Identification of Immune-Related Prognostic Markers in Gastric Cancer

Fructose-1, 6-Bisphosphate Aldolase B Suppresses Glycolysis and Tumor Progression of Gastric Cancer

OBJECTIVE

Gastric cancer (GC) is believed to be one of the most common digestive tract malignant tumors. However, mounting evidence indicates a link between the glycolysis and tumorigenesis, including gastric cancer.

METHODS

Our research identified 5508 differently expressed mRNAs in gastric cancer. Then, the genes highly associated with tumorigenesis were identified through weighted correlation network analysis (WGCNA). Bioinformatics analysis observed that these hub genes were significantly linked to the regulation of cell cycle, drug metabolism, and glycolysis. Among these hub genes, there is a critical gene involved in glycolysis regulation, namely fructose-bisphosphate B (ALDOB).

RESULTS

Analysis based on The Cancer Genome Atlas (TCGA) and three Gene Expression Omnibus (GEO) datasets revealed that ALDOB was significantly downregulated in GC compared with normal tissues. In addition, cell viability assay confirmed that ALDOB acted as a tumor suppressor. Finally, drug sensitivity analysis revealed that ALDOB increased the sensitivity of gastric cancer cells to most antitumor drugs, especially talazoparib, XAV939, and FTI-277. Our results showed that the expression of ALDOB was significantly lower in GC tissues than in normal tissues. And ALDOB significantly inhibited proliferation and migration, delayed glycolysis in GC cells. Consequently, our study suggests that ALDOB may be a potential target for the clinical treatment of gastric cancer.

Disulfidptosis-related lncRNA signature reveals immune microenvironment and novel molecular subtyping of stomach adenocarcinoma

The main challenge in treating stomach adenocarcinoma (STAD) is chemotherapy resistance, which is characterized by changes in the immune microenvironment. Disulfidptosis, a novel form of programmed cell death, is involved in STAD but its mechanism is not fully understood. Long non-coding RNAs (LncRNAs) may play a role in regulating disulfidptosis and influencing the immune microenvironment and chemotherapy resistance in STAD. This study aims to establish disulfidptosis-related lncRNA (DRL) features and explore their significance in the immune microenvironment and chemotherapy resistance in STAD patients. By analyzing RNA sequencing and clinical data from STAD patients and extracting disulfidptosis-related genes, we identified DRLs through co-expression, single-factor and multi-factor Cox regression, and Lasso regression analyses. We also investigated differences in the immune microenvironment, immune function, immune checkpoint gene expression, and chemotherapy resistance between different risk groups using various algorithms. A prognostic risk model consisting of 2 DRLs was constructed, with a strong predictive value for patient survival, outperforming other clinical-pathological factors in predicting 3-year and 5-year survival. Immune-related analysis revealed a strong positive correlation between T cell CD4+ cells and risk score across all algorithms, and higher expression of immune checkpoint genes in the high-risk group. In addition, high-risk patients showed better sensitivity to Erlotinib, Oxaliplatin, and Gefitinib. Furthermore, three novel molecular subtypes of STAD were identified based on the 2-DRLs features, with evaluation of the immune microenvironment and chemotherapy drug sensitivity for each subgroup, which holds significant implications for achieving precise treatment in STAD. Overall, our 2-DRLs prognostic model demonstrates high predictive value for patient survival in STAD, potentially providing new targets for individualized immune and chemical therapy.

The viral etiology of EBV-associated gastric cancers contributes to their unique pathology, clinical outcomes, treatment responses and immune landscape

Epstein-Barr virus (EBV) is a pathogen known to cause a number of malignancies, often taking years for them to develop after primary infection. EBV-associated gastric cancer (EBVaGC) is one such malignancy, and is an immunologically, molecularly and pathologically distinct entity from EBV-negative gastric cancer (EBVnGC). In comparison with EBVnGCs, EBVaGCs overexpress a number of immune regulatory genes to help form an immunosuppressive tumor microenvironment (TME), have improved prognosis, and overall have an "immune-hot" phenotype. This review provides an overview of the histopathology, clinical features and clinical outcomes of EBVaGCs. We also summarize the differences between the TMEs of EBVaGCs and EBVnGCs, which includes significant differences in cell composition and immune infiltration. A list of available EBVaGC and EBVnGC gene expression datasets and computational tools are also provided within this review. Finally, an overview is provided of the various chemo- and immuno-therapeutics available in treating gastric cancers (GCs), with a focus on EBVaGCs.

