Current methods in multiplex immunohistochemistry for formalin-fixed tissue samples
Authors:
Romana Hendrychová 1; Kateřina Čížková 2; Dominik Hraboš 1; Jan Bouchal 1
Authors‘ workplace:
Ústav klinické a molekulární patologie, Lékařská fakulta, Univerzita Palackého v Olomouci a Fakultní nemocnice Olomouc
1; Ústav histologie a embryologie, Lékařská fakulta, Univerzita Palackého v Olomouci
2
Published in:
Čes.-slov. Patol., 61, 2025, No. 4, p. 210-220
Category:
Original Article
Overview
Traditional histopathological methods, such as hematoxylin and eosin staining and chromogenic immunohistochemistry, are still primarily used in clinical practice, however, they are limited in their ability to simultaneously detect multiple biomarkers and analyze spatial relationships between cell populations. These limitations are overcome by multiplex immunohistochemistry (mIHC) methods that allow detailed spatial analysis of formalin-fixed paraffin-embedded tissues with detection of multiple epitopes in a single sample. Detailed characterization of immune cell populations within tumor microenvironment has significantly contributed to the development of immunotherapeutic approaches, which have fundamentally transformed the prognosis of many advanced malignancies. Modern multiplex methods use both chromogenic and immunofluorescence detection and include sequential cyclic labeling or tyramine signal amplification techniques. Alternative approaches, such as the use of nucleotide-conjugated antibodies, allow highly specific detection and facilitate quantitative analysis, while mass spectrometry-based approaches enable the profiling of extensive biomarker panels. Despite significant technological advances, the integration of mIHC into routine clinical diagnostics remains challenging, primarily due to the need for standardization, antibody validation, advanced image data analysis integration, and the regulation of laboratory-developed tests. With the continued automation and digitization of pathology, wider use of mIHC in clinical practice can be expected, which could significantly contribute to the deeper characterization of tumors and improved therapy.
Keywords:
Mass spectrometry – Immunofluorescence – Digital Pathology – multiplex immunohistochemistry
Sources
- World Health Organization. Guide for establishing a pathology laboratory in the context of cancer control. Geneva, CH: World Health Organization; 2019. ISBN: 9789241516938.
- Harms PW, Frankel TL, Mouta M, et al. Multiplex Immunohistochemistry and Immunofluorescence : A Practical Update for Pathologists. Mod Pathol 2023; 36(7): 100197.
- Taube JM, Akturk G, Angelo M, et al. 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(1): e000155.
- Leong AS, Leong TY. Standardization in Immunohistology. In: Al-Mulla F, eds. Formalin-Fixed Paraffin-Embedded Tissues: Methods and Protocols (1th ed). Totowa, NJ: Humana Press, 2011; 724 : 37–68.
- Sukswai N, Khoury JD. Immunohistochemistry Innovations for Diagnosis and Tissue-Based Biomarker Detection. Curr Hematol Malig Rep 2019; 14(5): 368–375.
- Lewis TL, Roth KA. Immunohistochemical Detection Methods. In: McManus ML, Mitchell NR, eds. Pathobiology of Human Disease: A Dynamic Encyclopedia of Disease Mechanisms (1th ed). Amsterdam NL: Elsevier, 2014; 3829–3840.
- Sheng W, Zhang C, Mohiuddin TM, et al. Multiplex Immunofluorescence: A Powerful Tool in Cancer Immunotherapy. Int J Mol Sci 2023; 24(4): 3086.
- Chang W, Tan C, Nerurkar SN, et al. Overview of multiplex immunohistochemistry/immunofluorescence techniques in the era of cancer immunotherapy. Cancer Commun (Lond) 2020; 40(4): 135–53.
- Im K, Mareninov S, Diaz MFP, et al. An introduction to Performing Immunofluorescence Staining. Methods Mol Biol 2019; 1897 : 299–311.
- Hernandez S, Rojas F, Laberiano C, et al. Multiplex Immunofluorescence Tyramide Signal Amplification for Immune Cell Profiling of Paraffin-Embedded Tumor Tissues. Front Mol Biosci 2021; 8 : 667067.
