Biology subjects

Chen, L.-Y.

Publications and source records attributed to Chen, L.-Y..

11 recordsLinked to original sources

bioRxiv2026

Integrative Transcriptomic and Functional Analysis Reveals Fatty Acyl Elongases Involved in Sex Pheromone Biosynthesis in Rice Leaffolder, Cnaphalocrocis medinalis (Lepidoptera: Pyraloidea)

Elongases are essential enzymes in the biosynthesis of sex pheromones in many lepidopteran species. Together with desaturases, they determine the carbon skeletons of many pheromone precursors, thereby contributing to the production of species-specific chemical signals. However, to date, such fatty acyl elongase gene has not been functionally characterized. The rice leaffolder, Cnaphalocrocis medinalis, utilizes a blend of C18 monounsaturated aldehydes and alcohols as its sex pheromone, implying a critical elongation step from C16 precursors. In this study, we performed pheromone gland transcriptome analysis and identified 45 candidate biosynthetic genes. Functional assays in Nicotiana benthamiana showed that the {Delta}11 desaturase Cmed070400 produces (Z)-11-hexadecenoic acid, which serves as the substrate for elongation. Multiple elongases catalyzed its conversion to (Z)-13-octadecenoic acid, with Cmed092440 showing the highest activity. These findings provide the first experimental evidence for elongase-mediated formation of C18 pheromone precursors in C. medinalis. The identification of a minimal set of functionally active enzymes further enables reconstruction of this pathway in plant systems, offering a basis for sustainable production of pheromone precursors for pest management applications.

zoology↗

bioRxiv2026

Co-option of ILF2/3 in primates restrains Alu hyper-editing to enable cell fate transitions

Understanding human specific mechanisms of cell fate control is essential for advancing developmental biology and regenerative medicine. Here, we identify the ILF2/3 complex as a critical regulator of primate cell fate transitions. Using genetically and epigenetically engineered gastruloids and adult stem cells, we show that ILF2/3 is required for gastrulation in primates but not mice, and for differentiation of adult progenitor cells. Mechanistically, ILF2/3 directly binds Alu elements in chromatin-associated RNAs and shields them from ADAR1-mediated adenosine-to-inosine (A-to-I) editing. Acute ILF2/3 degradation increases A-to-I editing at Alu elements, but not murine retrotransposons, leading to aberrant splicing and nonsense-mediated decay of transcripts encoding key chromatin regulators in primate cells. This in turn destabilizes the epigenetic landscape and blocks lineage commitment across all three germ layers. Re-expression of correctly spliced chromatin regulators rescues differentiation defects in ILF2/3-deficient cells, functionally linking Alu editing control to chromatin regulation and cell fate. These findings define an evolutionary mechanism that restrains retrotransposon-associated RNA editing to preserve proteome integrity and enable primate-specific developmental programs.

genetics↗

bioRxiv2025

Gut bacteria generate prodrugs in situ increasing systemic drug exposure

The human gut microbiome has been increasingly recognized as a metabolic compartment that influences health and therapeutic responses. While recent studies have cataloged diverse sets of drug biotransformation reactions as a result of microbial metabolism1-3, the pharmacological relevance of the resulting drug metabolites remains mostly uncharacterized. We investigated whether certain microbial drug metabolites can act as functional prodrugs. By systematically mining 871 putative drug metabolites produced by gut bacteria1, we identified microbial drug metabolites with key physicochemical properties of prodrugs. Using bacterial culturing, a genetic gain-of-function screen coupled to mass spectrometry and comparative genomics, we uncover that Bacteroidota bacteria encode conserved methyltransferases that can generate prodrugs through carboxyl methylation. As a case in point, we demonstrate that bezafibrate gets converted to a prodrug by a distinct bacterial enzyme, increasing epithelial drug permeability in vitro and systemic drug exposure in vivo in a gnotobiotic mouse model. Additionally, we tested 170 structurally and clinically diverse drugs, and demonstrate that microbial drug-prodrug conversion is a common result of gut bacterial drug biotransformation. Altogether, our findings suggest a novel mechanism of how the gut microbiota influences an individuals pharmacokinetics, and may generally cause interpersonal differences in microbiota-host metabolic interactions.

