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Infante T, Pepin ME, Ruocco A, Trama U, Mauro C, Napoli C. CDK5R1, GSE1, HSPG2 and WDFY3 as indirect epigenetic-sensitive genes in atrial fibrillation. Eur J Clin Invest 2024; 54:e14135. [PMID: 37991085 DOI: 10.1111/eci.14135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/14/2023] [Accepted: 11/14/2023] [Indexed: 11/23/2023]
Abstract
BACKGROUND Although mounting evidence supports that aberrant DNA methylation occurs in the hearts of patients with atrial fibrillation (AF), noninvasive epigenetic characterization of AF has not yet been defined. METHODS We investigated DNA methylome changes in peripheral blood CD4+ T cells isolated from 10 patients with AF relative to 11 healthy subjects (HS) who were enrolled in the DIANA clinical trial (NCT04371809) via reduced-representation bisulfite sequencing (RRBS). RESULTS An atrial-specific PPI network revealed 18 hub differentially methylated genes (DMGs), wherein ROC curve analysis revealed reasonable diagnostic performance of DNA methylation levels found within CDK5R1 (AUC = 0.76; p = 0.049), HSPG2 (AUC = 0.77; p = 0.038), WDFY3 (AUC = 0.78; p = 0.029), USP49 (AUC = 0.76; p = 0.049), GSE1 (AUC = 0.76; p = 0.049), AIFM1 (AUC = 0.76; p = 0.041), CDK5RAP2 (AUC = 0.81; p = 0.017), COL4A1 (AUC = 0.86; p < 0.001), SEPT8 (AUC = 0.90; p < 0.001), PFDN1 (AUC = 0.90; p < 0.01) and ACOT7 (AUC = 0.78; p = 0.032). Transcriptional profiling of the hub DMGs provided a significant overexpression of PSDM6 (p = 0.004), TFRC (p = 0.01), CDK5R1 (p < 0.001), HSPG2 (p = 0.01), WDFY3 (p < 0.001), USP49 (p = 0.004) and GSE1 (p = 0.021) in AF patients vs HS. CONCLUSIONS CDK5R1, GSE1, HSPG2 and WDFY3 resulted the best discriminatory genes both at methylation and gene expression level. Our results provide several candidate diagnostic biomarkers with the potential to advance precision medicine in AF.
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Affiliation(s)
- Teresa Infante
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Mark E Pepin
- Division of Internal Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Antonio Ruocco
- Cardiology Division, "A. Cardarelli" Hospital, Naples, Italy
| | - Ugo Trama
- General Direction of Health Care & Regional Health System Coordination, Drug & Device Politics, Campania Region, Naples, Italy
| | - Ciro Mauro
- Cardiology Division, "A. Cardarelli" Hospital, Naples, Italy
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Naples, Italy
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2
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Di Donato M, Di Zazzo E, Salvati A, Sorrentino C, Giurato G, Fiore D, Proto MC, Rienzo M, Casamassimi A, Gazzerro P, Bifulco M, Castoria G, Weisz A, Nassa G, Abbondanza C. RIZ2 at the crossroad of the EGF/EGFR signaling in colorectal cancer. J Transl Med 2023; 21:736. [PMID: 37853459 PMCID: PMC10585774 DOI: 10.1186/s12967-023-04621-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is the third most deadly and fourth most diagnosed cancer worldwide. Despite the progress in early diagnosis and advanced therapeutic options, CRC shows a poor prognosis with a 5 year survival rate of ~ 45%. PRDM2/RIZ, a member of PR/SET domain family (PRDM), expresses two main molecular variants, the PR-plus isoform (RIZ1) and the PR-minus (RIZ2). The imbalance in their expression levels in favor of RIZ2 is observed in many cancer types. The full length RIZ1 has been extensively investigated in several cancers where it acts as a tumor suppressor, whereas few studies have explored the RIZ2 oncogenic properties. PRDM2 is often target of frameshift mutations and aberrant DNA methylation in CRC. However, little is known about its role in CRC. METHODS We combined in-silico investigation of The Cancer Genome Atlas (TCGA) CRC datasets, cellular and molecular assays, transcriptome sequencing and functional annotation analysis to assess the role of RIZ2 in human CRC. RESULTS Our in-silico analysis on TCGA datasets confirmed that PRDM2 gene is frequently mutated and transcriptionally deregulated in CRC and revealed that a RIZ2 increase is highly correlated with a significant RIZ1 downregulation. Then, we assayed several CRC cell lines by qRT-PCR analysis for the main PRDM2 transcripts and selected DLD1 cell line, which showed the lowest RIZ2 levels. Therefore, we overexpressed RIZ2 in these cells to mimic TCGA datasets analysis results and consequently to assess the PRDM2/RIZ2 role in CRC. Data from RNA-seq disclosed that RIZ2 overexpression induced profound changes in CRC cell transcriptome via EGF pathway deregulation, suggesting that RIZ2 is involved in the EGF autocrine regulation of DLD1 cell behavior. Noteworthy, the forced RIZ2 expression increased cell viability, growth, colony formation, migration and organoid formation. These effects could be mediated by the release of high EGF levels by RIZ2 overexpressing DLD1 cells. CONCLUSIONS Our findings add novel insights on the putative RIZ2 tumor-promoting functions in CRC, although additional efforts are warranted to define the underlying molecular mechanism.
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Affiliation(s)
- Marzia Di Donato
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Erika Di Zazzo
- Department of Medicine and Health Sciences "V. Tiberio", University of Molise, Campobasso, Italy
| | - Annamaria Salvati
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, 84081, Baronissi, Italy
| | - Carmela Sorrentino
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, 84081, Baronissi, Italy
- CRGS-Genome Research Center for Health, University of Salerno Campus of Medicine, 84081, Baronissi, Italy
| | - Donatella Fiore
- Department of Pharmacy, University of Salerno, Fisciano, Italy
| | | | - Monica Rienzo
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Amelia Casamassimi
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy.
| | | | - Maurizio Bifulco
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Naples, Italy
| | - Gabriella Castoria
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, 84081, Baronissi, Italy
- CRGS-Genome Research Center for Health, University of Salerno Campus of Medicine, 84081, Baronissi, Italy
| | - Giovanni Nassa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, 84081, Baronissi, Italy
- CRGS-Genome Research Center for Health, University of Salerno Campus of Medicine, 84081, Baronissi, Italy
| | - Ciro Abbondanza
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy.
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3
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Di Zazzo E, Rienzo M, Casamassimi A, De Rosa C, Medici N, Gazzerro P, Bifulco M, Abbondanza C. Exploring the putative role of PRDM1 and PRDM2 transcripts as mediators of T lymphocyte activation. J Transl Med 2023; 21:217. [PMID: 36964555 PMCID: PMC10039509 DOI: 10.1186/s12967-023-04066-x] [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: 02/15/2023] [Accepted: 03/17/2023] [Indexed: 03/26/2023] Open
Abstract
BACKGROUND T cell activation and programming from their naïve/resting state, characterized by widespread modifications in chromatin accessibility triggering extensive changes in transcriptional programs, is orchestrated by several cytokines and transcription regulators. PRDM1 and PRDM2 encode for proteins with PR/SET and zinc finger domains that control several biological processes, including cell differentiation, through epigenetic regulation of gene expression. Different transcripts leading to main protein isoforms with (PR +) or without (PR-) the PR/SET domain have been described. Although many studies have established the critical PRDM1 role in hematopoietic cell differentiation, maintenance and/or function, the single transcript contribution has not been investigated before. Otherwise, very few evidence is currently available on PRDM2. Here, we aimed to analyze the role of PRDM1 and PRDM2 different transcripts as mediators of T lymphocyte activation. METHODS We analyzed the transcription signature of the main variants from PRDM1 (BLIMP1a and BLIMP1b) and PRDM2 (RIZ1 and RIZ2) genes, in human T lymphocytes and Jurkat cells overexpressing PRDM2 cDNAs following activation through different signals. RESULTS T lymphocyte activation induced an early increase of RIZ2 and RIZ1 followed by BLIMP1b increase and finally by BLIMP1a increase. The "first" and the "second" signals shifted the balance towards the PR- forms for both genes. Interestingly, the PI3K signaling pathway modulated the RIZ1/RIZ2 ratio in favor of RIZ1 while the balance versus RIZ2 was promoted by MAPK pathway. Cytokines mediating different Jak/Stat signaling pathways (third signal) early modulated the expression of PRDM1 and PRDM2 and the relationship of their different transcripts confirming the early increase of the PR- transcripts. Different responses of T cell subpopulations were also observed. Jurkat cells showed that the acute transient RIZ2 increase promoted the balancing of PRDM1 forms towards BLIMP1b. The stable forced expression of RIZ1 or RIZ2 induced a significant variation in the expression of key transcription factors involved in T lymphocyte differentiation. The BLIMP1a/b balance shifted in favor of BLIMP1a in RIZ1-overexpressing cells and of BLIMP1b in RIZ2-overexpressing cells. CONCLUSIONS This study provides the first characterization of PRDM2 in T-lymphocyte activation/differentiation and novel insights on PRDM1 and PRDM2 transcription regulation during initial activation phases.
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Affiliation(s)
- Erika Di Zazzo
- Department of Medicine and Health Sciences "V. Tiberio", University of Molise, 86100, Campobasso, Italy
| | - Monica Rienzo
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", 81100, Caserta, Italy
| | - Amelia Casamassimi
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138, Naples, Italy
| | - Caterina De Rosa
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138, Naples, Italy
| | - Nicola Medici
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138, Naples, Italy
| | - Patrizia Gazzerro
- Department of Pharmacy, University of Salerno, 84084, Salerno, Fisciano (SA), Italy
| | - Maurizio Bifulco
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", 80131, Naples, Italy
| | - Ciro Abbondanza
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138, Naples, Italy.
