Pharmacodynamic effects of the PARP inhibitor talazoparib (MDV3800, BMN 673) in patients with BRCA-mutated advanced solid tumors

PURPOSE

Talazoparib is an inhibitor of the poly (ADP-ribose) polymerase (PARP) family of enzymes and is FDA-approved for patients with (suspected) deleterious germline BRCA1/2-mutated, HER2‑negative, locally advanced or metastatic breast cancer. Because knowledge of the pharmacodynamic (PD) effects of talazoparib in patients has been limited to studies of PARP enzymatic activity (PARylation) in peripheral blood mononuclear cells, we developed a study to assess tumoral PD response to talazoparib treatment (NCT01989546).

METHODS

We administered single-agent talazoparib (1 mg/day) orally in 28-day cycles to adult patients with advanced solid tumors harboring (suspected) deleterious BRCA1 or BRCA2 mutations. The primary objective was to examine the PD effects of talazoparib; the secondary objective was to determine overall response rate (ORR). Tumor biopsies were mandatory at baseline and post-treatment on day 8 (optional at disease progression). Biopsies were analyzed for PARylation, DNA damage response (γH2AX), and epithelial‒mesenchymal transition.

RESULTS

Nine patients enrolled in this trial. Four of six patients (67%) evaluable for the primary PD endpoint exhibited a nuclear γH2AX response on day 8 of treatment, and five of six (83%) also exhibited strong suppression of PARylation. A transition towards a more mesenchymal phenotype was seen in 4 of 6 carcinoma patients, but this biological change did not affect γH2AX or PAR responses. The ORR was 55% with the five partial responses lasting a median of six cycles.

CONCLUSION

Intra-tumoral DNA damage response and inhibition of PARP enzymatic activity were confirmed in patients with advanced solid tumors harboring BRCA1/2 mutations after 8 days of talazoparib treatment.

Atezolizumab for Advanced Alveolar Soft Part Sarcoma

BACKGROUND

Alveolar soft part sarcoma (ASPS) is a rare soft-tissue sarcoma with a poor prognosis and no established therapy. Recently, encouraging responses to immune checkpoint inhibitors have been reported.

METHODS

We conducted an investigator-initiated, multicenter, single-group, phase 2 study of the anti-programmed death ligand 1 (PD-L1) agent atezolizumab in adult and pediatric patients with advanced ASPS. Atezolizumab was administered intravenously at a dose of 1200 mg (in patients ≥18 years of age) or 15 mg per kilogram of body weight with a 1200-mg cap (in patients <18 years of age) once every 21 days. Study end points included objective response, duration of response, and progression-free survival according to Response Evaluation Criteria in Solid Tumors (RECIST), version 1.1, as well as pharmacodynamic biomarkers of multistep drug action.

RESULTS

A total of 52 patients were evaluated. An objective response was observed in 19 of 52 patients (37%), with 1 complete response and 18 partial responses. The median time to response was 3.6 months (range, 2.1 to 19.1), the median duration of response was 24.7 months (range, 4.1 to 55.8), and the median progression-free survival was 20.8 months. Seven patients took a treatment break after 2 years of treatment, and their responses were maintained through the data-cutoff date. No treatment-related grade 4 or 5 adverse events were recorded. Responses were noted despite variable baseline expression of programmed death 1 and PD-L1.

CONCLUSIONS

Atezolizumab was effective at inducing sustained responses in approximately one third of patients with advanced ASPS. (Funded by the National Cancer Institute and others; ClinicalTrials.gov number, NCT03141684.).

Abstract 6008: Antibody validation for clinical pharmacodynamic assay reveals cross-reactivity of commercial DNMT3B clones

Cooperativity between the maintenance DNA methyltransferase, DNMT1, and de novo methyltransferases, DNMT3A and 3B, is essential for proper maintenance and integrity of the methylome, and deregulation of these enzymes and associated transcriptional silencing of multiple genes has been shown in many types of cancer. Two DNA methyltransferase inhibitors are currently in clinical use with several others undergoing clinical evaluation, and the pharmacodynamic response of DNMT enzymes is a crucial aspect of understanding therapeutic effects in preclinical studies and clinical trials. Vigorous fit-for-purpose validation of research-grade reagents and the application of effective quality control testing procedures to assess lot-to-lot variability (and reject unacceptable lots) are essential to assure robust and reproducible pharmacodynamic assay performance. During the antibody validation process for the DNMT3B enzyme target, two commercial monoclonal antibody clones were found to exhibit significant cross-reactivity to another cellular protein and inappropriate subcellular localization via immunohistochemistry (IHC), including diffuse cytoplasmic staining and significant staining in a DNMT3B knock out (KO) cell line. Two other commercial monoclonal antibody clones showed the expected nuclear expression in the HCT116 parental cell line and lack of staining in the DNMT KO cells. Further evaluation via western blot revealed that the cross-reacting antibodies detected a band of the approximate expected molecular weight (MW) of DNMT3B but of a protein that was expressed equivalently in the parental and DNMT3B KO cell line pair, whereas the two other antibody clones only detected a significant band of correct MW in the parental but not the KO cell line. These results suggest that some commercial antibody clones are binding to a protein other than DNMT3B and that they are unsuitable for use with IHC and western blot to evaluate subcellular localization and expression levels of DNMT3B protein. We presume that these non-specific antibody clones were chosen for commercial development based on target screening via Western blot that did not include evaluation of a validated DNMT3B knock out cell line, as is not uncommon for research-grade antibody clones. This data highlights the critical importance of thorough fit-for-purpose validation and quality control for crucial reagents used for pharmacodynamic biomarker studies. Funded by NCI Contract No HHSN261200800001E

Citation Format: Gabriel J. Benton, Manisha Mohandoss, James H. Doroshow, Ralph E. Parchment, Katherine V. Ferry-Galow. Antibody validation for clinical pharmacodynamic assay reveals cross-reactivity of commercial DNMT3B clones. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6008.

