1
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Tatsch JM, Furman DP, Nobre RM, Wurzer KM, da Silva LC, Picheth GF, Ramos EA, Acco A, Klassen G. Dulaglutide as a demethylating agent to improve the outcome of breast cancer. Epigenomics 2023; 15:1309-1322. [PMID: 38174426 DOI: 10.2217/epi-2023-0332] [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] [Indexed: 01/05/2024] Open
Abstract
Background: Dulaglutide emerged as a promising therapeutic option for diabetes mellitus Type 2 (DM2). Aims: Owing to epigenetic similarities between the pathophysiology of DM2 and breast cancer (BC), we investigated the antitumor effect of dulaglutide. Materials & methods: To investigate the effect of dulaglutide, we analyzed the expression of methylated gene promoter regions in BC (ESR1, CDH1 and ADAM33). Results: Dulaglutide increased the expression of ESR1, CDH1 and ADAM33 up to fourfold in the MDA-MB-231 lineage by demethylating the gene promoter regions. This effect was translated to in vivo antitumoral activity and revealed significant tumor inhibition by combining the half-dose of methotrexate with dulaglutide. Conclusion: This therapy may mitigate the severe side effects commonly associated with chemotherapy.
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Affiliation(s)
- Júlia M Tatsch
- Department of Basic Pathology, Laboratory of Epigenetics, Federal University of Paraná, Curitiba, PR, Brazil
| | - Diana P Furman
- Department of Basic Pathology, Laboratory of Epigenetics, Federal University of Paraná, Curitiba, PR, Brazil
| | - Rodrigo Mb Nobre
- Department of Basic Pathology, Laboratory of Epigenetics, Federal University of Paraná, Curitiba, PR, Brazil
| | - Karin M Wurzer
- Department of Basic Pathology, Laboratory of Epigenetics, Federal University of Paraná, Curitiba, PR, Brazil
| | - Liziane Cm da Silva
- Department of Pharmacology, Federal University of Paraná, Curitiba, PR, Brazil
| | - Guilherme F Picheth
- Department of Biochemistry Federal University of Paraná, Curitiba, PR, Brazil
| | - Edneia As Ramos
- Department of Basic Pathology, Laboratory of Epigenetics, Federal University of Paraná, Curitiba, PR, Brazil
| | - Alexandra Acco
- Department of Pharmacology, Federal University of Paraná, Curitiba, PR, Brazil
| | - Giseli Klassen
- Department of Basic Pathology, Laboratory of Epigenetics, Federal University of Paraná, Curitiba, PR, Brazil
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2
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Zhang R, Datta S. Adaptive Sparse Multi-Block PLS Discriminant Analysis: An Integrative Method for Identifying Key Biomarkers from Multi-Omics Data. Genes (Basel) 2023; 14:genes14050961. [PMID: 37239321 DOI: 10.3390/genes14050961] [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: 02/28/2023] [Revised: 04/06/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
With the growing use of high-throughput technologies, multi-omics data containing various types of high-dimensional omics data is increasingly being generated to explore the association between the molecular mechanism of the host and diseases. In this study, we present an adaptive sparse multi-block partial least square discriminant analysis (asmbPLS-DA), an extension of our previous work, asmbPLS. This integrative approach identifies the most relevant features across different types of omics data while discriminating multiple disease outcome groups. We used simulation data with various scenarios and a real dataset from the TCGA project to demonstrate that asmbPLS-DA can identify key biomarkers from each type of omics data with better biological relevance than existing competitive methods. Moreover, asmbPLS-DA showed comparable performance in the classification of subjects in terms of disease status or phenotypes using integrated multi-omics molecular profiles, especially when combined with other classification algorithms, such as linear discriminant analysis and random forest. We have made the R package called asmbPLS that implements this method publicly available on GitHub. Overall, asmbPLS-DA achieved competitive performance in terms of feature selection and classification. We believe that asmbPLS-DA can be a valuable tool for multi-omics research.
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Affiliation(s)
- Runzhi Zhang
- Department of Biostatistics, University of Florida, Gainesville, FL 32603, USA
| | - Susmita Datta
- Department of Biostatistics, University of Florida, Gainesville, FL 32603, USA
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3
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Lan J, Zhou Y, Liu Y, Xia Y, Wan Y, Cao J. Role of ADAM33 short isoform as a tumor suppressor in the pathogenesis of thyroid cancer via oncogenic function disruption of full-length ADAM33. Hum Cell 2023:10.1007/s13577-023-00898-3. [PMID: 36977901 DOI: 10.1007/s13577-023-00898-3] [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: 11/10/2022] [Accepted: 03/13/2023] [Indexed: 03/30/2023]
Abstract
Thyroid cancer is the most prevalent endocrine malignancy globally; however, its underlying pathogenesis remains unclarified. Reportedly, alternative splicing is involved in processes such as embryonic stem and precursor cell differentiation, cell lineage reprogramming, and epithelial-mesenchymal transitions. ADAM33-n, an alternative splicing isoform of ADAM33, encodes a small protein containing 138 amino acids of the N-terminal of full-length ADAM33, which constructs a chaperone-like domain that was previously reported to bind and block the proteolysis activity of ADAM33. In this study, we reported for the first time that ADAM33-n was downregulated in thyroid cancer. The results of cell counting kit-8 and colony formation assays showed that ectopic ADAM33-n in papillary thyroid cancer cell lines restricted cell proliferation and colony formation. Moreover, we demonstrated that ectopic ADAM33-n reversed the oncogenic function of full-length ADAM33 in cell growth and colony formation in the MDA-T32 and BCPAP cells. These findings indicate the tumor suppressor ability of ADAM33-n. Altogether, our study findings present a potential explanatory model of how the downregulation of the oncogenic gene ADAM33 promotes the pathogenesis of thyroid cancer.
