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Wen W, Li Y, Cao X, Li Y, Liu Z, Tang Z, Xie L, He R. Expression and Clinical Significance of NUDCD1, PI3K/AKT/mTOR Signaling Pathway-Related Molecules and Immune Infiltration in Breast Cancer. Clin Breast Cancer 2024; 24:e429-e451. [PMID: 38553373 DOI: 10.1016/j.clbc.2024.02.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/20/2024] [Accepted: 02/29/2024] [Indexed: 07/28/2024]
Abstract
BACKGROUND NUDCD1 (NudC Domain Containing 1) performs an essential function in biological processes such as cell progression, migration, cell cycle, and intracellular material transport. Many solid tumors express it highly, which is a prospective biomarker and therapeutic approach. However, the expression and clinical importance of NUDCD1 across breast cancer is unclear. METHODS The expressions of NUDCD1 in breast cancers and normal breast tissues were studied utilizing the TIMER database and immunohistochemical analysis. Subsequently, we validate the association between the expression of NUDCD1 and clinicopathologic features and prognosis of breast cancer. The immunohistochemical experiments of pathway-related molecules were done on 214 breast cancer tissue microarrays. The investigation of correlation between NUDCD1 expression and tumor immune infiltration was subsequently conducted. RESULTS Through the utilization of bioinformatics analysis and immunohistochemical experiments, it was determined that NUDCD1 exhibited upregulation within breast cancer. Furthermore, it was discovered that an elevated expression of NUDCD1 may potentially be linked to a worse prognosis in breast cancer. Our study reveals that the PI3K/AKT/mTOR signaling pathway may perform a function in NUDCD1 regulating breast cancer progression via enrichment analysis. Furthermore, the expression of NUDCD1 may be associated with the degree of immunological infiltration. CONCLUSION The expression of NUDCD1 was explored to be elevated in breast cancer and was observed to be correlated with a poorer prognosis. p-AKT, PI3K, AKT, mTOR, and p-mTOR expression levels underwent significant elevation in breast cancer. The function of NUDCD1 within breast cancer might be associated with the PI3K/AKT/mTOR signaling pathway.
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Affiliation(s)
- Wei Wen
- Department of Pathology, the First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, China; Department of Pathology, Yongchuan Hospital Of Chongqing Medical University, Yongchuan 402160, Chongqing, China
| | - Yuehua Li
- Department of Medical Oncology, the First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, China
| | - Xi Cao
- Department of Pathology, the First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, China
| | - Yanyan Li
- Department of Pathology, the First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, China
| | - Ziyi Liu
- Department of Pathology, the First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, China
| | - Zhuoqi Tang
- Department of Pathology, the First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, China
| | - Liming Xie
- Department of Medical Oncology, the First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, China.
| | - Rongfang He
- Department of Pathology, the First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, China.
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Zhuk AS, Stepchenkova EI, Zotova IV, Belopolskaya OB, Pavlov YI, Kostroma II, Gritsaev SV, Aksenova AY. G-Quadruplex Forming DNA Sequence Context Is Enriched around Points of Somatic Mutations in a Subset of Multiple Myeloma Patients. Int J Mol Sci 2024; 25:5269. [PMID: 38791307 PMCID: PMC11121618 DOI: 10.3390/ijms25105269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Multiple myeloma (MM) is the second most common hematological malignancy, which remains incurable despite recent advances in treatment strategies. Like other forms of cancer, MM is characterized by genomic instability, caused by defects in DNA repair. Along with mutations in DNA repair genes and genotoxic drugs used to treat MM, non-canonical secondary DNA structures (four-stranded G-quadruplex structures) can affect accumulation of somatic mutations and chromosomal abnormalities in the tumor cells of MM patients. Here, we tested the hypothesis that G-quadruplex structures may influence the distribution of somatic mutations in the tumor cells of MM patients. We sequenced exomes of normal and tumor cells of 11 MM patients and analyzed the data for the presence of G4 context around points of somatic mutations. To identify molecular mechanisms that could affect mutational profile of tumors, we also analyzed mutational signatures in tumor cells as well as germline mutations for the presence of specific SNPs in DNA repair genes or in genes regulating G-quadruplex unwinding. In several patients, we found that sites of somatic mutations are frequently located in regions with G4 context. This pattern correlated with specific germline variants found in these patients. We discuss the possible implications of these variants for mutation accumulation and specificity in MM and propose that the extent of G4 context enrichment around somatic mutation sites may be a novel metric characterizing mutational processes in tumors.
