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Nikiforova MN, Lepe M, Tolino LA, Miller ME, Ohori NP, Wald AI, Landau MS, Kaya C, Malapelle U, Bellevicine C, Troncone G, Nikiforov YE, Baloch Z. Thyroid cytology smear slides: An untapped resource for ThyroSeq testing. Cancer Cytopathol 2020; 129:33-42. [PMID: 32697051 DOI: 10.1002/cncy.22331] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 12/22/2022]
Abstract
BACKGROUND Molecular testing of thyroid nodules with indeterminate fine-needle aspiration (FNA) cytology is commonly used to guide patient management and is typically performed on freshly collected FNA samples. In this study, the authors evaluated the performance of the ThyroSeq test in cytology smear slides. METHODS Air-dried Diff-Quik (DQ)-stained and alcohol-fixed Papanicolaou (Pap)-stained smears were used to determine required cellularity and sensitivity of mutation detection and to compare ThyroSeq v3 Genomic Classifier (GC) results obtained in cytology smears and fresh FNA samples from the same nodules. RESULTS ThyroSeq testing of 31 cytology smears revealed that 25 smears (81%) were adequate for ThyroSeq analysis, including 14 Pap-stained smears (100%) and 11 DQ-stained smears (65%), whereas 6 DQ-stained smears (35%) failed RNA sequencing. The overall accuracy for detecting molecular alterations was 98%, with 100% concordance for mutations and gene expression alterations, 96% concordance for fusions, and 94% concordance for copy number alterations. Cytology smears were adequate for ThyroSeq analysis when at least 200 to 300 cells were present in 1 to 3 slides. ThyroSeq detected all studied mutations down to 5% allele frequency and BRAF mutations down to 1% allele frequency. Testing of smears yielded a positive ThyroSeq GC result in all nodules originally classified as positive. CONCLUSIONS Thyroid FNA cytology smear slides with adequate cellularity can be successfully used for ThyroSeq GC testing in approximately 80% of cases, with an even higher success rate in Pap-stained smears. Compared with FNA samples collected into preservative solution, 94% to 100% of different genetic alterations could be accurately detected in smears, validating cytology smears as an alternative for ThyroSeq testing in patients with indeterminate thyroid cytology.
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Affiliation(s)
- Marina N Nikiforova
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Marcos Lepe
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Medical Center, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Lindsey A Tolino
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Megan E Miller
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - N Paul Ohori
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Abigail I Wald
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Michael S Landau
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Cihan Kaya
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Umberto Malapelle
- Department of Public Health, University of Naples, Federico II, Naples, Italy
| | - Claudio Bellevicine
- Department of Public Health, University of Naples, Federico II, Naples, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples, Federico II, Naples, Italy
| | - Yuri E Nikiforov
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Zubair Baloch
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Medical Center, Perelman School of Medicine, Philadelphia, Pennsylvania
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2
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Abstract
There has been a paradigm shift in the practice of cytopathology with the advent of highly sensitive molecular tests using small amounts of tissue that can provide diagnostic, prognostic, and predictive information for clinical management. The cytopathologist plays a key role in providing a timely and accurate diagnosis as well as ensuring appropriate processing and handling of the specimen and judicious triaging of the tissue for molecular testing that guide therapeutic decisions. As the era of "precision medicine" continues to evolve and expand, cytopathology remains a dynamic field with advances in the practice of molecular cytopathology providing new paradigms in clinical care.
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Affiliation(s)
- Sinchita Roy-Chowdhuri
- Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard Unit 85, Houston, TX 77030, USA.
