Single-Cell Atlas of Lineage States, Tumor Microenvironment, and Subtype-Specific Expression Programs in Gastric Cancer

Single-cell transcriptomic analysis identifies tissue-specific fibroblasts as the main modulators of myeloid cells in peritoneal metastasis of different origin

Colorectal cancer (CRC) peritoneal metastasis (CPM) is related to limited therapy options and poor prognosis. Although stromal cells heavily infiltrate most CPMs, interactions between different cell types in their microenvironment remain unclear. Here, we investigated tumor and distant normal tissue from CPM and CRC patients using single-cell RNA sequencing. Investigating the incoming and outgoing signals between cells revealed that fibroblasts dominate the CPM signaling landscape with myeloid cells as their strongest interaction partner. Using immunohistochemistry, we confirmed that fibroblasts co-localize with macrophages in the CPM microenvironment. A fibroblast sub-population detected only in CPM and normal peritoneum demonstrated immunoregulatory properties in co-culture experiments, and was further detected in additional peritoneal malignancies derived from ovarian and gastric origin. This novel fibroblast type and its communication with macrophages could be attractive targets for therapeutic interventions in CPM and potentially peritoneal surface malignancies in general.

Single-cell technology for cell-based drug delivery and pharmaceutical research

Leveraging the capacity to precisely manipulate and analyze individual cells, single-cell technology has rapidly become an indispensable tool in the advancement of cell-based drug delivery systems and innovative cell therapies. This technology offers powerful means to address cellular heterogeneity and significantly enhance therapeutic efficacy. Recent breakthroughs in techniques such as single-cell electroporation, mechanical perforation, and encapsulation, particularly when integrated with microfluidics and bioelectronics, have led to remarkable improvements in drug delivery efficiency, reductions in cytotoxicity, and more precise targeting of therapeutic effects. Moreover, single-cell analyses, including advanced sequencing and high-resolution sensing, offer profound insights into complex disease mechanisms, the development of drug resistance, and the intricate processes of stem cell differentiation. This review summarizes the most significant applications of these single-cell technologies, highlighting their impact on the landscape of modern biomedicine. Furthermore, it provides a forward-looking perspective on future research directions aimed at further optimizing drug delivery strategies and enhancing therapeutic outcomes in the treatment of various diseases.

Role of m7G modification regulators as biomarkers in gastric cancer subtyping and precision immunotherapy

This study investigated the role of N7-methylguanosine (m7G) modification regulators as biomarkers in subtyping and precision immunotherapy of gastric cancer (GC). Through multi-omics analyses, including RNA sequencing, proteomics, and single-cell measurement, the study revealed heterogeneity in the m7G regulatory landscape among GC patients. Three m7G subtypes were identified, each with distinct pathways and phenotypes. Patients with low m7Gscores, based on an established scoring system, showed better survival outcomes and increased antitumor immune cell infiltration, as well as higher tumor mutation loads and lower PD-L1 expression. The predictive value of m7Gscore was confirmed in two immunotherapy cohorts. These findings highlight the potential of m7G modification in shaping the tumor microenvironment and provide new insights for immunotherapeutic strategies in GC patients.

The relationship between the gastric cancer microbiome and clinicopathological factors: a metagenomic investigation from the 100,000 genomes project and The Cancer Genome Atlas

BACKGROUND

Findings from previous gastric cancer microbiome studies have been conflicting, potentially due to patient and/or tumor heterogeneity. The intratumoral gastric cancer microbiome and its relationship with clinicopathological variables have not yet been characterized in detail. We hypothesized that variation in gastric cancer microbial abundance, alpha diversity, and composition is related to clinicopathological characteristics.

METHODS

Metagenomic analysis of 529 GC samples was performed, including whole exome sequencing data from The Cancer Genome Atlas (TCGA) and whole genome sequencing data from the 100,000 Genomes Project. Microbial abundance, alpha diversity, and composition were compared across patient age, sex, tumor location, geographic origin, pathological depth of invasion, pathological lymph node status, histological phenotype, microsatellite instability status, and TCGA molecular subtype.

RESULTS

Gastric cancer microbiomes resembled previous results, with Prevotella, Selenomonas, Stomatobaculum, Streptococcus, Lactobacillus, and Lachnospiraceae commonly seen across both cohorts. Within the TCGA cohort, microbial abundance and alpha diversity were greater in gastric cancers with microsatellite instability, lower pathological depth of invasion, intestinal-type histology, and those originating from Asia. Microsatellite instability status was associated with microbiome composition in both cohorts. Sex and pathological depth of invasion were associated with microbiome composition in the TCGA cohort.

CONCLUSION

The intratumoral gastric cancer microbiome appears to differ according to clinicopathological factors. Certain clinicopathological factors associated with favourable outcomes in gastric cancer were observed to be associated with greater microbial abundance and diversity. This highlights the need for further work to understand the underlying biological mechanisms behind the observed microbiome differences and their potential clinical and therapeutic impact.

Reshaping the immune microenvironment and reversing immunosenescence by natural products: Prospects for immunotherapy in gastric cancer

Gastric cancer (GC) represents a global health-care challenge. Recent progress in immunotherapy has elicited attracted considerable attention as a viable treatment option through modulating the host immune system and unleashing pre-existing immunity, which has profoundly revolutionized oncology, especially GC. Nonetheless, low clinical response and intrinsic and acquired resistance remain persistently challenging. The microenvironment of GC comprising multifarious stromal cell types has remarkable immunosuppressive elements that may impact the efficacy of immunotherapy. Immunosenescence is increasingly regarded as a factor that contributes to cancer development, remodels the tumor microenvironment and affects the efficacy of immunotherapy. Natural products are at the forefront of traditional medicine. Senotherapeutics is a class of drugs and natural products capable of delaying, preventing, or reversing the senescence process (i.e., senolytics) or suppressing senescence-associated secretory phenotype (i.e., senomorphics). Emerging evidence supports that natural products can improve the efficacy of existing immunotherapy and expand their indications in GC mainly based upon remodeling the immunosuppressive microenvironment and reversing immunosenescence. The review provides an integrated review of previously reported and ongoing clinical trials with immunotherapeutic regimens in GC and discusses current challenges. Next, we focus on natural compounds that exert anti-GC functions and possess immunomodulatory properties. More attention is paid to the potential of these natural compounds in modulating the immune microenvironment and immunosenescence. Lastly, we discuss the nanomedicine that can overcome the deficiencies of natural products. Altogether, our review suggests the enormous potential of natural compounds in GC immunotherapy, and provides an important direction for future research.

Spatial organization of B lymphocytes and prognosis prediction in patients with gastric cancer

BACKGROUND

Within the tumor microenvironment (TME), the association of B lymphocytes (B cells) with prognosis and therapy response in gastric cancer (GC) remains poorly characterized. We investigated the predictive and prognostic value of B cells, including their spatial organization within the TME, in one of the largest multi-cohort studies to date.

METHODS

Using CD20 immunohistochemistry, we evaluated B cell density in resection specimens from 977 patients with resectable GC across three cohorts, including the randomized phase III Korean CLASSIC trial. The relationship between CD20 density, clinicopathological characteristics, and overall survival (OS) was analyzed. Digital spatial profiling of 1063 regions of interest from 15 patients was performed to characterize B cell distribution within different regions of interest (ROIs) using the NanoString GeoMx platform.

RESULTS

CD20 density was significantly higher in diffuse-type GC compared to intestinal-type (p = 0.000012). Patients with CD20-low diffuse-type GC had the shortest OS in the CLASSIC trial (median OS: 49 vs 62 months, HR: 1.9, 95% CI: 1.2-3.0, p = 0.003) and in a Japanese cohort (median OS: 49 vs 67 months, HR: 2.2, 95% CI: 1.2-4.0, p = 0.011). This survival difference was not seen in patients treated with adjuvant chemotherapy (median OS: 62 vs 63 months, HR: 1.8, 95% CI: 0.88-3.5, p = 0.108). Spatial profiling revealed significant B cell enrichment within tumor ROIs compared to the stroma, particularly in diffuse-type GC.

CONCLUSIONS

Low CD20 positivity, especially in diffuse-type GC, is linked to poor prognosis and may identify patients who could benefit from chemotherapy. These findings underscore the role of B cells in GC.

USP14-IMP2-CXCL2 axis in tumor-associated macrophages facilitates resistance to anti-PD-1 therapy in gastric cancer by recruiting myeloid-derived suppressor cells

Resistance to anti-PD-1 therapy remains a significant challenge in gastric cancer (GC) treatment. Here, we revealed that the USP14-IMP2-CXCL2 axis in tumor-associated macrophages (TAMs) drove resistance by recruiting myeloid-derived suppressor cells (MDSCs). Endoscopic biopsy samples were obtained from patients with inoperable GC who were candidates for anti-PD-1 therapy. Single-cell RNA sequencing (scRNA-seq) analysis showed a higher prevalence of USP14+ TAMs in therapy-resistant cases, where USP14 was linked to the immunosuppressive phenotype of TAMs. Clinically, GC samples with elevated USP14+ TAM infiltration exhibited decreased CD8+ T cell presence and increased MDSC infiltration. In vivo experiments further confirmed that USP14+ TAMs facilitated resistance to anti-PD-1 therapy in GC, reduced the infiltration of CD8+ T cells, and significantly increased the infiltration of MDSCs. In particular, USP14+ TAMs markedly enhanced the recruitment of MDSCs into the GC microenvironment through the secretion of CXCL2. Mechanistically, USP14 stabilized the m6A reader IMP2 through deubiquitination, thus enhancing CXCL2 expression and secretion. Conversely, the E3 ligase RNF40 facilitated IMP2 degradation via increasing its ubiquitination, with USP14 and RNF40 dynamically balancing IMP2's protein abundance. Furthermore, animal experiments demonstrated that targeted intervention of USP14 markedly enhanced the sensitivity of GC to anti-PD-1 therapy. This study provided a comprehensive exploration of USP14's oncogenic roles in TAMs, suggesting a novel strategy to enhance the efficacy of anti-PD-1 therapy by inhibiting the USP14/IMP2/CXCL2 signaling axis in GC. The sc-RNA analysis revealed that infiltration of USP14+ TAM was significantly higher in anti-PD-1 resistant GC compared to anti-PD-1 sensitive GC (top). USP14 stabilized IMP2 protein in tumor-associated macrophages (middle-left), leading to recruitment of MDSCs into GC microenvironment through secretion of CXCL2 (middle-right), thus reducing the infiltration of CD8+ T cells and facilitating the resistance to anti-PD-1 therapy in GC (bottom). Comment: Dear editors, in formally published articles, figure legends could be placed beneath their corresponding figures. In this version, is this arrangement adopted for the sake of convenience during the proofreading process? If so, we understand and accept this layout.

