The ubiquitin (Ub)–proteasome system (UPS) is identified to regulate the cellular protein by ubiquitination modification. Ub is an important component in the UPS. It consists of a 76-amino-acid protein and is usually highly conserved in eukaryotes (Zheng and Shabek, 2017). Among the UPS, three significant enzymes function as enzyme cascade to transmit the Ub to the substrate. The three vital enzymes are identified as the Ub-activating enzyme (E1), the Ub-conjugating enzyme (E2), and the Ub-protein ligase (E3) (Pickart, 2001). The UPS process can be summarized as follows: at first, E1 activates Ub and transmits it to E2 by an adenosine triphosphate-dependent way. Then, E3 mediates the last step by interacting with E2 that is carried with the Ub and recognizing a specific substrate. E3 are usually identified as the most crucial component among the three-enzyme cascade because the interaction between E3 and the substrate is highly specific, and the ubiquitination of the substrate mainly depends on the E3.

The UPS, especially E3, is also proved to contribute a lot in the process of cancers. Dysregulated E3 were widely reported to occur in diverse cancers. For example, HERC3 was reported to mediate the ubiquitination and the degradation of SMAD7 in glioblastoma (Li et al., 2019). RNF6 was indicated to induce the progression of colorectal cancer (CRC) through mediating ubiquitination of TLE3 (Liu et al., 2018). Moreover, E3 can regulate the downstream substrate including many oncogenes and tumor suppressors. P53 was reported to be degraded by the E3 ligase RING1 (Shen et al., 2018). Cancer is featured as an uncontrolled cell proliferation that is also regulated by many cell cycle-related regulators (Williams and Stoeber, 2012; Otto and Sicinski, 2017). These regulators can also be ubiquitination modified and degraded by E3. Thus, the UPS especially E3 may be the key regulators in the proliferation of cancer cells and may also become the therapeutic targets to address the uncontrolled proliferation of cells (Nakayama and Nakayama, 2006).

Colorectal cancer was ranked the top in the aspect of mortality and morbidity among diverse cancer types (Siegel et al., 2020). Given the crucial role of E3 in cancers, it is urgent and necessary to research the UPS in CRC. However, the integrated analysis of UPS or the interaction between UPS and cell cycle-related regulators in CRC is still blank. In this present study, we integrated and analyzed the UPS, especially the E3 ligase in CRC; moreover, we constructed a prognostic signature based on UPS-associated regulators and further depicted the potential interactions between UPS and specific cell cycle-related genes in CRC. We provide a novel insight into the UPS and the latent interaction between cell cycle-associated genes and the UPS in the field of CRC.

Colorectal cancer is identified as one digestive system cancer type that has high morbidity and mortality (Siegel et al., 2020). Although the treatment of CRC progresses a lot during recent years, the potential regulatory mechanism of CRC is not clearly elucidated yet. The cell cycle is a crucial component in biological development. The cell cycle can be summarized into four phases: in the S phase, DNA replication is frequent; in the M phase, a single cell can divide into two daughter cells. There are also two gap phases between S and M, which can be characterized as G1 and G2. It is widely recognized that G1 is a phase in which a cell can be sensitive to stimulation of growth. G2 is the phase after S and specific for cell entering mitosis. Moreover, cancer is characterized as uncontrolled cell proliferation (Kastan and Bartek, 2004; Massagué, 2004). Uncontrolled cancer cell proliferation is also commonly observed in CRC. Zhang Z. et al. (2018) found that miR-1258 could regulate the CRC cell proliferation via regulating the cell cycle. Moreover, there was also a prognostic signature based on cell cycle specific in colon cancer (Zhang et al., 2020a). These studies implied that the cell cycle also has a significant function in the process of CRC. However, the detailed mechanism of the regulation of the cell cycle in CRC is not clear until now, and according to the vital role of the cell cycle in CRC, it is urgent to demonstrate the potential regulatory mechanism of the cell cycle in CRC.

The Ub–UPS is proved to be involved in the regulation of the process of many cancers. It can be summarized into many regulatory mechanisms. Firstly, the proteins that are involved in the UPS can be oncogenes or tumor suppressors. For instance, HERC3 was reported to be a tumor suppressor via regulating SMAD7 in glioblastoma (Li et al., 2019). RNF6 was reported to induce the progression of CRC through mediating ubiquitination of TLE3 (Liu et al., 2018). Secondly, many oncogenes or tumor suppressors can be regulated by E3, and P53 was indicated to be degraded by the E3 ligase RING1 (Shen et al., 2018). Given the important role of UPS in cancer, it is also urgent to comprehensively analyze the regulatory mechanism of UPS in CRC.