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3
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Bridge JA. Reverse transcription-polymerase chain reaction molecular testing of cytology specimens: Pre-analytic and analytic factors. Cancer Cytopathol 2016; 125:11-19. [DOI: 10.1002/cncy.21762] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 06/22/2016] [Accepted: 06/23/2016] [Indexed: 01/02/2023]
Affiliation(s)
- Julia A. Bridge
- Department of Pathology and Microbiology; University of Nebraska Medical Center; Omaha Nebraska
- Department of Pediatrics; University of Nebraska Medical Center; Omaha Nebraska
- Department of Orthopedic Surgery; University of Nebraska Medical Center; Omaha Nebraska
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4
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Distinct cervical microRNA profiles are present in women destined to have a preterm birth. Am J Obstet Gynecol 2014; 210:221.e1-11. [PMID: 24565431 DOI: 10.1016/j.ajog.2013.12.043] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 12/17/2013] [Accepted: 12/31/2013] [Indexed: 11/24/2022]
Abstract
OBJECTIVE Although premature cervical remodeling is involved in preterm birth (PTB), the molecular pathways that are involved have not been elucidated fully. MicroRNAs (miRNAs) that are highly conserved single-stranded noncoding RNAs that play a crucial role in gene regulation have now been identified as important players in disease states. The objective of this study was to determine whether miRNA profiles in cervical cells are different in women who are destined to have a PTB compared with a term birth. STUDY DESIGN A nested case-control study was performed. With the use of a noninvasive method, cervical cells were obtained at 2 time points in pregnancy. The cervical cell miRNA expression profiles were compared between women who ultimately had a PTB (n = 10) compared with a term birth (n = 10). MiRNA expression profiles were created with the Affymetrix GeneChip miRNA Array. The data were analyzed with the Significance of Analysis of Microarrays and Principle Components Analyses. A false-discovery rate of 20% was used to determine the most differentially expressed miRNAs. Validation was performed with quantitative polymerase chain reaction. In vitro studies were performed to confirm expression and regulation of select miRNAs. RESULTS With a false-discovery rate of 20% of the 5640 miRNAs that were analyzed on the array, 99 miRNAs differed between those with a PTB vs a term birth. Qualitative polymerase chain reaction validated the array findings. In vitro studies confirmed expression of select miRNAs in cervical cells. CONCLUSION MiRNA profiles in cervical cells may distinguish women who are at risk for PTB months before the outcome. With the large downstream effects of miRNAs on gene expression, these studies provide a new understanding of the processes that are involved in premature cervical remodeling and allow for the discovery of new therapeutic targets.
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Arbyn M, Andersson K, Bergeron C, Bogers JP, von Knebel-Doebertitz M, Dillner J. Cervical cytology biobanks as a resource for molecular epidemiology. Methods Mol Biol 2011; 675:279-298. [PMID: 20949396 DOI: 10.1007/978-1-59745-423-0_15] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A cervical cytology biobank (CCB) is an extension of current cytopathology laboratory practice consisting in the systematic storage of Pap smears or liquid-based cytology samples from women participating in cervical cancer screening with the explicit purpose of facilitating future scientific research and quality audit of preventive services. A CCB should use an internationally agreed uniform cytology terminology, be integrated in a national or regional screening registry, and linked to other registries (histology, cancer, and vaccination). Legal and ethical principles concerning personal integrity and data safety must be respected strictly. Biobank-based studies require approval from ethical review boards. A CCB constitutes a nearly inexhaustible resource to perform fundamental and applied biologic research. In particular, it can contribute in answering questions on the natural history of HPV infection and HPV-induced lesions and cancers, screening effectiveness, exploration of new biomarkers, and surveillance of short- and long-term effects of the introduction of HPV vaccination. To understand the limitations of CCB, more studies are needed on quality of samples in relation to sample type, storage procedures, and duration of storage.
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Affiliation(s)
- Marc Arbyn
- Unit of Cancer Epidemiology, Scientific Institute of Public Health, Brussels, Belgium.
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Rodriguez AS, Espina BH, Espina V, Liotta LA. Automated laser capture microdissection for tissue proteomics. Methods Mol Biol 2008; 441:71-90. [PMID: 18370312 DOI: 10.1007/978-1-60327-047-2_5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Laser Capture Microdissection (LCM) is a technique for isolating pure cell populations from a heterogeneous tissue section or cytological preparation through direct visualization of the cells. This technique is applicable to molecular profiling of diseased and disease-free tissue, permitting correlation of cellular molecular signatures with specific cell populations. DNA, RNA, or protein analysis may be performed with the microdissected tissue by any method with adequate sensitivity.Automated LCM platforms combine graphical user interfaces and annotation software for visualization of the tissue of interest in addition to robotically controlled microdissection. The principal components of LCM technology are (1) visualization of the cells of interest through microscopy, (2) transfer of laser energy to a thermolabile polymer with formation of a polymer-cell composite, and (3) removal of the cells of interest from the heterogeneous tissue section. Automated LCM is compatible with a variety of tissue types, cellular staining methods, and tissue preservation protocols allowing microdissection of fresh or archival specimens in a high-throughput manner. This protocol describes microdissection techniques compatible with downstream proteomic analyses.
