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Hickey JW, Neumann EK, Radtke AJ, Camarillo JM, Beuschel RT, Albanese A, McDonough E, Hatler J, Wiblin AE, Fisher J, Croteau J, Small EC, Sood A, Caprioli RM, Angelo RM, Nolan GP, Chung K, Hewitt SM, Germain RN, Spraggins JM, Lundberg E, Snyder MP, Kelleher NL, Saka SK. Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging. Nat Methods 2022; 19:284-295. [PMID: 34811556 PMCID: PMC9264278 DOI: 10.1038/s41592-021-01316-y] [Citation(s) in RCA: 138] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 09/15/2021] [Indexed: 02/07/2023]
Abstract
Tissues and organs are composed of distinct cell types that must operate in concert to perform physiological functions. Efforts to create high-dimensional biomarker catalogs of these cells have been largely based on single-cell sequencing approaches, which lack the spatial context required to understand critical cellular communication and correlated structural organization. To probe in situ biology with sufficient depth, several multiplexed protein imaging methods have been recently developed. Though these technologies differ in strategy and mode of immunolabeling and detection tags, they commonly utilize antibodies directed against protein biomarkers to provide detailed spatial and functional maps of complex tissues. As these promising antibody-based multiplexing approaches become more widely adopted, new frameworks and considerations are critical for training future users, generating molecular tools, validating antibody panels, and harmonizing datasets. In this Perspective, we provide essential resources, key considerations for obtaining robust and reproducible imaging data, and specialized knowledge from domain experts and technology developers.
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Affiliation(s)
- John W Hickey
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Elizabeth K Neumann
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
| | - Andrea J Radtke
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA.
| | - Jeannie M Camarillo
- Departments of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA
| | - Rebecca T Beuschel
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Alexandre Albanese
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Boston Children's Hospital, Division of Hematology/Oncology, Boston, MA, USA
| | | | - Julia Hatler
- Antibody Development Department, Bio-Techne, Minneapolis, MN, USA
| | - Anne E Wiblin
- Department of Research and Development, Abcam, Cambridge, UK
| | - Jeremy Fisher
- Department of Research and Development, Cell Signaling Technology, Danvers, MA, USA
| | - Josh Croteau
- Department of Applications Science, BioLegend, San Diego, CA, USA
| | | | | | - Richard M Caprioli
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - R Michael Angelo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kwanghun Chung
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Chemical Engineering, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Yonsei-IBS Institute, Yonsei University, Seoul, Republic of Korea
| | - Stephen M Hewitt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ronald N Germain
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Emma Lundberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Neil L Kelleher
- Departments of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA
| | - Sinem K Saka
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
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A new tool for technical standardization of the Ki67 immunohistochemical assay. Mod Pathol 2021; 34:1261-1270. [PMID: 33536573 PMCID: PMC8222064 DOI: 10.1038/s41379-021-00745-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 12/20/2022]
Abstract
Ki67, a nuclear proliferation-related protein, is heavily used in anatomic pathology but has not become a companion diagnostic or a standard-of-care biomarker due to analytic variability in both assay protocols and interpretation. The International Ki67 Working Group in breast cancer has published and has ongoing efforts in the standardization of the interpretation of Ki67, but they have not yet assessed technical issues of assay production representing multiple sources of variation, including antibody clones, antibody formats, staining platforms, and operators. The goal of this work is to address these issues with a new standardization tool. We have developed a cell line microarray system in which mixes of human Karpas 299 or Jurkat cells (Ki67+) with Sf9 (Spodoptera frugiperda) (Ki67-) cells are present in incremental standardized ratios. To validate the tool, six different antibodies, including both ready-to-use and concentrate formats from six vendors, were used to measure Ki67 proliferation indices using IHC protocols for manual (bench-top) and automated platforms. The assays were performed by three different laboratories at Yale and analyzed using two image analysis software packages, including QuPath and Visiopharm. Results showed statistically significant differences in Ki67 reactivity between each antibody clone. However, subsets of Ki67 assays using three clones performed in three different labs show no significant differences. This work shows the need for analytic standardization of the Ki67 assay and provides a new tool to do so. We show here how a cell line standardization system can be used to normalize the staining variability in proliferation indices between different antibody clones in a triple negative breast cancer cohort. We believe that this cell line standardization array has the potential to improve reproducibility among Ki67 assays and laboratories, which is critical for establishing Ki67 as a standard-of-care assay.
