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Hsu YC, Chiu YC, Lu TP, Hsiao TH, Chen Y. Predicting drug response through tumor deconvolution by cancer cell lines. PATTERNS (NEW YORK, N.Y.) 2024; 5:100949. [PMID: 38645769 PMCID: PMC11026976 DOI: 10.1016/j.patter.2024.100949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 02/07/2024] [Accepted: 02/12/2024] [Indexed: 04/23/2024]
Abstract
Large-scale cancer drug sensitivity data have become available for a collection of cancer cell lines, but only limited drug response data from patients are available. Bridging the gap in pharmacogenomics knowledge between in vitro and in vivo datasets remains challenging. In this study, we trained a deep learning model, Scaden-CA, for deconvoluting tumor data into proportions of cancer-type-specific cell lines. Then, we developed a drug response prediction method using the deconvoluted proportions and the drug sensitivity data from cell lines. The Scaden-CA model showed excellent performance in terms of concordance correlation coefficients (>0.9 for model testing) and the correctly deconvoluted rate (>70% across most cancers) for model validation using Cancer Cell Line Encyclopedia (CCLE) bulk RNA data. We applied the model to tumors in The Cancer Genome Atlas (TCGA) dataset and examined associations between predicted cell viability and mutation status or gene expression levels to understand underlying mechanisms of potential value for drug repurposing.
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Affiliation(s)
- Yu-Ching Hsu
- Bioinformatics Program, Taiwan International Graduate Program, National Taiwan University, Taipei 115, Taiwan
- Bioinformatics Program, Institute of Statistical Science, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan
- Institute of Health Data Analytics and Statistics, Department of Public Health, College of Public Health, National Taiwan University, Taipei 100, Taiwan
- Greehey Children’s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Yu-Chiao Chiu
- Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, USA
| | - Tzu-Pin Lu
- Institute of Health Data Analytics and Statistics, Department of Public Health, College of Public Health, National Taiwan University, Taipei 100, Taiwan
| | - Tzu-Hung Hsiao
- Department of Medical Research, Taichung Veterans General Hospital, Taichung 40705, Taiwan
| | - Yidong Chen
- Greehey Children’s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Department of Population Health Sciences, University of Texas Health San Antonio, San Antonio, TX 78229, USA
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Turkarslan S, He Y, Hothi P, Murie C, Nicolas A, Kannan K, Park JH, Pan M, Awawda A, Cole ZD, Shapiro MA, Stuhlmiller TJ, Lee H, Patel AP, Cobbs C, Baliga NS. An atlas of causal and mechanistic drivers of interpatient heterogeneity in glioma. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.05.24305380. [PMID: 38633778 PMCID: PMC11023657 DOI: 10.1101/2024.04.05.24305380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Grade IV glioma, formerly known as glioblastoma multiforme (GBM) is the most aggressive and lethal type of brain tumor, and its treatment remains challenging in part due to extensive interpatient heterogeneity in disease driving mechanisms and lack of prognostic and predictive biomarkers. Using mechanistic inference of node-edge relationship (MINER), we have analyzed multiomics profiles from 516 patients and constructed an atlas of causal and mechanistic drivers of interpatient heterogeneity in GBM (gbmMINER). The atlas has delineated how 30 driver mutations act in a combinatorial scheme to causally influence a network of regulators (306 transcription factors and 73 miRNAs) of 179 transcriptional "programs", influencing disease progression in patients across 23 disease states. Through extensive testing on independent patient cohorts, we share evidence that a machine learning model trained on activity profiles of programs within gbmMINER significantly augments risk stratification, identifying patients who are super-responders to standard of care and those that would benefit from 2 nd line treatments. In addition to providing mechanistic hypotheses regarding disease prognosis, the activity of programs containing targets of 2 nd line treatments accurately predicted efficacy of 28 drugs in killing glioma stem-like cells from 43 patients. Our findings demonstrate that interpatient heterogeneity manifests from differential activities of transcriptional programs, providing actionable strategies for mechanistically characterizing GBM from a systems perspective and developing better prognostic and predictive biomarkers for personalized medicine.
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Li Y, Yang Y. Label-free quantitative proteomics reveals the mechanisms of Aurora kinase B in renal cell carcinoma. SAGE Open Med 2024; 12:20503121241228474. [PMID: 38516642 PMCID: PMC10956137 DOI: 10.1177/20503121241228474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 01/05/2024] [Indexed: 03/23/2024] Open
Abstract
Background Renal cell carcinoma is the most common form of kidney cancer which is a global threat to human health, needing to explore effective therapeutic targets and treatment methods. Aurora kinase B acts as an important carcinogenic role in various kinds of tumors, while its mechanism in renal cell carcinoma is indistinct. Herein we explore the underlying mechanism of Aurora kinase B in renal cell carcinoma. Methods and results Label-free quantitative proteomics analysis was employed to analyze the differentially expressed proteins in 786-O cells which were treated with si-Aurora kinase B or si-ctrl. In the current study, 169 differentially expressed proteins were identified. The top 10 upregulated proteins were MX2, IFI44L, ISG20, DDX58, F3, IFI44, ECE1, PRIC285, NIT1, and IFIT2. The top 10 downregulated proteins were FKBP9, FSTL1, DDAH1, TGFB2, HMGN3, COIL, FAM65A, PTPN14, ARFGAP2, and EIF2C2. GO enrichment analysis showed that these differentially expressed proteins participated in biological processes, including defense response to virus, response to virus, and type I interferon signaling pathway. These differentially expressed proteins participated in cellular components, including focal adhesion, cell-substrate adherens junction, cell-substrate junction, and endoplasmic reticulum lumen. These differentially expressed proteins participated in molecule functions, including guanyl nucleotide binding, nucleotidase activity, double-stranded RNA binding, 2'-5'-oligoadenylate synthetase activity, and virus receptor activity. Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that the significantly changed proteins including OAS3, OAS2, JAK1, TAP1, and RAC1 were involved in Epstein-Barr virus infection. Conclusions Taken together, our results demonstrate the possible mechanisms that Aurora kinase B may participate in renal cell carcinoma. These findings may provide insights into tumorigenesis and a theoretical basis for developing potential therapies of renal cell carcinoma.
