DNA Methylation-Based Age Estimation in the Forensic Field

Ja Hyun An; Kyoung-Jin Shin; Ajin Choi; Woo Ick Yang; Hwan Young Lee

doi:10.7580/kjlm.2013.37.1.1

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An, Shin, Choi, Yang, and Lee: DNA Methylation-Based Age Estimation in the Forensic Field

종 설

Korean J Leg Med 2013;37(1):1-8.

Published online: 17 January 2013

DOI: https://doi.org/10.7580/kjlm.2013.37.1.1

DNA Methylation-Based Age Estimation in the Forensic Field

Ja Hyun An¹, Kyoung-Jin Shin^1,², Ajin Choi¹, Woo Ick Yang¹, Hwan Young Lee^1,²

¹Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, Korea

²Human Identification Research Center, Yonsei University, Seoul, Korea

이 논문은 2012년도 정부(교육과학기술 부)의 재원으로 한국연구재단의 일반연구 자지원사업의 지원을 받아 수행된 것임(과 제번호: 2012R1A1A2007031). 책임저자 : 이환영 (120-752) 서울시 서대문구 연세로 50, 연세대학교 의과대학 법의학과 전화 : +82-2-2228-2482 FAX : +82-2-362-0860 E-mail : hylee192@yuhs.ac

Received 31 January 2013 Revised 8 February 2013 Accepted 21 February 2013

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

The estimation of age is an important issue in forensic science, and the forensic community has attempted many times to establish methods for solving this issue. Aging leads to alterations in tissues and organs at the molecular level. These alterations at the molecular level may aid forensic scientists to estimate the age of a living person or a dead body. Initially, the focus was on the genetic components of aging, but recently, epigenetic mechanisms have emerged as the key contributors to the alterations in genome structure and function that accompany aging. In particular, DNA methylation is one of the best-understood mechanisms, and it has been suggested as a promising biomarker for age estimation in many studies. In this review, we summarize the recent studies on age-associated DNA methylation changes in different tissues and discuss its possible and practical applications in forensics.

Keywords: Key words, DNA methylation, Age estimation, Epigenetics, Forensics

REFERENCES

1. Kayser M, de Knijff P. Improving human forensics through advances in genetics, genomics and molecular biology. Nat Rev Genet. 2011; 12:179–92.

2. Kayser M, Schneider PM. DNA-based prediction of human externally visible characteristics in forensics: motivations, scientific challenges, and ethical considerations. Forensic Sci Int Genet. 2009; 3:154–61.

3. Ohtani S. Estimation of age from dentin by using the racemization reaction of aspartic acid. Am J Forensic Med Pathol. 1995; 16:158–61.

4. Sato Y, Kondo T, Ohshima T. Estimation of age of human cadavers by immunohistochemical assessment of ad-vanced glycation end products in the hippocampus. Histopathology. 2001; 38:217–20.

5. Harley C, Futcher AB, Greider CW. Telomeres shorten during ageing of human fibroblasts. Nature. 1990; 345:458–60.

6. Tsuji A, Ishiko A, Takasaki T, et al. Estimating age of humans based on telomere shortening. Forensic Sci Int. 2002; 126:197–9.

7. Meissner C, Ritz-Timme S. Molecular pathology and age estimation. Forensic Sci Int. 2010; 203:34–43.

8. Zubakov D, Liu F, van Zelm MC, et al. Estimating human age from T-cell DNA rearrangements. Curr Biol. 2010; 20:970–1.

9. Russo VEA, Martienssen RA, Riggas AD. Epigenetic mechanisms of gene regulation. New York: Cold Spring Harbor Laboratory Press;1996.

10. Gonzalo S. Epigenetic alterations in aging. J Appl Physiol. 2010; 109:586–97.

11. Miranda TB, Jones PA. DNA methylation: the nuts and bolts of repression. J Cell Physiol. 2007; 213:384–90.

12. Bird A. DNA methylation patterns and epigenetic memory. Genes Dev. 2002; 16:6–21.

13. Wilson VL, Smith RA, Ma S, et al. Genomic 5-methyldeoxycytidine decreases with age. J Biol Chem. 1987; 262:9948–51.

14. Vanyushin BF, Nemirovsky LE, Klimenko VV, et al. The 5-methylcytosine in DNA of rats. Tissue and age specificity and the changes induced by hydrocortisone and other agents. Gerontologia. 1973; 19:138–52.

15. Fuke C, Shimabukuro M, Petronis A, et al. Age related changes in 5-methylcytosine content in human peripheral leukocytes and placentas: an HPLC-based study. Ann Hum Genet. 2004; 68:196–204.

16. Casillas MA Jr, Lopatina N, Andrews LG, et al. Transcriptional control of the DNA methyltransferases is altered in aging and neoplastically-transformed human fibroblasts. Mol Cell Biochem. 2003; 252:33–43.

17. Murgatroyd C, Wu Y, Bockmuhl Y, et al. The Janus face of DNA methylation in aging. Aging. 2010; 2:107–10.

18. Rakyan VK, Down TA, Maslau S, et al. Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains. Genome Res. 2010; 20:434–9.

