Defective DNA Polymerases Can Lead to Colon and/or Endometrial Cancer

Anahita Bahreini-Esfahani

Unfaithful replication of the genome due to faulty Pol ε and Pol δ DNA polymerases can lead to predispositions of colorectal and endometrial cancers. Surprisingly, carriers of POLE/POLD1 germline mutations do not exhibit overt phenotypes of premature aging.

During each cycle of cell division, polymerases play a key role in replicating the genome. In humans, DNA replication is mainly performed by polymerases Pol ε and Pol δ, which are responsible for the synthesis of the leading and lagging strand, respectively. Both enzymes exhibit proof-reading activity1 (Figure 1).

Figure 1. During replication of the genome, as helicase unwinds the double-stranded DNA, synthesis of the new DNA molecule is initiated by the primers generated by Pol α-primase. DNA synthesis occurs in the 5’ to 3’ direction and the leading strand (shown in green) is synthesized continuously by DNA polymerase ε (Pol ε) whereas the lagging strand (shown in blue) is synthesized discontinuously by DNA polymerase δ (Pol δ). (Figure taken from2)

It has been previously shown that POLE exonuclease mutations lead to high single base substitutions (SBS) while POLD1 exonuclease mutations display less elevated SBS and high microsatellite instability. The mutations generated by defective POLE and POLD1 exonucleases reveal replication strand bias, which is expected due to their separate roles in replicating leading and lagging strands3. These findings have been confirmed using functional studies in yeast and mice4,5. If POLE and POLD1 exonuclease mutations occur in the germline, they can be inherited and cause a rare autosomal dominant cancer predisposition known as polymerase proofreading-associated polyposis (PPAP) which is mainly defined by early-onset tumors in the colon and endometrium6.

Accumulation of somatic mutations has been hypothesized as the main biological mechanism underlying aging7. There have been reports confirming increases in somatic mutation burden in a linear manner8; however, not all somatic mutations will have a significant biological consequence. The study of individuals with inherited POLE/POLD1 exonuclease mutations can shed light on the downstream effects of elevated mutation burdens and the genetics of aging.

In a study by Robinson et. al, samples were taken from 14 individuals aged 17-72 years and divided into 4 groups based on the germline exonuclease domain mutation they were carrying; All 14 individuals had a family history of colorectal cancer and/or other cancers. The researchers of this study focused on mutagenesis and mutational signatures in intestinal stem cells, mutagenesis in endometrial cells, mutagenesis during early embryogenesis, and differential mutational burdens across the genome.

Using whole-genome sequencing (WGS) methods, intestinal crypts from the 14 individuals revealed a range of 58-331 SBS rate per year in comparison to 49 SBS per year in crypts from healthy individuals. Thus, elevated rates of SBS rates are present in all otherwise normal intestinal cells of individuals harbouring POLE/POLD1 germline mutations. Moreover, small insertion and deletion (ID) mutation rates ranged from 12-44 per year in individuals with POLE/POLD1 compared with 1 per year in individuals without POLE/POLD1 mutations.

Eleven SBS mutational signatures were detected in normal intestinal crypts obtained from individuals with POLE/POLD1 germline mutations. Nine of these SBS mutational signatures were previously reported and the 2 previously unreported mutational signatures were revealed in normal crypts from individuals with POLD1 mutations. These mutational signatures allowed Robinson et. al to attribute the increases in SBS burdens from POLE/POLD1 germline mutation carriers to specific mutations. Similar trends were observed in the endometrial cells of the females in this study.

When Robinson et. al performed WGS on whole-blood samples of individuals carrying POLE/POLD1 mutations, the number of early embryogenesis single-base pair (bp) insertions was highly increased in some individuals. This heterogeneity is likely due to the maternal to zygotic transition of gene expression. If a POLE/POLD1 mutation is paternally inherited, the defective proof-reading polymerase is delayed until the zygote’s gene expression machinery is activated. However, If the mutation is maternally inherited, the faulty polymerase is also inherited by the zygote since the zygote inherits the proteins and mRNAs of the ovum. This leads to a high burden of mutations in early embryogenesis. These findings point to the fact that mutagenesis as a result of malfunctioning POLE/POLD1 proofreading is observed even at the earliest stages of life.

Robinson et al. also compared somatic mutations across the genome to the mutation load in the exome of individuals who carried germline POLE/POLD1 mutations. They found elevated mutation rates in cells of all types, but mutation rates were significantly increased in the colon and endometrium more than other tissues such as the skin. The hypothesis behind this finding is that differing stem cell division rates occur in the colon and endometrium. This finding can also partially explain why individuals with POLE/POLD1 mutations are more prone to colorectal and endometrial cancers including PPAP9.

In sum, this study demonstrates how normal cell types from carriers of POLE/POLD1 exonuclease germline mutations exhibit mutational signatures and elevated levels of somatic SBS and ID mutation rates. The amount of the increase in mutation rate seems to be larger in intestinal and endometrial epithelium than in the other cell types that were studied. This is important when discussing the somatic mutation theory of aging- a theory suggesting that as we age, we accumulate mutations that lead to a set of phenotypic features collectively known as aging10. This study shows that other than the increase in prevalence to colon and endometrial cancer, POLE/POLD1 germline exonuclease mutations do not cause premature aging. This indicates that many of our cells tolerate high SBS/ID mutations and somatic mutations alone do not underlie the process of aging. It is vital for future studies to address the shortcomings of this experiment, such as small sample size and to take a deeper dive into the genetics of aging. In a recent genome-wide association study (GWAS) done by Timmers et al., aging phenotypes such as healthspan, lifespan and longevity were found to be affected by 10 genomic loci. Follow-up studies using both GWAS studies and animal models can lead to therapeutic targets that can increase our chances of living longer, or to the very least, slow down the process of aging.

References

  1. Burgers, P. et al., Who is leading the replication fork, Pol ε or Pol δ? Molecular Cell. 4, 492-493 (2016).
  2. Marin-Garcia, J., Introduction to the molecular biology of the cell. Post-Genomic Cardiology. 2, 3-14 (2014).
  3. Morrison, A. et al., A third essential DNA polymerase in S. cerevisiae. Cell 62, 1143–1151 (1990).
  4. Venkatesan, R. N. et al., Mutation at the polymerase active site of mouse DNA polymerase increases genomic instability and accelerates tumorigenesis. Mol. Cell. Biol. 27, 7669–7682 (2007).
  5. Barbari, S. R. et al., Functional analysis of cancer-associated DNA polymerase ε variants in Saccharomyces cerevisiae. G3 (Bethesda) 8, 1019–1029 (2018).
  6. Palles, C. et al., Germline mutations affecting the proofreading domains of POLE and POLD1 predispose to colorectal adenomas and carcinomas. Nat. Genet. 45, 136–143 (2013).
  7. Vijg, J. & Dong, X. Pathogenic mechanisms of somatic mutation and genome mosaicism in aging. Cell 182, 12–23 (2020).
  8. Blokzijl, F. et al., Tissue-specific mutation accumulation in human adult stem cells during life. Nature 538, 260–264 (2016).
  9. Robinson, P. et al., Increased somatic mutation burdens in normal human cells due to defective DNA polymerases. Nat Genet 53, 1434–1442 (2021).
  10. Szilard, L. On the nature of the aging process. Proc. Natl Acad. Sci. USA 45, 30–45 (1959).
  11. Timmers, P. et al, Multivariate genomic scan implicates novel loci and haem metabolism in human ageing. Nat Commun 1, 3570-3571 (2020).

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