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Hosseiniyan Khatibi SM, Zununi Vahed S, Homaei Rad H, Emdadi M, Akbarpour Z, Teshnehlab M, Pirmoradi S, Alizadeh E. Uncovering key molecular mechanisms in the early and late-stage of papillary thyroid carcinoma using association rule mining algorithm. PLoS One 2023; 18:e0293335. [PMID: 37917782 PMCID: PMC10621943 DOI: 10.1371/journal.pone.0293335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 10/10/2023] [Indexed: 11/04/2023] Open
Abstract
OBJECTIVE Thyroid Cancer (TC) is the most frequent endocrine malignancy neoplasm. It is the sixth cause of cancer in women worldwide. The treatment process could be expedited by identifying the controlling molecular mechanisms at the early and late stages, which can contribute to the acceleration of treatment schemes and the improvement of patient survival outcomes. In this work, we study the significant mRNAs through Machine Learning Algorithms in both the early and late stages of Papillary Thyroid Cancer (PTC). METHOD During the course of our study, we investigated various methods and techniques to obtain suitable results. The sequence of procedures we followed included organizing data, using nested cross-validation, data cleaning, and normalization at the initial stage. Next, to apply feature selection, a t-test and binary Non-Dominated Sorting Genetic Algorithm II (NSGAII) were chosen to be employed. Later on, during the analysis stage, the discriminative power of the selected features was evaluated using machine learning and deep learning algorithms. Finally, we considered the selected features and utilized Association Rule Mining algorithm to identify the most important ones for improving the decoding of dominant molecular mechanisms in PTC through its early and late stages. RESULT The SVM classifier was able to distinguish between early and late-stage categories with an accuracy of 83.5% and an AUC of 0.78 based on the identified mRNAs. The most significant genes associated with the early and late stages of PTC were identified as (e.g., ZNF518B, DTD2, CCAR1) and (e.g., lnc-DNAJB6-7:7, RP11-484D2.3, MSL3P1), respectively. CONCLUSION Current study reveals a clear picture of the potential candidate genes that could play a major role not only in the early stage, but also throughout the late one. Hence, the findings could be of help to identify therapeutic targets for more effective PTC drug developments.
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Affiliation(s)
- Seyed Mahdi Hosseiniyan Khatibi
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
- Kidney Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Rahat Breath and Sleep Research Center, Tabriz University of Medical Science, Tabriz, Iran
| | | | - Hamed Homaei Rad
- Rahat Breath and Sleep Research Center, Tabriz University of Medical Science, Tabriz, Iran
| | - Manijeh Emdadi
- Department of Computer Engineering, Abadan Branch, Islamic Azad University, Abadan, Iran
| | - Zahra Akbarpour
- Rahat Breath and Sleep Research Center, Tabriz University of Medical Science, Tabriz, Iran
| | - Mohammad Teshnehlab
- Department of Electric and Computer Engineering, K.N. Toosi University of Technology, Tehran, Iran
| | - Saeed Pirmoradi
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Effat Alizadeh
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Faculty of Advanced Medical Sciences, Department of Medical Biotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
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Investigation of the clinical utility of adhesion molecules in the management of thyroid nodules. Sci Rep 2023; 13:4069. [PMID: 36906717 PMCID: PMC10008644 DOI: 10.1038/s41598-023-31302-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 03/09/2023] [Indexed: 03/13/2023] Open
Abstract
To better understand the relationship among cell adhesion molecules (CAM) and investigate the clinical diagnostic and prognostic application of ICAM-1 (ICAM1), LFA-1 (ITGAL), and L-selectin (SELL) proteins and mRNA corresponding expression in thyroid cancer. Gene expression was evaluated by RT-qPCR, and protein expression was evaluated by immunohistochemistry. We evaluated 275 patients (218 women, 57 men, 48.4 ± 14.5 years old), including 102 benign and 173 malignant nodules. The 143 papillary thyroid carcinoma (PTC) and 30 follicular thyroid carcinoma (FTC) patients were managed according to current guidelines and followed-up for 78.7 ± 54.2 months. Malignant and benign nodules differed concerning mRNA (p = 0.0027) and protein (p = 0.0020 for nuclear) expression of L-selectin and ICAM-1 (mRNA: p = 0.0001 and protein: p = 0.0014) and protein expression of LFA-1 (p = 0.0168), but not mRNA expression of LFA-1 (p = 0.2131). SELL expression was more intense in malignant tumors (p = 0.0027). ICAM1 (p = 0.0064) and ITGAL (p = 0.0244) mRNA expression was higher in tumors with lymphocyte infiltrate. ICAM-1 expression correlated with younger age at diagnosis (p = 0.0312) and smaller tumor size (p = 0.0443). Also, LFA-1 expression correlated with higher age at diagnosis (p = 0.0376) and was more intense at stage III and IV (p = 0.0077). In general, the protein expression of the 3 CAM decreased as the process of cellular dedifferentiation occurred. We suggest that the SELL and ICAM1 genes and L-selectin and LFA-1 protein expression may help confirm malignancy and assist in the histological characterization of follicular patterned lesions, but we were unable to correlate these CAMs with patient outcomes.