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MacNeil T, Vathiotis IA, Martinez-Morilla S, Yaghoobi V, Zugazagoitia J, Liu Y, Rimm DL. Antibody validation for protein expression on tissue slides: a protocol for immunohistochemistry. Biotechniques 2020; 69:460-468. [PMID: 32852223 PMCID: PMC7807291 DOI: 10.2144/btn-2020-0095] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Antibodies play a crucial role in basic research and clinical decision-making. However, there are no standardized algorithms or guidelines to ensure their accuracy and validity. There have been efforts to generate consensus, but, with the exception of clinical labs, antibody validation remains variable in the literature and sometimes in clinical practice. Here we focus on immunohistochemistry, an example of a scientific and clinical tool where validation of antibodies is critical. We describe a protocol that we use to validate antibodies specifically for immunohistochemistry, including some of the pillars of antibody validation from Uhlen et al. 2016, as an example of a rigorous approach to build antibody-based tests for both basic and translational science labs and for the clinic.
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Affiliation(s)
- Tyler MacNeil
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | | | | | - Vesal Yaghoobi
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Jon Zugazagoitia
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Yuting Liu
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - David L Rimm
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
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Cross-Platform Comparison of Computer-assisted Image Analysis Quantification of In Situ mRNA Hybridization in Investigative Pathology. Appl Immunohistochem Mol Morphol 2020; 27:15-26. [PMID: 28682833 DOI: 10.1097/pai.0000000000000542] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Although availability of automated platforms has proliferated, there is no standard practice for computer-assisted generation of scores for mRNA in situ hybridization (ISH) visualized by brightfield microscopic imaging on tissue sections. To address this systematically, an ISH for peptidylprolyl isomerase B (PPIB) (cyclophilin B) mRNA was optimized and applied to a tissue microarray of archival non-small cell lung carcinoma cases, and then automated image analysis for PPIB was refined across 4 commercially available software platforms. Operator experience and scoring results from ImageScope, HALO, CellMap, and Developer XD were systematically compared with each other and to manual pathologist scoring. Markup images were compared and contrasted for accuracy, the ability of the platform to identify cells, and the ease of visual assessment to determine appropriate interpretation. Comparing weighted scoring approaches using H-scores (Developer XD, ImageScope, and manual scoring) a correlation was observed (R value=0.7955), and association between the remaining 2 approaches (HALO and CellMap) was of similar value. ImageScope showed the highest R value in comparison with manual scoring (0.7377). Mean-difference plots showed that HALO produced the highest relative normalized values, suggesting higher relative sensitivity. ImageScope overestimated PPIB ISH signal at the high end of the range scores; however, this tendency was not observed in other platforms. HALO emerged with the highest number of favorable observations, no apparent systematic bias in score generation compared with the other methods, and potentially higher sensitivity to detect ISH. HALO may serve as a tool to empower teams of investigative pathology laboratory scientists to assist pathologists readily with quantitative scoring of ISH.
