Untangling the roles of TOP2A and TOP2B in transcription and cancer

SiRNA-mediated knockdown of TOP2B protects hiPSC-derived cardiomyocytes from doxorubicin-induced toxicity

AIMS

Doxorubicin (Dox) is a potent chemotherapeutic agent, but its use is limited by cardiotoxicity, primarily due to the disruption of Topoisomerase-2 beta (TOP2B) activity. Dexrazoxane (Dex), an FDA-approved cardioprotective drug, alleviates Dox-induced toxicity but lacks heart-specific targeting. This study investigates siRNA-mediated TOP2B knockdown as a more targeted strategy to protect cardiomyocytes from Dox-induced damage.

MATERIALS AND METHODS

Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) were treated with siRNA to knock down TOP2B and were then exposed to Dox. We compared the cardioprotective effects of siRNA-mediated knockdown to Dex treatment using cell viability, cell toxicity assay and electrophysiological evaluation was performed using a multielectrode array (MEA).

KEY FINDINGS

Our results demonstrate that TOP2B silencing significantly decreases apoptosis and improved cell viability, as compared to the Dex treatment. Additionally, electrophysiological assays using a Multielectrode Array (MEA) demonstrated enhanced contractility and conductivity in siRNA-treated hiPSC-CMs. Furthermore, transmission electron microscopy (TEM) data revealed that TOP2B knockdown preserves mitochondrial morphology and sarcomere structure, compared to Dox and Dex-treated groups.

SIGNIFICANCE

These findings suggest that siRNA-mediated TOP2B inhibition could provide a safer, more specific approach to mitigate Dox-induced cardiotoxicity.

Single-cell analyses unravel ecosystem dynamics and intercellular crosstalk during gallbladder cancer malignant transformation

BACKGROUND

Gallbladder cancer (GBC) is a rare but aggressive malignancy, often detected late due to early asymptomatic stages. Understanding cellular and molecular changes from normal tissue to high-grade intraepithelial neoplasia (HGIN) and invasive GBC is vital for identifying early biomarkers and therapeutic targets.

METHODS

We performed single-cell RNA sequencing on 98,113 cells derived from 2 normal adjacent tissues (NAT), 2 HGIN, and 6 GBC samples. The cellular diversity and heterogeneity, particularly within epithelial and immune cell populations in NAT-HGIN-GBC, were investigated utilizing single-cell RNA sequencing, bulk RNA sequencing (bulk RNA-seq), and 10 machine learning methodologies. Furthermore, the intercellular crosstalk between epithelial cells and tumor immune microenvironment cells was examined and validated through multiplex immunofluorescence staining.

RESULTS

The constructed cell atlas elucidated alterations in the immune landscape across various states of NAT-HGIN-GBC, highlighting a more pronounced inhibitory immune microenvironment in GBC. The epithelial subtype TOP2A+ Epi is markedly elevated in GBC and is correlated with a poor prognosis. Key genes associated with this subtype may include GMNN, CYTOR, KLK6, and BIRC5. Similarly, immunosuppressive macrophages, identified as TOP2A+ Macro, also increase along the NAT-HGIN-GBC sequence and are linked to reduced patient survival. Furthermore, TOP2A+ Macro and CD8+ exhausted T cells (CD8+ Tex) engage in intercellular communication with epithelial TOP2A+Epi cells via the TWEAK/FN14 signaling pathway, thereby promoting tumor progression and immune evasion in GBC. The findings were further corroborated through multiplex immunofluorescence staining conducted on specimens from patients.

CONCLUSIONS

This study elucidates significant alteration in the cellular ecosystems and intercellular signaling within the tumor immune microenvironment across the NAT-HGIN-GBC sequence. It identifies TOP2A, TWEAK, and FN14 as potential biomarkers and therapeutic targets for GBC.

Vincristine exerts antiglioma effects by inhibiting the PI3K/AKT signaling pathway: A mechanistic study based on network pharmacology, bioinformatics analysis, and experimental validation

In clinical settings, glioma patients often develop secondary resistance to first-line chemotherapy drugs. Vincristine has been reported for its application in cancer chemotherapy, but its molecular mechanism of action remains unclear. This study aimed to identify potential targets of vincristine in glioma using network pharmacology and to experimentally validate the possible molecular mechanisms against glioma. First, the potential targets of vincristine were predicted using CTD, SwissTargetPrediction, and TargetNet databases. Differential expression analysis and WGCNA algorithm were employed on glioma data from the GEO database to obtain important glioma-related target genes, which were then used to identify the anti-glioma targets of vincristine. The intersecting targets were input into the String database to construct a PPI network, and core targets were identified using the cytohubba plugin in Cytoscape. GO and KEGG analyses were conducted to investigate the functional and pathway enrichment of the intersecting targets. The expression and prognostic significance of the core targets were validated using data from the TCGA and HPA databases. Finally, the anti-glioma proliferation effect of vincristine was validated through CCK-8 assay, flow cytometry for cell cycle analysis, RT-qPCR, and Western blotting. A total of 175 vincristine targets and 1673 glioma targets were identified, with 11 shared targets between vincristine and glioma tissues. Network pharmacology studies suggested that CDC25B, CDK4, CDK6, TOP2A, and the PI3K/AKT signaling pathway might be important core targets and pathways through which vincristine exerts its anti-glioma effects. In vitro experiments confirmed that vincristine successfully inhibited U87 cell proliferation and induced G1 phase arrest via the PI3K/AKT signaling pathway, thereby reducing cell growth. The study results indicate that the PI3K/AKT signaling pathway may be involved in the mechanism by which vincristine inhibits the proliferation of glioma cells.

TOP2A Promotes Proliferation, Migration, and Inflammatory Response in M5-Treated Keratinocytes by Binding CTBP1 to Activate Wnt/β-Catenin Signaling

Psoriasis is a chronic cutaneous disease, affecting a significant portion of the global population. Topoisomerase II alpha (TOP2A) is upregulated in psoriasis samples, but the precise molecular mechanism remains unclear. We aimed to clarify the biological contribution of TOP2A in psoriasis progression. An in vitro psoriasis model was established on M5-induced keratinocytes (HaCaT cells) to simulate the psoriasis-like alterations. Following TOP2A knockdown without or with c terminal binding protein 1 (CTBP1) overexpression, CCK-8 and EDU staining were employed to analyze the viability and proliferation of HaCaT cells under M5 conditions. The capacities of HaCaT cell migration and invasion were examined with wound healing- and transwell assays. RT-qPCR and immunoblotting were adopted for evaluation of the inflammation and differentiation of M5-stimualted HaCaT cells. Additionally, the binding between TOP2A and CTBP1 was predicated using bioinformatics tools and detected by Co-IP. Finally, the expression of proteins in Wnt/β-catenin signaling was analyzed with the application of immunoblotting. Results suggested that TOP2A was upregulated in psoriasis skin lesions and M5-induced HaCaT cells. Interference with TOP2A attenuated the proliferation, migration, invasion, and inflammatory response in M5-treated HaCaT cells. In particular, TOP2A bound to CTBP1 and upregulated CTBP1 expression in HaCaT cells. Remarkably, CTBP1 upregulation blocked the impacts of TOP2A depletion on the biological behaviors of M5-treated HaCaT cells. Besides, TOP2A deficiency upregulated DKK1 expression as well as downregulated Wnt1, β-catenin, and c-Myc expression in HaCaT cells exposed to M5, which was restored by further CTBP1 overexpression. In summary, TOP2A binds CTBP1 to activate Wnt/β-catenin signaling, thereby promoting the progression of psoriasis.

Topobexin targets the Topoisomerase II ATPase domain for beta isoform-selective inhibition and anthracycline cardioprotection

Topoisomerase II alpha and beta (TOP2A and TOP2B) isoenzymes perform essential and non-redundant cellular functions. Anthracyclines induce their potent anti-cancer effects primarily via TOP2A, but at the same time they induce a dose limiting cardiotoxicity through TOP2B. Here we describe the development of the obex class of TOP2 inhibitors that bind to a previously unidentified druggable pocket in the TOP2 ATPase domain to act as allosteric catalytic inhibitors by locking the ATPase domain conformation with the capability of isoform-selective inhibition. Through rational drug design we have developed topobexin, which interacts with residues that differ between TOP2A and TOP2B to provide inhibition that is both selective for TOP2B and superior to dexrazoxane. Topobexin is a potent protectant against chronic anthracycline cardiotoxicity in an animal model. This demonstration of TOP2 isoform-specific inhibition underscores the broader potential to improve drug specificity and minimize adverse effects in various medical treatments.

Exploring the Anti-Leukemic Effect of the Synthetic Retinoid ST1926 on Malignant T Cells: A Comprehensive Proteomics Approach

T-cell malignancies represent a group of complex cancers arising from T cells and include aggressive subtypes such as Adult T-cell Leukemia/Lymphoma (ATL) and T-cell Acute Lymphoblastic Leukemia (T-ALL). Patients with these aggressive subtypes still represent an unmet medical condition. The synthetic adamantyl retinoid ST1926, a potent DNA polymerase-α inhibitor, proved a promising potency in preclinical models of ATL and peripheral T-cell lymphoma. Using advanced liquid chromatography-mass spectrometry (LC-MS/MS) techniques, we explored the effects of ST1926 on global protein expression in ATL (HuT-102) and T-ALL (MOLT-4) cells. We demonstrate that ST1926 triggers differentiation and apoptosis in malignant T-cells while halting tumor progression. Evidence at the proteomics level reveals the impact of ST1926 on crucial DNA replication enzymes and cell cycle regulation, highlighting its potential to reduce leukemogenesis and promote apoptosis. Our findings underscore the potential of ST1926 as an innovative therapeutic approach to address these aggressive T-cell malignancies, providing valuable insights into developing new targeted therapies and improving the outcomes and prognosis of patients with these challenging diseases.

