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Kim Y, Ko JY, Kong HK, Lee M, Chung W, Lim S, Son D, Oh S, Park JW, Kim DY, Lee M, Han W, Park WY, Yoo KH, Park JH. Hypomethylation of ATP1A1 Is Associated with Poor Prognosis and Cancer Progression in Triple-Negative Breast Cancer. Cancers (Basel) 2024; 16:1666. [PMID: 38730618 PMCID: PMC11083557 DOI: 10.3390/cancers16091666] [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: 03/22/2024] [Revised: 04/15/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Dysregulated DNA methylation in cancer is critical in the transcription machinery associated with cancer progression. Triple-negative breast cancer (TNBC) is the most aggressive breast cancer subtype, but no treatment targeting TNBC biomarkers has yet been developed. To identify specific DNA methylation patterns in TNBC, methyl-binding domain protein 2 (MBD) sequencing data were compared in TNBC and the three other major breast cancer subtypes. Integrated analysis of DNA methylation and gene expression identified a gene set showing a correlation between DNA methylation and gene expression. ATPase Na+/K+-transporting subunit alpha 1 (ATP1A1) was found to be specifically hypomethylated in the coding sequence (CDS) region and to show increased expression in TNBC. The Cancer Genome Atlas (TCGA) database also showed that hypomethylation and high expression of ATP1A1 were strongly associated with poor survival in patients with TNBC. Furthermore, ATP1A1 knockdown significantly reduced the viability and tumor-sphere formation of TNBC cells. These results suggest that the hypomethylation and overexpression of ATP1A1 could be a prognostic marker in TNBC and that the manipulation of ATP1A1 expression could be a therapeutic target in this disease.
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Affiliation(s)
- Yesol Kim
- Department of Biological Science, Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (Y.K.); (J.Y.K.)
| | - Je Yeong Ko
- Department of Biological Science, Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (Y.K.); (J.Y.K.)
| | - Hyun Kyung Kong
- Department of Biological Science, Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (Y.K.); (J.Y.K.)
| | - Minyoung Lee
- Department of Biological Science, Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (Y.K.); (J.Y.K.)
| | - Woosung Chung
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Republic of Korea
| | - Sera Lim
- Department of Biological Science, Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (Y.K.); (J.Y.K.)
| | - Dasom Son
- Department of Biological Science, Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (Y.K.); (J.Y.K.)
| | - Sumin Oh
- Department of Biological Science, Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (Y.K.); (J.Y.K.)
| | - Jee Won Park
- Department of Biological Science, Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (Y.K.); (J.Y.K.)
| | - Do Yeon Kim
- Department of Biological Science, Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (Y.K.); (J.Y.K.)
| | - Minju Lee
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Wonshik Han
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Department of Surgery, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Republic of Korea
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul 06355, Republic of Korea
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Kyung Hyun Yoo
- Department of Biological Science, Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (Y.K.); (J.Y.K.)
| | - Jong Hoon Park
- Department of Biological Science, Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (Y.K.); (J.Y.K.)
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Soumoy L, Genbauffe A, Mouchart L, Sperone A, Trelcat A, Mukeba-Harchies L, Wells M, Blankert B, Najem A, Ghanem G, Saussez S, Journe F. ATP1A1 is a promising new target for melanoma treatment and can be inhibited by its physiological ligand bufalin to restore targeted therapy efficacy. Cancer Cell Int 2024; 24:8. [PMID: 38178183 PMCID: PMC10765859 DOI: 10.1186/s12935-023-03196-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 12/26/2023] [Indexed: 01/06/2024] Open
Abstract
Despite advancements in treating metastatic melanoma, many patients exhibit resistance to targeted therapies. Our study focuses on ATP1A1, a sodium pump subunit associated with cancer development. We aimed to assess ATP1A1 prognostic value in melanoma patients and examine the impact of its ligand, bufalin, on melanoma cell lines in vitro and in vivo. High ATP1A1 expression (IHC) correlated with reduced overall survival in melanoma patients. Resistance to BRAF inhibitor was linked to elevated ATP1A1 levels in patient biopsies (IHC, qPCR) and cell lines (Western blot, qPCR). Additionally, high ATP1A1 mRNA expression positively correlated with differentiation/pigmentation markers based on data from The Cancer Genome Atlas (TCGA) databases and Verfaillie proliferative gene signature analysis. Bufalin specifically targeted ATP1A1 in caveolae, (proximity ligation assay) and influenced Src phosphorylation (Western blot), thereby disrupting multiple signaling pathways (phosphokinase array). In vitro, bufalin induced apoptosis in melanoma cell lines by acting on ATP1A1 (siRNA experiments) and, in vivo, significantly impeded melanoma growth using a nude mouse xenograft model with continuous bufalin delivery via an osmotic pump. In conclusion, our study demonstrates that ATP1A1 could serve as a prognostic marker for patient survival and a predictive marker for response to BRAF inhibitor therapy. By targeting ATP1A1, bufalin inhibited cell proliferation, induced apoptosis in vitro, and effectively suppressed tumor development in mice. Thus, our findings strongly support ATP1A1 as a promising therapeutic target, with bufalin as a potential agent to disrupt its tumor-promoting activity.
