Biology subjects

Wang, L.-C.

Publications and source records attributed to Wang, L.-C..

8 recordsLinked to original sources

bioRxiv2026

An integrated genome-wide resource reveals distinct replication environments of DNA breakage in human cancer cell lines

Replication stress is a major source of genome instability in cancer, yet the genomic features that determine where DNA double-strand breaks (DSBs) arise remain incompletely defined. Here, we establish an integrated genome-wide resource of DSBs, DNA replication, replication timing, transcription, and R-loops in two widely used cancer cell lines, U2-OS and HeLa, under steady-state conditions and following prolonged low-dose DNA polymerase inhibition. We combine these datasets with systematic statistical testing and comparative analytical approaches to define the replication environments associated with genome fragility. Endogenous DSBs preferentially accumulated at origin-rich initiation zones, where R-loops were enriched, whereas prolonged DNA polymerase inhibition redirected DSB formation toward origin-poor, late-replicating regions. Among the replication features examined, replication initiation zones and late-replicating areas were most sensitive to prolonged replication stress. R-loops were specifically enriched at initiation zones but depleted from late-replicating regions and recurrent DNA break clusters (RDCs), demonstrating that their association with genome fragility is context dependent. Replication stress further induced RDCs within long, actively transcribed genes, while their locations only partially overlapped with common fragile sites. Functional analyses identified MUS81 as a major regulator of RDC formation. MUS81 loss increased RDCs, whereas restoration of its catalytic activity suppressed them, indicating that MUS81 resolves replication intermediates before they persist into late-replicating fragile regions. Together, this resource and analytical framework provide a systematic basis for dissecting how replication architecture, transcription, and DNA processing shape genome fragility in cancer cells.

genomics↗

bioRxiv2026

Multiomic Spatial Imaging Assay (MSIA) -- A High-plex In Situ Detection Method for mRNAs, Proteins, and Protein-Protein Interactions using Manual And Semi-Automated Workflows

We report Multiomics Spatial Image Analysis (MSIA), a suite of technologies that include streamlined manual and semi-automated workflows to image 100s of RNAs from fresh frozen and formalin-fixed paraffin-embedded (FFPE) samples, contextualize RNAs with select protein markers including imaging synaptic protein interactions, a data analysis pipeline that includes corrections for chromatic aberration, algorithms for image stitching, deep learning models for image analysis (cell segmentation and RNA dot detection using hundreds of RNAscope images) from multiple stain-image cycles and proof of concept for a language model trained on extensive Parkinsons Disease (PD) literature. We used the language model to identify potential new biomarkers that were confirmed in MPTP-treated mouse model of PD. Furthermore, by incorporating more stain-image cycles alongside an additional fluorescent channel and advanced error-correcting decoding schemes, the MSIA workflow demonstrates the scalability to potentially quantify over 1,000 genes.

neuroscience↗

bioRxiv2026

Investigating the skin response of Striped Catfish to acute ammonia stress reveals a potential exosome-based ammonia excretion system

Ammonia can rapidly accumulate in intensive aquaculture and pose serious threats to fish health. Fish skin functions as a vital immune-related organ and a significant surface barrier against ammonia; however, little is known about the skins response and to acute ammonia stress. In this study, Striped catfish were exposed to a half-lethal concentration of ammonia to evaluate skin responses. We found generalized inflammation in the liver, spleen, and skin. However, the skin tissue showed subtle signs of damage, with tissue ammonia concentration accumulating and then decreasing. Further transcriptomic analysis of skin gene function suggested a hypothesized ammonia regulation occurring within cell compartments. Cellular examination by transmission electron microscopy further showed that accumulated exosome-suspecting vesicles near the epithelial surface were associated with ammonia regulation during acute ammonia stress. Using a newly established Striped catfish skin epithelial cell line, along with an exosome inhibitor, confirms the presence of exosome vesicles and their role in ammonia excretion. In conclusion, acute ammonia stress induces inflammation in Striped catfish skin, while active ammonia excretion via exosomes may alleviate ammonia accumulation, thereby maintaining skin tissue integrity. This study explores Striped catfish skin responses to acute ammonia stress and highlights a newly identified mechanism of ammonia regulation in the skin. HighlightsO_LIFish skin can regulate ammonia concentrations and stress. C_LIO_LIExosomal vesicles are involved in the excretion of ammonia from the skin. C_LI

immunology↗

bioRxiv2025

Female sex hormones enhance gonococcal colonization at the endocervix by modifying cervical mucus

