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Alontaga AY, Cano P, Ozakinci H, Puskas JA, Stewart PA, Welsh EA, Yoder SJ, Hicks JK, Saltos AN, Bossler AD, Haura EB, Koomen JM, Boyle TA. Implementation of a High-Accuracy Targeted Gene Expression Panel for Clinical Care. J Mol Diagn 2024:S1525-1578(24)00101-6. [PMID: 38777037 DOI: 10.1016/j.jmoldx.2024.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/29/2024] [Accepted: 04/17/2024] [Indexed: 05/25/2024] Open
Abstract
This study describes the validation of a clinical RNA expression panel with evaluation of concordance between gene copy gain by a next-generation sequencing (NGS) assay and high gene expression by an RNA expression panel. The RNA Salah Targeted Expression Panel (RNA STEP) was designed with input from oncologists to include 204 genes with utility for clinical trial prescreening and therapy selection. RNA STEP was validated with the nanoString platform using remnant formalin-fixed, paraffin-embedded-derived RNA from 102 patients previously tested with a validated clinical NGS panel. The repeatability, reproducibility, and concordance of RNA STEP results with NGS results were evaluated. RNA STEP demonstrated high repeatability and reproducibility, with excellent correlation (r > 0.97, P < 0.0001) for all comparisons. Comparison of RNA STEP high gene expression (log2 ratio ≥ 2) versus NGS DNA-based gene copy number gain (copies ≥ 5) for 38 mutually covered genes revealed an accuracy of 93.0% with a positive percentage agreement of 69.4% and negative percentage agreement of 93.8%. Moderate correlation was observed between platforms (r = 0.53, P < 0.0001). Concordance between high gene expression and gene copy number gain varied by specific gene, and some genes had higher accuracy between assays. Clinical implementation of RNA STEP provides gene expression data complementary to NGS and offers a tool for prescreening patients for clinical trials.
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Affiliation(s)
- Aileen Y Alontaga
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Pedro Cano
- Department of Pathology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Hilal Ozakinci
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - John A Puskas
- Department of Pathology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Paul A Stewart
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Eric A Welsh
- Department of Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Sean J Yoder
- Molecular Genomics Core Facility, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - J Kevin Hicks
- Department of Pathology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Andreas N Saltos
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Aaron D Bossler
- Department of Pathology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Eric B Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - John M Koomen
- Department of Pathology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida; Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Theresa A Boyle
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida; Department of Pathology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida.
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2
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Yan K, Liu Q, Huang R, Jiang Y, Bian Z, Li S, Li L, Shen F, Tsuneyama K, Zhang Q, Lian Z, Guan H, Xu B. Spatial transcriptomics reveals prognosis-associated cellular heterogeneity in the papillary thyroid carcinoma microenvironment. Clin Transl Med 2024; 14:e1594. [PMID: 38426403 PMCID: PMC10905537 DOI: 10.1002/ctm2.1594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 01/28/2024] [Accepted: 02/05/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Papillary thyroid carcinoma (PTC) is the most common malignant endocrine tumour, and its incidence and prevalence are increasing considerably. Cellular heterogeneity in the tumour microenvironment is important for PTC prognosis. Spatial transcriptomics is a powerful technique for cellular heterogeneity study. METHODS In conjunction with a clinical pathologist identification method, spatial transcriptomics was employed to characterise the spatial location and RNA profiles of PTC-associated cells within the tissue sections. The spatial RNA-clinical signature genes for each cell type were extracted and applied to outlining the distribution regions of specific cells on the entire section. The cellular heterogeneity of each cell type was further revealed by ContourPlot analysis, monocle analysis, trajectory analysis, ligand-receptor analysis and Gene Ontology enrichment analysis. RESULTS The spatial distribution region of tumour cells, typical and atypical follicular cells (FCs and AFCs) and immune cells were accurately and comprehensively identified in all five PTC tissue sections. AFCs were identified as a transitional state between FCs and tumour cells, exhibiting a higher resemblance to the latter. Three tumour foci were shared among all patients out of the 13 observed. Notably, tumour foci No. 2 displayed elevated expression levels of genes associated with lower relapse-free survival in PTC patients. We discovered key ligand-receptor interactions, including LAMB3-ITGA2, FN1-ITGA3 and FN1-SDC4, involved in the transition of PTC cells from FCs to AFCs and eventually to tumour cells. High expression of these patterns correlated with reduced relapse-free survival. In the tumour immune microenvironment, reduced interaction between myeloid-derived TGFB1 and TGFBR1 in tumour focus No. 2 contributed to tumourigenesis and increased heterogeneity. The spatial RNA-clinical analysis method developed here revealed prognosis-associated cellular heterogeneity in the PTC microenvironment. CONCLUSIONS The occurrence of tumour foci No. 2 and three enhanced ligand-receptor interactions in the AFC area/tumour foci reduced the relapse-free survival of PTC patients, potentially leading to improved prognostic strategies and targeted therapies for PTC patients.