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Affiliation(s)
- Jing Lan
- Department of General Surgery, The first affiliated hospital of Soochow University, 188 Shizi Street, Suzhou, 215000, People's Republic of China
| | - Yehui Zhou
- Department of General Surgery, The first affiliated hospital of Soochow University, 188 Shizi Street, Suzhou, 215000, People's Republic of China
| | - Yang Liu
- Department of General Surgery, The first affiliated hospital of Soochow University, 188 Shizi Street, Suzhou, 215000, People's Republic of China
| | - Yu Xia
- Department of General Surgery, The first affiliated hospital of Soochow University, 188 Shizi Street, Suzhou, 215000, People's Republic of China
| | - Yuqiu Wan
- Department of General Surgery, The first affiliated hospital of Soochow University, 188 Shizi Street, Suzhou, 215000, People's Republic of China.
| | - Jianbo Cao
- Department of General Surgery, The first affiliated hospital of Soochow University, 188 Shizi Street, Suzhou, 215000, People's Republic of China.
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4
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Muhammad A, Forcados GE, Katsayal BS, Bako RS, Aminu S, Sadiq IZ, Abubakar MB, Yusuf AP, Malami I, Faruk M, Ibrahim S, Pase PA, Ahmed S, Abubakar IB, Abubakar M, Yates C. Potential epigenetic modifications implicated in triple- to quadruple-negative breast cancer transition: a review. Epigenomics 2022; 14:711-726. [PMID: 35473304 DOI: 10.2217/epi-2022-0033] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Current research on triple-negative breast cancer (TNBC) has resulted in delineation into the quadruple-negative breast cancer (QNBC) subgroup. Epigenetic modifications such as DNA methylation, histone posttranslational modifications and associated changes in chromatin architecture have been implicated in breast cancer pathogenesis. Herein, the authors highlight genes with observed epigenetic modifications that are associated with more aggressive TNBC/QNBC pathogenesis and possible interventions. Advanced literature searches were done on PubMed/MEDLINE, Scopus and Google Scholar. The results suggest that nine epigenetically altered genes/differentially expressed proteins in addition to the downregulated androgen receptor are associated with TNBC aggressiveness and could be implicated in the TNBC to QNBC transition. Thus, restoring the normal expression of these genes via epigenetic reprogramming could be therapeutically beneficial to TNBC and QNBC patients.
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Affiliation(s)
- Aliyu Muhammad
- Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, P.M.B. 1044, Zaria, Kaduna State, Nigeria.,Center for Cancer Research, Department of Biology, Tuskegee University, Tuskegee, AL 36088, USA
| | | | - Babangida Sanusi Katsayal
- Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, P.M.B. 1044, Zaria, Kaduna State, Nigeria
| | - Rabiatu Suleiman Bako
- Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, P.M.B. 1044, Zaria, Kaduna State, Nigeria
| | - Suleiman Aminu
- Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, P.M.B. 1044, Zaria, Kaduna State, Nigeria
| | - Idris Zubairu Sadiq
- Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, P.M.B. 1044, Zaria, Kaduna State, Nigeria
| | - Murtala Bello Abubakar
- Department of Physiology, Usmanu Danfodiyo University, P.M.B 2254, Sokoto, Sokoto State, Nigeria.,Centre for Advanced Medical Research & Training (CAMRET), Usmanu Danfodiyo University, P.M.B 2254, Sokoto, Sokoto State, Nigeria
| | | | - Ibrahim Malami
- Department of Pharmacognosy & Ethnopharmacy, Faculty of Pharmaceutical Sciences, Usmanu Danfodiyo University, P.M.B 2254, Sokoto, Nigeria.,Centre for Advanced Medical Research & Training (CAMRET), Usmanu Danfodiyo University, P.M.B 2254, Sokoto, Sokoto State, Nigeria
| | - Mohammed Faruk
- Department of Pathology, Ahmadu Bello University, P.M.B. 1044, Zaria, Kaduna State, Nigeria
| | - Sani Ibrahim
- Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, P.M.B. 1044, Zaria, Kaduna State, Nigeria
| | - Peter Abur Pase
- Department of Surgery, Ahmadu Bello University, P.M.B. 1044, Zaria, Kaduna State, Nigeria
| | - Saad Ahmed
- Department of Pathology, Ahmadu Bello University, P.M.B. 1044, Zaria, Kaduna State, Nigeria
| | - Ibrahim Babangida Abubakar
- Deparment of Biochemistry, Kebbi State University of Science & Technology, PMB 1144, Aliero, Kebbi State, Nigeria
| | - Murtala Abubakar
- Department of Pathology, Ahmadu Bello University, P.M.B. 1044, Zaria, Kaduna State, Nigeria
| | - Clayton Yates