Loss of ubiquitin-specific peptidase 18 destabilizes 14-3-3ζ protein and represses lung cancer metastasis

Cancer metastasis is a major cause of cancer-related mortality. Strategies to reduce metastases are needed especially in lung cancer, the most common cause of cancer mortality. We previously reported increased ubiquitin-specific peptidase 18 (USP18) expression in lung and other cancers. Engineered reduction of USP18 expression repressed lung cancer growth and promoted apoptosis. This deubiquitinase (DUB) stabilized targeted proteins by removing the complex interferon-stimulated gene 15 (ISG15). This study explores if the loss of USP18 reduced lung cancer metastasis. USP18 knock-down in lung cancer cells was independently achieved using small hairpin RNAs (shRNAs) and small interfering RNAs (siRNAs). USP18 knock-down reduced lung cancer growth, wound-healing, migration, and invasion versus controls (P < .001) and markedly decreased murine lung cancer metastases (P < .001). Reverse Phase Protein Arrays (RPPAs) in shRNA knock-down lung cancer cells showed that 14-3-3ζ protein was regulated by loss of USP18. ISG15 complexed with 14-3-3ζ protein reducing its stability. Survival in lung adenocarcinomas (P < .0015) and other cancers was linked to elevated 14-3-3ζ expression as assessed by The Cancer Genome Atlas (TCGA). The findings were confirmed and extended using 14-3-3ζ immunohistochemical assays of human lung cancer arrays and syngeneic murine lung cancer metastasis models. A direct 14-3-3ζ role in controlling lung cancer metastasis came from engineered 14-3-3ζ knock-down in lung cancer cell lines and 14-3-3ζ rescue experiments that reversed migration and invasion inhibition. Findings presented here revealed that USP18 controlled metastasis by regulating 14-3-3ζ expression. These data provide a strong rationale for developing a USP18 inhibitor to combat metastases.

A phase 2 study of anti-PD-L1 antibody (atezolizumab) in grade 2 and 3 chondrosarcoma

11528

Background: Chondrosarcoma is one of the most common bone malignancies in adults, and the third most common in pediatric patients (pts). The most prevalent subtype, conventional chondrosarcoma, is a slow growing tumor that is historically known to be refractory to chemotherapy. Anecdotal reports indicated a role for anti-PD-(L)1 in the treatment of this disease. This is the first prospective report on the efficacy of the PD-L1-targeting agent, atezolizumab, in this rare disease. Methods: Patients (pts) ages 2 and older with unresectable grade 2 or 3 conventional chondrosarcoma were eligible. No prior anti-PD-(L)1 treatment was allowed, otherwise pts were eligible irrespective of prior therapies as long as protocol-specified washout period requirements were met. Pts received atezolizumab 1200 mg (15 mg/kg with 1200 mg cap in pediatric pts) once every 21 days. Imaging was carried out at end of cycle 3, and then every two cycles. Research biopsies were collected from adult pts prior to C1D1, prior to C3D1, and at progression. Immuno-pharmacodynamic (IO-PD) studies were performed on paired tumor samples and circulating immune cells to help elucidate signaling pathways mediating the immune response, with focus on subsets of effector cells in the tumor microenvironment. Results: A total of 9 pts (7 males, 2 females) were enrolled in 6 centers across the US and Canada. Six pts were Caucasian/White, 1 Asian, 1 Hispanic, and 1 unknown. Median age was 49 years (42-72). No objective responses were seen. Three pts (33%) experienced disease stability (SD) per RECIST 1.1, for a median duration of 21 weeks as of data cutoff (January 2022). A patient with SD remains on active treatment (tx) for 35 weeks. Three patients had no tx-related adverse events (AEs). Six pts (67%) experienced at least one tx-related AE. Two patients experienced > G2 AEs, but only one was considered tx-related (lymphopenia). Immune-related AEs were all G1/2 and included hepatitis (2), hypothyroidism (1), hyperthyroidism (1), and maculopapular rash (1). IO-PD studies are ongoing and will be reported at the conference if available. Conclusions: Atezolizumab was well-tolerated but demonstrated limited activity in this cohort of pts with few treatment options. Ongoing IO-PD studies will provide insight into atezolizumab’s effect upon immune cell content and activation in the tumor microenvironment that will help design future immunotherapy trials in this disease and other sarcoma types. The study was funded by NCI Contract HHSN261201500003I. Clinical trial information: NCT04458922.

