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Osuch E, Ursano R, Li H, Webster M, Hough C, Fullerton C, Leskin G. Brain Environment Interactions: Stress, Posttraumatic Stress Disorder, and the Need for a Postmortem Brain Collection. Psychiatry 2022; 85:113-145. [PMID: 35588486 DOI: 10.1080/00332747.2022.2068916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Stress, especially the extreme stress of traumatic events, can alter both neurobiology and behavior. Such extreme environmental situations provide a useful model for understanding environmental influences on human biology and behavior. This paper will review some of the evidence of brain alterations that occur with exposure to environmental stress. This will include recent studies using neuroimaging and will address the need for histological confirmation of imaging study results. We will review the current scientific approaches to understanding brain environment interactions, and then make the case for the collection and study of postmortem brain tissue for the advancement of our understanding of the effects of environment on the brain.Creating a brain tissue collection specifically for the investigation of the effects of extreme environmental stressors fills a gap in the current research; it will provide another of the important pieces to the puzzle that constitutes the scientific investigation of negative effects of environmental exposures. Such a resource will facilitate new discoveries related to the psychiatric illnesses of acute stress disorder and posttraumatic stress disorder, and can enable scientists to correlate structural and functional imaging findings with tissue abnormalities, which is essential to validate the results of recent imaging studies.
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Morlote D, Janowski KM, Siniard RC, Guo RJ, Winokur T, DeFrank G, Harada S. Effects of Improved DNA Integrity by Punch From Tissue Blocks as Compared to Pinpoint Extraction From Unstained Slides on Next-Generation Sequencing Quality Metrics. Am J Clin Pathol 2019; 152:27-35. [PMID: 30892602 DOI: 10.1093/ajcp/aqz014] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To compare the effects of two methods of formalin-fixed paraffin-embedded (FFPE) tissue harvesting on DNA quality and next-generation sequencing (NGS) quality metrics. METHODS DNA integrity number (DIN) and NGS quality metrics resulting from DNA extraction and sequencing of 199 sequential samples harvested via the Pinpoint Slide DNA Isolation System and the punch method were compared. RESULTS DNA extracted from FFPE tissue punches had higher DIN than that extracted from Pinpoint samples (mean ± SD, 6.18 ± 0.83 vs 5.09 ± 0.91; P < .0001), indicating less degradation. Lower DIN correlated with lower-quality metrics of NGS, that is lower percentage of unique on-target reads, average depth of coverage, and percentage of positions with coverage depth greater than or equal to 100×, 400×, and 1,000×. CONCLUSIONS Our study demonstrated methods to harvest tissue from FFPE blocks may affect quality of DNA, which in turn has an effect on other NGS quality metrics.
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Thennavan A, Sharma M, Chandrashekar C, Hunter K, Radhakrishnan R. Exploring the potential of laser capture microdissection technology in integrated oral biosciences. Oral Dis 2016; 23:737-748. [DOI: 10.1111/odi.12578] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Revised: 08/10/2016] [Accepted: 08/24/2016] [Indexed: 12/19/2022]
Affiliation(s)
- A Thennavan
- Department of Oral Pathology; Manipal College of Dental Sciences; Manipal Karnataka India
| | - M Sharma
- Pacific Academy of Higher Education and Research (PAHER) University; Udaipur Rajasthan India
- Department of Oral Pathology; ITS Dental College; Hospital and Research Center; Greater Noida India
| | - C Chandrashekar
- Department of Oral Pathology; Manipal College of Dental Sciences; Manipal Karnataka India
| | - K Hunter
- School of Clinical Dentistry; The University of Sheffield; Sheffield UK
| | - R Radhakrishnan
- Department of Oral Pathology; Manipal College of Dental Sciences; Manipal Karnataka India
- School of Clinical Dentistry; The University of Sheffield; Sheffield UK
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Snow AN, Stence AA, Pruessner JA, Bossler AD, Ma D. A simple and cost-effective method of DNA extraction from small formalin-fixed paraffin-embedded tissue for molecular oncologic testing. BMC Clin Pathol 2014; 14:30. [PMID: 25067909 PMCID: PMC4110377 DOI: 10.1186/1472-6890-14-30] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 07/01/2014] [Indexed: 02/14/2023] Open
Abstract
Background Extraction of DNA from formalin-fixed, paraffin-embedded (FFPE) tissue is a critical step in molecular oncologic testing. As molecular oncology testing becomes more important for prognostic and therapeutic decision making and tissue specimens become smaller due to earlier detection of suspicious lesions and the use of fine needle aspiration methods for tissue collection, it becomes more challenging for the typical molecular pathology laboratory to obtain reliable test results. We developed a DNA extraction method to obtain sufficient quantity and high quality genomic DNA from limited FFPE tissue for molecular oncology testing using a combination of H&E stained slides, a matrix capture method and the Qiagen DNA column. Methods Three DNA extraction methods were compared: our standard procedure of manually scraping tissue from unstained slides followed by DNA extraction using the QIAamp FFPE column (Qiagen, Valencia, CA), a glue capture method (Pinpoint Solution, Zymo Research Corp, Inc) on H&E stained slides followed by DNA extraction using either the QIAamp column or the column included with the Pinpoint kit (Zymo Research). The DNA extraction protocol was optimized. Statistical analysis was performed using the paired two-sample student’s t-test. Results The combination of the matrix capture method with the QIAamp column gave an equivalent amount of DNA as our standard extraction method using the unstained slides and a 4.6-fold higher DNA yield than using the Zymo column included in the Pinpoint Slide Solution kit. Several molecular tests were performed and DNA purified using the new method gave the same results as for the previous methods. Conclusions Using H&E stained slides allows visual confirmation of tumor cells during microdissection. The Pinpoint solution made removal of specific tissue from the slides easier and reduced the risk of contamination and tissue loss. This DNA extraction method is simple, cost-effective, and blends with our current workflow requiring no additional equipment.
