DNA Replication Licensing Factors: Novel Targets for Cancer Therapy via Inhibiting the Stemness of Cancer Cells

Comparative microRNAs profile of Schistosoma japonicum male worms derived from single-sex and bisexual infections: Implications of the multifunctional role of microRNA

Schistosoma japonicum is a dioecious parasite that requires constant pairing between male and female worms for female maturation and egg production. MicroRNAs (miRNAs) play crucial roles in regulating various biological processes, including parasite development and host-pathogen interactions, but their functions in schistosomes remain largely unexplored. This study aimed to investigate the differentially expressed miRNAs (DEMs) between mated male (MM) and single-sex male (SM) worms to gain insights into their regulatory roles in schistosome reproduction. Total RNA was extracted from 28-day-old MM and SM worms, followed by small RNA sequencing to identify DEMs. Bioinformatics analyses were used to predict the biological functions of DEM target genes. Comparative analysis with previously published miRNA datasets helped identify potentially significant miRNAs. Quantitative PCR (qPCR) validated the expression of selected miRNAs and mRNA levels of some target genes. A total of 20 DEMs were identified, with 9 upregulated in MM worms and 11 in SM worms. These DEMs may regulate processes such as intracellular transport, RNA processing, and cellular homeostasis. The study provides novel insights into the biological differences between SM and MM worms, suggesting that these miRNAs could be key regulators of parasite development and host adaptation, with potential diagnostic and therapeutic applications in schistosomiasis.

Rhodosporidium toruloides-a new surrogate model to study rapamycin induced effects on human aging and cancer

The haploid, olegenious yeast Rhodosporidium toruloides accumulates intracellular lipids and carotenoids upon metabolic stress. Target of Rapamycin (TOR) signaling, essential for cell proliferation, is known to affect cellular lipid accumulation. In contrast to the conventional surrugate cell model S. cerevisiae, which harbours two TOR kinases within its TOR complex, R. toruloides only harbours one TOR kinase, mimicking mammalian systems. We used a proteomics centered approach to probe the cellular response, of the two R. toruloides haplotypes, IFO0559 and IFO0880 upon treatment with the TOR inhibitor rapamycin, with an original focus on difference in carotenoid and lipid accumulation. Unexpectedly, IFO0880 displayed severe growth arrest in response to rapamycin, while IFO0559 did not. Proteomic anaysis revealed differential expression of several proteins involved in cell cycle control, lipogensis, amino acid metabolism and autophagy between the two haplotypes. Among those we identified several proteins previously described in both mammalian oncogenic and aging contexts. This differential haplotype response to rapamycin treatment positions R. toruloides as a promising cell surrugate model to study cellular mechanisms underlying rapamycin response especially for systems with high lipid contents, an emerging hallmark of different forms of mammalian cancer and age related disease.

NCBP2 predicts the prognosis and the immunotherapy response of cancers: a pan-cancer analysis

Background

The cap-binding complex (CBC) plays a crucial role in facilitating gene expression by safeguarding mRNA from nonsense-mediated decay, promoting mRNA splicing, 3'-end processing, and facilitating nuclear export. Nevertheless, the precise biological functions and clinical implications of CBC in cancer remain ambiguous, necessitating further investigation for clarification.

Methods

The present study utilized the cBioPortal database to investigate the genetic alterations of nuclear cap binding protein subunit 2 (NCBP2) in pan-cancer. The Cancer Genome Atlas (TCGA) and online web tools were employed to analyze the correlation between NCBP2 and prognosis, genome instability, immune infiltration, immune response, cancer stemness, and chemotherapeutic efficacy in pan-cancer. Furthermore, the expression of NCBP2 was confirmed by immunohistochemistry (IHC) and functional analysis at the single-cell level was conducted using the CancerSEA database.