COL1A1-positive endothelial cells promote gastric cancer progression via the ANGPTL4-SDC4 axis driven by endothelial-to-mesenchymal transition

Gastric cancer (GC) is an aggressive and heterogeneous disease with poor survival outcomes. The progression of GC involves complex, multi-step processes. Endothelial cells (ECs) play a crucial role in tumor angiogenesis, proliferation, invasion, and metastasis, particularly through the process of endothelial-to-mesenchymal transition (EndoMT). However, the specific role and mechanisms of EndoMT in gastric cancer remain unclear. Based on 6 GC single-cell RNA-sequencing (scRNA-seq) cohorts (samples = 97), we established an EndoMT-related gene signature, termed EdMTS. Leveraging this gene signature, ssGSEA was applied to calculate sample scores across multiple bulk RNA-seq datasets, which include information on immunotherapy, metastasis, GC progression, and survival. Moreover, we applied the Monocle2 method to calculate cell pseudotime and used CellChat to analyze interactions between malignant and EC cells. We verified the molecular mechanism by multiple immunofluorescence and cell function experiments. Findings In this study, we established a single-cell atlas of ECs in GC and identified a subpopulation of COL1A1+ ECs that play a critical role in tumor progression and metastasis. These COL1A1+ ECs were significantly associated with worse clinical outcomes in GC patients. Further analysis revealed that COL1A1+ ECs originated from lymphatic ECs and underwent EndoMT through the upregulation of CEBPB, driving tumor invasiveness. Moreover, COL1A1+ ECs interacted with malignant cells via ANGPTL4-SDC4 axis, enhancing invasion and migration. These findings provide a deeper understanding of the role of COL1A1+ ECs in GC progression and highlight potential therapeutic targets for disrupting the EndoMT process in these cells to provide a benefit for GC patients.

Multi-omics analysis identifies diagnostic circulating biomarkers and potential therapeutic targets, revealing IQGAP1 as an oncogene in gastric cancer

This study employed a multi-omics integration approach to identify circulating biomarkers for gastric cancer (GC). We analyzed plasma and tumor tissue single-cell RNA sequencing data, along with gene and protein quantitative trait loci analyses. Leveraging data from UK Biobank and FinnGen, we investigated genetic associations with GC. Through colocalization, Mendelian Randomization, and various filtering analyses, we identified four genes (IQGAP1, KRTCAP2, PARP1, MLF2) and four proteins (EGFL9 [DLK2], ECM1, PDIA5, TIMP4) as potential GC biomarkers. These were selected based on significant genetic colocation probabilities and significant associations with GC. Seven of these biomarkers demonstrated predictive capability for GC occurrence, with AUC ranging from 0.61 to 0.99. Drug prediction analysis identified seven protein biomarkers as potential targets for immunotherapy, targeted therapies, and tumor chemotherapy. Further scRNA-seq analysis revealed significant expression differences between gastric tumor and normal tissues, particularly the upregulation of IQGAP1, which highlights its role in tumor growth.

TPM4 influences the initiation and progression of gastric cancer by modulating ferroptosis via SCD1

Gastric cancer (GC) is a deadly disease with poor prognosis and few treatment options. Tropomyosin 4 (TPM4) is an actin-binding protein that stabilizes the cytoskeleton of cells and has an unclear role in GC. This study aimed to elucidate the role and underlying mechanisms of TPM4 in GC pathogenesis. The expression and diagnostic and prognostic value of TPM4 in GC were analyzed using bioinformatics. A nomogram based on TPM4 expression was created and validated with an external cohort. TPM4-knockdown GC cells and xenograft models in nude mice were used to study the function of TPM4 in vitro and in vivo. Proteomic and rescue experiments confirmed the regulatory effect of TPM4 on stearoyl-CoA desaturase 1 (SCD1) in GC. Immunohistochemistry verified the expression and correlation of the TPM4 and SCD1 proteins in GC tissues. Our study identified TPM4 as an oncogene in GC, suggesting its potential diagnostic and prognostic value. The TPM4-based nomogram showed potential prognostic value for clinical use. TPM4 knockdown inhibited GC cell proliferation, induced ferroptosis, and slowed tumor growth in vivo, which is achieved by inhibiting SCD1 expression. Immunohistochemical analysis of GC tissues revealed elevated expression levels of both TPM4 and SCD1 proteins, with a positive correlation observed between their expression. TPM4 is a promising target for new diagnostic, prognostic, and therapeutic strategies for GC. Downregulation of TPM4 inhibits GC cell growth and induces ferroptosis by suppressing SCD1 expression.

Spatial dissection of tumour microenvironments in gastric cancers reveals the immunosuppressive crosstalk between CCL2+ fibroblasts and STAT3-activated macrophages

BACKGROUND

A spatially resolved, niche-level analysis of tumour microenvironments (TME) can provide insights into cellular interactions and their functional impacts in gastric cancers (GC).

OBJECTIVE

Our goal was to translate the spatial organisation of GC ecosystems into a functional landscape of cellular interactions involving malignant, stromal and immune cells.

DESIGN

We performed spatial transcriptomics on nine primary GC samples using the Visium platform to delineate the transcriptional landscape and dynamics of malignant, stromal and immune cells within the GC tissue architecture, highlighting cellular crosstalks and their functional consequences in the TME.

RESULTS

GC spatial transcriptomes with substantial cellular heterogeneity were delineated into six regional compartments. Specifically, the fibroblast-enriched TME upregulates epithelial-to-mesenchymal transformation and immunosuppressive response in malignant and TME cells, respectively. Cell type-specific transcriptional dynamics revealed that malignant and endothelial cells promote the cellular proliferations of TME cells, whereas the fibroblasts and immune cells are associated with procancer and anticancer immunity, respectively. Ligand-receptor analysis revealed that CCL2-expressing fibroblasts promote the tumour progression via JAK-STAT3 signalling and inflammatory response in tumour-infiltrated macrophages. CCL2+ fibroblasts and STAT3-activated macrophages are co-localised and their co-abundance was associated with unfavourable prognosis. We experimentally validated that CCL2+ fibroblasts recruit myeloid cells and stimulate STAT3 activation in recruited macrophages. The development of immunosuppressive TME by CCL2+ fibroblasts were also validated in syngeneic mouse models.

CONCLUSION

GC spatial transcriptomes revealed functional cellular crosstalk involving multiple cell types among which the interaction between CCL2+ fibroblasts and STAT3-activated macrophages plays roles in establishing immune-suppressive GC TME with potential clinical relevance.

Spatially Resolved Tumor Ecosystems and Cell States in Gastric Adenocarcinoma Progression and Evolution

SIGNIFICANCE

Integration of spatial transcriptomic (GeoMx Digital Spatial Profiler) and single-cell RNA sequencing data from multiple gastric cancers identifies spatially resolved expression-based intratumoral heterogeneity, associated with distinct immune microenvironments. We uncovered two separate evolutionary trajectories associated with specific molecular subtypes, clinical prognoses, stromal neighborhoods, and genetic drivers. Tumor-stroma interfaces emerged as a unique state of tumor ecology.

PI3 expression predicts recurrence after chemotherapy with DNA-damaging drugs in gastric cancer

Despite recent advances in gastric cancer therapy, chemotherapy resistance and lack of methods for selecting combination regimens remain major problems. Organoids, which provide a culture system that more closely resembles tumor cell organization than traditional cell lines, can be established from surgical specimens with a high success rate and are widely used for drug sensitivity assays. In this study, we aimed to identify a novel biomarker for predicting multidrug resistance using gastric cancer organoids (GCOs). We evaluated 5-fluorouracil or oxaliplatin-resistant GCOs to find novel biomarkers that reflect multidrug resistance in gastric cancer. To examine the resistance mechanisms, RNA-sequencing analysis and ex vivo drug sensitivity testing were performed. The association of biomarkers with patient prognosis and chemotherapy efficacy was evaluated using three original cohorts with a total of 230 cases. The results were also validated with two independent public cohorts and single-cell RNA sequence data. Increased expression of peptidase inhibitor 3 (PI3) was detected in all 5-fluorouracil or oxaliplatin-resistant GCOs. Our findings suggest a potential association of PI3 expression with ribosome biosynthesis and RNA metabolism under organoid conditions. We also found that PI3 overexpression promoted 5-fluorouracil/oxaliplatin/cisplatin resistance but not paclitaxel resistance. Immunohistochemical evaluation of PI3 expression revealed that the PI3-positive gastric cancer group had a poorer outcome, especially in terms of time to recurrence. PI3 positivity was also an independent predictor of relapse after chemotherapy with DNA-damaging agents. PI3 promotes DNA-damaging drug resistance through multiple downstream regulations related to RNA and ribosomal metabolism. PI3 may be useful as a biomarker for the therapeutic selection of non-DNA-damaging agents. © 2025 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Loss of Kmt2c / d promotes gastric cancer initiation and confers vulnerability to mTORC1 inhibition and anti-PD1 immunotherapy

