Citations

Abstract Background Archived formalin fixed paraffin embedded (FFPE) samples are valuable clinical resources to examine clinically relevant morphology features and also to study genetic changes. However, DNA quality and quantity of FFPE samples are often sub-optimal, and resulting NGS-based genetics variant detections are prone to false positives. Evaluations of wet-lab and bioinformatics approaches are needed to optimize variant detection from FFPE samples. Results As a pilot study, we designed within-subject triplicate samples of DNA derived from paired FFPE and fresh frozen breast tissues to highlight FFPE-specific artifacts. For FFPE samples, we tested two FFPE DNA extraction methods to determine impact of wet-lab procedures on variant calling: QIAGEN QIAamp DNA Mini Kit ("QA"), and QIAGEN GeneRead DNA FFPE Kit ("QGR"). We also used negative-control (NA12891) and positive control samples (Horizon Discovery Reference Standard FFPE). All DNA sample libraries were prepared for NGS according to the QIAseq Human Breast Cancer Targeted DNA Panel protocol and sequenced on the HiSeq 4000. Variant calling and filtering were performed using QIAGEN Gene Globe Data Portal. Detailed variant concordance comparisons and mutational signature analysis were performed to investigate effects of FFPE samples compared to paired fresh frozen samples, along with different library preparations. In this study, we found that five times or more variants were called with FFPE samples, compared to their paired fresh-frozen tissue samples even after applying molecular barcoding error-correction and default bioinformatics filtering recommended by the vendor. We also found that QGR as an optimized FFPE-DNA extraction approach leads to much fewer discordant variants between paired fresh frozen and FFPE samples. Approximately 92% of the uniquely called FFPE variants were of low allelic frequency range (<5%), and collectively shared a “C>T|G>A” mutational signature known to be representative of FFPE artifacts resulting fromcytosine deamination. Based on control samples and FFPE-frozen replicates, we derived an effective filtering strategy with associated empirical false-discovery estimates. Conclusions Through this study, we demonstrated feasibility of calling and filtering genetic variants from FFPE tissue samples using a combined strategy with molecular barcodes, optimized DNA extraction, and bioinformatics methods incorporating genomics context such as mutational signature and variant allelic frequency.

Abstract Lung cancer (LC) is the primary cause of cancer-related deaths in the United States. Whereas smoking and other environmental factors strongly increase LC risk, multiple genetic variants also contribute to risk in smokers. Furthermore, among smokers, some families have been identified with an abnormally high prevalence of LC, suggesting that unknown genetic factors can greatly increase LC risk in smokers. The typically short survival after LC diagnosis impedes collection of detailed genotypic information on any single large family pedigree, impairing the identification of putative high-risk factors. Therefore, the Genetic Epidemiology of LC Consortium has collected epidemiological and genetic data from a number of families with high numbers of LC cases from eight different sites across the US. In this study, we have obtained whole exome sequences (WES) from 290 members of 28 families, including 66 LC cases. We used a gene-based approach to allow for the possibility that different families may contain different variants of the same gene. Variants were filtered for i) allele frequency, ii) functional effect using combined annotation-dependent depletion (CADD), and, iii) affecting a gene with either a known or suspected role in cancer. We further selected variants based on their segregation in family pedigrees in a pattern consistent with a large effect on LC risk. Candidate LC risk genes were then identified as those represented in at least two families by the same or different variants. We further culled the list of genes by requiring the presence of at least one rare, functional variant enriched in the WES of 1060 cases relative to 899 controls from the Transdisciplinary Research on Cancer of the Lung consortium. This analysis narrowed our results to two genes, one being E2A, a member of the E family of bHLH transcription factors. Whereas loss-of-function mutations in E2A drive lymphoid cancers, the E2A protein also participates in an oncogenic heterodimer with TWIST1 that promotes the epithelial-mesenchymal transition and is implicated in multiple cancer types. Furthermore, the E2A/TWIST1 heterodimer is the primary TWIST1-containing complex implicated in oncogenesis, and silencing of E2A in KRAS-mutant non-small cell lung cancer (NSCLC) cell lines results in oncogene-stimulated senescence and apoptosis. Our data identified three distinct E2A variants present in all 10 sequenced LC cases in the 5 families in which those variants are found. Finally, two of these E2A variants are located only 57 nucleotides from each other, immediately adjacent to sequences encoding a transcription activation domain, suggesting that both variants alter the same specific protein function. These data identify E2A variants as likely high risk factors for LC in smokers and validate our general approach for identifying genetic factors with a large impact on LC risk. Citation Format: Claudio W. Pikielny, Anthony M. Musolf, Mariza de Andrade, Diptasri Mandal, Colette Gaba, Ping Yang, yafang Li, Ming You, Richard Wilson, Elena Y. Kupert, Marshall W. Anderson, Ann G. Schwartz, Susan M. Pinney, Ambrose I. Granizo-Mackenzie, Yanhong Liu, Ramaswamy Govindan, James McKay, Rayjean Hung, John K. Field, David C. Christiani, Joan E. Bailey-Wilson, Christopher I. Amos. Familial studies identify variants in the E2A transcription factor as putative risk factors for lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-053.

