Bioinformatics analysis of the prognostic value of Tripartite Motif 28 in breast cancer

TRIM28 in cancer and cancer therapy

TRIM28 (tripartite motif protein 28) was initially believed to be a transcription inhibitor that plays an important role in DNA damage repair (DDR) and in maintaining cancer cellular stemness. As research has continued to deepen, several studies have found that TRIM28 not only has ubiquitin E3 ligase activity to promote degradation of substrates, but also can promote SUMOylation of substrates. Although TRIM28 is highly expressed in various cancer tissues and has oncogenic effects, there are still a few studies indicating that TRIM28 has certain anticancer effects. Additionally, TRIM28 is subject to complex upstream regulation. In this review, we have elaborated on the structure and regulation of TRIM28. At the same time, highlighting the functional role of TRIM28 in tumor development and emphasizing its impact on cancer treatment provides a new direction for future clinical antitumor treatment.

Emerging roles of tripartite motif family proteins (TRIMs) in breast cancer

Breast cancer (BC) is the most common malignant tumor worldwide. Despite enormous progress made in the past decades, the underlying mechanisms of BC remain further illustrated. Recently, TRIM family proteins proved to be engaged in BC progression through regulating various aspects. Here we reviewed the structures and basic functions of TRIM family members and first classified them into three groups according to canonical polyubiquitination forms that they could mediate: K48- only, K63- only, and both K48- and K63-linked ubiquitination. Afterwards, we focused on the specific biological functions and mechanisms of TRIMs in BCs, including tumorigenesis and invasiveness, drug sensitivity, tumor immune microenvironment (TIME), cell cycle, and metabolic reprogramming. We also explored the potential of TRIMs as novel biomarkers for predicting prognosis and future therapeutic targets in BC.

A systematic pan-cancer analysis identifies TRIM28 as an immunological and prognostic predictor and involved in immunotherapy resistance

Tripartite motif-containing protein 28 (TRIM28), as a transcriptional cofactor, has pleiotropic biological effects, such as silencing genes, promoting cellular proliferation and differentiation, and facilitating DNA repair. It is reported that TRIM28 is also correlated with immune infiltration in liver cancer that highlights an unnoticed function of TRIM28 in immune system. However, the prognostic and immunotherapeutic role of TRIM28 in human cancer has not been elucidated. In this study, we conducted a systematic pan-cancer analysis and partial experimental validation of TRIM28 as an immunological and prognostic predictor and its involvement in immunotherapy resistance. We found that TRIM28 expression was higher in various tumor tissues than in normal tissues. Higher TRIM28 expression was associated with poorer prognosis in multiple cancers. The expression of TRIM28 was positively correlated with the presence of T cells, macrophages and neutrophils, and TRIM28 also promoted the infiltration of a series of immune cell. Moreover, TRIM28 affected a wide range of cancer-related scores, and the abnormal expression of TRIM28 was also involved in tumor mutational burden, drug sensitivity, and microsatellite instability in cancer. The results suggest that TRIM28 is a potentially valuable immune response indicator and a molecular biomarker for predicting the prognosis of cancer patients.

The prognostic and biological importance of chromatin regulation-related genes for lung cancer is examined using bioinformatics and experimentally confirmed

BACKGROUND

The pathogenesis and clinical diagnosis of lung adenocarcinoma (LUAD), a malignant illness with substantial morbidity and mortality, are still being investigated. Genes involved in chromatin regulation are crucial in the biological function of LUAD.

METHODS

The prognostic prediction model for LUAD was developed using multivariables and least absolute shrinkage and selection operator (LASSO) regression. It consisted of 10 chromatin regulators. The LUAD has been divided into two groups, high- and low-risk, using a predictive model. The model was shown to be accurate in predicting survival by the nomogram, receiver operating characteristic (ROC) curves, and principal component analysis (PCA). An analysis of differences in immune-cell infiltration, immunologicalfunction, and clinical traits between low- and high-risk populations was conducted. Protein-protein interaction (PPI) networks and Gene Ontology (GO) pathways of differentially expressed genes (DEGs) in the high versus low risk group were also examined to investigate the association between genes and biological pathways. The biological roles of chromatin regulators (CRs) in LUAD were finally estimated using colony formation and cell movement. The important genes' mRNA expression has been measured using real-time polymerase chain reaction (RT-PCR).