KMT2C and KMT2D ( KMT2C/D ) are frequently mutated in gastric adenocarcinoma, yet their function in cancer initiation remains poorly understood. In this study, based on the observation that loss-of-function mutations of KMT2C and KMT2D are enriched and co-occur in gastric adenocarcinoma, we developed genetically engineered mouse models to selectively knock out Kmt2c and Kmt2d in gastric epithelial cells with Tmprss2-CreER T2 . Through histological staining and single-cell RNA sequencing, we observed that Kmt2c/d loss led to nuclear dysplasia and expansion of cells with mixed gastric lineage markers. When combined with Pten deletion, Kmt2c/d loss drove rapid development of muscle-invasive gastric adenocarcinoma as early as 3 weeks post Cre-mediated gene deletion. The adenocarcinoma exhibited decreased expression of gastric lineage markers and increased expression of intestinal differentiation markers, phenocopying human gastric adenocarcinoma. Kmt2c/d knockout reduced protein synthesis but upregulated transcription of ribosomal proteins, rendering sensitivity to mTORC1 inhibitors. Additionally, Kmt2c/d knockout increased MHC-I molecule expression and enhanced antigen presentation. Combination of mTROC1 inhibition and anti-PD1 immunotherapy significantly suppressed tumor growth in immune-competent mice. Together, these findings reveal the role of Kmt2c / d loss in gastric cancer initiation and suggest the potential therapeutic strategies for KMT2C/D -deficient gastric cancer.

Tumour-intrinsic alterations and stromal matrix remodelling promote Wnt-niche independence during diffuse-type gastric cancer progression

BACKGROUND

Development of diffuse-type gastric cancer (DGC) starts with intramucosal lesions that are primarily composed of differentiated, non-proliferative signet ring cells (SRCs). These indolent lesions can advance into highly proliferative and metastatic tumours, which requires suppression of DGC cell differentiation.

OBJECTIVE

Our goal was to identify molecular changes contributing to the progression of indolent to aggressive DGC lesions.

DESIGN

We conducted spatial transcriptomic analysis of patient tumours at different stages of hereditary DGC, comparing transcriptional differences in tumour cell populations and tumour-associated cells. We performed functional analysis of identified changes in a human gastric (CDH1 KO) organoid model recapitulating DGC initiation.

RESULTS

Our analysis reveals that distinct DGC cell populations exhibit varying levels of Wnt-signalling activity, and high levels of Wnt signalling prevent differentiation into SRCs. We identify multiple adaptations during DGC progression that converge on Wnt signalling, allowing tumour cells to remain in an undifferentiated state as they disseminate away from the gastric stem cell niche. First, DGC cells establish a cell-autonomous source for Wnt-pathway activation through upregulated expression of Wnt-ligands and 'secreted frizzled-related protein 2' (SFRP2) that potentiates ligand-induced Wnt signalling. Second, early tumour development is marked by extracellular matrix remodelling, including increased deposition of collagen I whose interactions with DGC cells suppress their differentiation in the absence of exogenous Wnt ligands.

CONCLUSIONS

Our findings demonstrate that tumour cell-derived ligand expression and extracellular matrix remodelling sustain Wnt signalling during DGC progression. These complementary mechanisms promote niche independence enabling expansion of undifferentiated DGC cells needed for the development of advanced tumours.

Integrative analysis of bulk and single-cell sequencing reveals TNFSF9 as a potential regulator in microsatellite instability stomach adenocarcinoma

BACKGROUND

Stomach adenocarcinoma (STAD) with microsatellite instability (MSI) is associated with a better prognosis compared to Non-MSI. This study aims to elucidate the differences in the tumor microenvironment (TME) of MSI and explore its underlying mechanisms in STAD.

METHODS

TME differences between MSI and Non-MSI were analyzed using single-cell RNA sequencing (MSI = 7, Non-MSI = 19) and bulk RNA sequencing (MSI = 39, Non-MSI = 198). Differentially expressed genes (DEGs) were used to identify enriched pathways and hub genes. TNFSF9 expression was validated by immunohistochemistry (IHC) on 23 STAD sections (MSI = 13, Non-MSI = 10) and confirmed in tumor epithelial cells using SNU-1 (MSI) and AGS (Non-MSI) cell lines through quantitative polymerase chain reaction (qPCR) and Western blot (WB).

RESULTS

The results showed MSI was significantly associated with a better prognosis (P < 0.05). Within the TME, MSI was associated with a higher abundance of antigen-presenting cells, including M1 macrophages (40.1% vs. 27.9%) and activated dendritic cells (22.1% vs. 10.5%), as well as pro-inflammatory Th1-like CD4⁺ T cells (15% vs. 11%). However, MSI also showed an increase in exhausted T cells, indicating a complex immune landscape. Signaling pathway and cell communication analyses revealed an enrichment of cytokine-related pathways in MSI. Hub gene analysis revealed that TNFSF9 was predominantly expressed in stromal cells and partially in tumor epithelial cells in MSI, with its upregulation further confirmed through IHC, qPCR, and WB. Correlation analysis demonstrated a positive relationship between TNFSF9 expression and the abundance of M1 macrophages.

CONCLUSIONS

These findings provide new insights into the TME of MSI in STAD, emphasizing the significant role of TNFSF9 in shaping MSI-specific TME, enhancing immunotherapy efficacy, and improving patient survival.

The fibroinflammatory response in cancer

Fibroinflammation refers to the highly integrated fibrogenic and inflammatory responses mediated by the concerted function of fibroblasts and innate immune cells in response to tissue perturbation. This process underlies the desmoplastic remodelling of the tumour microenvironment and thus plays an important role in tumour initiation, growth and metastasis. More specifically, fibroinflammation alters the biochemical and biomechanical signalling in malignant cells to promote their proliferation and survival and further supports an immunosuppressive microenvironment by polarizing the immune status of tumours. Additionally, the presence of fibroinflammation is often associated with therapeutic resistance. As such, there is increasing interest in targeting this process to normalize the tumour microenvironment and thus enhance the treatment of solid tumours. Herein, we review advances made in unravelling the complexity of cancer-associated fibroinflammation that can inform the rational design of therapies targeting this.

CNV-mediated dysregulation of the ceRNA network mechanism revealed heterogeneity in diffuse and intestinal gastric cancers

BACKGROUND

Gastric cancer (GC) is a highly heterogeneous tumour with high morbidity. Approximately 95% of GC cases are gastric adenocarcinomas, which are further categorized into two predominant subtypes: diffuse gastric cancer (DGC) and intestinal gastric cancer (IGC). These subtypes exhibit distinct pathophysiological and molecular characteristics, reflecting their unique tumorigenic mechanisms.

METHOD

In this study, we employed a comprehensive approach to identify driver genes associated with DGC and IGC by focusing on copy number variation (CNV) genes within the competing endogenous RNA (ceRNA) network. The influence of driver CNV genes on the molecular, cellular, and clinical differences between DGC and IGC was subsequently analysed. Finally, therapeutic strategies for DGC and IGC were evaluated based on the status and functional pathways of the driver CNV genes.

RESULTS

A total of 17 and 22 driver CNV genes were identified in DGC and IGC, respectively. These genes drive subtype differences through the ceRNA network, resulting in alterations in the tumour microenvironment (TME). Based on these differences, personalized treatment strategies for DGC or IGC could be developed. Immune checkpoint inhibitors may be an effective treatment option in IGC. Additionally, DGC patients with homozygous deletion of PPIF might benefit from adjuvant chemotherapy, whereas those with high-level amplification of MTAP could respond to targeted therapy.

CONCLUSION

Driver CNV genes were identified to reveal the underlying cause of heterogeneity in DGC and IGC. Furthermore, specific driver CNV genes were identified as potential therapeutic targets, facilitating personalized treatment.

Divergent lineage trajectories and genetic landscapes in human gastric intestinal metaplasia organoids associated with early neoplastic progression

BACKGROUND

Gastric intestinal metaplasia (IM) is a precancerous stage spanning a morphological spectrum that is poorly represented by human cell line models.

OBJECTIVE

We aim to establish and characterise human IM cell models to better understand IM progression along the cancer spectrum.

DESIGN

A large human gastric IM organoid (IMO) cohort (n=28), their clonal derivatives and normal gastric organoids (n=42) for comparison were established. Comprehensive multi-omics profiling and functional characterisation were performed.

RESULTS

Single-cell transcriptomes revealed IMO cells spanning a spectrum from hybrid gastric/intestinal to advanced intestinal differentiation. Their lineage trajectories connected different cycling and quiescent stem and progenitors, highlighting differences in gastric to IM transition and the potential origin of IM from STMN1 cycling isthmus stem cells. Hybrid IMOs showed impaired differentiation potential, high lineage plasticity beyond gastric or intestinal fates and reactivation of a fetal gene programme.Cell populations in gastric IM and cancer tissues were highly similar to those derived from IMOs and exhibited a fetal signature. Genomically, IMOs showed elevated mutation burden, frequent chromosome 20 gain and epigenetic deregulation of many intestinal and gastric genes. Functionally, IMOs were FGF10 independent and showed downregulated FGFR2. Several IMOs exhibited a cell-matrix adhesion independent subpopulation that displayed chromosome 20 gain but lacked key cancer driver mutations, potentially representing the earliest neoplastic precursor of IM-induced gastric cancer.

CONCLUSIONS

Overall, our IMO biobank captured the heterogeneous nature of IM, revealing mechanistic insights on IM pathogenesis and progression, offering an ideal platform for studying early gastric neoplastic transformation and chemoprevention.

Blood TCTP as a potential biomarker associated with immunosuppressive features and poor clinical outcomes in metastatic gastric cancer

BACKGROUND

No established biomarker exists for specific myeloid cell populations or in gastric cancer. This study aimed to explore the prognostic and immunological relevance of plasma translationally controlled tumor protein (TCTP) in patients with advanced gastric cancer treated with an immune checkpoint inhibitor and/or cytotoxic chemotherapy.

