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Lu X, Lu W, Hua D. A novel SERS-lateral flow assay (LFA) tray for monitoring of miR-155-5p during pyroptosis in breast cancer cells. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:3878-3894. [PMID: 38828902 DOI: 10.1039/d4ay00363b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
In the study, a novel surface-enhanced Raman scattering (SERS)-lateral flow assay (LFA) tray for the real-time detection of pyroptosis-associated miR-155-5p in breast cancer cells was established and validated. The SERS probe modified with monoclonal antibodies and functionalized HP1@5-FAM was first synthesized. When miR-155-5p was present, HP1@5-FAM on the SERS probe specifically recognized target miRNAs and hybridized with them, resulting in HP2 on the T line only capturing some SERS probes that were not bound to miR-155-5p. The T line appeared as a light orange band or there was no color change, and the corresponding Raman detection result showed a weak or insignificant Raman signal. The SERS probe showed high selectivity, satisfactory stability, and excellent reproducibility, and the limit of detection (LOD) for miR-155-5p was 7.26 aM. Finally, the proposed SERS-LFA tray was applied to detect miR-155-5p in MBA-MD-468 cells that underwent varying degrees of pyroptosis, and the detection results of SERS were consistent with those of the conventional real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) assay. The study demonstrated that the SERS-LFA tray was a convenient and ultrasensitive method for miR-155-5p real-time detection, which could provide more detailed information for pyroptosis and be of potential value in guiding the treatment of breast cancer.
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Affiliation(s)
- Xiaoxia Lu
- Department of Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, 214122, China.
- Department of Oncology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, 225000, China
| | - Wenlong Lu
- Department of Pharmacy and Equipment, Taizhou Women's and Children's Hospital, Taizhou, Jiangsu Province, 225300, China
| | - Dong Hua
- Department of Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, 214122, China.
- Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu Province, 21411, China
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Wang Y, Chen B, Fan J, Wang Z. A simple and efficient strategy for trace detection of ferroptosis-related miRNAs based on novel hydrophobic paper-based plasmonic substrate and "inverse molecular sentinel (iMS)" nanoprobes. Front Bioeng Biotechnol 2023; 11:1146111. [PMID: 36937763 PMCID: PMC10017978 DOI: 10.3389/fbioe.2023.1146111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 02/22/2023] [Indexed: 03/06/2023] Open
Abstract
Monitoring ferroptosis-related miRNAs is crucial for the treatment and prognosis of patients with intracerebral hemorrhage. In this work, a novel hydrophobic paper (h-paper)-based plasmonic substrate was produced by dropping DS Au nanorods with a narrow range of sizes and morphologies onto h-paper. Raman reporter molecules were adsorbed to the array surface, and surface-enhanced Raman scattering spectra at randomly selected points reveal uniform and significant SERS enhancement. Hairpin DNAs labelled with Raman reporters and hybridized with placeholder DNAs were decorated on SERS substrate to fabricate SERS biosensor. Target miRNAs initiated the "inverse Molecular Sentinel" process. During the process, PHs were removed and the conformation of HPs changed toward the hairpin structure, thus eliciting the proximity of Raman reporter to substrate and a stronger SERS signal. The proposed SERS biosensor performs well in terms of stability, reproducibility, and selectivity. The limits of detection of miR-122-5p and miR-140-5p in serum were 4.17 aM and 4.49 aM, respectively. Finally, the fabricated SERS biosensor was applied to detect miR-122-5p and miR-140-5p in ICH patients and healthy subjects, and the results obtained by SERS were consistent with the results from quantitative real-time polymerase chain reaction, revealing the accuracy of the method. This simple, rapid approach offers great potential for the simultaneous detection of miRNAs in practical clinical applications.
