Extranodal NK/T-cell lymphoma (ENKTL) is an aggressive, chemoresistant non-Hodgkin lymphoma subtype with poor patient outcomes linked to elevated PD-L1 expression. This study investigates miRNA-mediated regulation of PD-L1, focusing on miR-340-5p and miR-424-5p as novel therapeutic targets and predictive biomarkers for pembrolizumab response. Through miRNA sequencing and functional assays, miR-340-5p and miR-424-5p were identified as key modulators of PD-L1 in drug-resistant ENKTL cells, with their roles validated via ribonucleoprotein immunoprecipitation and luciferase reporter assays. Notably, elevated miR-340-5p levels in PD-L1-negative ENKTL tissues were inversely correlated with soluble PD-L1, implicating miR-340-5p in immune evasion mechanisms. Additionally, low serum levels of miR-340-5p were associated with reduced pembrolizumab efficacy, positioning miR-340-5p as a promising predictive biomarker for immune checkpoint blockade. These findings suggest that pre-treatment assessment of serum miR-340-5p could guide pembrolizumab therapy in ENKTL, optimizing treatment outcomes. Validation in larger cohorts is necessary to confirm the utility of miR-340-5p as a predictive biomarker for ENKTL immunotherapy.

Cholangiocarcinoma (CCA) is a highly aggressive bile duct cancer with a poor prognosis and high mortality rates, primarily due to the lack of early diagnosis and effective treatments. We have shown that cyclin D and CDK4/6, key regulators of cell cycle progression, are highly expressed in CCA patients. Moreover, high levels of cyclin D, CDK4, and CDK6 are associated with shorter survival in CCA patients, suggesting that cyclin D and CDK4/6 might be potential targets for CCA therapy. However, we have demonstrated that CDK4/6 inhibitor palbociclib monotherapy is less effective in CCA cells. We have identified Cellular Inhibitor of Apoptosis Proteins 1 and 2 (cIAP1/2), NF-κB target genes that their expression is associated with shorter survival in CCA patients, as potential key regulators of the CDK4/6 inhibitor response. We showed that palbociclib, a CDK4/6 inhibitor, increases phosphorylated p65 and its nuclear translocation, resulting in cIAP1/2 upregulation in CCA cells. Therefore, we hypothesized that the combination of a cIAP1/2 antagonist and a CDK4/6 inhibitor might enhance the CDK4/6 inhibitor response. Interestingly, combined treatment with the Smac mimetic LCL161, a cIAP1/2 antagonist, and palbociclib synergistically inhibits cell proliferation and induces cell death in both 2D monolayer and 3D spheroid CCA cultures. We further showed that this combination treatment has less effect on non-tumor cholangiocytes and human peripheral blood mononuclear cells (PBMCs). Our findings demonstrate for the first time that the combined treatment of Smac mimetics and CDK4/6 inhibitors is a promising novel targeted therapy for CCA patients.

All cancer cells must adopt a telomere maintenance mechanism to achieve replicative immortality. Most human cancer cells utilize the enzyme telomerase to maintain telomeres. Alternative splicing of TERT regulates the amount and function of telomerase, however many alternative splicing isoforms of TERT have unknown functions. Single molecule long read RNA/cDNA sequencing of TERT revealed 45 TERT mRNA variants including 13 known and 32 novel variants. Among the variants, TERT Delta 2-4, which lacks exons 2-4 but retains the original open reading frame, was selected for further study. Induced pluripotent stem cells and cancer cells express higher levels of TERT Delta 2-4 compared to primary human bronchial epithelial cells. Overexpression of TERT Delta 2-4 enhanced clonogenicity and resistance to cisplatin-induced cell death. Knockdown of endogenous TERT Delta 2-4 in Calu-6 cells reduced clonogenicity and resistance to cisplatin. Our results suggest that TERT Delta 2-4 enhances cancer cells' resistance to cell death. RNA sequencing following knockdown of Delta 2-4 TERT indicates that translation is downregulated and that mitochondrial related proteins are upregulated compared to controls. Overall, our data indicate that TERT produces many isoforms that influence the function of TERT and the abundance and activity of telomerase.

Triple negative breast cancer (TNBC) continues to be the most aggressive subtype of breast cancer that frequently develops resistance to chemotherapy. Doxorubicin (DOX) belongs to the anthracycline chemical class of the drug and is one of the widely used anticancer drugs. This study investigates the mechanism of m6A methyltransferase ZC3H13 in DOX resistance of TNBC.

