Knockdown of NDUFAF6 inhibits breast cancer progression via promoting mitophagy and apoptosis

BACKGROUND

While NDUFAF6 is implicated in breast cancer, its specific role remains unclear.

METHODS

The expression levels and prognostic significance of NDUFAF6 in breast cancer were assessed using The Cancer Genome Atlas, Gene Expression Omnibus, Kaplan-Meier plotter and cBio-Portal databases. We knocked down NDUFAF6 in breast cancer cells using small interfering RNA and investigated its effects on cell proliferation and migration ability. We performed gene expression analysis and validated key findings using protein analysis. We also assessed mitochondrial activity and cellular metabolism.

RESULTS

NDUFAF6 was highly expressed in breast cancer, which was associated with a poorer prognosis. Knockdown of NDUFAF6 reduced the proliferation and migration ability of breast cancer cells. Transcriptome analysis revealed 2,101 differentially expressed genes enriched in apoptosis and mitochondrial signaling pathways. Western blot results showed NDUFAF6 knockdown enhanced apoptosis. In addition, differential gene enrichment analysis was related to mitochondrial signaling pathways, and western blot results verified that mitophagy was enhanced in NDUFAF6 knockdown breast cancer cells. JC-1 assay also showed that mitochondrial dysfunction and reactive oxygen species content were increased after knocking down NDUFAF6. In addition, basal and maximal mitochondrial oxygen consumption decreased, and intracellular glycogen content increased.

CONCLUSIONS

Knockdown of NDUFAF6 resulted in apoptosis and mitophagy in breast cancer cells and NDUFAF6 may be a potential molecular target for breast cancer therapy.

Restriction of mitochondrial oxidation of glutamine or fatty acids enhances intracellular growth of Mycobacterium abscessus in macrophages

Mycobacterium abscessus (Mab), a nontuberculous mycobacterium, is increasing in prevalence worldwide and causes treatment-refractory pulmonary diseases. However, how Mab rewires macrophage energy metabolism to facilitate its survival is poorly understood. We compared the metabolic profiles of murine bone marrow-derived macrophages (BMDMs) infected with smooth (S)- and rough (R)-type Mab using extracellular flux technology. Mab infection shifted BMDMs towards a more energetic phenotype, marked by increased oxidative phosphorylation (OXPHOS) and glycolysis, with a significantly greater enhancement in OXPHOS. This metabolic adaptation was characterized by enhanced ATP production rates, particularly in cells infected with S-type Mab, highlighting OXPHOS as a key energy source. Notably, Mab infection also modulated mitochondrial substrate preferences, increasing fatty acid oxidation capabilities while revealing significant changes in glutamine dependency and flexibility. R-type Mab infections exhibited a marked decrease in glutamine reliance but enhanced metabolic flexibility and capacity. Furthermore, targeting metabolic pathways related to glutamine and fatty acid oxidation exacerbated Mab growth within macrophages, suggesting these pathways play a protective role against infection. These insights advance our understanding of Mab's impact on host cell metabolism and propose a novel avenue for therapeutic intervention. By manipulating host mitochondrial metabolism, we identify a potential host-directed therapeutic strategy against Mab, offering a promising alternative to conventional treatments beleaguered by drug resistance. This study underscores the importance of exploring metabolic interventions to combat Mab infection, paving the way for innovative approaches in the fight against this formidable pathogen.

Successful targeting of multidrug-resistant tumors with bispecific antibodies

Multidrug resistance (MDR) hinders efficacious cancer chemotherapy. Overexpression of the P-glycoprotein (P-gp) efflux pump (EP) on cancer cells is a primary cause of MDR since it expels numerous anticancer drugs. Small molecule intracellular P-gp antagonists have been investigated clinically to redress MDR but have failed primarily due to adverse effects on P-gp in normal tissue. We used a new approach to counteract P-gp with bispecific antibodies (BsAbs) that simultaneously bound P-gp and CD47 in cis on MDR cells but not normal tissue. Affinities of the individual arms of the BsAbs were low enough to minimize normal tissue binding, but, when the two targets were co-located on MDR cancer cells, both arms of the BsAb engaged with effective avidity. Proof-of-concept was shown in three different MDR xenograft tumor models with a non-humanized chimeric BsAb (targeting P-gp and CD47) that potently restored tumor sensitivity to paclitaxel. Fully humanized variants were successfully developed and characterized. Significant anti-tumor efficacy was observed with the BsAbs both when combined with paclitaxel and as single agents in the absence of paclitaxel. Treatment of MDR cancers with BsAbs using this novel approach has several distinct advantages over prior efforts with small molecule antagonists, including 1) invoking a direct immune attack on the tumors, 2) multimodal mechanisms of action, 3) tumor-specific targeting (with reduced toxicity to normal tissue), and 4) broad applicability as single agents and compatibility with other therapeutics.

Identification of host genetic factors modulating β-lactam resistance in Escherichia coli harbouring plasmid-borne β-lactamase through transposon-sequencing

Since β-lactam antibiotics are widely used, emergence of bacteria with resistance to them poses a significant threat to society. In particular, acquisition of genes encoding β-lactamase, an enzyme that degrades β-lactam antibiotics, has been a major contributing factor in the emergence of bacteria that are resistant to β-lactam antibiotics. However, relatively few genetic targets for killing these resistant bacteria have been identified to date. Here, we used a systematic approach called transposon-sequencing (Tn-Seq), to screen the Escherichia coli genome for host genetic factors that, when mutated, affect resistance to ampicillin, one of the β-lactam antibiotics, in a strain carrying a plasmid that encodes β-lactamase. This approach enabled not just the isolation of genes previously known to affect β-lactam resistance, but the additional loci skp, gshA, phoPQ and ypfN. Individual mutations in these genes modestly but consistently affected antibiotic resistance. We have identified that these genes are not only implicated in β-lactam resistance by itself but also play a crucial role in conditions associated with the expression of β-lactamase. GshA and phoPQ appear to contribute to β-lactam resistance by regulating membrane integrity. Notably, the overexpression of the uncharacterized membrane-associated protein, ypfN, has been shown to significantly enhance β-lactam resistance. We applied the genes identified from the screening into Salmonella Typhimurium and Pseudomonas aeruginosa strains, both critical human pathogens with antibiotic resistance, and observed their significant impact on β-lactam resistance. Therefore, these genes can potentially be utilized as therapeutic targets to control the survival of β-lactamase-producing bacteria.

Exploration of the feasibility of clinical application of phage treatment for multidrug-resistant Serratia marcescens-induced pulmonary infection

Serratia marcescens (S. marcescens) commonly induces refractory infection due to its multidrug-resistant nature. To date, there have been no reports on the application of phage treatment for S. marcescens infection. This study was conducted to explore the feasibility of phage application in treating refractory S. marcescens infection by collaborating with a 59-year-old male patient with a pulmonary infection of multidrug-resistant S. marcescens. Our experiments included three domains: i) selection of the appropriate phage, ii) verification of the efficacy and safety of the selected phage, iii) confirmation of phage-bacteria interactions. Our results showed that phage Spe5P4 is appropriate for S. marcescens infection. Treatment with phage Spe5P4 showed good efficacy, manifested as amelioration of symptoms, hydrothorax examinations, and chest computed tomography findings. Phage treatment did not worsen hepatic and renal function, immunity-related indices, or indices of routine blood examination. It did not induce or deteriorate drug resistance of the involved antibiotics. Importantly, no adverse events were reported during the treatment or follow-up periods. Thus, phage treatment showed satisfactory safety. Finally, we found that phage treatment did not increase the bacterial load, cytotoxicity, virulence, or phage resistance of S. marcescens, indicating satisfactory phage-bacteria interactions between Spe5P4 and S. marcescens, which are useful for the future application of phage Spe5P4 against S. marcescens. This work provides evidence and a working basis for further application of phage Spe5P4 in treating refractory S. marcescens infections. We also provided a methodological basis for investigating clinical application of phage treatment against multidrug-resistant bacterial infections in the future.

Tumor organoids in cancer medicine: from model systems to natural compound screening

CONTEXT

The advent of tissue engineering and biomedical techniques has significantly advanced the development of three-dimensional (3D) cell culture systems, particularly tumor organoids. These self-assembled 3D cell clusters closely replicate the histopathological, genetic, and phenotypic characteristics of primary tissues, making them invaluable tools in cancer research and drug screening.