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Taube JM, Akturk G, Angelo M, Engle EL, Gnjatic S, Greenbaum S, Greenwald NF, Hedvat CV, Hollmann TJ, Juco J, Parra ER, Rebelatto MC, Rimm DL, Rodriguez-Canales J, Schalper KA, Stack EC, Ferreira CS, Korski K, Lako A, Rodig SJ, Schenck E, Steele KE, Surace MJ, Tetzlaff MT, von Loga K, Wistuba II, Bifulco CB. The Society for Immunotherapy of Cancer statement on best practices for multiplex immunohistochemistry (IHC) and immunofluorescence (IF) staining and validation. J Immunother Cancer 2020; 8:e000155. [PMID: 32414858 PMCID: PMC7239569 DOI: 10.1136/jitc-2019-000155] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2020] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVES The interaction between the immune system and tumor cells is an important feature for the prognosis and treatment of cancer. Multiplex immunohistochemistry (mIHC) and multiplex immunofluorescence (mIF) analyses are emerging technologies that can be used to help quantify immune cell subsets, their functional state, and their spatial arrangement within the tumor microenvironment. METHODS The Society for Immunotherapy of Cancer (SITC) convened a task force of pathologists and laboratory leaders from academic centers as well as experts from pharmaceutical and diagnostic companies to develop best practice guidelines for the optimization and validation of mIHC/mIF assays across platforms. RESULTS Representative outputs and the advantages and disadvantages of mIHC/mIF approaches, such as multiplexed chromogenic IHC, multiplexed immunohistochemical consecutive staining on single slide, mIF (including multispectral approaches), tissue-based mass spectrometry, and digital spatial profiling are discussed. CONCLUSIONS mIHC/mIF technologies are becoming standard tools for biomarker studies and are likely to enter routine clinical practice in the near future. Careful assay optimization and validation will help ensure outputs are robust and comparable across laboratories as well as potentially across mIHC/mIF platforms. Quantitative image analysis of mIHC/mIF output and data management considerations will be addressed in a complementary manuscript from this task force.
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Affiliation(s)
- Janis M Taube
- Department of Dermatology, Johns Hopkins School of Medicine, Bloomberg~Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland, USA
| | - Guray Akturk
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York City, USA
| | - Michael Angelo
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California, USA
| | - Elizabeth L Engle
- Department of Dermatology, Johns Hopkins School of Medicine, Bloomberg~Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland, USA
| | - Sacha Gnjatic
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York City, USA
| | - Shirley Greenbaum
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California, USA
| | - Noah F Greenwald
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California, USA
- Cancer Biology Program, Stanford University School of Medicine, Palo Alto, California, USA
| | | | - Travis J Hollmann
- Dermatopathology, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | | | - Edwin R Parra
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - David L Rimm
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | - Kurt A Schalper
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | - Cláudia S Ferreira
- Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Penzberg, Germany
| | - Konstanty Korski
- Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Penzberg, Germany
| | - Ana Lako
- Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Scott J Rodig
- Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | | | | | | | - Michael T Tetzlaff
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Katharina von Loga
- Biomedical Research Centre, Royal Marsden NHS Foundation Trust, London, UK
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Carvajal-Hausdorf DE, Patsenker J, Stanton KP, Villarroel-Espindola F, Esch A, Montgomery RR, Psyrri A, Kalogeras KT, Kotoula V, Foutzilas G, Schalper KA, Kluger Y, Rimm DL. Multiplexed (18-Plex) Measurement of Signaling Targets and Cytotoxic T Cells in Trastuzumab-Treated Patients using Imaging Mass Cytometry. Clin Cancer Res 2019; 25:3054-3062. [PMID: 30796036 DOI: 10.1158/1078-0432.ccr-18-2599] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 12/09/2018] [Accepted: 02/08/2019] [Indexed: 12/15/2022]
Abstract
PURPOSE Imaging mass cytometry (IMC) uses metal-conjugated antibodies to provide multidimensional, objective measurement of protein targets. We used this high-throughput platform to perform an 18-plex assessment of HER2 ICD/ECD, cytotoxic T-cell infiltration and other structural and signaling proteins in a cohort of patients treated with trastuzumab to discover associations with trastuzumab benefit. EXPERIMENTAL DESIGN An antibody panel for detection of 18 targets (pan-cytokeratin, HER2 ICD, HER2 ECD, CD8, vimentin, cytokeratin 7, β-catenin, HER3, MET, EGFR, ERK 1-2, MEK 1-2, PTEN, PI3K p110 α, Akt, mTOR, Ki67, and Histone H3) was used with a selection of trastuzumab-treated patients from the Hellenic Cooperative Oncology Group 10/05 trial (n = 180), and identified a case-control series. RESULTS Patients that recurred after adjuvant treatment with trastuzumab trended toward a decreased fraction of HER2 ECD pixels over threshold compared with cases without recurrence (P = 0.057). After exclusion of the lowest HER2 expressers, 5-year recurrence events were associated with reduced total extracellular domain (ECD)/intracellular domain (ICD) ratio intensity in tumor (P = 0.044). These observations are consistent with our previous work using quantitative immunofluorescence, but represent the proof on identical cell content. We also describe the association of the ECD of HER2 with CD8 T-cell infiltration on the same slide. CONCLUSIONS The proximity of CD8 cells as a function of the expression of the ECD of HER2 provides further evidence for the role of the immune system in the mechanism of action of trastuzumab.