Neisseria gonorrhoeae is a human-exclusive pathogen that causes gonorrhea. Gonococci (GC) initiate female infections by colonizing the cervix, which can remain asymptomatic, cause cervicitis, or ascend to the upper female reproductive tract (FRT), leading to severe tissue damage. The FRT undergoes sex hormone-mediated changes during the menstrual cycle, which have long been implicated in the vulnerability to GC infection. One of the major changes is the increase and decrease in the production of the gel-forming mucin MUC5B by the endocervix in response to the level of estradiol (E2). This study examined the impact of sex hormones on GC infection of the human cervix, utilizing a human cervical tissue explant model. Tissue explants were treated without and with E2 alone or in combination with progesterone (E2+P4) to mimic various menstrual cycle phases. Treatment of E2 or E2+P4 enhanced GC colonization at the endocervix exclusively, but did not affect epithelial transmigration. While both treatments increased the number of GC microcolonies, E2+P4 increased GC colony size on the endocervical epithelium. These increases were independent of GC host receptors, carcinoembryonic antigen-related cell adhesion molecules. GC effectively diffused through cervical mucus to interact with the cervical epithelium under all hormone conditions and through mucin hydrogels with different MUC5B and MUC5AC compositions. Mucus gels collected from cervical explants and animal mucin mixtures enhanced GC aggregation in vitro. GC diffusion through mucin-hydrogels and aggregation in the presence of cervical mucus or animal mucins decreased as the MUC5B concentration increased. Our results suggest that female sex hormones promote GC colonization at the human endocervix by modulating the cervical mucus production, regulating womens susceptibility to GC infection, and further reveal the ability of GC to evade the mucus defense barrier for infection. Author SummaryNeisseria gonorrhoeae is a bacterial pathogen that primarily infects the human genital and female reproductive tracts, causing gonorrhea. While this bacterium can infect both men and women, the infection can lead to severe and permanent damage to womens reproductive systems. Currently, the relationship of gonococcal infection with the menstrual cycle is unknown. Here, we utilize a human cervical tissue explant model that mimics gonococcal infection in women to examine the impact of female sex hormones that drive the menstrual cycle on gonococcal infection. We found that estrogen alone or in combination with progesterone enhanced gonococcal colonization, increasing both the number and size of bacterial microcolonies on the cervical luminal surface, through regulating mucus production. Gonococci effectively penetrate through mucus layers to reach cervical epithelial cells and also prefer to aggregate with each other in the presence of mucus. Our results reveal that hormone-regulated mucus production changes the vulnerability of women to gonococcal infection, and that gonococci convert the mucus defense barrier into a colonization facilitator.

microbiology↗

bioRxiv2025

Adaptive Clonal Expansion Shapes Brain Development

Embryonic neural stem/progenitor cells (NSPCs) exhibit remarkable proliferative plasticity, allowing them to fully recover neuronal populations even after substantial cell loss 1,2. However, it remains unclear whether all embryonic NSPCs respond to brain lesions. To address this, we developed a mouse model to investigate NSPC proliferation dynamics, hypothesizing that the loss of progenitor cells would induce fitness competition among NSPCs. In this model, half of the founder NSPCs were ablated using diphtheria toxin A at the onset of neurogenesis, yet the surviving cells regenerated a brain containing all neuronal types within five of the total twenty embryonic days. Analysis of allelic variants revealed overrepresented somatic variants, indicating that only a small fraction of NSPCs underwent significant clonal expansion during early neurogenesis. Modelling proliferation dynamics predicted that as few as 10% of NSPCs could produce 83% of neurons by the time of birth. Single nucleotide substitution analysis suggested a potential link to oxidative metabolism in some of the expanded clones. Moreover, single-cell transcriptomics showed delayed development and a reduced NSPC pool as consequences of adaptive clonal expansion. Our findings highlight that NSPC exhibit varying expansion potential and that adaptive clonal expansion indirectly altered neuronal cell composition in the brain.