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Affiliation(s)
- Youwei Wang
- Department of neurosurgery, The First Affiliated Hospital of Soochow University, Suzhou, China
- Department of neurosurgery, The Affiliated Hospital of Yangzhou University, Yangzhou, China
| | - Bing Chen
- Department of neurosurgery, The Affiliated hospital of Qingdao University, Qingdao, China
| | - Jiang Fan
- Department of neurosurgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhong Wang
- Department of neurosurgery, The First Affiliated Hospital of Soochow University, Suzhou, China
- Department of neurosurgery and Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, China
- *Correspondence: Zhong Wang,
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Ge S, Li G, Zhou X, Mao Y, Gu Y, Li Z, Gu Y, Cao X. Pump-free microfluidic chip based laryngeal squamous cell carcinoma-related microRNAs detection through the combination of surface-enhanced Raman scattering techniques and catalytic hairpin assembly amplification. Talanta 2022; 245:123478. [DOI: 10.1016/j.talanta.2022.123478] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 04/07/2022] [Accepted: 04/10/2022] [Indexed: 01/14/2023]
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De Martino E, Medeot C, D'Amico L, Stanta G, Bonin S. Impact of standardization in tissue processing: the performance of different fixatives. N Biotechnol 2022; 71:30-36. [PMID: 35878783 DOI: 10.1016/j.nbt.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/21/2022] [Accepted: 07/21/2022] [Indexed: 10/31/2022]
Abstract
Most tissues in clinical practice are formalin-fixed and paraffin-embedded for histological as well as molecular analyses. The reproducibility and uniformity of molecular analyses is strictly dependent on the quality of the biomolecules, which is highly influenced by pre-analytical processes. In this study, the effect of different fixatives was compared, including formalin, Bouin's solution, RCL2® and TAG-1™ fixatives, by stringent application of ISO standards in mouse liver tissue processing, including formalin-free transport of tissues and tissue grossing in a refrigerated environment. The effect of fixatives was studied in terms of nucleic acid quality at the time of tissue processing and after one year of tissue storage at room temperature in the dark. Furthermore, a microcomputed tomography (CT) scan analysis was applied to investigate the paraffin embedding. The results show that the application of ISO standards in tissue processing allows analysis of 400 bases amplicons from RNA and 1000 bases from DNA, even in extracts from formalin-fixed and paraffin-embedded tissues. However, after one year storage at room temperature in the dark, a degradation of the nucleic acids was observed. Nevertheless, extracts can still be analyzed, but for metachronous tests it is highly recommended to repeat the quantitation of housekeeping genes in order to standardize the extent of nucleic acid degradation.
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Affiliation(s)
| | - Caterina Medeot
- Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Lorenzo D'Amico
- Department of Physics, University of Trieste, Trieste, Italy; Elettra-Sincrotrone Trieste S.C.p.A., Area Science Park, Trieste, Italy
| | - Giorgio Stanta
- Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Serena Bonin
- Department of Medical Sciences, University of Trieste, Trieste, Italy.
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Kos MZ, Puppala S, Cruz D, Neary JL, Kumar A, Dalan E, Li C, Nathanielsz P, Carless MA. Blood-Based miRNA Biomarkers as Correlates of Brain-Based miRNA Expression. Front Mol Neurosci 2022; 15:817290. [PMID: 35392269 PMCID: PMC8981579 DOI: 10.3389/fnmol.2022.817290] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/18/2022] [Indexed: 01/08/2023] Open
Abstract
The use of easily accessible peripheral samples, such as blood or saliva, to investigate neurological and neuropsychiatric disorders is well-established in genetic and epigenetic research, but the pathological implications of such biomarkers are not easily discerned. To better understand the relationship between peripheral blood- and brain-based epigenetic activity, we conducted a pilot study on captive baboons (Papio hamadryas) to investigate correlations between miRNA expression in peripheral blood mononuclear cells (PBMCs) and 14 different cortical and subcortical brain regions, represented by two study groups comprised of 4 and 6 animals. Using next-generation sequencing, we identified 362 miRNAs expressed at ≥ 10 read counts in 80% or more of the brain samples analyzed. Nominally significant pairwise correlations (one-sided P < 0.05) between peripheral blood and mean brain expression levels of individual miRNAs were observed for 39 and 44 miRNAs in each group. When miRNA expression levels were averaged for tissue type across animals within the groups, Spearman's rank correlations between PBMCs and the brain regions are all highly significant (r s = 0.47-0.57; P < 2.2 × 10-16), although pairwise correlations among the brain regions are markedly stronger (r s = 0.86-0.99). Principal component analysis revealed differentiation in miRNA expression between peripheral blood and the brain regions for the first component (accounting for ∼75% of variance). Linear mixed effects modeling attributed most of the variance in expression to differences between miRNAs (>70%), with non-significant 7.5% and 13.1% assigned to differences between blood and brain-based samples in the two study groups. Hierarchical UPGMA clustering revealed a major co-expression branch in both study groups, comprised of miRNAs globally upregulated in blood relative to the brain samples, exhibiting an enrichment of miRNAs expressed in immune cells (CD14+, CD15+, CD19+, CD3+, and CD56 + leukocytes) among the top blood-brain correlates, with the gene MYC, encoding a master transcription factor that regulates angiogenesis and neural stem cell activation, representing the most prevalent miRNA target. Although some differentiation was observed between tissue types, these preliminary findings reveal wider correlated patterns between blood- and brain-expressed miRNAs, suggesting the potential utility of blood-based miRNA profiling for investigating by proxy certain miRNA activity in the brain, with implications for neuroinflammatory and c-Myc-mediated processes.