Safety, pharmacodynamic, and clinical response evaluation of nilotinib and paclitaxel in adults with refractory solid tumors

3026

Background: The combination of the BCR-Abl kinase inhibitor nilotinib and the anti-tubulin agent paclitaxel was identified in the NCI-ALMANAC study to have greater-than-additive activity in the NCI-60 cell line panel and greater-than-single-agent antitumor activity in xenograft models, in which this combination induces tumor epithelial-mesenchymal transition (EMT). A phase 1 study was initiated to establish the safety, tolerability, and recommended phase 2 dose (RP2D) of this combination in patients (pts) with advanced solid tumors and to examine the pharmacokinetic (PK) and pharmacodynamic (PD) effects of the combination to understand the mechanism of action (NCT02379416). The dose escalation phase established the RP2D as 300 mg oral nilotinib twice daily and 80 mg/m2 intravenous paclitaxel on days (D) 1, 8, and 15 of each 28-day cycle. Here, we report the safety, preliminary PD, and efficacy data for this combination. Methods: Nilotinib and paclitaxel were administered as noted above, with a 1-day (escalation cohort) or 2-day (expansion cohort) paclitaxel-only run-in during the first cycle to enable comparison of the PK and PD effects of the combination vs. single-agent paclitaxel. Paired biopsies to assess tumor molecular response were collected from expansion cohort pts at baseline, cycle (C) 1 D2, and C1D28, with an optional biopsy at progression; accrual continued until ≥ 12 sufficient-quality paired biopsies were obtained. Blood specimens to assess molecular responses in circulating tumor cells (CTCs) were obtained at several timepoints during C1 and longitudinally every cycle thereafter. EMT biomarkers were measured in tumor and CTC specimens using quantitative immunofluorescence microscopy assays. Results: A total of 44 pts were enrolled. Three pts had partial responses (PR), and 1 had an unconfirmed PR (9%); 23 pts (52%) had a best response of stable disease (SD), including 7 pts on study for ≥ 10 cycles. The most common grade (Gr) 3-4 treatment-related adverse events were hematologic and hypophosphatemia. No pts experienced Gr ≥ 3 peripheral neuropathy. The median time on treatment was 67 days. Two pts with granulosa cell ovarian carcinoma had durable responses, completing 74+ and 64 cycles. Multiple patient biopsies and corresponding CTC specimens exhibited treatment-induced EMT. Longitudinal analysis of CTC EMT phenotypes in the 2 pts with extended PR revealed a substantial increase in mesenchymal-like CTCs prior to progression for the pt on study for 64 cycles; such increases were not observed in the pt still on study after 74+ cycles. Further PD analyses are ongoing. Conclusions: The combination of nilotinib and paclitaxel demonstrates promising disease control with durable response in select patients. Tumor PD analyses to discover the underlying pharmacology of this active regimen are ongoing. Funded by NCI Contract No. HHSN261201500003I. Clinical trial information: NCT02379416.

Phase II study of atezolizumab in advanced alveolar soft part sarcoma (ASPS)

11519

Background: ASPS constitutes < 1% of soft tissue sarcomas and frequently presents in adolescents and young adults. There are no approved therapies for ASPS. We are currently evaluating the clinical activity of atezolizumab (atezo), an anti-PD-L1 antibody, in patients (pts) with advanced ASPS. Methods: This is a multicenter, open-label, single-arm phase II study where atezo is administered at a fixed dose of 1200 mg in adults or 15 mg/kg (1200 mg max) in pediatric pts age ≥2 once Q21 days. The primary objective is to determine the objective response rate (ORR) of atezo using RECIST 1.1. Secondary objectives include duration of response and correlating response with the immune effects of atezo in blood and paired tumor biopsies (pre- and post-treatment). Tumor specimens were analyzed with multiplex immunofluorescence immuno-oncology panels to quantify CD8+, PD-1+, and PD-L1+ cells/mm2 in the tumor microenvironment. CD8+ density was calculated as the total number of CD8+ cells divided by the entire area (mm2) of the tumor and invasive margins of the biopsy. Results: As of February 4, 2021, 44 pts have been enrolled. The median age in the study was 31 years (range, 12–70) with equal male: female distribution. 54.5% of pts were Caucasian. Baseline ECOG ≤1 was present in 97.7%. The median time on study was 11.5 months (range, 0.8–40.3 months). At data cutoff, response evaluation was available for 43 pts with an ORR of 37.2% (16/43). One pt experienced a complete response and 15 pts experienced a partial response (PR), of which 14 were confirmed. The median time to confirmed response was 3.5 months (range, 2.1–14.9 months). The median duration of confirmed response was 16.5 months (range, 4.9–38.1 months). Stable disease (SD) was present in 58.1% (25/43). One or more grade 3 adverse events potentially related to atezo were identified in 16.3% (7/43) pts. These include diarrhea, hypothyroidism, transaminitis, anemia, vertigo, extremity pain, myalgia, pneumonitis, rash, and stroke (n = 1 each). No grade 4 or 5 events have been reported. Among 8 cases with evaluable biopsy pairs, both baseline and C3D1 specimens in all cases demonstrated CD8+ T cell infiltration and PD-L1 expression. PD-1 expression was detected at baseline in 5 cases and at C3D1 in 7 cases. In 6 cases (3 SDs and 3 PRs), treatment did not change CD8+ cell density. In the other 2 cases (both PRs), CD8+ density increased > 3x above baseline by C3D1. Analysis of T cell activation using pharmacodynamic response biomarkers, along with whole exome and RNA-seq to evaluate the genomic and transcriptomic landscape of ASPS, are ongoing. Conclusions: Atezo is well tolerated and demonstrates promising single agent activity with durable responses in advanced ASPS. Preliminary tumor biomarker analysis confirms the presence of multiple PD-1/PD-L1 immune checkpoint (IC) components, indicating that advanced ASPS is an ideal candidate for therapeutic IC inhibition. Funded by NCI Contract No HHSN261200800001E. Clinical trial information: NCT03141684.

Phase I trial of TRC102 (methoxyamine HCl) in combination with temozolomide in patients with relapsed solid tumors and lymphomas

Background: TRC102 inhibits base excision repair by binding abasic sites and preventing AP endonuclease processing; it potentiates the activity of alkylating agents, including temozolomide, in murine models. In published xenograft studies, TRC102 enhanced the antitumor effect of temozolomide regardless of cell line genetic characteristics, e.g., O6-methylguanine DNA methyltransferase (MGMT), mismatch repair (MMR), or p53 status.

