Clinical analysis combined with TCGA public data set
We downloaded the OSCC genome data from the GSE41613 in the GEO dataset. We identified 5266 differential gene using the R package Depseq2 (Fig 1)
The GSEA analysis showed the gene set was enriched in some biological pathway (Fig 2). For example, the gene set was significantly enriched in mononuclear cell differentiation. Monocytes are an important part of the immune system and play a complex role in the tumor microenvironment. In the tumor microenvironment, monocytes can differentiate into different types of cells such as tumor-associated macrophages ( TAMs ) and tumor-associated dendritic cells ( TADCs ). These cells affect the tumor microenvironment through a variety of mechanisms, including inducing immune tolerance, promoting angiogenesis, and helping tumor cell metastasis.
Subsequently, we focus on the p53 pathway in this gene set. The p53 signaling pathway is a very important regulatory network in cells. It plays a key role in cell response to DNA damage, cell cycle control, apoptosis, senescence, and cell metabolism. Patients with high level of p53 pathway show better survival comparing to those with low level of p53 pathway(Fig 3-4).
Additionally, We obtained key genes related to hyaluronic acid synthesis from the literature, specifically HAS2-AS1 (hyaluronan synthase), and conducted a differential expression analysis at the pan-cancer level. The results indicated that this gene is highly expressed in colorectal cancer, head and neck cancer, among others. Furthermore, high expression of HAS2-AS1 also predicts poor prognosis in hepatocellular carcinoma, indirectly supporting the role of hyaluronic acid in cancer treatment resistance and progression (Fig. 5-6).
linear regression model
We used linear regression to fit the cell viability of chassis bacteria and engineered bacteria measured at OD = 450 every two hours from 0 to 12 hours. By comparing Fig 1 and Fig 2, it can be found that there is no significant difference in activity between the chassis bacteria and the engineered bacteria after 12 hours of cultivation
The similarity in cell viability between the chassis bacteria and the engineered bacteria observed every two hours from 0 to 12 hours suggests that both types of bacteria maintain comparable cell viability under the same culture conditions. This indicates that the genetic modifications in the engineered bacteria do not significantly affect their basic survival capabilities. Further research could explore the impact of different culture conditions on cell viability to confirm the stability and adaptability of the engineered bacteria. If these bacteria consistently exhibit high cell viability, they could be valuable in industrial production and environmental remediation. Additionally, understanding the specific effects of genetic modifications on cell viability can help optimize the design of engineered bacteria for practical applications.