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Al-Ghazzawi K, Baum SH, Pförtner R, Philipp S, Bechrakis N, Görtz G, Eckstein A, Mairinger FD, Oeverhaus M. Evaluation of Orbital Lymphoproliferative and Inflammatory Disorders by Gene Expression Analysis. Int J Mol Sci 2022; 23:ijms23158609. [PMID: 35955742 PMCID: PMC9369106 DOI: 10.3390/ijms23158609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/28/2022] [Accepted: 07/28/2022] [Indexed: 11/21/2022] Open
Abstract
Non-specific orbital inflammation (NSOI) and IgG4-related orbital disease (IgG4-ROD) are often challenging to differentiate. Furthermore, it is still uncertain how chronic inflammation, such as IgG4-ROD, can lead to mucosa-associated lymphoid tissue (MALT) lymphoma. Therefore, we aimed to evaluate the diagnostic value of gene expression analysis to differentiate orbital autoimmune diseases and elucidate genetic overlaps. First, we established a database of NSOI, relapsing NSOI, IgG4-ROD and MALT lymphoma patients of our orbital center (2000−2019). In a consensus process, three typical patients of the above mentioned three groups (mean age 56.4 ± 17 years) at similar locations were selected. Afterwards, RNA was isolated using the RNeasy FFPE kit (Qiagen) from archived paraffin-embedded tissues. The RNA of these 12 patients were then subjected to gene expression analysis (NanoString nCounter®), including a total of 1364 target genes. The most significantly upregulated and downregulated genes were used for a machine learning algorithm to distinguish entities. This was possible with a high probability (p < 0.0001). Interestingly, gene expression patterns showed a characteristic overlap of lymphoma with IgG4-ROD and NSOI. In contrast, IgG4-ROD shared only altered expression of one gene regarding NSOI. To validate our potential biomarker genes, we isolated the RNA of a further 48 patients (24 NSOI, 11 IgG4-ROD, 13 lymphoma patients). Then, gene expression pattern analysis of the 35 identified target genes was performed using a custom-designed CodeSet to assess the prediction accuracy of the multi-parameter scoring algorithms. They showed high accuracy and good performance (AUC ROC: IgG4-ROD 0.81, MALT 0.82, NSOI 0.67). To conclude, genetic expression analysis has the potential for faster and more secure differentiation between NSOI and IgG4-ROD. MALT-lymphoma and IgG4-ROD showed more genetic similarities, which points towards progression to lymphoma.
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Affiliation(s)
- Karim Al-Ghazzawi
- Department of Ophthalmology, University Hospital Essen, 45147 Essen, Germany; (K.A.-G.); (S.P.); (N.B.); (G.G.); (A.E.)
| | - Sven Holger Baum
- Department of Oral and Maxillofacial Surgery, University of Duisburg-Essen, Kliniken-Essen-Mitte, 45136 Essen, Germany; (S.H.B.); (R.P.)
| | - Roman Pförtner
- Department of Oral and Maxillofacial Surgery, University of Duisburg-Essen, Kliniken-Essen-Mitte, 45136 Essen, Germany; (S.H.B.); (R.P.)
| | - Svenja Philipp
- Department of Ophthalmology, University Hospital Essen, 45147 Essen, Germany; (K.A.-G.); (S.P.); (N.B.); (G.G.); (A.E.)
| | - Nikolaos Bechrakis
- Department of Ophthalmology, University Hospital Essen, 45147 Essen, Germany; (K.A.-G.); (S.P.); (N.B.); (G.G.); (A.E.)
| | - Gina Görtz
- Department of Ophthalmology, University Hospital Essen, 45147 Essen, Germany; (K.A.-G.); (S.P.); (N.B.); (G.G.); (A.E.)
| | - Anja Eckstein
- Department of Ophthalmology, University Hospital Essen, 45147 Essen, Germany; (K.A.-G.); (S.P.); (N.B.); (G.G.); (A.E.)
| | - Fabian D. Mairinger
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
- Correspondence: (F.D.M.); (M.O.)
| | - Michael Oeverhaus
- Department of Ophthalmology, University Hospital Essen, 45147 Essen, Germany; (K.A.-G.); (S.P.); (N.B.); (G.G.); (A.E.)
- Correspondence: (F.D.M.); (M.O.)
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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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Development of Methods to Extract RNA From Archived Pediatric Needle Liver Biopsies to Produce Sequencing Data. J Pediatr Gastroenterol Nutr 2021; 72:436-441. [PMID: 33560759 DOI: 10.1097/mpg.0000000000003012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
ABSTRACT Genetic susceptibility has been proposed as etiopathogenic in several pediatric liver diseases including autoimmune hepatitis (AIH). High throughput sequencing (HTPS) has been applied to archived needle liver biopsies obtained from adults but rarely to pediatric biopsies. For conclusive diagnosis of AIH, most subjects have an initial formalin-fixed paraffin embedded (FFPE) needle liver biopsy that is eventually archived and may be stored for decades. OBJECTIVE Our goal was to develop methods to utilize tissue from archived needle liver biopsies for extraction of RNA sufficient to produce HTPS data. METHODS We extracted total RNA from 45 FFPE needle liver biopsy samples (24 AIH type 1 patients and 21 controls [ages 15_11 and 19_10]; biopsy storage time 0.5-20 years) and constructed cDNA libraries that were then sequenced on an Illumina HiSeq2000 platform. RESULTS Forty (89%) of the libraries produced high-quality sequences for further analyses. The average number of sequences obtained per library from HTPS was 55,136,519 (range 14,914,291-184,027,499). There was a significant inverse relationship between the number of human reads obtained and the age of the specimen (P < 2_10_7). It was possible to classify more than 90% of the reads as known genes in samples that had been stored for less than 10 years. CONCLUSIONS Archived needle liver biopsies can be used for sequence based interrogation of the etiologic origins of complex liver diseases of young subjects, such as AIH.
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Lopes C, Pereira C, Farinha M, Medeiros R, Dinis-Ribeiro M. Genetic Variations in Prostaglandin E 2 Pathway Identified as Susceptibility Biomarkers for Gastric Cancer in an Intermediate Risk European Country. Int J Mol Sci 2021; 22:ijms22020648. [PMID: 33440718 PMCID: PMC7827533 DOI: 10.3390/ijms22020648] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 02/06/2023] Open
Abstract
The cyclooxygenase-2 (COX-2)/prostaglandin E2 (PGE2) pathway exerts deleterious pleiotropic effects in inflammation-induced gastric carcinogenesis. We aimed to assess the association of genetic variants in prostaglandin-endoperoxide synthase 2 (PTGS2), ATP binding cassette subfamily C member 4 (ABCC4), hydroxyprostaglandin dehydrogenase 15-(NAD) (HPGD), and solute carrier organic anion transporter family member 2A1 (SLCO2A1) PGE2 pathway-related genes with gastric cancer (GC) risk in a European Caucasian population. A hospital-based case-control study gathering 260 GC cases and 476 cancer-free controls was implemented. Using a tagSNP approach, 51 single nucleotide polymorphisms (SNPs) were genotyped through MassARRAY® iPLEX Gold Technology or allelic discrimination by real-time polymerase chain reaction (PCR). Homozygous carriers of the minor allele for both rs689466 and rs10935090 SNPs were associated with a 2.98 and 4.30-fold increased risk for GC, respectively (95% confidence interval (CI): 1.14–7.74, p = 0.027; 95% CI: 1.22–15.16, p = 0.026), with the latter also being associated with an anticipated diagnosis age. A multifactor dimensionality reduction analysis identified an overall three-factor best interactive model composed of age, rs689466, and rs1678374 that was associated with a 17.6-fold GC increased risk (95% CI: 11.67–26.48, p < 0.0001, (cross-validation) CV consistency of 8/10 and accuracy of 0.807). In this preliminary study, several tagSNPs in PGE2 pathway-related genes were identified as risk biomarkers for GC development. This approach may help to identify higher-risk individuals and may contribute to the tailoring screening of GC in intermediate-risk European countries.
