are expressed in sensory neurons across species where they shape responses to varied sensory stimuli, on a wide range of timescales. In grasshoppers, visual detection of looming stimuli which simulate an approaching predator involves the sub-cellular expression pattern of a newly characterized Shaker channel in a single identified neuron, discovered using a newly sequenced genome and single cell RNA sequencing. This channel shapes selectivity for approaching threats and was characterized with electrophysiological recordings, RNA interference, pharmacology and biophysical compartmental simulations. Our results explain how a slowly activating and inactivating potassium conductance common in neuronal dendrites contributes to visual object segmentation and implements a complex neural computation within a single neuron.

neuroscience↗

bioRxiv2025

To jump or not to jump: Comparing effects of phenotypic plasticity on the visual responses and escape behavior of locusts and grasshoppers

Locusts exhibit remarkable phenotypic plasticity changing their appearance and behavior from solitary grasshoppers to gregarious locusts when population density increases. These changes include morphological differences in the size and shape of brain regions, but little is known about plasticity within individual neurons and alterations in behavior not directly related to aggregation or swarming. We examined looming escape behavior and the properties of a well-studied collision-detection neuron in gregarious and solitarious animals of three closely related species, the desert locust (Schistocerca gregaria), the Central American locust (S. piceifrons) and the American bird grasshopper (S. americana). For this neuron, the lobula giant movement detector (LGMD), we examined dendritic morphology, membrane properties, gene expression, and looming responses. Gregarious animals reliably jumped in response to looming stimuli, but surprisingly solitarious desert locusts did not produce escape jumps. These solitarious animals also had smaller LGMD dendrites. This is the first study done on three different species of grasshoppers to observe the effects of phenotypic plasticity on the jump escape behavior, physiology and transcriptomics of these animals. Surprisingly, there were little differences in these properties between the two phases except for behavior. For all the three species, gregarious animals jumped more than solitarious animals, but no significant differences were found between the two phases of animals in the electrophysiological and transcriptomics studies. Our results suggest that phase change impacts mainly the motor system and that the physiological properties of motor neurons need to be characterized to understand fully the variation in jump escape behavior across phases. New & Noteworthy (74 words): Swarming is observed in some grasshopper species, called locusts. We compared jump escape behavior between gregarious and solitarious grasshoppers and locusts, as well as LGMD responses to looming stimuli, and analyzed the morphological differences in this neuron. This study provides insights into the effects of phase change on the visual system of locusts and grasshoppers as it relates to looming-evoked jump escape behavior. In this context, our results suggest that phenotypic plasticity mainly impacts the motor system.

neuroscience↗

bioRxiv2025

Single-nucleotide Resolution Epitranscriptomic Profiling Uncovers Dynamic m6A Regulation in Bovine Preimplantation Development

RNA N6-methyladenosine (m6A) plays a crucial role in regulating gene expression during early embryonic development. However, the m6A dynamics at single-nucleotide resolution in preimplantation development remain uncharacterized, and the functional significance of site specific m6A modifications in key developmental regulators is largely unknown. Here, using SAC-seq, a single-base resolution, antibody-independent m6A profiling method, we generate the first comprehensive m6A landscape in bovine oocytes and preimplantation embryos. We identify a previously uncharacterized m6A site in RPL12 transcript that is essential for embryonic development. Loss of m6A at this site leads to reduced protein synthesis, disrupted expression of translation-related genes, and impaired zygotic genome activation and blastocyst formation. Notably, supplementation with wild-type RPL12 mRNA fails to rescue the developmental arrest, indicating that m6A regulation extends beyond transcript abundance. Our findings provide a valuable resource of m6A at single-nucleotide resolution in mammalian embryogenesis and uncover a critical mechanism by which precise, site-specific m6A regulates translation and developmental competence in early embryos.

developmental biology↗

bioRxiv2025

protPheMut: An Interpretable Machine Learning Tool for Classification of Cancer and Neurodevelopmental Disorders in Human Missense Variants

MotivationRecent advances in human genomics have revealed that missense mutations in a single protein can lead to distinctly different phenotypes. In particular, some mutations in oncoproteins like Ras, MEK, PI3K, PTEN, and SHP2 are linked various cancers and Neurodevelopmental Disorders (NDDs). While numerous tools exist for predicting the pathogenicity of missense mutations, linking these variants to certain phenotypes remains a major challenge, particularly in the context of personalized medicine. ResultsTo fill this gap, we developed protPheMut (Protein Phenotypic Mutations Analyzer), leveraging multiple interpretable machine learning methods and integrate diverse biophysics and network dynamics-based signatures, for the prediction of mutations of the same protein can promote cancer, or NDDs. We illustrate the utility of protPheMut in phenotypes (cancer/NDDs) prediction by the mutation analysis of two protein cases, that are PI3K and PTEN. Compared to seven other predictive tools, protPheMut demonstrated exceptional accuracy in forecasting phenotypic effects, achieving an AUROC of 0.8501 for PI3K mutations related to cancer and Cowden syndrome. For multi-phenotypes prediction of PTEN mutations related to cancer, PHTS, and HCPS, protPheMut achieved an AUC of 0.9349 through micro-averaging. Using SHAP model explanations, we gained insights into the mechanisms driving phenotype formation. A userfriendly website deployment is also provided. AvailabilitySource code and data are available at https://github.com/Spencer-JRWang/protPheMut. We also provide a user-friendly website at http://netprotlab.com/protPheMut. Supplementary informationSupplementary data are available at Bioinformatics online. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=64 SRC="FIGDIR/small/631365v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@df55e3org.highwire.dtl.DTLVardef@7fe3f9org.highwire.dtl.DTLVardef@501cccorg.highwire.dtl.DTLVardef@192c98e_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2023