- Center for Cancer Research, Department of Biology, Tuskegee University, Tuskegee, AL 36088, USA
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5
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Chequin A, Costa LE, de Campos FF, Moncada ADB, de Lima LTF, Sledz LR, Picheth GF, Adami ER, Acco A, Gonçalves MB, Manica GCM, Valdameri G, de Noronha L, Telles JEQ, Jandrey EHF, Costa ET, Costa FF, de Souza EM, Ramos EAS, Klassen G. Antitumoral activity of liraglutide, a new DNMT inhibitor in breast cancer cells in vitro and in vivo. Chem Biol Interact 2021; 349:109641. [PMID: 34534549 DOI: 10.1016/j.cbi.2021.109641] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 08/17/2021] [Accepted: 09/06/2021] [Indexed: 10/20/2022]
Abstract
Breast cancer (BC) is the most frequently diagnosed female cancer and second leading cause of death. Despite the discovery of many antineoplastic drugs for BC, the current therapy is not totally efficient. In this study, we investigated the potential of repurposing the well-known diabetes type II drug liraglutide to modulate epigenetic modifications in BC cells lines in vitro and in vivo via Ehrlich mice tumors models. The in vitro results revealed a significant reduction on cell viability, migration, DNMT activity and displayed lower levels of global DNA methylation in BC cell lines after liraglutide treatment. The interaction between liraglutide and the DNMT enzymes resulted in a decrease profile of DNA methylation for the CDH1, ESR1 and ADAM33 gene promoter regions and, consequently, increased their gene and protein expression levels. To elucidate the possible interaction between liraglutide and the DNMT1 protein, we performed an in silico study that indicates liraglutide binding in the catalytic cleft via hydrogen bonds and salt bridges with the interdomain contacts and disturbs the overall enzyme conformation. The in vivo study was also able to reveal that liraglutide and the combined treatment of liraglutide and paclitaxel or methotrexate were effective in reducing tumor growth. Moreover, the modulation of CDH1 and ADAM33 mouse gene expression by DNA demethylation suggests a role for liraglutide in DNMT activity in vivo. Altogether, these results indicate that liraglutide may be further analysed as a new adjuvant treatment for BC.
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Affiliation(s)
- Andressa Chequin
- Department of Basic Pathology, Laboratory of Epigenetics, Federal University of Paraná, Curitiba, PR, Brazil
| | - Luiz E Costa
- Department of Basic Pathology, Laboratory of Epigenetics, Federal University of Paraná, Curitiba, PR, Brazil
| | - Felipe F de Campos
- Department of Basic Pathology, Laboratory of Epigenetics, Federal University of Paraná, Curitiba, PR, Brazil
| | - Angie D B Moncada
- Department of Basic Pathology, Laboratory of Epigenetics, Federal University of Paraná, Curitiba, PR, Brazil
| | - Lucas T F de Lima
- Department of Basic Pathology, Laboratory of Epigenetics, Federal University of Paraná, Curitiba, PR, Brazil
| | - Lucas R Sledz
- Department of Basic Pathology, Laboratory of Epigenetics, Federal University of Paraná, Curitiba, PR, Brazil
| | - Guilherme F Picheth
- Department of Basic Pathology, Laboratory of Epigenetics, Federal University of Paraná, Curitiba, PR, Brazil
| | - Eliana R Adami
- Department of Pharmacology, Federal University of Paraná, Curitiba, PR, Brazil
| | - Alexandra Acco
- Department of Pharmacology, Federal University of Paraná, Curitiba, PR, Brazil
| | - Marcos B Gonçalves
- Department of Physics, Federal Technological University of Paraná, Curitiba, Parana, Brazil
| | - Graciele C M Manica
- Department of Clinical Analysis, Federal University of Paraná, Curitiba, PR, Brazil
| | - Gláucio Valdameri
- Department of Clinical Analysis, Federal University of Paraná, Curitiba, PR, Brazil
| | - Lucia de Noronha
- Department of Clinical Pathology, Pontifical Catholic University of Paraná, Curitiba, PR, Brazil
| | - José E Q Telles
- Department of Medical Pathology, Federal University of Paraná, Brazil
| | - Elisa H F Jandrey
- Molecular Oncology Center, Hospital Sírio-Libanês, São Paulo, SP, Brazil
| | - Erico T Costa
- Molecular Oncology Center, Hospital Sírio-Libanês, São Paulo, SP, Brazil
| | | | - Emanuel M de Souza
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, PR, Brazil
| | - Edneia A S Ramos
- Department of Basic Pathology, Laboratory of Epigenetics, Federal University of Paraná, Curitiba, PR, Brazil
| | - Giseli Klassen
- Department of Basic Pathology, Laboratory of Epigenetics, Federal University of Paraná, Curitiba, PR, Brazil.