OBJECTIVE

This review addresses the challenges in developing in vitro models that accurately reflect tumor heterogeneity and explores the application of tumor organoids in cancer research, with a specific focus on the screening of natural products for antitumor therapies.

METHODS

This review synthesizes information from major databases, including Chemical Abstracts, Medicinal and Aromatic Plants Abstracts, ScienceDirect, Google Scholar, Scopus, PubMed and Springer Link. Publications were selected without date restrictions, using terms such as 'organoid', 'natural product', 'pharmacological', 'extract', 'nanomaterial' and 'traditional uses'. Articles related to agriculture, ecology, synthetic work or published in languages other than English were excluded.

RESULTS AND CONCLUSIONS

The review identifies key challenges related to the efficiency and variability of organoid generation and discusses ongoing efforts to enhance their predictive capabilities in drug screening and personalized medicine. Recent studies utilizing patient-derived organoid models for natural compound screening are highlighted, demonstrating the potential of these models in developing new classes of anticancer agents. The integration of natural products with patient-derived organoid models presents a promising approach for discovering novel anticancer compounds and elucidating their mechanisms of action.

The emergence of highly resistant and hypervirulent Escherichia coli ST405 clone in a tertiary hospital over 8 years

The emergence of carbapenem-resistant Escherichia coli (CREC) poses crucial challenges in clinical management, requiring continuous monitoring to inform control and treatment strategies. This study aimed to investigate the genomic and epidemiological characteristics of CREC isolates obtained from a tertiary hospital in China between 2015 and 2022. Next-generation sequencing was used for genomic profiling, and clinical data from patients were integrated into the analysis. ST405 (21.2%), ST167 (20.3%) and ST410 (15.9%) were the most prevalent of the 30 distinct sequence types (STs) identified among the 113 unique CREC isolates. Infections caused by the ST405 CREC clone and severe underlying diseases were associated with higher in-hospital mortality rates, particularly in patients aged ≥65 years. Furthermore, the ST405 clone exhibited a greater number of virulence and resistance genes than non-ST405 CREC clones. The virulence gene eaeX and resistance genes mph(E) and msr(E) were exclusively found in ST405 clones, while other virulence genes (agn43, ipad and malX) and resistance genes (armA, catB3 and arr-3) were more prevalent in this clones. Additionally, ST405 showed higher minimum inhibitory concentrations for both meropenem and imipenem and showed superior growth under the meropenem challenge. Galleria mellonella virulence assays revealed that the ST405 CREC clone was more virulent than other predominant CREC STs. Our findings underscore the clinical threat posed by the ST405 CREC clone, which exhibits both enhanced virulence and extensive drug resistance. These results highlight the urgent need for stringent surveillance and targeted interventions to curb its further dissemination and prevent potential outbreaks.

The regulatory roles of RNA-binding proteins in the tumour immune microenvironment of gastrointestinal malignancies

The crosstalk between the tumour immune microenvironment (TIME) and tumour cells promote immune evasion and resistance to immunotherapy in gastrointestinal (GI) tumours. Post-transcriptional regulation of genes is pivotal to GI tumours progression, and RNA-binding proteins (RBPs) serve as key regulators via their RNA-binding domains. RBPs may exhibit either anti-tumour or pro-tumour functions by influencing the TIME through the modulation of mRNAs and non-coding RNAs expression, as well as post-transcriptional modifications, primarily N6-methyladenosine (m6A). Aberrant regulation of RBPs, such as HuR and YBX1, typically enhances tumour immune escape and impacts prognosis of GI tumour patients. Further, while targeting RBPs offers a promising strategy for improving immunotherapy in GI cancers, the mechanisms by which RBPs regulate the TIME in these tumours remain poorly understood, and the therapeutic application is still in its early stages. This review summarizes current advances in exploring the roles of RBPs in regulating genes expression and their effect on the TIME of GI tumours, then providing theoretical insights for RBP-targeted cancer therapies.

The role of cisplatin in modulating the tumor immune microenvironment and its combination therapy strategies: a new approach to enhance anti-tumor efficacy

Cisplatin is a platinum-based drug that is frequently used to treat multiple tumors. The anti-tumor effect of cisplatin is closely related to the tumor immune microenvironment (TIME), which includes several immune cell types, such as the tumor-associated macrophages (TAMs), cytotoxic T-lymphocytes (CTLs), dendritic cells (DCs), myeloid-derived suppressor cells (MDSCs), regulatory T cells (Tregs), and natural killer (NK) cells. The interaction between these immune cells can promote tumor survival and chemoresistance, and decrease the efficacy of cisplatin monotherapy. Therefore, various combination treatment strategies have been devised to enhance patient responsiveness to cisplatin therapy. Cisplatin can augment anti-tumor immune responses in combination with immune checkpoint blockers (such as PD-1/PD-L1 or CTLA4 inhibitors), lipid metabolism disruptors (like FASN inhibitors and SCD inhibitors) and nanoparticles (NPs), resulting in better outcomes. Exploring the interaction between cisplatin and the TIME will help identify potential therapeutic targets for improving the treatment outcomes in cancer patients.

Genomic and functional co-diversification imprint African Hominidae microbiomes to signal dietary and lifestyle adaptations

In the diverse landscape of African hominids, the obligate relationship between the host and its microbiome narrates signals of adaptation and co-evolution. Sequencing 546 African hominid metagenomes, including those from indigenous Hadza and wild chimpanzees, identified similar bacterial richness and diversity surpassing those of westernized populations. While hominids share core bacterial communities, they also harbor distinct, population-specific bacterial taxa tailored to specific diets, ecology and lifestyles, differentiating non-indigenous and indigenous humans and chimpanzees. Even amongst shared bacterial communities, several core bacteria have co-diversified to fulfil unique dietary degradation functions within their host populations. These co-evolutionary trends extend to non-bacterial elements, such as mitochondrial DNA, antimicrobial resistance, and parasites. Our findings indicate that microbiome-host co-adaptations have led to both taxonomic and within taxa functional displacements to meet host physiological demands. The microbiome, in turn, transcends its taxonomic interchangeable role, reflecting the lifestyle, ecology and dietary history of its host.

Innate immune cells in vascular lesions: mechanism and significance of diversified immune regulation

Angiogenesis is a complex physiological process. In recent years, the immune regulation of angiogenesis has received increasing attention, and innate immune cells, which are centred on macrophages, are thought to play important roles in vascular neogenesis and development. Various innate immune cells can act on the vasculature through a variety of mechanisms, with commonalities as well as differences and synergistic effects, which are crucial for the progression of vascular lesions. In recent years, monotherapy with antiangiogenic drugs has encountered therapeutic bottlenecks because of the short-term effect of 'vascular normalization'. The combination treatment of antiangiogenic therapy and immunotherapy breaks the traditional treatment pattern. While it has a remarkable curative effect and survival benefits, it also faces many challenges. This review focuses on innate immune cells and mainly introduces the regulatory mechanisms of monocytes, macrophages, natural killer (NK) cells, dendritic cells (DCs) and neutrophils in vascular lesions. The purpose of this paper was to elucidate the underlying mechanisms of angiogenesis and development and the current research status of innate immune cells in regulating vascular lesions in different states. This review provides a theoretical basis for addressing aberrant angiogenesis in disease processes or finding new antiangiogenic immune targets in inflammation and tumor.

Multifaceted quorum-sensing inhibiting activity of 3-(Benzo[d][1,3]dioxol-4-yl)oxazolidin-2-one mitigates Pseudomonas aeruginosa virulence

As antibiotic resistance escalates into a global health crisis, novel therapeutic approaches against infectious diseases are in urgent need. Pseudomonas aeruginosa, an adaptable opportunistic pathogen, poses substantial challenges in treating a range of infections. The quorum-sensing (QS) system plays a pivotal role in orchestrating the production of a large set of virulence factors in a cell density-dependent manner, and the anti-virulence strategy targeting QS may show huge potential. Here, we present a comprehensive investigation into the potential of the synthesized compound 3-(benzo[d][1,3]dioxol-4-yl)oxazolidin-2-one (OZDO, C10H9NO4) as a QS inhibitor to curb the virulence of P. aeruginosa. By employing an integrated approach encompassing in silico screening, in vitro and in vivo functional identification, we elucidated the multifaceted effects of OZDO. Molecular docking predicted that OZDO interfered with three core regulatory proteins of P. aeruginosa QS system. Notably, OZDO exhibited significant inhibition on the production of pyocyanin, rhamnolipid and extracellular proteases, biofilm formation, and cell motilities of P. aeruginosa. Transcriptomic analysis and quantitative real-time PCR displayed the down-regulation of QS-controlled genes in OZDO-treated PAO1, reaffirming the QS-inhibition activity of OZDO. In vivo assessments using a Caenorhabditis elegans-infection model demonstrated OZDO mitigated P. aeruginosa pathogenicity, particularly against the hypervirulent strain PA14. Moreover, OZDO in combination with polymyxin B and aztreonam presented a promising avenue for innovative anti-infective therapy. Our study sheds light on the multifaceted potential of OZDO as an anti-virulence agent and its significance in combating P. aeruginosa-associated infections.

