Cancer Genomics & Proteomics最新文献

Background/aim: Ewing's sarcoma is an aggressive pediatric malignancy driven by specific chromosomal translocations, predominantly leading to the oncogenic fusion protein EWS-FLI1. Runt-related transcription factors 1 and 2 (RUNX1 and RUNX2), which are key transcription factors involved in osteoblastic differentiation and skeletal morphogenesis, are not expressed in Ewing's sarcoma. Our study aimed to elucidate the relationship between the RUNX genes and EWS-FLI1.

Materials and methods: We used Ewing's sarcoma cell lines (A673 and NCR-EW2). EWS-FLI1 knockdown was achieved using shRNA, while inducible expression of RUNX1, RUNX2, EWS-FLI1, or EWS-ERG was performed using a Tet-on system. Gene and protein expression levels were quantitatively assessed by qPCR and Western blot analysis, respectively. Cell growth was evaluated using spheroid formation and cell viability assays. Truncated RUNX1 or RUNX2 constructs were employed to identify functional domains, with their intracellular localization confirmed by immunostaining.

Results: We observed low expression of RUNX1 and RUNX2 in Ewing's sarcoma cells. Notably, EWS-FLI1 knockdown increased RUNX2 gene expression. Conversely, inducible expressions of either RUNX1 or RUNX2 suppressed the expression of EWS-FLI1 target genes and inhibited cell proliferation and spheroid formation. Additionally, the RUNT domain of RUNX1 and RUNX2 was not essential for their inhibitory effect on EWS-FLI1 target gene expression. Importantly, both EWS-FLI1 and EWS-ERG down-regulated RUNX2 gene expression in hTert-RPE1 cells.

Conclusion: EWS-FLI1 suppresses RUNX2 gene expression in Ewing's sarcoma cells, and re-expressing RUNX2 inhibits cell growth. These findings suggest that RUNX2 has a negative impact on the oncogenic process in Ewing's sarcoma.

Background/aim: The expression of augmenter of liver regeneration (ALR), a potent growth factor, is significantly up-regulated in hepatocellular carcinoma (HCC). This study aims to investigate the potential functions and mechanisms of ALR in HCC.

Materials and methods: ALR expression in Huh7 cells was silenced using an RNA interference (RNAi) lentiviral vector, and differentially expressed genes (DEGs) were identified through DNA microarray analysis. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) were performed to explore the functional roles and mechanisms of ALR in HCC. A protein-protein interaction (PPI) network was constructed based on the identified DEGs, and hub genes with high connectivity were identified. The relationship between these hub genes, ALR, and HCC cell proliferation was further analyzed.

Results: A total of 299 DEGs were identified, including 171 up-regulated and 128 down-regulated genes. GO, KEGG, and GSEA analyses revealed that ALR is closely associated with receptor protein signaling pathways, cell proliferation, metabolism, mitochondrial homeostasis, and cell migration. Furthermore, ALR expression was associated with the enrichment of oncogenic pathways, including KRAS, Hedgehog, and IL-6/JAK/STAT3 signaling. Analysis of the PPI network and hub gene analysis identified Cyclooxygenase-2 [COX-2, also known as prostaglandin-endoperoxide synthase 2 (PTGS2)] as a key hub gene, which was selected for further investigation. Real-time quantitative PCR and Western blot results indicated that COX-2 is a downstream target of ALR. Additionally, ALR was shown to promote Huh7 cell proliferation by regulating COX-2.

Conclusion: These findings connect ALR to the dysregulation of multiple oncogenic signaling pathways in HCC. Additionally, ALR may promote the proliferation of HCC by modulating the downstream pro-inflammatory factor COX-2, suggesting that ALR could serve as a potential therapeutic target for HCC.

Background/aim: Prostate cancer is the second most commonly diagnosed malignancy and a leading cause of cancer-related mortality among men worldwide. While early-stage disease can often be managed effectively, advanced and treatment-resistant forms such as castration-resistant prostate cancer (CRPC) remain a major therapeutic challenge. Novel therapeutic strategies targeting alternative pathways are therefore urgently needed. Rutin, a natural flavonoid abundant in fruits and vegetables, has demonstrated antioxidant and anticancer properties. This study aimed to investigate the anticancer effects of Rutin in prostate cancer cells, focusing on epithelial-mesenchymal transition (EMT), mitochondrial biogenesis, and endoplasmic reticulum (ER) stress-linked signaling.

Materials and methods: Four prostate cancer cell lines (PC-3, DU-145, LNCaP, and LNCaP-Enz) were treated with rutin. Cell proliferation was assessed, and EMT markers [E-cadherin, α-smooth muscle actin (α-SMA), Snail, Slug], mitochondrial biogenesis-related proteins (AMPK, SIRT1, PGC-1α, NRF1, TFAM), and ER stress markers (BiP, IRE1, PERK, ATF6) were analyzed by standard molecular and cellular assays. Co-treatment with the ER stress inhibitor TUDCA and the eIF2α phosphorylation modulator Salubrinal was performed to determine pathway involvement.