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Affiliation(s)
- Yulong Li
- Department of Gastroenterology, Shaanxi Provincial People’s Hospital, Xi’an, China
| | - Yang Yang
- School of Public Health, Shaanxi University of Chinese Medicine, Xianyang, China
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4
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Ignatavicius P, Dauksa A, Zilinskas J, Kazokaite M, Riauka R, Barauskas G. DNA Methylation of HOXA11 Gene as Prognostic Molecular Marker in Human Gastric Adenocarcinoma. Diagnostics (Basel) 2022; 12:diagnostics12071686. [PMID: 35885590 PMCID: PMC9317388 DOI: 10.3390/diagnostics12071686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 12/24/2022] Open
Abstract
Hypermethylation of tumor suppressor genes and hypomethylation of oncogenes might be identified as possible biomarkers in gastric cancer (GC). We aimed to assess the DNA methylation status of selected genes in GC tissue samples and evaluate these genes’ prognostic importance on patient survival. Patients (99) diagnosed with GC and who underwent gastrectomy were included. We selected a group of genes (RAD51B, GFRA3, AKR7A3, HOXA11, TUSC3, FLI1, SEZ6L, GLDC, NDRG) which may be considered as potential tumor suppressor genes and oncogenes. Methylation of the HOXA11 gene promoter was significantly more frequent in GC tumor tissue (p = 0.006) than in healthy gastric mucosa. The probability of surviving longer (71.2 months (95% CI 57–85.3) vs. 44.3 months (95% CI 34.8–53.9)) was observed with unmethylated HOXA11 promoter in cancer tissues. Survival in patients with a methylation of HOXA11 promoter either in healthy gastric mucosa or gastric cancer tissue was twice as high as in patients with a methylation of HOXA11 promoter in both healthy gastric mucosa and cancer tissue (61.2 months (95% CI 50.9–71.4) vs. 28.5 months (95% CI 20.8–36.2)). Multivariate Cox analysis revealed the HOXA11 methylation as significantly associated with patients’ survival (HR = 2.4, 95% CI 1.19–4.86). Our results suggest that the HOXA11 gene might be a potential prognostic molecular marker in patients with gastric adenocarcinoma.
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Affiliation(s)
- Povilas Ignatavicius
- Department of Surgery, Medical Academy, Lithuanian University of Health Sciences, 50161 Kaunas, Lithuania; (A.D.); (J.Z.); (R.R.); (G.B.)
- Correspondence: ; Tel.: +370-37-326751
| | - Albertas Dauksa
- Department of Surgery, Medical Academy, Lithuanian University of Health Sciences, 50161 Kaunas, Lithuania; (A.D.); (J.Z.); (R.R.); (G.B.)
- Institute of Digestive Research, Medical Academy, Lithuanian University of Health Sciences, 50161 Kaunas, Lithuania
| | - Justas Zilinskas
- Department of Surgery, Medical Academy, Lithuanian University of Health Sciences, 50161 Kaunas, Lithuania; (A.D.); (J.Z.); (R.R.); (G.B.)
| | - Mintaute Kazokaite
- Institute of Endocrinology, Medical Academy, Lithuanian University of Health Sciences, 50161 Kaunas, Lithuania;
| | - Romualdas Riauka
- Department of Surgery, Medical Academy, Lithuanian University of Health Sciences, 50161 Kaunas, Lithuania; (A.D.); (J.Z.); (R.R.); (G.B.)
| | - Giedrius Barauskas
- Department of Surgery, Medical Academy, Lithuanian University of Health Sciences, 50161 Kaunas, Lithuania; (A.D.); (J.Z.); (R.R.); (G.B.)
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Hoxa11-mediated reduction of cell migration contributes to myeloid sarcoma formation induced by cooperation of MLL/AF10 with activating KRAS mutation in a mouse transplantation model. Neoplasia 2022; 29:100802. [PMID: 35500545 PMCID: PMC9065885 DOI: 10.1016/j.neo.2022.100802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 04/18/2022] [Indexed: 12/02/2022]
Abstract
Acute myeloid leukemia (AML) patients with MLL translocations (MLL-t) are frequently found to harbor N-/K-RAS activating mutations. Mouse models revealed that cooperating mutations accelerated leukemia development and myeloid sarcoma formation. The molecular mechanism of accelerated leukemia development and myeloid sarcoma formation is not clear. In this study, we demonstrate Hoxa10 accelerated leukemia development and are the first to show that Hoxa11 controls migration and retention of leukemia cell at extramedullary sites and is a key player in myeloid sarcoma formation.
The molecular mechanism of myeloid sarcoma (MS) formation remains nuclear. Our clinical and mouse model findings from a previous study revealed that cooperation of KMT2A (MLL) translocation (MLL-t) with activating N-/K-RAS mutations promoted MS formation in a shorter latency. To improve the understanding of MS formation, in this study, we performed imaging cell trafficking analysis and demonstrated that cells harboring cooperating mutations migrated more slowly to omental adipose tissues and more cells were retained in adipose tissues in vivo. Comparison of transcriptome profiling among three pairs of mouse MLL/AF10(OM-LZ) leukemia cell lines harboring activating and wild-type KRAS identified 77 differentially expressed genes (DEGs) with >1.5-fold change. Functional annotation of these 77 DEGs using Gene Ontology (GO) enrichment analysis followed by cluster analysis revealed that GO terms related to development/differentiation have the highest enrichment score. The roles of Hoxa10 and Hoxa11, two genes which mapped to this cluster, were further characterized. Silencing Hoxa10 and Hoxa11 in cells harboring cooperating mutations prolonged the survival and reduced MS formation, respectively, in the recipient mice. Data of imaging cell trafficking as well as competitive engraftment and clonal expansion analyses indicated that silencing or overexpressing Hoxa11 in mouse leukemia cells affected cell migration and retention in omental adipose tissue. Although silencing Hoxa11 in leukemia cells did not affect Cxcr4 expression, it resulted in increased transwell migration, motility in confined spaces 3 μm in size, and cell protrusion. Our results revealed that Hoxa10 plays an important role in survival and Hoxa11 contributes to MS formation in MLL-t acute myeloid leukemia with activating KRAS mutation.
