DNA Repair

Prostate cancer heterogeneity

Prostate cancer is a molecularly heterogeneous disease¹. Recent studies have utilised advanced molecular techniques to identify genetic alterations that are enriched in prostate cancer and its varying disease states². The aim of such studies is to identify prognostic and predictive biomarkers that may help to better stratify patients during treatment planning².

Alterations in advanced prostate cancer

Many gene alterations that are present in advanced prostate cancer have been identified to date (Figure 1). These genes encode proteins that are predominantly involved in^3,4:

• the PI3K pathway (for example, PTEN)
• DNA repair pathways (for example, BRCA2 and ATM)
• cell cycle regulation (for example, RB1)
• epigenetic regulation (for example, KMT2C and KMT2D)
• the WNT pathway (for example, APC and CTNNB1)

Other highly altered genes in metastatic prostate cancer include TP53 and AR that are involved in cellular survival and androgen receptor signalling, respectively, and the TMPRSS2:ERG gene fusion alteration^4–6.

Figure 1. Frequency of alterations identified in cellular pathways and genes for metastatic prostate cancer versus localised disease. Adapted from Armenia et al., 2018⁴. For DNA repair genes, genomic alterations were identified in 27% of metastatic tumours versus 10% in primary tumours. CTNNB1, catenin beta-1; MAPK, mitogen-activated protein kinase; PCa, prostate cancer; PI3K, phosphoinositide 3-kinase; RAF, rapidly accelerated fibrosarcoma; RAS, rat sarcoma.

It is important to understand which of the identified alterations are driver mutations that promote tumour evolution, and which are a consequence of selective pressure (for example, to promote treatment resistance). The former will allow for early stratification of patients that are more likely to develop aggressive disease. In a small study that analysed gene alterations in 61 matched patient samples from treatment naive and mCRPC tumours, AR alterations were the most commonly acquired mutation in mCRPC, followed by TP53 alterations⁷. AR and TP53 alterations are therefore likely to be the result of selective pressure to promote treatment resistance. Alterations in DNA repair genes (9/61) identified in mCRPC samples were all present in matched treatment naive samples⁷. The presence and stability of early DNA repair alterations, together with its enrichment in metastatic disease, may indicate a role in tumour evolution. Indeed, current data shows that germline (inherited) BRCA2 alteration is associated with poor prognosis and increased family risk^8–15.

These observations are in line with the role for DNA repair genes in preventing genome instability, a fundamental driver of tumour onset and progression¹⁶. DNA repair genes encode proteins that repair damaged DNA to prevent the forming of pathogenic mutations, thereby playing an important role in maintaining genome stability. They usually carry out this role as part of a cellular DNA repair pathway, each one evolved to repair specific damage types (Figure 2).

Figure 2. DNA repair pathways repair DNA damage from multiple sources to maintain genome stability. Adapted from Lord & Ashworth, 2012; Athie et al., 2019^2,17. The homologous recombination repair (HRR) pathway utilises genes like BRCA2, ATM, BRCA1, CHEK2, PALB2 and RAD51 to repair DNA double strand breaks. Loss of HRR leads to the error-prone repair of DNA double strand breaks to create mutations such as small base deletions and chromosomal rearrangements whereby the double strand break from one chromosome is re-joined to that of another. Mismatch repair genes like PMS2, MSH2 and MSH6 repair incorrectly paired DNA bases, and small insertion or deletion loops. Loss of MMR results in point mutations, as well as repeated insertions or deletions in genome regions that are prone to loop formation (identifiable as microsatellite repeats)¹⁸. A, adenine; ATM, ataxia telangiectasia mutated; BRCA1/2, breast cancer gene 1/2; CHEK2, checkpoint kinase 2; G, guanine; LIG3, ligase 3; MLH1, MutL homolog 1; MSH2/6, MutS Homolog 2/6; PALB2, partner and localizer of BRCA2; PARP1, poly (ADP-ribose) polymerase 1; PMS2, PMS1 homolog 2; UV, ultraviolet; XRCC1, X-Ray repair cross complementing 1.

A DNA repair alteration identified in early stage prostate cancer may therefore inform on patient risk to guide early treatment planning.

To find out more on the role for DNA repair genes in maintaining genome stability, see our section on cellular DNA damage response.  

Prevalence of DNA repair gene alterations in prostate cancer

Approximately 10–19% of primary prostate tumours and 23–27% of metastatic prostate tumours harbour both germline and somatic mutations in DNA repair genes^3,4,19. In the lethal form of prostate cancer, metastatic castration-resistant prostate cancer, approximately 12–15% of men have germline alterations in DNA damage response genes²⁰.  

