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Wang M, Fu L, Tian J, Zhang Y, Rossi L, Wang K. Function and prognosis analysis of nucleolus protein DCAF13 in breast cancer. Transl Cancer Res 2023; 12:3744-3751. [PMID: 38197079 PMCID: PMC10774066 DOI: 10.21037/tcr-23-1923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/22/2023] [Indexed: 01/11/2024]
Abstract
Background Breast cancer is one of the main causes of death among women. RNA binding proteins (RBPs) play a crucial role in the progression of breast cancer, with increasingly detailed understanding of RBP functional molecular mechanisms in breast cancer, the functional research of RBPs may help elucidate the potential mechanisms of tumor occurrence, development, invasion, metastasis and prognosis. DDB1- and CUL4-associated factor 13 (DCAF13) is an RBPs has been identified as a substrate receptor for the CUL4-DDB1 E3 ligase complex. Its expression is related to the prognosis of certain cancer. We tried to explore both co-expressed network and biological functions of DCAF13 in breast cancer. Methods The Cancer Genome Atlas (TCGA) database was used to analyze the different expression of DCAF13 messenger RNA (mRNA) between normal breast tissue and breast carcinoma tissue, and the clinical data about 960 samples were downloaded from the cBio Cancer Genomics Portal (cBioPortal). The expression level of DCAF13, co-expression network, and survival were analyzed. Those with a fold change ≥1 and FDR <0.05 were considered to have statistical significance. Unsupervised clustering of differentially expressed RBPs was performed based on log2-transformed FPKM values using the "pheatmap" package in R. Genes with a Spearman score >0.55 were regarded as moderately co-expressed genes. The Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database was used to construct a co-expression network. Meanwhile, the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were used to identify the biological process cluster and pathway cluster, respectively. Results Compared with normal breast tissue, DCAF13 mRNA expression was significantly increased in breast cancer tissue (P<0.01). The Database for Annotation, Visualization and Integrated Discovery (DAVID) was used to identify the functions of the co-expressed network. These genes were mainly enriched in mitosis, nuclear division, metabolic process, recombination, replication and repair of DNA, double-strand break repair, posttranscriptional regulation of gene expression, regulation of cell cycle, division and proliferation, regulation of protein stability and also participation in in regulation of poly(A) RNA binding, mRNA binding, tRNA binding, adenosine triphosphate (ATP) binding. KEGG pathway analysis revealed that the genes were mainly enriched in cell cycle, oocyte meiosis and oxidative phosphorylation. According to survival analysis, upregulation of DCAF13 mRNA was significant for overall survival (OS) (P=0.0163). Conclusions DCAF13 is up-regulated in breast cancer, the OS of patients with DCAF13 up-regulation was obviously reduced. DCAF13 was used as a diagnostic marker and therapeutic target for breast cancer. By building a co-expression network of DCAF13 and conducting bioinformatics analysis, it is possible to find the biomarker to evaluate patient prognosis. This finding provides a new target in mechanism and cell research of breast cancer.
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Affiliation(s)
- Mei Wang
- Clinical Laboratory, Yongchuan People’s Hospital of Chongqing, Chongqing, China
| | - Liang Fu
- Clinical Laboratory, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Jun Tian
- Clinical Laboratory, Yongchuan People’s Hospital of Chongqing, Chongqing, China
| | - Yongming Zhang
- Clinical Laboratory, Yongchuan People’s Hospital of Chongqing, Chongqing, China
| | - Lorenzo Rossi
- Ente Ospedaliero Cantonale, Institute of Oncology of Southern Switzerland (IOSI), Bellinzona, Switzerland
- Ente Ospedaliero Cantonale, Breast Unit of Southern Switzerland (CSSI), Lugano, Switzerland
| | - Ke Wang
- Clinical Laboratory, Yongchuan People’s Hospital of Chongqing, Chongqing, China
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Cui Y, Luo J, Bai N, Yu Z. Deltex E3 ubiquitin ligase 4 promotes thyroid cancer progression through stearoyl-CoA desaturase 1. Funct Integr Genomics 2023; 23:280. [PMID: 37612343 DOI: 10.1007/s10142-023-01215-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/06/2023] [Accepted: 08/15/2023] [Indexed: 08/25/2023]
Abstract
In this study, we aimed to explore the molecular role of Deltex E3 ubiquitin ligase 4 (DTX4) in thyroid cancer (TC) both in vitro and in vivo. The expression level of DTX4 in TC tissues was compared using The Cancer Genome Atlas (TCGA) database. We subsequently evaluated cell proliferation and migration in DTX4 knock down or DTX4 overexpression TC cell lines (TPC-1 and K1) by CCK-8, cell colony formation, and transwell assays. RNA sequencing and KEGG analysis were employed to identify potential genes that interact with DTX4. Our results showed that DTX4 was expressed at higher levels in both TC tissues and cells compared to normal controls. Knock down of DTX4 expression significantly inhibited TC cell progression in vitro. Furthermore, knockdown of endogenous DTX4 by shDTX4 markedly abrogated tumor growth, with significantly smaller tumor size and lower tumor weight in the shDTX4 group compared to the shCtrl group. Conversely, overexpression of DTX4 enhanced TC cell proliferation and migration. Through RNA sequencing, we identified 590 Differentially Expressed Genes (DEGs), with stearoyl-CoA desaturase 1 (SCD) ranking as the top gene. A positive correlation between DTX4 and SCD was observed in TC samples. Additionally, treatment with an SCD inhibitor, A939572, significantly rescued the enhanced growth effect induced by DTX4 overexpression. In conclusion, this study demonstrated that DTX4 promotes TC progression through SCD, indicating that the DTX4/SCD axis could be a promising target for TC therapy.