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The Diagnostic and Prognostic Values of HOXA Gene Family in Kidney Clear Cell Renal Cell Carcinoma. JOURNAL OF ONCOLOGY 2022; 2022:1762637. [PMID: 35342423 PMCID: PMC8942704 DOI: 10.1155/2022/1762637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 01/03/2022] [Accepted: 02/07/2022] [Indexed: 12/24/2022]
Abstract
Kidney renal clear cell carcinoma (KIRC) is one of the most common cancers with high mortality worldwide. As members of the homeobox (HOX) family, homeobox-A (HOXA) genes have been reported to play an increasingly important role in tumorigenesis and the progression of multiple cancers. However, limited studies have investigated the potential diagnostic and prognostic roles of HOXA genes in KIRC. In this research, we explored the expression pattern of the HOXA gene family in KIRC progression by differential analysis of expression profiles from The Cancer Genome Atlas (TCGA). By using univariate Cox analysis and lasso regression analysis, we comprehensively evaluated the prognostic value of HOXA genes and eventually identified a prognostic risk model consisting of five HOXA genes (HOXA2, HOXA3, HOXA7, HOXA11, and HOXA13). The risk model was further validated as a novel independent prognostic factor for KIRC patients based on the calculated risk score by Kaplan-Meier analysis, univariate and multivariate Cox regression analyses, and time-dependent receiver operating characteristic (ROC) curve analysis. Moreover, to explore the potential mechanism of tumorigenesis and clinical application of KIRC, we also developed the HOXA-based competing endogenous RNA (ceRNA) regulatory network and machine learning classification model. Valproic acid and tretinoin were predicted to be the most promising small molecules to adjuvant treatment of KIRC by mining the CMAP and DGIdb drug database. Subsequently, pathway and functional enrichment analyses provided us with new ways to search for a possible mechanism of action of drugs. Taken together, our study demonstrated the nonnegligible role of HOXA genes in KIRC and constructed an effective prognostic and diagnostic model, which offers novel insights into KIRC prognosis.
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Wang SS, Zhai GQ, Chen G, Huang ZG, He RQ, Huang SN, Liu JL, Cheng JW, Yan HB, Dang YW, Li SH. Decreased expression of transcription factor Homeobox A11 and its potential target genes in bladder cancer. Pathol Res Pract 2022; 233:153847. [DOI: 10.1016/j.prp.2022.153847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 03/04/2022] [Accepted: 03/17/2022] [Indexed: 10/18/2022]
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Morgan R, Hunter K, Pandha HS. Downstream of the HOX genes: explaining conflicting tumour suppressor and oncogenic functions in cancer. Int J Cancer 2022; 150:1919-1932. [PMID: 35080776 PMCID: PMC9304284 DOI: 10.1002/ijc.33949] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/24/2021] [Accepted: 01/07/2022] [Indexed: 11/07/2022]
Abstract
The HOX genes are a highly conserved group of transcription factors that have key roles in early development, but which are also highly expressed in most cancers. Many studies have found strong associative relationships between the expression of individual HOX genes in tumours and clinical parameters including survival. For the majority of HOX genes, high tumour expression levels seem to be associated with a worse outcome for patients, and in some cases this has been shown to result from the activation of pro-oncogenic genes and pathways. However, there are also many studies that indicate a tumour suppressor role for some HOX genes, sometimes with conclusions that contradict earlier work. In this review, we have attempted to clarify the role of HOX genes in cancer by focusing on their downstream targets as identified in studies that provide experimental evidence for their activation or repression. On this basis, the majority of HOX genes would appear to have a pro-oncogenic function, with the notable exception of HOXD10, which acts exclusively as a tumour suppressor. HOX proteins regulate a wide range of target genes involved in metastasis, cell death, proliferation, and angiogenesis, and activate key cell signalling pathways. Furthermore, for some functionally related targets, this regulation is achieved by a relatively small subgroup of HOX genes.
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Affiliation(s)
- Richard Morgan
- School of Biomedical SciencesUniversity of West LondonLondonUK
| | - Keith Hunter
- Unit of Oral and Maxillofacial Pathology, School of Clinical DentistryUniversity of SheffieldSheffieldUK
| | - Hardev S. Pandha
- Faculty of Health and Medical SciencesUniversity of SurreyGuildfordUK
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Chakravarthi S, Karikalan B. Molecular Biomarkers for Lung Adenocarcinoma: A Short Review. CURRENT CANCER THERAPY REVIEWS 2021. [DOI: 10.2174/1573394716666200724164654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Lung cancer is a disease with higher death rates and is responsible for around 2 million
deaths per year worldwide. Recently, several breakthroughs have been made in the field of lung
cancer that has led to a revolution in the management of lung cancer patients. Identification of
molecular markers and the implication of respective targeted therapies has been a great success in
the treatment of lung adenocarcinoma patients. Despite the fact that targeted therapy of lung adenocarcinomas
represents one of the significant milestones in the treatment of lung cancer that resulted
in increased survival rates even in advanced stages, the mortality rates of lung cancer still remain
to be significantly high. This warrants further research for gaining better insights into molecular alterations
that can lead to newer innovations in targeted drug therapy towards lung adenocarcinoma.
In this review, we briefly summarized the literature on molecular markers that are already in use.
We also consolidated newer molecular markers that are under study with the potential for being targeted
for therapies in future.
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Fu JF, Shih LY, Yen TH. HOXA11 plays critical roles in disease progression and response to cytarabine in AML. Oncol Rep 2021; 46:150. [PMID: 34080665 PMCID: PMC8185505 DOI: 10.3892/or.2021.8101] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/05/2021] [Indexed: 12/15/2022] Open
Abstract
Lysine methyltransferase 2A (KMT2A, also known as MLL) translocations (MLL-t) are frequently associated with mutations in RAS pathway genes in acute myeloid leukemia (AML). Previous findings with a mouse model showed that cooperation of MLL/AF10 with tyrosine-protein phosphatase non-receptor type 11 (PTPN11)G503A accelerated leukemia development, but increased cytarabine (Ara-C) sensitivity of leukemia cells. To identify the genes responsible for reduced survival and Ara-C resistance, transcriptomic profiling between six pairs of mouse MLL/AF10(OM-LZ) leukemia cells harboring activating and wild-type KRAS or PTPN11 was compared. A total of 23 differentially expressed genes (DEGs) with >1.5-fold-change between the paired cell lines were identified. The Gene Ontology (GO) terms overrepresented in these 23 DEGs included ‘immune system process’, ‘actin filament binding’, ‘cellular response to interferon-alpha’ and ‘sequence-specific DNA’. Among the four genes (Hoxa11, PR domain zinc finger protein 5, Iroquois-class homeodomain protein IRX-5 and homeobox protein PKNOX2) mapped to the GO term ‘sequence-specific DNA’, HOXA11 upregulation was associated with AML harboring MLL-t and RAS signaling mutations based on a meta-analysis using data deposited in Oncomine™ and analysis of the clinical samples in the present study. Microarray data revealed that only Hoxa11 was upregulated in those cells harboring activating PTPN11. Functional studies of Hoxa11 knockdown or overexpression in MLL/AF10(OM-LZ) cells revealed that Hoxa11 expression levels were associated with survival in vivo and Ara-C sensitivity/apoptosis in vitro. In addition, Hoxa11 regulated the expression of the apoptosis-related genes, NF-κB inhibitor α, transcription factor p65 and transformation-related protein p53. Furthermore, the results of a meta-analysis using Heuser's AML dataset supported the finding that chemotherapy responders have higher expression levels of HOXA11. These results indicated that the expression of HOXA11 increased cell apoptosis and predicted an improved response to Ara-C in AML.