Abstract Background Platinum chemotherapy (carboplatin or cisplatin) + etoposide is the current 1L standard of care treatment (tx) for ES-SCLC. Despite high response rates on this regimen, patient (pt) outcomes remain poor. IMpower133 is a Ph1/3, double-blind, randomized, placebo (PBO)-controlled trial that is evaluating the efficacy and safety of adding PD-L1-inhibitor atezo or PBO to 1L tx for ES-SCLC (NCT02763579). Methods IMpower133 enrolled pts without prior tx for ES-SCLC; PD-L1 testing was not required. Pts were randomized 1:1 to four 21-day cycles of carboplatin (AUC 5 mg/mL/min IV, Day 1) + etoposide (100 mg/m2 IV, Days 1-3) with either atezo (1200 mg IV, Day 1) or PBO, then maintenance atezo or PBO until PD, unacceptable toxicity or loss of clinical benefit. Maintenance prophylactic cranial irradiation (PCI) was allowed per protocol, while definitive thoracic radiation (TR) was not. Coprimary endpoints were OS and investigator-assessed PFS. A key exploratory endpoint was outcomes by blood tumor mutation burden (bTMB) analyzed at prespecified cutoffs (≥ 16 vs &lt; 16 and ≥ 10 vs &lt; 10 mutations/Mb). Results Adding atezo to carboplatin + etoposide demonstrated significant improvement in efficacy (OS and PFS) in 1L ES-SCLC (Table). Survival benefits were consistent across key subgroups and prespecified bTMB cutoffs. 44 pts (22 in each arm [per ITT]) received PCI, and 7 (3 in atezo arm, 4 in PBO arm) received TR. Gr 3-4 tx-related adverse events (AEs) occurred in 57% of atezo pts vs 56% of PBO pts; serious tx-related AEs occurred in 23% vs 19%. Occurrence of CNS-related AEs in pts who had PCI are shown in the Table. Conclusion Adding atezo to carboplatin + etoposide resulted in a significant improvement in survival in this 1L ES-SCLC all-comers population. There were no new safety signals, including in pts who received PCI or TR. Atezo + carboplatin + etoposide may represent a new standard regimen for untreated ES-SCLC. Atezo + carboplatin + etoposiden = 201PBO + carboplatin + etoposiden = 202Co-primary endpointsMedian OS, mo12.310.3HR 0.70 (95% CI: 0.54, 0.91); P = 0.0069Median PFS, mo5.24.3HR 0.77 (95% CI: 0.62, 0.96) P = 0.017Secondary efficacy endpointsInvestigator-assessed confirmed ORR, %60.264.4Median DoR, mo4.23.9CNS-related AEs in pts who had PCI, n (%)a,bn = 23n = 21Headache8 (34.8)4 (19.0)Asthenia5 (21.7)2 (9.5)Dizziness2 (8.7)0Insomnia2 (8.7)1 (4.8)Fall2 (8.7)1 (4.8)aSafety population; safety analyses conducted according to tx received (1 pt randomized to the control arm received a dose of atezo).bIncludes AEs occurring in ≥ 2 patients. Citation Format: Aaron S. Mansfield, Stephen V. Liu, Aleksandra Szczęsna, Libor Havel, Maciej Kzrakowski, Maximilian J. Hochmair, Florian Huemer, György Losonczy, Melissa L. Johnson, Makoto Nishio, Martin Reck, Tony S. Mok, Sivuonthanh Lam, David S. Shames, Juan Liu, Fairooz Kabbinavar, Alan Sandler, Leora Horn. IMpower133: Primary efficacy and safety + CNS-related adverse events in a Ph1/3 study of first-line (1L) atezolizumab (atezo) + carboplatin + etoposide in extensive-stage SCLC (ES-SCLC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr CT199.