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Affiliation(s)
- Kai Yan
- Guangdong Cardiovascular InstituteGuangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
| | - Qing‐Zhi Liu
- Chronic Disease LaboratoryInstitutes for Life SciencesSouth China University of TechnologyGuangzhouChina
| | - Rong‐Rong Huang
- Guangdong Cardiovascular InstituteGuangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
| | - Yi‐Hua Jiang
- Guangdong Cardiovascular InstituteGuangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhouChina
- Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and ApplicationGuangzhouChina
| | - Zhen‐Hua Bian
- School of Biomedical Sciences and EngineeringSouth China University of TechnologyGuangzhou International CampusGuangzhouChina
| | - Si‐Jin Li
- Department of Thyroid SurgeryGuangzhou First People's HospitalSouth China University of TechnologyGuangzhouChina
| | - Liang Li
- Medical Research InstituteGuangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences)Southern Medical UniversityGuangzhouChina
| | - Fei Shen
- Department of Thyroid SurgeryGuangzhou First People's HospitalSouth China University of TechnologyGuangzhouChina
| | - Koichi Tsuneyama
- Department of Pathology and Laboratory MedicineInstitute of Biomedical SciencesTokushima University Graduate SchoolTokushimaJapan
| | - Qing‐Ling Zhang
- Department of PathologyGuangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences)Southern Medical UniversityGuangzhouChina
| | - Zhe‐Xiong Lian
- Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences)Southern Medical UniversityGuangzhouChina
| | - Haixia Guan
- Department of EndocrinologyGuangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences)Southern Medical UniversityGuangzhouChina
| | - Bo Xu
- Department of Thyroid SurgeryGuangzhou First People's HospitalSouth China University of TechnologyGuangzhouChina
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Krappinger JC, Bonstingl L, Pansy K, Sallinger K, Wreglesworth NI, Grinninger L, Deutsch A, El-Heliebi A, Kroneis T, Mcfarlane RJ, Sensen CW, Feichtinger J. Non-coding Natural Antisense Transcripts: Analysis and Application. J Biotechnol 2021; 340:75-101. [PMID: 34371054 DOI: 10.1016/j.jbiotec.2021.08.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 06/30/2021] [Accepted: 08/04/2021] [Indexed: 12/12/2022]
Abstract
Non-coding natural antisense transcripts (ncNATs) are regulatory RNA sequences that are transcribed in the opposite direction to protein-coding or non-coding transcripts. These transcripts are implicated in a broad variety of biological and pathological processes, including tumorigenesis and oncogenic progression. With this complex field still in its infancy, annotations, expression profiling and functional characterisations of ncNATs are far less comprehensive than those for protein-coding genes, pointing out substantial gaps in the analysis and characterisation of these regulatory transcripts. In this review, we discuss ncNATs from an analysis perspective, in particular regarding the use of high-throughput sequencing strategies, such as RNA-sequencing, and summarize the unique challenges of investigating the antisense transcriptome. Finally, we elaborate on their potential as biomarkers and future targets for treatment, focusing on cancer.
