Histotechnical solutions for quality improvement of nucleic acid specimens extracted from paraffin blocks

Cover Page


Cite item

Full Text

Open Access Open Access
Restricted Access Access granted
Restricted Access Subscription or Fee Access

Abstract

With the growing body of information about molecular nature of a set of diseases, the question of molecular biology techniques acceptability for histological material study came up. Currently available pathology archives could provide vast quantity of material for retrospective studies, however, the most frequently used fixative formalin dramatically damages nucleic acids in the tissue. A similar problem arises with the material that come into the pathology department and undergoing conventional histological processing in nowadays. In recent years with the entry into the practice of diagnostic methods based on molecular biology methods it has become especially important to obtain high-quality samples of nucleic acids. Research devoted to development of new approaches of histological material handling from one side and solutions for nucleic acids extraction from tissue after standard histological treatment on the other side revealed a number of ways to overcome the problem of poor quality of nucleic acids isolated from the paraffin block. The aim of this review is to highlight the modifications histological processing techniques that allow prepare nucleic acids samples of higher quality.

About the authors

A. N Vaganova

BioVitrum Ltd, Moscow, Russia

References

  1. Goldsworthy S.M., Stockton P.S.,Trempus C. S. et al. Effects of fixation on RNA extraction and amplification from laser capture microdissected tissue. Mol Carcinog. 1999; 25(2): 86-91.
  2. Chung J.Y., Braunschweig T., Williams R. et al. Factors in tissue handling and processing that impact RNA obtained from formalin-fixed, paraffin-embedded tissue. J. Histochem. Cytochem. 2008; 56(11): 1033-42.
  3. Abrahamsen H.N., Steiniche T., Nexo E. et al. Towards quantitative mRNA analysis in paraffin-embedded tissues using real-time reverse transcriptase-polymerase chain reaction: a methodological study on lymph nodes from melanoma patients. J. Mol. Diagn. 2003; 5(1): 34-41.
  4. Srinivasan M., Sedmak D., Jewell S. Effect of fixatives and tissue processing on the content and integrity of nucleic acids. Am. J. Pathol. 2002; 161(6): 1961-71.
  5. Viertler C., Groelz D., Gundisch S. et al. A new technology for stabilization of biomolecules in tissues for combined histological and molecular analyses. J. Mol. Diagn. 2012; 14(5): 458-66.
  6. Nam S.K., Im J., Kwak Y. et al. Effects of fixation and storage of human tissue samples on nucleic Acid preservation. Korean J. Pathol. 2014; 48(1): 36-42.
  7. Arzt L., Kothmaier H., Quehenberger F. et al. Evaluation of formalin-free tissue fixation for RNA and microRNA studies. Exp. Mol. Pathol. 2011; 91(2): 490-5.
  8. Boon M.E., Kok L.P. Theory and practice of combining coagulant fixation and microwave histoprocessing. Biotech Histochem. 2008; 83(6): 261-77.
  9. Li J., Smyth P., Cahill S. et al. Improved RNA quality and TaqMan Pre-amplification method (PreAmp) to enhance expression analysis from formalin fixed paraffin embedded (FFPE) materials. BMC Biotechnol. 2008; 6; 8: 10.
  10. Turashvili G., Yang W., McKinney S. et al. Nucleic acid quantity and quality from paraffin blocks: defining optimal fixation, processing and DNA/RNA extraction techniques. Exp Mol Pathol. 2012; 92(1): 33-43.
  11. Kashofer K., Viertler C., Pichler M. et al. Quality control of RNA preservation and extraction from paraffin-embedded tissue: implications for RT-PCR and microarray analysis. PLoS One. 2013; 8(7): e70714.