Renal tubular epithelial cell related partial epithelial-mesenchymal transition in AAⅠ induced renal fibrosis via Wnt7b/β-catenin signaling

Introduction

This study investigates the pathological progressions in kidneys affected by aristolochic acid nephropathy (AAN) and explores the molecular mechanisms underlying the fibrotic process, specifically focusing on the Wnt7b/β-catenin signaling pathway.

Methods

Both mice and human kidney-2 (HK-2) cells were treated with aristolochic acid I (AAI). In mice, we monitored blood urea nitrogen (BUN), serum creatinine (Scr), kidney injury molecule-1 (KIM-1), pathological modifications of renal tubular epithelial cells (RTECs), and fibrosis degrees during acute/chronic disease phases. Wnt7b/β-catenin expression was evaluated through transcriptome analysis and laboratory assays (immunohistochemistry, Western blotting, immunoelectron microscopy) in acute AAN and cultured cells. Concurrent assays measured representative proteins: Aquaporin 1 (AQP1), Topoisomerase IIα (TOP2A), Vascular Cell Adhesion Molecule-1 (VCAM-1), and α-smooth muscle actin (α-SMA) in chronic AAN RTECs.

Results

AAI increased Scr, BUN, and KIM-1 levels by causing RTEC necrotic shedding in acute stages and promoted renal interstitial fibrosis chronically. Elevated Wnt7b pathway proteins enhanced damaged RTEC regeneration, with regenerated cells expressing mesenchymal proteins VCAM-1 and α-SMA.

Discussion

The Wnt7b/β-catenin signaling pathway connects acute tubule damage to fibrosis, explaining AAN's pathological continuum. These findings clarify how acute injury progresses to chronic fibrosis in AAN.

Integrative PPI network and random forest analysis identifies KIF4A, TOP2A, and ASPM protein macromolecules as novel protein biomarkers in renal carcinoma pathogenesis

The pathogenesis of kidney cancer is not fully understood, so there is an urgent need to identify new biomarkers to improve diagnosis and treatment. The study identified KIF4A, TOP2A and ASPM as novel protein biomarkers for renal cancer and explored their biological functions in the development and progression of renal cancer. A variety of bioinformatics methods were used to process and batch calibrate the transcriptome data of renal cancer. Differential gene expression analysis was performed using Limma packages, followed by functional enrichment analysis to identify biological pathways associated with kidney cancer. Construct a protein-protein interaction (PPI) network to prioritize core genes and use machine learning methods to further screen key signaling pathways. Epithelial-mesenchymal transition (EMT) marker score was used to evaluate the prognosis of renal carcinoma, and the results were validated by cell culture experiment. Integrated principal component analysis (PCA) showed significant effect of batch correction in the renal cancer cohort. Transcriptome analysis revealed dysregulation of conserved gene expression in renal carcinoma. Functional enrichment analysis showed that metabolic and immune signaling pathways play an important role in the pathogenesis of renal cancer. The integrated PPI network prioritising KIF4A, TOP2A and ASPM as key mitotic regulators and further confirming these three as core carcinogenic drivers through machine learning. Finally, integrated prognostic analyses identified genetic features associated with EMT that are clinically significant.

Dietary Intake of Octanoic Acid Restores UBE3A Expression and Improves the Behavioral Phenotypes in a Mouse Model of Angelman Syndrome

Angelman syndrome (AS) is a severe neurodevelopmental disorder with no effective therapies. Most of the behavioral deficits observed in AS patients arise from the absence of ubiquitin protein ligase E3A (UBE3A) in the brain during development, driven by the loss of maternally expressed UBE3A and silencing of the paternal copy of this gene through imprinting. Safe and effective therapies aiming at restoring the expression of the paternal UBE3A gene early in human life are currently lacking. In this study, we investigated whether octanoic acid (OA), a medium-chain fatty acid, could unsilence the paternal Ube3a allele in neurons and ameliorate the behavioral defects in a murine model of AS. To this end, Ube3am-/p+ and Ube3am+/pYFP mice, as well as their wild-type littermates, were fed either a control or OA-supplemented diet from postnatal day 0 through adulthood, and the improvements in AS-related cellular and behavioral deficits were characterized. We demonstrate that dietary intake of OA activates the expression of the silenced, paternal Ube3a in neurons and improves select AS behavioral phenotypes in mice. We further show that downregulation of topoisomerase II beta and restoration of dendritic spine development may underlie the unsilencing of Ube3a and the behavioral improvements in OA-supplemented animals, respectively. Together, our findings suggest that dietary supplementation with OA could serve as an early, safe, and clinically feasible therapeutic strategy for reactivation of the paternal UBE3A allele in patients with AS.

Discovery and therapeutic exploitation of Master Regulatory miRNAs in Glioblastoma

Glioblastoma is a fatal primary malignant brain tumor. Despite therapies involving surgical resection, chemotherapy, and radiation therapy, the average survival for glioblastoma patients remains at approximately 15 months. MicroRNAs (miRNAs) are short noncoding RNA molecules that regulate the expression of the majority of human genes. Numerous genes are concurrently deregulated in glioblastoma. Consequently, molecular monotherapies have failed to achieve improvements in clinical outcomes. Several lines of evidence suggest that simultaneous targeting of several deregulated molecules is required to achieve better therapies. However, the simultaneous targeting of several deregulated oncogenic drivers is severely limited by the fact that the drugs needed to target many deregulated molecules do not currently exist, and because combining several drugs in a clinical setting leads to an exponential increase in toxicity. We hypothesized that we can develop and use miRNA to simultaneously inhibit multiple deregulated genes for more efficacious glioblastoma therapies. The goal of this study was therefore to identify master regulatory microRNAs (miRNAs) and use them to simultaneously target multiple deregulated molecules for GBM therapy. We defined master regulatory miRNAs as those that target several deregulated genes in glioblastoma. To find master regulatory miRNAs, we first used PAR-CLIP screenings to identify all targets of all miRNAs in glioblastoma cells. We then analyzed TCGA tumor data to determine which of these targets are deregulated in human tumors. We developed and used an algorithm to rank these targets for significance in glioblastoma malignancy based on their magnitude of deregulation, frequency of deregulation, and correlation with patient survival. We then ranked the miRNAs for their capacity of targeting multiple glioblastoma-deregulated genes and therefore the potential to exhibit strong anti-tumor effects when delivered as therapy. Using this strategy, we selected two tumor suppressor master regulatory miRNAs, miR-340, miR-382 and an oncogenic master regulatory miRNA, miR-17. We validated the target genes of the miRNAs and showed that they form part of important glioblastoma regulatory pathways. We then showed that the miRNAs (miR-340 and miR-582) or the miR-17 inhibitor have strong inhibitory effects on glioblastoma cell growth, survival, invasion, stemness and in vivo tumor growth. Ultimately, we developed and successfully tested a new therapeutic approach to delivery miR-340 using MRI guided focused ultrasound and microbubbles (FUS-MB) and special brain penetrating nanoparticles (BPN). This approach resulted in a substantial reduction in tumor volume and prolongation of the survival of glioblastoma-bearing mice and can be translated into clinical trials. We therefore developed and successfully tested a novel strategy to discover and deliver miRNAs for glioblastoma and cancer therapy.

Identification of key hub genes and potential therapeutic drugs for nasopharyngeal carcinoma: Insights into molecular mechanisms and treatment strategies

OBJECTIVE

Nasopharyngeal Carcinoma (NPC) is a highly malignant cancer with a high incidence in East and Southeast Asia, including southern China. Despite advances in treatment, the prognosis for advanced NPC remains poor due to high recurrence and metastasis rates. The molecular mechanisms driving NPC progression are not fully understood, and identifying key genes and potential therapeutic agents is critical. This study aims to uncover critical genes and screen therapeutic drugs, providing insights into NPC pathogenesis and novel treatment strategies.

METHODS

Three GEO datasets (GSE12452, GSE53819, and GSE61218) were analyzed to identify overlapping Differentially Expressed Genes (DEGs) in NPC. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) were used to explore the biological roles of DEGs. Protein-Protein Interaction (PPI) and mRNA-miRNA-lncRNA interaction networks were constructed to identify key hub genes. Potential therapeutic drugs were predicted via a Drug-Gene Interaction network. The overexpression of hub genes was validated in NPC cells using CCK-8 assays, and the anti-proliferative effects of three drugs ‒ valproic acid, cyclosporine, and calcitriol ‒ were tested.

RESULTS

Eight hub genes (ASPM, BIRC5, BUB1B, CDK1, KIF23, PBK, TOP2A, and TTK) were identified, with ASPM reported for the first time in the context of NPC. Overexpression of these genes significantly promoted NPC cell proliferation. Among the tested drugs, calcitriol exhibited the most potent anti-proliferative effect, with IC50 values of 0.90 μM, 0.47 μM, and 0.31 μM at 24-, 48-, and 72-hs, respectively.