developmental biology↗

bioRxiv2023

Transcription-Replication Conflict Shapes DNA Break Dynamics

Recurrent DNA break clusters (RDCs) are replication-transcription collision hotspots; many are unique to neural progenitor cells. Through high-resolution replication sequencing and a capture-ligation assay in mouse neural progenitor cells experiencing replication stress, we unraveled the replication features dictating RDC location and orientation. Most RDCs occur at the replication forks traversing timing transition regions (TTRs), where sparse replication origins connect unidirectional forks. Leftward-moving forks generate telomere-connected DNA double-strand breaks (DSBs), while rightward-moving forks lead to centromere-connected DSBs. Strand-specific mapping for DNA-bound RNA revealed co-transcriptional dual-strand DNA:RNA hybrids present at a higher density in RDC than in other actively transcribed long genes. In addition, mapping RNA polymerase activity revealed that head-to-head interactions between replication and transcription machinery resulted in 60% DSB contribution to the head-on compared to 40% for co-directional. Our findings revealed TTR as a novel fragile class and highlighted how the linear interaction between transcription and replication impacts genome stability.

genomics↗

bioRxiv2022

Aeromonas hydrophila induces skin disturbance through mucosal microbiota dysbiosis in Pangasianodon hypophthalmus

Bacterial pathogens are well-equipped to adhere to and initiate infection in teleost fish. The fish skin mucus serves as the first barrier against environmental pathogens. The mucus harbors commensal microbes that form the microbiota, impacting the host physiological and immunological regulation. However, how the skin mucosal microbiota responds to the presence of pathogens remains largely unexplored. Thus, little is known about the status of skin mucus prior to the infection with noticeable symptoms. In this study, we aim to investigate the interaction between pathogen and skin mucosal microbiota, as well as the fish skin immune responses in the presence of pathogens. By challenging striped catfish (Pangasianodon hypophthalmus) with different concentrations of bacterial pathogen Aeromonas hydrophila (AH), the skin immune response and the mucosal microbiota were examined by qPCR and 16S rRNA gene sequencing analysis. We found a pathogen concentration able to stimulate the skin immune response associated with the significant mucosal microbiota change and re-confirmed with the ex vivo fish skin model. Further analysis indicated that the change was attributed to the significant increase in opportunistic pathogens over AH. We concluded that the presence and increase of AH results in dysbiosis of mucosal microbiota that can stimulate skin immune response. We believe our work can shed some light on host-pathogen-commensal microbiota interaction and therefore contribute to aquaculture infection prevention. IMPORTANCEThe fish skin mucosal microbiota is essentially the first barrier in response to the presence of pathogens. This study is the first study to elucidate the interaction between the AH, the skin mucosal microbiota, and the striped catfish skin at the initiation stage of infection. Our study provides a platform to study both the correlation and causation of the interaction between pathogen, the fish skin, and the skin mucosal microbiota. This work provides information that changes in the AH-induced mucosal microbiota result in skin disturbance with immune stimulation.

microbiology↗

bioRxiv2021

Gonococcal invasion into epithelial cells depends on both cell polarity and ezrin

Neisseria gonorrhoeae (GC) establishes symptomatic infection in women from the cervix, lined with heterogeneous epithelial cells from non-polarized stratified at the ectocervix to polarized columnar at the endocervix. We have previously shown that GC differentially colonize and transmigrate across the ecto and endocervical epithelia. However, whether and how GC invade into heterogeneous cervical epithelial cells is unknown. This study examined GC entry of epithelial cells with various properties, using human cervical tissue explant and non-polarized/polarized epithelial cell line models. While adhering to non-polarized and polarized epithelial cells at similar levels, GC invaded into non-polarized more efficiently than polarized epithelial cells. The enhanced GC invasion in non-polarized epithelial cells was associated with increased ezrin phosphorylation, F-actin and ezrin recruitment to GC adherent sites, and the elongation of GC-associated microvilli. Inhibition of ezrin phosphorylation inhibited F-actin and ezrin recruitment and microvilli elongation, leading to a reduction in GC invasion. The reduced GC invasion in polarized epithelial cells was associated with non-muscle myosin II-mediated F-actin disassembly and microvilli ablation at GC adherence sites. Surprisingly, intraepithelial GC were only detected inside epithelial cells shed from the cervix, but neither in the ectocervix nor the endocervix, by immunofluorescence microscopy. We observed similar ezrin and F-actin recruitment in exfoliated cervical epithelial cells but not in those that remained in the ectocervical epithelium, as the luminal layer of ectocervical epithelial cells expressed ten-fold lower levels of ezrin than those beneath. However, GC inoculation induced F-actin reduction and myosin recruitment in the endocervix, similar to what was seen in polarized epithelial cells. Thus, polarized expression of ezrin at the apical surface of epithelial cells inhibits GC invasion, while non-polarized expression of ezrin promotes GC invasion by driving actin accumulation and microvilli elongation.

cell biology↗