10–19% of primary prostate tumours and approximately 23–27% of metastatic prostate tumours harbour DNA repair gene alterations^3,4,19

DNA repair genes that are altered in prostate cancers are mostly involved in the homologous recombination repair (HRR) pathway that repairs DNA double strand breaks (for example, BRCA2, ATM, CHEK2, BRCA1 and PALB2) (Figure 3)²¹. Much less frequently, they are involved in the mismatch repair (MMR) pathway that repairs incorrectly paired DNA bases and DNA loops (for example, PMS2, MSH2 and MSH6)²¹. Of note, the less common ductal or intraductal prostate carcinomas display high levels of genome instability compared to adenocarcinomas. Indeed, these tumour types are more likely to harbour alterations in genes involved in MMR and HRR^22–25.

Figure 3. Distribution of presumed pathogenic germline mutations for 16 identified DNA repair genes in men with metastatic prostate cancer. Adapted from Pritchard et al., 2016²¹. Analysis of 20 DNA repair genes in 692 men with metastatic prostate cancer revealed that 82 men (11.8%) had at least one pathogenic mutation in 16 of the 20 DNA repair genes evaluated. In this study, 96% of alterations were found in genes of the homologous recombination repair (HRR) pathway that repairs DNA double strand breaks, whilst 4% were present in genes involved in mismatch repair (MMR). ATM, ataxia telangiectasia mutated; ATR, ataxia telangiectasia and Rad3 related; BRCA1/2, breast cancer gene 1/2; BRIP1, BRCA1 Interacting Protein C-Terminal Helicase 1; CHEK2, checkpoint kinase 2; FAM175A, family with sequence similarity 175 member; GEN1, GEN1 Holliday Junction 5' Flap Endonuclease; MRE11A, MRE11 homolog, double strand break repair nuclease A; MSH2/6, MutS Homolog 2/6; NBN, Nibrin; PALB2, partner and localizer of BRCA2; PMS2, PMS1 homolog 2; RAD51C/D, RAD51 recombinase C/D.

The most commonly altered DNA repair gene in metastatic prostate cancer is consistently BRCA2 (Figure 3)². Germline (heritable) pathogenic BRCA2 and BRCA1 alterations are associated with hereditary breast and ovarian cancer (HBOC) syndrome that is historically characterised by early onset breast and ovarian cancer in women²⁶. Despite its name, it is now clear that HBOC also impacts on the risk of other cancers in both men and women, including prostate cancer, pancreatic cancer and melanoma^13,26,27. Loss of mismatch repair genes are similarly associated with Lynch syndrome, a predisposition syndrome that is much less common in prostate cancer²⁸.

Distribution of germline and somatic DNA repair alterations in prostate cancer

Germline mutation
A mutation that is inherited from a parent and is found in all cells, including tumour cells²⁷ 

Somatic mutation
A mutation that arises spontaneously and can be found in any cell, including tumour cells, but not germ cells²⁷

Just under half of the DNA repair alterations identified in prostate cancer samples are of germline origin (inherited from a parent), and the rest is of somatic origin (a spontaneous mutation that is tumour-specific) (Figure 4)²⁹. This is true for alterations both in primary tumours (4.6% germline versus 10–19% tumour-associated) and metastatic prostate cancer (8–11.8% germline versus 23–27% tumour-associated)^3,4,19,21. Notably, germline alterations in DNA damage response genes are highest in metastatic castration-resistant prostate cancer, with a prevalence of approximately 12–15%²⁰. 

A recent study further suggested that metastatic castration-resistant prostate cancer may possess an even higher frequency of germline DNA repair gene alterations (16.2%; 68/419) compared to unspecified metastatic prostate cancer, as observed in another study (11.8%; 82/692)^21,30.

Figure 4. Frequency of germline and somatic DNA repair gene alterations in advanced prostate cancer. Adapted from Abida et al., 2017²⁹. Data represent alterations identified in archival and new biopsy samples from n = 50 locoregional, n = 53 biochemically recurrent and n = 358 metastatic samples. ATM, ataxia telangiectasia mutated; BRCA1/2, breast cancer gene 1/2; CHEK2, checkpoint kinase 2.

The V2.2020 Clinical Practice Guidelines In Oncology (NCCN Guidelines^®) for Prostate Cancer recommends germline testing for HRR and MMR gene alterations in high-risk, very-high-risk, regional or metastatic prostate cancer patients³¹. The V2.2020 NCCN Guidelines^® for Prostate Cancer also recommends germline testing in very-low, low and intermediate risk patients who have a family history of cancer, Ashkenazi Jewish ancestry or intraductal/cribriform histology³¹.