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Affiliation(s)
- Catarina Lopes
- Molecular Oncology and Viral Pathology Group, IPO Porto Research (CI-IPOP), Portuguese Institute of Oncology, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (C.L.); (R.M.)
| | - Carina Pereira
- Molecular Oncology and Viral Pathology Group, IPO Porto Research (CI-IPOP), Portuguese Institute of Oncology, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (C.L.); (R.M.)
- CINTESIS—Center for Health Technology and Services Research, University of Porto, Rua Dr. Plácido da Costa, 4200-450 Porto, Portugal;
- Correspondence: ; Tel.: +351-225-084-000; Fax: +351-225-084-001
| | - Mónica Farinha
- Pathology Department, Portuguese Institute of Oncology, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal;
| | - Rui Medeiros
- Molecular Oncology and Viral Pathology Group, IPO Porto Research (CI-IPOP), Portuguese Institute of Oncology, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (C.L.); (R.M.)
- Portuguese League Against Cancer, Estrada Interior da Circunvalação, 4200-172 Porto, Portugal
| | - Mário Dinis-Ribeiro
- CINTESIS—Center for Health Technology and Services Research, University of Porto, Rua Dr. Plácido da Costa, 4200-450 Porto, Portugal;
- Gastroenterology Department, Portuguese Institute of Oncology, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
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Walter RFH, Sydow SR, Berg E, Kollmeier J, Christoph DC, Christoph S, Eberhardt WEE, Mairinger T, Wohlschlaeger J, Schmid KW, Mairinger FD. Bortezomib sensitivity is tissue dependent and high expression of the 20S proteasome precludes good response in malignant pleural mesothelioma. Cancer Manag Res 2019; 11:8711-8720. [PMID: 31576173 PMCID: PMC6765394 DOI: 10.2147/cmar.s194337] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 07/22/2019] [Indexed: 01/13/2023] Open
Abstract
Background Bortezomib is an approved proteasome inhibitor for the treatment of certain lymphoma subtypes. Two clinical trials investigated bortezomib in patients with malignant pleural mesothelioma (MPM) and failed to improve outcome. We present a potential explanation for this event. Methods 171 patients with MPM were analyzed for their mRNA expression of proteasomal subunits PSMA1, PSMA5, PSMB1, PSMB2, PSMB4 and PSMB5 via qPCR (n=84) or sequencing (n=87 TCGA/cBioPortal data set “Mesothelioma”). Outcome and subunit expression were correlated. Four mesothelial and one fibroblast cell line were treated with bortezomib and cisplatin. Cellular response was measured after 0, 6, 12, 24, 48 and 72 hrs. Enzyme activity of proteasomal subunits was assessed via functional enzyme activity assays. Results Patients with MPM presented with elevated expression of proteasomal subunits compared to benign controls (p<0.001). PSMB4 correlated with outcome (Cox propotiortional-hazards model (COXPH): p<0.0175, TCGA/cBioPortal data). In cell lines, apoptosis was the main event with a peak after 48 hr incubation for bortezomib or cisplatin. Only two cell lines with comparably low proteasome activity (PSMB2 and PSMB5) responded to 50 nM and 100 nM bortezomib better than to cisplatin (MRC-5, NCI-H2052). MSTO-211H responded to cisplatin only, whereas the other two cell lines were considered therapy resistant (Met-5A, NCI-H2452). Interpretation Two clinical trials testing bortezomib in MPM failed, although MPM presents with high proteasome expression, which predicts bortezomib sensitivity in several tumors. Bortezomib induced apoptosis in MPM cell lines with low proteasome activity only. Bortezomib is not suitable for the treatment of MPM, and biomarker-based stratification could have improved both clinical trials. Trial registration NCT00513877 and NCT00458913
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Affiliation(s)
- Robert Fred Henry Walter
- Ruhrlandklinik, West German Lung Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | | | - Erika Berg
- Institute of Pathology, Charité Universitaetsmedizin, Berlin, Germany
| | - Jens Kollmeier
- Institute of Pathology, Helios Klinikum Emil Von Behring, Berlin, Germany
| | - Daniel Christian Christoph
- Department of Oncology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Department of Internistic Oncology, Kliniken Essen Mitte, Essen, Germany
| | - Sandra Christoph
- Department of Bone Marrow Transplantation, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | | | - Thomas Mairinger
- Institute of Pathology, Helios Klinikum Emil Von Behring, Berlin, Germany
| | - Jeremias Wohlschlaeger
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Kurt Werner Schmid
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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Schmeller J, Wessolly M, Mairinger E, Borchert S, Hager T, Mairinger T, Schmid KW, Wohlschlaeger J, Walter RFH, Mairinger FD. Setting out the frame conditions for feasible use of FFPE derived RNA. Pathol Res Pract 2018; 215:381-386. [PMID: 30606660 DOI: 10.1016/j.prp.2018.12.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 12/01/2018] [Accepted: 12/24/2018] [Indexed: 12/31/2022]
Abstract
INTRODUCTION The usage of formalin-fixed paraffin embedded (FFPE) tissue is characterized by its long shelf-life and simple handling. Therefore it is the most commonly available tissue specimen in routine diagnostics and histological studies. Formaldehyde fixation may result in RNA degradation and cross linking with proteins, while storage conditions also affect RNA integrity. The present study was designed to investigate the influence of these factors on RNA analysis. DESIGN FFPE-derived RNA from sections of 23 patients with spontaneous pneumothoraxes was used. Unstained sections of FFPE tissue were stored at various temperatures (-80 °C, -20 °C, 4 °C, 24 °C) prior to RNA extraction. The potential impact on RNA quality of semi-automatic and manual RNA isolation and three different deparaffinization agents (mineral oil, xylene and d-limonene) were compared. RESULTS The storage temperature of FFPE sections affects RNA concentration and fragmentation, with the optimal storage temperature below -20 °C. The RNA extracted with d-limonene shows equivalent quality to the RNA extracted using more toxic standard agents. The manual isolation provides a higher RNA yield compared to the semi-automatic isolation. However, no differences in the amount of longer RNA fragments were observed. Furthermore, the semi-automatic isolation showed an enhanced RNA quality. CONCLUSION FFPE sections not directly used for RNA extraction should be stored below -20 °C to increase quality and yield of the RNA. Usage of semi-automatic isolation produces superior results and simplifies routine processes by having less hands-on-time. Replacement of toxic xylene by d-limonene may contribute to improved occupational safety while not influencing analytical results.