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Affiliation(s)
- Jen-Fen Fu
- Department of Medical Research, Chang Gung Memorial Hospital, Graduate Institute of Clinical Medical Sciences, Chang Gung University, Taoyuan 333, Taiwan, R.O.C
| | - Lee-Yung Shih
- Department of Internal Medicine, Division of Hematology‑Oncology, Chang Gung Memorial Hospital, Taipei 105, Taiwan, R.O.C
| | - Tzung-Hai Yen
- Department of Nephrology, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan 333, Taiwan, R.O.C
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Wang L, Wang Z, Zhu Y, Tan S, Chen X, Yang X. SOX17 Antagonizes the WNT Signaling Pathway and is Epigenetically Inactivated in Clear-Cell Renal Cell Carcinoma. Onco Targets Ther 2021; 14:3383-3394. [PMID: 34079284 PMCID: PMC8163727 DOI: 10.2147/ott.s294164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/07/2021] [Indexed: 12/31/2022] Open
Abstract
Background SRY-box containing gene 17 (SOX17) was reported to be a candidate tumor suppressor gene in multiple tumors. Little is known about its role in clear-cell renal cell carcinoma (ccRCC). This study aims to identify the epigenetic regulation and tumor-suppressive function of SOX17 in ccRCC. Patients and Methods Fifty-five human ccRCC tissue samples, ten adjacent non-malignant kidney tissue samples, 20 paired paraffin section tissues and seven RCC cell lines were obtained. Immunohistochemistry (IHC) and real-time PCR were used to examine the expression of the target genes at the mRNA and protein levels. The methylation of SOX17 was analyzed using methylation-specific PCR (MSP) and bisulfite genomic sequencing (BGS) assay. The functions of SOX17 were examined by using CCK8, colony formation, wound healing assay and Matrigel invasion assays. Luciferase assay was used to analyze the function of SOX17 in the WNT signaling pathway. Results We investigated the SOX17 expression in ccRCC tissues and adjacent non-malignant kidney tissues using PCR and IHC. The expression of SOX17 was lower in ccRCC tissues. Next, we analyzed the DNA promoter methylation of SOX17 in 55 human ccRCC tissues, 10 adjacent non-malignant kidney tissues and RCC cell lines using MSP. DNA methylation of the SOX17 promoter region occurred in 60% of ccRCC tissues and 10% of adjacent non-malignant kidney tissues. In vitro experiments showed that SOX17 suppressed the proliferation of RCC cells. Furthermore, SOX17 inhibited the migration of RCC cells as shown in the wound healing and migration assays. In addition, we found that SOX17 overexpression affected the WNT signaling pathway by downregulating c-myc and cyclinD1. Conclusion In summary, our study showed that SOX17 is downregulated in ccRCC and the loss of SOX17 expression is regulated via epigenetic mechanisms in ccRCC. In addition, SOX17 negatively regulates the WNT signaling pathway and function as a tumor suppressor in ccRCC.
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Affiliation(s)
- Lu Wang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, 110004, People's Republic of China
| | - Zhe Wang
- Department of Pathology, Shengjing Hospital of China Medical University, Shenyang, 110004, People's Republic of China
| | - Yuze Zhu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, 110004, People's Republic of China
| | - Shutao Tan
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, 110004, People's Republic of China
| | - Xiaonan Chen
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, 110004, People's Republic of China
| | - Xianghong Yang
- Department of Pathology, Shengjing Hospital of China Medical University, Shenyang, 110004, People's Republic of China
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12
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Gan Y, Cao C, Li A, Song H, Kuang G, Ma B, Zhang Q, Zhang Q. Silencing of the TRIM58 Gene by Aberrant Promoter Methylation is Associated with a Poor Patient Outcome and Promotes Cell Proliferation and Migration in Clear Cell Renal Cell Carcinoma. Front Mol Biosci 2021; 8:655126. [PMID: 33816562 PMCID: PMC8012909 DOI: 10.3389/fmolb.2021.655126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 01/27/2021] [Indexed: 12/09/2022] Open
Abstract
To investigate the underlying molecular mechanism of tripartite motif-containing 58 (TRIM58) in the development of clear cell renal cell carcinoma (ccRCC), we explored TRIM58 expression and methylation in tumor tissues and the association with clinicopathological features and prognosis of tissue samples; Moreover, we examined the direct gene transcription of TRIM58-specific DNA demethyltransferase (TRIM58-TET1) by the CRISPR-dCas9 fused with the catalytic domain of TET1 and the biological functions in RCC cells. In this study, we demonstrate that TRIM58 is frequently downregulated by promoter methylation in ccRCC tissues, associated significantly with tumor nuclear grade and poor patient survival. TRIM58-TET1 directly induces demethylation of TRIM58 CpG islands, and activates TRIM58 transcription in RCC cell lines. Besides, DNA demethylation of TRIM58 by TRIM58-TET1 significantly inhibits cell proliferation and migration Overall, our results demonstrate that TRIM58 is inactivated by promoter methylation, associates with tumor nuclear grade and poor survival, and TRIM58 DNA demethylation could directly activate TRIM58 transcription and inhibit cell proliferation and migration in RCC cell lines.