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Affiliation(s)
- Daniel E Carvajal-Hausdorf
- Yale School of Medicine, New Haven, Connecticut.,Clínica Alemana-Facultad de Medicina U. del Desarrollo, Santiago, Chile
| | - Jonathan Patsenker
- Yale School of Medicine, New Haven, Connecticut.,Rensselaer Polytechnic Institute, Troy, New York
| | | | | | - Amanda Esch
- Fluidigm Corporation, Markham, Ontario, Canada
| | | | | | | | - Vassiliki Kotoula
- Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| | - George Foutzilas
- Department of Medical Oncology, "Papageorgiou" Hospital, Athens, Greece
| | | | | | - David L Rimm
- Yale School of Medicine, New Haven, Connecticut.
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7
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Jin BF, Yang F, Ying XM, Gong L, Hu SF, Zhao Q, Liao YD, Chen KZ, Li T, Tai YH, Cao Y, Li X, Huang Y, Zhan XY, Qin XH, Wu J, Chen S, Guo SS, Zhang YC, Chen J, Shen DH, Sun KK, Chen L, Li WH, Li AL, Wang N, Xia Q, Wang J, Zhou T. Signaling protein signature predicts clinical outcome of non-small-cell lung cancer. BMC Cancer 2018; 18:259. [PMID: 29510676 PMCID: PMC5840771 DOI: 10.1186/s12885-018-4104-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 02/06/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Non-small-cell lung cancer (NSCLC) is characterized by abnormalities of numerous signaling proteins that play pivotal roles in cancer development and progression. Many of these proteins have been reported to be correlated with clinical outcomes of NSCLC. However, none of them could provide adequate accuracy of prognosis prediction in clinical application. METHODS A total of 384 resected NSCLC specimens from two hospitals in Beijing (BJ) and Chongqing (CQ) were collected. Using immunohistochemistry (IHC) staining on stored formalin-fixed paraffin-embedded (FFPE) surgical samples, we examined the expression levels of 75 critical proteins on BJ samples. Random forest algorithm (RFA) and support vector machines (SVM) computation were applied to identify protein signatures on 2/3 randomly assigned BJ samples. The identified signatures were tested on the remaining BJ samples, and were further validated with CQ independent cohort. RESULTS A 6-protein signature for adenocarcinoma (ADC) and a 5-protein signature for squamous cell carcinoma (SCC) were identified from training sets and tested in testing sets. In independent validation with CQ cohort, patients can also be divided into high- and low-risk groups with significantly different median overall survivals by Kaplan-Meier analysis, both in ADC (31 months vs. 87 months, HR 2.81; P < 0.001) and SCC patients (27 months vs. not reached, HR 9.97; P < 0.001). Cox regression analysis showed that both signatures are independent prognostic indicators and outperformed TNM staging (ADC: adjusted HR 3.07 vs. 2.43, SCC: adjusted HR 7.84 vs. 2.24). Particularly, we found that only the ADC patients in high-risk group significantly benefited from adjuvant chemotherapy (P = 0.018). CONCLUSIONS Both ADC and SCC protein signatures could effectively stratify the prognosis of NSCLC patients, and may support patient selection for adjuvant chemotherapy.