Single-cell Total-RNA Profiling Unveils Regulatory Hubs of Transcription Factors

Recent development of RNA velocity uses master equations to establish the kinetics of the life cycle of RNAs from nascent RNA to mature RNA to degradation. To feed this kinetic analysis, simultaneous measurement of nascent RNA and mature RNA in single cells is greatly desired. However, the majority of single-cell RNA-seq chemistry only captures mature RNA species to measure gene expressions. Here, we develop a one-step total-RNA chemistry-based scRNA-seq method: snapTotal-seq. We benchmarked this method with multiple single-cell RNA-seq assays in their performance in kinetic analysis of cell cycle by RNA velocity. Next, with LASSO regression between transcription factors, we identified the critical regulatory hubs mediating the cell cycle dynamics. We also applied snapTotal-seq to profile the oncogene-induced senescence and identified the key regulatory hubs governing the entry of senescence. Furthermore, from the comparative analysis of nascent RNA and mature RNA, we identified a significant portion of genes whose expression changes occurred in mature RNA but not to the same degree in nascent RNA, indicating these gene expression changes are mainly controlled by post-transcriptional regulation. Overall, we demonstrate that snapTotal-seq can provide enriched information about gene regulation, especially during the transition between cell states.

genomics↗

bioRxiv2023

Characterization of Cancer Evolution Landscape Based on Accurate Detection of Somatic Mutations in Single Tumor Cells

Accurate detection of somatic mutations in single tumor cells is greatly desired as it allows us to quantify the single-cell mutation burden and construct the mutation-based phylogenetic tree. Here we developed scNanoSeq chemistry and profiled 842 single cells from 21 human breast cancer samples. The majority of the mutation-based phylogenetic trees comprise a characteristic stem evolution followed by the clonal sweep. We observed the subtype-dependent lengths in the stem evolution. To explain this phenomenon, we propose that the differences are related to different reprogramming required for different subtypes of breast cancer. Furthermore, we reason that the time that the tumor-initiating cell took to acquire the critical clonal-sweep-initiating mutation by random chance set the time limit for the reprogramming process. We refer to this model as a reprogramming and critical mutation co-timing (RCMC) subtype model. Next, in the sweeping clone, we observed that tumor cells undergo a branched evolution with rapidly decreasing selection. In the most recent clades, effectively neutral evolution has been reached, resulting in a substantially large number of mutational heterogeneities. Integrative analysis with 522-713X ultra-deep bulk whole genome sequencing (WGS) further validated this evolution mode. Mutation-based phylogenetic trees also allow us to identify the early branched cells in a few samples, whose phylogenetic trees support the gradual evolution of copy number variations (CNVs). Overall, the development of scNanoSeq allows us to unveil novel insights into breast cancer evolution.

genomics↗

bioRxiv2022

Fingerprint SRS Imaging Unveils Ergosteryl Ester as a Metabolic Signature of Azole-Resistant Candida albicans

Candida albicans (C. albicans), a major fungal pathogen, causes life-threatening infections in immunocompromised individuals. Fluconazole (FLC) is recommended as first-line therapy for treatment of invasive fungal infections. Yet, the widespread use of FLC has resulted in increased antifungal resistance among different strains of Candida, especially C. albicans, which is a leading source of hospital-acquired infections. Here, by hyperspectral stimulated Raman scattering (hSRS) imaging of single fungal cells in the fingerprint window and pixel-wise spectral unmixing, we report aberrant ergosteryl ester accumulation in azole-resistant C. albicans compared to azole-susceptible species. This accumulation was a consequence of de novo lipogenesis. Lipid profiling by mass spectroscopy identified ergosterol oleate to be the major species stored in azole-resistant C. albicans. Blocking ergosterol esterification by oleate and suppressing sterol synthesis by FLC synergistically suppressed the viability of C. albicans in vitro and limited the growth of biofilm on mouse skin in vivo. Our findings highlight a metabolic marker and a new therapeutic strategy for targeting azole-resistant C. albicans by interrupting the esterified ergosterol biosynthetic pathway. Significance StatementInvasive fungal infections and increasing antifungal resistance are emerging threats to public health with high morbidity and mortality. Despite the advances in azole resistance mechanisms, it remains unclear why some fungal species are intrinsically resistant to or easily acquire resistance to multiple antifungal drugs. Here, using fingerprint SRS microscopy, we uncovered a molecular signature, aberrant ergosteryl ester accumulation, linked to the azole resistance of Candida species. An antifungal treatment strategy combining oleate (inhibitor of ersgosteryl esterification) and azole significantly attenuates the azole resistance and the viability of C. albicans in vitro and in vivo. Our work opens a new way to detect and treat azole-resistant fungal infections by targeting ergosterol metabolism.