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3
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Chen H, Song A, Wang Y, He Y, Tong J, Di J, Li C, Zhou Z, Cai X, Zhong D, Da J. BRAF V600E mutation test on fine-needle aspiration specimens of thyroid nodules: Clinical correlations for 4600 patients. Cancer Med 2021; 11:40-49. [PMID: 34851044 PMCID: PMC8704181 DOI: 10.1002/cam4.4419] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 10/08/2021] [Accepted: 10/23/2021] [Indexed: 12/17/2022] Open
Abstract
Background The BRAFV600E mutation is valuable for the diagnosis, prognosis, and therapy of papillary thyroid cancer (PTC). However, studies related to this mutation have involved only a small number of patients. Therefore, we performed a large‐scale analysis from a single institute to evaluate the accuracy of combined fine‐needle aspiration (FNA) and BRAFV600E mutation tests for PTC diagnosis. Methods A total of 4600 patients with thyroid nodules who underwent both FNA cytology and BRAFV600E mutation analysis on FNA specimens were enrolled. The association between the BRAFV600E mutation and clinicopathological features was analyzed. A separate analysis was performed for the 311 patients who underwent repeated FNA for comparison of cytological evaluation and BRAFV600E mutation results. The diagnostic efficacy of the BRAFV600E mutation test and cytologic diagnoses was evaluated for 516 patients who underwent preoperative FNA tests in comparison with conclusive postoperative histopathologic results. Results The cytology results of all 4600 FNA samples were categorized according to The Bethesda System for Reporting Thyroid Cytology (TBSRTC) stages I–VI, which accounted for 11.76%, 60.02%, 6.46%, 3.61%, 6.71%, and 11.43% of the samples, respectively. The BRAFV600E mutation was detected in 762 (16.57%) FNA samples, with rates of 1.48%, 0.87%, 20.20%, 3.01%, 66.02%, and 87.81% for TBSRTC I–VI lesions, respectively. Among the 311 repeat FNA cases, 81.0% of the BRAFV600E‐positive and 4.3% of the BRAFV600E‐negative specimens with an initial indication of cytological non‐malignancy were ultimately diagnosed as malignant by repeat FNA (p < 0.001). Among the 516 patients who underwent thyroidectomy, the sensitivity and specificity of the BRAFV600E mutation test alone for PTC diagnosis were 76.71% and 100.0%, respectively, which increased to 96.62% and 88.03%, respectively, when combining the BRAFV600E mutation test with cytology. BRAFV600E mutation was significantly associated with lymph node metastasis (p < 0.001), but not with age, gender, or tumor size. Conclusions The BRAFV600E mutation test in FNA samples has potential to reduce false negatives in PTC diagnosis, and therefore plays an important role in the diagnosis of thyroid nodules, especially those with an indeterminate or nondiagnostic cytology, which should be considered for repeat FNA.