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6
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Liu Y, Teng L, Fu S, Wang G, Li Z, Ding C, Wang H, Bi L. Highly heterogeneous-related genes of triple-negative breast cancer: potential diagnostic and prognostic biomarkers. BMC Cancer 2021; 21:644. [PMID: 34053447 PMCID: PMC8165798 DOI: 10.1186/s12885-021-08318-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 05/04/2021] [Indexed: 02/07/2023] Open
Abstract
Background Triple-negative breast cancer (TNBC) is a highly heterogeneous subtype of breast cancer, showing aggressive clinical behaviors and poor outcomes. It urgently needs new therapeutic strategies to improve the prognosis of TNBC. Bioinformatics analyses have been widely used to identify potential biomarkers for facilitating TNBC diagnosis and management. Methods We identified potential biomarkers and analyzed their diagnostic and prognostic values using bioinformatics approaches. Including differential expression gene (DEG) analysis, Receiver Operating Characteristic (ROC) curve analysis, functional enrichment analysis, Protein-Protein Interaction (PPI) network construction, survival analysis, multivariate Cox regression analysis, and Non-negative Matrix Factorization (NMF). Results A total of 105 DEGs were identified between TNBC and other breast cancer subtypes, which were regarded as heterogeneous-related genes. Subsequently, the KEGG enrichment analysis showed that these genes were significantly enriched in ‘cell cycle’ and ‘oocyte meiosis’ related pathways. Four (FAM83B, KITLG, CFD and RBM24) of 105 genes were identified as prognostic signatures in the disease-free interval (DFI) of TNBC patients, as for progression-free interval (PFI), five genes (FAM83B, EXO1, S100B, TYMS and CFD) were obtained. Time-dependent ROC analysis indicated that the multivariate Cox regression models, which were constructed based on these genes, had great predictive performances. Finally, the survival analysis of TNBC subtypes (mesenchymal stem-like [MSL] and mesenchymal [MES]) suggested that FAM83B significantly affected the prognosis of patients. Conclusions The multivariate Cox regression models constructed from four heterogeneous-related genes (FAM83B, KITLG, RBM24 and S100B) showed great prediction performance for TNBC patients’ prognostic. Moreover, FAM83B was an important prognostic feature in several TNBC subtypes (MSL and MES). Our findings provided new biomarkers to facilitate the targeted therapies of TNBC and TNBC subtypes. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08318-1.
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Affiliation(s)
- Yiduo Liu
- School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, Jiangsu, China
| | - Linxin Teng
- School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, Jiangsu, China
| | - Shiyi Fu
- School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, Jiangsu, China
| | - Guiyang Wang
- School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, Jiangsu, China
| | - Zhengjun Li
- College of Health Economics Management, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, Jiangsu, China
| | - Chao Ding
- School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, Jiangsu, China
| | - Haodi Wang
- School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, Jiangsu, China
| | - Lei Bi
- School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, Jiangsu, China.
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7
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Wu Q, Li W, You C. The regulatory roles and mechanisms of the transcription factor FOXF2 in human diseases. PeerJ 2021; 9:e10845. [PMID: 33717680 PMCID: PMC7934645 DOI: 10.7717/peerj.10845] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 01/05/2021] [Indexed: 12/19/2022] Open
Abstract
Many studies have focused on the relationship between transcription factors and a variety of common pathological conditions, such as diabetes, stroke, and cancer. It has been found that abnormal transcription factor regulation can lead to aberrant expression of downstream genes, which contributes to the occurrence and development of many diseases. The forkhead box (FOX) transcription factor family is encoded by the FOX gene, which mediates gene transcription and follow-up functions during physiological and pathological processes. FOXF2, a member of the FOX transcription family, is expressed in various organs and tissues while maintaining their normal structural and functional development during the embryonic and adult stages. Multiple regulatory pathways that regulate FOXF2 may also be controlled by FOXF2. Abnormal FOXF2 expression induced by uncontrollable regulatory signals mediate the progression of human diseases by interfering with the cell cycle, proliferation, differentiation, invasion, and metastasis. FOXF2 manipulates downstream pathways and targets as both a pro-oncogenic and anti-oncogenic factor across different types of cancer, suggesting it may be a new potential clinical marker or therapeutic target for cancer. However, FOXF2’s biological functions and specific roles in cancer development remain unclear. In this study, we provide an overview of FOXF2’s structure, function, and regulatory mechanisms in the physiological and pathological conditions of human body. We also discussed the possible reasons why FOXF2 performs the opposite function in the same types of cancer.
