Reena Philip

Protein-Based Multiplex Assays: Mock Presubmissions to the US Food and Drug Administration

As a part of ongoing efforts of the NCI-FDA Interagency Oncology Task Force subcommittee on molecular diagnostics, members of the Clinical Proteomic Technology Assessment for Cancer program of the National Cancer Institute have submitted 2 protein-based multiplex assay descriptions to the Office of In Vitro Diagnostic Device Evaluation and Safety, US Food and Drug Administration. The objective was to evaluate the analytical measurement criteria and studies needed to validate protein-based multiplex assays. Each submission described a different protein-based platform: a multiplex immunoaffinity mass spectrometry platform for protein quantification, and an immunological array platform quantifying glycoprotein isoforms. Submissions provided a mutually beneficial way for members of the proteomics and regulatory communities to identify the analytical issues that the field should address when developing protein-based multiplex clinical assays.

Processing and localization of bovine β-casein expressed in transgenic soybean seeds under control of a soybean lectin expression cassette

We have examined the processing and subcellular localization of a chimeric gene consisting of the bovine milk protein, beta-casein, under the control of a soybean seed lectin promoter and its 32 amino acid signal sequence in the seeds of transgenic soybean plants. The beta-casein expressed in developing soybean seeds is a doublet with apparent molecular weight slightly smaller than the bovine beta-casein and expression of the protein was highest in immature cotyledons. The casein proteins were purified from the immature soybean seeds by immunoaffinity chromatography and were analyzed by two-dimensional gel electrophoresis, blotting, and amino terminal sequencing. The N-terminal sequences of both of the doublet soybean casein polypeptides were identical to the N-terminal sequence of the bovine beta-casein indicating that the 32 amino acid lectin signal sequence was cleaved precisely from the chimeric protein in developing soybean seeds. Analysis of the purified soybean beta-casein polypeptides by mass spectrometry (MALDI-MS) showed that they are not phosphorylated. Absence of added phosphate groups is the cause of the size difference between the soybean beta-casein and native bovine beta-casein protein. Immunolocalization experiments showed that the casein protein was found in the protein storage vacuoles (PSV) in developing and mature soybean seeds. The precise removal of the 32 amino acid lectin amino terminal sequence from the chimeric lectin-casein fusion suggests that the lectin expression cassette can be used for production of pharmaceutical or other recombinant proteins of added value in the developing soybean seed.

FDA Approval Summary: Rucaparib for the treatment of patients with deleterious BRCA mutation-associated advanced ovarian cancer

On December 19, 2016, the FDA granted accelerated approval to rucaparib (RUBRACA; Clovis Oncology, Inc.) for the treatment of patients with deleterious BRCA mutation (germline and/or somatic)–associated advanced ovarian cancer who have been treated with two or more chemotherapies. The FDA also approved the FoundationFocus CDxBRCA test (Foundation Medicine, Inc.), the first next-generation sequencing-based companion diagnostic, for identifying patients with advanced ovarian cancer eligible for treatment with rucaparib based on detection of deleterious BRCA1 and/or BRCA2 mutations in tumor tissue. Rucaparibs approval was based primarily on efficacy data from 106 patients with BRCA mutation–associated ovarian cancer who had prior treatment with two or more chemotherapies and safety data from 377 patients with ovarian cancer treated with rucaparib 600 mg orally twice daily on two open-label, single-arm trials. Investigator-assessed objective response rate was 54% [57/106; 95% confidence interval (CI), 44–64], and median duration of response was 9.2 months (95% CI, 6.6–11.7). The approved companion diagnostic verified tumor BRCA mutation status retrospectively in 96% (64/67) of patients. Common adverse reactions (≥20%) to rucaparib were nausea, fatigue, vomiting, anemia, abdominal pain, dysgeusia, constipation, decreased appetite, diarrhea, thrombocytopenia, and dyspnea. This article summarizes the FDA review and data supporting rucaparibs accelerated approval. Clin Cancer Res; 23(23); 7165–70. ©2017 AACR. See related commentary by Kohn et al., p. 7155

An FDA Perspective on the Regulatory Implications of Complex Signatures to Predict Response to Targeted Therapies.

As technologies evolve, and diagnostics move from detection of single biomarkers toward complex signatures, an increase in the clinical use and regulatory submission of complex signatures is anticipated. However, to date, no complex signatures have been approved as companion diagnostics. In this article, we will describe the potential benefit of complex signatures and their unique regulatory challenges, including analytic performance validation, complex signature simulation, and clinical performance evaluation. We also will review the potential regulatory pathways for clearance, approval, or acceptance of complex signatures by the FDA. These regulatory pathways include regulations applicable to in vitro diagnostic devices, including companion diagnostic devices, the potential for labeling as a complementary diagnostic, and the biomarker qualification program. Clin Cancer Res; 23(6); 1368–72. ©2016 AACR.