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Affiliation(s)
- Mark Z. Kos
- Department of Human Genetics, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Edinburg, TX, United States
| | - Sobha Puppala
- Department of Internal Medicine-Section of Molecular Medicine, Wake Forest Baptist Medical Center, Winston-Salem, NC, United States
| | - Dianne Cruz
- Duke University School of Medicine, Durham, NC, United States
| | - Jennifer L. Neary
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Ashish Kumar
- Department of Internal Medicine-Section of Molecular Medicine, Wake Forest Baptist Medical Center, Winston-Salem, NC, United States
| | - Emma Dalan
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, United States
| | - Cun Li
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, United States,Department of Animal Science, University of Wyoming, Laramie, WY, United States
| | - Peter Nathanielsz
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, United States,Department of Animal Science, University of Wyoming, Laramie, WY, United States
| | - Melanie A. Carless
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, United States,Population Health, Texas Biomedical Research Institute, San Antonio, TX, United States,*Correspondence: Melanie A. Carless,
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Frasquilho SG, Sanchez I, Yoo C, Antunes L, Bellora C, Mathieson W. Do Tissues Fixed in a Non-crosslinking Fixative Require a Dedicated Formalin-free Processor? J Histochem Cytochem 2021; 69:389-405. [PMID: 34010071 DOI: 10.1369/00221554211017859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We evaluate the consequences of processing alcohol-fixed tissue in a processor previously used for formalin-fixed tissue. Biospecimens fixed in PAXgene Tissue Fixative were cut into three pieces then processed in a flushed tissue processor previously used for formalin-fixed, paraffin-embedded (FFPE) blocks (neutral buffered formalin [NBF]+ve), a formalin-free system (NBF-ve), or left unprocessed. Histomorphology and immunohistochemistry were compared using hematoxylin/eosin staining and antibodies for MLH-1, Ki-67, and CK-7. Nucleic acid was extracted using the PAXgene Tissue RNA/DNA kits and an FFPE RNA extraction kit. RNA integrity was assessed using RNA integrity number (RIN), reverse transcription polymerase chain reaction (RT-PCR) (four amplicons), and quantitative RT-PCR (three genes). For DNA, multiplex PCR, quantitative PCR, DNA integrity number, and gel electrophoresis were used. Compared with NBF-ve, RNA from NBF+ve blocks had 88% lower yield and poorer purity; average RIN reduced from 5.0 to 3.8, amplicon length was 408 base pairs shorter, and Cq numbers were 1.9-2.4 higher. Using the FFPE extraction kit rescued yield and purity, but RIN further declined by 1.1 units. Differences between NBF+ve and NBF-ve in respect of DNA, histomorphology, and immunohistochemistry were either non-existent or small in magnitude. Formalin contamination of a tissue processor and its reagents therefore critically reduce RNA yield and integrity. We discuss the available options users can adopt to ameliorate this problem.
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Affiliation(s)
| | | | - Changyoung Yoo
- The Catholic University of Korea, St. Vincent's Hospital, Seoul, Korea
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Fernandez-Serra A, Moura DS, Sanchez-Izquierdo MD, Calabuig-Fariñas S, Lopez-Alvarez M, Martínez-Martínez A, Carrasco-Garcia I, Ramírez-Calvo M, Blanco-Alcaina E, López-Reig R, Obrador-Hevia A, Alemany R, Gutierrez A, Hindi N, Poveda A, Lopez-Guerrero JA, Martin-Broto J. Prognostic Impact of let-7e MicroRNA and Its Target Genes in Localized High-Risk Intestinal GIST: A Spanish Group for Research on Sarcoma (GEIS) Study. Cancers (Basel) 2020; 12:E2979. [PMID: 33066614 PMCID: PMC7602387 DOI: 10.3390/cancers12102979] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/09/2020] [Accepted: 10/10/2020] [Indexed: 12/16/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that negatively regulate gene expression at the post-transcriptional level, and they have been described as being associated with tumor prognosis. Here, miRNA profiling was planned to explore new molecular prognostic biomarkers in localized intestinal high-risk GIST. Paraffin tumor blocks of 14 and 86 patients were used in the discovery and expansion sets, respectively. GeneChip miRNA v3.0 was employed to identify the miRNAs differentially expressed between relapsed and non-relapsed patient samples, which were validated in the expansion set, by qRT-PCR. RT2 Profiler PCR Array was used for the screening of let-7e targets. Expression levels were correlated with relapse-free survival and overall survival. In the discovery set, 39 miRNAs were significantly deregulated, let-7e and miR-550 being the most underexpressed and overexpressed miRNAs in the relapsed group, respectively. In the expansion set, the underexpression of let-7e or the overexpression of 4 of its target genes (ACVR1B, CASP3, COL3A1, and COL5A2) were statistically associated with worse relapse-free survival. The expression of let-7e and 4 of its target genes are potential prognostic biomarkers in high-risk localized intestinal GIST. The expression of these genes is a potential molecular tool useful for a more accurate prognosis in this subset of GIST patients.
