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Malapelle U, Angerilli V, Pepe F, Fontanini G, Lonardi S, Scartozzi M, Memeo L, Pruneri G, Marchetti A, Perrone G, Fassan M. The ideal reporting of RAS testing in colorectal adenocarcinoma: a pathologists' perspective. Pathologica 2023; 115:1-11. [PMID: 37314870 PMCID: PMC10462993 DOI: 10.32074/1591-951x-895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 05/24/2023] [Indexed: 06/16/2023] Open
Abstract
RAS gene mutational status represents an imperative predictive biomarker to be tested in the clinical management of metastatic colorectal adenocarcinoma. Even if it is one of the most studied biomarkers in the era of precision medicine, several pre-analytical and analytical factors may still impasse an adequate reporting of RAS status in clinical practice, with significant therapeutic consequences. Thus, pathologists should be aware on the main topics related to this molecular evaluation: (i) adopt diagnostic limit of detections adequate to avoid the interference of sub-clonal cancer cell populations; (ii) choose the most adequate diagnostic strategy according to the available sample and its qualification for molecular testing; (iii) provide all the information regarding the mutation detected, since many RAS mutation-specific targeted therapeutic approaches are in development and will enter into routine clinical practice. In this review, we give a comprehensive description of the current scenario about RAS gene mutational testing in the clinic focusing on the pathologist's role in patient selection for targeted therapies.
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Affiliation(s)
- Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples (NA), Italy
| | | | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples (NA), Italy
| | - Gabriella Fontanini
- Department of Surgical, Medical and Molecular Pathology and Critical Care Medicine, University of Pisa, Pisa (PI), Italy
| | - Sara Lonardi
- Medical Oncology 3, Veneto Institute of Oncology IOV-IRCCS, Padua (PD), Italy
| | - Mario Scartozzi
- Medical Oncology, University Hospital and University of Cagliari, Cagliari (CA), Italy
| | - Lorenzo Memeo
- Department of Experimental Oncology, Mediterranean Institute of Oncology, Viagrande, Catania (CT), Italy
| | - Gianfranco Pruneri
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale Tumori and University of Milan, Milan (MI), Italy
| | - Antonio Marchetti
- Center for Advanced Studies and Technology (CAST), University Chieti-Pescara, Chieti (CH), Italy
- Diagnostic Molecular Pathology, Unit of Anatomic Pathology, SS Annunziata Hospital, Chieti (CH), Italy and Department of Medical, Oral, and Biotechnological Sciences University “G. D’Annunzio” of Chieti-Pescara, Chieti (CH), Italy
| | - Giuseppe Perrone
- Department of Medicine and Surgery, Research Unit of Anatomical Pathology, Università Campus Bio-Medico di Roma, Roma, Italy
- Anatomical Pathology Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, Roma, Italy
| | - Matteo Fassan
- Department of Medicine (DIMED), University of Padua, Padua (PD), Italy
- Veneto Institute of Oncology (IOV-IRCCS), Padua (PD), Italy
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Frankenstein Z, Uraoka N, Aypar U, Aryeequaye R, Rao M, Hameed M, Zhang Y, Yagi Y. Automated 3D scoring of fluorescence in situ hybridization (FISH) using a confocal whole slide imaging scanner. Appl Microsc 2021; 51:4. [PMID: 33835321 PMCID: PMC8035347 DOI: 10.1186/s42649-021-00053-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 03/29/2021] [Indexed: 11/10/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) is a technique to visualize specific DNA/RNA sequences within the cell nuclei and provide the presence, location and structural integrity of genes on chromosomes. A confocal Whole Slide Imaging (WSI) scanner technology has superior depth resolution compared to wide-field fluorescence imaging. Confocal WSI has the ability to perform serial optical sections with specimen imaging, which is critical for 3D tissue reconstruction for volumetric spatial analysis. The standard clinical manual scoring for FISH is labor-intensive, time-consuming and subjective. Application of multi-gene FISH analysis alongside 3D imaging, significantly increase the level of complexity required for an accurate 3D analysis. Therefore, the purpose of this study is to establish automated 3D FISH scoring for z-stack images from confocal WSI scanner. The algorithm and the application we developed, SHIMARIS PAFQ, successfully employs 3D calculations for clear individual cell nuclei segmentation, gene signals detection and distribution of break-apart probes signal patterns, including standard break-apart, and variant patterns due to truncation, and deletion, etc. The analysis was accurate and precise when compared with ground truth clinical manual counting and scoring reported in ten lymphoma and solid tumors cases. The algorithm and the application we developed, SHIMARIS PAFQ, is objective and more efficient than the conventional procedure. It enables the automated counting of more nuclei, precisely detecting additional abnormal signal variations in nuclei patterns and analyzes gigabyte multi-layer stacking imaging data of tissue samples from patients. Currently, we are developing a deep learning algorithm for automated tumor area detection to be integrated with SHIMARIS PAFQ.
