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. 2018 Dec;10(12):e9172.
doi: 10.15252/emmm.201809172.

A RAD51 assay feasible in routine tumor samples calls PARP inhibitor response beyond BRCA mutation

Marta Castroviejo-Bermejo  1 , Cristina Cruz  1   2   3 , Alba Llop-Guevara  1 , Sara Gutiérrez-Enríquez  4 , Mandy Ducy  5   6   7 , Yasir Hussein Ibrahim  1 , Albert Gris-Oliver  1 , Benedetta Pellegrino  1   8 , Alejandra Bruna  9 , Marta Guzmán  1 , Olga Rodríguez  1 , Judit Grueso  1 , Sandra Bonache  4 , Alejandro Moles-Fernández  4 , Guillermo Villacampa  10 , Cristina Viaplana  10 , Patricia Gómez  3   11 , Maria Vidal  3   11 , Vicente Peg  12   13 , Xavier Serres-Créixams  14 , Graham Dellaire  15 , Jacques Simard  7 , Paolo Nuciforo  13   16 , Isabel T Rubio  13   17 , Rodrigo Dienstmann  10 , J Carl Barrett  18 , Carlos Caldas  9   19 , José Baselga  20   21 , Cristina Saura  3   11 , Javier Cortés  13   22   23 , Olivier Déas  24 , Jos Jonkers  25 , Jean-Yves Masson  5   6 , Stefano Cairo  24 , Jean-Gabriel Judde  24 , Mark J O'Connor  26 , Orland Díez  4   27 , Judith Balmaña  28   3 , Violeta Serra  29   13
Affiliations

A RAD51 assay feasible in routine tumor samples calls PARP inhibitor response beyond BRCA mutation

Marta Castroviejo-Bermejo et al. EMBO Mol Med. 2018 Dec.

Abstract

Poly(ADP-ribose) polymerase (PARP) inhibitors (PARPi) are effective in cancers with defective homologous recombination DNA repair (HRR), including BRCA1/2-related cancers. A test to identify additional HRR-deficient tumors will help to extend their use in new indications. We evaluated the activity of the PARPi olaparib in patient-derived tumor xenografts (PDXs) from breast cancer (BC) patients and investigated mechanisms of sensitivity through exome sequencing, BRCA1 promoter methylation analysis, and immunostaining of HRR proteins, including RAD51 nuclear foci. In an independent BC PDX panel, the predictive capacity of the RAD51 score and the homologous recombination deficiency (HRD) score were compared. To examine the clinical feasibility of the RAD51 assay, we scored archival breast tumor samples, including PALB2-related hereditary cancers. The RAD51 score was highly discriminative of PARPi sensitivity versus PARPi resistance in BC PDXs and outperformed the genomic test. In clinical samples, all PALB2-related tumors were classified as HRR-deficient by the RAD51 score. The functional biomarker RAD51 enables the identification of PARPi-sensitive BC and broadens the population who may benefit from this therapy beyond BRCA1/2-related cancers.

Keywords: BRCA1; PALB2; PARP inhibitors; RAD51; homologous recombination.

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Figures

Figure 1
Figure 1. The antitumor activity of olaparib in PDXs identifies a subset of PARPi‐sensitive tumors
  1. A

    Waterfall plot showing the percentage of tumor volume change in olaparib‐treated tumors compared to the tumor volume on day 1. +20% and −30% are marked by dotted lines to indicate the range of PR, SD, and PD. The box underneath summarizes different characteristics of each model and the clinical context at the moment of PDX implantation. Black boxes indicate the presence of the phenotype. TNBC, triple negative breast cancer; ER+BC, estrogen receptor positive breast cancer; P, primary; M, metastasis. Error bars indicate SEM from independent tumors (n ≥ 3).

  2. B

    Graph showing the percentage of tumor volume change during olaparib treatment in PDXs from cohort‐1. Olaparib‐sensitive models are represented with discontinuous lines. Acquisition of PARPi resistance in PDX302, STG201, and PDX093 after prolonged exposure to olaparib is shown.

Figure 2
Figure 2. HRR‐related alterations in PDX cohort‐1 and PARPi response
  1. A

    Levels of BRCA1 promoter hypermethylation, levels of BRCA1 mRNA, and the presence of BRCA1 nuclear foci by immunofluorescence are shown (larger views and separate channels are shown in Appendix Fig S1). T127 and T162 were used as positive controls for hypermethylated BRCA1 promoter. Error bars indicate SEM from independent tumors (n ≥ 2). Dashed line indicates mean of BRCA1 mRNA levels in normal breast. PARPi response is shown in the summary underneath: white box: PD; black box: PR/CR. Alterations in HRR‐related genes in PDX are also indicated.

  2. B

    Western blot of PALB2 detected in U2OS cells and PDXs. Three biological replicates of PDX093 are shown; PDX302 is used as PALB2 wild‐type PDX control.

  3. C

    YFP‐PALB2 recruitment to laser‐induced DSBs is impaired in HeLa cells expressing PALB2 p.M296Nfs (n = 4, unpaired t‐test at 16 min). Error bars indicate SEM of >40 cells per condition.