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Affiliation(s)
- Qiong Wu
- Laboratory Medicine Center, Lanzhou University Second Hospital, Lanzhou, China
| | - Wei Li
- Laboratory Medicine Center, Lanzhou University Second Hospital, Lanzhou, China
| | - Chongge You
- Laboratory Medicine Center, Lanzhou University Second Hospital, Lanzhou, China
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8
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Liu D, Zhou D, Sun Y, Zhu J, Ghoneim D, Wu C, Yao Q, Gamazon ER, Cox NJ, Wu L. A Transcriptome-Wide Association Study Identifies Candidate Susceptibility Genes for Pancreatic Cancer Risk. Cancer Res 2020; 80:4346-4354. [PMID: 32907841 PMCID: PMC7572664 DOI: 10.1158/0008-5472.can-20-1353] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/25/2020] [Accepted: 08/14/2020] [Indexed: 12/13/2022]
Abstract
Pancreatic cancer is among the most well-characterized cancer types, yet a large proportion of the heritability of pancreatic cancer risk remains unclear. Here, we performed a large transcriptome-wide association study to systematically investigate associations between genetically predicted gene expression in normal pancreas tissue and pancreatic cancer risk. Using data from 305 subjects of mostly European descent in the Genotype-Tissue Expression Project, we built comprehensive genetic models to predict normal pancreas tissue gene expression, modifying the UTMOST (unified test for molecular signatures). These prediction models were applied to the genetic data of 8,275 pancreatic cancer cases and 6,723 controls of European ancestry. Thirteen genes showed an association of genetically predicted expression with pancreatic cancer risk at an FDR ≤ 0.05, including seven previously reported genes (INHBA, SMC2, ABO, PDX1, RCCD1, CFDP1, and PGAP3) and six novel genes not yet reported for pancreatic cancer risk [6q27: SFT2D1 OR (95% confidence interval (CI), 1.54 (1.25-1.89); 13q12.13: MTMR6 OR (95% CI), 0.78 (0.70-0.88); 14q24.3: ACOT2 OR (95% CI), 1.35 (1.17-1.56); 17q12: STARD3 OR (95% CI), 6.49 (2.96-14.27); 17q21.1: GSDMB OR (95% CI), 1.94 (1.45-2.58); and 20p13: ADAM33 OR (95% CI): 1.41 (1.20-1.66)]. The associations for 10 of these genes (SFT2D1, MTMR6, ACOT2, STARD3, GSDMB, ADAM33, SMC2, RCCD1, CFDP1, and PGAP3) remained statistically significant even after adjusting for risk SNPs identified in previous genome-wide association study. Collectively, this analysis identified novel candidate susceptibility genes for pancreatic cancer that warrant further investigation. SIGNIFICANCE: A transcriptome-wide association analysis identified seven previously reported and six novel candidate susceptibility genes for pancreatic cancer risk.
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Affiliation(s)
- Duo Liu
- Department of Pharmacy, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, P.R. China
- Division of Cancer Epidemiology, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Dan Zhou
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yanfa Sun
- Division of Cancer Epidemiology, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii
- College of Life Science, Longyan University, Longyan, Fujian, P.R. China
- Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Longyan, Fujian, P.R. China
- Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Fujian Province University, Longyan, Fujian, P.R. China
| | - Jingjing Zhu
- Division of Cancer Epidemiology, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Dalia Ghoneim
- Division of Cancer Epidemiology, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Chong Wu
- Department of Statistics, Florida State University, Tallahassee, Florida
| | - Qizhi Yao
- Division of Surgical Oncology, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas
- Center for Translational Research on Inflammatory Diseases (CTRID), Michael E. DeBakey VA Medical Center, Houston, Texas
| | - Eric R Gamazon
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Clare Hall, University of Cambridge, Cambridge, United Kingdom
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Nancy J Cox
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Lang Wu
- Division of Cancer Epidemiology, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii.
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9
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Accomando WP, Rao AR, Hogan DJ, Newman AM, Nakao A, Alizadeh AA, Diehn M, Diago OR, Gammon D, Haghighi A, Gruber HE, Jolly DJ, Ostertag D. Molecular and Immunologic Signatures are Related to Clinical Benefit from Treatment with Vocimagene Amiretrorepvec (Toca 511) and 5-Fluorocytosine (Toca FC) in Patients with Glioma. Clin Cancer Res 2020; 26:6176-6186. [PMID: 32816892 DOI: 10.1158/1078-0432.ccr-20-0536] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/30/2020] [Accepted: 08/13/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE High-grade gliomas (HGGs) are central nervous system tumors with poor prognoses and limited treatment options. Vocimagene amiretrorepvec (Toca 511) is a retroviral replicating vector encoding cytosine deaminase, which converts extended release 5-fluorocytosine (Toca FC) into the anticancer agent, 5-fluorouracil. According to preclinical studies, this therapy kills cancer cells and immunosuppressive myeloid cells in the tumor microenvironment, leading to T-cell-mediated antitumor immune activity. Therefore, we sought to elucidate this immune-related mechanism of action in humans, and to investigate potential molecular and immunologic indicators of clinical benefit from therapy. PATIENTS AND METHODS In a phase I clinical trial (NCT01470794), patients with recurrent HGG treated with Toca 511 and Toca FC showed improved survival relative to historical controls, and some had durable complete responses to therapy. As a part of this trial, we performed whole-exome DNA sequencing, RNA-sequencing, and multiplex digital ELISA measurements on tumor and blood samples. RESULTS Genetic analyses suggest mutations, copy-number variations, and neoantigens are linked to survival. Quantities of tumor immune infiltrates estimated by transcript abundance may potentially predict clinical outcomes. Peak values of cytokines in peripheral blood samples collected during and after therapy could indicate response. CONCLUSIONS These results support an immune-related mechanism of action for Toca 511 and Toca FC, and suggest that molecular and immunologic signatures are related to clinical benefit from treatment.
