The Case for Drug Development Tools
Scientific Director
Precision Cancer Care Program
ecent history has shown that pathologic complete response (pCR) in breast cancer is a critical drug development tool (DDT). Particularly, the I-SPY 2 trial has supported development of agents for FDA accelerated approval based on pCR data obtained in the neoadjuvant setting in breast cancer. Leukemias have similar characteristics in that tumor burden can be measured directly in the bone marrow as well as in the blood after treatment. As discussed below, the key concept of Minimal Residual Disease (MRD) is that there is a threshold of disease below which the likelihood of relapse is low. It is somewhat easier to identify leukemia cells than to measure pCR, because usually (not always) the leukemic cells express antigens that are distinct or in a pathological profile that distinguishes leukemic cells from normal cells.
Drug Development and the Importance of Minimal Residual Disease
RQ-PCR, adopted primarily in Europe, is quite sensitive, but it is time-consuming, labor intensive, expensive, and unable to measure blasts in some patients. So multiparametric flow cytometry (mpFCM), first with four-color and then with six-color assays, was developed by the US Children’s Oncology Group (COG) for its trials in ALL, employing a central laboratory for all studies.
Rise of Targeted Therapies for ALL
FDA-ASCO-NCI Workshops on MRD
As a result, the NCI workshop reported on a “bake-off” which compared the COG reference laboratories with two adult oncology group reference laboratories. The satellite COG laboratory was highly concordant with the base COG reference laboratory; however, the other laboratories were much less concordant with the base laboratory. The low concordance further demonstrated the need for standardizing MRD assays.
Questions in Standardizing MRD
- Was adult ALL like childhood ALL in the pattern of CD antigen presentation?
- What was the best MRD level for a positive test?
- Given the future use of targeted therapies that would alter clonal evolution, would mpFCM still be able to identify blasts which deleted the CDs that were targeted?
- Similar questions were raised in the FDA-ASCO workshops.
FDA supported initial focus on ALL since the disease is molecularly a little simpler than either CLL or AML. CLL has the problem of somatic hypermutation that mature B cells use to generate the B-cell antigen receptor repertoire, while AML is extremely heterogeneous with multiple subtypes that confound a simple strategy for identification of blasts. Since CAR T cells and biologics were beginning to come to the clinic, the FDA suggested that MRD may be useful as a DDT if it was shown to be a predictor of response. This led to the formulation of a project that was supported by a public-private partnership managed by the Foundation for the National Institutes of Health (FNIH).
MRD Detection in Adult ALL
The meta-analysis evaluated existing international literature to determine the utility of MRD for predicting event-free (EFS) and overall (OS) survival in pediatric and adult ALL. The major findings were: MRD behaves similarly in pediatric and adult ALL for EFS and overall survival (OS), e.g., for EFS the HR was 0.23 (0.18-.28 95% CT, N= 11249 patients) for MRD-negative patients compared to MRD-positive patients, while the EFS HR in adults was similar 0.28 (0.24-0.33, N = 2065 patients).
Subset analysis did not demonstrate significant interactions with the timing of MRD assessment, method of analysis, cytogenetics, or even the MRD cut-off. OS results were also alike in that both had HR’s of 0.28. Thus, this analysis established that MRD in adult ALL has the same importance as in childhood ALL as a prognostic factor. The analysis also demonstrated that MRD after therapy is likely to be a predictive biomarker after therapy and could be used as a DDT.
The standardization work was carried out in a cadre of eight laboratories including the cooperative oncology group reference laboratories, an academic laboratory, a government laboratory, the laboratory of a nonprofit healthcare organization, and an international laboratory. The goal was to develop a method for standardizing the demonstration of MRD by mpFCM. This goal had two parts: 1) harmonize the COG standard six-color panel; and 2) use the cadre of harmonized laboratories to develop new eight-color kits that could be commercialized as another method of MRD testing. Becton-Dickinson and Beckman Coulter, two of the main manufacturers of flow cytometers for clinical use, generously supported this effort by providing reagents for the project. Each manufacturer understood that the project would enable them to develop platform-specific reagents that could then be cleared by FDA. Commercialization of kits for these platforms would be a tremendous standardization driver because the kits would need to be used as cleared by the FDA.
A standard protocol was developed based on the COG panel, including a process for in silico training using electronic list mode data files from cases of ALL. This was a critical step because the files could be loaded into each laboratory’s analytic system independent of the platform on which it was collected, and each group could go through MRD assessment exercises in an anonymous manner. After several rounds and a wet lab challenge followed by more in silico training, the group was well harmonized and some of the laboratories were cleared to perform in COG trials. (This process is documented in detail in a publication by Keeney et al., along with addressing the challenging problem of identifying so-called “hematagones” [regenerating normal B cells] in adult bone marrow after recovery from treatment.) While a manuscript on standardizing MRD assessment by mpFCM in ALL is good, it does not necessarily promote adoption of the practice. However, the system has been accepted into the proficiency testing program of College of American Pathologists (CAP) Clinical Laboratory Improvement Amendments (CLIA) certification process based on these results. Another success of the standardization effort is increasing the number of laboratories certified to support NCI’s Cancer Therapy Evaluation Program from two to 18. Decentralization helps because a major problem for MRD by mpFCM is that samples must be analyzed fresh, within at most 96 hours of collection.
Manufacturers are also in the late stages of validating eight-color panels for mpFCM on their newest cytometers. We hope that the manufacturers will be able to bring their data forward to FDA for evaluation and possible clearance as in vitro medical devices.
Rise of Next Generation Sequencing
Adaptive Biotechnologies performed an NGS analysis of ~600 COG samples. These and other data enabled the company to gain de novo approval for its ClonoSeq assay in September 2018. ClonoSeq is now cleared for use to measure MRD in multiple myeloma and ALL and will enable laboratories that use it to perform standardized assessments of MRD.
Conclusions
And what about the original impetus for the development of the MRD project in ALL, blinatumomab? The eight-color panels will compensate for loss of CD19 or CD22. In addition, on March 29, 2018, FDA expanded its approval for the use of blinatumomab in patients with pre-B ALL who have an increased risk of relapse because the MRD level meets or exceeds 0.1%. MRD is now part of a drug approval!
Besides ALL, efforts in multiple myeloma and AML are in planning. All these hematologic malignancies support Dr. Radich’s statement: “MRD is the disease.”