Multidimensional fragmentomic profiling of cell-free DNA released from patient-derived organoids
Abstract Background Fragmentomics, 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 un...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-10-01
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| Series: | Human Genomics |
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| Online Access: | https://doi.org/10.1186/s40246-023-00533-0 |
| _version_ | 1797647273651339264 |
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| author | Jaeryuk Kim Seung-Pyo Hong Seyoon Lee Woochan Lee Dakyung Lee Rokhyun Kim Young Jun Park Sungji Moon Kyunghyuk Park Bukyoung Cha Jong-Il Kim |
| author_facet | Jaeryuk Kim Seung-Pyo Hong Seyoon Lee Woochan Lee Dakyung Lee Rokhyun Kim Young Jun Park Sungji Moon Kyunghyuk Park Bukyoung Cha Jong-Il Kim |
| author_sort | Jaeryuk Kim |
| collection | DOAJ |
| description | Abstract Background Fragmentomics, 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. Results We 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. Conclusions In 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. |
| first_indexed | 2024-03-11T15:13:55Z |
| format | Article |
| id | doaj.art-8b998c061fa34b3d9c74505a98d53d26 |
| institution | Directory Open Access Journal |
| issn | 1479-7364 |
| language | English |
| last_indexed | 2024-03-11T15:13:55Z |
| publishDate | 2023-10-01 |
| publisher | BMC |
| record_format | Article |
| series | Human Genomics |
| spelling | doaj.art-8b998c061fa34b3d9c74505a98d53d262023-10-29T12:30:24ZengBMCHuman Genomics1479-73642023-10-0117111510.1186/s40246-023-00533-0Multidimensional fragmentomic profiling of cell-free DNA released from patient-derived organoidsJaeryuk Kim0Seung-Pyo Hong1Seyoon Lee2Woochan Lee3Dakyung Lee4Rokhyun Kim5Young Jun Park6Sungji Moon7Kyunghyuk Park8Bukyoung Cha9Jong-Il Kim10Genomic Medicine Institute, Medical Research Center, Seoul National UniversityGenomic Medicine Institute, Medical Research Center, Seoul National UniversityGenomic Medicine Institute, Medical Research Center, Seoul National UniversityGenomic Medicine Institute, Medical Research Center, Seoul National UniversityGenomic Medicine Institute, Medical Research Center, Seoul National UniversityGenomic Medicine Institute, Medical Research Center, Seoul National UniversityGenomic Medicine Institute, Medical Research Center, Seoul National UniversityGenomic Medicine Institute, Medical Research Center, Seoul National UniversityGenomic Medicine Institute, Medical Research Center, Seoul National UniversityGenomic Medicine Institute, Medical Research Center, Seoul National UniversityGenomic Medicine Institute, Medical Research Center, Seoul National UniversityAbstract Background Fragmentomics, 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. Results We 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. Conclusions In 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.https://doi.org/10.1186/s40246-023-00533-0Cell-free DNA biologyIn vitro modelsFragmentomicsOrganoidsExtrachromosomal circular DNA |
| spellingShingle | Jaeryuk Kim Seung-Pyo Hong Seyoon Lee Woochan Lee Dakyung Lee Rokhyun Kim Young Jun Park Sungji Moon Kyunghyuk Park Bukyoung Cha Jong-Il Kim Multidimensional fragmentomic profiling of cell-free DNA released from patient-derived organoids Human Genomics Cell-free DNA biology In vitro models Fragmentomics Organoids Extrachromosomal circular DNA |
| title | Multidimensional fragmentomic profiling of cell-free DNA released from patient-derived organoids |
| title_full | Multidimensional fragmentomic profiling of cell-free DNA released from patient-derived organoids |
| title_fullStr | Multidimensional fragmentomic profiling of cell-free DNA released from patient-derived organoids |
| title_full_unstemmed | Multidimensional fragmentomic profiling of cell-free DNA released from patient-derived organoids |
| title_short | Multidimensional fragmentomic profiling of cell-free DNA released from patient-derived organoids |
| title_sort | multidimensional fragmentomic profiling of cell free dna released from patient derived organoids |
| topic | Cell-free DNA biology In vitro models Fragmentomics Organoids Extrachromosomal circular DNA |
| url | https://doi.org/10.1186/s40246-023-00533-0 |
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