- Hofman P, Badoual C, Henderson F, et al. Multiplexed Immunohistochemistry for Molecular and Immune Profiling in Lung Cancer – Just About Ready for Prime-Time? Cancers (Basel) 2019; 11(3): 283.
- Pugh M, Akarka AU, Hunter K, et al. Multiplex immunohistochemistry in lymphoma pathology: a research tool for study of the immune microenvironment. Diagnostic Histopathol 2020; 26(9): 407–420.
- Wharton KA, Wood D, Manesse M, et al. Tissue Multiplex Analyte Detection in Anatomic Pathology – Pathways to Clinical Implementation. Front Mol Biosci 2021; 8 : 672531.
- Lara H, Li Z, Abels E et al. Quantitative Image Analysis for Tissue Biomarker Use: A White Paper from the Digital Pathology Association. Appl Immunohistochem Mol Morphol 2021; 29(7): 479–493.
- Stack EC, Wang C, Roman KA, et al. Multiplexed immunohistochemistry, imaging, and quantitation : A review, with an assessment of Tyramide signal amplification, multispectral imaging and multiplex analysis. Methods 2014; 70(1): 46–58.
- Levenson RM, Borowsky AD, Angelo M. Immunohistochemistry and mass spectrometry for highly multiplexed cellular molecular imaging. Lab Investig 2015; 95(4): 397–405.
- Lin JR, Chen YA, Campton D et al. High-plex immunofluorescence imaging and traditional histology of the same tissue section for discovering image-based biomarkers. Nat Cancer 2023; 4(7): 1036–52.
- Remark R, Merghoub T, Grabe N et al. In-depth tissue profiling using multiplexed immunohistochemical consecutive staining on single slide. Sci Immunol 2016; 1(1): aaf6925.
- Akturk G, Sweeney R, Remark R, et al. Multiplexed Immunohistochemical Consecutive Staining on Single Slide (MICSSS): Multiplexed Chromogenic IHC Assay for High-Dimensional Tissue Analysis. Methods Mol Biol 2020; 2055 : 497–519.
- Chen T, Srinivas C. Group sparsity model for stain unmixing in brightfield multiplex immunohistochemistry images. Comput Med Imaging Graph 2015; 46 : 30–39.
- Zrazhevskiy P, Gao X. Quantum dot imaging platform for single-cell molecular profilin. Nat Commun 2013; 4 : 1619.
- Su T, Wang S, Huang S et al. Multiplex immunohistochemistry and high-throughput image analysis for evaluation of spatial tumor immune cell markers in human breast cancer. Cancer Biomark 2022; 35(2): 193–206.
- Muñoz-Castro C, Noori A, Magdamo CG et al. Cyclic multiplex fluorescent immunohistochemistry and machine learning reveal distinct states of astrocytes and microglia in normal aging and Alzheimer’s disease. J Neuroinflammation 2022; 19(1): 30.
- Viratham Pulsawatdi A, Craig SG, Bingham V, et al. A robust multiplex immunofluorescence and digital pathology workflow for the characterisation of the tumour immune microenvironment. Mol Oncol 2020; 14(10):2384–2402.
- Patel SS, Rodig SJ. Overview of Tissue Imaging Methods. In: Thurin M, Cesano A, Marincola F, eds. Biomarkers for Immunotherapy of Cancer: Methods in Molecular Biology. New York, NY: Humana; 2020; 2055 : 455–465.
- Glass G, Papin JA MJ. SIMPLE: A Sequential Immunoperoxidase Labeling and Erasing Method. J Histochem Cytochem 2009; 57(10): 899–905.
- Berndt U, Philipsen L, Bartsch S, et al. Research Comparative Multi-Epitope-Ligand-Cartography reveals essential immunological alterations in Barrett’s metaplasia and esophageal adenocarcinoma. Mol Cancer 2010; 9 : 117.
- Francisco-Cruz A, Parra ER, Tetzlaff MT, et al. Multiplex Immunofluorescence Assays. In: Thurin M, Cesano A, Marincola F, eds. Biomarkers for Immunotherapy of Cancer: Methods in Molecular Biology. New York, NY: Humana; 2020; 2055 : 467–495.
