Prognostic significance of mRNA expression of CASPs in gastric cancer

Predictive significance of MPT-driven necrosis-related genes signature in gastric cancer and their impact on the tumor microenvironment

BACKGROUND

Gastric cancer (GC) presents significant management challenges. MPT-driven necrosis (MPTDN) plays a significant role in various conditions, but its connection with GC is unclear. This study aimed to investigate the predictive significance of MPTDN-related genes (MPTDNRGs) in GC and their effect on the tumor immune microenvironment (TIME).

METHODS

RNA sequencing data for GC were sourced from TCGA and GEO databases. The mutation profiles and MPTDNRG expression between tumor and normal samples were assessed. Prognostic mRNAs were identified using univariate Cox regression and LASSO regression. GC patients were classified into high- and low-risk groups according to risk scores, followed by survival analysis and evaluation of correlations between MPTDN score and clinicopathological features, functional pathway, TIME, and responses to immunotherapy.

RESULTS

MPTDNRGs exhibited a 64% mutation rate in GC, with 22 showing significant expression differences. Univariate Cox and LASSO regression identified 15 independently prognostic MPTDNRGs. The prognostic risk model stratified patients into two groups, revealing significant differences in overall and disease-free survival. A nomogram incorporating the signature and clinical characteristics showed strong specificity and sensitivity in predicting prognosis. The MPTDN score was significantly associated with clinical characteristics, functional pathways, and TIME. scRNA-seq analysis indicated higher MPTDN-signature expression in CD8 + T cells, malignant cells, and myofibroblasts. TIDE analysis suggested high-risk patients have reduced responses to immunotherapy, while low-risk patients could benefit more. Importantly, validation using urothelial carcinoma data confirmed a better prognosis for low-risk patients with immunotherapy.

CONCLUSION

This study highlights the importance of MPTDN-related signatures in predicting GC prognosis and guiding therapeutic decisions.

Identification of genes predicting chemoresistance and short survival in ovarian cancer

Background

Ovarian cancer (OC) is a kind of lethiferous cancer in gynecology, and the development of chemoresistance is the brief reason for treatment failure. The genes which contribute to chemoresistance are often leading to short survival. Thus, this study aims to identify predictive markers for chemoresistance and survival from chemoresistant-related genes.

Methods

Coremine was used to retrieve of genes linked to OC chemoresistance. The relationship of genes with patient survival was analyzed in 489 OC patients of The Cancer Genome Atlas (TCGA) cohort, which the subgroup of 90 resistant and 197 sensitive samples was used to determine gene expression. Kaplan-Meier (KM) plotter of 1,816 OC patients with survival data was retrieved for survival analysis. Survival analysis was carried out by the R survival package in R (version 3.3.1). KM and receiver operating characteristic (ROC) curve were respectively used to access the ability of a gene to predict survival and chemoresistance.

Results

In this study, a group of genes potentially linked to OC chemoresistance was identified, which dysregulated in 90 chemoresistant tissues compared with 197 sensitive tissues. Of them, thirteen genes could predict chemoresistance in 1,347 patients, especially SOS1, MSH6, STAT5A were excellent for predicting chemoresistance to any drugs, platin and taxane, CASP2 and PARD6B for any drugs and platin, and HSP90AA1 and HSP90B1 for taxane. Meanwhile, 44 genes linked to OC chemoresistance could predict short overall survival (OS) and/or disease-free survival (DFS) in 489 OC patients, and 10 of them could predict short OS in large cohort of up to 1,657 patients. Finally, it is noteworthy that CASP2 was down-regulated in 90 chemoresistant samples, and low expression of the gene predicted chemoresistance in 1,347 patients, short OS and DFS in 489 patients, and short OS and progression-free survival (PFS) in 1,657 patients.

Conclusions

The identified genes specifically the CASP2 might be potentially used as predictive marker, prognostic marker and therapeutic target in management of OC.