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Affiliation(s)
- Yitong Cui
- Department of Endocrinology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Jia Luo
- Department of Endocrinology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Nanfang Bai
- Department of Endocrinology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Zhaoyan Yu
- Center for Integrative and Translational Medicine, Shandong Public Health Clinical Center, No.46, Lidong Road 250015, Jinan, 230601, Shandong, China.
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Liang L, Liu L, Mai S, Chen Y. A novel machine learning model based on ubiquitin-related gene pairs and clinical features to predict prognosis and treatment effect in colon adenocarcinoma. Eur J Med Res 2023; 28:41. [PMID: 36681855 PMCID: PMC9863211 DOI: 10.1186/s40001-023-00993-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 01/04/2023] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Ubiquitin and ubiquitin-like (UB/UBL) conjugations are essential post-translational modifications that contribute to cancer onset and advancement. In colon adenocarcinoma (COAD), nonetheless, the biological role, as well as the clinical value of ubiquitin-related genes (URGs), is unclear. The current study sought to design and verify a ubiquitin-related gene pairs (URGPs)-related prognostic signature for predicting COAD prognoses. METHODS Using univariate, least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression, URGP's predictive signature was discovered. Signatures differentiated high-risk and low-risk patients. ROC and Kaplan-Meier assessed URGPs' signature. Gene set enrichment analysis (GSEA) examined biological nomogram enrichment. Chemotherapy and tumor immune microenvironment were also studied. RESULTS The predictive signature used six URGPs. High-risk patients had a worse prognosis than low-risk patients, according to Kaplan-Meier. After adjusting for other clinical characteristics, the URGPs signature could reliably predict COAD patients. In the low-risk group, we found higher amounts of invading CD4 memory-activated T cells, follicular helper T cells, macrophages, and resting dendritic cells. Moreover, low-risk group had higher immune checkpoint-related gene expression and chemosensitivity. CONCLUSION Our research developed a nomogram and a URGPs prognostic signature to predict COAD prognosis, which may aid in patient risk stratification and offer an effective evaluation method of individualized treatment in clinical settings.