The ESMO Clinical Practice Guidelines for Prostate Cancer (2020) also recommends germline testing for BRCA2 and other DNA damage response (DDR) genes associated with predisposition syndromes in prostate cancer patients who have a family history of cancer³². It also suggests to consider germline testing for these genes in patients with metastatic prostate cancer³².

Germline testing is carried out on DNA extracted from normal cells taken from blood or buccal swab samples and is generally used to identify alterations that inform on familial risk of cancer³³. Since germline mutations are also present in tumour cells, germline testing also identifies tumour-associated alterations, but not those of somatic origin (approximately 50% of DNA repair gene alterations in prostate cancer)²⁹. Germline testing may therefore identify approximately half of prostate cancer patients who harbour tumour-associated alterations in DNA repair genes. The other half of patients who harbour only somatic mutations in DNA repair genes may be missed. The V2.2020 NCCN Guidelines for Prostate Cancer suggest to consider tumour multigene molecular testing in patients with low, intermediate and high-risk prostate cancer, who have a life expectancy of 10 years or more³¹. Indeed, this may help to inform on tumour aggressiveness. The V2.2020 NCCN Guidelines for Prostate Cancer also recommends tumour testing for HRR gene mutations in patients with metastatic prostate cancer, and suggest to consider tumour testing for MSI or defective MMR in these patients³¹. Tumour testing for HRR gene mutations, and MSI or defective MMR should also be considered in patients with regional disease³¹.

 The ESMO Clinical Practice Guidelines for Prostate Cancer (2020) suggest to consider tumour testing for homologous recombination repair genes and mismatch repair defects in patients with metastatic castration-resistant prostate cancer (mCRPC)³². Altogether, tumour testing may help to identify patients who could benefit from investigative treatments currently used in clinical trials.

The EAU guidelines (2020) do not currently provide any recommendations on molecular testing for DNA repair alterations in prostate cancer; however, the EAU guidelines recommend offering early PSA testing to men who have an elevated risk of prostate cancer, including men >40 years old who carry BRCA2 mutations³⁴.

Types of gene alterations in DNA repair genes

Germline mutations in DNA repair genes are often monoallelic (affecting only one of the two gene copies inherited from parents)^3,21,35. Biallelic loss occurs through somatic mutation of the second functional copy of the gene, to create two non-functional genes^3,21,35.

Monoallelic mutation
Only one copy of a gene is mutated, the other copy is still normal²⁷

Biallelic mutation
Both copies of the gene are mutated (not necessarily the same mutation)²⁷

For BRCA2, germline mutations are most often frameshift mutations that alter the reading frame of the genetic code, thereby creating truncated BRCA2 protein products that lack important functional domains (Figure 5)³. Inactivation of the second, functional BRCA2 gene is most often caused by loss of heterozygosity (LOH). Loss of heterozygosity may involve deletion of the functional BRCA2 allele (1 copy LOH), or replacement of the functional allele with the non-functional allele (copy neutral LOH) through conversion. Other less frequent alterations include missense, point and splice site mutations³.

Figure 5. Gene alterations identified in mCRPC patients. Adapted from Robinson et al., 2015³. Top panel: Patient-specific mutations identified in the panel of DNA repair genes assessed (homologous recombination repair genes; BRCA2, ATM, BRCA1, FANCA, RAD51B, RAD51C, and mismatch repair genes; MLH1 and MSH2). Lower panel: Amino acid alterations are indicated for the BRCA2 protein. ATM, ataxia telangiectasia mutated; BRCA1/2, breast cancer gene 1/2; FANCA, Fanconi anaemia, complementation group A; HELC, helical domain; LOH, loss of heterozygosity; MLH1, MutL homolog 1; MSH2, MutS Homolog 2; OB, oligonucleotide ssDNA-binding fold domain; RAD51B/C, RAD51 paralog B/C.

DNA damage response (DDR)

Prostate cancer is heterogeneous in nature and multiple mutations have been identified in genes that are involved in the cellular response to DNA damage². These genes include BRCA2, ATM and CHEK2 of the homologous recombination repair pathway (HRR) and MSH2, MSH6, MLH1 and PALB2 of the mismatch repair pathway (MMR)².

DNA damage

DNA possesses multiple chemical bonds that are susceptible to damage by both endogenous and exogenous damage sources (Figure 6). It is estimated that approximately 70,000 DNA lesions are created per cell per day³⁶. Endogenous damage is created by sources from within the cell, including reactive oxygen and nitrogen species, unregulated enzymatic activity (for example, by topoisomerases), and errors in DNA replication³⁷. Exogenous damage is inflicted from sources external to the cell, such as DNA alkylating agents (for example, mitomycin C and cisplatin), ultraviolet radiation and ionising radiation (Figure 6)³⁷. 