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Affiliation(s)
- Julian C Krappinger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Christian Doppler Laboratory for innovative Pichia pastoris host and vector systems, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria
| | - Lilli Bonstingl
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Center for Biomarker Research in Medicine, Stiftingtalstraße 5, 8010 Graz, Austria
| | - Katrin Pansy
- Division of Haematology, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Katja Sallinger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Center for Biomarker Research in Medicine, Stiftingtalstraße 5, 8010 Graz, Austria
| | - Nick I Wreglesworth
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Lukas Grinninger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Austrian Biotech University of Applied Sciences, Konrad Lorenz-Straße 10, 3430 Tulln an der Donau, Austria
| | - Alexander Deutsch
- Division of Haematology, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria; BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Amin El-Heliebi
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Center for Biomarker Research in Medicine, Stiftingtalstraße 5, 8010 Graz, Austria
| | - Thomas Kroneis
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Center for Biomarker Research in Medicine, Stiftingtalstraße 5, 8010 Graz, Austria
| | - Ramsay J Mcfarlane
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Christoph W Sensen
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria; Institute of Computational Biotechnology, Graz University of Technology, Petersgasse 14/V, 8010 Graz, Austria; HCEMM Kft., Római blvd. 21, 6723 Szeged, Hungary
| | - Julia Feichtinger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Christian Doppler Laboratory for innovative Pichia pastoris host and vector systems, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria.
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Suteau V, Seegers V, Munier M, Ben Boubaker R, Reyes C, Gentien D, Wery M, Croué A, Illouz F, Hamy A, Rodien P, Briet C. G Protein-coupled Receptors in Radioiodine-refractory Thyroid Cancer in the Era of Precision Medicine. J Clin Endocrinol Metab 2021; 106:2221-2232. [PMID: 34000025 DOI: 10.1210/clinem/dgab343] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Indexed: 12/11/2022]
Abstract
CONTEXT Radioiodine-refractory thyroid cancers have poor outcomes and limited therapeutic options (tyrosine kinase inhibitors) due to transient efficacy and toxicity of treatments. Therefore, combinatorial treatments with new therapeutic approaches are needed. Many studies link G protein-coupled receptors (GPCRs) to cancer cell biology. OBJECTIVE To perform a specific atlas of GPCR expression in progressive and refractory thyroid cancer to identify potential targets among GPCRs aiming at drug repositioning. METHODS We analyzed samples from tumor and normal thyroid tissues from 17 patients with refractory thyroid cancer (12 papillary thyroid cancers [PTCs] and 5 follicular thyroid cancers [FTCs]). We assessed GPCR mRNA expression using NanoString technology with a custom panel of 371 GPCRs. The data were compared with public repositories and pharmacological databases to identify eligible drugs. The analysis of prognostic value of genes was also performed with TCGA datasets. RESULTS With our transcriptomic analysis, 4 receptors were found to be downregulated in FTC (VIPR1, ADGRL2/LPHN2, ADGRA3, and ADGRV1). In PTC, 24 receptors were deregulated, 7 of which were also identified by bioinformatics analyses of publicly available datasets on primary thyroid cancers (VIPR1, ADORA1, GPRC5B, P2RY8, GABBR2, CYSLTR2, and LPAR5). Among all the differentially expressed genes, 22 GPCRs are the target of approved drugs and some GPCRs are also associated with prognostic factors. DISCUSSION For the first time, we performed GPCR mRNA expression profiling in progressive and refractory thyroid cancers. These findings provide an opportunity to identify potential therapeutic targets for drug repositioning and precision medicine in radioiodine-refractory thyroid cancer.