Aspartame carcinogenic potential revealed through network toxicology and molecular docking insights

The research employed network toxicology and molecular docking techniques to systematically examine the potential carcinogenic effects and mechanisms of aspartame (L-α-aspartyl-L-phenylalanine methyl ester). Aspartame, a commonly used synthetic sweetener, is widely applied in foods and beverages globally. In recent years, its safety issues, particularly the potential carcinogenic risk, have garnered widespread attention. The study first constructed an interaction network map of aspartame with gastric cancer targets using network toxicology methods and identified key targets and pathways. Preliminary validation was conducted through microarray data analysis and survival analysis, and molecular docking techniques were employed to further examine the binding affinity and modes of action of aspartame with key proteins. The findings suggest that aspartame has the potential to impact various cancer-related proteins, potentially raising the likelihood of cellular carcinogenesis by interfering with biomolecular function. Furthermore, the study found that the action patterns and pathways of aspartame-related targets are like the mechanisms of known carcinogenic pathways, further supporting the scientific hypothesis of its potential carcinogenicity. However, given the complexity of the in vivo environment, we also emphasize the necessity of validating these molecular-level findings in actual biological systems. The study introduces a fresh scientific method for evaluating the safety of food enhancers and provides a theoretical foundation for shaping public health regulations.

Identification of necroptosis-related gene signatures for predicting the prognosis of ovarian cancer

Ovarian cancer (OC) is one of the most prevalent and fatal malignant tumors of the female reproductive system. Our research aimed to develop a prognostic model to assist inclinical treatment decision-making.Utilizing data from The Cancer Genome Atlas (TCGA) and copy number variation (CNV) data from the University of California Santa Cruz (UCSC) database, we conducted analyses of differentially expressed genes (DEGs), gene function, and tumor microenvironment (TME) scores in various clusters of OC samples.Next, we classified participants into low-risk and high-risk groups based on the median risk score, thereby dividing both the training group and the entire group accordingly. Overall survival (OS) was significantly reduced in the high-risk group, and two independent prognostic factors were identified: age and risk score. Additionally, three genes-C-X-C Motif Chemokine Ligand 10 (CXCL10), RELB, and Caspase-3 (CASP3)-emerged as potential candidates for an independent prognostic signature with acceptable prognostic value. In Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses, pathways related to immune responses and inflammatory cell chemotaxis were identified. Cellular experiments further validated the reliability and precision of our findings. In conclusion, necroptosis-related genes play critical roles in tumor immunity, and our model introduces a novel strategy for predicting the prognosis of OC patients.

Prognostic significance of pyroptosis-associated molecules in endometrial cancer: a comprehensive immunohistochemical analysis

Introduction

Endometrial cancer, the most prevalent malignancy of the female genital tract, has a concerningly poor prognosis when diagnosed in advanced stages, with limited targeted therapy options available for advanced or recurrent cases. Pyroptosis, a type of nonapoptotic cell death mediated by caspase-1, has shown potential antitumor effects in various tumors. NLRP3, a cytosolic sensor, initiates the canonical pyroptotic pathway, leading to caspase-1 activation, subsequent gasdermin D cleavage, and plasma membrane pore formation. The ESCRT-III machinery, particularly CHMP4B, acts as a key inhibitor of pyroptosis by repairing gasdermin D-induced membrane damage. The current study aimed to evaluate the clinicopathologic relevance of key pyroptosis-associated molecules in endometrial cancer.

Methods

Immunohistochemistry was used to assess the expression of four pyroptosis-associated molecules (NLRP3, cleaved caspase-1 p20, cleaved gasdermin D, and CHMP4B) in 351 patients with endometrial cancer, and their associations with clinical, pathological, and survival outcomes were analyzed.

Results

High NLRP3 expression was significantly associated with age ≤ 50 years and premenopause. Increased cleaved caspase-1 p20 expression was associated with nonendometrioid carcinoma, Federation of Gynaecology and Obstetrics (FIGO) grade 3, and the p53 mutant pattern and was independently associated with poor recurrence-free survival (RFS) and overall survival. Increased cleaved gasdermin D expression was associated with a body mass index of >25 kg/m², FIGO grades 1-2, early FIGO stage (I-II), and absence of lymph node metastasis. High CHMP4B expression was associated with nonendometrioid carcinoma and poor RFS. Cleaved gasdermin D-high/CHMP4B-low endometrial cancer was associated with endometrioid carcinoma, FIGO grades 1-2 and favorable RFS.