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Affiliation(s)
- Laura Soumoy
- Laboratory of Human Anatomy and Experimental Oncology, Faculty of Medicine and Pharmacy, University of Mons (UMONS), 7000, Mons, Belgium.
- Institut National de la Santé et de la Recherche Médicale (INSERM) U981, Gustave Roussy Cancer Campus, Villejuif, France.
| | - Aline Genbauffe
- Laboratory of Human Anatomy and Experimental Oncology, Faculty of Medicine and Pharmacy, University of Mons (UMONS), 7000, Mons, Belgium
| | - Lena Mouchart
- Laboratory of Human Anatomy and Experimental Oncology, Faculty of Medicine and Pharmacy, University of Mons (UMONS), 7000, Mons, Belgium
| | - Alexandra Sperone
- Laboratory of Human Anatomy and Experimental Oncology, Faculty of Medicine and Pharmacy, University of Mons (UMONS), 7000, Mons, Belgium
| | - Anne Trelcat
- Laboratory of Human Anatomy and Experimental Oncology, Faculty of Medicine and Pharmacy, University of Mons (UMONS), 7000, Mons, Belgium
| | - Léa Mukeba-Harchies
- Laboratory of Human Anatomy and Experimental Oncology, Faculty of Medicine and Pharmacy, University of Mons (UMONS), 7000, Mons, Belgium
| | - Mathilde Wells
- Laboratory of Pharmaceutical Analysis, Faculty of Medicine and Pharmacy, University of Mons (UMONS), 7000, Mons, Belgium
| | - Bertrand Blankert
- Laboratory of Pharmaceutical Analysis, Faculty of Medicine and Pharmacy, University of Mons (UMONS), 7000, Mons, Belgium
| | - Ahmad Najem
- Laboratory of Clinical and Experimental Oncology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), 1000, Brussels, Belgium
| | - Ghanem Ghanem
- Laboratory of Clinical and Experimental Oncology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), 1000, Brussels, Belgium
| | - Sven Saussez
- Laboratory of Human Anatomy and Experimental Oncology, Faculty of Medicine and Pharmacy, University of Mons (UMONS), 7000, Mons, Belgium
- Department of Otolaryngology and Head and Neck Surgery, CHU Saint-Pierre, 1000, Brussels, Belgium
| | - Fabrice Journe
- Laboratory of Human Anatomy and Experimental Oncology, Faculty of Medicine and Pharmacy, University of Mons (UMONS), 7000, Mons, Belgium.
- Laboratory of Clinical and Experimental Oncology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), 1000, Brussels, Belgium.
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3
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Duardo RC, Guerra F, Pepe S, Capranico G. Non-B DNA structures as a booster of genome instability. Biochimie 2023; 214:176-192. [PMID: 37429410 DOI: 10.1016/j.biochi.2023.07.002] [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: 03/29/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/12/2023]
Abstract
Non-canonical secondary structures (NCSs) are alternative nucleic acid structures that differ from the canonical B-DNA conformation. NCSs often occur in repetitive DNA sequences and can adopt different conformations depending on the sequence. The majority of these structures form in the context of physiological processes, such as transcription-associated R-loops, G4s, as well as hairpins and slipped-strand DNA, whose formation can be dependent on DNA replication. It is therefore not surprising that NCSs play important roles in the regulation of key biological processes. In the last years, increasing published data have supported their biological role thanks to genome-wide studies and the development of bioinformatic prediction tools. Data have also highlighted the pathological role of these secondary structures. Indeed, the alteration or stabilization of NCSs can cause the impairment of transcription and DNA replication, modification in chromatin structure and DNA damage. These events lead to a wide range of recombination events, deletions, mutations and chromosomal aberrations, well-known hallmarks of genome instability which are strongly associated with human diseases. In this review, we summarize molecular processes through which NCSs trigger genome instability, with a focus on G-quadruplex, i-motif, R-loop, Z-DNA, hairpin, cruciform and multi-stranded structures known as triplexes.
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Affiliation(s)
- Renée C Duardo
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Federico Guerra
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Simona Pepe
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126, Bologna, Italy.
