Biology subjects

Yue, P.

Publications and source records attributed to Yue, P..

5 recordsLinked to original sources

bioRxiv2026

Pharmacologic eIF2B Activation Rescues Neuropathy in CMT2 Subtypes by Normalizing the Integrated Stress Response

Among the many subtypes of Charcot-Marie-Tooth (CMT) disease, several result from mutations in genes encoding aminoacyl-tRNA synthetases, enzymes required for tRNA charging during cytoplasmic and mitochondrial translation. We report that activation of the integrated stress response (ISR) pathway is a shared molecular feature of tRNA synthetase-associated and other axonal CMT subtypes. RTX-117, a CNS-penetrant small molecule currently in Phase 1 clinical trials, targets eukaryotic initiation factor 2B (eIF2B), a key modulator of protein synthesis and the ISR pathway. Using cryo-EM studies, we have characterized the binding mode of RTX-117 to the eIF2B decamer. In GarsP278KY/+ mice, which develop early onset motor defects and axonal pathology that recapitulate CMT2D symptoms from tRNA synthetase mutations, RTX-117 treatment started after disease onset reduced chronic ISR activation and produced significant functional and electrophysiological improvement. We further identify ISR targets, including secreted proteins such as GDF15 and FGF21 that may serve as translational biomarkers for treatment response to RTX-117 in CMT disease. Broader surveillance of the ISR pathway across models of neurodegeneration reveals strong activation in several diseases and a correlation with disease progression, particularly in models of Alzheimers disease. These findings identify chronic ISR activation as a recurrent, though not universal, pathological mechanism of neurodegenerative disease models. Overall, our study identifies candidate biomarkers for CMT disease subtypes associated with defects in translational homeostasis and supports eIF2[a]-ATF4 axis modulation as a promising therapeutic strategy for this disease class. One Sentence SummaryRTX-117, a clinical stage eIF2B activator, blunts chronic ISR activation and improves nerve and motor function in a mouse model of Charcot-Marie-Tooth Disease Type 2D.

cell biology↗

bioRxiv2025

CDDO-Imidazole regulates RBC alloimmunization to the KEL antigen by activating Nrf2

During red blood cell (RBC) transfusion, production of alloantibodies can promote significant hemolytic events. However, most transfusion recipients do not form anti-RBC alloantibodies. Identifying mechanisms that inhibit alloimmunization may lead to prophylactic interventions. One potential regulatory mechanism is activation of the transcription factor, nuclear factor erythroid-derived 2-like 2 (Nrf2), a master regulatory of antioxidant pathways. Pharmacologic Nrf2 activators improve sequelae of sickle cell disease in pre-clinical models. The Nrf2 activator, 1-[2-cyano-3-,12-dioxooleana-1,9(11)-dien-28-oyl]imidazole (CDDO-Im), suppresses production of inflammatory cytokines including type 1 interferons (IFN/{beta}), which have been implicated in promoting RBC alloimmunization in transfusion models. Thus, we tested the hypothesis that the Nrf2 activator, CDDO-Im, regulates RBC alloimmunization. Here, we report that CDDO-Im induced Nrf2 activated gene expression and suppressed poly(I:C)-induced IFN/{beta}-stimulated gene (ISG) expression in human macrophages and murine blood leukocytes. In addition, following transfusion of wildtype mice with RBCs expressing the KEL antigen, CDDO-Im treatment inhibited poly(I:C)-induced anti-KEL IgG production and promoted post-transfusion recovery of KEL+ RBCs, but failed to do so in Nrf2-/- mice. Results indicate that activation of the Nrf2 antioxidant pathway regulates RBC alloimmunization to the KEL antigen in a pre-clinical model. If findings translate to other models and human studies, Nrf2 activators may represent a potential prophylactic intervention to inhibit alloimmunization. Key PointsO_LIThe antioxidant pathway, Nrf2, inhibits anti-RBC alloantibody responses in a pre-clinical transfusion model. C_LIO_LINrf2 activation may represent a prophylactic strategy to inhibit RBC alloimmunization in transfusion recipients. C_LI

immunology↗

bioRxiv2021

Pan-Cancer Analysis of DNA Methylation Identifies Genes and Biological Functions Associated with Overall Survival