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Affiliation(s)
- Bao-Feng Jin
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, China National Center of Biomedical Analysis, Beijing, 100850 China
| | - Fan Yang
- Department of Thoracic Surgery, People’s Hospital, Peking University, Beijing, 100044 China
| | - Xiao-Min Ying
- Computational Medicine Laboratory, Beijing Institute of Basic Medical Sciences, Beijing, 100850 China
| | - Lin Gong
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, China National Center of Biomedical Analysis, Beijing, 100850 China
| | - Shuo-Feng Hu
- Computational Medicine Laboratory, Beijing Institute of Basic Medical Sciences, Beijing, 100850 China
| | - Qing Zhao
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, China National Center of Biomedical Analysis, Beijing, 100850 China
| | - Yi-Da Liao
- Department of Thoracic Surgery, People’s Hospital, Peking University, Beijing, 100044 China
| | - Ke-Zhong Chen
- Department of Thoracic Surgery, People’s Hospital, Peking University, Beijing, 100044 China
| | - Teng Li
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, China National Center of Biomedical Analysis, Beijing, 100850 China
| | - Yan-Hong Tai
- The 90th Hospital of Jinan, Jinan, 250031 China
- Department of Pathology, The 307th Hospital of Chinese PLA, Beijing, 100071 China
| | - Yuan Cao
- The 90th Hospital of Jinan, Jinan, 250031 China
| | - Xiao Li
- Department of Thoracic Surgery, People’s Hospital, Peking University, Beijing, 100044 China
| | - Yan Huang
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, China National Center of Biomedical Analysis, Beijing, 100850 China
| | - Xiao-Yan Zhan
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, China National Center of Biomedical Analysis, Beijing, 100850 China
| | - Xuan-He Qin
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, China National Center of Biomedical Analysis, Beijing, 100850 China
| | - Jin Wu
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, China National Center of Biomedical Analysis, Beijing, 100850 China
| | - Shuai Chen
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, China National Center of Biomedical Analysis, Beijing, 100850 China
| | - Sai-Sai Guo
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, China National Center of Biomedical Analysis, Beijing, 100850 China
| | - Yu-Cheng Zhang
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, China National Center of Biomedical Analysis, Beijing, 100850 China
| | - Jing Chen
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, China National Center of Biomedical Analysis, Beijing, 100850 China
| | - Dan-Hua Shen
- Department of Pathology, People’s Hospital, Peking University, Beijing, 100044 China
| | - Kun-Kun Sun
- Department of Pathology, People’s Hospital, Peking University, Beijing, 100044 China
| | - Lu Chen
- Institute of Pathology, Southwest Cancer Center, Southwest Hospital, Chongqing, 400038 China
| | - Wei-Hua Li
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, China National Center of Biomedical Analysis, Beijing, 100850 China
| | - Ai-Ling Li
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, China National Center of Biomedical Analysis, Beijing, 100850 China
| | - Na Wang
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, China National Center of Biomedical Analysis, Beijing, 100850 China
| | - Qing Xia
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, China National Center of Biomedical Analysis, Beijing, 100850 China
| | - Jun Wang
- Department of Thoracic Surgery, People’s Hospital, Peking University, Beijing, 100044 China
| | - Tao Zhou
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, China National Center of Biomedical Analysis, Beijing, 100850 China
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8
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Eskaros AR, Egloff SAA, Boyd KL, Richardson JE, Hyndman ME, Zijlstra A. Larger core size has superior technical and analytical accuracy in bladder tissue microarray. J Transl Med 2017; 97:335-342. [PMID: 28112755 DOI: 10.1038/labinvest.2016.151] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 11/16/2016] [Accepted: 12/05/2016] [Indexed: 12/17/2022] Open
Abstract
