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Köhler SA, Brandl L, Strissel PL, Gloßner L, Ekici AB, Angeloni M, Ferrazzi F, Bahlinger V, Hartmann A, Beckmann MW, Eckstein M, Strick R. Improved Bladder Tumor RNA Isolation from Archived Tissues Using Methylene Blue for Normalization, Multiplex RNA Hybridization, Sequencing and Subtyping. Int J Mol Sci 2022; 23:ijms231810267. [PMID: 36142180 PMCID: PMC9499321 DOI: 10.3390/ijms231810267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/26/2022] [Accepted: 09/02/2022] [Indexed: 12/02/2022] Open
Abstract
Methylene blue (MB) is a dye used for histology with clinical importance and intercalates into nucleic acids. After MB staining of formalin fixed paraffin embedded (FFPE) muscle invasive bladder cancer (MIBC) and normal urothelium, specific regions could be microdissected. It is not known if MB influences RNA used for gene expression studies. Therefore, we analyzed MIBC using five different RNA isolation methods comparing patient matched FFPE and fresh frozen (FF) tissues pre-stained with or without MB. We demonstrate a positive impact of MB on RNA integrity with FF tissues using real time PCR with no interference of its chemical properties. FFPE tissues showed no improvement of RNA integrity, which we propose is due to formalin induced nucleotide crosslinks. Using direct multiplex RNA hybridization the best genes for normalization of MIBC and control tissues were identified from 34 reference genes. In addition, 5SrRNA and 5.8SrRNA were distinctive reference genes detecting <200 bp fragments important for mRNA analyses. Using these normalized RNAs from MB stained MIBC and applying multiplex RNA hybridization and mRNA sequencing, a minimal gene expression panel precisely identified luminal and basal MIBC tumor subtypes, important for diagnosis, prognosis and chemotherapy response.
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Affiliation(s)
- Stefanie A. Köhler
- Laboratory for Molecular Medicine, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Universitaetsstrasse 21-23, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
| | - Lisa Brandl
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Pamela L. Strissel
- Laboratory for Molecular Medicine, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Universitaetsstrasse 21-23, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Laura Gloßner
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Arif B. Ekici
- Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Miriam Angeloni
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Fulvia Ferrazzi
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
- Department of Nephropathology, Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Veronika Bahlinger
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Arndt Hartmann
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Matthias W. Beckmann
- Laboratory for Molecular Medicine, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Universitaetsstrasse 21-23, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
| | - Markus Eckstein
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Reiner Strick
- Laboratory for Molecular Medicine, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Universitaetsstrasse 21-23, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Correspondence: ; Tel.: +49-91318536671
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Nendza R, Digweed M, Meyer HE, Erdmann VA, Mayr GW. 5S-rRNA-containing ribonucleoproteins from rabbit muscle and liver. Complex and partial primary structures. EUROPEAN JOURNAL OF BIOCHEMISTRY 1987; 169:85-95. [PMID: 2960523 DOI: 10.1111/j.1432-1033.1987.tb13584.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A 5S-rRNA-containing ribonucleoprotein was purified to homogeneity from a rabbit muscle extract through its affinity to phosphofructokinase-1 and then structurally characterized. This RNP was compared to the 5S-rRNA-containing ribonucleoprotein extracted from rabbit liver ribosomal 60S subunits with EDTA. Analytical gel filtration revealed a molecular mass of 70-80 kDa for both complexes. Gel electrophoresis of the ribosomal complex revealed three protein components, one migrating as a band of 35 kDa and two other small polypeptides of apparently 16.5 kDa and 17.5 kDa. In the sarcoplasmic RNP these small polypeptides were absent. However, besides a major component of 35 kDa, up to five slightly larger and smaller species of 31.5-36.5 kDa were detected. Despite this heterogeneity, only one N-terminal amino acid sequence was obtained for the isolated sarcoplasmic protein, suggesting a C-terminal heterogeneity of one single polypeptide. Within the first 46 amino acid residues no difference between the sequences of the isolated 35-kDa components of sarcoplasmic and ribosomal complexes was found. Homology criteria indicated that this component belongs to the ribosomal protein L5 family. The RNA was identified by complete enzymatic sequencing as 5S rRNA; it was also identical in both complexes and is strongly homologous to 5S rRNA of man. Both L5-5S-RNA complexes could be resolved by hydroxyapatite chromatography into three species still consisting of both protein and RNA. 5'-Terminal dephosphorylation experiments showed that this heterogeneity is exclusively due to the differing number (1-3) of 5'-terminal phosphates. The two additional low-molecular-mass proteins were stably associated to the ribosomal RNP at high salt concentrations in a stoichiometry of about 2:1. They were identified as the acidic phosphoproteins P2/P3 by N-terminal sequencing. High phosphate concentrations facilitated their dissociation from the L5-5S-RNA complex. For the sarcoplasmic L5-5S-RNA complex a hitherto unknown interaction with phosphofructokinase-1, affecting the enzymatic properties, was demonstrated.
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Affiliation(s)
- R Nendza
- Institut für Physiologische Chemie, Ruhr-Universität Bochum, Federal Republic of Germany
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