Discussion

Our study identified cleaved caspase-1 p20 as an independent predictor of adverse outcomes in endometrial cancer. CHMP4B, an inhibitor of pyroptosis, was associated with an unfavorable RFS, whereas high cleaved gasdermin D/low CHMP4B expression was associated with a favorable RFS. These findings underscore the prognostic significance of pyroptosis and the potential interaction between cleaved gasdermin D and CHMP4B in endometrial cancer.

Genetic polymorphisms in genes regulating cell death and prognosis of patients with rectal cancer receiving postoperative chemoradiotherapy

OBJECTIVE

The identification of biomarkers for predicting chemoradiotherapy efficacy is essential to optimize personalized treatment. This study determined the effects of genetic variations in genes involved in apoptosis, pyroptosis, and ferroptosis on the prognosis of patients with locally advanced rectal cancer receiving postoperative chemoradiotherapy (CRT).

METHODS

The Sequenom MassARRAY was used to detect 217 genetic variations in 40 genes from 300 patients with rectal cancer who received postoperative CRT. The associations between genetic variations and overall survival (OS) were evaluated using hazard ratios (HRs) and 95% confidence intervals (CIs) computed using a Cox proportional regression model. Functional experiments were performed to determine the functions of the arachidonate 5-lipoxygenase (ALOX5) gene and the ALOX5 rs702365 variant.

RESULTS

We detected 16 genetic polymorphisms in CASP3, CASP7, TRAILR2, GSDME, CASP4, HO-1, ALOX5, GPX4, and NRF2 that were significantly associated with OS in the additive model (P < 0.05). There was a substantial cumulative effect of three genetic polymorphisms (CASP4 rs571407, ALOX5 rs2242332, and HO-1 rs17883419) on OS. Genetic variations in the CASP4 and ALOX5 gene haplotypes were associated with a higher OS. We demonstrated, for the first time, that rs702365 [G] > [C] represses ALOX5 transcription and corollary experiments suggested that ALOX5 may promote colon cancer cell growth by mediating an inflammatory response.

CONCLUSIONS

Polymorphisms in genes regulating cell death may play essential roles in the prognosis of patients with rectal cancer who are treated with postoperative CRT and may serve as potential genetic biomarkers for individualized treatment.

Analysis of immunotherapeutic response-related signatures in esophageal squamous-cell carcinoma

Background

Esophageal squamous cell carcinoma (ESCC) is one of the most common and lethal malignant diseases. Immunotherapy has been widely studied and has exhibited potential in ESCC treatment. However, there are only a portion of ESCC patients have benefited from immunotherapy. We herein identified immunotherapeutic response-related signatures (IRRS) and evaluated their performance in ESCC prognosis and immunotherapeutic responsiveness.

Methods

We constructed an IRRS using the gene expression data of 274 ESCC patients based on y -30significantly differentially expressed genes, which were compared responders and non-responders from various patient cohorts treated with immunotherapy. Survival analysis was performed in both the GSE53625 and TCGA-ESCC cohorts. We also explored the differences in the tumor microenvironment between the high-IRRS and low-IRRS score groups using single-cell data as a reference. Three immunotherapy cohorts were used to verify the value of the IRRS in predicting immunotherapy response.

Results

Twelve immunotherapy-related genes were selected to construct a signature score and were validated as independent prognostic predictors for patients with ESCC. Patients with high IRRS scores exhibited an immunosuppressive phenotype. Therefore, patients with low IRRS scores may benefit from immunotherapy.

Conclusions

IRRS score is a biomarker for immunotherapy response and prognosis of ESCC.

