1
|
Evans M, Kendall T. Practical considerations for pathological diagnosis and molecular profiling of cholangiocarcinoma: an expert review for best practices. Expert Rev Mol Diagn 2024; 24:393-408. [PMID: 38752560 DOI: 10.1080/14737159.2024.2353696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024]
Abstract
INTRODUCTION Advances in precision medicine have expanded access to targeted therapies and demand for molecular profiling of cholangiocarcinoma (CCA) patients in routine clinical practice. However, pathologists face challenges in establishing a definitive intrahepatic CCA (iCCA) diagnosis while preserving sufficient tissue for molecular profiling. Additionally, they frequently face challenges in optimal tissue handling to preserve nucleic acid integrity. AREAS COVERED This article first identifies the challenges in establishing a definitive diagnosis of iCCA in a lesional liver biopsy while preserving sufficient tissue for molecular profiling. Then, the authors explore the clinical value of molecular profiling, the basic principles of single gene and next-generation sequencing (NGS) techniques, and the challenges in tissue sampling for genomic testing. They also propose an algorithm for best practice in tissue management for molecular profiling of CCA. EXPERT OPINION Several practical challenges face pathologists during tissue sampling and processing for molecular profiling. Optimized tissue processing, careful tissue handling, and selection of appropriate approaches to molecular testing are essential to ensure that the highest possible quality of diagnostic information is provided in the greatest proportion of cases.
Collapse
Affiliation(s)
- Matt Evans
- Cellular Pathologist, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | | |
Collapse
|
2
|
Navikas V, Kowal J, Rodriguez D, Rivest F, Brajkovic S, Cassano M, Dupouy D. Semi-automated approaches for interrogating spatial heterogeneity of tissue samples. Sci Rep 2024; 14:5025. [PMID: 38424144 PMCID: PMC10904364 DOI: 10.1038/s41598-024-55387-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 02/22/2024] [Indexed: 03/02/2024] Open
Abstract
Tissues are spatially orchestrated ecosystems composed of heterogeneous cell populations and non-cellular elements. Tissue components' interactions shape the biological processes that govern homeostasis and disease, thus comprehensive insights into tissues' composition are crucial for understanding their biology. Recently, advancements in the spatial biology field enabled the in-depth analyses of tissue architecture at single-cell resolution, while preserving the structural context. The increasing number of biomarkers analyzed, together with whole tissue imaging, generate datasets approaching several hundreds of gigabytes in size, which are rich sources of valuable knowledge but require investments in infrastructure and resources for extracting quantitative information. The analysis of multiplex whole-tissue images requires extensive training and experience in data analysis. Here, we showcase how a set of open-source tools can allow semi-automated image data extraction to study the spatial composition of tissues with a focus on tumor microenvironment (TME). With the use of Lunaphore COMET platform, we interrogated lung cancer specimens where we examined the expression of 20 biomarkers. Subsequently, the tissue composition was interrogated using an in-house optimized nuclei detection algorithm followed by a newly developed image artifact exclusion approach. Thereafter, the data was processed using several publicly available tools, highlighting the compatibility of COMET-derived data with currently available image analysis frameworks. In summary, we showcased an innovative semi-automated workflow that highlights the ease of adoption of multiplex imaging to explore TME composition at single-cell resolution using a simple slide in, data out approach. Our workflow is easily transferrable to various cohorts of specimens to provide a toolset for spatial cellular dissection of the tissue composition.
Collapse
Affiliation(s)
| | - Joanna Kowal
- Lunaphore Technologies SA, Tolochenaz, Switzerland
| | | | | | | | | | - Diego Dupouy
- Lunaphore Technologies SA, Tolochenaz, Switzerland.
| |
Collapse
|
3
|
Rivest F, Eroglu D, Pelz B, Kowal J, Kehren A, Navikas V, Procopio MG, Bordignon P, Pérès E, Ammann M, Dorel E, Scalmazzi S, Bruno L, Ruegg M, Campargue G, Casqueiro G, Arn L, Fischer J, Brajkovic S, Joris P, Cassano M, Dupouy D. Fully automated sequential immunofluorescence (seqIF) for hyperplex spatial proteomics. Sci Rep 2023; 13:16994. [PMID: 37813886 PMCID: PMC10562446 DOI: 10.1038/s41598-023-43435-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 09/23/2023] [Indexed: 10/11/2023] Open
Abstract
Tissues are complex environments where different cell types are in constant interaction with each other and with non-cellular components. Preserving the spatial context during proteomics analyses of tissue samples has become an important objective for different applications, one of the most important being the investigation of the tumor microenvironment. Here, we describe a multiplexed protein biomarker detection method on the COMET instrument, coined sequential ImmunoFluorescence (seqIF). The fully automated method uses successive applications of antibody incubation and elution, and in-situ imaging enabled by an integrated microscope and a microfluidic chip that provides optimized optical access to the sample. We show seqIF data on different sample types such as tumor and healthy tissue, including 40-plex on a single tissue section that is obtained in less than 24 h, using off-the-shelf antibodies. We also present extensive characterization of the developed method, including elution efficiency, epitope stability, repeatability and reproducibility, signal uniformity, and dynamic range, in addition to marker and panel optimization strategies. The streamlined workflow using off-the-shelf antibodies, data quality enabling downstream analysis, and ease of reaching hyperplex levels make seqIF suitable for immune-oncology research and other disciplines requiring spatial analysis, paving the way for its adoption in clinical settings.
Collapse
Affiliation(s)
| | - Deniz Eroglu
- Lunaphore Technologies SA, Tolochenaz, Switzerland
| | | | - Joanna Kowal
- Lunaphore Technologies SA, Tolochenaz, Switzerland
| | | | | | | | | | - Emilie Pérès
- Lunaphore Technologies SA, Tolochenaz, Switzerland
| | - Marco Ammann
- Lunaphore Technologies SA, Tolochenaz, Switzerland
| | | | | | | | | | | | | | - Lionel Arn
- Lunaphore Technologies SA, Tolochenaz, Switzerland
| | | | | | - Pierre Joris
- Lunaphore Technologies SA, Tolochenaz, Switzerland
| | | | - Diego Dupouy
- Lunaphore Technologies SA, Tolochenaz, Switzerland.
| |
Collapse
|
4
|
Draz MS, Dupouy D, Gijs MAM. Acoustofluidic large-scale mixing for enhanced microfluidic immunostaining for tissue diagnostics. LAB ON A CHIP 2023. [PMID: 37365861 DOI: 10.1039/d3lc00312d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
The usage of microfluidics for automated and fast immunoassays has gained a lot of interest in the last decades. This integration comes with certain challenges, like the reconciliation of laminar flow patterns of micro-scale systems with diffusion-limited mass transport. Several methods have been investigated to enhance microfluidic mixing in microsystems, including acoustic-based fluidic streaming. Here, we report both by numerical simulation and experiments on the beneficiary effect of acoustic agitation on the uniformity of immunostaining in large-size and thin microfluidic chambers. Moreover, we investigate by numerical simulation the impact of reducing the incubation times and the concentrations of the biochemical detection reagents on the obtained immunoassay signal. Finally, acoustofluidic mixing was successfully used to reduce by 80% the incubation time of the Her2 (human epidermal growth factor receptor 2) and CK (cytokeratins) biomarkers for the spatial immunostaining of breast cancer cell pellets, or reducing their concentration by 66% and achieving a higher signal-to-background ratio than comparable spatially resolved immunostaining with static incubation.