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Affiliation(s)
- Anna S. Zhuk
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.S.Z.); (I.V.Z.)
- Institute of Applied Computer Science, ITMO University, 197101 St. Petersburg, Russia
| | - Elena I. Stepchenkova
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia;
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Irina V. Zotova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.S.Z.); (I.V.Z.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia;
| | - Olesya B. Belopolskaya
- Resource Center “Bio-Bank Center”, Research Park of St. Petersburg State University, 198504 St. Petersburg, Russia;
- The Laboratory of Genogeography, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Youri I. Pavlov
- Eppley Institute for Research in Cancer, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA;
- Departments of Biochemistry and Molecular Biology, Microbiology and Pathology, Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Ivan I. Kostroma
- City Hospital No. 15, 198205 St. Petersburg, Russia; (I.I.K.); (S.V.G.)
| | | | - Anna Y. Aksenova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.S.Z.); (I.V.Z.)
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Wang C, Li Y, Miao X, Wang Y, Yang G. Knockdown of LRP5 Promotes Proliferation and Invasion of Tongue Squamous Cell Carcinoma through Compensatory Activation of Akt Signaling. J Cancer 2024; 15:3215-3226. [PMID: 38706907 PMCID: PMC11064261 DOI: 10.7150/jca.93585] [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: 12/25/2023] [Accepted: 04/03/2024] [Indexed: 05/07/2024] Open
Abstract
The role of LRP5, a critical receptor in the Wnt signaling pathway, remains unexplored in tongue squamous cell carcinoma (TSCC). This study investigates the impact of LRP5 knockdown on the biological behaviors of TSCC cell lines both in vitro and in vivo. Our findings indicate that LRP5 knockdown significantly enhances cell proliferation, migration, and invasion in CAL27 and SCC25 cell lines. RNA-seq analysis reveals compensatory activation of the Akt pathway, with 119 genes significantly upregulated post-LRP5 knockdown. Elevated MMP1 expression suggests its potential involvement in TSCC progression. Western blot analysis demonstrates increased Akt phosphorylation, upregulated proliferation-related PCNA, and downregulated apoptosis-related caspase-3 after LRP5 knockdown. Down-regulation of E-cadherin and β-Catenin, proteins associated with cell adhesion and invasion, further elucidates the molecular mechanism underlying increased cell migration and invasion. Our study concludes that compensatory Akt pathway activation is essential for the LRP5 knockdown-induced migration and proliferation of CAL27 and SCC25 cells. These results highlight LRP5 as a potential therapeutic target for TSCC. Simultaneous inhibition of Wnt and Akt signaling emerges as a promising approach for TSCC treatment.
