help button home button Am J Pathol ASIP MEMBERSHIP
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS

This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Purchase Article
Right arrow View Shopping Cart
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Gillespie, J. W.
Right arrow Articles by Emmert-Buck, M. R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Gillespie, J. W.
Right arrow Articles by Emmert-Buck, M. R.
(American Journal of Pathology. 2002;160:449-457.)
© 2002 American Society for Investigative Pathology

Technical Advance

Evaluation of Non-Formalin Tissue Fixation for Molecular Profiling Studies

John W. Gillespie*{dagger}, Carolyn J.M. Best{dagger}, Verena E. Bichsel{ddagger}, Kristina A. Cole{dagger}, Susan F. Greenhut§, Stephen M. Hewitt, Mamoun Ahram{dagger}, Yvonne B. Gathright§, Maria J. Merino, Robert L. Strausberg§, Jonathan I. Epstein||, Stanley R. Hamilton**, Gallya Gannot{dagger}{dagger}, Galina V. Baibakova{dagger}, Valerie S. Calvert{ddagger}, Michael J. Flaig{dagger}, Rodrigo F. Chuaqui{dagger}, Judi C. Herring{ddagger}{ddagger}, John Pfeifer§§, Emmanuel F. Petricoin{ddagger}, W. Marston Linehan¶¶, Paul H. Duray, G. Steven Bova|| and Michael R. Emmert-Buck{dagger}¶¶

From the Science Applications InternationalCorporation,*
National Cancer Institute, Frederick,Maryland; the Pathogenetics Unit,{dagger}
theLaboratory of Pathology, National Cancer Institute, Bethesda, Maryland;the Center for Biologics and Research,{ddagger}
Foodand Drug Administration, Bethesda, Maryland; the Cancer Genome AnatomyProject (CGAP),§
Office of the Director,National Cancer Institute, Bethesda, Maryland; the Laboratory ofPathology,
National Cancer Institute, Bethesda,Maryland; the Department of Pathology,||
Johns HopkinsUniversity, Baltimore, Maryland; the Department ofPathology,**
M.D. Anderson Cancer Center,Houston, Texas; the Faculty ofMedicine,{dagger}{dagger}
Tel Aviv University,Tel Aviv, Israel; the Center for Prostate DiseaseResearch,{ddagger}{ddagger}
Rockville, Maryland;the Center for Information Technology,§§
National Institutes of Health, Bethesda, Maryland; and the UrologicOncology Branch,
National CancerInstitute, Bethesda, Maryland

Correspondence: Address correspondence to M.R. Emmert-Buck, Pathogenetics Unit, Laboratory of Pathology and Urologic Oncology Branch, National Cancer Institute, Rm. 2A33, Bldg. 10, 9000 Rockville Pike, Bethesda, MD 20892. E-mail: mbuck\@helix.nih.gov.

Using a general strategy for evaluating clinical tissue specimens, we found that 70% ethanol fixation and paraffin embedding is a useful method for molecular profiling studies. Human prostate and kidney were used as test tissues. The protein content of the samples was analyzed by one-dimensional gel electrophoresis, immunoblot, two-dimensional gel electrophoresis, and layered expression scanning. In each case, the fixed and embedded tissues produced results similar to that obtained from snap-frozen specimens, although the protein quantity was somewhat decreased. Recovery of mRNA was reduced in both quantity and quality in the ethanol-fixed samples, but was superior to that obtained from formalin-fixed samples and sufficient to perform reverse transcription polymerase chain reactions. Recovery of DNA from ethanol-fixed specimens was superior to formalin-fixed samples as determined by one-dimensional gel electrophoresis and polymerase chain reaction. In conclusion, specimens fixed in 70% ethanol and embedded in paraffin produce good histology and permit recovery of DNA, mRNA, and proteins sufficient for several downstream molecular analyses. Complete protocols and additional discussion of relevant issues are available on an accompanying website (http://cgap-mf.nih.gov/).




