From degraded to deciphered: ATAC-seq’s application potential in forensic diagnosis

• Published in: International journal of legal medicine 2024-07, Vol.138 (4), p.1273-1285
• Main Authors: Li, Manrui, Jin, Yuntian, Xu, Yang, Sun, Yihan, Yuan, Ruixuan, Zhang, Xiao, Qu, Shengqiu, Lv, Meili, Liao, Miao, Liang, Weibo, Zhang, Lin, Chen, Xiameng
• Format: Article
• Language: English
• Subjects: Accessibility; Biology; Brain Injuries, Traumatic - diagnosis; Brain Injuries, Traumatic - genetics; Chromatin; Degradation; Diagnosis; DNA Degradation, Necrotic; Forensic Medicine; Forensic pathology; Gene sequencing; Head injuries; High-Throughput Nucleotide Sequencing; Humans; Medical diagnosis; Medical Law; Medicine; Medicine & Public Health; Molecular biology; Original Article; Pathology; Sequence Analysis, DNA - methods; Target recognition; Transposases - genetics; Traumatic brain injury
• ISSN: 0937-9827; 1437-1596
• DOI: 10.1007/s00414-024-03206-2

In recent years, molecular biology-based diagnostic techniques have made remarkable strides and are now extensively utilized in clinical practice, providing invaluable insights for disease diagnosis and treatment. However, forensic medicine, especially forensic pathology, has witnessed relatively limited progress in the application of molecular biology technologies. A significant challenge in employing molecular techniques for forensic diagnoses lies in the quantitative and qualitative changes observed in diagnostic markers due to sample degradation-a recognized and formidable obstacle. Inspired by the success of DNA sequencing in forensic practices, which enables accurate individual identification even in cases involving degraded and deteriorated tissues and organs, we propose the application of the assay for transposase-accessible chromatin with sequencing (ATAC-seq) to identify targets at the transcriptional onset, exploring chromatin and DNA-level alterations for injury and disease inference in forensic samples. This study employs ATAC-seq to explore alterations in chromatin accessibility post-injury and their subsequent changes over a 2-h degradation period, employing traumatic brain injury (TBI) as a representative model. Our findings reveal high sensitivity of chromatin accessibility sites to injury, evidenced by shifts in thousands of peak positions post-TBI. Remarkably, these alterations remain largely unaffected by early degradation. Our results robustly endorse the notion that integrating and incorporating these specific loci for injury and disease diagnosis in forensic samples holds tremendous promise for practical application. We further validated the above results using human cortical tissue, which supported that early degradation did not significantly affect chromatin accessibility. This pioneering advancement in molecular diagnostic techniques may revolutionize the field of forensic science, especially forensic pathology.