The introduction of next-generation androgen receptor signaling inhibitors (ARSIs) like enzalutamide (ENZ), has improved the clinical management of castration-resistant prostate cancer (CRPC). However, acquired resistance to these therapies often develops rapidly, and the underlying resistance mechanisms remain largely unclear. Here, we identified the aryl hydrocarbon receptor (AHR) as a crucial operator of ENZ-resistant CRPC. AHR is upregulated in three ENZ-resistant human CRPC cell lines (C4-2BENZR, CWR-R1ENZR, and VCaPENZR) as well as in high-grade prostate tumors from patients receiving ENZ treatment. Stable knockdown of AHR substantially reduced the growth of ENZ-resistant CRPC cells and xenografts. Mechanistically, AHR engages in distinct transcriptional programs in a cellular context-dependent manner. AHR directly regulates the transcription and expression of androgen receptor (AR)/glucocorticoid receptor (GR) co-target genes in CWR-R1ENZR cells, suggesting an AR-dependent mechanism of ENZ resistance. AHR promotes neuroendocrine differentiation while suppressing the expression of AR/GR targets in C4-2BENZR cells, indicating an AR-indifferent mechanism of ENZ resistance. The diverse mechanisms triggered by ENZ were also manifested in clinical samples. Collectively, these findings characterize AHR's contribution to ENZ resistance in CRPC and illuminate the potential of targeting AHR for treating ARSI-resistant advanced prostate cancer.

Epigenetic dysregulation is a fundamental cancer hallmark, and lysine demethylase 1 (LSD1) is a central target for cancer intervention. Developing novel LSD1 inhibitors with high selectivity, favorable bioavailability, and safety for acute myeloid leukemia (AML) remains challenging. We developed DC551040, a highly potent, selective irreversible LSD1 inhibitor with good tolerability in Phase I AML clinical trial (CTR20222026). DC551040-LSD1 complex crystal structure uncovered a new binding pocket, providing molecular insights for subsequent LSD1 inhibitor design. Given the significant role of LSD1 in epigenetic regulation, we performed comprehensive transcriptomic and proteomic analyses to investigate gene and protein expression dynamics following DC551040 treatment in an MV-4-11 xenograft model. These analyses revealed that multiple immune and inflammation related pathways are activated upon DC551040 treatment, including the key members STAT5, NF-κB, and AKT, suggesting the potential for adaptive resistance. Through a search of the Connectivity Map (CMAP) database, we identify homoharringtonine (HHT), an approved anti-leukemia drug, which mimics the anti-transcriptional activation of inflammatory pathways. Subsequent in vitro and in vivo experiments validated the efficacy of combining HHT with DC551040, demonstrating a synergistic antitumor effect and extended survival in MV-4-11 disseminated xenograft model mice. Together, this study not only introduces a novel LSD1 inhibitor but also delves into the molecular mechanisms underlying LSD1 inhibitors, while proposing a promising combination therapy for AML individuals in clinical trials.

Conventionally, KDM5C functions as a specific demethylase that targets histone H3 lysine 4 dimethyl and trimethyl modifications, crucial for gene expression. However, the role of KDM5C in multiple myeloma (MM) progression and bortezomib (BTZ) resistance has remained elusive. In this study, we found noncanonical functions of KDM5C in MM. Specifically, KDM5C binds to CBP and MYC, conferring BTZ resistance in MM through a demethylase-independent mechanism. Our investigations revealed that KDM5C is markedly upregulated in BTZ-resistant MM patients as well as those with relapsed MM. Significantly, the expression level of KDM5C exhibits an inverse correlation with the overall survival of MM patients. Moreover, KDM5C is indispensable for MM cell proliferation. Depletion of KDM5C augmented the sensitivity of MM cells to BTZ treatment both in vitro and in vivo. We found that KDM5C forms a novel complex with CBP and MYC via its PHD2 domain. This complex formation triggers lysine 27 acetylation in histone H3 (H3K27ac) and subsequent enrichment of H3K27ac on the PERK promoter. As a result, PERK transcription is activated, and Nrf2 phosphorylation is promoted, bolstering the unfolded protein response within the endoplasmic reticulum of MM cells. In contrast, the methylation status of histone H3 lysine 4 (H3K4me1/3) on the PERK promoter remains unaltered, regardless of the complex state. Taken together, the findings of this study underscore the key role of KDM5C as a driving force behind MM progression and BTZ resistance, indicating that KDM5C represents a novel and promising therapeutic target for the treatment of BTZ-resistant MM.