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4
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Benincasa G, Maron BA, Affinito O, D’Alto M, Franzese M, Argiento P, Schiano C, Romeo E, Bontempo P, Golino P, Berrino L, Loscalzo J, Napoli C. Association Between Circulating CD4 + T Cell Methylation Signatures of Network-Oriented SOCS3 Gene and Hemodynamics in Patients Suffering Pulmonary Arterial Hypertension. J Cardiovasc Transl Res 2023; 16:17-30. [PMID: 35960497 PMCID: PMC9944731 DOI: 10.1007/s12265-022-10294-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/19/2022] [Indexed: 02/06/2023]
Abstract
Pathogenic DNA methylation changes may be involved in pulmonary arterial hypertension (PAH) onset and its progression, but there is no data on potential associations with patient-derived hemodynamic parameters. The reduced representation bisulfite sequencing (RRBS) platform identified N = 631 differentially methylated CpG sites which annotated to N = 408 genes (DMGs) in circulating CD4+ T cells isolated from PAH patients vs. healthy controls (CTRLs). A promoter-restricted network analysis established the PAH subnetwork that included 5 hub DMGs (SOCS3, GNAS, ITGAL, NCOR2, NFIC) and 5 non-hub DMGs (NR4A2, GRM2, PGK1, STMN1, LIMS2). The functional analysis revealed that the SOCS3 gene was the most recurrent among the top ten significant pathways enriching the PAH subnetwork, including the growth hormone receptor and the interleukin-6 signaling. Correlation analysis showed that the promoter methylation levels of each network-oriented DMG were associated individually with hemodynamic parameters. In particular, SOCS3 hypomethylation was negatively associated with right atrial pressure (RAP) and positively associated with cardiac index (CI) (|r|≥ 0.6). A significant upregulation of the SOCS3, ITGAL, NFIC, NCOR2, and PGK1 mRNA levels (qRT-PCR) in peripheral blood mononuclear cells from PAH patients vs. CTRLs was found (P ≤ 0.05). By immunoblotting, a significant upregulation of the SOCS3 protein was confirmed in PAH patients vs. CTRLs (P < 0.01). This is the first network-oriented study which integrates circulating CD4+ T cell DNA methylation signatures, hemodynamic parameters, and validation experiments in PAH patients at first diagnosis or early follow-up. Our data suggests that SOCS3 gene might be involved in PAH pathogenesis and serve as potential prognostic biomarker.
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Affiliation(s)
- Giuditta Benincasa
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", 80138, Naples, Italy.
| | - Bradley A. Maron
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, MB Boston, USA ,Harvard Medical School, Boston, MA USA
| | | | - Michele D’Alto
- Department of Cardiology, Monaldi Hospital, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | | | - Paola Argiento
- Department of Cardiology, Monaldi Hospital, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Concetta Schiano
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Emanuele Romeo
- Department of Cardiology, Monaldi Hospital, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Paola Bontempo
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Paolo Golino
- Department of Cardiology, Monaldi Hospital, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Liberato Berrino
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Joseph Loscalzo
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, MB Boston, USA
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy ,IRCCS SDN, Naples, Italy
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5
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Yang K, Li J, Tao L. Purine metabolism in the development of osteoporosis. Biomed Pharmacother 2022; 155:113784. [DOI: 10.1016/j.biopha.2022.113784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022] Open
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6
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García-Pérez O, Melgar-Vilaplana L, Córdoba-Lanús E, Fernández-de-Misa R. Gene Expression Studies in Formalin-Fixed Paraffin-Embedded Samples of Cutaneous Cancer: The Need for Reference Genes. Curr Issues Mol Biol 2021; 43:2167-2176. [PMID: 34940125 PMCID: PMC8928935 DOI: 10.3390/cimb43030151] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/27/2021] [Accepted: 11/29/2021] [Indexed: 01/02/2023] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) tumour samples may provide crucial data regarding biomarkers for neoplasm progression. Analysis of gene expression is frequently used for this purpose. Therefore, mRNA expression needs to be normalized through comparison to reference genes. In this study, we establish which of the usually reported reference genes is the most reliable one in cutaneous malignant melanoma (MM) and cutaneous squamous cell carcinoma (CSCC). ACTB, TFRC, HPRT1 and TBP expression was quantified in 123 FFPE samples (74 MM and 49 CSCC biopsies) using qPCR. Expression stability was analysed by NormFinder and Bestkeeper softwares, and the direct comparison method between means and SD. The in-silico analysis with BestKeeper indicated that HPRT1 was more stable than ACTB and TFRC in MM (1.85 vs. 2.15) and CSCC tissues (2.09 vs. 2.33). The best option to NormFinder was ACTB gene (0.56) in MM and TFRC (0.26) in CSCC. The direct comparison method showed lower SD means of ACTB expression in MM (1.17) and TFRC expression in CSCC samples (1.00). When analysing the combination of two reference genes for improving stability, NormFinder indicated HPRT1 and ACTB to be the best for MM samples, and HPRT1 and TFRC genes for CSCC. In conclusion, HPRT1 and ACTB genes in combination are the most appropriate choice for normalization in gene expression studies in MM FFPE tissue, while the combination of HPRT1 and TFRC genes are the best option in analysing CSCC FFPE samples. These may be used consistently in forthcoming studies on gene expression in both tumours.
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Affiliation(s)
- Omar García-Pérez
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Ctra. Gral. del Rosario, 145, 38010 Santa Cruz de Tenerife, Spain;
- Universidad de La Laguna, Calle Padre Herrera, s/n, 38200 San Cristóbal de La Laguna, Spain
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC), 38296 San Cristóbal de La Laguna, Spain
| | - Leticia Melgar-Vilaplana
- Pathology Department, Hospital Universitario Nuestra Señora de Candelaria, Ctra. Gral. del Rosario, 145, 38010 Santa Cruz de Tenerife, Spain;
| | - Elizabeth Córdoba-Lanús
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Ctra. Gral. del Rosario, 145, 38010 Santa Cruz de Tenerife, Spain;
- Universidad de La Laguna, Calle Padre Herrera, s/n, 38200 San Cristóbal de La Laguna, Spain
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC), 38296 San Cristóbal de La Laguna, Spain
- Correspondence: (E.C.-L.); (R.F.-d.-M.)
| | - Ricardo Fernández-de-Misa
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Ctra. Gral. del Rosario, 145, 38010 Santa Cruz de Tenerife, Spain;
- Universidad de La Laguna, Calle Padre Herrera, s/n, 38200 San Cristóbal de La Laguna, Spain
- Dermatology Department, Hospital Universitario Nuestra Señora de Candelaria, Ctra. Gral. del Rosario, 145, 38010 Santa Cruz de Tenerife, Spain
- Correspondence: (E.C.-L.); (R.F.-d.-M.)
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7
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Infante T, Franzese M, Ruocco A, Schiano C, Affinito O, Pane K, Memoli D, Rizzo F, Weisz A, Bontempo P, Grimaldi V, Berrino L, Soricelli A, Mauro C, Napoli C. ABCA1, TCF7, NFATC1, PRKCZ, and PDGFA DNA methylation as potential epigenetic-sensitive targets in acute coronary syndrome via network analysis. Epigenetics 2021; 17:547-563. [PMID: 34151742 DOI: 10.1080/15592294.2021.1939481] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Acute coronary syndrome (ACS) is the most severe clinical manifestation of coronary heart disease.We performed an epigenome-wide analysis of circulating CD4+ and CD8+ T cells isolated from ACS patients and healthy subjects (HS), enrolled in the DIANA clinical trial, by reduced-representation bisulphite sequencing (RRBS). In CD4+ T cells, we identified 61 differentially methylated regions (DMRs) associated with 57 annotated genes (53% hyper- and 47% hypo-methylated) by comparing ACS patients vs HS. In CD8+ T cells, we identified 613 DMRs associated with 569 annotated genes (28% hyper- and 72% hypo-methylated) in ACS patients as compared to HS. In CD4+ vs CD8+ T cells of ACS patients we identified 175 statistically significant DMRs associated with 157 annotated genes (41% hyper- and 59% hypo-methylated). From pathway analyses, we selected six differentially methylated hub genes (NFATC1, TCF7, PDGFA, PRKCB, PRKCZ, ABCA1) and assessed their expression levels by q-RT-PCR. We found an up-regulation of selected genes in ACS patients vs HS (P < 0.001). ABCA1, TCF7, PDGFA, and PRKCZ gene expression was positively associated with CK-MB serum concentrations (r = 0.75, P = 0.03; r = 0.760, P = 0.029; r = 0.72, P = 0.044; r = 0.74, P = 0.035, respectively).This pilot study is the first single-base resolution map of DNA methylome by RRBS in CD4+ and CD8+ T cells and provides specific methylation signatures to clarify the role of aberrant methylation in ACS pathogenesis, thus supporting future research for novel epigenetic-sensitive biomarkers in the prevention and early diagnosis of this pathology.
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Affiliation(s)
- Teresa Infante
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Naples, Italy
| | | | - Antonio Ruocco
- Unit of Cardiovascular Diseases and Arrhythmias, "Antonio Cardarelli" Hospital, Naples, Italy
| | - Concetta Schiano
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Naples, Italy
| | | | | | - Domenico Memoli
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana," University of Salerno, Baronissi, SA, Italy.,Genome Research Center for Health, Campus of Medicine, Baronissi, SA, Italy
| | - Francesca Rizzo
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana," University of Salerno, Baronissi, SA, Italy.,Genome Research Center for Health, Campus of Medicine, Baronissi, SA, Italy
| | - Alessandro Weisz
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana," University of Salerno, Baronissi, SA, Italy.,Genome Research Center for Health, Campus of Medicine, Baronissi, SA, Italy
| | - Paola Bontempo
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Vincenzo Grimaldi
- IRCCS SDN, Naples, Italy.,U.O.C. Division of Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Liberato Berrino
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Andrea Soricelli
- IRCCS SDN, Naples, Italy.,Department of Exercise and Wellness Sciences, University of Naples Parthenope, Naples, Italy
| | - Ciro Mauro
- Unit of Cardiovascular Diseases and Arrhythmias, "Antonio Cardarelli" Hospital, Naples, Italy
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Naples, Italy.,IRCCS SDN, Naples, Italy
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8
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Rienzo M, Sorrentino A, Di Zazzo E, Di Donato M, Carafa V, Marino MM, De Rosa C, Gazzerro P, Castoria G, Altucci L, Casamassimi A, Abbondanza C. Searching for a Putative Mechanism of RIZ2 Tumor-Promoting Function in Cancer Models. Front Oncol 2021; 10:583533. [PMID: 33585202 PMCID: PMC7880127 DOI: 10.3389/fonc.2020.583533] [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: 07/15/2020] [Accepted: 12/08/2020] [Indexed: 12/16/2022] Open
Abstract
Positive Regulatory Domain (PRDM) gene family members commonly express two main molecular variants, the PR-plus isoform usually acting as tumor suppressor and the PR-minus one functioning as oncogene. Accordingly, PRDM2/RIZ encodes for RIZ1 (PR-plus) and RIZ2 (PR-minus). In human cancers, genetic or epigenetic modifications induce RIZ1 silencing with an expression level imbalance in favor of RIZ2 that could be relevant for tumorigenesis. Additionally, in estrogen target cells and tissues, estradiol increases RIZ2 expression level with concurrent increase of cell proliferation and survival. Several attempts to study RIZ2 function in HeLa or MCF-7 cells by its over-expression were unsuccessful. Thus, we over-expressed RIZ2 in HEK-293 cells, which are both RIZ1 and RIZ2 positive but unresponsive to estrogens. The forced RIZ2 expression increased cell viability and growth, prompted the G2-to-M phase transition and organoids formation. Accordingly, microarray analysis revealed that RIZ2 regulates several genes involved in mitosis. Consistently, RIZ silencing in both estrogen-responsive MCF-7 and -unresponsive MDA-MB-231 cells induced a reduction of cell proliferation and an increase of apoptosis rate. Our findings add novel insights on the putative RIZ2 tumor-promoting functions, although additional attempts are warranted to depict the underlying molecular mechanism.
