Cuproptosis‑related Gene CDKN2D is Linked to Prognosis in Esophageal Cancer

Intratumoral Fusobacterium nucleatum (Fn) infection is closely associated with poor prognosis in esophageal cancer (EC) due to its impact on the tumor microenvironment (TME). The tumor cell-intrinsic cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway is critical for regulating immune cell activation in the TME. However, the link between intratumoral Fn infection and the activation of the cGAS-STING pathway in tumor cells, as well as its effects on EC progression, remains largely unknown. In the present study, we investigated the impact of intratumoral Fn infection on the activation of the tumor cell-intrinsic cGAS-STING pathway and EC progression by analyzing our own EC cohort and performing in vitro experiments using co-cultures of EC-cell lines and Fn. The expression of tumor cell-intrinsic STING was significantly associated with worse prognosis in Fn-high EC patients. Exposure to Fn significantly activated the STING pathway in EC cells. RNA-seq analysis revealed that exposure to Fn markedly activated cytokine-chemokine-related signaling pathways and induced the expression of several cytokines and chemokines in STING-expressing EC cells. Among the differentially expressed cytokine and chemokine genes in EC cells co-cultured with Fn, analysis of TCGA datasets demonstrated that the expression of CCL20, CXCL10, and CSF2 may be associated with poor prognosis in EC patients. We revealed that the activation of the STING signaling pathway and the subsequent expression of cytokines and chemokines in EC cells induced by Fn infection may be closely associated with poor prognosis in EC patients.

Esophageal cancer (EC) is characterized by a high degree of malignancy and poor prognosis. N6-methyladenosine (m6A), a prominent post-transcriptional modification of mRNA in mammalian cells, plays a pivotal role in regulating various cellular and biological processes. Similarly, cuproptosis has garnered attention for its potential implications in cancer biology. This study seeks to elucidate the impact of m6A- and cuproptosis-related long non-coding RNAs (m6aCRLncs) on the prognosis of patients with EC. The EC transcriptional data and corresponding clinical information were retrieved from The Cancer Genome Atlas (TCGA) database, comprising 11 normal samples and 159 EC samples. Data on 23 m6A regulators and 25 cuproptosis-related genes were sourced from the latest literature. The m6aCRLncs linked to EC were identified through co-expression analysis. Differentially expressed m6aCRLncs associated with EC prognosis were screened using the limma package in R and univariate Cox regression analysis. Subtype clustering was performed to classify EC patients, enabling the investigation of differences in clinical outcomes and immune microenvironment across patient clusters. A risk prognostic model was constructed using least absolute shrinkage and selection operator (LASSO) regression. Its robustness was evaluated through survival analysis, risk stratification curves, and receiver operating characteristic (ROC) curves. Additionally, the model's applicability across various clinical features and molecular subtypes of EC patients was assessed. To further explore the model's utility in predicting the immune microenvironment, single-sample gene set enrichment analysis (ssGSEA), immune cell infiltration analysis, and immune checkpoint differential expression analysis were conducted. Drug sensitivity analysis was performed to identify potential therapeutic agents for EC. Finally, the mRNA expression levels of m6aCRLncs in EC cell lines were validated using reverse transcription quantitative polymerase chain reaction (RT-qPCR). We developed a prognostic risk model based on five m6aCRLncs, namely ELF3-AS1, HNF1A-AS1, LINC00942, LINC01389, and MIR181A2HG, to predict survival outcomes and characterize the immune microenvironment in EC patients. Analysis of molecular subtypes and clinical features revealed significant differences in cluster distribution, disease stage, and N stage between high- and low-risk groups. Immune profiling further identified distinct immune cell populations and functional pathways associated with risk scores, including positive correlations with naive B cells, resting CD4+ T cells, and plasma cells, and negative correlations with macrophages M0 and M1. Additionally, we identified key immune checkpoint-related genes with significant differential expression between risk groups, including TNFRSF14, TNFSF15, TNFRSF18, LGALS9, CD44, HHLA2, and CD40. Furthermore, nine candidate drugs with potential therapeutic efficacy in EC were identified: Bleomycin, Cisplatin, Cyclopamine, PLX4720, Erlotinib, Gefitinib, RO.3306, XMD8.85, and WH.4.023. Finally, RT-qPCR validation of the mRNA expression levels of m6aCRLncs in EC cell lines demonstrated that ELF3-AS1 expression was significantly upregulated in the EC cell lines KYSE-30 and KYSE-180 compared to normal esophageal epithelial cells. This study elucidates the role of m6aCRLncs in shaping the prognostic outcomes and immune microenvironment of EC. Furthermore, it identifies potential therapeutic agents with efficacy against EC. These findings hold significant promise for enhancing the survival of EC patients and provide valuable insights to inform clinical decision-making in the management of this disease.