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Wang B, Huang L, Ye S, Zheng Z, Liao S. Identification of Novel Prognostic Biomarkers That are Associated with Immune Microenvironment Based on GABA-Related Molecular Subtypes in Gastric Cancer. Pharmgenomics Pers Med 2023; 16:665-679. [PMID: 37405024 PMCID: PMC10315139 DOI: 10.2147/pgpm.s411862] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/10/2023] [Indexed: 07/06/2023] Open
Abstract
Background Gamma-aminobutyric acid (GABA) plays an important role in tumorigenesis and progression. Despite this, the role of Reactome GABA receptor activation (RGRA) on gastric cancer (GC) remains unclear. This study was intended to screen RGRA-related genes in GC and investigate their prognostic value. Methods GSVA algorithm was used to assess the score of RGRA. GC patients were divided into two subtypes based on the median score of RGRA. GSEA, functional enrichment analysis, and immune infiltration analysis were performed between the two subgroups. Then, differentially expressed analysis, and weighted gene co-expression network analysis (WGCNA) were used to identify RGRA-related genes. The prognosis and expression of core genes were analyzed and validated in the TCGA database, GEO database, and clinical samples. ssGSEA and ESTIMATE algorithms were used to assess the immune cell infiltration in the low- and high-core genes subgroups. Results High-RGRA subtype had a poor prognosis and activated immune-related pathways, as well as an activated immune microenvironment. ATP1A2 was identified to be the core gene. The expression of ATP1A2 was associated with the overall survival rate and tumor stage, and its expression was down-regulated in GC patients. Furthermore, ATP1A2 expression was positively correlated with the level of immune cells, including B cells, CD8 T cells, cytotoxic cells, DC, eosinophils, macrophages, mast cells, NK cells, and T cells. Conclusion Two RGRA-related molecular subtypes were identified that could predict the outcome in GC patients. ATP1A2 was a core immunoregulatory gene and was associated with prognosis and immune cell infiltration in GC.
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Affiliation(s)
- Beibei Wang
- Department of Gastroenterology and Hepatology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, 510080, People’s Republic of China
| | - Linlin Huang
- Department of Gastroenterology and Hepatology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, 510080, People’s Republic of China
| | - Shanliang Ye
- Department of Gastroenterology and Hepatology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, 510080, People’s Republic of China
| | - Zhongwen Zheng
- Department of Gastroenterology and Hepatology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, 510080, People’s Republic of China
| | - Shanying Liao
- Department of Gastroenterology and Hepatology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, 510080, People’s Republic of China
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5
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Ma J, Zhang L, Li S, Liu H. BRPCA: Bounded Robust Principal Component Analysis to Incorporate Similarity Network for N7-Methylguanosine(m 7G) Site-Disease Association Prediction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:3295-3306. [PMID: 34469307 DOI: 10.1109/tcbb.2021.3109055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Recent studies have revealed that N7-methylguanosine(m7G) plays a pivotal role in various biological processes and disease pathogenesis. To date, transcriptome-wide m7G modification sites have been identified by high-throughput sequencing approaches, and some related information has been recorded in a few biological databases. However, the mechanism of site action in disease remains uncharted. Wet experiments can help identify true m7G sites with high confidence, but it is time-consuming to find the true ones in such a large number of sites, which will also cost too much. Thus, computational methods are emergently needed to predict the associations between m7G sites and various diseases, thus help to uncover potential active sites for specific diseases. In this article, we proposed a bounded robust principal component analysis (BRPCA) method to predict unknown m7G-disease association based on similarity information. Importantly, BRPCA tolerates the noise and redundancy existing in association and similarity information. Moreover, a suitable bounded constraint is incorporated into BRPCA to ensure that the predicted association scores locate in a meaningful interval. The extensive experiments demonstrate the superiority and robustness of the BRPCA.
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Chen YI, Chang CC, Hsu MF, Jeng YM, Tien YW, Chang MC, Chang YT, Hu CM, Lee WH. Homophilic ATP1A1 binding induces activin A secretion to promote EMT of tumor cells and myofibroblast activation. Nat Commun 2022; 13:2945. [PMID: 35618735 PMCID: PMC9135720 DOI: 10.1038/s41467-022-30638-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 05/09/2022] [Indexed: 12/30/2022] Open
Abstract
Tumor cells with diverse phenotypes and biological behaviors are influenced by stromal cells through secretory factors or direct cell-cell contact. Pancreatic ductal adenocarcinoma (PDAC) is characterized by extensive desmoplasia with fibroblasts as the major cell type. In the present study, we observe enrichment of myofibroblasts in a juxta-tumoral position with tumor cells undergoing epithelial-mesenchymal transition (EMT) that facilitates invasion and correlates with a worse clinical prognosis in PDAC patients. Direct cell-cell contacts forming heterocellular aggregates between fibroblasts and tumor cells are detected in primary pancreatic tumors and circulating tumor microemboli (CTM). Mechanistically, ATP1A1 overexpressed in tumor cells binds to and reorganizes ATP1A1 of fibroblasts that induces calcium oscillations, NF-κB activation, and activin A secretion. Silencing ATP1A1 expression or neutralizing activin A secretion suppress tumor invasion and colonization. Taken together, these results elucidate the direct interplay between tumor cells and bound fibroblasts in PDAC progression, thereby providing potential therapeutic opportunities for inhibiting metastasis by interfering with these cell-cell interactions.
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Affiliation(s)
- Yi-Ing Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Chin-Chun Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Master Program for Cancer Biology and Drug Discovery, China Medical University and Academia Sinica, Taichung, Taiwan
| | - Min-Fen Hsu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yung-Ming Jeng
- Department of Pathology, National Taiwan University Hospital, Graduate Institute of Pathology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yu-Wen Tien
- Department of Surgery, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ming-Chu Chang
- Department of Internal Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Yu-Ting Chang
- Department of Internal Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chun-Mei Hu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.
| | - Wen-Hwa Lee
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.