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Affiliation(s)
- Monica Rienzo
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Anna Sorrentino
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Erika Di Zazzo
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy.,Department of Medicine and Health Sciences "V. Tiberio", University of Molise, Campobasso, Italy
| | - Marzia Di Donato
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Vincenzo Carafa
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Maria Michela Marino
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Caterina De Rosa
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | | | - Gabriella Castoria
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Amelia Casamassimi
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Ciro Abbondanza
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
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9
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Yang H, Zhang L, Liu S. Determination of reference genes for ovine pulmonary adenocarcinoma infected lung tissues using RNA-seq transcriptome profiling. J Virol Methods 2020; 284:113923. [PMID: 32615131 DOI: 10.1016/j.jviromet.2020.113923] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 02/25/2020] [Accepted: 06/25/2020] [Indexed: 01/08/2023]
Abstract
Ovine pulmonary adenocarcinoma (OPA) is a globally occurring tumor of lung epithelium which seriously affects the development of sheep farming. In our research, lung tissues of 3 naturally infected OPA individuals and 3 healthy individuals (2-4 years old) were collected. RNA was extracted for transcriptome analysis and reference gene selection. According to transcriptome analysis, 7 candidate reference genes (eukaryotic translation initiation factor 1, EIF1; glyceraldehyde-3-phosphate dehydrogenase, GAPDH; beta-actin, ACTB; GABA Type A receptor-associated protein, GABARAP; activating transcription factor 4, ATF4; ribosomal protein S15, RPS15; and Y-Box binding protein 1, YBX1) showed fragments per kilobase of transcript per million fragments mapped (FPKM) values > 200.0 and standard errors of the means (SEM) < 20.0. Expression of the above candidate reference genes was evaluated by Real-time quantitative polymerase chain reaction (RT-qPCR) combined with the analysis using GeNorm, NormFinder, and BestKeeper software. Comprehensive analysis of the results showed that ACTB was the most stable one, followed by EIF1 and GABARAP. Then, expression stability of the above three genes were validated, suggesting as suitable reference genes in sheep lung tissue, in additional 30 OPA-affected lung tissues and 10 healthy ovine lung tissues. Finally, our findings will be helpful for the subsequent study on the tumorigenic mechanism of OPA.
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Affiliation(s)
- Hui Yang
- Veterinary Medicine College of Inner Mongolia Agricultural University, Zhao Wu Da Road 306#, Hohhot 010018, People's Republic of China; Inner Mongolia Key Laboratory of Basic Veterinary Science, Hohhot 010018, People's Republic of China; Key Laboratory of Clinical Diagnosis and Treatment Technology in Animal Disease, Ministry of Agriculture, Hohhot 010018, People's Republic of China.
| | - Liang Zhang
- Veterinary Medicine College of Inner Mongolia Agricultural University, Zhao Wu Da Road 306#, Hohhot 010018, People's Republic of China; Inner Mongolia Key Laboratory of Basic Veterinary Science, Hohhot 010018, People's Republic of China; Key Laboratory of Clinical Diagnosis and Treatment Technology in Animal Disease, Ministry of Agriculture, Hohhot 010018, People's Republic of China.
| | - Shuying Liu
- Veterinary Medicine College of Inner Mongolia Agricultural University, Zhao Wu Da Road 306#, Hohhot 010018, People's Republic of China; Inner Mongolia Key Laboratory of Basic Veterinary Science, Hohhot 010018, People's Republic of China; Key Laboratory of Clinical Diagnosis and Treatment Technology in Animal Disease, Ministry of Agriculture, Hohhot 010018, People's Republic of China.
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Roy JG, McElhaney JE, Verschoor CP. Reliable reference genes for the quantification of mRNA in human T-cells and PBMCs stimulated with live influenza virus. BMC Immunol 2020; 21:4. [PMID: 32005148 PMCID: PMC6995044 DOI: 10.1186/s12865-020-0334-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 01/20/2020] [Indexed: 12/19/2022] Open
Abstract
Background Quantitative PCR (qPCR) is a powerful tool that is particularly well-suited to measure mRNA levels in clinical samples, especially those with relatively low cell counts. However, a caveat of this approach is that reliable, stably expressed reference (housekeeping) genes are vital in order to ensure reproducibility and appropriate biological inference. In this study, we evaluated the expression stability of six reference genes in peripheral blood mononuclear cells (PBMCs) and isolated CD3+ T-cells from young and old adults (n = 10), following ex vivo stimulation with mock (unstimulated) or live influenza virus. Our genes included: β-actin (ACTB), glyercaldehyde-3-phostphate dehydrogenase (GAPDH), ribosomal protein L13a (RPL13a), ribosomal protein S18 (RPS18), succinate dehydrogenase complex flavoprotein subunit A (SDHA), and ubiquitin-conjugating enzyme E2D2 (UBE2D2). Results Reference gene expression varied significantly depending on cell type and stimulation conditions, but not age. Using the comparative ΔCt method, and the previously published software BestKeeper, NormFinder, and geNorm, we show that in PBMCs and T-cells, UBE2D2 and RPS18 were the most stable reference genes, followed by ACTB; however, the expression of UBE2D2 and RPS18 was found to increase with viral stimulation in isolated T-cells, while ACTB expression did not change significantly. No age-related differences in stability were observed for any gene Conclusions This study suggests the use of a combination of UBE2D2, RPS18, and ACTB for the study of influenza responses in PBMCs and T-cells, although ACTB alone may be the most optimal choice if choosing to compare target gene expression before and after viral stimulation. Both GAPDH and RPL13a were found to be poor reference genes and should be avoided for studies of this nature.
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Affiliation(s)
- Justin G Roy
- Health Sciences North Research Institute, 41 Ramsey Lake Rd, Sudbury, ON, P3E5J1, Canada
| | - Janet E McElhaney
- Health Sciences North Research Institute, 41 Ramsey Lake Rd, Sudbury, ON, P3E5J1, Canada
| | - Chris P Verschoor
- Health Sciences North Research Institute, 41 Ramsey Lake Rd, Sudbury, ON, P3E5J1, Canada.
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11
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Postmenopausal Osteoporosis reference genes for qPCR expression assays. Sci Rep 2019; 9:16533. [PMID: 31712560 PMCID: PMC6848520 DOI: 10.1038/s41598-019-52612-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 10/14/2019] [Indexed: 02/05/2023] Open
Abstract
Osteoporosis (OP) is a multifactorial disease influenced by genetic factors in more than half of the cases. In spite of the efforts to clarify the relationship among genetic factors and susceptibility to develop OP, many genetic associations need to be further functionally validated. Besides, some limitations as the choice of stably expressed reference genes (RG) should be overcome to ensure the quality and reproducibility of gene expression assays. To our knowledge, a validation study for RG in OP is still missing. We compared the expression levels, using polymerase chain reaction quantitative real time (qPCR) of 10 RG (G6PD, B2M, GUSB, HSP90, EF1A, RPLP0, GAPDH, ACTB, 18 S and HPRT1) to assess their suitability in OP analysis by using GeNorm, Normfinder, BestKeeper and RefFinder programs. A minimal number of two RG was recommended by GeNorm to obtain a reliable normalization. RPLP0 and B2M were identified as the most stable genes in OP studies while ACTB, 18 S and HPRT1 were inadequate for normalization in our data set. Moreover, we showed the dramatic effects of suboptimal RG choice on the quantification of a target gene, highlighting the importance in the identification of the most appropriate reference gene to specific diseases. We suggest the use of RPLP0 and B2M as the most stable reference genes while we do not recommend the use of the least stable reference genes HPRT1, 18 S and ACTB in OP expression assays using PBMC as biological source. Additionally, we emphasize the importance of individualized and careful choice in software and reference genes selection.
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12
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Schiano C, Grimaldi V, Franzese M, Fiorito C, De Nigris F, Donatelli F, Soricelli A, Salvatore M, Napoli C. Non-nutritional sweeteners effects on endothelial vascular function. Toxicol In Vitro 2019; 62:104694. [PMID: 31655124 DOI: 10.1016/j.tiv.2019.104694] [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] [Received: 07/08/2019] [Revised: 10/04/2019] [Accepted: 10/17/2019] [Indexed: 12/27/2022]
Abstract
AIM Hyperglycemia status induces endothelial dysfunction, although the underlying pathogenic mechanisms are not fully understood. There are several studies connecting sugar/sweetened beverages to the cardiovascular disease. Currently, many sweeteners have been extensively introduced into lifestyle to normalize blood glucose levels without altering the sweet taste. However, there is growing concern for their impact on metabolic health. METHODS Human endothelial cells were treated with Glucose, Fructose, Aspartame, Rebaudioside A, Stevioside, or Steviol. Morphological characteristics, in vitro angiogenesis and array gene expression were analyzed. RESULTS High-glucose and fructose concentrations significantly decreased cell features such as angiogenic capability. Interestingly, non-caloric sweeteners did not significantly modified all cell characteristics and they did not compromised cell angiogenic ability. Array gene expression analysis revealed that the chemokine fractalkine (CX3CL1) and the enzyme transferase (HPRT1) were always significantly upregulated and downregulated respectively, after glucose and fructose treatments (P > .05), whereas they were non-differentially expressed with all the other sweeteners. Interestingly, both genes are considered as cardiovascular disease risk biomarkers. Specifically, upregulation of CX3CL1/CX3CR1 occurs in the human placenta and serum levels of the ligand are associated with markers of insulin resistance in GDM. CONCLUSIONS Differently from glucose and fructose, steviol glycosides do not damage endothelial cells. Prospective preclinical studies and clinical trials are warranted to confirm the long-term safety of such compounds.