- Schubert W. Topological Proteomics, Toponomics, MELK-Technology. Adv Biochem Eng Biotechnol 2003; 83 : 189–209.
- Schubert W, Bonnekoh B, Pommer AJ et al. Analyzing proteome topology and function by automated multidimensional fluorescence microscopy. Nat Biotechnol 2006; 24(10): 1270–1278.
- Dixon AR, Bathany C, Tsuei M, et al. Recent developments in multiplexing techniques for immunohistochemistry. Expert Rev Mol Diagn 2015; 15(9): 1171–1186.
- Schubert W, Gieseler A, Krusche A, et al. Next-generation biomarkers based on 100-parameter functional super-resolution microscopy TIS. N Biotechnol 2012; 29(5): 599–610.
- Lin JR, Fallahi-Sichani M, Chen JY, et al. Cyclic Immunofluorescence (CycIF), A Highly Multiplexed Method for Single-cell Imaging. Curr Protoc Chem Biol 2017; 8(4): 251–264.
- Gerdes MJ, Sevinsky CJ, Sood A et al. Highly multiplexed single-cell analysis of formalinfixed, paraffin-embedded cancer tissue. Proc Natl Acad Sci U S A 2013; 110(29): 11982 – 11987.
- Lin JR, Izar B, Wang S et al. Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes. eLife 2018; 7: e31657.
- Kinkhabwala A, Herbel C, Pankratz J et al. MACSima imaging cyclic staining (MICS) technology reveals combinatorial target pairs for CAR T cell treatment of solid tumors. Sci Rep 2022; 12(1): 19114.
- Aung TN, Bates KM, Rimm DL. High-Plex Assessment of Biomarkers in Tumors. Mod Pathol 2024; 37(3): 100425.
- Rivest F, Eroglu D, Pelz B, et al. Fully automated sequential immunofluorescence (seqIF) for hyperplex spatial proteomics. Sci Rep 2023; 13(1): 1–14.
- ToposNomos. ToposNomos Spatial Biology. Internet. Dostupné z: https://www.toposnomos.com/. Přístup dne 26.4.2025
- Miltenyi Biotec. MACSima™ Imaging Cyclic Staining (MICS) Technology. Internet. Dostupné z: https://www.miltenyibiotec.com/DE-en/ products/macs-imaging-and-spatial-biology/ macsima-platform/mics-technology.html. Přístup dne 26.4.2025.
- Lunaphore Technologies. Horizon™. Internet. Dostupné z https://lunaphore.com/products/horizon/. Přístup dne 26.6.2025
- Lunaphore Technologies. COMET™. Internet. Dostupné z https://lunaphore.com/products/ comet/. Přístup dne 26.6.2025
- Bobrow MN, Harris TD, Shaughnessy KJ, et al. Catalyzed reporter deposition, a novel method of signal amplification. Application to immunoassays. J Immunol Methods 1989; 125(1–2): 279–285.
- Bobrow MN, Shaughnessy KJ, Litt G. Catalyzed reporter deposition, a novel method of signal amplification. II. Application to membrane immunoassays. J Immunol Methods 1991; 137(1): 103–112. d
- Faget L, Hnasko TS. Tyramide Signal Amplification for Immunofluorescent Enhancement. In: Hnasko R, eds. ELISA: Methods and Protocols. New York, NY: Humana; 2015; 1318 : 161–172.
- Tumeh PC, Harview CL, Yearley JH et al. PD-1 blockade induces responses by inhibiting adaptive immune resistance. Nature 2015; 515(7528): 568–571.
- Hoyt CC. Multiplex Immunofluorescence and Multispectral Imaging: Forming the Basis of a Clinical Test Platform for Immuno-Oncology. Front Mol Biosci 2021; 8 : 674747.
- Goltsev Y, Samusik N, Kennedy-Darling J, et al. Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging. Cell 2018; 174(4): 968-981.e15.