microbiology↗

bioRxiv2025

Orphan nuclear receptors recruit TRIM28 to promote telomeric H3K9me3 for the alternative lengthening of telomeres pathway

Alternative lengthening of telomeres (ALT) is a telomere maintenance mechanism deployed in embryonic stem cells and cancer cells. High levels of the heterochromatin mark H3 lysine 9 trimethylation (H3K9me3) at telomeres are critical for ALT, but how that is achieved remains unclear. Telomeric association of orphan nuclear receptors (NRs)--such as COUP-TF1, COUP-TF2, TR2, and TR4--has been shown previously to promote ALT activation. Here, we show that orphan NRs regulate telomeric H3K9me3 through TRIM28, a corepressor of ZNF transcription factors, to drive ALT. We report that H3K9me3 is induced by telomeric association of orphan NRs in cultured human fibroblast and ALT cancer cell lines. Moreover, TRIM28 is required for the orphan NR-induced H3K9me3 and ALT phenotypes. Importantly, physical interaction of TRIM28 with orphan NRs facilitates a telomeric localization of TRIM28. A TRIM28 variant defective in orphan NR interaction fails to localize to telomeres and is unable to promote H3K9me3 and ALT phenotypes. These findings indicate that telomeric orphan NRs recruit TRIM28, driving telomeric H3K9me3 and ALT activation, emphasizing the role of changes in chromatin structure in ALT activation.

molecular biology↗

bioRxiv2024

Histone variant H3.3 mediates cGAS-STING pathway activation via telomere deprotection

The telomere damage response is a critical mechanism regulating human aging and disease progression. Deprotected telomeres activate the cytosolic DNA-sensing cGAS-STING pathway; however, the underlying mechanism remains unclear. Here, we discover that histone H3.3 is required for cGAS-STING pathway activation in cells with deprotected telomeres. Expression of the TRF2 dominant-negative mutant, TRF2{Delta}B{Delta}M, induces telomere dysfunction in fibroblast cells, triggering cGAS-STING pathway activation and growth inhibition. Histone H3.3 depletion significantly reduces this activation, highlighting its critical role in linking telomere deprotection to the cGAS-STING-mediated innate immune signaling. Furthermore, we assess the role of histone H3.3 in telomere fusion. Our finding reveal that histone H3.3 regulates cGAS-STING signaling by controlling telomere fusion. Additionally, depletion of histone H3.3 chaperones, including ATRX, DAXX, and HIRA, inhibits telomere fusion and cGAS-STING pathway activation, underscoring the role of histone H3.3 in telomere maintenance and the DNA damage response. Collectively, our study establishes histone H3.3 as a key regulator of telomere fusion and telomere dysfunction-induced cGAS-STING pathway activation, revealing the correlation between histones and telomeric DNA damage response.

molecular biology↗

bioRxiv2024

Endothelial PHD2 deficiency induces apoptosis resistance and inflammation via AKT activation and AIP1 loss independent of HIF2α