Generation of low phytic acid Arabidopsis seeds expressing an E. coli phytase during embryo development

An Escherichia coli phytase gene was introduced into Arabidopsis plants using an embryo-specific promoter and a signal peptide for vacuolar targeting. Three independent transgenic lines were analysed. Phytase activity in dry seeds was observed in transgenic lines, whereas no activity was detected in control, untransformed seeds. Transgenic seeds expressing the phytase gene had lower levels of phytic acid than the controls. Concomitant with the decrease in phytic acid was an increase in free phosphate. These results indicated that embryo-expressed phytase can reduce the levels of phytic acid stored during development.

Companion diagnostics: a regulatory perspective from the last 5 years of molecular companion diagnostic approvals

Companion diagnostics are essential for the safe and effective use of the corresponding therapeutic products. The US FDA has approved a number of companion diagnostics used to select cancer patients for treatment with contemporaneously approved novel therapeutics. The processes of co-development and co-approval of a therapeutic product and its companion diagnostic have been a learning experience that continues to evolve. Using several companion diagnostics as examples, this article describes the challenges associated with the scientific, clinical and regulatory hurdles faced by FDA and industry alike. Taken together, this discussion is intended to assist manufacturers toward a successful companion diagnostics development plan.

FDA Approval Summary: Niraparib for the maintenance treatment of patients with recurrent ovarian cancer in response to platinum-based chemotherapy

The FDA approved niraparib, a poly(ADP-ribose) polymerase (PARP) inhibitor, on March 27, 2017, for maintenance treatment of patients with recurrent epithelial ovarian, fallopian tube, or primary peritoneal cancer who are in response to platinum-based chemotherapy. Approval was based on data from the NOVA trial comparing niraparib with placebo in two independent cohorts, based on germline BRCA mutation status (gBRCAm vs. non-gBRCAm). Progression-free survival (PFS) in each cohort was the primary endpoint. In the gBRCAm cohort, estimated median PFS on niraparib was 21 months versus 5.5 months on placebo [HR, 0.26; 95% confidence interval (CI), 0.17–0.41; P < 0.0001]. In the non-gBRCAm cohort, estimated median PFS for niraparib and placebo was 9.3 and 3.9 months, respectively (HR, 0.45; 95% CI, 0.34–0.61; P < 0.0001). Common adverse reactions (>20% and higher incidence in the niraparib arm) with niraparib included thrombocytopenia, anemia, neutropenia, nausea, constipation, vomiting, mucositis, fatigue, decreased appetite, headache, insomnia, nasopharyngitis, dyspnea, rash, and hypertension. There were five cases of myelodysplastic syndrome and acute myeloid leukemia (1.4%) in patients treated with niraparib compared with two cases (1.1%) on placebo. Niraparib is the first PARP inhibitor approved as maintenance therapy for patients with ovarian, fallopian tube, or primary peritoneal cancer, with improvement in PFS, regardless of gBRCAm status. Clin Cancer Res; 24(17); 4066–71. ©2018 AACR. See related commentary by Konstantinopoulos and Matulonis, p. 4062

FDA Approval Summary: Dabrafenib and Trametinib for the Treatment of Metastatic Non‐Small Cell Lung Cancers Harboring BRAF V600E Mutations

This article summarizes the FDA review of the efficacy supplement supporting approval of dabrafenib and trametinib administered concurrently for BRAF V600E‐mutant non‐small cell lung cancer.

FDA Benefit‐Risk Assessment of Osimertinib for the Treatment of Metastatic Non‐Small Cell Lung Cancer Harboring Epidermal Growth Factor Receptor T790M Mutation

This article reviews the benefit‐risk assessment of osimertinib that led to approval of osimertinib for the treatment of patients with metastatic EGFR T790M mutation‐positive non‐small cell lung cancer whose disease had progressed after EGFR tyrosine kinase inhibitor therapy.

Neoadjuvant Breast Cancer Trials: Translational Research in Drug Development

In addition to reducing the size and extent of locally advanced breast cancer tumors, neoadjuvant trials allow for rapid assessment of drug efficacy and could expedite development and approval of treatments for early breast cancer. For these reasons, clinical trials in the neoadjuvant setting are prime opportunities to study translational science, pathologic response, genetic biomarkers, and imaging biomarkers. In this review, we provide a summary of the efforts to identify biomarkers aimed to understand tumor biology and to prognosticate and predict response to neoadjuvant therapy for early breast cancer. We also provide a perspective on how neoadjuvant trials can be used to pursue translational research and drug development.