Construction of an Amino Acid Metabolism-Related Prognostic Model for Colorectal Adenocarcinoma Patients
Authors: Yang# Feng , Zhu# Wenjun , Zhang Yiling , Peng Xiaohong , Chen Xin , Liu Yuanhui , Li Xiaoyu , Luo Na , Fu Min , Chen Ziqi , Zhang Qiang , Peng Bi , Zhang Yuanyuan , Li Qianxia , Hu Guangyuan 
Published: December 2023

Objective
The primary objective of this study was to develop an advanced prognostic model centered on amino acid metabolism-related genes(AAMG), specifically in the context of colon adenocarcinoma (COAD). Another aim was to delve into the prognostic significance of these genes and uncover the intricate mechanisms governing COAD.
Methods
Leveraging comprehensive transcriptome gene expression data alongside detailed clinical records sourced from The Cancer Genome Atlas (TCGA) database, it was attempted to meticulously develop a prognostic model rooted in the realm of amino acid metabolism. Rigorous validation of this model was executed utilizing the Gene Expression Omnibus (GEO) dataset. The comprehensive analysis encompassed a multifaceted approach, involving Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment assessments, meticulous exploration of immunotherapy effectiveness, intricate single-gene bioinformatics examinations, and cellular assays. This broad spectrum of analytical methods was employed to shed light on both the model's prognostic capacity and the intricate mechanisms underpinning its predictive capability.
Results
The derived prognostic risk model, a meticulously curated composite of five amino acid metabolism-related genes (PTH1R, HEYL, GABRD, NAT1, CALB2), exhibited remarkable prowess in prognostic prediction, a commendable achievement subsequently confirmed in the GEO cohort. The analytical exploration via KEGG pathway enrichment revealed a fascinating enrichment of both tumor-related and immune-related pathways within the high-risk group, prominently featuring key pathways, such as MAPK and T cell receptor signaling pathways. This exhaustive analysis unveiled the intricate nexus among amino acid metabolism and immune-related functions. Furthermore, the high-risk cohort displayed regrettably limited benefits in the realm of immunotherapy. The rigorous suite of cellular experiments furnished conclusive evidence supporting CALB2's pivotal role in driving COAD cells’ proliferation, migration, and the epithelial-mesenchymal transition (EMT). Lastly, the results hinted at the likelihood of the P53 signaling pathway as a probable mediator of CALB2's profound impact on the progression of colon cancer.
Conclusion
The meticulously developed prognostic model, specializing in amino acid metabolism within the realm of COAD, stands as a robust predictor of COAD prognosis. It was successfully demonstrated that amino acid metabolism-related genes, especially within high-risk group, wield a significant influence over COAD's immune function, with evident consequences of diminished immunotherapy efficacy. Furthermore, the analysis spotlighted the intriguing enrichment of crucial tumor and immune-related pathways in high-risk group. On a granular level, CALB2, a foundational gene within the model, emerged as a key driver in facilitating COAD cell proliferation, migration, and the complex process of EMT. Moreover, findings suggested a tantalizing link between CALB2's mechanistic actions and P53 signaling pathway in the context of colon cancer progression.