Biology subjects

Chen, J.-W.

Publications and source records attributed to Chen, J.-W..

8 recordsLinked to original sources

bioRxiv2026

Circular RNA aptamers act as superb sub-stoichiometric chaperones to prevent cytosolic TDP-43 condensation

Pathological protein misfolding and aggregation underlie many devastating human diseases, yet strategies to selectively neutralize aggregation-prone protein states without perturbing their normal functions remain limited. Here we identify loosely structured circular RNA (cRNA) aptamers, circT3 and its minimized 116-nt variant circT3-M3, as superb sub-stoichiometric RNA chaperones that suppress pathological assembly of TAR DNA-binding protein 43 (TDP-43), a defining feature of amyotrophic lateral sclerosis and frontotemporal dementia, in vitro and in cells. Rather than acting through simple stoichiometric sequestration, these cRNA aptamers engage TDP-43 transiently and iteratively through functionally and pathologically important residues in the RRM1 domain. Such interaction enables a single cRNA aptamer to promote rapid and multiple RRM1-dependent homomeric assembly, thereby stabilizing TDP-43 in a soluble oligomeric state to outcompete the C-terminal prion-like domain-driven condensation and supersaturation. Together, our findings establish cRNA aptamers as highly efficient subcellular RNA chaperones with exceptionally potent low-dose activity and highlight their promise as next-generation RNA therapeutics for certain protein-aggregation disorders.

molecular biology↗

bioRxiv2025

Characterization of Clinical Fusobacterium nucleatum Isolates from Oral Squamous Cell Carcinoma Patients

Fusobacterium nucleatum (Fn), a Gram-negative anaerobe primarily residing in the oral cavity, has garnered increasing attention for its role in a broad spectrum of human diseases. While typically absent or rarely detected outside the oral cavity in healthy individuals, Fn is frequently found at extra-oral sites under disease conditions and has been implicated in cancer progression and prognosis1. In oral squamous cell carcinoma (OSCC), the abundance of Fn significantly increases as the disease progresses, promoting cell invasion and metastasis. Furthermore, substantial evidence links Fn to accelerated tumor growth and metastatic progression in colorectal cancer (CRC), where its presence is also associated with chemotherapy resistance and poor prognosis. Here, to further elucidate the pathogenic mechanisms of Fn in cancer progression, this study characterized the physiological traits, virulence factor expression, and impacts on cancer cells of 10 Fn strains, including two well-characterized ATCC strains and eight clinical isolates. The clinical isolates consisted of three strains from saliva samples of 117 OSCC patients and five strains from 160 non-cancer individuals. Results indicated that oral isolates, regardless of disease origin, all belong to Fn subspecies polymorphum. The ATCC strains (23726 and 25586) exhibited shorter cell lengths and faster growth rates compared to the clinical isolates. Both ATCC strains formed stable biofilms and expressed key virulence genes, including aim1, fadA, fomA, and radD. All isolates tested showed sensitivity to a panel of eight different antibiotics. Interestingly, only one clinical isolate displayed similar stimulation of CRC cell migration as the two ATCC strains, while the other seven displayed no such ability. Collectively, these findings suggest that the most virulent strains, in terms of biofilm formation and virulence gene expression, are not necessarily the most pathogenic in the context of cancer cell interactions. Future pan-genomic analyses, incorporating whole-genome sequencing of the clinical isolates, will aim to delineate the genetic determinants contributing to the carcinogenic potential of Fn.

microbiology↗

bioRxiv2024

The protease interpain A of Prevotella intermedia promotes human OSCC cells proliferation and migration

