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Alzumaili B, Sadow PM. Update on Molecular Diagnostics in Thyroid Pathology: A Review. Genes (Basel) 2023; 14:1314. [PMID: 37510219 PMCID: PMC10379610 DOI: 10.3390/genes14071314] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/13/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
Thyroid nodules are quite common, and the determination of a nodule of concern is complex, involving serum testing, radiology and, in some cases, pathological evaluation. For those nodules that raise clinical concern of neoplasia, fine needle aspiration biopsy is the gold standard for evaluation; however, in up to 30% of cases, results are indeterminate for malignancy, and further testing is needed. Advances in molecular testing have shown it to be of benefit for both diagnostic and prognostic purposes, and its use has become an integral part of thyroid cancer management in the United States and in several global nations. After The Cancer Genome Atlas (TCGA) consortium published its molecular landscape of papillary thyroid carcinoma (PTC) and reduced the "black matter" in PTC from 25% to 3.5%, further work ensued to clarify the remaining fraction not neatly attributed to the BRAFV600E-like or RAS-like phenotypes of the TCGA. Over the past decade, commercial molecular platforms have been refined as data accrues, and they increasingly cover most genetic variants of thyroid carcinomas. Molecular reporting focuses on the nodule tested, including related clinical information for that nodule (size of nodule, Bethesda category, etc.). This results in a comprehensive report to physicians that may also include patient-directed, clear language that facilitates conversations about nodule management. In cases of advanced or recurrent disease, molecular testing may become essential for devising an individual therapeutic plan. In this review, we focus on the evolution of integrated molecular testing in thyroid nodules, and how our understanding of tumor genetics, combined with histopathology, is driving the next generation of rational patient management, particularly in the context of emerging small, targetable therapeutics.
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Affiliation(s)
- Bayan Alzumaili
- Departments of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Peter M Sadow
- Departments of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
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Huber F, Lang HP, Heller S, Bielicki JA, Gerber C, Meyer E, Egli A. Rapid Bacteria Detection from Patients' Blood Bypassing Classical Bacterial Culturing. BIOSENSORS 2022; 12:994. [PMID: 36354504 PMCID: PMC9688106 DOI: 10.3390/bios12110994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/26/2022] [Accepted: 11/08/2022] [Indexed: 06/16/2023]
Abstract
Sepsis is a life-threatening condition mostly caused by a bacterial infection resulting in inflammatory reaction and organ dysfunction if not treated effectively. Rapid identification of the causing bacterial pathogen already in the early stage of bacteremia is therefore vital. Current technologies still rely on time-consuming procedures including bacterial culturing up to 72 h. Our approach is based on ultra-rapid and highly sensitive nanomechanical sensor arrays. In measurements we observe two clearly distinguishable distributions consisting of samples with bacteria and without bacteria respectively. Compressive surface stress indicates the presence of bacteria. For this proof-of-concept, we extracted total RNA from EDTA whole blood samples from patients with blood-culture-confirmed bacteremia, which is the reference standard in diagnostics. We determined the presence or absence of bacterial RNA in the sample through 16S-rRNA hybridization and species-specific probes using nanomechanical sensor arrays. Via both probes, we identified two clinically highly-relevant bacterial species i.e., Escherichia coli and Staphylococcus aureus down to an equivalent of 20 CFU per milliliter EDTA whole blood. The dynamic range of three orders of magnitude covers most clinical cases. We correctly identified all patient samples regarding the presence or absence of bacteria. We envision our technology as an important contribution to early and sensitive sepsis diagnosis directly from blood without requirement for cultivation. This would be a game changer in diagnostics, as no commercial PCR or POCT device currently exists who can do this.
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Affiliation(s)
- François Huber
- Swiss Nanoscience Institute (SNI), Department of Physics, University of Basel, CH-4056 Basel, Switzerland
| | - Hans Peter Lang
- Swiss Nanoscience Institute (SNI), Department of Physics, University of Basel, CH-4056 Basel, Switzerland
| | - Stefanie Heller
- Applied Microbiology Research (Lab 315), Zentrum für Lehre und Forschung, Department of Biomedicine, University of Basel, CH-4031 Basel, Switzerland
| | - Julia Anna Bielicki
- University Children’s Hospital Basel (UKBB), Department of Medicine, University of Basel, CH-4056 Basel, Switzerland
| | - Christoph Gerber
- Swiss Nanoscience Institute (SNI), Department of Physics, University of Basel, CH-4056 Basel, Switzerland
| | - Ernst Meyer
- Swiss Nanoscience Institute (SNI), Department of Physics, University of Basel, CH-4056 Basel, Switzerland
| | - Adrian Egli
- Applied Microbiology Research (Lab 315), Zentrum für Lehre und Forschung, Department of Biomedicine, University of Basel, CH-4031 Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, CH-4031 Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, CH-8006 Zurich, Switzerland
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Poberezhnyi V, Marchuk O, Katilov O, Shvydiuk O, Lohvinov O. Basic concepts and physical-chemical phenomena, that have conceptual meaning for the formation of systemic clinical thinking and formalization of the knowledge of systemic structural-functional organization of the human’s organism. PAIN MEDICINE 2020. [DOI: 10.31636/pmjua.v5i2.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
