Introduction
It has historically been thought that Mendelian cancer predisposition syndromes are rarely, if ever, associated with a general predisposition to cancer. This is often perplexing, especially when the genes involved are ubiquitously expressed and/or are involved in fundamental processes such as cell metabolism or DNA repair. In fact, it is increasingly recognised that many of these syndromes confer a smaller, but definitely increased, risk of a wide range of cancers, this having been masked by a combination of early death from specific malignancies and ascertainment bias. Early reports of the spectrum of cancers associated with particular high-penetrance gene defects have often been revised in the light of improved treatment, longer follow-up and identification of gene heterozygotes in extended pedigrees. Almost without exception, these studies have confirmed that the cancers originally described are indeed the major risks, but lesser increased risks of other cancers are also present. Well established examples of the latter include prostate cancer in
BRCA1 and
BRCA2 heterozygotes [
1], gastric cancer in individuals with Li-Fraumeni syndrome [
2] and head and neck squamous cell cancer, gynaecological squamous cell cancer, oesophageal cancer, and liver, brain, skin and renal tumours in Fanconi anaemia patients [
3].
It is therefore premature to report the clinical features of new Mendelian syndromes until several years have elapsed since their identification. This problem is compounded by the fact that the recently identified syndromes inevitably tend to be rarer, so that accumulation of clinical information is slow and it is almost impossible to avoid all ascertainment bias. A recent example of the confusion that can arise is the phenotype of the recessive condition
NTHL1-associated polyposis (NAP), which initially was based on three families and largely comprises colorectal adenomas and carcinomas [
4]; yet, a single NAP patient with seven primary cancers (and multiple non-cancerous tumours) has also been described [
5]. Recent papers highlighting the now apparent extended tumour phenotype seen in individuals’ with two
NTHL1 mutations suggest
NTHL1 tumour syndrome as a more accurate name for this condition [
6].
In this manuscript, we report the clinical features of a set of families with polymerase proofreading-associated polyposis (PPAP), a Mendelian dominant condition caused by pathogenic variants in the exonuclease domains of
POLE and
POLD1, the genes encoding the catalytic subunits of DNA polymerases epsilon and delta. We assess the phenotype of those heterozygous for an exonuclease domain (ED) probably pathogenic variant in the context of dysfunction of the proof-reading capability of these genes being expected to cause a 100-fold increase in point mutations in theoretically every dividing cell type in the body. We provide an update of the phenotype of the families when we first described PPAP [
7] and combine this with a comprehensive literature review, resulting in a set of guidelines for PPAP management.
Discussion
In this study, we have provided a comprehensive description of the clinicopathological features of PPAP in those heterozygous for POLE and POLD1 ED variants with supporting evidence of a pathogenic impact. The cumulative incidence of CRC in
POLE and
POLD1 variant heterozygotes is estimated at approximately 90% and 50% respectively. These estimates are higher than previous reports [
30], probably because of the exclusion of variants of uncertain pathogenicity and the variable mixture between studies of PPAP patients who were screened because of family history and others whose first cancer occurred before surveillance began. Most patients have an attenuated polyposis phenotype (10–100 polyps), with greater polyp numbers in a few cases, but a minority of cases have a Lynch syndrome-like phenotype with early-onset CRC and few polyps. Individuals without CRAs were either young (aged 24 and 18 respectively), or carried a relatively rare probably pathogenic variant and presented with an extra-colonic tumour (
POLE p.Tyr458Phe,
POLD1 p. Asp316Gly,
POLD1 p. Asp316Asn,
POLD1 p. Leu474Pro).
We have expanded the spectrum of intestinal cancers to include benign and malignant duodenal tumours. 19% of all probably pathogenic ED variant heterozygotes had both a colorectal and a duodenal phenotype. Unfortunately, phenotypic data regarding the upper GI tract are somewhat limited and indeed many of the patients reported in the literature are likely not to have undergone upper GI endoscopy at all. When only those who have had an upper GI endoscopy were included, DAs were seen in over 50% of ED variant heterozygotes.