This study aims to systematically investigate the molecular mechanisms through which parabens may contribute to head and neck squamous cell carcinoma (HNSCC) carcinogenesis using integrated network toxicology and molecular docking.

Streptococcus mutans (S. mutans) is a primary cariogenic pathogen responsible for acid production, exopolysaccharides (EPS) production and biofilm formation. Two-component systems (TCS) regulate EPS metabolism, especially the VicRK TCS. Overexpression of antisense vicR (ASvicR) can reduce EPS production and thereby weaken the cariogenicity of S. mutans. Although the antimicrobial monomer dimethylaminohexadecyl methacrylate (DMAHDM) exhibits potent antibacterial properties, mature S. mutans biofilms can protect themselves by extracellular matrix. Emerging evidence suggests that genetic intervention enhances drug efficacy, yet the underlying regulatory mechanisms remain largely unexplored.

To explore the protective effects of cassia polysaccharides on myopia by examining their influence on ARPE-19 cells with reduced PAX6 expression.

The zebrafish vestibular otolith organs, like those of other vertebrate species, are organized into central (striolar) and peripheral (extrastriolar) zones that drive different vestibular circuits. How and when these spatial hair cell patterns develop in the zebrafish is unknown. We determined that early-developing hair cells (<36 h) expressed both striolar and extrastriolar transcriptomic markers. After 36 h, these hair cells become specified as extrastriolar hair cells. Later-developing hair cells (>36 h) mostly develop directly as striolar or extrastriolar. We observed complementary patterns of retinoic acid (RA) degrading and synthesizing enzymes that colocalize with striolar and extrastriolar hair cells, respectively, indicating evolutionarily conserved molecular signaling. RA treatment during development increased the proportion of extrastriolar and intermediate-type hair cells, indicating that increased RA reduces striolar development. However, in fish with mechanotransduction dysfunction from a cadherin 23 mutation, normal RA patterning is insufficient to finalize the fate of early-born hair cells, which remain transcriptomically unresolved. RA treatment further exacerbates this abnormal patterning. We conclude that hair cell fate, and thus normal zonal patterning, depends on both hair cell activity and the RA gradient.

Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer. Although an immune checkpoint blockade can reduce metastasis, its effectiveness is hindered by the immunosuppressive microenvironment in TNBC. EZH2 is overexpressed in TNBC, and patients with high EZH2 expression are associated with poor prognoses. The study developed EIP103 as a first-in-class peptide degrader that targets EZH2 through multivalent, high-affinity interactions and induces conformational destabilization, representing a mechanism distinct from that of the small molecule inhibitor EPZ-6438. The results demonstrated that EIP103 induces immunogenic cell death through lipid peroxidation, resulting in enhanced immune cell infiltration. Additionally, molecular dynamics (MD) simulations and biochemical assays revealed that the peptide EIP103 binds to the SET domain of EZH2, altering its structure and triggering proteasomal degradation via Praja Ring Finger Ubiquitin Ligase 2 (PJA2)-mediated ubiquitination. Harboring both enzymatic inhibition and post-translational regulation properties, EIP103 exerts durable efficacy and activates antitumor immunity, making it a promising therapeutic candidate for TNBC.