- Drug Development Center, China Medical University, Taichung, Taiwan.
- Department of Biological Chemistry, University of California, Irvine, USA.
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Identification of Potential Biomarkers for Progression and Prognosis of Bladder Cancer by Comprehensive Bioinformatics Analysis. JOURNAL OF ONCOLOGY 2022; 2022:1802706. [PMID: 35498536 PMCID: PMC9042640 DOI: 10.1155/2022/1802706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/22/2022] [Indexed: 11/23/2022]
Abstract
Background. Bladder cancer (BLCA) is a highly malignant tumor that develops in the urinary system. Identification of biomarkers in progression and prognosis is crucial for the treatment of BLCA. BLCA-related differentially expressed genes (DEGs) were authenticated by screening the DEGs and weighted gene coexpression network analysis (WGCNA). LASSO and SVM-RFE algorithms were utilized to screen the feature genes in BLCA. Survival analysis was performed using the Kaplan–Meier curve provided by the ‘survival' R package. The BLCA samples were clustered by hclust based on the immune score matrix calculated by the single-sample GSEA (ssGSEA) algorithm. The immune, stromal, and ESTIMATE scores of each BLCA patient were calculated by applying the ESTIMATE algorithm. ssGSEA was conducted to explore the function of characteristic genes in BLCA. The expression of characteristic genes in clinical cancer tissue, and the pericancerous tissue of BLCA patients was verified using qRT-PCR assays. A total of 189 BLCA-related DEGs were identified. Fourteen feature genes were defined by LASSO and SVM-RFE algorithms. Five characteristic genes, including SMYD2, GAPDHP1, ATP1A2, CILP, and THSD4, were related to the OS of BLCA. The correlation analysis of five characteristic genes and clinicopathological factors showed that five genes played a role in the progression of BLCA. Additionally, the expression of five characteristic genes in clinical cancer tissues and pericarcinomatous tissues from BLCA patients was verified by qRT-PCR, which was consistent with the result from the public database. Finally, we discovered five prognostic genes linked to BLCA progression, which might serve as a theoretical basis for prognosis and treatment targets for BLCA patients.
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das Chagas PF, de Sousa GR, Veronez LC, Martins-da-Silva A, Corrêa CAP, Cruzeiro GAV, Nagano LFP, Queiroz RGDP, Marie SKN, Brandalise SR, Scrideli CA, Tone LG, Valera ET. Identification of ITPR1 as a Hub Gene of Group 3 Medulloblastoma and Coregulated Genes with Potential Prognostic Values. J Mol Neurosci 2021; 72:633-641. [PMID: 34822110 DOI: 10.1007/s12031-021-01942-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/04/2021] [Indexed: 01/03/2023]
Abstract
The Group 3 Medulloblastoma (Grp3-MB) is an aggressive molecular subtype with a high incidence of metastasis and deaths. In this study, were used an RNA sequencing data (RNA-Seq) from a Brazilian cohort of MBs to identify hub genes associated with the metastatic risk. Data validation were performed by using multiple large datasets from MBs (GSE85217, GSE37418, and EGAS00001001953). DESeq2 package in R software was used to identify the differentially expressed genes (DEGs) in our RNA-Seq data. The DEGs data were accessed to construct the modules/graphs of co-expression and to identify hub genes through Cytoscape platform. The coregulated genes were enriched by the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and the protein-protein interaction (PPI) network was visualized by Cytoscape. The Kaplan-Meier plotter and ROC curves were used to validate the diagnostic and prognostic values of specific biomarkers identified through this model. We identified that inositol 1,4,5-trisphosphate receptor type 1 (ITPR1) as a downregulated hub gene, with a high diagnostic accuracy to Grp3-MBs and associated with tumor metastasis. In addition, we identified genes significantly correlated with ITPR1 that were associated with metastasis in Grp3-MB (ATP1A2, MTTL7A, and RGL1) and worst overall survival in MBs (ANTXR1 and RGL1). Our findings suggest that the ITPR1 hub gene is potentially involved in the metastatic process for Grp3-MB. Our data also provide evidence of targets that may serve as prognostic predictors and/or regulators for the metastatic process that maybe explored for further research of individualized therapy to Grp3-MBs.
