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Ram S, Mojtahedzadeh S, Aguilar JK, Coskran T, Powell EL, O'Neil SP. Quantitative performance assessment of Ultivue multiplex panels in formalin-fixed, paraffin-embedded human and murine tumor specimens. Sci Rep 2024; 14:8496. [PMID: 38605049 PMCID: PMC11009312 DOI: 10.1038/s41598-024-58372-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/28/2024] [Indexed: 04/13/2024] Open
Abstract
We present a rigorous validation strategy to evaluate the performance of Ultivue multiplex immunofluorescence panels. We have quantified the accuracy and precision of four different multiplex panels (three human and one mouse) in tumor specimens with varying levels of T cell density. Our results show that Ultivue panels are typically accurate wherein the relative difference in cell proportion between a multiplex image and a 1-plex image is less than 20% for a given biomarker. Ultivue panels exhibited relatively high intra-run precision (CV ≤ 25%) and relatively low inter-run precision (CV >> 25%) which can be remedied by using local intensity thresholding to gate biomarker positivity. We also evaluated the reproducibility of cell-cell distance estimates measured from multiplex images which show high intra- and inter-run precision. We introduce a new metric, multiplex labeling efficiency, which can be used to benchmark the overall fidelity of the multiplex data across multiple batch runs. Taken together our results provide a comprehensive characterization of Ultivue panels and offer practical guidelines for analyzing multiplex images.
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Affiliation(s)
- Sripad Ram
- Drug Safety Research and Development, Pfizer Inc., Groton, CT, USA.
| | | | | | - Timothy Coskran
- Drug Safety Research and Development, Pfizer Inc., Groton, CT, USA
| | - Eric L Powell
- Oncology Research and Development, Pfizer Inc., San Diego, CA, USA
| | - Shawn P O'Neil
- Drug Safety Research and Development, Pfizer Inc., Groton, CT, USA
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2
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Youssef O, Loukola A, Zidi-Mouaffak YHS, Tamlander M, Ruotsalainen S, Kilpeläinen E, Mars N, Ripatti S, Palotie A, Donner K, Carpén O. High-Resolution Genotyping of Formalin-Fixed Tissue Accurately Estimates Polygenic Risk Scores in Human Diseases. J Transl Med 2024; 104:100325. [PMID: 38220043 DOI: 10.1016/j.labinv.2024.100325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 12/11/2023] [Accepted: 01/05/2024] [Indexed: 01/16/2024] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues stored in biobanks and pathology archives are a vast but underutilized source for molecular studies on different diseases. Beyond being the "gold standard" for preservation of diagnostic human tissues, FFPE samples retain similar genetic information as matching blood samples, which could make FFPE samples an ideal resource for genomic analysis. However, research on this resource has been hindered by the perception that DNA extracted from FFPE samples is of poor quality. Here, we show that germline disease-predisposing variants and polygenic risk scores (PRS) can be identified from FFPE normal tissue (FFPE-NT) DNA with high accuracy. We optimized the performance of FFPE-NT DNA on a genome-wide array containing 657,675 variants. Via a series of testing and validation phases, we established a protocol for FFPE-NT genotyping with results comparable with blood genotyping. The median call rate of FFPE-NT samples in the validation phase was 99.85% (range 98.26%-99.94%) and median concordance with matching blood samples was 99.79% (range 98.85%-99.9%). We also demonstrated that a rare pathogenic PALB2 genetic variant predisposing to cancer can be correctly identified in FFPE-NT samples. We further imputed the FFPE-NT genotype data and calculated the FFPE-NT genome-wide PRS in 3 diseases and 4 disease risk variables. In all cases, FFPE-NT and matching blood PRS were highly concordant (all Pearson's r > 0.95). The ability to precisely genotype FFPE-NT on a genome-wide array enables translational genomics applications of archived FFPE-NT samples with the possibility to link to corresponding phenotypes and longitudinal health data.
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Affiliation(s)
- Omar Youssef
- Department of Pathology, University of Helsinki, Helsinki, Finland; Clinical and Chemical Pathology Department, National Cancer Institute, Cairo University, Cairo, Egypt; Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
| | - Anu Loukola
- Helsinki Biobank, Helsinki University Hospital (HUS), Helsinki, Finland
| | - Yossra H S Zidi-Mouaffak
- Department of Pathology, University of Helsinki, Helsinki, Finland; Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Helsinki Biobank, Helsinki University Hospital (HUS), Helsinki, Finland
| | - Max Tamlander
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Sanni Ruotsalainen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Elina Kilpeläinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Nina Mars
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland; Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland; Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Clinicum, Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland; Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Psychiatric and Neurodevelopmental Genetics Unit, Department of Psychiatry, Analytic and Translational Genetics Unit, Department of Medicine, and the Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts
| | - Kati Donner
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Olli Carpén
- Department of Pathology, University of Helsinki, Helsinki, Finland; Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Helsinki Biobank, Helsinki University Hospital (HUS), Helsinki, Finland
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3
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Thompson SD, Pichika R, Lieber RL, Lavasani M. Extracting high-quality RNA from formaldehyde-fixed naturally aged neuromusculoskeletal tissues. Biotechniques 2024; 76:153-160. [PMID: 38334498 PMCID: PMC10988388 DOI: 10.2144/btn-2023-0092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/22/2023] [Indexed: 02/10/2024] Open
Abstract
Modern approaches to discovering molecular mechanisms and validating treatments for age-related neuromusculoskeletal dysfunction typically rely on high-throughput transcriptome analysis. Previously harvested and fixed tissues offer an incredible reservoir of untapped molecular information. However, obtaining RNA from such formaldehyde-fixed neuromusculoskeletal tissues, especially fibrotic aged tissues, is technically challenging and often results in RNA degradation, chemical modification and yield reduction, prohibiting further analysis. Therefore, we developed a protocol to extract high-quality RNA from formaldehyde-fixed brain, cartilage, muscle and peripheral nerve isolated from naturally aged mice. Isolated RNA produced reliable gene expression data comparable to fresh and flash-frozen tissues and was sensitive enough to detect age-related changes, making our protocol valuable to researchers in the field of aging.
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Affiliation(s)
- Seth D Thompson
- Shirley Ryan AbilityLab, Chicago, IL 60611, USA
- Department of Physical Medicine & Rehabilitation, Northwestern University, Chicago, IL 60611, USA
- Northwestern University Interdepartmental Neuroscience Graduate Program, Northwestern University, Chicago, IL 60611, USA
| | - Rajeswari Pichika
- Shirley Ryan AbilityLab, Chicago, IL 60611, USA
- Department of Physical Medicine & Rehabilitation, Northwestern University, Chicago, IL 60611, USA
- Edward Hines Jr VA Medical Center, Maywood, IL 60153, USA
| | - Richard L Lieber
- Shirley Ryan AbilityLab, Chicago, IL 60611, USA
- Department of Physical Medicine & Rehabilitation, Northwestern University, Chicago, IL 60611, USA
- Edward Hines Jr VA Medical Center, Maywood, IL 60153, USA
| | - Mitra Lavasani
- Shirley Ryan AbilityLab, Chicago, IL 60611, USA
- Department of Physical Medicine & Rehabilitation, Northwestern University, Chicago, IL 60611, USA
- Northwestern University Interdepartmental Neuroscience Graduate Program, Northwestern University, Chicago, IL 60611, USA
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4
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Pang JMB, Byrne DJ, Bergin ART, Caramia F, Loi S, Gorringe KL, Fox SB. Spatial transcriptomics and the anatomical pathologist: Molecular meets morphology. Histopathology 2024; 84:577-586. [PMID: 37991396 DOI: 10.1111/his.15093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 11/23/2023]
Abstract
In recent years anatomical pathology has been revolutionised by the incorporation of molecular findings into routine diagnostic practice, and in some diseases the presence of specific molecular alterations are now essential for diagnosis. Spatial transcriptomics describes a group of technologies that provide up to transcriptome-wide expression profiling while preserving the spatial origin of the data, with many of these technologies able to provide these data using a single tissue section. Spatial transcriptomics allows expression profiling of highly specific areas within a tissue section potentially to subcellular resolution, and allows correlation of expression data with morphology, tissue type and location relative to other structures. While largely still research laboratory-based, several spatial transcriptomics methods have now achieved compatibility with formalin-fixed paraffin-embedded tissue (FFPE), allowing their use in diagnostic tissue samples, and with further development potentially leading to their incorporation in routine anatomical pathology practice. This mini review provides an overview of spatial transcriptomics methods, with an emphasis on platforms compatible with FFPE tissue, approaches to assess the data and potential applications in anatomical pathology practice.
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Affiliation(s)
- Jia-Min B Pang
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - David J Byrne
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Alice R T Bergin
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Franco Caramia
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Sherene Loi
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Kylie L Gorringe
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Stephen B Fox
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
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5
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Haqshenas G, Molano M, Phillips S, Balgovind P, Garland SM, Hawkes D, Brotherton JM, Machalek DA, Murray G. Evaluation of Seegene Anyplex II Performance for Detection of Human Papillomavirus Genotypes in Formalin-Fixed, Paraffin-Embedded Cervical Cancer Specimens. Arch Pathol Lab Med 2024; 148:353-358. [PMID: 37226838 DOI: 10.5858/arpa.2022-0317-oa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2023] [Indexed: 05/26/2023]
Abstract
CONTEXT.— Detection of human papillomavirus (HPV) in formalin-fixed, paraffin-embedded (FFPE) tissues may identify the cause of lesions and has value for the development of new diagnostic assays and epidemiologic studies. Seegene Anyplex II assays are widely used for HPV screening, but their performance using FFPE samples has not been fully explored. OBJECTIVE.— To validate Anyplex II HPV HR Detection (Anyplex II, Seegene) using FFPE samples. DESIGN.— We used 248 stored DNA extracts from cervical cancer FFPE samples collected during 2005-2015 that tested HPV positive using the RHA kit HPV SPF10-LiPA25, v1 (SPF10, Labo Biomedical Products) HPV genotyping assay, manufacturer-validated for FFPE samples. RESULTS.— Of the selected 248 samples, 243 were used in our analysis. Consistent with SPF10 genotyping results, Anyplex II detected all 12 oncogenic types and had an overall HPV detection rate of 86.4% (210 of 243 samples). Anyplex II and SPF10 showed very high agreement for the detection of the 2 most important oncogenic genotypes: HPV 16 (219 of 226; 96.9%; 95% CI, 93.7-98.75) and HPV 18 (221 of 226; 97.8%; 95% CI, 94.9-99.3). CONCLUSIONS.— Overall results showed that both platforms produced comparable HPV genotyping results, indicating the suitability of Anyplex II for FFPE samples. The Anyplex II assay has the added convenience of being an efficient, single-well semiquantitative polymerase chain reaction assay. Further optimization of Anyplex II may enhance its performance using FFPE samples by improving the detection limit.
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Affiliation(s)
- Gholamreza Haqshenas
- From the Departments of Obstetrics and Gynaecology (Haqshenas, Phillips, Balgovind, Garland, Murray)
| | - Monica Molano
- the Centre for Women's Infectious Diseases, The Royal Women's Hospital, Melbourne, Australia (Haqshenas, Molano, Phillips, Balgovind, Garland, Machalek, Murray)
| | - Samuel Phillips
- From the Departments of Obstetrics and Gynaecology (Haqshenas, Phillips, Balgovind, Garland, Murray)
- the Centre for Women's Infectious Diseases, The Royal Women's Hospital, Melbourne, Australia (Haqshenas, Molano, Phillips, Balgovind, Garland, Machalek, Murray)
- Murdoch Children's Research Institute, Melbourne, Australia (Haqshenas, Phillips, Balgovind, Garland, Murray)
| | - Prisha Balgovind
- From the Departments of Obstetrics and Gynaecology (Haqshenas, Phillips, Balgovind, Garland, Murray)
- the Centre for Women's Infectious Diseases, The Royal Women's Hospital, Melbourne, Australia (Haqshenas, Molano, Phillips, Balgovind, Garland, Machalek, Murray)
- Murdoch Children's Research Institute, Melbourne, Australia (Haqshenas, Phillips, Balgovind, Garland, Murray)
| | - Suzanne M Garland
- From the Departments of Obstetrics and Gynaecology (Haqshenas, Phillips, Balgovind, Garland, Murray)
- the Centre for Women's Infectious Diseases, The Royal Women's Hospital, Melbourne, Australia (Haqshenas, Molano, Phillips, Balgovind, Garland, Machalek, Murray)
- Murdoch Children's Research Institute, Melbourne, Australia (Haqshenas, Phillips, Balgovind, Garland, Murray)
| | - David Hawkes
- Biochemistry and Pharmacology (Hawkes)
- the Australian Centre for the Prevention of Cervical Cancer, Melbourne, Australia (Hawkes, Brotherton)
- the Department of Pathology, University of Malaya, Kuala Lumpur, Malaysia (Hawkes)
| | - Julia Ml Brotherton
- the School of Population and Global Health (Brotherton), University of Melbourne, Melbourne, Australia
| | - Dorothy A Machalek
- the Centre for Women's Infectious Diseases, The Royal Women's Hospital, Melbourne, Australia (Haqshenas, Molano, Phillips, Balgovind, Garland, Machalek, Murray)
- The Kirby Institute, University of New South Wales, Sydney, Australia (Machalek)
| | - Gerald Murray
- From the Departments of Obstetrics and Gynaecology (Haqshenas, Phillips, Balgovind, Garland, Murray)
- the Centre for Women's Infectious Diseases, The Royal Women's Hospital, Melbourne, Australia (Haqshenas, Molano, Phillips, Balgovind, Garland, Machalek, Murray)
- Murdoch Children's Research Institute, Melbourne, Australia (Haqshenas, Phillips, Balgovind, Garland, Murray)
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6
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Hiratsuka T, Yoshizawa A, Endo T, Yamamoto T, Toyokuni S, Tsuruyama T. Formalin-Fixed Paraffin-Embedded Proteomics of Malignant Mesothelioma and New Candidate Biomarkers Thioredoxin and Superoxide Dismutase 2 for Immunohistochemistry. J Transl Med 2024; 104:100299. [PMID: 38013118 DOI: 10.1016/j.labinv.2023.100299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/17/2023] [Accepted: 11/21/2023] [Indexed: 11/29/2023] Open
Abstract
The pathogenesis of malignant mesothelioma (MM) has been extensively investigated, focusing on stress derived from reactive oxygen species. We aimed to identify diagnostic biomarkers of MM by analyzing proteins in formalin-fixed paraffin-embedded specimens using liquid chromatography-mass spectrometry. We extracted proteins from formalin-fixed paraffin-embedded sections of MM tissues (n = 7) and compared their profiles with those of benign mesothelial tissues (n = 4) and alveolar tissue (n = 1). Proteomic data were statistically assessed and profiled using principal component analysis. We were successful in the classification of MM and healthy tissue. The levels of superoxide dismutase 2 (SOD2), an enzyme that converts superoxide anion into oxygen and hydrogen peroxide, and thioredoxin (TXN), which plays a crucial role in reducing disulfide bonds in proteins, primarily contributed to the classification. Other redox-related proteins, such as pyruvate dehydrogenase subunit X, and ceruloplasmin also contributed to the classification. Protein-protein interaction analysis demonstrated that these proteins play essential roles in MM pathogenesis. Immunohistochemistry revealed that TXN levels were significantly lower, whereas SOD2 levels were significantly higher in MM and lung cancer tissues than in controls. Proteomic profiling suggested that MM tissues experienced increased exposure to hydrogen peroxide and other reactive oxygen species. Combining immunohistochemistry for TXN and SOD2 allows for differentiation among MM, lung cancer, and control tissues; hence, TXN and SOD2 may be promising MM biomarkers and therapeutic targets.