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Affiliation(s)
- Liping Liang
- grid.284723.80000 0000 8877 7471Department of Gastroenterology, State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515 China
| | - Le Liu
- grid.284723.80000 0000 8877 7471Department of Gastroenterology, Integrated Clinical Microecology Center, Shenzhen Hospital, Southern Medical University, 1333 New Lake Road, Shenzhen, 518100 China
| | - Shijie Mai
- grid.284723.80000 0000 8877 7471Department of Thoracic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515 China
| | - Ye Chen
- grid.284723.80000 0000 8877 7471Department of Gastroenterology, State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515 China ,grid.284723.80000 0000 8877 7471Department of Gastroenterology, Integrated Clinical Microecology Center, Shenzhen Hospital, Southern Medical University, 1333 New Lake Road, Shenzhen, 518100 China
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Activities and binding partners of E3 ubiquitin ligase DTX3L and its roles in cancer. Biochem Soc Trans 2022; 50:1683-1692. [DOI: 10.1042/bst20220501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/27/2022] [Accepted: 11/15/2022] [Indexed: 11/25/2022]
Abstract
Ubiquitination is a protein post-translational modification that affects protein localisation, stability and interactions. E3 ubiquitin ligases regulate the final step of the ubiquitination reaction by recognising target proteins and mediating the ubiquitin transfer from an E2 enzyme. DTX3L is a multi-domain E3 ubiquitin ligase in which the N-terminus mediates protein oligomerisation, a middle D3 domain mediates the interaction with PARP9, a RING domain responsible for recognising E2 ∼ Ub and a DTC domain has the dual activity of ADP-ribosylating ubiquitin and mediating ubiquitination. The activity of DTX3L is known to be modulated by at least two different factors: the concentration of NAD+, which dictates if the enzyme acts as a ligase or as an ADP-ribosyltransferase, and its binding partners, which affect DTX3L activity through yet unknown mechanisms. In light of recent findings it is possible that DTX3L could ubiquitinate ADP-ribose attached to proteins. Different DTX3L–protein complexes have been found to be part of multiple signalling pathways through which they promote the adhesion, proliferation, migration and chemoresistance of e.g. lymphoma, glioma, melanoma, and prostate cancer. In this review, we have covered the literature available for the molecular functions of DTX3L especially in the context of cancer biology, different pathways it regulates and how these relate to its function as an oncoprotein.
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Jiang N, Hu Y, Wang M, Zhao Z, Li M. The Notch Signaling Pathway Contributes to Angiogenesis and Tumor Immunity in Breast Cancer. BREAST CANCER: TARGETS AND THERAPY 2022; 14:291-309. [PMID: 36193236 PMCID: PMC9526507 DOI: 10.2147/bctt.s376873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/08/2022] [Indexed: 11/23/2022]
Abstract
Breast cancer in women is the first leading tumor in terms of incidence worldwide. Some subtypes of BC lack distinct molecular targets and exhibit therapeutic resistance; these patients have a poor prognosis. Thus, the search for new molecular targets is an ongoing challenge for BC therapy. The Notch signaling pathway is found in both vertebrates and invertebrates, and it is a highly conserved in the evolution of the species, controlling cellular fates such as death, proliferation, and differentiation. Numerous studies have shown that improper activation of Notch signaling may lead to excessive cell proliferation and cancer, with tumor-promoting and tumor-suppressive effects in various carcinomas. Thus, inhibitors of Notch signaling are actively being investigated for the treatment of various tumors. The role of Notch signaling in BC has been widely studied in recent years. There is a growing body of evidence suggesting that Notch signaling has a pro-oncogenic role in BC, and the tumor-promoting effect is largely a result of the diverse nature of tumor immunity. Immunological abnormality is also a factor involved in the pathogenesis of BC, suggesting that Notch signaling could be a target for BC immunotherapies. Furthermore, angiogenesis is essential for BC growth and metastasis, and the Notch signaling pathway has been implicated in angiogenesis, so studying the role of Notch signaling in BC angiogenesis will provide new prospects for the treatment of BC. We summarize the potential roles of the current Notch signaling pathway and its inhibitors in BC angiogenesis and the immune response in this review and describe the pharmacological targets of Notch signaling in BC, which may serve as a theoretical foundation for future research into exploring this pathway for novel BC therapies.
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Affiliation(s)
- Nina Jiang
- Department of Oncology, the Second Hospital of Dalian Medical University, Dalian, Liaoning, People’s Republic of China
| | - Ye Hu
- Department of Oncology, the Second Hospital of Dalian Medical University, Dalian, Liaoning, People’s Republic of China
| | - Meiling Wang
- Department of Breast Surgery, the Second Hospital of Dalian Medical University, Dalian, Liaoning, People’s Republic of China
| | - Zuowei Zhao
- Department of Breast Surgery, the Second Hospital of Dalian Medical University, Dalian, Liaoning, People’s Republic of China
- Correspondence: Zuowei Zhao, Department of Breast Surgery, the Second Hospital of Dalian Medical University, Dalian, Liaoning, People’s Republic of China, Tel +86-0411-84671291, Fax +86-0411-84671230, Email
| | - Man Li
- Department of Oncology, the Second Hospital of Dalian Medical University, Dalian, Liaoning, People’s Republic of China
- Man Li, Department of Oncology, the Second Hospital of Dalian Medical University, Dalian, Liaoning, People’s Republic of China, Tel +86-0411-84671291, Fax +86-0411-84671230, Email
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