GC is a fatal disease with high heterogeneity and invasiveness. Recently, SPP1 has been reported to be involved in the tumor progression of multiple human cancers; however, the role of SPP1 in GC heterogeneity and whether it is associated with the invasiveness and mortality of GC remain unclear. Here, we combined multiple RNA sequencing approaches to evaluate the impact of SPP1 on GC. Through bulk RNA sequencing (bulk RNA-seq) and immunohistochemistry (IHC), we found that SPP1 was highly expressed in GC, and high levels of SPP1 were associated with macrophage infiltration, an advanced tumor stage, and higher mortality for advanced GC patients. Furthermore, through simultaneous single-cell and spatial analysis, we demonstrated that SPP1⁺ macrophages are tumor-specific macrophages unique to cancer and enriched in the deep layer of GC tissue. Cell—cell communication analysis revealed that SPP1/CD44 interactions between SPP1⁺ macrophages and their localized tumor epithelial cells could activate downstream target genes in epithelial cells to promote dynamic changes in intratumor heterogeneity. Moreover, these activated genes were found to be closely associated with poor clinical GC outcomes and with cancer-related pathways that promote GC progression, as shown by survival analysis and enrichment analysis, respectively. Collectively, our study reveals that tumor-specific SPP1⁺ macrophages drive the architecture of intratumor heterogeneity to evolve with tumor progression and that SPP1 may serve as a prognostic marker for advanced GC patients, as well as a potential therapeutic target for GC.

MDM4 is one of the major regulators of p53. The biological effect of MDM4 on tumor is controversial, its role and molecular mechanism in colon cancer progression and prognosis are still unclear. In this study, we identify that MDM4 is significantly overexpressed in human colon cancer and high MDM4 expression was associated with poor prognosis of colon cancer with mutant p53. MDM4 inhibits the ubiquitination of the ferroptosis marker protein GPX4 at K167 and K191 by upregulating the protein expression level of the E3 ubiquitin ligase TRIM21, which promotes the polyubiquitination of GPX4 transfer from K48- to K63- linked ubiquitination. Thereby, MDM4 enhances the stability of GPX4 protein, inhibiting ferroptosis, increasing the resistance of colon cancer patients to chemotherapy, and promoting colon cancer progression. These findings elucidate the ferroptosis inhibition effect of MDM4 via regulating TRIM21/GPX4 on p53-mutated colon cancer and provide a potential therapeutic strategy for colon cancer therapy.

Patients with infiltrative-type gastric cancer (GC) (Ming’s classification) have a poor prognosis due to more metastasis and recurrence. Cancer-associated fibroblasts (CAFs) in infiltrative-type extracellular matrix (ECM) have specific characteristics compared with those of expansive types with respect to metastasis, but the mechanism is still unclear. Based on our proteomics data, TCGA data analysis, and immunohistochemical staining results, significantly higher expression of IGFBP7 was observed in GC, especially in the infiltrative type, and was associated with a poor prognosis. Combining single-cell transcriptome data from GEO and multiple immunofluorescence staining on tissue showed that the differential expression of IGFBP7 mainly originated from myofibroblastic CAFs, the subgroup with higher expression of PDGFRB and α-SMA. After treating primary normal fibroblasts (NFs) with conditional medium or recombined protein, it was demonstrated that XGC-1-derived TGF-β1 upregulated the expression of IGFBP7 in the cells and its secretion via the P-Smad2/3 pathway and mediated its activation with higher FAP, PDGFRB, and α-SMA expression. Then, either conditional medium from CAFs with IGFBP7 overexpression or recombined IGFBP7 protein promoted the migration, invasion, colony formation, and sphere growth ability of XGC-1 and MGC-803, respectively. Moreover, IGFBP7 induced EMT in XGC-1. Therefore, our study clarified that in the tumor microenvironment, tumor-cell-derived TGF-β1 induces the appearance of the IGFBP7⁺ CAF subgroup, and its higher IGFBP7 extracellular secretion level accelerates the progression of tumors.

Gastric cancer (GC) is a major cause of cancer-related mortality worldwide. Despite the widespread recognition of tumor immunotherapy in treating unresectable GC, challenges, including ineffective immunotherapy and drug resistance, persist. Therefore, understanding the regulatory mechanisms of PD-L1, particularly in the context of super-enhancers (SEs) and zinc finger protein 36 ring finger protein-like 1 (ZFP36L1) RNA-binding protein, is crucial. In this study, we performed H3K27ac Cleavage Under Targets and Tagmentation (CUT&Tag) sequencing, investigated the heterogeneity of SEs between two GC subtypes with differential growth patterns, and revealed the immune escape signatures driven by ZFP36L1-SE in infiltrative GC through SEs inhibitors treatment. The regulation of ZFP36L1 to PD-L1 was evaluated by quantitative PCR, western blot, flow cytometry, and immunohistochemistry. Furthermore, we explored its regulatory mechanisms using a combination of molecular biology techniques, including luciferase reporter assay, GST/RNA pull-down, chromatin immunoprecipitation (ChIP)/RIP experiments, and in vivo functional assays. We demonstrated that ZFP36L1, driven by an SE, enhances IFN-γ-induced PD-L1 expression, with SPI1 identified as the specific transcription factor binding to ZFP36L1-SE. Mechanistically, ZFP36L1 binds to the adenylate uridylate-rich element in the 3ʹ untranslated region (3ʹUTR) of HDAC3 mRNA, exacerbating its mRNA decay, and thereby facilitating PD-L1 abnormal transcriptional activation. Collectively, our findings provide mechanistic insights into the role of the SPI1-ZFP36L1-HDAC3-PD-L1 signaling axis in orchestrating immune escape mechanisms in GC, thereby offering valuable insights into the potential targets for immune checkpoint therapy in GC management.