Enzalutamide resistance (EnzR) is a major challenge in the current treatment of castration-resistant prostate cancer, as tumors frequently progress to drug resistance after an initially effective treatment. Therefore, there is an urgent need to characterize the genes alterations that accompany EnzR in prostate cancer and to identify new therapeutic targets. In this study, we analyzed a total of 1273 publicly available transcriptomics datasets from patients who underwent prostate cancer surgery. We investigated transcriptomic changes after enzalutamide (ENZ) treatment, identified key genes involved in the process of EnzR, and developed EnzR scores to predict tumor progression. We further investigated the role of IGFBP3 in the regulation of EnzR in prostate cancer. The effect of IGFBP3 expression level on the malignant degree of EnzR cells was explored in vitro. In addition, we explored the downstream mechanism of IGFBP3 involvement in EnzR. We found that epithelial-mesenchymal transition (EMT), cancer stem cell-like properties, and neuroendocrine transformation occurred in tumor cells after ENZ treatment. Subsequently, we developed and validated EnzR scores to predict prostate cancer tumor progression. Furthermore, we experimentally confirmed that IGFBP3 promotes the proliferation of drug-resistant cells and enhances ENZ resistance via EMT signaling. Overall, we established a new EnzR scoring model through multidimensional analysis of EnzR patterns. This model can accurately predict the clinical prognosis of prostate cancer patients after surgery. Moreover, IGFBP3 can be used as a potential therapeutic target for ENZ resistance in prostate cancer.

Metastatic gastric cancer (GC) has a poor prognosis. Recent research demonstrated the aberrant expression of nuclear receptor HNF4α and the regulatory roles of its isoforms during the processes of tumorigenesis and development. However, the expression patterns of HNF4α and its potential as a therapeutic target in metastatic GC remain elusive. In this study, we unveiled that P2 promoter-driven HNF4α (P2-HNF4α) was highly expressed in distant metastasis of GC, playing a pivotal role in fostering the migration and metastasis of GC cells both in vitro and in vivo. The transactivational activity was essential for HNF4α to promote GC cell migration. An integrative analysis of transcriptome and metabolome implied the involvement of the glycolytic pathway in the promotion of GC cell migration by P2-HNF4α. We further found that P2-HNF4α directly bound to the enhancer of the HKDC1 gene and upregulated its expression, thereby orchestrating a metabolic rewiring conducive to promoting GC migration and metastasis. Mycophenolic acid, an active metabolite of the FDA-approved drug mycophenolate mofetil, demonstrated the ability to suppress HKDC1 expression and GC migration and metastasis in vitro and in vivo through antagonizing HNF4α. Therefore, this study sheds light on the HNF4α-HKDC1 axis as a key player in GC metastasis, providing a promising targeted therapeutic strategy for metastatic GC.

Vascular occlusions are a major cause of cardiovascular disease and require interventions including graft bypass surgery; yet, the development of synthetic vascular grafts remains a challenge due to the inability of synthetic biomaterials to support an anti-immunogenic endothelium. Topographical micropatterning of biophysical cues offers a promising strategy to enhance graft endothelialization. As the interface between the biomaterial and blood, endothelial cells provide a bioactive interface which regulates inflammation. We utilized topographical micropatterning of polyurethane biomaterial to induce endothelial cell elongation and alignment and measured the resultant transcriptional changes using bulk RNA-sequencing. Cell phenotype was characterized by gene and protein expression as well as chemokine secretion. The biomaterial micropatterning-modulated elongated and aligned morphology promoted an anti-inflammatory transcriptome, reduced pro-inflammatory chemokine secretion, and induced the transcription coregulator yes-associated protein (YAP) phosphorylation, supporting the anti-immunogenic properties of endothelial cells. Cytoskeletal regulation of this anti-immunogenic phenotype was quantified through measurement of intermediate filament vimentin regulation of YAP localization and endothelial pro-immunogenic gene expression. Aggregation of vimentin was positively correlated with YAP dephosphorylation and suppressed proinflammatory gene expression, indicating that endothelial elongation and alignment influence gene regulation and cellular function independent of vimentin-mediated mechanisms. The ability of micropatterned endothelial cells to maintain their anti-immunogenic functions under pro-inflammatory conditions was demonstrated by the increased phosphorylation of YAP and decrease in pro-inflammatory IL-8 release. Our study highlights the potential of biomaterial cues to regulate endothelial cell behavior for vascular graft design. STATEMENT OF SIGNIFICANCE: We used topographical micropatterning to separate the role of endothelial monolayer morphology from unidirectional blood flow and test how architecture alone regulates gene programs. Micropatterned substrates produced a reproducibly elongated, aligned endothelium with coordinated modeling of the vimentin intermediate filament network. Bulk transcriptomics revealed a distinct morphology-associated expression state, including reduced inflammatory signaling and altered secretory profiles, alongside shifts in mechanosensitive regulatory programs and downstream transcriptional signatures. Together, these findings link cytoskeletal organization to endothelial mechanotransduction and highlight biomaterial topography as a design lever to tune endothelial function for preclinical and clinical applications.