Results: Rutin significantly suppressed cell proliferation and EMT in all tested prostate cancer cell lines, as indicated by increased E-cadherin expression and decreased α-SMA, Snail, and Slug. It also promoted mitochondrial biogenesis through the up-regulation of AMPK, SIRT1, PGC-1α, NRF1, and TFAM. In parallel, rutin reduced ER stress marker expression, and these effects were reversed by co-treatment with TUDCA or Salubrinal.

Conclusion: Rutin inhibits prostate cancer progression by suppressing EMT, inducing mitochondrial biogenesis, and acting via ER stress-linked AMPK/SIRT1 signaling. These findings suggest that Rutin may serve as a potential therapeutic candidate for advanced prostate cancer.

Background/aim: Cancer remains a leading cause of mortality globally, driven by complex molecular mechanisms and characterized by significant biological heterogeneity across cancer types. We aimed to discover mitogen-activated protein kinases (MAPKs) family members as both biomarkers and therapeutic targets in different cancer types. MAPKs are key signaling molecules regulating cell proliferation, differentiation, stress response, and apoptosis. Dysregulation of MAPK pathways has been implicated in the onset and progression of multiple cancers, contributing to tumor growth, metastasis, and therapeutic resistance. Given their diverse roles across cancer types, systematic analysis of MAPK gene expression, mutations, and interactions with tumor microenvironment is essential.

Materials and methods: The present study undertakes a comprehensive transcriptomic analysis of MAPKs in nine major cancer types using RNA-Seq datasets from The Cancer Genome Atlas (TCGA). RNA-Seq data were analyzed to identify differentially expressed MAPKs across nine cancer types using DESeq2, NOIseq, and limma. Significant genes (adjusted p<0.05) were subjected to GO and KEGG enrichment (EnrichR), mutational profiling (cBioPortal), and Kaplan-Meier survival analysis. Tumor immune infiltration was further assessed using TIMER2.0 to explore immune-gene interactions.

Results: Through rigorous differential expression analysis, we identified key MAPKs that are significantly altered in liver hepatocellular carcinoma (LIHC) and lung adenocarcinoma (LUAD). Specifically, six MAPKs (MAPK3, MAPK7, MAPK9, MAPK10, MAPK12, and MAPK13) were found to be differentially expressed in LIHC, while MAPK6 emerged as the sole significant candidate in LUAD. Functional enrichment and pathway analysis revealed that these MAPKs are involved in critical oncogenic pathways, including MAPK-mediated transcriptional regulation and stress-activated signaling cascades. Mutational profiling and survival analysis further validated the prognostic significance of these genes, with several MAPKs showing strong associations with reduced patient survival. Tumor immune infiltration analysis indicated potential roles of these MAPKs in modulating immune responses within the tumor microenvironment. Also, MAPKs identified in this study are structurally related, suggesting that targeting them collectively may enhance therapeutic efficacy and overcome resistance mechanisms.

Conclusion: Our integrated approach underscores the value of MAPK family members as both biomarkers and therapeutic targets in LIHC and LUAD. This study contributes important insights into MAPK-related oncogenic processes and supports the development of targeted therapies under the framework of precision oncology.

Background/aim: Clear cell renal cell carcinoma (ccRCC), the most prevalent form of kidney cancer, often presents or recurs as an advanced, aggressive, and lethal disease. Thus, biomarkers are needed to identify patients at risk of developing advanced-stage or treatment-resistant ccRCC. SYNJ2BP, a cytoplasmic scaffolding protein, regulates ACVR2 activity, a key mediator of signaling pathways involved in tumor progression and metastasis. This study aimed to ascertain if SYNJ2BP, a gene highly expressed in normal kidney tissue, may serve as a predictive biomarker for ccRCC.

Materials and methods: Bioinformatic analysis and immunohistochemistry were applied to investigate the relationship between SYNJ2BP expression, the immune landscape, and survival outcomes in ccRCC. We utilized data from publicly available databases, including The Cancer Genome Atlas, Gene Set Cancer Analysis (TCGA), and various other databases.

Results: In-silico analyses revealed that SYNJ2BP expression was significantly down-regulated in ccRCC (Log2FC=0.40, p=2.65E-36; FDR=9.73E-34), compared to normal tissue. Moreover, SYNJ2BP expression was significantly reduced in advanced stages and grades (III and IV; p<0.001) compared to lower stages and grades (I and II). Decreased expression was associated with nodal invasion and metastasis (p<0.0001), unresponsive to treatment (p=0.0052), post-treatment recurrence (p=0.002), lower median overall survival (HR=0.39, 95% CI=0.28-0.54, p<0.0001), disease-specific survival (HR=0.16, 95% CI=0.09-0.27, p<0.0001) and shorter progression-free survival (HR=0.24, 95% CI=0.17-0.35, p<0.0001). Survival trends remained consistent in multivariate Cox regression, where expression remained independently associated with outcome. Consistent with transcript-level findings, immunohistochemistry demonstrated reduced protein expression of SYNJ2BP in ccRCC patients (p<0.05).