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Affiliation(s)
- Ying Gan
- Department of Urology, Peking University First Hospital and Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (male) Molecular Diagnosis and Treatment Center, Beijing, China
| | - Congcong Cao
- The Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Peking University Shenzhen Hospital, Institute of Urology of Shenzhen PKU-HKUST Medical Center, Shenzhen, China
| | - Aolin Li
- Department of Urology, Peking University First Hospital and Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (male) Molecular Diagnosis and Treatment Center, Beijing, China
| | - Haifeng Song
- Department of Urology, Peking University First Hospital and Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (male) Molecular Diagnosis and Treatment Center, Beijing, China
| | - Guanyu Kuang
- Department of Urology, Peking University First Hospital and Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (male) Molecular Diagnosis and Treatment Center, Beijing, China
| | - Binglei Ma
- Department of Urology, Peking University First Hospital and Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (male) Molecular Diagnosis and Treatment Center, Beijing, China
| | - Quan Zhang
- Department of Urology, Peking University First Hospital and Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (male) Molecular Diagnosis and Treatment Center, Beijing, China
| | - Qian Zhang
- Department of Urology, Peking University First Hospital and Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (male) Molecular Diagnosis and Treatment Center, Beijing, China
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Downregulation of HOXA11 enhances endometrial cancer malignancy and cisplatin resistance via activating PTEN/AKT signaling pathway. Clin Transl Oncol 2021; 23:1334-1341. [PMID: 33515421 DOI: 10.1007/s12094-020-02520-6] [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: 06/17/2020] [Accepted: 10/27/2020] [Indexed: 10/22/2022]
Abstract
PURPOSE Endometrial cancer is the most common malignant tumor of female genital system worldwide. Homeobox A11 (HOXA11) is an evolutionarily conserved Homeobox gene closely implicated in carcinogenesis. However, the mechanisms of HOXA11 in the progression and cisplatin resistance of endometrial cancer remain unclear. METHODS The expression of HOXA11 was analyzed based on 548 endometrial cancer and 35 control tissues from The Cancer Genome Atlas (TCGA) database. Transwell assay was performed to investigate the effect of HOXA11 on endometrial cell migration and invasion. TUNEL staining was carried out to assay the role of HOXA11 in endometrial cell apoptosis. Western blot was employed to detect the protein levels of B cell lymphoma-2 (Bcl-2), Bcl-2 associated X (Bax), cleaved caspase-3, matrix metalloproteinase-2/9 (MMP/9), phosphatase and tensin homolog (PTEN), protein kinase B (AKT) and p-AKT. RESULTS TCGA data showed that HOXA11 expression was significantly down-regulated in endometrial cancer tissue samples. The overexpression of HOXA11 promoted the apoptosis, but inhibited the proliferation, migration and invasion of endometrial cancer cells. HOXA11 knockdown with small interfering RNA (siRNA) considerably repressed cell apoptosis, while promoted cell proliferation, migration, and invasion through PTEN/AKT signaling pathway. Interestingly, HOXA11 was lowly expressed in Ishikawa cells treated with cisplatin. In addition, HOXA11 knockdown increased the resistance of endometrial cancer to cisplatin through activating PTEN/AKT signaling pathway. CONCLUSION Low HOXA11 expression may promote the proliferation, migration, invasion of endometrial cancer cells, and increase their resistance to cisplatin through activating PTEN/AKT pathway.
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Misawa A, Kondo Y, Takei H, Takizawa T. Long Noncoding RNA HOXA11-AS and Transcription Factor HOXB13 Modulate the Expression of Bone Metastasis-Related Genes in Prostate Cancer. Genes (Basel) 2021; 12:genes12020182. [PMID: 33514011 PMCID: PMC7912412 DOI: 10.3390/genes12020182] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/17/2021] [Accepted: 01/21/2021] [Indexed: 12/31/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are emerging as critical regulators of gene expression, which play fundamental roles in cancer development. In this study, we found that homeobox A11 antisense RNA (HOXA11-AS), a highly expressed lncRNA in cell lines derived from prostate cancer bone metastases, promoted the cell invasion and proliferation of PC3 prostate cancer cells. Transcription factor homeobox B13 (HOXB13) was identified as an upstream regulator of HOXA11-AS.HOXA11-AS regulated bone metastasis-associated C-C motif chemokine ligand 2 (CCL2)/C-C chemokine receptor type 2 (CCR2) signaling in both PC3 prostate cancer cells and SaOS2 osteoblastic cells. The HOXB13/HOXA11-AS axis also regulated integrin subunits (ITGAV and ITGB1) specific to prostate cancer bone metastasis. HOXB13, in combination with HOXA11-AS, directly regulated the integrin-binding sialoprotein (IBSP) promoter. Furthermore, conditioned medium containing HOXA11-AS secreted from PC3 cells could induce the expression of CCL2 and IBSP in SaOS2 osteoblastic cells. These results suggest that prostate cancer HOXA11-AS and HOXB13 promote metastasis by regulation of CCL2/CCR2 cytokine and integrin signaling in autocrine and paracrine manners.
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Affiliation(s)
- Aya Misawa
- Department of Molecular Medicine and Anatomy, Nippon Medical School, 1-1-5 Sendagi, Tokyo 113-8602, Japan;
| | - Yukihiro Kondo
- Department of Urology, Nippon Medical School, 1-1-5 Sendagi, Tokyo 113-8602, Japan;
| | - Hiroyuki Takei
- Department of Breast Surgical Oncology, Nippon Medical School, 1-1-5 Sendagi, Tokyo 113-8602, Japan;
| | - Toshihiro Takizawa
- Department of Molecular Medicine and Anatomy, Nippon Medical School, 1-1-5 Sendagi, Tokyo 113-8602, Japan;
- Correspondence: ; Tel.: +81-3-3822-2131; Fax: +81-3-5685-3052
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Paço A, de Bessa Garcia SA, Freitas R. Methylation in HOX Clusters and Its Applications in Cancer Therapy. Cells 2020; 9:cells9071613. [PMID: 32635388 PMCID: PMC7408435 DOI: 10.3390/cells9071613] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/26/2020] [Accepted: 06/29/2020] [Indexed: 02/08/2023] Open
Abstract
HOX genes are commonly known for their role in embryonic development, defining the positional identity of most structures along the anterior–posterior axis. In postembryonic life, HOX gene aberrant expression can affect several processes involved in tumorigenesis such as proliferation, apoptosis, migration and invasion. Epigenetic modifications are implicated in gene expression deregulation, and it is accepted that methylation events affecting HOX gene expression play crucial roles in tumorigenesis. In fact, specific methylation profiles in the HOX gene sequence or in HOX-associated histones are recognized as potential biomarkers in several cancers, helping in the prediction of disease outcomes and adding information for decisions regarding the patient’s treatment. The methylation of some HOX genes can be associated with chemotherapy resistance, and its identification may suggest the use of other treatment options. The use of epigenetic drugs affecting generalized or specific DNA methylation profiles, an approach that now deserves much attention, seems likely to be a promising weapon in cancer therapy in the near future. In this review, we summarize these topics, focusing particularly on how the regulation of epigenetic processes may be used in cancer therapy.