Collapse
Affiliation(s)
- Muaz S Draz
- Laboratory of Microsystems 2, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
- Lunaphore Technologies SA, CH-1131 Tolochenaz, Switzerland
| | - Diego Dupouy
- Lunaphore Technologies SA, CH-1131 Tolochenaz, Switzerland
| | - Martin A M Gijs
- Laboratory of Microsystems 2, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
| |
Collapse
|
5
|
Furia L, Pelicci S, Perillo F, Bolognesi MM, Pelicci PG, Facciotti F, Cattoretti G, Faretta M. Automated multimodal fluorescence microscopy for hyperplex spatial-proteomics: Coupling microfluidic-based immunofluorescence to high resolution, high sensitivity, three-dimensional analysis of histological slides. Front Oncol 2022; 12:960734. [PMCID: PMC9606676 DOI: 10.3389/fonc.2022.960734] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/27/2022] [Indexed: 11/13/2022] Open
Abstract
In situ multiplexing analysis and in situ transcriptomics are now providing revolutionary tools to achieve the comprehension of the molecular basis of cancer and to progress towards personalized medicine to fight the disease. The complexity of these tasks requires a continuous interplay among different technologies during all the phases of the experimental procedures. New tools are thus needed and their characterization in terms of performances and limits is mandatory to reach the best resolution and sensitivity. We propose here a new experimental pipeline to obtain an optimized costs-to-benefits ratio thanks to the alternate employment of automated and manual procedures during all the phases of a multiplexing experiment from sample preparation to image collection and analysis. A comparison between ultra-fast and automated immunofluorescence staining and standard staining protocols has been carried out to compare the performances in terms of antigen saturation, background, signal-to-noise ratio and total duration. We then developed specific computational tools to collect data by automated analysis-driven fluorescence microscopy. Computer assisted selection of targeted areas with variable magnification and resolution allows employing confocal microscopy for a 3D high resolution analysis. Spatial resolution and sensitivity were thus maximized in a framework where the amount of stored data and the total requested time for the procedure were optimized and reduced with respect to a standard experimental approach.
Collapse
Affiliation(s)
- Laura Furia
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Simone Pelicci
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Federica Perillo
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | | | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Federica Facciotti
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan, Italy
| | - Giorgio Cattoretti
- Department of Medicine and Surgery, Università di Milano-Bicocca, Monza, Italy
| | - Mario Faretta
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
- *Correspondence: Mario Faretta,
| |
Collapse
|
6
|
Fu C, Yang K, Zou Y, Huo R. Identification of Key microRNAs and Genes in Infantile Hemangiomas. Front Genet 2022; 13:766561. [PMID: 35360837 PMCID: PMC8963821 DOI: 10.3389/fgene.2022.766561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 02/21/2022] [Indexed: 11/29/2022] Open
Abstract
Infantile hemangiomas (IHs) are the most frequent vascular tumors that occur during infancy. Microribonucleic acids (miRNAs) have been demonstrated as critical regulators of gene expression in various diseases. However, the function of miRNAs in IH still remains largely unknown. In the present study, we performed a miRNA microarray analysis of IH and identified 68 differentially expressed miRNAs (DEMs). In addition, miRNA-gene networks and protein-protein interactions were constructed, and the hub miRNAs and genes of IH were screened out. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were used for biological analysis of DEMs and differentially expressed genes (DEGs). The pathway enrichment analysis of DEMs revealed several tumor-related pathways, including proteoglycans in cancer, signaling pathway regulating pluripotency of stem cells and TGF-beta signaling pathway. DEGs were mainly enriched in biological processes, including intracellular signal transduction, cell adhesion, and cell death. KEGG pathway analysis indicated that DEGs were enriched in tumorigenesis- and angiogenesis-related pathways such as proteoglycans in cancer, MAPK signaling pathway and Rap1 signaling pathway. Collectively, this study first established a comprehensive miRNA-gene network in IH, which should provide novel insights into IH pathogenesis and be beneficial to the understanding of neovascularization-related disorders.
Collapse
Affiliation(s)
- Cong Fu
- Department of Burn and Plastic Surgery, Shandong Provincial Hospital, Shandong First Medical University, Jinan, China
| | - Kun Yang
- Department of Medicine, Shandong University, Jinan, China
| | - Yuqing Zou
- Department of Medicine, Shandong University, Jinan, China
| | - Ran Huo
- Department of Burn and Plastic Surgery, Shandong Provincial Hospital, Shandong First Medical University, Jinan, China
- Department of Medicine, Shandong University, Jinan, China
- *Correspondence: Ran Huo,
| |
Collapse
|
7
|
Teixeira A, Carneiro A, Piairo P, Xavier M, Ainla A, Lopes C, Sousa-Silva M, Dias A, Martins AS, Rodrigues C, Pereira R, Pires LR, Abalde-Cela S, Diéguez L. Advances in Microfluidics for the Implementation of Liquid Biopsy in Clinical Routine. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1379:553-590. [DOI: 10.1007/978-3-031-04039-9_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
8
|
Fomitcheva-Khartchenko A, Rapsomaniki MA, Sobottka B, Schraml P, Kaigala GV. Spatial protein heterogeneity analysis in frozen tissues to evaluate tumor heterogeneity. PLoS One 2021; 16:e0259332. [PMID: 34797831 PMCID: PMC8604290 DOI: 10.1371/journal.pone.0259332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 10/19/2021] [Indexed: 11/19/2022] Open
Abstract
A new workflow for protein-based tumor heterogeneity probing in tissues is here presented. Tumor heterogeneity is believed to be key for therapy failure and differences in prognosis in cancer patients. Comprehending tumor heterogeneity, especially at the protein level, is critical for tracking tumor evolution, and showing the presence of different phenotypical variants and their location with respect to tissue architecture. Although a variety of techniques is available for quantifying protein expression, the heterogeneity observed in the tissue is rarely addressed. The proposed method is validated in breast cancer fresh-frozen tissues derived from five patients. Protein expression is quantified on the tissue regions of interest (ROI) with a resolution of up to 100 μm in diameter. High heterogeneity values across the analyzed patients in proteins such as cytokeratin 7, β-actin and epidermal growth factor receptor (EGFR) using a Shannon entropy analysis are observed. Additionally, ROIs are clustered according to their expression levels, showing their location in the tissue section, and highlighting that similar phenotypical variants are not always located in neighboring regions. Interestingly, a patient with a phenotype related to increased aggressiveness of the tumor presents a unique protein expression pattern. In summary, a workflow for the localized extraction and protein analysis of regions of interest from frozen tissues, enabling the evaluation of tumor heterogeneity at the protein level is presented.
