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Nguyen TPX, Roytrakul S, Buranapraditkun S, Shuangshoti S, Kitkumthorn N, Keelawat S. Proteomics profile in encapsulated follicular patterned thyroid neoplasms. Sci Rep 2024; 14:16343. [PMID: 39013964 PMCID: PMC11252349 DOI: 10.1038/s41598-024-67079-6] [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: 03/12/2024] [Accepted: 07/08/2024] [Indexed: 07/18/2024] Open
Abstract
Diagnosing encapsulated follicular-patterned thyroid tumors like Invasive Encapsulated Follicular Variant of Papillary Thyroid Carcinoma (IEFVPTC), Non-invasive Follicular Thyroid Neoplasm with Papillary-like Nuclear Features (NIFTP), and Well-Differentiated Tumor of Uncertain Malignant Potential (WDT-UMP) remains challenging due to their morphological and molecular similarities. This study aimed to investigate the protein distinctions among these three thyroid tumors and discover biological tumorigenesis through proteomic analysis. We employed total shotgun proteome analysis allowing to discover the quantitative expression of over 1398 proteins from 12 normal thyroid tissues, 13 IEFVPTC, 11 NIFTP, and 10 WDT-UMP. Principal component analysis revealed a distinct separation of IEFVPTC and normal tissue samples, distinguishing them from the low-risk tumor group (NIFTP and WDT-UMP). IEFVPTC exhibited the highest number of differentially expressed proteins (DEPs) compared to the other tumors. No discriminatory proteins between NIFTP and WDT-UMP were identified. Moreover, DEPs in IEFVPTC were significantly associated with thyroid tumor progression pathways. Certain hub genes linked to the response of immune checkpoint inhibitor therapy, revealing the potential predictor of prognosis. In conclusion, the proteomic profile of IEFVPTC differs from that of low-risk tumors. These findings may provide valuable insights into tumor biology and offer a basis for developing novel therapeutic strategies for follicular-patterned thyroid neoplasms.
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Affiliation(s)
- Truong Phan-Xuan Nguyen
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Sittiruk Roytrakul
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani 12120, Thailand
| | - Supranee Buranapraditkun
- Division of Allergy and Clinical Immunology, Department of Medicine, King Chulalongkorn Memorial Hospital, Faculty of Medicine, Chulalongkorn University, Thai Red Cross Society, Bangkok, 10330, Thailand
- Center of Excellence in Thai Pediatric Gastroenterology, Hepatology and Immunology (TPGHAI), Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Shanop Shuangshoti
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Chulalongkorn GenePRO Center, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Nakarin Kitkumthorn
- Department of Oral Biology, Faculty of Dentistry, Mahidol University, Bangkok, 10330, Thailand.
| | - Somboon Keelawat
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.
- Precision Pathology of Neoplasia Research Group, Department of Pathology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.
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Zhao D, Luo M, Zeng M, Yang Z, Guan Q, Wan X, Wang Y, Zhang H, Wang Y, Lu H, Xiang J. Deep convolutional neural network model ResNeSt for discrimination of papillary thyroid carcinomas and benign nodules in thyroid nodules diagnosed as atypia of undetermined significance. Gland Surg 2024; 13:619-629. [PMID: 38845827 PMCID: PMC11150190 DOI: 10.21037/gs-23-486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 04/11/2024] [Indexed: 06/09/2024]
Abstract
Background A deep convolutional neural network (DCNN) model was employed for the differentiation of thyroid nodules diagnosed as atypia of undetermined significance (AUS) according to the 2023 Bethesda System for Reporting Thyroid Cytopathology (TBSRTC). The aim of this study was to investigate the efficiency of ResNeSt in improving the diagnostic accuracy of fine-needle aspiration (FNA) biopsy. Methods Fragmented images were used to train and test DCNN models. A training dataset was built from 1,330 samples diagnosed as papillary thyroid carcinoma (PTC) or benign nodules, and a test dataset was built from 173 samples diagnosed as AUS. ResNeSt was trained and tested to provide a differentiation. With regard to AUS samples, the characteristics of the cell nuclei were compared using the Wilcoxon test. Results The ResNeSt model achieved an accuracy of 92.49% (160/173) on fragmented images and 84.78% (39/46) from a patient wise viewpoint in discrimination of PTC and benign nodules in AUS nodules. The sensitivity and specificity of ResNeSt model were 95.79% and 88.46%. The κ value between ResNeSt and the pathological results was 0.847 (P<0.001). With regard to the cell nuclei of AUS nodules, both area and perimeter of malignant nodules were larger than those of benign ones, which were 2,340.00 (1,769.00, 2,807.00) vs. 1,941.00 (1,567.50, 2,455.75), P<0.001 and 190.46 (167.64, 208.46) vs. 171.71 (154.95, 193.65), P<0.001, respectively. The grayscale (0 for black, 255 for white) of malignant lesions was lower than that of benign ones, which was 37.52 (31.41, 46.67) vs. 45.84 (31.88, 57.36), P <0.001, indicating nuclear staining of malignant lesions were deeper than benign ones. Conclusions In summary, the DCNN model ResNeSt showed great potential in discriminating thyroid nodules diagnosed as AUS. Among those nodules, malignant nodules showed larger and more deeply stained nuclei than benign nodules.
