DNA/RNA Degradation Rate in Long Term Fixed Museum Specimens
ABSTRACT
In today’s research driven society, it has become commonplace for institutions to rely upon DNA and RNA extraction techniques to help obtain genomic data from old specimens. Generally, specimens are preserved for future gross examination and/or teaching. Using histological examination of specimens from museum jars from the Pathology Department at the Indiana University School of Medicine, the sequential and chronological degradation of DNA and RNA has been studied. We examined gross specimens from 1920 to 2000. We evaluated histologic preservation of kidney, liver, heart, lung, spleen, uterus and brain for nuclear structure in these samples. Nuclear preservation was based on amount of nuclei per microscopic field and the crispness of the nuclear membrane and internal features. The nuclei in high lipid tissues such as the brain were found to degrade at a quicker rate than dense tissues such as the heart and uterus. Our study has shown that specimens preserved beyond fifty years were likely to have little to no nuclei left, thus indicating that there was little to no DNA and RNA remaining. This technique of histologic evaluation is an important finding and a general guideline which may save research institutions from the expensive process of DNA and RNA extraction.
In today’s research driven society, it has become commonplace for institutions to rely upon DNA and RNA extraction techniques to help obtain genomic data from old specimens. Generally, specimens are preserved for future gross examination and/or teaching. Using histological examination of specimens from museum jars from the Pathology Department at the Indiana University School of Medicine, the sequential and chronological degradation of DNA and RNA has been studied. We examined gross specimens from 1920 to 2000. We evaluated histologic preservation of kidney, liver, heart, lung, spleen, uterus and brain for nuclear structure in these samples. Nuclear preservation was based on amount of nuclei per microscopic field and the crispness of the nuclear membrane and internal features. The nuclei in high lipid tissues such as the brain were found to degrade at a quicker rate than dense tissues such as the heart and uterus. Our study has shown that specimens preserved beyond fifty years were likely to have little to no nuclei left, thus indicating that there was little to no DNA and RNA remaining. This technique of histologic evaluation is an important finding and a general guideline which may save research institutions from the expensive process of DNA and RNA extraction.
Cite this paper
Cook, S. , Dodge, C. , Morgan, R. and Sandusky, G. (2015) DNA/RNA Degradation Rate in Long Term Fixed Museum Specimens. Forensic Medicine and Anatomy Research, 3, 1-6. doi: 10.4236/fmar.2015.31001.
Cook, S. , Dodge, C. , Morgan, R. and Sandusky, G. (2015) DNA/RNA Degradation Rate in Long Term Fixed Museum Specimens. Forensic Medicine and Anatomy Research, 3, 1-6. doi: 10.4236/fmar.2015.31001.
References
[1] Miething, F., Hering, S., Hanschke, B. and Dressler, J. (2006) Effect of Fixation to the Degradation of Nuclear and Mitochondrial DNA in Different Tissues. Journal of Histochemistry & Cytology, 54, 371-374. [2] Stephen, M., Hewitt, M.D., et al. (2008) Tissue Handling and Specimen Preparation in Surgical Pathology Issues Concerning the Recovery of Nucleic Acids from Formalin-Fixed, Paraffin-Embedded Tissue. Archives of Pathology & Laboratory Medicine, 132, 1929-1935. [3] Xie, R., Chung, J.-Y., Ylaya, K., Williams, R.L., Guerrero, N., Nakatsuka, N., Badie, C. and Hewitt, S.M. (2011) Factors Influencing the Degradation of Archival Formalin-Fixed Paraffin-Embedded Tissue Sections. Journal of Histochemistry & Cytochemistry, 59, 356-365.
http://dx.doi.org/10.1369/0022155411398488 [4] Jewell, S., Sedmak, D. and Srinivasan, M. (2002) Effect of Fixatives and Tissue Processing on the Content and Integrity of Nucleic Acids. American Journal of Pathology, 161, 1961-1971. [5] Klopfleisch, R., Weiss, A.T. and Gruber, A.D. (2011) Excavation of a Buried Treasure—DNA, mRNA, miRNA and Protein Analysis in Formalin Fixed, Paraffin Embedded Tissues. Histology and Histopathology, 26, 797-810. [6] Turashvili, G., Yang, W., McKinney, S., Kalloger, S., Gale, N., Ng, Y., Chow, K., Bell, L., Lorette, J., Carrier, M., Luk, M., Aparicio, S., Huntsman, D. and Yip, S. (2011) Nucleic Acid Quantity and Quality from Paraffin Blocks: Defining Optimal Fixation, Processing and DNA/RNA Extraction Techniques. Experimental and Molecular Pathology, 92, 33- 43. http://dx.doi.org/10.1016/j.yexmp.2011.09.013 [7] Stan, A.D., Ghose, S., Gao, X.-M., Roberts, R.C., Lewis-Amezcua, K., Hatanpaa, K.K. and Tamminga, C.A. (2006) Human Postmortem Tissue: What Quality Markers Matter? Brain Research, 1123, 1-11.