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Affiliation(s)
- Pablo Ferreira das Chagas
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes, Ribeirão Preto, CEP, 390014049-900, Brazil.
| | - Graziella Ribeiro de Sousa
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes, Ribeirão Preto, CEP, 390014049-900, Brazil
| | - Luciana Chain Veronez
- Department of Pediatrics, Ribeirão Preto Medical School, Clinics Hospital, University of São Paulo Ribeirão Preto, Ribeirão, Brazil
| | - Andrea Martins-da-Silva
- Department of Pediatrics, Ribeirão Preto Medical School, Clinics Hospital, University of São Paulo Ribeirão Preto, Ribeirão, Brazil
| | - Carolina Alves Pereira Corrêa
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes, Ribeirão Preto, CEP, 390014049-900, Brazil
| | - Gustavo Alencastro Veiga Cruzeiro
- Department of Pediatrics, Ribeirão Preto Medical School, Clinics Hospital, University of São Paulo Ribeirão Preto, Ribeirão, Brazil.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Luis Fernando Peinado Nagano
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes, Ribeirão Preto, CEP, 390014049-900, Brazil
| | - Rosane Gomes de Paula Queiroz
- Department of Pediatrics, Ribeirão Preto Medical School, Clinics Hospital, University of São Paulo Ribeirão Preto, Ribeirão, Brazil
| | - Suely Kazue Nagahashi Marie
- Laboratory of Cellular and Molecular Biology, Department of Neurology, Faculdade de Medicina FMUSP, Universidade de SãoPaulo, São Paulo, SP, Brazil
| | | | - Carlos Alberto Scrideli
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes, Ribeirão Preto, CEP, 390014049-900, Brazil.,Department of Pediatrics, Ribeirão Preto Medical School, Clinics Hospital, University of São Paulo Ribeirão Preto, Ribeirão, Brazil
| | - Luiz Gonzaga Tone
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes, Ribeirão Preto, CEP, 390014049-900, Brazil.,Department of Pediatrics, Ribeirão Preto Medical School, Clinics Hospital, University of São Paulo Ribeirão Preto, Ribeirão, Brazil
| | - Elvis Terci Valera
- Department of Pediatrics, Ribeirão Preto Medical School, Clinics Hospital, University of São Paulo Ribeirão Preto, Ribeirão, Brazil
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9
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Themistocleous SC, Yiallouris A, Tsioutis C, Zaravinos A, Johnson EO, Patrikios I. Clinical significance of P-class pumps in cancer. Oncol Lett 2021; 22:658. [PMID: 34386080 PMCID: PMC8298992 DOI: 10.3892/ol.2021.12919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/12/2021] [Indexed: 12/16/2022] Open
Abstract
P-class pumps are specific ion transporters involved in maintaining intracellular/extracellular ion homeostasis, gene transcription, and cell proliferation and migration in all eukaryotic cells. The present review aimed to evaluate the role of P-type pumps [Na+/K+ ATPase (NKA), H+/K+ ATPase (HKA) and Ca2+-ATPase] in cancer cells across three fronts, namely structure, function and genetic expression. It has been shown that administration of specific P-class pumps inhibitors can have different effects by: i) Altering pump function; ii) inhibiting cell proliferation; iii) inducing apoptosis; iv) modifying metabolic pathways; and v) induce sensitivity to chemotherapy and lead to antitumor effects. For example, the NKA β2 subunit can be downregulated by gemcitabine, resulting in increased apoptosis of cancer cells. The sarcoendoplasmic reticulum calcium ATPase can be inhibited by thapsigargin resulting in decreased prostate tumor volume, whereas the HKA α subunit can be affected by proton pump inhibitors in gastric cancer cell lines, inducing apoptosis. In conclusion, the present review highlighted the central role of P-class pumps and their possible use and role as anticancer cellular targets for novel therapeutic chemical agents.
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Affiliation(s)
- Sophia C Themistocleous
- Department of Medicine, School of Medicine, European University Cyprus, 2404 Nicosia, Cyprus
| | - Andreas Yiallouris
- Department of Medicine, School of Medicine, European University Cyprus, 2404 Nicosia, Cyprus
| | - Constantinos Tsioutis
- Department of Medicine, School of Medicine, European University Cyprus, 2404 Nicosia, Cyprus
| | - Apostolos Zaravinos
- Department of Life Sciences, School of Sciences, European University Cyprus, 2404 Nicosia, Cyprus.,College of Medicine, Member of Qatar University Health, Qatar University, 2713 Doha, Qatar
| | - Elizabeth O Johnson
- Department of Medicine, School of Medicine, European University Cyprus, 2404 Nicosia, Cyprus
| | - Ioannis Patrikios
- Department of Medicine, School of Medicine, European University Cyprus, 2404 Nicosia, Cyprus
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10
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Bajaj R, Kundu ST, Grzeskowiak CL, Fradette JJ, Scott KL, Creighton CJ, Gibbons DL. IMPAD1 and KDELR2 drive invasion and metastasis by enhancing Golgi-mediated secretion. Oncogene 2020; 39:5979-5994. [PMID: 32753652 PMCID: PMC7539228 DOI: 10.1038/s41388-020-01410-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 07/14/2020] [Accepted: 07/23/2020] [Indexed: 01/12/2023]
Abstract
Non-small cell lung cancer (NSCLC) is the deadliest form of cancer worldwide, due in part to its proclivity to metastasize. Identifying novel drivers of invasion and metastasis holds therapeutic potential for the disease. We conducted a gain-of-function invasion screen, which identified two separate hits, IMPAD1 and KDELR2, as robust, independent drivers of lung cancer invasion and metastasis. Given that IMPAD1 and KDELR2 are known to be localized to the ER-Golgi pathway, we studied their common mechanism of driving in vitro invasion and in vivo metastasis and demonstrated that they enhance Golgi-mediated function and secretion. Therapeutically inhibiting matrix metalloproteases (MMPs) suppressed both IMPAD1- and KDELR2-mediated invasion. The hits from this unbiased screen and the mechanistic validation highlight Golgi function as one of the key cellular features altered during invasion and metastasis.