Proteomic Profiling of Advanced Melanoma Patients to Predict Therapeutic Response to Anti-PD-1 Therapy

PURPOSE

Despite high clinical need, there are no biomarkers that accurately predict the response of patients with metastatic melanoma to anti-PD-1 therapy.

EXPERIMENTAL DESIGN

In this multicenter study, we applied protein depletion and enrichment methods prior to various proteomic techniques to analyze a serum discovery cohort (n = 56) and three independent serum validation cohorts (n = 80, n = 12, n = 17). Further validation analyses by literature and survival analysis followed.

RESULTS

We identified several significantly regulated proteins as well as biological processes such as neutrophil degranulation, cell-substrate adhesion, and extracellular matrix organization. Analysis of the three independent serum validation cohorts confirmed the significant differences between responders (R) and nonresponders (NR) observed in the initial discovery cohort. In addition, literature-based validation highlighted 30 markers overlapping with previously published signatures. Survival analysis using the TCGA database showed that overexpression of 17 of the markers we identified correlated with lower overall survival in patients with melanoma.

CONCLUSIONS

Ultimately, this multilayered serum analysis led to a potential marker signature with 10 key markers significantly altered in at least two independent serum cohorts: CRP, LYVE1, SAA2, C1RL, CFHR3, LBP, LDHB, S100A8, S100A9, and SAA1, which will serve as the basis for further investigation. In addition to patient serum, we analyzed primary melanoma tumor cells from NR and found a potential marker signature with four key markers: LAMC1, PXDN, SERPINE1, and VCAN.

Gastric cancer-derived LBP promotes liver metastasis by driving intrahepatic fibrotic pre-metastatic niche formation

BACKGROUND

Liver metastasis (LM) is one of the most common distant metastases of gastric cancer (GC). However, the mechanisms underlying the LM of GC (GC-LM) remain poorly understood. This study aimed to identify the tumour-secreted protein associated with GC-LM and to investigate the mechanisms by which this secreted protein remodels the liver microenvironment to promote GC-LM.

METHODS

Data-independent acquisition mass spectrometry (DIA-MS), mRNA expression microarray, quantitative real-time PCR, enzyme-linked immunosorbent assay (ELISA) and immunohistochemistry (IHC) were performed to identify and validate the GC-secreted proteins associated with GC-LM. A modified intrasplenic injection mouse model of LM was used to evaluate the progression and tumour burden of LM in vivo. Flow cytometry, immunofluorescence (IF), western blots (WB) and IHC were performed to validate the pre-metastatic niche (PMN) formation in the pre-modelling mouse models. mRNA sequencing of PMA-treated THP-1 cells with or without lipopolysaccharide binding protein (LBP) treatment was used to identify the functional target genes of LBP in macrophages. Co-immunoprecipitation (Co-IP), WB, ELISA, IF and Transwell assays were performed to explore the underlying mechanism of LBP in inducing intrahepatic PMN formation.

RESULTS

LBP was identified as a critical secreted protein associated with GC-LM and correlated with a worse prognosis in patients with GC. LBP activated the TLR4/NF-κB pathway to promote TGF-β1 secretion in intrahepatic macrophages, which, in turn, activated hepatic satellite cells (HSCs) to direct intrahepatic fibrotic PMN formation. Additionally, TGF-β1 enhanced the migration and invasion of incoming metastatic GC cells in the liver. Consequently, selective targeting of the TGF-β/Smad signaling pathway with galunisertib demonstrated its efficacy in effectively preventing GC-LM in vivo.

CONCLUSIONS

The results of this study provide compelling evidence that serological LBP can serve as a valuable diagnostic biomarker for the early detection of GC-LM. Mechanistically, GC-derived LBP mediates the crosstalk between primary GC cells and the intrahepatic microenvironment by promoting TGF-β1 secretion in intrahepatic macrophages, which induces intrahepatic fibrotic PMN formation to promote GC-LM. Importantly, selectively targeting the TGF-β/Smad signaling pathway with galunisertib represents a promising preventive and therapeutic strategy for GC-LM.

Retracted: Identification of Immune-Related Prognostic Markers in Gastric Cancer

[This retracts the article DOI: 10.1155/2022/7897274.].

Delineation of fatty acid metabolism in gastric cancer: Therapeutic implications

BACKGROUND

The prognosis of gastric cancer is extremely poor. Metabolic reprogramming involving lipids has been associated with cancer occurrence and progression.