Figure 6. Endogenous and exogenous sources of DNA damage and damage types inflicted on to DNA. Adapted from Lord & Ashworth, 2012¹⁷. A, adenine; G, guanine; ROS, reactive oxygen species; UV, ultraviolet.

The type of damage inflicted on DNA depends on the source of damage (Figure 6)¹⁷. For instance, attack from reactive oxygen and nitrogen species can create base modifications that alter the base pairing preference to create base mismatches. DNA replication errors can also lead to base mismatches, or accidental base insertions and deletions. Cellular topoisomerases and radiation can cut the DNA backbone to create DNA single strand breaks or DNA double strand breaks. DNA double strand breaks are difficult to repair and can lead to cell death (the cytotoxic mechanism of radiation therapy) or genome rearrangements such as translocations. Unrepaired DNA single strand breaks may also be converted into DNA double strand breaks during DNA replication¹⁷. 

Cellular DNA damage response (DDR)

Unrepaired DNA damage can lead to the creation of a permanent mutation that is transmissible to daughter cells during cellular division and that can have catastrophic pathogenic effects^17,38. For instance, genes that regulate cellular proliferation and survival are frequently mutated in cancer cells¹⁶. It is therefore important to repair damaged DNA before a permanent mutation is created. Indeed, mutations that inactivate DNA damage repair genes often have been associated with cancer predisposition^2,37.

The importance of DNA damage repair is highlighted by the increased cancer susceptibility in patients who have pathogenic mutations in important DNA repair genes. These genes include BRCA1 and BRCA2 (hereditary breast and ovarian cancer syndrome) and MLH1, MSH2 and MSH6, PMS2 (Lynch syndrome), amongst others^27,28.  

The cellular DNA damage response broadly involves (Figure 7)^37,39,40:

1. Transcriptional activation of genes required for DNA damage signalling and repair
2. Cell cycle arrest to permit repair prior to DNA replication or cellular division
3. Damage-specific DNA repair using DNA repair proteins that identify and remove the damage, and restore the correct DNA sequence
4. Cell death (apoptosis) or senescence in cases where the damage is too severe, or repair is not possible

Figure 7. The DNA damage response (DDR). Adapted from Jackson & Bartek, 2009; Lord & Ashworth, 2012; O’Connor, 2015; Sahan et al., 2018^17,37,39,40. Sensing of DNA damage triggers transcriptional reprogramming to promote cell cycle checkpoint activation, DNA repair, and in cases where the damage is excessive or cannot be repaired, TP53-mediated cell death. A, adenine; DDR, DNA damage response; G, guanine; ROS, reactive oxygen species; UV, ultraviolet.

DNA repair

There are many DNA repair pathways, each optimised to repair a specific type of DNA damage (Figure 8)³⁷. The repair proteins involved in each pathway differ; however, they tend to be involved in one or more of the typical steps of repair²:

1. Damage detection
2. Damage signalling
3. Damage removal (excision) and/or DNA strand end processing
4. DNA synthesis to complete repair

Figure 8. DNA repair pathways for the indicated damage types. Adapted from Caldecott, 2008; Lord & Ashworth, 2012; Athie et al., 2019^2,17,41. A, adenine; APE1, apurinic/apyrimidinic endonuclease 1; ATM, ataxia telangiectasia mutated; BRCA1/2, breast cancer gene 1/2; CHEK2, checkpoint kinase 2; DNA-PKcs, DNA-dependent protein kinase catalytic subunit; ERCC1/4, excision repair cross-complementation group 1/4; G, guanine; Ku70/80, Ku autoantigen, 70kDa/80kDa; LIG3, ligase 3; MLH1, MutL homolog 1; MSH2/6, MutS Homolog 2/6; PALB2, partner and localizer of BRCA2; PARP1, poly (ADP-ribose) polymerase 1; PMS2, PMS1 homolog 2; UV, ultraviolet; XRCC1, X-Ray repair cross complementing 1.

Most modified bases are repaired by the base excision repair pathway (BER), whereas mismatched bases are predominantly repaired by the mismatch repair pathway (MMR) and bulky UV-induced DNA lesions are repaired by the nucleotide excision repair pathway (NER)¹⁷. DNA single strand breaks that occur in a single strand of duplex DNA are repaired by the single strand break repair pathway (SSBR)⁴¹. In dividing cells, the DNA replication machinery can collide with DNA single strand breaks that remain unrepaired (for example, through inhibition of enzymes involved in repair) to form a DNA double strand break, a highly toxic lesion that can trigger cell death if not repaired efficiently (Figure 9)^37,39. DNA double strand breaks are repaired predominantly by two DNA repair pathways; the non-homologous end joining pathway (NHEJ) which is error-prone, and the homologous recombination repair pathway (HRR) that utilises an existing undamaged DNA copy to complete accurate repair^17,36.