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Affiliation(s)
- Ziv Frankenstein
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
| | - Naohiro Uraoka
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Umut Aypar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Ruth Aryeequaye
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Mamta Rao
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Meera Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Yanming Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Yukako Yagi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
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Kofanova O, Bellora C, Garcia Frasquilho S, Antunes L, Hamot G, Mathay C, Mommaerts K, Muller A, DeWitt B, Betsou F. Standardization of the preanalytical phase of DNA extraction from fixed tissue for next-generation sequencing analyses. N Biotechnol 2020; 54:52-61. [DOI: 10.1016/j.nbt.2019.07.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 07/24/2019] [Accepted: 07/28/2019] [Indexed: 12/25/2022]
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Richardson SO, Huibers MMH, de Weger RA, de Leng WWJ, Hinrichs JWJ, Meijers RWJ, Willems SM, Peeters TLMG. One-fits-all pretreatment protocol facilitating Fluorescence In Situ Hybridization on formalin-fixed paraffin-embedded, fresh frozen and cytological slides. Mol Cytogenet 2019; 12:27. [PMID: 31236139 PMCID: PMC6580589 DOI: 10.1186/s13039-019-0442-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 06/06/2019] [Indexed: 05/30/2023] Open
Abstract
Background The Fluorescence In Situ Hybridization (FISH) technique is a very useful tool for diagnostic and prognostic purposes in molecular pathology. However, clinical testing on patient tissue is challenging due to variables of tissue processing that can influence the quality of the results. This emphasizes the necessity of a standardized FISH protocol with a high hybridization efficiency. We present a pretreatment protocol that is easy, reproducible, cost-effective, and facilitates FISH on all types of patient material simultaneously with good quality results. During validation, FISH analysis was performed simultaneously on formalin-fixed paraffin-embedded, fresh frozen and cytological patient material in combination with commercial probes using our optimized one-fits-all pretreatment protocol. An optimally processed sample is characterized by strong specific signals, intact nuclear membranes, non-disturbing autofluorescence and a homogeneous DAPI staining. Results In our retrospective cohort of 3881 patient samples, overall 93% of the FISH samples displayed good quality results leading to a patient diagnosis. All FISH were assessed on quality aspects such as adequacy and consistency of signal strength (brightness), lack of background and / or cross-hybridization signals, and additionally the presence of appropriate control signals were evaluated to assure probe accuracy. In our analysis 38 different FISH probes from 3 commercial manufacturers were used (Cytocell, Vysis and ZytoLight). The majority of the patients in this cohort displayed good signal quality and barely non-specific background fluorescence on all tissue types independent of which commercial probe was used. Conclusion The optimized one-fits-all FISH method is robust, reliable and reproducible to deliver an accurate result for patient diagnostics in a lean workflow and cost-effective manner. This protocol can be used for widespread application in cancer and non-cancer diagnostics and research.
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Affiliation(s)
- Shivanand O Richardson
- 1Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Manon M H Huibers
- 1Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands.,2Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Roel A de Weger
- 1Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands.,3Department of Pathology, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Wendy W J de Leng
- 1Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - John W J Hinrichs
- 1Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Ruud W J Meijers
- 1Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Stefan M Willems
- 1Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Ton L M G Peeters
- 1Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
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Mathieson W, Thomas G. Using FFPE Tissue in Genomic Analyses: Advantages, Disadvantages and the Role of Biospecimen Science. CURRENT PATHOBIOLOGY REPORTS 2019. [DOI: 10.1007/s40139-019-00194-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Mathieson W, Guljar N, Sanchez I, Sroya M, Thomas GA. Extracting DNA from FFPE Tissue Biospecimens Using User-Friendly Automated Technology: Is There an Impact on Yield or Quality? Biopreserv Biobank 2018; 16:191-199. [DOI: 10.1089/bio.2018.0009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
| | - Nafia Guljar
- Division of Surgery, Imperial College London, London, United Kingdom
| | | | - Manveer Sroya
- Division of Surgery, Imperial College London, London, United Kingdom
| | - Gerry A. Thomas
- Division of Surgery, Imperial College London, London, United Kingdom
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