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Affiliation(s)
- Rakhee Bajaj
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Samrat T Kundu
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA.
| | - Caitlin L Grzeskowiak
- Department of Molecular and Human Genetics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Medicine, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jared J Fradette
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Kenneth L Scott
- Department of Medicine, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chad J Creighton
- Department of Medicine, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Don L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA.
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA.
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11
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Chen F, Li Y, Qin N, Wang F, Du J, Wang C, Du F, Jiang T, Jiang Y, Dai J, Hu Z, Lu C, Shen H. RNA-seq analysis identified hormone-related genes associated with prognosis of triple negative breast cancer. J Biomed Res 2020; 34:129-138. [PMID: 32305967 DOI: 10.7555/jbr.34.20190111] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Triple negative breast cancer (TNBC) is an aggressive subtype of breast cancer that currently lacks effective biomarkers and therapeutic targets required to investigate the diagnosis and treatment of TNBC. Here we performed a comprehensive differential analysis of 165 TNBC samples by integrating RNA-seq data of breast tumor tissues and adjacent normal tissues from both our cohort and The Cancer Genome Atlas (TCGA). Pathway enrichment analysis was conducted to evaluate the biological function of TNBC-specific expressed genes. Further multivariate Cox proportional hazard regression was performed to evaluate the effect of these genes on TNBC prognosis. In this report, we identified a total of 148 TNBC-specific expressed genes that were primarily enriched in mammary gland morphogenesis and hormone levels related pathways, suggesting that mammary gland morphogenesis might play a unique role in TNBC patients differing from other breast cancer types. Further survival analysis revealed that nine genes ( FSIP1, ADCY5, FSD1, HMSD, CMTM5, AFF3, CYP2A7, ATP1A2, and C11orf86) were significantly associated with the prognosis of TNBC patients, while three of them ( ADCY5, CYP2A7, and ATP1A2) were involved in the hormone-related pathways. These findings indicated the vital role of the hormone-related genes in TNBC tumorigenesis and may provide some independent prognostic markers as well as novel therapeutic targets for TNBC.
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Affiliation(s)
- Fei Chen
- Department of Breast Surgery, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu 210004, China;Department of Epidemiology, Center for Global Health, School of Public Health
| | - Yuancheng Li
- Department of Epidemiology, Center for Global Health, School of Public Health
| | - Na Qin
- Department of Epidemiology, Center for Global Health, School of Public Health
| | - Fengliang Wang
- Department of Breast Surgery, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu 210004, China
| | - Jiangbo Du
- Department of Epidemiology, Center for Global Health, School of Public Health
| | - Cheng Wang
- Department of Epidemiology, Center for Global Health, School of Public Health
| | - Fangzhi Du
- Department of Clinical Management, National Center for STD Control, Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, Jiangsu 210042, China
| | - Tao Jiang
- Department of Epidemiology, Center for Global Health, School of Public Health
| | - Yue Jiang
- Department of Epidemiology, Center for Global Health, School of Public Health
| | - Juncheng Dai
- Department of Epidemiology, Center for Global Health, School of Public Health
| | - Zhibin Hu
- Department of Epidemiology, Center for Global Health, School of Public Health
| | - Cheng Lu
- Department of Breast Surgery, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu 210004, China
| | - Hongbing Shen
- Department of Epidemiology, Center for Global Health, School of Public Health
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12
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Lu J, Lu Y, Ding Y, Xiao Q, Liu L, Cai Q, Kong Y, Bai Y, Yu T. DNLC: differential network local consistency analysis. BMC Bioinformatics 2019; 20:489. [PMID: 31874600 PMCID: PMC6929334 DOI: 10.1186/s12859-019-3046-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 08/21/2019] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND The biological network is highly dynamic. Functional relations between genes can be activated or deactivated depending on the biological conditions. On the genome-scale network, subnetworks that gain or lose local expression consistency may shed light on the regulatory mechanisms related to the changing biological conditions, such as disease status or tissue developmental stages. RESULTS In this study, we develop a new method to select genes and modules on the existing biological network, in which local expression consistency changes significantly between clinical conditions. The method is called DNLC: Differential Network Local Consistency. In simulations, our algorithm detected artificially created local consistency changes effectively. We applied the method on two publicly available datasets, and the method detected novel genes and network modules that were biologically plausible. CONCLUSIONS The new method is effective in finding modules in which the gene expression consistency change between clinical conditions. It is a useful tool that complements traditional differential expression analyses to make discoveries from gene expression data. The R package is available at https://cran.r-project.org/web/packages/DNLC.