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Affiliation(s)
| | | | | | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California.,Department of Biomedical Data Science, Stanford University, Stanford, California
| | - Aki Nakao
- CiberMed Inc., Palo Alto, California
| | - Ash A Alizadeh
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California.,Stanford Cancer Institute, Stanford University, Stanford, California.,Division of Oncology, Department of Medicine, Stanford University, Stanford, California.,Division of Hematology, Department of Medicine, Stanford University, Stanford, California
| | - Maximilian Diehn
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California.,Stanford Cancer Institute, Stanford University, Stanford, California.,Department of Radiation Oncology, Stanford University, Stanford, California
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10
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Huang SH, Lin YC, Tung CW. Identification of Time-Invariant Biomarkers for Non-Genotoxic Hepatocarcinogen Assessment. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17124298. [PMID: 32560183 PMCID: PMC7345770 DOI: 10.3390/ijerph17124298] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/12/2020] [Accepted: 06/14/2020] [Indexed: 12/12/2022]
Abstract
Non-genotoxic hepatocarcinogens (NGHCs) can only be confirmed by 2-year rodent studies. Toxicogenomics (TGx) approaches using gene expression profiles from short-term animal studies could enable early assessment of NGHCs. However, high variance in the modulation of the genes had been noted among exposure styles and datasets. Expanding from our previous strategy in identifying consensus biomarkers in multiple experiments, we aimed to identify time-invariant biomarkers for NGHCs in short-term exposure styles and validate their applicability to long-term exposure styles. In this study, nine time-invariant biomarkers, namely A2m, Akr7a3, Aqp7, Ca3, Cdc2a, Cdkn3, Cyp2c11, Ntf3, and Sds, were identified from four large-scale microarray datasets. Machine learning techniques were subsequently employed to assess the prediction performance of the biomarkers. The biomarker set along with the Random Forest models gave the highest median area under the receiver operating characteristic curve (AUC) of 0.824 and a low interquartile range (IQR) variance of 0.036 based on a leave-one-out cross-validation. The application of the models to the external validation datasets achieved high AUC values of greater than or equal to 0.857. Enrichment analysis of the biomarkers inferred the involvement of chronic inflammatory diseases such as liver cirrhosis, fibrosis, and hepatocellular carcinoma in NGHCs. The time-invariant biomarkers provided a robust alternative for NGHC prediction.
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Affiliation(s)
- Shan-Han Huang
- Ph. D. Program in Toxicology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (S.-H.H.); (Y.-C.L.)
| | - Ying-Chi Lin
- Ph. D. Program in Toxicology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (S.-H.H.); (Y.-C.L.)
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Chun-Wei Tung
- Graduate Institute of Data Science, College of Management, Taipei Medical University, Taipei 11031, Taiwan
- National Institute of Environmental Health Sciences, National Health Research Institutes, Miaoli County 35053, Taiwan
- Correspondence:
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11
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Souza JSM, Lisboa ABP, Santos TM, Andrade MVS, Neves VBS, Teles-Souza J, Jesus HNR, Bezerra TG, Falcão VGO, Oliveira RC, Del-Bem LE. The evolution of ADAM gene family in eukaryotes. Genomics 2020; 112:3108-3116. [PMID: 32437852 DOI: 10.1016/j.ygeno.2020.05.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 03/17/2020] [Accepted: 05/08/2020] [Indexed: 12/12/2022]
Abstract
The ADAM (A Disintegrin And Metalloprotease) gene family encodes proteins with adhesion and proteolytic functions. ADAM proteins are associated with diseases like cancers. Twenty ADAM genes have been identified in humans. However, little is known about the evolution of the family. We analyzed the repertoire of ADAM genes in a vast number of eukaryotic genomes to clarify the main gene copy number expansions. For the first time, we provide compelling evidence that early-branching green algae (Mamiellophyceae) have ADAM genes, suggesting that they originated in the last common ancestor of eukaryotes, before the split of plants, fungi and animals. The ADAM family expanded in early metazoans, with the most significative gene expansion happening during the first steps of vertebrate evolution. We concluded that most of mammal ADAM diversity can be explained by gene duplications in early bone fish. Our data suggest that ADAM genes were lost early in green plant evolution.
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Affiliation(s)
- J S M Souza
- Biochemistry and Molecular Biology program, Institute of Health Sciences (ICS), Federal University of Bahia (UFBA), Salvador 40231-300, Brazil
| | - A B P Lisboa
- Biotechnology program, Institute of Health Sciences (ICS), Federal University of Bahia (UFBA), Salvador 40231-300, Brazil; Bioinformatics program, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil
| | - T M Santos
- Biochemistry and Molecular Biology program, Institute of Health Sciences (ICS), Federal University of Bahia (UFBA), Salvador 40231-300, Brazil; Bioinformatics program, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil
| | - M V S Andrade
- Biotechnology program, Institute of Health Sciences (ICS), Federal University of Bahia (UFBA), Salvador 40231-300, Brazil
| | - V B S Neves
- Biochemistry and Molecular Biology program, Institute of Health Sciences (ICS), Federal University of Bahia (UFBA), Salvador 40231-300, Brazil
| | - J Teles-Souza
- Biochemistry and Molecular Biology program, Institute of Health Sciences (ICS), Federal University of Bahia (UFBA), Salvador 40231-300, Brazil
| | - H N R Jesus
- Biochemistry and Molecular Biology program, Institute of Health Sciences (ICS), Federal University of Bahia (UFBA), Salvador 40231-300, Brazil
| | - T G Bezerra
- Biochemistry and Molecular Biology program, Institute of Health Sciences (ICS), Federal University of Bahia (UFBA), Salvador 40231-300, Brazil
| | - V G O Falcão
- Biotechnology program, Institute of Health Sciences (ICS), Federal University of Bahia (UFBA), Salvador 40231-300, Brazil
| | - R C Oliveira
- Biochemistry and Molecular Biology program, Institute of Health Sciences (ICS), Federal University of Bahia (UFBA), Salvador 40231-300, Brazil
| | - L E Del-Bem
- Institute of Health Sciences (ICS), Federal University of Bahia (UFBA), Salvador 40231-300, Brazil.