It has become increasingly recognised that MATN1-AS1 is involved in multiple tumour development. The role of MATN1-AS1 in clear cell renal cell carcinoma (ccRCC), however, is still largely unrecognised. This study investigated the molecular functions of MATN1-AS1 in promoting ccRCC metastasis and sunitinib resistance. MATN1-AS1 was found to be mainly located in the cytoplasm and was upregulated in ccRCC, and a positive association was seen between greater levels of MATN1-AS1 expression and worse clinical outcomes. Downregulating MATN1-AS1 significantly hindered cell proliferation, migration, invasion and epithelial-mesenchymal transition (EMT). MATN1-AS1 promoted tumour growth and metastasis in vivo. Mechanismly, MATN1-AS1 targeted microRNA miR-214-5p, thereby upregulating E2F2 and promoting E2F2-mediated EMT. We discovered that MATN1-AS1 also promoted sunitinib resistance via E2F2 in vitro. Collectively, our research uncovered the protumor characteristics of MATN1-AS1 and suggested it as a therapeutic target for reverse sunitinib resistance in ccRCC.

Serum is commonly added to culture medium to improve the production of bovine embryos in vitro. The main goals were to verify the actions of serum to increase blastocyst yield and test the hypothesis that fetal bovine serum alters blastocyst gene expression in a manner that could affect competence to establish pregnancy and dysregulate fetal development. Media used were synthetic oviduct fluid medium bovine embryo 2 (SOF-BE2) and a commercial medium from IVF Biosciences termed here as IVFB. Three experiments were conducted in which either adult or fetal bovine serum (10%, vol/vol) was added at day 1 or 5 of development. Overall, serum increased blastocyst production. Gene expression in blastocysts was measured in the experiment in which fetal bovine serum was added at day 5. Serum resulted in 215 differentially expressed genes for embryos cultured in SOF-BE2 and 194 genes for embryos cultured in IVFB (adjusted P value of <0.05 and a |log2| fold change >1). Only 24 genes were regulated by serum similarly for both media, including several transcription factors, imprinted genes, PSAT1 implicated in fetal growth in mice, and genes dysregulated in cloned embryos. Serum largely eliminated differences in gene expression between media. Expression data on eight biomarker genes were also used to calculate an embryo competence index previously related to embryo survival. Serum lowered the embryo competence index for both media. In conclusion, actions of fetal bovine serum on the preimplantation embryo include changes in gene expression indicative of reduced embryo competence and possible alterations in fetal development.NEW & NOTEWORTHY Serum is commonly added to the culture medium to improve the production of bovine embryos in vitro, but its molecular consequences for the resultant embryo are unclear. Here, we showed that blastocysts produced in serum experienced changes in gene expression, including transcription factors and imprinted genes. An embryo competence index that predicts embryo's ability to establish pregnancy based on gene expression was reduced by serum, suggesting serum can reduce embryo survivability.

Drug-induced liver injury (DILI), caused by chemical drugs and traditional Chinese medicine, often leads to severe outcomes like liver failure due to a lack of early detection markers. Farnesoid X receptor (FXR), a key regulator of bile acid (BA) and cholesterol metabolism, is a potential therapeutic target. This study investigates the pathogenesis, markers, and treatment strategies for DILI, focusing on the hepatoprotective effects of geniposidic acid (GPA) from Gardenia jasminoides J. Ellis. Using cellular and animal models of acute and chronic DILI induced by acetaminophen and triptolide, we explored GPA's mechanisms in BA and cholesterol metabolism. Lipidomic and BA analyses revealed that GPA alleviates DILI by enhancing bile acid synthesis and transport via FXR activation. Experiments using AAV-shFXR, Fxr-/- mice and molecular assays demonstrated that GPA targets Ser332 and His447 on FXR ligand-binding domain, promoting FXR nuclear translocation and initiating cytochrome P450 proteins (CYPs) transcriptional activation for BA metabolism. Additionally, miRNA sequencing and RNA-pulldown assays showed that GPA-activated FXR upregulates miR-19a-3p, binding to LXR 3'UTR to inhibit cholesterol production. These findings reveal the GPA-FXR "structure-target" relationship, highlighting a dual mechanism in which GPA promotes CYPs-mediated bile acid metabolism and miR-19a-3p-mediated cholesterol synthesis inhibition, providing a basis for FXR-targeted DILI therapies.