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Affiliation(s)
- Jianwei Lu
- School of Software Engineering, Tongji University, Shanghai, China
- Institute of Advanced Translational Medicine, Tongji University, Shanghai, China
| | - Yao Lu
- School of Software Engineering, Tongji University, Shanghai, China
| | - Yusheng Ding
- School of Software Engineering, Tongji University, Shanghai, China
| | - Qingyang Xiao
- Department of Environmental Health, Emory University, Atlanta, GA USA
| | - Linqing Liu
- School of Software Engineering, Tongji University, Shanghai, China
| | - Qingpo Cai
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA USA
| | - Yunchuan Kong
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA USA
| | - Yun Bai
- Department of Pharmaceutical Sciences, School of Pharmacy, Philadelphia College of Osteopathic Medicine, Georgia Campus, Suwanee, GA USA
| | - Tianwei Yu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA USA
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13
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A Humanized Yeast Phenomic Model of Deoxycytidine Kinase to Predict Genetic Buffering of Nucleoside Analog Cytotoxicity. Genes (Basel) 2019; 10:genes10100770. [PMID: 31575041 PMCID: PMC6826991 DOI: 10.3390/genes10100770] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/17/2019] [Accepted: 09/23/2019] [Indexed: 12/22/2022] Open
Abstract
Knowledge about synthetic lethality can be applied to enhance the efficacy of anticancer therapies in individual patients harboring genetic alterations in their cancer that specifically render it vulnerable. We investigated the potential for high-resolution phenomic analysis in yeast to predict such genetic vulnerabilities by systematic, comprehensive, and quantitative assessment of drug–gene interaction for gemcitabine and cytarabine, substrates of deoxycytidine kinase that have similar molecular structures yet distinct antitumor efficacy. Human deoxycytidine kinase (dCK) was conditionally expressed in the Saccharomyces cerevisiae genomic library of knockout and knockdown (YKO/KD) strains, to globally and quantitatively characterize differential drug–gene interaction for gemcitabine and cytarabine. Pathway enrichment analysis revealed that autophagy, histone modification, chromatin remodeling, and apoptosis-related processes influence gemcitabine specifically, while drug–gene interaction specific to cytarabine was less enriched in gene ontology. Processes having influence over both drugs were DNA repair and integrity checkpoints and vesicle transport and fusion. Non-gene ontology (GO)-enriched genes were also informative. Yeast phenomic and cancer cell line pharmacogenomics data were integrated to identify yeast–human homologs with correlated differential gene expression and drug efficacy, thus providing a unique resource to predict whether differential gene expression observed in cancer genetic profiles are causal in tumor-specific responses to cytotoxic agents.
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14
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Berral-Gonzalez A, Riffo-Campos AL, Ayala G. OMICfpp: a fuzzy approach for paired RNA-Seq counts. BMC Genomics 2019; 20:259. [PMID: 30940089 PMCID: PMC6444640 DOI: 10.1186/s12864-019-5496-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 01/29/2019] [Indexed: 12/16/2022] Open
Abstract
Background RNA sequencing is a widely used technology for differential expression analysis. However, the RNA-Seq do not provide accurate absolute measurements and the results can be different for each pipeline used. The major problem in statistical analysis of RNA-Seq and in the omics data in general, is the small sample size with respect to the large number of variables. In addition, experimental design must be taken into account and few tools consider it. Results We propose OMICfpp, a method for the statistical analysis of RNA-Seq paired design data. First, we obtain a p-value for each case-control pair using a binomial test. These p-values are aggregated using an ordered weighted average (OWA) with a given orness previously chosen. The aggregated p-value from the original data is compared with the aggregated p-value obtained using the same method applied to random pairs. These new pairs are generated using between-pairs and complete randomization distributions. This randomization p-value is used as a raw p-value to test the differential expression of each gene. The OMICfpp method is evaluated using public data sets of 68 sample pairs from patients with colorectal cancer. We validate our results through bibliographic search of the reported genes and using simulated data set. Furthermore, we compared our results with those obtained by the methods edgeR and DESeq2 for paired samples. Finally, we propose new target genes to validate these as gene expression signatures in colorectal cancer. OMICfpp is available at http://www.uv.es/ayala/software/OMICfpp_0.2.tar.gz. Conclusions Our study shows that OMICfpp is an accurate method for differential expression analysis in RNA-Seq data with paired design. In addition, we propose the use of randomized p-values pattern graphic as a powerful and robust method to select the target genes for experimental validation. Electronic supplementary material The online version of this article (10.1186/s12864-019-5496-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alberto Berral-Gonzalez
- Grupo de Investigación Bioinformática y Genómica Funcional. Laboratorio 19. Centro de Investigación del Cáncer (CiC-IBMCC, Universidad de Salamanca-CSIC, Campus Universitario Miguel de Unamuno s/n, Salamanca, 37007, Spain
| | - Angela L Riffo-Campos
- Universidad de La Frontera. Centro De Excelencia de Modelación y Computación Científica, C/ Montevideo 740, Temuco, Chile.