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Affiliation(s)
- Antonio Fernandez-Serra
- Laboratory of Molecular Biology, Fundación Instituto Valenciano de Oncología, 46009 Valencia, Spain; (A.F.-S.); (A.M.-M.); (M.R.-C.); (R.L.-R.)
| | - David S. Moura
- Institute of Biomedicine of Sevilla (IBIS, HUVR, CSIC, Universidad de Sevilla), 41013 Sevilla, Spain; (D.S.M.); (M.L.-A.); (I.C.-G.); (E.B.-A.); (N.H.)
| | | | - Silvia Calabuig-Fariñas
- Molecular Oncology Laboratory, Fundación Investigación, Hospital General Universitario de Valencia, 46014 Valencia, Spain;
- Centro de Investigación Biomédica en Red de Cáncer (CIBEROnc), 28029 Madrid, Spain
- Department of Pathology, Universitat de València, 46003 Valencia, Spain
| | - Maria Lopez-Alvarez
- Institute of Biomedicine of Sevilla (IBIS, HUVR, CSIC, Universidad de Sevilla), 41013 Sevilla, Spain; (D.S.M.); (M.L.-A.); (I.C.-G.); (E.B.-A.); (N.H.)
| | - Andrea Martínez-Martínez
- Laboratory of Molecular Biology, Fundación Instituto Valenciano de Oncología, 46009 Valencia, Spain; (A.F.-S.); (A.M.-M.); (M.R.-C.); (R.L.-R.)
| | - Irene Carrasco-Garcia
- Institute of Biomedicine of Sevilla (IBIS, HUVR, CSIC, Universidad de Sevilla), 41013 Sevilla, Spain; (D.S.M.); (M.L.-A.); (I.C.-G.); (E.B.-A.); (N.H.)
- Medical Oncology Department, University Hospital Virgen del Rocio, 41013 Sevilla, Spain
| | - Marta Ramírez-Calvo
- Laboratory of Molecular Biology, Fundación Instituto Valenciano de Oncología, 46009 Valencia, Spain; (A.F.-S.); (A.M.-M.); (M.R.-C.); (R.L.-R.)
| | - Elena Blanco-Alcaina
- Institute of Biomedicine of Sevilla (IBIS, HUVR, CSIC, Universidad de Sevilla), 41013 Sevilla, Spain; (D.S.M.); (M.L.-A.); (I.C.-G.); (E.B.-A.); (N.H.)
| | - Raquel López-Reig
- Laboratory of Molecular Biology, Fundación Instituto Valenciano de Oncología, 46009 Valencia, Spain; (A.F.-S.); (A.M.-M.); (M.R.-C.); (R.L.-R.)
| | - Antonia Obrador-Hevia
- Group of Advanced Therapies and Biomarkers in Clinical Oncology, Institut d’Investigació Sanitària de les Illes Balears (IdISBa-IUNICS), 07120 Palma de Mallorca, Spain;
- Sequencing Unit, University Hospital Son Espases, 07120 Palma de Mallorca, Spain
| | - Regina Alemany
- Department of Biology, Balearic Islands University, 07122 Palma de Mallorca, Spain;
| | - Antonio Gutierrez
- Hematology Department, University Hospital Son Espases, 07120 Mallorca, Spain;
| | - Nadia Hindi
- Institute of Biomedicine of Sevilla (IBIS, HUVR, CSIC, Universidad de Sevilla), 41013 Sevilla, Spain; (D.S.M.); (M.L.-A.); (I.C.-G.); (E.B.-A.); (N.H.)
- Medical Oncology Department, University Hospital Virgen del Rocio, 41013 Sevilla, Spain
| | - Andres Poveda
- Medical Oncology Department, Fundación Instituto Valenciano de Oncología, 46009 Valencia, Spain;
| | - Jose A. Lopez-Guerrero
- Laboratory of Molecular Biology, Fundación Instituto Valenciano de Oncología, 46009 Valencia, Spain; (A.F.-S.); (A.M.-M.); (M.R.-C.); (R.L.-R.)
- Department of Basic Medical Sciences, School of Medicine, Catholic University of Valencia ‘San Vicente Martir’, 46001 Valencia, Spain
| | - Javier Martin-Broto
- Institute of Biomedicine of Sevilla (IBIS, HUVR, CSIC, Universidad de Sevilla), 41013 Sevilla, Spain; (D.S.M.); (M.L.-A.); (I.C.-G.); (E.B.-A.); (N.H.)