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Affiliation(s)
- Takuya Hiratsuka
- Department of Drug Discovery Medicine, Medical Innovation Center, Kyoto University Graduate School of Medicine, Kyoto, Japan.
| | | | - Tatsuya Endo
- Department of Physics, Graduate School of Science, Tohoku University, Sendai, Japan
| | - Takushi Yamamoto
- Solutions COE, Analytical & Measuring Instruments Division, Shimadzu Corporation, Kyoto, Japan
| | - Shinya Toyokuni
- Department of Pathology and Biological Responses, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Tatsuaki Tsuruyama
- Department of Drug Discovery Medicine, Medical Innovation Center, Kyoto University Graduate School of Medicine, Kyoto, Japan; Department of Physics, Graduate School of Science, Tohoku University, Sendai, Japan; Tazuke Kofukai Medical Research Institute Kitano Hospital, Ohgimachi, Osaka, Japan.
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7
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Kassab M, Jehanzaib M, Başak K, Demir D, Keles GE, Turan M. FFPE++: Improving the quality of formalin-fixed paraffin-embedded tissue imaging via contrastive unpaired image-to-image translation. Med Image Anal 2024; 91:102992. [PMID: 37852162 DOI: 10.1016/j.media.2023.102992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 04/29/2023] [Accepted: 10/02/2023] [Indexed: 10/20/2023]
Abstract
Formalin-fixation and paraffin-embedding (FFPE) is a technique for preparing and preserving tissue specimens that has been utilized in histopathology since the late 19th century. This process is further complicated by FFPE preparation steps such as fixation, processing, embedding, microtomy, staining, and coverslipping, which often results in artifacts due to the complex histological and cytological characteristics of a tissue specimen. The term "artifacts" includes, but is not limited to, staining inconsistencies, tissue folds, chattering, pen marks, blurring, air bubbles, and contamination. The presence of artifacts may interfere with pathological diagnosis in disease detection, subtyping, grading, and choice of therapy. In this study, we propose FFPE++, an unpaired image-to-image translation method based on contrastive learning with a mixed channel-spatial attention module and self-regularization loss that drastically corrects the aforementioned artifacts in FFPE tissue sections. Turing tests were performed by 10 board-certified pathologists with more than 10 years of experience. These tests which were performed for ovarian carcinoma, lung adenocarcinoma, lung squamous cell carcinoma, and papillary thyroid carcinoma, demonstrate the clear superiority of the proposed method in many clinical aspects compared with standard FFPE images. Based on the qualitative experiments and feedback from the Turing tests, we believe that FFPE++ can contribute to substantial diagnostic and prognostic accuracy in clinical pathology in the future and can also improve the performance of AI tools in digital pathology. The code and dataset are publicly available at https://github.com/DeepMIALab/FFPEPlus.
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Affiliation(s)
- Mohamad Kassab
- Department of Computer Engineering, Bogazici University, Istanbul, Turkey
| | - Muhammad Jehanzaib
- Department of Computer Engineering, Bogazici University, Istanbul, Turkey
| | - Kayhan Başak
- Sağlık Bilimleri University, Kartal Dr.Lütfi Kırdar City Hospital, Department of Pathology, Istanbul, Turkey
| | - Derya Demir
- Faculty of Medicine, Department of Pathology, Ege University, Izmir, Turkey
| | | | - Mehmet Turan
- Department of Computer Engineering, Bogazici University, Istanbul, Turkey.
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8
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Mar D, Babenko IM, Zhang R, Noble WS, Denisenko O, Vaisar T, Bomsztyk K. A High-Throughput PIXUL-Matrix-Based Toolbox to Profile Frozen and Formalin-Fixed Paraffin-Embedded Tissues Multiomes. J Transl Med 2024; 104:100282. [PMID: 37924947 PMCID: PMC10872585 DOI: 10.1016/j.labinv.2023.100282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 11/06/2023] Open
Abstract
Large-scale high-dimensional multiomics studies are essential to unravel molecular complexity in health and disease. We developed an integrated system for tissue sampling (CryoGrid), analytes preparation (PIXUL), and downstream multiomic analysis in a 96-well plate format (Matrix), MultiomicsTracks96, which we used to interrogate matched frozen and formalin-fixed paraffin-embedded (FFPE) mouse organs. Using this system, we generated 8-dimensional omics data sets encompassing 4 molecular layers of intracellular organization: epigenome (H3K27Ac, H3K4m3, RNA polymerase II, and 5mC levels), transcriptome (messenger RNA levels), epitranscriptome (m6A levels), and proteome (protein levels) in brain, heart, kidney, and liver. There was a high correlation between data from matched frozen and FFPE organs. The Segway genome segmentation algorithm applied to epigenomic profiles confirmed known organ-specific superenhancers in both FFPE and frozen samples. Linear regression analysis showed that proteomic profiles, known to be poorly correlated with transcriptomic data, can be more accurately predicted by the full suite of multiomics data, compared with using epigenomic, transcriptomic, or epitranscriptomic measurements individually.
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Affiliation(s)
- Daniel Mar
- UW Medicine South Lake Union, University of Washington, Seattle, Washington; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington
| | - Ilona M Babenko
- Diabetes Institute, University of Washington, Seattle, Washington
| | - Ran Zhang
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, Washington; Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington
| | - Oleg Denisenko
- UW Medicine South Lake Union, University of Washington, Seattle, Washington
| | - Tomas Vaisar
- Diabetes Institute, University of Washington, Seattle, Washington
| | - Karol Bomsztyk
- UW Medicine South Lake Union, University of Washington, Seattle, Washington; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington; Matchstick Technologies, Inc, Kirkland, Washington.
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9
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Zong L, Zhu Y, Jiang Y, Xia Y, Liu Q, Jiang S. A comprehensive assessment of exome capture methods for RNA sequencing of formalin-fixed and paraffin-embedded samples. BMC Genomics 2023; 24:777. [PMID: 38102591 PMCID: PMC10722801 DOI: 10.1186/s12864-023-09886-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023] Open
Abstract
RNA-Seq analysis of Formalin-Fixed and Paraffin-Embedded (FFPE) samples has emerged as a highly effective approach and is increasingly being used in clinical research and drug development. However, the processing and storage of FFPE samples are known to cause extensive degradation of RNAs, which limits the discovery of gene expression or gene fusion-based biomarkers using RNA sequencing, particularly methods reliant on Poly(A) enrichment. Recently, researchers have developed an exome targeted RNA-Seq methodology that utilizes biotinylated oligonucleotide probes to enrich RNA transcripts of interest, which could overcome these limitations. Nevertheless, the standardization of this experimental framework, including probe designs, sample multiplexing, sequencing read length, and bioinformatic pipelines, remains an essential requirement. In this study, we conducted a comprehensive comparison of three main commercially available exome capture kits and evaluated key experimental parameters, to provide the overview of the advantages and limitations associated with the selection of library preparation protocols and sequencing platforms. The results provide valuable insights into the best practices for obtaining high-quality data from FFPE samples.
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Affiliation(s)
- Liang Zong
- Wuhan BGI Technology Service Co., Ltd. BGI-Wuhan, Wuhan, China
- College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan, China
| | - Yabing Zhu
- BGI Tech Solutions Co., Ltd. BGI-Shenzhen, Shenzhen, China
| | - Yuan Jiang
- Wuhan BGI Technology Service Co., Ltd. BGI-Wuhan, Wuhan, China
| | - Ying Xia
- Wuhan BGI Technology Service Co., Ltd. BGI-Wuhan, Wuhan, China
| | - Qun Liu
- Wuhan BGI Technology Service Co., Ltd. BGI-Wuhan, Wuhan, China
| | - Sanjie Jiang
- BGI Tech Solutions Co., Ltd. BGI-Shenzhen, Shenzhen, China.
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10
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Amemiya K, Hirotsu Y, Nagakubo Y, Mochizuki H, Oyama T, Omata M. Influence of formalin fixation duration on RNA quality and quantity from formalin-fixed paraffin-embedded hepatocellular carcinoma tissues. Pathol Int 2023; 73:593-600. [PMID: 37933792 DOI: 10.1111/pin.13385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/14/2023] [Indexed: 11/08/2023]
Abstract
Analyzing RNA samples from formalin-fixed paraffin-embedded (FFPE) tissues is essential for precision medicine. We investigated RNA quantity and quality from FFPE tumor tissues fixed in formalin for various times and compared sequencing metrics from next-generation sequencing (NGS). Hepatocellular carcinoma (HCC) tissues were fixed in 10% neutral buffered formalin (1-240 h) and FFPE blocks were prepared. Total RNA was extracted, and the quantity and quality were assessed using the NanoDrop, Qubit and Bioanalyzer. After preparing sequencing libraries, NGS was performed on the Oncomine Dx Multi-CDx system. Total RNA yields of all samples met the threshold required for NGS, but longer fixation times resulted in decreased total RNA and long RNA fragment (>200 nt) yields. NGS analysis showed fewer sequencing reads of internal control genes from RNA with longer fixation times. RNA extracted from FFPE blocks stored for 500 days had reduced RNA yield and quality compared with RNA obtained from FFPE blocks prepared immediately. In conclusion, short and over-fixation should be avoided because of their negative impact on sequencing quality. Fixation process should be finished promptly within recommended guidelines (6-72 h) for cancer patients.
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Affiliation(s)
- Kenji Amemiya
- Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Yosuke Hirotsu
- Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Yuki Nagakubo
- Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Hitoshi Mochizuki
- Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Toshio Oyama
- Pathology Division, Laboratory Department, Yamanashi Prefectural Central Hospital, Yamanashi, Japan
| | - Masao Omata
- Department of Gastroenterology, Yamanashi Central Hospital, Yamanashi, Japan
- The University of Tokyo, Tokyo, Japan
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Tüshaus J, Sakhteman A, Lechner S, The M, Mucha E, Krisp C, Schlegel J, Delbridge C, Kuster B. A region-resolved proteomic map of the human brain enabled by high-throughput proteomics. EMBO J 2023; 42:e114665. [PMID: 37916885 PMCID: PMC10690467 DOI: 10.15252/embj.2023114665] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 11/03/2023] Open
Abstract
Substantial efforts are underway to deepen our understanding of human brain morphology, structure, and function using high-resolution imaging as well as high-content molecular profiling technologies. The current work adds to these approaches by providing a comprehensive and quantitative protein expression map of 13 anatomically distinct brain regions covering more than 11,000 proteins. This was enabled by the optimization, characterization, and implementation of a high-sensitivity and high-throughput microflow liquid chromatography timsTOF tandem mass spectrometry system (LC-MS/MS) capable of analyzing more than 2,000 consecutive samples prepared from formalin-fixed paraffin embedded (FFPE) material. Analysis of this proteomic resource highlighted brain region-enriched protein expression patterns and functional protein classes, protein localization differences between brain regions and individual markers for specific areas. To facilitate access to and ease further mining of the data by the scientific community, all data can be explored online in a purpose-built R Shiny app (https://brain-region-atlas.proteomics.ls.tum.de).
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Affiliation(s)
- Johanna Tüshaus
- Proteomics and Bioanalytics, Department of Molecular Life Sciences, School of Life SciencesTechnical University of MunichMunichGermany
| | - Amirhossein Sakhteman
- Proteomics and Bioanalytics, Department of Molecular Life Sciences, School of Life SciencesTechnical University of MunichMunichGermany
| | - Severin Lechner
- Proteomics and Bioanalytics, Department of Molecular Life Sciences, School of Life SciencesTechnical University of MunichMunichGermany
| | - Matthew The
- Proteomics and Bioanalytics, Department of Molecular Life Sciences, School of Life SciencesTechnical University of MunichMunichGermany
| | - Eike Mucha
- Bruker Daltonics GmbH & Co. KGBremenGermany
| | | | - Jürgen Schlegel
- Department of Neuropathology, Klinikum Rechts der ISAR, School of MedicineTechnical University MunichMunichGermany
| | - Claire Delbridge
- Department of Neuropathology, Klinikum Rechts der ISAR, School of MedicineTechnical University MunichMunichGermany
| | - Bernhard Kuster
- Proteomics and Bioanalytics, Department of Molecular Life Sciences, School of Life SciencesTechnical University of MunichMunichGermany
- German Cancer Consortium (DKTK), Munich SiteHeidelbergGermany
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Uzoma IC, Taiwo IA, Ugwu NI, Durosinmi MA, Akinloye O. Quality and Quantity of Nucleic Acids Extracted from Formalin-Fixed Paraffin-Embedded Lymphoma Biopsies from Nigerian Archived Biopsy. Niger J Clin Pract 2023; 26:1854-1860. [PMID: 38158353 DOI: 10.4103/njcp.njcp_389_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/17/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND Integrity of nucleic acids derived from archived formalin-fixed paraffin-embedded (FFPE) cancer specimens affects diagnosis, prognosis, and therapy. Several factors affect the quality and quantity of extracted nucleic acids and one of such factors is storage period. AIM We investigated the impact of storage duration on the quality and quantity of nucleic acids extracted from archived FFPE lymphoma biopsies in Nigeria. MATERIALS AND METHODS A total of 53 FFPE biopsies diagnosed as lymphoma stored over several years (2008-2019) were analyzed. They were 22 chronic lymphocytic leukemia (CLL) cases, 17 Hodgkin lymphoma (HL) cases, and 14 diffuse large B-cell lymphoma, not otherwise specified (DLBCL, NOS). DNA was extracted from all the lymphoma samples which were analyzed for integrity and amplifiability using the four pairs of control genes polymerase chain reaction (PCR) primers of BIOMED-2 protocol, whereas RNA extraction was from 6 CLL cases used for qPCR analysis of RNU43. RESULTS For CLL, the mean DNA yield was 193.6 ng/µl (range: 3.0-533.0 ng/µl), whereas the mean A260/A280 ratio was 1.7 (1.2-1.9). For DLBCL, NOS, and HL, 255.5 ng/µl (range: 32.9-605.4 ng/µl), 1.8 (1.5-2.0) and 242.7 ng/µl (range: 1.3-886.0 ng/µl), and 1.7 (0.9-1.8), respectively. The extracted DNA gave amplifiable products of at least 200bp, whereas the RNA analysis showed CT values of <38 in all the samples. The mean RNA yield was 462.2 ng/µl (range: 74.7-1082.1), whereas the mean A260/A280 was 1.7 (1.5-1.8). CONCLUSION Quantity and quality of nucleic acids from FFPE tissues stored for different time periods showed no significant difference in yield and quality.
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Affiliation(s)
- I C Uzoma
- Department of Medical Laboratory Science, Faculty of Health Sciences and Technology, Molecular Hematology and Immunogenetics Laboratory, College of Medicine, University of Nigeria, Enugu Campus, Nsukka, Nigeria
| | - I A Taiwo
- Department of Cell Biology and Genetics, Faculty of Science, Genetics Laboratory, University of Lagos, Lagos, Nigeria
| | - N I Ugwu
- Department of Hematology and Immunology, Faculty of Clinical Medicine, College of Health Sciences, Ebonyi State University, Abakaliki, Nigeria
| | - M A Durosinmi
- Department of Hematology and Blood Transfusion, Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Nigeria
| | - O Akinloye
- Department of Medical Laboratory Science, Faculty of Basic Medical Sciences, Clinical Chemistry and Molecular Diagnostics Laboratory, College of Medicine, University of Lagos, Lagos, Nigeria
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13
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Cho A, Ahn J, Kim A, Lee JH, Ryu HS, Kim KM, Yi EC. Proteomics analysis of an individual formalin-fixed paraffin-embedded tissue section using isobaric-tag amplification. Rapid Commun Mass Spectrom 2023; 37:e9616. [PMID: 37817342 DOI: 10.1002/rcm.9616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 10/12/2023]
Abstract
RATIONALE The comprehensive analysis of formalin-fixed paraffin-embedded (FFPE) tissues is essential for retrospective clinical studies. However, detecting low-abundance proteins and obtaining proteome-scale data from FFPE samples pose analytical challenges in mass spectrometry-based proteomics. To overcome this challenge, our study focuses on implementing an isobaric labeling approach to improve the detection of low-abundance target proteins in FFPE tissues, thereby enhancing the qualitative and quantitative analysis. METHODS We employed an isobaric labeling approach utilizing synthetic peptides or proteins to enable the qualitative and quantitative measurement of target proteins in FFPE tissue samples. To achieve this, we incorporated tandem mass tag (TMT)-labeled recombinant proteins or synthetic peptides into TMT-labeled metastatic breast cancer FFPE tissues. Through this strategy, we successfully detect coexisting CD276 (B7-H3) and CD147 proteins while identifying over 6000 proteins using targeted analysis of individual FFPE tissue sections. RESULTS Our findings provide compelling evidence that the incorporation of isobaric labeling, along with the inclusion of TMT-labeled peptides or proteins, greatly enhances the detection of target proteins in FFPE tissue samples. By employing this approach, we were able to obtain robust qualitative measurements of CD276 and CD147 proteins, showcasing its effectiveness in identifying more than 6000 proteins in FFPE samples. CONCLUSIONS The integration of an isobaric labeling approach, in conjunction with synthetic peptides or proteins, presents a valuable strategy for enhancing the detection and validation of target proteins in FFPE tissue analysis. This technique holds immense potential in retrospective clinical studies, as it enables comprehensive analysis of low-abundance proteins and facilitating proteome-scale investigations in FFPE samples. By leveraging this methodology, researchers can unlock new insights into disease mechanisms and advance our understanding of complex biological processes.
