The Effect of Fibrosis on DNA Yield from Formalin Fixed Paraffin Embedded Tissues

Muhammad Naveed; Hassan  Tariq; Asma Gul; Natasha Arzo; Muhammad Hussain; Sumaira Buksh

doi:10.51253/pafmj.v74i3.8923

Authors

Muhammad Naveed Department of Histopathology, Armed Forces Institute of Pathology/National University of Medical Sciences (NUMS) Rawalpindi Pakistan
Hassan Tariq Department of Histopathology, Armed Forces Institute of Pathology/National University of Medical Sciences (NUMS) Rawalpindi Pakistan
Asma Gul Department of Histopathology, Armed Forces Institute of Pathology/National University of Medical Sciences (NUMS) Rawalpindi Pakistan
Natasha Arzo Department of Histopathology, Armed Forces Institute of Pathology/National University of Medical Sciences (NUMS) Rawalpindi Pakistan
Muhammad Hussain Department of Histopathology, Armed Forces Institute of Pathology/National University of Medical Sciences (NUMS) Rawalpindi Pakistan
Sumaira Buksh Department of Histopathology, Combined Military Hospital, Malir/National University of Medical Sciences (NUMS) Rawalpindi Pakistan

DOI:

https://doi.org/10.51253/pafmj.v74i3.8923

Keywords:

Deoxyribonucleic acid, Formalin-fixed paraffin-embedded, Fibrosis

Abstract

Objective: To report the effect of fibrosis on yield of Deoxyribonucleic Acid extraction from Formalin-Fixed Paraffin-Embedded tissue.

Study Design: Cross sectional study.

Place and Duration of Study: Department of Molecular Pathology, Armed Forces Institute of Pathology, Rawalpindi Pakistan, Jul to Dec 2021.

Methodology: Fifty-four Formalin-Fixed Paraffin-Embedded tissues having size <2cm containing fibrosis (Mild, Moderate, Severe) were included in the study. Formalin-Fixed Paraffin-Embedded tissues having tissue size > 2cm were excluded. Deoxyribonucleic Acid was extracted and quantified from Formalin-Fixed Paraffin-Embedded blocks.

Results: Nine (17%) Formalin-Fixed Paraffin-Embedded tissues had no fibrosis, 28(51%) had Mild fibrosis, 9(17%) and 8(15%) had Moderate and Severe fibrosis. Measurement scale in 5 different stages for evaluation of our quantified results were used. For specimens with no fibrosis the DNA quantity fell on scale 1, 0(0%); on scale 2, 1(11%); on scale 3, 0(0%); on scale 4, 1(11%); and on scale 5, 7(78%). Deoxyribonucleic Acid yield in moderate fibrosis specimens fell on scale 1, 0(0%)’ on scale 2, 7(78%); on scale 3, 0(0%); on scale 4, 1(11%); and on scale 5, 1(11%). Among severe fibrosis the Deoxyribonucleic Acid quantity fall on scale 1, 5(62%); on scale 2, 3(38%); on scale 3, 0(0%); on scale 4, 0(0%); and on scale 5, 0(0%).

Conclusion: Formalin-Fixed Paraffin-Embedded tissues having severe fibrosis resulted in significantly lower Deoxyribonucleic Acid yield as compared to Formalin-Fixed Paraffin-Embedded tissues having no fibrosis

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Author Biography

Natasha Arzo, Department of Histopathology, Armed Forces Institute of Pathology/National University of Medical Sciences (NUMS) Rawalpindi Pakistan

The author contributed in data analysis and proof reading

References

Blow N. Tissue issues. Nature. 2007; 448(7156): 959–960.

https://doi.org/10.1038/448959a

Mathieson W, Thomas GA. Why Formalin-fixed, Paraffin-embedded Biospecimens Must Be Used in Genomic Medicine: An Evidence-based Review and Conclusion. J Histochem Cytochem 2020; 68(8): 543–552.

https://doi.org/10.1369/0022155420945050

Chung MJ, Lin W , Dong L, Li X. Tissue Requirements and DNA Quality Control for Clinical Targeted Next-Generation Sequencing of Formalin-Fixed, Paraffin-Embedded Samples: A Mini-Review of Practical Issues. J Mol Genet Med 2017; 11(262): 1747–0862. https://doi.org/10.4172/1747-0862.1000262

Zhu Y, Weiss T, Zhang Q, Sun R, Wang B, Yi X, et al. High-throughput proteomic analysis of FFPE tissue samples facilitates tumor stratification. Mol Oncol 2019; 13(11): 2305–2328.

https://doi.org/10.1002/1878-0261.12570

Austin MC, Smith C, Pritchard CC, Tait JF. DNA Yield from Tissue Samples in Surgical Pathology and Minimum Tissue Requirements for Molecular Testing. Arch Pathol Lab Med 2016; 140(2): 130–133. https://doi.org/10.5858/arpa.2015-0082-OA

Gaffney EF, Riegman PH, Grizzle WE, Watson PH. Factors that drive the increasing use of FFPE tissue in basic and translational cancer research. Biotech Histochem 2018; 93(5): 373–386.

