Table 3.
Analysis of PAR Levels and Pharmacodynamic Biomarkers of DNA Damage Response in Paired Tumor Biopsy Specimens
| Patient Number |
Dose Level ABT-888 (mg) |
Best Response |
Validated PAR-IA | Validated Nuclear γH2Ax-qIFA1 (all cells in fields without necrosis) |
Exploratory Nuclear γH2Ax-qIFA1 (only fields with high content of viable tumor cells) |
Exploratory Nuclear pNBS1-qIFA2 (only fields with high content of viable tumor cells) |
|||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Day 2 Tumor PAR Content 28-hr of CPT-11 w/o ABT-888 (pg/µg protein) |
Day 9 Tumor PAR Content 28-hr of CPT-11 4-hr after a.m. ABT-888 dose (pg/µg protein) |
Decline in Tumor PAR from Day 2→9 (%) |
Day 2 Nuclear γH2Ax 28-hr of CPT-11 w/o ABT-888 (% NAP) |
Day 9 Nuclear γH2Ax 28-hr of CPT-11 4-hr after a.m. ABT-888 dose (% NAP) |
Day 2 Nuclear γH2Ax 28-hr of CPT-11 w/o ABT-888 (% NAP) |
Day 9 Nuclear γH2Ax 28-hr of CPT-11 4-hr after a.m. ABT-888 dose (% NAP) |
Day 2 Nuclear pNBS1 28-hr of CPT-11 w/o ABT-888 (% NAP) |
Day 9 Nuclear pNBS1 28-hr of CPT-11 4-hr after a.m. ABT-888 dose (% NAP) |
|||
| 002 | 10 | PD | 25.6 | 12.5 | −51 | < 5.0 | 9.5 | < 5.0 | < 5.0 | background | background |
| 010 | 20 | PD | 57.3 | 2.4 | −96 | 7.9 | 7.0 | < 5.0 | < 5.0 | background | background |
| 014 | 20 | PD | 19.6 | 1.2 | −94 | 9.8 | 7.1 | 8.4 | n/a | ++ | n/a |
| 016 | 20 | PD | 5.7 | 2.2 | −60 | < 5.0 | < 5.0 | n/a | n/a | ||
| 034 | 40 | PD | 68.8 | 1.2 | −98 | < 5.0 | 9.9 | 6.7 | < 5.0 | detectable | background |
| 006 | 10 | SD | n/a | n/a | n/a | < 5.0 | < 5.0 | < 5.0 | < 5.0 | background | background |
| 007 | 10 | SD | 2.3 | 0.3 | −87 | < 5.0 | < 5.0 | < 5.0 | < 5.0 | detectable | detectable |
| 028 | 40 | SD | 12.8 | 0.6 | −95 | < 5.0 | < 5.0 | < 5.0 | < 5.0 | detectable | + |
| 009 | 20 | PR | 13.6 | 1.6 | −89 | < 5.0 | < 5.0 | n/a | n/a | ||
| 012 | 20 | PR | n/a | n/a | n/a | 6.0 | < 5.0 | n/a | n/a | ||
| 013 | 20 | PR | 33.7 | 6.1 | −82 | < 5.0 | 5.7 | < 5.0 | < 5.0 | ++ | ++++ |
Paired biopsies for evaluation of PAR levels in first-pass core specimens also yielded second-pass core specimens in some patients that were sufficient for analysis of nuclear PD-biomarkers of DNA damage response (DDR). Note that nuclear pNBS1 was the only PD-biomarker of DDR that exhibited a signal at sampling times selected for evaluating PAR levels. Samples demonstrating evidence of increased DNA damage or persistent DNA repair after combined irinotecan/veliparib compared to irinotecan alone are bolded.
The validated single-plex IFA for nuclear γ-H2AX employs ImagePro-based image analysis and reports %NAP (nuclear area positivity) for all viable cells in non-necrotic fields. The exploratory multi-plex IFA for nuclear γ-H2AX employs a Definiens-based image analysis algorithm that reports %NAP only in fields predominantly composed of viable tumor cells. Background %NAP values of nuclear γ-H2AX in untreated tumor specimens are <5%, so %NAP values must exceed this threshold to demonstrate an increase in DDR.
The term “background” means <1% positive nuclei in all fields, “detectable” means a few positive nuclei in only some fields, and “++” and “++++” indicate progressively higher numbers of strongly positive nuclei in every field.
n/a-not assessable (insufficient cells for analysis); PD – progressive disease; PR – partial response; SD – stable disease