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Affiliation(s)
- Ana Paço
- Centre Bio: Bioindustries, Biorefineries and Bioproducts, BLC3 Association—Technology and Innovation Campus, 3405-169 Oliveira do Hospital, Portugal;
| | | | - Renata Freitas
- I3S—Institute for Innovation & Health Research, University of Porto, 4200-135 Porto, Portugal;
- ICBAS—Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal
- Correspondence:
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Cui Y, Yan M, Zhang C, Xue J, Zhang Q, Ma S, Guan F, Cao W. Comprehensive analysis of the HOXA gene family identifies HOXA13 as a novel oncogenic gene in kidney renal clear cell carcinoma. J Cancer Res Clin Oncol 2020; 146:1993-2006. [PMID: 32444962 DOI: 10.1007/s00432-020-03259-x] [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] [Received: 01/15/2020] [Accepted: 05/13/2020] [Indexed: 12/30/2022]
Abstract
OBJECTIVES Kidney renal clear cell carcinoma (KIRC) is one of the most common lethal cancers in the human urogenital system. As members of the Homeobox (HOX) family, Homeobox-A (HOXA) cluster genes have been reported to be involved in the development of many cancer types. However, the expression and clinical significance of HOXA genes in KIRC remain largely unknown. MATERIALS AND METHODS In this study, we comprehensively analyzed the mRNA expression and prognostic values of HOXA genes in KIRC using The Cancer Genome Atlas (TCGA) analysis databases online. Colony formation assay, flow cytometry and Western blot were used to detect cell proliferation, apoptosis, cell cycle, and protein level of the indicated gene. RESULTS We found that the HOXA genes were differentially expressed in KIRC tissues when compared with normal tissues. The expression of HOXA4 and HOXA13 were significantly up-regulated, while HOXA7 and HOXA11 were down-regulated in KIRC. High mRNA levels of HOXA2, HOXA3 and HOXA13, and low level of HOXA7 predicted poor overall survival (OS) of KIRC patients. High mRNA level of HOXA13 further indicated a poor disease-free survival (DFS) of KIRC patients. Functionally, knockdown of HOXA13 significantly suppressed cell proliferation of KIRC in vitro, increased the protein level of p53 and decreased the protein level of cyclin D1 in KIRC cells. Over-expression of HOXA13 had the opposite effects on KIRC cells. CONCLUSION Collectively, our findings suggest that HOXA13 functions as a novel oncogene in KIRC and may be a potential biomarker for this malignancy.
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Affiliation(s)
- Yuanbo Cui
- Department of Translational Medicine Center, Zhengzhou Central Hospital Affiliated To Zhengzhou University, Zhengzhou, 450007, China. .,School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China.
| | - Ming Yan
- Basic Medical College, Zhengzhou University, Zhengzhou, 450001, China
| | - Chunyan Zhang
- Department of Clinical Laboratory, Zhengzhou Central Hospital Affiliated To Zhengzhou University, Zhengzhou, 450007, China
| | - Jinhui Xue
- Department of Pathology, Zhengzhou Central Hospital Affiliated To Zhengzhou University, Zhengzhou, 450007, China
| | - Quanwu Zhang
- Department of Pathology, Zhengzhou Central Hospital Affiliated To Zhengzhou University, Zhengzhou, 450007, China
| | - Shanshan Ma
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Fangxia Guan
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China.
| | - Wei Cao
- Department of Translational Medicine Center, Zhengzhou Central Hospital Affiliated To Zhengzhou University, Zhengzhou, 450007, China.
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Wang C, Shi M, Ji J, Cai Q, Jiang J, Zhang H, Zhu Z, Zhang J. A self-enforcing HOXA11/Stat3 feedback loop promotes stemness properties and peritoneal metastasis in gastric cancer cells. Am J Cancer Res 2019; 9:7628-7647. [PMID: 31695791 PMCID: PMC6831465 DOI: 10.7150/thno.36277] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 09/05/2019] [Indexed: 12/13/2022] Open
Abstract
Rationale: Peritoneal metastasis is one of the most common and life-threatening metastases in gastric cancer patients. The disseminated gastric cancer cells forming peritoneal metastasis exhibit a variety of characteristics that contrast with those of adjacent epithelial cell of gastric mucosa and even primary gastric cancer cells. We hypothesized that the gene expression profiles of peritoneal foci could reveal the identities of genes that might function as metastatic activator. Methods: In this study, we show, using in vitro, in vivo, in silico and gastric cancer tissues studies in humans and mice, that Homoebox A11 (HOXA11) potently promote peritoneal metastasis of gastric cancer cells. Results: Its mechanism of action involves alternation of cancer stemness and subsequently enhancement of the adhesion, migration and invasion and anti-apoptosis. This is achieved, mainly, through formation of a positive feedback loop between HOXA11 and Stat3, which is involved in the stimulation of Stat3 signaling pathway. Conclusions: These observations uncover a novel peritoneal metastatic activator and demonstrate the association between HOXA11, Stat3 and cancer stemness of gastric cancer cells, thereby revealing a previously undescribed mechanism of peritoneal metastasis.
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Zhang Y, Yuan Y, Li Y, Zhang P, Chen P, Sun S. An inverse interaction between HOXA11 and HOXA11-AS is associated with cisplatin resistance in lung adenocarcinoma. Epigenetics 2019; 14:949-960. [PMID: 31144606 DOI: 10.1080/15592294.2019.1625673] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
HOXA11, which is a member of the homeobox (HOX) gene family, and its natural antisense transcript (NAT) HOXA11-AS have been reported to be closely related to the development of lung cancer. We aimed to investigate their specific roles in cisplatin (DDP) resistance in lung adenocarcinoma (LUAD). First, we found that HOXA11 is hypermethylated and significantly downregulated in a DDP-resistant A549 cell line (A549/DDP) and LUAD tissues, while the HOXA11-AS expression level is elevated. Although HOXA11 and HOXA11-AS mRNA overlap in the 5'-untranslated region (5' UTR) and share two CpG islands, DNA methylation only regulates the expression of HOXA11. Then, we found that HOXA11 and HOXA11-AS have an inverse interaction by transfecting their siRNAs and overexpression vectors into A549 and A549/DDP cells. A dual-luciferase reporter assay further confirmed that the overlapping 5'UTR is essential for the bidirectional regulation between HOXA11 and HOXA11-AS. Functional analysis showed that knockdown of HOXA11 expression in A549 cells induced DDP resistance and activated Akt/β-catenin signaling, while overexpression of HOXA11 in A549/DDP cells increased DDP sensitivity and inhibited Akt/β-catenin signaling. Moreover, HOXA11-AS knockdown in A549 cells increased DDP sensitivity and inhibited Akt/β-catenin signaling, while the overexpression of HOXA11-AS in A549/DDP cells induced DDP resistance and activated Akt/β-catenin signaling. In conclusion, our study demonstrates that the inverse interaction between HOXA11 and HOXA11-AS promotes DDP resistance in LUAD.