Collapse
Affiliation(s)
| | | | - Bettina Sobottka
- Department of Pathology and Molecular Pathology, University Hospital Zurich and University Zurich, Zurich, Switzerland
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, University Hospital Zurich and University Zurich, Zurich, Switzerland
| | | |
Collapse
|
9
|
Vázquez M, Anfossi L, Ben-Yoav H, Diéguez L, Karopka T, Della Ventura B, Abalde-Cela S, Minopoli A, Di Nardo F, Shukla VK, Teixeira A, Tvarijonaviciute A, Franco-Martínez L. Use of some cost-effective technologies for a routine clinical pathology laboratory. LAB ON A CHIP 2021; 21:4330-4351. [PMID: 34664599 DOI: 10.1039/d1lc00658d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Classically, the need for highly sophisticated instruments with important economic costs has been a major limiting factor for clinical pathology laboratories, especially in developing countries. With the aim of making clinical pathology more accessible, a wide variety of free or economical technologies have been developed worldwide in the last few years. 3D printing and Arduino approaches can provide up to 94% economical savings in hardware and instrumentation in comparison to commercial alternatives. The vast selection of point-of-care-tests (POCT) currently available also limits the need for specific instruments or personnel, as they can be used almost anywhere and by anyone. Lastly, there are dozens of free and libre digital tools available in health informatics. This review provides an overview of the state-of-the-art on cost-effective alternatives with applications in routine clinical pathology laboratories. In this context, a variety of technologies including 3D printing and Arduino, lateral flow assays, plasmonic biosensors, and microfluidics, as well as laboratory information systems, are discussed. This review aims to serve as an introduction to different technologies that can make clinical pathology more accessible and, therefore, contribute to achieve universal health coverage.
Collapse
Affiliation(s)
- Mercedes Vázquez
- National Centre For Sensor Research, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Laura Anfossi
- Department of Chemistry, University of Turin, Via Giuria, 5, I-10125 Turin, Italy
| | - Hadar Ben-Yoav
- Nanobioelectronics Laboratory (NBEL), Department of Biomedical Engineering, Ilse Katz Institute of Nanoscale Science and Technology, Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Lorena Diéguez
- Medical Devices Research Group, International Iberian Nanotechnology Laboratory - INL, 4715-330 Braga, Portugal
| | | | - Bartolomeo Della Ventura
- Department of Physics "E. Pancini", University of Naples Federico II, Via Cintia 26, I-80126 Napoli, Italy
| | - Sara Abalde-Cela
- Medical Devices Research Group, International Iberian Nanotechnology Laboratory - INL, 4715-330 Braga, Portugal
| | - Antonio Minopoli
- Department of Physics "E. Pancini", University of Naples Federico II, Via Cintia 26, I-80126 Napoli, Italy
| | - Fabio Di Nardo
- Department of Chemistry, University of Turin, Via Giuria, 5, I-10125 Turin, Italy
| | - Vikas Kumar Shukla
- Nanobioelectronics Laboratory (NBEL), Department of Biomedical Engineering, Ilse Katz Institute of Nanoscale Science and Technology, Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Alexandra Teixeira
- Medical Devices Research Group, International Iberian Nanotechnology Laboratory - INL, 4715-330 Braga, Portugal
| | - Asta Tvarijonaviciute
- Interdisciplinary Laboratory of Clinical Pathology, Interlab-UMU, Regional Campus of International Excellence 'Campus Mare Nostrum', University of Murcia, 30100 Murcia, Spain.
| | - Lorena Franco-Martínez
- Interdisciplinary Laboratory of Clinical Pathology, Interlab-UMU, Regional Campus of International Excellence 'Campus Mare Nostrum', University of Murcia, 30100 Murcia, Spain.
| |
Collapse
|
10
|
Mahmoudi R, Dianat-Moghadam H, Poorebrahim M, Siapoush S, Poortahmasebi V, Salahlou R, Rahmati M. Recombinant immunotoxins development for HER2-based targeted cancer therapies. Cancer Cell Int 2021; 21:470. [PMID: 34488747 PMCID: PMC8422749 DOI: 10.1186/s12935-021-02182-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/26/2021] [Indexed: 01/07/2023] Open
Abstract
Understanding the molecular mechanisms of cancer biology introduces targeted therapy as a complementary method along with other conventional therapies. Recombinant immunotoxins are tumor specific antibodies that their recognizing fragment is utilized for delivering modified toxins into tumor cells. These molecules have been considered as a targeted strategy in the treatment of human cancers. HER2 tumor biomarker is a transmembrane tyrosine kinase receptor that can be used for targeted therapies in the forms of anti-HER2 monoclonal antibodies, antibody-drug conjugates and immunotoxins. There have been many studies on HER2-based immunotoxins in recent years, however, little progress has been made in the clinical field which demanded more improvements. Here, we summarized the HER2 signaling and it's targeting using immunotherapeutic agents in human cancers. Then, we specifically reviewed anti-HER2 immunotoxins, and their strengths and drawbacks to highlight their promising clinical impact.
Collapse
Affiliation(s)
- Reza Mahmoudi
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hassan Dianat-Moghadam
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Mansour Poorebrahim
- Targeted Tumor Vaccines Group, Clinical Cooperation Unit Applied Tumor Immunity, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Samaneh Siapoush
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Vahdat Poortahmasebi
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Reza Salahlou
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Rahmati
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.
- Department of Clinical Biochemistry, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
| |
Collapse
|
11
|
Multifunctional nanoparticles as optical biosensing probe for breast cancer detection: A review. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2021; 127:112249. [PMID: 34225888 DOI: 10.1016/j.msec.2021.112249] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 05/11/2021] [Accepted: 06/05/2021] [Indexed: 12/15/2022]
Abstract
Optical biosensors show attractive performance in medical sensing in the event of using different nanoparticles in their design. Owing to their unique optical characteristics and biological compatibility, gold nanoparticles (GNPs), silver nanoparticles (AgNPs), bimetallic nanoparticles and magnetic nanoparticles have been broadly implemented in making sensing tools. The functionalization of these nanoparticles with different components provides an excellent opportunity to assemble selective and sensitive sensing materials to detect various biological molecules related to breast cancer. This review summarizes the recent application of optical biosensing devices based on nanomaterials and discusses their pros and cons to improve breast cancer detection in real samples. In particular, the main constituent elements of these optical biosensors including recognition and transducer elements, types of applied nanostructures, analytical sensing procedures, sensor detection ranges and limit of detection (LOD), are expressed in detail.