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Affiliation(s)
- Huang Chen
- Department of Pathology, The China-Japan Friendship Hospital, Beijing, China
| | - Aiping Song
- Department of Pathology, The China-Japan Friendship Hospital, Beijing, China
| | - Ye Wang
- Department of Pathology, The China-Japan Friendship Hospital, Beijing, China
| | - Yifan He
- Department of Pathology & Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Jie Tong
- Department of Pathology, The China-Japan Friendship Hospital, Beijing, China
| | - Jinxi Di
- Department of Pathology, The China-Japan Friendship Hospital, Beijing, China
| | - Chun Li
- Department of Pathology, The China-Japan Friendship Hospital, Beijing, China
| | - Zhongren Zhou
- Department of Endocrinology, The China-Japan Friendship Hospital, Beijing, China
| | - Xiaopin Cai
- Department of Pathology & Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Dingrong Zhong
- Department of Pathology, The China-Japan Friendship Hospital, Beijing, China
| | - Jiping Da
- Department of Pathology, The China-Japan Friendship Hospital, Beijing, China.,Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hosptial, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
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4
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Bhalla S, Kaur H, Kaur R, Sharma S, Raghava GPS. Expression based biomarkers and models to classify early and late-stage samples of Papillary Thyroid Carcinoma. PLoS One 2020; 15:e0231629. [PMID: 32324757 PMCID: PMC7179925 DOI: 10.1371/journal.pone.0231629] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 03/27/2020] [Indexed: 12/19/2022] Open
Abstract
INTRODUCTION Recently, the rise in the incidences of thyroid cancer worldwide renders it to be the sixth most common cancer among women. Commonly, Fine Needle Aspiration biopsy predominantly facilitates the diagnosis of the nature of thyroid nodules. However, it is inconsiderable in determining the tumor's state, i.e., benign or malignant. This study aims to identify the key RNA transcripts that can segregate the early and late-stage samples of Thyroid Carcinoma (THCA) using RNA expression profiles. MATERIALS AND METHODS In this study, we used the THCA RNA-Seq dataset of The Cancer Genome Atlas, consisting of 500 cancer and 58 normal (adjacent non-tumorous) samples obtained from the Genomics Data Commons (GDC) data portal. This dataset was dissected to identify key RNA expression features using various feature selection techniques. Subsequently, samples were classified based on selected features employing different machine learning algorithms. RESULTS Single gene ranking based on the Area Under the Receiver Operating Characteristics (AUROC) curve identified the DCN transcript that can classify the early-stage samples from late-stage samples with 0.66 AUROC. To further improve the performance, we identified a panel of 36 RNA transcripts that achieved F1 score of 0.75 with 0.73 AUROC (95% CI: 0.62-0.84) on the validation dataset. Moreover, prediction models based on 18-features from this panel correctly predicted 75% of the samples of the external validation dataset. In addition, the multiclass model classified normal, early, and late-stage samples with AUROC of 0.95 (95% CI: 0.84-1), 0.76 (95% CI: 0.66-0.85) and 0.72 (95% CI: 0.61-0.83) on the validation dataset. Besides, a five protein-coding transcripts panel was also recognized, which segregated cancer and normal samples in the validation dataset with F1 score of 0.97 and 0.99 AUROC (95% CI: 0.91-1). CONCLUSION We identified 36 important RNA transcripts whose expression segregated early and late-stage samples with reasonable accuracy. The models and dataset used in this study are available from the webserver CancerTSP (http://webs.iiitd.edu.in/raghava/cancertsp/).