AIM

To illustrate fatty acid metabolic mechanisms in gastric cancer, detect core genes, develop a prognostic model, and provide treatment options.

METHODS

Raw data from The Cancer Genome Atlas and Gene Expression Omnibus databases were collected and analyzed. Differentially expressed fatty acid metabolism genes were identified and incorporated into a risk model based on least absolute shrinkage and selection operator regression analysis. Then, patients from The Cancer Genome Atlas were assigned to high- and low-risk cohorts according to the mean value of the risk score as the threshold, which was verified in the Gene Expression Omnibus database. Relationships between chemotherapeutic sensitivity and tumor microenvironment features were assessed.

RESULTS

An integrated evaluation was performed in this study. Fatty acid metabolism-related genes were used to construct the risk model. Patients classified into the high-risk cohort were considered to be resistant to chemotherapy based on results of the "pRRophetic" R package. Patients in the high-risk cohort were associated with type I/II interferon activation, increased inflammation level, immune cell infiltration, and tumor immune dysfunction based on the exclusion algorithm, indicating the potential benefit of immunotherapy in these patients.

CONCLUSION

We constructed a fatty acid-related risk score model to assess the comprehensive fatty acid features in gastric cancer and validated its vital role in prognosis, chemotherapy sensitivity, and immunotherapy.

Delineation of fatty acid metabolism in gastric cancer: Therapeutic implications

BACKGROUND

The prognosis of gastric cancer is extremely poor. Metabolic reprogramming involving lipids has been associated with cancer occurrence and progression.

AIM

To illustrate fatty acid metabolic mechanisms in gastric cancer, detect core genes, develop a prognostic model, and provide treatment options.

METHODS

Raw data from The Cancer Genome Atlas and Gene Expression Omnibus databases were collected and analyzed. Differentially expressed fatty acid metabolism genes were identified and incorporated into a risk model based on least absolute shrinkage and selection operator regression analysis. Then, patients from The Cancer Genome Atlas were assigned to high- and low-risk cohorts according to the mean value of the risk score as the threshold, which was verified in the Gene Expression Omnibus database. Relationships between chemotherapeutic sensitivity and tumor microenvironment features were assessed.

RESULTS

An integrated evaluation was performed in this study. Fatty acid metabolism-related genes were used to construct the risk model. Patients classified into the high-risk cohort were considered to be resistant to chemotherapy based on results of the “pRRophetic” R package. Patients in the high-risk cohort were associated with type I/II interferon activation, increased inflammation level, immune cell infiltration, and tumor immune dysfunction based on the exclusion algorithm, indicating the potential benefit of immunotherapy in these patients.

CONCLUSION

We constructed a fatty acid-related risk score model to assess the comprehensive fatty acid features in gastric cancer and validated its vital role in prognosis, chemotherapy sensitivity, and immunotherapy.

Analysis of the characteristics of immune infiltration in endometrial carcinoma and its relationship with prognosis based on bioinformatics

To explore immune-related molecules that affect the prognosis of endometrial carcinoma (EC) using bioinformatic data mining. The expression data related to EC were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus databases. After differential expression analysis, the intersection with immune related genes in the ImmPort database was used to obtain immune related differentially expressed genes (IRDEGs). The correlation between clinicopathological information and the prognosis of IRDEGs was further analyzed to obtain prognosis related differentially expressed immune genes (PRDEIG). Gene correlation analysis and Gene Set Enrichment Analysis (GSEA) enrichment analysis showed that PRDEIG was enriched in cancer-related functional pathways. We then analyzed the relationship between PRDEIG and immune cell infiltration, and further analyzed the mRNA and protein expression of PRDEIG in EC using TCGA and the human protein expression atlas (THPA) databases. After the intersection of the differential expression analysis results and immune-related genes, 4 IRDEGs were obtained: osteoglycin (OGN), LTBP4, CXCL12, and SPP1. After analyzing the relationship between 4 IRDEGs and clinicopathological parameters and prognosis of patients with EC, revealed that only OGN was not only related to tumor immunity, but also affected the prognosis of patients with EC. Gene correlation and GSEA enrichment of OGN were analyzed. The results showed that OGN was significantly enriched in 6 functional pathways: epithelial mesenchymal transition, KRAS signaling up, myogenesis, UV response, allograft rejection and apical junction. In addition, it was also found that OGN was significantly correlated with a variety of immune cells. The results of TCGA and THPA database showed that the mRNA and protein expression levels of OGN decreased in EC. OGN may affect the epithelial mesenchymal transformation (EMT) of tumor by affecting the infiltration of tumor immune cells.