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Affiliation(s)
- Concetta Schiano
- Department of Advanced Clinical and Surgical Sciences, University of Campania "L. Vanvitelli", Naples, Italy.
| | - Vincenzo Grimaldi
- Department of Advanced Clinical and Surgical Sciences, University of Campania "L. Vanvitelli", Naples, Italy
| | | | - Carmela Fiorito
- Department of Advanced Clinical and Surgical Sciences, University of Campania "L. Vanvitelli", Naples, Italy
| | - Filomena De Nigris
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Naples, Italy
| | - Francesco Donatelli
- Department of Clinical and Community Sciences, University of Milan, Milan, Italy
| | | | | | - Claudio Napoli
- Department of Advanced Clinical and Surgical Sciences, University of Campania "L. Vanvitelli", Naples, Italy; IRCCS SDN, Naples, Italy
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Schiano C, Franzese M, Pane K, Garbino N, Soricelli A, Salvatore M, de Nigris F, Napoli C. Hybrid 18F-FDG-PET/MRI Measurement of Standardized Uptake Value Coupled with Yin Yang 1 Signature in Metastatic Breast Cancer. A Preliminary Study. Cancers (Basel) 2019; 11:cancers11101444. [PMID: 31561604 PMCID: PMC6827137 DOI: 10.3390/cancers11101444] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/18/2019] [Accepted: 09/18/2019] [Indexed: 12/24/2022] Open
Abstract
Purpose: Detection of breast cancer (BC) metastasis at the early stage is important for the assessment of BC progression status. Image analysis represents a valuable tool for the management of oncological patients. Our preliminary study combined imaging parameters from hybrid 18F-FDG-PET/MRI and the expression level of the transcriptional factor Yin Yang 1 (YY1) for the detection of early metastases. Methods: The study enrolled suspected n = 217 BC patients that underwent 18F-FDG-PET/MRI scans. The analysis retrospectively included n = 55 subjects. n = 40 were BC patients and n = 15 imaging-negative female individuals were healthy subjects (HS). Standard radiomics parameters were extracted from PET/MRI image. RNA was obtained from peripheral blood mononuclear cells and YY1 expression level was evaluated by real time reverse transcription polymerase chain reactions (qRT-PCR). An enzyme-linked immuosorbent assay (ELISA) was used to determine the amount of YY1 serum protein. Statistical comparison between subgroups was evaluated by Mann-Whitney U and Spearman’s tests. Results: Radiomics showed a significant positive correlation between Greg-level co-occurrence matrix (GLCM) and standardized uptake value maximum (SUVmax) (r = 0.8 and r = 0.8 respectively) in BC patients. YY1 level was significant overexpressed in estrogen receptor (ER)-positive/progesteron receptor-positive/human epidermal growth factor receptor2-negative (ER+/PR+/HER2-) subtype of BC patients with synchronous metastasis (SM) at primary diagnosis compared to metachronous metastasis (MM) and HS (p < 0.001) and correlating significantly with 18F-FDG-uptake parameter (SUVmax) (r = 0.48). Conclusions: The combination of functional 18F-FDG-PET/MRI parameters and molecular determination of YY1 could represent a novel integrated approach to predict synchronous metastatic disease with more accuracy than 18F-FDG-PET/MRI alone.
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Affiliation(s)
| | | | | | | | - Andrea Soricelli
- IRCCS SDN, 80134 Naples, Italy
- Department of Motor Sciences and Healthiness, University of Naples Parthenope, 80134 Naples, Italy
| | | | - Filomena de Nigris
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Claudio Napoli
- IRCCS SDN, 80134 Naples, Italy
- Department of Advanced Medical and Surgical Sciences, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
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Correlation of Circulating miR-765, miR-93-5p, and miR-433-3p to Obstructive Coronary Heart Disease Evaluated by Cardiac Computed Tomography. Am J Cardiol 2019; 124:176-182. [PMID: 31084998 DOI: 10.1016/j.amjcard.2019.04.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/01/2019] [Accepted: 04/05/2019] [Indexed: 12/13/2022]
Abstract
Epigenetic-sensitive mechanisms may be correlated both to pathogenesis and prognosis of coronary heart disease (CHD). We prospectively investigated some plasma circulating microRNA levels in patients undergoing cardiac computed tomography for suspected CHD (n = 95). We show that let-7c-5p, miR-765, miR-483-5p, miR-31-5p, and miR-206 were upregulated in CHD patients (n = 66) versus healthy subjects HS (n = 29); moreover, let-7c-5p, miR-765, miR- 483-5p showed higher expression in obstructive CHD (n = 36) compared to no obstructive CHD patients (n = 66). Remarkably, miR-765, miR-93-5p, and miR-433-3p showed an upregulation in patients with critical coronary stenosis. Multivariate regression analysis demonstrated that miR-765, miR-31-5p, and miR-206 were independently associated with CHD while circulating levels of miR-765 (p = 0.035), miR-433-3p (p = 0.043), and miR-93-5p (p = 0.041) were significantly higher in critical stenosis patients. Receiver operating characteristic curve analysis revealed a good performance for miR-765, miR-93-5p, and miR-433-3p on predicting CHD severity. In conclusion, our study represents a combined epigenetic/imaging approach useful to support the diagnosis and prediction of CHD.
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Fede C, Stecco C, Angelini A, Fan C, Belluzzi E, Pozzuoli A, Ruggieri P, De Caro R. Variations in contents of hyaluronan in the peritumoral micro-environment of human chondrosarcoma. J Orthop Res 2019; 37:503-509. [PMID: 30444002 DOI: 10.1002/jor.24176] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 10/30/2018] [Indexed: 02/04/2023]
Abstract
A concept consolidated in recent years is that tumor growth depends to a great extent on the micro-environment surrounding the tumor, which has a fundamental role in tumor progression and in determining the effectiveness of therapies. Our analysis focuses on chondrosarcoma, the second primary malignant bone tumor, resistant to both chemotherapeutic and radiation therapy. We quantified hyaluronan, one of the main components of the extracellular matrix, with the aim of comparing its amount in the connective tissue surrounding the tumor with intra-tumoral tissue and healthy fascia of the same anatomic district, viewed as a health control. We demonstrate that hyaluronan increased significantly in the peritumoral stroma compared with the healthy fascia, which showed an average amount according to the physical characteristics of body districts by a mean value of 26.9 μg/g. In the peritumoral stroma, the mean hyaluronan content reached 132.6 μg/g (mean value of 63.2 μg/g). The p-value was less than 0.01, showing a highly significant statistical difference. Surprisingly, no significant differences were detected as a function of age, gender, or tumor grade. The levels of hyaluronan were comparable in peritumoral and tumor tissues, although there were differences depending on the state of necrosis. In addition, data on the expression of hyaluronic acid synthetase showed a decrease of about 50% in peritumoral and tumor tissues, indicating alterations in hyaluronan turnover and synthesis. This work demonstrates a variation in hyaluronan contents around the chondrosarcoma, likely correlated with the aggressiveness and resistance to chemotherapy of this tumors. Statement of Clinical Significance: Deeper knowledge about the composition of the peritumoral stroma, rich in extracellular matrix, will enhance better study and understanding of the metastatic potential of tumors and their prognostic indices. © 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 37:503-509, 2019.
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Affiliation(s)
- Caterina Fede
- Department of Neuroscience, Anatomy Institute, University of Padova, via Gabelli 65, Padova 35121, Italy
| | - Carla Stecco
- Department of Neuroscience, Anatomy Institute, University of Padova, via Gabelli 65, Padova 35121, Italy
| | - Andrea Angelini
- Department of Orthopedics and Orthopedic Oncology, University of Padova, via Giustiniani 2, Padova 35121, Italy
| | - Chenglei Fan
- Department of Neuroscience, Anatomy Institute, University of Padova, via Gabelli 65, Padova 35121, Italy
| | - Elisa Belluzzi
- Department of Orthopedics and Orthopedic Oncology, University of Padova, via Giustiniani 2, Padova 35121, Italy
| | - Assunta Pozzuoli
- Department of Orthopedics and Orthopedic Oncology, University of Padova, via Giustiniani 2, Padova 35121, Italy
| | - Pietro Ruggieri
- Department of Orthopedics and Orthopedic Oncology, University of Padova, via Giustiniani 2, Padova 35121, Italy
| | - Raffaele De Caro
- Department of Neuroscience, Anatomy Institute, University of Padova, via Gabelli 65, Padova 35121, Italy
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Evidence of association of circulating epigenetic-sensitive biomarkers with suspected coronary heart disease evaluated by Cardiac Computed Tomography. PLoS One 2019; 14:e0210909. [PMID: 30673762 PMCID: PMC6343931 DOI: 10.1371/journal.pone.0210909] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 01/03/2019] [Indexed: 12/22/2022] Open
Abstract
Circulating biomarkers available in clinical practice do not allow to stratify patients with coronary heart disease (CHD) prior the onset of a clinically relevant event. We evaluated the methylation status of specific genomic segments and gene expression in peripheral blood of patients undergoing Cardiac Computed Tomography (CCT) for CHD (n = 95). We choose to investigate cholesterol metabolism. Methylation and gene expression of low density lipoprotein receptor (LDLR), sterol regulatory element-binding factor 2 (SREBF2) and ATP-binding cassette transporter 1 (ABCA1) were evaluated by qRT-PCR. Calcium score (CACS), stenosis degree, total plaque volume (TPV), calcified plaque volume (CPV), non-calcified plaque volume (NCPV) and plaque burden (PB) were assessed in all CHD patients (n = 65). The percentage of methylation at the specific analyzed segment of LDLR promoter was higher in CHD patients vs healthy subjects (HS) (n = 30) (p = 0.001). LDLR, SREBF2 and ABCA1 mRNAs were up-regulated in CHD patients vs HS (p = 0.02; p = 0.019; p = 0.008). SREBF2 was overexpressed in patients with coronary stenosis ≥50% vs subjects with stenosis <50% (p = 0.036). After adjustment for risk factors and clinical features, ABCA1 (p = 0.005) and SREBF2 (p = 0.010) gene expression were identified as independent predictors of CHD and severity. ROC curve analysis revealed a good performance of ABCA1 on predicting CHD (AUC = 0.768; p<0.001) and of SREBF2 for the prediction of disease severity (AUC = 0.815; p<0.001). Moreover, adjusted multivariate analysis demonstrated SREBF2 as independent predictor of CPV, NCPV and TPV (p = 0.022; p = 0.002 and p = 0.006) and ABCA1 as independent predictor of NCPV and TPV (p = 0.002 and p = 0.013). CHD presence and characteristics are related to selected circulating transcriptional and epigenetic-sensitive biomarkers linked to cholesterol pathway. More extensive analysis of CHD phenotypes and circulating biomarkers might improve and personalize cardiovascular risk stratification in the clinical settings.