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Affiliation(s)
- Youwei Zhang
- a Department of Medical Oncology, Affiliated Xuzhou Central Hospital, Southeast University , Xuzhou , China
| | - Yuan Yuan
- a Department of Medical Oncology, Affiliated Xuzhou Central Hospital, Southeast University , Xuzhou , China
| | - Yang Li
- b Department of Molecular Laboratory, Affiliated Xuzhou Central Hospital, Southeast University , Xuzhou , China
| | - Peiying Zhang
- a Department of Medical Oncology, Affiliated Xuzhou Central Hospital, Southeast University , Xuzhou , China
| | - Pingsheng Chen
- c Department of Pathology, School of Basic Medical Sciences, Southeast University , Nanjing , China
| | - Sanyuan Sun
- a Department of Medical Oncology, Affiliated Xuzhou Central Hospital, Southeast University , Xuzhou , China
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Long non-coding RNA HOTTIP affects renal cell carcinoma progression by regulating autophagy via the PI3K/Akt/Atg13 signaling pathway. J Cancer Res Clin Oncol 2018; 145:573-588. [DOI: 10.1007/s00432-018-2808-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 11/30/2018] [Indexed: 12/12/2022]
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20
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Yang X, Deng Y, He RQ, Li XJ, Ma J, Chen G, Hu XH. Upregulation of HOXA11 during the progression of lung adenocarcinoma detected via multiple approaches. Int J Mol Med 2018; 42:2650-2664. [PMID: 30106131 PMCID: PMC6192730 DOI: 10.3892/ijmm.2018.3826] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 08/10/2018] [Indexed: 12/22/2022] Open
Abstract
The altered expression of homeobox (HOX)A11 has been observed in various malignant tumor types, but it has remained to be determined in human lung adenocarcinoma (LUAD). In the present study, the expression of HOXA11 in LUAD and the potential associated mechanisms were assessed. Data from The Cancer Genome Atlas and Oncomine microarrays were gathered and in‑house polymerase chain reaction data were produced to investigate the altered expression of HOXA11 in LUAD and its association with various clinicopathological characteristics. Genes co‑expressed with HOXA11 were also identified by searching the cBioPortal and Multi Experiment Matrix databases, and performing a bioinformatics analysis, through which the potential molecular mechanisms of HOXA11 in LUAD were explored. The data analyses indicated that HOXA11 was overexpressed in the LUAD samples, and together with its co‑expressed genes, it was indicated to participate in various key signaling pathways, including the focal adhesion, extracellular matrix‑receptor interaction, axon guidance and small cell lung cancer signaling pathways. Furthermore, collagen type III α 1 chain (COL3A1), ephrin B2 (EFNB2), integrin subunit α 8 (ITGA8) and syndecan 2 (SDC2) were confirmed to be differentially expressed in LUAD vs. normal controls at the mRNA and protein level. Of note, LUAD patients with low expression of HOXA11 and ITGB1 had better overall survival rates. The present study indicated that HOXA11 may function as an oncogene in LUAD, and HOXA11 protein probably combines with ITGB1, COL3A1, EFNB2, ITGA8 and SDC2 to have a role in the focal adhesion pathway.
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Affiliation(s)
- Xia Yang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Yun Deng
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Rong-Quan He
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Xiao-Jiao Li
- Department of Positron Emission Tomography‑Computed Tomography, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Jie Ma
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Xiao-Hua Hu
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
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Zhang R, Zhang TT, Zhai GQ, Guo XY, Qin Y, Gan TQ, Zhang Y, Chen G, Mo WJ, Feng ZB. Evaluation of the HOXA11 level in patients with lung squamous cancer and insights into potential molecular pathways via bioinformatics analysis. World J Surg Oncol 2018; 16:109. [PMID: 29914539 PMCID: PMC6006563 DOI: 10.1186/s12957-018-1375-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 03/26/2018] [Indexed: 01/11/2023] Open
Abstract
Background This study was carried out to discover the underlying role that HOXA11 plays in lung squamous cancer (LUSC) and uncover the potential corresponding molecular mechanisms and functions of HOXA11-related genes. Methods Twenty-three clinical paired LUSC and non-LUSC samples were utilized to examine the level of HOXA11 using quantitative real-time polymerase chain reaction (qRT-PCR). The clinical significance of HOXA11 was systematically analyzed based on 475 LUSC and 18 non-cancerous adjacent tissues from The Cancer Genome Atlas (TCGA) database. A total of 102 LUSC tissues and 121 non-cancerous tissues were available from Oncomine to explore the expressing profiles of HOXA11 in LUSC. A meta-analysis was carried out to further assess the differential expression of HOXA11 in LUSC, including in-house qRT-PCR data, expressing data extracted from TCGA and Oncomine databases. Moreover, the enrichment analysis and potential pathway annotations of HOXA11 in LUSC were accomplished via Gene Oncology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The expression of hub genes and according correlations with HOXA11 were assessed to further explore the biological role of HOXA11 in LUSC. Results HOXA11 expression in LUSC had a tendency to be upregulated in comparison to adjacent non-cancerous tissues by qRT-PCR. TCGA data displayed that HOXA11 was remarkably over-expressed in LUSC compared with that in non-LUSC samples, and the area under curves (AUC) was 0.955 (P < 0.001). A total of 1523 co-expressed genes were sifted for further analysis. The most significant term enriched in the KEGG pathway was focal adhesion. Among the six hub genes of HOXA11, including PARVA, ILK, COL4A1, COL4A2, ITGB1, and ITGA5, five (with the exception of COL4A1) were significantly decreased compared with the normal lung tissues. Moreover, the expression of ILK was negatively related to HOXA11 (r = − 0.141, P = 0.002). Conclusion High HOXA11 expression may lead to carcinogenesis and the development of LUSC. Furthermore, co-expressed genes might affect the prognosis of LUSC.