- Medical Oncology Department, University Hospital Virgen del Rocio, 41013 Sevilla, Spain
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Fattorini P, Forzato C, Tierno D, De Martino E, Azzalini E, Canzonieri V, Stanta G, Bonin S. A Novel HPLC-Based Method to Investigate on RNA after Fixation. Int J Mol Sci 2020; 21:ijms21207540. [PMID: 33066070 PMCID: PMC7588918 DOI: 10.3390/ijms21207540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/24/2020] [Accepted: 10/09/2020] [Indexed: 12/13/2022] Open
Abstract
RNA isolated from fixed and paraffin-embedded tissues is widely used in biomedical research and molecular pathology for diagnosis. In the present study, we have set-up a method based on high performance liquid chromatography (HPLC) to investigate the effects of different fixatives on RNA. By the application of the presented method, which is based on the Nuclease S1 enzymatic digestion of RNA extracts followed by a HPLC analysis, it is possible to quantify the unmodified nucleotide monophosphates (NMPs) in the mixture and recognize their hydroxymethyl derivatives as well as other un-canonical RNA moieties. The results obtained from a set of mouse livers fixed/embedded with different protocols as well from a set of clinical samples aged 0 to 30 years-old show that alcohol-based fixatives do not induce chemical modification of the nucleic acid under ISO standard recommendations and confirm that pre-analytical conditions play a major role in RNA preservation.
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Affiliation(s)
- Paolo Fattorini
- DSM-Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (P.F.); (D.T.); (E.D.M.); (E.A.); (V.C.); (G.S.)
| | - Cristina Forzato
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, 34127 Trieste, Italy;
| | - Domenico Tierno
- DSM-Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (P.F.); (D.T.); (E.D.M.); (E.A.); (V.C.); (G.S.)
- Doctorate of Nanotechnology, University of Trieste, 34100 Trieste, Italy
| | - Eleonora De Martino
- DSM-Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (P.F.); (D.T.); (E.D.M.); (E.A.); (V.C.); (G.S.)
| | - Eros Azzalini
- DSM-Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (P.F.); (D.T.); (E.D.M.); (E.A.); (V.C.); (G.S.)
| | - Vincenzo Canzonieri
- DSM-Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (P.F.); (D.T.); (E.D.M.); (E.A.); (V.C.); (G.S.)
- Pathology Unit, IRCCS CRO Aviano-National Cancer Institute, 33081 Aviano, Italy
| | - Giorgio Stanta
- DSM-Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (P.F.); (D.T.); (E.D.M.); (E.A.); (V.C.); (G.S.)
| | - Serena Bonin
- DSM-Department of Medical Sciences, University of Trieste, 34149 Trieste, Italy; (P.F.); (D.T.); (E.D.M.); (E.A.); (V.C.); (G.S.)
- Correspondence: ; Tel.: +39-040-399-3266
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Pre-analytics and tumor heterogeneity. N Biotechnol 2020; 55:30-35. [DOI: 10.1016/j.nbt.2019.09.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 09/19/2019] [Accepted: 09/29/2019] [Indexed: 12/11/2022]
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10
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Esteva-Socias M, Gómez-Romano F, Carrillo-Ávila JA, Sánchez-Navarro AL, Villena C. Impact of different stabilization methods on RT-qPCR results using human lung tissue samples. Sci Rep 2020; 10:3579. [PMID: 32108147 PMCID: PMC7046779 DOI: 10.1038/s41598-020-60618-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 01/20/2020] [Indexed: 02/06/2023] Open
Abstract
Aiming to increase the reproducibility of biomedical research results, biobanks obtain human tissues of the highest quality and carry out different storage methods adapted to the needs of analytical technique to be performed by the biomedical researchers. However, there is much controversy and little data concerning the real impact of different stabilization methods on tissue quality, integrity and functionality of derived biomolecules. The influence of four stabilization methods [RNAlater (RNL), snap freezing (SF), snap freezing using Optimal Cutting Tissue compound (SF-OCT) and formalin-fixed paraffin-embedded (FFPE)] on RNA quality and integrity was evaluated in paired samples of lung tissue. RNA integrity was evaluated through PCR-endpoint assays amplifying six fragments of different length of the HPRT1 gene and RNA Integrity Number (RIN). To evaluate the difference of tissue functionality among the stabilization methods tested, RT-qPCRs were performed focusing on the differential expression of the HPRT1, SNRPD3 and Jun genes. RNA from the samples preserved with the RNL or SF-OCT method showed better integrity compared to SF and FFPE, measured by PCR-endpoint and RT-qPCR assays. However, only statistically significant differences were observed between the RNA from FFPE and other stabilization methods when gene expression of HPRT1, SNRPD3 and Jun housekeeping genes were determined by RT-qPCR. For the three mentioned genes, Cq and RIN values were highly correlated. The present work describes the fragility of SF samples, being critical the moment just before RNA extraction, although further experiments of tissue RNA are needed. Standardization pre-analytic workflow can lead to improved reproducibility between biomedical research studies. The present study demonstrated clear evidences about the impact of the stabilization method on RNA derived from lung human tissue samples.