- Black S, Phillips D, Hickey JW, et al. CODEX multiplexed tissue imaging with DNA-conjugated antibodies. Nat Protoc 2022; 16(8): 3802–3835.
- Wang Y, Liu X, Zeng Y, et al. Multiplexed in situ protein imaging using DNA-barcoded antibodies with extended hybridization chain reactions. Nucleic Acids Res 2024; 52(15): e71.
- Choi J, Love KR, Gong Y, et al. Immuno-Hybridization Chain Reaction for Enhancing Detection of Individual Cytokine-Secreting Human Peripheral Mononuclear Cells. Anal Chem 2011; 83(17): 6890–6895.
- Wang Y, Woehrstein JB, Donoghue N, et al. Rapid Sequential in Situ Multiplexing with DNA Exchange Imaging in Neuronal Cells and Tissues. Nano Lett 2017; 17(10): 6131–6139.
- Saka SK, Wang Y, Kishi JY, et al. Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues. Nat Biotechnol 2019; 37(9): 1080–1090.
- Manesse M, Patel KK, Bobrow M, et al. The InSituPlex® Staining Method for Multiplexed Immunofluorescence Cell Phenotyping and Spatial Profiling of Tumor FFPE Samples In: Thurin M, Cesano A, Marincola F, eds. Biomarkers for Immunotherapy of Cancer: Methods in Molecular Biology. New York, NY: Humana; 2020; 2055 : 585–592.
- Cell Signaling Technology. Spatial Profiling with SignalStar™ Multiplex IHC. Internet. Dostupné z https://www.cellsignal.com/appli- cations/signalstar-multiplex-ihc-overview. Přístup dne 13.6.2025
- Merritt CR, Ong GT, Church SE, et al. Multiplex digital spatial profiling of proteins and RNA in fixed tissue. Nat Biotechnol 2020; 38(5): 586–99.
- Einhaus J, Rochwarger A, Mattern S, et al. High-multiplex tissue imaging in routine pathology–are we there yet?. Virchows Arch 2023; 482(5): 801–812.
- Eyers M, Irlam J, Marshall G, et al. Digital spatial profiling of the microenvironment of muscle invasive bladder cancer. Commun Biol 2024; 7(1): 737.
- Bandura DR, Baranov VI, Ornatsky OI, et al. Mass Cytometry: Technique for Real Time Single Cell Multitarget Immunoassay Based on Inductively Coupled Plasma Time-of-Flight Mass Spectrometry. Anal Chem 2009; 81(16): 6813–6822.
- Bjornson ZB, Nolan GP FW. Single Cell Mass Cytometry for Analysis of Immune System Functional States. Curr Opin Immunol 2013; 25(4): 484–494.
- Giesen C, Wang HAO, Schapiro D, et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nat Methods 2014; 11(4): 417–422.
- Angelo M, Bendall SC, Finck R, et al. Multiplexed ion beam imaging of human breast tumors. Nat Med 2014; 20(4): 436–442.
- Akoya Biosciences. PhenoImager HT. Internet. Dostupné z: https://www.akoyabio.com/ phenoimager/instruments/phenoimager-ht/. Přístup dne 28.4.2025.
- Akoya Biosciences. inForm Tissue Analysis Software. Internet. Dostupné z: https://www. akoyabio.com/phenoimager/inform-tissue-finder/. Přístup dne 28.4.2025.
- HPST. PhenoImager HT – Akoya Biosciences. Internet. Dostupné z: https://hpst.cz/bunecna-biologie-mikroskopie/spatial-omics-akoya-biosciences/phenoimager-ht#. Přístup dne 28.4.2025.
- Roche. Discovery Ultra. Internet. Dostupné z: https://diagnostics.roche.com/us/en/products/product-category/immunohistochemistry--ihc-/discovery-ultra.html. Přístup dne 28.4.2025.
- Akoya Biosciences. PhenoCycler. Internet. Dostupné z: https://www.akoyabio.com/phe- nocycler/. Přístup dne 28.4.2025.
- NanoString. GeoMx® Digital Spatial Profiler. Internet. Dostupné z: https://nanostring.com/ products/geomx-digital-spatial-profiler/. Přístup dne 28.4.2025.