This article has been cited by other articles:


Home page
 Proc. Natl. Acad. Sci. USAHome page
V. A. Burzio, C. Villota, J. Villegas, E. Landerer, E. Boccardo, L. L. Villa, R. Martinez, C. Lopez, F. Gaete, V. Toro, et al.
Expression of a family of noncoding mitochondrial RNAs distinguishes normal from cancer cells
PNAS, June 9, 2009; 106(23): 9430 - 9434.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
V. Espina, K. H. Edmiston, M. Heiby, M. Pierobon, M. Sciro, B. Merritt, S. Banks, J. Deng, A. J. VanMeter, D. H. Geho, et al.
A Portrait of Tissue Phosphoprotein Stability in the Clinical Tissue Procurement Process
Mol. Cell. Proteomics, October 1, 2008; 7(10): 1998 - 2018.
[Abstract] [Full Text] [PDF]

Home page
 J. Mol. Diagn.Home page
M. Doleshal, A. A. Magotra, B. Choudhury, B. D. Cannon, E. Labourier, and A. E. Szafranska
Evaluation and Validation of Total RNA Extraction Methods for MicroRNA Expression Analyses in Formalin-Fixed, Paraffin-Embedded Tissues
J. Mol. Diagn., May 1, 2008; 10(3): 203 - 211.
[Abstract] [Full Text] [PDF]

Home page
 J. Mol. Diagn.Home page
G. Gannot, M. A. Tangrea, H. S. Erickson, P. A. Pinto, S. M. Hewitt, R. F. Chuaqui, J. W. Gillespie, and M. R. Emmert-Buck
Layered Peptide Array for Multiplex Immunohistochemistry
J. Mol. Diagn., July 1, 2007; 9(3): 297 - 304.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
M. W.B. Spencer, S. A. Casson, and K. Lindsey
Transcriptional Profiling of the Arabidopsis Embryo
Plant Physiology, February 1, 2007; 143(2): 924 - 940.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
C. C. Whiteford, S. Bilke, B. T. Greer, Q. Chen, T. A. Braunschweig, N. Cenacchi, J. S. Wei, M. A. Smith, P. Houghton, C. Morton, et al.
Credentialing Preclinical Pediatric Xenograft Models Using Gene Expression and Tissue Microarray Analysis
Cancer Res., January 1, 2007; 67(1): 32 - 40.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Cancer Res.Home page
K. Sircar, L. Gaboury, L. Ouadi, M. Mecteau, E. Scarlata, F. Saad, A. Aprikian, S. Tanguay, S. Lapointe, C. Lussier, et al.
Isolation of human prostatic epithelial plasma membranes for proteomics using mirror image tissue banking of radical prostatectomy specimens.
Clin. Cancer Res., July 15, 2006; 12(14): 4178 - 4184.
[Abstract] [Full Text] [PDF]

Home page
 J. Histochem. Cytochem.Home page
W.-S. Chu, Q. Liang, Y. Tang, R. King, K. Wong, M. Gong, M. Wei, J. Liu, S.-H. Feng, S.-C. Lo, et al.
Ultrasound-accelerated Tissue Fixation/Processing Achieves Superior Morphology and Macromolecule Integrity with Storage Stability
J. Histochem. Cytochem., May 1, 2006; 54(5): 503 - 513.
[Abstract] [Full Text] [PDF]

Home page
 J. Clin. Pathol.Home page
A A Ghazani, N C R Arneson, K Warren, and S J Done
Limited tissue fixation times and whole genomic amplification do not impact array CGH profiles.
J. Clin. Pathol., March 1, 2006; 59(3): 311 - 315.
[Abstract] [Full Text] [PDF]

Home page
 JNCI J Natl Cancer InstHome page
J. A. Hanson, J. W. Gillespie, A. Grover, M. A. Tangrea, R. F. Chuaqui, M. R. Emmert-Buck, J. A. Tangrea, S. K. Libutti, W. M. Linehan, and K. G. Woodson
Gene promoter methylation in prostate tumor-associated stromal cells.
J Natl Cancer Inst, February 15, 2006; 98(4): 255 - 261.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
B. L. Hood, M. M. Darfler, T. G. Guiel, B. Furusato, D. A. Lucas, B. R. Ringeisen, I. A. Sesterhenn, T. P. Conrads, T. D. Veenstra, and D. B. Krizman
Proteomic Analysis of Formalin-fixed Prostate Cancer Tissue
Mol. Cell. Proteomics, November 1, 2005; 4(11): 1741 - 1753.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Cancer Res.Home page
C. J.M. Best, J. W. Gillespie, Y. Yi, G. V.R. Chandramouli, M. A. Perlmutter, Y. Gathright, H. S. Erickson, L. Georgevich, M. A. Tangrea, P. H. Duray, et al.
Molecular Alterations in Primary Prostate Cancer after Androgen Ablation Therapy
Clin. Cancer Res., October 1, 2005; 11(19): 6823 - 6834.
[Abstract] [Full Text] [PDF]