Collapse
|
12
|
Bekaii-Saab TS, Bridgewater J, Normanno N. Practical considerations in screening for genetic alterations in cholangiocarcinoma. Ann Oncol 2021; 32:1111-1126. [PMID: 33932504 DOI: 10.1016/j.annonc.2021.04.012] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 04/06/2021] [Accepted: 04/18/2021] [Indexed: 12/14/2022] Open
Abstract
Cholangiocarcinoma (CCA) encompasses diverse epithelial tumors historically associated with poor outcomes due to an aggressive disease course, late diagnosis, and limited benefit of standard chemotherapy for advanced disease. Comprehensive molecular profiling has revealed a diverse landscape of genomic alterations as oncogenic drivers in CCA. TP53 mutations, CDKN2A/B loss, and KRAS mutations are the most common genetic alterations in CCA. However, intrahepatic CCA (iCCA) and extrahepatic CCA (eCCA) differ substantially in the frequency of many alterations. This includes actionable alterations, such as isocitrate dehydrogenase 1 (IDH1) mutations and a large variety of FGFR2 rearrangements, which are found in up to 29% and ∼10% of patients with iCCA, respectively, but are rare in eCCA. FGFR2 rearrangements are currently the only genetic alteration in CCA for which a targeted therapy, the fibroblast growth factor receptor 1-3 inhibitor pemigatinib, has been approved. However, favorable phase III results for IDH1-targeted therapy with ivosidenib in iCCA have been published, and numerous other alterations are actionable by targeted therapies approved in other indications. Recent advances in next-generation sequencing (NGS) have led to the development of assays that allow comprehensive genomic profiling of large gene panels within 2-3 weeks, including in vitro diagnostic tests approved in the United States. These assays vary regarding acceptable source material (tumor tissue or peripheral whole blood), genetic source for library construction (DNA or RNA), target selection technology, gene panel size, and type of detectable genomic alterations. While some large commercial laboratories offer rapid and comprehensive genomic profiling services based on proprietary assay platforms, clinical centers may use commercial genomic profiling kits designed for clinical research to develop their own customized laboratory-developed tests. Large-scale genomic profiling based on NGS allows for a detailed and precise molecular diagnosis of CCA and provides an important opportunity for improved targeted treatment plans tailored to the individual patient's genetic signature.
Collapse
Affiliation(s)
| | - J Bridgewater
- University College London Cancer Institute, London, UK
| | - N Normanno
- Istituto Nazionale Tumori 'Fondazione Giovanni Pascale' IRCCS, Naples, Italy
| |
Collapse
|
13
|
Subia B, Dahiya UR, Mishra S, Ayache J, Casquillas GV, Caballero D, Reis RL, Kundu SC. Breast tumor-on-chip models: From disease modeling to personalized drug screening. J Control Release 2021; 331:103-120. [PMID: 33417986 PMCID: PMC8172385 DOI: 10.1016/j.jconrel.2020.12.057] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/30/2020] [Accepted: 12/31/2020] [Indexed: 02/06/2023]
Abstract
Breast cancer is one of the leading causes of mortality worldwide being the most common cancer among women. Despite the significant progress obtained during the past years in the understanding of breast cancer pathophysiology, women continue to die from it. Novel tools and technologies are needed to develop better diagnostic and therapeutic approaches, and to better understand the molecular and cellular players involved in the progression of this disease. Typical methods employed by the pharmaceutical industry and laboratories to investigate breast cancer etiology and evaluate the efficiency of new therapeutic compounds are still based on traditional tissue culture flasks and animal models, which have certain limitations. Recently, tumor-on-chip technology emerged as a new generation of in vitro disease model to investigate the physiopathology of tumors and predict the efficiency of drugs in a native-like microenvironment. These microfluidic systems reproduce the functional units and composition of human organs and tissues, and importantly, the rheological properties of the native scenario, enabling precise control over fluid flow or local gradients. Herein, we review the most recent works related to breast tumor-on-chip for disease modeling and drug screening applications. Finally, we critically discuss the future applications of this emerging technology in breast cancer therapeutics and drug development.
Collapse
Affiliation(s)
- Bano Subia
- Elvesys Microfluidics Innovation Centre, Paris 75011, France..
| | | | - Sarita Mishra
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India..
| | - Jessica Ayache
- Elvesys Microfluidics Innovation Centre, Paris 75011, France..
| | | | - David Caballero
- 3B's Research Group, I3Bs-Institute on Biomaterials, Biodegradables and Biomimetics, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, University of Minho, AvePark, Barco, Guimarãaes 4805-017, Portugal; ICVS/3B's - PT Government Associate Laboratory, 4805-017, Braga/Guimarães, Portugal.
| | - Rui L Reis
- 3B's Research Group, I3Bs-Institute on Biomaterials, Biodegradables and Biomimetics, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, University of Minho, AvePark, Barco, Guimarãaes 4805-017, Portugal; ICVS/3B's - PT Government Associate Laboratory, 4805-017, Braga/Guimarães, Portugal.
| | - Subhas C Kundu
- 3B's Research Group, I3Bs-Institute on Biomaterials, Biodegradables and Biomimetics, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, University of Minho, AvePark, Barco, Guimarãaes 4805-017, Portugal; ICVS/3B's - PT Government Associate Laboratory, 4805-017, Braga/Guimarães, Portugal.
| |
Collapse
|
14
|
Lovchik RD, Taylor D, Kaigala G. Rapid micro-immunohistochemistry. MICROSYSTEMS & NANOENGINEERING 2020; 6:94. [PMID: 34567704 PMCID: PMC8433409 DOI: 10.1038/s41378-020-00205-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 05/04/2023]
Abstract
We present a new and versatile implementation of rapid and localized immunohistochemical staining of tissue sections. Immunohistochemistry (IHC) comprises a sequence of specific biochemical reactions and allows the detection of specific proteins in tissue sections. For the rapid implementation of IHC, we fabricated horizontally oriented microfluidic probes (MFPs) with functionally designed apertures to enable square and circular footprints, which we employ to locally expose a tissue to time-optimized sequences of different biochemicals. We show that the two main incubation steps of IHC protocols can be performed on MDAMB468-1510A cell block sections in less than 30 min, compared to incubation times of an hour or more in standard protocols. IHC analysis on the timescale of tens of minutes could potentially be applied during surgery, enabling clinicians to react in more dynamically and efficiently. Furthermore, this rapid IHC implementation along with conservative tissue usage has strong potential for the implementation of multiplexed assays, allowing the exploration of optimal assay conditions with a small amount of tissue to ensure high-quality staining results for the remainder of the sample.