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Affiliation(s)
- Dan Zhao
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Mukun Luo
- Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Min Zeng
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Nursing Administration, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Zhou Yang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qing Guan
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaochun Wan
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yu Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hao Zhang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yunjun Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hongtao Lu
- Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Jun Xiang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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Hu P, Luo S, Qu G, Luo Q, Tian Y, Huang K, Sun T. Identification and validation of feature genes associated with M1 macrophages in preeclampsia. Aging (Albany NY) 2023; 15:13822-13839. [PMID: 38048229 PMCID: PMC10756132 DOI: 10.18632/aging.205264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/23/2023] [Indexed: 12/06/2023]
Abstract
Preeclampsia (PE) is a pregnancy-specific cardiovascular complication that is the leading cause of maternal and neonatal morbidity and mortality. Previous studies have indicated the importance of immune cells, such as M1 and M2 macrophages, in the pathogenesis of PE. However, the mechanisms leading to immune dysregulation are unclear. Data-independent acquisition proteomic analysis was performed on placental tissues collected from patients with PE and healthy controls. Transcriptome data for placenta samples from patients with PE and their corresponding controls were obtained from the Gene Expression Omnibus database. Differential analysis of transcriptome and proteome data between PE and control groups was performed using R software. Immunocytic infiltration scoring was performed using the quantiseq algorithm. Weighted gene co-expression network analysis (WGCNA) screened for feature genes associated with M1 cell infiltration. Protein-protein interaction (PPI) analysis identified hub genes. We confirm that the infiltration score of M1 macrophages was significantly increased in the placental tissues of patients with PE. Differential analysis, WGCNA, and PPI analysis identified four hub molecules associated with M1 cell infiltration (HTRA4, POGK, MFAP5, and INHBA). The hub molecules displayed dysregulated expression in PE tissues. The qPCR, Western blots, and immunohistochemistry analyses confirmed that Inhibin, beta A (INHBA) was highly expressed in placental tissues of patients with PE. Immunofluorescence revealed the extensive infiltration of M1 macrophages in the placental tissues of patients with PE and their co-localization with INHBA. The collective results identified hub genes associated with M1 macrophage infiltration, providing potential targets for the pathogenesis and treatment of PE.
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Affiliation(s)
- Panpan Hu
- Department of Gerontology, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Shanshun Luo
- Department of Gerontology, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Guangjin Qu
- Department of Gerontology, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Qiqi Luo
- Department of Gerontology, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Yu Tian
- Department of Gerontology, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Kun Huang
- Department of Gerontology, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Tingting Sun
- Department of Gerontology, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
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Piga I, L'Imperio V, Capitoli G, Denti V, Smith A, Magni F, Pagni F. Paving the path toward multi-omics approaches in the diagnostic challenges faced in thyroid pathology. Expert Rev Proteomics 2023; 20:419-437. [PMID: 38000782 DOI: 10.1080/14789450.2023.2288222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/22/2023] [Indexed: 11/26/2023]
Abstract
INTRODUCTION Despite advancements in diagnostic methods, the classification of indeterminate thyroid nodules still poses diagnostic challenges not only in pre-surgical evaluation but even after histological evaluation of surgical specimens. Proteomics, aided by mass spectrometry and integrated with artificial intelligence and machine learning algorithms, shows great promise in identifying diagnostic markers for thyroid lesions. AREAS COVERED This review provides in-depth exploration of how proteomics has contributed to the understanding of thyroid pathology. It discusses the technical advancements related to immunohistochemistry, genetic and proteomic techniques, such as mass spectrometry, which have greatly improved sensitivity and spatial resolution up to single-cell level. These improvements allowed the identification of specific protein signatures associated with different types of thyroid lesions. EXPERT COMMENTARY Among all the proteomics approaches, spatial proteomics stands out due to its unique ability to capture the spatial context of proteins in both cytological and tissue thyroid samples. The integration of multi-layers of molecular information combining spatial proteomics, genomics, immunohistochemistry or metabolomics and the implementation of artificial intelligence and machine learning approaches, represent hugely promising steps forward toward the possibility to uncover intricate relationships and interactions among various molecular components, providing a complete picture of the biological landscape whilst fostering thyroid nodule diagnosis.
