Cancer Genomics & Proteomics最新文献

Background/aim: In this study, we provide a comprehensive characterization of HPV-positive primary cervical cancers (CC) and HPV-positive head and neck squamous cell carcinomas (HNSCC) through whole genome next-generation sequencing. Human papillomavirus (HPV) infection, recognized as a definitive human carcinogen, is increasingly acknowledged for its role in development of human cancers. HPV-driven cervical cancers are among the leading causes of cancer-related deaths worldwide, while HPV-driven head and neck cancers exhibit distinct biological and clinical characteristics. Recent data has provided convincing evidence that HPV-related cervical cancer, like HPV head and neck cancer also predict better outcomes, with viral integration patterns further predicting disease related outcomes.

Materials and methods: We designed an experimental study that encompasses four pairs of HPV-positive patient samples with controls, utilizing state-of-the-art Next Generation Sequencing (NGS) technology including whole genome sequencing, transcriptome sequencing and virus integration.

Results: Multiple mutated genes, including TTN, COL6A3, and FLNA, were identified shared between CC and HNSCC. Additionally, we observed a notable proportion of pathways affected by oncogenic alterations, particularly in the RTK-RAS and NOTCH pathways, in both CC and HNSCC. Furthermore, we discovered a shared down-regulation of the Hedgehog signaling pathway based on transcriptome expression analysis in KEGG. We also identified RUNX2 and TFPI as sites of virus integration, and upstream as well as downstream pathway modulators, and represent potential targets for therapeutic interventions.

Conclusion: Overall, this study showed a thorough comparison between CC and HNSCC from multiple aspects, including gene variations, oncogenic pathways, KEGG enrichment and virus integration sites. However, further studies, which involve larger patient cohorts should be undertaken to further support these findings.

Background/aim: Metachronous biliary tract cancer (BTC) is a rare occurrence after curative resection of primary BTC. The genetic alterations and pathogenesis associated with metachronous BTC remain poorly understood.

Patients and methods: We analyzed four patients with metachronous BTC who underwent resection at the Nagoya University Hospital between 2010 and 2024. Gene panel examination was performed on both primary and secondary tumors using next-generation sequencing.

Results: The median interval between resection of the primary tumor and diagnosis of metachronous BTC was 24 months. Genetic alterations were observed in all paired primary and metachronous carcinomas. The number of genetic mutations was higher in metachronous lesions than in primary lesions. CDKN2A and SMAD4 were the most frequently mutated genes in all metachronous lesions. Common genetic mutations between primary and metachronous lesions were confirmed in all four cases, suggesting a common clonal origin.

Conclusion: This study demonstrated that characteristic genetic alterations and their accumulation play important roles in metachronous BTC. This suggests that the increasing burden of gene mutations may play a crucial role in the carcinogenesis of metachronous BTC. Further investigation is required to validate these findings and elucidate the underlying molecular mechanisms.

Background/aim: We previously developed Salmonella typhimurium A1-R, which selectively targets and kills tumors. In the present study, we established recombinant methioninase (rMETase)-producing Salmonella typhimurium A1-R (A1-R-rMETase), by transfer of the Pseudomonas putida methioninase gene, to target methionine addiction of syngeneic-cancer mouse models.

Materials and methods: A plasmid containing the Pseudomonas putida methioninase gene was extracted from METase-producing recombinant E. coli and inserted into Salmonella typhimurium A1-R using electroporation. Lewis Lung Carcinoma (LLC) cells (10⁶) were injected subcutaneously in male C57BL/6 mice aged 4-6 weeks. We determined that 10⁸ Salmonella typhimurium A1-R-rMETase administered iv was a safe dosage in C57BL/6 mice and was used for efficacy studies on LLC tumors in C57BL/6 mice. Tumor size was measured with calipers three times per week for 3 weeks. On day 22, tumor methionine levels were measured using HPLC in the control mice injected with phosphate-buffered saline (PBS) and the mice injected with Salmonella typhimurium A1-R-rMETase.

Results: The mean LLC tumor size of each group on day 22 was as follows: PBS control: 741.5 mm³; mice injected with Salmonella typhimurium A1-R: 566.3 mm³ (p=0.370); and mice injected with Salmonella typhimurium A1-R-rMETase: 198.8 mm³ (p=0.0003 vs control and p=0.0117 vs. Salmonella A1-R). The mice injected with Salmonella typhimurium A1-R-rMETase showed a significantly lower mean tumor methionine level than mice injected with PBS (5.9 nM/mg protein vs 11.1 nM/mg protein, p=0.0095). Salmonella typhimurium A1-R-rMETase grew continuously in the tumors but not in the liver or spleen.

Conclusion: Tumor-targeting Salmonella typhimurium A1-R engineered to express the Pseudomonas putida methioninase gene, inhibited LLC tumor growth in a syngeneic mouse model and reduced the methionine level in the tumor. Salmonella typhimurium A1-R-rMETase combines the tumor targeting and killing capability of Salmonella typhimurium A1-R plus rMETase which targets the methionine addiction of cancer.