The construction of tissue microarrays (TMAs) with cores from a large number of paraffin-embedded tissues (donors) into a single paraffin block (recipient) is an effective method of analyzing samples from many patient specimens simultaneously. For the TMA to be successful, the cores within it must capture the correct histologic areas from the donor blocks (technical accuracy) and maintain concordance with the tissue of origin (analytical accuracy). This can be particularly challenging for tissues with small histological features such as small islands of carcinoma in situ (CIS), thin layers of normal urothelial lining of the bladder, or cancers that exhibit intratumor heterogeneity. In an effort to create a comprehensive TMA of a bladder cancer patient cohort that accurately represents the tumor heterogeneity and captures the small features of normal and CIS, we determined how core size (0.6 vs 1.0 mm) impacted the technical and analytical accuracy of the TMA. The larger 1.0 mm core exhibited better technical accuracy for all tissue types at 80.9% (normal), 94.2% (tumor), and 71.4% (CIS) compared with 58.6%, 85.9%, and 63.8% for 0.6 mm cores. Although the 1.0 mm core provided better tissue capture, increasing the number of replicates from two to three allowed with the 0.6 mm core compensated for this reduced technical accuracy. However, quantitative image analysis of proliferation using both Ki67+ immunofluorescence counts and manual mitotic counts demonstrated that the 1.0 mm core size also exhibited significantly greater analytical accuracy (P=0.004 and 0.035, respectively, r2=0.979 and 0.669, respectively). Ultimately, our findings demonstrate that capturing two or more 1.0 mm cores for TMA construction provides superior technical and analytical accuracy over the smaller 0.6 mm cores, especially for tissues harboring small histological features or substantial heterogeneity.
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Affiliation(s)
- Adel Rh Eskaros
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Shanna A Arnold Egloff
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Kelli L Boyd
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Joyce E Richardson
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M Eric Hyndman
- Department of Surgery, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Andries Zijlstra
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
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9
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Peck AR, Girondo MA, Liu C, Kovatich AJ, Hooke JA, Shriver CD, Hu H, Mitchell EP, Freydin B, Hyslop T, Chervoneva I, Rui H. Validation of tumor protein marker quantification by two independent automated immunofluorescence image analysis platforms. Mod Pathol 2016; 29:1143-54. [PMID: 27312066 PMCID: PMC5047958 DOI: 10.1038/modpathol.2016.112] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 05/05/2016] [Accepted: 05/06/2016] [Indexed: 12/27/2022]
Abstract
Protein marker levels in formalin-fixed, paraffin-embedded tissue sections traditionally have been assayed by chromogenic immunohistochemistry and evaluated visually by pathologists. Pathologist scoring of chromogen staining intensity is subjective and generates low-resolution ordinal or nominal data rather than continuous data. Emerging digital pathology platforms now allow quantification of chromogen or fluorescence signals by computer-assisted image analysis, providing continuous immunohistochemistry values. Fluorescence immunohistochemistry offers greater dynamic signal range than chromogen immunohistochemistry, and combined with image analysis holds the promise of enhanced sensitivity and analytic resolution, and consequently more robust quantification. However, commercial fluorescence scanners and image analysis software differ in features and capabilities, and claims of objective quantitative immunohistochemistry are difficult to validate as pathologist scoring is subjective and there is no accepted gold standard. Here we provide the first side-by-side validation of two technologically distinct commercial fluorescence immunohistochemistry analysis platforms. We document highly consistent results by (1) concordance analysis of fluorescence immunohistochemistry values and (2) agreement in outcome predictions both for objective, data-driven cutpoint dichotomization with Kaplan-Meier analyses or employment of continuous marker values to compute receiver-operating curves. The two platforms examined rely on distinct fluorescence immunohistochemistry imaging hardware, microscopy vs line scanning, and functionally distinct image analysis software. Fluorescence immunohistochemistry values for nuclear-localized and tyrosine-phosphorylated Stat5a/b computed by each platform on a cohort of 323 breast cancer cases revealed high concordance after linear calibration, a finding confirmed on an independent 382 case cohort, with concordance correlation coefficients >0.98. Data-driven optimal cutpoints for outcome prediction by either platform were reciprocally applicable to the data derived by the alternate platform, identifying patients with low Nuc-pYStat5 at ~3.5-fold increased risk of disease progression. Our analyses identified two highly concordant fluorescence immunohistochemistry platforms that may serve as benchmarks for testing of other platforms, and low interoperator variability supports the implementation of objective tumor marker quantification in pathology laboratories.