Collapse
Affiliation(s)
- Robert D. Lovchik
- IBM Research Europe, Saeumerstrasse 4, 8803 Rueschlikon, Switzerland
| | - David Taylor
- IBM Research Europe, Saeumerstrasse 4, 8803 Rueschlikon, Switzerland
- Present Address: Eidgenössische Technische Hochschule Zürich, Department of Mechanical and Process Engineering, Sonneggstrasse 3, 8092 Zurich, Switzerland
| | - Govind Kaigala
- IBM Research Europe, Saeumerstrasse 4, 8803 Rueschlikon, Switzerland
| |
Collapse
|
15
|
Zhong R, Hou L, Zhao Y, Wang T, Wang S, Wang M, Xu D, Sun Y. A 3D mixing-based portable magnetic device for fully automatic immunofluorescence staining of γ-H2AX in UVC-irradiated CD4 + cells. RSC Adv 2020; 10:29311-29319. [PMID: 35521108 PMCID: PMC9055984 DOI: 10.1039/d0ra03925j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/02/2020] [Indexed: 11/22/2022] Open
Abstract
Immunofluorescence (IF) is a common method used in cell biology. The conventional protocol for IF staining is time and labor-intensive, operator dependent and reagent-consuming. Magnetic Bead (MB)-based microdevices are frequently utilized in cellular assays, but integration of simple and efficient mixing with downstream multi-step manipulation of MBs for automatic IF staining is still challenging. We herein present a portable, inexpensive and integratable device for MB-based automatic IF staining. First, a front-end cell capture step is performed using a 3D-mixing module, which is built upon a novel mechanism named ec-2MagRotors and generates periodically changing 3D magnetic fields. A 5-fold enhancement of cell capture efficiency was attained even with a low bead-to-cell concentration ratio (5 : 1), when conducting magnetic 3D mixing. Second, a 1D-moving module is employed downstream to automatically manipulate MB–cell complexes for IF staining. Further, a simplified protocol for staining of γ-H2AX, a biomarker widely used in evaluation of cell radiation damage, is presented for proof-of-principle study of the magnetic device. Using UVC-irradiated CD4+ cells as samples, our device achieved fully automatic γ-H2AX staining within 40 minutes at room temperature and showed a linear dose–response relationship. The developed portable magnetic device is automatic, efficient, cost-effective and simple-to-use, holding great potential for applications in different IF assays. A 3D mixing-based portable magnetic device to perform on-chip efficient cell capture and automatic intracellular immunofluorescence (IF) staining is presented.![]()
Collapse
Affiliation(s)
- Runtao Zhong
- Institute of Environmental Systems Biology
- Dalian Maritime University
- Dalian 116026
- China
| | - Liangsheng Hou
- College of Marine Engineering
- Dalian Maritime University, Dalian
- Dalian 116026
- China
| | - Yingbo Zhao
- Institute of Environmental Systems Biology
- Dalian Maritime University
- Dalian 116026
- China
| | - Tianle Wang
- Institute of Environmental Systems Biology
- Dalian Maritime University
- Dalian 116026
- China
| | - Shaohua Wang
- Institute of Environmental Systems Biology
- Dalian Maritime University
- Dalian 116026
- China
| | - Mengyu Wang
- Institute of Environmental Systems Biology
- Dalian Maritime University
- Dalian 116026
- China
| | - Dan Xu
- Institute of Environmental Systems Biology
- Dalian Maritime University
- Dalian 116026
- China
| | - Yeqing Sun
- Institute of Environmental Systems Biology
- Dalian Maritime University
- Dalian 116026
- China
| |
Collapse
|
16
|
Migliozzi D, Pelz B, Dupouy DG, Leblond AL, Soltermann A, Gijs MAM. Microfluidics-assisted multiplexed biomarker detection for in situ mapping of immune cells in tumor sections. MICROSYSTEMS & NANOENGINEERING 2019; 5:59. [PMID: 31700674 PMCID: PMC6831597 DOI: 10.1038/s41378-019-0104-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 08/19/2019] [Accepted: 08/24/2019] [Indexed: 06/10/2023]
Abstract
Because of the close interaction between tumors and the immune system, immunotherapies are nowadays considered as the most promising treatment against cancer. In order to define the diagnosis and the subsequent therapy, crucial information about the immune cells at the tumor site is needed. Indeed, different types or activation status of cells may be indicative for specific and personalized treatments. Here, we present a quantitative method to identify ten different immuno-markers in the same tumor cut section, thereby saving precious samples and enabling correlative analysis on several cell families and their activation status in a tumor microenvironment context. We designed and fabricated a microfluidic chip with optimal thermomechanical and optical properties for fast delivery of reagents on tissue slides and for fully automatic imaging by integration with an optical microscope. The multiplexing capability of the system is enabled by an optimized cyclic immunofluorescence protocol, with which we demonstrated quantitative sequential immunostaining of up to ten biomarkers on the same tissue section. Furthermore, we developed high-quality image-processing algorithms to map each cell in the entire tissue. As proof-of-concept analyses, we identified coexpression and colocalization patterns of biomarkers to classify the immune cells and their activation status. Thanks to the quantitativeness and the automation of both the experimental and analytical methods, we believe that this multiplexing approach will meet the increasing clinical need of personalized diagnostics and therapy in cancer pathology.
Collapse
Affiliation(s)
- Daniel Migliozzi
- Laboratory of Microsystems, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, CH Switzerland
| | - Benjamin Pelz
- Laboratory of Microsystems, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, CH Switzerland
- Lunaphore Technologies SA, EPFL Innovation Park, Building C, 1015 Lausanne, CH Switzerland
| | - Diego G. Dupouy
- Lunaphore Technologies SA, EPFL Innovation Park, Building C, 1015 Lausanne, CH Switzerland
| | - Anne-Laure Leblond
- Universitätsspital Zürich, Schmelzbergstrasse 12, 8091 Zürich, CH Switzerland
| | - Alex Soltermann
- Universitätsspital Zürich, Schmelzbergstrasse 12, 8091 Zürich, CH Switzerland
| | - Martin A. M. Gijs
- Laboratory of Microsystems, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, CH Switzerland
| |
Collapse
|
17
|
Aimi F, Procopio MG, Alvarez Flores MT, Brouland JP, Piazzon N, Brajkovic S, Dupouy DG, Gijs M, de Leval L. Microfluidic-based immunohistochemistry for breast cancer diagnosis: a comparative clinical study. Virchows Arch 2019; 475:313-323. [PMID: 31267199 DOI: 10.1007/s00428-019-02616-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 06/18/2019] [Accepted: 06/23/2019] [Indexed: 12/20/2022]
Abstract
Breast cancer is a highly heterogeneous disease. The efficacy of tailored therapeutic strategies relies on the precise detection of diagnostic biomarkers by immunohistochemistry (IHC). Therefore, considering the increasing incidence of breast cancer cases, a concomitantly time-efficient and accurate diagnosis is clinically highly relevant. Microfluidics is a promising innovative technology in the field of tissue diagnostic, enabling for rapid, reliable, and automated immunostaining. We previously reported the microfluidic-based HER2 (human epidermal growth factor receptor 2) detection in breast carcinomas to greatly correlate with the HER2 gene amplification level. Here, we aimed to develop a panel of microfluidic-based IHC protocols for prognostic and therapeutic markers routinely assessed for breast cancer diagnosis, namely HER2, estrogen/progesterone receptor (ER/PR), and Ki67 proliferation factor. The microfluidic IHC protocol for each marker was optimized to reach high staining quality comparable to the standard procedure, while concomitantly shortening the staining time to 16 min-excluding deparaffinization and antigen retrieval step-with a turnaround time reduction up to 7 folds. Comparison of the diagnostic score on 50 formaldehyde-fixed paraffin-embedded breast tumor resections by microfluidic versus standard staining showed high concordance (overall agreement: HER2 94%, ER 95.9%, PR 93.6%, Ki67 93.7%) and strong correlation (ρ coefficient: ER 0.89, PR 0.88, Ki67 0.87; p < 0.0001) for all the analyzed markers. Importantly, HER2 genetic reflex test for all discordant cases confirmed the scores obtained by the microfluidic technique. Overall, the microfluidic-based IHC represents a clinically validated equivalent approach to the standard chromogenic staining for rapid, accurate, and automated breast cancer diagnosis.