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Affiliation(s)
- Anthony N Snow
- Department of Pathology, Brown University, Rhode Island Hospital, Providence, Rhode Island 02806, USA
| | - Aaron A Stence
- Department of Pathology, University of Iowa Hospitals and Clinics, 200 Hawkins Drive, BT6008GH, Iowa City, IA 52242, USA
| | - Jonathan A Pruessner
- Department of Pathology, University of Iowa Hospitals and Clinics, 200 Hawkins Drive, BT6008GH, Iowa City, IA 52242, USA
| | - Aaron D Bossler
- Department of Pathology, University of Iowa Hospitals and Clinics, 200 Hawkins Drive, BT6008GH, Iowa City, IA 52242, USA
| | - Deqin Ma
- Department of Pathology, University of Iowa Hospitals and Clinics, 200 Hawkins Drive, BT6008GH, Iowa City, IA 52242, USA
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DeVilliers P, Suggs C, Simmons D, Murrah V, Wright JT. Microgenomics of ameloblastoma. J Dent Res 2011; 90:463-9. [PMID: 21282726 DOI: 10.1177/0022034510391791] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Gene expression profiles of human ameloblastoma microdissected cells were characterized with the purpose of identifying genes and their protein products that could be targeted as diagnostic and prognostic markers as well as for potential therapeutic interventions. Five formalin-fixed, decalcified, paraffin-embedded samples of ameloblastoma were subjected to laser capture microdissection, linear mRNA amplification, and hybridization to oligonucleotide human 41,000 RNA arrays and compared with universal human reference RNA, to determine the gene expression signature. Assessment of the data by Significance Analysis of Microarrays (SAM) and cluster analysis showed that 38 genes were highly expressed (two-fold increase) in all samples, while 41 genes were underexpressed (two-fold reduction). Elements of the sonic hedgehog pathway and Wingless type MMTV integration site family were validated by immunohistochemistry. We have identified the expression of multiple genes and protein products that could serve as potential diagnostic, prognostic, and therapeutic targets.
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Affiliation(s)
- P DeVilliers
- Department of Pathology, University of Alabama at Birmingham, USA
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Kolbert CP, Chari S, Sreekumar R. Microarray Technologies for Gene Transcript Analysis in Pancreatic Cancer. Technol Cancer Res Treat 2008; 7:55-9. [DOI: 10.1177/153303460800700107] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Pancreatic cancer is a devastating condition that is most often characterized by a poor prognosis. Microarray technologies are promising screening methods for the identification of potential markers for early diagnosis and chemotherapeutic intervention. In this article, we review the current state of pancreatic cancer research as it relates to the measurement of gene transcript levels by DNA microarray analysis.
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Affiliation(s)
| | | | - R. Sreekumar
- Clinical Research Unit
- Division of Endocrinology Mayo Clinic Rochester, MN 55905, USA
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Reis SA, Oostra BA, Willemsen R. Isolation of mouse neuritic mRNAs. J Mol Histol 2006; 37:79-86. [PMID: 16821094 DOI: 10.1007/s10735-006-9036-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2006] [Accepted: 05/22/2006] [Indexed: 11/26/2022]
Abstract
Impaired local protein translation at postsynaptic sites has been hypothesized to be the cause of several neurological disorders such as fragile X syndrome, neurofibromatosis-1, Rett syndrome, and other syndromic and non-specific forms of mental retardation. Identification of which mRNAs are present in dendrites and the identification of the molecular pathways that they promote will be imperative to the understanding of the neuropathology of these diseases. Since mouse models are the most widely used animal models of human diseases we developed a cell culture based technique to isolate mRNAs from mouse neurites.