| | - Guillermo Ayala
- Universidad de Valencia. Departamento de Estadística e Investigación Operativa, Avda. Vicent Andrés Estellés, 1, Burjasot, 46100, Spain
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15
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Wang Q, Li SB, Zhao YY, Dai DN, Du H, Lin YZ, Ye JC, Zhao J, Xiao W, Mei Y, Xiao YT, Liu SC, Li Y, Xia YF, Song EW, Tang GH, Zhang WG, Li ZJ, Zheng XB, Cao DH, Li MZ, Zhong Q, Chen ZP, Qian CN, Fan W, Feng GK, Zeng MS. Identification of a sodium pump Na +/K + ATPase α1-targeted peptide for PET imaging of breast cancer. J Control Release 2018; 281:178-188. [PMID: 29777796 DOI: 10.1016/j.jconrel.2018.05.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 04/03/2018] [Accepted: 05/16/2018] [Indexed: 02/07/2023]
Abstract
The sodium pump Na+/K+ ATPase a1 subunit(NKA a1), an attractive cancer-related biomarker and therapeutic target, is closely related to the development and progression of several cancers including breast cancer. Currently, a NKA a1 inhibitor, UNBS1450, has already evidenced its great therapeutic potential in personalized cancer treatment. The ability of non-invasive imaging of NKA a1 expression would be useful for selecting cancer patients who may benefit from this drug. Here, we identified an S3 peptide that is specifically homed to breast cancer by phage display. All data of in vitro and in vivo experiments suggested the excellent targeting character of the S3 peptide. As the binding activity of the S3 phage was positively correlated to the level of NKA α1 expression in various breast cancer cells, NKA α1 was validated as the primary target of the S3 peptide. Based on immunohistochemistry staining result of 107 breast cancer patients, NKA α1 was verified to be a novel tracking marker and a prognostic predictor for breast cancer. Importantly, we proposed and validated an S3 peptide-based radiotracer 18F-ALF-NOTA-S3 for PET (Positron Emission Tomography) imaging of breast cancer and other NKA α1-overexpressing cancers, including hepatocellular carcinoma and non-small cell lung cancer, in mouse models. Our findings demonstrated the potential application of 18F-ALF-NOTA-S3 for visualization of NKA α1-positive lesions, which provide a new approach to character tumor phenotypic imaging.
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Affiliation(s)
- Qian Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Shi-Bing Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Yi-Ying Zhao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China; Department of Neurosurgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Da-Nian Dai
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Hui Du
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Yan-Zhu Lin
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Jia-Cong Ye
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Jing Zhao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Wei Xiao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Yan Mei
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Yi-Tai Xiao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Shi-Chu Liu
- Shenzhen Pingshan District People's Hospital, Shenzhen 518118, China
| | - Yan Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Yun-Fei Xia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Er-Wei Song
- Breast Cancer Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Gang-Hua Tang
- PET-CT Center, Department of Nuclear Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Wei-Guang Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Zhi-Jian Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Xiao-Bin Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - De-Hai Cao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Man-Zhi Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Qian Zhong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Zhong-Ping Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Chao-Nan Qian
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Wei Fan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China.
| | - Guo-Kai Feng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China.
| | - Mu-Sheng Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China.
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16
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Ogburn RN, Jin L, Meng H, Fitzgerald MC. Discovery of Tamoxifen and N-Desmethyl Tamoxifen Protein Targets in MCF-7 Cells Using Large-Scale Protein Folding and Stability Measurements. J Proteome Res 2017; 16:4073-4085. [PMID: 28927269 DOI: 10.1021/acs.jproteome.7b00442] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The proteins in an MCF-7 cell line were probed for tamoxifen (TAM) and n-desmethyl tamoxifen (NDT) induced stability changes using the Stability of Proteins from Rates of Oxidation (SPROX) technique in combination with two different quantitative proteomics strategies, including one based on SILAC and one based on isobaric mass tags. Over 1000 proteins were assayed for TAM- and NDT-induced protein stability changes, and a total of 163 and 200 protein hits were identified in the TAM and NDT studies, respectively. A subset of 27 high-confidence protein hits were reproducibly identified with both proteomics strategies and/or with multiple peptide probes. One-third of the high-confidence hits have previously established experimental links to the estrogen receptor, and nearly all of the high-confidence hits have established links to breast cancer. One high-confidence protein hit that has known estrogen receptor binding properties, Y-box binding protein 1 (YBX1), was further validated as a direct binding target of TAM using both the SPROX and pulse proteolysis techniques. Proteins with TAM- and/or NDT-induced expression level changes were also identified in the SILAC-SPROX experiments. These proteins with expression level changes included only a small fraction of those with TAM- and/or NDT-induced stability changes.
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Affiliation(s)
- Ryenne N Ogburn
- Department of Chemistry, Duke University , Durham, North Carolina 27708, United States
| | - Lorrain Jin
- Department of Chemistry, Duke University , Durham, North Carolina 27708, United States
| | - He Meng
- Department of Chemistry, Duke University , Durham, North Carolina 27708, United States
| | - Michael C Fitzgerald
- Department of Chemistry, Duke University , Durham, North Carolina 27708, United States
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