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Tumor Discovery BAK1 as a novel prognostic biomarker

was performed on them. To assess the relationship between Table 1. 33 cancer types used in this study
high and low BAK1 expression groups and immune cell
infiltration content, the CIBERSORT algorithm was Abbreviation Full name
used, and the filter condition for immune cell infiltration ACC Adrenocortical carcinoma
findings was set to pFilter = 0.05. Immune checkpoint BLCA Bladder urothelial carcinoma
correlation analysis was then performed to investigate the BRCA Breast invasive carcinoma
relationship between immune checkpoint genes and BAK1, CESC Cervical squamous cell carcinoma and endocervical
with the filter condition of correlation test P-value set to adenocarcinoma
pFilter = 0.001. The immunoscores of liver cancer patients CHOL Cholangiocarcinoma
were gathered from http://tcia.at/, and immunotherapy COAD Colon adenocarcinoma
analysis was performed in R studio program using “limma” DLBC Lymphoid neoplasm diffuse large B-cell
and “ggpubr” packages. The immunohistochemical pictures ESCA Esophageal carcinoma
of BAK1 protein in various cancer and normal tissues
were obtained from http://www.proteinatlas.org/(Human GBM Glioblastoma multiforme
Protein Atlas [HPA] database). We estimated the half HNSC Head and neck squamous cell carcinoma
maximal inhibitory concentrations (IC50s) of compounds KICH Kidney chromophobe
collected from the Genomics of Drug Sensitivity in Cancer KIRC Kidney renal clear cell carcinoma
(GDSC) website in the TCGA project of the LIHC dataset KIRP Kidney renal papillary cell carcinoma
to identify possible medications for clinical application in LAML Acute myeloid leukemia
LIHC therapy. The IC50 of the chemical, acquired from LGG Low grade glioma
the GDSC website, in LIHC patients was predicted using R LIHC Liver hepatocellular carcinoma
studio’s “pRRophetic” package, with the filter condition for
P-value set to pFilter = 0.001. LUAD Lung adenocarcinoma
LUSC Lung squamous cell carcinoma
2.5. Building a nomogram scoring system MESO Mesothelioma
The clinical variables and risk scores were integrated to OV Ovarian serous cystadenocarcinoma
construct a predictive nomogram in R studio using “rms,” PAAD Pancreatic adenocarcinoma
“survival,” and “regplot” packages. Each clinical feature and PCPG Pheochromocytoma and paraganglioma
risk rating in the nomogram was assigned a score; the total PRAD Prostate adenocarcinoma
score was calculated by summing the scores for all clinical PEAD Rectum adenocarcinoma
features and risk ratings in each sample. The accuracy of
anticipated 1-, 3-, and 5-year survival events was described SARC Sarcoma
using calibration plots. SKCM Skin cutaneous melanoma
STAD Stomach adenocarcinoma
2.6. Statistical analysis TGCT Testicular germ cell tumors
R version 4 was used for all statistical studies. Statistical THCA Thyroid carcinoma
significance was defined as P < 0.05. THYM Thymoma
3. Results UCEC Uterine corpus endometrial carcinoma
UCS Uterine carcinosarcoma
3.1. Expression and survival analysis of BAK1 UVM Uveal melanoma
Table 1 lists the 33 cancers studied in this work. The HCC
cohort (GSE76427) used has 115 patients in total. We in pan-cancer. Figure 1B shows that the expression of BAK1
analyzed the PRGs in 115 HCC patients using R studio was significantly upregulated in 11 cancer types (bladder
packages “survival” and “limma.” P < 0.05 was deemed urothelial carcinoma [BLCA], breast invasive carcinoma
statistically significant for prognosis. Figure 1A depicts [BRCA], cholangiocarcinoma [CHOL], esophageal
the gene coexpression relationship, revealing that GSDME, carcinoma [ESCA], glioblastoma multiforme [GBM],
CHMP4B, CHMP3, BAK1, and NOD2 are high-risk genes head-and-neck squamous cell carcinoma [HNSC], liver
that are strongly associated with prognosis. In view of the hepatocellular carcinoma [LIHC], lung adenocarcinoma
limited number of research on the prognosis and immunity [LUAD], lung squamous cell carcinoma [LUSC], stomach
of BAK1 expression in liver cancer, we chose BAK1 and adenocarcinoma [STAD], and uterine corpus endometrial
used TIMER 2.0 database to investigate BAK1 expression carcinoma [UCEC]; all P < 0.001), whereas it was

Volume 1 Issue 2 (2022) 3 https://doi.org/10.36922/td.v1i2.221