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Affiliation(s)
- Sherry Bhalla
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
- Centre for Systems Biology and Bioinformatics, Panjab University, Chandigarh, India
| | - Harpreet Kaur
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Rishemjit Kaur
- CSIR-Central Scientific Instruments Organization, Chandigarh, India
| | - Suresh Sharma
- Centre for Systems Biology and Bioinformatics, Panjab University, Chandigarh, India
| | - Gajendra P. S. Raghava
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
- * E-mail:
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5
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Baloch Z, LiVolsi VA. The Bethesda System for Reporting Thyroid Cytology (TBSRTC): From look-backs to look-ahead. Diagn Cytopathol 2020; 48:862-866. [PMID: 31999070 DOI: 10.1002/dc.24385] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 01/13/2020] [Indexed: 02/06/2023]
Abstract
The Bethesda System for Reporting Thyroid Cytopathology (TBSRTC) was formalized in October 2007 by experts in thyroidology at the National Institute of Health in Bethesda, Maryland. The first edition of the TBSRTC book was published in 2010 and the second edition in 2018. The TBSRTC is widely employed in cytology practices in the United States and has also served as a model for similar tiered classification schemes for reporting thyroid cytopathology specimens. The tremendous success of TBSRTC cannot be underscored, it has provided a diagnostic framework which is well aligned with the present and the future of thyroid nodule management.
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Affiliation(s)
- Zubair Baloch
- Perelman School of Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Virginia A LiVolsi
- Perelman School of Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
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Fulciniti F, Cipolletta Campanile A, Malzone MG, Chiofalo MG, Capiluongo A, Monaco M, Di Maio N, Sandomenico F, Botti G, Chiappetta G, Vuttariello E, Pezzullo L. Impact of ultrasonographic features, cytomorphology and mutational testing on malignant and indeterminate thyroid nodules on diagnostic accuracy of fine needle cytology samples: A prospective analysis of 141 patients. Clin Endocrinol (Oxf) 2019; 91:851-859. [PMID: 31483883 PMCID: PMC6972562 DOI: 10.1111/cen.14089] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 08/28/2019] [Accepted: 08/29/2019] [Indexed: 12/30/2022]
Abstract
OBJECTIVE Fine needle cytology (FNC) is the first-line diagnostic method to determine the benign or malignant nature of thyroid nodules. The gray zone of cytological classifications remains, however, a crucial and challenging area for cytopathologists. DESIGN, PATIENTS AND MEASUREMENTS In the present study, 141 thyroid cytological samples, with ultrasonographic suspicious features, have been prospectively analysed. Molecular analyses were performed by an innovative technology using two multiplex PCRs for the amplification of BRAF, N-H-K-RAS and RET exon genes. RNA samples were studied for RET/PTC1 and RET/PTC3 rearrangements by PCR amplification, and the conditions were set-up to study, with a single experiment, both wild-type PAX8 and PAX8/PPARɣ rearrangements. In total, 111 samples were examined for BRAF, N-H-KRAS and RET genes. An ultrasonographic, cytological and molecular correlation was also carried out in an attempt to suggest a possible way to manage the patients with thyroid nodules. Cyto-histological correlation was available in 115 cases, and it was used to verify the global diagnostic accuracy of this combined approach. RESULTS According to the histopathological diagnosis, FNC accuracy was 100% for TIR5 and metastases; 89% for TIR4; 84% for TIR3A and 58% for TIR3B. About 11% of the studied samples showed either RET-PTC1 or RET/PTC3 chromosomal rearrangements, and only one sample simultaneously presented RET/PTC1 and RET/PTC3 rearrangements. PAX8/PPARɣ rearrangement was found in 6% of the samples. CONCLUSIONS A multidisciplinary approach to the thyroid is therefore necessary to develop innovative methods suitable for an improved diagnostic and prognostic definition of thyroid cancer.