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Affiliation(s)
- Ara Cho
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Jinsung Ahn
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Andrew Kim
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Jeong Hyun Lee
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Han Suk Ryu
- Department of Pathology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Kristine M Kim
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, Republic of Korea
- Department of Bio-Health Convergence, Kangwon National University, Chuncheon, Republic of Korea
| | - Eugene C Yi
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Medicine, Seoul National University, Seoul, Republic of Korea
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14
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Chardin D, Jing L, Chazal-Ngo-Mai M, Guigonis JM, Rigau V, Goze C, Duffau H, Virolle T, Pourcher T, Burel-Vandenbos F. Identification of Metabolomic Markers in Frozen or Formalin-Fixed and Paraffin-Embedded Samples of Diffuse Glioma from Adults. Int J Mol Sci 2023; 24:16697. [PMID: 38069019 PMCID: PMC10705927 DOI: 10.3390/ijms242316697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
The aim of this study was to identify metabolomic signatures associated with the gliomagenesis pathway (IDH-mutant or IDH-wt) and tumor grade of diffuse gliomas (DGs) according to the 2021 WHO classification on frozen samples and to evaluate the diagnostic performances of these signatures in tumor samples that are formalin-fixed and paraffin-embedded (FFPE). An untargeted metabolomic study was performed using liquid chromatography/mass spectrometry on a cohort of 213 DG samples. Logistic regression with LASSO penalization was used on the frozen samples to build classification models in order to identify IDH-mutant vs. IDH-wildtype DG and high-grade vs low-grade DG samples. 2-Hydroxyglutarate (2HG) was a metabolite of interest to predict IDH mutational status and aminoadipic acid (AAA) and guanidinoacetic acid (GAA) were significantly associated with grade. The diagnostic performances of the models were 82.6% AUC, 70.6% sensitivity and 80.4% specificity for 2HG to predict IDH status and 84.7% AUC, 78.1% sensitivity and 73.4% specificity for AAA and GAA to predict grade from FFPE samples. Thus, this study showed that AAA and GAA are two novel metabolites of interest in DG and that metabolomic data can be useful in the classification of DG, both in frozen and FFPE samples.
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Affiliation(s)
- David Chardin
- Laboratory Transporter in Imaging and Radiotherapy in Oncology (TIRO), Direction de la Recherche Fondamentale (DRF), Institut des Sciences du Vivant Frederic Joliot, Commissariat a l’Energie Atomique et aux Energies Alternatives (CEA), Université Cote d’Azur (UCA), 06000 Nice, France; (D.C.); (L.J.); (J.-M.G.); (T.P.)
- Service de Médecine Nucléaire, Centre Antoine Lacassagne, Université Cote d’Azur, 06000 Nice, France
| | - Lun Jing
- Laboratory Transporter in Imaging and Radiotherapy in Oncology (TIRO), Direction de la Recherche Fondamentale (DRF), Institut des Sciences du Vivant Frederic Joliot, Commissariat a l’Energie Atomique et aux Energies Alternatives (CEA), Université Cote d’Azur (UCA), 06000 Nice, France; (D.C.); (L.J.); (J.-M.G.); (T.P.)
| | | | - Jean-Marie Guigonis
- Laboratory Transporter in Imaging and Radiotherapy in Oncology (TIRO), Direction de la Recherche Fondamentale (DRF), Institut des Sciences du Vivant Frederic Joliot, Commissariat a l’Energie Atomique et aux Energies Alternatives (CEA), Université Cote d’Azur (UCA), 06000 Nice, France; (D.C.); (L.J.); (J.-M.G.); (T.P.)
| | - Valérie Rigau
- Department of Pathology and Oncobiology, Institute for Neurosciences of Montpellier, INSERM U1051, University Hospital of Montpellier, 34000 Montpellier, France;
| | - Catherine Goze
- Laboratory of Solid Tumors Biology, Institute for Neurosciences of Montpellier, INSERM U1051, University Hospital of Montpellier, 34000 Montpellier, France;
| | - Hugues Duffau
- Neurosurgery Department, Institute for Neurosciences of Montpellier, INSERM U1051, University Hospital of Montpellier, 34000 Montpellier, France;
| | - Thierry Virolle
- Team INSERM “Cancer Stem Cell Plasticity and Functional Intra-Tumor Heterogeneity”, Institut de Biologie Valrose, Université Côte D’Azur, CNRS, INSERM, 06000 Nice, France;
| | - Thierry Pourcher
- Laboratory Transporter in Imaging and Radiotherapy in Oncology (TIRO), Direction de la Recherche Fondamentale (DRF), Institut des Sciences du Vivant Frederic Joliot, Commissariat a l’Energie Atomique et aux Energies Alternatives (CEA), Université Cote d’Azur (UCA), 06000 Nice, France; (D.C.); (L.J.); (J.-M.G.); (T.P.)
| | - Fanny Burel-Vandenbos
- Department of Pathology, University Hospital of Nice, 06000 Nice, France;
- Laboratory “Cancer Stem Cell Plasticity and Functional Intra-Tumor Heterogeneity”, UMR CNRS 7277-UMR INSERM 1091, Institute of Biology Valrose, University Côte d’Azur, 06000 Nice, France
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15
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Chen H, Zhang Y, Zhou H, Chen W, Peng J, Feng Y, Fan L, Li J, Zi J, Ren Y, Li Q, Liu S. Routine Workflow of Spatial Proteomics on Micro-formalin-Fixed Paraffin-Embedded Tissues. Anal Chem 2023; 95:16733-16743. [PMID: 37922386 DOI: 10.1021/acs.analchem.3c03848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2023]
Abstract
In the era of single-cell biology, spatial proteomics has emerged as an important frontier. However, it still faces several challenges in technology. Formalin-fixed paraffin-embedded (FFPE) tissues are an important material in spatial proteomics, in which fixed tissues are excised using laser capture microdissection (LCM), followed by protein identification with mass spectrometry. For a satisfied spatial proteomics upon FFPE tissues, the excision area is expected to be as small as possible, and the identified proteins are countered upon as much as possible. For a general laboratory for spatial proteomics, a routine workflow is required, not relying on any special device, and is easily operating. In view of these challenges in technology, we initiated a technology evaluation throughout the entire procedure of proteomic analysis with micro-FFPE tissues. In contrast to the protocols reported previously, several innovations in technology were proposed and conducted, such as removal of destaining, decross-linking with "hang-down", solution simplification for peptide generation and balancing to excision area, and capture rate of micro-FFPE tissues. After optimization of all the necessary steps, a routine workflow was established, in which the minimized area for protein identification was 0.002 mm2, while the excision area for a consistent proteomic analysis was 0.05 mm2. Using the developed workflow and collecting the micro-FFPE tissues continuously, for the first time, a spatial proteomic atlas of mouse brain was preliminarily constructed, which exhibited the typical characteristics of spatial-dependent protein abundance and functional enrichment.
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Affiliation(s)
- Hao Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Yuefei Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Haichao Zhou
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Weiran Chen
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- College of Pharmaceutical Science, Zhejiang University of Technology, Gongda Road 1, Huzhou 313200, China
| | - Jiayi Peng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Yang Feng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Linyuan Fan
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Jun Li
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- College of Pharmaceutical Science, Zhejiang University of Technology, Gongda Road 1, Huzhou 313200, China
| | - Jin Zi
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Yan Ren
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Shanghai University of Traditional Chinese Medicine, Shanghai 200120, China
| | - Qidan Li
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Siqi Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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16
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Song K, Elboudwarej E, Zhao X, Zhuo L, Pan D, Liu J, Brachmann C, Patterson SD, Yoon OK, Zavodovskaya M. RNA-seq RNAaccess identified as the preferred method for gene expression analysis of low quality FFPE samples. PLoS One 2023; 18:e0293400. [PMID: 37883360 PMCID: PMC10602291 DOI: 10.1371/journal.pone.0293400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 10/11/2023] [Indexed: 10/28/2023] Open
Abstract
Clinical tumor tissues that are preserved as formalin-fixed paraffin-embedded (FFPE) samples result in extensive cross-linking, fragmentation, and chemical modification of RNA, posing significant challenges for RNA-seq-based gene expression profiling. This study sought to define an optimal RNA-seq protocol for FFPE samples. We employed a common RNA extraction method and then compared RNA-seq library preparation protocols including RNAaccess, RiboZero and PolyA in terms of sequencing quality and concordance of gene expression using FFPE and case-matched fresh-frozen (FF) triple-negative breast cancer (TNBC) tissues. We found that RNAaccess, a method based on exome capture, produced the most concordant results. Applying RNAaccess to FFPE gastric cancer tissues, we established a minimum RNA DV200 requirement of 10% and a RNA input amount of 10ng that generated highly reproducible gene expression data. Lastly, we demonstrated that RNAaccess and NanoString platforms produced highly concordant expression profiles from FFPE samples for shared genes; however, RNA-seq may be preferred for clinical biomarker discovery work because of the broader coverage of the transcriptome. Taken together, these results support the selection of RNA-seq RNAaccess method for gene expression profiling of FFPE samples. The minimum requirements for RNA quality and input established here may allow for inclusion of clinical FFPE samples of sub-optimal quality in gene expression analyses and ultimately increasing the statistical power of such analyses.
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Affiliation(s)
- Kai Song
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Emon Elboudwarej
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Xi Zhao
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Luting Zhuo
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - David Pan
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Jinfeng Liu
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Carrie Brachmann
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Scott D. Patterson
- Gilead Sciences, Inc., Foster City, California, United States of America
| | - Oh Kyu Yoon
- Gilead Sciences, Inc., Foster City, California, United States of America
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17
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KUROKAWA A, YAMAMOTO Y. Immunohistochemical identification of T and B lymphocytes in formalin-fixed, paraffin-embedded tissues of 53 avian species using commercial antibodies. J Vet Med Sci 2023; 85:1121-1130. [PMID: 37661384 PMCID: PMC10600538 DOI: 10.1292/jvms.23-0255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 08/16/2023] [Indexed: 09/05/2023] Open
Abstract
Providing a method to detect avian lymphocytes by immunohistochemistry (IHC) would be helpful for analyzing immune function and diagnosing diseases in birds. In this study, we comprehensively examined the immunohistochemical identification of avian T and B lymphocytes in formalin-fixed, paraffin-embedded tissues from 53 avian species across 15 orders, using eight commercially available lymphocyte markers. T lymphocytes from all 53 avian species tested were specifically detected by IHC using the anti-CD3 antibody (clone F7.2.38). The appropriate antibody for detecting avian B lymphocytes in IHC varied depending on the avian species. B lymphocytes were specifically labeled by IHC in 46 of 53 avian species (86.8%) using any of seven B cell markers. The anti-PAX5 antibody (clone SP34) immunohistochemically detected B lymphocytes from the majority of avian species (41 out of 53 species), excluding those in the orders Falconiformes (falcons) and Passeriformes (oscines). The anti-BAFF-R antibody (clone 2C4) proved suitable for detecting B lymphocytes in the orders Galliformes (landfowls) and Anseriformes (waterfowls) in IHC. Caution is advised when using the anti-BLA36 (clone A27-42) and two anti-CD20 (clone L26 and product No. PA5-16701) antibodies, which are commonly used as B cell markers in mammals, for detecting avian B lymphocytes. These antibodies reacted with cells located in both T and B cell areas in certain avian species. The anti-Bu-1a/b (clone AV20) and anti-CD79a (clone HM57) antibodies were found not to bind to B lymphocytes in various avian species in IHC.
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Affiliation(s)
- Aoi KUROKAWA
- National Institute of Animal Health, National Agriculture
and Food Research Organization, Ibaraki, Japan
| | - Yu YAMAMOTO
- National Institute of Animal Health, National Agriculture
and Food Research Organization, Ibaraki, Japan
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18
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Feldiorean A, Bena J, Nakashima MO, McShane AJ, Cotta CV. Formalin Fixation Followed by Paraffin Embedding Allows Long-Term Storage of Proteins for Liquid Chromatography-Tandem Mass Spectrometry Analysis. J Transl Med 2023; 103:100224. [PMID: 37517701 DOI: 10.1016/j.labinv.2023.100224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/15/2023] [Accepted: 07/13/2023] [Indexed: 08/01/2023] Open
Abstract
In an anatomical pathology laboratory, liquid chromatography-tandem mass spectrometry (LC-MS/MS) is used to characterize amyloid deposits identified in formalin-fixed paraffin-embedded tissue (FFPET). However, the development of additional tests is partially limited by the lack of information the passage of time has on the proteins in FFPET. To investigate the reliability of LC-MS/MS in the analysis of old FFPET specimens, 1 bone marrow aspirate clot was analyzed by LC-MS/MS yearly from 2014 to 2018, in 3 consecutive months. Peptide-spectrum match, number of peptides identified, and percentage of the proteins covered were the parameters collected for the hemoglobin subunits alpha (HbA), beta (HbB), delta (HbD), and gamma (HbG). These proteins are constant components of the peripheral blood and are present in high and low abundance, allowing the monitorization of the performance of the test across varying protein concentrations. The hemoglobin subunits were stable over the years studied; 71% to 74% of HbA, 77% to 80% of HbB, 69% to 77% of HbD, and 57% to 63% of HbG were covered, with no statistical difference between 2014 and 2018. The number of peptides identified was also constant, 11 to 13 for HbA, 13 to 15 for HbB, 11 to 14 for HbD, and 7 to 9 for HbG. Peptide spectrum match was only slightly more variable: 209 to 327 for HbA, 569 to 1052 for HbB, 286 to 533 HbD, and 142 to 292 for HbG. In conclusion, high abundance hemoglobins, HbA and HbB, and relatively low abundance ones, HbD and HbG, are preserved in FFPET and confidently identified by LC-MS/MS for at least 5 years.
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Affiliation(s)
| | - James Bena
- Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, Ohio
| | - Megan O Nakashima
- Department of Laboratory Medicine, RJ Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Adam J McShane
- Department of Laboratory Medicine, RJ Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Claudiu V Cotta
- Department of Laboratory Medicine, RJ Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio.
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19
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Stelloo E, Meijers RWJ, Swennenhuis JF, Allahyar A, Hajo K, Cangiano M, de Leng WWJ, van Helvert S, Van der Meulen J, Creytens D, van Kempen LC, Cleton-Jansen AM, Bovee JVMG, de Laat W, Splinter E, Feitsma H. Formalin-Fixed, Paraffin-Embedded-Targeted Locus Capture: A Next-Generation Sequencing Technology for Accurate DNA-Based Gene Fusion Detection in Bone and Soft Tissue Tumors. J Mol Diagn 2023; 25:758-770. [PMID: 37517473 DOI: 10.1016/j.jmoldx.2023.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/23/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023] Open
Abstract
Chromosomal rearrangements are important drivers in cancer, and their robust detection is essential for diagnosis, prognosis, and treatment selection, particularly for bone and soft tissue tumors. Current diagnostic methods are hindered by limitations, including difficulties with multiplexing targets and poor quality of RNA. A novel targeted DNA-based next-generation sequencing method, formalin-fixed, paraffin-embedded-targeted locus capture (FFPE-TLC), has shown advantages over current diagnostic methods when applied on FFPE lymphomas, including the ability to detect novel rearrangements. We evaluated the utility of FFPE-TLC in bone and soft tissue tumor diagnostics. FFPE-TLC sequencing was successfully applied on noncalcified and decalcified FFPE samples (n = 44) and control samples (n = 19). In total, 58 rearrangements were identified in 40 FFPE tumor samples, including three previously negative samples, and none was identified in the FFPE control samples. In all five discordant cases, FFPE-TLC could identify gene fusions where other methods had failed due to either detection limits or poor sample quality. FFPE-TLC achieved a high specificity and sensitivity (no false positives and negatives). These results indicate that FFPE-TLC is applicable in cancer diagnostics to simultaneously analyze many genes for their involvement in gene fusions. Similar to the observation in lymphomas, FFPE-TLC is a good DNA-based alternative to the conventional methods for detection of rearrangements in bone and soft tissue tumors.
