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Olmos R, Domínguez JM, Vargas-Salas S, Mosso L, Fardella CE, González G, Baudrand R, Guarda F, Valenzuela F, Arteaga E, Forenzano P, Nilo F, Lustig N, Martínez A, López JM, Cruz F, Loyola S, Leon A, Droppelmann N, Montero P, Domínguez F, Camus M, Solar A, Zoroquiain P, Roa JC, Muñoz E, Bruce E, Gajardo R, Miranda G, Riquelme F, Mena N, González HE. ThyroidPrint®: clinical utility for indeterminate thyroid cytology. Endocr Relat Cancer 2023; 30:e220409. [PMID: 37671897 PMCID: PMC10563504 DOI: 10.1530/erc-22-0409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 09/06/2023] [Indexed: 09/07/2023]
Abstract
Molecular testing contributes to improving the diagnosis of indeterminate thyroid nodules (ITNs). ThyroidPrint® is a ten-gene classifier aimed to rule out malignancy in ITN. Post-validation studies are necessary to determine the real-world clinical benefit of ThyroidPrint® in patients with ITN. A single-center, prospective, noninterventional clinical utility study was performed, analyzing the impact of ThyroidPrint® in the physicians' clinical decisions for ITN. Demographics, nodule characteristics, benign call rates (BCRs), and surgical outcomes were measured. Histopathological data were collected from surgical biopsies of resected nodules. Of 1272 fine-needle aspirations, 109 (8.6%) were Bethesda III and 135 (10.6%) were Bethesda IV. Molecular testing was performed in 155 of 244 ITN (63.5%), of which 104 were classified as benign (BCR of 67.1%). After a median follow-up of 15 months, 103 of 104 (99.0%) patients with a benign ThyroidPrint® remained under surveillance and one patient underwent surgery which was a follicular adenoma. Surgery was performed in all 51 patients with a suspicious for malignancy as per ThyroidPrint® result and in 56 patients who did not undergo testing, with a rate of malignancy of 70.6% and 32.1%, respectively. A higher BCR was observed in follicular lesion of undetermined significance (87%) compared to atypia of undetermined significance (58%) (P < 0.05). False-positive cases included four benign follicular nodules and six follicular and four oncocytic adenomas. Our results show that, physicians chose active surveillance instead of diagnostic surgery in all patients with a benign ThyroidPrint® result, reducing the need for diagnostic surgery in 67% of patients with preoperative diagnosis of ITN.
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Affiliation(s)
- Roberto Olmos
- Department of Endocrinology, School of Medicine Pontificia Universidad Católica de Chile
| | - José Miguel Domínguez
- Department of Endocrinology, School of Medicine Pontificia Universidad Católica de Chile
| | - Sergio Vargas-Salas
- Department of Surgical Oncology, School of Medicine Pontificia Universidad Católica de Chile
| | - Lorena Mosso
- Department of Endocrinology, School of Medicine Pontificia Universidad Católica de Chile
| | - Carlos E Fardella
- Department of Endocrinology, School of Medicine Pontificia Universidad Católica de Chile
| | - Gilberto González
- Department of Endocrinology, School of Medicine Pontificia Universidad Católica de Chile
| | - René Baudrand
- Department of Endocrinology, School of Medicine Pontificia Universidad Católica de Chile
| | - Francisco Guarda
- Department of Endocrinology, School of Medicine Pontificia Universidad Católica de Chile
| | - Felipe Valenzuela
- Department of Endocrinology, School of Medicine Pontificia Universidad Católica de Chile
| | - Eugenio Arteaga
- Department of Endocrinology, School of Medicine Pontificia Universidad Católica de Chile
| | - Pablo Forenzano
- Department of Endocrinology, School of Medicine Pontificia Universidad Católica de Chile
| | - Flavia Nilo
- Department of Endocrinology, School of Medicine Pontificia Universidad Católica de Chile
| | - Nicole Lustig
- Department of Endocrinology, School of Medicine Pontificia Universidad Católica de Chile
| | - Alejandra Martínez
- Department of Endocrinology, School of Medicine Pontificia Universidad Católica de Chile
| | - José M López
- Department of Endocrinology, School of Medicine Pontificia Universidad Católica de Chile
| | - Francisco Cruz
- Department of Radiology, School of Medicine Pontificia Universidad Católica de Chile
| | - Soledad Loyola
- Department of Radiology, School of Medicine Pontificia Universidad Católica de Chile
| | - Augusto Leon
- Department of Surgical Oncology, School of Medicine Pontificia Universidad Católica de Chile
| | - Nicolás Droppelmann
- Department of Surgical Oncology, School of Medicine Pontificia Universidad Católica de Chile
| | - Pablo Montero
- Department of Surgical Oncology, School of Medicine Pontificia Universidad Católica de Chile
| | - Francisco Domínguez
- Department of Surgical Oncology, School of Medicine Pontificia Universidad Católica de Chile
| | - Mauricio Camus
- Department of Surgical Oncology, School of Medicine Pontificia Universidad Católica de Chile
| | - Antonieta Solar
- Department of Anatomic Pathology, School of Medicine Pontificia Universidad Católica de Chile
| | - Pablo Zoroquiain
- Department of Anatomic Pathology, School of Medicine Pontificia Universidad Católica de Chile
| | - Juan Carlos Roa
- Department of Anatomic Pathology, School of Medicine Pontificia Universidad Católica de Chile
| | - Estefanía Muñoz
- Department of Surgical Oncology, School of Medicine Pontificia Universidad Católica de Chile
| | - Elsa Bruce
- Department of Surgical Oncology, School of Medicine Pontificia Universidad Católica de Chile
| | - Rossio Gajardo
- Department of Surgical Oncology, School of Medicine Pontificia Universidad Católica de Chile
| | - Giovanna Miranda
- Department of Surgical Oncology, School of Medicine Pontificia Universidad Católica de Chile
| | - Francisco Riquelme
- Department of Surgical Oncology, School of Medicine Pontificia Universidad Católica de Chile
| | - Natalia Mena
- Department of Surgical Oncology, School of Medicine Pontificia Universidad Católica de Chile
| | - Hernán E González
- Department of Surgical Oncology, School of Medicine Pontificia Universidad Católica de Chile