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Affiliation(s)
- Franco Fulciniti
- Clinical Cytopathology ServiceIstituto Cantonale di PatologiaLocarnoSwitzerland
| | | | | | - Maria Grazia Chiofalo
- Thyroid and Parathyroid Surgery UnitIstituto Nazionale Tumori – IRCCS – Fondazione G. PascaleNaplesItaly
| | - Anna Capiluongo
- Functional Genomics UnitIstituto Nazionale Tumori – IRCCS – Fondazione G. PascaleNaplesItaly
| | - Mario Monaco
- Functional Genomics UnitIstituto Nazionale Tumori – IRCCS – Fondazione G. PascaleNaplesItaly
| | | | - Fabio Sandomenico
- Radiology UnitIstituto Nazionale Tumori – IRCCS – Fondazione G. PascaleNaplesItaly
| | - Gerardo Botti
- Scientific DirectorateIstituto Nazionale Tumori – IRCCS – Fondazione G. PascaleNaplesItaly
| | | | - Emilia Vuttariello
- Functional Genomics UnitIstituto Nazionale Tumori – IRCCS – Fondazione G. PascaleNaplesItaly
| | - Luciano Pezzullo
- Thyroid and Parathyroid Surgery UnitIstituto Nazionale Tumori – IRCCS – Fondazione G. PascaleNaplesItaly
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7
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Wang Z, Sun K, Jing C, Cao H, Ma R, Wu J. Comparison of droplet digital PCR and direct Sanger sequencing for the detection of the BRAF V600E mutation in papillary thyroid carcinoma. J Clin Lab Anal 2019; 33:e22902. [PMID: 31021028 PMCID: PMC6642310 DOI: 10.1002/jcla.22902] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/27/2019] [Accepted: 03/28/2019] [Indexed: 12/19/2022] Open
Abstract
Background The BRAFV600E mutation status is a useful diagnostic and prognostic marker for papillary thyroid carcinoma (PTC). Although it is a commonly used method, Sanger sequencing has several limitations in detecting the BRAFV600E mutation. The aim of this study was to evaluate the efficiency of droplet digital PCR (ddPCR) as an alternative method for the detection of the BRAFV600E mutation in PTC patients. Methods Samples from a total of 120 patients with PTC and 30 patients with benign nodular thyroid disease who underwent thyroid surgery were collected. The BRAFV600E mutation status of the PTC patients was tested by Sanger sequencing and ddPCR. Results The BRAFV600E mutation was detected in 67 samples (44.67%) by Sanger sequencing and 92 samples (61.33%) by ddPCR. The detection of the mutation by the two methods was inconsistent in twenty‐five samples (16.67%). The sensitivity and specificity of the ddPCR method were 100% and 69.88%, respectively, and the positive predictive and negative predictive values were 72.83% and 100%, respectively. The concordance rate between the two methods in detecting the BRAFV600E mutation was 83.33%. Neither Sanger sequencing nor ddPCR detected BRAFV600E in 30 patients with benign nodular thyroid disease. The 92 samples with the BRAFV600E mutation were detected by ddPCR at a fractional abundance from 0.28% to 45.40% as follows: ≥10% (59 samples, 64.13%), 5%‐10% (8 samples, 8.70%), and ≤5% (25 samples, 27.17%). The BRAFV600E mutation was detected in all 59 samples at a fractional abundance ≥10% and in four samples at a fractional abundance from 5% to 10%, and no BRAFV600E mutation was detected at a fractional abundance ≤5% by Sanger sequencing. Conclusions ddPCR was a reliable, highly sensitive alternative method for the detection of the BRAFV600E mutation in PTC patients.
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Affiliation(s)
- Zhuo Wang
- Clinical Cancer Research Center, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | | | - Changwen Jing
- Clinical Cancer Research Center, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Haixia Cao
- Clinical Cancer Research Center, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Rong Ma
- Clinical Cancer Research Center, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Jianzhong Wu
- Clinical Cancer Research Center, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
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Ferrari SM, Fallahi P, Ruffilli I, Elia G, Ragusa F, Paparo SR, Ulisse S, Baldini E, Giannini R, Miccoli P, Antonelli A, Basolo F. Molecular testing in the diagnosis of differentiated thyroid carcinomas. Gland Surg 2018; 7:S19-S29. [PMID: 30175060 DOI: 10.21037/gs.2017.11.07] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Different genetic mutations and other molecular alterations in papillary thyroid cancer (PTC) and follicular thyroid cancer (FTC) can be detected in fine-needle aspiration (FNA) of thyroid nodules, and can be used successfully to ameliorate cancer diagnosis and management of patients with thyroid nodules. The greatest experience has been obtained with the diagnostic use of BRAF mutation that is strongly specific for malignancy when detected using well-validated techniques. The strongest diagnostic result can be obtained testing FNA samples for a panel of mutations that typically involve TERT, BRAF, PAX8/PPARγ, RAS, and RET/PTC. Finding any of these mutations in a thyroid nodule provides strong indication for malignancy and helps to refine clinical management for a significant proportion of patients with indeterminate cytology. The use of molecular markers, as TERT, BRAF, PAX8/PPARγ, RAS, and RET/PTC, may be considered for patients with indeterminate FNA cytology (FNAC) to help guide management. In patients with indeterminate TIR3 FNA, the combination of precise molecular marker expression analysis with molecular mutations evaluations could ameliorate significantly the accuracy of cancer diagnosis. However other prospective studies are needed to identify more accurate molecular markers. Finally, the knowledge of these molecular pathways has permitted the development of new targeted therapies for aggressive TC.