Abstract Background: Most patients with advanced OC relapse after initial standard platinum-based chemotherapy, and eventually the disease becomes platinum-resistant. Niraparib (ZEJULA®) was the first selective poly(ADP-ribose) polymerase inhibitor (PARPi) approved in the United States and Europe for maintenance treatment in patients with recurrent OC regardless of BRCA mutation status. Preclinical evidence suggests that niraparib activates the stimulator of interferon genes pathway to increase immune cell infiltration and synergizes with anti-PD-1 therapy. Additionally, hypoxia induces contextual synthetic lethality by impairing homologous recombination, and therefore induction of hypoxia by inhibition of angiogenesis could lead to synergy with PARPi. In the TOPACIO/KEYNOTE-162 trial, niraparib in combination with pembrolizumab has shown efficacy in recurrent, platinum-resistant OC. Niraparib in combination with the anti-angiogenic agent bevacizumab is under study for the treatment of recurrent platinum-sensitive OC (AVANOVA trial) and advanced OC following response on frontline platinum-based chemotherapy (OVARIO trial). TSR-042 is an anti-PD-1 humanized monoclonal antibody that has shown clinical activity as monotherapy in early phase trials. Cohort A of the OPAL trial will evaluate the novel triple combination of the PARPi niraparib, angiogenesis inhibitor bevacizumab, and PD-1 inhibitor TSR-042 in patients with platinum-resistant OC who are naïve to PARPi therapy. Methods: Eligible patients will have high-grade recurrent epithelial ovarian, fallopian tube, or primary peritoneal cancer of the ovary and progressed ≤6 months from completion of ≥4 cycles of platinum-based chemotherapy. Additional key eligibility criteria include 1-2 prior lines of anticancer therapy for OC, no prior therapy with an anti-PD-1 or anti-PD-L1 antibody, and no prior therapy for OC with a PARPi. Patients will receive a combination regimen of 500 mg TSR-042 on day 1 of each 3-week cycle for 4 cycles, then 1000 mg on day 1 of every other cycle beginning on cycle 5 until progression or toxicity, 15 mg/kg bevacizumab on day 1 of each 3-week cycle for up to 15 months, and niraparib 300 mg or 200 mg (for patients &lt;77 kg or platelet count &lt;150,000/µL at screening) daily until disease progression or toxicity. The primary endpoint is to evaluate treatment efficacy by confirmed objective response rate per investigator-assessed RECIST v1.1 criteria. Secondary objectives are evaluation of progression-free survival, overall survival, duration of response, and disease control rate. Exploratory objectives are to identify potential biomarkers of tumor response, including BRCA status and homologous recombination repair gene status and to evaluate the evolution of the molecular profile of the tumor and tumor microenvironment in response to treatment. Clinical trial identification: NCT03574779 Citation Format: Joyce Liu, Camille Gunderson, Andrea Wahner Hendrickson, Elena Ratner, Elisabeth Diver, John Moroney, Rebecca C. Arend, Melinda Louie-Gao, Sarah Wang, Katarina Luptakova, Gottfried E. Konecny. An open-label Phase II study of combination of TSR-042, bevacizumab, and niraparib in patients with platinum-resistant ovarian cancer (OC): Cohort A of the OPAL trial [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr CT157.