  12. Macabeo-Ong M., Ginzinger D. G., Dekker N. et al. Effect of duration of fixation on quantitative reverse transcription polymerase chain reaction analyses. Mod. Pathol. 2002;15(9): 979-87.
  13. Roberts L., Bowers J., Sensinger K. et al. Identification of methods for use of formalin-fixed, paraffin-embedded tissue samples in RNA expression profiling. Genomics. 2009; 94(5): 341-8.
  14. Gilbert M.T., Haselkorn T., Bunce M. et al. The isolation of nucleic acids from fixed, paraffin-embedded tissues-which methods are useful when? PLoS One. 2007; 2(6): e537.
  15. Имянитов Е.Н., Григорьев М.Ю., Городинская В.М. и др. Способ восстановления ДНК, изолированной из архивных патоморфологических образцов тканей. Патент РФ № 2219243. 20.12.2003.
  16. Ben-Ezra J., Johnson D.A., Rossi J. et al. Effect of fixation on the amplification of nucleic acids from paraffin-embedded material by the polymerase chain reaction. J. Histochem. Cytochem. 1991; 39(3): 351-4.
  17. Bresters D., Schipper M.E, Reesink H.W. et al. The duration of fixation influences the yield of HCV cDNA-PCR products from formalin-fixed, paraffin-embedded liver tissue. J. Virol. Methods. 1994; 48(2/3): 267-72.
  18. Gillespie J.W., Best C.J., Bichsel V.E. et al. Evaluation of nonformalin tissue fixation for molecular profiling studies. Am. J. Pathol. 2002; 160(2): 449-57.
  19. Matsuda Y., Fujii T., Suzuki T. et al. Comparison of fixation methods for preservation of morphology, RNAs, and proteins from paraffin-embedded human cancer cell-implanted mouse models. J. Histochem. Cytochem. 2011; 59(1): 68-75.
  20. Cox M.L., Schray C.L., Luster C.N. et al. Assessment of fixatives, fixation, and tissue processing on morphology and RNA integrity. Exp Mol Pathol. 2006; 80(2): 183-91.
  21. Howat W.J., Wilson B.A. Tissue fixation and the effect of molecular fixatives on downstream staining procedures. Methods. 2014. pii: S1046-2023(14)00060-7.
  22. Belloni B., Lambertini C., Nuciforo P. et al. Will PAXgene substitute formalin? A morphological and molecular comparative study using a new fixative system. J. Clin. Pathol. 2013; 66(2): 124-35.
  23. Groelz D., Sobin L., Branton P. et al. Non-formalin fixative versus formalin-fixed tissue: a comparison of histology and RNA quality. Exp. Mol. Pathol. 2013; 94(1): 188-94.
  24. Vincek V., Nassiri M., Nadji M. et al. A tissue fixative that protects macromolecules (DNA, RNA, and protein) and histomorphology in clinical samples. Lab. Invest. 2003; 83(10): 1427-35.
  25. Talaulikar D., Shadbolt B., McNiven M. et al. DNA amplification from formalin-fixed decalcified paraffin-embedded bone marrow trephine specimens: does the duration of storage matter? Pathology 2008; 40(7):702-6.
  26. Talaulikar D., Gray J. X., Shadbolt B. et al. A comparative study of the quality of DNA obtained from fresh frozen and formalin-fixed decalcified paraffin-embedded bone marrow trephine biopsy specimens using two different methods. J Clin Pathol. 2008; 61(1): 119-23.
  27. Mangham D.C., Williams A., McMullan D.J. et al. Ewing's sarcoma of bone: the detection of specific transcripts in a large, consecutive series of formalin-fixed, decalcified, paraffin-embedded tissue samples using the reverse transcriptase-polymerase chain reaction. Histopathology 2006; 48(4): 363-76.
  28. Wickham C.L., Sarsfield P., Joyner M.V. et al. Formic acid decalcification of bone marrow trephines degrades DNA: alternative use of EDTA allows the amplification and sequencing of relatively long PCR products. Mol. Pathol. 2000; 53(6): 336.
  29. Wickham C.L., Boyce M., Joyner M.V. et al. Amplification of PCR products in excess of 600 base pairs using DNA extracted from decalcified, paraffin wax embedded bone marrow trephine biopsies. Mol. Pathol. 2000; 53(1): 19-23.