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Affiliation(s)
- Margalida Esteva-Socias
- Centro de Investigación Biomédica en Red in Respiratory Diseases (CIBERES), Plataforma Biobanco Pulmonar CIBERES, Hospital Universitari Son Espases, Palma, Spain
- Grupo de Inflamación, reparación y cáncer en enfermedades respiratorias, Institut d'Investigació Sanitària de les Illes Balears (IdISBa), Hospital Universitari Son Espases, Palma, Spain
- Spanish Biobank Network, Instituto de Salud Carlos III, Madrid, Spain
| | - Fernando Gómez-Romano
- Centro de Investigación Biomédica en Red in Respiratory Diseases (CIBERES), Plataforma Biobanco Pulmonar CIBERES, Hospital Universitari Son Espases, Palma, Spain
- Grupo de Inflamación, reparación y cáncer en enfermedades respiratorias, Institut d'Investigació Sanitària de les Illes Balears (IdISBa), Hospital Universitari Son Espases, Palma, Spain
- Spanish Biobank Network, Instituto de Salud Carlos III, Madrid, Spain
| | - José Antonio Carrillo-Ávila
- Spanish Biobank Network, Instituto de Salud Carlos III, Madrid, Spain
- Andalusian Public Health System Biobank, Granada. Instituto de Investigación Biosanitaria ibs. Granada. Complejo Universitario de Granada/Universidad de Granada, Granada, Spain
| | - Alicia Loreto Sánchez-Navarro
- Centro de Investigación Biomédica en Red in Respiratory Diseases (CIBERES), Plataforma Biobanco Pulmonar CIBERES, Hospital Universitari Son Espases, Palma, Spain
- Grupo de Inflamación, reparación y cáncer en enfermedades respiratorias, Institut d'Investigació Sanitària de les Illes Balears (IdISBa), Hospital Universitari Son Espases, Palma, Spain
- Spanish Biobank Network, Instituto de Salud Carlos III, Madrid, Spain
| | - Cristina Villena
- Centro de Investigación Biomédica en Red in Respiratory Diseases (CIBERES), Plataforma Biobanco Pulmonar CIBERES, Hospital Universitari Son Espases, Palma, Spain.
- Grupo de Inflamación, reparación y cáncer en enfermedades respiratorias, Institut d'Investigació Sanitària de les Illes Balears (IdISBa), Hospital Universitari Son Espases, Palma, Spain.
- Spanish Biobank Network, Instituto de Salud Carlos III, Madrid, Spain.
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Azzalini E, De Martino E, Fattorini P, Canzonieri V, Stanta G, Bonin S. Reliability of miRNA Analysis from Fixed and Paraffin-Embedded Tissues. Int J Mol Sci 2019; 20:ijms20194819. [PMID: 31569791 PMCID: PMC6801416 DOI: 10.3390/ijms20194819] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/23/2019] [Accepted: 09/26/2019] [Indexed: 11/23/2022] Open
Abstract
In clinical practice, patients’ tissues are fixed and paraffin-embedded in order to enable histological diagnosis. Nowadays, those tissues are also used for molecular characterization. Formalin is the most used fixative worldwide, and Bouin’s solution in some worldwide institutions. Among molecular targets, micro RNAs (miRNAs), the single-stranded non-coding RNAs comprised of 18 to 24 nucleotides, have been demonstrated to be resistant to fixation and paraffin-embedding processes, with consequent possible application in clinical practice. In the present study, let-7e-5p, miR-423-3p, miR-92a-1-5p, miR-30d-5p, miR-155-5p, miR-200a-3p, and miR-429 were investigated in formalin and matched Bouin’s solution-fixed tissues of high grade serous ovarian cancers by means of real-time and droplet digital PCR (ddPCR). Micro RNAs were detectable and analyzable in both formalin- and Bouin’s-fixed specimens, but on average, higher Ct values and lower copies/µL were found in Bouin’s-fixed samples. Data from formalin-fixed samples correlated significantly for most targets with Bouin’s ones, except for let-7e-5p and miR-155-5p. This study shows that miRNAs are analyzable in both formalin- and Bouin’s-fixed specimens, with the possibility, after proper data normalization, to compare miRNA-based data from formalin-fixed samples to those of Bouin’s-fixed ones.
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Affiliation(s)
- Eros Azzalini
- DSM-Department of Medical Sciences-University of Trieste, 34149 Trieste, Italy.
