1
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Guo Y, Wang W, Ye K, He L, Ge Q, Huang Y, Zhao X. Single-Nucleus RNA-Seq: Open the Era of Great Navigation for FFPE Tissue. Int J Mol Sci 2023; 24:13744. [PMID: 37762049 PMCID: PMC10530744 DOI: 10.3390/ijms241813744] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/28/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Single-cell sequencing (scRNA-seq) has revolutionized our ability to explore heterogeneity and genetic variations at the single-cell level, opening up new avenues for understanding disease mechanisms and cell-cell interactions. Single-nucleus RNA-sequencing (snRNA-seq) is emerging as a promising solution to scRNA-seq due to its reduced ionized transcription bias and compatibility with richer samples. This approach will provide an exciting opportunity for in-depth exploration of billions of formalin-fixed paraffin-embedded (FFPE) tissues. Recent advancements in single-cell/nucleus gene expression workflows tailored for FFPE tissues have demonstrated their feasibility and provided crucial guidance for future studies utilizing FFPE specimens. In this review, we provide a broad overview of the nuclear preparation strategies, the latest technologies of snRNA-seq applicable to FFPE samples. Finally, the limitations and potential technical developments of snRNA-seq in FFPE samples are summarized. The development of snRNA-seq technologies for FFPE samples will lay a foundation for transcriptomic studies of valuable samples in clinical medicine and human sample banks.
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Affiliation(s)
| | | | | | | | | | | | - Xiangwei Zhao
- State Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China; (Y.G.); (W.W.); (K.Y.); (L.H.); (Q.G.); (Y.H.)
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2
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Vucevic DD, Seidman MA, Mesaki K, Guan Z, Juvet S, Liu M, Keshavjee S, Murphy K. A Novel Tissue Preservation and Transport Solution as a Substitute for Formalin. J Transl Med 2023; 103:100198. [PMID: 37321542 DOI: 10.1016/j.labinv.2023.100198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/17/2023] Open
Abstract
Formalin, a common laboratory fixative, is a type 1 carcinogen; a biohazard with risks, environmental, disposal, and legal costs; and a chemical modifier of protein epitopes in tissues. A less-toxic tissue preservation method is therefore badly needed. We have developed a novel tissue preservation medium, Amber, composed of low-potassium dextran glucose, 10% honey, and 1% coconut oil. This study investigates Amber as compared with formalin with respect to the following aspects: (1) histologic preservation, (2) epitope integrity with immunohistochemistry (IHC) and immunofluorescence (IF), and (3) integrity of tissue RNA. Rat and human lung, liver, kidney, and heart tissues were collected and stored for 24 hours at 4 °C in Amber or formalin. The tissues were evaluated with hematoxylin and eosin; IHC: thyroid transcription factor, muscle-specific actin, hepatocyte-specific antigen, and common acute lymphoblastic leukemia antigen; and IF: VE-cadherin, vimentin, and muscle-specific actin. RNA quality upon extraction was also assessed. Amber demonstrated superior and/or noninferior performance in rat and human tissue evaluation with respect to standard techniques of histology, IHC, IF, and extracted RNA quality. Amber maintains high-quality morphology without compromising the ability to perform IHC and nucleic acid extraction. As such, Amber could be a safer and superior substitute to formalin for clinical tissue preservation for contemporary pathological examination.
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Affiliation(s)
- Diana D Vucevic
- Biomedical Engineering Institute, University of Toronto, Toronto, Ontario, Canada; Division of Thoracic Surgery and Latner Thoracic Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Michael A Seidman
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine & Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Kumi Mesaki
- Division of Thoracic Surgery and Latner Thoracic Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Zehong Guan
- Division of Thoracic Surgery and Latner Thoracic Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Stephen Juvet
- Biomedical Engineering Institute, University of Toronto, Toronto, Ontario, Canada; Division of Thoracic Surgery and Latner Thoracic Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada; Department of Surgery, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada; Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Mingyao Liu
- Division of Thoracic Surgery and Latner Thoracic Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada; Department of Surgery, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada; Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Shaf Keshavjee
- Biomedical Engineering Institute, University of Toronto, Toronto, Ontario, Canada; Division of Thoracic Surgery and Latner Thoracic Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada; Department of Surgery, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada; Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Kieran Murphy
- Joint Department of Medical Imaging, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.
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3
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Ball JB, McNulty CJ, Green-Fulgham SM, Dragavon JM, Correia Rocha IR, Finch MR, Prévost ED, Siddique II, Woodall BJ, Watkins LR, Baratta MV, Root DH. Combining RNAscope and immunohistochemistry to visualize inflammatory gene products in neurons and microglia. Front Mol Neurosci 2023; 16:1225847. [PMID: 37664240 PMCID: PMC10470653 DOI: 10.3389/fnmol.2023.1225847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/31/2023] [Indexed: 09/05/2023] Open
Abstract
A challenge for central nervous system (CNS) tissue analysis in neuroscience research has been the difficulty to codetect and colocalize gene and protein expression in the same tissue. Given the importance of identifying gene expression relative to proteins of interest, for example, cell-type specific markers, we aimed to develop a protocol to optimize their codetection. RNAscope fluorescent in situ hybridization (FISH) combined with immunohistochemistry (IHC) in fixed (CNS) tissue sections allows for reliable quantification of gene transcripts of interest within IHC-labeled cells. This paper describes a new method for simultaneous visualization of FISH and IHC in thicker (14-μm), fixed tissue samples, using spinal cord sections. This method's effectiveness is shown by the cell-type-specific quantification of two genes, namely the proinflammatory cytokine interleukin-1beta (IL-1b) and the inflammasome NLR family pyrin domain containing 3 (NLRP3). These genes are challenging to measure accurately using immunohistochemistry (IHC) due to the nonspecificity of available antibodies and the hard-to-distinguish, dot-like visualizations of the labeled proteins within the tissue. These measurements were carried out in spinal cord sections after unilateral chronic constriction injury of the sciatic nerve to induce neuroinflammation in the spinal cord. RNAscope is used to label transcripts of genes of interest and IHC is used to label cell-type specific antigens (IBA1 for microglia, NeuN for neurons). This combination allowed for labeled RNA transcripts to be quantified within cell-type specific boundaries using confocal microscopy and standard image analysis methods. This method makes it easy to answer empirical questions that are intractable with standard IHC or in situ hybridization alone. The method, which has been optimized for spinal cord tissue and to minimize tissue preparation time and costs, is described in detail from tissue collection to image analysis. Further, the relative expression changes in inflammatory genes NLRP3 and IL-1b in spinal cord microglia vs. neurons of somatotopically relevant laminae are described for the first time.