- NanoString. nCounter® Analysis Systems for Biomarker Validation and Biomarker Development. Internet. Dostupné z: https://nanostring.com/products/ncounter-analysis-system/ncounter-systems-overview/. Přístup dne 28.4.2025.
- Ultivie. InSituPlex® technology. Internet. Dostupné z https://ultivue.com/insituplex-technology/. Přístup dne 13.6.2025
- Cell Signaling Technology. SignalStar™ Multiplex Immunohistochemistry Assay Manual. Internet. Dostupné z https://www.cellsignal. com/learn-and-support/protocols/signal star-multiplex-ihc-assay-manual. Přístup dne 13.6.2025
- Standard BioTools. Imaging Mass Cytometry™ (IMC™). Internet. Dostupné z: https:// www.standardbio.com/products/technolo- gies/imaging-mass-cytometry#workflow-anchor. Přístup dne 28.4.2025.
- Standard BioTools. Hyperion XTi Imaging System. Internet. Dostupné z: https://www.standardbio.com/support/instrument-support/hyperion-xti-support. Přístup dne 28.4.2025.
- Immune Dynamics. Spectre Spatial Visualisation. Internet. Dostupné z: https://immunedynamics.io/spectre/spatial/visualisation/. Přístup dne 28.4.2025.
- Moen E, Bannon D, Kudo T, et al. Deep learning for cellular image analysis. Nat Methods 2019; 16(12): 1233–1246.
- Rojas F, Hernandez S, Lazcano R, et al. Multiplex Immunofluorescence and the Digital Image Analysis Workflow for Evaluation of the Tumor Immune Environment in Translational Research. Front Oncol 2022; 12: 889886.
- Zeng W. Image data augmentation techniques based on deep learning: A survey. Math Biosci Eng. 2024; 21(6): 6190–6224.
- Aleynick N, Li Y, Xie Y, et al. Cross-platform dataset of multiplex fluorescent cellular object image annotations. Sci Data 2023; 10(1): 193.
- Parra ER, Jiang M, Solis L, et al. Procedural Requirements and Recommendations for Multiplex Immunofluorescence Tyramide Signal Amplification Assays to Support Translational Oncology Studies. Cancers (Basel) 2020; 12(2): 255.
- Bankhead P, Loughrey MB, Fernández JA, et al. QuPath: Open source software for digital pathology image analysis. Sci Rep 2017; 7(1): 16878.
- Varghese F, Bukhari AB, Malhotra R, et al. Profiler: an open source plugin for the quantitative evaluation and automated scoring of immunohistochemistry images of human tissue samples. PLoS One 2014; 9(5): e96801.
- Marée R. Open Practices and Resources for Collaborative Digital Pathology. Front Med 2019; 6 : 255.
- Schneider CA, Rasband WS, Eliceiri KW. NIH Image to ImageJ: 25 years of image analysis. Nat Methods 2012; 9(7): 671–675.
- Schapiro D, Jackson HW, Raghuraman S, et al. histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data. Nat Methods 2017; 14(9): 873–876.
- Schapiro D, Sokolov A, Yapp C, et al. MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging. Nat Methods 2022; 19(3): 311–315.
- Wan G, Maliga Z, Yan B, et al. SpatialCells : automated profiling of tumor microenvironments with spatially resolved multiplexed single-cell data. Brief Bioinform 2024; 25(3): bbae189.
- Mascaux C, Angelova M, Vasaturo A, et al. Immune evasion before tumour invasion in early lung squamous carcinogenesis. Nature 2019; 571(7766): 570–575.
- Giraldo NA, Nguyen P, Engle EL, et al. Multidimensional, quantitative assessment of PD-1/PD-L1 expression in patients with Merkel cell carcinoma and association with response to pembrolizumab. J Immunother Cancer 2018; 6(1): 99.
- Dawe M, Shi W, Liu TY, et al. Reliability and Variability of Ki-67 Digital Image Analysis Methods for Clinical Diagnostics in Breast Cancer. Lab Invest 2024; 104(5): 100341.