METHODS

Plasma samples were prospectively collected from the cohorts of patients with gastric cancer treated with first-line fluoropyrimidine plus platinum chemotherapy (n=143, cohort 1) and third-line nivolumab (n=165, cohort 2). Plasma TCTP levels were quantified using ELISA, and multiplex proteomic analysis (Olink) was conducted to assess expression levels of immune-related proteins. External single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics datasets were employed to validate the findings.

RESULTS

Patients with high plasma TCTP levels (TCTP-high group) exhibited poor progression-free survival (PFS) and overall survival (OS) with first-line chemotherapy compared with those with low levels (TCTP-low group) in cohort 1 (HR: 1.73 for PFS; 1.77 for OS). In the TCTP-high group, proteins associated with immunosuppressive myeloid cells, angiogenesis, and immune exclusion of T/natural killer (NK) cell function were upregulated, whereas proteins involved in T-cell activation/exhaustion were significantly upregulated in the TCTP-low group. scRNA-seq analyses identified a myeloid subset with high TPT1 (encoding TCTP) expression and TCTP-related molecules, enriched with inhibitory myeloid inflammation gene signatures and providing inhibitory signals to T/NK cells (Macrophage-chemokine). Spatial transcriptomics analyses revealed a tumor-cell-enriched cluster co-localized with the Macrophage-chemokine subset, which exhibited the highest TPT1 expression and a positive correlation between its abundance and average TPT1 levels. In nivolumab-treated patients (cohort 2), the high TCTP group was associated with poor survival outcomes (HR: 1.39 for PFS; 1.47 for OS).

CONCLUSIONS

Plasma TCTP is a prognostic biomarker, reflecting clinically relevant immunosuppressive myeloid signals in patients with gastric cancer.

Cellular heterogeneity and communication networks in gastric cancer: Single-cell analysis reveals β-hydroxybutyrylation-associated genes and immune infiltration characteristics

Gastric cancer is characterized by high heterogeneity, with its complex microenvironment and intercellular communications playing critical roles in disease progression and treatment responses. In this study, we utilized single-cell sequencing to dissect the intricate landscape of gastric cancer, identifying diverse cell populations and their interactions. We focused on the role of β-hydroxybutyrylation (Kbhb)-associated genes and their impact on the tumor microenvironment. By analyzing 189,700 single-cell profiles, we identified four distinct malignant epithelial cell subpopulations characterized by unique gene expression patterns. Among these, 20 β-hydroxybutyrylation (Kbhb)-associated genes were identified, including key genes such as MRPL13, LDHB, COX6C, FABP5, and RPS13, which were significantly associated with immune infiltration and tumor microenvironment remodeling. Hierarchical clustering based on these genes classified gastric cancer patients into two subgroups with distinct prognostic outcomes. Patients in the high-risk subgroup exhibited increased expression of pro-tumor genes and reduced immune infiltration, correlating with poorer survival. We further constructed a robust risk scoring model incorporating these genes, achieving AUC values of 0.72, 0.69, and 0.66 for predicting 1-, 3-, and 5-year survival in the TCGA dataset. These findings underscore the prognostic value of Kbhb-associated genes and their potential as therapeutic targets. This study not only provides insights into the molecular underpinnings of gastric cancer but also offers potential biomarkers for patient stratification and targets for therapeutic intervention.

YTHDF2-mediated m6A modification of ONECUT2 promotes stemness and oxaliplatin resistance in gastric cancer through transcriptionally activating TFPI

AIMS

Chemoresistance results in poor outcomes of patients with gastric cancer (GC). This study aims to identify oxaliplatin resistance-related cell subpopulations in the tumor microenvironment (TME) and decipher the involved molecular mechanisms.

METHODS

Through single-cell RNA sequencing, a unique ONECUT2+TFPI+ GC cell subset was identified in the oxaliplatin-resistant TME. The functional roles and molecular mechanisms of ONECUT2 in oxaliplatin resistance were investigated in cellular and mouse models. Therapeutic efficacy of small molecule inhibitor of ONECUT2 was also evaluated.

RESULTS

The abundance of ONECUT2+TFPI+ GC cell subset was elevated in oxaliplatin-resistant GC tumors. ONECUT2 was up-regulated and associated with undesirable prognostic outcomes of patients with GC. ONECUT2 facilitated GC cell migration, stemness properties and oxaliplatin resistance. YTHDF2, an m6A "reader", was down-regulated in GC, and its overexpression facilitated ONECUT2 mRNA degradation through m6A modification. Furthermore, ONECUT2 transcriptionally activated TFPI through binding to its promoter. Small molecule inhibitor CSRM617 targeting ONECUT2 was well tolerated in GC mouse models, and could effectively improve therapeutic efficacy of oxaliplatin against GC.

CONCLUSIONS

Our study demonstrates that YTHDF2-mediated m6A modification of ONECUT2 results in stemness and oxaliplatin resistance in GC through transcriptionally activating TFPI, which provides a novel therapeutic target against oxaliplatin-resistant GC.

Prognostic value of [68Ga]Ga-FAPI-04 PET in patients with newly diagnosed gastric carcinoma

PURPOSE

Gallium-68-labeled fibroblast activation protein inhibitor ([68Ga]Ga-FAPI) positron emission tomography (PET) has demonstrated excellent diagnostic performance in various malignancies, including gastric carcinoma. However, its prognostic utility is unclear. This study evaluates the prognostic value of [68Ga]Ga-FAPI-04 PET/MRI(CT) in gastric carcinoma.

METHODS

We retrospectively analyzed patients with gastric cancer who underwent [68Ga]Ga-FAPI-04 PET/MRI(CT) between June 2020 and June 2023. Semi-quantitative parameters, including maximum and mean standard uptake value (SUVmax, SUVmean), FAPI-avid tumor volume (FTV), total lesion FAP expression (TLF), tumor to background ratio (TBR), heterogeneity factor (HF) and coefficient of variation (CV) of the primary tumor were measured or calculated. Overall survival (OS) and progression-free survival (PFS) were obtained through follow-up. The relationships between disease prognosis and potential predictors were analyzed， and predictive models were established.

RESULTS

Eighty-six patients (median age 59 years) were included. Thirty-five patients experienced disease progression, and 26 of them died. Univariable analysis revealed SUVmax, FTV, TLF, TBR, HF and CV were significant prognostic factors for both OS and PFS. In multivariate Cox regression analysis, a nomogram model for OS was established, incorporating body mass index (BMI) and CV as independent predictors. The time-dependent C-index of the nomogram model > 0.75 indicates good predictive performance. When predicting PFS, a stratified analysis was performed based on distant metastasis, FTV was an independent prognostic factor among patients without distant metastasis.

CONCLUSION

CV and FTV, derived from [68Ga]Ga-FAPI-04 PET imaging, could serve as independent prognostic factor for OS and PFS in patients with gastric cancer, respectively.

Single-Cell Sequencing: Genomic and Transcriptomic Approaches in Cancer Cell Biology

This article reviews the impact of single-cell sequencing (SCS) on cancer biology research. SCS has revolutionized our understanding of cancer and tumor heterogeneity, clonal evolution, and the complex interplay between cancer cells and tumor microenvironment. SCS provides high-resolution profiling of individual cells in genomic, transcriptomic, and epigenomic landscapes, facilitating the detection of rare mutations, the characterization of cellular diversity, and the integration of molecular data with phenotypic traits. The integration of SCS with multi-omics has provided a multidimensional view of cellular states and regulatory mechanisms in cancer, uncovering novel regulatory mechanisms and therapeutic targets. Advances in computational tools, artificial intelligence (AI), and machine learning have been crucial in interpreting the vast amounts of data generated, leading to the identification of new biomarkers and the development of predictive models for patient stratification. Furthermore, there have been emerging technologies such as spatial transcriptomics and in situ sequencing, which promise to further enhance our understanding of tumor microenvironment organization and cellular interactions. As SCS and its related technologies continue to advance, they are expected to drive significant advances in personalized cancer diagnostics, prognosis, and therapy, ultimately improving patient outcomes in the era of precision oncology.

Cancer-Associated Fibroblasts Genes and Transforming Growth Factor Beta Pathway in Gastric Cancer for Novel Therapeutic Strategy

Background-Objective: Cancer-associated fibroblasts (CAFs) play a crucial role in the tumor microenvironment of gastric cancer (GC). Understanding the molecular characteristics of CAFs-associated genes (CAFGs) is essential for elucidating their role in tumor progression and prognosis. This review aims to summarize the current knowledge on CAFGs, highlighting their expression patterns, prognostic significance, and potential functional mechanisms. Methods: A comprehensive review of existing literature was conducted, focusing on molecular features of CAFGs in GC. Single-cell RNA sequencing (scRNA-seq) analyses were examined to assess the expression patterns of CAFGs in broad-sense CAFs, which include both CAFs and pericytes. Additionally, clinicopathological studies validating the prognostic significance of CAFGs were reviewed. Results: ScRNA-seq analyses revealed that CAFGs are not necessarily restricted to CAFs alone but may also reflect the activation status of surrounding cells. Several CAFGs, including SPARC, THBS2, COL1A1, COL3A1, INHBA, PDGFC, and SDC2, have been validated for their prognostic relevance in GC. However, compared with other cancers, the functional mechanisms of these genes in GC remain poorly understood. While CAFGs exhibit synchronized expression with TGFB1 in colorectal cancer (CRC), such patterns have yet to be confirmed in GC due to the limitations of available microdissected data. Conclusions: A comprehensive understanding of CAFGs and their interaction with the TGFB pathway, including LTBP family genes, may be critical for developing novel therapeutic strategies for GC. Further research is needed to elucidate their functional mechanisms and therapeutic potential.