  4. D, E

    Gene targeting efficiency using Cas9/mClover‐LMNA1 homologous recombination assay of (D) siRNA PALB2 cells (n = 4, one‐way ANOVA) or (E) cells with no PALB2 depletion complemented with wild‐type and p.M296Nfs siRNA‐resistant constructs (n = 7, one‐way ANOVA). Western blots of PALB2 wild‐type and PALB2 p.M296Nfs for each condition are shown. Error bars indicate SEM from independent experiments.

Source data are available online for this figure.
Figure EV1
Figure EV1. Analysis of PALB2 mutation in PDX093; RAD51 assay scoring and validation
  1. A

    Sanger sequencing reverse plots of DNA and RNA from PDX093 showing 1 nt (T) insertion in one PALB2 allele (PALB2 c.886dupA).

  2. B

    Flow diagram of the RAD51 scoring criteria and quality controls.

  3. C

    Quantification of geminin‐positive cells with RAD51 foci (Mann–Whitney U‐test) following treatment with vehicle and olaparib in PARPi‐sensitive (CR/PR) versus PARPi‐resistant (PD) PDXs.

  4. D

    Pearson correlation between the RAD51 score (percentage of RAD51 (+)/Geminin (+) cells, assessed in untreated FFPE tumor samples) and the percentage of tumor volume change in olaparib‐treated tumors from PDX cohort‐1. Each dot represents one PDX model. Error bars indicate SEM from independent tumors (n ≥ 3) treated with olaparib.

  5. E

    Quantification of geminin‐positive cells (paired t‐test in vehicle‐ versus olaparib‐treated tumors; unpaired t‐test in CR/PR versus PD tumors) following treatment with vehicle and olaparib in PARPi‐sensitive (CR/PR) versus PARPi‐resistant (PD) PDXs.

  6. F

    Spearman correlation of the percentage of RAD51 (+)/Geminin (+) cells in PDX cohort‐1 assessed with two different antibodies against RAD51 both in vehicle‐ and olaparib‐treated PDX samples.

Figure 3
Figure 3. Lack of RAD51 nuclear foci identifies PARPi‐sensitive PDX tumors
  1. A

    Percentage of geminin‐positive, RAD51 nuclear foci‐containing cells detected by immunofluorescence in FFPE samples from PDX tumors treated with vehicle or PARPi (larger views and separate channels are shown in Appendix Fig S2). Error bars indicate SEM from independent tumors (n ≥ 2). PARPi response is shown in the summary underneath: white box: PD; black box: PR/CR. Immunofluorescence staining of RAD51 foci in PARPi‐ and vehicle‐treated PDX tumors is shown. Alterations in HRR‐related genes are also summarized: hBRCA1: BRCA1 promoter hypermethylation and lack of BRCA1 expression and BRCA1 nuclear foci formation.

  2. B

    Restoration of RAD51 foci formation in PARPi acquired‐resistant PDXs. Immunofluorescence staining of BRCA1 and RAD51 foci in PARPi‐treated tumors from STG201, PDX302, and the corresponding PARPi acquired‐resistant models (STG201OR and PDX302OR). Scale bars: 10 μm.

  3. C

    Quantification of geminin‐positive cells that exhibit γ‐H2AX nuclear foci following treatment with vehicle and olaparib. Paired t‐test in PARPi‐sensitive (CR/PR) versus PARPi‐resistant (PD) PDXs.

Figure 4
Figure 4. RAD51 score predicts PDX response to PARPi in an independent PDX panel (cohort‐2)
  1. A

    Percentage of geminin‐positive, RAD51 nuclear foci‐containing cells in FFPE samples from untreated PDX tumors. Color bars indicate the presence of pathogenic variants in the indicated genes. Error bars indicate SEM from independent tumors (n ≥ 2). PARPi response is shown in the summary underneath: black box: PR/CR; white box: PD. Box colors indicate the PARP inhibitor treatment. Boxes with two colors indicate the same response to both treatments. Olaparib 100 and 50 mg/kg indicates that both doses were tested and resulted in the same response categorization.

  2. B

    ROC curves of the RAD51 score and HRD score, for PARPi response prediction capacity in the PDX cohort‐2. Bootstrap statistical test.

  3. C

    Immunofluorescence staining of 53BP1 and BRCA1 nuclear foci [with an antibody toward the N‐terminus (B1‐NT) or C‐terminus (B1‐CT) of BRCA1] in three BRCA1‐mutant, PARPi‐resistant models from PDX cohort‐2. The location of the mutation within the gene is indicated. Scale bars: 10 μm.

Figure 5
Figure 5. RAD51 score in tumors from patients with HBOC syndrome, including germline PALB2 mutation carriers
  1. A

    Consort diagram of the collected and analyzed FFPE tumor samples from patients with HBOC syndrome following the scoring criteria for the RAD51 assay.

  2. B

    Percentage of geminin‐positive, RAD51, or γ‐H2AX nuclear foci‐containing cells in FFPE tumor samples from patients with HBOC syndrome. The box underneath summarizes the patient's young onset (< 35 years), her family history (FH, purple box for PALB2‐related tumors) and the presence of BRCA1 nuclear foci in the analyzed tumor samples.

  3. C

    Immunofluorescence staining of γ‐H2AX, BRCA1, and RAD51 foci in three representative FFPE tumors from patients: one RAD51‐ and BRCA1‐positive tumor (Pt03), one RAD51‐ and BRCA1‐negative tumor (Pt11), and one PALB2‐related tumor, with BRCA1 but not RAD51 nuclear foci (Pt20.1). Scale bars: 10 μm.

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