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Affiliation(s)
- Jan Schmeller
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
| | - Michael Wessolly
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Elena Mairinger
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Sabrina Borchert
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Thomas Hager
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Thomas Mairinger
- Department of Pathology, Helios Klinikum Emil von Behring, Berlin, Germany
| | - Kurt Werner Schmid
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Jeremias Wohlschlaeger
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Robert F H Walter
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany; Ruhrlandklinik, West German Lung Centre, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Fabian D Mairinger
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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Gyvyte U, Kupcinskas J, Juzenas S, Inciuraite R, Poskiene L, Salteniene V, Link A, Fassan M, Franke A, Kupcinskas L, Skieceviciene J. Identification of long intergenic non-coding RNAs (lincRNAs) deregulated in gastrointestinal stromal tumors (GISTs). PLoS One 2018; 13:e0209342. [PMID: 30557328 PMCID: PMC6296525 DOI: 10.1371/journal.pone.0209342] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/04/2018] [Indexed: 12/12/2022] Open
Abstract
Long intergenic non-coding RNAs (lincRNAs) are >200 nucleotides long non-coding RNAs, which have been shown to be implicated in carcinogenic processes by interacting with cancer associated genes or other non-coding RNAs. However, their role in development of rare gastrointestinal stromal tumors (GISTs) is barely investigated. Therefore, the aim of this study was to define lincRNAs deregulated in GIST and find new GIST-lincRNA associations. Next-generation sequencing data of paired GIST and adjacent tissue samples from 15 patients were subjected to a web-based lincRNA analysis. Three deregulated lincRNAs (MALAT1, H19 and FENDRR; adjusted p-value < 0.05) were selected for expression validation in a larger group of patients (n = 22) by RT-qPCR method. However, only H19 and FENDRR showed significant upregulation in the validation cohort (adjusted p < 0.05). Further, we performed correlation analyses between expression levels of deregulated lincRNAs and GIST-associated oncogenes or GIST deregulated microRNAs. We found high positive correlations between expression of H19 and known GIST related oncogene ETV1, and between H19 and miR-455-3p. These findings expand the knowledge on lincRNAs deregulated in GIST and may be an important resource for the future studies investigating lincRNAs functionally relevant to GIST carcinogenesis.
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Affiliation(s)
- Ugne Gyvyte
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Juozas Kupcinskas
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Simonas Juzenas
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
- Institute of Clinical Molecular Biology, Christian-Albrechts University, Kiel, Germany
| | - Ruta Inciuraite
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Lina Poskiene
- Department of Pathological Anatomy, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Violeta Salteniene
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Alexander Link
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University, Magdeburg, Germany
| | - Matteo Fassan
- Department of Medicine (DMID), Surgical Pathology & Cytopathology Unit, University of Padua, Padua, Italy
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts University, Kiel, Germany
| | - Limas Kupcinskas
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Jurgita Skieceviciene
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
- * E-mail:
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Boldrini L, Giordano M, Lucchi M, Melfi F, Fontanini G. Expression profiling and microRNA regulation of the LKB1 pathway in young and aged lung adenocarcinoma patients. Biomed Rep 2018; 9:198-205. [PMID: 30271594 PMCID: PMC6158392 DOI: 10.3892/br.2018.1122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/11/2018] [Indexed: 12/14/2022] Open
Abstract
Lung cancer in young patients appears to have distinct clinicopathological features. The present study focused on the role of the serine/threonine kinase liver kinase B1 (LKB1), a known tumor suppressor gene, and its miRNA regulation in lung adenocarcinoma, particularly in young versus elderly patients. A total of 88 patients with lung adenocarcinoma were retrospectively analysed. A simultaneous quantification was performed of the expression of LKB1 mRNA and 15 microRNAs (miRNA/miRs; miRs −93, −96, −34a, −34c, −214, −33a, −30b, −145, −182, −30c, −183, −29b, −29c, −153 and −138) involved in the LKB1 pathway, as well as of 5 identified target mRNAs [cyclin D1 (CCND1), catenin β-1 (CTNNB1), lysyl oxidase (LOX), yes-associated protein 1 (YAP1) and survivin], using NanoString technology. KRAS mutations were investigated by pyrosequencing analysis. Patients ≤50 years were defined as a younger group, while patients >50 years old as an older group (n=44/group). No difference between the two groups was identified in terms of survival times analysed using the Kaplan-Meier method or KRAS mutations. Subsequently, the LKB1 signalling pathway was focused on, as a target for therapy in lung adenocarcinoma, and assessed with regards to clinicopathological features; we found that LOX levels in adenocarcinoma patients were significantly associated with histological subtype (P=0.03), stage (P<0.0001) and prognosis (P=0.02 for disease-free interval and P=0.005 for overall survival), but not with age. Furthermore, the miRNA target prediction model indicated that miR-93 and miR-30b appeared to have functional binding sites and downregulate the gene expression of LKB1 and LOX, respectively. In conclusion, young patients appeared have similar survival rates to elderly patients. The assessment of LKB1, its downstream genes and its regulation by miRNAs may have an impact on future research on lung adenocarcinoma in young and elderly patients. Further investigations will be necessary to elucidate the potential of this pathway as a novel target for therapy.
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Affiliation(s)
- Laura Boldrini
- Department of Surgical, Medical, Molecular Pathology and Critical Care Medicine, University of Pisa, I-56126 Pisa, Italy
| | - Mirella Giordano
- Department of Surgical, Medical, Molecular Pathology and Critical Care Medicine, University of Pisa, I-56126 Pisa, Italy
| | - Marco Lucchi
- Department of Surgical, Medical, Molecular Pathology and Critical Care Medicine, University of Pisa, I-56126 Pisa, Italy
| | - Franca Melfi
- Department of Surgical, Medical, Molecular Pathology and Critical Care Medicine, University of Pisa, I-56126 Pisa, Italy
| | - Gabriella Fontanini
- Department of Surgical, Medical, Molecular Pathology and Critical Care Medicine, University of Pisa, I-56126 Pisa, Italy
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Folic acid phenotype (FAP) is a superior biomarker predicting response to pemetrexed-based chemotherapy in malignant pleural mesothelioma. Oncotarget 2018; 8:37502-37510. [PMID: 28415584 PMCID: PMC5514925 DOI: 10.18632/oncotarget.16398] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 03/01/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Malignant pleural mesothelioma (MPM) is a rare tumor linked to a dismal prognosis. Even the most effective chemotherapeutical regime of pemetrexed combined with cisplatin leads to a remission-rate of only about 40%. The reasons for the rather poor efficacy remain largely unknown. RESULTS Phenotypes were significantly associated with progression (p=0.0279) and remission (p=0.0262). Cox-regression revealed significant associations between SLC19A1/TYMS-ratio (p=0.0076) as well as FPGS/TYMS-ratio (p=0.0026) and OS. For differentiation by risk-groups, COXPH identified a strong correlation (p=0.0008). METHODS 56 MPM specimens from patients treated with pemetrexed were used for qPCR analysis. Phenotypes and risk groups were defined by their expression levels of members of the folic acid metabolism and correlated to survival and objective response. CONCLUSION Our results indicate that the balance between folic acid uptake, activation and metabolism plays a crucial role in response to pemetrexed-based chemotherapy and the prognosis of MPM patients. Implementing this marker profile in MPM stratification may help to individualize MPM-therapy more efficiently.