Benzo[a]pyrene (B[a]P), a prominent persistent organic pollutant that is widespread in marine environment due to anthropogenic activities, poses considerable threats to marine ecosystem and public health. Although prior research has documented the adverse impacts of B[a]P on organisms and their response to relieve injury, there are relatively few studies on marine crustaceans that show commercial significance. In this study, we investigated the dose- and time-dependent effects of B[a]P on the lipid peroxidation and gene expression in the hepatopancreas and gill of Marsupenaeus japonicus. The results revealed that malondialdehyde contents in the hepatopancreas and gills of M. japonicus increased at 5 μg/L and 50 μg/L B[a]P exposure, indicating that higher B[a]P concentrations could induce lipid peroxidation. Exposure to 50 μg/L B[a]P resulted in the downregulated expression of several antimicrobial protein genes, including C-type lectins, i-type lysozyme, and stylicin. In contrast, B[a]P exposure significantly upregulated the gene expression of heat shock proteins and antioxidant enzymes. Moreover, correlation analysis suggested that malondialdehyde (MDA) content and gene expression levels in the hepatopancreas and gill of M. japonicus could serve as candidate biomarkers for B[a]P. Overall, this study provided basic insights into the effects of B[a]P on oxidative stress and gene expression in M. japonicus, enriched the understanding of molecular mechanisms in crustaceans responding to B[a]P stress, and identified candidate biomarkers for B[a]P.

Nanoplastics (NPs) and heat stress co-occur in agricultural systems, yet their interactive effects on crops under different heat regimes remain unclear. Here, we investigated rice (Oryza sativa L.) responses to polystyrene NPs under chronic (CH; 36°C, 10 d) and acute (AH; 45°C, 3 h) heat stress using integrated transcriptomics, metabolomics, and alternative splicing analyses. Combined stressors produced additive biomass reductions; however, molecular responses exhibited regime-dependent non-additivity. Under CH, NPs induced widespread antagonistic interactions, suppressing the transcriptional acclimation program by ∼50%. Rather than alleviating stress, this antagonism reflected a systemic failure of heat defense activation, mediated by the disruption of a core regulatory module governing cell wall biosynthesis, phenylpropanoid production, and oxidative stress responses. This resulted in depletion of structural phospholipids and defense compounds (e.g., sakuranetin). Under AH, NPs altered the alternative splicing of circadian clock genes (OsCRY1, OsPRR73, OsGI). These findings reveal that NPs induce regime-specific, non-additive molecular effects despite additive phenotypic responses, demonstrating that traditional organism-level endpoints (e.g., biomass) lack the sensitivity to detect substantial disruption of molecular acclimation programs. This work highlights the need for integrating quantitative interaction modeling and systems-level analyses into multi-stressor risk assessments for agricultural systems facing concurrent pollution and climate stress.