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Affiliation(s)
| | | | | | | | - Guoli Yang
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Clinical Research Center for Oral Diseases of Zhejiang Province, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310006, China
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Wei S, Xing J, Chen J, Chen L, Lv J, Chen X, Li T, Yu T, Wang H, Wang K, Yu W. DCAF13 inhibits the p53 signaling pathway by promoting p53 ubiquitination modification in lung adenocarcinoma. J Exp Clin Cancer Res 2024; 43:3. [PMID: 38163876 PMCID: PMC10759521 DOI: 10.1186/s13046-023-02936-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024] Open
Abstract
BACKGROUND Lung cancer is a malignant tumor with the highest mortality worldwide. Abnormalities in the ubiquitin proteasome system are considered to be contributed to lung cancer progression with deleterious effects. DDB1 and CUL4 associated factor 13 (DCAF13) is a substrate receptor of the E3 ubiquitin ligase CRL4, but its role in lung cancer remains unknown. In this study, we aimed to investigate the regulatory mechanisms of DCAF13 in lung adenocarcinoma (LUAD). METHODS So as to investigate the effect of DCAF13 on lung adenocarcinoma cell function using in vivo and in vitro. Mechanistically, we have identified the downstream targets of DCAF13 by using RNA-sequencing, as well as ubiquitination assays, co-immunoprecipitation, immunofluorescence, immunohistochemistry and chromatin immunoprecipitation - qPCR experiments. RESULTS Our findings reveal that DCAF13 is a carcinogenic factor in LUAD, as it is highly expressed and negatively correlated with clinical outcomes in LUAD patients. Through RNA-sequencing, it has been shown that DCAF13 negatively regulates the p53 signaling pathway and inhibits p53 downstream targets including p21, BAX, FAS, and PIDD1. We also demonstrate that DCAF13 can bind to p53 protein, leading to K48-linked ubiquitination and degradation of p53. Functionally, we have shown that DCAF13 knockdown inhibits cell proliferation and migration. Our results highlight the significant role of DCAF13 in promoting LUAD progression by inhibiting p53 protein stabilization and the p53 signaling pathway. Furthermore, our findings suggest that high DCAF13 expression is a poor prognostic indicator in LUAD, and DCAF13 may be a potential therapeutic target for treating with this aggressive cancer. CONCLUSIONS The DCAF13 as a novel negative regulator of p53 to promote LUAD progression via facilitating p53 ubiquitination and degradation, suggesting that DCAF13 might be a novel biomarker and therapeutical target for LUAD.
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Affiliation(s)
- Shan Wei
- Department of Respiratory and Critical Care Medicine, The Affiliated People's Hospital of Ningbo University (Ningbo Yinzhou People's Hospital), 251, Baizhang Road, Ningbo, Zhejiang, 315040, People's Republic of China
| | - Jing Xing
- Department of Respiratory and Critical Care Medicine, The Affiliated People's Hospital of Ningbo University (Ningbo Yinzhou People's Hospital), 251, Baizhang Road, Ningbo, Zhejiang, 315040, People's Republic of China
| | - Jia Chen
- Department of Respiratory and Critical Care Medicine, The Affiliated People's Hospital of Ningbo University (Ningbo Yinzhou People's Hospital), 251, Baizhang Road, Ningbo, Zhejiang, 315040, People's Republic of China
| | - Liping Chen
- Department of Respiratory and Critical Care Medicine, The Affiliated People's Hospital of Ningbo University (Ningbo Yinzhou People's Hospital), 251, Baizhang Road, Ningbo, Zhejiang, 315040, People's Republic of China
| | - Jiapei Lv
- Department of Respiratory and Critical Care Medicine, The Affiliated People's Hospital of Ningbo University (Ningbo Yinzhou People's Hospital), 251, Baizhang Road, Ningbo, Zhejiang, 315040, People's Republic of China
| | - Xiaofei Chen
- Department of Respiratory and Critical Care Medicine, The Affiliated People's Hospital of Ningbo University (Ningbo Yinzhou People's Hospital), 251, Baizhang Road, Ningbo, Zhejiang, 315040, People's Republic of China
| | - Tang Li
- Department of Respiratory and Critical Care Medicine, The Affiliated People's Hospital of Ningbo University (Ningbo Yinzhou People's Hospital), 251, Baizhang Road, Ningbo, Zhejiang, 315040, People's Republic of China
| | - Tao Yu
- Department of Respiratory and Critical Care Medicine, The Affiliated People's Hospital of Ningbo University (Ningbo Yinzhou People's Hospital), 251, Baizhang Road, Ningbo, Zhejiang, 315040, People's Republic of China
| | - Huaying Wang
- Department of Respiratory and Critical Care Medicine, The Affiliated People's Hospital of Ningbo University (Ningbo Yinzhou People's Hospital), 251, Baizhang Road, Ningbo, Zhejiang, 315040, People's Republic of China
| | - Kai Wang
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, Zhejiang, 322000, People's Republic of China
| | - Wanjun Yu
- Department of Respiratory and Critical Care Medicine, The Affiliated People's Hospital of Ningbo University (Ningbo Yinzhou People's Hospital), 251, Baizhang Road, Ningbo, Zhejiang, 315040, People's Republic of China.