Studies have indicated that cyclin dependent protein kinase inhibitor 2B (CDKN2B) deletion is one of the most common changes in esophageal cancer (EC) which affects its progression and prognosis. This study explored the association between CDKN2B deletion, immunophenotype, and the prognosis of EC. We investigated CDKN2B status and RNA expression, identified differentially expressed immune-associated genes between wild-type CDKN2B (CDKN2BWT) and deleted CDKN2B (CDKN2Bdeletion) in Cancer Genome Atlas (TCGA) EC samples. We also a constructed an immune prognostic model (IPM) based on these genes. Thereafter, the effects of IPM on the immune microenvironment of EC were analyzed. Finally, we established a nomogram by integrating the IPM and other clinical factors. CDKN2B deletion leads to downregulation of the immune response in EC. A total of 136 immune-associated genes were identified based on the CDKN2B deletion status, and three genes with remarkable potential as individual targets were selected for model construction. An IPM was developed and validated, it showed good performance in differentiating patients with a low or high risk of poor prognosis, and its predictive ability was independent of traditional clinical features. High-risk patients with EC had increased T follicular helper cells (Tfh) and M0 macrophages, and lower infiltration levels of resting CD4 memory T cells resting, and naive B cells. The nomogram developed for clinical application showed good predictive performance. Our results suggested that CDKN2B deletion was associated with the survival and immune microenvironment in EC. IPM is not only an effective indicator of the immune response and prognosis, but also suggest potential targets for immunotherapy in patients with EC.

To explore the molecular mechanisms of FAM129A in regulating the progression of esophageal cancer and its prognosis. FAM129A levels in esophageal cancer tissues and paracancerous ones were detected by quantitative real-time polymerase chain reaction (qRT-PCR). Its influences on clinical features and prognosis in esophageal cancer patients were analyzed. Changes in proliferation and apoptosis in esophageal cancer cells after knockdown of FAM129A were examined by cell counting kit-8 (CCK-8), 5-Ethynyl-2'- deoxyuridine (EdU) assay and flow cytometry, respectively. The feedback loop FAM129A/CXCL14 was finally assessed. FAM129A was upregulated in esophageal cancer tissues. High level of FAM129A predicted advanced tumor staging, large tumor size and poor prognosis in esophageal cancer patients. Knockdown of FAM129A inhibited proliferative ability and induced apoptosis in OE19 and OE33 cells. In addition, knockdown of FAM129A upregulated protein level of CXCL14 in esophageal cancer cells. CXCL14 was downregulated in esophageal cancer tissues and negatively correlated to FAM129A level. The negative feedback loop FAM129A/CXCL14 was responsible for aggravating the malignant phenotypes of esophageal cancer cells. FAM129A is upregulated in esophageal cancer samples, and it is linked to tumor staging, tumor size and poor prognosis. FAM129A aggravates the progression of esophageal cancer by negatively regulating CXCL14 level.