From the point of view of perception and generalization processes there are complex, logic and conceptual forms of thinking. Its conceptual form is the highest result of interaction between thinking and speech. While realizing it, human uses the concept, which are logically formed thoughts, that are the meaning of representation in thinking of unity of meaningful features, relations of subjects or phenomena of objective reality. Special concepts, that are used in the science and technique are called terms. They perform a function of corresponding, special, precise marking of subjects and phenomena, their features and interactions. Scientific knowledge are in that way an objective representation of material duality in our consciousness. Certain complex of terms forms a terminological system, that lies in the basis of corresponding sphere of scientific knowledge and conditions a corresponding form and way of thinking. Clinical thinking is a conceptual form, that manifests and represents by the specialized internal speech with gnostic motivation lying in its basis. Its structural elements are corresponding definitions, terms and concepts. Cardinal features of clinical systems are consistency, criticality, justification and substantiation. Principles of perception and main concepts are represented in the article along with short descriptions of physical and chemical phenomena, that have conceptual meaning for the formation of systematic clinical thinking and formalization of systemic structural-functional organization of the human’s organism
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Wu L, Garrido-Maestu A, Guerreiro JRL, Carvalho S, Abalde-Cela S, Prado M, Diéguez L. Amplification-free SERS analysis of DNA mutation in cancer cells with single-base sensitivity. NANOSCALE 2019; 11:7781-7789. [PMID: 30951061 DOI: 10.1039/c9nr00501c] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Accurate and sensitive identification of DNA mutations in tumor cells is critical to the diagnosis, prognosis and personalized therapy of cancer. Conventional polymerase chain reaction (PCR)-based methods are limited by the complicated amplification process. Herein, an amplification-free surface enhanced Raman spectroscopy (SERS) approach which directly detects point mutations in cancer cells has been proposed. A highly sensitive and uniform SERS substrate was fabricated using gold@silver core-shell nanorods, achieving an enhancement factor of 1.85 × 106. By combining the SERS-active nanosubstrate with molecular beacon probes, the limit of detection reached as low as 50 fM. To enable parallel analysis and automated operation, the SERS sensor was integrated into a microfluidic chip. This novel chip-based assay was able to differentiate between mutated and wild-type KRAS genes among a variety of other nucleic acids from cancer cells in 40 min. Owing to the simple operation and fast analysis, the SERS-based DNA assay chip could potentially provide insights into clinical cancer theranostics in an easy and inexpensive manner at the point of care.
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Affiliation(s)
- Lei Wu
- International Iberian Nanotechnology Laboratory (INL), 4715-330 Braga, Portugal.
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Domínguez CM, Ramos D, Mingorance J, Fierro JLG, Tamayo J, Calleja M. Direct Detection of OXA-48 Carbapenemase Gene in Lysate Samples through Changes in Mechanical Properties of DNA Monolayers upon Hybridization. Anal Chem 2018; 90:968-973. [PMID: 29186953 DOI: 10.1021/acs.analchem.7b04094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Carbapenem-resistant Enterobacteriaceae have recently become an important cause of morbidity and mortality due to healthcare-associated infections. Most commonly used diagnostic methods are incompatible with fast and accurate directed therapy. We report here the direct identification of the blaOXA48 gene, which codes for the carbapenemase OXA-48, in lysate samples from Klebsiella pneumoniae. The method is PCR-free and label-free. It is based on the measurement of changes in the stiffness of DNA self-assembled monolayers anchored to microcantilevers that occur as a consequence of the hybridization. The stiffness of the DNA layer is measured through changes of the sensor resonance frequency upon hybridization and at varying relative humidity.
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Affiliation(s)
- Carmen M Domínguez
- IMN-Instituto de Micro y Nanotecnología (CNM-CSIC) , Isaac Newton 8, PTM, Tres Cantos, Madrid E-28760, Spain
| | - Daniel Ramos
- IMN-Instituto de Micro y Nanotecnología (CNM-CSIC) , Isaac Newton 8, PTM, Tres Cantos, Madrid E-28760, Spain
| | - Jesús Mingorance
- Servicio de Microbiología, Hospital Universitario La Paz , IdiPAZ, Paseo de la Castellana, 261, Madrid, E-28046, Spain
| | - José L G Fierro
- ICP-Instituto de Catálisis y Petroleoquímica (CSIC) , Marie Curie, 2 Cantoblanco, Madrid, E-28049, Spain
| | - Javier Tamayo
- IMN-Instituto de Micro y Nanotecnología (CNM-CSIC) , Isaac Newton 8, PTM, Tres Cantos, Madrid E-28760, Spain
| | - Montserrat Calleja
- IMN-Instituto de Micro y Nanotecnología (CNM-CSIC) , Isaac Newton 8, PTM, Tres Cantos, Madrid E-28760, Spain
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Wu S, Zhang Z, Zhou X, Liu H, Xue C, Zhao G, Cao Y, Zhang Q, Wu X. Nanomechanical sensors for direct and rapid characterization of sperm motility based on nanoscale vibrations. NANOSCALE 2017; 9:18258-18267. [PMID: 28890972 DOI: 10.1039/c7nr03688d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Infertility, whether of male or female origin, is a critical challenge facing the low birth rate and aging population throughout the world, and semen analysis is a cornerstone of the diagnostic evaluation of the male contribution to infertility. This means that tools which can characterize sperm properties in an effective manner are very much needed. The conventional approaches are essentially image-based, which have a limited value for analyzing sperm properties. Here, we show that an assay using nanomechanical sensors can detect sperm motility based on nanomotion. We use microcantilever sensors to directly characterize the mechanical response of the sperm based on the fluctuations of microcantilevers. We applied this methodology to sperms exposed to different chemical or physical agents. Real-time nanomechanical fluctuations showed that living sperms produced smaller fluctuations after treatment with inhibitory chemicals, and larger fluctuations after treatment with stimulatory chemicals. Our preliminary experiments suggest that the frequency of fluctuation is associated with sperm motility. This technique offers a brand-new perspective in the characterization of the sperm. By combining conventional measurements, reproductive medicine doctors and researchers should now be able to achieve unprecedented depth in the sperm properties.
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Affiliation(s)
- Shangquan Wu
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei 230027, China.
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