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Zhang S, Bai X, Li F, Ni C, Li Y, Che N, Zhao N, Zhao X, Liu T. UTP23 Functions in Breast Cancer Progression and Predicts Poor Prognosis of Luminal a Breast Cancer. Clin Breast Cancer 2024; 24:e20-e30.e6. [PMID: 37880005 DOI: 10.1016/j.clbc.2023.09.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/27/2023]
Abstract
BACKGROUND Luminal A breast cancer is the most common molecular subtype of breast cancer. Exploring biomarkers to identify luminal A breast cancer patients at high risk of recurrence and metastasis has important clinical significance. UTP23 is a component of ribosomal small-subunit processome, which is involved in ribosome synthesis and RNA maturation. The role of UTP23 in breast cancer has not been reported. METHODS TCGA-BRCA data, LinkedOmics, STRING, Metascape and ssGSEA were used to analyze UTP23 expression in breast cancer and evaluate prognosis. Quantitative real-time PCR, western blot and in vitro cell experiment were used to demonstrate the role of UTP23 in breast cancer. RESULTS UTP23 showed abnormally high expression in multiple cancers and was associated with poor prognosis. UTP23 was associated with T stage, lymph node metastasis, race, histological type, molecular subtypes and survival status in breast cancer. Importantly, UTP23 was significantly associated with poor OS in luminal A or early breast cancer, not in non-luminal A or advanced breast cancer. UTP23 expression was significantly correlated with immune cells infiltration. Enrichment analysis suggested that UTP23 might regulate cell cycle and cell division. Bioinformatics analysis showed DCAF13 might be downstream factor of UTP23. UTP23 expression promoted MCF-7 cells proliferation, migration and invasion possibly through regulating DCAF13 expression. CONCLUSIONS UTP23 may function in breast cancer progression. The elevated UTP23 may be a potential prognostic biomarker for luminal A or early breast cancer.
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Affiliation(s)
- Sida Zhang
- Department of Pathology, Tianjin Medical University, Tianjin, China
| | - Xiaoyu Bai
- Department of Pathology, Tianjin Medical University, Tianjin, China
| | - Fan Li
- Department of Pathology, Tianjin Medical University, Tianjin, China
| | - Chunsheng Ni
- Department of Pathology, Tianjin Medical University, Tianjin, China; Department of Pathology, General Hospital of Tianjin Medical University, Tianjin, China
| | - Yanlei Li
- Department of Pathology, Tianjin Medical University, Tianjin, China; Department of Pathology, General Hospital of Tianjin Medical University, Tianjin, China
| | - Na Che
- Department of Pathology, Tianjin Medical University, Tianjin, China; Department of Pathology, General Hospital of Tianjin Medical University, Tianjin, China
| | - Nan Zhao
- Department of Pathology, Tianjin Medical University, Tianjin, China; Department of Pathology, General Hospital of Tianjin Medical University, Tianjin, China
| | - Xiulan Zhao
- Department of Pathology, Tianjin Medical University, Tianjin, China; Department of Pathology, General Hospital of Tianjin Medical University, Tianjin, China.
| | - Tieju Liu
- Department of Pathology, Tianjin Medical University, Tianjin, China; Department of Pathology, General Hospital of Tianjin Medical University, Tianjin, China.