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12
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Saha N, Robev D, Himanen JP, Nikolov DB. ADAM proteases: Emerging role and targeting of the non-catalytic domains. Cancer Lett 2019; 467:50-57. [PMID: 31593799 DOI: 10.1016/j.canlet.2019.10.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 09/27/2019] [Accepted: 10/01/2019] [Indexed: 12/11/2022]
Abstract
ADAM proteases are multi domain transmembrane metalloproteases that cleave a range of cell surface proteins and activate signaling pathways implicated in tumor progression, including those mediated by Notch, EFGR, and the Eph receptors. Consequently, they have emerged as key therapeutic targets in the efforts to inhibit tumor initiation and progression. To that end, two main approaches have been taken to develop ADAM antagonists: (i) small molecule inhibitors, and (ii) monoclonal antibodies. In this mini-review we describe the distinct features of ADAM proteases, particularly of ADAM10 and ADAM17, their domain organization, conformational rearrangements, regulation, as well as their emerging importance as therapeutic targets in cancer. Further, we highlight an anti-ADAM10 monoclonal antibody that we have recently developed, which has shown significant promise in inhibiting Notch signaling and deterring growth of solid tumors in pre-clinical settings.
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Affiliation(s)
- Nayanendu Saha
- Sloan-Kettering Institute for Cancer Research, 1275 York Avenue, New York, NY, 10065, USA.
| | - Dorothea Robev
- Sloan-Kettering Institute for Cancer Research, 1275 York Avenue, New York, NY, 10065, USA
| | - Juha P Himanen
- Sloan-Kettering Institute for Cancer Research, 1275 York Avenue, New York, NY, 10065, USA
| | - Dimitar B Nikolov
- Sloan-Kettering Institute for Cancer Research, 1275 York Avenue, New York, NY, 10065, USA
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13
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Wang D, Li J, Cai F, Xu Z, Li L, Zhu H, Liu W, Xu Q, Cao J, Sun J, Tang J. Overexpression of MAPT-AS1 is associated with better patient survival in breast cancer. Biochem Cell Biol 2018; 97:158-164. [PMID: 30074401 DOI: 10.1139/bcb-2018-0039] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Breast cancer is the most frequent malignant disease in women worldwide. It is a heterogeneous and complex genetic disease with different molecular characteristics. MAPT-AS1, a long non-coding RNA (lncRNA) existing at the anti-sense strand of the MAPT (microtubule associated protein tau) promoter region, was believed to regulate MAPT, which was associated with disease state in Parkinson's disease. But the role of MAPT-AS1 in breast cancer has never been reported. In our study we found that MAPT-AS1 is overexpressed in breast cancer but not in triple negative breast cancer (TNBC), and that high expression of MAPT-AS1 was correlated with better patient survival. In addition, the level of MAPT-AS1 was correlated with the expression of MAPT, and MAPT was associated with survival time in breast cancer. Our study suggests that MAPT-AS1 may play a role and be a potential survival predictive biomarker in breast cancer.
