Colorectal cancers (CRC) with KRAS mutations (KRAS^mut) are frequently included in consensus molecular subtype 3 (CMS3) with profound metabolic deregulation. We explored the transcriptomic impact of KRAS^mut, focusing on the tumor microenvironment (TME) and pathways beyond metabolic deregulation. The status of KRAS^mut in patients with CRC was investigated and overall survival (OS) was compared with wild-type KRAS (KRAS^wt). Next, we identified CMS, and further investigated differentially expressed genes (DEG) of KRAS^mut and distinctive pathways. Lastly, we used spatially resolved gene expression profiling to define the effect of KRAS^mut in the TME regions of CMS3-classified CRC tissues. CRC patients with KRAS^mut were mainly enriched in CMS3. Their specific enrichments of immune gene signatures in immunosuppressive TME were associated with worse OS. Activation of TGFβ signaling by KRAS^mut was related to reduced pro-inflammatory and cytokine gene signatures, leading to suppression of immune infiltration. Digital spatial profiling in TME regions of KRAS^mut CMS3-classified tissues suggested up-regulated genes, CD40, CTLA4, ARG1, STAT3, IDO, and CD274, that could be characteristic of immune suppression in TME. This study may help to depict the complex transcriptomic profile of KRAS^mut in immunosuppressive TME. Future studies and clinical trials in CRC patients with KRAS^mut should consider these transcriptional landscapes.

Stage 4 colon cancer (CC) presents a significant global health challenge due to its poor prognosis and limited treatment options. Tetraspanins, the transmembrane proteins involved in crucial cancer processes, have recently gained attention as diagnostic markers and therapeutic targets. However, their spatial expression and potential roles in stage 4 CC tissues remain unknown. Using the GeoMx digital spatial profiler, we profiled all 33 human tetraspanin genes in 48 areas within stage 4 CC tissues, segmented into immune, fibroblast, and tumor compartments. Our results unveiled diverse gene expression patterns across different primary tumor sub-regions. CD53 exhibited distinct overexpression in the immune compartment, hinting at a potential role in immune modulation. TSPAN9 was specifically overexpressed in the fibroblast compartment, suggesting involvement in tumor invasion and metastasis. CD9, CD151, TSPAN1, TSPAN3, TSPAN8, and TSPAN13 displayed specific overexpression in the tumor compartment, indicating potential roles in tumor growth. Furthermore, our differential analysis revealed significant spatial changes in tetraspanin expression between patient-matched stage 4 primary CC and metastatic liver tissues. These findings provide spatially resolved insights into the expression and potential roles of tetraspanins in stage 4 CC progression, proposing their utility as diagnostic markers and therapeutic targets. Understanding this landscape is beneficial for tailoring therapeutic strategies to specific sub-tumor regions in the context of stage 4 CC and liver metastasis.

Spatial transcriptomic technology enables resolving a tumor microenvironment heterogeneity of colorectal cancer (CRC) tissue samples. However, there is limited evidence regarding the relative strengths and weaknesses of different CRC sample types and preservation methods, including formalin-fixed paraffin-embedded (FFPE), fresh frozen (FF) and snap frozen (SF). Here, we examine gene expression profiles in 36 tissue areas, FFPE, FF and SF samples, derived from a patient with stage IV CRC, using spatial analysis of the whole transcriptome. The tissue samples obtained from surgical resection of the cancer were subjected to a detailed histological evaluation and spatial transcriptomics analysis to compare the quality of the sample between different preservation methods. Spatial transcriptomic analysis demonstrated that FFPE tissue samples offered improved resolution of cellular morphology in the tumor microenvironment, facilitating greater detail of gene expression and cell types. In contrast, gene expression analysis of FF and SF tissues embedded in optimal cutting temperature compound revealed a high level of CRC gene expression. FFPE, FF and SF samples shared a significant overlap among the top 300 genes that were strongly associated with key biological processes in CRC. In summary, the spatial analysis of the whole transcriptome across FFPE, FF and SF CRC tissues revealed intratumoral heterogeneity and highlighted key transcriptomic signatures, suggesting the specific value of different tissue preservation methods in the profiling of CRC.

Esophageal cancer is frequently diagnosed at an advanced stage, limiting opportunities for curative treatment and contributing to poor clinical outcomes. We aimed to identify clinicopathological predictors of advanced-stage presentation and use these findings to inform a registry-informed framework for earlier detection of esophageal adenocarcinoma (AC) in Thailand. A retrospective cohort study was conducted using the Siriraj Cancer Registry. Among 1451 patients diagnosed with esophageal cancer between 2009 and 2024, 591 patients with sufficient clinical and/or pathological information for stage assignment were included. Patients were classified as having early-stage (Stage I–II) or advanced-stage (Stage III–IV) disease. Univariable and multivariable logistic regression analyses were performed to identify independent predictors of advanced-stage presentation. Among patients with sufficient information for reliable stage assignment, 77.5% presented with advanced-stage disease. AC histology was independently associated with increased odds of advanced-stage presentation compared with squamous cell carcinoma (adjusted odds ratio 4.16, 95% confidence interval 1.21–14.30; p = 0.024). A trend toward earlier-stage diagnosis was observed during 2017–2024 compared with 2009–2016 (adjusted odds ratio 0.66, 95% confidence interval 0.43–1.00; p = 0.052). These findings provide hypothesis-generating evidence to inform a risk-based approach to earlier evaluation of individuals at increased risk of esophageal AC in Thailand, which requires prospective validation.