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Płuciennik A, Płaczek A, Wilk A, Student S, Oczko-Wojciechowska M, Fujarewicz K. Data Integration–Possibilities of Molecular and Clinical Data Fusion on the Example of Thyroid Cancer Diagnostics. Int J Mol Sci 2022; 23:ijms231911880. [PMID: 36233181 PMCID: PMC9569592 DOI: 10.3390/ijms231911880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/24/2022] [Accepted: 09/28/2022] [Indexed: 11/23/2022] Open
Abstract
(1) Background: The data from independent gene expression sources may be integrated for the purpose of molecular diagnostics of cancer. So far, multiple approaches were described. Here, we investigated the impacts of different data fusion strategies on classification accuracy and feature selection stability, which allow the costs of diagnostic tests to be reduced. (2) Methods: We used molecular features (gene expression) combined with a feature extracted from the independent clinical data describing a patient’s sample. We considered the dependencies between selected features in two data fusion strategies (early fusion and late fusion) compared to classification models based on molecular features only. We compared the best accuracy classification models in terms of the number of features, which is connected to the potential cost reduction of the diagnostic classifier. (3) Results: We show that for thyroid cancer, the extracted clinical feature is correlated with (but not redundant to) the molecular data. The usage of data fusion allows a model to be obtained with similar or even higher classification quality (with a statistically significant accuracy improvement, a p-value below 0.05) and with a reduction in molecular dimensionality of the feature space from 15 to 3–8 (depending on the feature selection method). (4) Conclusions: Both strategies give comparable quality results, but the early fusion method provides better feature selection stability.
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Affiliation(s)
- Alicja Płuciennik
- Department of Systems Biology and Engineering, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland
- Department of Technology Development, Gabos Software Sp z o.o., Mikołowska 100, 40-065 Katowice, Poland
- Correspondence: (A.P.); (S.S.)
| | - Aleksander Płaczek
- Department of Technology Development, Gabos Software Sp z o.o., Mikołowska 100, 40-065 Katowice, Poland
- Department of Applied Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland
| | - Agata Wilk
- Department of Systems Biology and Engineering, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland
- Department of Biostatistics and Bioinformatics, Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, Wybrzeze AK 14, 44-100 Gliwice, Poland
| | - Sebastian Student
- Department of Systems Biology and Engineering, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland
- Biotechnology Center, Silesian University of Technology, Bolesława Krzywoustego 8, 44-100 Gliwice, Poland
- Correspondence: (A.P.); (S.S.)
| | - Małgorzata Oczko-Wojciechowska
- Department of Clinical and Molecular Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, Wybrzeze AK 14, 44-100 Gliwice, Poland
| | - Krzysztof Fujarewicz
- Department of Systems Biology and Engineering, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland
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Haaga E, Kalfert D, Ludvíková M, Kholová I. Non-Invasive Follicular Thyroid Neoplasm with Papillary-Like Nuclear Features Is Not a Cytological Diagnosis, but It Influences Cytological Diagnosis Outcomes: A Systematic Review and Meta-Analysis. Acta Cytol 2021; 66:85-105. [PMID: 34781293 DOI: 10.1159/000519757] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/16/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND A low-risk thyroid tumour, non-invasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP) was introduced in 2016. NIFTP criteria require a thorough histological examination to rule out capsular and lymphovascular invasion, which denies the possibility of preoperative cytological diagnosis. Nevertheless, since the adoption of the new entity, the cytology of NIFTP has been a subject of interest. OBJECTIVES The present systematic review and meta-analysis investigate the cytological diagnosis of NIFTP. METHOD An online PubMed literature search was conducted between March 1, 2020, and June 30, 2020, for all original articles considering the cytology of histologically proven NIFTP. The studies including data on fine needle aspiration specimens classified by The Bethesda System for Reporting Thyroid Cytology (TBSRTC) categories, risk of malignancy (ROMs) in the TBSRTC categories, and cytomorphological features of NIFTP were included in the meta-analysis. Non-English studies and case reports were excluded. The data were tabulated and statistical analysis was performed with Open Meta-Analyst program. RESULTS Fifty-eight studies with a total of 2,553 NIFTP cases were included in the study. The pooled prevalence of NIFTP cases was calculated among 25,892 surgically resected cases from 20 studies and the results show that NIFTP consisted 4.4% (95% confidence interval [CI]: 3.5-5.4%) of all cases. Most of the NIFTP cases (79.0%) belonged to the intermediate categories of TBSRTC. The pooled distribution of NIFTP cases in each TBSRTC category was 1.3% (95% CI: 0.8-1.7%) in non-diagnostic (ND), 8.9% (95% CI: 6.9-10.8%) in benign, 29.2% (95% CI: 25.0-33.4%) in atypia of undetermined significance or follicular lesion of undetermined significance (AUS/FLUS), 24.2% (95% CI: 19.6-28.9%) in follicular neoplasm (FN), 19.5% (95% CI: 16.1-22.9%) in suspicious for malignancy (SM), and 6.9% (95% CI: 5.2-8.7%) in malignant. Compared to pre-NIFTP era, the pooled risk differences of ROM were reduced by 2.4% in ND, 2.7% in benign, 8.2% in AUS/FLUS, 8.2% in FN, 7.3% in SM, and 1.1% in the malignant category. The cytomorphological features of NIFTP were similar to follicular variant of papillary thyroid carcinoma (FVPTC) but lesser to papillary thyroid carcinoma (PTC). CONCLUSIONS Based on our results, NIFTP remains a histological diagnosis. Although cytomorphological features cannot be used in differentiating NIFTP from FVPTC, they may guide in separating NIFTP from PTC. Features such as papillae, microfollicles, giant cells, psammoma bodies, and the amount of papillary-like nuclear features should be taken into account when suspicious of NIFTP. NIFTP should not have papillae or psammoma bodies, and giant cells were rarely observed.