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Affiliation(s)
- Amy R Peck
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Melanie A Girondo
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Chengbao Liu
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Albert J Kovatich
- John P. Murtha Cancer Center, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Jeffrey A Hooke
- John P. Murtha Cancer Center, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Craig D Shriver
- John P. Murtha Cancer Center, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Hai Hu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | - Edith P Mitchell
- Department of Medical Oncology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Boris Freydin
- Division of Biostatistics, Thomas Jefferson University, Philadelphia, PA, USA
| | - Terry Hyslop
- Duke Cancer Institute, Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Inna Chervoneva
- Division of Biostatistics, Thomas Jefferson University, Philadelphia, PA, USA
| | - Hallgeir Rui
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, USA
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10
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Engelberg JA, Retallack H, Balassanian R, Dowsett M, Zabaglo L, Ram AA, Apple SK, Bishop JW, Borowsky AD, Carpenter PM, Chen YY, Datnow B, Elson S, Hasteh F, Lin F, Moatamed NA, Zhang Y, Cardiff RD. "Score the Core" Web-based pathologist training tool improves the accuracy of breast cancer IHC4 scoring. Hum Pathol 2015; 46:1694-704. [PMID: 26410019 DOI: 10.1016/j.humpath.2015.07.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 07/07/2015] [Accepted: 07/15/2015] [Indexed: 01/27/2023]
Abstract
Hormone receptor status is an integral component of decision-making in breast cancer management. IHC4 score is an algorithm that combines hormone receptor, HER2, and Ki-67 status to provide a semiquantitative prognostic score for breast cancer. High accuracy and low interobserver variance are important to ensure the score is accurately calculated; however, few previous efforts have been made to measure or decrease interobserver variance. We developed a Web-based training tool, called "Score the Core" (STC) using tissue microarrays to train pathologists to visually score estrogen receptor (using the 300-point H score), progesterone receptor (percent positive), and Ki-67 (percent positive). STC used a reference score calculated from a reproducible manual counting method. Pathologists in the Athena Breast Health Network and pathology residents at associated institutions completed the exercise. By using STC, pathologists improved their estrogen receptor H score and progesterone receptor and Ki-67 proportion assessment and demonstrated a good correlation between pathologist and reference scores. In addition, we collected information about pathologist performance that allowed us to compare individual pathologists and measures of agreement. Pathologists' assessment of the proportion of positive cells was closer to the reference than their assessment of the relative intensity of positive cells. Careful training and assessment should be used to ensure the accuracy of breast biomarkers. This is particularly important as breast cancer diagnostics become increasingly quantitative and reproducible. Our training tool is a novel approach for pathologist training that can serve as an important component of ongoing quality assessment and can improve the accuracy of breast cancer prognostic biomarkers.