HNF4G accelerates glioma progression by facilitating NRP1 transcription

Hepatocyte nuclear factor 4γ (HNF4G) is considered to be a transcription factor and functions as an oncogene in certain types of human cancer. However, the precise functions and the potential molecular mechanisms of HNF4G in glioma remain unclear. Therefore, the present study aimed to elucidate the role of HNF4G in glioma and the underlying mechanism. Western blotting and reverse transcription-quantitative PCR (RT-qPCR) demonstrated that HNF4G was highly expressed in glioma tissues and cell lines. The overexpression of HNF4G in LN229 and U251 glioma cells promoted cell proliferation and cell cycle progression, and inhibited apoptosis, while the knockdown of HNF4G suppressed cell proliferation, cell cycle progression and tumor growth, and induced apoptosis. A significant positive association was detected between HNF4G and neuropilin-1 (NRP1) mRNA expression in glioma tissues. Bioinformatics analysis, chromatin immunoprecipitation-RT-qPCR and promoter reporter assays confirmed that HNF4G promoted NRP1 transcription in glioma by binding to its promoter. NRP1 overexpression facilitated glioma cell proliferation and cell cycle progression, and suppressed apoptosis in vitro, while the knockdown of NRP1 inhibited cell proliferation and cell cycle progression, and facilitated apoptosis. NRP1 overexpression reversed the effects induced by HNF4G knockdown on glioma cell proliferation, cell cycle progression and apoptosis. In summary, the present study demonstrated that HNF4G promotes glioma cell proliferation and suppresses apoptosis by activating NRP1 transcription. These findings indicate that HNF4G acts as an oncogene in glioma and may thus be an effective therapeutic target for glioma.

Pyroptosis-related genes regulate proliferation and invasion of pancreatic cancer and serve as the prognostic signature for modeling patient survival

OBJECTIVE

Pancreatic ductal adenocarcinoma (PDAC) has high mortality and poor prognosis. Pyroptosis can influence the prognosis of patients by regulating the proliferation, invasion, and metastasis of cancer cells. However, the role of pyroptosis-related genes (PRGs) in PDAC remains unclear.

METHODS

In this study, based on the Cancer Genome Atlas (TCGA) cohort of PDAC samples, univariate Cox analysis and LASSO regression analysis were used to screen the prognostic PRGs and establish the gene signature. To further evaluate the functional significance of CASP4 and NLRP1 in PDAC, we also conducted an in vitro study to explore the mechanism of CASP4 and NLRP1 regulating the occurrence and development of PDAC. Finally, we investigated the relationship between CASP4 and NLRP1 expression levels and drug sensitivity in pancreatic cancer cells.

RESULTS

A risk prediction model based on CASP4 and NLRP1 was established, which can distinguish high-risk patients from low-risk patients (P < 0.001). Both internal validation and external GEO data sets validation demonstrate good predictive capability of the model (AUC = 0.732, AUC = 0.802, AUC = 0.632, P < 0.05). In vitro, CCK8 and Transwell assay suggested that CASP4 may accelerate the progression of PDAC by promoting proliferation and migration of pancreatic cancer cells, while NLRP1 has been found to have tumor suppressive effect. It should be noted that knockdown of CASP4 reduced the level of coke death, the expression levels of acetyl-CoA carboxylase, FASN, SREBP-1 and SREBP-2 were decreased, and the number of lipid droplets was also significantly reduced. Moreover, the enrichment of signaling pathways showed that NLRP1 was significantly correlated with MAPK and RAS/ERK signaling pathways, and knocking down NLRP1 could indeed up-regulate p-ERK expression. Finally, high expression of CASP4 and low expression of NLRP1 increased the sensitivity of pancreatic cancer cells to ERK inhibitors.

CONCLUSIONS

In especial, CASP4 can promote tumor progression by promoting the synthesis and accumulation of fatty acids, while NLRP1 acts on RAS/ERK signaling pathway. Both of genes play an important role in the diagnosis and treatment of PDAC, which may also affect the inhibitors of MAPK/ERK efficiency.

Prognostic signature of esophageal adenocarcinoma based on pyroptosis-related genes

Background

The role of pyroptosis-related genes (PRGs) in esophageal adenocarcinoma (EAC) remains unknown.

Methods

In this study, the first PRGs prognostic signature (PPS) of EAC was constructed based on the results of multivariate stepwise Cox regression analysis. Based on 1,047 samples of EAC and normal esophagus (NE), differentially expressed PRGs were selected for the establishment of the PPS. The discrimination effect of this PPS was detected by receiver operating characteristic curves, and the prognosis value of this PPS was determined through Cox regression analysis and Kaplan-Meier curves. Net benefits of the EAC patients from the nomogram (constructed based on the PPS and some clinical parameters) were assessed via decision curve analysis. The potential molecular mechanism of the PPS in EAC was explored via gene set enrichment analysis. The ability of PPS to distinguish EAC and NE was evaluated based on the results of summary receiver operating characteristic curves.