19. Bocklandt S, Lin W, Sehl ME, et al. Epigenetic predictor of age. PLoS ONE. 2011; 6:e14821.

20. Koch CM, Suschek CV, Lin Q, et al. Specific Age-associated DNA methylation changes in human dermal fibroblasts. PLoS ONE. 2011; 6:e16679.

21. Gronniger E, Weber B, Heil O, et al. Aging and chronic sun exposure cause distinct epigenetic changes in human skin. PLoS Genet. 2010; 6:e1000971.

22. Bocker MT, Hellwig I, Breiling A, et al. Genomewide promoter DNA methylation dynamics of human hematopoietic progenitor cells during differentiation and aging. Blood. 2011; 117:e182–9.

23. Teschendorff AE, Menon U, Gentry-Maharaj A, et al. Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer. Genome Res. 2010; 20:440–6.

24. Koch C, Wagner W. Epigenetic-aging-signature to determine age in different tissues. Aging. 2011; 3:1018–27.

25. Bell JT, Tsai PC, Yang TP, et al. Epigenomewide scans identify differentially methylated regions for age and age-related phenotypes in a healthy ageing population. PLoS Genet. 2012; 8:e1002629.

26. Simm A, Nass N, Bartling B, et al. Potential biomarkers of ageing. Biol Chem. 2008; 389:257–65.

27. Dedeurwaerder S, Defrance M, Calonne E, et al. Evaluation of the infinium methylation 450K technology.

28. Garagnani P, Bacalini MG, Pirazzini C, et al. Methylation of ELOVL2 gene as a new epigenetic marker of age. Aging Cell. 2012; 11:1132–4.

29. Hannum G, Ginney J, Zhao L, et al. Genomewide methylation profiles reveal quantitative views of human aging rates. Mol Cell. 2013; 49:359–67.

30. Zou H, Hastie T. Regularization and variable selection via the elastic net. J R Statist Soc B. 2005; 67:301–20.

31. Heyn H, Li N, Ferreira HJ, et al. Distinct DNA methy-lomes of newborns and centenarians. Proc Natl Acad Sci USA. 2012; 109:10522–7.

32. Bibikova M, Le J, Barnes B, et al. Genomewide DNA methylation profiling using Infinium^� assay. Epigenomics. 2009; 1:177–200.

33. Shames DS, Minna JD, Gazdar AF. Methods for detecting DNA methylation in tumors: from bench to bedside. Cancer Lett. 2007; 251:187–98.

34. Frommer M, McDonald LE, Millar DS, et al. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci U S A. 1992; 89:1827–31.

35. Zhang Y, Rohde C, Tierling S, et al. DNA methylation analysis by bisulfite conversion, cloning, and sequencing of individual clones. Methods Mol Biol. 2009; 507:177–87.

36. van den Boom D, Ehrich M. Mass spectrometric analysis of cytosine methylation by base-specific cleavage and primer extension methods. Methods Mol Biol. 2009; 507:207–27.

37. Dejeux E, El abdalaoui H, Gut IG, et al. Identification and quantification of differentially methylated loci by the pyrosequencing technology. Methods Mol Biol. 2009; 507:189–205.

38. Licchesi JD, Herman JG. Methylation-specific PCR. Methods Mol Biol. 2009; 507:305–23.

39. Brena RM, Plass C. Bio-COBRA: absolute quantification of DNA methylation in electrofluidics chips. Methods Mol Biol. 2009; 507:257–69.

40. Kaminsky Z, Petronis A. Methylation SNaPshot: a method for the quantification of site-specific DNA methylation levels. Methods Mol Biol. 2009; 507:241–55.

41. Oakes CC, La Salle S, Trasler JM, et al. Restriction digestion and real-time PCR (qAMP). Methods Mol Biol. 2009; 507:271–80.

42. Frumkin D, Wasserstrom A, Budowle B, et al. DNA methylation-based forensic tissue identification. Forensic Sci Int Genet. 2011; 5:517–24.

43. Lee HY, Park MJ, Choi A, et al. Potential forensic application of DNA methylation profiling to body fluid identification. Int J Legal Med. 2012; 126:55–62.

44. Kayser M, Liu F, Janssens AC, et al. Three genomewide association studies and a linkage analysis identify HERC2 as a human iris color gene. Am J Hum Genet. 2008; 82:411–23.

45. Liu F, Wollstein A, Hysi PG, et al. Digital quantification of human eye color highlights genetic association of three new loci. PLoS Genet. 2010; 6:e1000934.

46. Branicki W, Brudnik U, Kupiec T, et al. Determination of phenotype associated SNPs in the MC1R gene. J Forensic Sci. 2007; 52:349–54.

Table 1.