BACKGROUNDIn hypoxic and pseudohypoxic rodent models of pulmonary arterial hypertension (PAH), hypoxia-inducible factor (HIF) inhibition reduces disease severity. However, HIF activation alone, due to genetic alterations or use of inhibitors of prolyl hydroxylase domain (PHD) enzymes, has not been definitively shown to cause PAH in humans, indicating the involvement of other mechanisms. METHODSPseudohypoxia was investigated in primary human lung endothelial cells by silencing PHD2, and in Tie2-Cre/Phd2 knockout mice, a rodent model of PAH. Lung vascular endothelial cells from PAH patients, and lung tissue from both SU5416/hypoxia PAH rats and PAH patients, were examined for validation. RESULTSPHD2 silencing or inhibition, while activating HIF2, induces apoptosis-resistance, hypo-proliferation, and IFN/STAT activation in endothelial cells, independent of HIF signaling. Mechanistically, PHD2 deficiency activates AKT and ERK, inhibits JNK, and reduces AIP1 (ASK1-interacting protein 1), all independent of HIF2. Like PHD2, AIP1 silencing affects these same kinase pathways and produces a similar dysfunctional endothelial cell phenotype, which can be partially reversed by AKT inhibition. These findings are corroborated in lung tissues of rodent PAH models and pulmonary vascular endothelial cells and tissues from PAH patients. CONCLUSIONSPHD2 deficiency in lung vascular endothelial cells induces an apoptosis-resistant, inflammatory, and hypo-proliferative phenotype. AKT activation and AIP1 loss, but not HIF signaling, drive these aberrant phenotypic changes. Our study suggests that HIF blockade alone may not suffice for PAH therapy; targeting PHD2, AKT, and AIP1 has the potential for developing more effective treatment. GRAPHIC ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/578286v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@1fd0a0borg.highwire.dtl.DTLVardef@19e6ba9org.highwire.dtl.DTLVardef@1ae2827org.highwire.dtl.DTLVardef@ce31ec_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIPHD2 silencing in human lung vascular endothelial cells suppresses apoptosis, inhibits proliferation, and activates STAT signaling, effects that persist despite HIF2 inhibition or knockdown. C_LIO_LIPHD2 silencing activates AKT and ERK, inhibits JNK, and decreases AIP1, all independently of HIF2 C_LIO_LILike PHD2, AIP1 silencing led to similar alterations in kinase signaling and endothelial cell phenotypes, which are partially reversed by ATK inhibition. C_LIO_LIThese in vitro findings align with observations in lung vascular endothelial cells and tissues from rodent models of PAH as well as PAH patients. C_LI

cell biology↗

bioRxiv2023

Hematopoietic Transfer of the Anti-Cancer and Lifespan-Extending Capabilities of A Genetically Engineered Blood System

A causal relationship exists among the aging process, organ decay and dis-function, and the occurrence of various diseases including cancer. A genetically engineered mouse model, termed Klf1K74R/K74R or Klf1(K74R), carrying mutation on the well-conserved sumoylation site of the hematopoietic transcription factor KLF1/ EKLF has been generated that possesses extended lifespan and healthy characteristics including cancer resistance. We show that the healthy longevity characteristics of the Klf1(K74R) mice, as exemplified by their higher anti- cancer capability, are likely gender-, age- and genetic background-independent. Significantly, the anti-cancer capability, in particular that against melanoma as well as hepatocellular carcinoma, and lifespan-extending property of Klf1(K74R) mice could be transferred to wild-type mice via transplantation of their bone marrow mononuclear cells at young age of the latter. Furthermore, NK(K74R) cells carry higher in vitro cancer cell-killing ability than wild type NK cells. Targeted/global gene expression profiling analysis has identified changes of the expression of specific proteins, including the immune checkpoint factors PDCD and CD274, and cellular pathways in the leukocytes of the Klf1(K74R) that are in the directions of anti-cancer and/or anti-aging. This study demonstrates the feasibility of developing a transferable hematopoietic/ blood system for long-term anti-cancer and, potentially, for anti-aging.

cancer biology↗

bioRxiv2023

SCCA1/SERPINB3 promotes suppressive immune environment via STAT-dependent chemokine production, blunting the therapy-induced T cell responses

Radiotherapy is a commonly used cancer treatment; however, patients with high serum squamous cell carcinoma antigen (SCCA1/SERPINB3) are associated with resistance and poor prognosis. Despite being a strong clinical biomarker, the modulation of SERPINB3 in tumor immunity is poorly understood. We investigated the microenvironment of SERPINB3 high tumors through RNAseq of primary cervix tumors and found that SERPINB3 was positively correlated with CXCL1/8, S100A8/A9 and myeloid cell infiltration. Induction of SERPINB3 in vitro resulted in increased CXCL1/8 and S100A8/A9 production, and supernatants from SERPINB3-expressing cultures attracted monocytes and MDSCs. In murine tumors, the orthologue mSerpinB3a promoted MDSC, TAM, and M2 macrophage infiltration contributing to an immunosuppressive phenotype, which was further augmented upon radiation. Radiation-enhanced T cell response was muted in SERPINB3 tumors, whereas Treg expansion was observed. A STAT-dependent mechanism was implicated, whereby inhibiting STAT signaling with ruxolitinib abrogated suppressive chemokine production. Patients with elevated pre-treatment serum SCCA and high pSTAT3 had increased intratumoral CD11b+ myeloid cell compared to patients with low SCCA and pSTAT3 cohort that had overall improved cancer specific survival after radiotherapy. These findings provide a preclinical rationale for targeting STAT signaling in tumors with high SERPINB3 to counteract the immunosuppressive microenvironment and improve response to radiation.