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Affiliation(s)
| | - Ruud W J Meijers
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Amin Allahyar
- Oncode Institute, Hubrecht Institute-Royal Netherlands Academy of Arts and Sciences, and University Medical Center Utrecht, Utrecht, the Netherlands
| | | | | | - Wendy W J de Leng
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Sjoerd van Helvert
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - David Creytens
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Léon C van Kempen
- Department of Pathology, University Hospital Antwerp, University of Antwerp, Antwerp, Belgium; Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | | | - Judith V M G Bovee
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Wouter de Laat
- Oncode Institute, Hubrecht Institute-Royal Netherlands Academy of Arts and Sciences, and University Medical Center Utrecht, Utrecht, the Netherlands
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20
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Mangalaparthi KK, Singh S, Garapati K, Garcia JJ, Kipp BR, Roden AC, Pandey A. Identification of SARS-CoV-2 from Human Lung Formalin-Fixed Paraffin-Embedded Tissue Sections Using Mass Spectrometry. OMICS 2023; 27:494-496. [PMID: 37815798 PMCID: PMC10615085 DOI: 10.1089/omi.2023.0157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Affiliation(s)
| | - Smrita Singh
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Manipal Academy of Higher Education, Manipal, India
- Institute of Bioinformatics, International Tech Park, Bangalore, India
| | - Kishore Garapati
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Manipal Academy of Higher Education, Manipal, India
| | - Joaquin J. Garcia
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Benjamin R. Kipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Anja C. Roden
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
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21
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Zhang JJ, Long ZB, Luo LL, Li LH, Yang H, Cao Y, Wang L, Wang WP. Feasibility analysis of rapid gene detection using intraoperative frozen tissues: comparison of intraoperative frozen tissues with paraffin-embedded tissues in epidermal growth factor receptor gene mutation detection of lung adenocarcinoma. J Cancer Res Clin Oncol 2023; 149:12025-12032. [PMID: 37421459 DOI: 10.1007/s00432-023-05056-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 06/28/2023] [Indexed: 07/10/2023]
Abstract
BACKGROUND Epidermal growth factor receptor (EGFR) is the driver gene with the highest frequency of mutations in lung adenocarcinoma and can guide the development of targeted therapies. The detection of routine gene mutations must be performed after the preparation of paraffin samples in a standard polymerase chain reaction (PCR) laboratory, which is time-consuming. The Idylla™ EGFR fully automatic PCR system for rapid detection requires no special detection environment and completes the process in only 2.5 h. It has been applied to tissues embedded in paraffin. METHODS The Idylla™ EGFR automated PCR system was used to detect EGFR gene mutations in intraoperative frozen fresh tissues and paraffin-embedded tissues from 47 enrolled patients with lung adenocarcinoma. The gold standard amplification refractory mutation system (ARMS) method for gene mutation detection was used for verification, and the concordance between the three detection results was compared, to investigate the feasibility of detecting rapid gene mutations in intraoperative frozen samples. RESULTS The EGFR mutation rate in 47 fresh samples of lung adenocarcinoma was 61.7% (29/47), which is consistent with the mutation level of lung adenocarcinoma in the Asian population (38.8-64.0%). The concordance rate between the Idylla™ frozen tissues and paraffin-embedded tissues was 91.4% (43/47) when compared to the ARMS method, while the coincidence rate between the two methods was 93.6% (44/47). The three methods had a total consistency rate of 89.4% (42/47). CONCLUSIONS The Idylla™ EGFR fully automatic PCR system directly detects EGFR mutations in fresh tissues. The operation is simple, the detection time is short, and the accuracy is high. The detection time is reduced to 1/4-1/3 of the original time while meeting clinical standards for detecting the gene status of patients, thus saving crucial time for individualized and accurate treatment of patients. The method has promising clinical application prospects.
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Affiliation(s)
- Juan-Juan Zhang
- Department of Pathology, The First People's Hospital of Yunnan Province, No. 157 Jinbi Road, Xishan District, Kunming, 650032, Yunnan, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, 650032, Yunnan, China
| | - Zheng-Bo Long
- Kunming University of Science and Technology, Kunming, 650031, Yunnan, China
| | - Li-Lin Luo
- Department of Pathology, The First People's Hospital of Yunnan Province, No. 157 Jinbi Road, Xishan District, Kunming, 650032, Yunnan, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, 650032, Yunnan, China
| | - Lin-Hui Li
- Department of Pathology, The First People's Hospital of Yunnan Province, No. 157 Jinbi Road, Xishan District, Kunming, 650032, Yunnan, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, 650032, Yunnan, China
| | - Hui Yang
- Department of Pathology, The First People's Hospital of Yunnan Province, No. 157 Jinbi Road, Xishan District, Kunming, 650032, Yunnan, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, 650032, Yunnan, China
| | - Yue Cao
- Kunming University of Science and Technology, Kunming, 650031, Yunnan, China
| | - Li Wang
- Department of Pathology, The First People's Hospital of Yunnan Province, No. 157 Jinbi Road, Xishan District, Kunming, 650032, Yunnan, China.
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, 650032, Yunnan, China.
| | - Wan-Pu Wang
- Department of Pathology, The First People's Hospital of Yunnan Province, No. 157 Jinbi Road, Xishan District, Kunming, 650032, Yunnan, China.
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, 650032, Yunnan, China.
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22
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Dupont ME, Jacobsen SB, Christiansen SNN, Tfelt-Hansen J, Smerup MH, Andersen JD, Morling N. Fresh and frozen cardiac tissue are comparable in DNA methylation array β-values, but formalin-fixed, paraffin-embedded tissue may overestimate DNA methylation levels. Sci Rep 2023; 13:16381. [PMID: 37773256 PMCID: PMC10541404 DOI: 10.1038/s41598-023-43788-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 09/28/2023] [Indexed: 10/01/2023] Open
Abstract
Untreated fresh cardiac tissue is the optimal tissue material for investigating DNA methylation patterns of cardiac biology and diseases. However, fresh tissue is difficult to obtain. Therefore, tissue stored as frozen or formalin-fixed, paraffin-embedded (FFPE) is widely used for DNA methylation studies. It is unknown whether storage conditions alter the DNA methylation in cardiac tissue. In this study, we compared the DNA methylation patterns of fresh, frozen, and FFPE cardiac tissue to investigate if the storage method affected the DNA methylation results. We used the Infinium MethylationEPIC assay to obtain genome-wide methylation levels in fresh, frozen, and FFPE tissues from nine individuals. We found that the DNA methylation levels of 21.4% of the examined CpG sites were overestimated in the FFPE samples compared to that of fresh and frozen tissue, whereas 5.7% were underestimated. Duplicate analyses of the DNA methylation patterns showed high reproducibility (precision) for frozen and FFPE tissues. In conclusion, we found that frozen and FFPE tissues gave reproducible DNA methylation results and that frozen and fresh tissues gave similar results.
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Affiliation(s)
- Mikkel Eriksen Dupont
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Stine Bøttcher Jacobsen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Steffan Noe Niikanoff Christiansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Jacob Tfelt-Hansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Cardiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Morten Holdgaard Smerup
- Department of Cardiothoracic Surgery, Rigshospitalet Copenhagen University Hospital, Copenhagen, Denmark
| | - Jeppe Dyrberg Andersen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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23
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Soni RK. Protocol for deep proteomic profiling of formalin-fixed paraffin-embedded specimens using a spectral library-free approach. STAR Protoc 2023; 4:102381. [PMID: 37355991 PMCID: PMC10319319 DOI: 10.1016/j.xpro.2023.102381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/20/2023] [Accepted: 05/23/2023] [Indexed: 06/27/2023] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) samples are valuable archived bio-specimens of individuals and are commonly used in biomedical research. Here, we present a protocol for deep proteomic profiling of FFPE specimens using a spectral library-free approach. We describe steps for FFPE tissue collection, tissue lysis, homogenization, protein lysate cleanup, on-beads digestion, and de-salting. We then detail data acquisition and statistical analysis. This protocol is highly sensitive, reproducible, and applicable for high-throughput proteomic profiling and can be used on various types of specimens.
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Affiliation(s)
- Rajesh Kumar Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Columbia University Irving Medical Center, New York, NY, USA; Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA.
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24
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Wang LC, Hsieh YH, Hung YL, Jiang YT, Lin YC, Chang MDT, Lin YY, Chou TY. Panoramic Tissue Examination That Integrates 3-Dimensional Pathology Imaging and Gene Mutation: Potential Utility in Non-Small Cell Lung Cancer. J Transl Med 2023; 103:100195. [PMID: 37302529 DOI: 10.1016/j.labinv.2023.100195] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/12/2023] [Accepted: 06/05/2023] [Indexed: 06/13/2023] Open
Abstract
Novel therapeutics have significantly improved the survival and quality of life of patients with malignancies in this century. Versatile precision diagnostic data were used to formulate personalized therapeutic strategies for patients. However, the cost of extensive information depends on the consumption of the specimen, raising the challenges of effective specimen utilization, particularly in small biopsies. In this study, we proposed a tissue-processing cascaded protocol that obtains 3-dimensional (3D) protein expression spatial distribution and mutation analysis from an identical specimen. In order to reuse the thick section tissue evaluated after the 3D pathology technique, we designed a novel high-flatness agarose-embedded method that could improve tissue utilization rate by 1.52 fold, whereas it reduced the tissue-processing time by 80% compared with the traditional paraffin-embedding method. In animal studies, we demonstrated that the protocol would not affect the results of DNA mutation analysis. Furthermore, we explored the utility of this approach in non-small cell lung cancer because it is a compelling application for this innovation. We used 35 cases including 7 cases of biopsy specimens of non-small cell lung cancer to simulate future clinical application. The cascaded protocol consumed 150-μm thickness of formalin-fixed, paraffin-embedded specimens, providing 3D histologic and immunohistochemical information approximately 38 times that of the current paraffin-embedding protocol, and 3 rounds of DNA mutation analysis, offering both essential guidance for routine diagnostic evaluation and advanced information for precision medicine. Our designed integrated workflow provides an alternative way for pathological examination and paves the way for multidimensional tumor tissue assessment.
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Affiliation(s)
- Lei-Chi Wang
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan; Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | | | | | | | | | | | | | - Teh-Ying Chou
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan; Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Pathology, Taipei Medical University Hospital, Taipei Medical University, Taipei, Taiwan; Graduate Institute of Clinical Medicine, Taipei Medical University, Taipei, Taiwan.
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25
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Steiert TA, Parra G, Gut M, Arnold N, Trotta JR, Tonda R, Moussy A, Gerber Z, Abuja P, Zatloukal K, Röcken C, Folseraas T, Grimsrud M, Vogel A, Goeppert B, Roessler S, Hinz S, Schafmayer C, Rosenstiel P, Deleuze JF, Gut I, Franke A, Forster M. A critical spotlight on the paradigms of FFPE-DNA sequencing. Nucleic Acids Res 2023; 51:7143-7162. [PMID: 37351572 PMCID: PMC10415133 DOI: 10.1093/nar/gkad519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 05/24/2023] [Accepted: 06/05/2023] [Indexed: 06/24/2023] Open
Abstract
In the late 19th century, formalin fixation with paraffin-embedding (FFPE) of tissues was developed as a fixation and conservation method and is still used to this day in routine clinical and pathological practice. The implementation of state-of-the-art nucleic acid sequencing technologies has sparked much interest for using historical FFPE samples stored in biobanks as they hold promise in extracting new information from these valuable samples. However, formalin fixation chemically modifies DNA, which potentially leads to incorrect sequences or misinterpretations in downstream processing and data analysis. Many publications have concentrated on one type of DNA damage, but few have addressed the complete spectrum of FFPE-DNA damage. Here, we review mitigation strategies in (I) pre-analytical sample quality control, (II) DNA repair treatments, (III) analytical sample preparation and (IV) bioinformatic analysis of FFPE-DNA. We then provide recommendations that are tested and illustrated with DNA from 13-year-old liver specimens, one FFPE preserved and one fresh frozen, applying target-enriched sequencing. Thus, we show how DNA damage can be compensated, even when using low quantities (50 ng) of fragmented FFPE-DNA (DNA integrity number 2.0) that cannot be amplified well (Q129 bp/Q41 bp = 5%). Finally, we provide a checklist called 'ERROR-FFPE-DNA' that summarises recommendations for the minimal information in publications required for assessing fitness-for-purpose and inter-study comparison when using FFPE samples.
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Affiliation(s)
- Tim A Steiert
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, Kiel 24105, Germany
| | - Genís Parra
- Center for Genomic Regulation, Centro Nacional de Análisis Genómico, Barcelona 08028, Spain
| | - Marta Gut
- Center for Genomic Regulation, Centro Nacional de Análisis Genómico, Barcelona 08028, Spain
| | - Norbert Arnold
- Department of Gynaecology and Obstetrics, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel 24105, Germany
| | - Jean-Rémi Trotta
- Center for Genomic Regulation, Centro Nacional de Análisis Genómico, Barcelona 08028, Spain
| | - Raúl Tonda
- Center for Genomic Regulation, Centro Nacional de Análisis Genómico, Barcelona 08028, Spain
| | - Alice Moussy
- Le Centre de référence, d’innovation, d’expertise et de transfert (CRefIX), PFMG 2025, Évry 91057, France
| | - Zuzana Gerber
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Évry 91057, France
| | - Peter M Abuja
- Diagnostic & Research Center for Molecular Biomedicine, Diagnostic & Research Institute of Pathology, Medical University of Graz, Graz 8010, Austria
| | - Kurt Zatloukal
- Diagnostic & Research Center for Molecular Biomedicine, Diagnostic & Research Institute of Pathology, Medical University of Graz, Graz 8010, Austria
| | - Christoph Röcken
- Department of Pathology, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel 24105, Germany
| | - Trine Folseraas
- Norwegian PSC Research Center Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo 0372, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo 0372, Norway
| | - Marit M Grimsrud
- Norwegian PSC Research Center Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo 0372, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo 0372, Norway
| | - Arndt Vogel
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hanover 30625, Germany
| | - Benjamin Goeppert
- Institute of Pathology, University Hospital Heidelberg, Heidelberg 69120, Germany
- Institute of Pathology and Neuropathology, RKH Klinikum Ludwigsburg, Ludwigsburg 71640, Germany
| | - Stephanie Roessler
- Institute of Pathology, University Hospital Heidelberg, Heidelberg 69120, Germany
| | - Sebastian Hinz
- Department of General Surgery, University Medicine Rostock, Rostock 18057, Germany
| | - Clemens Schafmayer
- Department of General Surgery, University Medicine Rostock, Rostock 18057, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, Kiel 24105, Germany
| | - Jean-François Deleuze
- Le Centre de référence, d’innovation, d’expertise et de transfert (CRefIX), PFMG 2025, Évry 91057, France
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Évry 91057, France
| | - Ivo G Gut
- Center for Genomic Regulation, Centro Nacional de Análisis Genómico, Barcelona 08028, Spain
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, Kiel 24105, Germany
| | - Michael Forster
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, Kiel 24105, Germany
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26
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Li J, Greytak SR, Guan P, Engel KB, Goerlitz DS, Islam M, Varghese RS, Moore HM, Ressom HW. Formalin Fixation, Delay to Fixation, and Time in Fixative Adversely Impact Copy Number Variation Analysis by aCGH. Biopreserv Biobank 2023; 21:407-416. [PMID: 36169416 PMCID: PMC10460690 DOI: 10.1089/bio.2022.0036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Although molecular profiling of DNA isolated from formalin-fixed, paraffin-embedded (FFPE) tumor specimens has become more common in recent years, it remains unclear how discrete FFPE processing variables may affect detection of copy number variation (CNV). To better understand such effects, array comparative genomic hybridization (aCGH) profiles of FFPE renal cell carcinoma specimens that experienced different delays to fixation (DTFs; 1, 2, 3, and 12 hours) and times in fixative (TIFs; 6, 12, 23, and 72 hours) were compared to snap-frozen tumor and blood specimens from the same patients. A greater number of regions containing CNVs relative to commercial reference DNA were detected in DNA from FFPE tumor specimens than snap-frozen tumor specimens even though they originated from the same tumor blocks. Extended DTF and TIF affected the number of DNA segments with a copy number status that differed between FFPE and frozen tumor specimens; a DTF ≥3 hours led to more segments, while a TIF of 72 hours led to fewer segments. Importantly, effects were not random as a higher guanine-cytosine (GC) content and/or a higher percentage of repeats were observed among stable regions. While limiting aCGH analysis to FFPE specimens with a DTF <3 hours and a TIF <72 hours may circumvent some effects, results from FFPE specimens should be validated against fresh or frozen specimens whenever possible.