- Doctorate of Nanotechnology-University of Trieste, 34100 Trieste, Italy.
| | - Eleonora De Martino
- DSM-Department of Medical Sciences-University of Trieste, 34149 Trieste, Italy.
| | - Paolo Fattorini
- DSM-Department of Medical Sciences-University of Trieste, 34149 Trieste, Italy.
| | - Vincenzo Canzonieri
- DSM-Department of Medical Sciences-University of Trieste, 34149 Trieste, Italy.
- Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081 Aviano, Italy.
| | - Giorgio Stanta
- DSM-Department of Medical Sciences-University of Trieste, 34149 Trieste, Italy.
| | - Serena Bonin
- DSM-Department of Medical Sciences-University of Trieste, 34149 Trieste, Italy.
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Akahane T, Yamaguchi T, Kato Y, Yokoyama S, Hamada T, Nishida Y, Higashi M, Nishihara H, Suzuki S, Ueno S, Tanimoto A. Comprehensive validation of liquid-based cytology specimens for next-generation sequencing in cancer genome analysis. PLoS One 2019; 14:e0217724. [PMID: 31199826 PMCID: PMC6568385 DOI: 10.1371/journal.pone.0217724] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 05/07/2019] [Indexed: 12/20/2022] Open
Abstract
In addition to conventional cytology, liquid-based cytology (LBC) is also used for immunocytochemistry and gene analysis. However, an appropriate method to obtain high quality DNA for next-generation sequencing (NGS) using LBC specimens remains controversial. We determined the optimal conditions for fixation with an alcohol-based fixative for LBC and DNA extraction using cultured cancer cell lines and clinical specimens. The extracted DNA was processed for NGS after the DNA quality was confirmed based on the DNA concentration and degree of degradation. The optimal conditions for cultured cells to obtain high quality DNA were to fix the cells at a density of 6 × 103 or 2 × 104 cells/mL and to use the magnetic bead-based DNA extraction method. Even after storing the fixed cells for 90 days, DNA extracted using the above and other extraction kits, including membrane-based methods, did not undergo degradation. Furthermore, 5-year-old residual LBC samples demonstrated high DNA quality that was suitable for NGS. Furthermore, a cancer genome panel analysis was successfully performed with DNA extracted from cultured cells fixed at 6 × 103 cells/mL for 90 days, and with DNA from residual LBC samples even after 1 year of storage. Residual LBC samples may be a useful source of DNA for clinical NGS to promote genome-based cancer medicine.
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Affiliation(s)
- Toshiaki Akahane
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
- Center for Human Genome and Gene Analysis, Kagoshima University Hospital, Kagoshima, Japan
| | - Tomomi Yamaguchi
- Department of Pathology, Laboratory of Cancer Medical Science, Hokuto Hospital, Obihiro, Japan
| | - Yasutaka Kato
- Department of Pathology, Laboratory of Cancer Medical Science, Hokuto Hospital, Obihiro, Japan
| | - Seiya Yokoyama
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Taiji Hamada
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Yukari Nishida
- Department Surgical Pathology, Kagoshima University Hospital, Kagoshima, Japan
| | - Michiyo Higashi
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
- Department Surgical Pathology, Kagoshima University Hospital, Kagoshima, Japan
| | - Hiroshi Nishihara
- Department of Biology and Genetics, Laboratory of Cancer Medical Science, Hokuto Hospital, Obihiro, Japan
- Keio Cancer Center, Keio University School of Medicine, Tokyo, Japan
| | - Shinsuke Suzuki
- Department of Clinical Cancer Research, Kagoshima University Graduate School of Medical and Dental Sciences, 890–8544 Kagoshima, Japan
- Kagoshima University Hospital Cancer Center, Kagoshima University Hospital, Kagoshima, Japan
| | - Shinichi Ueno
- Department of Clinical Cancer Research, Kagoshima University Graduate School of Medical and Dental Sciences, 890–8544 Kagoshima, Japan
- Kagoshima University Hospital Cancer Center, Kagoshima University Hospital, Kagoshima, Japan
| | - Akihide Tanimoto
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
- Center for Human Genome and Gene Analysis, Kagoshima University Hospital, Kagoshima, Japan
- Department Surgical Pathology, Kagoshima University Hospital, Kagoshima, Japan
- * E-mail:
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13
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Mathieson W, Mommaerts K, Trouet JM, Mathay C, Guan P, Carithers LJ, Rohrer D, Valley DR, Blanski A, Jewell S, Moore HM, Betsou F. Cold Ischemia Score: An mRNA Assay for the Detection of Extended Cold Ischemia in Formalin-Fixed, Paraffin-Embedded Tissue. J Histochem Cytochem 2019; 67:159-168. [PMID: 30562131 PMCID: PMC6393842 DOI: 10.1369/0022155418819967] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/26/2018] [Indexed: 02/08/2023] Open
Abstract
Although there are thousands of formalin-fixed paraffin-embedded (FFPE) tissue blocks potentially available for scientific research, many are of questionable quality, partly due to unknown preanalytical variables. We analyzed FFPE tissue biospecimens as part of the National Cancer Institute (NCI) Biospecimen Preanalytical Variables program to identify mRNA markers denoting cold ischemic time. The mRNA was extracted from colon, kidney, and ovary cancer FFPE blocks (40 patients, 10-12 hr fixation time) with 1, 2, 3, and 12 hr cold ischemic times, then analyzed using qRT-PCR for 23 genes selected following a literature search. No genes tested could determine short ischemic times (1-3 hr). However, a combination of three unstable genes normalized to a more stable gene could generate a "Cold Ischemia Score" that could distinguish 1 to 3 hr cold ischemia from 12 hr cold ischemia with 62% sensitivity and 84% specificity.