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Affiliation(s)
- Jesse A Engelberg
- Center for Comparative Medicine, University of California Davis, Davis, CA 95616.
| | - Hanna Retallack
- School of Medicine, University of California San Francisco, San Francisco, CA 94143
| | - Ronald Balassanian
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143
| | - Mitchell Dowsett
- Centre for Molecular Pathology, Royal Marsden Hospital, London, SW3 6JJ United Kingdom
| | - Lila Zabaglo
- Institute of Cancer Research, London, SM2 5NG United Kingdom
| | - Arishneel A Ram
- Center for Comparative Medicine, University of California Davis, Davis, CA 95616
| | - Sophia K Apple
- Department of Pathology, University of California Los Angeles, Los Angeles, CA 90404
| | - John W Bishop
- Department of Pathology, University of California Davis, Davis, CA 95616
| | | | - Philip M Carpenter
- Department of Pathology, University of California Irvine, Orange, CA 92697
| | - Yunn-Yi Chen
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143
| | - Brian Datnow
- Department of Pathology, University of California San Diego, San Diego, CA 92093
| | - Sarah Elson
- Center for Comparative Medicine, University of California Davis, Davis, CA 95616
| | - Farnaz Hasteh
- Department of Pathology, University of California San Diego, San Diego, CA 92093
| | - Fritz Lin
- Department of Pathology, University of California Irvine, Orange, CA 92697
| | - Neda A Moatamed
- Department of Pathology, University of California Los Angeles, Los Angeles, CA 90404
| | - Yanhong Zhang
- Department of Pathology, University of California Davis, Davis, CA 95616
| | - Robert D Cardiff
- Department of Pathology, University of California Davis, Davis, CA 95616
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11
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Carvajal-Hausdorf D, Schalper KA, Neumeister V, Rimm DL. Quantitative measurement of cancer tissue biomarkers in the lab and in the clinic. J Transl Med 2015; 95:385-96. [PMID: 25502176 PMCID: PMC4383674 DOI: 10.1038/labinvest.2014.157] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 11/18/2014] [Indexed: 02/06/2023] Open
Abstract
Detection of biomolecules in tissues provides contextual information and the possibility to assess the interaction of different cell types and markers. Routine qualitative assessment of immune- and oligonucleotide-based methods in research and the clinic has been associated with assay variability because of lack of stringent validation and subjective interpretation of results. As a result, the vast majority of in situ assays in clinical usage are nonquantitative and, although useful, often of questionable scientific validity. Here, we revisit the reporters and methods used for single- and multiplexed in situ visualization of protein and RNA. Then we examine methods for the use of quantitative platforms for in situ measurement of protein and mRNA levels. Finally, we discuss the challenges of the transition of these methods to the clinic and their potential role as tools for development of companion diagnostic tests.
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Affiliation(s)
| | - Kurt A. Schalper
- Department of Pathology, Yale University School of Medicine, New Haven, CT
| | | | - David L. Rimm
- Department of Pathology, Yale University School of Medicine, New Haven, CT
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12
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Kricka LJ, Polsky TG, Park JY, Fortina P. The future of laboratory medicine - a 2014 perspective. Clin Chim Acta 2014; 438:284-303. [PMID: 25219903 DOI: 10.1016/j.cca.2014.09.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 09/03/2014] [Accepted: 09/04/2014] [Indexed: 12/20/2022]
Abstract
Predicting the future is a difficult task. Not surprisingly, there are many examples and assumptions that have proved to be wrong. This review surveys the many predictions, beginning in 1887, about the future of laboratory medicine and its sub-specialties such as clinical chemistry and molecular pathology. It provides a commentary on the accuracy of the predictions and offers opinions on emerging technologies, economic factors and social developments that may play a role in shaping the future of laboratory medicine.
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Affiliation(s)
- Larry J Kricka
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, 7.103 Founders Pavilion, 3400 Spruce Street, Philadelphia, PA 19104, USA.
| | - Tracey G Polsky
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, 7.103 Founders Pavilion, 3400 Spruce Street, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jason Y Park
- Department of Pathology and the Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Children's Medical Center, 1935 Medical District Drive, Dallas, TX 75235, USA
| | - Paolo Fortina
- Cancer Genomics Laboratory, Kimmel Cancer Center, Department of Cancer Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA; Department of Molecular Medicine, Universita' La Sapienza, Rome, Italy
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