Esophageal cancer (EC) and gastric cancer (GC) often have an unfavorable prognosis. Therefore, research is being conducted to identify the molecular mechanisms underlying the tumorigenesis and progression of GC and EC, and to indicate novel therapeutic targets and clinically applicable biomarkers. The dysregulations and roles of long non-coding RNAs (lncRNAs) have been widely reported, and current published literature has shown that lncRNAs play important regulatory roles in the carcinogenesis and progression of EC and GC. The lncRNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) has been investigated in a number of studies with regard to its pathogenic pathways and association with the prognosis of gastric and esophageal malignancies. As literature on the topic of MALAT1 in EC and GC continues to emerge, the present review aims to summarize all current knowledge on the association between MALAT1 expression and esophagogastric malignancies and to describe the pathogenic pathways and possible prognostic role of MALAT1 in esophagogastric cancer. As research studies on MALAT1 pathways in esophagogastric malignancies are ongoing, new possibilities for the diagnosis, prognosis and therapy of GC and EC are likely to be identified.

C-X-C motif chemokine 8 (CXCL-8), known as interleukin-8, is a pro-inflammatory cytokine which acts as a chemotactic factor, mainly for leukocytes. CXCL-8 is produced by malignant cells, and therefore it can stimulate the growth and progression of various neoplasms, including oesophageal cancer (OC). The aim of the current study was to measure serum concentrations of chemokine CXCL-8 in OC patients and establish whether this protein might be considered a potential candidate for a tumor marker in the diagnosis and progression of OC. The study included 50 OC subjects (32 patients with squamous cell carcinoma of oesophagus—OSCC, 18 patients with adenocarcinoma—OAC) and 26 healthy volunteers. Serum CXCL-8 concentrations were measured using immunoenzymatic assay (ELISA). CRP levels were determined by immunoturbidimetric method, while classical tumor marker levels were measured using chemiluminescent immunoassay. CXCL-8 concentrations were significantly higher in OC patients compared to healthy controls. We demonstrated significant differences between CXCL-8 concentrations and depth of tumor invasion (T factor) in OC patients and OSCC subgroup. In addition, CXCL-8 levels were found to correlate positively with T factor and CRP concentrations. The diagnostic sensitivity, negative predictive value and the area under ROC curve (AUC) of CXCL-8 were higher than those of classical tumor markers. Our findings suggest the potential usefulness of CXCL-8 in the diagnosis and progression of OC. However, due to the non-specific nature of this chemokine, further research is needed to clarify the usefulness of CXCL-8 as a tumor marker of OC.

Recent studies have shown that oral microbiota play an important role in the esophageal cancer (EC) initiation and progression, suggesting that oral microbiota is a new risk factor for EC. The composition of the microbes inhabiting the oral cavity could be perturbed with continuous factors such as smoking, alcohol consumption, and inflammation. The microbial alteration involves the decrease of beneficial species and the increase of pathogenic species. Experimental evidences suggest a significant role of oral commensal organisms in protecting hosts against EC. By contrast, oral pathogens, especially Porphyromonas gingivalis and Fusobacterium nucleatum, give rise to the risk for developing EC through their pro-inflammatory and pro-tumorigenic activities. The presences of oral dysbiosis, microbial biofilm, and periodontitis in EC patients are found to be associated with invasive cancer phenotypes and poor prognosis. The mechanism of oral bacteria in EC progression is complex, which involves a combination of cytokines, chemokines, oncogenic signaling pathways, cell surface receptors, the degradation of extracellular matrix, and cell apoptosis. From a clinical perspective, good oral hygiene, professional oral care, and rational use of antibiotics bring positive impacts on oral microbial balance, thus helping individuals reduce the risk of EC, inhibiting postoperative complications among EC patients, and improving the efficiency of chemoradiotherapy. However, current oral hygiene practices mainly focus on the oral bacteria-based predictive and preventive purposes. It is still far from implementing microbiota-dependent regulation as a therapy for EC. Further explorations are needed to render oral microbiota a potential target for treating EC.