Figure 9. Unrepaired DNA single strand breaks are converted into DNA double strand breaks in replicating cells. Adapted from O’Connor, 2015³⁹.

DNA repair gene alterations identified in prostate cancer are mostly involved in the homologous recombination repair pathway that repairs DNA double strand breaks in replicating cells, or much less frequently in the mismatch repair pathway that replaces mismatched DNA bases².

Homologous recombination repair (HRR)  

The homologous recombination repair (HRR) pathway repairs DNA double strand breaks in cells that have a second copy of DNA (the homologue) available as a template for repair¹⁷. This second copy of DNA is mainly available during the S and G2 phases of the cell cycle, when cells have already replicated their DNA¹⁷. HRR therefore plays an important repair role in dividing cells, such as cancer cells.

During HRR, damage is detected by the MRN complex (MRE11-RAD50-NBS1) that activates ATM and ATR, two kinases that activate and recruit multiple repair proteins and regulators to the damage site (Figure 10)². ATM, together with the ATR kinase, also activate the cell cycle regulators CHEK1 and CHEK2 to halt the cell cycle². Multiple repair proteins process the DNA ends (for example, CtIP and EXO1) to create single stranded DNA overhangs⁴². Regulatory repair proteins, including BRCA1-BARD1 together with BRCA2 and PALB2, enable RAD51 protein binding to the single stranded overhangs⁴². RAD51 then guides the single stranded DNA to the complementary region of the undamaged DNA copy, using it as a template for accurate synthesis and repair completion².    

Figure 10. The homologous recombination repair pathway (HRR). Adapted from Athie et al., 2019². ATM, ataxia telangiectasia mutated; ATR, ataxia telangiectasia and Rad3 related; BRCA1/2, breast cancer gene 1/2; Chk1/2, checkpoint kinase 1/2; MRE11, MRE11 homolog, double strand break repair nuclease; NBS1, nibrin; PALB2, partner and localizer of BRCA2; RAD50, RAD50 double strand break repair protein.

HRR deficiency (HRD) is caused by pathogenic alteration in HRR DNA repair genes such as BRCA1, BRCA2, ATM and PALB2⁴³. In the absence of HRR, DNA double strand breaks are repaired by non-homologous end joining (NHEJ), an error-prone process that can lead to the loss or gain of nucleotides at the broken DNA ends prior to ligation^17,36. Persisting DNA double strand breaks also increases the possibility of chromosomal rearrangements³⁶. HRD therefore leads to genome instability that is identifiable as loss of heterozygosity (LOH), large scale transitions, and telomeric allelic imbalance, which are sometimes altogether referred to as scars or signatures⁴³.

HRR proteins are also involved in the repair of DNA inter-strand cross links, a complex damage type generated by alkylating chemotherapy agents such as cisplatin and mitomycin C⁴⁴. This complex damage type is resolved through the Fanconi Anaemia (FA) repair pathway that utilises proteins from multiple repair pathways to complete repair, including the HRR pathway. Some HRR repair proteins therefore have FA aliases, including BRCA2 (FANCD1), PALB2 (FANCN), RAD51 (FANCR) and BRCA1 (FANCS)⁴⁴. 

Mismatch repair (MMR)

The mismatch repair pathway (MMR) replaces incorrect bases mis-inserted during DNA synthesis². It also repairs accidental base insertions and deletions caused by slippage of the DNA replication machinery. During MMR, damage recognition is carried out by the MSH2-MSH6 or MSH2-MSH3 complexes (Figure 11)^2,45. This recruits the MLH1-PMS2 proteins that together with the EXO1 nuclease removes a small stretch of nucleotides on the newly synthesised DNA strand, including the mismatched or misplaced base². Repair is completed by DNA re-synthesis using the replication machinery.

Figure 11. The mismatch repair pathway (MMR). Adapted from Athie et al., 2019². MSH2-MSH6 or MSH2-MSH3 recognise the mismatched base and recruits MLH1-PMS2 and EXO1 to remove the stretch of newly synthesised DNA containing the base mismatch^2,45. The replicative polymerase (Polδ) and Ligase I complete repair. DNA Pol, DNA polymerase; EXO1, exonuclease 1; LIG1, DNA ligase 1; MLH1, MutL homolog 1; MSH2/3/6, MutS Homolog 2/3/6; PMS2, PMS1 homolog 2.