cancer biology↗

bioRxiv2022

Orphan nuclear receptors promote alternative lengthening of telomeres (ALT) through ALT-associated PML bodies

Alternative lengthening of telomeres (ALT) is a telomerase-independent telomere maintenance mechanism utilized by about 15% of cancers. Orphan nuclear receptors (NRs), such as COUP-TF1, COUP-TF2, EAR2, TR2, and TR4, associate with telomeres of ALT cells by binding to variant telomeric repeats. However, how these orphan NRs function in the ALT pathway remains to be characterized. Here, we have established an ALT-inducing cell model by tethering orphan NRs to telomeres in non-ALT BJ fibroblast cells. We demonstrate that recruitment of orphan NRs to telomeres is sufficient to initiate formation of ALT-associated promyelocytic leukemia nuclear bodies (APBs) and telomeric DNA synthesis at APBs. We found that the ability of orphan NRs to initiate APB formation and recombination is dependent on the orphan NR AF2 domain, the zinc-finger protein ZNF827, and PML protein. Depletion of orphan NRs in ALT cell lines reduced APB formation and telomeric DNA synthesis, confirming the role of orphan NRs in ALT cells. Furthermore, we found that ATRX/DAXX depletion, together with the telomeric localization of orphan NRs, induces APB formation, telomere clustering, and telomeric DNA synthesis more dramatically in non-ALT cells. Accordingly, we propose that these events in ALT, orphan NR recruitment to telomeres and ATRX/DAXX loss, operate in concert to activate the ALT pathway.

molecular biology↗

bioRxiv2021

Targeted Protein Acetylation in Cells Using Heterobifunctional Molecules

Protein acetylation is a central event in orchestrating diverse cellular processes. However, current strategies to investigate protein acetylation in cells are often non-specific or lack temporal and magnitude control. Here, we developed an acetylation tagging system, AceTAG, to induce acetylation of targeted proteins. The AceTAG system utilizes bifunctional molecules to direct the lysine acetyltransferase p300/CBP to proteins fused with the small protein tag FKBP12F36V, resulting in their induced acetylation. Using AceTAG, we induced targeted acetylation of a diverse array of proteins in cells, specifically histone H3.3, the NF-{kappa}B subunit p65/RelA, and the tumor suppressor p53. We demonstrate that targeted acetylation with the AceTAG system is rapid, selective, reversible, and can be controlled in a dose-dependent fashion. AceTAG represents a useful strategy to modulate protein acetylation and will enable the exploration of targeted acetylation in basic biological and therapeutic contexts. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=67 SRC="FIGDIR/small/454011v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@e7eeddorg.highwire.dtl.DTLVardef@f2fbf1org.highwire.dtl.DTLVardef@7a9d23org.highwire.dtl.DTLVardef@1e2a5b4_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2018

Performance of gene expression analyses using de novo assembled transcripts in polyploid species

MotivationQuality of gene expression analyses using de novo assembled transcripts in species experienced recent polyploidization is yet unexplored.\n\nResultsFive plant species with various polyploidy history were used for differential gene expression (DGE) analyses. DGE analyses using putative genes inferred by Trinity performed similar to or better than Corset and Grouper in precision, but lower in sensitivity. In species that lack polyploidy event in the past few million years, DGE analyses using de novo assembled transcriptome identified 50-76% of the differentially expressed genes recovered by mapping reads to the reference genes. However, in species with more recent polyploidy event, the percentage decreased to 7-30%. In addition, 7-89% of differentially expressed genes from de novo assembly are contaminations. Gene co-expression network analyses using de novo assemblies vs. mapping to the reference genes recovered the same module that significantly correlated with treatment in one of the five species tested.\n\nAvailability and ImplementationCommands and scripts used in this study are available at https://bitbucket.org/lychen83/chen_et_al_2018_benchmark_dge/; Analysis files are available at Dryad doi: XXXXXX.\n\nContactlychen83@qq.com\n\nSupplementary informationSupplementary data are available at Bioinformatics online

bioinformatics↗