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Affiliation(s)
- Jayson B. Ball
- Department of Psychology and Neuroscience, Center for Neuroscience, University of Colorado Boulder, Boulder, CO, United States
| | - Connor J. McNulty
- Department of Psychology and Neuroscience, Center for Neuroscience, University of Colorado Boulder, Boulder, CO, United States
| | - Suzanne M. Green-Fulgham
- Department of Psychology and Neuroscience, Center for Neuroscience, University of Colorado Boulder, Boulder, CO, United States
| | - Joseph M. Dragavon
- Advanced Light Microscopy Core, Biofrontiers Institute, University of Colorado Boulder, Boulder, CO, United States
| | - Igor R. Correia Rocha
- Department of Psychology and Neuroscience, Center for Neuroscience, University of Colorado Boulder, Boulder, CO, United States
| | - Maggie R. Finch
- Department of Psychology and Neuroscience, Center for Neuroscience, University of Colorado Boulder, Boulder, CO, United States
| | - Emily D. Prévost
- Department of Psychology and Neuroscience, Center for Neuroscience, University of Colorado Boulder, Boulder, CO, United States
| | - Imaad I. Siddique
- Department of Psychology and Neuroscience, Center for Neuroscience, University of Colorado Boulder, Boulder, CO, United States
| | - Brodie J. Woodall
- Department of Psychology and Neuroscience, Center for Neuroscience, University of Colorado Boulder, Boulder, CO, United States
| | - Linda R. Watkins
- Department of Psychology and Neuroscience, Center for Neuroscience, University of Colorado Boulder, Boulder, CO, United States
| | - Michael V. Baratta
- Department of Psychology and Neuroscience, Center for Neuroscience, University of Colorado Boulder, Boulder, CO, United States
| | - David H. Root
- Department of Psychology and Neuroscience, Center for Neuroscience, University of Colorado Boulder, Boulder, CO, United States
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4
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Montero-Macías R, Coronado PJ, Robillard N, Veyer D, Villefranque V, Le Frére-Belda MA, Auberger E, Bitolog P, Stankovic I, Bélec L, Bats AS, Lécuru F, Péré H. HPV Molecular Genotyping as a Differential Diagnosis Tool in Cervical Cancer Metastasis. J Pers Med 2023; 13:jpm13020177. [PMID: 36836411 PMCID: PMC9961249 DOI: 10.3390/jpm13020177] [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: 12/30/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Differentiating metastatic cervical cancer from another primary tumor can be difficult in patients with a history of cervical cancer and a distant lesion. The use of routine HPV molecular detection and genotyping tests could help in these cases. The objective of this study was to identify if an easy-to-use HPV molecular genotyping assay would allow differentiating between HPV tumor metastasis and a new independent primary non-HPV-induced tumor. MATERIALS AND METHODS Between 2010 and 2020, we identified patients with a primary cervical carcinoma who also had another secondary lesion. This identification included a clinical and histologic differential diagnosis of metastatic cervical cancer versus a new primary cancer or metastatic cancer from another site. We used a routine multiplex real-time PCR (rt-PCR) AnyplexTM II HPV28 (Seegene, Seoul, Republic of Korea) to detect the high-risk (HR)-HPV genome in the distant lesions in these patients. RESULTS Eight cases of cervical cancer with a new secondary lesion were identified. In seven, HR-HPV DNA was detected in the biopsy of the distant lesion, which confirmed the diagnosis of cervical cancer metastasis. In the remaining case, no HPV was detected in the secondary lung biopsy, confirming the diagnosis of new primary lung cancer. CONCLUSION Our results pave the way for HPV molecular genotyping use in cases of newly diagnosed distant lesions in patients with a history of HPV cervical neoplasia by using a routine diagnosis process to complete the clinical and histologic differential diagnosis when confronted with ambiguous situations.
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Affiliation(s)
- Rosa Montero-Macías
- Obstetrics and Gynecology Department, Centre Hospitalier Simone Veil, 95602 Eaubonne, France
- Complutense University of Madrid, 28223 Madrid, Spain
| | - Pluvio J. Coronado
- Women’s Health Institute José Botella Llusiá, Fundación de Investigación del Hospital Clínico San Carlos (IdISSC), Universidad Complutense, 28040 Madrid, Spain
| | - Nicolas Robillard
- Virology Laboratory, Georges Pompidou European Hospital, 75015 Paris, France
| | - David Veyer
- Virology Laboratory, Georges Pompidou European Hospital, 75015 Paris, France
- INSERM, Functional Genomics of Solid Tumors (FunGeST), Centre de Recherche des Cordeliers, Université de Paris and Sorbonne Université, 75013 Paris, France
| | - Vincent Villefranque
- Obstetrics and Gynecology Department, Centre Hospitalier Simone Veil, 95602 Eaubonne, France
| | | | | | - Pauline Bitolog
- Pathology Department, Simone Veil Hospital, 95600 Eaubonne, France
| | - Ivana Stankovic
- Pathology Department, Georges Pompidou European Hospital, 75015 Paris, France
| | - Laurent Bélec
- Virology Laboratory, Georges Pompidou European Hospital, 75015 Paris, France
- Faculty of Medicine, Paris University, 75015 Paris, France
| | - Anne-Sophie Bats
- Faculty of Medicine, Paris University, 75015 Paris, France
- Gynecologic and Breast Oncologic Surgery Department, Georges Pompidou European Hospital, 75015 Paris, France
| | - Fabrice Lécuru
- Faculty of Medicine, Paris University, 75015 Paris, France
- Breast, Gynecology and Reconstructive Surgery Unit, Curie Institute, 75005 Paris, France
| | - Hélène Péré
- Virology Laboratory, Georges Pompidou European Hospital, 75015 Paris, France
- Faculty of Medicine, Paris University, 75015 Paris, France
- Correspondence:
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5
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Mena J, Ariyama N, Navarro C, Quezada M, Brevis C, Rojas D, Medina RA, Brito B, Ruiz Á, Neira V. Ubiquitous influenza A virus in Chilean swine before the H1N1pdm09 introduction. Transbound Emerg Dis 2021; 68:3174-3179. [PMID: 34288514 PMCID: PMC8684045 DOI: 10.1111/tbed.14243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 07/16/2021] [Indexed: 12/16/2022]
Abstract
Influenza A virus (IAV) was a neglected swine pathogen in South America before the 2009 H1N1 pandemic (A(H1N1)pdm2009). The A(H1N1)pdm2009 strain has widely spread among the Chilean swine population and co-circulates with endemic H1N2 and H3N2 viruses. The presence of IAV as a swine pathogen in Chilean swine before the 2009 pandemic is unknown. To understand the IAV in swine prior to 2009, aY retrospective study of samples from pigs affected with respiratory diseases was conducted. Ninety formalin-fixed and paraffin-embedded lung tissues belonging to 21 intensive pig production companies located in five different administrative regions of Chile, collected between 2005 and 2008, were evaluated. The tissues were tested by immunohistochemistry (IHC), identifying that 9 out of 21 farms (42.8%) and 31 out of 90 (34.4%) samples were IAV positive. Only three out of the 31 IHC-positive samples were positive upon RNA extraction and rtRT-PCR analysis. Partial nucleotide sequences were obtained from one sample and characterized as an H3N2 subtype closely related to a human seasonal H3N2 IAVs that circulated globally in the mid-90s. These results indicate that IAV was circulating in swine before 2009 and highlight the value of conducting retrospective studies through genomic strategies to analyse historical samples.
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Affiliation(s)
- Juan Mena
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Universidad de Chile, Santiago, Chile
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
- Animales y Ambientes (ICA3), Instituto de Ciencias Agroalimentarias, Universidad de O'Higgins, San Fernando, Chile
| | - Naomi Ariyama
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Camila Navarro
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Manuel Quezada
- Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile
| | - Cristina Brevis
- Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile
| | - Daniela Rojas
- Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile
| | - Rafael A Medina
- Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Barbara Brito
- The ithree institute - University of Technology Sydney, Sydney, New South Wales, Australia
| | - Álvaro Ruiz
- Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile
| | - Victor Neira
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
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6
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Against All Odds: RNA Extraction From Different Protocols Adapted to Formalin-fixed Paraffin-embedded Tissue. Appl Immunohistochem Mol Morphol 2021; 28:403-410. [PMID: 31135444 DOI: 10.1097/pai.0000000000000772] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
For the preservation of tissue samples, formalin fixation followed by paraffin embedding (FFPE) has been the method of choice for decades, mainly because it maintains the morphologic characteristics of the original tissue particularly preserved, as well as its genetic material. FFPE cells can be used to perform molecular tests, such as conventional (c) or quantitative (q) reverse transcriptase polymerase chain reaction (RT-PCR), in retrospective investigations. However, extracting RNA from archived FFPE tissues is a challenging procedure, as it requires time and the use of complex extraction methods. As specific FFPE extraction methods are not always available in the laboratories, the objective of this study was to evaluate the performance of a method based on phenol-chloroform (PC) and 2 commercial methods for RNA extraction, adapting their protocols for FFPE tissues. For this study, a pool of FFPE tissues underwent RNA extraction by PC, QIAmp Viral RNA Mini, and RNeasy Mini Kit. Both the RT-cPCR and the RT-qPCR results were favorable, demonstrating the viability of the RNA. As these results expanded the alternatives for low-budget FFPE extraction, the choice of the ideal method to be used will depend on the availability of reagents and kits.