Collapse
Affiliation(s)
- Fabio Aimi
- Laboratory of Microsystems, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Maria-Giuseppina Procopio
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, CH-8091, Zurich, Switzerland
| | | | - Jean-Philippe Brouland
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, CH-1011, Lausanne, Switzerland
| | - Nathalie Piazzon
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, CH-1011, Lausanne, Switzerland
| | - Saška Brajkovic
- Lunaphore Technologies SA, EPFL Innovation Park-Building C, CH-1015, Lausanne, Switzerland.
| | - Diego Gabriel Dupouy
- Lunaphore Technologies SA, EPFL Innovation Park-Building C, CH-1015, Lausanne, Switzerland
| | - Martin Gijs
- Laboratory of Microsystems, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Laurence de Leval
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, CH-1011, Lausanne, Switzerland
| |
Collapse
|
18
|
Leblond AL, Rechsteiner M, Jones A, Brajkovic S, Dupouy D, Soltermann A. Microfluidic-Based Immunohistochemistry Combined With Next-Generation Sequencing on Diagnostic Tissue Sections for Detection of Tumoral BRAF V600E Mutation. Am J Clin Pathol 2019; 152:59-73. [PMID: 31065676 DOI: 10.1093/ajcp/aqz028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
OBJECTIVES Tailored diagnostics requires immunohistochemistry (IHC) and next generation sequencing (NGS). Here we combined on a single paraffin-embedded slide microfluidic-based IHC (micro-IHC) and NGS for BRAF V600E mutation detection in BRAFomas. METHODS For micro-IHC, we performed the primary antibody incubation step of conventional chromogenic IHC in a LabSat device (Lunaphore Technologies SA). Tumor areas immunoreactive for pan-cytokeratin, pan-melanoma, and BRAF V600E mutation-specific antibody were H-scored, microdissected, and analyzed by NGS. RESULTS After 2 minutes, pan-cytokeratin and BRAF micro-IHC increased exponentially (half-time values: 1.7 and 3.2 minutes). Pan-melanoma displayed a higher half-time value of 15 minutes. There was no significant difference in H-score and staining quality, respectively, between conventional and micro-IHC. BRAF V600E mutation was detected in all pan-cytokeratin and pan-melanoma stained samples without amplification but in only 40% of BRAF V600E stained samples with amplification. CONCLUSIONS Micro-IHC enables short antibody incubation times and subsequent NGS. Preprocessing is critical for preservation of DNA quality.
Collapse
Affiliation(s)
- Anne-Laure Leblond
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Markus Rechsteiner
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Amy Jones
- Lunaphore Technologies SA, Lausanne, Switzerland
| | | | - Diego Dupouy
- Lunaphore Technologies SA, Lausanne, Switzerland
| | - Alex Soltermann
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| |
Collapse
|
19
|
High-content, cell-by-cell assessment of HER2 overexpression and amplification: a tool for intratumoral heterogeneity detection in breast cancer. J Transl Med 2019; 99:722-732. [PMID: 30659272 PMCID: PMC6522386 DOI: 10.1038/s41374-018-0172-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/04/2018] [Accepted: 12/04/2018] [Indexed: 01/25/2023] Open
Abstract
Immunohistochemistry and fluorescence in situ hybridization are the two standard methods for human epidermal growth factor receptor 2 (HER2) assessment. However, they have severe limitations to assess quantitatively intratumoral heterogeneity (ITH) when multiple subclones of tumor cells co-exist. We develop here a high-content, quantitative analysis of breast cancer tissues based on microfluidic experimentation and image processing, to characterize both HER2 protein overexpression and HER2 gene amplification at the cellular level. The technique consists of performing sequential steps on the same tissue slide: an immunofluorescence (IF) assay using a microfluidic protocol, an elution step for removing the IF staining agents, a standard FISH staining protocol, followed by automated quantitative cell-by-cell image processing. Moreover, ITH is accurately detected in both cluster and mosaic form using an analysis of spatial association and a mathematical model that allows discriminating true heterogeneity from artifacts due to the use of thin tissue sections. This study paves the way to evaluate ITH with high accuracy and content while requiring standard staining methods.
Collapse
|
20
|
Ultra-fast and automated immunohistofluorescent multistaining using a microfluidic tissue processor. Sci Rep 2019; 9:4489. [PMID: 30872751 PMCID: PMC6418167 DOI: 10.1038/s41598-019-41119-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 02/28/2019] [Indexed: 12/04/2022] Open
Abstract
Multistaining of a tissue section targeting multiple markers allows to reveal complex interplays in a tumor environment. However, the resource-intensive and impractically long nature of iterative multiplexed immunostainings prohibits its practical implementation in daily routine, even when using work-flow automation systems. Here, we report a fully automated and ultra-fast multistaining using a microfluidic tissue processor (MTP) in as short as 20 minutes per marker, by immunofluorescent staining employing commercially available tyramide signal amplification polymer precipitation by horse-radish peroxidase (HRP) activation. The reported duration includes (i) 15 minutes for the entire fluidic exchange and reagent incubation necessary for the immunostaining and (ii) 5 minutes for the heat-induced removal of the applied antibodies. Using the automated MTP, we demonstrated a 4-plex automated multistaining with clinically relevant biomarkers within 84 minutes, showing perfect agreement with the state-of-the-art microwave treatment antibody removal. The presented HRP-based method is in principle extendable to multistaining by both tyramides accommodating higher number of fluorescent channels and multi-color chromogenic staining. We anticipate that our automated multi-staining with a turn-around time shorter than existing monoplex immunohistochemistry methods has the potential to enable multistaining in routine without disturbing the current laboratory workflow, opening perspectives for implementation of -omics approaches in tissue diagnostics.
Collapse
|
21
|
A microfluidic platform towards automated multiplexed in situ sequencing. Sci Rep 2019; 9:3542. [PMID: 30837556 PMCID: PMC6401021 DOI: 10.1038/s41598-019-40026-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 02/08/2019] [Indexed: 01/06/2023] Open
Abstract
Advancements in multiplexed in situ RNA profiling techniques have given unprecedented insight into spatial organization of tissues by enabling single-molecule quantification and sub-micron localization of dozens to thousands of RNA species simultaneously in cells and entire tissue sections. However, the lack of automation of the associated complex experimental procedures represents a potential hurdle towards their routine use in laboratories. Here, we demonstrate an approach towards automated generation and sequencing of barcoded mRNA amplicons in situ, directly in fixed cells. This is achieved through adaptation of a microfluidic tool compatible with standard microscope slides and cover glasses. The adapted tool combines a programmable reagent delivery system with temperature controller and flow cell to perform established in situ sequencing protocols, comprising hybridization and ligation of gene-specific padlock probes, rolling circle amplification of the probes yielding barcoded amplicons and identification of amplicons through barcode sequencing. By adapting assay parameters (e.g. enzyme concentration and temperature), we achieve a near-identical performance in identifying mouse beta-actin transcripts, in comparison with the conventional manual protocol. The technically adapted assay features i) higher detection efficiency, ii) shorter protocol time, iii) lower consumption of oligonucleotide reagents but slightly more enzyme. Such an automated microfluidic tissue processor for in situ sequencing studies would greatly enhance its research potentials especially for cancer diagnostics, thus paving way to rapid and effective therapies.