Identification of pyrimidine metabolism-based molecular subtypes and prognostic signature to predict immune landscape and guide clinical treatment in prostate cancer

BACKGROUND

We previously described the enrichment of plasma exosome metabolites in CRPC, PCa, and TFC cohorts, and found significant differences in pyrimidine metabolites. The PMGs is associated with the clinical prognosis of several cancers, but its biological role in PCa is still unclear.

METHODS

This study extracted 98 reliable PMGs, and analyzed their somatic mutations, expression levels, and prognostic significance. Unsupervised clustering was applied to classify patients with PCa into clusters based on six PMGs that were related to the prognosis of PCa. The TME, gene mutations, and immune escape ability were compared among the clusters. A scoring algorithm based on prognostic PMGs, referred to as the PMGscore, was developed. TK1 was identified and the biological functions of TK1 were determined using loss-of-function experiments. RNA sequencing was subsequently performed to determine the molecules associated with the underlying mechanisms of TK1 function.

RESULTS

In total, six out of 98 PMGs simultaneously exhibited differential expression in PCa and were correlated with BCR. Patients were clustered into two clusters according to the expression levels of these six PMGs, which reflected distinct clinical outcomes and immune cell infiltration characteristics. Clinical features, tumor prognosis, and functional annotation were analyzed. Subsequently, we constructed a prognostic signature using these six PMGs. In combination with other clinical traits, we found that the six PMGs' prognostic signature was an independent prognostic factor for patients with PCa. Finally, we found that the expression of TK1 was higher in CRPC tissues than in PCa tissues in three GEO datasets. The results indicated that TK1 promotes the growth and metastasis of PCa cells.

CONCLUSIONS

We provide evidence for a PMG signature for PCa patients to accurately predict clinical prognosis. TK1 plays crucial roles in the progression of PCa cells and can be used as a potential therapeutic target for CRPC.

Acyl-CoA dehydrogenase long chain acts as a tumor-suppressive factor in lung adenocarcinoma progression

This study investigated the role of long-chain acyl-CoA dehydrogenase (ACADL) in lung adenocarcinoma (LUAD). ACADL was significantly downregulated in human LUAD tissues compared to normal lung tissues. In vitro, ectopic expression of ACADL in murine LLC cells decreased cell viability, migration, and invasion, while ACADL knockdown exhibited the opposite effect. In vivo, ACADL overexpression impeded tumor growth and metastasis. Mechanistically, ACADL hindered tumor progression by inducing cell cycle arrest, promoting apoptosis, and suppressing the epithelial-mesenchymal transition (EMT) process. These findings suggest ACADL acts as a tumor suppressor in LUAD progression.

Total flavonoids of litchi seed inhibit breast cancer metastasis by regulating the PI3K/AKT/mTOR and MAPKs signaling pathways

CONTEXT

Total flavonoids from Litchi chinensis Sonn. (Sapindaceae) seeds (TFLS) effectively attenuate stem cell-like properties in breast cancer cells. However, their pharmacological effects and mechanisms in suppressing breast cancer metastasis remain unclear.

OBJECTIVE

This study aimed to elucidate the inhibitory effects and underlying mechanisms of TFLS on breast cancer metastasis.

MATERIALS AND METHODS

The antiproliferative, migratory, and invasive activities of breast cancer cells following TFLS treatment were evaluated using CCK-8, wound-healing, and transwell assays. The epithelial-mesenchymal transition (EMT) biomarkers were evaluated via Western blot analysis. The anti-metastatic effects of TFLS were further validated in vivo using zebrafish and mouse models. Network pharmacology methodology was utilized to predict potential targets and signaling pathways, which were subsequently corroborated by Western blot. Potential active compounds were identified through molecular docking, and the chemical constituents of TFLS were analyzed and characterized using UPLC-QTOF/MS.

RESULTS

TFLS suppressed the proliferation of MDA-MB-231 and MDA-MB-468 cells, with IC50 values of 44.47 μg/mL and 37.35 μg/mL at 72 h, respectively. It effectively suppressed breast cancer metastasis in vitro, demonstrated by a marked reduction in cellular motility and invasiveness, alongside the reversal of EMT. Consistent with pathway enrichment analysis, network pharmacology revealed that TFLS reduced the phosphorylation levels of PI3K, AKT, mTOR, JNK, ERK, and p38 in breast cancer cells. Molecular docking identified seven potential active ingredients, and UPLC-MS/MS confirmed the presence of key compounds, including procyanidin A2.

DISCUSSION AND CONCLUSION

TFLS effectively inhibits breast cancer cell proliferation, migration, and invasion in vitro by reversing the EMT phenotype, while suppressing metastasis in vivo. These effects are likely mediated via the attenuation of the PI3K/AKT/mTOR and MAPK signaling pathways.

Research trends of neoadjuvant therapy for breast cancer: A bibliometric analysis

The approach of neoadjuvant therapy for breast cancer, which involves administering systemic treatment prior to primary surgery, has undergone substantial advancements in recent decades. This strategy is intended to reduce tumor size, thereby enabling less invasive surgical procedures and enhancing patient outcomes. This study presents a comprehensive bibliometric analysis of research trends in neoadjuvant therapy for breast cancer from 2009 to 2024. Using data extracted from the Web of Science Core Collection, a total of 3,674 articles were analyzed to map the research landscape in this field. The analysis reveals a steady increase in publication output, peaking in 2022, with the United States and China identified as the leading contributors. Key institutions, such as the University of Texas System and MD Anderson Cancer Center, have been instrumental in advancing the research on neoadjuvant therapy. The study also highlights the contributions of influential authors like Sibylle Loibl and Gunter von Minckwitz, as well as major journals such as the Journal of Clinical Oncology. Emerging research topics, including immunotherapy, liquid biopsy, and artificial intelligence, are gaining prominence and represent potential future directions for clinical applications. This bibliometric analysis provides critical insights into global research trends, key contributors, and future developments in the field of neoadjuvant therapy for breast cancer, offering a foundation for future research and clinical practice advancements.

Advancing the understanding of the role of apoptosis in lung cancer immunotherapy: Global research trends, key themes, and emerging frontiers

Apoptosis is vital for improving the efficacy of lung cancer (LC) immunotherapy by targeting cancer cell elimination. Despite its importance, there is a lack of comprehensive bibliometric studies analyzing global research on apoptosis in LC immunotherapy. This analysis aims to address this gap by highlighting key trends, contributors, and future directions. A total of 969 publications from 1996 to 2024 were extracted from the Web of Science Core Collection. Analysis was conducted using VOSviewer, CiteSpace, and the R package 'bibliometrix.' The study included contributions from 6,894 researchers across 1,469 institutions in 61 countries, with research published in 356 journals. The volume of publications has steadily increased, led by China and the United States, with Sichuan University as the top contributor. The journal Cancers published the most articles, while Cancer Research had the highest co-citations. Yu-Quan Wei was the leading author, and Jemal, A. was the most frequently co-cited. Key research themes include "cell death mechanisms," "immune regulation," "combination therapies," "gene and nanomedicine applications," and "traditional Chinese medicine (TCM)." Future research is likely to focus on "coordinated regulation of multiple cell death pathways," "modulation of the tumor immune microenvironment," "optimization of combination therapies," "novel strategies in gene regulation," and the "integration of TCM" for personalized treatment. This is the first bibliometric analysis on the role of apoptosis in LC immunotherapy, providing an landscape of global research patterns and emerging therapeutic strategies. The findings offer insights to guide future research and optimize treatment approaches.