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van der Linden AJ, Pieters PA, Bartelds MW, Nathalia BL, Yin P, Huck WTS, Kim J, de Greef TFA. DNA Input Classification by a Riboregulator-Based Cell-Free Perceptron. ACS Synth Biol 2022; 11:1510-1520. [PMID: 35381174 PMCID: PMC9016768 DOI: 10.1021/acssynbio.1c00596] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ability to recognize molecular patterns is essential for the continued survival of biological organisms, allowing them to sense and respond to their immediate environment. The design of synthetic gene-based classifiers has been explored previously; however, prior strategies have focused primarily on DNA strand-displacement reactions. Here, we present a synthetic in vitro transcription and translation (TXTL)-based perceptron consisting of a weighted sum operation (WSO) coupled to a downstream thresholding function. We demonstrate the application of toehold switch riboregulators to construct a TXTL-based WSO circuit that converts DNA inputs into a GFP output, the concentration of which correlates to the input pattern and the corresponding weights. We exploit the modular nature of the WSO circuit by changing the output protein to the Escherichia coli σ28-factor, facilitating the coupling of the WSO output to a downstream reporter network. The subsequent introduction of a σ28 inhibitor enabled thresholding of the WSO output such that the expression of the downstream reporter protein occurs only when the produced σ28 exceeds this threshold. In this manner, we demonstrate a genetically implemented perceptron capable of binary classification, i.e., the expression of a single output protein only when the desired minimum number of inputs is exceeded.
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Affiliation(s)
- Ardjan J. van der Linden
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Pascal A. Pieters
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Mart W. Bartelds
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Bryan L. Nathalia
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Wilhelm T. S. Huck
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Jongmin Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Tom F. A. de Greef
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands
- Center for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, 3584 CB Utrecht, The Netherlands
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Ragia G, Manolopoulos VG. Assessing COVID-19 susceptibility through analysis of the genetic and epigenetic diversity of ACE2-mediated SARS-CoV-2 entry. Pharmacogenomics 2020; 21:1311-1329. [PMID: 33243086 PMCID: PMC7694444 DOI: 10.2217/pgs-2020-0092] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
There is considerable variation in disease course among individuals infected with SARS-CoV-2. Many of them do not exhibit any symptoms, while some others proceed to develop COVID-19; however, severity of COVID-19 symptoms greatly differs among individuals. Focusing on the early events related to SARS-CoV-2 entry to cells through the ACE2 pathway, we describe how variability in (epi)genetic factors can conceivably explain variability in disease course. We specifically focus on variations in ACE2, TMPRSS2 and FURIN genes, as central components for SARS-CoV-2 infection, and on other molecules that modulate their expression such as CALM, ADAM-17, AR and ESRs. We propose a genetic classifier for predicting SARS-CoV-2 infectivity potential as a preliminary tool for identifying the at-risk-population. This tool can serve as a dynamic scaffold being updated and adapted to validated (epi)genetic data. Overall, the proposed approach holds potential for better personalization of COVID-19 handling.
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Affiliation(s)
- Georgia Ragia
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, 68100, Greece
| | - Vangelis G Manolopoulos
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, 68100, Greece.,Clinical Pharmacology & Pharmacogenetics Unit, Academic General Hospital of Alexandroupolis, Alexandroupolis, 68100, Greece
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Sayeg MK, Weinberg BH, Cha SS, Goodloe M, Wong WW, Han X. Rationally Designed MicroRNA-Based Genetic Classifiers Target Specific Neurons in the Brain. ACS Synth Biol 2015; 4:788-795. [PMID: 25848814 DOI: 10.1021/acssynbio.5b00040] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Targeting transgene expression to specific cell types in vivo has proven instrumental in characterizing the functional role of defined cell populations. Genetic classifiers, synthetic transgene constructs designed to restrict expression to particular classes of cells, commonly rely on transcriptional promoters to define cellular specificity. However, the large size of many natural promoters complicates their use in viral vectors, an important mode of transgene delivery in the brain and in human gene therapy. Here, we expanded upon an emerging classifier platform, orthogonal to promoter-based strategies, that exploits endogenous microRNA regulation to target gene expression. Such classifiers have been extensively explored in other tissues; however, their use in the nervous system has thus far been limited to targeting gene expression between neurons and supporting cells. Here, we tested the possibility of using combinatory microRNA regulation to specify gene targeting between neuronal subtypes, and successfully targeted inhibitory cells in the neocortex. These classifiers demonstrate the feasibility of designing a new generation of microRNA-based neuron-type- and brain-region-specific gene expression targeting neurotechnologies.
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Affiliation(s)
- Marianna K. Sayeg
- Department of Biomedical
Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Benjamin H. Weinberg
- Department of Biomedical
Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Susie S. Cha
- Department of Biomedical
Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Michael Goodloe
- Department of Biomedical
Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Wilson W. Wong
- Department of Biomedical
Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Xue Han
- Department of Biomedical
Engineering, Boston University, Boston, Massachusetts 02215, United States
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