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Haynes HR, Killick-Cole CL, Hares KM, Redondo J, Kemp KC, Moutasim KA, Faulkner C, Wilkins A, Kurian KM. Evaluation of the quality of RNA extracted from archival FFPE glioblastoma and epilepsy surgical samples for gene expression assays. J Clin Pathol 2018; 71:695-701. [DOI: 10.1136/jclinpath-2017-204969] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 01/29/2018] [Accepted: 01/30/2018] [Indexed: 01/05/2023]
Abstract
AimsHistopathological tissue samples are being increasingly used as sources of nucleic acids in molecular pathology translational research. This study investigated the suitability of glioblastoma and control central nervous system (CNS) formalin-fixed paraffin embedded (FFPE) tissue-derived RNA for gene expression analyses.MethodsTotal RNA was extracted from control (temporal lobe resection tissue) and glioblastoma FFPE tissue samples. RNA purity (260/280 ratios) was determined and RNA integrity number (RIN) analysis was performed. RNA was subsequently used for RT-qPCR for two reference genes,18SandGAPDH.ResultsReference gene expression was equivalent between control and glioblastoma tissue when using RNA extracted from FFPE tissue, which has key implications for biological normalisation for CNS gene expression studies. There was a significant difference between the mean RIN values of control and glioblastoma FFPE tissue. There was no significant correlation between 260/280 or RIN values versus total RNA yield. The age of the tissue blocks did not influence RNA yield, fragmentation or purity. There was no significant correlation between RIN or 260/280 ratios and mean qPCR cycle threshold for either reference gene.ConclusionsThis study showed that routinely available CNS FFPE tissue is suitable for RNA extraction and downstream gene expression studies, even after 60 months of storage. Substantial RNA fragmentation associated with glioblastoma and control FFPE tissue blocks did not preclude downstream RT-qPCR gene expression analyses. Cross validation with both archival and prospectively collated FFPE specimens is required to further demonstrate that CNS tissue blocks can be used in novel translational molecular biomarker studies.
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Walter RFH, Mairinger FD, Werner R, Vollbrecht C, Hager T, Schmid KW, Wohlschlaeger J, Christoph DC. Folic-acid metabolism and DNA-repair phenotypes differ between neuroendocrine lung tumors and associate with aggressive subtypes, therapy resistance and outcome. Oncotarget 2018; 7:20166-79. [PMID: 27064343 PMCID: PMC4991445 DOI: 10.18632/oncotarget.7737] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 01/30/2016] [Indexed: 02/02/2023] Open
Abstract
Purpose 25% of all lung cancer cases are neuroendocrine (NELC) including typical (TC) and atypical carcinoid (AC), large-cell neuroendocrine (LCNEC) and small cell lung cancer (SCLC). Prognostic and predictive biomarkers are lacking. Experimental Design Sixty patients were used for nCounter mRNA expression analysis of the folic-acid metabolism (ATIC, DHFR, FOLR1, FPGS, GART, GGT1, SLC19A1, TYMS) and DNA-repair (ERCC1, MLH1, MSH2, MSH6, XRCC1). Phenotypic classification classified tumors (either below or above the median expression level) with respect to the folic acid metabolism or DNA repair. Results Expression of FOLR1, FPGS, MLH1 and TYMS (each p<0.0001) differed significantly between all four tumor types. FOLR1 and FPGS associated with tumor differentiation (both p<0.0001), spread to regional lymph nodes (FOLR1 p=0.0001 and FPGS p=0.0038), OS and PFS (FOLR1 p<0.0050 for both and FPGS p<0.0004 for OS). Phenotypic sorting revealed the Ft-phenotype to be the most prominent expression profile in carcinoids, whereas SCLC presented nearly univocal with the fT and LCNEC with fT or ft. These results were significant for tumor subtype (p<0.0001). Conclusions The assessed biomarkers and phenotypes allow for risk stratification (OS, PFS), diagnostic classification and enhance the biological understanding of the different subtypes of neuroendocrine tumors revealing potential new therapy options and clarifying known resistance mechanisms.
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Affiliation(s)
- Robert Fred Henry Walter
- Ruhrlandklinik Essen, West German Lung Centre, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Fabian Dominik Mairinger
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Institute of Pathology, Division of Molecular Pathology, Charité, Berlin, Germany
| | - Robert Werner
- Department of Pathology, Helios Klinikum Emil von Behring, Berlin, Germany
| | - Claudia Vollbrecht
- Institute of Pathology, Division of Molecular Pathology, Charité, Berlin, Germany
| | - Thomas Hager
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Kurt Werner Schmid
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Jeremias Wohlschlaeger
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Institute of Pathology, Ev.-Luth. Diakonissenkrankenhaus Flensburg, Flensburg, Germany
| | - Daniel Christian Christoph
- Department of Medical Oncology, West German Cancer Centre, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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12
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Wang DZ, Liu P, Yao L, Hao YH, Zhu RJ, Zhang T, Tang XB. Aberrant expression of thyroid transcription factor-1 in schwannomas. Hum Pathol 2017; 71:84-90. [PMID: 29104109 DOI: 10.1016/j.humpath.2017.10.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/15/2017] [Accepted: 10/18/2017] [Indexed: 10/18/2022]
Abstract
Aberrant expression of thyroid transcription factor-1 (TTF-1) has been observed in tumors arising in locations other than thyroid gland, lung and ventral forebrain. However, TTF-1 expression in schwannomas has not yet been studied. Meanwhile, a few inconsistent changes in protein expression have been identified between schwannomas and other peripheral nerve sheath tumors. We evaluated TTF-1 expression in 161 schwannomas and 43 other peripheral nervous system lesions, including ganglioneuromas (n = 8), malignant peripheral nerve sheath tumors (MPNSTs) (n = 11), neurofibromas (n = 24), and traumatic neuromas (n = 9), using immunohistochemistry and verified it using quantitative real-time reverse-transcription polymerase chain reaction (qPCR) to explore TTF-1 expression in peripheral nervous system lesions. Formalin-fixed paraffin-embedded (FFPE) tissues were obtained for both analyses. In this study, we observed nuclear TTF-1 staining in 109 (67.7%) schwannomas, including 102 of 131 (77.9%) conventional, 1 of 20 (5.0%) cellular and 6 of 10 (60.0%) plexiform schwannomas. Nuclear staining was not observed in normal peripheral nerves and non-schwannoma lesions. qPCR verified the aberrant expression and revealed a correlation between TTF-1 protein and mRNA levels (r = 0.633, P = .003). In conclusion, the data from our study show that TTF-1 is selectively expressed in the majority of schwannomas, particularly the conventional variants. Based on this observation, the TTF-1 protein and mRNA are specifically expressed in schwannomas. This highly aberrant expression of varying amounts of TTF-1 may provide new clues to reveal the pathogenesis of schwannoma.
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Affiliation(s)
- Dai-Zhong Wang
- Department of Pathology, Taihe Hospital, Hubei University of Medicine, Hubei, China 442000
| | - Ping Liu
- Department of Pathology, Taihe Hospital, Hubei University of Medicine, Hubei, China 442000
| | - Li Yao
- Department of Pathology, Taihe Hospital, Hubei University of Medicine, Hubei, China 442000
| | - Ying-Hua Hao
- Department of Pathology, Taihe Hospital, Hubei University of Medicine, Hubei, China 442000
| | - Rui-Juan Zhu
- Department of Pathology, Taihe Hospital, Hubei University of Medicine, Hubei, China 442000
| | - Tao Zhang
- Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, Hubei, China 442000
| | - Xian-Bin Tang
- Department of Pathology, Taihe Hospital, Hubei University of Medicine, Hubei, China 442000.