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Affiliation(s)
- James Li
- Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University, Washington, District of Columbia, USA
| | | | - Ping Guan
- Biorepositories & Biospecimen Research Branch, National Cancer Institute, Bethesda, Maryland, USA
| | | | - David S. Goerlitz
- Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University, Washington, District of Columbia, USA
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA
| | - Md Islam
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA
| | - Rency S. Varghese
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA
| | - Helen M. Moore
- Biorepositories & Biospecimen Research Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Habtom W. Ressom
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA
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27
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Shi Y, Yee-Chang M, Shi SR. Application of Immunohistochemistry in Cytology. Appl Immunohistochem Mol Morphol 2023; 31:459-466. [PMID: 36730366 DOI: 10.1097/pai.0000000000001086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 10/19/2022] [Indexed: 02/04/2023]
Abstract
Immunohistochemistry (IHC), also referred to as immunocytochemistry in cytology literature, has revolutionized the practice of cytopathology. Because of the complexity of cytology preparation and limited diagnostic material, performing IHC remains a challenge. Formalin-fixed paraffin-embedded (FFPE) cell block (CB) is the optimal choice for IHC. In this review, the approaches for improving CB preparation will be discussed. When CB material is not available, various cytology specimens can also be used for IHC. With the utilization of Antigen Retrieval (AR) technique, these nonformalin-fixed cytology specimens can achieve successful IHC staining, comparable with the results from FFPE tissue sections. In the last part of this review, we will discuss the use of positive controls and the important role of AR in standardization of IHC in cytology.
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Affiliation(s)
- Yan Shi
- Department of Pathology, New York University Grossman School of Medicine, New York, NY
| | - Melissa Yee-Chang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY
| | - Shan-Rong Shi
- Department of Pathology, University of Southern California Keck School of Medicine, Los Angeles, CA
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28
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Marczyk M, Fu C, Lau R, Du L, Trevarton AJ, Sinn BV, Gould RE, Pusztai L, Hatzis C, Symmans WF. Assessment of stained direct cytology smears of breast cancer for whole transcriptome and targeted messenger RNA sequencing. Cancer Cytopathol 2023; 131:289-299. [PMID: 36650408 PMCID: PMC10614161 DOI: 10.1002/cncy.22679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/04/2022] [Accepted: 11/28/2022] [Indexed: 01/19/2023]
Abstract
BACKGROUND Rather than surgical resection, cytologic specimens are often used as first-line clinical diagnostic procedures due to higher safety, speed, and cost-effectiveness. Archival diagnostic cytology slides containing cancer can be equivalent to tissue biopsies for DNA mutation testing, but the accuracy of transcriptomic profiling by RNA sequencing (RNA-seq) is less understood. METHODS This study compares the results from whole transcriptome RNA-seq and a targeted RNA-seq assay of stained cytology smears (CS) versus matched tumor tissue samples preserved fresh-frozen (FF) and processed as formalin-fixed paraffin-embedded (FFPE) sections. Cellular cytology scrapes from all 11 breast cancers were fixed and stained using three common protocols: Carnoy's (CS_C) or 95% ethanol (CS_E) fixation and then Papanicolaou stain or air-dried then methanol fixation and DiffQuik stain (CS_DQ). Agreement between samples was assessed using Lin's concordance correlation coefficient. RESULTS Library yield for CS_DQ was too low, therefore it was not sequenced. The distributions of concordance correlation coefficient of gene expression levels in comparison to FF were comparable between CS_C and CS_E, but expression of genes enriched in stroma was lower in cytosmear samples than in FF or FFPE. Six signatures showed similar concordance to FF for all methods and two were slightly worse in CS_C and CS_E. Genomic signatures were highly concordant using targeted RNA-seq. The allele fraction of selected mutations calculated on cytosmear specimens was highly correlated with FF tissues using both RNA-seq methods. CONCLUSION RNA can be reliably extracted from cytology smears and is suitable for transcriptome profiling or mutation detection, except for signatures of tumor stroma.
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Affiliation(s)
- Michal Marczyk
- Yale Cancer Center Yale School of Medicine, New Haven, Connecticut, USA
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Chunxiao Fu
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Rosanna Lau
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lili Du
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Alexander J. Trevarton
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Bruno V. Sinn
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Rebekah E. Gould
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lajos Pusztai
- Yale Cancer Center Yale School of Medicine, New Haven, Connecticut, USA
| | - Christos Hatzis
- Yale Cancer Center Yale School of Medicine, New Haven, Connecticut, USA
| | - William Fraser Symmans
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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29
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Abuja PM, Pabst D, Bourgeois B, Loibner M, Ulz C, Kufferath I, Fackelmann U, Stumptner C, Kraemer R, Madl T, Zatloukal K. Residual Humidity in Paraffin-Embedded Tissue Reduces Nucleic Acid Stability. Int J Mol Sci 2023; 24:8010. [PMID: 37175716 PMCID: PMC10178321 DOI: 10.3390/ijms24098010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/11/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Molecular diagnostics in healthcare relies increasingly on genomic and transcriptomic methodologies and requires appropriate tissue specimens from which nucleic acids (NA) of sufficiently high quality can be obtained. Besides the duration of ischemia and fixation type, NA quality depends on a variety of other pre-analytical parameters, such as storage conditions and duration. It has been discussed that the improper dehydration of tissue during processing influences the quality of NAs and the shelf life of fixed tissue. Here, we report on establishing a method for determining the amount of residual water in fixed, paraffin-embedded tissue (fixed by neutral buffered formalin or a non-crosslinking fixative) and its correlation to the performance of NAs in quantitative real-time polymerase chain reaction (qRT-PCR) analyses. The amount of residual water depended primarily on the fixative type and the dehydration protocol and, to a lesser extent, on storage conditions and time. Moreover, we found that these parameters were associated with the qRT-PCR performance of extracted NAs. Besides the cross-linking of NAs and the modification of nucleobases by formalin, the hydrolysis of NAs by residual water was found to contribute to reduced qRT-PCR performance. The negative effects of residual water on NA stability are not only important for the design and interpretation of research but must also be taken into account in clinical diagnostics where the reanalysis of archived tissue from a primary tumor may be required (e.g., after disease recurrence). We conclude that improving the shelf life of fixed tissue requires meticulous dehydration and dry storage to minimize the degradative influence of residual water on NAs.
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Affiliation(s)
- Peter M. Abuja
- Diagnostic & Research Centre for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Daniela Pabst
- Diagnostic & Research Centre for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Benjamin Bourgeois
- Gottfried Schatz Research Centre for Cell Signalling, Metabolism and Ageing, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| | - Martina Loibner
- Diagnostic & Research Centre for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Christine Ulz
- Diagnostic & Research Centre for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Iris Kufferath
- Diagnostic & Research Centre for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Ulrike Fackelmann
- Diagnostic & Research Centre for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Cornelia Stumptner
- Diagnostic & Research Centre for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Rainer Kraemer
- Berghof Products & Instruments GmbH, 72800 Eningen, Germany
| | - Tobias Madl
- Gottfried Schatz Research Centre for Cell Signalling, Metabolism and Ageing, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| | - Kurt Zatloukal
- Diagnostic & Research Centre for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
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30
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Birrer F, Brodie T, Stroka D. OMIP-088: Twenty-target imaging mass cytometry panel for major cell populations in mouse formalin fixed paraffin embedded liver. Cytometry A 2023; 103:189-192. [PMID: 36602064 DOI: 10.1002/cyto.a.24714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/08/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023]
Abstract
The purpose of this 20-target imaging mass cytometry (IMC) panel is to identify the main cell types in formalin fixed paraffin embedded (FFPE) mouse liver tissue with the Hyperion™ mass cytometer from Standard BioTools (formerly Fluidigm). The antibody panel includes markers to identify hepatocytes (E-cadherin, HNF4α (hepatocyte nuclear factor 4 alpha), Arginase-1), liver sinusoidal endothelial cells (LSECs; CD206), Kupffer cells (F4/80, CD206), neutrophils (Ly6G, CD11b), bone marrow derived myeloid cells (BMDMs; CD11b), cholangiocytes (E-cadherin high), endothelial cells (CD31, α-SMA), plasmacytoid dendritic cells (CD317), B cells (CD19), T cells (CD3e, CD4, CD8a), NK cells (CD161) as well markers of cell activation (CD44, CD74), proliferation (Ki-67) and to aid in cell segmentation (Pan-Actin, E-cadherin, histone H3). The panel has been tested in other mouse tissues, namely the spleen, colon and lung, and therefore is likely to work across various mouse FFPE samples of interest. It has not been tested using human samples, frozen samples or in suspension mass cytometry because FFPE treatment profoundly changes epitope conformation. In summary, this panel is a powerful tool for pre-clinical research to determine cellular abundance and spatial distribution within mouse tissues and serves as a scaffold, to which more targets can be added for project specific requirements.
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Affiliation(s)
- Fabienne Birrer
- Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Switzerland
| | - Tess Brodie
- Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Switzerland
| | - Deborah Stroka
- Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Switzerland
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31
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Barnabas G, Goebeler V, Tsui J, Bush JW, Lange PF. ASAP─Automated Sonication-Free Acid-Assisted Proteomes─from Cells and FFPE Tissues. Anal Chem 2023; 95:3291-3299. [PMID: 36724070 PMCID: PMC9933881 DOI: 10.1021/acs.analchem.2c04264] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 01/17/2023] [Indexed: 02/02/2023]
Abstract
Formalin-fixed, paraffin-embedded (FFPE) tissues are an invaluable resource for retrospective studies, but protein extraction and subsequent sample processing steps have been shown to be challenging for mass spectrometry (MS) analysis. Streamlined high-throughput sample preparation workflows are essential for efficient peptide extraction from complex clinical specimens such as fresh frozen tissues or FFPE. Overall, proteome analysis has gained significant improvements in the instrumentation, acquisition methods, sample preparation workflows, and analysis pipelines, yet even the most recent FFPE workflows remain complex and are not readily scalable. Here, we present an optimized workflow for automated sonication-free acid-assisted proteome (ASAP) extraction from FFPE sections. ASAP enables efficient protein extraction from FFPE specimens, achieving similar proteome coverage as established methods using expensive sonicators, resulting in reduced sample processing time. The broad applicability of ASAP on archived pediatric tumor FFPE specimens resulted in high-quality data with increased proteome coverage and quantitative reproducibility. Our study demonstrates the practicality and superiority of the ASAP workflow as a streamlined, time- and cost-effective pipeline for high-throughput FFPE proteomics of clinical specimens.
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Affiliation(s)
- Georgina
D. Barnabas
- Department
of Pathology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Michael
Cuccione Childhood Cancer Research Program, BC Children’s Hospital and Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
| | - Verena Goebeler
- Department
of Pediatrics, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Michael
Cuccione Childhood Cancer Research Program, BC Children’s Hospital and Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
| | - Janice Tsui
- Department
of Pathology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Michael
Cuccione Childhood Cancer Research Program, BC Children’s Hospital and Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
| | - Jonathan W. Bush
- Department
of Pathology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Philipp F. Lange
- Department
of Pathology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Michael
Cuccione Childhood Cancer Research Program, BC Children’s Hospital and Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
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32
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Jiang J, Tang C, Li Y, Lin Z, Li Z, Zhou C, Gu Y, He P, Tang Q, Zhang Y, Deng Q, Ge Y, Liang W, He J. Cell pellet from fixative medium of transbronchial lung biopsy sample improves lung cancer ancillary test. Lung Cancer 2023; 175:9-16. [PMID: 36436242 DOI: 10.1016/j.lungcan.2022.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 11/20/2022]
Abstract
OBJECTIVES Lung cancer tissue obtained using small biopsies are relatively fragile, leaving behind some tiny tissue fragments or cell clusters in the fixative medium that are difficult to collect for processing as a paraffin-embedded tissue block. Usually, the cellular component of the residual fixative medium is discarded as medical waste as per routine laboratory protocol. No protocol exists for utilizing the cellular component of the residual fixative medium after processing the tissue blocks to improve lung cancer ancillary testing. This study aimed to undercover the potential value of these samples for lung cancer diagnosis and targeted therapy development. MATERIALS AND METHODS A protocol was developed for cell pellet sample collection from the residual fixative medium of a transbronchial forceps lung biopsy sample. Tumour cell number and fraction in a paired cell pellet and matching formalin-fixed paraffin-embedded tissue section were evaluated from 324 non-smallcell lung carcinoma (NSCLC) cases. We defined the adequacy of the cell pellet for molecular analysis as ≥ 200 tumour cells and ≥ 10 % tumour cells. Real-time polymerase chain reaction and next-generation sequencing were performed on adequate cell pellet samples. RESULTS We discovered that the fixative medium of most transbronchial forceps lung biopsy samples was enriched in tumour cells. Among 324 biopsy samples, 70 (21.6%) exhibited inadequate formalin-fixed paraffin-embedded tissue sections, whereas 53 (75.7%) yielded adequate cell pellet samples. Somatic mutations detected in the formalin-fixed paraffin-embedded tissue section samples were also detected in the matching cell pellets. CONCLUSIONS Cell pellets collected from the fixative medium of thoracic small biopsies are a beneficial supplemental material for ancillary testing. Combined use of cell pellets with traditional tissue-based samples can enhance the detection rate of informative mutations in patients with advanced NSCLC.
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Affiliation(s)
- Juhong Jiang
- China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Chunli Tang
- China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yuqin Li
- China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zeyun Lin
- China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhi Li
- Department of Pathology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Chengzhi Zhou
- China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yingying Gu
- China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ping He
- Department of Pathology, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qing Tang
- Department of Ultrasound, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yuxin Zhang
- Department of Ultrasound, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qiuhua Deng
- Department of Clinical Laboratory, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yimin Ge
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Wenhua Liang
- China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jianxing He
- China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
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33
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Latimer CS, Melief EJ, Ariza-Torres J, Howard K, Keen AR, Keene LM, Schantz AM, Sytsma TM, Wilson AM, Grabowski TJ, Darvas M, O'Connor KD, Nolan AL, Edlow BL, Mac Donald CL, Keene CD. Protocol for the Systematic Fixation, Circuit-Based Sampling, and Qualitative and Quantitative Neuropathological Analysis of Human Brain Tissue. Methods Mol Biol 2023; 2561:3-30. [PMID: 36399262 DOI: 10.1007/978-1-0716-2655-9_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Human brain tissue has long been a critical resource for neuroanatomy and neuropathology, but with the advent of advanced imaging and molecular sequencing techniques, it has become possible to use human brain tissue to study, in great detail, the structural, molecular, and even functional underpinnings of human brain disease. In the century following the first description of Alzheimer's disease (AD), numerous technological advances applied to human tissue have enabled novel diagnostic approaches using diverse physical and molecular biomarkers, and many drug therapies have been tested in clinical trials (Schachter and Davis, Dialogues Clin Neurosci 2:91-100, 2000). The methods for brain procurement and tissue stabilization have remained somewhat consistently focused on formalin fixation and freezing. Although these methods have enabled research protocols of multiple modalities, new, more advanced technologies demand improved methodologies for the procurement, characterization, stabilization, and preparation of both normal and diseased human brain tissues. Here, we describe our current protocols for the procurement and characterization of fixed brain tissue, to enable systematic and precisely targeted diagnoses, and describe the novel, quantitative molecular, and neuroanatomical studies that broadly expand the use of formalin-fixed, paraffin-embedded (FFPE) tissue that will further our understanding of the mechanisms underlying human neuropathologies.
