Dissecting single-cell genomes through the clonal organoid technique

Youk, Jeonghwan; Kwon, Ho Jang; Kim, Ryul; Ju, Young Seok

doi:10.1038/s12276-021-00680-1

Cited by 13 publications

(13 citation statements)

References 115 publications

(130 reference statements)

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“…SVs, and particularly complex SVs, play a significant yet underappreciated role in determining how cancer genomes evolve. Single-cell WGS applied to organoid systems [126,127] has enabled high-resolution phylogenetic studies and functional interrogation of subclonal SVs [128]. In addition, longitudinal single-cell WGS of patient-derived xenografts from tumour samples has demonstrated that CNAs have an underappreciated impact on clonal fitness [129].…”

Section: Structural Variation As a Critical Dimension In Tumour Evolu...mentioning

confidence: 99%

Unravelling the tumour genome: The evolutionary and clinical impacts of structural variants in tumourigenesis

Hamdan

Ewing

2022

The Journal of Pathology

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Structural variants (SVs) represent a major source of aberration in tumour genomes. Given the diversity in the size and type of SVs present in tumours, the accurate detection and interpretation of SVs in tumours is challenging. New classes of complex structural events in tumours are discovered frequently, and the definitions of the genomic consequences of complex events are constantly being refined. Detailed analyses of short-read whole-genome sequencing (WGS) data from large tumour cohorts facilitate the interrogation of SVs at orders of magnitude greater scale and depth. However, the inherent technical limitations of short-read WGS prevent us from accurately detecting and investigating the impact of all the SVs present in tumours. The expanded use of long-read WGS will be critical for improving the accuracy of SV detection, and in fully resolving complex SV events, both of which are crucial for determining the impact of SVs on tumour progression and clinical outcome. Despite the present limitations, we demonstrate that SVs play an important role in tumourigenesis. In particular, SVs contribute significantly to late-stage tumour development and to intratumoural heterogeneity. The evolutionary trajectories of SVs represent a window into the clonal dynamics in tumours, a comprehensive understanding of which will be vital for influencing patient outcomes in the future. Recent findings have highlighted many clinical applications of SVs in cancer, from early detection to biomarkers for treatment response and prognosis. As the methods to detect and interpret SVs improve, elucidating the full breadth of the complex SV landscape and determining how these events modulate tumour evolution will improve our understanding of cancer biology and our ability to capitalise on the utility of SVs in the clinical management of cancer patients.

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Section: Structural Variation As a Critical Dimension In Tumour Evolu...mentioning

confidence: 99%

Unravelling the tumour genome: The evolutionary and clinical impacts of structural variants in tumourigenesis

Hamdan

Ewing

2022

The Journal of Pathology

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“…Our approaches allowed for the sensitive and precise investigation soL1Rs in single genomes with minimal amplification and dropout artifacts that frequently occur in whole-genome amplification (WGA)-based single-genome sequencing 28 and in laser capture microdissection (LCM)-based clonal patch sequencing ( Supplementary Discussion ). In addition, our approach enabled us to combine DNA methylation and gene expression profiles from the same clones, which are challenging in other approaches 29 . Furthermore, by integrating early developmental lineages of clones reconstructed by somatic mutations as cellular barcodes 8 , the early molecular dynamics of the mutational, transcriptional, and epigenetic profiles of L1s were also investigated.…”

Section: Introductionmentioning

confidence: 99%

Extensive mosaicism by somatic L1 retrotransposition in normal human cells

Nam

Youk

Kim

et al. 2022

Preprint

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Over the course of an individual's lifetime, genomic alterations accumulate in somatic cells. However, the mutational landscape by retrotranspositions of long interspersed nuclear element-1 (L1), a widespread mobile element in the human genome, is poorly understood in normal cells. Here, we explored the whole-genome sequences of 892 single-cell clones established from various tissues collected from 28 individuals. Remarkably, 88% of colorectal epithelial cells acquired somatic L1 retrotranspositions (soL1Rs), carrying ~3 events per cell on average with substantial intra- and inter-individual variances, which was accelerated at least 10-fold during tumourigenesis. Breakpoints of soL1Rs suggested that a few variant mechanisms can be involved in the L1 retrotransposition processes. Fingerprinting of donor L1s using source-specific unique sequences revealed 34 hot L1s, 44% of which were newly discovered in this study, and many ultra-rare hot L1s in the human population showed higher retrotransposition potential in somatic lineages than common sources. Multi-dimensional analysis of soL1Rs with early embryonic developmental relationships, genome-wide methylation, and gene expression profiles of the clones demonstrated that (1) soL1Rs occur from early embryogenesis at a substantial rate, (2) epigenetic activation of hot L1s is stochastically acquired during the wave of early global epigenomic reprogramming, rather than by the sporadic loss-of-methylation at the late stage, and (3) most L1 transcripts in the cytoplasm do not generate soL1Rs in somatic lineages. In summary, this study provides insights into the retrotransposition dynamics of L1s in the human genome and the resultant somatic mosaicism in normal human cells.

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“…In between both approaches, MALBAC starts with an isothermal preamplification followed by PCR amplification. An important caveat of these techniques is the mutation rate, up to 1–40 mutations per 100 kb [ 4 ], which needs to be considered in the variant calling process and subsequent analyses. Primary template-directed amplification (PTA) is an improved alternative that takes advantage of the low error rate of the polymerase used in MDA with some modifications in the amplification [ 5 ].…”

Section: Somatic Variant Detectionmentioning

confidence: 99%

“…Induced pluripotent stem cell (iPSC) culture is another option. However, the culture conditions and environmental agents can be a selective bottleneck to a group of cells and can induce de novo mutations during culture [ 4 ]. In contrast, organoid culture technologies have the advantage of being compatible with multiple human cell types, and long-term genome-stable cultures can be obtained.…”

Section: Somatic Variant Detectionmentioning

confidence: 99%

Somatic genetic variation in healthy tissue and non-cancer diseases

et al. 2022

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Somatic genetic variants have been studied for several years mostly concerning cancer, where they contribute to its origin and development. It is also clear that the somatic variants load is greater in aged individuals in comparison to younger ones, pointing to a cause/consequence of the senescence process. More recently, researchers have focused on the role of this type of variation in healthy tissue and its dynamics in cell lineages and different organs. In addition, somatic variants have been described to contribute to monogenic diseases, and the number of evidences of their role in complex disorders is also increasing. Thanks to recent advances in next-generation sequencing technologies, this type of genetic variation can be now more easily studied than in the past, although we still face some important limitations. Novel strategies for sampling, sequencing and filtering are being investigated to detect these variants, although validating them with an orthogonal approach will most likely still be needed. In this review, we aim to update our knowledge of somatic variation detection and its relation to healthy tissue and non-cancer diseases.

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Dissecting single-cell genomes through the clonal organoid technique

Cited by 13 publications

References 115 publications

Unravelling the tumour genome: The evolutionary and clinical impacts of structural variants in tumourigenesis

Unravelling the tumour genome: The evolutionary and clinical impacts of structural variants in tumourigenesis

Extensive mosaicism by somatic L1 retrotransposition in normal human cells

Somatic genetic variation in healthy tissue and non-cancer diseases

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