Results

NCBP2 exhibited distinct genetic alterations in pan-cancer with an increased expression in 24/32, while decreased expression in 3/32, types of cancers. IHC confirmed the aberrant expression of NCBP2 in lung squamous cell carcinoma (LUSC), pancreatic adenocarcinoma (PAAD), kidney renal papillary cell carcinoma (KIRP) and kidney renal clear cell carcinoma (KIRC). NCBP2 was correlated with overall survival (OS), disease-specific survival (DSS), and progression-free survival (PFS) in various cancers. Importantly, it was identified as a risk factor for OS, DSS and PFS in PAAD and uterine corpus endometrial carcinoma (UCEC). Gene Set Enrichment Analysis (GSEA) demonstrated that elevated NCBP2 was linked to immune and proliferation related pathways across multiple cancer types. Furthermore, a negative association between NCBP2 and stromal score, immune score, and ESTIMATE score was detected, and a positive correlation was observed between NCBP2 and diverse immune cells as well as stemness-indexes in the majority of cancer types. Drug sensitivity analysis revealed that drugs associated with NCBP2 primarily targeted DNA replication, chromatin histone methylation, ABL signaling, cell cycle, and PI3K signaling. Additionally, an examination at the single-cell level indicated that NCBP2 was positively correlated with cell cycle progression, DNA damage, DNA repair, invasion, and stemness in most cancer types, while negatively correlated with apoptosis, inflammation, and hypoxia in certain cancers.

Conclusion

In this study, we revealed the correlation of NCBP2 with prognosis, microenvironment and stemness, indicating that NCBP2 might be a potential therapeutic target for more effective and personalized therapy strategies in pan-cancer.

DeOri 10.0: An Updated Database of Experimentally Identified Eukaryotic Replication Origins

DNA replication is a complex and crucial biological process in eukaryotes. To facilitate the study of eukaryotic replication events, we present a database of eukaryotic DNA replication origins (DeOri), which collects genome-wide data on eukaryotic DNA replication origins currently available. With the rapid development of high-throughput experimental technology in recent years, the number of datasets in the new release of DeOri 10.0 increased from 10 to 151 and the number of sequences increased from 16,145 to 9,742,396. Besides nucleotide sequences and browser extensible data (BED) files, corresponding annotation files, such as coding sequences (CDSs), mRNAs, and other biological elements within replication origins, are also provided. The experimental techniques used for each dataset, as well as related statistical data, are also presented on web page. Differences in experimental methods, cell lines, and sequencing technologies have resulted in distinct replication origins, making it challenging to differentiate between cell-specific and non-specific replication origins. Based on multiple replication origin datasets at the species level, we scored and screened replication origins in Homo sapiens, Gallus gallus, Mus musculus, Drosophila melanogaster, and Caenorhabditis elegans. The screened regions with high scores were considered as species-conservative origins, which are integrated and presented as reference replication origins (rORIs). Additionally, we analyzed the distribution of relevant genomic elements associated with replication origins at the genome level, such as CpG island (CGI), transcription start site (TSS), and G-quadruplex (G4). These analysis results can be browsed and downloaded as needed at http://tubic.tju.edu.cn/deori/.

Integrated network pharmacology and transcriptomic approach reveal the role of equol in reducing colorectal cancer via regulating multiple cell cycle genes in HCT116 cells

Equol is an isoflavone-derived metabolite known to exhibit strong estrogenic and antioxidant activities. The aim of this paper is twofold: first, to confirm the anticancer potential of equol against colorectal cancer, and second, to reveal the underlying mechanisms. After treatment with 40 μg/mL equol, cell proliferation, cell migration, and colony formation of HCT116 colon cancer cells were inhibited. Network pharmacology and transcriptomics analysis revealed the downregulation of genes related to DNA replication (CCND1, E2F1, CDC6, CDC45, MCM4), leading to G1/S cell cycle arrest and the induction of cell apoptosis, which was confirmed by flow cytometry. Genes associated with the G2-to-M transition (CDK1, CCNA2, CCNB1) were also downregulated. In addition, equol downregulated genes (FOXM1 and ASPM) that control cell migration and invasion. Our data indicate that equol can inhibit colorectal cancer by targeting multiple pathways, suggesting its potential as a key component in the adjuvant treatment of colorectal cancer.