Collapse
|
22
|
Migliozzi D, Nguyen HT, Gijs MAM. Combining fluorescence-based image segmentation and automated microfluidics for ultrafast cell-by-cell assessment of biomarkers for HER2-type breast carcinoma. JOURNAL OF BIOMEDICAL OPTICS 2018; 24:1-8. [PMID: 30484294 PMCID: PMC6987647 DOI: 10.1117/1.jbo.24.2.021204] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 11/02/2018] [Indexed: 06/09/2023]
Abstract
Immunohistochemistry (IHC) is one of the main clinical techniques for biomarker assessment on tissue biopsies. It consists in chromogenic labeling with specific antibodies, followed by optical imaging, and it is used for diagnosis and therapeutic targeting. A well-known drawback of IHC is its limited robustness, which often precludes quantitative biomarker assessment. We combine microfluidic immunostaining, fluorescence imaging, and image-based cell segmentation to create an ultrafast procedure for accurate biomarker assessment via IHC. The experimental protocol is very simple and based on fast delivery of reagents in a microfluidic chamber created by clamping a half-chamber patterned in a silicon chip on top of a tumor tissue section. Also, the imaging procedure simply requires a standard fluorescence microscope, already widely used in clinical practice. The image processing is based on local-contrast enhancement and thresholding of the obtained fluorescence image, with subsequent Voronoi segmentation. To assess the experimental and analytical procedure on robust biological controls, we apply our method to well-characterized cell lines, which guarantee higher reproducibility than whole-tissue samples and therefore enable to disentangle the technical variability from the biological variability. To increase the potential translationality, we address the detection and quantification of the human epidermal growth factor receptor 2 (HER2) protein, which is a biomarker for HER2-type breast carcinoma diagnosis and therapy. We report both ultrafast immunofluorescence staining (5 min per sample) of two breast cancer biomarkers and ultrafast cell segmentation (1 min per sample = processing of thousands of cells). This provides a quantitative, cell-based immunofluorescent signal, with which we propose a potential diagnostic criterion to separate HER2-positive and HER2-negative breast cancer cells at high sensitivity and specificity.
Collapse
Affiliation(s)
- Daniel Migliozzi
- École Polytechnique Fédérale de Lausanne, Laboratory of Microsystems, Lausanne, Switzerland
| | - Huu T. Nguyen
- École Polytechnique Fédérale de Lausanne, Laboratory of Microsystems, Lausanne, Switzerland
| | - Martin A. M. Gijs
- École Polytechnique Fédérale de Lausanne, Laboratory of Microsystems, Lausanne, Switzerland
| |
Collapse
|
23
|
Microfluidics-based immunofluorescence for fast staining of ALK in lung adenocarcinoma. Diagn Pathol 2018; 13:79. [PMID: 30326973 PMCID: PMC6192181 DOI: 10.1186/s13000-018-0757-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 10/02/2018] [Indexed: 02/06/2023] Open
Abstract
Background Anaplastic lymphoma kinase (ALK) is a key oncogenic driver in lung adenocarcinoma patients and its fusion proteins are routinely assessed. The microfluidic tissue processor (MTP) device is based on a chip-confined low-volume technology allowing for rapid immunohistochemistry/immunofluorescence (IHC/IF) stainings of formalin-fixed paraffin-embedded (FFPE) or frozen tissue samples. Methods A novel ALK IF protocol was developed for the MTP device using the primary mouse anti-human ALK antibody clone 5A4. FFPE tumor whole sections from 14 resected lung adenocarcinoma patients documented to be ALK positive (ALK+) by automated chromogenic IHC and/or FISH were used. MTP-derived IF immunoreactivity was measured by computerized analysis of digitalized images on individual frames of tumor epithelia and surrounding stroma, using an ImageJ plug-in. Results The 5A4 antibody yielded saturated immunoreactivity at an incubation time of 4 min on a titration curve ranging from 2 to 32 min. Total staining time on the MTP device was 18 min including secondary IgG Alexa Fluor 647. MTP-based ALK IF confirmed all 12 cases; with epithelial signal above stromal staining based on computerized pixel-based measurement. MTP-IF (mean intensity levels 458 to 1301) and chromogenic IHC (H-score 120 to 300) showed an equal range of variation of 2.8 and 2.5 folds, respectively, and a trend for direct correlation (p-value 0.051). Conclusion The newly developed protocol for immunofluorescent detection of ALK protein with the MTP device confirms chromogenic IHC results on FFPE lung adenocarcinoma specimens. MTP-based IF is fast and reliable. We foresee this study to be a first step opening the road for further realization of microfluidic-based assays for rapid simultaneous detection of targetable oncogenic and immune-system related markers in their topographical context to investigate tumour heterogeneity and micro-environmental interactions. Electronic supplementary material The online version of this article (10.1186/s13000-018-0757-1) contains supplementary material, which is available to authorized users.
Collapse
|
24
|
Kang CC, Ward TM, Bockhorn J, Schiffman C, Huang H, Pegram MD, Herr AE. Electrophoretic cytopathology resolves ERBB2 forms with single-cell resolution. NPJ Precis Oncol 2018; 2:10. [PMID: 29872719 PMCID: PMC5871910 DOI: 10.1038/s41698-018-0052-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 02/10/2018] [Accepted: 02/20/2018] [Indexed: 12/20/2022] Open
Abstract
In addition to canonical oncoproteins, truncated isoforms and proteolysis products are implicated in both drug resistance and disease progression. In HER2-positive breast tumors, expression of truncated HER2 isoforms resulting from alternative translation and/or carboxy-terminal fragments (CTFs) resulting from proteolysis (collectively, t-erbB2) have been associated with shortened progression-free survival of patients. Thus, to advance clinical pathology and inform treatment decisions, we developed a high-selectivity cytopathology assay capable of distinguishing t-erbB2 from full-length HER2 expression without the need for isoform-specific antibodies. Our microfluidic, single-cell western blot, employs electrophoretic separations to resolve full-length HER2 from the smaller t-erbB2 in each ~28 pL single-cell lysate. Subsequently, a pan-HER2 antibody detects all resolved HER2 protein forms via immunoprobing. In analysis of eight breast tumor biopsies, we identified two tumors comprised of 15% and 40% t-erbB2-expressing cells. By single-cell western blotting of the t-erbB2-expressing cells, we observed statistically different ratios of t-erbB2 proteins to full-length HER2 expression. Further, target multiplexing and clustering analyses scrutinized signaling, including ribosomal S6, within the t-erbB2-expressing cell subpopulation. Taken together, cytometric assays that report both protein isoform profiles and signaling state offer cancer classification taxonomies with unique relevance to precisely describing drug resistance mechanisms in which oncoprotein isoforms/fragments are implicated.