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Anbazhagan A, Sridharan P, Pratheesh P. Validation of suitable housekeeping genes for 3T3-L1 derived adipocytes cultured in obesity mimicking conditions and RAW 264.7 macrophage cells lines in hypoxic and normoxic conditions. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Sorrentino A, Federico A, Rienzo M, Gazzerro P, Bifulco M, Ciccodicola A, Casamassimi A, Abbondanza C. PR/SET Domain Family and Cancer: Novel Insights from the Cancer Genome Atlas. Int J Mol Sci 2018; 19:ijms19103250. [PMID: 30347759 PMCID: PMC6214140 DOI: 10.3390/ijms19103250] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 10/12/2018] [Accepted: 10/17/2018] [Indexed: 12/17/2022] Open
Abstract
The PR/SET domain gene family (PRDM) encodes 19 different transcription factors that share a subtype of the SET domain [Su(var)3-9, enhancer-of-zeste and trithorax] known as the PRDF1-RIZ (PR) homology domain. This domain, with its potential methyltransferase activity, is followed by a variable number of zinc-finger motifs, which likely mediate protein⁻protein, protein⁻RNA, or protein⁻DNA interactions. Intriguingly, almost all PRDM family members express different isoforms, which likely play opposite roles in oncogenesis. Remarkably, several studies have described alterations in most of the family members in malignancies. Here, to obtain a pan-cancer overview of the genomic and transcriptomic alterations of PRDM genes, we reanalyzed the Exome- and RNA-Seq public datasets available at The Cancer Genome Atlas portal. Overall, PRDM2, PRDM3/MECOM, PRDM9, PRDM16 and ZFPM2/FOG2 were the most mutated genes with pan-cancer frequencies of protein-affecting mutations higher than 1%. Moreover, we observed heterogeneity in the mutation frequencies of these genes across tumors, with cancer types also reaching a value of about 20% of mutated samples for a specific PRDM gene. Of note, ZFPM1/FOG1 mutations occurred in 50% of adrenocortical carcinoma patients and were localized in a hotspot region. These findings, together with OncodriveCLUST results, suggest it could be putatively considered a cancer driver gene in this malignancy. Finally, transcriptome analysis from RNA-Seq data of paired samples revealed that transcription of PRDMs was significantly altered in several tumors. Specifically, PRDM12 and PRDM13 were largely overexpressed in many cancers whereas PRDM16 and ZFPM2/FOG2 were often downregulated. Some of these findings were also confirmed by real-time-PCR on primary tumors.
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Affiliation(s)
- Anna Sorrentino
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio, 80138 Naples, Italy.
- Department of Science and Technology, University of Naples "Parthenope", 80143 Naples, Italy.
| | - Antonio Federico
- Department of Science and Technology, University of Naples "Parthenope", 80143 Naples, Italy.
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso", CNR, 80131 Naples, Italy.
| | - Monica Rienzo
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy.
| | - Patrizia Gazzerro
- Department of Pharmacy, University of Salerno, 84084 Salerno, Italy.
| | - Maurizio Bifulco
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", 80131 Naples, Italy.
| | - Alfredo Ciccodicola
- Department of Science and Technology, University of Naples "Parthenope", 80143 Naples, Italy.
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso", CNR, 80131 Naples, Italy.
| | - Amelia Casamassimi
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio, 80138 Naples, Italy.
| | - Ciro Abbondanza
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio, 80138 Naples, Italy.
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Absence of Beta-2 microgloblulin ( B2M ) and hypoxanthine-guanine phosphoribosyl transferase-1( HPRT1 ) gene modulation in U87MG and U251 Glioblastoma cell lines subjected to cobalt chloride mediated hypoxia. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.03.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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Schiano C, Rienzo M, Casamassimi A, Soricelli A, Napoli C. Splicing regulators in endothelial cell differentiation. J Cardiovasc Med (Hagerstown) 2017; 18:742-749. [PMID: 28661931 DOI: 10.2459/jcm.0000000000000536] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
AIMS Alternative splicing represents a key mechanism of gene regulation. Despite its role in regulating cell pluripotency and differentiation being well known, the underlining mechanisms are still poorly studied. Here, we investigated the possible involvement of splicing regulators during the different steps of endothelial cell differentiation through expression studies on human circulating progenitors. METHODS Total RNAs were extracted from all cells and reverse-transcribed. Semiquantitative and real-time RT-PCR was performed using selective oligonucleotides. Differences between group means were considered significant at P value less than 0.05 and more significant at P value less than 0.01. Protein extracts were incubated with an antibody directed against MED23. Immunoprecipitation of supernatants and pellets was probed with both anti-Muscleblind-like splicing regulator (MBNL)1 and anti-MBNL2 antibodies. RESULTS Several clinical trials demonstrated the safety and efficacy of progenitor cells in regenerative therapy of the cardiovascular system. Particularly, we analyzed the expression of genes belonging to muscleblind family members and MED complex subunits, which are known to be involved during differentiation in other models. This study shows that MED23, MBNL1 and MBNL2 were all expressed at high levels only in differentiated cells. Moreover, immunoprecipitation assays indicated that MED23 is able to bind MBNLs in endothelial cells. CONCLUSION Our data suggest that MED23, MBNL1 and MBNL2 could regulate alternative splicing events activated during differentiation through a common mechanism. Hence, these observations corroborate previous evidence that splicing regulators may have an essential role in the basic apparatus required for cell pluripotency and reprogramming, allowing identification of novel biomarkers to use for early diagnosis in cardiovascular diseases.
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Affiliation(s)
- Concetta Schiano
- aIRCCS SDN bDepartment of Biochemistry, Biophysics and General Pathology, Università degli Studi della Campania 'Luigi Vanvitelli' cDepartment of Diagnostic Imaging, University of Naples "Parthenope" dU.O.C. Immunohematology, Transfusion Medicine and Transplant Immunology, Regional Reference Laboratory of Transplant Immunology, Department of Medical, Surgical, Neurological, Metabolic and Geriatric Sciences, Università degli Studi della Campania 'Luigi Vanvitelli', Naples, Italy
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Li T, Diao H, Zhao L, Xing Y, Zhang J, Liu N, Yan Y, Tian X, Sun W, Liu B. Identification of suitable reference genes for real-time quantitative PCR analysis of hydrogen peroxide-treated human umbilical vein endothelial cells. BMC Mol Biol 2017; 18:10. [PMID: 28381210 PMCID: PMC5381023 DOI: 10.1186/s12867-017-0086-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 03/21/2017] [Indexed: 11/25/2022] Open
Abstract
Background Oxidative stress can induce cell injury in vascular endothelial cells, which is the initial event in the development of atherosclerosis. Although quantitative real-time polymerase chain reaction (qRT-PCR) has been widely used in gene expression studies in oxidative stress injuries, using carefully validated reference genes has not received sufficient attention in related studies. The objective of this study, therefore, was to select a set of stably expressed reference genes for use in qRT-PCR normalization in oxidative stress injuries in human umbilical vein endothelial cells (HUVECs) induced by hydrogen peroxide (H2O2). Results Using geNorm analysis, we found that five stably expressed reference genes were sufficient for normalization in qRT-PCR analysis in HUVECs treated with H2O2. Genes with the most stable expression according to geNorm were U6, TFRC, RPLP0, GAPDH, and ACTB, and according to NormFinder were ALAS1, TFRC, U6, GAPDH, and ACTB. Conclusion Taken together, our study demonstrated that the expression stability of reference genes may differ according to the statistical program used. U6, TFRC, RPLP0, GAPDH, and ACTB was the optimal set of reference genes for studies on gene expression performed by qRT-PCR assays in HUVECs under oxidative stress study.
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Affiliation(s)
- Tianyi Li
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China
| | - Hongying Diao
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China
| | - Lei Zhao
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China
| | - Yue Xing
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China
| | - Jichang Zhang
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China
| | - Ning Liu
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China
| | - Youyou Yan
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China
| | - Xin Tian
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China
| | - Wei Sun
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China
| | - Bin Liu
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China.
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Characterizing biomarkers in osteosarcoma metastasis based on an ego-network. Biotechnol Lett 2017; 39:841-848. [PMID: 28229297 DOI: 10.1007/s10529-017-2305-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 02/08/2017] [Indexed: 02/02/2023]
Abstract
OBJECTIVES To characterize biomarkers that underlie osteosarcoma (OS) metastasis based on an ego-network. RESULTS From the microarray data, we obtained 13,326 genes. By combining PPI data and microarray data, 10,520 shared genes were found and constructed into ego-networks. 17 significant ego-networks were identified with p < 0.05. In the pathway enrichment analysis, seven ego-networks were identified with the most significant pathway. CONCLUSIONS These significant ego-modules were potential biomarkers that reveal the potential mechanisms in OS metastasis, which may contribute to understanding cancer prognoses and providing new perspectives in the treatment of cancer.