Harnessing Macrophages in Cancer Therapy: from Immune Modulators to Therapeutic Targets

Macrophages, as the predominant phagocytes, play an essential role in pathogens defense and tissue homeostasis maintenance. In the context of cancer, tumor-associated macrophages (TAMs) have evolved into cunning actors involved in angiogenesis, cancer cell proliferation and metastasis, as well as the construction of immunosuppressive microenvironment. Once properly activated, macrophages can kill tumor cells directly through phagocytosis or attack tumor cells indirectly by stimulating innate and adaptive immunity. Thus, the prospect of targeting TAMs has sparked significant interest and emerged as a promising strategy in immunotherapy. In this review, we summarize the diverse roles and underlying mechanisms of TAMs in cancer development and immunity and highlight the TAM-based therapeutic strategies such as inhibiting macrophage recruitment, inhibiting the differentiation reprogramming of TAMs, blocking phagocytotic checkpoints, inducing trained macrophages, as well as the potential of engineered CAR-armed macrophages in cancer therapy.

Sialic acid metabolism-based classification reveals novel metabolic subtypes with distinct characteristics of tumor microenvironment and clinical outcomes in gastric cancer

BACKGROUND

High heterogeneity in gastric cancer (GC) remains a challenge for standard treatments and prognosis prediction. Dysregulation of sialic acid metabolism (SiaM) is recognized as a key metabolic hallmark of tumor immune evasion and metastasis. Herein, we aimed to develop a SiaM-based metabolic classification in GC.

METHODS

SiaM-related genes were obtained from the MsigDB database. Bulk and single-cell transcriptional data of 956 GC patients were acquired from the GEO, TCGA, and MEDLINE databases. Proteomic profiles of 20 GC samples were derived from our institution. The consensus clustering algorithm was applied to identify SiaM-based clusters. The SiaM-based model was established via LASSO regression and evaluated via Kaplan‒Meier curve and ROC curve analyses. In vitro and in vivo experiments were conducted to explore the function of ST3GAL1 in GC.

RESULTS

Three SiaM clusters presented distinct patterns of clinicopathological features, transcriptomic alterations, and tumor immune microenvironment landscapes in GC. Compared with clusters A and B, cluster C presented elevated SiaM activity, higher metastatic potential, more abundant immunosuppressive features, and a worse prognosis. Based on the differentially expressed genes between these clusters, a risk model for six genes (ARHGAP6, ST3GAL1, ADAM28, C7, PLCL1, and TTC28) was then constructed. The model exhibited robust performance in predicting peritoneal metastasis and prognosis in four independent cohorts. As a hub gene in the model, ST3GAL1 promoted GC cell migration and invasion in vitro and in vivo.

CONCLUSIONS

Our study proposed a novel SiaM-based classification that identified three metabolic subtypes with distinct characteristics of tumor microenvironment and clinical outcomes in GC.

Single-cell transcriptomics reveals the multidimensional dynamic heterogeneity from primary to metastatic gastric cancer

Reprogramming of the tumor microenvironment (TME) plays a critical role in gastric cancer (GC) progression and metastasis. However, the multidimensional features between primary tumors and organ-specific metastases remain poorly understood. In this study, we characterized the dynamic heterogeneity of GC from primary to metastatic stages. We identified seven major cell types and 27 immune and stromal subsets. Immune cells decreased, while immunosuppressive cells increased in ovarian and peritoneal metastases. A 30-gene signature for ovarian metastasis was validated in GC cohorts. Additionally, critical ligand-receptor interactions, including LGALS9-MET in liver metastasis and PVR-TIGIT in lymph node metastasis, were identified as potential therapeutic targets. Furthermore, CLOCK, a transcription factor, was associated with poor prognosis and influenced immune cell interactions and migration. Collectively, this study provides valuable insights into TME dynamics in GC and highlights potential avenues for targeted therapies.

IQGAP3 signalling mediates intratumoral functional heterogeneity to enhance malignant growth

BACKGROUND

The elevation of IQGAP3 expression in diverse cancers indicates a key role for IQGAP3 in carcinogenesis. Although IQGAP3 was established as a proliferating stomach stem cell factor and a regulator of the RAS-ERK pathway, how it drives cancer growth remains unclear.

OBJECTIVE

We define the function of IQGAP3 in gastric cancer (GC) development and progression.

DESIGN

We studied the phenotypic changes caused by IQGAP3 knockdown in three molecularly diverse GC cell lines by RNA-sequencing. In vivo tumorigenesis and lung metastasis assays corroborated IQGAP3 as a mediator of oncogenic signalling. Spatial analysis was performed to evaluate the intratumoral transcriptional and functional differences between control tumours and IQGAP3 knockdown tumours.

RESULTS

Transcriptomic profiling showed that IQGAP3 inhibition attenuates signal transduction networks, such as KRAS signalling, via phosphorylation blockade. IQGAP3 knockdown was associated with significant inhibition of MEK/ERK signalling-associated growth factors, including TGFβ1, concomitant with gene signatures predictive of impaired tumour microenvironment formation and reduced metastatic potential. Xenografts involving IQGAP3 knockdown cells showed attenuated tumorigenesis and lung metastasis in immunodeficient mice. Accordingly, immunofluorescence staining revealed significant reductions of TGFβ/SMAD signalling and αSMA-positive stromal cells; digital spatial analysis indicated that IQGAP3 is indispensable for the formation of two phenotypically diverse cell subpopulations, which played crucial but distinct roles in promoting oncogenic functions.

CONCLUSION

IQGAP3 knockdown suppressed the RAS-TGFβ signalling crosstalk, leading to a significant reduction of the tumour microenvironment. In particular, IQGAP3 maintains functional heterogeneity of cancer cells to enhance malignant growth. IQGAP3 is thus a highly relevant therapy target in GC.

Multiple programmed cell death patterns predict the prognosis and drug sensitivity in gastric cancer

Background

Gastric cancer (GC) is a malignant tumor with poor prognosis. The diverse patterns of programmed cell death (PCD) are significantly associated with the pathogenesis and progression of GC, and it has the potential to serve as prognostic and drug sensitivity indicators for GC.

Method

The sequencing data and clinical characteristics of GC patients were downloaded from The Cancer Genome Atlas and GEO databases. LASSO cox regression method was used to screen feature genes and develop the PCD score (PCDS). Immune cell infiltration, immune checkpoint expression, Tumor Immune Dysfunction and Exclusion (TIDE) algorithm and drug sensitivity analysis were used to explore immunotherapy response. By integrating PCDS with clinical characteristics, we constructed and validated a nomogram that demonstrated robust predictive performance.

Results

We screened nine PCD-related genes (SERPINE1, PLPPR4, CDO1, MID2, NOX4, DYNC1I1, PDK4, MYB, TUBB2A) to create the PCDS. We found that GC patients with high PCDS experienced significantly poorer prognoses, and PCDS was identified as an independent prognostic factor. Furthermore, there was a significant difference in immune profile between high PCDS and low PCDS groups. Additionally, drug sensitivity analysis indicated that patients with a high PCDS may exhibit resistance to immunotherapy and standard adjuvant chemotherapy regimens; however, they may benefit from the FDA-approved drug Dasatinib.

Conclusion

Overall, we confirmed that the PCDS is a prognostic risk factor and a valuable predictor of immunotherapy response in GC patients, which provides new evidence for the potential application of GC.

Single-cell profiling reveals a reduced epithelial defense system, decreased immune responses and the immune regulatory roles of different fibroblast subpopulations in chronic atrophic gastritis

PURPOSE

To identify key cellular changes and molecular events in atrophic mucosa, we aimed to elucidate the molecular mechanisms driving the occurrence of chronic atrophic gastritis (CAG).

METHODS

We used single-cell RNA sequencing (scRNA-seq) to characterize changes in the epithelial state and tissue microenvironment associated with CAG. The molecular changes were identified by comparing differentially expressed genes (DEGs) between the two mucosa states. Gene Ontology (GO) pathway enrichment analysis was used to explore the potential functional changes in each cell subtype in atrophic mucosa. Gene set score analysis was conducted to compare the functional roles of different fibroblast subtypes and functional changes in cell subtypes between the CAG and control groups. Metabolic analysis was performed to compare the metabolic activity of C1Q+ macrophages under different conditions. NichNet analysis was used to analyze the regulatory relationships between CCL11+APOE+ fibroblasts and C1Q+ macrophages and between CCL11+APOE+ fibroblasts and CD8+ effector T cells. Transcription factor (TF) analysis was performed to determine the transcription status of different T-cell subtypes in atrophic and normal mucosa.

RESULTS

We generated a single-cell transcriptomic atlas from 3 CAG biopsy samples and paired adjacent normal tissues. Our analysis revealed that chief cells and parietal cells exhibited a loss of detoxification ability and that surface mucous cells displayed a reduced antimicrobial defense ability in CAG lesions. The mucous neck cells in CAG lesions showed upregulation of genes related to cell cycle transition, which may lead to aberrant DNA replication. Additionally, cells with the T exhaustion phenotype infiltrated under CAG condition. C1Q+ macrophages exhibited reduced phagocytosis, downregulated expression of pattern recognition receptors and decreased metabolic activity. NichNet analysis revealed that a subpopulation of CXCL11+APOE+ fibroblasts regulated the inflammatory response in the pathogenesis of atrophic gastritis. APSN+CXCL11+APOE+ fibroblasts were found to be associated with gastric cancer (GC) development.

CONCLUSIONS

The main goal of this study was to comprehensively elucidate the cellular changes in CAG lesions. We observed an immune decline in the mucosal microenvironment during the development of CAG, including a reduced immune response of C1Q+ macrophages, reduced cytotoxicity of T cells, and increased infiltration of exhausted T cells. Specifically, we demonstrated that different epithelial subtypes aberrantly express genes related to susceptibility to external bacterial infection and aberrant cell cycle progression. Our study provides new insights into the functions of epithelial changes and immune alterations during the development of CAG.