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Affiliation(s)
| | - Poupak Fallahi
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Ilaria Ruffilli
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Giusy Elia
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Francesca Ragusa
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | | | - Salvatore Ulisse
- Department of Surgical Sciences, 'Sapienza' University of Rome, Rome, Italy
| | - Enke Baldini
- Department of Surgical Sciences, 'Sapienza' University of Rome, Rome, Italy
| | - Riccardo Giannini
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
| | - Paolo Miccoli
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
| | - Alessandro Antonelli
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Fulvio Basolo
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
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9
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de Koster EJ, de Geus-Oei LF, Dekkers OM, van Engen-van Grunsven I, Hamming J, Corssmit EPM, Morreau H, Schepers A, Smit J, Oyen WJG, Vriens D. Diagnostic Utility of Molecular and Imaging Biomarkers in Cytological Indeterminate Thyroid Nodules. Endocr Rev 2018; 39:154-191. [PMID: 29300866 DOI: 10.1210/er.2017-00133] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 12/27/2017] [Indexed: 12/21/2022]
Abstract
Indeterminate thyroid cytology (Bethesda III and IV) corresponds to follicular-patterned benign and malignant lesions, which are particularly difficult to differentiate on cytology alone. As ~25% of these nodules harbor malignancy, diagnostic hemithyroidectomy is still custom. However, advanced preoperative diagnostics are rapidly evolving.This review provides an overview of additional molecular and imaging diagnostics for indeterminate thyroid nodules in a preoperative clinical setting, including considerations regarding cost-effectiveness, availability, and feasibility of combining techniques. Addressed diagnostics include gene mutation analysis, microRNA, immunocytochemistry, ultrasonography, elastosonography, computed tomography, sestamibi scintigraphy, [18F]-2-fluoro-2-deoxy-d-glucose positron emission tomography (FDG-PET), and diffusion-weighted magnetic resonance imaging.The best rule-out tests for malignancy were the Afirma® gene expression classifier and FDG-PET. The most accurate rule-in test was sole BRAF mutation analysis. No diagnostic had both near-perfect sensitivity and specificity, and estimated cost-effectiveness. Molecular techniques are rapidly advancing. However, given the currently available techniques, a multimodality stepwise approach likely offers the most accurate diagnosis, sequentially applying one sensitive rule-out test and one specific rule-in test. Geographical variations in cytology (e.g., Hürthle cell neoplasms) and tumor genetics strongly influence local test performance and clinical utility. Multidisciplinary collaboration and implementation studies can aid the local decision for one or more eligible diagnostics.