CUL4A Ubiquitin Ligase Is an Independent Predictor of Overall Survival in Pancreatic Adenocarcinoma

BACKGROUND/AIM

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy with dismal prognosis. Genomic instability due to defects in cell-cycle regulation/mitosis or deficient DNA-damage repair is a major driver of PDAC progression with clinical relevance. Deregulation of licensing of DNA replication leads to DNA damage and genomic instability, predisposing cells to malignant transformation. While overexpression of DNA replication-licensing factors has been reported in several human cancer types, their role in PDAC remains largely unknown. We aimed here to examine the expression and prognostic significance of the DNA replication-licensing factors chromatin licensing and DNA replication factor 1 (CDT1), cell-division cycle 6 (CDC6), minichromosome maintenance complex component 7 (MCM7) and also of the ubiquitin ligase regulator of CDT1, cullin 4A (CUL4A), in PDAC.

MATERIALS AND METHODS

Expression levels of CUL4, CDT1, CDC6 and MCM7 were evaluated by immunohistochemistry in 76 formalin-fixed paraffin-embedded specimens of PDAC patients in relation to DNA-damage response marker H2AX, clinicopathological parameters and survival. We also conducted bioinformatics analysis of data from online available databases to corroborate our findings.

RESULTS

CUL4A and DNA replication-licensing factors were overexpressed in patients with PDAC and expression of CDT1 positively correlated with H2AX. Expression of CUL4A and CDT1 positively correlated with lymph node metastasis. Importantly, elevated CUL4A expression was associated with reduced overall survival and was an independent indicator of poor prognosis on multivariate analysis.

CONCLUSION

Our findings implicate CUL4A, CDT1, CDC6 and MCM7 in PDAC progression and identify CUL4A as an independent prognostic factor for this disease.

Pathway-dependent toxic interaction between polystyrene microbeads and methylmercury on the brackish water flea Diaphanosoma celebensis: Based on mercury bioaccumulation, cytotoxicity, and transcriptomic analysis

Given their worldwide distribution and toxicity to aquatic organisms, methylmercury (MeHg) and microplastics (MP) are major pollutants in marine ecosystems. Although they commonly co-exist in the ocean, information on their toxicological interactions is limited. Therefore, to understand the toxicological interactions between MeHg and MP (6-μm polystyrene), we investigated the bioaccumulation of MeHg, its cytotoxicity, and transcriptomic modulation in the brackish water flea Diaphanosoma celebensis following single and combined exposure to MeHg and MP. After single exposure to MeHg for 48-h, D. celebensis showed high Hg accumulation (34.83 ± 0.40 μg/g dw biota) and cytotoxicity, which was reduced upon co-exposure to MP. After transcriptomic analysis, 2, 253, and 159 differentially expressed genes were detected in the groups exposed to MP, MeHg, and MeHg+MP, respectively. Genes related to metabolic pathways and the immune system were significantly affected after MeHg exposure, but the effect of MeHg on these pathways was alleviated by MP co-exposure. However, MeHg and MP exhibited synergistic effects on the expression of gene related to DNA replication. These findings suggest that MP can reduce the toxicity of MeHg but that their toxicological interactions differ depending on the molecular pathway.

DNA replication: Mechanisms and therapeutic interventions for diseases

Accurate and integral cellular DNA replication is modulated by multiple replication-associated proteins, which is fundamental to preserve genome stability. Furthermore, replication proteins cooperate with multiple DNA damage factors to deal with replication stress through mechanisms beyond their role in replication. Cancer cells with chronic replication stress exhibit aberrant DNA replication and DNA damage response, providing an exploitable therapeutic target in tumors. Numerous evidence has indicated that posttranslational modifications (PTMs) of replication proteins present distinct functions in DNA replication and respond to replication stress. In addition, abundant replication proteins are involved in tumorigenesis and development, which act as diagnostic and prognostic biomarkers in some tumors, implying these proteins act as therapeutic targets in clinical. Replication-target cancer therapy emerges as the times require. In this context, we outline the current investigation of the DNA replication mechanism, and simultaneously enumerate the aberrant expression of replication proteins as hallmark for various diseases, revealing their therapeutic potential for target therapy. Meanwhile, we also discuss current observations that the novel PTM of replication proteins in response to replication stress, which seems to be a promising strategy to eliminate diseases.