A comprehensive analysis of molecular characteristics of hot and cold tumor of gastric cancer

BACKGROUND

The advent of immunotherapy has revolutionized the treatment paradigm for gastric cancer (GC), offering unprecedented clinical benefits. However, a detailed molecular characterization of the tumor immune microenvironment in GC is essential to further optimize these therapies and enhance their efficacy.

METHODS

Consensus clustering was utilized to classify GC patients into distinct immune states, followed by an in-depth analysis of differences in mutation profiles, copy number variations, and DNA methylation patterns. Weighted gene co-expression network analysis (WGCNA) and correlation analysis were applied to identify gene modules underlying the classification of immune "hot" and "cold" tumors. Subsequently, 101 machine learning algorithm combinations were employed to construct a prognostic model based on the identified gene modules. Single-cell analysis was conducted to investigate cellular interactions associated with the immune-determinant gene module. Finally, immunofluorescence staining for CD8, CD45, and CXCR4 was performed on human GC tissue samples.

RESULTS

A total of 1,298 GC patients were included in this comprehensive analysis. For the first time, we identified and characterized immune "hot" and "cold" tumors in GC patients, revealing distinct molecular features associated with these tumor types. Immune "hot" tumor-related genes were identified, and their functional roles were validated through biological behavior analysis. A prognostic signature, termed the hot tumor top regulators (HTTR), was developed using 101 machine learning algorithm combinations. The HTTR signature emerged as an independent prognostic factor, effectively stratifying patients into low- and high-risk groups with significant differences in overall survival. High-risk groups demonstrated strong associations with immune checkpoint regulation, antigen presentation, and inhibitory pathways. Notably, single-cell analysis revealed that HTTR genes were highly active in CD8 + T cells, with the CXCL12-CXCR4 axis playing a critical role in mediating interactions between CD8 + T cells and endothelial cells.

CONCLUSION

In conclusion, the HTTR signature served as a robust prognostic biomarker for GC patients and effectively identified those with immune "hot" tumors. This finding provided valuable insights into the molecular mechanisms of tumor immunity in GC, offering potential avenues for targeted therapeutic interventions.

Single-cell RNA Sequencing Analysis Reveals Cancer-associated Fibroblast Signature for Prediction of Clinical Outcomes and Immunotherapy in Gastric Cancer

Gastric cancer (GC) is a significant worldwide health concern and is a leading cause of cancer-related mortality. Immunotherapy has arisen as a promising strategy to stimulate the patient's immune system in combating cancer cells. Nevertheless, the effectiveness of immunotherapy in individuals with gastric cancer (GC) is not yet optimal. Thus, it is crucial to discover biomarkers capable appof predicting the advantages of immunotherapy for tailored treatment. The tumor microenvironment (TME) and its constituents, including cancer-associated fibroblasts (CAFs), exert a substantial influence on immune responses and treatment outcomes. In this investigation, we utilized single-cell RNA sequencing to profile CAFs in GC and established a scoring method, referred to as the CAF score (CAFS), for the prediction of patient prognosis and response to immunotherapy. Through our analysis, we successfully identified distinct subgroups within CAFs based on CAF score (CAFS), namely CAFS-high and CAFS-low subgroups. Notably, we noted that individuals within the CAFS-high subgroup experienced a lessF favorable prognosis and displayed diminished responsiveness to immunotherapy in contrast to the CAFS low subgroup. Furthermore, we analyzed the mutation and immune characteristics of these subgroups, identifying differentially mutated genes and immune cell compositions. We established that CAFS could forecast treatment advantages in patients with gastric cancer, both for chemotherapy and immunotherapy. Its efficacy was additionally confirmed in contrast to other biomarkers, including Tumor Immune Dysfunction and Exclusion (TIDE) and Immunophenotypic Score (IPS). These findings emphasize the clinical relevance and potential utility of CAFS in guiding personalized treatment strategies for gastric cancer.

Constructing methylation-driven ceRNA networks unveil tumor heterogeneity and predict patient prognosis

Cancer development involves a complex interplay between genetic and epigenetic factors, with emerging evidence highlighting the pivotal role of competitive endogenous RNA (ceRNA) networks in regulating gene expression. However, the influence of ceRNA networks by aberrant DNA methylation remains incompletely understood. In our study, we proposed DMceNet, a computational method to characterize the effects of DNA methylation on ceRNA regulatory mechanisms and apply it across eight prevalent cancers. By integrating methylation and transcriptomic data, we constructed methylation-driven ceRNA networks and identified a dominant role of lncRNAs within these networks in two key ways: (i) 17 cancer-shared differential methylation lncRNAs (DMlncs), including PVT1 and CASC2, form a Common Cancer Network (CCN) affecting key pathways such as the G2/M checkpoint, and (ii) 24 cancer-specific DMlncs construct unique ceRNA networks for each cancer type. For instance, in LUAD and STAD, hypomethylation drives DMlncs like PCAT6 and MINCR, disrupting the Wnt signaling pathway and apoptosis. We further investigated the characteristics of these methylation-driven ceRNA networks at the cellular level, revealing how methylation-driven dysregulation varies across distinct cell populations within the tumor microenvironment. Our findings also demonstrate the prognostic potential of cancer-specific ceRNA relationships, highlighting their relevance in predicting patient survival outcomes. This integrated transcriptomic and epigenomic analysis provides new insights into cancer biology and regulatory mechanisms.

Integrated analysis of single-cell and bulk transcriptomes uncovers clinically relevant molecular subtypes in human prostate cancer

Objective

Prostate cancer (PCa) is a complex disease characterized by diverse cellular ecosystems within the tumor microenvironment (TME) and high tumor heterogeneity, which challenges clinically stratified management and reinforces the need for novel strategies to fight against castration-resistant PCa (CRPC).

Methods

We performed single-cell RNA sequencing (scRNA-seq) on 10 untreated primary PCa tissues and integrated public scRNA-seq resources from three normal prostate tissues, two untreated primary PCa tissues, and six CRPC tumors to portray a comprehensive cellular and molecular interaction atlas of PCa. We further integrated the single-cell and bulk transcriptomes of PCa to establish a molecular classification system.

Results

scRNA-seq profiles revealed substantial inter- and intra-tumoral heterogeneity across different cell subpopulations in untreated PCa and CRPC tumors. In the malignant epithelial reservoir, cells evolved along decoupled paths in treatment-naive PCa and CRPC tumors, and distinct transcriptional reprogramming processes were activated, highlighting anti-androgen therapy-induced lineage plasticity. Based on the specifically expressed markers of the epithelial subpopulations, we conducted unsupervised clustering analysis in The Cancer Genome Atlas prostate adenocarcinoma (TCGA-PRAD) cohort and identified three molecularly and clinically distinct subtypes. The C1 subtype, characterized by high enrichment of CRPC-enriched epithelial cells, had a high risk of rapid development of anti-androgen resistance and might require active surveillance and additional promising intervention treatments, such as integrin A3 (ITGA3) + integrin B1 (ITGB1) inhibition. The C2 subtype resembled the immune-modulated subtype that was most likely to benefit from anti-LAG3 immunotherapy. The C3 subtype had a favorable prognosis.

Conclusions

Our study provides a comprehensive and high-resolution landscape of the intricate architecture of the PCa TME, and our trichotomic molecular taxonomy could help facilitate precision oncology.

To describe the subsets of malignant epithelial cells in gastric cancer, their developmental trajectories and drug resistance characteristics

Gastric cancer is an aggressive malignancy characterized by significant clinical heterogeneity arising from complex genetic and environmental interactions. This study employed single-cell RNA sequencing, using the 10 × Genomics platform, to analyze 262,532 cells from gastric cancer samples, identifying 32 distinct clusters and 10 major cell types, including immune cells (e.g., T cells, monocytes) and epithelial subpopulations. Among 27 epithelial subgroups, five malignant subpopulations were identified, each defined by unique marker gene expressions and playing diverse roles in tumor progression. Developmental trajectory analysis revealed potential stem-like characteristics in certain clusters, suggesting their involvement in therapeutic resistance and disease recurrence. Cell-cell communication analysis uncovered a dynamic network of interactions within the tumor microenvironment, potentially influencing tumor growth and metastasis. Differential gene expression analysis identified key genes (LDHA, GPC3, MIF, CD44, and TFF3) that were used to construct a prognostic risk score model. This model demonstrated robust predictive power, achieving AUC values of 0.77, 0.77, and 0.76 for 1-, 3-, and 5-year overall survival in the TCGA training dataset, with validation across independent cohorts. These findings deepen our understanding of gastric cancer's cellular and molecular heterogeneity, offering insights into potential therapeutic targets and biomarkers. By facilitating the development of targeted therapies and personalized treatment strategies, these results hold promise for improving clinical outcomes in gastric cancer patients.

Hypoxia signature derived from tumor-associated endothelial cells predict prognosis in gastric cancer

Background

A hypoxic metabolism environment in the tumors is often associated with poor prognostic events such as tumor progression and treatment resistance. In gastric cancer, the mechanism of how hypoxia metabolism affects the tumor microenvironment and immunotherapy efficacy remains to be elucidated.

Methods

We used the bulk-mapping method to analyze the signatures correlated with the response of immunotherapy in the single-cell dataset. Cellular, pathway, and gene were systematically analyzed in both single-cell and bulk validation datasets.