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7
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Toohey-Kurth KL, Mulrooney DM, Hinkley S, Lea Killian M, Pedersen JC, Bounpheng MA, Pogranichniy R, Bolin S, Maes R, Tallmadge RL, Goodman LB, Crossley BM. Best practices for performance of real-time PCR assays in veterinary diagnostic laboratories. J Vet Diagn Invest 2020; 32:815-825. [PMID: 32996402 PMCID: PMC7649542 DOI: 10.1177/1040638720962076] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The exquisite sensitivity of in vitro amplification assays such as real-time polymerase chain reaction (rtPCR) requires the establishment of thorough and robust laboratory practices. To this end, an American Association of Veterinary Laboratory Diagnosticians (AAVLD) committee of subject matter experts was convened to develop a set of best practices for performance of nucleic acid amplification assays. Consensus advice for the performance of preanalytical, analytical, and postanalytical steps is presented here, along with a review of supporting literature.
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Affiliation(s)
- Kathy L. Toohey-Kurth
- California Animal Health and Food Safety Laboratory, University of California–Davis, San Bernardino
| | - Donna M. Mulrooney
- Oregon Veterinary Diagnostic Laboratory, Oregon State University, Corvallis, OR
| | | | | | | | | | - Roman Pogranichniy
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS
| | - Steve Bolin
- Veterinary Diagnostic Laboratory, Michigan State University, Lansing, MI
| | - Roger Maes
- Veterinary Diagnostic Laboratory, Michigan State University, Lansing, MI
| | | | - Laura B. Goodman
- Population Medicine & Diagnostic Sciences, Cornell University, Ithaca, NY
| | - Beate M. Crossley
- California Animal Health and Food Safety Laboratory, University of California–Davis, San Bernardino and Davis branches, CA
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8
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Guerini-Rocco E, Taormina SV, Vacirca D, Ranghiero A, Rappa A, Fumagalli C, Maffini F, Rampinelli C, Galetta D, Tagliabue M, Ansarin M, Barberis M. SARS-CoV-2 detection in formalin-fixed paraffin-embedded tissue specimens from surgical resection of tongue squamous cell carcinoma. J Clin Pathol 2020; 73:754-757. [PMID: 32366599 PMCID: PMC7431818 DOI: 10.1136/jclinpath-2020-206635] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 04/17/2020] [Accepted: 04/17/2020] [Indexed: 12/12/2022]
Abstract
In the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, pathologists can be exposed to infection handling surgical specimens. Guidelines related to safety procedures in the laboratory have been released. However, there is a lack of studies performed on biopsy and surgical resection specimens. Here we report the detection of SARS-CoV-2 in formalin-fixed paraffin-embedded samples from surgical resection of tongue squamous cell carcinoma of a patient who developed COVID-19 postsurgery. RNA of SARS-CoV-2 strain was detected in the tumour and the normal submandibular gland samples using real-time PCR-based assay. No viral RNA was found in metastatic and reactive lymph nodes. We demonstrated that SARS-CoV-2 RNA can be detected in routine histopathological samples even before COVID-19 disease development. These findings may give important information on the possible sites of infection or virus reservoir, and highlight the necessity of proper handling and fixation before sample processing.
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Affiliation(s)
- Elena Guerini-Rocco
- Division of Pathology and Laboratory Medicine, IEO, European Institute of Oncology, IRCCS, Milano, Italy
- Department of Oncology and Hemato-Oncology, University of Milano, Milano, Italy
| | - Sergio Vincenzo Taormina
- Division of Pathology and Laboratory Medicine, IEO, European Institute of Oncology, IRCCS, Milano, Italy
| | - Davide Vacirca
- Division of Pathology and Laboratory Medicine, IEO, European Institute of Oncology, IRCCS, Milano, Italy
| | - Alberto Ranghiero
- Division of Pathology and Laboratory Medicine, IEO, European Institute of Oncology, IRCCS, Milano, Italy
| | - Alessandra Rappa
- Division of Pathology and Laboratory Medicine, IEO, European Institute of Oncology, IRCCS, Milano, Italy
| | - Caterina Fumagalli
- Division of Pathology and Laboratory Medicine, IEO, European Institute of Oncology, IRCCS, Milano, Italy
| | - Fausto Maffini
- Division of Pathology and Laboratory Medicine, IEO, European Institute of Oncology, IRCCS, Milano, Italy
| | - Cristiano Rampinelli
- Division of Radiology, IEO, European Institute of Oncology, IRCCS, Milano, Italy
| | - Domenico Galetta
- Division of Thoracic Surgery, IEO, European Institute of Oncology, IRCCS, Milano, Italy
| | - Marta Tagliabue
- Division of Otolaryngology and Head-Neck Surgery, IEO, European Institute of Oncology, IRCCS, Milano, Italy
| | - Mohssen Ansarin
- Division of Otolaryngology and Head-Neck Surgery, IEO, European Institute of Oncology, IRCCS, Milano, Italy
| | - Massimo Barberis
- Division of Pathology and Laboratory Medicine, IEO, European Institute of Oncology, IRCCS, Milano, Italy
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9
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Bain W, Lee JS, Watson AM, Stitt-Fischer MS. Practical Guidelines for Collection, Manipulation and Inactivation of SARS-CoV-2 and COVID-19 Clinical Specimens. ACTA ACUST UNITED AC 2020; 93:e77. [PMID: 32502333 PMCID: PMC7300551 DOI: 10.1002/cpcy.77] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
SARS-CoV-2 is a novel coronavirus that causes the acute respiratory disease-Coronavirus disease 2019 (COVID-19)-which has led to a global health crisis. Currently, no prophylactics or therapies exist to control virus spread or mitigate the disease. Thus, the risk of infection for physicians and scientists is high, requiring work to be conducted in Biosafety Level-3 (BSL-3) facilities if virus will be isolated or propagated. However, inactivation of the virus can enable safe handling at a reduced biosafety level, making samples accessible to a diverse array of institutions and investigators. Institutions of all types have an immediate need for guidelines that outline safe collection, handling, and inactivation of samples suspected to contain active virus. Here we provide a practical guide for physicians and researchers wishing to work with materials from patients who are COVID-19 positive or suspected positive. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Practical guidelines for the safe collection and handling of specimens collected from COVID-19 and suspected COVID-19 patients Basic Protocol 2: Inactivating SARS-CoV-2.
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Affiliation(s)
- William Bain
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Janet S Lee
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Alan M Watson
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Molly S Stitt-Fischer
- Department of Environmental Health and Safety, University of Pittsburgh, Pittsburgh, Pennsylvania
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10
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Gottdenker NL, Gregory CR, Ard MB, Lorenz WW, Nilsen RA, Ritchie BW. Histopathologic Changes, Ultrastructure, and Molecular Characterization of an Adenovirus in a Sun Conure ( Aratinga solstitialis). Avian Dis 2020; 63:531-538. [PMID: 31967440 DOI: 10.1637/aviandiseases-d-19-00080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 05/21/2019] [Indexed: 11/05/2022]
Abstract
In this case report, we describe the pathologic changes and the ultrastructural and molecular characteristics of an adenovirus in a sun conure (Aratinga solstitialis) that presented with a history of sudden death. On histologic examination, there was multifocal hepatic and splenic necrosis. Within some hepatocytes and unidentified cells in the spleen, renal interstitial fibroblasts, and ovarian stroma were intranuclear amphophilic inclusion bodies. Electron microscopy of affected tissue showed intranuclear icosahedral viral particles with an inner capsid (29.2-33.8 nm in diameter) and an outer capsid (70.2-71.7 nm in diameter). Next-generation sequencing and BLAST analysis of complementary DNA synthesized from RNA extracted from formalin-fixed tissues showed an adenovirus, designated sun conure adenovirus (SCAdv). A DNA in situ hybridization (ISH) probe, constructed from the SCAdv and similar sequences from GenBank, was also positive in the intranuclear inclusion bodies, whereas standard ISH for psittacine adenovirus 1 was negative. These results show that ancillary diagnostic testing, such as next-generation sequencing, even using formalin-fixed, paraffin-embedded tissues, along with ISH, can be useful in identifying additional, unknown viruses that show similar pathology to commonly known viruses but do not show up as positive on routine diagnostic tests.
