Multidimensional fragmentomic profiling of cell-free DNA released from patient-derived organoids

Human Genomics

Research

Kyunghyuk Park¹  Bukyoung Cha¹  Seyoon Lee²  Jaeryuk Kim²  Dakyung Lee²  Woochan Lee²  Rokhyun Kim²  Seung-Pyo Hong²  Jong-Il Kim³  Young Jun Park⁴  Sungji Moon⁵ 

[1] Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea;Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea;Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea;Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea;Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea;Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea;Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea;Department of Translational Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea;Interdisciplinary Program in Cancer Biology, Seoul National University College of Medicine, Seoul, Republic of Korea;Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea;Cancer Research Institute, Seoul National University, Seoul, Republic of Korea;Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea;Department of Translational Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea;Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea;Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea;Interdisciplinary Program in Cancer Biology, Seoul National University College of Medicine, Seoul, Republic of Korea;Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea;

关键词: Cell-free DNA biology;    In vitro models;    Fragmentomics;    Organoids;    Extrachromosomal circular DNA;   

DOI  :  10.1186/s40246-023-00533-0

 received in 2023-05-10, accepted in 2023-09-11,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundFragmentomics, the investigation of fragmentation patterns of cell-free DNA (cfDNA), has emerged as a promising strategy for the early detection of multiple cancers in the field of liquid biopsy. However, the clinical application of this approach has been hindered by a limited understanding of cfDNA biology. Furthermore, the prevalence of hematopoietic cell-derived cfDNA in plasma complicates the in vivo investigation of tissue-specific cfDNA other than that of hematopoietic origin. While conventional two-dimensional cell lines have contributed to research on cfDNA biology, their limited representation of in vivo tissue contexts underscores the need for more robust models. In this study, we propose three-dimensional organoids as a novel in vitro model for studying cfDNA biology, focusing on multifaceted fragmentomic analyses.ResultsWe established nine patient-derived organoid lines from normal lung airway, normal gastric, and gastric cancer tissues. We then extracted cfDNA from the culture medium of these organoids in both proliferative and apoptotic states. Using whole-genome sequencing data from cfDNA, we analyzed various fragmentomic features, including fragment size, footprints, end motifs, and repeat types at the end. The distribution of cfDNA fragment sizes in organoids, especially in apoptosis samples, was similar to that found in plasma, implying occupancy by mononucleosomes. The footprints determined by sequencing depth exhibited distinct patterns depending on fragment sizes, reflecting occupancy by a variety of DNA-binding proteins. Notably, we discovered that short fragments (< 118 bp) were exclusively enriched in the proliferative state and exhibited distinct fragmentomic profiles, characterized by 3 bp palindromic end motifs and specific repeats.ConclusionsIn conclusion, our results highlight the utility of in vitro organoid models as a valuable tool for studying cfDNA biology and its associated fragmentation patterns. This, in turn, will pave the way for further enhancements in noninvasive cancer detection methodologies based on fragmentomics.

【 授权许可】

CC BY   
© The Author(s) 2023

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