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Affiliation(s)
- Elina Haaga
- Pathology, Fimlab Laboratories, Tampere, Finland
- Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
| | - David Kalfert
- Department of Otorhinolaryngology and Head and Neck Surgery, First Faculty of Medicine, Charles University, University Hospital Motol, Prague, Czechia
| | - Marie Ludvíková
- Department of Biology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia
| | - Ivana Kholová
- Pathology, Fimlab Laboratories, Tampere, Finland
- Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
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Abstract
The Italian SIAPEC-AIT 2014 classification, the 2017 Bethesda System for Reporting Thyroid Cytology (TBSRTC), the 2016 UK Royal College of Pathologists (RCPath) thyroid reporting system, and the 2019 Japanese reporting system for thyroid aspiration cytology (JRSTAC2019) represent the most widely used reporting systems among clinicians and pathologists for the purpose of cytologically diagnosing, estimating the potential risk of malignancy (ROM), and defining the most appropriate treatment for a patient with a thyroid nodule. Although all the systems use overlapping diagnostic categories and morphologic criteria, they differ on the basis of the criteria for inclusion in the cytologic categories, which may, in turn, affect the ROM of a given category and the clinical management of the patient, particularly with regard to the “indeterminate” categories. The aim of this review is to analyze the main differences that emerge between the systems and to propose possible solutions for a comprehensive reporting system that integrates and harmonizes all the criteria of the Italian classification and the Bethesda system, also taking into account the impact that the new tumor entity NIFTP (non-invasive follicular tumor with papillary-like nuclear features) that has, in many instances, replaced the non-invasive form of the follicular variant of papillary carcinoma, has had on the modification of malignancy risks.
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Suzuki M, Moriya S, Kobayashi S, Nishijima Y, Fujii T, Ikota H, Yokoo H, Saio M. Computer-assisted image analysis of cytological specimens clarify the correlation between nuclear size and intranuclear cytoplasmic inclusions regardless of BRAFV600E mutation in papillary thyroid carcinoma. Cytopathology 2021; 32:718-731. [PMID: 34159645 DOI: 10.1111/cyt.13022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/29/2021] [Accepted: 06/08/2021] [Indexed: 11/28/2022]
Abstract
OBJECTIVE The morphological features of nuclei in cytological and histological specimens were compared and examined for the presence of BRAFV600E mutation and the appearance rate of intranuclear cytoplasmic inclusions (NI). METHODS BRAFV600E mutation was identified using a mutation-specific antibody (clone; VE1) in 103 thyroid papillary carcinoma cases at Gunma University Hospital. The nuclear area, perimeter, and roundness of the corresponding cytological specimens and haematoxylin and eosin-stained specimens were analysed using image analysis software, and the appearance rate of NI was calculated and compared. RESULTS BRAFV600E mutation was detected in 71 (69%) cases. The appearance rate of NI was significantly higher in the BRAFV600E mutation-positive group in cytological and histological specimens (P = .0070 and .0184, respectively). Significant differences were observed between the BRAFV600E mutation-negative and -positive groups in the average nuclear area and average nuclear perimeter in cytological specimens (P = .0137 and .0152, respectively). In addition, nuclear enlargement was correlated with the appearance rate of NI regardless of the presence of BRAFV600E mutation in cytological specimens. In the BRAFV600E mutation-negative group, the nuclear area and perimeter were significantly smaller in the lymph node metastasis-positive cases (P = .0182 and .0260, respectively). CONCLUSION This study found that the appearance rate of NI was positively correlated with the nuclear area and perimeter and negatively correlated with nuclear roundness in cytological specimens. Furthermore, these results were observed regardless of the existence of BRAFV600E mutation. These results have never been previously reported and clearly demonstrate the usefulness of cytological specimens in computer-assisted image analysis.