Tissue-Specific Age-Associated DNA Methylation Changes

Target ID^∗	Symbol	Description	Methylation change^†	Tissue or cell type	Ref.
cg00059225	GLRA1	Glycine receptor alpha 1	Increase	Blood, saliva	18,19
cg15747595	TSPYL5	TSPY-like 5	Increase	Blood, saliva	18,19
cg16232126	SLC5A7	Solute carrier family 5 member 7	Increase	Blood, saliva	18,19
cg18236477	ATP8A2	ATPase aminophospholipid transporter class I type 8A member 2	Increase	Blood, saliva	18,19
cg19594666	LEP	Leptin	Increase	Blood, saliva	18,19
cg19885761	CPLX2	Complexin 2	Increase	Blood, saliva	18,19
cg19945840	B3GALT6	BetaGal beta 1, 3-galactosyltransferase polypeptide 6	Increase	Blood, saliva	18,19
cg21801378	BRUNOL6	CUGBP Elav-like family member 6	Increase	Blood, saliva	18,19
cg09809672	EDARADD	Edar associated death domain	Decrease	Saliva	19
cg27210390	TOM1L1	Target of myb1-like 1	Decrease	Saliva	19
cg12815142	SPAG7	Sperm associated antigen 7	Increase	Fibroblasts	20
			Decrease	MSC^†	20
cg10210238	CDKN2B	Cyclin-dependent kinase inhibitor 2B isoform 2	Increase	Fibroblasts	20
			Decrease	MSC	20
cg16601385	CFD	Complement factor D preproprotein	Decrease	Fibroblasts	20
			Increase	MSC	20
cg06144905	PIPOX	L-pipecolic acid oxidase	Increase	Fibrblasts, MSC	20
cg23081213	PRKAG3	AMP-activated protein kinase; non-catalytic gamma-3 subunit	Decrease	Fibrblasts, MSC	20
cg21660392	ABCA8	ATP-binding cassette; sub-family A member 8	Decrease	Fibrblasts, MSC	20
cg13870866	TBX20	T-box 20	Increase	Blood	25
cg06639320	FHL2	Four and a half LIM domains 2	Increase	Blood	28
cg16419235	PENK	Proenkephalin	Increase	Blood	28

^∗ Target ID: Reference ID of the Infinium HumanMethylation Beadchip platform

^† Methylation change: Methylation change upon aging

^† MSC: Mesenchymal stem cells

Table 2.

Age-Associated DNA Methylation Changes Common to Various Cell Types

Target ID	Symbol	Description	Methylation change^†	Cell type	Ref.
cg03664992	BMP8A	Bone morphogenetic protein 8a	Increase	Various cell type	23
cg13921352	FAM19A4	Family with sequence similarity 19 member A4	Increase	Various cell type	23
cg27320127	KCNK12	Potassium channel subfamily K member 12	Increase	Various cell type	18, 19, 23
cg04528819	KLF14	Kruppel-like factor 14	Increase	Various cell type	23
cg02620013	MLNR	Motilin receptor	Increase	Various cell type	23
cg02844545	GCM2	Glial cells missing homolog 2	Increase	Various cell type	23
cg04084157	VGF	VGF nerve growth factor inducible	Increase	Various cell type	23
cg21530890	SOX8	SRY (sex determining region Y)-box 8	Increase	Various cell type	23
cg07533148	TRIM58	Tripartite motif-containing 58	Increase	Various cell type	24
cg01530101	KCNQ1DN	KCNQ1 downstream neighbor	Increase	Various cell type	24
cg12799895	NPTX2	Neuronal pentraxin II	Increase	Various cell type	18, 19, 23, 24
cg25148589	GRIA2	Glutamate receptor ionotropic AMPA 2	Increase	Various cell type	23, 24
cg23571857	BIRC4BP	XIAP associated factor-1	Decrease	Various cell type	24
cg16867657	ELOVL2	ELOVL fatty acid elongase 2	Increase	Various cell type	28, 29

^∗ Target ID: Reference ID of the Infinium HumanMethylation Beadchip platform

^† Methylation change: Methylation change upon aging

Table 3.

Techniques Allowing the Analysis of DNA Methylation at Specific Gene Loci

Technique^∗	Bisulfite conversion	CpG sites^†	Advantages	Inconveniences	Ref.
Bisulfite sequencing	Yes	5-50	Gold standard	Labor-intensive	35
EpiTYPER^©	Yes	5-50	Commercial service available	Cost	36
Pyrosequencing	Yes	5-20	Commercial service available	Cost	37
MSP	Yes	1-3	Simplicity	Lack of quantitative result	38
COBRA	Yes	1	Sensitivity	Limited to specific restriction targets	39
MS-SnuPE	Yes	1	Sensitivity	Requires a capillary electrophoresis instrument^†	40
MSRE-PCR	No	1	Cost and time-saving	Limited to specific restriction targets	41

^∗ MSP: Methylation specific PCR; COBRA: Combined bisulfite restriction analysis of DNA; MS-SnuPE: Methylation-sensitive single nucleotide primer extension; MSRE-PCR: Methylation-sensitive restriction endonuclease PCR

^† CpG sites: Number of CpG sites interrogated per monoplex assay

^† Requiring a capillary electrophoresis instrument is no problem in general forensic laboratories.

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