Neisseria gonorrhoeae uses the Type IV pilus (T4p) to colonize several sites within humans by adhering to host cells and tissues. Previously, we identified a periplasmic M23B zinc metallopeptidase, Mpg, that is necessary to protect from oxidative and nonoxidative killing and these phenotypes are mediated by Mpg activities on T4p expression. Here, we use a high-throughput, target-based screening approach to identify novel inhibitors of Mpg's enzymatic activity. We identified two natural compounds, punicalagin and chebulinic acid, which inhibit the peptidoglycan-hydrolyzing activity of Mpg in a dose-dependent manner. Moreover, treatment of N. gonorrhoeae with these compounds leads to a concomitant decrease in the number of T4p, similar to an mpg mutant. However, these compounds are not toxic to N. gonorrhoeae. These compounds exhibit activity against Mpg orthologs from other bacterial species. Notably, these natural compounds inhibit N. gonorrhoeae colonization and survival in cell culture models of infection. This work provides the characterization of two natural compounds with activity against N. gonorrhoeae T4p through the Mpg M23B class zinc metallopeptidase.

Recent studies have investigated RNA modifications in response to stressors like chemical agents, including the anticancer drug 5-fluorouracil (5-FU). Traditionally, 5-FU's mechanism of action was believed to involve inhibition of thymidylate synthase, leading to thymidine depletion and cancer cell death. However, recent findings suggest that ribosome collisions and defects in ribosomal RNA (rRNA) processing drive 5-FU toxicity, potentially through RNA writer inhibition. To explore the effects of 5-FU on rRNA and transfer RNA (tRNA) modifications, we exposed HEK293T cells to 5-FU and quantified key RNA modifications. We found 55% and 40% reduction in 5-methyluridine and pseudouridine (Ψ), respectively, in tRNAs, but only minor changes in rRNA. Using nucleic acid isotope labeling coupled mass spectrometry (NAIL-MS), we identified that pre-existing tRNA and rRNA retained their modification profiles, while newly synthesized RNAs lost various modifications. In addition, new tRNAs exhibited modification reprogramming, particularly important for cell survival after 5-FU removal. In rRNA, we observed reduced levels of mature rRNA, with hypomodification in newly transcribed mature rRNA, particularly in Ψ and ribose methylations. In summary, we observe RNA hypomodification in both tRNA and rRNA due to 5-FU, which might be the molecular basis of 5-FU's mechanism of action.

Phaeodactylum tricornutum is a marine diatom with significant biotechnological potential, particularly in producing high-value bioactive compounds such as fucoxanthin and unsaturated fatty acids, which possess significant pharmaceutical and nutraceutical properties. However, the naturally low yields of these compounds present a major challenge for large-scale production. Methyl jasmonic acid (MeJA), a plant-derived signaling molecule, has been shown to enhance the biosynthesis of these metabolites in P. tricornutum. While transcriptional regulation has been extensively studied, the role of post-transcriptional modifications, such as RNA editing, in mediating MeJA-induced metabolic changes remains largely unexplored. RNA editing can alter nucleotide sequences, leading to functional changes in gene expression and protein activity, thus providing a potential regulatory mechanism for enhanced biosynthesis of target metabolites. In this study, we investigated the role of RNA editing in Phaeodactylum tricornutum under methyl jasmonic acid (MeJA) treatment, focusing on its impact on the accumulation of bioactive compounds such as fucoxanthin and fatty acids. We conducted a comprehensive comparative analysis of RNA editing events across MeJA-treated and control groups. Our findings reveal that MeJA treatment induces significant variations in RNA editing levels, affecting key metabolic pathways. Notably, two genes, Lhcr10 (Phatr3_J16481) and Phatr3_J43665, were identified as potential contributors to increased RNA editing enzyme activity and to energy metabolism and fatty acid biosynthesis under MeJA treatment. These results provide a foundation for the discovery of molecular mechanisms underlying adaptive responses in P. tricornutum and highlight RNA editing as a critical regulatory mechanism in MeJA-induced metabolic reprogramming.