Materials and Methods: We conducted a phase 1 trial of TRC102 with temozolomide given orally on days 1-5 of 28-day cycles in adult patients with refractory solid tumors that had progressed on standard therapy. Tumor induction of nuclear biomarkers of DNA damage response (DDR) γH2AX, pNBs1, and Rad51 was assessed in the context of MGMT and MMR protein expression for expansion cohort patients.

Results: Fifty-two patients were enrolled (37 escalation, 15 expansion) with 51 evaluable for response. The recommended phase 2 dose was 125 mg TRC102, 150 mg/m² temozolomide QDx5. Common adverse events (grade 3/4) included anemia (19%), lymphopenia (12%), and neutropenia (10%). Four patients achieved partial responses (1 non-small cell lung cancer, 2 granulosa cell ovarian cancer, and 1 colon cancer) and 13 patients had a best response of stable disease. Retrospective analysis of 15 expansion cohort patients did not demonstrate a correlation between low tumor MGMT expression and patient response, but treatment induced nuclear Rad51 responses in 6 of 12 patients.

Conclusions: The combination of TRC 102 with temozolomide is active, with 4 of 51 patients experiencing a partial response and 13 of 51 experiencing stable disease, and the side effect profile is manageable.

Abstract 802: Implementation of optimized research biopsy analyses for clinical pharmacodynamic (PD) studies

Research biopsies collected for evaluation of pharmacodynamic (PD) biomarkers present requirements beyond those obtained for diagnostic purposes. Despite establishing stringent post-collection handling and processing procedures, we have found that many biopsy pairs collected from the early phase trial patient population demonstrate significant tissue heterogeneity and viable tumor content too low to adequately assess biomarker response in the tumor cell population. A retrospective analysis of samples collected from NCI's Developmental Therapeutics Clinic (DTC) from 1/2010-9/2016 revealed an initial success rate for analysis of paired biopsies of only 53%; this was primarily due to a high incidence of biopsies with no or very low tumor content. Based on this initial high failure rate, several clinical and laboratory initiatives were undertaken to identify and mitigate factors which contribute to biopsy unsuitability. After consultation with other translational oncology teams to review best practices, we have published and implemented critical recommendations to improve research biopsy quality at the clinical project team level (PMID: 30285529). In addition to important updates to the clinical trial strategy, several actionable improvements have been identified and implemented at the laboratory level to significantly increase the success rate of research biopsy analyses. Improvements in the biopsy processing approach include use of multiple 18-gauge biopsy cores per timepoint as a standard approach for all PD trials, implementation of methods to prevent biopsy curling during fixation and processing to ensure full longitudinal facing of the tissue during sectioning, and deeper sectioning of the blocks with H&E evaluation of flanking slides by an anatomic pathologist with subsequent release of nonadjacent slides from the most optimal slide range for the primary PD analyses. Development of advanced image analysis methods including the use of β-catenin as a tissue segmentation marker for multiplex immunofluorescence assays has allowed for successful analysis of biopsies with significant heterogeneity and low tumor content. Additionally, defining the minimum cell number required to reach significance for PD marker measurements and capturing additional image fields in low tumor content biopsies to reach the required threshold has led to the implementation of highly robust methods across multiple clinical trials and laboratories. An analysis of biopsies collected from 10/2016-9/2019, after which several clinical and laboratory improvements had been implemented, revealed a significantly improved success rate for paired biopsies of 83%. Funded by NCI Contract No HHSN261200800001E.

Citation Format: Katherine V. Ferry-Galow, Deborah Wilsker, Robert J. Kinders, Hala R. Makhlouf, Angie Dull, Tony Navas, Rachel E. Andrews, Geraldine O'Sullivan Coyne, Alice P. Chen, James H. Doroshow, Ralph E. Parchment. Implementation of optimized research biopsy analyses for clinical pharmacodynamic (PD) studies [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 802.

Abstract 6495: Development of robust and reproducible controls to support clinical implementation of quantitative immunofluorescence assays for pharmacodynamic biomarkers

Robust pharmacodynamic (PD) assays are valuable to confirm putative drug mechanisms and downstream effects in support of early phase clinical trials. Evolving methods to achieve consistent performance across patients, clinical trials, and laboratories is critical for the success of clinical pharmacodynamic measurements. We have developed integral quality control tools to support clinical implementation of quantitative multiplex immunofluorescence assays (qmIFAs) that include xenograft tissue reference calibrators. These reference slides help to provide confirmation that the pharmacodynamic assay is reporting biomarker levels within designated target ranges with expected subcellular localization, helping to control for run-to-run issues with the assay procedures, reagents, or equipment; however, significant challenges are faced in producing these key reagents. Compared to conventional cell pellets, xenograft controls require more time, expense and specialized facilities; however, the tumor tissues are much more representative of the heterogeneity found in clinical biopsies. The challenges associated with xenograft controls include tissue and biomarker variability attributed to necrotic areas, fixation artifacts, and variable drug distribution. During our qualification process, xenografts undergo multiple rounds of selection and analysis to identify specimens that exhibit good tissue quality, adequate regions of interest (ROI), and appropriate target signal levels to support the intended biomarker measurements. Slide lots are produced, qualified, and stored in a manner that ensures adequate lot sizes, robust and reproducible slide to slide performance, and appropriate shelf life. Xenograft tissue reference standards representing a range of basal or drug-induced biomarker expression in appropriate models have been developed for several informative PD markers including Epithelial Mesenchymal Transition (EMT) markers such as E-Cadherin, Vimentin, and Beta-Catenin; DNA damage response markers γH2AX, pNBS1 and Rad51; apoptosis induction markers for colocalized γH2AX/cleaved Caspase 3; and the cell cycle markers pY15cdk and pHH3 among others and have been used as important tools to support ongoing clinical pharmacodynamic analyses of research biopsies at the NCI and other institutions (PMIDs 25964244, 29682208, 30792217, 31732654). In summary, generalized methods and workflows that will be made public have been developed by the NCI to optimize the production of qualified reference slide lots of sufficient reproducibility, stability, and quantity to support ongoing NCI-supported clinical trial pharmacodynamic assays for several key biomarkers. Funded by NCI Contract No HHSN261200800001E.