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Freitag D, Koch A, Lawson McLean A, Kalff R, Walter J. Validation of Reference Genes for Expression Studies in Human Meningiomas under Different Experimental Settings. Mol Neurobiol 2017; 55:5787-5797. [PMID: 29079997 DOI: 10.1007/s12035-017-0800-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/11/2017] [Indexed: 02/06/2023]
Abstract
Quantitative polymerase chain reaction (qPCR) is a sensitive technique for the quantitative analysis of gene expression levels. To compare mRNA transcripts across tumour and non-pathological tissue, appropriate reference genes are required for internal standardisation. Validation of these reference genes in meningiomas has not yet been reported. After mRNA transcription of meningioma (WHO grade I-III) and meningeal tissue from three different experimental sample types (fresh tissue, primary cell cultures and FFPE tissue), 13 candidate reference genes (ACTB, B2M, HPRT, VIM, GAPDH, YWHAZ, EIF4A2, MUC1, ATP5B, GNB2L, TUBB, CYC1, RPL13A) were chosen for quantitative expression analysis. Two statistical algorithms (GeNorm and NormFinder) were used for validation of gene expression stability. All candidate housekeepers tested for stability were checked within and across the three tissue analysis groups. Pearson correlation, the ΔC t method and ranking analysis identified the most non-regulated genes suitable for internal standardisation. TUBB, HPRT and ACTB were the most stably expressed genes for all analysis groups across meningioma and non-pathological meningeal tissue combined. In contrast, analysis of the consistency of reference gene expression within specific meningioma and meningeal tissues resulted in specific reference gene rankings for each tissue type. Future gene expression analyses require reference genes to be chosen that are suitable for the tissue types and for the experimental paradigms being studied. Validation of candidate housekeeper genes in meningiomas for quantitative real-time polymerase chain reaction revealed for the first time TUBB, ACTB and HPRT as the most consistently expressed genes among meningioma and non-pathological meningeal tissue across a range of experimental settings.
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Affiliation(s)
- Diana Freitag
- Department of Neurosurgery, Section of Experimental Neurooncology, Jena University Hospital - Friedrich Schiller University Jena, Am Klinikum 1, 07747, Jena, Germany.
| | - Arend Koch
- Institute of Neuropathology, Charité-Universitätsmedizin Berlin, Charitéplatz 1 - Virchowweg 15, 10117, Berlin, Germany
| | - Aaron Lawson McLean
- Department of Neurosurgery, Section of Experimental Neurooncology, Jena University Hospital - Friedrich Schiller University Jena, Am Klinikum 1, 07747, Jena, Germany
| | - Rolf Kalff
- Department of Neurosurgery, Section of Experimental Neurooncology, Jena University Hospital - Friedrich Schiller University Jena, Am Klinikum 1, 07747, Jena, Germany
| | - Jan Walter
- Department of Neurosurgery, Section of Experimental Neurooncology, Jena University Hospital - Friedrich Schiller University Jena, Am Klinikum 1, 07747, Jena, Germany
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15
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Haynes HR, White P, Hares KM, Redondo J, Kemp KC, Singleton WGB, Killick-Cole CL, Stevens JR, Garadi K, Guglani S, Wilkins A, Kurian KM. The transcription factor PPARα is overexpressed and is associated with a favourable prognosis in IDH-wildtype primary glioblastoma. Histopathology 2017; 70:1030-1043. [PMID: 27926792 DOI: 10.1111/his.13142] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 11/29/2016] [Indexed: 12/26/2022]
Abstract
AIMS PPARα agonists are in current clinical use as hypolipidaemic agents and show significant antineoplastic effects in human glioblastoma models. To date however, the expression of PPARα in large-scale glioblastoma datasets has not been examined. We aimed to investigate the expression of the transcription factor PPARα in primary glioblastoma, the relationship between PPARα expression and patients' clinicopathological features and other molecular markers associated with gliomagenesis. METHODS AND RESULTS With protein immunoblotting techniques and reverse transcription quantitative real-time PCR, PPARα was found to be significantly overexpressed in glioblastoma compared with control brain tissue (P = 0.032 and P = 0.005). PPARA gene expression was found to be enriched in the classical glioblastoma subtype within The Cancer Genome Atlas (TCGA) dataset. Although not associated with overall survival when assessed by immunohistochemistry, cross-validation with the TCGA dataset and multivariate analyses identified PPARA gene expression as an independent prognostic marker for overall survival (P = 0.042). Finally, hierarchical clustering revealed novel, significant associations between high PPARA expression and a putative set of glioblastoma molecular mediators including EMX2, AQP4, and NTRK2. CONCLUSIONS PPARα is overexpressed in primary glioblastoma and high PPARA expression functions as an independent prognostic marker in the glioblastoma TCGA dataset. Further studies are required to explore genetic associations with high PPARA expression and to analyse the predictive role of PPARα expression in glioblastoma models in response to PPARα agonists.
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Affiliation(s)
- Harry R Haynes
- Brain Tumour Research Group, Institute of Clinical Neurosciences, University of Bristol, Bristol, UK
| | - Paul White
- Applied Statistics Group, University of the West of England, Bristol, UK
| | - Kelly M Hares
- MS and Stem Cell Research Group, Institute of Clinical Neurosciences, University of Bristol, Bristol, UK
| | - Juliana Redondo
- MS and Stem Cell Research Group, Institute of Clinical Neurosciences, University of Bristol, Bristol, UK
| | - Kevin C Kemp
- MS and Stem Cell Research Group, Institute of Clinical Neurosciences, University of Bristol, Bristol, UK
| | - William G B Singleton
- Functional Neurosurgery Research Group, Institute of Clinical Neurosciences, University of Bristol, Bristol, UK
| | - Clare L Killick-Cole
- Functional Neurosurgery Research Group, Institute of Clinical Neurosciences, University of Bristol, Bristol, UK
| | | | - Krishnakumar Garadi
- Bristol Haematology and Oncology Centre, University Hospital Bristol Trust, Bristol, UK
| | - Sam Guglani
- Gloucestershire Oncology Centre, Gloucestershire Hospitals NHS Foundation Trust, Cheltenham, UK
| | - Alastair Wilkins
- MS and Stem Cell Research Group, Institute of Clinical Neurosciences, University of Bristol, Bristol, UK
| | - Kathreena M Kurian
- Brain Tumour Research Group, Institute of Clinical Neurosciences, University of Bristol, Bristol, UK
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ACTB, CDKN1B, GAPDH, GRB2, RHOA and SDCBP Were Identified as Reference Genes in Neuroendocrine Lung Cancer via the nCounter Technology. PLoS One 2016; 11:e0165181. [PMID: 27802291 PMCID: PMC5089548 DOI: 10.1371/journal.pone.0165181] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 10/08/2016] [Indexed: 01/18/2023] Open
Abstract
Background Neuroendocrine lung cancer (NELC) represents 25% of all lung cancer cases and large patient collectives exist as formalin-fixed, paraffin-embedded (FFPE) tissue only. FFPE is controversially discussed as source for molecular biological analyses and reference genes for NELC are poorly establishes. Material and methods Forty-three representative FFPE-specimens were used for mRNA expression analysis using the digital nCounter technology (NanoString). Based on recent literature, a total of 91 mRNA targets were investigated as potential tumor markers or reference genes. The geNorm, NormFinder algorithms and coefficient of correlation were used to identify the most stable reference genes. Statistical analysis was performed by using the R programming environment (version 3.1.1) Results RNA integrity (RIN) ranged from 1.8 to 2.6 and concentrations from 34 to 2,109 ng/μl. However, the nCounter technology gave evaluable results for all samples tested. ACTB, CDKN1B, GAPDH, GRB2, RHOA and SDCBP were identified as constantly expressed genes with high stability (M-)values according to geNorm, NormFinder and coefficients of correlation. Conclusion FFPE-derived mRNA is suitable for molecular biological investigations via the nCounter technology, although it is highly degraded. ACTB, CDKN1B, GAPDH, GRB2, RHOA and SDCBP are potent reference genes in neuroendocrine tumors of the lung.
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Meira-Strejevitch CS, Pereira-Chioccola VL, Maia MM, Carnietto de Hipólito DD, Wang HTL, Motoie G, de Souza Gomes AH, Kanamura CT, Martines RB, de Mattos CCB, Frederico FB, de Mattos LC, de Mattos CCB, Frederico FB, Siqueira RC, Previato M, Barbosa AP, Murata FHA. WITHDRAWN: Selection of reference genes in five types of human tissues for normalization of gene expression studies in infectious diseases. Gene 2016:S0378-1119(16)30816-2. [PMID: 27743995 DOI: 10.1016/j.gene.2016.10.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 10/09/2016] [Indexed: 11/23/2022]
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.