Prenatal exposure to metals can influence fetal programming via DNA methylation and has been linked to adverse birth outcomes and long-term consequences. Epigenetic clocks estimate the biological age of a given tissue based on DNA methylation and are potential health biomarkers. This study leveraged the Extremely Low Gestational Age Newborn (ELGAN) study (n = 265) to evaluate associations between umbilical cord tissue concentrations of 11 metals as single exposures as well as mixtures in relation to (1) placental epigenetic gestational age acceleration (eGAA) and the (2) methylation status of the Robust Placental Clock (RPC) CpGs. Linear mixed effect regression models were stratified by infant sex. Both copper (Cu) and manganese (Mn) were significantly associated with a decelerated placental eGA of -0.98 (95% confidence interval (CI): -1.89, -0.07) and -0.90 weeks (95% CI: -1.78, -0.01), respectively, in male infants. Cu and Mn levels were also associated with methylation at RPC CpGs within genes related to processes including energy homeostasis and inflammatory response in placenta. Overall, these findings suggest that prenatal exposures to Cu and Mn impact placental eGAA in a sex-dependent manner in ELGANs, and future work could examine eGAA as a potential mechanism mediating in utero metal exposures and later life consequences.

Aspirin has consistently shown preventive effects in some solid cancers, notably colorectal cancer. However, the precise molecular mechanisms underlying this positive effect have remained elusive. In this study, we used an azoxymethane-induced mouse model of colon carcinogenesis to identify aspirin-associated molecular alterations that could account for its cancer-preventive effect. Transcriptomic analysis of aspirin-treated mice showed a strong reduction in c-Myc protein levels and effects on the Myc-dependent transcriptional program in colonic cells. Proto-oncogene c-Myc cooperates with AMP-activated protein kinase (AMPK) to control cellular energetics. Here, we show that salicylate, the active metabolite of aspirin, reduces c-Myc protein expression levels through multiple mechanisms that are both AMPK dependent and independent. This effect is cell-type dependent and occurs at both the transcriptional and post-translational levels. Salicylate-induced AMPK activation leads to the phosphorylation of c-Myc at Thr400, as well as its destabilization and degradation. Our results reveal a complex, multilayered, negative effect of salicylate on c-Myc protein abundance and suggest that chronic depletion of c-Myc can counteract the neoplastic transformation of colorectal epithelium, underpinning the preventive effect of aspirin on colorectal cancer.

Crohn's disease (CD) is an inflammatory bowel disease marked by an abnormal immune response and excessive pro-inflammatory cytokines, leading to impaired protein processing and endoplasmic reticulum (ER) stress. This stress, caused by the accumulation of misfolded proteins, triggers the unfolded protein response (UPR) through IRE1/Xbp-1, PERK/eIF2α, and ATF6 pathways, which are linked to intestinal inflammation. This study aimed to investigate ER stress in CD patients' intestinal mucosa and evaluate phenylbutyrate (PBA) as an ER stress inhibitor.

Despite extensive efforts to develop new treatments, the prognosis for glioblastoma multiforme (GBM) is extremely unfavorable, urging the identification of new chemotherapeutics. A previous work identified the cyclic decapeptide uPAcyclin as a potent inhibitor of GBM cell migration, matrix invasion and vascular-like structures' formation, acting through binding to αV integrins and not interfering with cell proliferation or survival. These clearcut activities prompted us to design and test novel derivatives on cultured U87-MG and U251 GBM-MG human cells. With the exception of the residues involved in peptide cyclization, residues were Ala-substituted one by one and the single peptides tested for binding affinity for the αV target integrin, the inhibition of migration, invasion and vasculogenic mimicry. The first screening highlighted peptides with a low binding affinity and low inhibitory ability (Ala4,7,9 derivatives) and peptides with affinity and inhibitory capacity higher than uPAcyclin (Ala2,5,6,8 derivatives). The integration of these results with conformational studies led to the design of the di-substituted variant uPAcyclin. Intriguingly, at least ten-fold greater anti-migratory and anti-invasive effects of the [Ala2,Ala5]uPAcyclin variant compared to uPAcyclin were found. The latter variant also exhibited a greater inhibitory potential for vascular-like structures' formation by matrix-seeded GBM cells. These studies shed light on the functional relevance of single amino acid residues in uPAcyclin and lead to the identification of therapeutically interesting new variants as promising candidates for anti-GBM therapies.

TAVO412, a multi-specific antibody targeting epidermal growth factor receptor (EGFR), mesenchymal epithelial transition factor (c-Met), and vascular endothelial growth factor A (VEGF-A), is undergoing clinical development for the treatment of solid tumors. TAVO412 has multiple mechanisms of action for tumor growth inhibition that include shutting down the EGFR, c-Met, and VEGF signaling pathways, having enhanced Fc effector functions, addressing drug resistance that can be mediated by the crosstalk amongst these three targets, as well as inhibiting angiogenesis. TAVO412 demonstrated strong in vivo tumor growth inhibition in 23 cell-line derived xenograft (CDX) models representing diverse cancer types, as well as in 9 patient-derived xenograft (PDX) lung tumor models.