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Affiliation(s)
- Midori Suzuki
- Laboratory of Histopathology and Cytopathology, Department of Laboratory Sciences, Gunma University Graduate School of Health Sciences, Gunma, Japan
| | - Shunichi Moriya
- Laboratory of Histopathology and Cytopathology, Department of Laboratory Sciences, Gunma University Graduate School of Health Sciences, Gunma, Japan
| | - Sayaka Kobayashi
- Laboratory of Histopathology and Cytopathology, Department of Laboratory Sciences, Gunma University Graduate School of Health Sciences, Gunma, Japan
| | - Yoshimi Nishijima
- Laboratory of Histopathology and Cytopathology, Department of Laboratory Sciences, Gunma University Graduate School of Health Sciences, Gunma, Japan
| | - Takaaki Fujii
- Division of Breast and Endocrine Surgery, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Hayato Ikota
- Clinical Department of Pathology, Gunma University Hospital, Gunma, Japan
| | - Hideaki Yokoo
- Department of Human Pathology, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Masanao Saio
- Laboratory of Histopathology and Cytopathology, Department of Laboratory Sciences, Gunma University Graduate School of Health Sciences, Gunma, Japan
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Girolami I, Pantanowitz L, Mete O, Brunelli M, Marletta S, Colato C, Trimboli P, Crescenzi A, Bongiovanni M, Barbareschi M, Eccher A. Programmed Death-Ligand 1 (PD-L1) Is a Potential Biomarker of Disease-Free Survival in Papillary Thyroid Carcinoma: a Systematic Review and Meta-Analysis of PD-L1 Immunoexpression in Follicular Epithelial Derived Thyroid Carcinoma. Endocr Pathol 2020; 31:291-300. [PMID: 32468210 DOI: 10.1007/s12022-020-09630-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The expression of programmed death-ligand 1 (PD-L1) is an established prerequisite for the administration of checkpoint inhibitor therapy and is of prognostic value in several cancer types. Data concerning the potential effect of PD-L1 on the prognosis of thyroid carcinoma are limited. Therefore, this study aimed to provide a systematic review of the published data on this topic. The literature was reviewed to gather and quantify evidence on the prognostic role of PD-L1 in follicular epithelial derived thyroid carcinomas and determine its association with clinicopathological parameters. A meta-analysis was performed using the DerSimonian-Laird random-effects model. The quality of studies was evaluated with the Newcastle-Ottawa Scale and a modified GRADE approach used to rate the quality of evidence. Out of 445 papers, 18 were included and 15 provided adequate data for meta-analysis. The quality of evidence ranged from low to high. PD-L1 expression was significantly associated with a reduced disease-free survival (DFS) (RR 1.63, CI 1.04-2.56, p = 0.03, I2 68%, τ2 0.19 and HR 1.90, CI 1.33-2.70, p< 0.001, I2 0%, τ2 0.00); however, no association was found with the overall survival (OS). Furthermore, a significant association was found with respect to underlying chronic lymphocytic thyroiditis and BRAFV600E mutation status in papillary thyroid carcinomas. In the subgroup analysis, the association of PD-L1 and DFS remained strong in papillary thyroid carcinoma when compared with dedifferentiated thyroid carcinomas (anaplastic and poorly differentiated thyroid carcinomas) that failed to demonstrate a significant association with respect to PD-L1. These findings underscore the role of PD-L1 immunohistochemistry as a potential prognostic biomarker of disease recurrence in patients with papillary thyroid carcinoma.
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MESH Headings
- Adenocarcinoma, Follicular/diagnosis
- Adenocarcinoma, Follicular/metabolism
- Adenocarcinoma, Follicular/mortality
- Adenocarcinoma, Follicular/therapy
- Adult
- Aged
- Aged, 80 and over
- B7-H1 Antigen/analysis
- B7-H1 Antigen/metabolism
- Biomarkers, Tumor/analysis
- Biomarkers, Tumor/metabolism
- Disease-Free Survival
- Female
- Humans
- Immunohistochemistry
- Male
- Middle Aged
- Neoplasm Recurrence, Local/diagnosis
- Neoplasm Recurrence, Local/metabolism
- Neoplasm Recurrence, Local/mortality
- Prognosis
- Thyroid Cancer, Papillary/diagnosis
- Thyroid Cancer, Papillary/metabolism
- Thyroid Cancer, Papillary/mortality
- Thyroid Cancer, Papillary/therapy
- Thyroid Neoplasms/diagnosis
- Thyroid Neoplasms/metabolism
- Thyroid Neoplasms/mortality
- Thyroid Neoplasms/therapy
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Affiliation(s)
- Ilaria Girolami
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, P.le Stefani n. 1, 37126, Verona, Italy
| | - Liron Pantanowitz
- Department of Pathology, UPMC Shadyside Hospital, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ozgur Mete
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Matteo Brunelli
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, P.le Stefani n. 1, 37126, Verona, Italy
| | - Stefano Marletta
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, P.le Stefani n. 1, 37126, Verona, Italy
| | - Chiara Colato
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, P.le Stefani n. 1, 37126, Verona, Italy
| | - Pierpaolo Trimboli
- Clinic for Nuclear Medicine and Competence Centre for Thyroid Disease, Imaging Institute of Southern Switzerland, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana (USI), Lugano, Switzerland
| | - Anna Crescenzi
- Section of Pathology, University Hospital Campus Bio Medico, Rome, Italy
| | | | | | - Albino Eccher
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, P.le Stefani n. 1, 37126, Verona, Italy.
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