“…The mutation rate of actively cycling sperm precursors is approximately 27-fold lower than that of the colorectal epithelium (Moore et al, 2021). The comparison of various tissue samples across organs from the same individual indicated 2.4 mutations per cell division during the first few embryonic divisions (Table 2) (Coorens et al, 2021;Park et al, 2021). The rate of mutagenesis is subsequently reduced, presumably due to enhanced DNA repair activity.…”
Next-generation sequencing (NGS) of single cells and micro-dissected tissues has demonstrated that the number of somatic mutations in normal cells increases linearly with age. The majority of somatic mutations are single base substitutions (SBSs). NGS has revealed the mutagenic effect of various metabolic and environmental genotoxic agents on different cells, such as normal colonic epithelial cells, hematopoietic cells, hepatocytes, and neurons. NGS has also uncovered the clonal expansion of cells in normal tissues of the elderly driven by oncogenic mutations. There are two main mechanisms for the generation of mutations, namely, replication errors and DNA damage, with both being followed by inaccurate repair. NGS studies of normal tissues highlight the substantial contribution of the latter mechanism by revealing the significant accumulation of somatic mutations in mitotically inactive hepatocytes and neurons. This review describes the nature of spontaneously arising SBSs in normal tissues, the causes of mutagenesis, cellular pathways of the DNA damage response that suppress mutagenesis, as well as unsolved questions on the matter.
KeywordsSpontaneous mutagenesis • Error-reduced NGS technology • Replication errors • Inaccurate repair of DNA damage • de novo mutation * Shunichi Takeda
“…The mutation rate of actively cycling sperm precursors is approximately 27-fold lower than that of the colorectal epithelium (Moore et al, 2021). The comparison of various tissue samples across organs from the same individual indicated 2.4 mutations per cell division during the first few embryonic divisions (Table 2) (Coorens et al, 2021;Park et al, 2021). The rate of mutagenesis is subsequently reduced, presumably due to enhanced DNA repair activity.…”
Next-generation sequencing (NGS) of single cells and micro-dissected tissues has demonstrated that the number of somatic mutations in normal cells increases linearly with age. The majority of somatic mutations are single base substitutions (SBSs). NGS has revealed the mutagenic effect of various metabolic and environmental genotoxic agents on different cells, such as normal colonic epithelial cells, hematopoietic cells, hepatocytes, and neurons. NGS has also uncovered the clonal expansion of cells in normal tissues of the elderly driven by oncogenic mutations. There are two main mechanisms for the generation of mutations, namely, replication errors and DNA damage, with both being followed by inaccurate repair. NGS studies of normal tissues highlight the substantial contribution of the latter mechanism by revealing the significant accumulation of somatic mutations in mitotically inactive hepatocytes and neurons. This review describes the nature of spontaneously arising SBSs in normal tissues, the causes of mutagenesis, cellular pathways of the DNA damage response that suppress mutagenesis, as well as unsolved questions on the matter.
KeywordsSpontaneous mutagenesis • Error-reduced NGS technology • Replication errors • Inaccurate repair of DNA damage • de novo mutation * Shunichi Takeda
“…To implement these strategies, researchers have applied various cell culture techniques, such as classical 2D culture, induced pluripotent stem cell (iPSC) culture, and organoid culture technologies. Some cell types, such as hematopoietic stem cells 61 , bronchial epithelial cells 62 , and fibroblasts 63 , can be successfully clonalized using primary 2D culture techniques. However, unlike cancer cell lines, most primary human cells are difficult to expand in vitro using the classical technique, particularly when a single cell is isolated.…”
Section: Main Textmentioning
confidence: 99%
“…These efforts demonstrated that (1) the two cells of the two-cell stage mouse embryo do not contribute equally to adult cells and that (2) anatomically adjacent cells in adult tissue are not always developmentally closer than distant cells 88 . Most importantly, the work suggested that similar approaches may be applicable to human cells 63 for understanding human embryogenesis, where the direct investigation is not possible. Fig.…”
Section: Main Textmentioning
confidence: 99%
“…It would not be very surprising, in fact, if the entire human population were to be sequenced in the next several decades. In parallel, an individual may be sequenced multiple times, at least for medical purposes, for instance, to longitudinally trace the genomic evolution of cancer tissues 110 or to decompose the genomic heterogeneity of a specific individual 63 , 111 .…”
Section: Main Textmentioning
confidence: 99%
“…We first need to record the mutational and clonal complexity of human tissues on a massive scale to extract common features and principles. Technically, as mentioned throughout this manuscript, the landscape of somatic mosaicism is becoming fundamentally explorable, as seen in recent studies involving clones from diverse anatomical regions of human bodies 63 , 111 .…”
The revolution in genome sequencing technologies has enabled the comprehensive detection of genomic variations in human cells, including inherited germline polymorphisms, de novo mutations, and postzygotic mutations. When these technologies are combined with techniques for isolating and expanding single-cell DNA, the landscape of somatic mosaicism in an individual body can be systematically revealed at a single-cell resolution. Here, we summarize three strategies (whole-genome amplification, microdissection of clonal patches in the tissue, and in vitro clonal expansion of single cells) that are currently applied for single-cell mutational analyses. Among these approaches, in vitro clonal expansion, particularly via adult stem cell-derived organoid culture technologies, yields the most sensitive and precise catalog of somatic mutations in single cells. Moreover, because it produces living mutant cells, downstream validation experiments and multiomics profiling are possible. Through the synergistic combination of organoid culture and genome sequencing, researchers can track genome changes at a single-cell resolution, which will lead to new discoveries that were previously impossible.
Humans had acquired a tremendously enlarged cerebral cortex containing a huge quantity and variety of cells during evolution. Such evolutionary uniqueness offers a neural basis of our cognitive innovation and human‐specific features of neurodevelopmental and psychiatric disorders. Since human brain is hardly examined in vivo with experimental approaches commonly applied on animal models, the recent advancement of sequencing technologies offers an indispensable viewpoint of human brain anatomy and development. This review introduces the recent findings on the unique features in the adult and the characteristic developmental processes of the human cerebral cortex, based on high‐throughput DNA sequencing technologies.
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