RESULTS AND CONCLUSION

Risk score and stage based on the model could be seen as separate prognostic indicators for patients with LUAD. The main signaling pathway difference across various risk groups was in cell cycle. The immunoinfiltration profile of the tumor microenvironment (TME) and individuals with different risk levels were correlated, suggesting that the interaction of immune cells with the tumor led to the creation of a favorable immunosuppressive microenvironment. These discoveries aid in the creation of individualized therapies for LUAD patients.

TRIM28 promotes luminal cell plasticity in a mouse model of prostate cancer

The Tripartite motif-containing 28 (TRIM28) transcriptional cofactor is significantly upregulated in high-grade and metastatic prostate cancers. To study the role of TRIM28 in prostate cancer progression in vivo, we generated a genetically-engineered mouse model, combining prostate-specific inactivation of Trp53, Pten and Trim28. Trim28 inactivated NPp53T mice developed an inflammatory response and necrosis in prostate lumens. By conducting single-cell RNA sequencing, we found that NPp53T prostates had fewer luminal cells resembling proximal luminal lineage cells, which are cells with progenitor activity enriched in proximal prostates and prostate invagination tips in wild-type mice with analogous populations in human prostates. However, despite increased apoptosis and reduction of cells expressing proximal luminal cell markers, we found that NPp53T mouse prostates evolved and progressed to invasive prostate carcinoma with a shortened overall survival. Altogether, our findings suggest that TRIM28 promotes expression of proximal luminal cell markers in prostate tumor cells and provides insights into TRIM28 function in prostate tumor plasticity.

Analytical Computation of Interleukin17A Activity in Breast Cancer Patients Using Bioinformatics Methods

Interleukin-17A (IL-17A) is a member of the Interleukin-17 family, which belongs to the pro-inflammatory cystine-knot cytokines. Recent studies on the etiology of breast cancer have focused on the role of immunity and inflammation. The pro-inflammatory cytokines IL-17A can medicate cancer-related inflammation. The present study aimed to analyze the mutation in physicochemical properties and structure of the Interleukin-17 A gene in developing breast cancer using bioinformatics methods. A total of 60 blood samples were obtained from Iraqi women aged 25 to 75 with breast cancer. Twenty blood samples were obtained from healthy women in the same age range as a control group. Deletion and missense mutations detected by BLAST in samples with breast cancer. The present study determined the physicochemical properties of IL-17A such as hydrophilic nature, alpha-helical and 3D structure. The results of this study indicated that IL-17A is considered a marker for a patient with breast cancer. Also, mutations in the IL-17A gene affect the structure and physicochemical properties of the IL-17A protein complex.

UBE2S interacting with TRIM28 in the nucleus accelerates cell cycle by ubiquitination of p27 to promote hepatocellular carcinoma development

Genomic sequencing analysis of tumors provides potential molecular therapeutic targets for precision medicine. However, identifying a key driver gene or mutation that can be used for hepatocellular carcinoma (HCC) treatment remains difficult. Here, we performed whole-exome sequencing on genomic DNA obtained from six pairs of HCC and adjacent tissues and identified two novel somatic mutations of UBE2S (p. Gly57Ala and p. Lys63Asn). Predictions of the functional effects of the mutations showed that two amino-acid substitutions were potentially deleterious. Further, we observed that wild-type UBE2S, especially in the nucleus, was significantly higher in HCC tissues than that in adjacent tissues and closely related to the clinicopathological features of patients with HCC. Functional assays revealed that overexpression of UBE2S promoted the proliferation, invasion, metastasis, and G1/S phase transition of HCC cells in vitro, and promoted the tumor growth significantly in vivo. Mechanistically, UBE2S interacted with TRIM28 in the nucleus, both together enhanced the ubiquitination of p27 to facilitate its degradation and cell cycle progression. Most importantly, the small-molecule cephalomannine was found by a luciferase-based sensitive high-throughput screen (HTS) to inhibit UBE2S expression and significantly attenuate HCC progression in vitro and in vivo, which may represent a promising strategy for HCC therapy.