Background Esophageal cancer remains one of the most lethal malignant diseases globally. Previous studies indicated that TRIM9 (Tripartite Motif Containing 9) is a potential marker in breast cancer patients. Therefore, in the current research, we intended to clarify the regulatory network of TRIM9 and its relative role in esophageal cancer patients. We aimed to elucidate the regulatory role of TRIM9 in esophageal cancer. Methods Clinical tumor tissue samples combined with cancer cell line models were utilized to explore the TRIM9 expression pattern. Functional experiments including transwell assay, cell viability assay, and ubiquitination blocking experiments were performed to evaluate the role of the TRIM9/ZEB1 (zinc finger E-box binding homeobox 1) axis and UPP pathway in esophageal cancer progression and exacerbation. Results Both esophageal cancer samples and cell line models showed significantly suppressed levels of TRIM9. Functional experiments confirmed that TRIM9 overexpression inhibited the cell viability, invasiveness, and stem-like phenotype of cancer cells. Subsequent investigations suggested that TRIM9-ZEB1 interaction accelerated ZEB1 protein degradation through the modulation of the UPP pathway, which confirmed the protective role of TRIM9 in esophageal cancer progression and metastasis. Conclusion This study concluded that TRIM9 was a tumor suppressor that interacted with ZEB1 and accelerated ZEB1 protein degradation via the ubiquitin-proteasome pathway (UPP). Our research emphasized TRIM9-ZEB1 interaction as a valuable target for esophageal cancer treatment in future development. More detailed studies are needed to further consolidate our findings.

The underlying causes of esophageal cancer (EC) are unknown. To explore the molecular mechanisms that lead to EC, gene expression profiles of large cohorts of patients with EC were obtained from The Cancer Genome Atlas and the Gene Expression Omnibus (GEO) databases (GSE5364, GSE20347 and GSE23400). The present study identified 83 upregulated and 22 downregulated genes between EC and normal tissue using R statistical software and the GEO2R web tool. The Database for Annotation, Visualization and Integrated Discovery was used to identify the associated pathways, and for functional annotation of the differentially expressed genes (DEGs). Protein-protein interactions of these DEGs were analyzed based on the Search Tool for the Retrieval of Interacting Genes database, and hub genes were visualized using Cytoscape software. An online Kaplan-Meier plotter survival analysis tool was utilized to evaluate the prognostic value of hub gene expression in patients with EC. Further analysis of an additional dataset from GEO (GSE21293) revealed that these genes were associated with infiltration and metastasis in EC. In addition, the Gene Expression Profiling Interactive Analysis tool was used to evaluate expression levels of hub genes in patients with EC for different pathological stages. The Ualcan analysis tool was used to evaluate the expression levels of hub genes for different histological types. Overall, ubiquitin conjugating enzyme E2 C, cyclin dependent kinase inhibitor 3, CDC28 protein kinase regulatory subunit 2, kinesin family member 20A (KIF20A) and RAD51 associated protein 1 (RAD51AP1) were upregulated in EC tissues compared with normal tissues, and upregulation of these genes was a poor prognostic factor for patients with EC, indicating that these genes may mediate EC cell infiltration and metastasis. Among the hub genes, KIF-20A had potential value for predicting the pathological stage of EC. KIF20A and RAD51AP1 were more informative biomarkers of esophageal squamous cell carcinoma. Further studies are required to explore the value of these genes in the treatment of EC.