EC is the most common extra-intestinal malignancy in PPAP, with lower risks than CRC. The risk is higher in POLD1 heterozygotes. OC is also relatively frequent, sometimes synchronous with EC, although no consistent assessment of histology or clonal origins was possible. There is also growing evidence that a variety of brain tumours can occur as part of PPAP.
Caution is advised in interpreting the details of some of our findings, including the quantitative cancer risk estimates and the intriguing possibility of genotype–phenotype correlations. Potential problems include the small numbers of affected individuals from a limited number of families, the variable extent of cancer screening, and ascertainment bias for genetic testing. Such issues are unavoidable for rare conditions, and must be take into account wherever possible in the clinical setting.
How do our data inform clinical management? Colorectal surveillance is clearly advisable. Bellido et al. [
27] suggested colonoscopy from the age of 18 years. Given that we identified an individual with a CRA aged 15 and Wimmer et al. [
20] identified a CRC in a 14 year old, we suggest that earlier colonoscopic assessment at age 14 should be performed in all PPAP patients. It is noteworthy that 26/86 (30%) CRC cases were in patients who did not have adenomas and no clear correlation between polyp burden and cancer risk has been demonstrated. Furthermore, although the tumours we originally described in
POLE and
POLD1 carriers were microsatellite-stable, the frequency of MSI (12.5%) that we now describe in CRCs is similar to that in sporadic CRCs, despite the earlier onset of the former. Whether MSI in PPAP CRC results from somatic loss of mismatch repair or an unappreciated direct effect of constitutive proofreading deficiency, it could result in accelerated progression to cancer. Given the above uncertainties, we recommend at least biennial colonoscopy, compared with 1–2 yearly suggested by Bellido et al. [
27]. Prophylactic surgical intervention may be appropriate for PPAP cases with a severe polyp phenotype: our data suggest that colectomy and ileo-rectal or ileo-distal sigmoid anastomosis would usually be most appropriate. Surgery for those with PPAP in whom CRC has already arisen needs to be individualised and no strong recommendation can be given; factors including phenotype, expected functional outcome and the metachronous cancer risk all need to be considered.
The finding of frequent DAs and DC suggests that routine upper gastrointestinal tract surveillance would be beneficial. In the absence of robust data, we suggest that surveillance is based on the system advocated for FAP [
31], starting at age 25. The role of duodenal polypectomy is unproven, even in FAP, but it would seem reasonable to consider polypectomy in PPAP when adenomas reach 1 cm in size.
Endometrial cancer is common in PPAP and it is logical to think that gynaecological surveillance would be warranted. Indeed, Bellido and colleagues [
27] proposed endometrial surveillance in patients with
POLD1 pathogenic variants, commencing age 40 years. However, there are no robust data to support gynaecological screening in Lynch syndrome, which has a comparable or higher risk of gynaecological cancer, even though it is performed in some centres. Instead of gynaecological surveillance, Lynch syndrome patients are usually counselled regarding the possibility of risk-reducing surgery when they have completed their family [
32]. For
POLE carriers, given the finding of 5 cases with ovarian cancer, this counselling should include a discussion of both risk reducing hysterectomy and bilateral salpingo-oophorectomy (BSO). We suggest a similar approach for women with PPAP, since the EC risk is appreciable with either
POLD1 or
POLE ED variant heterozygotes.