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Affiliation(s)
- Caitlin S Latimer
- University of Washington, Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Erica J Melief
- University of Washington, Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Jeanelle Ariza-Torres
- University of Washington, Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Kim Howard
- University of Washington, Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Amanda R Keen
- University of Washington, Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Lisa M Keene
- University of Washington, Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Aimee M Schantz
- University of Washington, Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Trevor M Sytsma
- University of Washington, Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Angela M Wilson
- University of Washington, Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | | | - Martin Darvas
- University of Washington, Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | | | - Amber L Nolan
- University of Washington, Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Brian L Edlow
- Massachusetts General Hospital, Department of Neurology, Boston, MA, USA
| | | | - C Dirk Keene
- University of Washington, Department of Laboratory Medicine and Pathology, Seattle, WA, USA.
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34
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Bürgisser GM, Heuberger DM, Schaffner N, Giovanoli P, Calcagni M, Buschmann J. Delineation of the healthy rabbit heart by immunohistochemistry - A technical note. Acta Histochem 2023; 125:151993. [PMID: 36584538 DOI: 10.1016/j.acthis.2022.151993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/22/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022]
Abstract
Heart failure poses a big health problem and may result from obesity, smoking, alcohol and/or growing age. Studying pathological heart tissue demands accurate histological and immunohistochemical stainings in animal models, including chromogenic and fluorescent approaches. Moreover, a reliable set of healthy heart stainings and labeling are required, in order to provide a reference for the pathological situation. Heart and brain tissue of a healthy rabbit were collected, and different histological key steps were compared, such as paraffin embedding after formalin fixation versus cryopreservation; an antigen retrieval (AR) step in processing paraffin sections versus the same procedure without AR; or a chromogenic with a fluorescent detection system, respectively. Using serial sections, we stained the same morphological structure with classic approaches (HE, Masson Goldner Trichrome (GT) and Elastica van Gieson (EL)) and with different markers, including collagen I, collagen III, fibronectin, α-SMA, protease-activated receptor-2 (PAR-2) which is an inflammation-related marker, and ki67 for proliferating cells. Differences between conditions were quantitatively assessed by measuring the color intensity. Generally, cryosections exhibited a more prominent signal intensity in immunohistochemically labeled sections than in paraffin sections, but the strong staining was slurry, which sometimes impeded proper identification of morphological structures, particularly at higher magnifications. In addition, the advantage of an AR step was observed when compared to the condition without AR, where signal intensities were significantly lower. Different stainings of the heart arteries and the myocardium revealed a clear distribution of extracellular matrix components, with prominent collagen III in the artery wall, but an absence of collagen III in the myocardium. Moreover, paraffin-embedded sections provided more distinct structures compared to cryosections after collagen III, ki67, fibronectin, and α-SMA labeling. As for the Purkinje cells that were depicted in the heart and the cerebellum (Purkinje neurons), we found GT staining most suitable to depict them in the heart, while HE as well as EL staining was ideal to depict Purkinje neurons in the cerebellum. In sum, we provide useful reference images with different stainings for researchers using the rabbit heart or brain model. Such images can help to decide which of the immunohistochemical protocols are valuable to reach a specific aim. Recommendations are given for the best visualization of the target structures and specific (immunohistochemical) staining.
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Affiliation(s)
- Gabriella Meier Bürgisser
- Division of Plastic Surgery and Hand Surgery, University Hospital Zurich, Sternwartstrasse 14, 8091 Zurich, Switzerland
| | - Dorothea M Heuberger
- Institute of Intensive Care Medicine, University Hospital Zurich, Sternwartstrasse 14, 8091 Zurich, Switzerland
| | - Nicola Schaffner
- Division of Plastic Surgery and Hand Surgery, University Hospital Zurich, Sternwartstrasse 14, 8091 Zurich, Switzerland
| | - Pietro Giovanoli
- Division of Plastic Surgery and Hand Surgery, University Hospital Zurich, Sternwartstrasse 14, 8091 Zurich, Switzerland
| | - Maurizio Calcagni
- Division of Plastic Surgery and Hand Surgery, University Hospital Zurich, Sternwartstrasse 14, 8091 Zurich, Switzerland
| | - Johanna Buschmann
- Division of Plastic Surgery and Hand Surgery, University Hospital Zurich, Sternwartstrasse 14, 8091 Zurich, Switzerland.
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35
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Dowling P. DIGE Saturation Labeling for Scarce Amounts of Protein from Formalin-Fixed Paraffin-Embedded (FFPE) Tissue. Methods Mol Biol 2023; 2596:113-118. [PMID: 36378435 DOI: 10.1007/978-1-0716-2831-7_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In this chapter, we describe the utility of fluorescence two-dimensional difference gel electrophoresis (2D-DIGE) as a proteomics platform for the global detection of expressed proteins in formalin-fixed paraffin-embedded (FFPE) tissues and its use for biomarker discovery/identification of proteins that may contribute to cancer development and progression. Formalin fixation and paraffin embedding of tissue is the standard processing methodology practiced in pathology laboratories worldwide, resulting in a highly stable form of tissue that is easily stored due to its inherent stability at room temperature. Consequently, FFPE tissues represent an attractive reservoir of clinical material for conducting retrospective protein biomarker analysis. A limitation for proteomics research in this type of clinical sample is the amount of viable protein that can be obtained from fixed tissues. Tissue biopsies are precious samples that can generally be acquired in very small amounts due to the invasive nature of the sample collection, mainly during surgery or biopsy. Subsequently, the amount of extracted protein can be, in many cases, very limited. The saturation 2D-DIGE technology has emerged as a useful method for protein analysis where only scarce amounts of protein are available. This approach can be adapted successfully to label low-level protein isolated from FFPE tissue.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
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36
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Sánchez-Porras D, Bermejo-Casares F, Carmona R, Weiss T, Campos F, Carriel V. Tissue Fixation and Processing for the Histological Identification of Lipids. Methods Mol Biol 2023; 2566:175-186. [PMID: 36152251 DOI: 10.1007/978-1-0716-2675-7_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Lipids are a heterogeneous group of substances characterized by their solubility in organic solvents and insolubility in water. Lipids can be found as normal components of different tissues and organs, and they can be affected by several pathological conditions. The histochemical identification of lipids plays an important role in the histopathological diagnosis and research, but successful staining depends on adequate fixation and processing of the tissue. Here we describe methods to fix, cryoprotect, and process tissue samples for the histochemical identification of lipids in frozen or paraffin-embedded tissues.
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Affiliation(s)
- David Sánchez-Porras
- Department of Histology (Tissue Engineering Group), Faculty of Medicine, University of Granada, Granada, Spain.
- Instituto de Investigación Biosanitaria, Ibs.GRANADA, Granada, Spain.
| | - Fabiola Bermejo-Casares
- Department of Histology (Tissue Engineering Group), Faculty of Medicine, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria, Ibs.GRANADA, Granada, Spain
| | - Ramón Carmona
- Department of Cell Biology, Faculty of Science, University of Granada, Granada, Spain
| | - Tamara Weiss
- Department of Plastic, Reconstructive and Aesthetic Surgery, Medical University of Vienna, Vienna, Austria
| | - Fernando Campos
- Department of Histology (Tissue Engineering Group), Faculty of Medicine, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria, Ibs.GRANADA, Granada, Spain
| | - Víctor Carriel
- Department of Histology (Tissue Engineering Group), Faculty of Medicine, University of Granada, Granada, Spain.
- Instituto de Investigación Biosanitaria, Ibs.GRANADA, Granada, Spain.
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37
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Ramsower C, Wisner L, Zellner K, Glinsmann-Gibson B, Larsen B, McGrath M, Maguire A, Rimsza L. Assessment of 2-Year Storage Conditions on Protein, RNA, and DNA in Unstained Human Tissue Sections, Including a Novel Multiplex Digital Gene Expression Profiling Method with Implications for Biobanking. Biopreserv Biobank 2022; 20:473-484. [PMID: 34591685 PMCID: PMC9810356 DOI: 10.1089/bio.2021.0023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Background: Formalin-fixed, paraffin-embedded (FFPE) tissues are a valuable resource for clinical and basic science research. Paraffin blocks and the resulting unstained sections (USS) are often stored for years before being used. Previous studies have evaluated the effects of time, temperature, humidity, and inert gases on preservation of USS; however, no study has examined all four variables together. Methods: In the current work, we prospectively and blindly assessed time points from 0 to 24 months, room versus refrigerated temperature, and presence of a desiccant and/or nitrogen atmosphere on a variety of benign and malignant tissues from North America and Africa. End points included immunohistochemistry (IHC), in situ hybridization (ISH), extracted RNA and DNA quantity and quality, and messenger RNA performance in a novel, multiplexed digital gene expression profiling assay of both housekeeping and tumor-specific genes. Results: We found that using current methods of antigen retrieval, staining, and extraction, the end points of IHC, ISH, RNA, and DNA were well preserved under the various conditions tested, with implications that pre-embedding factors contribute to variability in subsequent tissue integrity. We also document that spectrophotometric estimations of nucleic acid concentrations were in general estimated to be higher than with fluorimetric methods, which may be pertinent to end assay development. We further describe a new multiplex assay, the PlexSet digital gene expression assay, suitable for evaluating RNA quality in FFPE tissues. Conclusion: Altogether, these results may provide helpful guidance with regard to approaches for long-term storage conditions for USS.
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Affiliation(s)
- Colleen Ramsower
- Department of Research, and Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | - Lee Wisner
- Department of Research, and Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | - Katie Zellner
- Department of Research, and Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | | | - Brandon Larsen
- Department of Laboratory Medicine and Pathology, Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | - Michael McGrath
- Department of Medicine, University of California, San Francisco, California, USA
| | - Alanna Maguire
- Department of Research, and Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | - Lisa Rimsza
- Department of Laboratory Medicine and Pathology, Mayo Clinic Arizona, Scottsdale, Arizona, USA
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38
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Köhler SA, Brandl L, Strissel PL, Gloßner L, Ekici AB, Angeloni M, Ferrazzi F, Bahlinger V, Hartmann A, Beckmann MW, Eckstein M, Strick R. Improved Bladder Tumor RNA Isolation from Archived Tissues Using Methylene Blue for Normalization, Multiplex RNA Hybridization, Sequencing and Subtyping. Int J Mol Sci 2022; 23:ijms231810267. [PMID: 36142180 PMCID: PMC9499321 DOI: 10.3390/ijms231810267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/26/2022] [Accepted: 09/02/2022] [Indexed: 12/02/2022] Open
Abstract
Methylene blue (MB) is a dye used for histology with clinical importance and intercalates into nucleic acids. After MB staining of formalin fixed paraffin embedded (FFPE) muscle invasive bladder cancer (MIBC) and normal urothelium, specific regions could be microdissected. It is not known if MB influences RNA used for gene expression studies. Therefore, we analyzed MIBC using five different RNA isolation methods comparing patient matched FFPE and fresh frozen (FF) tissues pre-stained with or without MB. We demonstrate a positive impact of MB on RNA integrity with FF tissues using real time PCR with no interference of its chemical properties. FFPE tissues showed no improvement of RNA integrity, which we propose is due to formalin induced nucleotide crosslinks. Using direct multiplex RNA hybridization the best genes for normalization of MIBC and control tissues were identified from 34 reference genes. In addition, 5SrRNA and 5.8SrRNA were distinctive reference genes detecting <200 bp fragments important for mRNA analyses. Using these normalized RNAs from MB stained MIBC and applying multiplex RNA hybridization and mRNA sequencing, a minimal gene expression panel precisely identified luminal and basal MIBC tumor subtypes, important for diagnosis, prognosis and chemotherapy response.
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Affiliation(s)
- Stefanie A. Köhler
- Laboratory for Molecular Medicine, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Universitaetsstrasse 21-23, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
| | - Lisa Brandl
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Pamela L. Strissel
- Laboratory for Molecular Medicine, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Universitaetsstrasse 21-23, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Laura Gloßner
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Arif B. Ekici
- Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Miriam Angeloni
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Fulvia Ferrazzi
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
- Department of Nephropathology, Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Veronika Bahlinger
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Arndt Hartmann
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Matthias W. Beckmann
- Laboratory for Molecular Medicine, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Universitaetsstrasse 21-23, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
| | - Markus Eckstein
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Reiner Strick
- Laboratory for Molecular Medicine, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Universitaetsstrasse 21-23, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Correspondence: ; Tel.: +49-91318536671
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Mukherjee A, Ghosh S, Biswas D, Rao A, Shetty P, Epari S, Moiyadi A, Srivastava S. Clinical Proteomics for Meningioma: An Integrated Workflow for Quantitative Proteomics and Biomarker Validation in Formalin-Fixed Paraffin-Embedded Tissue Samples. OMICS 2022; 26:512-520. [PMID: 36036964 DOI: 10.1089/omi.2022.0082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Clinical proteomics is a rapidly emerging frontier in laboratory medicine. High-throughput proteomic investigations of biopsy tissues provide mechanistic insights into complex human diseases. For large-scale proteomics, formalin-fixed and paraffin-embedded (FFPE) tissue samples offer a viable alternative to fresh-frozen (FF) tissues that have restricted availability. In this context, meningioma is one of the most common primary brain tumors where innovation in diagnostics and therapeutic targets can benefit from clinical proteomics. We present here an integrated workflow for quantitative proteomics and biomarker validation of meningioma FFPE tissues. Applying label-free quantitative (LFQ) proteomics, we reproducibly (Pearson's correlation: 0.84-0.91) obtained an in-depth proteome coverage (nearly 4000 proteins per sample) from 120 min gradient of single unfractionated mass spectrometry run. Furthermore, building upon LFQ data and literature curated set of meningioma-associated proteins, we validated VIM, AHNAK, and CLU from FFPE tissues using selected reaction monitoring (SRM) assay and compared its performance with FF tissues. This study illustrates how knowledge from label-free proteomics can be integrated for selecting peptides for targeted validation and suggests that FFPE tissues are comparable to FF tissues for SRM assays. This quantitative clinical proteomics workflow is scalable for large-scale clinical diagnostics studies in the future, for example, utilizing the global repository of FFPE tissues in meningioma and possibly in other cancers.
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Affiliation(s)
- Arijit Mukherjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Susmita Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Deeptarup Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Aishwarya Rao
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | | | | | | | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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Ondracek RP, Chen J, Marosy B, Szewczyk S, Medico L, Mohan AS, Nair P, Pratt R, Roh JM, Khoury T, Carpten J, Kushi LH, Palmer JR, Doheny K, Davis W, Higgins MJ, Yao S, Ambrosone CB. Results and lessons from dual extraction of DNA and RNA from formalin-fixed paraffin-embedded breast tumor tissues for a large Cancer epidemiologic study. BMC Genomics 2022; 23:614. [PMID: 36008758 PMCID: PMC9404650 DOI: 10.1186/s12864-022-08837-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The use of archived formalin-fixed paraffin-embedded (FFPE) tumor tissues has become a common practice in clinical and epidemiologic genetic research. Simultaneous extraction of DNA and RNA from FFPE tissues is appealing but can be practically challenging. Here we report our results and lessons learned from processing FFPE breast tumor tissues for a large epidemiologic study. METHODS Qiagen AllPrep DNA/RNA FFPE kit was adapted for dual extraction using tissue punches or sections from breast tumor tissues. The yield was quantified using Qubit and fragmentation analysis by Agilent Bioanalyzer. A subset of the DNA samples were used for genome-wide DNA methylation assays and RNA samples for sequencing. The QC metrices and performance of the assays were analyzed with pre-analytical variables. RESULTS A total of 1859 FFPE breast tumor tissues were processed. We found it critical to adjust proteinase K digestion time based on tissue volume to achieve balanced yields of DNA and RNA. Tissue punches taken from tumor-enriched regions provided the most reliable output. A median of 1475 ng DNA and 1786 ng RNA per sample was generated. The median DNA integrity number (DIN) was 3.8 and median DV200 for RNA was 33.2. Of 1294 DNA samples used in DNA methylation assays, 97% passed quality check by qPCR and 92% generated data deemed high quality. Of the 130 RNA samples with DV200 ≥ 20% used in RNA-sequencing, all but 5 generated usable transcriptomic data with a mapping rate ≥ 60%. CONCLUSIONS Dual DNA/RNA purification using Qiagen AllPrep FFPE extraction protocol is feasible for clinical and epidemiologic studies. We recommend tissue punches as a reliable source material and fine tuning of proteinase K digestion time based on tissue volume. IMPACT Our protocol and recommendations may be adapted by future studies for successful extraction of archived tumor tissues.