Citation Format: Gabriel J. Benton, Katherine V. Ferry-Galow, Victor E. Lonsberry, Manisha Mohandoss, Howard Stotler, Debbie Trail, Kyle Georgius, Melinda Hollingshead, Deborah Wilsker, Robert Kinders, James H. Doroshow, Ralph E. Parchment. Development of robust and reproducible controls to support clinical implementation of quantitative immunofluorescence assays for pharmacodynamic biomarkers [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6495.

Clinical Evolution of Epithelial-Mesenchymal Transition in Human Carcinomas

The significance of the phenotypic plasticity afforded by epithelial-mesenchymal transition (EMT) for cancer progression and drug resistance remains to be fully elucidated in the clinic. We evaluated epithelial-mesenchymal phenotypic characteristics across a range of tumor histologies using a validated, high-resolution digital microscopic immunofluorescence assay (IFA) that incorporates β-catenin detection and cellular morphology to delineate carcinoma cells from stromal fibroblasts and that quantitates the individual and colocalized expression of the epithelial marker E-cadherin (E) and the mesenchymal marker vimentin (V) at subcellular resolution ("EMT-IFA"). We report the discovery of β-catenin⁺ cancer cells that coexpress E-cadherin and vimentin in core-needle biopsies from patients with various advanced metastatic carcinomas, wherein these cells are transitioning between strongly epithelial and strongly mesenchymal-like phenotypes. Treatment of carcinoma models with anticancer drugs that differ in their mechanism of action (the tyrosine kinase inhibitor pazopanib in MKN45 gastric carcinoma xenografts and the combination of tubulin-targeting agent paclitaxel with the BCR-ABL inhibitor nilotinib in MDA-MB-468 breast cancer xenografts) caused changes in the tumor epithelial-mesenchymal character. Moreover, the appearance of partial EMT or mesenchymal-like carcinoma cells in MDA-MB-468 tumors treated with the paclitaxel-nilotinib combination resulted in upregulation of cancer stem cell (CSC) markers and susceptibility to FAK inhibitor. A metastatic prostate cancer patient treated with the PARP inhibitor talazoparib exhibited similar CSC marker upregulation. Therefore, the phenotypic plasticity conferred on carcinoma cells by EMT allows for rapid adaptation to cytotoxic or molecularly targeted therapy and could create a form of acquired drug resistance that is transient in nature. SIGNIFICANCE: Despite the role of EMT in metastasis and drug resistance, no standardized assessment of EMT phenotypic heterogeneity in human carcinomas exists; the EMT-IFA allows for clinical monitoring of tumor adaptation to therapy.

What Can Be Done to Improve Research Biopsy Quality in Oncology Clinical Trials?

PURPOSE:

Research biopsy specimens collected in clinical trials often present requirements beyond those of tumor biopsy specimens collected for diagnostic purposes. Research biopsies underpin hypothesis-driven drug development, pharmacodynamic assessment of molecularly targeted anticancer agents, and, increasingly, genomic assessment for precision medicine; insufficient biopsy specimen quality or quantity therefore compromises the scientific value of a study and the resources devoted to it, as well as each patient's contribution to and potential benefit from a clinical trial.

METHODS:

To improve research biopsy specimen quality, we consulted with other translational oncology teams and reviewed current best practices.

RESULTS:

Among the recommendations were improving communication between oncologists and interventional radiologists, providing feedback on specimen sufficiency, increasing academic recognition and financial support for the time investment required by radiologists to collect and preserve research biopsy specimens, and improving real-time assessment of tissue quality.

CONCLUSION:

Implementing these recommendations at the National Cancer Institute's Developmental Therapeutics Clinic has demonstrably improved the quality of biopsy specimens collected; more widespread dissemination of these recommendations beyond large clinical cancer centers is possible and will be of value to the community in improving clinical research and, ultimately, patient care.

A phase I trial of TRC102 (methoxyamine HCl) with temozolomide (TMZ) in patients with solid tumors and lymphomas