For the other cancers observed in PPAP families, the absolute risk appears relatively small and below the threshold at which routine surveillance would be recommended. The lifetime risk of breast cancer in the female UK population is 12% and the risk of developing breast cancer in the next 10 years if aged 50 is 3.54% whereas the risk of breast cancer by age 60 is approximately 30% in POLD1 and 20% in
POLE ED pathogenic variant heterozygotes included in our analysis (Supplementary Figure S4). Whilst this is based on only 40 female
POLE ED heterozygotes and 17 female
POLD1 heterozygotes, we conclude that female
POLD1 ED heterozygotes in particular may be at an increased risk of developing breast cancer compared to the general population, but this is not proven. Specifically, there is, as yet, insufficient evidence that the risk observed is high enough to fulfil the criteria for moderate risk breast screening according to UK NICE (Familial breast cancer: classification, care and managing breast cancer and related risks in people with a family history of breast cancer, Clinical guideline [CG164] updated: March 2017 [
33]). We suggest
POLE and
POLD1 ED heterozygotes could be referred to a high risk breast screening service for discussion. The lack of data about type of breast cancer, hormone receptor status and the inherent bias in our cohort make it difficult to give robust recommendations. Discussion in a specialised unit is sensible particularly where there is clustering of breast cancer cases or the presence of very young onset breast cancer in a first degree relative. Certainly, breast awareness and self-examination should be encouraged in all female patients with PPAP. Whilst there are no data to support that it is effective, increasing awareness and empowering patients to be involved in the management of their condition should be supported.
The PPAP phenotype is in some ways a hybrid between attenuated adenomatous polyposis (as seen in other DNA repair deficiency syndromes such as MAP) and Lynch syndrome, especially as regards the high EC risk. CRC and EC cancer patients with somatic
POLE ED mutations have been shown to have a favourable prognosis [
34,
35] and it would be interesting in future studies to investigate whether the prognosis of cancer patients with germline
POLE or
POLD1 mutations is also better. There is currently no consensus as to who should have diagnostic testing for PPAP (screening of EDs of
POLE and
POLD1 for pathogenic variants); we suggest that it should be considered for those with unexplained adenomatous polyposis, as well as those with a family history fulfilling the Amsterdam or modified Bethesda criteria, especially if no pathogenic mismatch repair variants have been found. Distinguishing pathogenic, PPAP-causing variants from non-pathogenic variants in
POLE and
POLD1 may be challenging. Based on the features of the mutations described here and the likely absence of functional data to help assessment of novel mutations in the clinic, we suggest applying the following filtering steps to distinguish a likely pathogenic variant:
(1)
Maps to the exonuclease domain of POLE (amino acids 268–471) or POLD1 (amino acids 304–533)
(2)
Allele frequency of < 1 × 10–5 in non-Finnish European gnomAD data
(3)
Maps to or flanks an exo motif and affects an amino acid that is perfectly or highly conserved in a POLE-POLD1 protein alignment
(4)
Classed as pathogenic by two or more in silico tools
(5)
Results in a protein predicted to retain polymerase and regulatory functions.
Additional DNA samples from relatives for co-segregation studies, and from tumours for mutation burden, spectrum and signature analysis are also very helpful. It remains desirable to find an in vitro system for rapid testing of novel variants. Design of functional assays in accordance with American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) guidelines would aid greatly with variant interpretation [
36]. The set of variants selected here as probably pathogenic all had supporting evidence from at least one of the following: co-segregation studies, mutator phenotype assessment in yeast assays or biochemical proof reading assays, in addition to fulfilling the five criteria above. If any of these supporting lines of evidence were conflicting or inconclusive, the variant was classed as being of unknown significance (e.g.
POLE W347C and
POLE L460M). It is possible that we have excluded variants that are pathogenic, but we decided that strict classification criteria for pathogenic variants was required in order to give an accurate survey of the clinical features of those with PPAP.
This manuscript is a step forward in describing the clinical features of PPAP based on variants with strong evidence of pathogenicity with implications for diagnostic testing algorithms and hence screening. With time, the understanding of this condition and its cancer risk will no doubt evolve and inform updates to our recommendations for clinical management. We highlight the difficulties in identifying truly pathogenic variants and provide suggestions that could be incorporated in a more formal variant classification system for suspected PPAP-causing variants.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.