Results

The significant prognostic value of PPS can be observed at all of the training cohort, test cohort, and validation cohort, such as its independent risk role in the prognosis of the EAC patients (hazard ratio > 0; 95% CI not including 0). The positive net benefits of the nomogram for the EAC patients can be detected via decision curve analysis, and the potential molecular mechanism of the PPS in EAC is likely related to cell pyroptosis. Last, some of the PRGs (particularly CASP5) included in this PPS specifically support its feasibility for identifying EAC (area under the curves > 0.7).

Conclusions

The construction of this PPS in EAC enhances the present understanding of the relationship between PRGs and EAC, thus representing a novel approach to the clinical identification and management of EAC based on PRGs.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12920-022-01196-x.

A Novel Pyroptosis-Related Signature for Predicting Prognosis and Indicating Immune Microenvironment Features in Osteosarcoma

Osteosarcoma is a common malignant bone tumor with a propensity for drug resistance, recurrence, and metastasis. A growing number of studies have elucidated the dual role of pyroptosis in the development of cancer, which is a gasdermin-regulated novel inflammatory programmed cell death. However, the interaction between pyroptosis and the overall survival (OS) of osteosarcoma patients is poorly understood. This study aimed to construct a prognostic model based on pyroptosis-related genes to provide new insights into the prognosis of osteosarcoma patients. We identified 46 differentially expressed pyroptosis-associated genes between osteosarcoma tissues and normal control tissues. A total of six risk genes affecting the prognosis of osteosarcoma patients were screened to form a pyroptosis-related signature by univariate and LASSO regression analysis and verified using GSE21257 as a validation cohort. Combined with other clinical characteristics, including age, gender, and metastatic status, we found that the pyroptosis-related signature score, which we named “PRS-score,” was an independent prognostic factor for patients with osteosarcoma and that a low PRS-score indicated better OS and a lower risk of metastasis. The result of ssGSEA and ESTIMATE algorithms showed that a lower PRS-score indicated higher immune scores, higher levels of tumor infiltration by immune cells, more active immune function, and lower tumor purity. In summary, we developed and validated a pyroptosis-related signature for predicting the prognosis of osteosarcoma, which may contribute to early diagnosis and immunotherapy of osteosarcoma.

The Antitriple Negative Breast cancer Efficacy of Spatholobus suberectus Dunn on ROS-Induced Noncanonical Inflammasome Pyroptotic Pathway

Breast cancer (BCa) is the leading cause of women's death worldwide; among them, triple-negative breast cancer (TNBC) is one of the most troublesome subtypes with easy recurrence and great aggressive properties. Spatholobus suberectus Dunn has been used in the clinic of Chinese society for hundreds of years. Shreds of evidence showed that Spatholobus suberectus Dunn has a favorable outcome in the management of cancer. However, the anti-TNBC efficacy of Spatholobus suberectus Dunn percolation extract (SSP) and its underlying mechanisms have not been fully elucidated. Hence, the present study is aimed at evaluating the anti-TNBC potential of SSP both in vitro and in vivo, through the cell viability, morphological analysis of MDA-MB-231, LDH release assay, ROS assay, and the tests of GSH aborted pyroptotic noninflammasome signaling pathway. Survival analysis using the KM Plotter and TNM plot database exhibited the inhibition of transcription levels of caspase-4 and 9 related to low relapse-free survival in patients with BCa. Based on the findings, SSP possesses anti-TNBC efficacy that relies on ROS-induced noncanonical inflammasome pyroptosis in cancer cells. In this study, our preclinical evidence is complementary to the preceding clinic of Chinese society; studies on the active principles of SPP remain underway in our laboratory.

