2.4.2. Case A153: Biopsy Right Iliac Crest Corresponding to Metastatic Deposit on Imaging

This *TMPRSS2-ERG* positive metastatic tumour harboured a pathogenic *TP53* mutation (rs121912656, c.734G > T; p.Gly245Val) and a high PGA (25.5%). SCNAs include losses in *APC, PTEN, CHD1, BRCA2, FANCA, PIK3R1* and *LRP1B*. A complex SV on chromosome 5 encompassing *PPAP2A, PDE4D, MAP3K1* and *IL6ST,* was previously associated with a worse prognosis [8].

*TP53* loss is associated with a worse prognosis and decreased response to abiraterone in CRPC. *APC* loss, through its activation of Wnt signalling, may promote ASI resistance [32,62]. These two features would make docetaxel a better option than an ASI in the first instance for this patient at metastatic relapse. *BRCA2* and *FANCA* alterations were predictive for sensitivity to olaparib in the TOPARP studies [23,53] and, as previously discussed, *PTEN* and *CDH1* losses may sensitize this patient to PARP inhibition [54,77].

2.4.3. Case PCSD13: Biopsy Left Femur during Total Hip Replacement for Pathological Fracture

PCSD13 presented with a pathogenic germline *IDH2* mutation (rs121913502, c.419G > A; p.Arg140Gln). Reported to have an allele frequency of 0.00003 in The Genome Aggregation Database (gnomAD) [86], while associated with several other cancers, this mutation has not yet been reported in PCa [87]. In addition to an SNV in *AKT1*, there is a copy number gain in this gene. There are losses in the DDR genes *CDK12* and *MLH1*, and SVs also overlap multiple DDR genes. The COSMIC Mutational Signatures in this case show a subclonal increase in the proportion of Signature 3, whereas the majority of the other samples showed a decrease in this signature, which is associated with failure of double-strand DNA repair (Figure 2B).

The *AKT1* alterations may have contributed to his early ADT resistance (within 3 months of starting ADT) and confer sensitivity to AKT inhibitors [19]. These alterations could influence decisions on escalating ADT treatment with the addition of abiraterone, an androgen targeting drug, or docetaxel. However, the crosstalk between AR and PI3K/AKT signalling is well-established, [88,89] and additional pressure on the androgen axis in the context of an *AKT1* amplification may only drive further growth via the PI3K pathway. In the absence of a clinical trial with an AKT inhibitor, the addition of docetaxel rather than an AR targeting agent may have been more prudent. Immune checkpoint inhibition may have been another treatment option for this patient with his *CDK12* and *MLH1* SCNAs. This patient succumbed to his cancer shortly after developing CRPC.

2.4.4. Case 1135: Biopsy Right Posterior Iliac Crest Corresponding to Metastatic Deposit on Imaging

Despite having CRPC at the time of biopsy, case 1135 had very few alterations of interest with a TMB of 0.73 and PGA of 3.1%. This tumour contained SNVs in *KMT2C* and *IDH2* (rs121913502, c.419G > A; p.Arg140Gln) and SCNAs in *BCOR, NCOA7,* and *NOTCH2*. No significant SVs were identified with WGS but a homozygous deletion overlapping *TNS3* was identified using WGM.

The somatic SNV in *IDH2* is the same as the germline alteration seen in PCSD13 that has not been reported in PCa. It is unclear whether this mutation would drive the progression of this patient's cancer and if IDH inhibitor therapy, used to treat IDH-mutant AML, would be relevant. Based on preclinical studies, *KMT2C* alterations may confer sensitivity to PARP inhibition via its effects on the epigenetic status and expression of DDR genes. However, alterations in *KMT2C* are frequent in PCa [7] and responses to PARP inhibition only occur in a small proportion of patients [23]; therefore, it is unlikely this SNV alone will be enough to predict sensitivity to PARP monotherapy. ATRX is a DDR pathway gene while *BCOR, NCOA7* and *NOTCH2* are involved in androgen signalling. However, these alterations do not yet have any targeted therapeutic strategies for CRPC. While the impact of the deletion in *TNS3* is again unclear, it is noted that Tensins are a family of scaffolding proteins that regulate cell motility and growth and *TNS3* in involved in MET signalling [90], a target of the tyrosine kinase inhibiting drug, cabozantinib. Overall, though this case's alterations do not yet have any therapeutic relevance, the knowledge of molecular features in PCa is rapidly evolving and future findings may bring useful drugs to light.