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Affiliation(s)
- Rochelle Payne Ondracek
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, 14263, USA
| | - Jianhong Chen
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, 14263, USA.
| | - Beth Marosy
- Center for Inherited Disease Research, Johns Hopkins Genomics, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Sirinapa Szewczyk
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Leonard Medico
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, 14263, USA
| | - Amrutha Sherly Mohan
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, 14263, USA
| | - Priya Nair
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, 14263, USA
| | - Rachel Pratt
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, 14263, USA
| | - Janise M Roh
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Thaer Khoury
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - John Carpten
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lawrence H Kushi
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Julie R Palmer
- Slone Epidemiology Center, Boston University, Boston, MA, USA
| | - Kim Doheny
- Center for Inherited Disease Research, Johns Hopkins Genomics, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Warren Davis
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, 14263, USA
| | - Michael J Higgins
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, 14263, USA
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, 14263, USA
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Walsh EM, Halushka MK. A Comparison of Tissue Dissection Techniques for Diagnostic, Prognostic, and Theragnostic Analysis of Human Disease. Pathobiology 2022; 90:199-208. [PMID: 35952628 PMCID: PMC9918608 DOI: 10.1159/000525979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/05/2022] [Indexed: 11/19/2022] Open
Abstract
Histopathology has historically been the critical technique for the diagnosis and treatment of human disease. Today, genomics, transcriptomics, and proteomics from specific cells, rather than bulk tissue, have become key to understanding underlying disease mechanisms and rendering useful diagnostic information. Extraction of desired analytes, i.e., nucleic acids or proteins, from easily accessible formalin-fixed paraffin-embedded tissues allows for clinically relevant activities, such as sequencing biomarker mutations or typing amyloidogenic proteins. Genetic profiling has become routine for cancers as varied as non-small cell lung cancer and prostatic carcinoma. The five main tissue dissection techniques that have been developed thus far include: bulk scraping, manual macrodissection, manual microdissection, laser-capture microdissection, and expression microdissection. In this review, we discuss the importance of tissue dissection in clinical practice and research, the basic methods, applications, as well as some advantages and disadvantages for each modality.
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Affiliation(s)
- Elise M. Walsh
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marc K. Halushka
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Waszut U, Taylor NF. Use of dissected paraffin block tissue as a source of mRNA for transcriptional profiling and biomarker identification: a review, with preliminary findings in adrenocortical carcinoma tissue. Acta Biochim Pol 2022; 69:273-281. [PMID: 35623010 DOI: 10.18388/abp.2020_5611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 02/03/2022] [Indexed: 11/10/2022]
Abstract
Cancer tissue obtained by biopsy or at surgery is usually handled and stored as formalin-fixed, paraffin-embedded (FFPE) blocks. While primarily prepared for histological examination, this material represents a valuable resource that is stable and transportable, and which is ideal for examination in 3 dimensions. It has been used for DNA and protein analysis but the potential for transcriptional profiling has been little exploited: the quality of the extracted RNA is uncertain and there are few reports of its efficient use. We review the background and practicalities of this approach and describe a pilot study as a worked example in which RNA of good yield and quality could be consistently obtained from differentiated areas of adrenocortical carcinoma (ACC) tissue.
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Affiliation(s)
- Urszula Waszut
- Department of Nuclear Medicine, Medical University of Gdansk, Gdańsk, Poland
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Iwaya K, Arai H, Takatou N, Morita Y, Ozeki R, Nakaoka H, Sakamoto M, Kouno T, Soma M. A sheet pocket to prevent cross-contamination of formalin-fixed paraffin-embedded block for application in next generation sequencing. PLoS One 2022; 17:e0266947. [PMID: 35507545 PMCID: PMC9067696 DOI: 10.1371/journal.pone.0266947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 03/31/2022] [Indexed: 11/23/2022] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) blocks are used as biomaterials for next-generation sequencing of cancer panels. Cross-contamination is detected in approximately 5% of the DNA extracted from FFPE samples, which reduces the detection rate of genetic abnormalities. There are no effective methods available for processing FFPE blocks that prevent cells from mixing with other specimens. The present study evaluated 897 sheets that could potentially prevent cell transmission but allow for the movement of various solvents used in FFPE blocks. According to the International Organization for Standardization and Japanese Industrial Standards, six requirements were established for the screening of packing sheets: 1) filter opening ≤5 μm, 2) thickness ≤100 μm, 3) chemical resistance, 4) permeability ≥1.0 × 10−3 cm/s, 5) water retention rate <200%, and 6) cell transit test (≤2 cells/10 high-power fields). Polyamide, polyethylene terephthalate, and polypropylene/polyethylene composite sheets met all criteria. A pocket, which was designed to wrap the tissue uniformly, was made of these sheets and was found to effectively block the entry of all cell types during FFPE block processing. Using a sheet pocket, no single cell from the cell pellet could pass through the outer layer. The presence or absence of the sheet pocket did not affect hematoxylin and eosin staining. When processing FFPE blocks as a biomaterial for next-generation sequencing, the sheet pocket was effective in preventing cross-contamination. This technology will in part support the precise translation of histopathological data into genome sequencing data in general pathology laboratories.
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Affiliation(s)
- Keiichi Iwaya
- Department of Pathology, SASAKI Institute, Kyoundo Hospital, Chiyoda-ku, Tokyo, Japan
- * E-mail:
| | - Hisae Arai
- Department of Pathology, SASAKI Institute, Kyoundo Hospital, Chiyoda-ku, Tokyo, Japan
| | - Nanao Takatou
- Department of Pathology, SASAKI Institute, Kyoundo Hospital, Chiyoda-ku, Tokyo, Japan
| | - Yuka Morita
- Department of Pathology, SASAKI Institute, Kyoundo Hospital, Chiyoda-ku, Tokyo, Japan
| | - Rinko Ozeki
- Department of Pathology, SASAKI Institute, Kyoundo Hospital, Chiyoda-ku, Tokyo, Japan
| | - Hirofumi Nakaoka
- Department of Cancer Genome Research, SASAKI Institute, Chiyoda-ku, Tokyo, Japan
| | - Masaru Sakamoto
- Department of Gynecology, SASAKI Institute, Kyoundo Hospital, Chiyoda-ku, Tokyo, Japan
| | - Tsutomu Kouno
- Department of Medical Oncology, SASAKI Institute, Kyoundo Hospital, Chiyoda-ku, Tokyo, Japan
| | - Masayoshi Soma
- Department of Internal Medicine, SASAKI Institute, Kyoundo Hospital, Chiyoda-ku, Tokyo, Japan
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Talukdar FR, Abramović I, Cuenin C, Carreira C, Gangane N, Sincic N, Herceg Z. A protocol for good quality genomic DNA isolation from formalin-fixed paraffin-embedded tissues without using commercial kits. Mol Biol Rep 2022; 49:4115-4121. [PMID: 35359238 DOI: 10.1007/s11033-022-07394-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 03/16/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND DNA isolation from formalin-fixed paraffin-embedded (FFPE) tissues for molecular analysis has become a frequent procedure in cancer research. However, the yield or quality of the isolated DNA is often compromised, and commercial kits are used to overcome this to some extent. METHODS We developed a new protocol (IARCp) to improve the quality and yield of DNA from FFPE tissues without using any commercial kit. To evaluate the IARCp's performance, we compared the quality and yield of DNA with two commercial kits, namely NucleoSpin® DNA FFPE XS (MN) and QIAamp DNA Micro (QG) isolation kit. RESULTS Total DNA yield for QG ranged from 120.0 to 282.0 ng (mean 216.5 ng), for MN: 213.6-394.2 ng (mean 319.1 ng), and with IARCp the yield was much higher ranging from 775.5 to 1896.9 ng (mean 1517.8 ng). Moreover, IARCp has also performed well in qualitative assessments by spectrophotometer, fluorometer, and real-time PCR assay. CONCLUSION Overall, IARCp represents a novel approach to DNA isolation from FFPE which results in good quality and significant amounts of DNA suitable for many downstream genome-wide and targeted molecular analyses. This protocol does not require the use of any commercial kits or phenol for isolating DNA from FFPE tissues, making it suitable to implement in low-resource settings such as low and middle-income countries.
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Affiliation(s)
- Fazlur Rahman Talukdar
- International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, 69008, Lyon Cedex 08, France.
| | - Irena Abramović
- Scientific Group for Research on Epigenetic Biomarkers, School of Medicine, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
- Department of Medical Biology, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Cyrille Cuenin
- International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, 69008, Lyon Cedex 08, France
| | - Christine Carreira
- International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, 69008, Lyon Cedex 08, France
| | - Nitin Gangane
- Mahatma Gandhi Institute of Medical Sciences, Sevagram, India
| | - Nino Sincic
- Scientific Group for Research on Epigenetic Biomarkers, School of Medicine, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
- Department of Medical Biology, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Zdenko Herceg
- International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, 69008, Lyon Cedex 08, France
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Makutani Y, Sakai K, Yamada M, Wada T, Chikugo T, Satou T, Iwasa Y, Yamamoto H, de Velasco MA, Nishio K, Kawamura J. Performance of Idylla ™ RAS-BRAF mutation test for formalin-fixed paraffin-embedded tissues of colorectal cancer. Int J Clin Oncol 2022; 27:1180-1187. [PMID: 35474548 PMCID: PMC9209352 DOI: 10.1007/s10147-022-02167-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/03/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND The Biocartis Idylla™ platform is a fully automated, real-time PCR-based diagnostic system. The Idylla™ KRAS and NRAS-BRAF Mutation Tests have been developed for the qualitative detection of mutations in KRAS, NRAS and BRAF genes, facilitating the genomic profiling of patients with colorectal cancer. The aim of the present study was to evaluate clinical performances of these tests in Japan. METHODS The RAS and BRAF mutation statuses of 253 formalin-fixed paraffin-embedded (FFPE) colorectal cancer tissues were analyzed using the Investigational Use Only Idylla™ KRAS Mutation Test and the Idylla™ NRAS-BRAF Mutation Test and an in vitro diagnostics (IVD) kit (MEBGEN RASKET™-B kit). RESULTS The success rate for obtaining a valid mutational data without retest of the Idylla tests was 97.6% (247/253): 111 KRAS mutations (43.8%), 9 NRAS mutations (3.6%), and 36 BRAF V600E mutations (14.2%) were detected using the Idylla tests. Compared with the MEBGEN RASKET-B results, the positive concordance rate was 97.4%, the negative concordance rate was 95.7%, and the overall concordance rate was 95.3% (κ = 0.919, 95% CI 0.871-0.967). The average turnaround time to Idylla™ KRAS and NRAS-BRAF Mutation Test was 5.6 working days (range: 3-11 days). CONCLUSION This result demonstrates a high concordance between the Idylla™ KRAS and NRAS-BRAF Mutation Tests and an existing IVD kit. In this manner, the Idylla™ mutation tests were validated for the detection of clinically significant KRAS, NRAS, and BRAF mutations in FFPE samples from colorectal cancer patients.
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Affiliation(s)
- Yusuke Makutani
- Department of Surgery, Faculty of Medicine, Kindai University, Osaka-sayama, Osaka, 589-8511, Japan
| | - Kazuko Sakai
- Department of Genome Biology, Faculty of Medicine, Kindai University, Ohnohigashi 377-2, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Masahiro Yamada
- Department of Surgery, Shiga General Hospital, Moriyama, Shiga, 524-8524, Japan
| | - Toshiaki Wada
- Department of Surgery, Faculty of Medicine, Kindai University, Osaka-sayama, Osaka, 589-8511, Japan
| | - Takaaki Chikugo
- Department of Diagnostic Pathology, Kindai University Hospital, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Takao Satou
- Department of Diagnostic Pathology, Kindai University Hospital, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Yoko Iwasa
- Department of Diagnostic Pathology, Shiga General Hospital, Moriyama, Shiga, 524-8524, Japan
| | - Hidekazu Yamamoto
- Department of Surgery, Shiga General Hospital, Moriyama, Shiga, 524-8524, Japan
- Department of Diagnostic Pathology, Shiga General Hospital, Moriyama, Shiga, 524-8524, Japan
| | - Marco A de Velasco
- Department of Genome Biology, Faculty of Medicine, Kindai University, Ohnohigashi 377-2, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Kazuto Nishio
- Department of Genome Biology, Faculty of Medicine, Kindai University, Ohnohigashi 377-2, Osaka-Sayama, Osaka, 589-8511, Japan.
| | - Junichiro Kawamura
- Department of Surgery, Faculty of Medicine, Kindai University, Osaka-sayama, Osaka, 589-8511, Japan
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Mitiushkina NV, Yanus GA, Kuligina ES, Laidus TA, Romanko AA, Kholmatov MM, Ivantsov AO, Aleksakhina SN, Imyanitov EN. Preparation of Duplex Sequencing Libraries for Archival Paraffin-Embedded Tissue Samples Using Single-Strand-Specific Nuclease P1. Int J Mol Sci 2022; 23:4586. [PMID: 35562977 PMCID: PMC9105346 DOI: 10.3390/ijms23094586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 12/04/2022] Open
Abstract
DNA from formalin-fixed paraffin-embedded (FFPE) tissues, which are frequently utilized in cancer research, is significantly affected by chemical degradation. It was suggested that approaches that are based on duplex sequencing can significantly improve the accuracy of mutation detection in FFPE-derived DNA. However, the original duplex sequencing method cannot be utilized for the analysis of formalin-fixed paraffin-embedded (FFPE) tissues, as FFPE DNA contains an excessive number of damaged bases, and these lesions are converted to false double-strand nucleotide substitutions during polymerase-driven DNA end repair process. To resolve this drawback, we replaced DNA polymerase by a single strand-specific nuclease P1. Nuclease P1 was shown to efficiently remove RNA from DNA preparations, to fragment the FFPE-derived DNA and to remove 5'/3'-overhangs. To assess the performance of duplex sequencing-based methods in FFPE-derived DNA, we constructed the Bottleneck Sequencing System (BotSeqS) libraries from five colorectal carcinomas (CRCs) using either DNA polymerase or nuclease P1. As expected, the number of identified mutations was approximately an order of magnitude higher in libraries prepared with DNA polymerase vs. nuclease P1 (626 ± 167/Mb vs. 75 ± 37/Mb, paired t-test p-value 0.003). Furthermore, the use of nuclease P1 but not polymerase-driven DNA end repair allowed a reliable discrimination between CRC tumors with and without hypermutator phenotypes. The utility of newly developed modification was validated in the collection of 17 CRCs and 5 adjacent normal tissues. Nuclease P1 can be recommended for the use in duplex sequencing library preparation from FFPE-derived DNA.
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Affiliation(s)
- Natalia V. Mitiushkina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia; (N.V.M.); (G.A.Y.); (E.S.K.); (T.A.L.); (A.A.R.); (M.M.K.); (A.O.I.); (S.N.A.)
| | - Grigory A. Yanus
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia; (N.V.M.); (G.A.Y.); (E.S.K.); (T.A.L.); (A.A.R.); (M.M.K.); (A.O.I.); (S.N.A.)