microbiology↗

bioRxiv2020

Single-PanIN-seq Unveils that ARID1A Deficiency Promotes Pancreatic Tumorigenesis by Attenuating KRAS Induced Senescence

ARID1A is one of the most frequently mutated epigenetic regulators in a wide spectrum of cancers. Recent studies have shown that ARID1A deficiency induces global changes in the epigenetic landscape of enhancers and promoters. These broad and complex effects make it challenging to identify the driving mechanisms of ARID1A deficiency in promoting cancer progression. Here we identified the anti-senescence effect of ARID1A deficiency in the progression of pancreatic intraepithelial neoplasia (PanIN) by profiling the transcriptome of individual PanINs in the mouse model. Interestingly, we found that ARID1A deficiency upregulates the expression of Aldehyde dehydrogenase ALDH1A1, which plays an essential role in attenuating the senescence induced by oncogenic KRAS. Despite that ALDH proteins have been commonly used as cancer stem cell markers, their effect in promoting attenuation of senescence is not known before. Therefore, ALDH proteins could be considered a potential adjuvant drug target in treating pancreatic cancer.

cancer biology↗

bioRxiv2019

Topological Dependent Abundance of Spontaneous DNA Damage in Single Human Cells

In the studies of single-cell genomics, the large endeavor has been focused on the detection of the permanent changes in the genome. On the other hand, spontaneous DNA damage frequently occurs and results in transient single-stranded changes to the genome until they are repaired. So far, successful profiling of these dynamic changes has not been demonstrated by single-cell whole-genome amplification methods. Here we reported a novel single-cell WGA method: Linearly Produced Semiamplicon based Split Amplification Reaction (LPSSAR), which allows, for the first time, the genome-wide detection of the DNA damage associated single nucleotide variants (dSNVs) in single human cells. The sequence-based detection of dSNVs allows the direct characterization of the major damage signature that occurred in human cells. In the analysis of the abundance of dSNVs along the genome, we observed two modules of dSNV abundance, instead of a homogeneous abundance of dSNVs. Interestingly, we found that the two modules are associated with the A/B topological compartments of the genome. This result suggests that the genome topology directly influences genome stability. Furthermore, with the detection of a large number of dSNVs in single cells, we showed that only under a stringent filtering condition, can we distinguish the de novo mutations from the dSNVs and achieve a reliable estimation of the total level of de novo mutations in a single cell.

genomics↗

bioRxiv2019

Establishment of the trans-resveratrol-induced mouse pulmonary fibrosis model and its comparison with the bleomycin-induced model

Pulmonary fibrosis (PF) is a progressive, fatal disease, and its pathogenic mechanism has not yet been identified. The bleomycin (BLM)-induced animal model has several shortcomings that cannot be overcome. We accidentally found that the continuous oral administration of trans-resveratrol (TR) at levels above the prescribed dose can induce PF within a certain period of time, and this model can be successfully replicated in mice, as indicated by the hydroxyproline (HYP) test and pathological analysis. The TR model requires no anesthesia or surgery and thus causes less damage to mice than the BLM model. The progress of fibrosis in the TR model was slow but progressed steadily compared with the BLM model, and the TR model was more comparable to human PF. Although the pathogenesis is not understood, the TR-induced PF model indicated that there may be a close relationship between PF and tumors and antitumor drugs, which requires further exploration.

pharmacology and toxicology↗

bioRxiv2019

Photo-Disassembly of Membrane Microdomains Revives Conventional Antibiotics against MRSA

Confronted with the rapid evolution and dissemination of antibiotic resistance, there is an urgent need to develop alternative treatment strategies for drug-resistant pathogens. Here, we present an unconventional approach to restore the susceptibility of methicillin-resistant S. aureus (MRSA) to a broad spectrum of conventional antibiotics via photo-disassembly of functional membrane microdomains. The photo-disassembly of microdomains is based on effective photolysis of staphyloxanthin, the golden carotenoid pigment that gives its name. Upon pulsed laser treatment, cell membranes are found severely disorganized and malfunctioned to defense antibiotics, as unveiled by membrane permeabilization, membrane fluidification, and detachment of membrane protein, PBP2a. Consequently, our photolysis approach increases susceptibility and inhibits development of resistance to a broad spectrum of antibiotics including penicillins, quinolones, tetracyclines, aminoglycosides, lipopeptides, and oxazolidinones.\n\nOne Sentence SummaryUsing photons to crash S. aureus cell membrane and its formidable defense against a broad spectrum of antibiotics.

microbiology↗