Background/aim: This study investigated the relationship between E-cadherin down-regulation and enhanced pERK1/2 signaling in cervical cancer, evaluated their combined prognostic impact, and explored potential therapeutic targets.

Materials and methods: We analyzed 188 cervical cancer specimens and 300 normal cervical tissue samples using tissue microarray and immunohistochemistry. Small interfering RNA transfection and western blotting were used to study molecular interactions in cervical cancer cell lines.

Results: We observed a significant inverse correlation between E-cadherin and pERK1/2 expression, as well as poor disease-free survival and overall survival. Additionally, molecular analysis indicated that E-cadherin silencing enhanced ERK signaling and promoted cancer cell proliferation.

Conclusion: The findings suggest that E-cadherin and pERK1/2 are crucial biomarkers for cervical cancer prognosis and their interaction provides a potential target for therapeutic interventions. Further studies are recommended to explore these pathways in the clinical setting.

Background/aim: The tumor microenvironment greatly influences cancer occurrence, progression, and treatment resistance, making it a key target alongside cancer cells. In squamous cell carcinoma, the invasive front is crucial for studying invasion mechanisms driven by the surrounding microenvironment and for identifying biomarkers to diagnose and predict invasive cancer. In this study, we aimed to elucidate the regulation of cancer characteristics through the interactions between factors at the invasive tumor front and the surrounding tumor microenvironment.

Materials and methods: The invasive tumor front (ITF) and tumor center (TC) of collective cancer invasion were analyzed using microarray to compare gene expression. A stable cell line with depleted DEFA1 expression was established, and its effect on cancer growth was observed using a mouse tongue xenograft model. Invasive activity was assessed using Transwell assays. Gene profiling of cancer cells and analysis of secreted proteins interacting with U937 monocytic cells during co-culture were conducted using QuantSeq 3' mRNA sequencing and LC-MS/MS analysis.

Results: DEFA1 was overexpressed at the ITF of collective cancer invasion. YD10B cells with depleted DEFA1 expression exhibited significantly reduced invasiveness and tumor growth without changes in the cell cycle distribution. Co-culture with U937 cells significantly enhanced the invasiveness of YD10B cells, which was inhibited by anti-DEFA1 treatment. QuantSeq 3' mRNA sequencing and LC-MS/MS analyses confirmed that DEFA1 derived from U937 cells increased the invasiveness of YD10B cells. Recombinant DEFA1 (rDEFA1) significantly enhanced the invasiveness of YD10B cells via the JNK MAPK/NF-[Formula: see text]B signaling pathway, independent of changes in DEFA1 expression within YD10B cells.

Conclusion: DEFA1 is crucial for cancer invasion and growth, and monocyte-derived DEFA1 exacerbates these traits. This study highlights DEFA1's role in promoting invasion at the tumor front, where interactions with the microenvironment are active.

Background/aim: Cholangiocarcinoma (CCA) is an epithelial malignancy that is most prevalent in Southeast Asia, particularly in the northeast of Thailand. Identifying and establishing specific biomarkers of CCA is crucial for ensuring accurate prognosis and enabling effective treatment. High-mobility group box 1 (HMGB1) is a damage-associated molecular pattern (DAMP) molecule that can be released by dead or injured cells and is associated with tumor progression. This study aimed to investigate the expression levels of HMGB1 in CCA.

Materials and methods: The clinical significance of HMGB1 levels was assessed by examining their correlation with patients' clinicopathological data. A bioinformatics analysis was conducted to examine HMGB1 mRNA expression and perform survival analysis. The expression levels of 137 tissue cases were evaluated using the immunohistochemical technique, whereas the serum levels of 31 cases were evaluated using indirect ELISA.

Results: The GEPIA analysis demonstrated that HMGB1 exhibited elevated mRNA expression in CCA compared to the normal group. Immunohistochemical staining revealed that HMGB1 expression was primarily localized in the nucleus. High HMGB1 expression was observed in 57.6% of tissue samples, while low expression was detected in 42.4%. There was a significant positive correlation between high HMGB1 expression and the extrahepatic type of CCA as well as lymph node metastasis. The measurement of HMGB1 levels were assessed using indirect ELISA in 31 CCA serum samples, where 51.6% exhibited elevated concentrations of HMGB1. Elevated serum HMGB1 levels were significantly associated with advanced tumor stages and high levels of bilirubin levels.

Conclusion: HMGB1 in both tissue biopsies and blood serum shows potential as a predictive biomarker in CCA patients. These biomarkers could form the basis for facilitating more effective treatment planning.

Background/aim: Treatment with retinoic acid (RA) often promotes neuroblastoma differentiation and growth inhibition, including the suppression of the expression of the MYCN oncogene. However, RA also targets protumoral chemokines, such as CCL2, which may contribute to the development of resistance. The present study aimed to investigate the regulation and function of CCL2 and N-Myc in RA-treated neuroblastoma cells.

Materials and methods: In Kelly or SH-SY5Y cells, viability was quantified by cell fitness assays. Expression was analyzed using quantitative PCR and the regulation of proteins using enzyme-linked immunoabsorbent assays (ELISA) or western blots.