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Affiliation(s)
- N L Gottdenker
- Department of Veterinary Pathology, The University of Georgia, Athens, GA 30602,
| | - C R Gregory
- Infectious Disease Laboratory, The University of Georgia, Athens, GA 30602
| | - M B Ard
- Department of Veterinary Pathology, The University of Georgia, Athens, GA 30602
| | - W W Lorenz
- Institute of Bioinformatics, The University of Georgia, Athens, GA 30602
| | - R A Nilsen
- Georgia Genomics and Bioinformatics Core, The University of Georgia, Athens, GA 30602
| | - B W Ritchie
- Infectious Disease Laboratory, The University of Georgia, Athens, GA 30602
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11
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Bertran K, Pantin-Jackwood MJ, Criado MF, Lee DH, Balzli CL, Spackman E, Suarez DL, Swayne DE. Pathobiology and innate immune responses of gallinaceous poultry to clade 2.3.4.4A H5Nx highly pathogenic avian influenza virus infection. Vet Res 2019; 50:89. [PMID: 31675983 PMCID: PMC6824115 DOI: 10.1186/s13567-019-0704-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/27/2019] [Indexed: 11/10/2022] Open
Abstract
In the 2014-2015 Eurasian lineage clade 2.3.4.4A H5 highly pathogenic avian influenza (HPAI) outbreak in the U.S., backyard flocks with minor gallinaceous poultry and large commercial poultry (chickens and turkeys) operations were affected. The pathogenesis of the first H5N8 and reassortant H5N2 clade 2.3.4.4A HPAI U.S. isolates was investigated in six gallinaceous species: chickens, Japanese quail, Bobwhite quail, Pearl guinea fowl, Chukar partridges, and Ring-necked pheasants. Both viruses caused 80-100% mortality in all species, except for H5N2 virus that caused 60% mortality in chickens. The surviving challenged birds remained uninfected based on lack of clinical disease and lack of seroconversion. Among the infected birds, chickens and Japanese quail in early clinical stages (asymptomatic and listless) lacked histopathologic findings. In contrast, birds of all species in later clinical stages (moribund and dead) had histopathologic lesions and systemic virus replication consistent with HPAI virus infection in gallinaceous poultry. These birds had widespread multifocal areas of necrosis, sometimes with heterophilic or lymphoplasmacytic inflammatory infiltrate, and viral antigen in parenchymal cells of most tissues. In general, lesions and antigen distribution were similar regardless of virus and species. However, endotheliotropism was the most striking difference among species, with only Pearl guinea fowl showing widespread replication of both viruses in endothelial cells of most tissues. The expression of IFN-γ and IL-10 in Japanese quail, and IL-6 in chickens, were up-regulated in later clinical stages compared to asymptomatic birds.
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Affiliation(s)
- Kateri Bertran
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, 30605, USA.,IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Mary J Pantin-Jackwood
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, 30605, USA
| | - Miria F Criado
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, 30605, USA
| | - Dong-Hun Lee
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, 30605, USA.,Department of Pathobiology & Veterinary Science, University of Connecticut, Storrs, CT, 06269, USA
| | - Charles L Balzli
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, 30605, USA.,Battelle National Biodefense Institute, National Biodefense Analysis and Countermeasures Center, 8300 Research PI, Fort Detrick, MD, 21702, USA
| | - Erica Spackman
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, 30605, USA
| | - David L Suarez
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, 30605, USA
| | - David E Swayne
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, 30605, USA.
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Kawanami AE, Oliveira JPD, Arenales A, Crossley B, Woods LW, Duarte JM, Werther K. Detection of bluetongue virus in Brazilian cervids in São Paulo state. PESQUISA VETERINÁRIA BRASILEIRA 2018. [DOI: 10.1590/1678-5150-pvb-4550] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
ABSTRACT: Viral hemorrhagic diseases in cervids occur worldwide and include epizootic hemorrhagic disease (EHD), bluetongue (BT), and adenoviral hemorrhagic disease (AHD). Since gross lesions in all three hemorrhagic diseases are identical (hemorrhagic enteropathy, pulmonary edema, systemic petechial and suffusion hemorrhages), it is necessary to use accurate techniques for a definitive etiologic diagnosis. Archival material (paraffin blocks) at the Department of Veterinary Pathology of FCAV - Unesp was reviewed for lesions of hemorrhagic disease and 42 captive and free-living Brazilian deer were selected to include in this study. Paraffin-embedded tissues were evaluated using immunohistochemistry and tested negative for adenovirus. Using real time RT-PCR, EHD virus was not detected in paraffin-embedded tissues in any of the cases evaluated. The same technique was used for detection of BT virus and seven positive animals (16,66%) were confirmed after agarose 4% gel electrophoresis and gene sequencing. The main macroscopic changes observed in the positive animals were hemorrhagic intestinal contents, reddish mucous membrane of the gastrointestinal tract, ulcers on tongue and petechiae in various organs. Microscopic changes observed were lymphocytic inflammatory infiltrate in liver, kidney and lungs, hemorrhage, and congestion in various organs. All positive cases were from captive animals, three females (two young and one adult), and four young males. This study demonstrates that the bluetongue virus is involved in hemorrhagic disease outbreaks of deer in Brazil.
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13
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Mubemba B, Thompson P, Odendaal L, Coetzee P, Venter E. Evaluation of positive Rift Valley fever virus formalin-fixed paraffin embedded samples as a source of sequence data for retrospective phylogenetic analysis. J Virol Methods 2017; 243:10-14. [DOI: 10.1016/j.jviromet.2017.01.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 01/06/2017] [Accepted: 01/06/2017] [Indexed: 10/20/2022]
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The Utilization of Formalin Fixed-Paraffin-Embedded Specimens in High Throughput Genomic Studies. Int J Genomics 2017; 2017:1926304. [PMID: 28246590 PMCID: PMC5299160 DOI: 10.1155/2017/1926304] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 01/09/2017] [Indexed: 01/09/2023] Open
Abstract
High throughput genomic assays empower us to study the entire human genome in short time with reasonable cost. Formalin fixed-paraffin-embedded (FFPE) tissue processing remains the most economical approach for longitudinal tissue specimen storage. Therefore, the ability to apply high throughput genomic applications to FFPE specimens can expand clinical assays and discovery. Many studies have measured the accuracy and repeatability of data generated from FFPE specimens using high throughput genomic assays. Together, these studies demonstrate feasibility and provide crucial guidance for future studies using FFPE specimens. Here, we summarize the findings of these studies and discuss the limitations of high throughput data generated from FFPE specimens across several platforms that include microarray, high throughput sequencing, and NanoString.