Results

The most significant cell proportion difference between the response and non-response groups was in endothelial cells, which represent the malignant cells. VWF was specifically overexpressed in endothelial cells and was the hub gene of differential genes. EPAS1 was a VWF trans-regulated gene and highly positively correlated with VWF in expression. Knockdown experiments demonstrated that siVWF reduced the expression of VWF, EPAS1, and HIF1A, as well as the synthesis of lactate and adenosine which are indicators of hypoxic metabolism. These results suggest that the overexpression of core malign endothelial genes such as VWF drives hypoxic metabolism in tumors and creates an immunosuppressive environment that reduces the efficacy of immunotherapy. The adverse prognosis of the hypoxia signature was validated in the bulk cohort and significance was further enhanced after selecting core genes and combined survival weight scoring.

Conclusion

In summary, high expression of the malignant endothelial cell driver genes VWF and EPAS1 enhances hypoxic metabolism, and malignant cell-immune cell interactions suppress the immune response. Therefore, the two core genes of hypoxic metabolism might represent potential therapeutic and predicting biomarkers for immunotherapy of gastric cancer in the future.

Exosomal Galectin-3 promotes peritoneal metastases in gastric adenocarcinoma via microenvironment alterations

Peritoneal carcinomatosis (PC) in gastric adenocarcinoma (GAC) is the most common metastatic site and leads to a short median survival. Exosomes have been shown to remodel the microenvironment, facilitating tumor metastases. However, the functional component in GAC cell-derived exosomes that remodel the landscape in the peritoneal cavity remains unclear. To address this, we performed in-depth proteomic profiling of ascites-derived exosomes from patients with PC, and we found that Galectin-3 was highly enriched in exosomes derived from malignant ascites. exosomal Galectin-3 was the crucial regulator of PC. Blockage of exosomal Galectin-3 significantly inhibited tumor metastases and prolonged overall survival. Exosomal Galectin-3 activated cancer-associated fibroblasts through integrin α1β1/FAK/Akt/mTOR/CXCL12 signaling. Combined inhibition of the CXCL12-CXCR4 axis and exosomal Galectin-3 enhanced the efficacy of anti-PD-1 immunotherapy, leading to significantly diminished PC progression and durable antitumor responses. These findings provide a rationale for clinical strategy of targeting exosomal Galectin-3 to treat PC.

KHSRP promotes cancer stem cell maintenance, tumorigenesis, and suppresses anti-tumor immunity in gastric cancer

Objectives

KH-type splicing regulatory protein (KHSRP) is an RNA-binding protein involved in several cellular processes, including nuclear splicing, mRNA localization, and cytoplasmic degradation. While KHSRP's role has been studied in other cancers, its specific involvement in gastric cancer remains poorly understood. This study aims to explore KHSRP expression in gastric cancer and its potential effects on tumor progression and immune response.

Methods

KHSRP expression in gastric cancer tissues and normal tissues was analyzed using data from The Cancer Genome Atlas (TCGA) database. The correlation between KHSRP expression, patient survival, and immune response was also assessed. Immunohistochemistry was performed to evaluate KHSRP expression in gastric cancer tissues. Gain- and loss-of-function experiments were conducted to assess KHSRP's effects on gastric cancer cell proliferation, stemness, and migration. Furthermore, the impact of KHSRP silencing on tumor volume and immune cell infiltration was evaluated in a C3H/He mouse xenograft model.

Results

KHSRP was found to be overexpressed in gastric cancer tissues compared to normal tissues, with a positive correlation to tumor stage and a negative correlation with patient prognosis. Functional assays revealed that KHSRP promotes gastric cancer cell proliferation, enhances cancer stem cell properties, and increases migratory capabilities in vitro. In vivo, KHSRP silencing led to a significant reduction in tumor volume and increased immune cell infiltration in the mouse xenograft model.

Conclusions

KHSRP acts as an oncogene in gastric cancer by promoting tumorigenesis and suppressing anti-tumor immune responses. Its overexpression is associated with poor prognosis, making KHSRP a potential prognostic marker and therapeutic target in gastric cancer.

Investigation of Exome-Wide Tumor Heterogeneity on Colorectal Tissue-Based Single Cells

The progression of colorectal cancer is strongly influenced by environmental and genetic conditions. One of the key factors is tumor heterogeneity which is extensively studied by cfDNA and bulk sequencing methods; however, we lack knowledge regarding its effects at the single-cell level. Motivated by this, we aimed to employ an end-to-end single-cell sequencing workflow from tissue-derived sample isolation to exome sequencing. Our main goal was to investigate the heterogeneity patterns by laser microdissecting samples from different locations of a tissue slide. Moreover, by studying healthy colon control, tumor-associated normal, and colorectal cancer tissues, we explored tissue-specific heterogeneity motifs. For completeness, we also compared the performance of the whole-exome bulk, cfDNA, and single-cell sequencing methods based on variation at the level of a single nucleotide.

FAP+ gastric cancer mesenchymal stromal cells via paracrining INHBA and remodeling ECM promote tumor progression

Gastric cancer (GC) mesenchymal stromal cells (GCMSCs) are the predominant components of the tumor microenvironment (TME) and play a role in the occurrence, development, and metastasis of tumors. However, GCMSCs exhibit phenotypic and functional heterogeneity. The key population of GCMSCs which are vital to tumor progression remains elusive. The expression of fibroblast activation protein (FAP) in gastric cancer was analyzed and verified using clinical pathology data and single-cell RNA sequencing database of gastric cancer patients. FAP positive GCMSCs (FAP+ GCMSCs) were isolated via flow cytometry and characterized through transcriptomic sequencing. The impact of conditioned medium from FAP+ GCMSCs on gastric cancer cell lines was assessed using Enzyme-linked immunosorbent assay (ELISA) and Western blot analyses. Additionally, immunohistochemistry (IHC) and Masson's trichrome staining were employed to explore the association between FAP+ GCMSCs and extracellular matrix (ECM) deposition in gastric cancer tissues. Our study demonstrates that FAP is predominantly expressed in the mesenchymal stromal cells within the gastric cancer milieu. FAP+ GCMSCs exhibited enhanced proliferation, migration, contraction, and tumor-promoting capabilities compared to their FAP- counterparts. These cells significantly increased proliferation and migration of gastric cancer cells through the paracrine secretion of Inhibin Subunit Beta A (INHBA) and activation of the SMAD2/3 signaling pathway. Moreover, FAP+ GCMSCs also induced collagen deposition in ECM and then up-regulated invasion and stemness of GC cells. Mechanistically, this process was mediated by the interaction of collagen with Integrin Subunit Beta 1 (ITGB1), triggering the phosphorylation of Focal Adhesion Kinase (FAK) and Yes Associated Transcriptional Regulator (YAP). Our findings reveal that FAP+ GCSMCs enhanced the GC progression via releasing cytokine INHBA and remodeling ECM providing a theoretical basis for further exploration of tumor stromal-targeting therapy of gastric cancer.

Intestinal Subtype as a Biomarker of Response to Neoadjuvant Immunochemotherapy in Locally Advanced Gastric Adenocarcinoma: Insights from a Prospective Phase II Trial

PURPOSE

Neoadjuvant immunochemotherapy (NAIC) markedly induces pathologic regression in locally advanced gastric adenocarcinoma. However, specific biomarkers are still lacking to effectively identify the beneficiary patients for NAIC.

PATIENTS AND METHODS

A prospective, single-arm, phase II study was conducted to treat locally advanced gastric adenocarcinoma with NAIC (NCT05515796). Correlation between clinicopathologic characteristics and neoadjuvant efficacy was investigated. Bulk RNA sequencing data from 104 samples (from 75 patients in two independent cohorts) and single-cell RNA sequencing data from 105 treatment-naïve gastric adenocarcinomas were comprehensively analyzed to decipher the association of epithelial and microenvironmental characteristics and clinical responses.

RESULTS

The prespecified primary endpoints were achieved: pathologic complete regression rate was 30%, major pathologic regression rate was 43%, and the regimen was well tolerated. Analysis of baseline clinical-pathologic parameters revealed the intestinal subtype of Lauren's classification as a key feature stratifying patients with increased sensitivity to NAIC. Mechanistically, an increased pool of DNA damage repair-active cancer cells and enrichment of CLEC9A+ dendritic cells in the tumor microenvironment were associated with enhanced responsiveness of the intestinal subtype gastric adenocarcinoma to NAIC. More importantly, an intestinal subtype-specific signature model was constructed by the machine learning algorithm NaiveBayes via integrating the transcriptomic features of both DNA damage repair-active cancer cells and CLEC9A+ dendritic cells, which accurately predicted the efficacy of NAIC in multiple independent gastric adenocarcinoma cohorts.

CONCLUSIONS

Intestinal subtype is a histologic biomarker of enhanced sensitivity of gastric adenocarcinoma to NAIC. The intestinal subtype-specific signature model is applicable to guide NAIC for patients with locally advanced gastric adenocarcinoma.

Identification of disulfidptosis-related subtypes in gastric cancer and GAMT is a key gene during disulfidptosis

Recent studies have found that disulfidptosis occurs in cells under glucose starvation. The role of this programmed death method in gastric cancer remains to be explored. Cluster analysis based on disulfidptosis related genes to analyze the differential characteristics of disulfidptosis subtypes. We construct a prognostic risk model using 12 differentially expressed genes of disulfidptosis subtypes. We also analyzed the disulfidptosis subtypes at single-cell resolution. We found that cluster 1 has a poor prognosis and is characterized by a younger age. Inhibiting the expression of GAMT genes associated with disulfidptosis subtypes can significantly inhibit the proliferation of gastric cancer cells, which may be an important target for gastric cancer treatment. Cluster 2 patients are more sensitive to various chemotherapy drugs and immunotherapy. Mesenchymal cells, especially myCAF, endothelial cells, and smooth muscle cells, have strong disulfidptosis scores. In summary, our study provides new insights into the role of disulfidptosis in gastric cancer, and this may be used to guide the treatment of gastric cancer.