http://dx.doi.org/10.1016/j.brainres.2006.09.025 [8] Chung, J.-Y., Braunschweig, T., Williams, R., Guerrero, N., Hoffman, K.M., Kwon, M., Song, Y.K., Libutti, S.L. and Hewitt, S.M. (2008) Factors in Tissue Handling and Processing That Impact RNA Obtained from Formalin-Fixed, Paraffin-Embedded Tissue. Journal of Histochemistry & Cytochemistry, 56, 1033-1042. [9] Schander, C. and Halaynch, K.M. (2003) DNA, PCR and Formalinized Animal Tissue—A Short Review and Protocols. Organisms Diversity & Evolution, 3, 195-205. http://dx.doi.org/10.1078/1439-6092-00071 [10] Niland, E.E., McGuire, A., Cox, M.H. and Sandusky, G.E. (2012) High Quality DNA Obtained with an Automated DNA Extraction Method with 70+ Year Old Formalin-Fixed Celloidin-Embedded (FFCE) Blocks from the Indiana Medical History Museum. American Journal of Translational Research, 4, 198-205.
[1] Miething, F., Hering, S., Hanschke, B. and Dressler, J. (2006) Effect of Fixation to the Degradation of Nuclear and Mitochondrial DNA in Different Tissues. Journal of Histochemistry & Cytology, 54, 371-374. [2] Stephen, M., Hewitt, M.D., et al. (2008) Tissue Handling and Specimen Preparation in Surgical Pathology Issues Concerning the Recovery of Nucleic Acids from Formalin-Fixed, Paraffin-Embedded Tissue. Archives of Pathology & Laboratory Medicine, 132, 1929-1935. [3] Xie, R., Chung, J.-Y., Ylaya, K., Williams, R.L., Guerrero, N., Nakatsuka, N., Badie, C. and Hewitt, S.M. (2011) Factors Influencing the Degradation of Archival Formalin-Fixed Paraffin-Embedded Tissue Sections. Journal of Histochemistry & Cytochemistry, 59, 356-365.
http://dx.doi.org/10.1369/0022155411398488 [4] Jewell, S., Sedmak, D. and Srinivasan, M. (2002) Effect of Fixatives and Tissue Processing on the Content and Integrity of Nucleic Acids. American Journal of Pathology, 161, 1961-1971. [5] Klopfleisch, R., Weiss, A.T. and Gruber, A.D. (2011) Excavation of a Buried Treasure—DNA, mRNA, miRNA and Protein Analysis in Formalin Fixed, Paraffin Embedded Tissues. Histology and Histopathology, 26, 797-810. [6] Turashvili, G., Yang, W., McKinney, S., Kalloger, S., Gale, N., Ng, Y., Chow, K., Bell, L., Lorette, J., Carrier, M., Luk, M., Aparicio, S., Huntsman, D. and Yip, S. (2011) Nucleic Acid Quantity and Quality from Paraffin Blocks: Defining Optimal Fixation, Processing and DNA/RNA Extraction Techniques. Experimental and Molecular Pathology, 92, 33- 43. http://dx.doi.org/10.1016/j.yexmp.2011.09.013 [7] Stan, A.D., Ghose, S., Gao, X.-M., Roberts, R.C., Lewis-Amezcua, K., Hatanpaa, K.K. and Tamminga, C.A. (2006) Human Postmortem Tissue: What Quality Markers Matter? Brain Research, 1123, 1-11.
http://dx.doi.org/10.1016/j.brainres.2006.09.025 [8] Chung, J.-Y., Braunschweig, T., Williams, R., Guerrero, N., Hoffman, K.M., Kwon, M., Song, Y.K., Libutti, S.L. and Hewitt, S.M. (2008) Factors in Tissue Handling and Processing That Impact RNA Obtained from Formalin-Fixed, Paraffin-Embedded Tissue. Journal of Histochemistry & Cytochemistry, 56, 1033-1042. [9] Schander, C. and Halaynch, K.M. (2003) DNA, PCR and Formalinized Animal Tissue—A Short Review and Protocols. Organisms Diversity & Evolution, 3, 195-205. http://dx.doi.org/10.1078/1439-6092-00071 [10] Niland, E.E., McGuire, A., Cox, M.H. and Sandusky, G.E. (2012) High Quality DNA Obtained with an Automated DNA Extraction Method with 70+ Year Old Formalin-Fixed Celloidin-Embedded (FFCE) Blocks from the Indiana Medical History Museum. American Journal of Translational Research, 4, 198-205.