2518

Background: TRC102 inhibits BER by binding to abasic sites and acting as a topo II poison to cause DNA strand breaks; it potentiates the activity of alkylating agents including TMZ in murine models. In xenograft studies, TRC102 efficiently enhanced the antitumor effect of TMZ regardless of cell line genetic characteristics, e.g., O6-methylguanine DNA-methyltransferase, mismatch repair (MMR), or p53 status. This is the first report for the expansion phase (the escalation phase was reported previously (ASCO2016)). Methods: We conducted a phase 1 trial of TRC102with TMZ in patients (pts) with refractory solid tumors. Eligibility criteria included adults that had progressed on standard therapy, ECOG PS of 0-2, and adequate organ function. TRC102 and TMZ were given orally days 1-5, in 28-day cycles. The pharmacokinetic and pharmacodynamic profile of TRC102 with TMZ was evaluated. Antitumor responses were determined using RECIST 1.1 criteria. The DNA damage response (DDR) markers γH2Ax, pNbs1, and Rad51 were evaluated in the expansion cohort at DL6, tested by previously described methods on paired tumor biopsies prior to and after the first course of therapy. Results: After the recommended Phase 2 Dose was defined as DL6 (TRC102 125mg, TMZ 150mg/m2 D1-5), 15 pts were accrued to the expansion cohort between 9/2015 to 11/2016. A total of 52 pts were enrolled (37 escalation, 15 expansion). Grade 3/4 adverse events included neutropenia (13%), anemia (the DLT;10%), thrombocytopenia (7%), hemolysis (5%) or hypophosphatemia (3%). 4 pts had a partial response (PR) (NSCLC, ovarian (2), and colon); 13 pts had stable disease (SD), 29 progressive disease (PD), and 6 were not evaluable; three pts remain on study. 11/14 paired biopsies were suitable for analysis. Rad51 signal was induced in 6/11pts. One patient showed γH2Ax and 2 showed pNbs1 induction. 4/5 colon cancer specimens had evidence of DDR marker induction. Conclusions: The combination of TRC 102/TMZ is active with 4 PRs and 13 SDs, and the side effect profile is manageable. DDR markers were induced in 4 of 5 paired colon biopsies indicating DNA damage following treatment. A phase 2 trial of patients with colon cancer, NSCLC, and granulosa cell ovarian cancer is accruing. Clinical trial information: NCT01851369.

Efficacy of the PARP Inhibitor Veliparib with Carboplatin or as a Single Agent in Patients with Germline BRCA1- or BRCA2-Associated Metastatic Breast Cancer: California Cancer Consortium Trial NCT01149083

Purpose: We aimed to establish the MTD of the poly (ADP-ribose) (PAR) polymerase inhibitor, veliparib, in combination with carboplatin in germline BRCA1- and BRCA2- (BRCA)-associated metastatic breast cancer (MBC), to assess the efficacy of single-agent veliparib, and of the combination treatment after progression, and to correlate PAR levels with clinical outcome.Experimental Design: Phase I patients received carboplatin (AUC of 5-6, every 21 days), with escalating doses (50-20 mg) of oral twice-daily (BID) veliparib. In a companion phase II trial, patients received single-agent veliparib (400 mg BID), and upon progression, received the combination at MTD. Peripheral blood mononuclear cell PAR and serum veliparib levels were assessed and correlated with outcome.Results: Twenty-seven phase I trial patients were evaluable. Dose-limiting toxicities were nausea, dehydration, and thrombocytopenia [MTD: veliparib 150 mg po BID and carboplatin (AUC of 5)]. Response rate (RR) was 56%; 3 patients remain in complete response (CR) beyond 3 years. Progression-free survival (PFS) and overall survival (OS) were 8.7 and 18.8 months. The PFS and OS were 5.2 and 14.5 months in the 44 patients in the phase II trial, with a 14% RR in BRCA1 (n = 22) and 36% in BRCA2 (n = 22). One of 30 patients responded to the combination therapy after progression on veliparib. Higher baseline PAR was associated with clinical benefit.Conclusions: Safety and efficacy are encouraging with veliparib alone and in combination with carboplatin in BRCA-associated MBC. Lasting CRs were observed when the combination was administered first in the phase I trial. Further investigation of PAR level association with clinical outcomes is warranted. Clin Cancer Res; 23(15); 4066-76. ©2017 AACR.

Pharmacodynamic analyses in a multi-laboratory network: lessons from the poly(ADP-ribose) assay

Clinical pharmacodynamic assays need to meet higher criteria for sensitivity, precision, robustness, and reproducibility than those expected for research-grade assays because of the long duration of clinical trials and the potentially unpredictable number of laboratories running the assays. This report describes the process of making an immunoassay based on commercially available reagents "clinically ready". The assay was developed to quantify poly(ADP-ribose) (PAR) levels as a marker of PAR polymerase inhibitor activity for a proof-of-concept phase 0 clinical trial at the National Cancer Institute (NCI) and subsequent clinical trials. In this publication, we retrospectively examine the measures taken to validate the published PAR immunoassay and outline key lessons learned during the development and implementation of these procedures at both internal and external clinical trial sites; these measures included optimizing PAR measurements in tumor biopsies and peripheral blood mononuclear cells (PBMCs), reagent qualification, analytical validation and assay quality control, instrument qualification and method quality control, and support for external laboratories.

The root causes of pharmacodynamic assay failure

Robust pharmacodynamic assay results are valuable for informing go/no-go decisions about continued development of new anti-cancer agents and for identifying combinations of targeted agents, but often pharmacodynamic results are too incomplete or variable to fulfill this role. Our experience suggests that variable reagent and specimen quality are two major contributors to this problem. Minimizing all potential sources of variability in procedures for specimen collection, processing, and assay measurements is essential for meaningful comparison of pharmacodynamic biomarkers across sample time points. This is especially true in the evaluation of pre- and post-dose tumor biopsies, which suffer from high levels of tumor insufficiency due to variations in biopsy collection techniques and significant specimen heterogeneity within and across patients. Developing methods to assess heterogeneous biopsies is necessary in order to evaluate a majority of tumor biopsies collected for pharmacodynamic biomarker studies. Improved collection devices and standardization of methods are being sought in order to improve the tumor content and quality of tumor biopsies. In terms of reagent variability, we have found that stringent initial reagent qualification and quality control of R&D-grade reagents is critical to minimize lot-to-lot variability and prevent assay failures, especially for clinical pharmacodynamic questions, which often demand assay performance that meets or exceeds clinical diagnostic assay standards. Rigorous reagent specifications and use of appropriate assay quality control methodologies help to ensure consistency between assay runs, laboratories and trials to provide much needed pharmacodynamic insights into the activity of investigational agents.