Prognostic significances of PD-L1- and CTLA-4-positive T cells and positive correlations of immunosuppressive marker expression between cancer tissue and peripheral blood in patients with gastric cancer

Introduction

Although tumor, node, metastasis (TNM) staging has been used for prognostic assessment of gastric cancer (GC), the prognosis may vary among patients with the same TNM stage. Recently, the TNM-Immune (TNM-I) classification staging system has been used for prognostic assessment of colorectal cancer based on intra-tumor T-cell status, which is a superior prognostic factor compared with the American Joint Committee on Cancer staging manual. However, an immunoscoring system with prognostic significance for GC has not been established.

Method

Here, we evaluated immune phenotypes in cancer and normal tissues, then examined correlations between tissues and peripheral blood. GC patients who underwent gastrectomy at Seoul St. Mary's Hospital between February 2000 and May 2021 were included. We collected 43 peripheral blood samples preoperatively and a pair of gastric mucosal samples postoperatively, including normal and cancer mucosa, which did not influence tumor diagnosis and staging. Tissue microarray samples of GC were collected from 136 patients during surgery. We investigated correlations of immune phenotypes between tissues and peripheral blood using immunofluorescence imaging and flow cytometry, respectively. GC mucosa exhibited an increased number of CD4⁺ T cells, as well as increased expression levels of immunosuppressive markers (e.g., programmed death-ligand-1 [PD-L1], cytotoxic T lymphocyte antigen-4 [CTLA-4], and interleukin-10), in CD4+ T cells and non-T cells.

Result

The expression levels of immunosuppressive markers were significantly increased in cancer tissues and peripheral blood mononuclear cells. In gastric mucosal tissues and peripheral blood of GC patients, similar immunosuppression phenotypes were observed, including increased numbers of PD-L1- and CTLA-4-positive T cells.

Discussion

Therefore, peripheral blood analysis may be an important tool for prognostic assessment of GC patients.

Oncogenic roles of LINC01234 in various forms of human cancer

Abnormal expression of long non-coding RNAs (lncRNAs) plays an essential role in various malignant neoplasia. As a newly identified lncRNA, LINC01234 is abnormally expressed in several types of cancers and promotes the development of cancers. Accumulating evidence indicates that overexpression of LINC01234 is associated with poor clinical outcomes. Moreover, LINC01234 modulates many cellular events as a putative proto-oncogene, including proliferation, migration, invasion, apoptosis, cell cycle progression, and EMT. In terms of molecular mechanism, LINC01234 regulates gene expression by acting as ceRNA, participating in signaling pathways, interacting with proteins and other molecules, and encoding polypeptide. It reveals that LINC01234 may serve as a potential biomarker for cancer diagnosis, treatment, and prognosis. This review summarizes the expression pattern, biological function, and molecular mechanism of LINC01234 in human cancer and discusses its potential clinical utility.

Immune Profiling in Gastric Cancer Reveals the Dynamic Landscape of Immune Signature Underlying Tumor Progression

The profiling of the tumor immune microenvironment (TIME) is critical for guiding immunotherapy strategies. However, how the composition of the immune landscape affects the tumor progression of gastric cancer (GC) is ill-defined. Here, we used mass cytometry to perform simultaneous in-depth immune profiling of the tumor, adjacent tissues, and blood cells from GC patients and revealed a unique GC tumor-immune signature, where CD8⁺ T cells were present at a lower frequency in tumor tissues compared to adjacent tissues, whereas regulatory T cells and tumor-associated macrophages (TAMs) were significantly increased, indicating strong suppressive TIME in GC. Incorporated with oncogenic genomic traits, we found that the unique immunophenotype was interactively shaped by a specific GC gene signature across tumor progression. Earlier-stage GC lesions with IFN signaling enrichment harbored significantly altered T-cell compartments while advanced GC featured by metabolism signaling activation was accumulated by TAMs. Interestingly, PD-1 expression on CD8⁺ T cells was relatively higher in earlier-stage GC patients, indicating that these patients may derive more benefits from PD-1 inhibitors. The dynamic properties of diverse immune cell types revealed by our study provide new dimensions to the immune landscape of GC and facilitate the development of novel immunotherapy strategies for GC patients.