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Craig S, Stretch C, Farshidfar F, Sheka D, Alabi N, Siddiqui A, Kopciuk K, Park YJ, Khalil M, Khan F, Harvey A, Bathe OF. A clinically useful and biologically informative genomic classifier for papillary thyroid cancer. Front Endocrinol (Lausanne) 2023; 14:1220617. [PMID: 37772080 PMCID: PMC10523308 DOI: 10.3389/fendo.2023.1220617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/22/2023] [Indexed: 09/30/2023] Open
Abstract
Clinical management of papillary thyroid cancer depends on estimations of prognosis. Standard care, which relies on prognostication based on clinicopathologic features, is inaccurate. We applied a machine learning algorithm (HighLifeR) to 502 cases annotated by The Cancer Genome Atlas Project to derive an accurate molecular prognostic classifier. Unsupervised analysis of the 82 genes that were most closely associated with recurrence after surgery enabled the identification of three unique molecular subtypes. One subtype had a high recurrence rate, an immunosuppressed microenvironment, and enrichment of the EZH2-HOTAIR pathway. Two other unique molecular subtypes with a lower rate of recurrence were identified, including one subtype with a paucity of BRAFV600E mutations and a high rate of RAS mutations. The genomic risk classifier, in addition to tumor size and lymph node status, enabled effective prognostication that outperformed the American Thyroid Association clinical risk stratification. The genomic classifier we derived can potentially be applied preoperatively to direct clinical decision-making. Distinct biological features of molecular subtypes also have implications regarding sensitivity to radioactive iodine, EZH2 inhibitors, and immune checkpoint inhibitors.
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Affiliation(s)
- Steven Craig
- Department of Surgery, Illawarra Shoalhaven Local Health District, Wollongong, NSW, Australia
- Graduate School of Medicine, University of Wollongong, Wollongong, NSW, Australia
| | - Cynthia Stretch
- Department of Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Farshad Farshidfar
- Department of Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Dropen Sheka
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Nikolay Alabi
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Ashar Siddiqui
- O’Brien Centre for the Bachelor of Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Karen Kopciuk
- Department of Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Cancer Epidemiology and Prevention Research, Alberta Health Services, Calgary, AB, Canada
| | - Young Joo Park
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea
| | - Moosa Khalil
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Faisal Khan
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- OncoHelix, Calgary, AB, Canada
| | - Adrian Harvey
- Department of Surgery, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Oliver F. Bathe
- Department of Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Surgery, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Research and Development, Qualisure Diagnostics Inc., Calgary, AB, Canada
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Yoon J, Kym D, Hur J, Won JH, Yim H, Cho YS, Chun W. Time-varying discrimination accuracy of longitudinal biomarkers for the prediction of mortality compared to assessment at fixed time point in severe burns patients. BMC Emerg Med 2021; 21:1. [PMID: 33407163 PMCID: PMC7786914 DOI: 10.1186/s12873-020-00394-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/11/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The progression of biomarkers over time is considered an indicator of disease progression and helps in the early detection of disease, thereby reducing disease-related mortality. Their ability to predict outcomes has been evaluated using conventional cross-sectional methods. This study investigated the prognostic performance of biomarkers over time. METHODS Patients aged > 18 years admitted to the burn intensive care unit within 24 h of a burn incident were enrolled. Information regarding longitudinal biomarkers, including white blood cells; platelet count; lactate, creatinine, and total bilirubin levels; and prothrombin time (PT), were retrieved from a clinical database. Time-dependent receiver operating characteristic curves using cumulative/dynamic and incident/dynamic (ID) approaches were used to evaluate prognostic performance. RESULTS Overall, 2259 patients were included and divided into survival and non-survival groups. By determining the area under the curve using the ID approach, platelets showed the highest c-index [0.930 (0.919-0.941)] across all time points. Conversely, the c-index of PT and creatinine levels were 0.862 (0.843-0.881) and 0.828 (0.809-0.848), respectively. CONCLUSIONS Platelet count was the best prognostic marker, followed by PT. Total bilirubin and creatinine levels also showed good prognostic ability. Although lactate was a strong predictor, it showed relatively poor prognostic performance in burns patients.
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Affiliation(s)
- Jaechul Yoon
- Department of Surgery and Critical Care, Burn Center, Hangang Sacred Heart Hospital, College of Medicine, Hallym University Medical Center, 12, Beodeunaru-ro 7-gil, Youngdeungpo-gu, Seoul, 07247, South Korea
- Graduate School of Medicine, Kangwon National University, Chuncheon, Republic of Korea
| | - Dohern Kym
- Department of Surgery and Critical Care, Burn Center, Hangang Sacred Heart Hospital, College of Medicine, Hallym University Medical Center, 12, Beodeunaru-ro 7-gil, Youngdeungpo-gu, Seoul, 07247, South Korea
| | - Jun Hur
- Department of Surgery and Critical Care, Burn Center, Hangang Sacred Heart Hospital, College of Medicine, Hallym University Medical Center, 12, Beodeunaru-ro 7-gil, Youngdeungpo-gu, Seoul, 07247, South Korea.
| | - Jae Hee Won
- Department of Surgery and Critical Care, Burn Center, Hangang Sacred Heart Hospital, College of Medicine, Hallym University Medical Center, 12, Beodeunaru-ro 7-gil, Youngdeungpo-gu, Seoul, 07247, South Korea
| | - Haejun Yim
- Department of Surgery and Critical Care, Burn Center, Hangang Sacred Heart Hospital, College of Medicine, Hallym University Medical Center, 12, Beodeunaru-ro 7-gil, Youngdeungpo-gu, Seoul, 07247, South Korea
| | - Yong Suk Cho
- Department of Surgery and Critical Care, Burn Center, Hangang Sacred Heart Hospital, College of Medicine, Hallym University Medical Center, 12, Beodeunaru-ro 7-gil, Youngdeungpo-gu, Seoul, 07247, South Korea
| | - Wook Chun
- Department of Surgery and Critical Care, Burn Center, Hangang Sacred Heart Hospital, College of Medicine, Hallym University Medical Center, 12, Beodeunaru-ro 7-gil, Youngdeungpo-gu, Seoul, 07247, South Korea
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