Conclusion: SYNJ2BP is a novel prognostic biomarker for ccRCC and the down-regulation of SYNJ2BP expression is associated with poor survival outcomes and reduced treatment response.

Background/aim: Regional differences in genomic mutation profiles of uterine cervical cancer have been reported. Japanese people are divided into two genetic background clusters, originating from mainland Japan and Okinawa. Okinawa is an island prefecture surrounded by the sea, located more than 800 km from the southernmost point of mainland Japan. No studies have examined gene mutation profiles of cervical cancer in Okinawa. This study aimed to investigate the mutation profile of cervical cancer in Okinawa.

Patients and methods: Twenty-three patients with biopsy-proven squamous cell carcinoma and adenocarcinoma of the intact uterine cervix who were treated with definitive radiotherapy were analyzed. Genomic DNA was extracted from fresh frozen tissue samples collected by tumor biopsy prior to treatment. Variants of 224 cancer-related genes were identified using next-generation sequencing.

Results: A total of 29 gene mutations were observed in 16 patients, including nine genes mutated in multiple samples: SCN7A (17%), PIK3CA (13%), FGFR4 (13%), USP6 (13%), SETD2 (9%), KIT (9%), TSC1 (9%), SERPING1 (9%), and NOTCH3 (9%). Compared to a report from mainland Japan, significant differences in mutation frequency were observed in PIK3CA, FBXW7, and ARID1A. Significant mutations in ARID1A, FBXW7, PTEN, TP53, and EP300, reported as relatively common in cervical cancer in other regions were not detected in this study. The rate of 2-year overall survival and progression-free survival was 95.5% and 73.4%, respectively.

Conclusion: Gene mutation profiles of cervical cancer in Okinawa may differ from those in other regions.

Background/aim: Metastatic Ewing sarcoma (EWS) causes high mortality. Precision medicine can help to mitigate dismal outcomes by targeted and more effective eradication of cancer cells. The aim of the study was to propose a targeted immunoliposome (IL) that has a potential of selectively binding to and destroying EWS cells. EWS expresses CD99 used for diagnostics. If CD99 is used for targeted IL, its payload must be more damaging to EWS than normal cells, which may also express CD99. Poly(ADP-ribose) polymerase (PARP) inhibitors are potential payload candidates, since they may enhance apoptosis of EWS-cells treated with DNA-damaging agents.

Materials and methods: The R2 genomics platform was used to explore the differential expression of CD99 and PARP1 in seven different databases (two EWS and five various normal tissues). Kaplan-Meier analysis was conducted for prognostic significance of PARP1 expression. The side-effect profile of PARP inhibitors allowed selection of a potential payload for proposed IL.

Results: EWS samples (Savola/Surdez, n=196) had higher CD99 expression than 737 normal tissues. Endothelial compartment had twice-higher CD99 compared to other normal tissues but lower CD99 and PARP1 than EWS. Recurrent/metastatic EWS expressed more PARP1 than primary tumors (ANOVA p=0.02, Savola). Ten-year survival respectively for low versus high PARP1 expression was 36% vs. 14% for EFS (p=0.016), and 50% vs. 7% for OS (p<0.001). Normal hematopoietic/B-cell compartments had ≥2-times higher PARP1 than other tissues; therefore, niraparib (least lymphotoxic of PARP inhibitors), was favored as a payload for anti-EWS IL.

Conclusion: Immunoliposomes covered with anti-CD99 mAbs and loaded with small-molecule niraparib may be developed as an adjuvant therapy for advanced EWS. Projected 100 nm IL should provide vascular permeability and tumor tropism; however, extensive preclinical evaluations will also be required regarding hematopoietic and endothelial damage.

Background/aim: Oxysterol-binding protein-like 3 (OSBPL3) is a member of the intracellular lipid receptor and transporter protein family involved in regulating lipid metabolism. Altered OSBPL3 expression has been observed in various cancers, where it has been associated with both oncogenic and tumor-suppressive roles. However, its precise functions and underlying mechanisms in colorectal cancer (CRC) remain unclear. This study aimed to investigate the role of OSBPL3 in CRC cells and evaluate its prognostic significance.

Materials and methods: A small interfering RNA vector targeting OSBPL3 was employed to silence its expression in CRC cell lines. OSBPL3 levels in CRC tissues were assessed using reverse transcription-polymerase chain reaction and immunohistochemistry. Tumor cell apoptosis, proliferation, and angiogenesis were evaluated via a terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling assay, and immunohistochemical staining for Ki-67 and CD34.