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Affiliation(s)
- Adrianna S Rodriguez
- Center for Cancer Research, Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA
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Gopee NV, Howard PC. A time course study demonstrating RNA stability in postmortem skin. Exp Mol Pathol 2007; 83:4-10. [PMID: 17174950 DOI: 10.1016/j.yexmp.2006.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2006] [Revised: 11/08/2006] [Accepted: 11/08/2006] [Indexed: 11/22/2022]
Abstract
Knowledge of the factors regulating the rate of mRNA degradation, including postmortem delay, is important in determining the reliability of gene expression patterns in dermal tissue. Since RNA stability can be tissue dependent, this study evaluates the effect of postmortem interval on the integrity of total RNA or the levels of representative mRNA species in murine cutaneous tissue. Pieces of fresh skin tissue were excised for periods of 0-60 min from SKH-1 female hairless mice that were maintained at room temperature post-sacrifice. Total RNA was subsequently isolated and RNA integrity from each specimen was evaluated. Bioanalyzer profiles showed no apparent change in 28S/18S rRNA ratio or RNA integrity number at time points up to 60 min. Changes in mRNA expression levels of five selected genes were determined by real-time quantitative PCR. There were no statistical differences in the relative gene expressions of Ccnd1, Hif1alpha, cMyc and Cyr61 as a function of postmortem interval. Our data suggest that the molecular quality of cutaneous tissue is well preserved for at least 60 min after death, which can be regarded as important information for consideration of the order for tissue procurement in in vivo studies and acute ex vivo dermal studies.
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Affiliation(s)
- Neera V Gopee
- Division of Biochemical Toxicology, and National Toxicology Program Center for Phototoxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Department of Health and Human Services, Jefferson, Arkansas 72079, USA
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Mattu R, Sorbara L, Filie AC, Little R, Wilson W, Raffeld M, Abati A. Utilization of polymerase chain reaction on archival cytologic material: a comparison with fresh material with special emphasis on cerebrospinal fluids. Mod Pathol 2004; 17:1295-301. [PMID: 15195110 DOI: 10.1038/modpathol.3800185] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Use of the polymerase chain reaction (PCR) for the detection of B- and T-cell clonality, Epstein-Barr virus (EBV) and Human Herpes Virus 8 (HHV 8) infection is gaining increasing importance as a diagnostic modality. These tests are usually performed on fresh specimens. There are instances when fresh material is not available and there is a clinical utility for the performance of PCR on archival material via slide scrape lysates (SSL). However, the suitability of archival material may be questioned. Records were searched for all archival cytology cases submitted for SSL molecular diagnostics tests since 1998. Results for each case were analyzed for PCR amplification status and individual test results. A randomly chosen control group of equivalent cytologic samples submitted fresh was evaluated for comparison of amplification status. In all, 241 PCR runs were performed on SSL of archival material from 112 cytologic samples (89 cerebrospinal fluids (CSFs), 13 fine-needle aspirates (FNAs), 10 effusions). Out of these samples, 95 (85%) had amplifiable DNA, as assessed by a positive reaction for glyceraldehyde phosphate dehydrogenase (GAPDH). For the control group, 320 PCR runs were performed on 112 fresh cytologic samples (89 CSFs, 13 FNAs, 10 effusions). In total, 102 samples (91%) had amplifiable DNA. There was no statistical difference in the amplification yield between the two groups (P = 0.2177). A morphologic review of 16 of the 17 SSL archival cytologic cases that did not show amplification revealed 11/16 to be of sparse cellularity. Molecular diagnostic tests are performed routinely on fresh cytologic samples with excellent results. At times critical decisions on patient care may need to be made when fresh tissue is not available for molecular diagnostic tests. SSL of archival cytologic material can be used with excellent results for molecular diagnostic tests when fresh material is not available or when the cytologic diagnosis needs further clarification.
