Gastric cancer peritoneal metastasis related signature predicts prognosis and sensitivity to immunotherapy in gastric cancer

Unraveling the Role of Programmed Cell Death Gene Signature and THBS1 in Gastric Cancer Progression and Therapy Response

BACKGROUND

Programmed cell death (PCD) genes play crucial roles in cancer progression and response to therapies, yet their impact on gastric cancer remains inadequately elucidated. This study aimed to create a prognostic cell death signature (PCDs) for gastric cancer, providing insights into potential therapeutic targets and survival predictors.

METHODS

We utilized TCGA-STAD and five GEO datasets, representing thousands of gastric cancer samples, for a comprehensive analysis of PCD genes. Differential gene expression, functional enrichment, survival, and machine learning analyses were conducted to construct a PCD-based prognostic model.

RESULTS

A total of 249 differentially expressed PCD genes were identified between cancerous and noncancerous gastric tissues. Subsequently, a PCD signature based on seven genes was developed and cross-validated across multiple cohorts. The high-PCD subtype correlated with poorer survival outcomes, lower tumor mutational burden, higher infiltration of M2 macrophages, lower levels of immune checkpoint expression, and decreased response to immunotherapy. A nomogram incorporating the PCDs provided accurate survival rate predictions. Additionally, nine machine learning algorithms were implemented for recurrence prediction, with the random forest model displaying high effectiveness. In this model, thrombospondin 1 (THBS1) showed the highest weight, and its knockdown significantly reduced gastric cancer cell proliferation and invasion.

CONCLUSION

This study underscores the significance of PCD genes, particularly THBS1, in gastric cancer progression and highlights their value as potential therapeutic targets. The predictive models developed here can aid in assessing patient prognosis and tailoring personalized treatment strategies.

Integrative analysis of ubiquitination-related genes identifies HSPA1A as a critical regulator in colorectal cancer progression

Colorectal cancer (CRC) is a prevalent and lethal malignancy, with ubiquitination significantly influencing cellular processes involved in cancer progression. However, the contributions of ubiquitination-related genes in CRC remain unclear. This study conducted a detailed analysis of gene expression profiles associated with ubiquitination in CRC, evaluating 1006 genes across 46 pathways. By comparing CRC tissues to adjacent normal tissues, we identified differentially expressed genes and developed a ubiquitination-related pathway gene signature (URPGS) using LASSO regression analysis on genes with prognostic significance. The prognostic capability of the URPGS was validated in independent cohorts, and its associations with clinical characteristics, including post-chemotherapy survival outcomes, were examined. Machine learning techniques identified HSPA1A as a key gene relevant to CRC both in vitro and in vivo. Our analysis revealed 307 differentially expressed ubiquitination-related genes, with 24 significantly associated with patient prognosis. The developed 14-gene URPGS exhibited strong prognostic value, effectively stratifying patients into high-risk and low-risk groups for overall survival. The URPGS correlated with advanced clinical stages, lymph node metastasis, and recurrence, with higher scores linked to poorer post-chemotherapy survival outcomes. Knockdown of HSPA1A significantly inhibited CRC cell proliferation, migration, and invasion in vitro, as well as tumor growth and metastasis in vivo. This research establishes a novel URPGS that effectively predicts prognosis and chemotherapy outcomes in CRC, enhancing our understanding of ubiquitination's role and suggesting personalized treatment strategies.

Single-cell RNA-sequencing and genome-wide Mendelian randomisation along with abundant machine learning methods identify a novel B cells signature in gastric cancer

BACKGROUND

Gastric cancer (GC) has a poor prognosis, considerable cellular heterogeneity, and ranks fifth among malignant tumours. Understanding the tumour microenvironment (TME) and intra-tumor heterogeneity (ITH) may lead to the development of novel GC treatments.

METHODS

The single-cell RNA sequencing (scRNA-seq) dataset was obtained from the Gene Expression Omnibus (GEO) database, where diverse immune cells were isolated and re-annotated based on cell markers established in the original study to ascertain their individual characteristics. We conducted a weighted gene co-expression network analysis (WGCNA) to identify genes with a significant correlation to GC. Utilising bulk RNA sequencing data, we employed machine learning integration methods to train specific biomarkers for the development of novel diagnostic combinations. A two-sample Mendelian randomisation study was performed to investigate the causal effect of biomarkers on gastric cancer (GC). Ultimately, we utilised the DSigDB database to acquire associations between signature genes and pharmaceuticals.

RESULTS

The 18 genes that made up the signature were as follows: ZFAND2A, PBX4, RAMP2, NNMT, RNASE1, CD93, CDH5, NFKBIE, VWF, DAB2, FAAH2, VAT1, MRAS, TSPAN4, EPAS1, AFAP1L1, DNM3. Patients were categorised into high-risk and low-risk groups according to their risk scores. Individuals in the high-risk cohort exhibited a dismal outlook. The Mendelian randomisation study demonstrated that individuals with a genetic predisposition for elevated NFKBIE levels exhibited a heightened likelihood of acquiring GC. Molecular docking indicates that gemcitabine and chloropyramine may serve as effective therapeutics against NFKBIE.

CONCLUSIONS

We developed and validated a signature utilising scRNA-seq and bulk sequencing data from gastric cancer patients. NFKBIE may function as a novel biomarker and therapeutic target for GC.

Treatment strategy and therapy based on immune response in patients with gastric cancers

In this editorial, we highlight the significance of a retrospective study "Analysis of the impact of immunotherapy efficacy and safety in patients with gastric cancer and liver metastasis" performed by Liu et al. The authors utilized data collected from gastric cancer (GC) patients and assessed immunotherapy effectiveness and survival status. They found significant differences in treatment response. Because immunotherapy seems to be a beneficial strategy for advanced GC patients, stratification of the data based on metastasis status may further improve treatment strategies.

SYNPO2 promotes the development of BLCA by upregulating the infiltration of resting mast cells and increasing the resistance to immunotherapy

Synaptopodin 2 (SYNPO2) plays a pivotal role in regulating tumor growth, development and progression in bladder urothelial Carcinoma (BLCA). However, the precise biological functions and mechanisms of SYNPO2 in BLCA remain unclear. Based on TCGA database‑derived BLCA RNA sequencing data, survival analysis and prognosis analysis indicate that elevated SYNPO2 expression was associated with poor survival outcomes. Notably, exogenous SYNPO2 expression significantly promoted tumor invasion and migration by upregulating vimentin expression in BLCA cell lines. Enrichment analysis revealed the involvement of SYNPO2 in humoral immune responses and the PI3K/AKT signaling pathway. Moreover, increased SYNPO2 levels increased the sensitivity of BLCA to PI3K/AKT pathway‑targeted drugs while being resistant to conventional chemotherapy. In in vivo BLCA mouse models, SYNPO2 overexpression increased pulmonary metastasis of 5637 cells. High SYNPO2 expression led to increased infiltration of innate immune cells, particularly mast cells, in both nude mouse model and clinical BLCA samples. Furthermore, tumor immune dysfunction and exclusion score showed that patients with BLCA patients and high SYNPO2 expression exhibited worse clinical outcomes when treated with immune checkpoint inhibitors. Notably, in the IMvigor 210 cohort, SYNPO2 expression was significantly associated with the population of resting mast cells in BLCA tissue following PD1/PDL1 targeted therapy. In conclusion, SYNPO2 may be a promising prognostic factor in BLCA by modulating mast cell infiltration and exacerbating resistance to immune therapy and conventional chemotherapy.