Abstract 5279: Establishing robust pharmacodynamic (PD) immunofluorescence assays of clinical biopsies at the National Cancer Institute: Optimized quality control procedures for the evaluation of DNA damage response and epithelial-mesenchymal transition (EMT) biomarkers

Robust PD assay results are valuable for informing decisions about continued preclinical and clinical development of new agents and for identifying effective combinations of targeted agents. The National Cancer Institute's Division of Cancer Treatment and Diagnosis (DCTD) develops and validates PD assays to obtain accurate information about drug effect on intended molecular targets in first-in-human clinical trials. Our group utilizes quantitative immunofluorescence assays (qIFA) of PD biomarkers in FFPE slides prepared from pre- and post-dose tumor biopsies collected from patients on early phase clinical trials. Paired biopsies are fixed and paraffin embedded, in parallel with tissue controls, such that all tissues are sectioned onto the same slide. Stringent methods to maintain the biopsy orientation are utilized during fixation, blocking and microtomy. A large number of sections are generated to increase the likelihood of finding optimal tumor regions of interest for biomarker analyses. Flanking H&E slides are utilized to assess the quality of the tumor biopsies. Whole slide scans of the H&E slides are shared with a clinical pathologist who determines whether the sections are sufficient or insufficient for the intended analysis. The pathology review allows the assay operator to select the optimal range of slides to stain and quantitatively analyze for the biomarker(s) of interest. Pathology-guided regions allow the operator to focus on tumor regions of interest and avoid normal tissue and/or confounding regions compromised by handling and processing artifacts. For nuclear biomarkers such as γH2AX and related DNA damage response biomarkers the pathologist annotates areas of sufficient tumor content and viability. For biomarker changes in tissue architecture such as that seen in Epithelial Mesenchymal Transition biomarkers, including E-Cadherin, Vimentin and β-catenin, the pathology annotation denotes areas of normal tissue and necrosis to eliminate from the qIFA analysis. All other areas of sufficient tumor cellularity from the entire slide are evaluated for the EMT biomarkers. Use of the pathology-annotated whole slide image as a tool for guidance of the operator performing the quantitative evaluation of the PD biomarker helps to ensure a non-subjective analysis. Finally, steps are taken to ensure proper storage of the paraffin slides, including paraffin dipping after microtomy, which is critical for preservation of labile epitopes such as phosphorylated proteins. We will present details of these optimized methods as well as key lessons learned during the preclinical and clinical implementation of qIFA measurements of PD biomarkers for various molecular targeted agents. Funded by NCI Contract No HHSN261200800001E.

Citation Format: Katherine V. Ferry-Galow, Scott M. Lawrence, Tony Navas, Hala R. Makhlouf, Donna O. Butcher, Brad A. Gouker, William H. Yutzy, Jiuping Ji, Robert Kinders, Ralph E. Parchment, Shivaani Kummar, Joseph E. Tomaszewski, James H. Doroshow. Establishing robust pharmacodynamic (PD) immunofluorescence assays of clinical biopsies at the National Cancer Institute: Optimized quality control procedures for the evaluation of DNA damage response and epithelial-mesenchymal transition (EMT) biomarkers [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5279. doi:10.1158/1538-7445.AM2015-5279

Creating clinical target validation groups via quality assured transfer of robust clinical pharmacodynamic (PD) assays from the NCI: Clinical implementation of a PAR immunoassay in tumor biopsies

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Background: Early phase clinical trials of investigational agents benefit from laboratory assays that quantify intended mechanism of action on molecular target (1° PD effects), desired changes in mechanistic biomarkers (2° PD effects), and 3° PD effects on cell survival. Robust PD assay results are valuable for informing go/no‐go decisions about continued development of new agents and for identifying combinations of targeted agents that cover the multiple molecular defects underlying many malignancies. Methods: Readying PD assays for clinical use involves validating analytical performance, identifying and qualifying critical reagents, demonstrating fit‐for‐purpose for the clinical protocol, and finalizing companion SOPs specifying specimen handling and processing. Because clinical PD questions often demand assay performance that meets or even exceeds clinical diagnostic assay standards, but key assay reagents are usually R and D‐rather than GMP‐grade, stringent reagent Quality Control is critical for preventing assay failures due to lot-to-lot variability. Results: The poly(ADP-ribose) (PAR) Immunoassay was the first qualified assay developed by NCI for implementation in early phase clinical trials. Development of stringent production and internal Quality Control specifications for accepting/rejecting new lots of critical reagents and a defined Quality Assurance Plan allowed a network of users to achieve consistent results and quality using R&D-grade source materials. Conclusions: The NCI’s Division of Cancer Treatment and Diagnosis is developing a clinical PD assay portfolio capable of quantifying 1°, 2°, and 3° PD effects. Proven clinical assays are formally transferred from the NCI to requesting sites in academia and industry via laboratory‐based certification and training, centralized access to SOPs, assistance with assay transfer, and participation in the assay’s Quality Assurance Plan. Funded by NCI Contract No HHSN261200800001E.