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Affiliation(s)
- Isabella Piga
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano - Bicocca, Monza, Italy
| | - Vincenzo L'Imperio
- Department of Medicine and Surgery, Pathology, Fondazione IRCCS San Gerardo dei Tintori, University of Milan-Bicocca, Monza, Italy
| | - Giulia Capitoli
- Department of Medicine and Surgery, Bicocca Bioinformatics Biostatistics and Bioimaging B4 Center, University of Milan - Bicocca (UNIMIB), Monza, Italy
| | - Vanna Denti
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano - Bicocca, Monza, Italy
| | - Andrew Smith
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano - Bicocca, Monza, Italy
| | - Fulvio Magni
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano - Bicocca, Monza, Italy
| | - Fabio Pagni
- Department of Medicine and Surgery, Pathology, Fondazione IRCCS San Gerardo dei Tintori, University of Milan-Bicocca, Monza, Italy
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Luvhengo TE, Bombil I, Mokhtari A, Moeng MS, Demetriou D, Sanders C, Dlamini Z. Multi-Omics and Management of Follicular Carcinoma of the Thyroid. Biomedicines 2023; 11:biomedicines11041217. [PMID: 37189835 DOI: 10.3390/biomedicines11041217] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/05/2023] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
Follicular thyroid carcinoma (FTC) is the second most common cancer of the thyroid gland, accounting for up to 20% of all primary malignant tumors in iodine-replete areas. The diagnostic work-up, staging, risk stratification, management, and follow-up strategies in patients who have FTC are modeled after those of papillary thyroid carcinoma (PTC), even though FTC is more aggressive. FTC has a greater propensity for haematogenous metastasis than PTC. Furthermore, FTC is a phenotypically and genotypically heterogeneous disease. The diagnosis and identification of markers of an aggressive FTC depend on the expertise and thoroughness of pathologists during histopathological analysis. An untreated or metastatic FTC is likely to de-differentiate and become poorly differentiated or undifferentiated and resistant to standard treatment. While thyroid lobectomy is adequate for the treatment of selected patients who have low-risk FTC, it is not advisable for patients whose tumor is larger than 4 cm in diameter or has extensive extra-thyroidal extension. Lobectomy is also not adequate for tumors that have aggressive mutations. Although the prognosis for over 80% of PTC and FTC is good, nearly 20% of the tumors behave aggressively. The introduction of radiomics, pathomics, genomics, transcriptomics, metabolomics, and liquid biopsy have led to improvements in the understanding of tumorigenesis, progression, treatment response, and prognostication of thyroid cancer. The article reviews the challenges that are encountered during the diagnostic work-up, staging, risk stratification, management, and follow-up of patients who have FTC. How the application of multi-omics can strengthen decision-making during the management of follicular carcinoma is also discussed.
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Affiliation(s)
- Thifhelimbilu Emmanuel Luvhengo
- Department of Surgery, Charlotte Maxeke Johannesburg Academic Hospital, University of the Witwatersrand, Parktown, Johannesburg 2193, South Africa
| | - Ifongo Bombil
- Department of Surgery, Chris Hani Baragwanath Academic Hospital, University of the Witwatersrand, Johannesburg 1864, South Africa
| | - Arian Mokhtari
- Department of Surgery, Dr. George Mukhari Academic Hospital, Sefako Makgatho Health Sciences University, Ga-Rankuwa 0208, South Africa
| | - Maeyane Stephens Moeng
- Department of Surgery, Charlotte Maxeke Johannesburg Academic Hospital, University of the Witwatersrand, Parktown, Johannesburg 2193, South Africa
| | - Demetra Demetriou
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Cancer Research Institute (PACRI), University of Pretoria, Hatfield 0028, South Africa
| | - Claire Sanders
- Department of Surgery, Helen Joseph Hospital, University of the Witwatersrand, Auckland Park, Johannesburg 2006, South Africa
| | - Zodwa Dlamini
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Cancer Research Institute (PACRI), University of Pretoria, Hatfield 0028, South Africa
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