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, 194100 St.-Petersburg, Russia
| | - Ekatherina Sh. Kuligina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia; (N.V.M.); (G.A.Y.); (E.S.K.); (T.A.L.); (A.A.R.); (M.M.K.); (A.O.I.); (S.N.A.)
| | - Tatiana A. Laidus
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia; (N.V.M.); (G.A.Y.); (E.S.K.); (T.A.L.); (A.A.R.); (M.M.K.); (A.O.I.); (S.N.A.)
| | - Alexandr A. Romanko
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia; (N.V.M.); (G.A.Y.); (E.S.K.); (T.A.L.); (A.A.R.); (M.M.K.); (A.O.I.); (S.N.A.)
| | - Maksim M. Kholmatov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia; (N.V.M.); (G.A.Y.); (E.S.K.); (T.A.L.); (A.A.R.); (M.M.K.); (A.O.I.); (S.N.A.)
| | - Alexandr O. Ivantsov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia; (N.V.M.); (G.A.Y.); (E.S.K.); (T.A.L.); (A.A.R.); (M.M.K.); (A.O.I.); (S.N.A.)
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, 194100 St.-Petersburg, Russia
| | - Svetlana N. Aleksakhina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia; (N.V.M.); (G.A.Y.); (E.S.K.); (T.A.L.); (A.A.R.); (M.M.K.); (A.O.I.); (S.N.A.)
| | - Evgeny N. Imyanitov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia; (N.V.M.); (G.A.Y.); (E.S.K.); (T.A.L.); (A.A.R.); (M.M.K.); (A.O.I.); (S.N.A.)
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, 194100 St.-Petersburg, Russia
- Department of Oncology, I.I. Mechnikov North-Western Medical University, 191015 St.-Petersburg, Russia
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Jouinot A, Lippert J, Sibony M, Violon F, Jeanpierre L, De Murat D, Armignacco R, Septier A, Perlemoine K, Letourneur F, Izac B, Ragazzon B, Leroy K, Pasmant E, North MO, Gaujoux S, Dousset B, Groussin L, Libe R, Terris B, Fassnacht M, Ronchi CL, Bertherat J, Assie G. Transcriptome in paraffin samples for the diagnosis and prognosis of adrenocortical carcinoma. Eur J Endocrinol 2022; 186:607-617. [PMID: 35266879 PMCID: PMC9066577 DOI: 10.1530/eje-21-1228] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/10/2022] [Indexed: 11/08/2022]
Abstract
DESIGN Molecular classification is important for the diagnosis and prognosis of adrenocortical tumors (ACT). Transcriptome profiles separate adrenocortical adenomas 'C2' from carcinomas, and identify two groups of carcinomas 'C1A' and 'C1B', of poor and better prognosis respectively. However, many ACT cannot be profiled because of improper or absent freezing procedures, a mandatory requirement so far. The main aim was to determine transcriptome profiles on formalin-fixed paraffin-embedded (FFPE) samples, using the new 3'-end RNA-sequencing technology. A secondary aim was to demonstrate the ability of this technique to explore large FFPE archives, by focusing on the rare oncocytic ACT variants. METHODS We included 131 ACT: a training cohort from Cochin hospital and an independent validation cohort from Wuerzburg hospital. The 3' transcriptome was generated from FFPE samples using QuantSeq (Lexogen, Vienna, Austria) and NextSeq500 (Illumina, San Diego, CA, USA). RESULTS In the training cohort, unsupervised clustering identified three groups: 'C1A' aggressive carcinomas (n = 28, 29%), 'C1B' more indolent carcinomas (n = 28, 29%), and 'C2' adenomas (n = 39, 41%). The prognostic value of FFPE transcriptome was confirmed in the validation cohort (5-year OS: 26% in 'C1A' (n = 26) and 100% in 'C1B' (n = 10), P = 0.003). FFPE transcriptome was an independent prognostic factor in a multivariable model including tumor stage and Ki-67 (OS HR: 7.5, P = 0.01). Oncocytic ACT (n = 19) did not form any specific cluster. Oncocytic carcinomas (n = 6) and oncocytic ACT of uncertain malignant potential (n = 4) were all in 'C1B'. CONCLUSIONS The 3' RNA-sequencing represents a convenient solution for determining ACT molecular class from FFPE samples. This technique should facilitate routine use and large retrospective studies.
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Affiliation(s)
- Anne Jouinot
- Université de Paris, Institut Cochin, INSERM U-1016, CNRS UMR-8104, Paris, France
- Endocrinology, AP-HP Hôpital Cochin, Paris, France
- Institut Curie, INSERM U900, MINES ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, Paris, France
| | - Juliane Lippert
- Division of Endocrinology and Diabetes, Department of Internal Medicine I, University Hospital, University of Wuerzburg, Wuerzburg, Germany
| | - Mathilde Sibony
- Université de Paris, Institut Cochin, INSERM U-1016, CNRS UMR-8104, Paris, France
- Pathology, AP-HP Hôpital Cochin, Paris, France
| | - Florian Violon
- Université de Paris, Institut Cochin, INSERM U-1016, CNRS UMR-8104, Paris, France
- Pathology, AP-HP Hôpital Cochin, Paris, France
| | - Lindsay Jeanpierre
- Université de Paris, Institut Cochin, INSERM U-1016, CNRS UMR-8104, Paris, France
- Pathology, AP-HP Hôpital Cochin, Paris, France
| | - Daniel De Murat
- Université de Paris, Institut Cochin, INSERM U-1016, CNRS UMR-8104, Paris, France
| | - Roberta Armignacco
- Université de Paris, Institut Cochin, INSERM U-1016, CNRS UMR-8104, Paris, France
| | - Amandine Septier
- Université de Paris, Institut Cochin, INSERM U-1016, CNRS UMR-8104, Paris, France
| | - Karine Perlemoine
- Université de Paris, Institut Cochin, INSERM U-1016, CNRS UMR-8104, Paris, France
| | - Franck Letourneur
- Université de Paris, Institut Cochin, INSERM U-1016, CNRS UMR-8104, Paris, France
| | - Brigitte Izac
- Université de Paris, Institut Cochin, INSERM U-1016, CNRS UMR-8104, Paris, France
| | - Bruno Ragazzon
- Université de Paris, Institut Cochin, INSERM U-1016, CNRS UMR-8104, Paris, France
| | - Karen Leroy
- Genetics and Molecular Biology, AP-HP Hôpital Cochin, Paris, France
| | - Eric Pasmant
- Genetics and Molecular Biology, AP-HP Hôpital Cochin, Paris, France
| | | | - Sébastien Gaujoux
- Université de Paris, Institut Cochin, INSERM U-1016, CNRS UMR-8104, Paris, France
- Digestive and Endocrine Surgery, AP-HP Hôpital Cochin, Paris, France
| | - Bertrand Dousset
- Université de Paris, Institut Cochin, INSERM U-1016, CNRS UMR-8104, Paris, France
- Digestive and Endocrine Surgery, AP-HP Hôpital Cochin, Paris, France
| | - Lionel Groussin
- Université de Paris, Institut Cochin, INSERM U-1016, CNRS UMR-8104, Paris, France
- Endocrinology, AP-HP Hôpital Cochin, Paris, France
| | - Rossella Libe
- Université de Paris, Institut Cochin, INSERM U-1016, CNRS UMR-8104, Paris, France
- Endocrinology, AP-HP Hôpital Cochin, Paris, France
| | | | - Martin Fassnacht
- Division of Endocrinology and Diabetes, Department of Internal Medicine I, University Hospital, University of Wuerzburg, Wuerzburg, Germany
| | - Cristina L Ronchi
- Division of Endocrinology and Diabetes, Department of Internal Medicine I, University Hospital, University of Wuerzburg, Wuerzburg, Germany
- Institute of Metabolism and System Research, University of Birmingham, Birmingham, UK
- Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, UK
- Correspondence should be addressed to C L Ronchi or G Assié; or
| | - Jérôme Bertherat
- Université de Paris, Institut Cochin, INSERM U-1016, CNRS UMR-8104, Paris, France
- Endocrinology, AP-HP Hôpital Cochin, Paris, France
| | - Guillaume Assie
- Université de Paris, Institut Cochin, INSERM U-1016, CNRS UMR-8104, Paris, France
- Endocrinology, AP-HP Hôpital Cochin, Paris, France
- Correspondence should be addressed to C L Ronchi or G Assié; or
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48
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Hockney R, Orr CH, Waring GJ, Christiaens I, Taylor G, Cummings SP, Robson SC, Nelson A. Formalin-Fixed Paraffin-Embedded (FFPE) samples are not a beneficial replacement for frozen tissues in fetal membrane microbiota research. PLoS One 2022; 17:e0265441. [PMID: 35298530 PMCID: PMC8929612 DOI: 10.1371/journal.pone.0265441] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/01/2022] [Indexed: 12/19/2022] Open
Abstract
Formalin-Fixed Paraffin-Embedded (FFPE) tissues are routinely collected, archived, and used for clinical diagnosis, including maternal and neonatal health. Applying FFPE samples to microbiota research would be beneficial to reduce preparation, storage and costs associated with limited available frozen samples. This research aims to understand if FFPE fetal membrane samples are comparable to frozen tissues, which are the current gold standard for DNA microbiota analysis. Extracted DNA from nine matched paired patients were sequenced by Illumina sequencing of the V4 16S rRNA gene region. This included duplicate frozen amnion and chorion fetal membrane rolls or FFPE combined amniochorionic samples. Negative controls of surrounding wax blocks and DNA extraction reagents were processed alongside samples using identical methods. DNA quality and quantity was assessed by NanoDrop, agarose gel electrophoresis and Bioanalyzer. Decontam and SourceTracker were integrated into microbiota analysis to identify the presence of contaminating sources. The bacterial profile and nine genera differed between FFPE and frozen fetal membranes. There were no differences in bacterial profiles between FFPE samples and corresponding wax negative controls, with 49% of bacteria in FFPE fetal membrane samples matched to the source origin of paraffin wax, and 40% originating from DNA extraction reagent sources. FFPE samples displayed high fragmentation and low quantity of extracted DNA compared to frozen samples. The microbiota of FFPE fetal membrane samples is influenced by processing methods, with the inability to differentiate between the microbiota of the tissue sample and the surrounding wax block. Illumina sequencing results of FFPE and frozen fetal membrane samples should not be compared using the methods employed here. Variation could be influenced by limitations including storage time, DNA extraction and purification methods. To utilise FFPE fetal membrane samples in microbiota research then contamination prevention and detection methods must be included into optimised and standardised protocols, with recommendations presented here.
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Affiliation(s)
- Rochelle Hockney
- School of Health, Leeds Beckett University, Leeds, United Kingdom
- School of Health and Life Sciences, Teesside University, Middlesbrough, United Kingdom
- National Horizons Centre, Teesside University, John Dixon Lane, Darlington, United Kingdom
- * E-mail:
| | - Caroline H. Orr
- School of Health and Life Sciences, Teesside University, Middlesbrough, United Kingdom
- National Horizons Centre, Teesside University, John Dixon Lane, Darlington, United Kingdom
| | - Gareth J. Waring
- Institute of Cellular Medicine, Newcastle University, Newcastle, United Kingdom
| | - Inge Christiaens
- Institute of Cellular Medicine, Newcastle University, Newcastle, United Kingdom
| | - Gillian Taylor
- School of Health and Life Sciences, Teesside University, Middlesbrough, United Kingdom
- National Horizons Centre, Teesside University, John Dixon Lane, Darlington, United Kingdom
| | - Stephen P. Cummings
- School of Health and Life Sciences, Teesside University, Middlesbrough, United Kingdom
- National Horizons Centre, Teesside University, John Dixon Lane, Darlington, United Kingdom
| | - Stephen C. Robson
- Institute of Cellular Medicine, Newcastle University, Newcastle, United Kingdom
| | - Andrew Nelson
- Faculty of Health and Life Sciences, Northumbria University, Newcastle, United Kingdom
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49
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Wisner L, Larsen B, Maguire A. Enhancing Tumor Content through Tumor Macrodissection. J Vis Exp 2022:10.3791/62961. [PMID: 35225270 PMCID: PMC10448995 DOI: 10.3791/62961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023] Open
Abstract
The presence of contaminating non-tumor tissues in formalin-fixed paraffin-embedded (FFPE) tissues can greatly undermine genomic studies. Herein we describe macrodissection, a method designed to augment the percentage tumor content of a tissue specimen by removing and eliminating unwanted tissue prior to performing downstream nucleic acid extractions. FFPE tissue blocks were sectioned to produce 4-5 µm slide-mounted tissue sections. A representative section was submitted for hematoxylin and eosin (H&E) staining and subsequently reviewed by a board-certified pathologist. During the review, the pathologist identified and marked the regions of tumor tissue in the H&E. Once complete, the demarked H&E was used to guide resection of the serial unstained sections from the same tissue block. To demonstrate the effects of macrodissection, RNA extracted from matched macrodissected and non-dissected Diffuse Large B-Cell Lymphomas (DLBCL) were run on a digital gene expression assay capable of determining DLBCL subtype and BCL2 translocation status. The results showed that macrodissection changed the subtype or BCL2 translocation status calls in 60% of the samples examined. In conclusion, macrodissection is a simple and effective method for performing tumor enrichment prior to nucleic acid extractions, the product of which can then be confidently used in downstream genomic studies.
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Affiliation(s)
| | - Brandon Larsen
- Department of Laboratory Medicine and Pathology, Mayo Clinic
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50
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Sabo AR, Winfree S, Bledsoe SB, Phillips CL, Lingeman JE, Eadon MT, Williams JC, El‐Achkar TM. Label-free imaging of non-deparaffinized sections of the human kidney to determine tissue quality and signatures of disease. Physiol Rep 2022; 10:e15167. [PMID: 35133089 PMCID: PMC8822874 DOI: 10.14814/phy2.15167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 12/18/2021] [Accepted: 12/22/2021] [Indexed: 11/24/2022] Open
Abstract
Label-free fluorescence imaging of kidney sections can provide important morphological information, but its utility has not been tested in a histology processing workflow. We tested the feasibility of label-free imaging of paraffin-embedded sections without deparaffinization and its potential usefulness in generating actionable data. Kidney tissue specimens were obtained during percutaneous nephrolithotomy or via diagnostic needle biopsy. Unstained non-deparaffinized sections were imaged using widefield fluorescence microscopy to capture endogenous fluorescence. Some samples were also imaged with confocal microscopy and multiphoton excitation to collect second harmonic generation (SHG) signal to obtain high-quality autofluorescence images with optical sectioning. To adjudicate the label-free signal, the samples or corresponding contiguous sections were subsequently deparaffinized and stained with Lillie's allochrome. Label-free imaging allowed the recognition of various kidney structures and enabled morphological qualification for adequacy. SHG and confocal imaging yielded quantifiable high-quality images for tissue collagens and revealed specific patterns in glomeruli and various tubules. Disease specimens from patients with diabetic kidney disease and focal segmental glomerulosclerosis showed distinctive signatures compared to specimens from healthy controls with normal kidney function. Quantitative cytometry could also be performed when DAPI is added in situ before imaging. These results show that label-free imaging of non-deparaffinized sections provides useful information about tissue quality that could be beneficial to nephropathologists by maximizing the use of scarce kidney tissue. This approach also provides quantifiable features that could inform on the biology of health and disease.
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Affiliation(s)
- Angela R. Sabo
- Department of Anatomy, Cell Biology, and PhysiologyIndiana University School of MedicineIndianapolisIndianaUSA
- Department of MedicineIndiana University School of MedicineIndianapolisIndianaUSA
| | - Seth Winfree
- Department of Pathology and MicrobiologyEppley InstituteUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Sharon B. Bledsoe
- Department of Anatomy, Cell Biology, and PhysiologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - Carrie L. Phillips
- Department of PathologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - James E. Lingeman
- Department of UrologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - Michael T. Eadon
- Department of MedicineIndiana University School of MedicineIndianapolisIndianaUSA
| | - James C. Williams
- Department of Anatomy, Cell Biology, and PhysiologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - Tarek M. El‐Achkar
- Department of Anatomy, Cell Biology, and PhysiologyIndiana University School of MedicineIndianapolisIndianaUSA
- Department of MedicineIndiana University School of MedicineIndianapolisIndianaUSA
- Indianapolis VA Medical CenterIndianapolisIndianaUSA
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