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Affiliation(s)
- Elizabeth J de Koster
- Department of Radiology and Nuclear Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Lioe-Fee de Geus-Oei
- Department of Radiology, Section of Nuclear Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Olaf M Dekkers
- Department of Endocrinology, Leiden University Medical Center, Leiden, the Netherlands.,Department of Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Jaap Hamming
- Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands
| | - Eleonora P M Corssmit
- Department of Endocrinology, Leiden University Medical Center, Leiden, the Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Abbey Schepers
- Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands
| | - Jan Smit
- Department of Endocrinology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Wim J G Oyen
- Department of Radiology and Nuclear Medicine, Radboud University Medical Center, Nijmegen, the Netherlands.,Division of Radiotherapy and Imaging, Institute of Cancer Research, and Department of Nuclear Medicine, Royal Marsden Hospital, London, United Kingdom
| | - Dennis Vriens
- Department of Radiology, Section of Nuclear Medicine, Leiden University Medical Center, Leiden, the Netherlands
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10
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Oh HS, Kwon H, Park S, Kim M, Jeon MJ, Kim TY, Shong YK, Kim WB, Choi J, Kim WG, Song DE. Comparison of Immunohistochemistry and Direct Sanger Sequencing for Detection of the BRAF(V600E) Mutation in Thyroid Neoplasm. Endocrinol Metab (Seoul) 2018; 33:62-69. [PMID: 29388401 PMCID: PMC5874197 DOI: 10.3803/enm.2018.33.1.62] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/27/2017] [Accepted: 12/05/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The BRAF(V600E) mutation is the most common genetic alteration identified in papillary thyroid carcinoma (PTC). Because of its costs effectiveness and sensitivity, direct Sanger sequencing has several limitations. The aim of this study was to evaluate the efficiency of immunohistochemistry (IHC) as an alternative method to detect the BRAF(V600E) mutation in preoperative and postoperative tissue samples. METHODS We evaluated 71 patients who underwent thyroid surgery with the result of direct sequencing of the BRAF(V600E) mutation. IHC staining of the BRAF(V600E) mutation was performed in 49 preoperative and 23 postoperative thyroid specimens. RESULTS Sixty-two patients (87.3%) had PTC, and of these, BRAF(V600E) was confirmed by direct sequencing in 57 patients (91.9%). In 23 postoperative tissue samples, the BRAF(V600E) mutation was detected in 16 samples (70%) by direct sequencing and 18 samples (78%) by IHC. In 24 fine needle aspiration (FNA) samples, BRAF(V600E) was detected in 18 samples (75%) by direct sequencing and 16 samples (67%) by IHC. In 25 core needle biopsy (CNB) samples, the BRAF(V600E) mutation was detected in 15 samples (60%) by direct sequencing and 16 samples (64%) by IHC. The sensitivity and specificity of IHC for detecting the BRAF(V600E) mutation were 77.8% and 66.7% in FNA samples and 99.3% and 80.0% in CNB samples. CONCLUSION IHC could be an alternative method to direct Sanger sequencing for BRAF(V600E) mutation detection both in postoperative and preoperative samples. However, application of IHC to detect the BRAF(V600E) mutation in FNA samples is of limited value compared with direct sequencing.
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Affiliation(s)
- Hye Seon Oh
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Hyemi Kwon
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
- Division of Endocrinology and Metabolism, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Suyeon Park
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Mijin Kim
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Min Ji Jeon
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Tae Yong Kim
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Young Kee Shong
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Won Bae Kim
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jene Choi
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Won Gu Kim
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
| | - Dong Eun Song
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
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Ahmed AA, Abedalthagafi M. Cancer diagnostics: The journey from histomorphology to molecular profiling. Oncotarget 2018; 7:58696-58708. [PMID: 27509178 PMCID: PMC5295463 DOI: 10.18632/oncotarget.11061] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 07/19/2016] [Indexed: 12/15/2022] Open
Abstract
Although histomorphology has made significant advances into the understanding of cancer etiology, classification and pathogenesis, it is sometimes complicated by morphologic ambiguities, and other shortcomings that necessitate the development of ancillary tests to complement its diagnostic value. A new approach to cancer patient management consists of targeting specific molecules or gene mutations in the cancer genome by inhibitory therapy. Molecular diagnostic tests and genomic profiling methods are increasingly being developed to identify tumor targeted molecular profile that is the basis of targeted therapy. Novel targeted therapy has revolutionized the treatment of gastrointestinal stromal tumor, renal cell carcinoma and other cancers that were previously difficult to treat with standard chemotherapy. In this review, we discuss the role of histomorphology in cancer diagnosis and management and the rising role of molecular profiling in targeted therapy. Molecular profiling in certain diagnostic and therapeutic difficulties may provide a practical and useful complement to histomorphology and opens new avenues for targeted therapy and alternative methods of cancer patient management.