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Affiliation(s)
| | | | - Marta Marques Maia
- Centro de Parasitologia e Micologia, Instituto Adolfo Lutz, Sao Paulo Brazil
| | | | - Hui-Tzu Lin Wang
- Laboratório de Investigação Molecular em Cardiologia, Instituto Dante Pazzanese de Cardiologia, Sao Paulo Brazil
| | - Gabriela Motoie
- Centro de Parasitologia e Micologia, Instituto Adolfo Lutz, Sao Paulo Brazil
| | | | | | | | - Cinara Cássia Brandão de Mattos
- Laboratório de Imunogenética, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, Brazil
| | - Fábio Batista Frederico
- Ambulatório de Oftalmologia, Fundação Faculdade Regional de Medicina-Hospital de Base, São José do Rio Preto, Brazil
| | - Luiz Carlos de Mattos
- Laboratório de Imunogenética, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, Brazil
| | - Cinara Cássia Brandão de Mattos
- Laboratório de Imunogenética, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, Brazil
| | - Fábio Batista Frederico
- Ambulatório de Oftalmologia, Fundação Faculdade Regional de Medicina-Hospital de Base, São José do Rio Preto, Brazil
| | - Rubens Camargo Siqueira
- Laboratório de Imunogenética, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, Brazil
| | - Mariana Previato
- Laboratório de Imunogenética, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, Brazil
| | - Amanda Pires Barbosa
- Ambulatório de Oftalmologia, Fundação Faculdade Regional de Medicina-Hospital de Base, São José do Rio Preto, Brazil
| | - Fernando Henrique Antunes Murata
- Laboratório de Imunogenética, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, Brazil
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Walter RFH, Werner R, Ting S, Vollbrecht C, Theegarten D, Christoph DC, Schmid KW, Wohlschlaeger J, Mairinger FD. Identification of deregulation of apoptosis and cell cycle in neuroendocrine tumors of the lung via NanoString nCounter expression analysis. Oncotarget 2016; 6:24690-8. [PMID: 26008974 PMCID: PMC4694788 DOI: 10.18632/oncotarget.3992] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 04/15/2015] [Indexed: 01/16/2023] Open
Abstract
Background Neuroendocrine tumors of the lung comprise typical (TC) and atypical carcinoids (AC), large-cell neuroendocrine cancer (LCNEC) and small-cell lung cancer (SCLC). Cell cycle and apoptosis are key pathways of multicellular homeostasis and deregulation of these pathways is associated with cancerogenesis. Materials and Methods Sixty representative FFPE-specimens (16 TC, 13 AC, 16 LCNEC and 15 SCLC) were used for mRNA expression analysis using the NanoString technique. Eight genes related to apoptosis and ten genes regulating key points of cell cycle were investigated. Results ASCL1, BCL2, CASP8, CCNE1, CDK1, CDK2, CDKN1A and CDKN2A showed lower expression in carcinoids compared to carcinomas. In contrast, CCNE1 and CDK6 showed elevated expression in carcinoids compared to carcinomas. The calculated BCL2/BAX ratio showed increasing values from TC to SCLC. Between SCLC and LCNEC CDK2, CDKN1B, CDKN2A and PNN expression was significantly different with higher expression in SCLC. Conclusion Carcinoids have increased CDK4/6 and CCND1 expression controlling RB1 phosphorylation via this signaling cascade. CDK2 and CCNE1 were increased in carcinomas showing that these use the opposite way to control RB1. BAX and BCL2 are antagonists in regulating apoptosis. BCL2 expression increased over BAX expression with increasing malignancy of the tumor from TC to SCLC.
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Affiliation(s)
- Robert Fred Henry Walter
- Ruhrlandklinik, West German Lung Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Robert Werner
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Saskia Ting
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | | | - Dirk Theegarten
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Daniel Christian Christoph
- Department of Medical Oncology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Kurt Werner Schmid
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Jeremias Wohlschlaeger
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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Ostasiewicz B, Ostasiewicz P, Duś-Szachniewicz K, Ostasiewicz K, Ziółkowski P. Quantitative analysis of gene expression in fixed colorectal carcinoma samples as a method for biomarker validation. Mol Med Rep 2016; 13:5084-92. [PMID: 27121919 PMCID: PMC4878534 DOI: 10.3892/mmr.2016.5200] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 03/09/2016] [Indexed: 02/06/2023] Open
Abstract
Biomarkers have been described as the future of oncology. Modern proteomics provide an invaluable tool for the near-whole proteome screening for proteins expressed differently in neoplastic vs. healthy tissues. However, in order to select the most promising biomarkers, an independent method of validation is required. The aim of the current study was to propose a methodology for the validation of biomarkers. Due to material availability the majority of large scale biomarker studies are performed using formalin-fixed paraffin-embedded (FFPE) tissues, therefore these were selected for use in the current study. A total of 10 genes were selected from what have been previously described as the most promising candidate biomarkers, and the expression levels were analyzed with reverse transcription-quantitative polymerase chain reaction (RT-qPCR) using calibrator normalized relative quantification with the efficiency correction. For 6/10 analyzed genes, the results were consistent with the proteomic data; for the remaining four genes, the results were inconclusive. The upregulation of karyopherin α 2 (KPNA2) and chromosome segregation 1-like (CSE1L) in colorectal carcinoma, in addition to downregulation of chloride channel accessory 1 (CLCA1), fatty acid binding protein 1 (FABP1), sodium channel, voltage gated, type VII α subunit (SCN7A) and solute carrier family 26 (anion exchanger), member 3 (SLC26A3) was confirmed. With the combined use of proteomic and genetic tools, it was reported, for the first time to the best of our knowledge, that SCN7A was downregulated in colorectal carcinoma at mRNA and protein levels. It had been previously suggested that the remaining five genes served an important role in colorectal carcinogenesis, however the current study provided strong evidence to support their use as biomarkers. Thus, it was concluded that combination of RT-qPCR with proteomics offers a powerful methodology for biomarker identification, which can be used to analyze FFPE samples.