Mapping the rapid growth of multi-omics in tumor immunotherapy: Bibliometric evidence of technology convergence and paradigm shifts

This study aims to fill the knowledge gap in systematically mapping the evolution of omics-driven tumor immunotherapy research through a bibliometric lens. While omics technologies (genomics, transcriptomics, proteomics, metabolomics)provide multidimensional molecular profiling, their synergistic potential with immunotherapy remains underexplored in large-scale trend analyses. A comprehensive search was conducted using the Web of Science Core Collection for literature related to omics in tumor immunotherapy, up to August 2024. Bibliometric analyses, conducted using R version 4.3.3, VOSviewer 1.6.20, and Citespace 6.2, examined publication trends, country and institutional contributions, journal distributions, keyword co-occurrence, and citation bursts. This analysis of 9,494 publications demonstrates rapid growth in omics-driven tumor immunotherapy research since 2019, with China leading in output (63% of articles) yet exhibiting limited multinational collaboration (7.9% vs. the UK's 61.8%). Keyword co-occurrence and citation burst analyses reveal evolving frontiers: early emphasis on "PD-1/CTLA-4 blockade" has transitioned toward "machine learning," "multi-omics," and "lncRNA," reflecting a shift to predictive modeling and biomarker discovery. Multi-omics integration has facilitated the development of immune infiltration-based prognostic models, such as TIME subtypes, which have been validated across multiple tumor types, which inform clinical trial design (e.g. NCT06833723). Additionally, proteomic analysis of melanoma patients suggests that metabolic biomarkers, particularly oxidative phosphorylation and lipid metabolism, may stratify responders to PD-1 blockade therapy. Moreover, spatial omics has confirmed ENPP1 as a potential novel therapeutic target in Ewing sarcoma. Citation trends underscore clinical translation, particularly mutation-guided therapies. Omics technologies are transforming tumor immunotherapy by enhancing biomarker discovery and improving therapeutic predictions. Future advancements will necessitate longitudinal omics monitoring, AI-driven multi-omics integration, and international collaboration to accelerate clinical translation. This study presents a systematic framework for exploring emerging research frontiers and offers insights for optimizing precision-driven immunotherapy.

Ultrasound-triggered lysosomal alkalinization to block autophagy in tumor therapy

Lysosomes play a crucial role in regulating cancer progression and drug resistance. However, there is a pressing need for the development of drugs that can safely and effectively modulate the pH of cancerous lysosomes in a controlled manner. In this study, we propose a novel strategy for lysosomal alkalinization triggered by piezoelectricity. Our findings indicate that the electrons generated by (BaTiO3/Zr/Ca) BCZT under sonication effectively alkalinize the lysosomes. Molecular dynamics simulations further demonstrate that alterations in lysosomal pH lead to modifications in the conformation of V-ATPase (proton pump), enhancing its interaction with sodium ions while partially excluding hydrogen ions from entering the lysosomes. This mechanism helps maintain lysosomal alkalization, resulting in reduced hydrolase activity and preventing the degradation of proteins and damaged organelles. The accumulation of nanoparticles within the lysosomes causes swelling and gradual destruction of the lysosomal membrane. Consequently, this lysosomal dysfunction hampers the fusion with autophagosomes, inhibiting autophagy in tumor cells and promoting apoptosis in various tumor types. Our strategy significantly inhibited tumor volume growth in mice during animal studies. In conclusion, our piezoelectric-triggered lysosomal alkalinization strategy holds promise for innovative breakthroughs in the treatment of multiple cancers.

Unique methotrexate polyglutamates distributions in peripheral blood mononuclear cells of rheumatoid arthritis patients: Development and validation of a UPLC-MS/MS method

Methotrexate is pivotal in treating immune-mediated inflammatory diseases. Intracellularly, methotrexate is metabolized to methotrexate-polyglutamates (MTX-PG1-7), comprising up to six additional glutamate moieties, crucial for cellular retention and therapeutic efficacy. Hitherto, quantification of MTX-PG1-6 in peripheral blood mononuclear cells (PBMCs) from methotrexate-treated patients was challenging due to their low abundance in blood and matrix effects. We present a robust validated UPLC-MS/MS method to quantify individual MTX-PG1-6 in PBMCs. Stable-isotope labelled internal standard mixture of MTX-PG1-6 was added to 5 million PBMCs, followed by deproteinization with perchloric acid, and additional sample clean-up using solid phase extraction columns. MTX-PG1-6 were detected and quantified using UPLC-MS/MS. The method was validated for lower limit of quantification (LLOQ), linearity, carryover, recovery, matrix effects, precision and stability. We assessed MTX-PG1-6 in PBMCs derived from five methotrexate-treated rheumatoid arthritis patients. For all MTX-PG1-6, LLOQs were < 1 fmol-MTX-PG1-6/million cells with linearities R2 > 0.995. The recoveries, carryover and stability were acceptable and no matrix effects were observed. The intraday and interday precision %CVs of quality controls ranged from 2.7 % to 11.4 % and 3.5-14.9 % respectively. Interday precision using nine PBMCs aliquots from a single MTX-treated patient aligned similarly (%CV <15 %). In patient-derived PBMC samples, MTX-PG1 was the highest, with decreasing concentrations of MTX-PG2 to MTX-PG5. No signal for MTX-PG6 was detected in the patient samples. We validated a new UPLC-MS/MS method to quantify MTX-PG1-6 in PBMCs, thus facilitating PBMC-based therapeutic drug monitoring studies and understand associations between MTX-PG1-6 concentration and therapy efficacy or adherence.

Design of NanoBiT-Nanobody-based FGL1 biosensors for early assisted diagnosis of esophageal cancer

Esophageal cancer (EC) is one of the most common causes of cancer-related mortality due in part to challenges in early diagnosis. Biomarker identification is crucial for improved early screening and treatment strategies for patients. Firstly, we employed serum proteomics techniques to screen for potential biomarkers in 15 early-stage EC patients and 5 healthy individuals. Among the differentially expressed proteins, FGL1 emerged as a promising candidate (AUC = 0.974) for early detection of EC. Subsequently, we developed NanoBiT-conjugated dual nanobodies (NBNB) sensors for robust and quantitative signal detection in fetal bovine serum (FBS) in 30 min or less, with a limit of detection (LoD) of 11.38 pM. In a case-control study recruiting 96 EC patients and 99 control samples, testing serum samples with the developed NBNB sensors revealed significantly elevated serum level of FGL1 in all-stage EC patients (AUC = 0.7880) and early-stage EC patients (AUC = 0.8286). Additionally, the combined diagnostic performance of FGL1 and CEA in EC samples is notably enhanced (AUC = 0.8847). These findings propose FGL1 as a novel and promising target for the early-stage EC diagnosis and treatment selection. Furthermore, we applied the assay to patients across six types of cancer, suggesting FGL1 as a potential pan-cancer marker. This study introduces a rapid, easy-to-use, cost-effective, reliable, universal, and high-throughput alternative to meet the growing demand for cancer biomarker testing in both academic and clinical settings.

Invariant set theory for predicting potential failure of antibiotic cycling

Collateral sensitivity, where resistance to one drug confers heightened sensitivity to another, offers a promising strategy for combating antimicrobial resistance, yet predicting resultant evolutionary dynamics remains a significant challenge. We propose here a mathematical model that integrates fitness trade-offs and adaptive landscapes to predict the evolution of collateral sensitivity pathways, providing insights into optimizing sequential drug therapies. Our approach embeds collateral information into a network of switched systems, allowing us to abstract the effects of sequential antibiotic exposure on antimicrobial resistance. We analyze the system stability at disease-free equilibrium and employ set-control theory to tailor therapeutic windows. Consequently, we propose a computational algorithm to identify effective sequential therapies to counter antibiotic resistance. By leveraging our theory with data on collateral sensivity interactions, we predict scenarios that may prevent bacterial escape for chronic Pseudomonas aeruginosa infections.