Prevotella intermedia has been increasingly recognized as a potential contributor to oral squamous cell carcinoma (OSCC), yet the underlying mechanisms remain poorly defined. In this study, we identified interpain A (InpA), a cysteine protease secreted by P. intermedia, as a key virulence factor that promotes oral epithelial cell proliferation and OSCC cell migration. Conditioned medium (CM) derived from P. intermedia strain ATCC 25611 enhanced proliferation in both normal oral keratinocytes (SG cells) and OSCC cell lines (SCC-15, SAS). The pro-proliferative effect was abolished upon heat inactivation of the CM and inhibited by E64, a cysteine protease inhibitor, and FSLLRY-NH2, a PAR-2 antagonist, suggesting the involvement of protease-activated receptor-2 (PAR-2) signaling. InpA was highly secreted by strain ATCC 25611 but not by clinical isolates lacking proliferative effects, and RT-qPCR confirmed higher inpA expression in OSCC-derived strains compared to non-cancer controls. Recombinant InpA (rInpA) mimicked the effect of CM, inducing proliferation and migration, which were blocked by PAR-2 inhibition. Transcriptomic and protein-level screening in SG cells revealed activation of EGFR and downstream RAS-RAF-MEK-ERK signaling. Furthermore, in a colorectal cancer (CRC) mouse model, oral administration of P. intermedia led to increased tumor formation, suggesting a broader oncogenic potential. These findings highlight InpA as a PAR-2-activating protease that may contribute to OSCC and potentially other cancers associated with oral microbiota dysbiosis.

cancer biology↗

bioRxiv2024

Combination of mitomycin C and low-dose metronidazole synergistically against Clostridioides difficile infection and recurrence prevention

Clostridioides difficile is an anaerobic, spore-forming, Gram-positive pathogen responsible for various conditions from mild diarrhea to severe toxic megacolon and potentially death. Current treatments for C. difficile infection (CDI) rely on antibiotics like vancomycin and metronidazole (MTZ); however, the high doses required often disrupt gut microbiota, leading to a high recurrence rate. Mitomycin C (MMC), a chemotherapy drug approved by the FDA, is known for inducing phage production in lysogenic bacterial strains, effectively targeting the host bacteria. Given that 70% of C. difficile strains harbor prophages, this study investigates MMCs potential to enhance antibiotic efficacy against CDI. Our in vitro experiments indicate that MMC acts synergistically with MTZ to inhibit the growth of C. difficile strain R20291. Furthermore, this combination decreases biofilm-resident vegetative cell resistance and reduces the MTZ concentration needed to kill C. difficile in stool samples ex vivo. In a CDI mouse relapse model, in vivo results show that MMC combined with a low dose of MTZ significantly improves survival rates and reduces fecal spore counts after antibiotic treatment. Overall, these findings suggest that a low-dose combination of MMC and MTZ offers enhanced therapeutic efficacy for CDI, both in vitro and in vivo, and may provide a promising new approach for treatment.

microbiology↗

bioRxiv2024

The tumor-maintaining function of UTX/KDM6A in DNA replication and the PARP1-dependent repair pathway