Results: In MYCN-amplified Kelly cells, endogenous CCL2 levels were significantly lower compared to MYCN non-amplified SH-SY5Y cells. Treatment with 5 μM RA increased CCL2 release in both cell lines, but reduced N-Myc levels and cell numbers in Kelly cells. Over-expression of MYCN enhanced viability in SH-SY5Y cells, but did not affect RA-induced CCL2 release, while supplementation of CCL2 in Kelly cells did not prevent RA-mediated growth reduction. Impaired N-Myc or CCL2 signaling reduced the survival of all RA-treated cells and inhibition of N-Myc also decreased CCL2 levels. However, attenuated survival signaling was not generally associated with reduced levels of N-Myc or CCL2. Co-application of RA and the growth factor receptor inhibitors cediranib or crizotinib decreased N-Myc levels only in Kelly cells, while CCL2 release was dependent on the cell type and stimulus.

Conclusion: CCL2 and N-Myc promote the viability of RA-treated cells, although the levels of these mediators were not consistently correlated with cellular outcomes, especially during apoptotic signaling.

Background/aim: Replication factor C subunit 3 (RFC3) is a critical component of the replication factor C complex, which is essential for DNA replication and repair. Recent studies have highlighted the RFC3's significance in various cancer types. Herein, we aimed to elucidate its biological role in cervical cancer.

Materials and methods: Cervical cancer cells were transfected with RFC3 or control siRNA. Cell viability was assessed using the MTT assay over a 4-day period and its clonogenic potential was determined using colony formation assays. Flow cytometry analysis was performed to evaluate cell cycle distribution. Transwell migration and invasion assays were performed to assess the migration and invasion abilities of cervical cancer cells.

Results: RFC3 knockdown significantly inhibited cell proliferation, induced cell-cycle arrest, and decreased migration and invasion in HeLa and ME-180 cells compared to control siRNA-transfected cells.

Conclusion: The crucial role of RFC3 in cervical cancer progression is highlighted. RFC3 knockdown resulted in decreased cervical cancer cell proliferation, migration and invasion, suggesting its potential as a therapeutic target in cervical cancer.

Background/aim: Glioblastoma is the most malignant brain tumor, and despite advances in treatment, survival rates are still dismal. Therefore, a comprehensive understanding of the underlying molecular mechanisms of glioblastoma is needed. This study suggests potential therapeutic targets in glioblastoma that may provide new therapeutic insights.

Materials and methods: To identify hub genes in glioblastoma, three datasets were selected from the GEO database. After screening DEGs using GEO2R, GO and KEGG analyses were performed using DAVID. The PPI network was visualized using Cytoscape and 7 hub genes were extracted. The prognostic potential of 7 hub genes was investigated using the Gliovis and GEPIA2 databases.

Results: In total, 176 up-regulated and 263 down-regulated genes were identified. From the PPI network, 7 hub genes were identified including CAMK2A, DLG4, SNAP25, SYT1, MYC, FN1, and VEGFA. Out of the 7 hub genes identified, FN1 and VEGFA have been associated with a poor prognosis in glioblastoma based on the survival analysis.

Conclusion: This study suggests that high levels of FN1 and VEGFA expression are associated with a poor prognosis in glioblastoma and that both genes are promising targets for glioblastoma therapy. Bioinformatics analysis of DEGs revealed putative targets that might reveal the molecular mechanisms underlying glioblastoma.

Background/aim: The development of new biomarkers to predict cancer patient prognosis is expected to aid in treatment selection, contributing to improved outcomes. In this study, we extracted a candidate gene associated with patient prognosis from a public database and investigated the molecular and biological functions and clinical significance of the gene in gastric cancer.

Materials and methods: We analyzed The Cancer Genome Atlas database and identified the family with sequence similarity 32 member a (FAM32A) as a candidate gene. We investigated the clinicopathological significance of FAM32A mRNA and protein expression in 300 and 176 gastric cancer patients respectively. We evaluated the molecular and biological functions by suppressing FAM32A expression in gastric cancer cell lines using small interfering RNA.

Results: In the polymerase chain reaction (PCR) cohort, low FAM32A expression group showed significantly shorter disease-specific survival (DSS) [hazard ratio (HR)=1.586; 95% confidence interval (95% CI)=1.056-2.382, p=0.026]. In the immunohistochemistry cohort, the FAM32A(-) group had significantly shorter overall survival (HR=1.703; 95% CI=1.050-2.764, p=0.031) and DSS (HR=2.123; 95% CI=1.185-3.804, p=0.011). Multivariate Cox hazard analysis revealed that FAM32A(-) was an independent adverse prognostic factor for DSS (p<0.001). AGS cell lines with FAM32A knockdown exhibited significant resistance to 5-fluorouracil (5-FU) and reduced apoptosis upon 5-FU administration. Gene set enrichment analysis indicated decreased gene expression related to the p53 signaling pathway in AGS cells with FAM32A knockdown that were treated with 5-FU.

Conclusion: FAM32A suppression decreases 5-FU-induced apoptosis. Low FAM32A expression is associated with a poor prognosis in gastric cancer, suggesting its potential as a biomarker.