Fluorescent sensor array for rapid bacterial identification using antimicrobial peptide-functionalized gold nanoclusters and machine learning

Bacterial infectious diseases pose significant challenges to public health, emphasizing the need for rapid and accurate diagnostic tools. Here, we introduced a multichannel fluorescent sensor array based on antimicrobial peptide-functionalized gold nanoclusters (AMP-AuNCs) designed for precise bacterial identification. By utilizing the unique electrostatic and hydrophobic properties of three AMP-AuNCs, this sensor array generated distinct fluorescence patterns upon binding to different bacterial species. Machine learning algorithms, including Principal Component Analysis (PCA), Hierarchical Clustering Analysis (HCA), and Linear Discriminant Analysis (LDA), were employed to analyze fluorescence fingerprint patterns and identify bacterial strains with high accuracy. The sensor array achieved 100 % accuracy in identifying six common bacterial species and demonstrated an 86.7 % accuracy in classifying clinical Escherichia coli isolates from urinary tract infections. This AMP-AuNC-based sensor array offers a promising approach for rapid and precise bacterial diagnostics, with potential applications in clinical settings for combating antibiotic resistance.

Nanotherapeutic strategies exploiting biological traits of cancer stem cells

Cancer stem cells (CSCs) represent a distinct subpopulation of cancer cells that orchestrate cancer initiation, progression, metastasis, and therapeutic resistance. Despite advances in conventional therapies, the persistence of CSCs remains a major obstacle to achieving cancer eradication. Nanomedicine-based approaches have emerged for precise CSC targeting and elimination, offering unique advantages in overcoming the limitations of traditional treatments. This review systematically analyzes recent developments in nanomedicine for CSC-targeted therapy, emphasizing innovative nanomaterial designs addressing CSC-specific challenges. We first provide a detailed examination of CSC biology, focusing on their surface markers, signaling networks, microenvironmental interactions, and metabolic signatures. On this basis, we critically evaluate cutting-edge nanomaterial engineering designed to exploit these CSC traits, including stimuli-responsive nanodrugs, nanocarriers for drug delivery, and multifunctional nanoplatforms capable of generating localized hyperthermia or reactive oxygen species. These sophisticated nanotherapeutic approaches enhance selectivity and efficacy in CSC elimination, potentially circumventing drug resistance and cancer recurrence. Finally, we present an in-depth analysis of current challenges in translating nanomedicine-based CSC-targeted therapies from bench to bedside, offering critical insights into future research directions and clinical implementation. This review aims to provide a comprehensive framework for understanding the intersection of nanomedicine and CSC biology, contributing to more effective cancer treatment modalities.

Application of Machine Learning (ML) approach in discovery of novel drug targets against Leishmania: A computational based approach

Molecules with potent anti-leishmanial activity play a crucial role in identifying treatments for leishmaniasis and aiding in the design of novel drugs to combat the disease, ultimately protecting individuals and populations. Various methods have been employed to represent molecular structures and predict effective anti-leishmanial molecules. However, each method faces challenges and limitations that must be addressed to optimize the drug discovery and design process. Recently, machine learning approaches have gained significant importance in overcoming the limitations of traditional methods across various fields. Therefore, there is an urgent need to build a computational pipeline using advanced machine learning and deep learning methods that help to predict anti-leishmanial activity of drug candidates. The proposed pipeline in this paper involves data collection, feature extraction, feature selection and prediction techniques. This review presents a comprehensive computational pipeline for anti-leishmanial drug discovery, highlighting its strengths, limitations, challenges, and future directions to improve treatment for this neglected tropical disease.

Metabolic reprogramming in cholangiocarcinoma cancer stem cells: Emerging therapeutic paradigms

Cholangiocarcinoma (CCA) is an aggressive malignancy characterized by limited therapeutic options and poor prognosis, largely attributed to the presence of cancer stem cells (CSCs). These CSCs serve as pivotal drivers of tumor heterogeneity, chemotherapy resistance, and disease recurrence. CSCs in CCA exhibit remarkable plasticity, a characteristic sustained through metabolic state alterations and intricate interactions with the tumor microenvironment (TME), which collectively enhance their self-renewal and survival potential. While advancements have been made in understanding metabolic reprogramming of CCA CSCs, translating these findings into clinical applications encounters significant challenges, including insufficient target specificity, complex metabolic heterogeneity, and the profound complexity of the TME. This review provides a systematic evaluation of metabolic reprogramming mechanisms in CCA CSCs, with critical analysis of stemness-maintaining signaling pathways, oxidative phosphorylation (OXPHOS), nutrient utilization, metabolic crosstalk within the TME, autophagy regulation, and ferroptosis resistance. We emphasize emerging strategies to therapeutically target the interconnected metabolic networks essential for CSC functionality and survival, with the goal of establishing a theoretical basis for innovative precision therapies to enhance clinical outcomes for CCA patients.

Metformin inhibits the progression of castration-resistant prostate cancer by regulating PDE6D induced purine metabolic alternation and cGMP / PKG pathway activation

The castration-resistant prostate cancer (CRPC) remains an incurable disease. Metformin has demonstrated a potential therapeutic effect on CRPC. However, the poor clinical performance of metformin against cancer may be due to its clinical dose being much lower than the anticancer concentration used in pre-clinical experiments. The challenge is to determine a way to enhance sensitivity to metformin at an appropriate concentration on CRPC. In this study, a mouse model of low-dose metformin treatment for CRPC cells were established. Metabolomic-seq and transcriptomic-seq was used to investigate changes in CRPC xenografts. We discovered that low-dose metformin inhibits the progression of CRPC by regulating PDE6D, which induces alterations in purine metabolism and activates the cGMP/PKG pathway. Furthermore, we found that cells with high expression of PDE6D were more resistant to metformin. When combined with the PDE6D inhibitor TMX-4100, the inhibitory effect on tumors was enhanced, and TMX-4100 demonstrated favorable biosafety in animal models. In conclusion, we found that low-dose metformin inhibits the progression of CRPC by regulating PDE6D-induced alterations in purine metabolism and activating the cGMP/PKG pathway. Moreover, patients with high PDE6D expression may exhibit greater resistance to metformin. Combining metformin with TMX-4100 could further improve the inhibitory effects on tumors.

Design, synthesis, and biological activity study of 6,7-dimethoxy-1,2,3,4-tetrahydroisoquinoline derivatives against multidrug resistance in Eca109/VCR cells

The advent of multidrug resistance (MDR) in tumors markedly diminishes the effectiveness of anticancer therapies. P-glycoprotein (P-gp) plays a crucial role in tumor MDR by mediating the efflux of drugs and cytotoxic agents. Presently, small molecule agents targeting P-gp are among the promising therapeutic approaches to counteract MDR. In previous research, our team identified a novel class of P-gp inhibitors featuring a 6,7-dimethoxy-1,2,3,4-tetrahydroisoquinoline scaffold. To further delineate the structure-activity relationship, this study conducted an extensive structural optimization, synthesizing 42 novel compounds. Evaluation on the drug-resistant cell line Eca109/VCR indicated that the majority of these compounds exhibited remarkable MDR-reversing activity. Notably, the optimized compound 41 demonstrated an outstanding ability to reverse MDR, with a reversal fold of up to 467.7, surpassing the efficacy of the standard third-generation P-gp inhibitor TQ, as evidenced by plate cloning assay and flow cytometry analysis. Subsequent mechanism validation experiments-including western blotting, chemosensitization tests, and fluorescent substrate accumulation assays-complemented by molecular docking studies, confirmed that compound 41 exerts its MDR-reversing effects through P-gp inhibition. This research offers new perspectives for the development of drug sensitizers targeting resistant tumors based on the tetrahydroisoquinoline scaffold.

A new short pH-responsive anticancer peptide derived by intramolecular charge shielding strategy

The pH-responsive anticancer peptides (ACPs) have been regarded as a new generation of prospective antitumor candidates due to their selectivity. However, the successful utilizations have been hampered by their narrow therapeutic index, poor stability and long sequence. Here, a new type of short pH-responsive ACPs was constructed by smart intramolecular charge shielding in histidine-rich peptide LH. This design would not depend on the introduction of additional anionic binding peptide, which might be an effective method for appreciably shortening the sequence of pH-responsive ACPs while improving their safety and stability. As expected, 2E-K stood out from the acquired peptides as it exhibited a considerable pH-dependent antitumor activity concomitant with remarkably improved therapeutic selectivity (14.5-fold increase) and extended serum half-life (3.6-fold enhancement) compared to LH. Experimental results showed that acid-activated 2E-K could efficiently induce tumor cell death by rapid membrane damage. Notably, the in vivo experiments further confirmed its excellent antitumor efficacy and low toxicity when compared with PTX, which demonstrating its superiority for in vivo application. In conclusion, our work opened a new avenue for developing short pH-responsive ACPs as promising alternative drugs in cancer treatment.