https://doi.org/10.1080/10520295.2018.1446101

Lu XJD, Liu KYP, Zhu YS, Cui C, Poh CF. Using ddPCR to assess the DNA yield of FFPE samples. Biomol Detect Quantif 2018; 16: 5–11. https://doi.org/10.1016/j.bdq.2018.10.001

Singh H, Narayan B, Urs AB, Kumar Polipalli S, Kumar S. A novel approach for extracting DNA from formalin-fixed paraffin-embedded tissue using microwave. Med J Armed Forces India 2020; 76(3): 307–311. https://doi.org/10.1016/j.mjafi.2019.02.007

Andreassen CN, Sørensen FB, Overgaard J, Alsner J. Optimisation and validation of methods to assess single nucleotide polymorphisms (SNPs) in archival histological material. Radiother Oncol 2004; 72(3): 351–356.

https://doi.org/10.1016/j.radonc.2004.07.006

Nechifor-Boilǎ A, Banescu C, Zahan AE, Moldovan V, Szasz E, Borda A. DNA isolation from achieved formalin-fixed paraffin-embedded tissues in a series of 212 thyroid carcinoma cases: The influence of preanalytical factors on DNA quantity and purity. J Investig Med 2020; 68(3): 792–798.

https://doi.org10.1136/jim-2019-001134

Arreaza G, Qiu P, Pang L, Albright A, Hong LZ, Marton MJ, et al. Pre-analytical considerations for successful next-generation sequencing (NGS): Challenges and opportunities for formalin-fixed and paraffin-embedded tumor tissue (FFPE) samples. Int J Mol Sci 2016; 17(9): 1579. https://doi.org/10.3390/ijms17091579

Bhagwate AV, Liu Y, Winham SJ, McDonough SJ, Stallings-Mann ML, Heinzen EP, et al. Bioinformatics and DNA-extraction strategies to reliably detect genetic variants from FFPE breast tissue samples. BMC Med Genomic 2019; 20(1).

https://doi.org/10.1186/s12864-019-6056-8

Shi SR, Cote RJ, Wu L, Liu C, Datar R, Shi Y, et al. DNA extraction from archival formalin-fixed, paraffin-embedded tissue sections based on the antigen retrieval principle: Heating under the influence of pH. J Histochem Cytochem 2002; 50(8): 1005–1011. https://doi.org/10.1177/002215540205000802

Jillwin J, Rudramurthy SM, Singh S, Bal A, Das A, Radotra B, et al. Molecular identification of pathogenic fungi in formalin-fixed and paraffin-embedded tissues. J Med Microbiol 2020; 70(2): 001282. https://doi.org/10.1099/JMM.0.001282

Patel PG, Selvarajah S, Guérard KP, Bartlett JMS, Lapointe J, Berman DM, et al. Reliability and performance of commercial RNA and DNA extraction kits for FFPE tissue cores. PLoS One 2017; 12(6): e0179732.

https://doi.org/10.1371/journal.pone.0179732

Kakimoto Y, Tanaka M, Kamiguchi H, Ochiai E, Osawa M. MicroRNA stability in FFPE tissue samples: Dependence on gc content. PLoS One 2016; 11: 387–388.

https://doi.org/10.1371/journal.pone.0163125

Yi QQ, Yang R, Shi JF, Zeng NY, Liang DY, Sha S, et al. Effect of preservation time of formalin-fixed paraffin-embedded tissues on extractable DNA and RNA quantity. J Int Med Res 2020; 48(6): 0300060520931259. https://doi.org/10.1177/0300060520931259

Frazer Z, Yoo C, Sroya M, Bellora C, DeWitt BL, Sanchez I, et al. Effect of different proteinase k digest protocols and deparaffinization methods on yield and integrity of DNA extracted from formalin-fixed, paraffin-embedded tissue. J Histochem Cytochem 2020; 68(3): 171–184.

https://doi.org/10.1369/0022155420906234

Lee HS, Park KU, Park JO, Chang HE, Song J, Choe G. Rapid, sensitive, and specific detection of Mycobacterium tuberculosis complex by real-time PCR on paraffin-embedded human tissues. J Mol Diagnostics 2011; 13(4): 390–394.

https://doi.org/10.1016/j.jmoldx.2011.02.004

Zsikla V, Baumann M, Cathomas G. Effect of buffered formalin on amplification of DNA from paraffin wax embedded small biopsies using real-time PCR. J Clin Pathol 2004; 57(6): 654–656.

https://doi.org/10.1136/jcp.2003.013961

Kim S, Labbe RG, Ryu S. Inhibitory effects of collagen on the PCR for detection of Clostridium perfringens. Appl Environ Microbiol 2000; 66(3): 1213-1215.

https://doi.org/10.1128/AEM.66.3.1213-1215.2000

Piersma B, Hayward MK, Weaver VM. Fibrosis and cancer: A strained relationship. Biochim Biophys Acta Rev Cancer 2020; 1873(2): 188356.

https://doi.org/10.1016/j.bbcan.2020.188356