Colorectal cancer subtyping and immune landscape analysis based on natural killer cell-related genes.

BACKGROUND AND STUDY AIMS: The prognosis of colorectal cancer (CRC) is related to natural killer (NK) cells, but the molecular subtype features of CRC based on NK cells are still unknown. This study aimed to identify NK cell-related molecular subtypes of CRC and analyze the survival status and immune landscape of patients with different subtypes. PATIENTS/MATERIAL AND METHODS: mRNA expression data, single nucleotide variant (SNV) data, and clinical information of CRC patients were obtained from The Cancer Genome Atlas. Differentially expressed genes (DEGs) were obtained through differential analysis, and the intersection was taken with NK cell-associated genes to obtain 103 NK cell-associated CRC DEGs (NCDEGs). Based on NCDEGs, CRC samples were divided into three clusters through unsupervised clustering analysis. Survival analysis, immune analysis, Gene Set Enrichment Analysis (GSEA), and tumor mutation burden (TMB) analysis were performed. Finally, NCDEG-related small-molecule drugs were screened using the CMap database. RESULTS: Survival analysis revealed that cluster2 had a lower survival rate than cluster1 and cluster3 (p < 0.05). Immune infiltration analysis found that the immune infiltration levels and immune checkpoint expression levels of cluster1_3 were substantially higher than those of cluster2, and the tumor purity was the opposite (p < 0.05). GSEA presented that cluster1_3 was significantly enriched in the chemokine signaling pathway, ECM receptor interaction, and antigen processing and presentation pathways (p < 0.05). The TMB of cluster1_3 was significantly higher than that of cluster2 (p < 0.05). Genes with the highest mutation rate in CRC were APC, TP53, TTN, and KRAS. Drug prediction results showed that small-molecule drugs that reverse the upregulation of NCDEGs, deoxycholic acid, dipivefrine, phenformin, and other drugs may improve the prognosis of CRC. CONCLUSION: NK cell-associated CRC subtypes can be used to evaluate the tumor characteristics of CRC patients and provide an important reference for CRC patients.

Effects of dietary combination of corn and rice as whole crop silage and grain sources on carbohydrate digestion and nitrogen use in steers.

Four Holstein steers were used to evaluate the combination effects of whole crop corn (Cs) or rice (Rs) silage with steam-flaked corn (Cg) or rice (Rg) grain (four dietary treatments) on ruminal carbohydrate digestion, duodenal nitrogen (N) flow and plasma essential amino acid (EAA) concentration. The ruminal digestibility of starch and nonfiber carbohydrate (NFC) for Rs and Rg diets compared with Cs and Cg diets was greater, but that of neutral detergent fiber (aNDFom) was less. Because the ruminal disappearance of NFC plus aNDFom was similar across four dietary treatments, microbial N flow was not affected by the diets. There was an interaction of methionine (Met) flow by silage and grain sources: greatest for CsRg and least for RsRg diet, and blood plasma concentration of Met after feeding was lower for Rg than Cg diets. Postprandial reduction degree of plasma EAA varied with the diets and individual EAA. The Cs diets compared with the Rs diets tended to be greater in N retention because of greater digestible organic matter (OM) intake. These results suggest that silage source combined with corn or rice grain affects N use in steers through the digestible OM intake, and the kinds of limiting AA may differ among the combination of silage and grain sources.