Development of 9H-purine scaffold as novel CDK2 inhibitors: Design, synthesis, and biological evaluation

Cyclin-dependent kinase 2 (CDK2), a crucial regulator in multiple oncogenic signaling pathways, has emerged as a promising target for the development of innovative anticancer therapies and overcoming resistance to CDK4/6 inhibitors. In this study, three series of compounds were designed and synthesized, using the CDK2 inhibitor fadraciclib (CYC065) as the lead compound, with 9H-purine as the core structure. The design incorporated reported structure-activity relationship data and utilized computer-aided drug design techniques. Compounds in series 1 explored the binding mode between the ATP ribose binding site in CDK2 and C2 substituents, while compounds in series 2 and 3 validated the feasibility of modifying the specific binding region with different substituents and investigated the effects of filling the CDK2 hydrophobic pocket at the N9 position with alkyl substituents. Three compounds, 1f, 2e, and 3a, demonstrated remarkable activity against CDK2-cyclin E2. Notably, 3a exhibited the most potent effect, with a CDK2-cyclin E2 IC50 value of 6.0 ± 0.1 nM, an MV4-11 IC50 value of 489.2 ± 0.2 nM, and excellent selectivity for CDK2. This study evaluated the impact of substitutions at the 2, 6, and 9 positions of the purine ring on the activity of CDK2 small molecule inhibitors. The findings offer a theoretical foundation for future research, broadening the structural diversity and scope of CDK2 inhibitor studies.

Enhancing PD-1 blockade in NSCLC: Reprogramming tumor immune microenvironment with albumin-bound statins targeting lipid rafts and mitochondrial respiration

Non-small cell lung cancer (NSCLC) has shown limited response to immunotherapy, primarily due to an immunosuppressive tumor microenvironment characterized by hypoxia and lipid raft formation, which together inhibit T-cell infiltration and function, impeding effective immune responses. To address these challenges, we developed Abstatin, an albumin-bound fluvastatin formulation that targets lipid raft disruption and mitochondrial respiration inhibition, aiming to reduce hypoxia and destabilize lipid rafts to enhance T-cell activity within the tumor. Using bioinformatics analysis, in vitro assays, and in vivo studies in both murine and humanized PDX models, we demonstrated that Abstatin reprograms the NSCLC microenvironment by concurrently lowering hypoxia levels and lipid raft integrity, thereby restoring T-cell infiltration, enhancing cytotoxic T-cell function, and ultimately improving response to Anti-PD-1 therapy. Results showed that Abstatin significantly amplifies Anti-PD-1 efficacy with minimal toxicity, indicating a favorable safety profile for clinical use. This study highlights Abstatin as a promising immunotherapy adjuvant that addresses critical barriers in NSCLC by modulating metabolic pathways linked to immune resistance. Abstatin's approach, which combines modulation of cellular metabolism with immune sensitization, broadens the potential of immunotherapy and provides a practical, scalable strategy to enhance treatment outcomes in NSCLC and potentially other tumors, offering insights into combinatory cancer therapies.

Exploring the molecular mechanisms through which overexpression of TET3 alleviates liver fibrosis in mice via ferroptosis in hepatic stellate cells

Hepatic stellate cell (HSC) activation is crucial in the onset and progression of liver fibrosis, and inhibiting or eliminating activated HSCs is a key therapeutic strategy. Ferroptosis may help eliminate activated HSCs; however, its role and regulatory pathways in liver fibrosis remain unclear. As a DNA demethylase, TET3 regulates gene expression via DNA demethylation. We previously demonstrated that TET3 overexpression alleviates CCL4-induced liver fibrosis in mice; however, the specific mechanisms, including whether TET3 affects ferroptosis in HSCs, remain unexplored. Thus, we aimed to explore the molecular mechanisms wherein TET3 overexpression improves liver fibrosis in mice via ferroptosis in HSCs. Our in vivo observations showed that overexpression of TET3 ameliorate liver fibrosis in mice, and is associated with increased levels of malondialdehyde (MDA) and Fe2+ in liver tissue, as well as decreased protein expression of SLC7A11, GPX4, and FTH1. Further in vitro studies on HSCs showed that TET3 overexpression inhibits the expression of SLC7A11, GPX4, and FTH1, and reduces intracellular GSH levels, leading to accumulation of MDA and iron ions. This induces ferroptosis in HSC-LX2 cells, while simultaneously decreasing ECM accumulation in HSCs. Furthermore, hMeDIP-SEQ and ChIP-qPCR analyses revealed that TET3 directly interacts with the promoter regions of GPX4 and FTH1 to regulate their transcriptional expression. We propose that overexpression of TET3 modulates the gene methylation status of ferroptosis-related proteins, thereby regulating HSC ferroptosis, reducing activated HSCs, and decreasing ECM deposition in the liver. This may represent one of the molecular mechanisms wherein TET3 overexpression ameliorates liver fibrosis in mice.

SQLE amplification accelerates esophageal squamous cell carcinoma tumorigenesis and metastasis through oncometabolite 2,3-oxidosqualene repressing Hippo pathway

Esophageal squamous cell carcinoma (ESCC) is one of the most prevalent cancers worldwide, characterized by a dismal prognosis and elusive therapeutic targets. Dysregulated cholesterol metabolism is a critical hallmark of cancer cells, facilitating tumor progression. Here, we used whole genome sequencing data from several ESCC cohorts to identify the important role of squalene epoxidase (SQLE) in promoting ESCC tumorigenesis and metastasis. Specifically, our findings highlight the significance of 2,3-oxidosqualene, an intermediate metabolite of cholesterol biosynthesis, synthesized by SQLE and metabolized by lanosterol synthase (LSS), as a key regulator of ESCC progression. Mechanistically, the interaction between 2,3-oxidosqualene and vinculin enhances the nuclear accumulation of Yes-associated protein 1 (YAP), thereby increasing YAP/TEAD-dependent gene expression and accelerating both tumor growth and metastasis. In a 4-nitroquinoline 1-oxide (4-NQO)-induced ESCC mouse model, overexpression of Sqle resulted in accelerated tumorigenesis compared to wild-type controls, highlighting the pivotal role of SQLE in vivo. Furthermore, elevated SQLE expression in ESCC patients correlates with a poorer prognoses, suggesting potential therapeutic avenues for treatment. In conclusion, our study elucidates the oncogenic function of 2,3-oxidosqualene as a naturally occurring metabolite and proposes modulation of its levels as a promising therapeutic strategy for ESCC.

Protein succinylation mechanisms and potential targeted therapies in urinary disease

Succinylation is a relatively common post-translational modification. It occurs in the cytoplasm, mitochondria, and the nucleus, where its essential precursor, succinyl-CoA, is present, allowing for the modification of non-histone and histone proteins. In normal cells, succinylation levels are carefully regulated to sustain a dynamic balance, necessitating the involvement of various regulatory mechanisms, including non-enzymatic reactions, succinyltransferases, and desuccinylases. Among these regulatory factors, sirtuin 5, the first identified desuccinylase, plays a significant role and has been extensively researched. The level of succinylation has a significant effect on multiple metabolic pathways, including the tricarboxylic acid cycle, redox balance, and fatty acid metabolism. Dysregulated succinylation can contribute to the progression or exacerbation of various urinary diseases. Succinylation predominantly affects disease progression by altering the expression of key genes and modulating the activity of enzymes involved in vital metabolic processes. Desuccinylases primarily affect enzymes associated with Warburg's effect, thereby affecting the energy supply of tumor cells, while succinyltransferases can regulate gene transcription to alter cell phenotype, thereby involving the development of urinary diseases. Considering these effects, targeting succinylation-related enzymes to regulate metabolic pathways or gene expression may offer a promising therapeutic strategy for treating urinary diseases.