CONCLUSION

This study identified eight key genes as potential biomarkers for NPC and validated calcitriol as a promising therapeutic agent, providing a foundation for further research into NPC treatment.

LEVEL OF EVIDENCE

Level 2 (Individual cross-sectional studies or systematic review of surveys that allow matching to local circumstances).

Extrachromosomal DNA replication and maintenance couple with DNA damage pathway in tumors

Extrachromosomal DNA (ecDNA) drives the evolution of cancer cells. However, the functional significance of ecDNA and the molecular components involved in its replication and maintenance remain largely unknown. Here, using CRISPR-C technology, we generated ecDNA-carrying (ecDNA+) cell models. By leveraging these models alongside other well-established systems, we demonstrated that ecDNA can replicate and be maintained in ecDNA+ cells. The replication of ecDNA activates the ataxia telangiectasia mutated (ATM)-mediated DNA damage response (DDR) pathway. Topoisomerases, such as TOP1 and TOP2B, play a role in ecDNA replication-induced DNA double-strand breaks (DSBs). A subset of these elevated DSBs persists into the mitotic phase and is primarily repaired by the alternative non-homologous end joining (alt-NHEJ) pathway, which involves POLθ and LIG3. Correspondingly, ecDNA maintenance requires DDR, and inhibiting DDR impairs the circularization of ecDNA. In summary, we demonstrate reciprocal interactions between ecDNA maintenance and DDR, providing new insights into the detection and treatment of ecDNA+ tumors.

Investigation of multi-drug resistant Candida auris using species-specific molecular markers in immunocompromised patients from a tertiary care hospital in Quetta, Pakistan

INTRODUCTION

Candida auris is an emerging multidrug-resistant pathogen responsible for nosocomial infections worldwide, characterized by high mortality rates and significant challenges in detection due to frequent misidentification. Classified by the WHO as a pathogen of critical importance since it exhibits resistance to multiple antifungal agents, particularly fluconazole, and is highly transmissible in healthcare settings. Conventional detection methods often lack the accuracy required for effective infection control. This study aimed to conduct inferential and molecular analyses of C. auris and other yeast species infecting immunocompromised patients in the Special and Intensive Care Units (SCU and ICU) of a tertiary care hospital in Quetta, Pakistan. In this region, C. auris remains rarely studied and is frequently misdiagnosed by clinical staff due to limited awareness and diagnostic challenges. Notably, no prior research has been conducted on C. auris in Quetta. The study also sought to develop reliable diagnostic methods suitable for resource-limited settings, addressing a critical gap in healthcare infrastructure.

MATERIALS AND METHODS

Samples (150 each) from the ear, axilla, groin, and saliva of SCU/ICU patients were collected and processed on yeast malt agar, with preliminary identification using Brilliance Candida Agar (BCA) and CHROMagar Candida Plus (CCP). Advanced techniques, including PCR amplification of ITS regions, DNA sequencing, RFLP with Msp1, MALDI-TOF, Vitek 2, and species-specific primers, were used for identification. Antifungal susceptibility to fluconazole, amphotericin B, and voriconazole were also assessed.

RESULTS

The culture test revealed that 42.6% samples were positive for yeast infections. In addition to detecting Candida auris in 4 cultures, chromogenic media identified 6 other Candida species: C. albicans, C. dubliniensis, C. glabrata, C. krusei, C. parapsilosis, and C. tropicalis. Further validation through advanced techniques, including molecular diagnostics and MALDI-TOF, enabled the identification of additional species: C. famata, C. kefyr, C. lusitaniae, and Meyerozyma (Candida) guilliermondii. Out of all identified yeast species C. dubliniensis was the most common, followed by C. albicans and C. tropicalis, with the highest infection rates observed in saliva samples. Antifungal Susceptibility Tests (AST) revealed that C. auris isolates were resistant to Fluconazole, Amphotericin B, and Voriconazole, highlighting multidrug resistance. This study represents the first report of novel multidrug-resistant C. auris from Quetta, Pakistan, indicating that C. auris is prevalent among ICU and SCU patients. Novel species specific primers targeting phospholipase B, topoisomerase II, CDR and 18s genes were designed in our laboratory and not previously reported in earlier studies, proved highly effective for the rapid identification of Candida species. The established protocol using these primers is recommended for implementation in resource-limited laboratory settings. The statistical analysis demonstrated significant correlations between Candida species infection (dependent variable) and several independent factors (variables) emphasizing the importance of targeted diagnostics and intervention strategies.

Hsa_circ_0072088 promotes non-small cell lung cancer progression through modulating miR-1270/TOP2A axis

According to the data released by the International Agency for Research on Cancer (IARC) in 2020, lung cancer ranks second among newly diagnosed malignant tumors globally. As a special class of non-coding RNA, circRNA has become a new hotspot in the field of biomarker research. With the continuous deepening of molecular-level investigations, the underlying mechanisms of circRNA are being gradually unveiled. The more widely studied mechanism is the competitive endogenous RNA mechanism of circRNA. Studies related to circRNA expression were searched in GEO database and statistically analyzed using the "limma" package and weighted gene co-expression network analysis. The expression of circRNA, microRNA and mRNA in cells and tissues were examined via qRT-PCR. MTS assay was used to measure cell proliferation, Transwell assay was used to measure cell migration, and apoptosis assay was carried out to detect cell apoptosis. Additionally, a dual-luciferase reporter assay was further executed to explore the targeted binding relationships between circRNA-microRNA and microRNA-mRNA. It was discovered that hsa_circRNA_103809 was differentially highly expressed in non-small cell lung cancer cells, whereas miR-1270 was differentially lowly expressed. The knockdown of circ_0072088 inhibited the cell proliferation and migration, while promoting cell apoptosis. The same biological function was found with the overexpression of miR-1270. The rescue experiment further validated that circ_0072088 could regulate the biological function of cells by influencing miR-1270. Finally, the targeted binding relationship was verified by dual luciferase reporting experiment. In conclusion, circ_0072088 is differentially highly expressed in non-small cell lung cancer and can affect the progression of non-small cell lung cancer through the circ_0072088/miR-1270/TOP2A axis.

Deciphering the heterogeneity of epithelial cells in pancreatic ductal adenocarcinoma: implications for metastasis and immune evasion

OBJECTIVE

This study examines the cellular heterogeneity of epithelial cells within pancreatic ductal adenocarcinoma (PDAC) and their contributions to tumor progression, metastasis, and immunosuppressive interactions using single-cell RNA sequencing.

METHODS

Single-cell RNA-sequencing data from two datasets (GSE154778 and GSE158356) were integrated using the Harmony algorithm, followed by quality control, clustering, and differential gene expression analysis. Distinct subpopulations of epithelial cells were identified, and their gene expression profiles were analyzed. To assess the malignancy of these subpopulations, single-cell copy number variation (CNV) analysis and trajectory analysis were conducted. Additionally, intercellular communication was examined using the CellChat platform.

RESULTS

The analysis revealed pronounced heterogeneity among PDAC epithelial cells, with specific subpopulations exhibiting distinct roles in tumor proliferation, extracellular matrix remodeling, and metastatic dissemination. Subpopulations 4 and 6 were characterized by increased CNV levels and a more malignant phenotype, suggesting an enhanced capacity for metastasis. Single-cell trajectory analysis, along with CellChat, mapped the temporal evolution of epithelial cells, identifying key regulatory genes such as DCBLD2 and JUN. A prognostic model incorporating five key genes, including KLF6, was developed and demonstrated strong predictive accuracy for patient outcomes. Notably, KLF6 emerged as a critical prognostic marker associated with immune modulation, particularly through interactions with M2 macrophages.

CONCLUSION

The study highlights the pronounced heterogeneity of epithelial cells in PDAC and their distinct contributions to tumor progression, metastasis, and immune modulation. Through single-cell transcriptomic and CNV analyses, we identified epithelial subpopulations with varying malignant potentials and distinct interactions with the tumor microenvironment. Among these, KLF6 emerged as a key regulator associated with immune modulation and metastasis. Our findings emphasize the significance of epithelial cell heterogeneity in shaping pancreatic cancer progression. These insights provide a foundation for future investigations into novel prognostic markers and therapeutic strategies.

HJURP modulates cell proliferation and chemoresistance via the MYC/TOP2A transcriptional axis in gastric cancer

Background

The histone chaperone Holliday Junction Recognition Protein (HJURP) has been associated with multiple types of cancers, but its role in GC is not yet fully understood. Considering its functions in centromere stability and DNA repair, investigating HJURP's role in GC may offer novel therapeutic perspectives.

Methods

HJURP expression was examined in a dataset comprising TCGA-STAD samples and an internal group of GC patients, utilizing RNA sequencing and Western blot techniques. Functional experiments were carried out on the AGS and HGC-27 GC cell lines. The expression levels of HJURP, MYC, and Topoisomerase II alpha (TOP2A) were assessed via quantitative real-time PCR and Western blot. Proliferation rates of the cells were determined through EdU, CCK-8, and colony formation assays.

Results

Compared to adjacent normal tissues, HJURP expression was notably increased in GC tissues, a finding consistent across both the TCGA-STAD database and our internal patient group. Silencing HJURP markedly reduced GC cell growth and chemoresistance. Mechanistically, HJURP enhanced MYC stability, which in turn promoted TOP2A transcription. Rescue experiments confirmed that overexpression of TOP2A alters proliferation and chemoresistance of GC cells with HJURP knockdown, indicating the dependency of this axis on MYC activity.