Effects of neoadjuvant therapies on genetic regulation of targeted pathways in ER+ primary ductal breast carcinoma: A meta-analysis of microarray datasets

Breast cancer arises as a result of multiple interactions between environmental and genetic factors. Conventionally, breast cancer is treated based on histopathological and clinical features. DNA technologies like the human genome microarray are now partially integrated into clinical practice and are used for developing new "personalized medicines" and "pharmacogenetics" for improving the efficiency and safety of cancer medications. We investigated the effects of four established therapies-for ER+ ductal breast cancer-on the differential gene expression. The therapies included single agent tamoxifen, two-agent docetaxel and capecitabine, or combined three-agents CAF (cyclophosphamide, doxorubicin, and fluorouracil) and CMF (cyclophosphamide, methotrexate, and fluorouracil). Genevestigator 8.1.0 was used to compare five datasets from patients with infiltrating ductal carcinoma, untreated or treated with selected drugs, to those from the healthy control. We identified 74 differentially expressed genes involved in three pathways, i.e., apoptosis (extrinsic and intrinsic), oxidative signaling, and PI3K/Akt signaling. The treatments affected the expression of apoptotic genes (TNFRSF10B [TRAIL], FAS, CASP3/6/7/8, PMAIP1 [NOXA], BNIP3L, BNIP3, BCL2A1, and BCL2), the oxidative stress-related genes (NOX4, XDH, MAOA, GSR, GPX3, and SOD3), and the PI3K/Akt pathway gene (ERBB2 [HER2]). Breast cancer treatments are complex with varying drug responses and efficacy among patients. This necessitates identifying novel biomarkers for predicting the drug response, using available data and new technologies. GSR, NOX4, CASP3, and ERBB2 are potential biomarkers for predicting the treatment response in primary ER+ ductal breast carcinoma.

Proinflammatory Interleukin-33 Induces Dichotomic Effects on Cell Proliferation in Normal Gastric Epithelium and Gastric Cancer

Interleukin (IL)-33 is a member of the interleukin (IL)-1 family of cytokines linked to the development of inflammatory conditions and cancer in the gastrointestinal tract. This study is designed to investigate whether IL-33 has a direct effect on human gastric epithelial cells (GES-1), the human gastric adenocarcinoma cell line (AGS), and the gastric carcinoma cell line (NCI-N87) by assessing its role in the regulation of cell proliferation, migration, cell cycle, and apoptosis. Cell cycle regulation was also determined in ex vivo gastric cancer samples obtained during endoscopy and surgical procedures. Cell lines and tissue samples underwent stimulation with rhIL-33. Proliferation was assessed by XTT and CFSE assays, migration by wound healing assay, and apoptosis by caspase 3/7 activity assay and annexin V assay. Cell cycle was analyzed by means of propidium iodine assay, and gene expression regulation was assessed by RT-PCR profiling. We found that IL-33 has an antiproliferative and proapoptotic effect on cancer cell lines, and it can stimulate proliferation and reduce apoptosis in normal epithelial cell lines. These effects were also confirmed by the analysis of cell cycle gene expression, which showed a reduced expression of pro-proliferative genes in cancer cells, particularly in genes involved in G0/G1 and G2/M checkpoints. These results were confirmed by gene expression analysis on bioptic and surgical specimens. The aforementioned results indicate that IL-33 may be involved in cell proliferation in an environment- and cell-type-dependent manner.

Caspase 4 Overexpression as a Prognostic Marker in Clear Cell Renal Cell Carcinoma: A Study Based on the Cancer Genome Atlas Data Mining