Background: Colorectal laterally spreading tumors (LSTs) are clinically important premalignant lesions with distinctive endoscopic morphology and malignant potential. Although microbiome and metabolome alterations have been reported in colorectal cancer and conventional adenomas, the microbial and metabolic features associated with LSTs remain insufficiently characterized. Objective: We investigated whether LSTs are associated with a coordinated carcinogenic eco-metabolic shift (CES) involving stool microbial, metagenomic functional, and circulating metabolic alterations, hereafter referred to a CES, a finding consistent with its high-risk premalignant biology. Methods: Building on our LST multi-omics cohort, we focused on stool metagenomic, serum metabolomic, and paired stool–serum datasets from 35 LST patients and 35 healthy controls. LST-associated microbial taxa, serum metabolites, and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional features were organized into CES modules according to their biological direction and functional themes. Cross-layer Spearman’s analyses, functional pathway analyses, and sign-aligned CES scores were used to assess coordination across microbial, functional, and metabolic layers. Publicly available MetaGenoPolis stool metagenomic data were used as a reference cohort for comparisons across healthy controls, adenoma, and colorectal cancer (CRC) disease sequences. Results: LST patients showed a CES characterized by the depletion of protective anaerobe-associated taxa; enrichment of facultative/pathobiont-associated taxa; remodeling of dicarboxylate/TCA axis metabolism; alterations in amino acid and choline/glycerophospholipid metabolism; and enrichment of microbial functions related to carbohydrate uptake, central carbon metabolism, transport, and biofilm-associated adaptation. In paired stool–serum samples, four cross-layer associations were retained, including an exploratory inverse Roseburia –succinate relationship. In the MetaGenoPolis cohort, the matched microbial component of the CES showed a CRC-oriented pattern: CRC patients had higher microbial CES scores than healthy controls and adenoma patients, whereas the microbial CES scores of healthy controls and adenoma patients were not significantly different. Sign-aligned CES scores were higher in LST patients than in healthy controls across stool, serum, and paired multi-omics analyses; the paired integrated CES score showed a rank-biserial effect size of 0.952. A compact five-anchor CES representation, based on Roseburia depletion, succinate elevation, phosphotransferase system (PTS) elevation, 3-hydroxybutyric acid depletion, and Escherichia enrichment, preserved the main signal. Conclusion: LSTs are associated with a coordinated CES involving stool microbial, microbial functional, and serum metabolic alterations. These findings support the CES as a testable framework for understanding high-risk premalignant colorectal biology and warrant validation in larger cohorts with adenoma and serrated lesion comparators.

Background: Gastric cancer is a heterogeneous disease shaped by the co-evolution of malignant epithelial programs, stromal remodeling, and immune contexture. Transfer RNA (tRNA) regulation sits at a strategic junction in this biology: it governs translational capacity and selectivity while generating tRNA-derived fragments (tRFs) and tRNA halves (tiRNAs)—a family of regulatory small RNAs detectable in both tissue and blood. Objective: We asked whether the coordinated machinery responsible for tRNA transcription, maturation, modification, charging, and cleavage defines biologically meaningful gastric cancer ecosystem states, and whether a corresponding circulating small-RNA phenotype can be detected across independent cohorts of chronic atrophic gastritis (CAG), early gastric cancer (EGC), and gastric cancer (GC). Methods: We integrated transcriptomic, genomic, proteomic, and tissue small-RNA data across complementary gastric cancer series and localized the program in single-cell expression maps. The clinical arm comprised independent serum samples from CAG, EGC, and GC participants. Results: A 70-gene tRNA-regulatory program resolved three ecosystem states (TRES-1, TRES-2, and TRES-3). TRES-3 exhibited high tRNA-regulatory activity coupled with proliferative and DNA-repair protein expression, whereas TRES-1 was enriched for receptor-signaling and cell-cycle-restraint proteins. These states also differed in copy-number alterations and non-synonymous variant burden at the program level. Direct tissue small-RNA profiling revealed a marked expansion of tRF output and repertoire breadth in TRES-2 and TRES-3, with state-specific tRF classes, parent-tRNA modules, and exact sequences. A shared set of 446 exact tRF sequences connected the tissue and serum catalogues. In an independent gastric cancer series, the three-state architecture aligned with ACRG molecular subtypes, RNA cargo selection, extracellular vesicle release, and stress-response programs. Single-cell mapping placed tRNA-regulatory activity across epithelial, stromal, and immune compartments. In our serum cohort, the 14-30-nt fraction declined from 47.4% in CAG to 37.8% in EGC and 33.6% in GC, while the 31-40-nt fraction rose from 52.6% to 62.2% and 66.4% (absolute Spearman rho = 0.791; BH-adjusted P = 0.0112; exact-permutation P = 0.0214). Conclusion: tRNA regulation defines gastric cancer ecosystem states with distinct genomic, proteomic, and tissue small-RNA correlates. In our serum cohort, the reciprocal shift in circulating tRF/tiRNA length composition—a decline in the 14-30-nt fraction and a rise in the 31-40-nt fraction—parallels the transition from CAG to EGC to GC. These findings establish a testable molecular framework for paired tissue-serum validation and position circulating tRF/tiRNA architecture as a candidate readout of gastric cancer ecosystem biology.