Given the important role of cell cycle and UPS in CRC, we comprehensively analyzed differentially expressed UPS-associated genes in CRC through three differential analyses. Moreover, we discovered that the cell cycle is one of the most important biological processes in the progression of CRC. We also used WGCNA to identify some cell cycle-associated genes that are specific in CRC. Furthermore, we used the differentially expressed UPS-associated genes and cell cycle-associated genes to construct the PPI network. Afterward, we used UPS-associated genes to construct the OS prognostic signature in CRC with relative considerable AUC.

Among the UPS, E3 ligase is undoubtedly the most important component because the interaction between E3 and the substrate is highly specific, and the ubiquitination of the substrate mainly depends on the E3. In this research, we found a total of 60 differentially expressed UPS-associated genes, among them, 24 genes were identified as E3 ligases. Among these 24 differentially expressed E3 ligases, many were proved to have relevant regulatory roles in the process of CRC. For example, AURKA was upregulated by ARID3 in CRC (Tang et al., 2020). CBX4 was reported to involve in the process of long non-coding RNA RAMS11 regulating the metastasis of CRC (Silva-Fisher et al., 2020). ASB8 was reported to be controlled by miR-452 in CRC cells (Mo and Chae, 2021). FBXO45 could be regulated by RP11 through the Siah1-Fbxo45/Zeb1 axis (Wu et al., 2019). TRIM27 was also reported to be an oncogene in CRC (Zhang Y. et al., 2018). Previous researches also confirmed that our analysis was reliable. Combing the results of survival analysis and the results of differential analysis, we found that HERC3 is an E3 ligase that owns the same trend of survival analysis and differential analysis, indicating the potential research value of HERC3 in CRC.

Through three differential analyses, we identified 3,323 upregulated genes and 3,635 downregulated genes in CRC. GSEA indicated that the cell cycle is an important component in CRC. Via WGCNA, we also identified cell cycle-associated genes specific in CRC. Moreover, the PPI network based on UPS-associated genes and cell cycle-associated genes provided many latent research orientations for the mechanism of uncontrolled cell proliferation in CRC.

Finally, we constructed an OS-associated signature based on the 60 differentially expressed UPS-associated genes. However, the signature still lacks enough validation, and this limitation is also a novel research direction for us. Compared with other signatures in CRC, our signature can predict the prognosis in colon cancer and rectal cancer with a considerate AUC; other signatures mainly focus on one cancer type only (colon cancer or rectal cancer) (Zhang et al., 2020a,b,c,d, 2021). Among these genes involved in the signature, some of them were previously reported to perform latent jobs in the progression of cancer. ZBTB18 was reported to be upregulated by circTP63 and further promote hepatocellular carcinoma progression (Wang and Che, 2021). RNF113A was revealed to promote the proliferation, migration, and invasion in esophageal squamous cell carcinoma (Wang et al., 2018). SKP1 was demonstrated to be involved in an axis to promote bladder cancer proliferation and is controlled by circGLIS3 (Wu et al., 2021).

In conclusion, we used bioinformatic analysis to reveal the potential regulatory mechanism between UPS-associated genes and potential cell cycle-related substrates specific in CRC. Besides, we constructed a prognostic signature based on the UPS-associated genes. Our research provides a novel insight of the UPS and cell cycle system in CRC.

The raw microarray data and relevant clinical information of CRC patients that were based on TCGA (The Cancer Genome Atlas) database, and raw microarray data of normal colon samples that were based on GTEx (The Genotype-Tissue Expression) database were downloaded from XENA (http://xena.ucsc.edu/).

The studies involving human participants were reviewed and approved by the data was obtained from TCGA and GTEx database. The patients/participants provided their written informed consent to participate in this study. Written informed consent was obtained from the individual(s) for the publication of any potentially identifiable images or data included in this article.

ZZ, JX, and LR designed and conducted the study. ZZ and QF wrote the manuscript. JC and WT helped to improve and design the study. All authors contributed to the article and approved the submitted version.

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.