DNA methylation influences gene expression and is altered in many cancers, but the relationship between DNA methylation and cancer outcomes is not yet fully understood. If methylation of specific genes is associated with better or worse outcomes, it could implicate genes in driving cancer and suggest therapeutic strategies. To advance our understanding of DNA methylation in cancer biology, we conducted a pan-cancer analysis of the relationship between methylation and overall survival. Using data on 28 tumor types from The Cancer Genome Atlas (TCGA), we identified genes and genomic regions whose methylation was recurrently associated with survival across multiple cancer types. While global DNA methylation levels are associated with outcome in some cancers, we found that the gene-specific associations were largely independent of these global effects. Genes with recurrent associations across cancer types were enriched for certain biological functions, such as immunity and cell-cell adhesion. While these recurrently associated genes were found throughout the genome, they were enriched in certain genomic regions, which may further implicate certain gene families and gene clusters in affecting survival. By finding common features across cancer types, our results link DNA methylation to patient outcomes, identify biological mechanisms that could explain survival differences, and support the potential value of treatments that modulate the methylation of tumor DNA.

cancer biology↗

bioRxiv2020

Brassinosteroids Suppress Ethylene Biosynthesis via Transcription Factor BZR1 in Pear and Apple Fruit

The plant hormone ethylene is important for the ripening of climacteric fruit, such as pear (Pyrus ussuriensis), and the brassinosteroid (BR) class of phytohormones affects ethylene biosynthesis during ripening, although via an unknown molecular mechanism. Here, we observed that exogenous BR treatment suppressed ethylene production during pear fruit ripening, and that the expression of the transcription factor PuBZR1 was enhanced by epibrassinolide (EBR) treatment during pear fruit ripening. PuBZR1 was shown to interact with PuACO1, which converts 1-aminocyclopropane-1-carboxylic acid (ACC) to ethylene, and suppress its activity. We also observed that BR-activated PuBZR1 bound to the promoters of PuACO1 and of PuACS1a, which encodes ACC synthase, and directly suppressed their transcription. Moreover, PuBZR1 suppressed the expression of transcription factor PuERF2 by binding its promoter, and PuERF2 bound to the promoters of PuACO1 and PuACS1a. We concluded that PuBZR1 indirectly suppresses the transcription of PuACO1 and PuACS1a through its regulation of PuERF2. Ethylene production and the expression profiles of the corresponding apple (Malus domestica) homologs showed similar changes following EBR treatment. Together, these results suggest that BR-activated BZR1 suppresses ACO1 activity and the expression of ACO1 and ACS1a, thereby reducing ethylene production during pear and apple fruit ripening. This likely represents a conserved mechanism by which exogenous BR suppresses ethylene biosynthesis during climacteric fruit ripening. One-sentence summaryBR-activated BZR1 suppresses ACO1 activity and expression of ACO1 and ACS1a, which encode two ethylene biosynthesis enzymes, thereby reducing ethylene production during pear and apple fruit ripening.

plant biology↗

bioRxiv2019

STAT3 and GR cooperate to drive basal-like triple negative breast cancer gene expression and proliferation.

Breast cancers can be divided into subtypes with different prognoses and treatment responses based on global gene expression differences. Luminal breast cancer gene expression and proliferation are driven by the transcription factors Estrogen Receptor (ER), FOXA1 and GATA3. Targeting ER is the most effective therapy for treating luminal breast cancer because ER is the master regulator of the luminal gene expression program. In contrast, it is unclear which transcription factors are responsible for driving the gene expression signature that defines basal-like triple negative breast cancer, and there are no targeted therapies approved to treat this aggressive subtype of the disease. This study utilized integrated analysis of DNA methylation, chromatin accessibility, transcription factor binding, and gene expression in large collections of breast cancer cell lines and patient tumors to identify transcription factors responsible for the basal-like gene expression program. The results of this study indicate that glucocorticoid receptor (GR) and signal transducer and activator of transcription 3 (STAT3) bind to the same genomic regulatory regions that are specifically open and unmethylated in basal-like breast cancer. These transcription factors cooperate to regulate expression of hundreds of genes in the basal-like gene expression signature and these downstream genes are associated with poor prognosis in patients. Furthermore, combination treatment with small molecule drugs that inhibit both transcription factors leads to synergistic decreases in cell proliferation in cell lines and patient-derived organoid models. This study demonstrates that GR and STAT3 cooperate to regulate the basal-like breast cancer gene expression program and provides the basis for improved therapy for basal-like triple negative breast cancer through rational combination of STAT3 and GR inhibitors.

cancer biology↗