TRIM28 is a distinct prognostic biomarker that worsens the tumor immune microenvironment in lung adenocarcinoma

The tumor immune microenvironment (TIME) is an important determinant of cancer prognosis and treatment efficacy. To identify immune-related prognostic biomarkers of lung adenocarcinoma, we used the ESTIMATE algorithm to calculate the immune and stromal scores of 517 lung adenocarcinoma patients from The Cancer Genome Atlas (TCGA). We detected 985 differentially expressed genes (DEGs) between patients with high and low immune and stromal scores, and we analyzed their functions and protein-protein interactions. TRIM28 was upregulated in lung adenocarcinoma patients with low immune and stromal scores, and was associated with a poor prognosis. The TISIDB and TIMER databases indicated that TRIM28 expression correlated negatively with immune infiltration. We then explored genes that were co-expressed with TRIM28 in TCGA, and investigated DEGs based on TRIM28 expression in GSE43580 and GSE7670. The 429 common DEGs from these analyses were functionally analyzed. We also performed a Gene Set Enrichment Analysis using TCGA data, and predicted substrates of TRIM28 using UbiBrowser. The results indicated that TRIM28 may negatively regulate the TIME by increasing the SUMOylation of IRF5 and IRF8. Correlation analyses and validations in two lung adenocarcinoma cell lines (PC9 and H1299) confirmed these findings. Thus, TRIM28 may worsen the TIME and prognosis of lung adenocarcinoma.

Identification of prognostic biomarkers in colorectal cancer using a long non-coding RNA-mediated competitive endogenous RNA network

Colorectal cancer (CRC) is a highly malignant gastrointestinal tumor accompanied by poor prognosis. Long non-coding RNA (lncRNA) plays an important role in the progression and physiology of tumors as it competes with endogenous RNAs, including miRNA and mRNA. In the present study, a multi-step computational method was used to build a CRC-related functional lncRNA-mediated competitive endogenous RNA (ceRNA) network (LMCN). lncRNAs with more degrees and betweenness centrality (BC) were screened out as hub lncRNAs. Then functional enrichment analyses of lncRNAs were carried out from the Gene Ontology (GO) and Reactome pathway databases based on the 'guilt by association' principle. As a result, lncRNAs in the LMCN displayed specific topological characteristics in accordance with the regulatory correlation of coding mRNAs in CRC pathology. HCP5, EPB41L4A-AS1, SNHG12, and LINC00649 were screened out as hub lncRNAs which were more significantly related to the development and prognosis of CRC. The hub lncRNAs in CRC were obviously involved in functions of cell cycle arrest, vacuolar transport, histone modification, and in pathways of GPCR, signaling by Rho GTPases, axon guidance pathways, meaning that they might be potential biomarkers for diagnosis, evaluation and gene-targeted therapy of CRC. Thus, the LMCN construction method could accelerate lncRNA discovery and therapeutic development in CRC.

[Bioinformatics analysis of expression and function of EXD3 gene in gastric cancer]

OBJECTIVE

To investigate the differentially expressed genes between gastric cancer and normal gastric mucosa by bioinformatics analysis, identify the important gene participating in the occurrence and progression of gastric cancer, and predict the functions of these genes.