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Affiliation(s)
- Surya A Reis
- CBG-Department of Clinical Genetics, Erasmus MC, P.O. Box 1738, 3000, DR, Rotterdam, The Netherlands
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Player A, Barrett JC, Kawasaki ES. Laser capture microdissection, microarrays and the precise definition of a cancer cell. Expert Rev Mol Diagn 2004; 4:831-40. [PMID: 15525225 DOI: 10.1586/14737159.4.6.831] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Most expression profiling studies of solid tumors have used biopsy samples containing large numbers of contaminating stromal and other cell types, thereby complicating any precise delineation of gene expression in nontumor versus tumor cell types. Combining laser capture microdissection, RNA amplification protocols, microarray technologies and our knowledge of the human genome sequence, it is possible to isolate pure populations of cells or even a single cell and interrogate the expression of thousands of sequences for the purpose of more precisely defining the biology of the tumor cell. Although many of the studies that currently allow for characterization of small sample preparations and single cells were performed utilizing noncancer cell types, and in some cases isolation protocols other than laser capture microdissection, a list of protocols are described that could be used for the expression analysis of individual tumor cells. Application of these experimental approaches to cancer studies may permit a more accurate definition of the biology of the cancer cell, so that ultimately, more specific targeted therapies can be developed.
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Affiliation(s)
- Audrey Player
- National Cancer Institute, Advanced Technology Center, Microarray Facility, Gaithersburg, MD 20877, USA.
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Abstract
With completion of the human genome sequence, it is now possible to study the expression of the entire human gene complement of approximately 30,000-35,000 genes. To accomplish this goal, microarrays have become the leading methodology for the analysis of global gene expression. Improvements in technology have increased the sensitivity of microarrays to the point where it is feasible to study gene expression in a small number of cells and even at the single cell level. A summary of developments in the area of expression profiling in single cells will be described, and the rationale for these types of studies will be presented. In addition, from a biologist's point of view, some bioinformatic challenges of expression analysis of single cells will be discussed.
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Affiliation(s)
- Ernest S Kawasaki
- Advanced Technology Center, National Cancer Institute, National Institutes of Health, 8717 Grovemont Circle, Bethesda, MD 20892, USA.
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Meyers BC, Galbraith DW, Nelson T, Agrawal V. Methods for transcriptional profiling in plants. Be fruitful and replicate. PLANT PHYSIOLOGY 2004; 135:637-52. [PMID: 15173570 PMCID: PMC514100 DOI: 10.1104/pp.104.040840] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2004] [Revised: 03/19/2004] [Accepted: 03/19/2004] [Indexed: 05/18/2023]
Affiliation(s)
- Blake C Meyers
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA.
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Osuch E, Ursano R, Li H, Webster M, Hough C, Fullerton C, Leskin G. Brain environment interactions: stress, posttraumatic stress disorder, and the need for a postmortem brain collection. Psychiatry 2004; 67:353-83. [PMID: 15801377 DOI: 10.1521/psyc.67.4.353.56565] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Stress, especially the extreme stress of traumatic events, can alter both neurobiology and behavior. Such extreme environmental situations provide a useful model for understanding environmental influences on human biology and behavior. This paper will review some of the evidence of brain alterations that occur with exposure to environmental stress. This will include recent studies using neuroimaging and will address the need for histological confirmation of imaging study results. We will review the current scientific approaches to understanding brain environment interactions, and then make the case for the collection and study of postmortem brain tissue for the advancement of our understanding of the effects of environment on the brain. Creating a brain tissue collection specifically for the investigation of the effects of extreme environmental stressors fills a gap in the current research; it will provide another of the important pieces to the puzzle that constitutes the scientific investigation of negative effects of environmental exposures. Such a resource will facilitate new discoveries related to the psychiatric illnesses of acute stress disorder and posttraumatic stress disorder, and can enable scientists to correlate structural and functional imaging findings with tissue abnormalities, which is essential to validate the results of recent imaging studies.
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MESH Headings
- Acoustic Stimulation/adverse effects
- Axons/physiology
- Brain/metabolism
- Brain/pathology
- Brain/physiopathology
- Environment
- Epinephrine/blood
- Epinephrine/urine
- Humans
- Limbic System/anatomy & histology
- Limbic System/metabolism
- Limbic System/pathology
- Limbic System/physiopathology
- Norepinephrine/blood
- Norepinephrine/urine
- Reflex, Startle
- Stress Disorders, Post-Traumatic/metabolism
- Stress Disorders, Post-Traumatic/physiopathology
- Stress Disorders, Post-Traumatic/psychology
- Stress Disorders, Traumatic, Acute/metabolism
- Stress Disorders, Traumatic, Acute/physiopathology
- Stress Disorders, Traumatic, Acute/psychology
- Tissue Banks
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Affiliation(s)
- Elizabeth Osuch
- Department of Psychiatry, Uniformed Services Universityof the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814, USA.
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