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Affiliation(s)
- Dongfeng Wang
- a Jiangsu Provincial Cancer Hospital, Affiliated to Nanjing Medical University, No. 42 of Baiziting, Nanjing, 210009, China.,b Institute of Jiangsu Provincial Cancer Prevention, No. 42 of Baiziting, Nanjing, 210009, China
| | - Jian Li
- a Jiangsu Provincial Cancer Hospital, Affiliated to Nanjing Medical University, No. 42 of Baiziting, Nanjing, 210009, China.,b Institute of Jiangsu Provincial Cancer Prevention, No. 42 of Baiziting, Nanjing, 210009, China
| | - Fengling Cai
- a Jiangsu Provincial Cancer Hospital, Affiliated to Nanjing Medical University, No. 42 of Baiziting, Nanjing, 210009, China.,b Institute of Jiangsu Provincial Cancer Prevention, No. 42 of Baiziting, Nanjing, 210009, China
| | - Zhi Xu
- a Jiangsu Provincial Cancer Hospital, Affiliated to Nanjing Medical University, No. 42 of Baiziting, Nanjing, 210009, China.,b Institute of Jiangsu Provincial Cancer Prevention, No. 42 of Baiziting, Nanjing, 210009, China
| | - Li Li
- a Jiangsu Provincial Cancer Hospital, Affiliated to Nanjing Medical University, No. 42 of Baiziting, Nanjing, 210009, China.,b Institute of Jiangsu Provincial Cancer Prevention, No. 42 of Baiziting, Nanjing, 210009, China
| | - Huanfeng Zhu
- a Jiangsu Provincial Cancer Hospital, Affiliated to Nanjing Medical University, No. 42 of Baiziting, Nanjing, 210009, China.,b Institute of Jiangsu Provincial Cancer Prevention, No. 42 of Baiziting, Nanjing, 210009, China
| | - Wei Liu
- a Jiangsu Provincial Cancer Hospital, Affiliated to Nanjing Medical University, No. 42 of Baiziting, Nanjing, 210009, China.,b Institute of Jiangsu Provincial Cancer Prevention, No. 42 of Baiziting, Nanjing, 210009, China
| | - Qingyu Xu
- a Jiangsu Provincial Cancer Hospital, Affiliated to Nanjing Medical University, No. 42 of Baiziting, Nanjing, 210009, China.,b Institute of Jiangsu Provincial Cancer Prevention, No. 42 of Baiziting, Nanjing, 210009, China
| | - Jian Cao
- a Jiangsu Provincial Cancer Hospital, Affiliated to Nanjing Medical University, No. 42 of Baiziting, Nanjing, 210009, China.,b Institute of Jiangsu Provincial Cancer Prevention, No. 42 of Baiziting, Nanjing, 210009, China
| | - Jingfeng Sun
- a Jiangsu Provincial Cancer Hospital, Affiliated to Nanjing Medical University, No. 42 of Baiziting, Nanjing, 210009, China.,b Institute of Jiangsu Provincial Cancer Prevention, No. 42 of Baiziting, Nanjing, 210009, China
| | - Jinhai Tang
- c Department of Surgery, The First Affiliated Hospital of Nanjing Medical University, No. 300 of Gangzhou Road, Nanjing 210029, China
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14
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Comparative analysis of Adam33 mutations in murine lung cancer cell lines by droplet digital PCR, real-time PCR and Insight Onco™ NGS. Mol Cell Toxicol 2018. [DOI: 10.1007/s13273-018-0024-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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15
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Li W, Jia G, Qu Y, Du Q, Liu B, Liu B. Long Non-Coding RNA (LncRNA) HOXA11-AS Promotes Breast Cancer Invasion and Metastasis by Regulating Epithelial-Mesenchymal Transition. Med Sci Monit 2017; 23:3393-3403. [PMID: 28701685 PMCID: PMC5521048 DOI: 10.12659/msm.904892] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND To detect the expression of lncRNA HOXA11-AS and its biological effect in breast cancer. MATERIAL AND METHODS In this study, fluorescent quantitative real-time PCR (qRT-PCR), MTT assay and clone formation assay, flow cytometry, Transwell assay and wound healing assay, immunofluorescence, and Western blot analysis were conducted to detect the expression of lncRNA HOXA11-AS, cell proliferation activity, cell apoptosis rate and cell cycle distribution, the changes of cell invasion and metastasis capacity, and the expressions of molecular markers of epithelial-mesenchymal transition (EMT), respectively. Additionally, a nude mouse metastatic tumor model was established to study the influence of lncRNA HOXA11-AS on invasion and metastasis capacity of breast cancer cells. RESULTS The qRT-PCR experiment results showed that HOXA11-AS expression in breast cancer tissue of 50 patients was relatively higher than that in tissue adjacent to cancer. MTT assay suggested that tumor cell proliferation capacity was suppressed followed by the knockdown of lncRNA HOXA11-AS expression in MDA-MB-231 and MCF-7 cells; flow cytometry results demonstrated that interfering in lncRNA HOXA11-AS could induce tumor cell apoptosis and promote cell cycle progression to be arrested in G1/G0 stage; experiments in vivo/vitro manifested that interfering in lncRNA HOXA11-AS could inhibit tumor cell invasion and migration capacity by affecting the expressions of EMT-related molecular markers (E-cadherin, N-cadherin, Vimentin). CONCLUSIONS High expression of lncRNA HOXA11-AS promotes breast cancer invasion and metastasis by affecting EMT, and interfering in lncRAN HOXA11-AS expression provides a theoretical basis and important molecular target for inhibiting the distant metastasis of breast cancer in clinical practice.
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Affiliation(s)
- Wenlei Li
- Department of Breast and Thyroid Surgery, Liaocheng People's Hospital, Liaocheng, Shandong, China (mainland)
| | - Guotao Jia
- Department of Pathology, Liaocheng People's Hospital, Liaocheng, Shandong, China (mainland)
| | - Yanwen Qu
- Department of Gynecologic Oncology, Qingdao Cancer Hospital, Qingdao, Shandong, China (mainland)
| | - Qian Du
- Department of Pediatrics, Liaocheng People's Hospital, Liaocheng, Shandong, China (mainland)
| | - Baoguo Liu
- Department of Breast and Thyroid Surgery, Liaocheng People's Hospital, Liaocheng, Shandong, China (mainland)
| | - Bin Liu
- Department of Thyroid and Breast Surgery, Tengzhou Central People's Hospital, Tengzhou, Shandong, China (mainland)
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