METHODS

The gene expression microarray data GSE100935 (including 18 gastric cancer samples and normal gastric mucosal tissues) downloaded from the GEO expression profile database were analyzed using Morpheus to obtain the differentially expressed genes in gastric cancer, and a cluster analysis heat map was constructed. The online database UALCAN was used to obtain the expression levels of these differentially expressed genes in gastric cancer and normal gastric mucosa. The prognostic value of the differentially expressed genes in gastric cancer was evaluated with Kaplan-Meier survival analysis. GO functional enrichment analysis was performed using Fun-Rich software, and the STRING database was exploited to establish a PPI network for the differentially expressed genes.

RESULTS

A total of 45119 differentially expressed genes were identified from GSE100935 microarray data. Analysis with UALCAN showed an obvious high expression of EXD3 gene in gastric cancer, and survival analysis suggested that a high expression level of EXD3 was associated with a poorer prognosis of the patients with gastric cancer. GO functional enrichment analysis found that the differentially expressed genes in gastric cancer were involved mainly in the regulation of nucleotide metabolism and the activity of transcription factors in the cancer cells.

CONCLUSIONS

EXD3 may be a potential oncogene in gastric cancer possibly in relation to DNA damage repair. The up-regulation of EXD3 plays an important role in the development and prognosis of gastric cancer, and may serve as an important indicator for prognostic evaluation of the patients.

miR-140-3p inhibits breast cancer proliferation and migration by directly regulating the expression of tripartite motif 28

The present study aimed to determine the expression profile and significance of microRNA-140-3p (miR-140-3p) in breast cancer (BC). miR-140-3p expression in BC tumor tissues and cell lines was measured by reverse transcription-quantitative polymerase chain reaction. Luciferase activity reporter assay and western blotting were used to assess the effect of miR-140-3p expression on tripartite motif 28 (TRIM28). Cell growth, migration, and invasion were assessed by Cell Counting Kit-8 assay, wound-healing assay and Transwell invasion assay, respectively. miR-140-3p expression was significantly reduced in BC tumor tissues compared with in adjacent normal tissues. Additionally, low miR-140-3p expression was found to predict poor prognosis of patients with BC. TRIM28 expression was significantly reduced by miR-140-3p overexpression in BC cell lines, and was inversely correlated with miR-140-3p in BC tissues. Overexpression of miR-140-3p also inhibited cell proliferation, migration and invasion compared with in the control group. In conclusion, the present study revealed that miR-140-3p inhibited the progression of BC partially by regulating TRIM28.

Expression and Significance of TRIM 28 in Squamous Carcinoma of Esophagus

Tripartite motif-containing protein 28 (TRIM28) has been proved to accelerate cell proliferation and metastasis in a variety of human cancers. However, the role of TRIM28 in esophageal squamous cell carcinoma (ESCC) remains unclear. In this study, to compare the biological effect and significance of TRIM28 expression in ESCC, immunohistochemistry (streptavidin-perosidase, S-P) method was used firstly to examine the expression of TRIM28 in 136 cases of ESCC, 35 cases of high grade intraepithelial neoplasia (HGIN), 29 cases of low grade intraepithelial neoplasia (LGIN) and 37 cases of normal esophageal epithelium (NEE). Then the associations of TRIM28 expression with clinicopathological data and overall survival (OS) were also analyzed. Western blot was performed to evaluate TRIM28 protein in a total of 20 matched human ESCC and NEE tissues. Moreover, the localization of TRIM28 protein in ESCC and NEE tissues was also detected by immunofluorescence. TRIM28 protein was mainly distributed in the nucleus of ESCC. The expression of TRIM28 increased progressively from NEE to LGIN, to HGIN, and to ESCC, and it was also related to invasive depth, pTNM stage and lymph node metastasis in ESCC (P < 0.05). The results of western blot and immunofluorescence all showed that the relative expression of TRIM28 protein was markedly upregulated in ESCC compared with the NEE tissues (P < 0.01). However, prognostic analysis showed that TRIM28 may not be a prognostic factor of patients with ESCC. In conclusion, the overexpression of TRIM28 may play an important role for development and metastasis in ESCC.