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Dambach DM, Misner D, Brock M, Fullerton A, Proctor W, Maher J, Lee D, Ford K, Diaz D. Safety Lead Optimization and Candidate Identification: Integrating New Technologies into Decision-Making. Chem Res Toxicol 2015; 29:452-72. [DOI: 10.1021/acs.chemrestox.5b00396] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Donna M. Dambach
- Department of Safety Assessment, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
| | - Dinah Misner
- Department of Safety Assessment, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
| | - Mathew Brock
- Department of Safety Assessment, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
| | - Aaron Fullerton
- Department of Safety Assessment, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
| | - William Proctor
- Department of Safety Assessment, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
| | - Jonathan Maher
- Department of Safety Assessment, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
| | - Dong Lee
- Department of Safety Assessment, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
| | - Kevin Ford
- Department of Safety Assessment, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
| | - Dolores Diaz
- Department of Safety Assessment, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
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Xiao Y, Sheng ZM, Taubenberger JK. Isolating Viral and Host RNA Sequences from Archival Material and Production of cDNA Libraries for High-Throughput DNA Sequencing. ACTA ACUST UNITED AC 2015; 37:1E.8.1-16. [PMID: 26344216 DOI: 10.1002/9780471729259.mc01e08s37] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The vast majority of surgical biopsy and post-mortem tissue samples are formalin-fixed and paraffin-embedded (FFPE), but this process leads to RNA degradation that limits gene expression analysis. As an example, the viral RNA genome of the 1918 pandemic influenza A virus was previously determined in a 9-year effort by overlapping RT-PCR from post-mortem samples. Using the protocols described here, the full genome of the 1918 virus was determined at high coverage in one high-throughput sequencing run of a cDNA library derived from total RNA of a 1918 FFPE sample after duplex-specific nuclease treatments. This basic methodological approach should assist in the analysis of FFPE tissue samples isolated over the past century from a variety of infectious diseases.
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Affiliation(s)
- Yongli Xiao
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Zong-Mei Sheng
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Jeffery K Taubenberger
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
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Kotani O, Iwata‐Yoshikawa N, Suzuki T, Sato Y, Nakajima N, Koike S, Iwasaki T, Sata T, Yamashita T, Minagawa H, Taguchi F, Hasegawa H, Shimizu H, Nagata N. Establishment of a panel of in-house polyclonal antibodies for the diagnosis of enterovirus infections. Neuropathology 2015; 35:107-21. [PMID: 25263613 PMCID: PMC7168124 DOI: 10.1111/neup.12171] [Citation(s) in RCA: 6] [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: 08/24/2014] [Accepted: 09/02/2014] [Indexed: 11/30/2022]
Abstract
The aim of this study was to establish a reliable method of virus detection for the diagnosis of critical enterovirus infections such as acute infective encephalitis, encephalomyelitis and myocarditis. Because histopathological and immunohistochemical analyses of paraffin-embedded tissues play an important role in recognizing infectious agents in tissue samples, six in-house polyclonal antibodies raised against three representative enteroviruses using an indirect immunofluorescence assay and immunohistochemistry were examined. This panel of polyclonal antibodies recognized three serotypes of enterovirus. Two of the polyclonal antibodies were raised against denatured virus particles from enterovirus A71, one was raised against the recombinant VP1 protein of coxsackievirus B3, and the other for poliovirus type 1 were raised against denatured virus particles, the recombinant VP1 protein and peptide 2C. Western blot analysis revealed that each of these antibodies recognized the corresponding viral antigen and none cross-reacted with non-enteroviruses within the family Picornaviridae. However, all cross-reacted to some extent with the antigens derived from other serotypes of enterovirus. Indirect immunofluorescence assay and immunohistochemistry revealed that the virus capsid and non-structural proteins were localized in the cytoplasm of affected culture cells, and skeletal muscles and neurons in neonatal mice experimentally-infected with human enterovirus. The antibodies also recognized antigens derived from recent clinical isolates of enterovirus A71, coxsackievirus B3 and poliovirus. In addition, immunohistochemistry revealed that representative antibodies tested showed the same recognition pattern according to each serotype. Thus, the panel of in-house anti-enterovirus polyclonal antibodies described herein will be an important tool for the screening and pathological diagnosis for enterovirus infections, and may be useful for the classification of different enterovirus serotypes, including coxsackieviruses A and B, echoviruses, enterovirus A71 and poliovirus.
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Affiliation(s)
- Osamu Kotani
- Department of PathologyNational Institute of Infectious DiseasesAichiJapan
- Department of Virology and Viral InfectionsFaculty of Veterinary MedicineNippon Veterinary and Life Science UniversityAichiJapan
| | | | - Tadaki Suzuki
- Department of PathologyNational Institute of Infectious DiseasesAichiJapan
| | - Yuko Sato
- Department of PathologyNational Institute of Infectious DiseasesAichiJapan
| | - Noriko Nakajima
- Department of PathologyNational Institute of Infectious DiseasesAichiJapan
| | - Satoshi Koike
- Neurovirology ProjectTokyo Metropolitan Institute of Medical ScienceAichiJapan
| | - Takuya Iwasaki
- Department of PathologyNational Institute of Infectious DiseasesAichiJapan
| | - Tetsutaro Sata
- Department of PathologyNational Institute of Infectious DiseasesAichiJapan
| | - Teruo Yamashita
- Department of Microbiology and Medical ZoologyAichi Prefectural Institute of Public HealthAichiJapan
| | - Hiroko Minagawa
- Department of Microbiology and Medical ZoologyAichi Prefectural Institute of Public HealthAichiJapan
| | - Fumihiro Taguchi
- Department of Virology and Viral InfectionsFaculty of Veterinary MedicineNippon Veterinary and Life Science UniversityAichiJapan
| | - Hideki Hasegawa
- Department of PathologyNational Institute of Infectious DiseasesAichiJapan
| | - Hiroyuki Shimizu
- Department of Virology IINational Institute of Infectious DiseasesAichiJapan
| | - Noriyo Nagata
- Department of PathologyNational Institute of Infectious DiseasesAichiJapan
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Wang Z, Lebron JA, Wolf JJ. Reliable quantification of mRNA in archived formalin-fixed tissue with or without paraffin embedding. J Pharmacol Toxicol Methods 2014; 71:103-9. [PMID: 25280797 DOI: 10.1016/j.vascn.2014.09.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 09/20/2014] [Accepted: 09/22/2014] [Indexed: 12/19/2022]
Abstract
INTRODUCTION Formalin fixation and paraffin embedding (FFPE) is a standard method for tissue sample storage and preservation in pathology archives. The Reverse Transcriptase Quantitative Polymerase Chain Reaction (RT-qPCR) is a useful method for gene expression analysis, but its sensitivity is significantly decreased in FFPE tissue due to the fixation process. This process results in chemical modifications of RNA, cross-links proteins to RNA, and degrades RNA in these archived samples, hindering the reverse transcription step of the conventional RT-pPCR method and preventing generation of a cDNA that is long enough for the subsequent quantitative PCR step. METHODS In this study, we used a multi-species RT-qPCR method originally developed to detect mRNA in tissue homogenate samples (Wang et al., 2011) and applied it to effectively detect a specific mRNA in formalin-fixed tissues with or without paraffin-embedding by targeting mRNA sequences as short as 24 nucleotides. RESULTS Target sizes ranging from 24 to 91 nucleotides were evaluated using this multi-species RT-qPCR assay. Data generated with FFPE tissues demonstrated that use of short target sequences relieved the dependence on RNA quality and could reliably quantify mRNA. This method was highly sensitive, reproducible, and had a dynamic range of five orders of magnitude. Importantly, this method could quantify mRNA in prolonged formalin-fixed and FFPE tissue, where conventional RT-qPCR assays failed. Moreover, a similar result for small interfering RNA (siRNA)-mediated Apob mRNA knockdown was obtained from tissues fixed in formalin solution for 3months to 4years, and was found to be comparable to results obtained with frozen liver tissues. DISCUSSION Therefore, the method presented here allows for preclinical and clinical retrospective and prospective studies on mRNA derived from archived FFPE and prolonged formalin-fixed tissue.
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Affiliation(s)
- Zhibin Wang
- Department of Safety Assessment & Laboratory Animal Resources, Merck Research Laboratories, Merck & Co, Inc., 770 Sumneytown Pike, West Point, PA 19486, USA
| | - Jose A Lebron
- Department of Safety Assessment & Laboratory Animal Resources, Merck Research Laboratories, Merck & Co, Inc., 770 Sumneytown Pike, West Point, PA 19486, USA
| | - Jayanthi J Wolf
- Department of Safety Assessment & Laboratory Animal Resources, Merck Research Laboratories, Merck & Co, Inc., 770 Sumneytown Pike, West Point, PA 19486, USA.
