Stem Cell DNA Damage and Genome Mutation in the Context of Aging and Cancer Initiation

Abstract

Adult stem cells fuel tissue homeostasis and regeneration through their unique ability to self-renew and differentiate into specialized cells. Thus, their DNA provides instructions that impact the tissue as a whole. Since DNA is not an inert molecule, but rather dynamic, interacting with a myriad of chemical and physical factors, it encounters damage from both endogenous and exogenous sources. Damage to DNA introduces deviations from its normal intact structure and, if left unrepaired, may result in a genetic mutation. In turn, mutant genomes of stem and progenitor cells are inherited in cells of the lineage, thus eroding the genetic information that maintains homeostasis of the somatic cell population. Errors arising in stem and progenitor cells will have a substantially larger impact on the tissue in which they reside than errors occurring in postmitotic differentiated cells. Therefore, maintaining the integrity of genomic DNA within our stem cells is essential to protect the instructions necessary for rebuilding healthy tissues during homeostatic renewal. In this review, we will first discuss DNA damage arising in stem cells and cell- and tissue-intrinsic mechanisms that protect against harmful effects of this damage. Secondly, we will examine how erroneous DNA repair and persistent DNA damage in stem and progenitor cells impact stem cells and tissues in the context of cancer initiation and aging. Finally, we will discuss the use of invertebrate and vertebrate model systems to address unanswered questions on the role that DNA damage and mutation may play in aging and precancerous conditions.

Figure 1.

Mechanisms of stem cell protection from DNA damage by repair, elimination or cell cycle exit. (A) Repair: depending on the cell cycle status of the cell, the cell undergoes repair by either nonhomologous end-joining (NHEJ) (top panel) or homologous recombination (HR) (bottom panel). NHEJ is the quick and efficient mechanism used by quiescent stem cells when they are faced with damage. It involves the ligation of the broken ends and often results in the introduction of small deletions, but can also lead to translocation and genome rearrangements. HR is used if the cell is cycling and goes through S phase, duplicating its chromosomes, providing a template for the repair of the damaged chromosome. This is usually more accurate repair than NHEJ, though erroneous choice of the homologous chromosome, rather than the sister, can lead to loss of heterozygosity (LOH). (B) Elimination: by apoptosis. Some cells undergo apoptosis rather than repair. If this mechanism is preferentially used in the stem cell, there is a higher chance of stem cell depletion. (C) Cell-cycle exit: by differentiation (top panel) on DNA damage, or remaining in a state of quiescence.

Figure 2.

Cell competition selects for “winner” cells and weeds out less fit “loser” cells. (A) Differential Myc levels drive cell competition in both Drosophila (progenitors in the disc) and mammalian cells (mouse developing epidermal cells and adult epidermis). This figure shows that Myc mutants are “losers” and are outcompeted by adjacent wild-type (WT) cells. Extra levels of Myc also renders cells “winners” compared with WT cells (not shown). (B) DNA damage creates differences in fitness and this can drive cell competition. Irradiation of mouse hematopoietic stem and progenitor cells creates DNA damage, which results in increased Trp53 levels. When these cells are transplanted into mice with nonirradiated cells (4 days after the irradiation), the irradiated cells are outcompeted by the nonirradiated cells that have lower Trp53 levels and a higher expression of more competitive signaling molecules. Thus, DNA damage via irradiation creates a long-lasting “loser” cell status by inducing p53-mediated apoptosis or cell-cycle arrest. (C) Stem cell lineages with higher levels of COL17A1 and Mycn become “winners” in mouse skin epidermis. Genomic stress leads to the proteolytic degradation of COL17A1 and thus results in differential levels of COL17A1 expressed in the epidermis. Cells with higher levels of COL17A1 outcompete the cells expressing lower levels via symmetric cell division and the elimination of the losers. The higher expression of COL17A1 maintains a healthy skin phenotype, whereas COL17A1 deficiency causes skin atrophy, fragility, dyspigmentation, and alopecia. Similarly, during epidermal stratification skin lineages with higher levels of Mycn outcompete the cells expressing lower levels of Mycn, but it remains unclear whether genomic stress is what drives differential Mycn expression.

Figure 3.

Somatic mosaicism with age. (A) Mutations arise in stem cells of young tissues. (B) Age-dependent clonal expansion of mutant stem cells via positive selection or neutral drift give rise to mosaic patches. These may have a premalignant capacity and their persistence can lead to cancer initiation. (C) Clonal expansion can lead to the age-related collapse in clonal diversity with very few stem cells contributing to the aging tissue. The functional impact of collapse of clonal diversity is still not fully understood but it can impact age-associated lineage skewing in some cases. (D) Clonal expansion of cancer driver genes can lead to cancer initiation.

Figure 4.

The use of model systems to assay spontaneous mutations in adult tissues. (A) A LacZ reporter to assay spontaneous mutations (Dolle et al. 2000). In this assay, genomic DNA extracted from young/old hearts and small intestines of transgenic mice containing the LacZ reporter is assessed for spontaneous mutation. LacZ encoding plasmids are recovered in bacteria tested for intact LacZ activity. A significant age-related increase in point mutations was detected in small intestines, whereas a significant age-related increase in genomic rearrangements was detected in hearts. (B) A transgenic nucleotide repeat reporter assay to mark spontaneous mutations in mouse intestinal crypts (Kozar et al. 2013). In this system, spontaneous slippage of the cassette during replication allows for expression of the reporter. Wholly populated crypts indicative of the fixation of mutations were shown to increase in an age-dependent manner. (C) Spontaneously arising somatic Notch mutations in Drosophila intestinal stem cells (ISCs) can be detected as clonally expanded Notch mutants/neoplasia in aged flies (Siudeja et al. 2015). Inactivation of Notch leads to neoplasia with an accumulation of ISCs and enteroendocrine cells. Whole-genome sequencing of aged male neoplasia revealed that Notch is inactivated via deletions or structural rearrangements.