Histone H3K27 demethylase UTX (aka KDM6A) is mutated in many human cancers, suggesting its tumor suppressive role during cancer development. However, most tumors still express wild-type UTX/KDM6A and its function is not always linked to tumor suppression. Here, we present evidence of UTX/KDM6As role in sustaining tumor growth, revealing its function in tumor maintenance. We find that UTX/KDM6A sustains tumor cell cycling and survival via regulating DNA replication-associated transcriptional programs in a demethylase-independent manner. UTX/KDM6A can also interact with PARP1 and facilitate its recruitment to DNA lesions. Therefore, UTX/KDM6A depletion disrupts DNA replication and repair pathways, activating ATM-CHK2 and ATR-CHK1 signaling pathways and triggering S and G2/M checkpoints, leading to a pronounced defect in tumor growth. Analysis of human cancer xenograft models further demonstrates that knockdown of UTX/KDM6A by RNA-interference, rather than inhibition of its enzymatic activity via GSK-J4, shows potent anticancer effects. Dual inhibition of UTX/KDM6A and ATR further demonstrates synergistic anticancer activities. Our work highlights UTX/KDM6A as a potential therapeutic target for cancer treatment, especially when combined with ATR inhibition. HighlightsO_LIUTX/KDM6A contributes to tumor maintenance by promoting the growth and survival of tumor cells C_LIO_LITumor cells rely on UTX/KDM6A to maintain DNA replication, cell cycling, and DNA damage repair C_LIO_LIUTX/KDM6A depletion triggers S and G2/M checkpoints via activating ATM-CHK2 and ATR-CHK1 signaling pathways C_LIO_LITargeting UTX/KDM6A may prove to be an innovative strategy for cancer therapy, whether employed independently or in conjunction with ATR inhibitors. C_LI The Paper ExplainedO_ST_ABSProblemC_ST_ABSThe aggressive growth of tumors relies significantly on heightened proliferation rates and genomic instability, which necessitate robust DNA replication machinery and efficient DNA damage repair mechanisms for tumor cell survival and proliferation. UTX/KDM6A, a histone demethylase central to chromatin and epigenetic regulation, is commonly mutated in various human cancers. However, its role as a tumor suppressor or promoter remains unclear across different cancer contexts. This study delves into the potential tumor-maintaining role of UTX/KDM6A in cancer progression and tumorigenesis, establishing the mechanistic foundation for its tumor-promoting function. ResultsWe uncover UTX/KDM6As crucial role in tumor maintenance via its participation in DNA replication and repair pathways. Surprisingly, we find that its histone demethylase activity is dispensable for these functions, implying an alternative role as a scaffold protein. Consequently, our findings suggest that targeting the entire UTX/KDM6A gene or protein, rather than inhibiting its enzymatic activity, holds promise as a therapeutic strategy for tumors dependent on its tumor-maintaining function. ImpactThis study unveils UTX/KDM6As multifaceted role in cancer progression, shedding light on its diverse contributions to tumorigenesis. Our findings suggest promising therapeutic strategies for cancer treatment, highlighting the importance of targeting UTX/KDM6A and its impact on DNA replication and repair pathways. These discoveries set the stage for further exploration of UTX/KDM6A-mediated mechanisms in clinical settings, indicating potential applications in future clinical trials and combination therapy strategies.

cancer biology↗

bioRxiv2023

Phage transcriptional regulator X (PtrX)-mediated augmentation of toxin production and virulence in Clostridioides difficile strain R20291

Clostridioides difficile is a Gram-positive, anaerobic, and spore-forming bacterial member of the human gut microbiome. The primary virulence factors of C. difficile are toxin A and toxin B. These toxins damage the cell cytoskeleton and cause various diseases, from diarrhea to severe pseudomembranous colitis. Evidence suggests that bacteriophages can regulate the expression of the pathogenic locus (PaLoc) genes of C. difficile. We previously demonstrated that the genome of the C. difficile strain RT027 (NCKUH-21) contains a prophage-like DNA sequence, which was found to be markedly similar to that of the {varphi}CD38-2 phage. In the present study, we investigated the mechanisms underlying the {varphi}NCKUH-21-mediated regulation of the pathogenicity and the PaLoc genes expression in the lysogenized C. difficile strain R20291. The carriage of {varphi}NCKUH-21 in R20291 cells substantially enhanced toxin production, bacterial motility, biofilm formation, and spore germination in vitro. Subsequent mouse studies revealed that the lysogenized R20291 strain caused a more severe infection than the wild-type strain. We screened three {varphi}NCKUH-21 genes encoding DNA-binding proteins to check their effects on PaLoc genes expression. The overexpression of NCKUH-21_03890, annotated as a transcriptional regulator (phage transcriptional regulator X, PtrX), considerably enhanced toxin production, biofilm formation, and bacterial motility of R20291. Transcriptome analysis further confirmed that the overexpression of ptrX led to the upregulation of the expression of toxin genes, flagellar genes, and csrA. In the ptrX-overexpressing R20291 strain, PtrX influenced the expression of flagellar genes and the sigma factor gene sigD, possibly through an increased flagellar phase ON configuration ratio. Author SummaryClostridioides difficile is a Gram-positive, spore-forming anaerobic bacterium that can lead to antibiotic-associated diarrhea and pseudomembranous colitis. During the C. difficile infection (CDI), the major virulence factor is the secretion of two exotoxins, toxin A and B, to destroy host intestinal epithelium cells. The investigation of bacteriophages affecting the toxicity of C. difficile has increasingly been research. We previously isolated a C. difficile clinical strain NCKUH-21, which carried a phage-like DNA sequence, and named it {varphi}NCKUH-21. However, whether this prophage could enhance the virulence of C. difficile and the mechanism for regulating the pathogenicity are still unclear. We successfully created a {varphi}NCKUH-21-lysogenized R20291 strain and showed that lysogenized R20291 performed stronger pathogenicity than the wild-type R20291. We found that a {varphi}NCKUH-21-specific protein (encoded by NCKUH-21_03890 gene) might influence C. difficile flagellar phase variation to promote toxin production further. These findings are expected to clarify the mechanism for controlling the pathogenicity of {varphi}NCKUH-21-infected C. difficile. Moreover, we also believe that the existence of hypervirulent C. difficile strains carrying a prophage should be monitored proactively in hospitals to prevent severe CDI.