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Affiliation(s)
- Beata Ostasiewicz
- Department of Pathology, Wrocław Medical University, Wrocław 50‑368, Poland
| | - Paweł Ostasiewicz
- Department of Pathology, Wrocław Medical University, Wrocław 50‑368, Poland
| | | | | | - Piotr Ziółkowski
- Department of Pathology, Wrocław Medical University, Wrocław 50‑368, Poland
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Bradley WH, Eng K, Le M, Mackinnon AC, Kendziorski C, Rader JS. Comparing gene expression data from formalin-fixed, paraffin embedded tissues and qPCR with that from snap-frozen tissue and microarrays for modeling outcomes of patients with ovarian carcinoma. BMC Clin Pathol 2015; 15:17. [PMID: 26412982 PMCID: PMC4582729 DOI: 10.1186/s12907-015-0017-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 09/08/2015] [Indexed: 12/18/2022] Open
Abstract
Background Previously, we have used clinical and gene expression data from The Cancer Genome Atlas (TCGA) to model a pathway-based index predicting outcomes in ovarian carcinoma. This data were obtained from snap-frozen tissue measured with the Affymetrix U133 platform. In the current study, we correlate the data used to model with data derived from TaqMan qPCR both snap frozen and paraffin embedded (FFPE) samples. Methods To compare the effect of preservation methods on gene expression measured by qPCR, we assessed 18 patient and tumor sample matched snap-frozen and FFPE ovarian carcinoma samples. To compare gene measurement technologies, we correlated qPCR data from 10 patients with tumor sample matched snap-frozen ovarian carcinoma samples with the microarray data from TCGA. We normalized results to the average expression of three housekeeping genes. We scaled and centered the data for comparison to the Affymetrix output. Results For the 18 specimens, gene expression data obtained from snap-frozen tissue correlated highly with that from FFPE samples in our TaqMan assay (r > 0.82). For the 10 duplicate TCGA specimens, the reported microarray data correlated well (r = 0.6) with our qPCR data, and ranges of expression along pathways were similar. Conclusions Gene expression data obtained by qPCR from FFPE serous ovarian carcinoma samples can be used to assess in the pathway-based predictive model. The normalization procedures described control variations in expression, and the range calculated along a specific pathway can be interpreted for a patient’s risk profile. Electronic supplementary material The online version of this article (doi:10.1186/s12907-015-0017-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- William H Bradley
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226 USA
| | - Kevin Eng
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53792 USA ; Current Address: Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY USA
| | - Min Le
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226 USA
| | - A Craig Mackinnon
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226 USA
| | - Christina Kendziorski
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53792 USA
| | - Janet S Rader
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226 USA
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21
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Walter RFH, Mairinger FD, Ting S, Vollbrecht C, Mairinger T, Theegarten D, Christoph DC, Schmid KW, Wohlschlaeger J. MDM2 is an important prognostic and predictive factor for platin-pemetrexed therapy in malignant pleural mesotheliomas and deregulation of P14/ARF (encoded by CDKN2A) seems to contribute to an MDM2-driven inactivation of P53. Br J Cancer 2015; 112:883-90. [PMID: 25668009 PMCID: PMC4453955 DOI: 10.1038/bjc.2015.27] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 01/01/2015] [Accepted: 01/12/2015] [Indexed: 12/28/2022] Open
Abstract
Background: Malignant pleural mesothelioma (MPM) is a highly aggressive tumour that is
first-line treated with a combination of cisplatin and pemetrexed. Until
now, predictive and prognostic biomarkers are lacking, making it a
non-tailored therapy regimen with unknown outcome. P53 is frequently
inactivated in MPM, but mutations are extremely rare. MDM2 and P14/ARF
are upstream regulators of P53 that may contribute to P53 inactivation. Methods: A total of 72 MPM patients were investigated. MDM2 immunoexpression was
assessed in 65 patients. MDM2 and P14/ARF mRNA
expression was analysed in 48 patients of the overall collective. The
expression results were correlated to overall survival (OS) and
progression-free survival (PFS). Results: OS and PFS correlated highly significantly with MDM2 mRNA and protein
expression, showing a dismal prognosis for patients with elevated MDM2
expression (for OS: Score (logrank) test: P⩽0.002, and for PFS:
Score (logrank) test; P<0.007). MDM2 was identified as robust
prognostic and predictive biomarker for MPM on the mRNA and protein level.
P14/ARF mRNA expression reached no statistical
significance, but Kaplan–Meier curves distinguished patients with low
P14/ARF expression and hence shorter survival from patients
with higher expression and prolonged survival. Conclusions: MDM2 is a prognostic and predictive marker for a platin–pemetrexed
therapy of patients with MPMs. Downregulation of P14/ARF expression
seems to contribute to MDM2-overexpression-mediated P53 inactivation in MPM
patients.
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Affiliation(s)
- R F H Walter
- 1] Ruhrlandklinik, West German Lung Center, University Hospital Essen, University of Duisburg-Essen, Tüschener Weg 40, Essen D-45239, Germany [2] Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - F D Mairinger
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - S Ting
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - C Vollbrecht
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - T Mairinger
- Department of Pathology, Helios Klinikum Emil von Behring, Berlin, Germany
| | - D Theegarten
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - D C Christoph
- 1] Department of Medical Oncology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany [2] Department of Medicine, Division of Medical Oncology, University of Colorado Denver, Aurora, CO, USA
| | - K W Schmid
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - J Wohlschlaeger
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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22
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Gerdes MJ, Sood A, Sevinsky C, Pris AD, Zavodszky MI, Ginty F. Emerging understanding of multiscale tumor heterogeneity. Front Oncol 2014; 4:366. [PMID: 25566504 PMCID: PMC4270176 DOI: 10.3389/fonc.2014.00366] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 12/02/2014] [Indexed: 12/12/2022] Open
Abstract
Cancer is a multifaceted disease characterized by heterogeneous genetic alterations and cellular metabolism, at the organ, tissue, and cellular level. Key features of cancer heterogeneity are summarized by 10 acquired capabilities, which govern malignant transformation and progression of invasive tumors. The relative contribution of these hallmark features to the disease process varies between cancers. At the DNA and cellular level, germ-line and somatic gene mutations are found across all cancer types, causing abnormal protein production, cell behavior, and growth. The tumor microenvironment and its individual components (immune cells, fibroblasts, collagen, and blood vessels) can also facilitate or restrict tumor growth and metastasis. Oncology research is currently in the midst of a tremendous surge of comprehension of these disease mechanisms. This will lead not only to novel drug targets but also to new challenges in drug discovery. Integrated, multi-omic, multiplexed technologies are essential tools in the quest to understand all of the various cellular changes involved in tumorigenesis. This review examines features of cancer heterogeneity and discusses how multiplexed technologies can facilitate a more comprehensive understanding of these features.
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Affiliation(s)
- Michael J. Gerdes
- Diagnostic Imaging and Biomedical Technologies, GE Global Research, Niskayuna, NY, USA
| | - Anup Sood
- Diagnostic Imaging and Biomedical Technologies, GE Global Research, Niskayuna, NY, USA
| | - Christopher Sevinsky
- Diagnostic Imaging and Biomedical Technologies, GE Global Research, Niskayuna, NY, USA
| | - Andrew D. Pris
- Diagnostic Imaging and Biomedical Technologies, GE Global Research, Niskayuna, NY, USA
| | - Maria I. Zavodszky
- Diagnostic Imaging and Biomedical Technologies, GE Global Research, Niskayuna, NY, USA
| | - Fiona Ginty
- Diagnostic Imaging and Biomedical Technologies, GE Global Research, Niskayuna, NY, USA
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23
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Aggerholm-Pedersen N, Safwat A, Bærentzen S, Nordsmark M, Nielsen OS, Alsner J, Sørensen BS. The importance of reference gene analysis of formalin-fixed, paraffin-embedded samples from sarcoma patients - an often underestimated problem. Transl Oncol 2014; 7:687-93. [PMID: 25500077 PMCID: PMC4311021 DOI: 10.1016/j.tranon.2014.09.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 09/24/2014] [Accepted: 09/26/2014] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE Reverse transcription quantitative real-time polymerase chain reaction is efficient for quantification of gene expression, but the choice of reference genes is of paramount importance as it is essential for correct interpretation of data. This is complicated by the fact that the materials often available are routinely collected formalin-fixed, paraffin-embedded (FFPE) samples in which the mRNA is known to be highly degraded. The purpose of this study was to investigate 22 potential reference genes in sarcoma FFPE samples and to study the variation in expression level within different samples taken from the same tumor and between different histologic types. METHODS Twenty-nine patients treated for sarcoma were enrolled. The samples encompassed 82 (FFPE) specimens. Extraction of total RNA from 7-μm FFPE sections was performed using a fully automated, bead-base RNA isolation procedure, and 22 potential reference genes were analyzed by reverse transcription quantitative real-time polymerase chain reaction. The stability of the genes was analyzed by RealTime Statminer. The intrasamples variation and the interclass correlation coefficients were calculated. The linear regression model was used to calculate the degradation of the mRNA over time. RESULTS The quality of RNA was sufficient for analysis in 84% of the samples. Recommended reference genes differed with histologic types. However, PPIA, SF3A1, and MRPL19 were stably expressed regardless of the histologic type included. The variation in ∆Cq value for samples from the same patients was similar to the variation between patients. It was possible to compensate for the time-dependent degradation of the mRNA when normalization was made using the selected reference genes. CONCLUSION PPIA, SF3A1, and MRPL19 are suitable reference genes for normalization in gene expression studies of FFPE samples from sarcoma regardless of the histology.