Home page
 J. Histochem. Cytochem.Home page
G. Gannot, J. W. Gillespie, R. F. Chuaqui, M. A. Tangrea, W. M. Linehan, and M. R. Emmert-Buck
Histomathematical Analysis of Clinical Specimens: Challenges and Progress
J. Histochem. Cytochem., February 1, 2005; 53(2): 177 - 185.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
C. C. Xiang, E. Mezey, M. Chen, S. Key, L. Ma, and M. J. Brownstein
Using DSP, a reversible cross-linker, to fix tissue sections for immunostaining, microdissection and expression profiling
Nucleic Acids Res., December 16, 2004; 32(22): e185 - e185.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Epidemiol. Biomarkers Prev.Home page
T. M. Beer, A. Myrthue, M. Garzotto, M. F. O'Hara, R. Chin, B. A. Lowe, M. A. Montalto, C. L. Corless, and W. D. Henner
Randomized Study of High-Dose Pulse Calcitriol or Placebo prior to Radical Prostatectomy
Cancer Epidemiol. Biomarkers Prev., December 1, 2004; 13(12): 2225 - 2232.
[Abstract] [Full Text] [PDF]

Home page
 IOVSHome page
T. W. Olsen and X. Feng
The Minnesota Grading System of Eye Bank Eyes for Age-Related Macular Degeneration
Invest. Ophthalmol. Vis. Sci., December 1, 2004; 45(12): 4484 - 4490.
[Abstract] [Full Text] [PDF]

Home page
 J. Mol. Diagn.Home page
A. Gloghini, B. Canal, U. Klein, L. Dal Maso, T. Perin, R. Dalla-Favera, and A. Carbone
RT-PCR Analysis of RNA Extracted from Bouin-Fixed and Paraffin-Embedded Lymphoid Tissues
J. Mol. Diagn., November 1, 2004; 6(4): 290 - 296.
[Abstract] [Full Text] [PDF]

Home page
 J. Mol. Diagn.Home page
M. A. Perlmutter, C. J.M. Best, J. W. Gillespie, Y. Gathright, S. Gonzalez, A. Velasco, W. M. Linehan, M. R. Emmert-Buck, and R. F. Chuaqui
Comparison of Snap Freezing versus Ethanol Fixation for Gene Expression Profiling of Tissue Specimens
J. Mol. Diagn., November 1, 2004; 6(4): 371 - 377.
[Abstract] [Full Text] [PDF]

Home page
 INT J SURG PATHOLHome page
Z. Suo, K. U. Daehli, C. Fr. Lindboe, E. Borgen, A. Bassarova, and J. M. Nesland
Real-Time PCR Quantification of c-erbB-2 Gene is an Alternative for Fish in the Clinical Management of Breast Carcinoma Patients
International Journal of Surgical Pathology, October 1, 2004; 12(4): 311 - 318.
[Abstract] [PDF]

Home page
 J Natl Cancer Inst MonogrHome page
M. E. Sherman
Chapter 11: Future Directions in Cervical Pathology
J Natl Cancer Inst Monographs, June 1, 2003; 2003(31): 72 - 79.
[Abstract] [Full Text] [PDF]

Home page
 Am. J. Pathol.Home page
O. Kabbarah, K. Pinto, D. G. Mutch, and P. J. Goodfellow
Expression Profiling of Mouse Endometrial Cancers Microdissected from Ethanol-Fixed, Paraffin-Embedded Tissues
Am. J. Pathol., March 1, 2003; 162(3): 755 - 762.
[Abstract] [Full Text] [PDF]

Home page
 Am. J. Pathol.Home page
A. B. Rogers, C. K. Mathiason, and E. A. Hoover
Immunohistochemical Localization of Feline Immunodeficiency Virus Using Native Species Antibodies
Am. J. Pathol., October 1, 2002; 161(4): 1143 - 1151.
[Abstract] [Full Text] [PDF]


HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
Copyright © 2002 by the American Society for Investigative Pathology.