Abstract 1186: Creating clinical target validation groups via quality assured transfer of robust clinical pharmacodynamic (PD) assays from the NCI: clinical implementation of a HIF1α immunoassay in tumor biopsies

Robust pharmacodynamic (PD) assay results are valuable for informing go/no-go decisions about preclinical and clinical development of new agents and for identifying optimal combinations of targeted agents. The NCI's Division of Cancer Treatment and Diagnosis (DCTD) develops and validates PD assays to obtain accurate information about target engagement in first-in-human clinical trials. The Pharmacodynamic Assay Development and Implementation Section (PADIS) and National Clinical Target Validation Laboratory (NCTVL) were established at SAIC-Frederick to develop and validate PD assays by validating analytical performance, demonstrating fitness-for-purpose for the clinical protocol, and finalizing companion standard operating procedures (SOPs) for specimen handling and processing. Proven clinical assays are transferred from the NCI to requesting sites in academia and industry through laboratory-based certification and training, centralized access to current SOPs, assistance with assay transfer, and participation in the assay's Quality Assurance Plan. One such validated assay is the HIF1α Immunoassay, which is currently in clinical evaluation at NCTVL. Procedures to clinically implement HIF1α analysis in tumor biopsies from patients treated with angiogenesis inhibitors required consideration of many factors including the low abundance and oxygen sensitivity of the analyte. A customized extraction process for HIF1α was developed and optimized using mouse xenograft biopsies. Use of a customized extraction buffer containing 2-hydroxyglutarate, which was degassed to minimize dissolved oxygen, was shown to improve analyte recovery. Optimized extraction procedures also include use of an automated ceramic bead homogenizer to improve both the efficiency and reproducibility of extraction of HIF1α over sonication. The immunoassay procedure uses lyophilized reagents from a commercially available kit and a modified procedure together with quality control specimens that serve to qualify the performance of each run. Finally, pre-defined data analyses and quality control evaluation criteria are used to perform a semi-automated process to analyze data and evaluate acceptability of performance for both the assay run and individual clinical specimens. In total, five SOPs have been developed to define procedures from collection and freezing of the needle biopsies in the radiology suite to data analyses and reporting. Together, these defined procedures are being used to perform PD analyses as key parts of two clinical trial evaluations at the NCI and will be launched to the community once clinical utility is demonstrated. Funded by NCI Contract No HHSN261200800001E.

Citation Format: Ralph E. Parchment, Robert J. Kinders, Sook Ryun Park, Katherine V. Ferry-Galow, Yvonne A. Evrard, Jiuping Ji, Shivaani Kummar, Joseph E. Tomaszewski, James H. Doroshow. Creating clinical target validation groups via quality assured transfer of robust clinical pharmacodynamic (PD) assays from the NCI: clinical implementation of a HIF1α immunoassay in tumor biopsies. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1186. doi:10.1158/1538-7445.AM2013-1186

Abstract 1173: Development of calibrators and controls as quality control tools for clinical implementation of quantitative immunofluorescence assays for pharmacodynamic biomarkers of molecular targeted agents in tumor biopsies

The application of robust pharmacodynamic (PD) assays as part of clinical trial design is valuable for confirming putative drug mechanisms in patients. Our group supports the development, validation and clinical implementation of these PD assays including quantitative immunofluorescence (qIFA) measurements in formalin-fixed, paraffin-embedded (FFPE) human tissue biopsies. One such assay is a multiplex qIFA method for evaluating histone H2AX phosphorylated at serine 139 (γH2AX), activated caspase 3 (cCasp3), Ki67, and DAPI (referred to as Rx1-IFA4) in response to DNA-damaging agents. Integral PD quality control tools were developed as part of the Rx1-IFA4 and included xenograft tissue calibrators, which are used as visual and quantitative reference standards representing a range of biomarker expression levels for drug effect on tumor, and mouse testis and jejunum tissues, which are used as positive or negative controls for endogenous tissue expression for each biomarker. Rx1-IFA4 tissue calibrators were prepared with tumor quadrants derived from human breast MDA-MB-231 xenografts treated with vehicle, low, or high doses of a cIAP inhibitor. Xenografts were prescreened for levels of each biomarker, and tissues containing defined ranges of biomarker expression were re-embedded in a block to represent each of the treatment groups. Use of tumor quadrants as opposed to biopsies allows for a large number of calibrator slides to be produced from a single qualified block. Qualification of each lot of calibrator slides includes qIFA analysis of representative slides from which specifications for acceptable ranges of biomarker expression for that lot are determined. Whole fluorescent slide imaging using Aperio® was performed to document distribution patterns of the biomarkers within each tumor quadrant. Staining analysis of control tissues also enabled performance assessment of all assay antibodies applied on each clinical slide without the need for duplicate slides as controls. Application of tissue calibrators and controls to the qIFA assay, as opposed to the more typical use of cell pellet-derived controls provides many advantages. Biomarker expression levels with drug treated cells rarely correlate with expression levels in vivo. Additionally, quantitative image analysis for this assay utilizes image analysis software and custom macros that require the appropriate selection of a representative area of background for each analyzed image and tissue context is critical for accurate quantitation. These quality control tools are effective for monitoring the performance of the qIFA assay across laboratories and clinical assay runs. The first three authors listed contributed to this work equally. Funded by NCI Contract No HHSN261200800001E.

Citation Format: Katherine V. Ferry-Galow, Tony Navas, Scott M. Lawrence, Karun Mutreja, Donna Butcher, Melinda Hollingshead, Ralph Parchment, Joseph E. Tomaszewski, James H. Doroshow, Robert J. Kinders. Development of calibrators and controls as quality control tools for clinical implementation of quantitative immunofluorescence assays for pharmacodynamic biomarkers of molecular targeted agents in tumor biopsies. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1173. doi:10.1158/1538-7445.AM2013-1173