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Affiliation(s)
- Valentine Suteau
- Département d'Endocrinologie-diabétologie nutrition, CHU Angers, Angers, France
- Faculty of Health, University of Angers (CHU Angers), Inserm 1083, CNRS 6015, MITOVASC, SFR ICAT, Angers, France
| | - Valérie Seegers
- Institut de Cancérologie de l'Ouest, Service de Biométrie, Angers, France
| | - Mathilde Munier
- Département d'Endocrinologie-diabétologie nutrition, CHU Angers, Angers, France
- Faculty of Health, University of Angers (CHU Angers), Inserm 1083, CNRS 6015, MITOVASC, SFR ICAT, Angers, France
- Centre de référence des maladies rares de la Thyroïde et des Récepteurs Hormonaux, Endo-ERN centre for rare endocrine diseases, Angers, France
| | - Rym Ben Boubaker
- Faculty of Health, University of Angers (CHU Angers), Inserm 1083, CNRS 6015, MITOVASC, SFR ICAT, Angers, France
| | - Cécile Reyes
- Institut Curie, Plateforme Génomique, Paris, France
| | | | - Méline Wery
- Faculty of Health, University of Angers (CHU Angers), SFR ICAT, Angers, France
| | - Anne Croué
- Département de Pathologie Cellulaire et Tissulaire, CHU Angers, Angers, France
| | - Frédéric Illouz
- Département d'Endocrinologie-diabétologie nutrition, CHU Angers, Angers, France
- Centre de référence des maladies rares de la Thyroïde et des Récepteurs Hormonaux, Endo-ERN centre for rare endocrine diseases, Angers, France
- Centre de compétence TUTHYREF, TUTHYREF Network, Angers, France
| | - Antoine Hamy
- Service de chirurgie viscérale, CHU d'Angers, Angers, France
| | - Patrice Rodien
- Département d'Endocrinologie-diabétologie nutrition, CHU Angers, Angers, France
- Faculty of Health, University of Angers (CHU Angers), Inserm 1083, CNRS 6015, MITOVASC, SFR ICAT, Angers, France
- Centre de référence des maladies rares de la Thyroïde et des Récepteurs Hormonaux, Endo-ERN centre for rare endocrine diseases, Angers, France
- Centre de compétence TUTHYREF, TUTHYREF Network, Angers, France
| | - Claire Briet
- Département d'Endocrinologie-diabétologie nutrition, CHU Angers, Angers, France
- Faculty of Health, University of Angers (CHU Angers), Inserm 1083, CNRS 6015, MITOVASC, SFR ICAT, Angers, France
- Centre de référence des maladies rares de la Thyroïde et des Récepteurs Hormonaux, Endo-ERN centre for rare endocrine diseases, Angers, France
- Centre de compétence TUTHYREF, TUTHYREF Network, Angers, France
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Molecular Genetics of Follicular-Derived Thyroid Cancer. Cancers (Basel) 2021; 13:cancers13051139. [PMID: 33799953 PMCID: PMC7961716 DOI: 10.3390/cancers13051139] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Thyroid tumors that derive from follicular cells are not a homogeneous entity, showing variable morphological appearance and different degrees of differentiation. Molecular markers are useful for both diagnostic purposes and prognostic stratification of patients. In presurgical setting, molecular testing of indeterminate thyroid nodules on aspirates provides useful diagnostic information; the molecular analysis on tumor tissues can also reveal the presence of genetic alterations related to patients’ prognosis. In recent years, the molecular characterization of these tumors has acquired even more importance thanks to the introduction of targeted drugs. This review summarizes the current literature on the molecular landscape of follicular-derived thyroid tumors. Abstract Thyroid cancer is the most common type of endocrine-related malignancy, whose incidence rates have increased dramatically in the last few decades. Neoplasms of follicular origin generally have excellent prognosis, with the exception of less differentiated tumors. Follicular-derived thyroid cancer can manifest as a variety of morphologically distinct entities, characterized by various degrees of differentiation and invasiveness. Histological evaluation is thus crucial for the definition of patients’ prognosis. However, within each histological subtype, tumor behavior can be highly variable, and, in this respect, molecular characterization can provide insightful information to refine the risk stratification of tumors. In addition to the importance of its prognostic role, molecular testing can be used to support the differential diagnosis of thyroid nodules in the absence of marked cyto-morphological aberrations. Finally, with the advent of targeted drugs, the presence of molecular alterations will guide the therapeutic strategies for patients with advanced tumors who do not respond to standard treatment. This review aims to describe the genetic landscape of follicular-derived thyroid tumors also highlighting differences across histological subtypes.
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