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High rate of chronic villitis in placentas of pregnancies complicated by influenza A/H1N1 infection. Infect Dis Obstet Gynecol 2014; 2014:768380. [PMID: 24693211 PMCID: PMC3947755 DOI: 10.1155/2014/768380] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 12/30/2013] [Accepted: 01/02/2014] [Indexed: 11/17/2022] Open
Abstract
INTRODUCTION Pandemic influenza A/H1N1 infection during pregnancy has a negative impact on several aspects of pregnancy outcome. As yet, no elucidating mechanism has been revealed for these effects. We investigated whether placentas of pregnancies complicated by 2009 influenza A/H1N1 infection demonstrated an increased rate of chronic villitis and whether this villitis was caused by influenza virus. METHODS We performed a cohort study on 145 pregnant outpatients during the 2009-2010 influenza A H1N1 pandemic. The placentas of patients with influenza infection were examined for histologic signs of chronic villitis. In case of villitis, polymerase chain reaction (PCR) on influenza virus was performed on placental tissue. RESULTS 29 patients had influenza infection. Placentas of 15 of these patients were collected and examined. In 7 cases (47%) chronic villitis was detected. Placental weight and birth weight of the neonates did not differ between cases with and without chronic villitis. In all cases PCR was negative for influenza. CONCLUSION In our series, chronic villitis was present in a high proportion of placentas of pregnancies complicated by 2009 influenza A/H1N1 infection. We could not demonstrate the presence of influenza virus in placental tissue.
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Maes RK, Langohr IM, Wise AG, Smedley RC, Thaiwong T, Kiupel M. Beyond H&E: integration of nucleic acid-based analyses into diagnostic pathology. Vet Pathol 2013; 51:238-56. [PMID: 24129897 DOI: 10.1177/0300985813505878] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Veterinary pathology of infectious, particularly viral, and neoplastic diseases has advanced significantly with the advent of newer molecular methodologies that can detect nucleic acid of infectious agents within microscopic lesions, differentiate neoplastic from nonneoplastic cells, or determine the suitability of a targeted therapy by detecting specific mutations in certain cancers. Polymerase chain reaction-based amplification of DNA or RNA and in situ hybridization are currently the most commonly used methods for nucleic acid detection. In contrast, the main methodology used for protein detection within microscopic lesions is immunohistochemistry. Other methods that allow for analysis of nucleic acids within a particular cell type or individual cells, such as laser capture microdissection, are also available in some laboratories. This review gives an overview of the factors that influence the accurate analysis of nucleic acids in formalin-fixed tissues, as well as of different approaches to detect such targets.
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Affiliation(s)
- R K Maes
- College of Veterinary Medicine, Michigan State University, 4125 Beaumont Road, Lansing, MI 48910, USA. and
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Speers DJ, Moss DM, Minney-Smith C, Levy A, Smith DW. Influenza and respiratory syncytial virus are the major respiratory viruses detected from prospective testing of pediatric and adult coronial autopsies. Influenza Other Respir Viruses 2013; 7:1113-21. [PMID: 23855988 PMCID: PMC4634247 DOI: 10.1111/irv.12139] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2013] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND To ascertain the full mortality of influenza and other respiratory viruses, the testing of community autopsy specimens is essential. METHODS Respiratory virus PCR and culture were performed on 2418 fresh unfrozen respiratory samples collected from 1611 coronial cases where the death was either unknown or infection was suspected, from July 2007 to June 2011, to detect the common respiratory viruses in children and adults, using standardized microbiological testing. RESULTS The respiratory virus positive rate was 8·3% (134 cases) with a peak of 28% (42 of 151 cases) in children under 10 years of age. Influenza virus was the commonest respiratory virus (50 cases, 3%), followed by respiratory syncytial virus (RSV) (30 cases, 2%). All tested respiratory viruses were found in children, most commonly adenovirus, enterovirus and RSV, and influenza A and RSV predominated in those over 60 years, but coinfection was uncommon. Almost all influenza cases occurred when influenza was widely circulating in the community but few were diagnosed pre-mortem. Influenza and RSV detection was associated with bronchitis or bronchiolitis in 7 (9%) of the 80 cases and caused pneumonia in 14 (0·8%) deaths overall. CONCLUSIONS Our prospective review of respiratory viruses using standardized testing found a single lower respiratory tract autopsy specimen for respiratory virus PCR would detect most community infections at the time of death.
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Affiliation(s)
- David J Speers
- Department of Microbiology, PathWest Laboratory Medicine WA, Queen Elizabeth II Medical Centre, Nedlands, WA, Australia; School of Medicine and Pharmacology, University of Western Australia, Crawley, WA, Australia
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Xiao YL, Kash JC, Beres SB, Sheng ZM, Musser JM, Taubenberger JK. High-throughput RNA sequencing of a formalin-fixed, paraffin-embedded autopsy lung tissue sample from the 1918 influenza pandemic. J Pathol 2013. [PMID: 23180419 DOI: 10.1002/path.4145] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Most biopsy and autopsy tissues are formalin-fixed and paraffin-embedded (FFPE), but this process leads to RNA degradation that limits gene expression analysis. The RNA genome of the 1918 pandemic influenza virus was previously determined in a 9-year effort by overlapping RT-PCR from post-mortem samples. Here, the full genome of the 1918 virus at 3000× coverage was determined in one high-throughput sequencing run of a library derived from total RNA of a 1918 FFPE sample after duplex-specific nuclease treatments. Bacterial sequences associated with secondary bacterial pneumonias were also detected. Host transcripts were well represented in the library. Compared to a 2009 pandemic influenza virus FFPE post-mortem library, the 1918 sample showed significant enrichment for host defence and cell death response genes, concordant with prior animal studies. This methodological approach should assist in the analysis of FFPE tissue samples isolated over the past century from a variety of diseases.
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Affiliation(s)
- Yong-Li Xiao
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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The impact of regulations, safety considerations and physical limitations on research progress at maximum biocontainment. Viruses 2013; 4:3932-51. [PMID: 23342380 PMCID: PMC3528297 DOI: 10.3390/v4123932] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
We describe herein, limitations on research at biosafety level 4 (BSL-4) containment laboratories, with regard to biosecurity regulations, safety considerations, research space limitations, and physical constraints in executing experimental procedures. These limitations can severely impact the number of collaborations and size of research projects investigating microbial pathogens of biodefense concern. Acquisition, use, storage, and transfer of biological select agents and toxins (BSAT) are highly regulated due to their potential to pose a severe threat to public health and safety. All federal, state, city, and local regulations must be followed to obtain and maintain registration for the institution to conduct research involving BSAT. These include initial screening and continuous monitoring of personnel, controlled access to containment laboratories, accurate and current BSAT inventory records. Safety considerations are paramount in BSL-4 containment laboratories while considering the types of research tools, workflow and time required for conducting both in vivo and in vitro experiments in limited space. Required use of a positive-pressure encapsulating suit imposes tremendous physical limitations on the researcher. Successful mitigation of these constraints requires additional time, effort, good communication, and creative solutions. Test and evaluation of novel vaccines and therapeutics conducted under good laboratory practice (GLP) conditions for FDA approval are prioritized and frequently share the same physical space with important ongoing basic research studies. The possibilities and limitations of biomedical research involving microbial pathogens of biodefense concern in BSL-4 containment laboratories are explored in this review.