Advances in antimicrobial peptides: From mechanistic insights to chemical modifications

This review provides a comprehensive analysis of antimicrobial peptides (AMPs), exploring their diverse sources, secondary structures, and unique characteristics. The review explores into the mechanisms underlying the antibacterial, immunomodulatory effects, antiviral, antiparasitic and antitumour of AMPs. Furthermore, it discusses the three principal synthesis pathways for AMPs and assesses their current clinical applications and preclinical research status. The paper also addresses the limitations of AMPs, including issues related to stability, resistance, and toxicity, while offering insights into strategies for their enhancement. Recent advancements in AMP research, such as chemical modifications (including amino acid sequence optimisation, terminal and side-chain modifications, PEGylation, conjugation with small molecules, conjugation with photosensitisers, metal ligands, polymerisation, cyclisation and specifically targeted antimicrobial peptides) are highlighted. The goal is to provide a foundation for the future design and optimisation of AMPs.

The role of Bcl‑2 in controlling the transition between autophagy and apoptosis (Review)

The Bcl‑2 protein family serves a key role in maintaining cellular homeostasis by regulating the balance between autophagy and apoptosis. The present review aimed to summarize interactions of Bcl‑2 with key proteins, including Beclin 1, Bax and Bcl‑2 homologous antagonist/killer, as well as its influence on cellular processes such as mitophagy, nutrient sensing and endoplasmic reticulum stress response. The impact of post‑translational modifications of Bcl‑2, including phosphorylation, ubiquitination and sumoylation, is discussed with respect to their regulatory roles under stress. In pathological states, Bcl‑2 upregulation in cancer suppresses apoptosis and autophagy, thereby facilitating tumor survival and resistance to chemotherapy. Conversely, in neurodegenerative diseases, impaired autophagy and increased apoptosis contribute to neuronal loss. Therapeutic strategies targeting Bcl‑2 (for example inhibitors such as venetoclax, navitoclax, obatoclax and combination therapies involving autophagy modulators) were evaluated for their potential efficacy. There is lack of understanding of tissue‑specific functions of Bcl‑2 and its interactions with non‑coding RNAs. Future research should prioritize these areas and leverage advanced single‑cell technologies to elucidate the real‑time dynamics of Bcl‑2 in cell processes. The present review highlights the key role of Bcl‑2 in cell fate determination and highlights its potential as a therapeutic target, offering insight for the development of innovative treatments for cancer, neurodegenerative disorder and age‑related diseases.

A narrative review: Ultrasound-Assisted drug delivery: Improving treatments via multiple mechanisms

Safe and efficient drug delivery is as important as drug development. Biological barriers, such as cell membranes, present significant challenges in drug delivery, especially for newly developed protein-, nucleic acid-, and cell-based drugs. Ultrasound-mediated drug delivery systems offer a promising strategy to overcome these challenges. Ultrasound, a mechanical wave with energy, produces thermal effects, cavitation, acoustic radiation, and other biophysical effects. Used alone or in combination with microbubbles or sonosensitizers, it breaks biological barriers, enhances targeted drug delivery, reduces adverse reactions, controls drug release, switches on/off drug functions, and ultimately improves therapeutic efficiency. Various ultrasound-mediated drug delivery methods, including transdermal drug delivery, nebulization, targeted microbubble destruction, and sonodynamic therapy, are being actively explored for the treatment of various diseases. This review article introduces the principles, advantages, and applications of ultrasound-mediated drug delivery methods for improved therapeutic outcomes and discusses future prospects in this field.

Macrophage polarization-mediated PKM2/mTORC1/YME1L signaling pathway activation in fibrosis associated with Cardiorenal syndrome

BACKGROUND

Cardiorenal syndrome (CRS) is a complex condition characterized by the interplay between cardiac and renal dysfunction, often culminating in renal fibrosis. The role of macrophage polarization and its downstream effects in CRS-induced renal fibrosis remains an area of active investigation.

METHODS

Single-cell RNA sequencing (scRNA-seq) and immune infiltration analyses were employed to identify key immune cells and genes involved in renal fibrosis in CRS. Meta-analysis and pseudo-time analysis were conducted to validate the functional relevance of these genes. Functional studies utilizing CRISPR/Cas9 gene editing and lentiviral vectors assessed macrophage polarization and epithelial-to-mesenchymal transition (EMT). In vivo, a CRS mouse model was established, and fibrosis progression was tracked using histological and imaging methods.

RESULTS

The PKM2/mTORC1/YME1L signaling axis was identified as a critical pathway driving renal fibrosis, mediated by HIF-1α-induced M1 macrophage polarization. Inhibition of HIF-1α significantly alleviated renal fibrosis by restricting M1 polarization and suppressing the PKM2/mTORC1/YME1L axis. Co-culture models further demonstrated the involvement of EMT and metabolic reprogramming in affected cells.

CONCLUSION

Targeting the HIF-1α signaling pathway offers a promising therapeutic strategy for renal fibrosis by modulating macrophage polarization and the PKM2/mTORC1/YME1L axis.

Discovery of structurally diverse diazatricyclododecenes as lysosomotropic autophagy inhibitors

Lysosomotropic autophagy inhibitors were identified from a structurally diverse library of diazatricycloundecanes. Structure activity relationship (SAR) studies on the three side chain substituents (R1-R3) of diazatricycloundecane identified compound 1e as the most potent inducer of LC3-II protein accumulation. Mechanistic analysis revealed that compound 1e functions as a lysosomotropic agent, increasing lysosomal pH and inhibiting autophagy through lysosomal dysfunction. Furthermore, compound 1e was less cytotoxic compared to previously reported lysosomotropic agents and exhibited excellent drug-like physicochemical properties, surpassing those of classical lysosomotropic agents such as chloroquine and hydroxychloroquine.

Organelle-oriented nanomedicines in tumor therapy: Targeting, escaping, or collaborating?

Precise tumor therapy is essential for improving treatment specificity, enhancing efficacy, and minimizing side effects. Targeting organelles is a key strategy for achieving this goal and is a frontier research area attracting a considerable amount of attention. The concept of organelle targeting has a significant effect on the structural design of the nanodrugs employed. Most notably, the intricate interactions among different organelles in a tumor cell essentially create a unified system. Unfortunately, this aspect might have been somewhat overlooked when existing organelle-targeting nanodrugs were designed. In this review, we underscore the synergistic relationship among the various organelles and advocate for a holistic view of organelle-targeting design. Through the integration of biology and material science, recent advancements in organelle targeting, escaping, and collaborating are consolidated to offer fresh perspectives for the development of antitumor nanomedicines.

Regulation of mitochondrial apoptosis via siRNA-loaded metallo-alginate hydrogels: A localized and synergistic antitumor therapy

Preventing relapse after resection of a primary tumor continues to be an unmet clinical need. Development of adjuvant biomaterials with the capacity to kill residual cancer cells after tumor resection is of clinical importance. Here we developed a library of metallo-alginate hydrogels containing high concentrations of metallic ions such as Ca2+ in combination with Zn2+, Li+, or Mg2+ to disrupt Ca2+ homeostasis in the mitochondria of cancer cells by local hyperthermia. To synergistically kill tumor cells and suppress the growth of rechallenged tumors, we embedded oncogene-silencing nucleic acids (mTOR siRNA) loaded into polymerc nanoparticles (NPs) composed of poly (β-amino esters) in the metallo-alginate hydrogels, targeting cancer cells that activate multi-drug resistance pathways such PI3K/AKT/mTOR. Metabolomic studies showed alterations in the Warburg effect, mitochondrial transport, and the TCA cycle, confirming cancer cell damage. In vivo studies of this targeted therapy in mice demonstrated a sex-dependent effect. Male B16F10-tumor-bearing mice treated with the synergistic therapy showed restrained tumor growth. In contrast, no therapeutic effect was observed in female counterparts. Our results demonstrate that in situ-formed NP-loaded metallo-alginate hydrogels can modulate two distinct immune signaling networks that are relevant for enhancing cancer cell death. On the basis of our findings, this combination therapy emerges as a promising sex-dependent strategy for clinical translation.