Conclusion

Our study demonstrates that HJURP is critical for promoting GC proliferation and chemoresistance through the regulation of the MYC/TOP2A transcriptional network. Targeting HJURP might offer a novel therapeutic avenue for GC, necessitating further exploration of its clinical potential. This work underscores the value of investigating histone chaperones as potential targets in cancer treatment.

Causes and consequences of DNA double-stranded breaks in cardiovascular disease

The genome, whose stability is essential for survival, is incessantly exposed to internal and external stressors, which introduce an estimated 104 to 105 lesions, such as oxidation, in the nuclear genome of each mammalian cell each day. A delicate homeostatic balance between the generation and repair of DNA lesions maintains genomic stability. To initiate transcription, DNA strands unwind to form a transcription bubble and provide a template for the RNA polymerase II (RNAPII) complex to synthesize nascent RNA. The process generates DNA supercoils and introduces torsional stress. To enable RNAPII processing, the supercoils are released by topoisomerases by introducing strand breaks, including double-stranded breaks (DSBs). Thus, DSBs are intrinsic genomic features of gene expression. The breaks are quickly repaired upon processing of the transcription. DNA lesions and damaged proteins involved in transcription could impede the integrity and efficiency of RNAPII processing. The impediment, which is referred to as transcription stress, not only could lead to the generation of aberrant RNA species but also the accumulation of DSBs. The latter is particularly the case when topoisomerase processing and/or the repair mechanisms are compromised. The DSBs activate the DNA damage response (DDR) pathways to repair the damaged DNA and/or impose cell cycle arrest and cell death. In addition, the release of DSBs into the cytosol activates the cytosolic DNA-sensing proteins (CDSPs), which along with the nuclear DDR pathways induce the expression of senescence-associated secretory phenotype (SASP), cell cycle arrest, senescence, cell death, inflammation, and aging. The primary stimulus in hereditary cardiomyopathies is a mutation(s) in genes encoding the protein constituents of cardiac myocytes; however, the phenotype is the consequence of intertwined complex interactions among numerous stressors and the causal mutation(s). Increased internal DNA stressors, such as oxidation, alkylation, and cross-linking, are expected to be common in pathological conditions, including in hereditary cardiomyopathies. In addition, dysregulation of gene expression also imposes transcriptional stress and collectively with other stressors provokes the generation of DSBs. In addition, the depletion of nicotinamide adenine dinucleotide (NAD), which occurs in pathological conditions, impairs the repair mechanism and further facilitates the accumulation of DSBs. Because DSBs activate the DDR pathways, they are expected to contribute to the pathogenesis of cardiomyopathies. Thus, interventions to reduce the generation of DSBs, enhance their repair, and block the deleterious DDR pathways would be expected to impart salubrious effects not only in pathological states, as in hereditary cardiomyopathies but also aging.

A Multicenter Prospective Observational Study to Examine the Experience of Using Phosphocreatine in Combination Therapy for Heart Failure Caused by Cancer Treatment. Rationale and Design of the Study

Enhanced cancer treatment efficacy has resulted in a significant increase in the number of cancer survivors after the cure of malignant tumors. However, cardiovascular morbidity, including chronic heart failure, has become the leading cause of death and decreased life expectancy among cancer survivors. This is due, in particular, to the cardiotoxic effects of anticancer drugs and associated factors. Cardioprotective approaches aim to reduce the incidence and severity of cardiotoxicity through the use of cardioprotective agents (e.g., dexrazoxane), liposomal drug delivery systems (e.g., liposomal doxorubicin), and optimization of drug administration schedules. Reducing the cardiotoxicity of cancer treatments is a clinically important goal. Phosphocreatine-based therapy represents a potentially valuable new strategy in this area. In this regard, the study "Multicenter prospective observational study to investigate the experience of using phosphocreatine in combination therapy for heart failure caused by cancer treatment" was initiated. This publication presents the protocol of the observational non-interventional NEOCARD study.

Unravelling the transcriptomic characteristics of bronchoalveolar lavage in post-covid pulmonary fibrosis

BACKGROUND

Post-Covid Pulmonary Fibrosis (PCPF) has emerged as a significant global issue associated with a poor quality of life and significant morbidity. Currently, our understanding of the molecular pathways of PCPF is limited. Hence, in this study, we performed whole transcriptome sequencing of the RNA isolated from the bronchoalveolar lavage (BAL) samples of PCPF and compared it with idiopathic pulmonary fibrosis (IPF) and non-ILD (Interstitial Lung Disease) control to understand the gene expression profile and associated pathways.

METHODS

BAL samples from PCPF (n = 3), IPF (n = 3), and non-ILD Control (n = 3) (individuals with apparent healthy lung without interstitial lung disease) groups were obtained and RNA were isolated for whole transcriptomic sequencing. Differentially Expressed Genes (DEGs) were determined followed by functional enrichment analysis and qPCR validation.

RESULTS

A panel of differentially expressed genes were identified in bronchoalveolar lavage fluid cells (BALF) of PCPF as compare to control and IPF. Our analysis revealed dysregulated pathways associated with cell cycle regulation, immune responses, and neuroinflammatory processes. Real-time validation further supported these findings. The PPI network and module analysis shed light on potential biomarkers and underscore the complex interplay of molecular mechanisms in PCPF. The comparison of PCPF and IPF identified a significant downregulation of pathways that were more prominent in IPF.

CONCLUSION

This investigation provides crucial insights into the molecular mechanism of PCPF and also outlines avenues for prospective research and the development of therapeutic approaches.

Comprehensive genomic dependency landscape of a human colon cancer organoid

Identifying genetic dependencies in human colon cancer could help identify effective treatment strategies. Genome-wide CRISPR-Cas9 dropout screens have the potential to reveal genetic dependencies, some of which could be exploited as therapeutic targets using existing drugs. In this study, we comprehensively characterized genetic dependencies present in a colon cancer organoid avatar, and validated tumor-specific selectivity of select pharmacologic agents. We conducted a genome-wide CRISPR dropout screen to elucidate the genetic dependencies that interacted with select driver somatic mutations. We found distinct genetic dependencies that interacted with WNT, MAPK, PI3K, TP53, and mismatch repair pathways and validated targets that could be exploited as treatments for this specific subtype of colon cancer. These findings demonstrate the utility of functional genomic screening in the context of personalized medicine.

A convenient single-cell newly synthesized transcriptome assay reveals FLI1 downregulation during T-cell activation

Sequencing newly synthesized transcriptome alongside regular transcriptome in single cells enables the study of gene expression temporal dynamics during rapid chromatin and gene regulation processes. Existing assays for profiling single-cell newly synthesized transcriptome often require specialized technical expertise to achieve high cellular throughput, limiting their accessibility. Here, we developed NOTE-seq, a method for simultaneous profiling of regular and newly synthesized transcriptomes in single cells with high cellular throughput. NOTE-seq integrates 4-thiouridine labeling of newly synthesized RNA, thiol-alkylation-based chemical conversion, and a streamlined 10X Genomics workflow, making it accessible and convenient for biologists without extensive single-cell expertise. Using NOTE-seq, we investigated the temporal dynamics of gene expression during early-stage T-cell activation, identified transcription factors and regulons in Jurkat and naïve T cells, and uncovered the down-regulation of FLI1 as a master transcription factor upon T-cell stimulation. Notably, topoisomerase inhibition led to the depletion of both topoisomerases and FLI1 in T cells through a proteasome-dependent mechanism driven by topoisomerase cleavage complexes, highlighting potential complications topoisomerase-targeting cancer chemotherapies could pose to the immune system.

CENPF (+) cancer cells promote malignant progression of early-stage TP53 mutant lung adenocarcinoma

The prevention and precise treatment of early-stage lung adenocarcinoma (LUAD) characterized by small nodules (stage IA) remains a significant challenge for clinicians, which is due largely to the limited understanding of the oncogenic mechanisms spanning from preneoplasia to invasive adenocarcinoma. Our study highlights the pivotal role of cancer cells exhibiting high expression of centromere protein F (CENPF), driven by TP53 mutations, which become increasingly prevalent during the transition from preneoplasia to invasive LUAD. Biologically, cancer cells (CENPF+) exhibited robust proliferative and stem-like capabilities, thereby propelling the malignant progression of early-stage LUAD. Clinically, autoantibodies against CENPF in the serum and elevated cancer cells (CENPF+) in tissue correlated positively with the progression of early-stage LUAD, especially those in stage IA. Our findings suggest that cancer cells (CENPF+) play a central role in orchestrating the malignant evolution of LUAD and hold potential as a novel biomarker for early-stage detection and management of the disease.