e16000 Background: Homologous recombination deficiency (HRD) is associated with tumorigenesis and could predict the response of PARP inhibitor (PARPi) therapy and immunotherapy. Loss of function or deleterious mutations in homologous recombination-related (HRR) genes contribute to HRD phenotype. Methods: Tumor tissue samples from 1237 Chinese patients with esophageal and gastric cancer were sequenced with 551 cancer-related genes. Based on the clinical evidence, 15 HRR genes ( ATM, BRCA1, BRCA2, BARD1, BRIP1, CDK12, CHEK1, CHEK2, FANCL, PALB2, RAD51B, RAD51C, RAD51D, RAD54L, PPP2R2A) were selected. 623 patients with WES data from the TCGA datasets were included for analysis. Results: In the Chinese cohort, 25.1% (62/247) esophageal cancer (EC) patients and 20.71% (205/990) gastric cancer (GC) patients exhibited somatic HRR (sHRR) gene mutations. The most frequently mutated genes were CHEK2 (7%) in EC and ATM (8%) in GC. The germline HRR (gHRR) gene mutations were identified in 48.16% (118/245) EC patients and 50.66% (498/983) GC patients. BRCA2 was the most common mutant gene (22% in EC and 9% in GC). 4.84% EC patients and 4.14% GC patients carried both germline and somatic HRR gene mutations. The sHRR-Mut patients had a higher median TMB compared to the sHRR-WT patients (EC, 8.09 vs 4.41, p < 0.001; GC, 8.09 vs 4.26, p < 0.001). However, the median TMB was similar between the gHRR-Mut and the gHRR-WT patients (EC, 5.67 vs 5.67, p = 0.903; GC, 4.96 vs 4.41, p = 0.356). In the TCGA cohort, 15.68% (29/185) EC patients and 23.97% (105/438) GC patients exhibited sHRR gene mutations. The most common mutant gene was ATM (5% in EC and 10% in GC). The sHRR-Mut patients had a higher median TMB compared to the sHRR-WT patients (EC, 4.78 vs 2.75, p < 0.001; GC, 21.23 vs 2.65, p < 0.001). For the TCGA gastric cancer cohort, the patients with sHRR-Mut had a significantly better median overall survival compared to the ones with sHRR-WT (46.9 months vs 26.5 months, p = 0.043). Conclusions: Our data reported the genetic landscape of HRR genes in Chinese esophageal and gastric cancer patients. Patients with somatic HRR gene mutations had a significantly elevated TMB level. In gastric cancer, patients carried somatic HRR gene mutations had a significantly prolonged OS.

Role of mitochondrial DNA 4977-bp deletions in esophageal cancer susceptibility and prognosis in a northern Indian population

BackgroundHeat shock protein family D (Hsp60) member 1 (HSPD1) has been reported as a potential survival-related biomarker in some cancers. However, the correlation between HSPD1 expression with prognosis and clinical features of esophageal cancer (EC) is poorly understood. Our research aimed to explore the clinical and prognostic significance of HSPD1 expression in EC patients.MethodsIn our study, HSPD1 expression was detected by immunochemistry in 87 EC tissue specimens and 20 normal cancerous peripheral tissue specimens. Meanwhile, we also analyzed the expression of HSPD1 in EC by The Cancer Genome Atlas (TCGA) database. Then Chi-squared and Fisher’s exact tests and Wilcoxon signed-rank test and logistic regression models were separately used to test the correlation between clinical characteristics and HSPD1 expression in our and TCGA cohort. Moreover, we evaluated the value of HSPD1 in prognosis by Kaplan-Meier curves and Cox analysis. Finally, gene set enrichment analysis (GSEA) was performed using the data accessed from TCGA.ResultsThe results showed that HSPD1 was overexpressed in EC, and the expression was related to histological type, histological grade, N classification, and clinical stage. Moreover, Kaplan-Meier curves and Cox analysis indicated that high expression of HSPD1 correlated with poor prognosis, and HSPD1 was an independent risk factor for EC. GSEA identified pathways involved in cysteine and methionine metabolism, spliceosome, selenoamino acid metabolism, mismatch repair, RNA degration, DNA replication, and cell cycle as differentially enriched in ECs with high HSPD1 expression.ConclusionsOur results suggest that HSPD1 is expressed at high levels in EC, and has potential to be used as a novel biomarker for the prognosis of patients with EC.