Defective mismatch repair (dMMR) has been studied widely in colorectal cancers, where approximately 15–20% of cancers display microsatellite instability (MSI), and those with dMMR display a high mutation rate, 100–1000-fold more than normal cells¹⁸. Microsatellites are repetitive sequences in DNA that are highly susceptible to accidental base insertions and deletions caused by slippage of the DNA replication machinery¹⁸. Mismatch repair normally corrects this error, and irregularities in the length of these repetitive sequences, MSI, indicate dMMR¹⁸. MSI is therefore a marker (sometimes referred to as a scar, or signature) that is used to characterise the MMR status of tumours¹⁸. Lynch syndrome, which is caused by hereditary pathogenic mutation of mismatch repair genes (MSH2, MSH6, MLH1, PMS2), is characterised by early onset cancers that display high levels of MSI across multiple cancer types, including colorectal cancer and prostate cancer^28,46. 

Clinical implications of DNA repair gene alterations

The clinical implications of DNA repair gene alterations in prostate cancer is mostly under investigation. DNA repair gene alterations may serve as a marker for personal and family risk of developing cancer³¹. The V2.2020 NCCN Guidelines for Prostate Cancer therefore recommends germline testing for HRR and MMR gene alterations in prostate cancer patients who have a family history of cancer, or who have high-risk, very-high-risk, regional or metastatic disease³¹. This testing may identify DNA repair gene alterations that can inform on personal and family risk of cancer.

The possible implications of DNA repair gene alterations in prostate cancer that are under investigation include: 

• Familial risk stratification
• Prognostic biomarker for aggressive disease and metastasis
• Predictive biomarker for sensitivity to treatments

Personal and family risk of cancer

A family history of prostate cancer increases the risk of prostate cancer^47–49. Additionally, a family history of hereditary breast and ovarian cancer (HBOC) syndrome and Lynch syndrome also increases the risk of prostate cancer^{13,28,46,50,51}.

Both HBOC and Lynch Syndrome are caused by inherited germline alterations to genes involved in processes that repair damaged DNA. For HBOC, altered genes include BRCA1 and BRCA2 that are involved in DNA double strand break repair through the homologous recombination repair (HRR) pathway²⁷. Sufferers of Lynch syndrome possess gene alterations for DNA repair proteins involved in the mismatch repair (MMR) pathway that removes and replaces mismatched DNA bases²⁸. An inability to efficiently repair DNA damage increases the likelihood of random mutations forming, thereby promoting genome instability that is the likely cause of increased cancer predisposition in people who have these gene alterations^2,16.

Dr Alexander Wyatt, who leads a prostate cancer genomics research group at the Vancouver Prostate Centre comments on the clinical impact of identifying DNA repair alterations on the family members of a prostate cancer patient.

As with breast and ovarian cancer, multiple studies have now associated germline BRCA1 and BRCA2 mutations to an increased risk for prostate cancer^{9,13,50,52–55}. Early studies on patients with primary prostate cancer identified inherited (germline) mutations in BRCA2 that were more common in younger patients and patients who had a family history of cancer^56,57. More than 2% of Ashkenazi Jews carry germline alterations in BRCA1 and BRCA2, and in one study, carriers were found to be over-represented in those with prostate cancer (5.2% versus 1.9% of control Ashkenazi Jewish men)^58,59. It is now thought that BRCA2 is associated with a 2 to 6-fold increased risk of prostate cancer, whilst the association is not clear for the less frequent BRCA1 mutation^{9,13,50,55,59,60}. Other DNA damage response factors including ATM, PALB2 and CHEK2 have also been associated with an increased risk of prostate cancer^61–64.

Lynch syndrome is caused by mutations in genes that are involved in the mismatch repair (MMR) pathway, including MLH1, MSH2, MSH6 and PMS2²⁸. Loss of efficient mismatch repair results in high levels of random point mutations and tumour microsatellite instability (MSI). In one study, approximately 5% of 1,048 prostate cancer patients possessed high or intermediate levels of microsatellite instability, 5.6% of whom were found to have Lynch Syndrome (a total of 0.29% of PC patients tested)²⁸. In another prospective study, 3.1% of 1,033 prostate cancer patients displayed high MSI levels, 21.9% of whom had Lynch syndrome (a total of 0.68% of PC patients)⁶⁵. In another study, 1.74% of 3,607 prostate cancer patients who were referred for genetic testing had mutations in PMS2, MLH1, MSH2 or MSH6⁶⁶. Interestingly, a higher level of genomic instability is apparent in the rarer ductal or intraductal prostate carcinomas compared to adenocarcinomas. Indeed, these tumour types are more likely to harbour MMR and HRR alterations^22–25.

Despite enrichment of DNA repair mutations in patients who have a family history of cancer, germline mutations were also identified in patients who did not possess a significant family history of cancer, as well as in older patients who did not fit within ‘early-onset’ disease that is often ascribed to patients with inherited predispositions^2,21,67.