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Infante T, Forte E, Aiello M, Salvatore M, Cavaliere C. In Vivo and In Vitro Analysis in Coronary Artery Disease Related to Type 2 Diabetes. Front Endocrinol (Lausanne) 2017; 8:209. [PMID: 28871240 PMCID: PMC5566996 DOI: 10.3389/fendo.2017.00209] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 08/08/2017] [Indexed: 12/11/2022] Open
Abstract
AIM The leading cause of morbidity and mortality in patients with type 2 diabetes mellitus (DM) is coronary artery disease (CAD), a condition often asymptomatic but severe in these patients. Although glucose metabolism impairment and oxidative stress are known actors in the endothelial dysfunction/remodeling that occurs in diabetic patients, the relationship between cardiovascular disorders and DM is not fully understood. We have performed both an in vivo imaging and in vitro molecular analysis to investigate diabetic-specific CAD alterations. METHODS Computed tomography coronary angiography (CTCA) was performed in a group of 20 diabetic patients with CAD (DM+CAD+), 20 non-diabetic with CAD (DM-CAD+), 10 diabetic non-CAD patients (DM+CAD-), and 20 non-diabetic healthy subjects (HS). Imaging quantitative parameters such as calcium score (Cascore), calcified plaque volume (CPV), non-calcified plaque volume (NCPV), total plaque volume (TPV), remodeling index (RI), and plaque burden were extracted for each CAD subject. Moreover, the expression levels of superoxide dismutase 2 (SOD2) and liver X receptor alpha (LXRα) genes were analyzed in the peripheral blood mononuclear cells, whereas hyaluronan (HA) concentrations were evaluated in the plasma of each subject. RESULTS Imaging parameters, such as Cascore, CPV, RI, and plaque burden, were significantly higher in DM+CAD+ group, compared to DM-CAD+ (P = 0.019; P = 0.014; P < 0.001, P < 0.001, respectively). SOD2 mRNA was downregulated, while LXRα gene expression was upregulated in DM+CAD-, DM+CAD+, and DM-CAD+ groups compared to HS (P = 0.001, P = 0.03, and P = 0.001 for SOD2 and P = 0.006, P = 0.008, and P < 0.001 for LXRα, respectively). Plasmatic levels of HA were higher in DM-CAD+, DM+CAD-, and DM+CAD+ groups, compared to HS (P = 0.001 for the three groups). When compared to DM-CAD+, HA concentration was higher in DM+CAD- (P = 0.008) and DM+CAD+ (P < 0.001) with a significant difference between the two diabetic groups (P = 0.003). Moreover, HA showed a significant association with diabetes (P = 0.01) in the study population, and the correlation between HA levels and glycemia was statistically significant (ρ = 0.73, P < 0.001). CONCLUSION In our population, imaging parameters highlight a greater severity of CAD in diabetic patients. Among molecular parameters, HA is modulated by diabetic CAD-related alterations while SOD2 and LXRα are found to be more associated with CAD but do not discriminate between diabetic and non-diabetic subgroups.
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Affiliation(s)
| | - Ernesto Forte
- IRCCS SDN, Naples, Italy
- *Correspondence: Ernesto Forte,
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Fede C, Albertin G, Petrelli L, Sfriso MM, Biz C, De Caro R, Stecco C. Hormone receptor expression in human fascial tissue. Eur J Histochem 2016; 60:2710. [PMID: 28076930 PMCID: PMC5134680 DOI: 10.4081/ejh.2016.2710] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/18/2016] [Accepted: 10/21/2016] [Indexed: 01/06/2023] Open
Abstract
Many epidemiologic, clinical, and experimental findings point to sex differences in myofascial pain in view of the fact that adult women tend to have more myofascial problems with respect to men. It is possible that one of the stimuli to sensitization of fascial nociceptors could come from hormonal factors such as estrogen and relaxin, that are involved in extracellular matrix and collagen remodeling and thus contribute to functions of myofascial tissue. Immunohistochemical and molecular investigations (real-time PCR analysis) of relaxin receptor 1 (RXFP1) and estrogen receptor-alpha (ERα) localization were carried out on samples of human fascia collected from 8 volunteers patients during orthopedic surgery (all females, between 42 and 70 yrs, divided into pre- and post-menopausal groups), and in fibroblasts isolated from deep fascia, to examine both protein and RNA expression levels. We can assume that the two sex hormone receptors analyzed are expressed in all the human fascial districts examined and in fascial fibroblasts culture cells, to a lesser degree in the post-menopausal with respect to the pre-menopausal women. Hormone receptor expression was concentrated in the fibroblasts, and RXFP1 was also evident in blood vessels and nerves. Our results are the first demonstrating that the fibroblasts located within different districts of the muscular fasciae express sex hormone receptors and can help to explain the link between hormonal factors and myofascial pain. It is known, in fact, that estrogen and relaxin play a key role in extracellular matrix remodeling by inhibiting fibrosis and inflammatory activities, both important factors affecting fascial stiffness and sensitization of fascial nociceptors.
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Affiliation(s)
- C Fede
- University of Padua, Department of Neuroscience.
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Mining for genes related to choroidal neovascularization based on the shortest path algorithm and protein interaction information. Biochim Biophys Acta Gen Subj 2016; 1860:2740-9. [PMID: 26987808 DOI: 10.1016/j.bbagen.2016.03.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/05/2016] [Accepted: 03/10/2016] [Indexed: 12/24/2022]
Abstract
BACKGROUND Choroidal neovascularization (CNV) is a serious eye disease that may cause visual loss, especially for older people. Many factors have been proven to induce this disease including age, gender, obesity, and so on. However, until now, we have had limited knowledge on CNV's pathogenic mechanism. Discovering the genes that underlie this disease and performing extensive studies on them can help us to understand how CNV occurs and design effective treatments. METHODS In this study, we designed a computational method to identify novel CNV-related genes in a large protein network constructed using the protein-protein interaction information in STRING. The candidate genes were first extracted from the shortest paths connecting any two known CNV-related genes and then filtered by a permutation test and using knowledge of their linkages to known CNV-related genes. RESULTS A list of putative CNV-related candidate genes was accessed by our method. These genes are deemed to have strong relationships with CNV. CONCLUSIONS Extensive analyses of several of the putative genes such as ANK1, ITGA4, CD44 and others indicate that they are related to specific biological processes involved in CNV, implying they may be novel CNV-related genes. GENERAL SIGNIFICANCE The newfound putative CNV-related genes may provide new insights into CNV and help design more effective treatments. This article is part of a Special Issue entitled "System Genetics" Guest Editor: Dr. Yudong Cai and Dr. Tao Huang.
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Andrusiewicz M, Słowikowski B, Skibińska I, Wołuń-Cholewa M, Dera-Szymanowska A. Selection of reliable reference genes in eutopic and ectopic endometrium for quantitative expression studies. Biomed Pharmacother 2016; 78:66-73. [PMID: 26898426 DOI: 10.1016/j.biopha.2015.12.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/16/2015] [Accepted: 12/21/2015] [Indexed: 01/16/2023] Open
Abstract
PURPOSE Physiological changes during menstrual cycle cause the endometrium and endometriosis to develop specific kind of tissues, especially in regard to the gene expression profiles, which may include also housekeeping genes, commonly used as reference genes (RGs) in quantitative studies. Reverse transcription, followed by quantitative polymerase chain reaction (RT-qPCR) is the most precise and commonly used method in gene expression studies. In order to reduce effects of technical approaches and biological variability of gene's expression level, the studies often employ RGs in experimental data normalization. However, the expression of RGs is not always stable and depends on several variables. Thus, the selection of appropriate RG is one of the most significant steps to obtain reliable results in RT-qPCR-based methods. MATERIAL AND METHODS With the usage of RT-qPCR, we researched the expression of seven genes (ACTB, B2M, G6PD, GAPD, GUSB, HPRT and PPIA) as reliable reference genes in eutopic and ectopic endometrial tissue specimens obtained during standard surgery of women of reproductive age. Stability of expression level was analyzed by the most universal MS Excel plug-ins including: geNorm, NormFinder and BestKeeper. The descriptive statistics were evaluated using Statistica software. RESULTS The distribution of threshold (Ct) values was not equal. We identified genes with higher expression level (referring to Ct values) such as ACTB and B2M, medium e.g., GAPD and low expression level, e.g., G6PD and HPRT. We demonstrated that the stability of the analyzed reference genes was not homogenous, and different algorithms pointed to PPIA, GAPD and B2M as the most stable ones in eutopic and ectopic endometrium. On the contrary to these, GUSB and G6PD were the most unstable ones. CONCLUSIONS In RT-qPCR-based analyses of gene expression level in eutopic and ectopic endometrium, we strongly recommend that a minimum of two reference genes are to be used and we determined that the most suitable seem to be PPIA and GAPD.
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Affiliation(s)
- Mirosław Andrusiewicz
- Department of Cell Biology, Health Sciences Faculty, Poznan University of Medical Sciences, Rokietnicka str. 5D, 60-806 Poznan, Poland.
| | - Bartosz Słowikowski
- Department of Cell Biology, Health Sciences Faculty, Poznan University of Medical Sciences, Rokietnicka str. 5D, 60-806 Poznan, Poland; Department of Biochemistry and Molecular Biology, Faculty of Medicine I, Poznan University of Medical Sciences, Swiecickiego str. 6, 60-781 Poznan, Poland.
| | - Izabela Skibińska
- Department of Cell Biology, Health Sciences Faculty, Poznan University of Medical Sciences, Rokietnicka str. 5D, 60-806 Poznan, Poland.
| | - Maria Wołuń-Cholewa
- Department of Cell Biology, Health Sciences Faculty, Poznan University of Medical Sciences, Rokietnicka str. 5D, 60-806 Poznan, Poland.
| | - Anna Dera-Szymanowska
- Department of Perinatology and Gynecology, Faculty of Medicine II, Poznan University of Medical Sciences, Polna Street 33, 60-535 Poznan, Poland.
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Abstract
The invention of polymerase chain reaction (PCR) in 1983 revolutionized many areas of science, due to its ability to multiply a number of copies of DNA sequences (known as amplicons). Here we report on a method to double the throughput of quantitative PCR which could be especially useful for PCR-based mass screening. We concurrently amplified two target genes using only single fluorescent dye. A FAM probe labelled olionucleotide was attached to a quencher for one amplicon while the second one was without a probe. The PCR was performed in the presence of the intercalating dye SYBR Green I. We collected the fluorescence amplitude at two points per PCR cycle, at the denaturation and extension steps. The signal at denaturation is related only to the amplicon with the FAM probe while the amplitude at the extension contained information from both amplicons. We thus detected two genes within the same well using a single fluorescent channel. Any commercial real-time PCR systems can use this method doubling the number of detected genes. The method can be used for absolute quantification of DNA using a known concentration of housekeeping gene at one fluorescent channel.
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Affiliation(s)
| | - Pavel Neužil
- 1] Kist-Europe, Saarbrücken, Saarland, 66123, Germany [2] Central European Institute of Technology, Brno University of Technology, Technická 3058/10, CZ-616 00 Brno, Czech Republic [3] Northwestern Polytechnical University, School of Mechanical Engineering, 127 West Youyi Road, Xi'an, Shaanxi, 710072, P.R.China
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Liang J, Liu L, Cheung M, Lee MP, Wang H, Li CH, Chan CC, Nishiura K, Tang X, Tan Z, Peng J, Cheung KW, Yam WC, Chen Z. Community-Based HIV-1 Early Diagnosis and Risk Behavior Analysis of Men Having Sex with Men in Hong Kong. PLoS One 2015; 10:e0125715. [PMID: 25915755 PMCID: PMC4410921 DOI: 10.1371/journal.pone.0125715] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 03/17/2015] [Indexed: 11/19/2022] Open
Abstract
The increasing prevalence of HIV-1 among men having sex with men (MSM) calls for an investigation of HIV-1 prevalence and incidence in MSM by early diagnosis to assist with early preventive interventions in Hong Kong. The participants were recruited randomly from MSM communities within a one-year period. Rapid HIV Test (RHT) and real-time dried blood spot (DBS)-based quantitative polymerase chain reaction (DBS-qPCR) were used for the early diagnosis of 474 participants. Risk behavior analysis was performed by studying information obtained from the participants during the study period. The HIV-1 prevalence and incident rates in the studied MSM population were 4.01% (19/474) and 1.47% (7/474), respectively. Three infected participants were found at the acute phase of infection by DBS-qPCR. Only 46.4% (220/474) MSM were using condoms regularly for anal sex. HIV infection significantly correlated with unprotected receptive anal sex and syphilis infection. An increased number of infections was found among foreign MSM in Hong Kong. This study is the first to use DBS-qPCR to identify acutely infected individuals in a community setting and to provide both the prevalence and incident rates of HIV-1 infection among MSM in Hong Kong. The risk analysis provided evidence that behavior intervention strengthening is necessary to fight against the increasing HIV-1 epidemic among MSM in Hong Kong and surrounding regions in Asia.