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Wong KT, Ng KY, Ong KC, Ng WF, Shankar SK, Mahadevan A, Radotra B, Su IJ, Lau G, Ling AE, Chan KP, Macorelles P, Vallet S, Cardosa MJ, Desai A, Ravi V, Nagata N, Shimizu H, Takasaki T. Enterovirus 71 encephalomyelitis and Japanese encephalitis can be distinguished by topographic distribution of inflammation and specific intraneuronal detection of viral antigen and RNA. Neuropathol Appl Neurobiol 2012; 38:443-53. [PMID: 22236252 DOI: 10.1111/j.1365-2990.2011.01247.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS To investigate if two important epidemic viral encephalitis in children, Enterovirus 71 (EV71) encephalomyelitis and Japanese encephalitis (JE) whose clinical and pathological features may be nonspecific and overlapping, could be distinguished. METHODS Tissue sections from the central nervous system of infected cases were examined by light microscopy, immunohistochemistry and in situ hybridization. RESULTS All 13 cases of EV71 encephalomyelitis collected from Asia and France invariably showed stereotyped distribution of inflammation in the spinal cord, brainstem, hypothalamus, cerebellar dentate nucleus and, to a lesser extent, cerebral cortex and meninges. Anterior pons, corpus striatum, thalamus, temporal lobe, hippocampus and cerebellar cortex were always uninflamed. In contrast, the eight JE cases studied showed inflammation involving most neuronal areas of the central nervous system, including the areas that were uninflamed in EV71 encephalomyelitis. Lesions in both infections were nonspecific, consisting of perivascular and parenchymal infiltration by inflammatory cells, oedematous/necrolytic areas, microglial nodules and neuronophagia. Viral inclusions were absent. CONCLUSIONS Immunohistochemistry and in situ hybridization assays were useful to identify the causative virus, localizing viral antigens and RNA, respectively, almost exclusively to neurones. The stereotyped distribution of inflammatory lesions in EV71 encephalomyelitis appears to be very useful to help distinguish it from JE.
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Affiliation(s)
- K T Wong
- Faculty of Medicine, University of Malaya, Kuala Lumpur, Kuching, Malaysia.
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25
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The Non-Crosslinking Fixative RCL2®-CS100 is Compatible with Both Pathology Diagnosis and Molecular Analyses. Pathol Oncol Res 2012; 19:41-53. [DOI: 10.1007/s12253-012-9556-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 07/10/2012] [Indexed: 12/16/2022]
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Thunnissen E, Kerr KM, Herth FJF, Lantuejoul S, Papotti M, Rintoul RC, Rossi G, Skov BG, Weynand B, Bubendorf L, Katrien G, Johansson L, López-Ríos F, Ninane V, Olszewski W, Popper H, Jaume S, Schnabel P, Thiberville L, Laenger F. The challenge of NSCLC diagnosis and predictive analysis on small samples. Practical approach of a working group. Lung Cancer 2011; 76:1-18. [PMID: 22138001 DOI: 10.1016/j.lungcan.2011.10.017] [Citation(s) in RCA: 158] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 10/20/2011] [Accepted: 10/22/2011] [Indexed: 12/17/2022]
Abstract
Until recently, the division of pulmonary carcinomas into small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC) was adequate for therapy selection. Due to the emergence of new treatment options subtyping of NSCLC and predictive testing have become mandatory. A practical approach to the new requirements involving interaction between pulmonologist, oncologist and molecular pathology to optimize patient care is described. The diagnosis of lung cancer involves (i) the identification and complete classification of malignancy, (ii) immunohistochemistry is used to predict the likely NSCLC subtype (squamous cell vs. adenocarcinoma), as in small diagnostic samples specific subtyping is frequently on morphological grounds alone not feasible (NSCLC-NOS), (iii) molecular testing. To allow the extended diagnostic and predictive examination (i) tissue sampling should be maximized whenever feasible and deemed clinically safe, reducing the need for re-biopsy for additional studies and (ii) tissue handling, processing and sectioning should be optimized. Complex diagnostic algorithms are emerging, which will require close dialogue and understanding between pulmonologists and others who are closely involved in tissue acquisition, pathologists and oncologists who will ultimately, with the patient, make treatment decisions. Personalized medicine not only means the choice of treatment tailored to the individual patient, but also reflects the need to consider how investigative and diagnostic strategies must also be planned according to individual tumour characteristics.
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Affiliation(s)
- Erik Thunnissen
- Department of Pathology, VU Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands.
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Mostegl MM, Richter B, Dinhopl N, Weissenböck H. Influence of prolonged formalin fixation of tissue samples on the sensitivity of chromogenic in situ hybridization. J Vet Diagn Invest 2011; 23:1212-6. [PMID: 22362804 DOI: 10.1177/1040638711425584] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Chromogenic in situ hybridization (ISH) is a commonly used tool in diagnostic pathology to detect pathogens in formalin-fixed, paraffin-embedded (FFPE) tissue sections. Prolonged formalin fixation time was identified to be a limiting factor for the successful detection of nucleic acid from different pathogens, most probably due to the cross-linking activity of formalin between RNA, DNA, and proteins. Therefore, in the current study, the influence of formalin fixation time on ISH signal intensity of 2 viral (Porcine circovirus-2 [PCV-2] and Porcine respiratory and reproductive virus [PRRSV]) and 2 protozoal agents (Cryptosporidium serpentis and Tritrichomonas sp.) was evaluated. Tissue samples were fixed in 7% neutral buffered formaldehyde solution, and at defined intervals, pieces were embedded in paraffin wax and subjected to pathogen-specific ISH. For all 4 pathogens, the signal intensity remained comparable with the starting ISH signal for different periods of fixation (PCV-2: 6 weeks, PRRSV: 23 weeks, C. serpentis: 55 weeks, Tritrichomonas sp.: 53 weeks). Thereafter, the signal started to decline until loss of nucleic acid detection. The influence of increased proteinase K concentrations for inverting the formalin-induced cross-linking activity was examined compared with the standard protocol. With all 4 infectious agents, a 4-fold proteinase K concentration restored the ISH signals to a level comparable with 1 day of fixation. In conclusion, the influence of prolonged formalin fixation on the intensity of detected ISH signal highly depends on the analyzed infectious agent and the pretreatment protocol.
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Affiliation(s)
- Meike M Mostegl
- Institute of Pathology and Forensic Veterinary Medicine, Department of Pathobiology, University of Veterinary Medicine, Veterinärplatz 1, A-1210 Vienna, Austria
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Denison AM, Blau DM, Jost HA, Jones T, Rollin D, Gao R, Liu L, Bhatnagar J, Deleon-Carnes M, Shieh WJ, Paddock CD, Drew C, Adem P, Emery SL, Shu B, Wu KH, Batten B, Greer PW, Smith CS, Bartlett J, Montague JL, Patel M, Xu X, Lindstrom S, Klimov AI, Zaki SR. Diagnosis of influenza from respiratory autopsy tissues: detection of virus by real-time reverse transcription-PCR in 222 cases. J Mol Diagn 2011; 13:123-8. [PMID: 21354045 DOI: 10.1016/j.jmoldx.2010.09.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Revised: 09/02/2010] [Accepted: 09/08/2010] [Indexed: 12/15/2022] Open
Abstract
The recent influenza pandemic, caused by a novel H1N1 influenza A virus, as well as the seasonal influenza outbreaks caused by varieties of influenza A and B viruses, are responsible for hundreds of thousands of deaths worldwide. Few studies have evaluated the utility of real-time reverse transcription-PCR to detect influenza virus RNA from formalin-fixed, paraffin-embedded tissues obtained at autopsy. In this work, respiratory autopsy tissues from 442 suspect influenza cases were tested by real-time reverse transcription-PCR for seasonal influenza A and B and 2009 pandemic influenza A (H1N1) viruses and the results were compared to those obtained by immunohistochemistry. In total, 222 cases were positive by real-time reverse transcription-PCR, and of 218 real-time, reverse transcription-PCR-positive cases also tested by immunohistochemistry, only 107 were positive. Although formalin-fixed, paraffin-embedded tissues can be used for diagnosis, frozen tissues offer the best chance to make a postmortem diagnosis of influenza because these tissues possess nucleic acids that are less degraded and, as a consequence, provide longer sequence information than that obtained from fixed tissues. We also determined that testing of all available respiratory tissues is critical for optimal detection of influenza virus in postmortem tissues.