  30. Reineke T., Jenni B., Abdou M. T. et al. Ultrasonic decalcification offers new perspectives for rapid FISH, DNA, and RT-PCR analysis in bone marrow trephines. Am. J. Surg. Pathol. 2006; 30(7): 892-6.
  31. Imaizumi K., Taniguchi K., Ogawa Y. An evaluation of the effect of microwave irradiation on bone decalcification aimed to DNA extraction. Leg. Med. (Tokyo) 2013; 15(5): 272-7.
  32. Farahani R. M., Nguyen K.A., Simonian M. et al. Adaptive calcified matrix response of dental pulp to bacterial invasion is associated with establishment of a network of glial fibrillary acidic protein+/glutamine synthetase+ cells. Am. J. Pathol. 2010; 177(4): 1901-14.
  33. Sano M., Sugitani M., Ishige T. et al. Supplemental utility of nested PCR for the pathological diagnosis of disseminated trichosporonosis. Virchows Arch. 2007; 451(5): 929-35.
  34. Yamasaki H., Nagase T., Kiyoshige Y. et al. A case of intramuscular cysticercosis diagnosed definitively by mitochondrial DNA analysis of extremely calcified cysts. Parasitol. Int. 2006;55(2):127-30.
  35. Evers D.L., Fowler C.B., Cunningham B.R. et al. The effect of formaldehyde fixation on RNA: optimization of formaldehyde adduct removal. J. Mol. Diagn. 2011; 13(3): 282-8.
  36. Vincek V., Nassiri M., Knowles J. et al. Preservation of tissue RNA in normal saline. Lab. Invest. 2003; 83(1): 137-8.
  37. Chu W. S., Liang Q., Tang Y. et al. Ultrasound-accelerated tissue fixation/processing achieves superior morphology and macromolecule integrity with storage stability. J. Histochem. Cytochem. 2006; 54(5): 503-13.
  38. Morales A.R., Essenfeld H., Essenfeld E. et al. Continuous-specimen-flow, high-throughput, 1-hour tissue processing. A system for rapid diagnostic tissue preparation. Arch. Pathol. Lab. Med. 2002; 126(5): 583-90.
  39. Nassiri M., Nadji M. Experience with a Molecular-friendly Histology System for Preservation of Biomolecules in Breast Cancer Tissue. Connection 2008; 12: 72-74.
  40. van Eijk R., Stevens L., Morreau H. et al. Assessment of a fully automated high-throughput DNA extraction method from formalin-fixed, paraffin-embedded tissue for KRAS, and BRAF somatic mutation analysis. Exp. Mol. Pathol. 2013; 94(1):121-5.
  41. Bonin S., Hlubek F., Benhattar J. et al. Multicentre validation study of nucleic acids extraction from FFPE tissues. Virchows Arch. 2010; 457(3): 309-17.
  42. Hu Y. C., Zhang Q., Huang Y. H. et al. Comparison of two methods to extract DNA from formalin-fixed, paraffin-embedded tissues and their impact on EGFR mutation detection in non-small cell lung carcinoma. Asian. Pac. J. Cancer Prev. 2014; 15(6): 2733-7.
  43. Steinau M., Patel S.S. 0, Unger E.R. et al. Efficient DNA extraction for HPV genotyping in formalin-fixed, paraffin-embedded tissues. J. Mol. Diagn. 2011; 13(4): 377-81.
  44. Lin J., Kennedy S. H., Svarovsky T. et al. High-quality genomic DNA extraction from formalin-fixed and paraffin-embedded samples deparaffinized using mineral oil. Anal. Biochem. 2009; 395(2): 265-7.
  45. Senguven B., Baris E., Oygur T. et al. Comparison of methods for the extraction of DNA from formalin-fixed, paraffin-embedded archival tissues. Int. J. Med. Sci. 2014; 11(5): 494-9.
  46. Dedhia P., Tarale S., Dhongde G. et al. Evaluation of DNA extraction methods and real time PCR optimization on formalin-fixed paraffin-embedded tissues. Asian Pac. J. Cancer Prev. 2007; 8 (1): 55-9.

Supplementary files

Supplementary Files
Action
1. JATS XML

Copyright (c) 2014 Eco-Vector



СМИ зарегистрировано Федеральной службой по надзору в сфере связи, информационных технологий и массовых коммуникаций (Роскомнадзор).
Регистрационный номер и дата принятия решения о регистрации СМИ: 

This website uses cookies

You consent to our cookies if you continue to use our website.

About Cookies