Unravelling the epigenetic based mechanism in discovery of anticancer phytomedicine: Evidence based studies

Epigenetic mechanisms play a crucial role in the normal development and maintenance of tissue-specific gene expression patterns in mammals. Disruption of these processes can result in changes to gene function and the transformation of cells into a malignant state. Cancer is characterized by widespread alterations in the epigenetic landscape, revealing that it involves not only genetic mutations but also epigenetic abnormalities. Recent progress in the field of cancer epigenetics has demonstrated significant reprogramming of various components of the epigenetic machinery in cancer, such as DNA methylation, modifications to histones, positioning of nucleosomes, and the expression of non-coding RNAs, particularly microRNAs. The ability to reverse epigenetic abnormalities has given rise to the hopeful field of epigenetic therapy, which has shown advancement with the recent approval by the FDA of three drugs targeting epigenetic mechanisms for the treatment of cancer. In the present manuscript, a comprehensive review has been presented about the role of understanding the epigenetic link between cancer and mechanisms by which phytomedicine offers treatment avenues. Further, this review deciphers the significance of natural products in the identification of epigenetic therapeutics, the diversity of their molecular targets, the use of nanotechnology, and the creation of new strategies for overcoming the inherent clinical challenges associated with developing these drug leads.

Apatinib combined with paclitaxel suppresses synergistically TNBC progression through enhancing ferroptosis susceptibility regulated SLC7A11/GPX4/ACSL4 axis

Triple-negative breast cancer (TNBC) is highly heterogeneous, often leading to resistance to chemotherapy agents like paclitaxel (PTX) and resulting in suboptimal outcomes. The anti-angiogenic agent apatinib not only enhances chemotherapy sensitivity but also involves in regulating ferroptosis. However, the potential of combining apatinib with PTX to improve treatment efficacy in refractory TNBC by increasing tumor cell susceptibility to ferroptosis remains elusive. This study aims to elucidate whether inducing ferroptosis participates in the beneficial effects of apatinib combined with PTX to synergistically suppress TNBC. Herein, we demonstrated that the coadministration of apatinib and PTX exerted significant inhibitory effects on both primary tumor progression and distant metastases to pulmonary and hepatic tissues in TNBC-bearing murine models. Transcriptomic and proteomic analyses indicated that ferroptosis induction is a key mechanism by which the drug combination suppresses TNBC, as evidenced by a marked downregulation of SLC7A11, GPX4, NRF2, and FTH1, and a significant upregulation of ACSL4. In vitro, the combination of 5 μM apatinib and 8 nM PTX synergistically inhibited tumor cell proliferation, migration, and invasion. Notably, the combination therapy markedly augmented ferroptosis in tumor cells through the regulation of the SLC7A11/GPX4/ACSL4 axis, leading to increased intracellular iron accumulation and lipid peroxide generation, concomitant with a reduction in GSH levels. The effect of apatinib combined with PTX on enhancing ferroptosis susceptibility could be exploited as a combination treatment regimen for future TNBC therapy.

CircRUNX1 enhances the Warburg effect and immune evasion in non-small cell lung cancer through the miR-145/HK2 pathway

Non-small cell lung cancer (NSCLC) is acknowledged as the primary subtype of lung cancer. The Warburg effect, marked by elevated glucose consumption and lactate fermentation, is a prevalent characteristic of NSCLC. The mechanisms by which circRNA mediates the regulation of the Warburg effect and immune evasion in NSCLC remain unclear. This study found an elevated circRNA, circRUNX1, whiche promotes glycolysis and lactate generation, resulting in the infiltration of regulatory T cell (Treg) in NSCLC. circRUNX1 acts as a miR-145 sponge, inhibiting its negative regulation of the target gene HK2, therefore facilitating glycolysis and lactate generation. The accumulation of lactic acid in the tumor microenvironment promotes Treg cell proliferation and aids immune evasion. Functionally, the suppression of circRUNX1 significantly impedes tumor development both in vitro and in vivo. These findings collectively clarity a previously unexamined mechanism linking the circRUNX1/miR-145/HK2 axis in regulation of the Warburg effect and immune evasion in NSCLC.

Anticancer therapy-induced peripheral neuropathy in solid tumors: diagnosis, mechanisms, and treatment strategies

Anticancer therapy-induced peripheral neuropathy (PN) is a common adverse event during the diagnosis and treatment of solid tumors. The drug class, cumulative dose, and individual susceptibility affect the incidence and severity of PN. Owing to the lack of specific biomarkers and imaging tests, the diagnostic criteria for PN remain unclear. Moreover, the available and effective clinical treatment strategies are very limited, and most of the current drugs focus on symptom management rather than fundamental reversal of the disease course. The morbidity mechanisms of PN are diverse, including direct neurotoxicity, mitochondrial dysfunction, and disruption of axonal transport. Here, we summarize the diagnosis, mechanisms, and neuroprotective strategies of PN and discuss potential intervention treatments.

Vestigial-like family member 1 (VGLL1): An emerging candidate in tumor progression

Vestigial-like family member 1 (VGLL1), a product of an X-linked gene (VGLL1), belongs to a family of transcriptional co-activators including VGLL2, VGLL3 and VGLL4. These proteins are called vestigial-like because of the structural and functional similarities with the Drosophila ortholog vestigial (vg). VGLL1 is usually expressed in human placenta, and has also been detected in many aggressive cancers. For this reason, it is called an onco-placental protein. It can bind and activate the TEA-domain containing transcription factors TEAD1-4, and the interaction is mediated through a conserved 'valine-x-x-histidine-phenylalanine' domain (VxxHF, x denotes any amino acid) present in VGLL1 protein. Prior studies indicate a pro-tumorigenic role for this protein in several cancers including carcinoma of the breast. This review aims at summarizing our present knowledge about the functions of VGLL1, and the mechanisms that regulate its expression in cancer.

Unveiling EIF5A2: A multifaceted player in cellular regulation, tumorigenesis and drug resistance

The eukaryotic initiation factor 5A2 gene (EIF5A2) is a highly conserved and multifunctional gene that significantly influences various cellular processes, including translation elongation, RNA binding, ribosome binding, protein binding and post-translational modifications. Overexpression of EIF5A2 is frequently observed in multiple cancers, where it functions as an oncoprotein. Additionally, EIF5A2 is implicated in drug resistance through the regulation of various molecular pathways. In the review, we describe the structure and functions of EIF5A2 in normal cells and its role in tumorigenesis. We also elucidate the molecular mechanisms associated with EIF5A2 in the context of tumorigenesis and drug resistance. We propose that the biological roles of EIF5A2 in regulating diverse cellular processes and tumorigenesis are clinically significant and warrant further investigation.

Targeting sensitive and multidrug resistant leukemia cells with a novel benzofuran-isatin conjugate

Benzofuran-isatin conjugates are considered as promising compounds in cancer prevention and treatment. However, it is not known yet whether these compounds are useful to effectively treat multidrug-resistant tumors. In this study, we investigated the activity of G-5e, a novel benzofuran-isatin conjugate in a panel of cell lines exhibiting well-known drug resistance mechanisms (P-gp, BCRP, TP53, EGFR). P-glycoprotein overexpressing CEM/ADR5000 cell line displayed notable hypersensitivity (collateral sensitivity) to G-5e, which was mediated through autophagic cell death activation including downregulation of the autophagy suppressor RND2, upregulation of the autophagy inducer LC3B, and G0/G1 phase arrest during cell cycle progression. Independent of collateral sensitivity, transcriptomic analyses also revealed that G-5e caused downregulation of NF-κB and ERK1/2 pathways. Our findings highlight the potential of benzofuran-isatin conjugates to combat multidrug resistance and the role of RND2 for collateral sensitivity.

RNAa: Mechanisms, therapeutic potential, and clinical progress

RNA activation (RNAa), a gene regulatory mechanism mediated by small activating RNAs (saRNAs) and microRNAs (miRNAs), has significant implications for therapeutic applications. Unlike small interfering RNA (siRNA), which is known for gene silencing in RNA interference (RNAi), synthetic saRNAs can stably upregulate target gene expression at the transcriptional level through the assembly of the RNA-induced transcriptional activation (RITA) complex. Moreover, the dual functionality of endogenous miRNAs in RNAa (hereafter referred to as mi-RNAa) reveals their complex role in cellular processes and disease pathology. Emerging studies suggest saRNAs' potential as a novel therapeutic modality for diseases such as metabolic disorders, hearing loss, tumors, and Alzheimer's. Notably, MTL-CEBPA, the first saRNA drug candidate, shows promise in hepatocellular carcinoma treatment, while RAG-01 is being explored for non-muscle-invasive bladder cancer, highlighting clinical advancements in RNAa. This review synthesizes our current understanding of the mechanisms of RNAa and highlights recent advancements in the study of mi-RNAa and the therapeutic development of saRNAs.