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MESH Headings
- B-Lymphocytes/cytology
- B-Lymphocytes/metabolism
- Biopsy, Fine-Needle
- Cell Line, Tumor
- Cerebrospinal Fluid
- Clone Cells/metabolism
- Cytodiagnosis/methods
- DNA, Viral/cerebrospinal fluid
- DNA, Viral/genetics
- DNA, Viral/isolation & purification
- Gene Rearrangement, B-Lymphocyte/genetics
- Gene Rearrangement, T-Lymphocyte/genetics
- Gene Rearrangement, gamma-Chain T-Cell Antigen Receptor/genetics
- Herpesvirus 4, Human/genetics
- Herpesvirus 8, Human/genetics
- Humans
- Immunoglobulin Heavy Chains/genetics
- Molecular Diagnostic Techniques/methods
- Pleural Effusion
- Polymerase Chain Reaction/methods
- T-Lymphocytes/cytology
- T-Lymphocytes/metabolism
- Vaginal Smears
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Affiliation(s)
- Rubina Mattu
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD 20892, USA
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Vielemeyer O, Crouch JY, Edberg SC, Howe JG. Identification of Bordetella pertussis in a critically ill human immunodeficiency virus-infected patient by direct genotypical analysis of Gram-stained material and discrimination from B. holmesii by using a unique recA gene restriction enzyme site. J Clin Microbiol 2004; 42:847-9. [PMID: 14766870 PMCID: PMC344463 DOI: 10.1128/jcm.42.2.847-849.2004] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bordetella pertussis was diagnosed in a human immunodeficiency virus-infected patient by a newly developed method in which bacterial DNA is amplified directly from sputum Gram-stained slides. The validation of the method is described along with an additional new PCR-based assay that can distinguish between B. pertussis and Bordetella holmesii.
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Affiliation(s)
- Ole Vielemeyer
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut 06520-8035, USA
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10
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Jewell SD, Srinivasan M, McCart LM, Williams N, Grizzle WH, LiVolsi V, MacLennan G, Sedmak DD. Analysis of the molecular quality of human tissues: an experience from the Cooperative Human Tissue Network. Am J Clin Pathol 2002; 118:733-41. [PMID: 12428794 DOI: 10.1309/vpql-rt21-x7yh-xdxk] [Citation(s) in RCA: 119] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
The scientific usefulness of the data obtained from tissue analysis is related to specimen quality, which may be affected by conditions that may contribute to the degradation of the specimen before processing and analysis. We determined the usability of nucleic acids extracted from banked human tissues for further molecular analyses. We assayed 151 tissue specimens, storedfor various times at 4 divisions of the Cooperative Human Tissue Network, National Cancer Institute, Bethesda, MD, for DNA and RNA degradation. Simple electrophoresis, polymerase chain reaction (PCR), reverse-transcriptase (RT)-PCR, and Northern blot analysis were compared to determine the optimal quality control procedure. In addition, a time course degradation procedure was performed on human lung tissue. Gel electrophoresis was as informative as PCR, RT-PCR, and Northern blot analysis in determining the molecular usefulness of the human tissues. Overall, 80% of the stored human tissues had good-quality DNA, and 60% had good-quality RNA. Electrophoresis procedures for DNA and RNA offer a quick and valuable measure of the molecular quality of stored human tissues. The DNA and RNA degradation of one tissue type (lung) was stable for both nucleic acids for up to 5 hours after excision.
