Proof of concept study of age-dependent DNA methylation markers across different tissues by massive parallel sequencing

• Published in: Forensic science international : genetics Vol. 36; pp. 152 - 159
• Main Authors: Naue, Jana, Sänger, Timo, Hoefsloot, Huub C.J., Lutz-Bonengel, Sabine, Kloosterman, Ate D., Verschure, Pernette J.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01-09-2018
• Subjects: Adolescent; Adult; Age determination; Aged; Aged, 80 and over; Aging - genetics; Bone and Bones - chemistry; Brain Chemistry; Child; Child, Preschool; CpG Islands - genetics; DNA Methylation; Female; Forensic epigenetics; Genetic Markers; High-Throughput Nucleotide Sequencing; Humans; Infant; Infant, Newborn; Linear Models; Male; Massive parallel sequencing; Middle Aged; Mouth Mucosa - chemistry; Muscle, Skeletal - chemistry; Pilot Projects; Polymerase Chain Reaction; Polymorphism, Single Nucleotide; Proof of Concept Study; Saliva - chemistry; Sequence Analysis, DNA; Young Adult; DNA methylation; Massive parallel sequencing; Forensic epigenetics; Age determination
• ISSN: 1872-4973; 1878-0326
• DOI: 10.1016/j.fsigen.2018.07.007

•DNA methylation (DNAm) changes are a powerful tool for age prediction.•DNAm of 13 blood age-dependent loci were investigated in other tissues.•Blood, bone, brain, buccal swabs and muscle from 29 individuals were analyzed by MPS.•Some markers are multi-tissue informative others are highly tissue-specific.
The use of DNA methylation (DNAm) for chronological age determination has been widely investigated within the last few years for its application within the field of forensic genetics. The majority of forensic studies are based on blood, saliva, and buccal cell samples, respectively. Although these types of samples represent an extensive amount of traces found at a crime scene or are readily available from individuals, samples from other tissues can be relevant for forensic investigations. Age determination could be important for cases involving unidentifiable bodies and based on remaining soft tissue e.g. brain and muscle, or completely depend on hard tissue such as bone. However, due to the cell type specificity of DNAm, it is not evident whether cell type specific age-dependent CpG positions are also applicable for age determination in other cell types. Within this pilot study, we investigated whether 13 previously selected age-dependent loci based on whole blood analysis including amongst others ELOVL2, TRIM59, F5, and KLF14 also have predictive value in other forensically relevant tissues.
Samples of brain, bone, muscle, buccal swabs, and whole blood of 29 deceased individuals (age range 0–87 years) were analyzed for these 13 age-dependent markers using massive parallel sequencing. Seven of these loci did show age-dependency in all five tissues. The change of DNAm during lifetime was different in the set of tissues analyzed, and sometimes other CpG sites within the loci showed a higher age-dependency.
This pilot study shows the potential of existing blood DNAm markers for age-determination to analyze other tissues than blood. We identified seven known blood-based DNAm markers for use in muscle, brain, bone, buccal swabs, and blood. Nevertheless, a different reference set for each tissue is needed to adapt for tissue-specific changes of the DNAm over time.