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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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Zheng X, Zhao D, Liu Y, Jin Y, Liu T, Li H, Liu D. Regeneration and anti-inflammatory effects of stem cells and their extracellular vesicles in gynecological diseases. Biomed Pharmacother 2023; 168:115739. [PMID: 37862976 DOI: 10.1016/j.biopha.2023.115739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/10/2023] [Accepted: 10/16/2023] [Indexed: 10/22/2023] Open
Abstract
There are many gynecological diseases, among which breast cancer (BC), cervical cancer (CC), endometriosis (EMs), and polycystic ovary syndrome (PCOS) are common and difficult to cure. Stem cells (SCs) are a focus of regenerative medicine. They are commonly used to treat organ damage and difficult diseases because of their potential for self-renewal and multidirectional differentiation. SCs are also commonly used for difficult-to-treat gynecological diseases because of their strong directional differentiation ability with unlimited possibilities, their tendency to adhere to the diseased tissue site, and their use as carriers for drug delivery. SCs can produce exosomes in a paracrine manner. Exosomes can be produced in large quantities and have the advantage of easy storage. Their safety and efficacy are superior to those of SCs, which have considerable potential in gynecological treatment, such as inhibiting endometrial senescence, promoting vascular reconstruction, and improving anti-inflammatory and immune functions. In this paper, we review the mechanisms of the regenerative and anti-inflammatory capacity of SCs and exosomes in incurable gynecological diseases and the current progress in their application in genetic engineering to provide a foundation for further research.
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Affiliation(s)
- Xu Zheng
- Changchun University of Chinese Medicine, Changchun 130117, China
| | - Dan Zhao
- Affiliated Hospital of Changchun University of Traditional Chinese Medicine, Changchun 130000, China
| | - Yang Liu
- Affiliated Hospital of Changchun University of Traditional Chinese Medicine, Changchun 130000, China
| | - Ye Jin
- Changchun University of Chinese Medicine, Changchun 130117, China
| | - Tianjia Liu
- Changchun University of Chinese Medicine, Changchun 130117, China; Baicheng Medical College, Baicheng 137000, China.
| | - Huijing Li
- Changchun University of Chinese Medicine, Changchun 130117, China.
| | - Da Liu
- Changchun University of Chinese Medicine, Changchun 130117, China.
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Zhang X, Feng R, Guo J, Pan L, Yao Y, Gao J. Integrated single-cell and bulk RNA sequencing analysis identifies a neoadjuvant chemotherapy-related gene signature for predicting survival and therapy in breast cancer. BMC Med Genomics 2023; 16:300. [PMID: 37996875 PMCID: PMC10666338 DOI: 10.1186/s12920-023-01727-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 11/05/2023] [Indexed: 11/25/2023] Open
Abstract
Neoadjuvant chemotherapy (NAC) is a well-established treatment modality for locally advanced breast cancer (BC). However, it can also result in severe toxicities while controlling tumors. Therefore, reliable predictive biomarkers are urgently needed to objectively and accurately predict NAC response. In this study, we integrated single-cell and bulk RNA-seq data to identify nine genes associated with the prognostic response to NAC: NDRG1, CXCL14, HOXB2, NAT1, EVL, FBP1, MAGED2, AR and CIRBP. Furthermore, we constructed a prognostic risk model specifically linked to NAC. The clinical independence and generalizability of this model were effectively demonstrated. Additionally, we explore the underlying cancer hallmarks and microenvironment features of this NAC response-related risk score, and further assess the potential impact of risk score on drug response. In summary, our study constructed and validated a nine-gene signature associated with NAC prognosis, which was accomplished through the integration of single-cell and bulk RNA data. The results of our study are of crucial significance in the prediction of the efficacy of NAC in BC, and may have implications for the clinical management of this disease.