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Affiliation(s)
- Scott D Jewell
- Department of Pathology, Ohio State University, Columbus 43210, USA
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11
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Siddiqui MT, Greene KL, Clark DP, Xydas S, Udelsman R, Smallridge RC, Zeiger MA, Saji M. Human telomerase reverse transcriptase expression in Diff-Quik-stained FNA samples from thyroid nodules. DIAGNOSTIC MOLECULAR PATHOLOGY : THE AMERICAN JOURNAL OF SURGICAL PATHOLOGY, PART B 2001; 10:123-9. [PMID: 11385322 DOI: 10.1097/00019606-200106000-00009] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Fine-needle aspiration (FNA) is a highly sensitive method in the differential diagnosis of thyroid nodules. However, 10% of thyroid FNAs are indeterminate for cancer, and thus additional markers may be useful diagnostically. The authors have demonstrated previously that human telomerase reverse transcriptase (hTERT) gene expression is useful in the distinction of benign lesions from malignant lesions. They therefore wondered whether the detection of hTERT gene expression was feasible using archival slides. To establish an experimental system, ribonucleic acid was extracted from human anaplastic thyroid carcinoma cell line (ARO) in cytologic specimens, and reverse transcription-polymerase chain reaction (RT-PCR) for hTERT expression was performed. RT-PCR analysis for hTERT gene detection was then performed using 58 Diff-Quik-stained archival FNA samples collected retrospectively. RT-PCR for human thyroglobulin (hTg) or beta-actin gene expression served as a positive control. Successful PCR results were obtained from 48 of the 58 cases. All 10 slides in which no RT-PCR products were noted were older than 3 years. hTERT gene expression was demonstrated in FNAs from two of seven cases (29%) of hyperplastic nodule, one of one case (100%) of Hashimoto's thyroiditis, three of eight cases (38%) of follicular adenoma, three of eight cases (38%) of Hürthle cell adenoma, three of four cases (75%) of follicular carcinoma, two of two cases (100%) of Hürthle cell carcinoma, and 11 of 18 cases (61%) of papillary carcinoma. All but one of the available 33 corresponding frozen samples exhibited the same RT-PCR results. This study demonstrates that Diff-Quik-stained thyroid FNA specimens less than 3 years old can be used for the detection of hTERT gene expression by RT-PCR. This test, along with careful cytopathologic examination, may improve our ability to differentiate benign lesions from malignant lesions in indeterminate FNA samples from thyroid nodules.
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MESH Headings
- Actins/genetics
- Actins/metabolism
- Adenocarcinoma, Follicular/enzymology
- Adenocarcinoma, Follicular/genetics
- Adenocarcinoma, Follicular/pathology
- Adenoma/enzymology
- Adenoma/genetics
- Adenoma/pathology
- Biomarkers, Tumor
- Biopsy, Needle
- DNA-Binding Proteins
- Gene Expression Regulation, Neoplastic
- Humans
- Hyperplasia
- RNA
- RNA, Messenger/analysis
- RNA, Neoplasm/analysis
- Reverse Transcriptase Polymerase Chain Reaction
- Sensitivity and Specificity
- Telomerase/genetics
- Telomerase/metabolism
- Thyroglobulin/genetics
- Thyroglobulin/metabolism
- Thyroid Neoplasms/enzymology
- Thyroid Neoplasms/genetics
- Thyroid Neoplasms/pathology
- Thyroid Nodule/enzymology
- Thyroid Nodule/genetics
- Thyroid Nodule/pathology
- Thyroiditis, Autoimmune/enzymology
- Thyroiditis, Autoimmune/genetics
- Thyroiditis, Autoimmune/pathology
- Tumor Cells, Cultured
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Affiliation(s)
- M T Siddiqui
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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12
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Abstract
An understanding of the relationship between gene expression, protein expression and the influences of genetic responses upon gene function is vital before we can understand the complexity of genomes. Traditional methods for the study of gene expression are limited to studying small groups of genes at a time and a source of pure starting material has been difficult to obtain. Recent technological advances have enabled large numbers of genes, from specific cell populations, to be studied in a single experiment. Laser capture microdissection (LCM) and microarray technology are providing the next revolution in the study of gene expression. LCM-based molecular analysis of histopathological lesions can be applied to any disease process that is accessible through tissue sampling. Examples include: (i) mapping the field of genetic changes associated with oxidative stress; (ii) analysis of gene expression patterns in atherosclerotic tissues, sites of inflammation and Alzheimer's disease plaques; (iii) infectious micro-organism diagnosis; and (iv) typing of cells within disease foci. Microarray hybridisation glass chips spotted with sets of genes can then be used to obtain a molecular fingerprint of gene expression in the microdissected cells. The variation of expressed genes or alterations in the cellular DNA that correlate with a particular disease state can be compared within or between individual samples. The identification of gene expression patterns may provide vital information for the understanding of the disease process and may contribute to diagnostic decisions and therapies tailored to the individual patient. Molecules found to be associated with defined pathological lesions may provide clues about new therapeutic targets in the future.
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Affiliation(s)
- J K Burgess
- Department of Pharmacology, University of Sydney, New South Wales, Australia.
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