Cellular stresses regulate transcriptional readthrough, whereby RNA polymerase II elongates past a gene's polyadenylation cleavage site without RNA cleavage. Readthrough has been reported in several cancer types. Here, we use long-read sequencing of nascent RNA to quantify transcriptional readthrough in chronic myeloid leukemia (CML) cells and characterize early responses to the targeted therapeutic, imatinib. We show that the amount, length, and gene specificity of readthrough increase within 1 hour, before gene expression and alternative splicing alterations emerge. Notably, imatinib-dependent messenger RNA (mRNA) isoform changes involved "readthrough chimeras," in which exons from an upstream gene are alternatively spliced to exons in a downstream gene. Altered mRNA isoforms and chimera levels were detected in imatinib-resistant K562 cells as well as cells of patients with CML. Thus, imatinib can provoke a cascade of early changes to transcription and splicing fidelity that may lead to longer-term adjustments in gene expression, cancer cell differentiation, and the development of therapy resistance.

Preoperative systemic chemotherapy plays a crucial role in enhancing the outcomes of patients with locally advanced esophageal squamous cell carcinoma (ESCC). Andrographis (major bioactive diterpenoid lactone isolated from Andrographis paniculata; PubChem ID: 5318517), a safe and cost‑effective dietary compound, has demonstrated antitumor effects against various gastrointestinal adenocarcinomas. However, its impact on squamous cell carcinoma remains unclear. The present study explored the antitumor effects of Andrographis and its potential to augment the antitumor efficacy of 5‑fluorouracil (5‑FU). A series of in vitro experiments was conducted, including cell proliferation, colony formation and apoptosis assays, using the ESCC cell lines KYSE410 and TE1. Compared with the controls, Andrographis significantly inhibited cell proliferation (P<0.05), suppressed colony formation (P<0.05), induced apoptosis (P<0.05), and upregulated the expression of ferroptosis‑related genes and proteins, such as HMOX1 (P<0.01), GCLC (P<0.05) and GCLM (P<0.001). Notably, even at a sub‑IC50 dose of 5‑FU, its combination with Andrographis resulted in additive antitumor effects (P<0.05) and further upregulation of ferroptosis‑related gene expression, particularly HMOX1 (P<0.05), compared with either mono‑treatment. The findings of the present study indicate that Andrographis exerts antitumor effects and enhances the efficacy of 5‑FU in ESCC by activating both apoptosis and ferroptosis, suggesting its potential as an adjunctive therapy for ESCC to improve efficacy and reduce 5‑FU dosage and toxicity.

Exposure to waste anesthetic gases (WAGs) is an underestimated occupational hazard in veterinary operating rooms (VORs), where insufficient ventilation and the absence of scavenging systems remain common worldwide. Veterinarians occupationally exposed to WAGs have been poorly investigated to date. Addressing this critical gap, we present the first integrative study evaluating circulating microRNAs (miRNAs), global DNA methylation, and urinary anesthetic quantification in veterinarians occupationally exposed to WAGs isoflurane and sevoflurane. In a case-control design, plasma profiling revealed 11 dysregulated miRNAs in the exposed group (n = 29) compared to the control group (n = 28) based on nominal p-values (p < 0.05), as part of an exploratory screening approach, including seven upregulated miRNAs meeting a predefined fold-change criterion (FC≥1.5). Among these, hsa-miR-1252-5p and hsa-miR-520f-3p showed robust discriminatory performance based on Receiver Operating Characteristic (ROC) curve analysis (AUC≥0.70). Functional enrichment analysis highlighted epigenetic regulators as major network hubs. For hsa-miR-1252-5p, hubs included EP300, TP53, CREBBP, HDAC1 and SIRT1, linking miRNAs modulation to histone acetylation/deacetylation, DNA damage response, apoptosis, and stress regulation. For hsa-miR-520f-3p, included MAPK1, TNRC6B, MECP2 and KMT2A, associated with cell signaling pathways, proliferation and epigenetic regulation. Global DNA methylation levels did not differ significantly between groups, suggesting that exposure under the evaluated conditions may not trigger genome-wide alterations. Occupational exposure was confirmed by urinary quantification of isoflurane and sevoflurane, indicating highly polluted workplaces. In conclusion, although global DNA methylation remained unchanged, WAG exposure was associated with modulation of circulating miRNAs, and our findings suggest that hsa-miR-1252-5p and hsa-miR-520f-3p emerge as potential biomarkers of effect associated to WAG occupational exposure in veterinarians who work in inadequately equipped VORs.