Topoisomerase IIβ binding protein 1 serves as a novel prognostic biomarker for stage II-III colorectal cancer patients

BACKGROUND

Colorectal cancer (CRC) is a commonly diagnosed human malignancy worldwide. Accumulating evidence has suggested DNA repair related proteins widely participate in CRC initiation and development. TOPBP1 is recently identified as a novel regulator for DNA repair, however, its biological role in CRC remains unknown.

METHODS

Firstly, the bioinformatics analysis was utilized to investigate the expression and clinical significance of TOPBP1 in CRC patients. Then, a retrospective study enrolling 129 stage II/III CRC patients was performed for validation. The CCK-8, colony formation, transwell assay and xenograft model were used to clarify the biological impact of TOPBP1 on CRC cells. Finally, transcriptome sequencing was performed to investigate the potential oncogenic mechanisms regulated by TOPBP1 in CRC development.

RESULTS

The expression of TOPBP1 was significantly higher in CRC tissues than that in normal tissues. High TOPBP1 expression was an independent unfavorable prognostic factor for overall and disease-free survival in II/III CRC patients. Knockdown of TOPBP1 not only significantly inhibited the proliferation, colony formation, invasion, migration and epithelial-mesenchymal transition (EMT) molecular phenotype of CRC cells, while the opposite was for TOPBP1 expression. Moreover, knockdown of TOPBP1 slowed down the growth speed of xenografts. The transcriptome sequencing identified MAP3K3 as a downstream gene of TOPBP1 and MAP3K3 knockdown inhibited the EMT molecular phenotype in CRC cells. Finally, the rescue assay indicated MAP3K3 overexpression counteracted the inhibitory effect of TOPBP1 knockdown on the proliferation, colony formation, invasion, migration and EMT phenotype of CRC cells.

CONCLUSION

TOPBP1 promotes the malignant progression of CRC through MAP3K3 induced EMT. TOPBP1 is a promising clinical biomarker or therapeutical target for CRC patients.

Bioinformatics Analysis of RNA-seq Data Reveals Genes Related to Cancer Stem Cells in Colorectal Cancerogenesis

Cancer stem cells (CSC) play one of the crucial roles in the pathogenesis of various cancers, including colorectal cancer (CRC). Although great efforts have been made regarding our understanding of the cancerogenesis of CRC, CSC involvement in CRC development is still poorly understood. Using bioinformatics and RNA-seq data of normal mucosa, colorectal adenoma, and carcinoma (n = 106) from GEO and TCGA, we identified candidate CSC genes and analyzed pathway enrichment analysis (PEI) and protein–protein interaction analysis (PPI). Identified CSC-related genes were validated using qPCR and tissue samples from 47 patients with adenoma, adenoma with early carcinoma, and carcinoma without and with lymph node metastasis and were compared to normal mucosa. Six CSC-related genes were identified: ANLN, CDK1, ECT2, PDGFD, TNC, and TNXB. ANLN, CDK1, ECT2, and TNC were differentially expressed between adenoma and adenoma with early carcinoma. TNC was differentially expressed in CRC without lymph node metastases whereas ANLN, CDK1, and PDGFD were differentially expressed in CRC with lymph node metastases compared to normal mucosa. ANLN and PDGFD were differentially expressed between carcinoma without and with lymph node metastasis. Our study identified and validated CSC-related genes that might be involved in early stages of CRC development (ANLN, CDK1, ECT2, TNC) and in development of metastasis (ANLN, PDGFD).