Limited guidelines currently exist to support consideration of familial testing. The V2.2020 NCCN Guidelines for Prostate Cancer recommend germline testing for HRR and MMR germline alterations in all patients with high-risk, very-high-risk, regional or metastatic prostate cancer³¹. For patients with very-low, low and intermediate risks, the V2.2020 NCCN Guidelines for Prostate Cancer recommend germline testing for DNA repair alterations if patients have a family history of cancer, Ashkenazi Jewish ancestry or intraductal/cribriform histology³¹. Germline testing may be performed with or without pre-test counselling; however, genetic counselling should be carried out if a pathogenic germline mutation is identified³¹.

The ESMO Clinical Practice Guidelines for Prostate Cancer (2020) also recommends germline testing for BRCA2 and other DNA damage response (DDR) genes associated with predisposition syndromes in prostate cancer patients who have a family history of cancer³². It also suggests to consider germline testing for these genes in patients with metastatic prostate cancer³². The EAU Guidelines for Prostate Cancer (2020) does not currently provide recommendations on molecular testing for DNA repair alterations in prostate cancer; however it recommends offering early PSA testing to men who have an elevated risk of prostate cancer, including men >40 years old who carry BRCA2 mutations³⁴.

Discover more on the types of molecular tests for identifying DNA repair gene alterations in prostate cancer. 

Prognostic biomarker for aggressive disease

The presence of DNA repair gene alterations in both treatment naive and mCRPC samples matched from the same patient, together with its enrichment in metastatic disease, suggests a role in tumour aggressiveness^4,7. Indeed, several large retrospective studies have found an association between germline BRCA2 alterations and aggressive prostate cancer disease phenotype^8–12,14,15. BRCA2 germline mutations may therefore serve as a prognostic marker for aggressive disease in patients with early stage prostate cancer^9–12,14,15. More recently, biallelic loss of CDK12 that regulates the expression of many DNA damage response genes, has also been shown to be enriched in patients with more aggressive disease at the outset⁶⁸.  

In one study, median cancer-specific survival of 8.6 years was identified in carriers of BRCA1 and BRCA2 alterations (n = 79) versus 15.7 years in noncarriers (n = 1,940) (Figure 12)¹¹. This study also found significant associations between germline BRCA mutations and Gleason scores ≥ 8 (P=0.00003), T3/T4 stage (P=0.003), nodal involvement (P=0.00005), and metastases at diagnosis (P=0.005)¹¹. A later study by Castro and colleagues showed that BRCA1 and BRCA2 germline mutation carriers had reduced cause-specific survival and were more likely to develop metastatic disease¹².

Figure 12. Cause-specific (a) and metastasis-free (b) survival for early prostate cancer carriers of BRCA1 and BRCA2 mutations (n = 79) versus noncarriers (n = 1,940). Adapted from Castro et al., 2013¹¹. BRCA1/2, breast cancer gene 1/2.

A more recent study also identified an association between the incidence of prostate tumour grade reclassification among patients undergoing active surveillance and germline BRCA1, BRCA2 and ATM mutation (Figure 13)¹⁵. The degree of association was highest for tumours with a BRCA2 mutation, where the incidence of an upgrade was higher at both the early stages (2–year follow-up) and later (10–year follow-up).

Figure 13. Cumulative incidence of upgrading grade groups on biopsies taken after the diagnostic biopsy in noncarriers and (a) carriers of germline BRCA1 and/or BRCA2 and/or ATM mutations or (b) carriers of BRCA2 mutations only. Adapted from Carter et al., 2019¹⁵. ATM, ataxia-telangiesctasia mutated; BRCA1/2, breast cancer gene 1/2.

Germline BRCA2 gene alterations have been shown to impact survival even at the later stages of prostate cancer disease. Whilst the primary endpoint of this study was not met, cause specific survival in metastatic castration-resistant prostate cancer was halved in BRCA2 carriers compared to noncarriers (17 versus 33 months, P=0.027), though this was not significant in the comparison of carriers of any assessed DNA repair mutation (BRCA2, ATM, BRCA1, PALB2) versus noncarriers (23 versus 33.2 months, p=0.264)³⁰. Larger cohort studies that include more patients with potential prognostic markers such as BRCA1 and ATM mutations are needed to better understand the contributions of individual germline DDR mutations to disease aggressiveness and progression. 