Ursolic Acid as a Protective Agent against UVB-Induced Metabolic and Epigenetic Alterations in Human Skin Keratinocytes: An Omics-Based Study

This study aimed to assess how ursolic acid (UA) can protect human skin keratinocytes from damage caused by UVB radiation. Utilizing an omics-based approach, we characterized the features of photodamage and investigated the potential of UA to reverse HaCaT cell subpopulation injury caused by UVB radiation. The most significant changes in metabolite levels after UA treatment were in pathways associated with phosphatidylcholine biosynthesis and arginine and proline metabolism. Treatment with UA can reverse the levels of certain metabolites, including creatinine, creatine phosphate, and succinic acid. Pathways activated by UA treatment in UVB-irradiated HaCaT cells were associated with several biological processes, including the positive regulation of protein modification process, cell division, and enzyme-linked receptor protein signaling pathway. Treatment with UA demonstrates the capability to mitigate the effects of UVB radiation on specific genes, including S100 calcium-binding protein A9 and IL6 receptor. DNA/CpG methylation indicates that UA can partially reverse some of the alterations in the UVB-induced CpG methylome. Utilizing integrated RNA sequencing and methylation sequencing data, starburst plots illustrate the correlation between mRNA expression and CpG methylation status. UA potentially influences the metabolic pathway of glycerophospholipid metabolism by modulating the expression of several key enzymes, including phospholipase A2 group IIA and lipin 2. Altogether, these results indicate that UVB radiation induces metabolic reprogramming, epigenetic changes, and transcriptomic shifts. Meanwhile, UA demonstrates the capacity to inhibit or reduce the severity of these alterations, which may underlie its potential protective role against skin damage caused by UVB exposure. Prevention Relevance: Our research indicates that UA has the potential to mitigate or lessen the impact of UVB radiation, which is known to cause metabolic reprogramming, epigenetic alterations, and transcriptomic changes. These effects could be responsible for UA's possible protective function against skin damage induced by UVB exposure.

Multi-omics analysis reveals the panoramic picture of TOP2A in pan-cancer

Topoisomerases are critical nuclear enzymes that resolve DNA topological challenges during genetic processes. However, there is currently a lack of comprehensive multi-omics analysis of TOP2A from a pan-cancer perspective, despite its significance. A multiomics analysis was conducted to investigate TOP2A across various cancer types. This study involved the integration of over 10,000 multidimensional genomic datasets from 33 distinct cancer types, obtained from The Cancer Genome Atlas (TCGA). The analysis focused on evaluating the overall activity levels of TOP2A in pan-cancers, which encompassed differential expression, clinical significance, immune cell infiltration, and the regulation of pathways related to cancer. Aberrant epigenetic modifications and genomic alterations have been identified as being associated with the dysregulation of TOP2A expression levels. These molecular changes have substantial impacts on cancer progression, intratumoral heterogeneity, immunological status, and the regulation of pathways related to cancer biomarkers. Consequently, patient prognosis varies significantly based on the presence and specific nature of these alterations. The potential of TOP2A to serve as a novel biomarker for prognosis may offer valuable insights into the diagnosis and treatment of cancer.

Targeting the AURKB-MAD2L2 Axis Disrupts the DNA Damage Response and Glycolysis to Inhibit Colorectal Cancer Progression

BACKGROUND

Dysregulated metabolic pathways, including glycolysis and a compromised DNA damage response (DDR), are linked to the progression of colorectal cancer (CRC). The mitotic arrest deficient-like 2 (MAD2L2) and aurora kinase B (AURKB) genes play roles in cell cycle regulation and the DDR, making them potential targets for CRC therapy.

METHODS

Differential expression analysis was performed using The Cancer Genome Atlas-Colon Adenocarcinoma (TCGA-COAD) and GSE47074 datasets. A predictive model was established, and gene expression levels were further analyzed. The Gene Expression Profiling Interaction Analysis database and co-immunoprecipitation experiments assessed the correlation between AURKB and MAD2L2. Knockdown experiments in CRC cell lines further investigated the role of AURKB, followed by analyses of cell behavior, oxidative stress, glycolysis, DDR, and interaction with MAD2L2.

RESULTS

The risk model identified six prognostic genes (BUB1 mitotic checkpoint serine/threonine kinase B (BUB1B), AURKB, aurora kinase A (AURKA), exonuclease 1 (EXO1), topoisomerase II alpha (TOP2A), cyclin A2 (CCNA2)) associated with CRC, which were significantly expressed in tumor samples from the TCGA-COAD and GSE47074 datasets. In vitro assays confirmed that AURKB knockdown inhibited CRC cell behavior, induced G1 cell cycle arrest, and increased oxidative stress and apoptosis. AURKB knockdown also impaired glycolysis, reducing lactate production, glucose uptake, and ATP levels. Overexpression of MAD2L2 partially reversed these effects, restored glycolytic activity, and mitigated the cell cycle arrest and DDR caused by AURKB knockdown.

CONCLUSION

AURKB regulates CRC progression by modulating glycolysis and DDR pathways. Targeting the AURKB-MAD2L2 axis offers a promising therapeutic strategy for disrupting fundamental metabolic and DNA repair mechanisms in CRC.

Mechanisms of Picrasma quassioides against hepatocellular carcinoma elucidated by network pharmacology and experimental validation

OBJECTIVE

The medicinal plant Picrasma quassioides (P. quassioides) Benn exerts an inhibitory effect on the growth of hepatocellular carcinoma (HCC) cells via an unknown mechanism. This study explored the targets and signaling pathways underlying the mechanism of P. quassioides against HCC.

METHODS

Targets of P. quassioides active compounds were identified using the HERB database, and the HCC targets were found with the GeneCards database. The optimal serum concentration and intervention time were determined using the CCK-8 assay. Apoptosis, cell cycle, invasion, cloning, and wound-healing abilities were assessed using flow cytometry. Core protein targets and signaling pathway-related metabolic enzymes were evaluated with Western blotting. The anti-HCC effect of P. quassioides medicated serum was verified using arachidonic acid (AA)-related enzyme agonists.

RESULTS

Network pharmacology identified 19 effective compounds of P. quassioides and 105 HCC-associated targets. It also revealed the AA pathway was the central pathway of P. quassioides against HCC, with AURKA, AURKB, KIF11, and TOP2A identified as core targets that inhibit excessive HCC cell proliferation and promote apoptosis. Flow cytometry findings supported that P. quassioides medicated serum significantly inhibited HCC cell proliferation and promoted apoptosis. By contrast, enzyme agonists related to the AA pathway markedly counteracted the anti-HCC effect of P. quassioides, promoting HCC growth.

CONCLUSION

P. quassioides medicated serum exerts a prominent anti-HCC effect in vitro. The AA pathway constitutes the mechanism by which P. quassioides medicated serum inhibits excessive proliferation and promotes apoptosis of HCC cells.

Reduction of DNA Topoisomerase Top2 Reprograms the Epigenetic Landscape and Extends Health and Life Span Across Species

DNA topoisomerases are essential molecular machines that manage DNA topology in the cell and play important roles in DNA replication and transcription. We found that knocking down the enzyme topoisomerase Top2 or its mammalian homolog TOP2B increases the lifespan of S. cerevisiae, C. elegans, and mice. TOP2B reduction also extends the health span of mice and alleviates the pathologies of aging in multiple tissues. At the cellular/molecular level, TOP2B reduction alleviates the major hallmarks of aging, including senescence, DNA damage, and deregulated nutrient sensing. We observed that TOP2B reduction changes the epigenetic landscape of various tissues in old mice toward that of the young animals, and differentially downregulates genes with active promoter and high expression. Our observations suggest that Top2 reduction confers pro-longevity effect across species possibly through a conserved mechanism and may be a promising strategy for longevity intervention.

Bioinformatics analysis of coronary microvascular dysfunction in rats based on single-cell RNA sequencing

Coronary microvascular dysfunction serves as one of the etiological factors for ischemic heart disease and represents a novel therapeutic direction for coronary artery diseases; however, the research on its pathogenesis remains inconsistent. This study aims to explore the single-cell gene expression profiles in rats with coronary microvascular dysfunction using single-cell RNA sequencing, with a particular focus on the in-depth analysis of endothelial cell gene expression characteristics. By establishing a rat model of coronary microvascular dysfunction, we collected cardiac apical tissue to prepare single-cell suspensions and further analyzed them using bioinformatics methods. From a total of 55,419 cells, we identified 28 distinct cell clusters, with endothelial cells and fibroblasts being the predominant cell types. Compared to the NC group, the proportion of endothelial cells in the CMD group was significantly reduced, while the number of fibroblasts was significantly increased. Through further analysis of the endothelial cells, we classified them into normal phenotype endothelial cells, mesenchymal phenotype endothelial cells, proliferative phenotype endothelial cells, and lymphatic endothelial cells, with mesenchymal and proliferative endothelial cells originating from normal phenotype endothelial cells. Additionally, the CMD group exhibited an increase in immune cells, enhanced inflammatory response, and increased oxidative stress. These findings may provide novel potential therapeutic targets for the treatment of Coronary microvascular dysfunction.

The emerging regulatory interface between DNA repair and steroid hormone receptors in cancer

Human cells potentiate highly diverse functions through tight transcriptional regulation and maintenance of genome integrity. While the DNA damage response (DDR) safeguards the genome, ligand-activated transcription factors, such as steroid hormone receptors (SHRs), provide complex transcriptional outputs. Interestingly, an increasing body of evidence reveals a direct biological and functional interplay between DDR factors and SHR cascades in cancer. SHRs can directly affect DDR gene expression, but DDR factors in turn act as transcriptional coregulators, enabling oncogenic SHR-mediated signaling, which has the potential for novel therapeutic interventions. With a focus on breast and prostate cancer, we describe in this review recent developments in, and insights into, the complex interplay between SHR signaling and the DDR, highlighting opportunities for future clinical interventions.

