Table 3.

Analysis of PAR levels and PD biomarkers of the DNA damage response in paired tumor biopsy specimens

			Validated PAR-IA			Validated nuclear γ-H2Ax-qIFA^a (all cells in fields without necrosis)		Exploratory nuclear γ-H2Ax-qIFA^a (only fields with high content of viable tumor cells)		Exploratory nuclear pNBS1-qIFA^b (only fields with high content of viable tumor cells)
			Day 2 tumor PAR content	Day 9 tumor PAR content	Decline in tumor PAR from days 2→9 (%)	Day 2 nuclear γ-H2Ax	Day 9 nuclear γ-H2Ax	Day 2 nuclear γ-H2Ax	Day 9 nuclear γ-H2Ax	Day 2 nuclear pNBS1	Day 9 nuclear pNBS1
			28-hr of CPT-11 w/o ABT-888	28-hr of CPT-11 4-hr after a.m. ABT-888 dose		28-hr of CPT-11 w/o ABT-888	28-hr of CPT-11 4-hr after a.m. ABT-888 dose	28-hr of CPT-11 w/o ABT-888	28-hr of CPT-11 4-hr after a.m. ABT-888 dose	28-hr of CPT-11 w/o ABT-888	28-hr of CPT-11 4-hr after a.m. ABT-888 dose
Patient number	Dose level ABT-888 (mg)	Best response	(pg/μg protein)	(pg/μg protein)		(% NAP)	(% NAP)	(% NAP)	(% NAP)	(% NAP)	(% 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	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	n/a	n/a
012	20	PR	n/a	n/a	n/a	6.0	<5.0	n/a	n/a	n/a	n/a
013	20	PR	33.7	6.1	−82	<5.0	5.7	<5.0	<5.0	++	++++

NOTE: 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 the DNA damage response (DDR). Note that nuclear pNBS1 was the only PD biomarker of the 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 with irinotecan alone are bolded.
Abbreviations: hr, hour; n/a, not assessable (insufficient cells for analysis).
↵^aThe validated single-plex IFA for nuclear γ-H2AX employs ImagePro-based image analysis and reports %NAP 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.
↵^bThe 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.