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Affiliation(s)
- Jianguo Liang
- AIDS Institute and Department of Microbiology, Research Center for Infection and Immunity, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong Special Administrative Region, China
| | - Li Liu
- AIDS Institute and Department of Microbiology, Research Center for Infection and Immunity, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong Special Administrative Region, China
- * E-mail: (LL); (ZC)
| | - Mandy Cheung
- AIDS Concern, 17B, Block F, 3 Lok Man Road, Chai Wan, Hong Kong Special Administrative Region, China
| | - Man-Po Lee
- Department of Medicine, Queen Elizabeth Hospital Hong Kong, Hong Kong Special Administrative Region, China
| | - Haibo Wang
- AIDS Institute and Department of Microbiology, Research Center for Infection and Immunity, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong Special Administrative Region, China
| | - Chun-ho Li
- AIDS Concern, 17B, Block F, 3 Lok Man Road, Chai Wan, Hong Kong Special Administrative Region, China
| | - Chun-Chung Chan
- AIDS Concern, 17B, Block F, 3 Lok Man Road, Chai Wan, Hong Kong Special Administrative Region, China
| | - Kenji Nishiura
- AIDS Institute and Department of Microbiology, Research Center for Infection and Immunity, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong Special Administrative Region, China
| | - Xian Tang
- AIDS Institute and Department of Microbiology, Research Center for Infection and Immunity, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong Special Administrative Region, China
| | - Zhiwu Tan
- AIDS Institute and Department of Microbiology, Research Center for Infection and Immunity, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jie Peng
- AIDS Institute and Department of Microbiology, Research Center for Infection and Immunity, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong Special Administrative Region, China
| | - Ka-Wai Cheung
- AIDS Institute and Department of Microbiology, Research Center for Infection and Immunity, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong Special Administrative Region, China
| | - Wing-Cheong Yam
- Department of Microbiology, Queen Mary Hospital, the University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Zhiwei Chen
- AIDS Institute and Department of Microbiology, Research Center for Infection and Immunity, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong Special Administrative Region, China
- * E-mail: (LL); (ZC)
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Evaluation and application of the strand-specific protocol for next-generation sequencing. BIOMED RESEARCH INTERNATIONAL 2015; 2015:182389. [PMID: 25893191 PMCID: PMC4393923 DOI: 10.1155/2015/182389] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 02/03/2015] [Indexed: 12/02/2022]
Abstract
Next-generation sequencing (NGS) has become a powerful sequencing tool, applied in a wide range of biological studies. However, the traditional sample preparation protocol for NGS is non-strand-specific (NSS), leading to biased estimates of expression for transcripts overlapped at the antisense strand. Strand-specific (SS) protocols have recently been developed. In this study, we prepared the same RNA sample by using the SS and NSS protocols, followed by sequencing with Illumina HiSeq platform. Using real-time quantitative PCR as a standard, we first proved that the SS protocol more precisely estimates gene expressions compared with the NSS protocol, particularly for those overlapped at the antisense strand. In addition, we also showed that the sequence reads from the SS protocol are comparable with those from conventional NSS protocols in many aspects. Finally, we also mapped a fraction of sequence reads back to the antisense strand of the known genes, originally without annotated genes located. Using sequence assembly and PCR validation, we succeeded in identifying and characterizing the novel antisense genes. Our results show that the SS protocol performs more accurately than the traditional NSS protocol and can be applied in future studies.
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Mohapatra S, Chakraborty T, Miyagawa S, Zhou L, Ohta K, Iguchi T, Nagahama Y. Steroid responsive regulation of IFNγ2 alternative splicing and its possible role in germ cell proliferation in medaka. Mol Cell Endocrinol 2015; 400:61-70. [PMID: 25458697 DOI: 10.1016/j.mce.2014.10.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 10/13/2014] [Accepted: 10/14/2014] [Indexed: 11/23/2022]
Abstract
Interferon gamma (IFNγ) is an active player in estrogen dependent immuno-regulation of fish. The present work was aimed to characterize the alternatively spliced isoforms of IFNγ2 in the gonadal sex development in medaka. Phylogenetic analysis demonstrated that IFNγ2a and 2b were clustered with fish specific interferon gamma. Our in vitro promoter and mini-genome analysis data confirmed that alternative splicing of IFNγ2 is regulated by estrogens and androgens. Tissue distribution, quantitative PCR and ISH data demonstrated ubiquitous expression of IFNγ2a, while IFNγ2b was only expressed predominantly in female germ cells than males. This was further confirmed by germ cell specific GFP signals in the IFNγ2b-GFP over-expressed embryos and specific induction of IFNγ2b expression in the BrdU positive cells. All together our data suggest that steroid responsive alternatively spliced IFNγ2b isoforms might have some indirect roles in germ cell proliferation and thus can be an important candidate for immuno-reproductive interaction studies.
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Affiliation(s)
- Sipra Mohapatra
- South Ehime Fisheries Research Center, Ehime University, 798-4206, Matsuyama, Japan; Key Laboratory of Freshwater Fish Reproduction and Development, Southwest University, Chongqing, 400715, China; Division of Molecular Environmental Endocrinology, National Institute of Natural Sciences, Okazaki, 444-8585, Japan
| | - Tapas Chakraborty
- South Ehime Fisheries Research Center, Ehime University, 798-4206, Matsuyama, Japan; Division of Molecular Environmental Endocrinology, National Institute of Natural Sciences, Okazaki, 444-8585, Japan.
| | - Shinichi Miyagawa
- Division of Molecular Environmental Endocrinology, National Institute of Natural Sciences, Okazaki, 444-8585, Japan
| | - Linyan Zhou
- Key Laboratory of Freshwater Fish Reproduction and Development, Southwest University, Chongqing, 400715, China
| | - Kohei Ohta
- South Ehime Fisheries Research Center, Ehime University, 798-4206, Matsuyama, Japan
| | - Taisen Iguchi
- Division of Molecular Environmental Endocrinology, National Institute of Natural Sciences, Okazaki, 444-8585, Japan
| | - Yoshitaka Nagahama
- South Ehime Fisheries Research Center, Ehime University, 798-4206, Matsuyama, Japan.
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David KA, Unger FT, Uhlig P, Juhl H, Moore HM, Compton C, Nashan B, Dörner A, de Weerth A, Zornig C. Surgical procedures and postsurgical tissue processing significantly affect expression of genes and EGFR-pathway proteins in colorectal cancer tissue. Oncotarget 2014; 5:11017-28. [PMID: 25526028 PMCID: PMC4294341 DOI: 10.18632/oncotarget.2669] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 11/03/2014] [Indexed: 12/02/2022] Open
Abstract
An understanding of tissue data variability in relation to processing techniques during and postsurgery would be desirable when testing surgical specimens for clinical diagnostics, drug development, or identification of predictive biomarkers. Specimens of normal and colorectal cancer (CRC) tissues removed during colon and liver resection surgery were obtained at the beginning of surgery and postsurgically, tissue was fixed at 10, 20, and 45 minutes. Specimens were analyzed from 50 patients with primary CRC and 43 with intrahepatic metastasis of CRC using a whole genome gene expression array. Additionally, we focused on the epidermal growth factor receptor pathway and quantified proteins and their phosphorylation status in relation to tissue processing timepoints. Gene and protein expression data obtained from colorectal and liver specimens were influenced by tissue handling during surgery and by postsurgical processing time. To obtain reliable expression data, tissue processing for research and diagnostic purposes needs to be highly standardized.
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Affiliation(s)
| | | | | | | | - Helen M. Moore
- Biorepositories and Biospecimen Research Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | | | - Björn Nashan
- Clinic for Hepatobiliary Surgery and Transplantation Surgery, University Hospital Hamburg Eppendorf, Hamburg, Germany
| | - Arnulf Dörner
- Clinic for General and Visceral Surgery and Clinic for Gastroenterology, Agaplesion Diakonieklinikum Hamburg, Hamburg, Germany
| | - Andreas de Weerth
- Clinic for General and Visceral Surgery and Clinic for Gastroenterology, Agaplesion Diakonieklinikum Hamburg, Hamburg, Germany
| | - Carsten Zornig
- Surgical Clinic, Israelitisches Krankenhaus in Hamburg, Hamburg, Germany
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RNA-Seq for the identification of novel Mediator transcripts in endothelial progenitor cells. Gene 2014; 547:98-105. [PMID: 24952135 DOI: 10.1016/j.gene.2014.06.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Revised: 05/30/2014] [Accepted: 06/17/2014] [Indexed: 11/22/2022]
Abstract
Mediator (MED) complex is a multiprotein playing a key role in the eukaryotic transcription. Alteration of MED function may have enormous pathophysiological consequences and several MED genes have been implicated in human diseases. Here, we have combined computational and experimental approaches to identify and characterize, new transcripts generated by alternative splicing (AS) for all MED genes, through the analysis of our recently published RNA-Sequencing datasets of endothelial progenitor cells (EPCs). This combined strategy allowed us to identify novel transcripts for MED4, MED9, MED11, MED14, MED27 and CDK8 most of them generated by AS. All the newly identified transcripts, except MED11, are predicted to encode novel protein isoforms. The identification of novel MED variants could lead to the finding of other MED complexes with different functions depending on their subunit composition. Finally, the expression profile of all MED genes, together with an extensive gene expression analysis, may be useful to better classify the diverse subsets of cell populations that contribute to neovascularization.