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Affiliation(s)
- Xiaojun Zhang
- General Surgery Department, Third Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030032, China.
| | - Ran Feng
- General Surgery Department, Third Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030032, China
| | - Junbin Guo
- Yangquan Coal Industry (Group) General Hospital, Yangquan, Shanxi, 045008, China
| | - Lihui Pan
- General Surgery Department, Third Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030032, China
| | - Yarong Yao
- General Surgery Department, Third Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030032, China
| | - Jinnan Gao
- General Surgery Department, Third Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030032, China
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Liu ZY, Li YH, Zhang QK, Li BW, Xin L. Development and validation of a ubiquitin-proteasome system gene signature for prognostic prediction and immune microenvironment evaluation in hepatocellular carcinoma. J Cancer Res Clin Oncol 2023; 149:13363-13382. [PMID: 37490101 DOI: 10.1007/s00432-023-05189-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 07/14/2023] [Indexed: 07/26/2023]
Abstract
BACKGROUND The ubiquitin proteasome has a major role in the development of many tumors. However, the prognostic importance of ubiquitin proteasome-system genes (UPSGs) in hepatocellular carcinoma (HCC) is not fully defined. METHODS The TCGA and ICGC datasets were utilized to obtain transcriptional profiling data as well as clinicopathological information about HCC. The 3-UPSGs signature for the TCGA cohort was developed via univariate and LASSO Cox regression analyses. Differential expression of genes was demonstrated by qRT-PCR and immunohistochemistry (IHC). Biological pathways were studied using GSVA and GSEA. Six algorithms were used to compare immune infiltration between the two risk groups. Furthermore, drug sensitivity was measured using the "pRRophetic" R package. The predictive capacity of the 3-UPSGs signature for sensitivity to immunotherapy was also explored. Moreover, we performed a pan-cancer analysis of the 3-UPSGs signature. RESULTS A risk model containing 3 UPSGs (DCAF13, CDC20 and PSMB5) was developed. IHC and qRT-PCR results showed that signature genes were significantly overexpressed in HCC tissues. The high-risk group had a worse prognosis, with a higher clinicopathological grade, higher levels of tumor mutation burden (TMB), elevated levels of immune checkpoint (IC) expression, as well as increased sensitivity to immunotherapy. The two risk groups also differ in their sensitivity to chemotherapeutic drugs. Furthermore, the three UPSGs may play crucial roles in the progression of multiple types of cancers. CONCLUSION We created a 3-UPSGs signature to estimate the prognosis of HCC and to assist in individualized treatment.
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Affiliation(s)
- Zhi-Yang Liu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Donghu District, Nanchang, Jiangxi, 330006, China
| | - Yi-He Li
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Qing-Kun Zhang
- Department of Otorhinolaryngology, Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bo-Wen Li
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Donghu District, Nanchang, Jiangxi, 330006, China
| | - Lin Xin
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Donghu District, Nanchang, Jiangxi, 330006, China.
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Géci I, Bober P, Filová E, Amler E, Sabo J. The Role of ARHGAP1 in Rho GTPase Inactivation during Metastasizing of Breast Cancer Cell Line MCF-7 after Treatment with Doxorubicin. Int J Mol Sci 2023; 24:11352. [PMID: 37511111 PMCID: PMC10379778 DOI: 10.3390/ijms241411352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 07/05/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
Breast cancer is the most prevalent cancer type in women worldwide. It proliferates rapidly and can metastasize into farther tissues at any stage due to the gradual invasiveness and motility of the tumor cells. These crucial properties are the outcome of the weakened intercellular adhesion, regulated by small guanosine triphosphatases (GTPases), which hydrolyze to the guanosine diphosphate (GDP)-bound conformation. We investigated the inactivating effect of ARHGAP1 on Rho GTPases involved signaling pathways after treatment with a high dose of doxorubicin. Label-free quantitative proteomic analysis of the proteome isolated from the MCF-7 breast cancer cell line, treated with 1 μM of doxorubicin, identified RAC1, CDC42, and RHOA GTPases that were inactivated by the ARHGAP1 protein. Upregulation of the GTPases involved in the transforming growth factor-beta (TGF-beta) signaling pathway initiated epithelial-mesenchymal transitions. These findings demonstrate a key role of the ARHGAP1 protein in the disruption of the cell adhesion and simultaneously allow for a better understanding of the molecular mechanism of the reduced cell adhesion leading to the subsequent metastasis. The conclusions of this study corroborate the hypothesis that chemotherapy with doxorubicin may increase the risk of metastases in drug-resistant breast cancer cells.