Advances in research on malignant tumors and targeted agents for TOP2A (Review)

The DNA topoisomerase isoform topoisomerase IIα (TOP2A) is essential for the condensation and segregation of cellular mitotic chromosomes and the structural maintenance. It has been demonstrated that TOP2A is highly expressed in various malignancies, including lung adenocarcinoma (LUAD), hepatocellular carcinoma (HCC) and breast cancer (BC), associating with poor prognosis and aggressive tumor behavior. Additionally, TOP2A has emerged as a promising target for cancer therapy, with widespread clinical application of associated chemotherapeutic agents. The present study explored the impact of TOP2A on malignant tumor growth and the advancements in research on its targeted drugs. The fundamental mechanisms of TOP2A have been detailed, its specific roles in tumor cells are analyzed, and its potential as a biomarker for tumor prognosis and therapeutic targeting is highlighted. Additionally, the present review compiles findings from the latest clinical trials of relevant targeted agents, information on newly developed inhibitors, and discusses future research directions and clinical application strategies in cancer therapy, aiming to propose novel ideas and methods.

MYBL2 promotes proliferation of clear cell renal cell carcinoma by regulating TOP2A and activating AKT/mTOR signaling pathway

Renal cell carcinoma (RCC) is one of the most common malignancies in the urinary system, and clear cell renal cell carcinoma (ccRCC) is the most common subtype. MYBL2 has been reported to be overexpressed in various tumors and associated with poor prognosis in patients, but its biological role in ccRCC remains unclear. In this study, we investigated the mRNA and protein expression levels of MYBL2 in ccRCC samples and evaluated the prognostic value of MYBL2 using TCGA dataset. In vitro functional assays were performed using CCK-8, EdU, colony formation, cell scratch, and transwell assays, as well as in vivo tumorigenesis assays to investigate the biological functions of MYBL2 in ccRCC. Additionally, gene set enrichment analysis (GSEA) was used to explore the downstream pathways of MYBL2, which were further validated. Finally, we predicted the target genes of MYBL2 using bioinformatics and validated them using ChIP and dual-luciferase reporter gene assays. MYBL2 expression was significantly higher in ccRCC than in adjacent normal tissues and was associated with poor prognosis. MYBL2 expression was positively correlated with the pathological tumor grade and clinical TNM stage of ccRCC patients. Knockdown of MYBL2 significantly inhibited the proliferation of renal cancer cells in vitro and in vivo, and knockdown of MYBL2 could inhibit cell invasion and migration, while overexpression of MYBL2 had the opposite effect. GSEA revealed that MYBL2 was associated with the mTOR signaling pathway and cell cycle pathway, which was confirmed by our study. Finally, we found that TOP2A was a target gene of MYBL2, and MYBL2 could bind to the TOP2A promoter to regulate its transcriptional activity, promoting the proliferation of clear cell renal cell carcinoma cells. MYBL2 emerges as a highly expressed factor that significantly correlates with adverse patient prognosis in ccRCC. Mechanistically, MYBL2 transcriptionally upregulates TOP2A, thereby modulating the proliferation of ccRCC cells. Furthermore, MYBL2 activates the mTOR signaling pathway, a critical node in the progression of ccRCC. Collectively, these findings position MYBL2 as a promising candidate for both a biological marker and a therapeutic target in the management of ccRCC.

PICH, A protein that maintains genomic stability, can promote tumor growth

Genomic instability is regardedas a hallmark of cancer cells. It can be presented in many ways, among which chromosome instability has received attention. Ultrafine anaphase bridges are a typeof chromatin bridges, the untimely resolution of which can also lead to chromosome instability. PICH can play a role in maintaining chromosome stability by regulating chromosome morphologyand resolving ultrafine anaphase bridges. Recently, PICH has been found to be overexpressed in various cancers. Overexpression of PICH is related to the proliferation of tumors and poor prognosis. In this article, we consider that PICH can maintain genomic stability by regulating appropriate chromosome structure, ensuring proper chromosome segregation, and facilitating replication fork reversal. We summarize how PICH regulates chromosome stability, how PICH resolves Ultrafine anaphase bridges with other proteins, and how PICH promotes tumor progression.

Identification of a novel TOP2B::AFF2 fusion gene in B-cell acute lymphoblastic leukemia

Genetic alterations play a pivotal role in leukemic clonal transformation, significantly influencing disease pathogenesis and clinical outcomes. Here, we report a novel fusion gene and investigate its pathogenic role in acute lymphoblastic leukemia (ALL). We engineer a transposon transfection system expressing the TOP2B::AFF2 transcript and introduce it into Ba/F3 cells. Functional studies, including proliferation, cell cycle, and apoptosis assays, were conducted to assess the fusion gene's impact. In vitro assays reveal that the TOP2B::AFF2 fusion significantly enhances Ba/F3 cell proliferation and G1/S phase transition while suppressing differentiation and apoptosis. This study identifies TOP2B::AFF2 as a potential oncogenic driver. However, further validation through in vivo studies are warranted to fully elucidate the fusion gene's role in leukemogenesis.

Topoisomerase-modulated genome-wide DNA supercoiling domains colocalize with nuclear compartments and regulate human gene expression

DNA supercoiling is a biophysical feature of the double helix with a pivotal role in biological processes. However, understanding of DNA supercoiling in the chromatin remains limited. Here, we developed azide-trimethylpsoralen sequencing (ATMP-seq), a DNA supercoiling assay offering quantitative accuracy while minimizing genomic bias and background noise. Using ATMP-seq, we directly visualized transcription-dependent negative and positive twin-supercoiled domains around genes and mapped kilobase-resolution DNA supercoiling throughout the human genome. Remarkably, we discovered megabase-scale supercoiling domains (SDs) across all chromosomes that are modulated mainly by topoisomerases I and IIβ. Transcription activities, but not the consequent supercoiling accumulation in the local region, contribute to SD formation, indicating the long-range propagation of transcription-generated supercoiling. Genome-wide SDs colocalize with A/B compartments in both human and Drosophila cells but are distinct from topologically associating domains (TADs), with negative supercoiling accumulation at TAD boundaries. Furthermore, genome-wide DNA supercoiling varies between cell states and types and regulates human gene expression, underscoring the importance of supercoiling dynamics in chromatin regulation and function.

TOP2A modulates signaling via the AKT/mTOR pathway to promote ovarian cancer cell proliferation

Ovarian cancer (OC) is a form of gynecological malignancy that is associated with worse patient outcomes than any other cancer of the female reproductive tract. Topoisomerase II α (TOP2A) is commonly regarded as an oncogene that is associated with malignant disease progression in a variety of cancers, its mechanistic functions in OC have yet to be firmly established. We explored the role of TOP2A in OC through online databases, clinical samples, in vitro and in vivo experiments. And initial analyses of public databases revealed high OC-related TOP2A expression in patient samples that was related to poorer prognosis. This was confirmed by clinical samples in which TOP2A expression was elevated in OC relative to healthy tissue. Kaplan-Meier analyses further suggested that higher TOP2A expression levels were correlated with worse prognosis in OC patients. In vitro, TOP2A knockdown resulted in the inhibition of OC cell proliferation, with cells entering G1 phase arrest and undergoing consequent apoptotic death. In rescue assays, TOP2A was confirmed to regulate cell proliferation and cell cycle through AKT/mTOR pathway activity. Mouse model experiments further affirmed the key role that TOP2A plays as a driver of OC cell proliferation. These data provide strong evidence supporting TOP2A as an oncogenic mediator and prognostic biomarker related to OC progression and poor outcomes. At the mechanistic level, TOP2A can control tumor cell growth via AKT/mTOR pathway modulation. These preliminary results provide a foundation for future research seeking to explore the utility of TOP2A inhibitor-based combination treatment regimens in platinum-resistant recurrent OC patients.

Targeting TOP2A in Ovarian Cancer: Biological and Clinical Implications

The enzyme topoisomerase II alpha (TOP2A) plays a critical role in DNA replication and cell proliferation, making it a promising target for cancer therapy. In epithelial ovarian cancer (EOC), TOP2A overexpression is associated with poor prognosis and resistance to conventional treatments. This review explores the biological functions of TOP2A in EOC and discusses its potential as a therapeutic target. We highlight studies on the mechanisms through which TOP2A contributes to tumor progression and recurrence. Additionally, we evaluate the clinical implications of targeting TOP2A, including the use of TOP2A inhibitors and their combination with novel drugs. We provide a comprehensive overview of the current understanding and future directions for targeting TOP2A in the management of EOC.

