SPP1 as a Potential Stage-Specific Marker of Colorectal Cancer

<b>Background:</b> Colorectal cancer is the third most diagnosed cancer and a leading cause of cancer-related deaths worldwide. Early detection significantly improves patient outcomes, yet many cases are identified only at late stages. The high molecular and genetic heterogeneity of colorectal cancer presents major challenges in accurate diagnosis, prognosis, and therapeutic stratification. Recent advances in gene expression profiling offer new opportunities to discover genes that play a role in colorectal cancer carcinogenesis and may contribute to early diagnosis, prognosis prediction, and the identification of novel therapeutic targets. <b>Methods:</b> This study involved 142 samples: 84 primary tumor samples, 27 liver metastases, and 31 adjacent non-tumor tissues serving as controls. RNA sequencing was performed on a subset of tissues (12 liver metastases and 3 adjacent non-tumor tissues) using a targeted RNA panel covering 395 cancer-related genes. Data processing and differential gene expression analysis were carried out using the DRAGEN RNA and DRAGEN Differential Expression tools. The expression of six genes involved in hypoxia and epithelial-to-mesenchymal transition (EMT) pathways (<i>SLC16A3</i>, <i>ANXA2</i>, <i>P4HA1</i>, <i>SPP1</i>, <i>KRT19</i>, and <i>LGALS3</i>) identified as significantly differentially expressed was validated across the whole cohort via quantitative real-time PCR. The relative expression levels were determined using the ΔΔct method and log2FC, and compared between different groups based on the sample type; clinical parameters; and mutational status of the genes <i>KRAS</i>, <i>PIK3CA</i>, <i>APC</i>, <i>SMAD4</i>, and <i>TP53</i>. <b>Results:</b> Our results suggest that the expression of all the validated genes is significantly altered in metastases compared to non-tumor control samples (<i>p</i> < 0.05). The most pronounced change occurred for the genes <i>P4HA1</i> and <i>SPP1</i>, whose expression was significantly increased in metastases compared to non-tumor and primary tumor samples, as well as between clinical stages of CRC (<i>p</i> < 0.001). Furthermore, all genes, except for <i>LGALS3</i>, exhibited significantly altered expression between non-tumor samples and samples in stage I of the disease, suggesting that they play a role in the early stages of carcinogenesis (<i>p</i> < 0.05). Additionally, the results suggest the mutational status of the <i>KRAS</i> gene did not significantly affect the expression of any of the validated genes, indicating that these genes are not involved in the carcinogenesis of <i>KRAS</i>-mutated CRC. <b>Conclusions:</b> Based on our results, the genes <i>P4HA1</i> and <i>SPP1</i> appear to play a role in the progression and metastasis of colorectal cancer and are candidate genes for further investigation as potential biomarkers in CRC.