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Rauh J, Jacobi A, Stiehler M. Identification of stable reference genes for gene expression analysis of three-dimensional cultivated human bone marrow-derived mesenchymal stromal cells for bone tissue engineering. Tissue Eng Part C Methods 2014; 21:192-206. [PMID: 25000821 DOI: 10.1089/ten.tec.2014.0230] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The principles of tissue engineering (TE) are widely used for bone regeneration concepts. Three-dimensional (3D) cultivation of autologous human mesenchymal stromal cells (MSCs) on porous scaffolds is the basic prerequisite to generate newly formed bone tissue. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is a specific and sensitive analytical tool for the measurement of mRNA-levels in cells or tissues. For an accurate quantification of gene expression levels, stably expressed reference genes (RGs) are essential to obtain reliable results. Since the 3D environment can affect a cell's morphology, proliferation, and gene expression profile compared with two-dimensional (2D) cultivation, there is a need to identify robust RGs for the quantification of gene expression. So far, this issue has not been adequately investigated. The aim of this study was to identify the most stably expressed RGs for gene expression analysis of 3D-cultivated human bone marrow-derived MSCs (BM-MSCs). For this, we analyzed the gene expression levels of n=31 RGs in 3D-cultivated human BM-MSCs from six different donors compared with conventional 2D cultivation using qRT-PCR. MSCs isolated from bone marrow aspirates were cultivated on human cancellous bone cube scaffolds for 14 days. Osteogenic differentiation was assessed by cell-specific alkaline phosphatase (ALP) activity and expression of osteogenic marker genes. Expression levels of potential reference and target genes were quantified using commercially available TaqMan(®) assays. mRNA expression stability of RGs was determined by calculating the coefficient of variation (CV) and using the algorithms of geNorm and NormFinder. Using both algorithms, we identified TATA box binding protein (TBP), transferrin receptor (p90, CD71) (TFRC), and hypoxanthine phosphoribosyltransferase 1 (HPRT1) as the most stably expressed RGs in 3D-cultivated BM-MSCs. Notably, genes that are routinely used as RGs, for example, beta actin (ACTB) and ribosomal protein L37a (RPL37A), were among the least stable genes. We recommend the combined use of TBP, TFRC, and HPRT1 for the accurate and robust normalization of qRT-PCR data of 3D-cultivated human BM-MSCs.
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Affiliation(s)
- Juliane Rauh
- University Center for Orthopedics and Trauma Surgery, Centre for Translational Bone, Joint and Soft Tissue Research, University Hospital Carl Gustav Carus at Technische Universität Dresden , Dresden, Germany
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Zhan C, Zhang Y, Ma J, Wang L, Jiang W, Shi Y, Wang Q. Identification of reference genes for qRT-PCR in human lung squamous-cell carcinoma by RNA-Seq. Acta Biochim Biophys Sin (Shanghai) 2014; 46:330-7. [PMID: 24457517 DOI: 10.1093/abbs/gmt153] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Although the accuracy of quantitative real-time polymerase chain reaction (qRT-PCR) is highly dependent on the reliable reference genes, many commonly used reference genes are not stably expressed and as such are not suitable for quantification and normalization of qRT-PCR data. The aim of this study was to identify novel reliable reference genes in lung squamous-cell carcinoma. We used RNA sequencing (RNA-Seq) to survey the whole genome expression in 5 lung normal samples and 44 lung squamous-cell carcinoma samples. We evaluated the expression profiles of 15 commonly used reference genes and identified five additional candidate reference genes. To validate the RNA-Seq dataset, we used qRT-PCR to verify the expression levels of these 20 genes in a separate set of 100 pairs of normal lung tissue and lung squamous-cell carcinoma samples, and then analyzed these results using geNorm and NormFinder. With respect to 14 of the 15 common reference genes (B2M, GAPDH, GUSB, HMBS, HPRT1, IPO8, PGK1, POLR2A, PPIA, RPLP0, TBP, TFRC, UBC, and YWHAZ), the expression levels were either too low to be easily detected, or exhibited a high degree of variability either between lung normal and squamous-cell carcinoma samples, or even among samples of the same tissue type. In contrast, 1 of the 15 common reference genes (ACTB) and the 5 additional candidate reference genes (EEF1A1, FAU, RPS9, RPS11, and RPS14) were stably and constitutively expressed at high levels in all the samples tested. ACTB, EEF1A1, FAU, RPS9, RPS11, and RPS14 are ideal reference genes for qRT-PCR analysis of lung squamous-cell carcinoma, while 14 commonly used qRT-PCR reference genes are less appropriate in this context.
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Affiliation(s)
- Cheng Zhan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200031, China
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Gene expression profile of the whole Mediator complex in human osteosarcoma and normal osteoblasts. Med Oncol 2013; 30:739. [PMID: 24101134 DOI: 10.1007/s12032-013-0739-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 09/24/2013] [Indexed: 10/26/2022]
Abstract
Mediator complex (MED) is an essential multi-subunit component of the transcription apparatus and plays a key role in the transcription regulation of many genes involved in several diseases, including cancer. Recently, numerous MED subunits have been implicated in cancer development and metastasis, and specific alterations in their coding genes have been found to correlate with some malignancies. It is conceivable that a specific MED alteration pattern can characterize each cancer type. However, to date, no study has reported the complete picture of MED subunits in a specific tumor. Thus, the aim of this study was to investigate for the first time the gene expression profile of the whole MED complex in human osteosarcoma (OS). To this purpose, we have examined all the MED subunit genes in three OS cell lines compared to normal osteoblasts by real-time RT-PCR. Interestingly, our findings indicate that the expression of most of the MED genes is altered in OS. Moreover, a very high overexpression of MED20 and MED31 can be observed in all the analyzed OS cells, thus suggesting for the first time a potential role of these subunits in human malignancies. Overall, this study may open the way to other functional studies exploring the role of the whole complex in cancer development and progression. These findings may lead to the identification of novel biomarkers, which can be used also in combination with imaging techniques for early detection, and/or to develop novel targets for innovative therapeutic approaches.
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Kılıç Y, Çelebiler AÇ, Sakızlı M. Selecting housekeeping genes as references for the normalization of quantitative PCR data in breast cancer. Clin Transl Oncol 2013; 16:184-90. [PMID: 23720140 DOI: 10.1007/s12094-013-1058-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 05/21/2013] [Indexed: 02/02/2023]
Abstract
OBJECTIVE The common reference genes of choice in relative gene expression studies based on quantitative real time polymerase chain reaction, ACTB and B2M, were shown to be regulated differently in respect to tissue type. In this study, the stability of the selected housekeeping genes for normalizing the qPCR data were identified in the tumor and its adjacent tissues in invasive breast cancer, and the variability of their levels according to the stages and the histopathologic subtypes was analyzed. METHODS Four housekeeping genes: PUM1, RPL13A, B2M, and ACTB were analyzed in 99 surgically excised tissue specimens (50 tumor, 45 tumor adjacent and 4 normal breast tissues). Three of the most common softwares (GeNorm, NormFinder, and BestKeeper) were used for calculation purposes. RESULTS When all of the tissue samples were included in analyses, PUM1 was the most stable gene according to calculations made with both NormFinder and BestKeeper; while PUM1/RPL13A combination was the most stable by GeNorm software. The PUM1 gene was also identified as the most stable gene among the four in all sample groups (in both Estrogen Receptor positive and Estrogen Receptor negative subgroups of invasive breast carcinoma and in normal breast tissue) according to calculations made using the NormFinder software. CONCLUSION While suggesting PUM1 is one of the most stable single gene and the PUM1/RPL13A pair as one of the best housekeeping genes for the normalization of expression studies in invasive breast tumor studies, it will be more practical to evaluate stability once more and decide upon the reference gene accordingly within the sample group itself.
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Affiliation(s)
- Y Kılıç
- Department of Medical Biology and Genetics, Faculty of Medicine, Dokuz Eylül University, Konak, İzmir, Turkey,
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Li B, Matter EK, Hoppert HT, Grayson BE, Seeley RJ, Sandoval DA. Identification of optimal reference genes for RT-qPCR in the rat hypothalamus and intestine for the study of obesity. Int J Obes (Lond) 2013; 38:192-7. [PMID: 23736358 DOI: 10.1038/ijo.2013.86] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Revised: 03/28/2013] [Accepted: 04/28/2013] [Indexed: 02/02/2023]
Abstract
BACKGROUND Obesity has a complicated metabolic pathology, and defining the underlying mechanisms of obesity requires integrative studies with molecular end points. Real-time quantitative PCR (RT-qPCR) is a powerful tool that has been widely utilized. However, the importance of using carefully validated reference genes in RT-qPCR seems to have been overlooked in obesity-related research. The objective of this study was to select a set of reference genes with stable expressions to be used for RT-qPCR normalization in rats under fasted vs re-fed and chow vs high-fat diet (HFD) conditions. DESIGN Male long-Evans rats were treated under four conditions: chow/fasted, chow/re-fed, HFD/fasted and HFD/re-fed. Expression stabilities of 13 candidate reference genes were evaluated in the rat hypothalamus, duodenum, jejunum and ileum using the ReFinder software program. The optimal number of reference genes needed for RT-qPCR analyses was determined using geNorm. RESULTS Using geNorm analysis, we found that it was sufficient to use the two most stably expressed genes as references in RT-qPCR analyses for each tissue under specific experimental conditions. B2M and RPLP0 in the hypothalamus, RPS18 and HMBS in the duodenum, RPLP2 and RPLP0 in the jejunum and RPS18 and YWHAZ in the ileum were the most suitable pairs for a normalization study when the four aforementioned experimental conditions were considered. CONCLUSIONS Our study demonstrates that gene expression levels of reference genes commonly used in obesity-related studies, such as ACTB or RPS18, are altered by changes in acute or chronic energy status. These findings underline the importance of using reference genes that are stable in expression across experimental conditions when studying the rat hypothalamus and intestine, because these tissues have an integral role in the regulation of energy homeostasis. It is our hope that this study will raise awareness among obesity researchers on the essential need for reference gene validation in gene expression studies.
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Affiliation(s)
- B Li
- Department of Internal Medicine, Division of Endocrinology University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - E K Matter
- Department of Internal Medicine, Division of Endocrinology University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - H T Hoppert
- Department of Internal Medicine, Division of Endocrinology University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - B E Grayson
- Department of Internal Medicine, Division of Endocrinology University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - R J Seeley
- Department of Internal Medicine, Division of Endocrinology University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - D A Sandoval
- Department of Internal Medicine, Division of Endocrinology University of Cincinnati College of Medicine, Cincinnati, OH, USA
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