Collapse
Affiliation(s)
- Chi-Chih Kang
- 1Department of Bioengineering, University of California Berkeley, Berkeley, CA 94720 USA
| | - Toby M Ward
- 2Division of Medical Oncology, Department of Medicine, Stanford University, Stanford, CA 94305 USA
| | - Jessica Bockhorn
- 2Division of Medical Oncology, Department of Medicine, Stanford University, Stanford, CA 94305 USA
| | - Courtney Schiffman
- 3Division of Biostatistics, School of Public Health, University of California Berkeley, Berkeley, CA 94720 USA
| | - Haiyan Huang
- 4Department of Statistics, University of California Berkeley, Berkeley, CA 94720 USA
| | - Mark D Pegram
- 2Division of Medical Oncology, Department of Medicine, Stanford University, Stanford, CA 94305 USA
| | - Amy E Herr
- 1Department of Bioengineering, University of California Berkeley, Berkeley, CA 94720 USA
| |
Collapse
|
25
|
Li H, Brewer G, Ongo G, Normandeau F, Omeroglu A, Juncker D. Immunohistochemistry Microarrays. Anal Chem 2017; 89:8620-8625. [DOI: 10.1021/acs.analchem.7b00807] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Huiyan Li
- Biomedical
Engineering Department, ‡McGill University and Genome Quebec Innovation
Centre, §Department of Pathology, McGill University Health Centre, and ∥Department of
Neurology and Neurosurgery, McGill University, Montreal, Quebec H3A0G1, Canada
| | - Gabrielle Brewer
- Biomedical
Engineering Department, ‡McGill University and Genome Quebec Innovation
Centre, §Department of Pathology, McGill University Health Centre, and ∥Department of
Neurology and Neurosurgery, McGill University, Montreal, Quebec H3A0G1, Canada
| | - Grant Ongo
- Biomedical
Engineering Department, ‡McGill University and Genome Quebec Innovation
Centre, §Department of Pathology, McGill University Health Centre, and ∥Department of
Neurology and Neurosurgery, McGill University, Montreal, Quebec H3A0G1, Canada
| | - Frederic Normandeau
- Biomedical
Engineering Department, ‡McGill University and Genome Quebec Innovation
Centre, §Department of Pathology, McGill University Health Centre, and ∥Department of
Neurology and Neurosurgery, McGill University, Montreal, Quebec H3A0G1, Canada
| | - Atilla Omeroglu
- Biomedical
Engineering Department, ‡McGill University and Genome Quebec Innovation
Centre, §Department of Pathology, McGill University Health Centre, and ∥Department of
Neurology and Neurosurgery, McGill University, Montreal, Quebec H3A0G1, Canada
| | - David Juncker
- Biomedical
Engineering Department, ‡McGill University and Genome Quebec Innovation
Centre, §Department of Pathology, McGill University Health Centre, and ∥Department of
Neurology and Neurosurgery, McGill University, Montreal, Quebec H3A0G1, Canada
| |
Collapse
|
26
|
Microfluidics for rapid cytokeratin immunohistochemical staining in frozen sections. J Transl Med 2017; 97:983-991. [PMID: 28553936 PMCID: PMC5533214 DOI: 10.1038/labinvest.2017.49] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 03/24/2017] [Accepted: 04/11/2017] [Indexed: 01/28/2023] Open
Abstract
Frozen sections (FS) of tumor samples represent a cornerstone of pathological intraoperative consultation and have an important role in the microscopic analysis of specimens during surgery. So far, immunohistochemical (IHC) stainings on FS have been demonstrated for a few markers using manual methods. Microfluidic technologies have proven to bring substantial improvement in many fields of diagnostics, though only a few microfluidic devices have been designed to improve the performance of IHC assays. In this work, we show optimization of a complete pan-cytokeratin chromogenic immunostaining protocol on FS using a microfluidic tissue processor into a protocol taking <12 min. Our results showed specificity and low levels of background. The dimensions of the microfluidic prototype device are compatible with the space constraints of an intraoperative pathology laboratory. We therefore anticipate that the adoption of microfluidic technologies in the field of surgical pathology can significantly improve the way FSs influence surgical procedures.
Collapse
|
27
|
Kim S, Kwon S, Cho CH, Park JK. Pipetting-driven microfluidic immunohistochemistry to facilitate enhanced immunoreaction and effective use of antibodies. LAB ON A CHIP 2017; 17:702-709. [PMID: 28145545 DOI: 10.1039/c6lc01495j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Immunohistochemistry (IHC), which has been used to detect antigens in cells of a tissue section using an immunoreaction between an antibody and an antigen, is a practical tool for identifying the type and stage of diseases in cancer diagnosis and scientific research. However, conventional IHC requires long, laborious process times and high costs. Although microfluidic IHC platforms have been developed to overcome these limitations, the application of microfluidic IHC in real-world environments is still limited due to the additional equipment needed to operate the microfluidic systems. In addition, continuous flow in a microfluidic channel leads to a waste of unbound antibodies. In this study, we demonstrate a novel and easy-to-use microfluidic IHC platform operated only using a manual pipette that is commonly available in research laboratories or hospitals. No other device such as a pump or a controller is required to operate our system. Bidirectional flows of the antibody solution in a microfluidic device are induced by repetitive manual pipetting which facilitates the enhanced antigen-antibody reaction and enables the effective use of a limited amount of antibody. When breast cancer cell and tissue sections are reacted with antibodies using our platform, pipetting for less than 2 min is sufficient to obtain immunostaining results without damaging the sample. The staining intensity by our method is similar to that of the sample stained for 1 h by a conventional batch process. We believe that this pipetting-based approach to the operation of a microfluidic system allows end users to use microfluidic IHC more conveniently and easily in real-world environments.
Collapse
Affiliation(s)
- Segi Kim
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Seyong Kwon
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Chang Hyun Cho
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Je-Kyun Park
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea. and KAIST Institute for Health Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| |
Collapse
|
28
|
Microfluidics-assisted fluorescence in situ hybridization for advantageous human epidermal growth factor receptor 2 assessment in breast cancer. J Transl Med 2017; 97:93-103. [PMID: 27892928 DOI: 10.1038/labinvest.2016.121] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/20/2016] [Accepted: 10/20/2016] [Indexed: 11/08/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) is one of the recommended techniques for human epidermal growth factor receptor 2 (HER2) status assessment on cancer tissues. Here we develop microfluidics-assisted FISH (MA-FISH), in which hybridization of the FISH probes with their target DNA strands is obtained by applying square-wave oscillatory flows of diluted probe solutions in a thin microfluidic chamber of 5 μl volume. By optimizing the experimental parameters, MA-FISH decreases the consumption of the expensive probe solution by a factor 5 with respect to the standard technique, and reduces the hybridization time to 4 h, which is four times faster than in the standard protocol. To validate the method, we blindly conducted HER2 MA-FISH on 51 formalin-fixed paraffin-embedded tissue slides of 17 breast cancer samples, and compared the results with standard HER2 FISH testing. HER2 status classification was determined according to published guidelines, based on average number of HER2 copies per cell and average HER2/CEP17 ratio. Excellent agreement was observed between the two methods, supporting the validity of MA-FISH and further promoting its short hybridization time and reduced reagent consumption.
Collapse
|
29
|
Karle M, Vashist SK, Zengerle R, von Stetten F. Microfluidic solutions enabling continuous processing and monitoring of biological samples: A review. Anal Chim Acta 2016; 929:1-22. [DOI: 10.1016/j.aca.2016.04.055] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 04/26/2016] [Accepted: 04/30/2016] [Indexed: 01/25/2023]
|