In Vitro Evaluation, Chemical Profiling, and In Silico ADMET Prediction of the Pharmacological Activities of Artemisia absinthium Root Extract

Artemisia absinthium L., is a plant with established pharmacological properties, but the A. absinthium root extract (AARE) remains unexplored. The aim of this study was to examine the chemical composition of AARE and assess its biological activity, which included antidiabetic, antibacterial, anticancer, and antioxidant properties. GC-MS was used to analyze the chemical components. The antioxidant activity of the total phenolic and flavonoid content was evaluated. Antibacterial activity and cytotoxic effects were identified. Enzyme inhibition experiments were performed to determine its antidiabetic potential. Molecular docking was utilized to evaluate the potential antioxidant, antibacterial, and anticancer activities of the compounds from AARE using Maestro 11.5 from the Schrödinger suite. AARE exhibited moderate antioxidant activity in DPPH (IC50: 172.41 ± 3.15 μg/mL) and ABTS (IC50: 378.94 ± 2.18 μg/mL) assays. Cytotoxicity tests on MCF-7 and HepG2 cancer cells demonstrated significant anticancer effects, with IC50 values of 150.12 ± 0.74 μg/mL and 137.11 ± 1.33 μg/mL, respectively. Apoptotic studies indicated an upregulation of pro-apoptotic genes (caspase-3, 8, 9, Bax) and a downregulation of anti-apoptotic markers (Bcl-2 and Bcl-Xl). AARE also inhibited α-amylase and α-glucosidase, suggesting potential antidiabetic effects, with IC50 values of 224.12 ± 1.17 μg/mL and 243.35 ± 1.51 μg/mL. Antibacterial assays revealed strong activity against Gram-positive bacteria. Molecular docking and pharmacokinetic analysis identified promising inhibitory effects of key AARE compounds on NADPH oxidase, E. coli Gyrase B, and Topoisomerase IIα, with favorable drug-like properties. These findings suggest AARE's potential in treating cancer, diabetes, and bacterial infections, warranting further in vivo and clinical studies.

Time-resolved scRNA-seq reveals transcription dynamics of polarized macrophages with influenza A virus infection and antigen presentation to T cells

Throughout history, the influenza A virus has caused numerous devastating global pandemics. Macrophages, as pivotal innate immune cells, exhibit a wide range of immune functions characterized by distinct polarization states, reflecting their intricate heterogeneity. In this study, we employed the time-resolved single-cell sequencing technique coupled with metabolic RNA labelling to elucidate the dynamic transcriptional changes in distinct polarized states of bone marrow-derived macrophages (BMDMs) upon infection with the influenza A virus. Our approach not only captures the temporal dimension of transcriptional activity, which is lacking in conventional scRNA-seq methods, but also reveals that M2-polarized Arg1_macrophage cluster is the sole state supporting successful replication of influenza A virus. Furthermore, we identified distinct antigen presentation capabilities to CD4+ T and CD8+ T cells across diverse polarized states of macrophages. Notably, the M1 phenotype, exhibited by (BMDMs) and murine alveolar macrophages (AMs), demonstrated superior conventional and cross-presentation abilities for exogenous antigens, with a particular emphasis on cross-presentation capacity. Additionally, as CD8+ T cell differentiation progressed, M1 polarization exhibited an enhanced capacity for cross-presentation. All three phenotypes of BMDMs, including M1, demonstrated robust presentation to CD4+ regulatory T cells, while displaying limited ability to present to naive CD4+ T cells. These findings offer novel insights into the immunological regulatory mechanisms governing distinct polarized states of macrophages, particularly their roles in restricting the replication of influenza A virus and modulating antigen-specific T cell responses through innate immunity.

Mime: A flexible machine-learning framework to construct and visualize models for clinical characteristics prediction and feature selection

The widespread use of high-throughput sequencing technologies has revolutionized the understanding of biology and cancer heterogeneity. Recently, several machine-learning models based on transcriptional data have been developed to accurately predict patients' outcome and clinical response. However, an open-source R package covering state-of-the-art machine-learning algorithms for user-friendly access has yet to be developed. Thus, we proposed a flexible computational framework to construct a machine learning-based integration model with elegant performance (Mime). Mime streamlines the process of developing predictive models with high accuracy, leveraging complex datasets to identify critical genes associated with prognosis. An in silico combined model based on de novo PIEZO1-associated signatures constructed by Mime demonstrated high accuracy in predicting the outcomes of patients compared with other published models. Furthermore, the PIEZO1-associated signatures could also precisely infer immunotherapy response by applying different algorithms in Mime. Finally, SDC1 selected from the PIEZO1-associated signatures demonstrated high potential as a glioma target. Taken together, our package provides a user-friendly solution for constructing machine learning-based integration models and will be greatly expanded to provide valuable insights into current fields. The Mime package is available on GitHub (https://github.com/l-magnificence/Mime).

Type II topoisomerases shape multi-scale 3D chromatin folding in regions of positive supercoils

Type II topoisomerases (TOP2s) resolve torsional stress accumulated during various cellular processes and are enriched at chromatin loop anchors and topologically associated domain (TAD) boundaries, where, when trapped, can lead to genomic instability promoting the formation of oncogenic fusions. Whether TOP2s relieve topological constraints at these positions and/or participate in 3D chromosome folding remains unclear. Here, we combine 3D genomics, imaging, and GapRUN, a method for the genome-wide profiling of positive supercoiling, to assess the role of TOP2s in shaping chromosome organization in human cells. Acute TOP2 depletion led to the emergence of new, large-scale contacts at the boundaries between active, positively supercoiled, and lamina-associated domains. TOP2-dependent changes at the higher-order chromatin folding were accompanied by remodeling of chromatin-nuclear lamina interactions and of gene expression, while at the chromatin loop level, TOP2 depletion predominantly remodeled transcriptionally anchored, positively supercoiled loops. We propose that TOP2s act as a fine regulator of chromosome folding at multiple scales.

Multilevel Mechanisms of Cancer Drug Resistance

Cancer drug resistance represents one of the most significant challenges in oncology and manifests through multiple interconnected molecular and cellular mechanisms. Objective: To provide a comprehensive analysis of multilevel processes driving treatment resistance by integrating recent advances in understanding genetic, epigenetic, and microenvironmental factors. This is a systematic review of the recent literature focusing on the mechanisms of cancer drug resistance, including genomic studies, clinical trials, and experimental research. Key findings include the following: (1) Up to 63% of somatic mutations can be heterogeneous within individual tumors, contributing to resistance development; (2) cancer stem cells demonstrate enhanced DNA repair capacity and altered metabolic profiles; (3) the tumor microenvironment, including cancer-associated fibroblasts and immune cell populations, plays a crucial role in promoting resistance; and (4) selective pressure from radiotherapy drives the emergence of radioresistant phenotypes through multiple adaptive mechanisms. Understanding the complex interplay between various resistance mechanisms is essential for developing effective treatment strategies. Future therapeutic approaches should focus on combination strategies that target multiple resistance pathways simultaneously, guided by specific biomarkers.

Identification and validation of a novel prognostic signature and key genes related to development of anaplastic thyroid carcinoma

BACKGROUND

Anaplastic thyroid carcinoma (ATC) is a rare but the most aggressive type of thyroid carcinoma. Nevertheless, limited advances were made to reduce mortality and improve survival over the last decades. Therefore, identifying novel diagnostic biomarkers and therapeutic targets for ATC patients is still needed.

MATERIALS AND METHODS

RNA sequencing data and corresponding clinical features were available from GEO and TCGA databases. We integrated WGCNA and PPI network analysis to identify hub genes associated with ATC development, and RT-qPCR was employed for data verification. Univariate and LASSO Cox regression analyses were used to generate prognostic signatures.

RESULTS

Based on PPI and WGCNA, 6 hub genes were identified, namely KIF2C, PBK, TOP2A, CDK1, KIF20A, and ASPM, which play vital roles in ATC development. Subsequently, RT-qPCR experiments showed that most of these genes were significantly upregulated in CAL-62 cells compared to Nthy-ori 3-1 cells. Moreover, a prognostic signature featuring GPSM2, FGF5, ASXL3, CYP4B1, CLMP, and DUXAP9 was generated, which was also verified by RT-qPCR results and proved as an independent predictor of poorer prognosis of ATC. Additionally, a nomogram incorporating the risk score and clinicopathological parameters was further constructed for accurate prediction of 1-, 3- and 5-year survival probabilities of ATC.

CONCLUSIONS

Our study identified 6 key genes critical to ATC development and constructed a prognostic signature. These findings provide reliable biomarkers and a relatively comprehensive tumorigenesis profile of ATC, which may inform future strategies for clinical diagnosis and pharmaceutical design.

Elucidating the prognostic and therapeutic significance of TOP2A in various malignancies

Topoisomerase IIα (TOP2A) is a crucial enzyme that plays a vital role in DNA replication and transcription mechanisms. Dysregulated expression of TOP2A has been associated with various malignancies, including hepatocellular carcinoma, prostate cancer, colon cancer, lung cancer and breast cancer. In this review, we summarized the prognostic relevances of TOP2A in various types of cancer. The increased expression of TOP2A has been linked to resistance to therapy and reduced survival rates. Therefore, evaluating TOP2A levels could assist in identifying patients who may derive advantages from molecular targeted therapy. The amplification of TOP2A has been linked to a positive response to chemotherapy regimens that contain anthracycline. Nevertheless, the overexpression of TOP2A also indicates a heightened likelihood of disease recurrence and unfavorable prognosis. The prognostic significance of TOP2A has been extensively studied in various types of cancer. The increased expression of TOP2A is associated with poor clinical outcomes, indicating its potential as a valuable biomarker for assessing risk and stratifying treatment in these malignancies. However, further investigation is needed to elucidate the underlying mechanisms by which TOP2A influences cancer progression and to explore its potential as a therapeutic target.

