Secondary analysis of existing microarray data reveals potential gene drivers of cutaneous squamous cell carcinoma

Abstract

Cutaneous squamous‐cell carcinoma (cSCC) is the second most common skin cancer, with an increasing incidence in recent years. To define the molecular basis that drive cSCC development and progression, this study aimed at identifying potential novel molecular targets for the diagnosis and therapy of patients with cSCC. Two data sets with the accession number GSE45164 and GSE66359 were downloaded from Gene Expression Omnibus (GEO) database. After the identification of differentially expressed genes (DEGs) from these two data sets, respectively, between cSCC samples and controls, a combination of DEGs from these two data sets were subjected to the following analyses, including functional annotation, protein–protein interaction (PPI) network and module construction, transcription factor (TF)‐target regulation prediction, and drug–gene interaction predictive analysis. A total of 204 upregulated genes and 213 downregulated genes were found in two data sets which were used for the follow‐up analysis. Upregulated and downregulated genes were mainly involved in the functions such as cell division, mitotic nuclear division, cell cycle, and p53 signaling pathway. Interferon induced protein family members and proteasome subunit members were involved in the TF‐target regulatory network, such as PSMB8, CXCL10, and IFIT3. Eight upregulated genes ( TOP2A, CXCL8, RRM2, PSMB8, PSMB9, PBK, CXCL10, and ISG15) that were hub genes in the PPI network and significant modules were identified in the predicted drug–gene interaction. In conclusion, TOP2A, CXCL8, RRM2, PSMB8, PSMB9, PBK, CXCL10, and ISG15 may be potential targets for the diagnosis and therapy of patients with cSCC.

OmicsARules: a R package for integration of multi-omics datasets via association rules mining

“…PSMB9 locates in the class II region of the MHC (major histocompatibility complex) and encodes the proteasome subunit. In previous studies, there is no evidence of positive relationship between PSMB9 and ESCA, but PSMB9 has been suggested to be potential targets for the diagnosis and therapy for several other cancers, such as cutaneous squamous cell carcinoma and cervical cancer [18, 19]. As shown in Fig.…”

3-Deoxysappanchalcone Inhibits Skin Cancer Proliferation by Regulating T-Lymphokine-Activated Killer Cell-Originated Protein Kinase in vitro and in vivo

“…TOPK and p-TOPK were highly expressed in skin cancer cell lines (Figure 1A) and in metastatic melanoma tumors compared with primary melanoma tumors according to GTEx and TCGA patient samples (Figure 1B). Independent cohort data presented within the Gene Expression Omnibus (GEO) database provide further evidence of heightened TOPK expression in cancer (Liu et al, 2019). In esophageal squamous cell carcinoma, TOPK was positively correlated with tumor metastasis (Seol et al, 2017;Zykova et al, 2017;Ma et al, 2019) by activating Src/GSK3β/STAT3 signaling pathway (Jiang et al, 2019).…”

Transcriptome analysis of the procession from chronic pancreatitis to pancreatic cancer and metastatic pancreatic cancer

“…PSMB8 and PSMB9 can be the alternative subunits to help the constructive proteasome transform to the immune proteasome induced by interferon γ 42 . PSMB8, PSMB9 were identified as potential targets for the diagnosis and therapy of cutaneous squamous-cell carcinoma and melanoma 42,43 .…”