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Affiliation(s)
- Rui Zhang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | | | - Gao-Qiang Zhai
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Xian-Yu Guo
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Yuan Qin
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Ting-Qing Gan
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Yu Zhang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Wei-Jia Mo
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.
| | - Zhen-Bo Feng
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.
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Lauber C, Klink B, Seifert M. Comparative analysis of histologically classified oligodendrogliomas reveals characteristic molecular differences between subgroups. BMC Cancer 2018; 18:399. [PMID: 29631562 PMCID: PMC5892046 DOI: 10.1186/s12885-018-4251-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 03/20/2018] [Indexed: 11/24/2022] Open
Abstract
Background Molecular data of histologically classified oligodendrogliomas are available offering the possibility to stratify these human brain tumors into clinically relevant molecular subtypes. Methods Gene copy number, mutation, and expression data of 193 histologically classified oligodendrogliomas from The Cancer Genome Atlas (TCGA) were analyzed by well-established computational approaches (unsupervised clustering, statistical testing, network inference). Results We applied hierarchical clustering to tumor gene copy number profiles and revealed three molecular subgroups within histologically classified oligodendrogliomas. We further screened these subgroups for molecular glioma markers (1p/19q co-deletion, IDH mutation, gain of chromosome 7 and loss of chromosome 10) and found that our subgroups largely resemble known molecular glioma subtypes. We excluded glioblastoma-like tumors (7a10d subgroup) and derived a gene expression signature distinguishing histologically classified oligodendrogliomas with concurrent 1p/19q co-deletion and IDH mutation (1p/19q subgroup) from those with predominant IDH mutation alone (IDHme subgroup). Interestingly, many signature genes were part of signaling pathways involved in the regulation of cell proliferation, differentiation, migration, and cell-cell contacts. We further learned a gene regulatory network associated with the gene expression signature revealing novel putative major regulators with functions in cytoskeleton remodeling (e.g. APBB1IP, VAV1, ARPC1B), apoptosis (CCNL2, CREB3L1), and neural development (e.g. MYTIL, SCRT1, MEF2C) potentially contributing to the manifestation of differences between both subgroups. Moreover, we revealed characteristic expression differences of several HOX and SOX transcription factors suggesting the activity of different glioma stemness programs in both subgroups. Conclusions We show that gene copy number profiles alone are sufficient to derive molecular subgroups of histologically classified oligodendrogliomas that are well-embedded into general glioma classification schemes. Moreover, our revealed novel putative major regulators and characteristic stemness signatures indicate that different developmental programs might be active in these subgroups, providing a basis for future studies. Electronic supplementary material The online version of this article (10.1186/s12885-018-4251-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chris Lauber
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Barbara Klink
- Institute for Clinical Genetics, Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Dresden, Germany.,National Center for Tumor Diseases, Dresden, Germany
| | - Michael Seifert
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Dresden, Germany. .,National Center for Tumor Diseases, Dresden, Germany.
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Yang C, Zheng J, Xue Y, Yu H, Liu X, Ma J, Liu L, Wang P, Li Z, Cai H, Liu Y. The Effect of MCM3AP-AS1/miR-211/KLF5/AGGF1 Axis Regulating Glioblastoma Angiogenesis. Front Mol Neurosci 2018; 10:437. [PMID: 29375300 PMCID: PMC5767169 DOI: 10.3389/fnmol.2017.00437] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 12/18/2017] [Indexed: 01/23/2023] Open
Abstract
Glioblastoma (GBM) is the most aggressive and malignant primary tumor. Angiogenesis plays a critical role in the progression of GBM. Previous studies have indicated that long non-coding RNAs (lncRNAs) are abnormally expressed in various cancers and participate in the regulation of the malignant behaviors of tumors. The present study demonstrated that lncRNA antisense 1 to Micro-chromosome maintenance protein 3-associated protein (MCM3AP-AS1) was upregulated whereas miR-211 was downregulated in glioma-associated endothelial cells (GECs). Knockdown of MCM3AP-AS1 suppressed the cell viability, migration, and tube formation of GECs and played a role in inhibiting angiogenesis of GBM in vitro. Furthermore, knockdown of MCM3AP-AS1 increased the expression of miR-211. Luciferase reporter assay implicated that miR-211 targeted KLF5 3'-UTR and consequently inhibited KLF5 expression. Besides, in this study we found that MCM3AP-AS1 knockdown decreased KLF5 and AGGF1 expression by upregulating miR-211. In addition, KLF5 was associated with the promoter region of AGGF1. Knockdown of KLF5 decreased AGGF1 expression by transcriptional repression, and also inhibited the activation of PI3K/AKT and ERK1/2 signaling pathways. Overall, this study reveals that MCM3AP-AS1/miR-211/KLF5/AGGF1 axis plays a prominent role in the regulation of GBM angiogenesis and also serves as new therapeutic target for the anti-angiogenic therapy of glioma.
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Affiliation(s)
- Chunqing Yang
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
- Liaoning Research Center for Clinical Medicine in Nervous System Disease, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Jian Zheng
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
- Liaoning Research Center for Clinical Medicine in Nervous System Disease, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Yixue Xue
- Department of Neurobiology, College of Basic Medicine, China Medical University, Shenyang, China
- Key Laboratory of Cell Biology, Ministry of Public Health of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, Shenyang, China
| | - Hai Yu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
- Liaoning Research Center for Clinical Medicine in Nervous System Disease, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Xiaobai Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
- Liaoning Research Center for Clinical Medicine in Nervous System Disease, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Jun Ma
- Department of Neurobiology, College of Basic Medicine, China Medical University, Shenyang, China
- Key Laboratory of Cell Biology, Ministry of Public Health of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, Shenyang, China
| | - Libo Liu
- Department of Neurobiology, College of Basic Medicine, China Medical University, Shenyang, China
- Key Laboratory of Cell Biology, Ministry of Public Health of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, Shenyang, China
| | - Ping Wang
- Department of Neurobiology, College of Basic Medicine, China Medical University, Shenyang, China
- Key Laboratory of Cell Biology, Ministry of Public Health of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, Shenyang, China
| | - Zhen Li
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
- Liaoning Research Center for Clinical Medicine in Nervous System Disease, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Heng Cai
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
- Liaoning Research Center for Clinical Medicine in Nervous System Disease, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Yunhui Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
- Liaoning Research Center for Clinical Medicine in Nervous System Disease, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
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