Poly (ADP-ribose) Polymerase Inhibitor Resistance Driven by Emergence of Polyclonal Mutations With Convergent Evolution: A Molecular Tumor Board Discussion

Abstract

Polyclonal convergent evolution to PARPi resistance in a patient with metastatic breast cancer with gPALB2.

FIG 1.

Radiographic response to PARPi in the context of germline, tumor, and plasma genotyping revealing germline PALB2 loss and emergent somatic polyclonal PALB2 reversion mutations. (A) RECIST disease assessment of metastatic lesions for a patient receiving olaparib showing dynamics of total tumor burden over time and indicating a decrease in overall tumor burden upon treatment until an eventual increase occurred at the time of resistance to therapy. Tumor dimensions of each individual target lesion over time are also plotted and highlight their heterogeneity throughout the therapeutic period. (B) Lollipop plot showing the PALB2 germline mutation detected in both tissue and plasma sequencing and the reversion mutations detected in ctDNA next-generation sequencing. The VAF found in plasma of each PALB2 mutation is shown on the y-axis. (C) Restoration of DNA reading frame by PALB2 reversion mutations; the wild-type sequence is shown in the top row together with expected sequence from the truncating germline mutation (second row) and 13 of the 17 reversion mutations (remaining rows). The germline frameshift mutation leads to the formation of a premature stop codon, whereas the somatic reversion mutations restore the DNA reading frame, resulting in frame restoration. ctDNA, circulating tumor DNA; PARPi, poly (ADP-ribose) polymerase inhibitor; VAF, variant allele frequency.

FIG 2.

Evolutionary trajectories, restoration of HR, and development of PARPi resistance. (A) Convergent evolution of metastatic subclones under selective pressure. Selective pressure via targeted therapy results in the emergence of multiple unique subclones with similar evolutionary advantage. These subclones, arising in different metastatic sites after seeding by the parental clone, may acquire distinct reversion mutations that result in the same resistant phenotype. By sampling the entire tumor genomic landscape, liquid biopsies allow for detection of these polyclonal mutations in a minimally invasive manner. (B) This figure depicts the role of PARP in HR repair, the mechanism of action of PARP inhibitors, and potential mechanisms of acquired PARPi resistance as well as strategies to overcome this resistance. When DNA damage occurs, single-stranded DNA breaks use PARP for repair. However, PARP inhibitors prevent release of PARP from the DNA, leading to formation of a double-stranded break. Double-strand breaks lead to the recruitment of HR proteins (such as BRCA1/2, PALB2, RAD51, and others) for HR repair, resulting in cell survival. In case of a defective HR protein, such as a loss of PALB2 function, HRD occurs, and DNA repair takes place through alternate, error-prone repair mechanisms (such as NHEJ or MMEJ) that ultimately lead to cell cycle failure and death. Cancer cells that are exposed to PARP inhibition develop resistance mechanisms such as replication fork stabilization that promotes single-strand break repair, changes in PARP function that decrease sensitivity to PARP inhibition, increased activity of the efflux pump that removes PARP inhibitors from the cell, and restoration of HR protein proficiency that re-enables HRR. Therapeutic strategies that may be able to overcome PARPi resistance include inhibiting replication stress response pathways with ATR, CHK1, or WEE1 inhibitors or causing synthetic lethality by inhibiting a crucial alternative pathway for double-stranded DNA break repair with a polQ inhibitor. HR, homologous recombination; HRD, homologous recombination deficiency; MMEJ, microhomology-mediated end joining; NHEJ, non-homologous end joining; PARPi, poly (ADP-ribose) polymerase inhibitor.