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Affiliation(s)
| | - Akmal Safwat
- Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Steen Bærentzen
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | | | | | - Jan Alsner
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Brita S Sørensen
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark
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24
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Mairinger FD, Ting S, Werner R, Walter RFH, Hager T, Vollbrecht C, Christoph D, Worm K, Mairinger T, Sheu-Grabellus SY, Theegarten D, Schmid KW, Wohlschlaeger J. Different micro-RNA expression profiles distinguish subtypes of neuroendocrine tumors of the lung: results of a profiling study. Mod Pathol 2014; 27:1632-40. [PMID: 24875640 DOI: 10.1038/modpathol.2014.74] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 02/12/2014] [Indexed: 12/30/2022]
Abstract
MicroRNAs (miRNAs) are a class of small (∼22 nucleotides), non-coding, highly conserved single-stranded RNAs with posttranscriptional regulatory features, including the regulation of cell proliferation, differentiation, survival, and apoptosis. They are deregulated in a broad variety of tumors showing characteristic expression patterns and can, thus, be used as a diagnostic tool. In contrast to non-small cell carcinoma of the lung neuroendocrine lung tumors, encompassing typical and atypical carcinoids, small cell lung cancer and large cell neuroendocrine lung cancer, no data about deregulation of tumor entity-specific miRNAs are available to date. miRNA expression differences might give useful information about the biological characteristics of these tumors, as well as serve as helpful markers.In 12 pulmonary neuroendocrine tumors classified as either typical carcinoid, atypical, large cell neuroendocrine or small cell lung cancer, screening for 763 miRNAs known to be involved in pulmonary cancerogenesis was conducted by performing 384-well TaqMan low-density array real-time qPCR. In the entire cohort, 44 miRNAs were identified, which showed a significantly different miRNA expression. For 12 miRNAs, the difference was highly significant (P<0.01). Eight miRNAs showed a negative (miR-22, miR-29a, miR-29b, miR-29c, miR-367*; miR-504, miR-513C, miR-1200) and four miRNAs a positive (miR-18a, miR-15b*, miR-335*, miR-1201) correlation to the grade of tumor biology. The miRNAs let-7d; miR-19; miR-576-5p; miR-340*; miR-1286 are significantly associated with survival. Members of the miR-29 family seem to be extremely important in this group of tumors. We found a number of miRNAs, which showed a highly significant deregulation in pulmonary neuroendocrine tumors. Moreover, some of these deregulated miRNAs seem to allow discrimination of the various subtypes of pulmonary neuroendocrine tumors. Thus, the analysis of specific sets of miRNAs can be proposed as diagnostic and/or predictive markers in this group of neoplasias.
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Affiliation(s)
- Fabian Dominik Mairinger
- Institute of Pathology and Neuropathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Saskia Ting
- Institute of Pathology and Neuropathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Robert Werner
- Institute of Pathology and Neuropathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Robert Fred Henry Walter
- 1] Institute of Pathology and Neuropathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany [2] Department of interventional Pneumology, Ruhrlandklinik, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Thomas Hager
- Institute of Pathology and Neuropathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | | | - Daniel Christoph
- Department of Medical Oncology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Karl Worm
- Institute of Pathology and Neuropathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Thomas Mairinger
- Department of Pathology, Helios Klinikum Emil von Behring, Berlin, Germany
| | - Sien-Yi Sheu-Grabellus
- Institute of Pathology and Neuropathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Dirk Theegarten
- Institute of Pathology and Neuropathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Kurt Werner Schmid
- Institute of Pathology and Neuropathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Jeremias Wohlschlaeger
- Institute of Pathology and Neuropathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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25
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Prokopec SD, Watson JD, Pohjanvirta R, Boutros PC. Identification of reference proteins for Western blot analyses in mouse model systems of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) toxicity. PLoS One 2014; 9:e110730. [PMID: 25329058 PMCID: PMC4201576 DOI: 10.1371/journal.pone.0110730] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 09/24/2014] [Indexed: 01/15/2023] Open
Abstract
Western blotting is a well-established, inexpensive and accurate way of measuring protein content. Because of technical variation between wells, normalization is required for valid interpretation of results across multiple samples. Typically this involves the use of one or more endogenous controls to adjust the measured levels of experimental molecules. Although some endogenous controls are widely used, validation is required for each experimental system. This is critical when studying transcriptional-modulators, such as toxicants like 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD).To address this issue, we examined hepatic tissue from 192 mice representing 47 unique combinations of strain, sex, Ahr-genotype, TCDD dose and treatment time. We examined 7 candidate reference proteins in each animal and assessed consistency of protein abundance through: 1) TCDD-induced fold-difference in protein content from basal levels, 2) inter- and intra- animal stability, and 3) the ability of each candidate to reduce instability of the other candidates. Univariate analyses identified HPRT as the most stable protein. Multivariate analysis indicated that stability generally increased with the number of proteins used, but gains from using >3 proteins were small. Lastly, by comparing these new data to our previous studies of mRNA controls on the same animals, we were able to show that the ideal mRNA and protein control-genes are distinct, and use of only 2–3 proteins provides strong stability, unlike in mRNA studies in the same cohort, where larger control-gene batteries were needed.
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Affiliation(s)
- Stephenie D. Prokopec
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - John D. Watson
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Raimo Pohjanvirta
- Laboratory of Toxicology, National Institute for Health and Welfare, Kuopio, Finland
- Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland
| | - Paul C. Boutros
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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26
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Fisher KE, Smith GH, Neill SG, Rossi MR. Section I: integrating laboratory medicine with tissue specimens. Curr Probl Cancer 2014; 38:144-58. [PMID: 25239562 DOI: 10.1016/j.currproblcancer.2014.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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27
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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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28
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Neumeister VM. Tools to assess tissue quality. Clin Biochem 2014; 47:280-7. [PMID: 24565988 DOI: 10.1016/j.clinbiochem.2014.02.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 02/12/2014] [Accepted: 02/13/2014] [Indexed: 01/21/2023]
Abstract
Biospecimen science has recognized the importance of tissue quality for accurate molecular and biomarker analysis and efforts are made to standardize tissue procurement, processing and storage conditions of tissue samples. At the same time the field has emphasized the lack of standardization of processes between different laboratories, the variability inherent in the analytical phase and the lack of control over the pre-analytical phase of tissue processing. The problem extends back into tissue samples in biorepositories, which are often decades old and where documentation about tissue processing might not be available. This review highlights pre-analytical variations in tissue handling, processing, fixation and storage and emphasizes the effects of these variables on nucleic acids and proteins in harvested tissue. Finally current tools for quality control regarding molecular or biomarker analysis are summarized and discussed.
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Affiliation(s)
- Veronique M Neumeister
- Department of Pathology, Yale University School of Medicine, 310 Cedar Street, LMP101, New Haven, CT 06520, USA.
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