Emodin, a natural compound derived mainly from Reynoutria japonica (Huzhang), has demonstrated notable antitumor effects, though its epigenetic regulatory mechanisms in cervical cancer remain largely unclear. In this study, we show that emodin suppresses cervical cancer cell proliferation and induces oxidative stress. Integrated transcriptomic and metabolomic analyses further demonstrated that emodin markedly disrupted lipid metabolism, particularly by increasing phospholipid accumulation and promoting phospholipid peroxidation. Epigenetic profiling using Western blotting showed that emodin treatment altered global histone modification patterns, with notable increases in H3K27ac and H3K27me3 levels. Subsequent CUT&Tag analysis combined with ChIP-qPCR validation indicated that emodin modulates these two histone marks to regulate the transcription of key phospholipid metabolism-related genes, thereby contributing to enhanced phospholipid peroxidation and antitumor activity. Together, these findings provide new insights into the epigenetic antitumor mechanisms of emodin and highlight potential histone modification targets involved in phospholipid metabolism.

Body axial curvature is a common toxic effect of fish after exposure to environmental pollutants, but the molecular mechanism remains unclear. To investigate the underlying mechanisms, zebrafish were exposed to different persistent organic pollutants (POPs) including polychlorinated biphenyl (PCB) and 2,2',4,4'-tetrabromodiphenyl ether (BDE-47). PCB40 was chosen as the typical POP to discover the mechanism because of its remarkable body axial developmental toxicity. The PCB40 exposure reduced the density of spinal cord cilia. We observed the upregulation of neuropeptides urotensin II-related peptide (urp2), which is downstream of cilia signaling. Further analysis revealed an upregulation of lysine (K)-specific demethylase 1a (Kdm1a, also known as LSD1), and the microscale thermophoresis and chromatin immunoprecipitation assays indicated Kdm1a directly bound PCB40 and enriched in urp2 promoter regions to enhance urp2 expression. Both interventions of Kdm1a using a specific inhibitor and CRISPR/Cas9-mediated knockout partially rescued the body axial curvature induced by PCB40. Further molecular docking suggested that the previously reported pollutants which induced zebrafish body axial curvature could interact with Kdm1a. We found that PCB95 and BDE-47 also induced body axial curvature through Kdm1a and urp2. In conclusion, the study identified a previously unrecognized molecular pathway, specific POPs induced zebrafish body axial curvature by binding to Kdm1a, with urp2 emerging as a key candidate downstream mediator via Kdm1a-dependent upregulation. The study provides a new mechanism for fish body axial curvature caused by specific POPs and provides new insights for pollutant toxicity evaluation and prevention.

The effectiveness of immunotherapy is significantly limited by the inherently low immunogenicity and immunosuppressive phenotypes of tumors. To address this challenge, we develop assemblies composed of chlorin e6 and regorafenib (designated as CeRe), which combine photodynamic therapy (PDT) with immune regulatiing functions. CeRe exhibits uniform nanoscale distribution and good stability without requiring additional carriers. Upon light activation, CeRe eradicate tumor cells via PDT-induced reactive oxygen species (ROS) while simultaneously triggering immunogenic cell death (ICD). Furthermore, CeRe downregulates PD-L1 expression in tumor cells, promotes macrophage polarization, and relieves the immunosuppressive tumor microenvironment (TME). These synergistic immunomodulatory effects substantially improve tumor responsiveness to αPD-L1 treatment, leading to the effective inhibition of both primary and metastatic tumor growth. Collectively, this work presents a carrier-free nanodrug assembly strategy with multifaceted mechanisms, offering a promising approach for precise tumor therapy and metastasis suppression.

Evidence suggests that environmental exposures induce epigenetic modifications that can have long-lasting effects on multiple health outcomes, and an in-depth review of the epidemiological evidence is urgent. We aimed to comprehensively assess the associations between long-term exposure to air pollution and epigenetic changes in adults.