Identification of cancer-associated fibrolast subtypes and distinctive role of MFAP5 in CT-detected extramural venous invasion in gastric cancer

Extramural venous invasion (EMVI) detected by computed tomography has been identified as an independent risk factor for distant metastasis in patients with advanced gastric cancer (GC). Cancer-associated fibroblasts (CAFs) are critical for remodeling the tumor microenvironment in GCs. Here, we report that MFAP5+ CAFs promote the formation of EMVI imaging in GC. We detected gene expression in pathological samples from 13 advanced GC patients with EMVI. Radiogenomics results showed the degree of CAFs infiltration was directly proportional to the EMVI score and EMT pathway in GC patients. Single-cell sequencing data analysis results showed that MFAP5+CAFs subtypes in GC were negatively correlated with patient prognosis and were enriched in tumor lactylation modification and EMT pathways. Immunohistochemistry results showed that the expression of MFAP5, L-lactyl and EMT markers in GC tissues was proportional to the EMVI score. CAF from gastric cancer tissue was extracted using collagenase method and co-cultured with GC cell line in vitro. After lentivirus knockdown of MFAP5 in CAFs, the levels of L-lactoyl and histone lactylation modifications were significantly reduced, and the sphere-forming and vascularization abilities of CAFs were significantly inhibited. Cell function experiments showed that MFAP5+ CAFs can affect the EMT, metastasis and invasion capabilities of GC cells. In vivo experimental results of the nude mouse in situ EMVI model suggest that MFAP5+ CAF may promote the formation of EMVI imaging features in GC by regulating lactylation modification. This innovative work may provide important new references for the diagnosis and treatment of GC.

Identification of core immune-related genes CTSK, C3, and IFITM1 for diagnosing Helicobacter pylori infection-associated gastric cancer through transcriptomic analysis

OBJECTIVES

To identify diagnostic genes and mechanisms linking Helicobacter pylori (H. pylori) infection to gastric cancer.

METHODS

Gene expression profiles from GEO were analyzed using differential expression gene (DEG) analysis, weighted gene co-expression network analysis (WGCNA), and functional enrichment. A random forest (RF) model assessed immune-related diagnostic genes, examining their expression, diagnostic performance, prognostic value, and immune cell relationships. Expression patterns of core genes were evaluated with single-cell RNA sequencing (scRNA-seq), and a regulatory network involving miRNA, mRNA, and transcription factors was built.

RESULTS

We identified 75 genes and developed an RF model including 15 immune-related genes, notably CTSK, NR4A3, C3, and IFITM1. Except for NR4A3, these genes showed higher expression in datasets, confirmed by in vitro tests. Their diagnostic performance had an AUC > 0.7, enhancing to >0.85 in a multi-gene model. Survival analysis linked gene upregulation to poorer prognosis, and scRNA-seq and immune cell infiltration analysis underscored their roles in immune dysregulation and pathogenicity in H. pylori-related gastric cancer.

CONCLUSIONS

CTSK, C3, and IFITM1 are crucial in H. pylori-related gastric cancer, forming a robust diagnostic model and guiding future diagnostic and therapeutic research.

Role and value of the tumor microenvironment in the progression and treatment resistance of gastric cancer (Review)

Gastric cancer (GC) is characterized by a complex and heterogeneous tumor microenvironment (TME) that significantly influences disease progression and treatment outcomes. The tumor stroma, which is composed of a variety of cell types such as cancer‑associated fibroblasts, immune cells and vascular components, displays significant spatial and temporal diversity. These stromal elements engage in dynamic crosstalk with cancer cells, shaping their proliferative, invasive and metastatic potential. Furthermore, the TME is instrumental in facilitating resistance to traditional chemotherapy, specific treatments and immunotherapy strategies. Understanding the underlying mechanisms by which the GC microenvironment evolves and supports tumor growth and therapeutic resistance is critical for developing effective treatment strategies. The present review explores the latest progress in understanding the intricate interactions between cancer cells and their immediate environment in GC, highlighting the implications for disease pathogenesis and therapeutic interventions.

Advances in the diagnosis of colorectal cancer: the application of molecular biomarkers and imaging techniques: a literature review

Background

Following neoplasms of the lung and breast, colorectal cancer (CRC) is the third most frequent malignancy globally. Screening for CRC at the age of 50 years is strongly encouraged for prompt earlier diagnosis owing to prognoses being greatly correlated with time of detection and cancer staging.

Aim

This review aimed to elucidate the most recent advancements in the detection of CRC, with an emphasis on the latest innovations in diagnostic molecular biomarkers in conjunction with radiological imaging alongside stool-based tests for CRC screening.

Methods

A comprehensive review of the literature was performed, focusing on specific terms in different electronic databases, including that of PubMed/MEDLINE. Keywords pertaining to "colorectal cancer," "diagnosis," "screening," "imaging," and "biomarkers," among others, were employed in the search strategy. Articles screened and evaluated were deemed relevant to the study aim and were presented in the medium of the English language.

Results

There have been several innovations in the diagnostics and identification of CRC. These generally comprise molecular biomarkers, currently being studied for suitability in disease detection. Examples of these include genetic, epigenetic, and protein biomarkers. Concurrently, recent developments in CRC diagnostics highlight the advancements made in radiological imaging that offer precise insights on tumor biology in addition to morphological information. Combining these with statistical methodologies will increase the sensitivity and specificity of CRC diagnostics. However, putting these strategies into reality is hampered by several issues.

Conclusion

Progress in diagnostic technology alongside the identification of a few prognostic predictive molecular biomarkers suggested great promise for prompt detection and management of CRC. This clearly necessitates further efforts to learn more in this specific sector.

Computer-aided analysis reveals metallothionein-positive cancer-associated fibroblasts promote angiogenesis in gastric adenocarcinoma

Gastric adenocarcinoma (GC), along with its tumor microenvironment (TME), poses great challenges for clinical treatment strategies. Single-cell sequencing has become an important tool for analyzing TME heterogeneity, cell subpopulation, and gene expression patterns. 56 GC single-cell sequencing samples were analyzed, focusing on TME by delineating cancer cells, cancer-associated fibroblasts (CAFs), and macrophages. The spatial transcriptome was used to clarify the distribution characteristics of each cellular component in the tissue slice. Despite the widespread genetic mutations observed in cancer cells, certain recurrent alterations were identified in specific chromosomal regions. The heterogeneity among GC cells is profound, four cancer cell subpopulations were identified through drug sensitivity profiling. Subtype 4, although only present in some samples, demonstrates the strongest stemness and metabolic activity, possibly indicative of an early-stage cancer subpopulation. Their drug sensitivity profiles may hold promise for guiding clinical intervention. In addition, robust spatial co-localization patterns were observed between CAFs, M2 macrophages, and endothelial cells. CAFs were further categorized into six subgroups, among which a novel subgroup termed metallothionein(mt)-positive CAF (mtCAF), characterized by elevated expression of metallothionein 1X (MT1X) and subsequent vascular endothelial growth factor A (VEGFA) secretion, was identified. Immunohistochemistry preliminary confirmed the presence of this unique CAF subgroup. Additionally, M2d macrophages, besides exhibiting high VEGFA expression, also demonstrated various growth factors such as Aamphiregulin (AREG). The M2d-mtCAF axis may play an important role in GC angiogenesis. This study not only enhances our understanding of the TME heterogeneity in GC but also sheds light on the interaction between CAFs and tumor-associated macrophages (TAMs) in tumor angiogenesis.

Single-cell multi-omics in the study of digestive system cancers

Digestive system cancers are prevalent diseases with a high mortality rate, posing a significant threat to public health and economic burden. The diagnosis and treatment of digestive system cancer confront conventional cancer problems, such as tumor heterogeneity and drug resistance. Single-cell sequencing (SCS) emerged at times required and has developed from single-cell RNA-seq (scRNA-seq) to the single-cell multi-omics era represented by single-cell spatial transcriptomics (ST). This article comprehensively reviews the advances of single-cell omics technology in the study of digestive system tumors. While analyzing and summarizing the research cases, vital details on the sequencing platform, sample information, sampling method, and key findings are provided. Meanwhile, we summarize the commonly used SCS platforms and their features, as well as the advantages of multi-omics technologies in combination. Finally, the development trends and prospects of the application of single-cell multi-omics technology in digestive system cancer research are prospected.

Comprehensive integration of single-cell RNA and transcriptome RNA sequencing to establish a pyroptosis-related signature for improving prognostic prediction of gastric cancer

Cell pyroptosis, a Gasdermin-dependent programmed cell death characterized by inflammasome, plays a complex and dynamic role in Gastric cancer (GC), a serious threat to human health. Therefore, the value of pyroptosis-related genes (PRGs) as prognostic biomarkers and therapeutic indicators for patients needs to be exploited in GC. This study integrates single-cell RNA sequencing (scRNA-seq) dataset GSE183904 with GC transcriptome data from the TCGA database, focusing on the expression and distribution of PRGs in GC at the single-cell level. The prognostic signature of PRGs was established by using Cox and LASSO analyses. The differences in long-term prognosis, immune infiltration, mutation profile, CD274 and response to chemotherapeutic drugs between the two groups were analyzed and evaluated. A tissue array was used to verify the expression of six PRGs, CD274, CD163 and FoxP3. C12orf75, VCAN, RGS2, MKNK2, SOCS3 and TNFAIP2 were successfully screened out to establish a signature to potently predict the survival time of GC patients. A webserver (https://pumc.shinyapps.io/GastricCancer/) for prognostic prediction in GC patients was developed based on this signature. High-risk score patients typically had worse prognoses, resistance to classical chemotherapy, and a more immunosuppressive tumor microenvironment. VCAN, TNFAIP2 and SOCS3 were greatly elevated in the GC while RGS2 and MKNK2 were decreased in the tumor samples. Further, VCAN was positively related to the infiltrations of Tregs and M2 TAMs in GC TME and the CD274 in tumor cells. In summary, a potent pyroptosis-related signature was established to accurately forecast the survival time and treatment responsiveness of GC patients.