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Affiliation(s)
- Imrich Géci
- Department of Medical and Clinical Biophysics, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Trieda SNP 1, 04011 Košice, Slovakia
| | - Peter Bober
- Department of Medical and Clinical Biophysics, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Trieda SNP 1, 04011 Košice, Slovakia
| | - Eva Filová
- Institute of Experimental Medicine, Czech Academy of Sciences, Vídeňská 1083, 142 00 Prague, Czech Republic
| | - Evžen Amler
- Institute of Experimental Medicine, Czech Academy of Sciences, Vídeňská 1083, 142 00 Prague, Czech Republic
| | - Ján Sabo
- Department of Medical and Clinical Biophysics, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Trieda SNP 1, 04011 Košice, Slovakia
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11
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Bhattacharya A. A fresh cup of DCAF: DCAF13 implicated in a neuromuscular disorder. Eur J Hum Genet 2023; 31:613-614. [PMID: 36991069 PMCID: PMC10250295 DOI: 10.1038/s41431-023-01340-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 03/13/2023] [Indexed: 03/31/2023] Open
Affiliation(s)
- Aniket Bhattacharya
- Department of Neuroscience and Cell Biology, Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, 08901, USA.
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Wei S, Lu K, Xing J, Yu W. A multidimensional pan-cancer analysis of DCAF13 and its protumorigenic effect in lung adenocarcinoma. FASEB J 2023; 37:e22849. [PMID: 36884358 DOI: 10.1096/fj.202201022rrr] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 01/31/2023] [Accepted: 02/17/2023] [Indexed: 03/09/2023]
Abstract
DCAF13 is a substrate recognition protein in the ubiquitin-proteasome system with oncogenic effects in several malignant tumors. However, it is unclear that the relationship between DCAF13 expression pattern and prognosis across different cancer types. Also unknown is the biological function or effects on the immune microenvironment of DCAF13. In this study, we parsed multiple public databases to explore the potential tumorigenic actions of DCAF13, including correlations with prognosis, microsatellite instability (MSI), tumor mutational burden (TMB), immune checkpoint genes, immune cell infiltration, and immunotherapy response in pan-cancer. Moreover, we validated DCAF13 expression in a tissue microarray by immunohistochemistry and investigate its effects in vitro and in vivo. The results showed that DCAF13 was upregulated in 17 cancer types and correlated with poor prognosis in many cancers. Also, the correlation between DCAF13 and TMB was found in 14 cancers as well as MSI in nine. The expression level of DCAF13 was found to be notably correlated with immune cell infiltration, showing a negative correlation with CD4 T cell infiltration and a positive correlation with neutrophil infiltration. The oncogene DCAF13 expression was shown to have a positive correlation with CD274 or ADORA2A and negative correlation with VSIR, TNFRSF4, or TNFRSF14 across large subsets of human cancers. Finally, we observed that DCAF13 was highly expressed in a tissue microarray of lung cancer. In immunocompromised mouse models, xenograft growth of human lung cancer cells was significantly inhibited by DCAF13 knockdown. Our results highlighted the value of DCAF13 as a promising independent predictor of poor prognosis through numerous biological processes. High DCAF13 expression often predicts suppressive immune microenvironment and immunotherapy resistance in a pan-cancer context.