Proteomic profiling identifies a direct interaction between heat shock transcription factor 2 and the focal adhesion adapter talin-1

Heat shock factor 2 (HSF2) is a versatile transcription factor that regulates gene expression under stress conditions, during development, and in disease. Despite recent advances in characterizing HSF2-dependent target genes, little is known about the protein networks associated with this transcription factor. In this study, we performed co-immunoprecipitation coupled with mass spectrometry analysis to identify the HSF2 interactome in mouse testes, where HSF2 is required for normal sperm development. Endogenous HSF2 was discovered to form a complex with several adhesion-associated proteins, a finding substantiated by mass spectrometry analysis conducted in human prostate carcinoma PC-3 cells. Notably, this group of proteins included the focal adhesion adapter protein talin-1 (TLN1). Through co-immunoprecipitation and proximity ligation assays, we demonstrate the conservation of the HSF2-TLN1 interaction from mouse to human. Additionally, employing sequence alignment analyses, we uncovered a TLN1-binding motif in the HSF2 C terminus that binds directly to multiple regions of TLN1 in vitro. We provide evidence that the 25 C-terminal amino acids of HSF2, fused to EGFP, are sufficient to establish a protein complex with TLN1 and modify cell-cell adhesion in human cells. Importantly, this TLN1-binding motif is absent in the C-terminus of a closely related HSF family member, HSF1, which does not form a complex with TLN1. These results highlight the unique molecular characteristics of HSF2 in comparison to HSF1. Taken together, our data unveil the protein partners associated with HSF2 in a physiologically relevant context and identifies TLN1 as the first adhesion-related HSF2-interacting partner.

Flavonoids and their derivatives as DNA topoisomerase inhibitors with anti-cancer activity in various cell models: Exploring a novel mode of action

Flavonoids, a diverse group of plant-derived secondary metabolites, have garnered significant attention for their potential anti-cancer properties. This review explores the role of flavonoids as inhibitors of DNA topoisomerases, key enzymes essential for DNA replication, transcription, and cell division. The article offers a comprehensive overview of flavonoid classification, biosynthesis, and their widespread natural occurrence. It further delves into the molecular mechanisms through which flavonoids exert their anti-cancer effects, emphasizing their interactions with topoisomerases. The review provides a thorough analysis of both in vitro and in vivo studies that highlight the topoisomerase inhibitory activities of various flavonoids and their derivatives. Key findings demonstrate that flavonoids can function as catalytic inhibitors, poisons, or DNA intercalators, affecting both type I and type II topoisomerases. The structure-activity relationships of flavonoids concerning their topoisomerase inhibitory potency are also examined. This review underscores the potential of flavonoids as promising lead compounds for the development of novel topoisomerase inhibitors, which could have important implications for cancer therapy. However, it also acknowledges the need for further research to fully understand the intricate interactions between flavonoids and topoisomerases within the cellular environment.

DIA proteomic and PRM validation through human granulose cells profiles screen suitable biomarkers for polycystic ovary syndrome patients

The aim of this study is to identify differentially expressed proteins (DEPs) in granulose cells (GCs) from women with or withoutpolycystic ovary syndrome (PCOS) via data independent acquisition (DIA) proteomic analysis.A total of 63 women were recruited for this study, 34 PCOS patients as experimental group (P), and 29 women without PCOS as Normal group (NP). DIA-based proteomic analysis was performed to identify DEPs in GCs between the P and NP samples. Certain typical DEPs were further validated by Parallel reaction monitoring (PRM), and correlation analysis was performed between these DEPs and the clinical characteristics.Cell vitality was measured by CCK-8 assay. DIA analysis revealed 174 significantly DEPs, of which 7 were upregulated and 167 downregulated. Bioinformatics analysis was performed to analysis the significantly DEPs. The PRM experiment confirmed TOP2A and SPHKAP were upregulated significantly in P by comparing to NP, while GM2A, MRPS16, APOA2 and FGF2 were downregulated significantly. Most notably, Correlation analysis revealed that TOP2A, SPHKAP, MRPS16 and FGF2were positively correlated with TG, AMH and Age, but negatively correlated with Menarche age, DBIL, FT3, Basal serum FSH and LH.Meanwhile, CCK-8 assay has shown that downregulation of FGF2 could weaken cell viability. Finally, a panel of DEPs were identified in the GCs of patients with PCOS, of which certain significant DEPs might play essential roles in the pathogenesis of PCOS, could be regarded as candidate biomarkers for PCOS.

Targeting the 3D genome by anthracyclines for chemotherapeutic effects

The chromatins are folded into three-dimensional (3D) structures inside cells, which coordinates the regulation of gene transcription by the non-coding regulatory elements. Aberrant chromatin 3D folding has been shown in many diseases, such as acute myeloid leukemia (AML), and may contribute to tumorigenesis. The anthracycline topoisomerase II inhibitors can induce histone eviction and DNA damage. We performed genome-wide high-resolution mapping of the chemotherapeutic effects of various clinically used anthracycline drugs. ATAC-seq was used to profile the histone eviction effects of different anthracyclines. TOP2A ChIP-seq was used to profile the potential DNA damage regions. Integrated analyses show that different anthracyclines have distinct target selectivity on epigenomic regions, based on their respective ATAC-seq and ChIP-seq profiles. We identified the underlying molecular mechanism that unique anthracycline variants selectively target chromatin looping anchors via disrupting CTCF binding, suggesting an additional potential therapeutic effect on the 3D genome. We further performed Hi-C experiments, and data from K562 cells treated with the selective anthracycline drugs indicate that the 3D chromatin organization is disrupted. Furthermore, AML patients receiving anthracycline drugs showed altered chromatin structures around potential looping anchors, which linked to distinct clinical outcomes. Our data indicate that anthracyclines are potent and selective epigenomic targeting drugs and can target the 3D genome for anticancer therapy, which could be used for personalized medicine to treat tumors with aberrant 3D chromatin structures.

Protein turnover regulation is critical for influenza A virus infection

The abundance of a protein is defined by its continuous synthesis and degradation, a process known as protein turnover. Here, we systematically profiled the turnover of proteins in influenza A virus (IAV)-infected cells using a pulse-chase stable isotope labeling by amino acids in cell culture (SILAC)-based approach combined with downstream statistical modeling. We identified 1,798 virus-affected proteins with turnover changes (tVAPs) out of 7,739 detected proteins (data available at pulsechase.innatelab.org). In particular, the affected proteins were involved in RNA transcription, splicing and nuclear transport, protein translation and stability, and energy metabolism. Many tVAPs appeared to be known IAV-interacting proteins that regulate virus propagation, such as KPNA6, PPP6C, and POLR2A. Notably, our analysis identified additional IAV host and restriction factors, such as the splicing factor GPKOW, that exhibit significant turnover rate changes while their total abundance is minimally affected. Overall, we show that protein turnover is a critical factor both for virus replication and antiviral defense.

Integrated bioinformatics reveals genetic links between visceral obesity and uterine tumors

Visceral obesity (VO), characterized by excess fat around internal organs, is a recognized risk factor for gynecological tumors, including benign uterine leiomyoma (ULM) and malignant uterine leiomyosarcoma (ULS). Despite this association, the shared molecular mechanisms remain underexplored. This study utilizes an integrated bioinformatics approach to elucidate common molecular pathways and identify potential therapeutic targets linking VO, ULM, and ULS. We analyzed gene expression datasets from the Gene Expression Omnibus (GEO) to identify differentially expressed genes (DEGs) in each condition. We found 101, 145, and 18 DEGs in VO, ULM, and ULS, respectively, with 37 genes overlapping across all three conditions. Functional enrichment analysis revealed that these overlapping DEGs were significantly enriched in pathways related to cell proliferation, immune response, and transcriptional regulation, suggesting shared biological processes. Protein-protein interaction network analysis identified 14 hub genes, of which TOP2A, APOE, and TYMS showed significant differential expression across all three conditions. Drug-gene interaction analysis identified 26 FDA-approved drugs targeting these hub genes, highlighting potential therapeutic opportunities. In conclusion, this study uncovers shared molecular pathways and actionable drug targets across VO, ULM, and ULS. These findings deepen our understanding of disease etiology and offer promising avenues for drug repurposing. Experimental validation is needed to translate these insights into clinical applications and innovative treatments.

Genome Instability Induced by Topoisomerase Misfunction

Topoisomerases alter DNA topology by making transient DNA strand breaks (DSBs) in DNA. The DNA cleavage reaction mechanism includes the formation of a reversible protein/DNA complex that allows rapid resealing of the transient break. This mechanism allows changes in DNA topology with minimal risks of persistent DNA damage. Nonetheless, small molecules, alternate DNA structures, or mutations in topoisomerase proteins can impede the resealing of the transient breaks, leading to genome instability and potentially cell death. The consequences of high levels of enzyme/DNA adducts differ for type I and type II topoisomerases. Top1 action on DNA containing ribonucleotides leads to 2-5 nucleotide deletions in repeated sequences, while mutant Top1 enzymes can generate large deletions. By contrast, small molecules that target Top2, or mutant Top2 enzymes with elevated levels of cleavage lead to small de novo duplications. Both Top1 and Top2 have the potential to generate large rearrangements and translocations. Thus, genome instability due to topoisomerase mis-function is a potential pathogenic mechanism especially leading to oncogenic progression. Recent studies support the potential roles of topoisomerases in genetic changes in cancer cells, highlighting the need to understand how cells limit genome instability induced by topoisomerases. This review highlights recent studies that bear on these questions.