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Copaciu R, Rashidian J, Lloyd J, Yahyabeik A, McClure J, Cummings K, Su Q. Characterization of an IDH1 R132H Rabbit Monoclonal Antibody, MRQ-67, and Its Applications in the Identification of Diffuse Gliomas. Antibodies (Basel) 2023; 12:antib12010014. [PMID: 36810519 PMCID: PMC9944093 DOI: 10.3390/antib12010014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/26/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
The current diagnosis of diffuse glioma involves isocitrate dehydrogenase (IDH) mutation testing. Most IDH mutant gliomas carry a G-to-A mutation at IDH1 position 395, resulting in the R132H mutant. R132H immunohistochemistry (IHC), therefore, is used to screen for the IDH1 mutation. In this study, the performance of MRQ-67, a recently generated IDH1 R132H antibody, was characterized in comparison with H09, a frequently used clone. Selective binding was demonstrated by an enzyme-linked immunosorbent assay for MRQ-67 to the R132H mutant, with an affinity higher than that for H09. By Western and dot immunoassays, MRQ-67 was found to bind specifically to the IDH1 R1322H, with a higher capacity than H09. IHC testing with MRQ-67 demonstrated a positive signal in most diffuse astrocytomas (16/22), oligodendrogliomas (9/15), and secondary glioblastomas tested (3/3), but not in primary glioblastomas (0/24). While both clones demonstrated a positive signal with similar patterns and equivalent intensities, H09 exhibited a background stain more frequently. DNA sequencing on 18 samples showed the R132H mutation in all IHC positive cases (5/5), but not in negative cases (0/13). These results demonstrate that MRQ-67 is a high-affinity antibody suitable for specific detection of the IDH1 R132H mutant by IHC and with less background as compared with H09.
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Affiliation(s)
| | | | | | | | | | | | - Qin Su
- Correspondence: ; Tel.: +1-916-746-8961
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Chardin D, Humbert O, Bailleux C, Burel-Vandenbos F, Rigau V, Pourcher T, Barlaud M. Primal-dual for classification with rejection (PD-CR): a novel method for classification and feature selection-an application in metabolomics studies. BMC Bioinformatics 2021; 22:594. [PMID: 34911437 PMCID: PMC8672607 DOI: 10.1186/s12859-021-04478-w] [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: 01/19/2021] [Accepted: 10/29/2021] [Indexed: 11/25/2022] Open
Abstract
Background Supervised classification methods have been used for many years for feature selection in metabolomics and other omics studies. We developed a novel primal-dual based classification method (PD-CR) that can perform classification with rejection and feature selection on high dimensional datasets. PD-CR projects data onto a low dimension space and performs classification by minimizing an appropriate quadratic cost. It simultaneously optimizes the selected features and the prediction accuracy with a new tailored, constrained primal-dual method. The primal-dual framework is general enough to encompass various robust losses and to allow for convergence analysis. Here, we compare PD-CR to three commonly used methods: partial least squares discriminant analysis (PLS-DA), random forests and support vector machines (SVM). We analyzed two metabolomics datasets: one urinary metabolomics dataset concerning lung cancer patients and healthy controls; and a metabolomics dataset obtained from frozen glial tumor samples with mutated isocitrate dehydrogenase (IDH) or wild-type IDH. Results PD-CR was more accurate than PLS-DA, Random Forests and SVM for classification using the 2 metabolomics datasets. It also selected biologically relevant metabolites. PD-CR has the advantage of providing a confidence score for each prediction, which can be used to perform classification with rejection. This substantially reduces the False Discovery Rate. Conclusion PD-CR is an accurate method for classification of metabolomics datasets which can outperform PLS-DA, Random Forests and SVM while selecting biologically relevant features. Furthermore the confidence score provided with PD-CR can be used to perform classification with rejection and reduce the false discovery rate. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04478-w.