Esophageal cancer (EC) is a common malignant tumor of the digestive system with high mortality and morbidity. Current evidence suggests that immune cells and molecules regulate the initiation and progression of EC. Accordingly, it is necessary to identify immune-related genes (IRGs) affecting the biological behaviors and microenvironmental characteristics of EC. Bioinformatics methods, including differential expression analysis, Cox regression, and immune infiltration prediction, were conducted using R software to analyze the Gene Expression Omnibus (GEO) dataset. The Cancer Genome Atlas (TCGA) cohort was used to validate the prognostic signature. Patients were stratified into high- and low-risk groups for further analyses, including functional enrichment, immune infiltration, checkpoint relevance, clinicopathological characteristics, and therapeutic sensitivity analyses. A prognostic signature was established based on 21 IRGs (S100A7, S100A7A, LCN1, CR2, STAT4, GAST, ANGPTL5, TRAV39, F2RL2, PGLYRP3, KLRD1, TRIM36, PDGFA, SLPI, PCSK2, APLN, TICAM1, ITPR3, MAPK9, GATA4, and PLAU). Compared with high-risk patients, better overall survival rates and clinicopathological characteristics were found in low-risk patients. The areas under the curve of the two cohorts were 0.885 and 0.718, respectively. Higher proportions of resting CD4+ memory T lymphocytes, M2 macrophages, and resting dendritic cells and lower proportions of follicular helper T lymphocytes, plasma cells, and neutrophils were found in the high-risk tumors. Moreover, the high-risk group showed higher expression of CD44 and TNFSF4, lower expression of PDCD1 and CD40, and higher TIDE scores, suggesting they may respond poorly to immunotherapy. High-risk patients responded better to chemotherapeutic agents such as docetaxel, doxorubicin, and gemcitabine. Furthermore, IRGs associated with tumor progression, including PDGFA, ITPR3, SLPI, TICAM1, and GATA4, were identified. Our immune-related signature yielded reliable value in evaluating the prognosis, microenvironmental characteristics, and therapeutic sensitivity of EC and may help with the precise treatment of this patient population.

38P - A novel ADS prognostic score containing prospective AFR, Alb and dNLR predicted overall survival in esophageal cancer patients

Aim of this study was to explore the immune-related lncRNAs having prognostic role and establishing risk score model for better prognosis and immunotherapeutic coherence for esophageal cancer (EC) patients. To determine the role of immune-related lncRNAs in EC, we analyzed the RNA-seq expression data of 162 EC patients and 11 non-cancerous individuals and their clinically relevant information from the cancer genome atlas (TCGA) database. Bioinformatic and statistical analysis such as Differential expression analysis, co-expression analysis, Kaplan Meier survival analysis, Cox proportional hazards model, ROC analysis of risk model was employed. Utilizing a cutoff criterion (log2FC > 1 + log2FC < -1 and FDR < 0.01), we identified 3737 RNAs were significantly differentially expressed in EC patients. Among these, 2222 genes were classified as significantly differentially expressed mRNAs (demRNAs), and 966 were significantly differentially expressed lncRNAs (delncRNA). Through Pearson correlation analysis between differentially expressed lncRNAs and immune related-mRNAs, we identified 12 immune-related lncRNAs as prognostic signatures for EC. Notably, through Kaplan-Meier analysis on these lncRNAs, we found the low-risk group patients showed significantly improved survival compared to the high-risk group. Moreover, this prognostic signature has consistent performance across training, testing and entire validation cohort sets. Using ESTIMATE and CIBERSORT algorithm we further observed significant enriched infiltration of naive B cells, regulatory T cells resting CD4+ memory T cells, and, plasma cells in the low-risk group compared to high-risk EC patients group. On the contrary, tumor-associated M2 macrophages were highly enriched in high-risk patients. Additionally, we confirmed immune-related biological functions and pathways such as inflammatory, cytokines, chemokines response and natural killer cell-mediated cytotoxicity, toll-like receptor signaling pathways, JAK-STAT signaling pathways, chemokine signaling pathways significantly associated with identified IRlncRNA signature and their co-expressed immune genes. Furthermore, we assessed the predictive potential of the lncRNA signature in immune checkpoint inhibitors; we found that programed cell death ligand 1 (PD-L1; P-value = .048), programed cell death ligand 2 (PD-L2; P-value = .002), and T cell immunoglobulin and mucin-domain containing-3 (TIM-3; P-value = .045) expression levels were significantly higher in low-risk patients compared to high-risk patients. We believe this study will contribute to better prognosis prediction and targeted treatment of EC in the future.