Hakea laurina, a woody Proteaceae, naturally occurs in severely phosphorus (P)-impoverished habitats in southwest Australia. It develops distinctive cluster roots that exhibit a high capacity for carboxylate exudation and acid phosphatase activity, contributing to its P acquisition. However, the molecular mechanisms underlying these physiological functions remain poorly understood. We explored the cluster-root transcriptome using de novo RNA-Seq and identified Hakea laurina Aluminum-activated Malate Transporter 1 (HalALMT1), encoding an aluminum (Al)-activated malate transporter induced in mature cluster roots. We characterized HalALMT1 through electrophysiological assays and overexpression in Arabidopsis thaliana, and localized HalALMT1 expression, acid phosphatase activity, and suberized boundaries in cluster roots. Differentially expressed genes highlighted multiple increased carboxylate-related processes at cluster-root maturity. HalALMT1 released malate, an activity further enhanced by exposure to Al3+. Notably, HalALMT1 was specifically expressed in mature cortex cells of cluster rootlets, which lack a suberized exodermis. Acid phosphatase activity was pronounced throughout the cluster rootlets, unlike in noncluster roots where it was limited to the epidermis and stele. Substantial malate release and acid phosphatase activity in the cortex cells in cluster rootlets, which lack a suberized exodermis, allowed massive exudation. This study sheds light on an exquisite P-acquisition strategy of Proteaceae, enabling survival under extremely low P availability.

Enterococcus faecalis is a significant pathogen in healthcare settings and is frequently resistant to multiple antibiotics. This resistance is compounded by its ability to form biofilms, dense bacterial communities that are challenging to eliminate via standard antibiotic therapies. As such, targeting biofilm formation is considered a viable strategy for addressing these infections. This study assessed the effectiveness of surfactin, a cyclic lipopeptide biosurfactant synthesized by Bacillus subtilis natto NTU-18, in preventing biofilm formation by E. faecalis. Analytical characterization of surfactin was performed via liquid chromatography‒mass spectrometry (LC‒MS). Additionally, transcriptomic sequencing and quantitative PCR (qPCR) were used to investigate alterations in E. faecalis gene expression following treatment with surfactin. The data revealed notable suppression of crucial virulence-related genes responsible for pilus construction and exopolysaccharide synthesis, both of which are vital for E. faecalis adhesion and biofilm structure. Functional tests confirmed that surfactin treatment substantially reduced E. faecalis attachment to Caco-2 cell monolayers and curtailed exopolysaccharide production. Moreover, confocal laser scanning microscopy revealed significant thinning of the biofilms. These observations support the potential utility of surfactin as a therapeutic agent to manage biofilm-associated infections caused by E. faecalis.

Silicon (Si) is a beneficial nutrient well-known for its functions in enhancing plant resistance to abiotic and biotic stresses. How Si application affects tomato yield and quality and underlying physiological mechanisms remain largely unclear.

Drug resistance in metastatic lung cancer significantly contributes to patient mortality. This study explores the role of circulating tumor cells (CTCs), the precursors to metastasis, in driving this resistance. We aim to delineate the unique biological traits of CTC clusters in lung cancer and elucidate the mechanisms underlying their resistance to chemotherapy.

The circadian clock regulates key physiological processes, including cellular responses to DNA damage. Circadian-based therapeutic strategies optimize treatment timing to enhance drug efficacy and minimize side effects, offering potential for precision cancer treatment. However, applying these strategies in cancer remains limited due to a lack of understanding of the clock's function across cancer types and incomplete insights into how the circadian clock affects drug responses. To address this, we conducted deep circadian phenotyping across a panel of breast cancer cell lines. Observing diverse circadian dynamics, we characterized metrics to assess circadian rhythm strength and stability in vitro. This led to the identification of four distinct circadian-based phenotypes among 14 breast cancer cell models: functional, weak, unstable, and dysfunctional clocks. Furthermore, we demonstrate that the circadian clock plays a critical role in shaping pharmacological responses to various anti-cancer drugs and we identify circadian features descriptive of drug sensitivity. Collectively, our findings establish a foundation for implementing circadian-based treatment strategies in breast cancer, leveraging clock phenotypes and drug sensitivity patterns to optimize therapeutic outcomes.