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Affiliation(s)
- David Chardin
- Transporters in imaging and Radiotherapy in Oncology (TIRO), Direction de la Recherche Fondamentale (DRF), Institute des sciences du vivant Fréderic Joliot, Commissariat à l'Energie Atomique et aux énergies alternatives (CEA), Université Côte d'Azur (UCA), Nice, France.,Department of Nuclear Medicine, Centre Antoine Lacassagne, Université Côte d'Azur (UCA), Nice, France
| | - Olivier Humbert
- Transporters in imaging and Radiotherapy in Oncology (TIRO), Direction de la Recherche Fondamentale (DRF), Institute des sciences du vivant Fréderic Joliot, Commissariat à l'Energie Atomique et aux énergies alternatives (CEA), Université Côte d'Azur (UCA), Nice, France.,Department of Nuclear Medicine, Centre Antoine Lacassagne, Université Côte d'Azur (UCA), Nice, France
| | - Caroline Bailleux
- Transporters in imaging and Radiotherapy in Oncology (TIRO), Direction de la Recherche Fondamentale (DRF), Institute des sciences du vivant Fréderic Joliot, Commissariat à l'Energie Atomique et aux énergies alternatives (CEA), Université Côte d'Azur (UCA), Nice, France.,Department of Oncology, Centre Antoine Lacassagne, Université Côte d'Azur (UCA), Nice, France
| | - Fanny Burel-Vandenbos
- Central Laboratory of Pathology, University Hospital and Institute of Biology Valrose, Inserm U1091 - CNRS UMR7277, University Côte d'Azur, Nice, France
| | - Valerie Rigau
- Department of Pathology and Oncobiology, University Hospital, Montpellier, France.,Institute for Neurosciences of Montpellier, INSERM U1051, Montpellier, France
| | - Thierry Pourcher
- Transporters in imaging and Radiotherapy in Oncology (TIRO), Direction de la Recherche Fondamentale (DRF), Institute des sciences du vivant Fréderic Joliot, Commissariat à l'Energie Atomique et aux énergies alternatives (CEA), Université Côte d'Azur (UCA), Nice, France
| | - Michel Barlaud
- Laboratoire d'Informatique, Signaux et Systèmes de Sophia Antipolis (I3S), Université Côte d'Azur (UCA), Centre de Recherche Scientifique (CNRS), Sophia Antipolis, France.
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Fischer EG. Morphological changes in previously frozen formalin-fixed paraffin-embedded (FFPE) tissue. J Clin Pathol 2021; 75:431-432. [PMID: 34697031 DOI: 10.1136/jclinpath-2021-207922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 09/30/2021] [Indexed: 11/04/2022]
Affiliation(s)
- Edgar G Fischer
- Pathology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
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Santisukwongchote S, Teerapakpinyo C, Chankate P, Techavichit P, Boongird A, Sathornsumetee S, Thammachantha S, Cheunsuchon P, Tanboon J, Thorner PS, Shuangshoti S. Simplified approach for pathological diagnosis of diffuse gliomas in adult patients. Pathol Res Pract 2021; 223:153483. [PMID: 34022681 DOI: 10.1016/j.prp.2021.153483] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 05/08/2021] [Accepted: 05/10/2021] [Indexed: 01/22/2023]
Abstract
The most recent WHO classification (2016) for gliomas introduced integrated diagnoses requiring both phenotypic and genotypic data. This approach presents difficulties for countries with limited resources for laboratory testing. The present study describes a series of 118 adult Thai patients with diffuse gliomas, classified by the WHO 2016 classification. The purpose was to demonstrate how a diagnosis can still be achieved using a simplified approach that combines clinical, morphological, immunohistochemical, and fewer molecular assays than typically performed. This algorithm starts with tumor location (midline vs. non-midline) with diffuse midline glioma identified by H3 K27M immunostaining. All other tumors are placed into one of 6 categories, based on morphologic features rather than specific diagnoses. Molecular testing is limited to IDH1/IDH2 mutations, plus co-deletion of 1p/19q for cases with oligodendroglial features and TERT promoter mutation for cases without such features. Additional testing for co-deletion of 1p/19q, TERT promoter mutation and BRAF mutations are only used in selected cases to refine diagnosis and prognosis. With this approach, we were able to reach the integrated diagnosis in 117/118 cases, saving 50 % of the costs of a more inclusive testing panel. The demographic data and tumor subtypes were found to be similar to series from other regions of the world. To the best of our knowledge, this is to the first reported series of diffuse gliomas in South-East Asia categorized by the WHO 2016 classification system.
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Affiliation(s)
- Sakun Santisukwongchote
- Dept. of Pathology, Faculty of Medicine, Chulalongkorn Memorial Hospital, Bangkok, 10330, Thailand
| | - Chinnachote Teerapakpinyo
- Chulalongkorn GenePRO Center, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Piyamai Chankate
- Chulalongkorn GenePRO Center, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Piti Techavichit
- Division of Hematology and Oncology, Dept. of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Atthaporn Boongird
- Neurosurgical Unit, Dept. of Surgery, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
| | - Sith Sathornsumetee
- Dept. of Medicine (Neurology), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Samasuk Thammachantha
- Dept. of Pathology, Neurological Institute of Thailand, Dept. of Medical Service, Ministry of Public Health, Bangkok, 10400, Thailand
| | - Pornsuk Cheunsuchon
- Dept. of Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Jantima Tanboon
- Dept. of Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Paul Scott Thorner
- Dept. of Pathology, Faculty of Medicine, Chulalongkorn Memorial Hospital, Bangkok, 10330, Thailand; Dept. of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, M5S1A8, Canada
| | - Shanop Shuangshoti
- Dept. of Pathology, Faculty of Medicine, Chulalongkorn Memorial Hospital, Bangkok, 10330, Thailand; Chulalongkorn GenePRO Center, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.
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