The V2.2020 NCCN Guidelines for Prostate Cancer suggests to consider tumour multigene molecular testing in patients with low, intermediate and high-risk prostate cancer, who have a life expectancy of 10 years or more³¹. This may inform patients on risk of aggressive disease, and may impact on their decision to have curative intent treatment options versus active surveillance¹⁵. The V2.2020 NCCN Guidelines for Prostate Cancer also recommend tumour testing for HRR gene mutations in patients with metastatic prostate cancer, and suggest to consider tumour testing for MSI or defective MMR in these patients³¹. Tumour testing for HRR gene mutations, and MSI or defective MMR should also be considered in patients with regional disease³¹.

The ESMO Clinical Practice Guidelines for Prostate Cancer (2020) suggest to consider tumour testing for homologous recombination repair genes and mismatch repair defects in patients with metastatic castration-resistant prostate cancer (mCRPC)³².

Predictive biomarker for current treatments

Prostate cancer patients with DNA repair gene alterations may respond differently to some treatments compared to those without DNA repair gene alterations².

Dr Alexander Wyatt leads a prostate cancer genomics and molecular diagnostics research group at the Vancouver Prostate Centre. Here, he highlights key learnings from identifying predictive biomarkers for treatment response in other cancer types.

Localised prostate cancer

Currently, treatment options for men with localised prostate cancer include active surveillance, radiotherapy or radical prostatectomy³⁴. Since DNA repair gene alterations have been associated with aggressive disease, it is likely that carrier patients with localised disease will opt for radiotherapy or radical prostatectomy instead of active surveillance¹⁵. Very little data exists on whether radiotherapy or radical prostatectomy is preferable. One retrospective study found that BRCA1 or BRCA2 mutation carriers had worse outcome when treated with standard therapies compared to noncarriers; however, they did not conclusively identify a difference in response between carriers who had radical prostatectomy versus those who were treated with external beam radiation therapy¹². Whilst surgery appeared better (89% and 67% of BRCA1 or BRCA2 carriers were metastasis free at 5– and 10–years, respectively) compared to radiation therapy (57% and 39% of BRCA1 or BRCA2 carriers were metastasis free at 5– and 10–years, respectively), patients were not blindly selected for treatment and those who received radiotherapy presented more advanced disease than those who were treated with surgery¹².

Castration-resistant and advanced disease

Prostate cancer patients are often treated with androgen deprivation therapy (ADT) early on. The recent prospective PROREPAIR-B study found that carriers of BRCA2 alterations progressed from ADT responsive recurrent or metastatic disease to ADT-resistant (castration-resistant) disease more quickly compared to noncarriers (13.2 months versus 22.8 months, P=0.048)³⁰. Patients who develop castration-resistant disease are commonly treated with taxanes and/or new hormonal agents (NHA) such as enzalutamide or abiraterone^34,69,70. Currently, the androgen receptor variant, AR-V7, is being considered as a possible biomarker for response to NHAs; otherwise, there are no well validated molecular markers of response for approved systemic therapies⁷¹. For metastatic castration-resistant prostate cancer (mCRPC), the impact of DNA damage repair gene alterations on response to enzalutamide or abiraterone and taxanes is currently unclear (Table 1).

Table 1. Treatment outcome in mCRPC patients who carry DNA repair gene alterations^30,35,72,73.

Overall, the studies summarised in Table 1 show conflicting data on the impact of DNA repair alterations on treatment response. Only the PROREPAIR-B study was wholly prospective in terms of patient recruitment. PROREPAIR-B found that germline mutations in ATM/BRCA1/BRCA2/PALB2 showed a non-significant trend toward worse progression free survival and cancer specific survival following any first-line treatment. Germline BRCA2 mutation carriers had a significantly lower cancer specific survival when treated with first-line taxanes compared to noncarriers but not to androgen signalling inhibitors (ASI)³⁰. In an earlier retrospective study by Mateo and colleagues on patients who may have received multiple treatments, no significant difference was observed for overall survival or progression-free survival following taxane or NHA treatments between either germline DDR mutation carriers or BRCA2 mutations carriers and noncarriers⁷³. In two retrospective studies by Annala and colleagues, less time to PSA progression was observed in DNA repair alteration carriers treated with NHAs but not with taxanes, and a positive correlation with NHA resistance was observed^35,74. Conversely, a prospective study that included retrospective data by Antonarakis et al indicated that carriers of germline DNA repair gene alterations showed a non-significant trend toward better progression-free survival following NHA treatment⁷². These studies all vary in study design with only PROREPAIR-B being wholly prospective². They also assess different DNA repair gene alterations for a small number of patients in the carrier arm who may have complex treatment histories². Larger prospective studies that include detailed assessment of multiple DNA damage response genes and that distinguish between germline and somatic mutations are needed.

See our section on molecular diagnostics highlighting the molecular tests available for assessing DNA repair gene alterations.

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