microbiology↗

bioRxiv2023

Mechanism of glucocorticoid receptor activation regulated expression of thrombospondin-1

Objective: Thrombospondin-1 (TSP-1) plays an important role in platelet activation and aggregation and aggravates thrombosis. Chronic stress can cause a variety of diseases, including coagulation disorders, increased thrombosis, atherosclerosis, and a series of cardiovascular and cerebrovascular diseases. However, it is still unknown how chronic stress regulates the expression of TSP-1 after glucocorticoid receptor activation. Approach and Results: rats chronic unpredictable mild stress model was applied and the changes of TSP-1 and microRNAs in plasma were examined. Effects of glucocorticoid receptor activation on human umbilical vein endothelial cells and platelets were observed. Glucocorticoid receptor (GR) activation upregulated the expression of TSP-1 and downregulated the expression of microRNA-1-3p accompanied with increase of phosphorylation of p38 mitogen-activated protein kinase (MAPK) and argonaute-2 (AGO-2). Blockade of p38 MAPK phosphorylation resulted in decrease of phosphorylation level of AGO-2, increase of microRNA-1-3p expression, and decrease of TSP-1 expression. Transfection of AGO-2 Y393F point mutant plasmid, increased microRNA-1-3p expression and decreased TSP-1 expression, transfection of microRNA-1-3p mimic also decreased TSP-1 expression, while transfection of microRNA-1-3p inhibitor increased TSP-1 expression. Finally, GR activation led to an increase in the phosphorylation level of p38 MAPK in platelets and an increase in the level of TSP-1 in the supernatant. Conclusions: our study demonstrates that GR activation in HUVEC stimulates the phosphorylation of p38 MAPK, which in turn promotes the phosphorylation of AGO-2 and inhibits the maturation of microRNA-1-3p, leading to elevated expression of TSP-1, GR activation in platelets leads to the release of TSP-1. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=147 SRC="FIGDIR/small/536820v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@86e8ecorg.highwire.dtl.DTLVardef@126094eorg.highwire.dtl.DTLVardef@2d13c3org.highwire.dtl.DTLVardef@16c79c3_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO HSS: Hydrocortisone sodium succinate C_FIG

pathology↗

bioRxiv2022

Natural selection and neutral mutations through the lens of viruses

The Neutral Theory and the Modern Synthesis, a modified version of Darwins theory, have been arguing for decades about the influence of natural selection on molecular evolution1-10. Here we elucidate through the lens of viruses that a frequently used method11-17 employing the ratio of nonsynonymous versus synonymous substitution rates has dramatically underestimated the influence of natural selection on molecular evolution. We also find novel evidence from viral sequences to support the co-existence of the crucial role of natural selection in molecular evolution and the ubiquity of neutral mutations. The co-existence has perplexed biologists for decades2,5,7. We then elucidate for the first time the causality between natural selection and the ubiquity of neutral mutations with a novel interpretation of natural selection. This novel interpretation incorporates biochemistry, genetics, epigenetics, physiology, and dynamics. It holds that natural selection acts directly on the overall phenotypic performance of organisms and indirectly on each genomic site or phenotypic trait. It highlights not only restrictions and competitions but also freedom and diversity, besides the overall harmonious development of organisms and human societies. Therefore, this novel interpretation could have far-reaching implications in the natural and social sciences.

evolutionary biology↗