Results: OSBPL3 silencing inhibited tumor cell migration and invasion in CRC. OSBPL3 knockdown reduced proliferation and induced apoptosis through caspase activation and cell cycle arrest mediated by the regulation of cyclins, cyclin dependent kinases (CDKs), and CDK inhibitors. OSBPL3 suppression impaired the invasion and tube formation of human umbilical vein endothelial cells by down-regulating angiogenic factors and up-regulating angiostatic factors. OSBPL3 expression correlated significantly with tumor size, tumor stage, invasion depth, lymph node involvement, distant metastasis, and reduced survival. The apoptotic index was lower and microvessel density was higher in OSBPL3-positive tumors than in OSBPL3-negative tumors.

Conclusion: OSBPL3 contributes to CRC progression by regulating tumor cell apoptosis and angiogenesis.

Background/aim: Cross-talk between forkhead box O1 (FOXO1), a transcriptional factor known to function as a tumor suppressor via the PI3K/AKT pathway, and glucocorticoid receptor (GR) has been implied in non-urothelial cells. The present study aimed to investigate the association of FOXO1 and GR expression in bladder cancer and its prognostic significance.

Materials and methods: Immunohistochemical staining for GR, FOXO1, and p-FOXO1 (a phosphorylated/inactivated form) was performed in a set of bladder cancer tissue microarray comprising 50 low-grade non-invasive tumors, 28 high-grade non-muscle-invasive tumors, and 51 high-grade muscle-invasive tumors. Western blotting for FOXO1 and p-FOXO1 was also conducted in human bladder cancer cells.

Results: GR expression was detected in 109 [84.5%; 39 (30.2%) weakly positive (1+), 39 (30.2%) moderately positive (2+), 31 (24.0%) strongly positive (3+)] tumors, whereas FOXO1 and p-FOXO1 were immunoreactive in 17 [13.2%; 16 (12.4%) 1+, 1 (0.8%) 2+] and 71 [55.0%; 57 (44.2%) 1+, 14 (10.9%) 2+] tumors, respectively. The expression levels of GR were positively and negatively correlated with those of FOXO1 (p=0.003) and p-FOXO1 (p=0.009), respectively. GR(0/1+)/FOXO1(0) and GR(0/1+)/p-FOXO1(1+/2+) were significantly more often observed in high-grade (vs. low-grade) or muscle-invasive (vs. non-muscle-invasive) tumors. Both univariate and multivariate analyses revealed that GR(0/1+)/FOXO1(0) and GR(0/1+)/p-FOXO1(1+/2+) were associated with a significantly higher risk for the recurrence of non-invasive disease or progression of muscle-invasive disease. In 2 GR-positive bladder cancer lines, glucocorticoids (i.e., dexamethasone, prednisone) and a GR antagonist (i.e., RU486) induced the levels of FOXO1 and p-FOXO1 expression, respectively.

Conclusion: The expression levels of GR and FOXO1 or p-FOXO1 were strongly correlated in bladder cancer. Specific GR/FOXO1 and GR/p-FOXO1 expression profiles served as independent predictors of disease recurrence or progression.

Background/aim: The incidence of cancer continues to rise, highlighting the urgent need for reliable, non-invasive biomarkers to support early diagnosis and improve treatment outcomes. In addition to circulating microRNAs, circulating PIWI-interacting RNAs (cir-piRNAs) have emerged as promising candidates. Although the biological functions of piRNAs are not yet fully understood, they are known to suppress transposable elements and may regulate structural genes involved in tumorigenesis. In this two-phase study, we aimed to identify serum piRNAs with diagnostic potential for clear cell renal cell carcinoma (ccRCC).

Materials and methods: A total of 238 serum samples from ccRCC patients and 208 healthy controls were analyzed. In the exploratory phase, next-generation sequencing (NGS) was performed on pooled samples representing different clinical stages of ccRCC and healthy controls.

Results: We identified 35 piRNAs with significantly different expression (p<0.01) between groups. Based on statistical significance, read abundance, and fold change, six piRNAs were selected for the training phase and subsequently, three piRNAs, piR-24672, piR-27140, and piR-28876, were selected for validation. Validation by RT-qPCR in an independent cohort confirmed significantly reduced levels of all three piRNAs in ccRCC patients. ROC analysis demonstrated that piR-28876 is a superior diagnostic biomarker, reaching AUC=0.787, with 85.0% specificity and 66.3% sensitivity in distinguishing ccRCC patients from healthy controls.

Conclusion: Circulating piRNAs, particularly piR-24672, piR-27140, and piR-28876, may serve as potential non-invasive biomarkers for the early detection of ccRCC.