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Affiliation(s)
- Amy M Denison
- Infectious Diseases Pathology Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
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Ecco R, Brown C, Susta L, Cagle C, Cornax I, Pantin-Jackwood M, Miller PJ, Afonso CL. In vivo transcriptional cytokine responses and association with clinical and pathological outcomes in chickens infected with different Newcastle disease virus isolates using formalin-fixed paraffin-embedded samples. Vet Immunol Immunopathol 2011; 141:221-9. [DOI: 10.1016/j.vetimm.2011.03.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Revised: 01/13/2011] [Accepted: 03/03/2011] [Indexed: 01/04/2023]
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Quantitative assessment of the sensitivity of various commercial reverse transcriptases based on armored HIV RNA. PLoS One 2010; 5:e13931. [PMID: 21085668 PMCID: PMC2978101 DOI: 10.1371/journal.pone.0013931] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Accepted: 10/18/2010] [Indexed: 12/11/2022] Open
Abstract
Background The in-vitro reverse transcription of RNA to its complementary DNA, catalyzed by the enzyme reverse transcriptase, is the most fundamental step in the quantitative RNA detection in genomic studies. As such, this step should be as analytically sensitive, efficient and reproducible as possible, especially when dealing with degraded or low copy RNA samples. While there are many reverse transcriptases in the market, all claiming to be highly sensitive, there is need for a systematic independent comparison of their applicability in quantification of rare RNA transcripts or low copy RNA, such as those obtained from archival tissues. Methodology/Principal Findings We performed RT-qPCR to assess the sensitivity and reproducibility of 11 commercially available reverse transcriptases in cDNA synthesis from low copy number RNA levels. As target RNA, we used a serially known number of Armored HIV RNA molecules, and observed that 9 enzymes we tested were consistently sensitive to ∼1,000 copies, seven of which were sensitive to ∼100 copies, while only 5 were sensitive to ∼10 RNA template copies across all replicates tested. Despite their demonstrated sensitivity, these five best performing enzymes (Accuscript, HIV-RT, M-MLV, Superscript III and Thermoscript) showed considerable variation in their reproducibility as well as their overall amplification efficiency. Accuscript and Superscript III were the most sensitive and consistent within runs, with Accuscript and Superscript II ranking as the most reproducible enzymes between assays. Conclusions/Significance We therefore recommend the use of Accuscript or Superscript III when dealing with low copy number RNA levels, and suggest purification of the RT reactions prior to downstream applications (eg qPCR) to augment detection. Although the results presented in this study were based on a viral RNA surrogate, and applied to nucleic acid lysates derived from archival formalin-fixed paraffin embedded tissue, their relative performance on RNA obtained from other tissue types may vary, and needs future evaluation.
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Bonin S, Hlubek F, Benhattar J, Denkert C, Dietel M, Fernandez PL, Höfler G, Kothmaier H, Kruslin B, Mazzanti CM, Perren A, Popper H, Scarpa A, Soares P, Stanta G, Groenen PJTA. Multicentre validation study of nucleic acids extraction from FFPE tissues. Virchows Arch 2010; 457:309-17. [PMID: 20665046 PMCID: PMC2933807 DOI: 10.1007/s00428-010-0917-5] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2009] [Revised: 02/12/2010] [Accepted: 03/31/2010] [Indexed: 10/25/2022]
Abstract
In most pathology laboratories worldwide, formalin-fixed paraffin embedded (FFPE) samples are the only tissue specimens available for routine diagnostics. Although commercial kits for diagnostic molecular pathology testing are becoming available, most of the current diagnostic tests are laboratory-based assays. Thus, there is a need for standardized procedures in molecular pathology, starting from the extraction of nucleic acids. To evaluate the current methods for extracting nucleic acids from FFPE tissues, 13 European laboratories, participating to the European FP6 program IMPACTS (www.impactsnetwork.eu), isolated nucleic acids from four diagnostic FFPE tissues using their routine methods, followed by quality assessment. The DNA-extraction protocols ranged from homemade protocols to commercial kits. Except for one homemade protocol, the majority gave comparable results in terms of the quality of the extracted DNA measured by the ability to amplify differently sized control gene fragments by PCR. For array-applications or tests that require an accurately determined DNA-input, we recommend using silica based adsorption columns for DNA recovery. For RNA extractions, the best results were obtained using chromatography column based commercial kits, which resulted in the highest quantity and best assayable RNA. Quality testing using RT-PCR gave successful amplification of 200 bp-250 bp PCR products from most tested tissues. Modifications of the proteinase-K digestion time led to better results, even when commercial kits were applied. The results of the study emphasize the need for quality control of the nucleic acid extracts with standardised methods to prevent false negative results and to allow data comparison among different diagnostic laboratories.
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Affiliation(s)
- Serena Bonin
- ACADEM Department-University of Trieste and ICGEB, University of Trieste, Cattinara Hospital, 34149 Trieste, Italy
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Hofman V, Ilie M, Gavric-Tanga V, Lespinet V, Mari M, Lassalle S, Butori C, Coelle C, Bordone O, Selva E, Lamy A, Sabourin JC, Hofman P. [Role of the surgical pathology laboratory in the pre-analytical approach of molecular biology techniques]. Ann Pathol 2010; 30:85-93. [PMID: 20451063 DOI: 10.1016/j.annpat.2010.03.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2010] [Revised: 03/04/2010] [Accepted: 03/09/2010] [Indexed: 11/15/2022]
Abstract
The advent of the targeted cancer therapies administered to patients, according to the results of molecular biology techniques (in particular, in situ hybridization, "polymerase chain reaction" amplification and sequencing), has modified the practice of the surgical pathology laboratories. The necessity to answer to the needs of physicians for optimizing the medical care for patients who develop cancer has led to a policy of national debate, spurred by the National Institute of Cancer (INCa), in order to implement new procedures in the pathology laboratories. Thus, in addition to the structuring of molecular biology platforms and their labeling by INCa, the upstream control of the steps present between resection of tumor samples and molecular analysis has proved to be crucial. Indeed, the quality of this upstream time, called "pre-analytical" phase, determines the reliability of the molecular biology results and therefore the therapeutic strategy. We describe here the main steps to be checked in the pre-analytical phase. The optimization of this pre-analytical phase within the surgical pathology laboratory aims to reduce or render insignificant the risk of errors of molecular biology tests. These errors can indeed lead to false negative or false positive results whose therapeutic consequences can be particularly harmful to patients with cancer.
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Affiliation(s)
- Véronique Hofman
- Laboratoire de pathologie clinique et expérimentale, hôpital Pasteur, CHU de Nice, 30, avenue de Voie-Romaine, BP 69, 06002 Nice cedex, France.
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Nguyen BT, Koh G, Lim HS, Chua AJS, Ng MML, Toh CS. Membrane-Based Electrochemical Nanobiosensor for the Detection of Virus. Anal Chem 2009; 81:7226-34. [DOI: 10.1021/ac900761a] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Binh T.T. Nguyen
- Department of Chemistry, Faculty of Science, and Department of Microbiology, Yong Loo Lin School of Medicine, 3 Science Drive 3, National University of Singapore, Singapore 117543
| | - Guiwan Koh
- Department of Chemistry, Faculty of Science, and Department of Microbiology, Yong Loo Lin School of Medicine, 3 Science Drive 3, National University of Singapore, Singapore 117543
| | - Hui Si Lim
- Department of Chemistry, Faculty of Science, and Department of Microbiology, Yong Loo Lin School of Medicine, 3 Science Drive 3, National University of Singapore, Singapore 117543
| | - Anthony J. S. Chua
- Department of Chemistry, Faculty of Science, and Department of Microbiology, Yong Loo Lin School of Medicine, 3 Science Drive 3, National University of Singapore, Singapore 117543
| | - Mary M. L. Ng
- Department of Chemistry, Faculty of Science, and Department of Microbiology, Yong Loo Lin School of Medicine, 3 Science Drive 3, National University of Singapore, Singapore 117543
| | - Chee-Seng Toh
- Department of Chemistry, Faculty of Science, and Department of Microbiology, Yong Loo Lin School of Medicine, 3 Science Drive 3, National University of Singapore, Singapore 117543
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