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Affiliation(s)
- Atif A Ahmed
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri, USA
| | - Malak Abedalthagafi
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,The Saudi Human Genome Laboratory, Department of Pathology, King Fahad Medical City, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
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12
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Onenerk AM, Pusztaszeri MP, Canberk S, Faquin WC. Triage of the indeterminate thyroid aspirate: What are the options for the practicing cytopathologist? Cancer Cytopathol 2017; 125:477-485. [PMID: 28609009 DOI: 10.1002/cncy.21828] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 12/17/2016] [Accepted: 12/22/2016] [Indexed: 12/26/2022]
Abstract
Fine-needle aspiration (FNA) plays a key role in the early evaluation of patients with thyroid nodules; however, from 15% to 30% of FNA specimens are cytologically indeterminate. Molecular testing has proven useful when applied to indeterminate thyroid FNAs, and its use has been endorsed in the American Thyroid Association guidelines. In addition to the noncommercial ("in-house") application of v-Raf murine sarcoma viral oncogene homolog B1 (BRAF), rat sarcoma (RAS), rearranged in transformation/papillary thyroid carcinoma (RET/PTC), and peroxisome proliferator-activated receptor γ/paired box gene 8 (PPARγ/PAX8) testing, there are currently 3 commercially available molecular panels that vary in their relative reported performances, strengths, and limitations. Here, we discuss the role of molecular testing for indeterminate thyroid aspirates, taking into consideration the recent reclassification of the encapsulated follicular variant of papillary thyroid carcinoma (PTC) as "noninvasive follicular neoplasm with papillary-like nuclear features (NIFTP)." Cancer Cytopathol 2017;125(6 suppl):477-85. © 2017 American Cancer Society.
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Affiliation(s)
- Ayse M Onenerk
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Marc P Pusztaszeri
- Department of Pathology, Geneva University Hospitals, Geneva, Switzerland
| | - Sule Canberk
- Acibadem University, Department of Pathology, Istanbul, Turkey
| | - William C Faquin
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
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13
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De Luca C, Vigliar E, d'Anna M, Pisapia P, Bellevicine C, Malapelle U, Troncone G. KRAS detection on archival cytological smears by the novel fully automated polymerase chain reaction-based Idylla mutation test. Cytojournal 2017; 14:5. [PMID: 28331530 PMCID: PMC5348988 DOI: 10.4103/1742-6413.200936] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 12/22/2016] [Indexed: 01/04/2023] Open
Abstract
Background: Molecular techniques are relevant to modern cytopathology, but their implementation is difficult without molecular expertise and infrastructure. The assessment of KRAS mutational status on cytological preparations may be useful either to refine uncertain diagnoses on pancreatic aspirates or to yield predictive information to plan targeted treatment of metastatic colorectal cancer (mCRC). The novel test Idylla™ enables fully automated KRAS genotyping in approximately 2 h, even in less experienced hands. Materials and Methods: This study aims to validate this methodology to detect KRAS mutations on archival cytological preparations of pancreatic cancer (n = 9) and mCRC (n = 9) by comparing the Idylla™ performance to that of standard real-time polymerase chain reaction. Results: The same 11 mutations (n = 4: p.G12D; n = 2: p.G12V; n = 2: p.A59E/G/T; n = 1: p.G12R; n = 1: p.G13D; n = 1: p.Q61H) were detected by both techniques. Conclusion: Even in less experienced laboratories, a cytopathologist may easily integrate morphological diagnostic report with accurate KRAS mutation detection, which is relevant for diagnostic and treatment decisions.
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Affiliation(s)
- Caterina De Luca
- Address: Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Elena Vigliar
- Address: Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Melania d'Anna
- Address: Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Pasquale Pisapia
- Address: Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Claudio Bellevicine
- Address: Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Umberto Malapelle
- Address: Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Giancarlo Troncone
- Address: Department of Public Health, University of Naples Federico II, Naples, Italy
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