The dysregulation of caspase 4 (CASP4) expression is related to the occurrence, development, and outcome of many malignant tumors; however, its role in clear cell renal cell carcinoma (ccRCC) remains unclear. Herein, we investigated the expression of CASP4 in tumor tissues and its relationship with clinical prognosis, immune infiltration, and drug sensitivity status of ccRCC patients. Oncomine and The Cancer Genome Atlas (TCGA) databases were used to determine CASP4 mRNA expression in ccRCC patients. The correlation between CASP4 expression and disease prognosis was evaluated using Kaplan–Meier analysis. Related pathways were obtained from TCGA database via gene set enrichment analysis (GSEA) and gene set variation analysis (GSVA). Meanwhile, genes co-expressing with CASP4 in ccRCC were investigated. Finally, we analyzed the proportion of tumor-infiltrating immune cells (TICs) using the CIBERSORT computational method and assessed CASP4 methylation and its relationship with drug sensitivity. Immunohistochemical analysis of 30 paired ccRCC and adjacent normal tissues confirmed the in silico results. CASP4 mRNA expression in ccRCC was significantly higher than that in the normal tissues, positively correlated with clinicopathological features (clinical stage and pathological grade), and negatively correlated with patient overall survival (OS). GSEA and GSVA showed that the genes in the CASP4-high expression group were primarily enriched in immune-related activities. Moreover, CIBERSORT analysis of TIC proportions revealed that activated CD4 memory T cells were positively correlated with CASP4 expression. Notably, methylation analysis revealed that the abnormal upregulation of CASP4 might be caused by hypomethylation. Finally, we found that the abnormal expression of CASP4 may be related to tumor drug resistance. Overall, our study shows that CASP4 is overexpressed in ccRCC and is an important factor affecting disease prognosis. Hence, CASP4 may serve as a potential prognostic biomarker and therapeutic target in ccRCC.

Transcriptomic Analysis of Glycolysis-Related Genes Reveals an Independent Signature of Bladder Carcinoma

Background

Bladder carcinoma (BC) is one of the most prevalent and malignant tumors. Multiple gene signatures based on BC metabolism, especially regarding glycolysis, remain unclear. Thus, we developed a glycolysis-related gene signature to be used for BC prognosis prediction.

Methods

Transcriptomic and clinical data were divided into a training set and a validation set after they were downloaded and analyzed from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Gene-set enrichment analysis (GSEA) and differential analysis were used to screen differentially expressed genes (DEGs), while univariate Cox regression and lasso-penalized Cox regression were employed for signature establishment. To evaluate the prognostic power of the signature, receiver operating characteristic (ROC) curve and Kaplan-Meier (KM) survival analysis were also used. Additionally, we developed a nomogram to predict patients' survival chances using the identified prognostic gene signature. Further, gene mutation and protein expression, as well as the independence of signature genes, were also analyzed. Finally, we also performed qPCR and western blot to detect the expression and potential pathways of signature genes in BC samples.

Results

Ten genes were selected for signature construction among 71 DEGs, including nine risk genes and one protection gene. KM survival analysis revealed that the high-risk group had poor survival and the low-risk group had increased survival. ROC curve analysis and the nomogram validated the accurate prediction of survival using a gene signature composed of 10 glycolysis-related genes. Western blot and qPCR analysis demonstrated that the expression trend of signature genes was basically consistent with previous results. These 10 glycolysis-related genes were independent and suitable for a signature.

Conclusion

Our current study indicated that we successfully built and validated a novel 10-gene glycolysis-related signature for BC prognosis.

Identification of biomarkers predicting the chemotherapeutic outcomes of capecitabine and oxaliplatin in patients with gastric cancer

The capecitabine and oxaliplatin (CapeOX) regimen is a commonly used adjuvant chemotherapeutic regimen for gastric cancer (GC). However, some patients exhibit a poor chemotherapy response due to genetic differences among individuals. Therefore, finding an effective sensitization strategy for CapeOX is important in the treatment of GC. The present study aimed to investigate the predictive biomarkers of the CapeOX chemotherapeutic outcomes for patients with GC. A total of 30 differentially expressed genes (DEGs) were identified using the gene expression profiles from The Cancer Genome Atlas capecitabine and oxaliplatin treatment GC cases and seven key DEGs [uroplakin-1b (UPK1B), fatty acid-binding protein, heart (FABP3), cystatin-M, caspase-5 (CASP5), corticosteroid 11-β-dehydrogenase isozyme 2, cytochrome P450 4X1 (CYP4X1) and epidermal growth factor receptor kinase substrate 8-like protein 3] were associated with survival. Gene validation was performed in clinical samples divided into recurrence and nonrecurrence groups. Patients with high or low expression of UPK1B, FABP3, CASP5 and CYP4X1 had markedly different overall survival rates. A model was established and the area under the curve of the receiver operating characteristic reached 0.875 (0.793–0.957), indicating that the model had good sensitivity and specificity.