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Affiliation(s)
- Shan Wei
- Department of Respiratory and Critical Care Medicine, The Affiliated People's Hospital of Ningbo University (Ningbo Yinzhou People's Hospital), Ningbo, People's Republic of China
| | - Kaining Lu
- Department of Urology, Ningbo First Hospital, Ningbo, People's Republic of China
| | - Jing Xing
- Department of Respiratory and Critical Care Medicine, The Affiliated People's Hospital of Ningbo University (Ningbo Yinzhou People's Hospital), Ningbo, People's Republic of China
| | - Wanjun Yu
- Department of Respiratory and Critical Care Medicine, The Affiliated People's Hospital of Ningbo University (Ningbo Yinzhou People's Hospital), Ningbo, People's Republic of China
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Ten Years of CRISPRing Cancers In Vitro. Cancers (Basel) 2022; 14:cancers14235746. [PMID: 36497228 PMCID: PMC9738354 DOI: 10.3390/cancers14235746] [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: 10/11/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 11/24/2022] Open
Abstract
Cell lines have always constituted a good investigation tool for cancer research, allowing scientists to understand the basic mechanisms underlying the complex network of phenomena peculiar to the transforming path from a healthy to cancerous cell. The introduction of CRISPR in everyday laboratory activity and its relative affordability greatly expanded the bench lab weaponry in the daily attempt to better understand tumor biology with the final aim to mitigate cancer's impact in our lives. In this review, we aim to report how this genome editing technique affected in the in vitro modeling of different aspects of tumor biology, its several declinations, and analyze the advantages and drawbacks of each of them.
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Tang J, Wu Z, Wang X, Hou Y, Bai Y, Tian Y. Hypoxia-Regulated lncRNA USP2-AS1 Drives Head and Neck Squamous Cell Carcinoma Progression. Cells 2022; 11:3407. [PMID: 36359803 PMCID: PMC9655520 DOI: 10.3390/cells11213407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/16/2022] [Accepted: 10/24/2022] [Indexed: 07/30/2023] Open
Abstract
The role of hypoxia-regulated long non-coding RNA (lncRNA) in the development of head and neck squamous cell carcinoma (HNSCC) remains to be elucidated. In the current study, we initially screened hypoxia-regulated lncRNA in HNSCC cells by RNA-seq, before focusing on the rarely annotated lncRNA USP2 antisense RNA 1 (USP2-AS1). We determined that USP2-AS1 is a direct target of HIF1α and is remarkably elevated in HNSCC compared with matched normal tissues. Patients with a higher level of USP2-AS1 suffered a poor prognosis. Next, loss- and gain-of-function assays revealed that USP2-AS1 promoted cell proliferation and invasion in vitro and in vivo. Mechanically, RNA pulldown and LC-MS/MS demonstrated that the E3 ligase DDB1- and CUL4-associated factor 13 (DCAF13) is one of the binding partners to USP2-AS1 in HNSCC cells. In addition, we assumed that USP2-AS1 regulates the activity of DCAF13 by targeting its substrate ATR. Moreover, the knockdown of DCAF13 restored the elevated cell proliferation and growth levels achieved by USP2-AS1 overexpression. Altogether, we found that lncRNA USP2-AS1 functions as a HIF1α-regulated oncogenic lncRNA and promotes HNSCC cell proliferation and growth by interacting and modulating the activity of DCAF13.
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Affiliation(s)
- Jianmin Tang
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China
- Institute of Radiotherapy and Oncology, Soochow University, Suzhou 215004, China
- Department of Radiation Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, No.160 Pujian Road, Shanghai 200127, China
| | - Zheng Wu
- Department of Radiation Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, No.160 Pujian Road, Shanghai 200127, China
| | - Xiaohang Wang
- Department of Radiation Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, No.160 Pujian Road, Shanghai 200127, China
| | - Yanli Hou
- Department of Radiation Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, No.160 Pujian Road, Shanghai 200127, China
| | - Yongrui Bai
- Department of Radiation Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, No.160 Pujian Road, Shanghai 200127, China
| | - Ye Tian
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China
- Institute of Radiotherapy and Oncology, Soochow University, Suzhou 215004, China
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