- Flotte TJ, Derauf SA, Byrd RK, et al. Democratizing Artificial Intelligence in Anatomic Pathology. Arch Pathol Lab Med 2025; 149(1): 55–59.
- Yoder A, Inge LJ, Chen CC, et al. Computer-aided scoring of erb-b2 receptor tyrosine kinase 2 (HER2) gene amplification status in breast cancer. J Pathol Inform 2022; 13 : 100116.
- Bankhead P. QuPath User Documentation. Internet. Dostupné z: https://qupath.readthedocs.io/en/stable/index.html. Přístup dne 28.4.2025.
- National Institutes of Health. ImageJ. Internet. Dostupné z: https://imagej.net/imagej-wiki-static/Welcome. Přístup dne 28.4.2025.
- Rau A, Bodenmiller B. HistoCAT. Internet. Dostupné z https://bodenmillergroup.github. io/histocat-web/#overview. Přístup dne 28.4.2025.
- Indica Labs. HALO – Quantitative Image Analysis for Pathology. Internet. Dostupné z https://indicalab.com/halo/. Přístup dne 28.4.2025.
- Aiforia Technologies. Aiforia: AI – for image analysis. Internet. Dostupné z https://www. aiforia.com/. Přístup dne 28.4.2025.
- Roche. uPath Image Analysis Algorithms. Internet. Dostupné z https://diagnostics. roche.com/us/en/products/other/upath-image-analysis-algorithms.html. Přístup dne 28.4.2025.
- Singh V, Manu V, Malik A, et al. Diagnostic utility of p63 and α-methyl acyl Co A racemase in resolving suspicious foci in prostatic needle biopsy and transurethral resection of prostate specimens. J Cancer Res Ther 2014; 10(3): 686–692. doi: 10.4103/0973-1482.138194.
- Trpkov K, Bartczak-McKay J, Yilmaz A. Usefulness of cytokeratin 5/6 and AMACR applied as double sequential immunostains for diagnostic assessment of problematic prostate specimens. Am J Clin Pathol 2009; 132(2): 211–307.
- Obiorah IE, Wang HW, Ma D, et al. The Effectiveness of Dual-Staining Immunohistochemistry in the Detection of Mantle Cell Lymphoma in the Bone Marrow. Am J Clin Pathol 2022; 157(5): 709-717.
- Taube JM, Roman K, Engle EL, et al. Multi-institutional TSA-amplified Multiplexed Immunofluorescence Reproducibility Evaluation (MITRE) Study. J Immunother Cancer 2021; 9(7): e002197.
- Kimura A, Tsujikawa T, Morimoto H, et al. Rapid multiplex immunohistochemistry for characterizing tumor-immune microenvironment. Heliyon 2024; 10(13): e33830.
- Státní ústav pro kontrolu léčiv (SÚKL). Metodické doporučení pro implementaci požadavků IVDR na prostředky vyráběné a používané pouze v rámci zdravotnického zařízení. Praha, CZ: SÚKL; 2024 : 1-46.
Labels
Anatomical pathology Forensic medical examiner ToxicologyArticle was published in
Czecho-Slovak Pathology
2025 Issue 4
-
All articles in this issue
- Editorial
- Interview
- Monitor
- Papillary Breast Lesions: Diagnostic Challenges and Overview of Entities
- Immunohistochemical assessment of HER2 protein in breast carcinomas – current status
- Predictive factors assessment in breast cancer treatment
- Unusual histopathologic finding in axillary lymph node in patient with invasive breast carcinoma NST: Case report and literature review
- An unusual case of late recurrent adult granulosa cell tumor and mature teratoma arising within the same ovary, confirmed by NGS analysis
- Current methods in multiplex immunohistochemistry for formalin-fixed tissue samples
- Czecho-Slovak Pathology
- Journal archive
- Current issue
- About the journal
Most read in this issue
- Editorial
- An unusual case of late recurrent adult granulosa cell tumor and mature teratoma arising within the same ovary, confirmed by NGS analysis
- Interview
- Monitor