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Affiliation(s)
| | | | | | | | - Ping Guan
- National Cancer Institute, Bethesda, Maryland
| | | | | | | | | | | | | | - Fay Betsou
- Integrated Biobank of Luxembourg, Luxembourg
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14
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Impact of storage conditions on the quality of nucleic acids in paraffin embedded tissues. PLoS One 2018; 13:e0203608. [PMID: 30192857 PMCID: PMC6128582 DOI: 10.1371/journal.pone.0203608] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 08/23/2018] [Indexed: 01/02/2023] Open
Abstract
RNA and DNA analyses from paraffin-embedded tissues (PET) are an important diagnostic tool for characterization of a disease, exploring biomarkers and treatment options. Since nucleic acids from formalin-fixed and paraffin-embedded (FFPE) tissue are of limited use for molecular analyses due to chemical modifications of biomolecules alternate, formalin-free fixation reagents such as the PAXgene Tissue system are of evolving interest. Furthermore, biomedical research and biomarker development critically relies on using long-term stored PET from medical archives or biobanks to correlate molecular features with long-term disease outcomes. We therefore performed a comparative study to evaluate the effect of long term storage of FFPE and PAXgene Tissue-fixed and paraffin-embedded (PFPE) tissue at different temperatures on nucleic acid stability and usability in PCR. Matched FFPE and PFPE human tissues from routine clinical setting or rat tissues from a highly controlled animal model were stored at room temperature and 4°C, as well as in case of animal tissues frozen at -20°C and -80°C. RNA and DNA were extracted in intervals for up to nine years, and examined for integrity, and usability in quantitative RT-PCR (RT-qPCR) or PCR (qPCR) assays. PET storage at room temperature led to a degradation of nucleic acids which was slowed down by storage at 4°C and prevented by storage at -20°C or -80°C. Degradation was associated with an amplicon length depending decrease of RT-qPCR and qPCR efficiency. Storage at 4°C improved amplifiability in RT-qPCR and qPCR profoundly. Chemically unmodified nucleic acids from PFPE tissue performed superior compared to FFPE tissue, regardless of storage time and temperature in both human and rat tissues. In conclusion molecular analyses from PET can be greatly improved by using a non-crosslinking fixative and storage at lower temperatures such as 4°C, which should be considered in prospective clinical studies.
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xMD-miRNA-seq to generate near in vivo miRNA expression estimates in colon epithelial cells. Sci Rep 2018; 8:9783. [PMID: 29955168 PMCID: PMC6023933 DOI: 10.1038/s41598-018-28198-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 06/19/2018] [Indexed: 01/09/2023] Open
Abstract
Accurate, RNA-seq based, microRNA (miRNA) expression estimates from primary cells have recently been described. However, this in vitro data is mainly obtained from cell culture, which is known to alter cell maturity/differentiation status, significantly changing miRNA levels. What is needed is a robust method to obtain in vivo miRNA expression values directly from cells. We introduce expression microdissection miRNA small RNA sequencing (xMD-miRNA-seq), a method to isolate cells directly from formalin fixed paraffin-embedded (FFPE) tissues. xMD-miRNA-seq is a low-cost, high-throughput, immunohistochemistry-based method to capture any cell type of interest. As a proof-of-concept, we isolated colon epithelial cells from two specimens and performed low-input small RNA-seq. We generated up to 600,000 miRNA reads from the samples. Isolated epithelial cells, had abundant epithelial-enriched miRNA expression (miR-192; miR-194; miR-200b; miR-200c; miR-215; miR-375) and overall similar miRNA expression patterns to other epithelial cell populations (colonic enteroids and flow-isolated colon epithelium). xMD-derived epithelial cells were generally not contaminated by other adjacent cells of the colon as noted by t-SNE analysis. xMD-miRNA-seq allows for simple, economical, and efficient identification of cell-specific miRNA expression estimates. Further development will enhance rapid identification of cell-specific miRNA expression estimates in health and disease for nearly any cell type using archival FFPE material.
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