The Childhood Cancer Data Initiative: Using the Power of Data to Learn From and Improve Outcomes for Every Child and Young Adult With Pediatric Cancer

Data-driven basic, translational, and clinical research has resulted in improved outcomes for children, adolescents, and young adults (AYAs) with pediatric cancers. However, challenges in sharing data between institutions, particularly in research, prevent addressing substantial unmet needs in children and AYA patients diagnosed with certain pediatric cancers. Systematically collecting and sharing data from every child and AYA can enable greater understanding of pediatric cancers, improve survivorship, and accelerate development of new and more effective therapies. To accomplish this goal, the Childhood Cancer Data Initiative (CCDI) was launched in 2019 at the National Cancer Institute. CCDI is a collaborative community endeavor supported by a 10-year, $50-million (in US dollars) annual federal investment. CCDI aims to learn from every patient diagnosed with a pediatric cancer by designing and building a data ecosystem that facilitates data collection, sharing, and analysis for researchers, clinicians, and patients across the cancer community. For example, CCDI's Molecular Characterization Initiative provides comprehensive clinical molecular characterization for children and AYAs with newly diagnosed cancers. Through these efforts, the CCDI strives to provide clinical benefit to patients and improvements in diagnosis and care through data-focused research support and to build expandable, sustainable data resources and workflows to advance research well past the planned 10 years of the initiative. Importantly, if CCDI demonstrates the success of this model for pediatric cancers, similar approaches can be applied to adults, transforming both clinical research and treatment to improve outcomes for all patients with cancer.

Topical therapy for regression and melanoma prevention of congenital giant nevi

Giant congenital melanocytic nevi are NRAS-driven proliferations that may cover up to 80% of the body surface. Their most dangerous consequence is progression to melanoma. This risk often triggers preemptive extensive surgical excisions in childhood, producing severe lifelong challenges. We have presented preclinical models, including multiple genetically engineered mice and xenografted human lesions, which enabled testing locally applied pharmacologic agents to avoid surgery. The murine models permitted the identification of proliferative versus senescent nevus phases and treatments targeting both. These nevi recapitulated the histologic and molecular features of human giant congenital nevi, including the risk of melanoma transformation. Cutaneously delivered MEK, PI3K, and c-KIT inhibitors or proinflammatory squaric acid dibutylester (SADBE) achieved major regressions. SADBE triggered innate immunity that ablated detectable nevocytes, fully prevented melanoma, and regressed human giant nevus xenografts. These findings reveal nevus mechanistic vulnerabilities and suggest opportunities for topical interventions that may alter the therapeutic options for children with congenital giant nevi.

A Trans-Governmental Collaboration to Independently Evaluate SARS-CoV-2 Serology Assays

The emergence of SARS-CoV-2 created a crucial need for serology assays to detect anti-SARS-CoV-2 antibodies, which led to many serology assays entering the market. A trans-government collaboration was created in April 2020 to independently evaluate the performance of commercial SARS-CoV-2 serology assays and help inform U.S. Food and Drug Administration (FDA) regulatory decisions. To assess assay performance, three evaluation panels with similar antibody titer distributions were assembled. Each panel consisted of 110 samples with positive (n = 30) serum samples with a wide range of anti-SARS-CoV-2 antibody titers and negative (n = 80) plasma and/or serum samples that were collected before the start of the COVID-19 pandemic. Each sample was characterized for anti-SARS-CoV-2 antibodies against the spike protein using enzyme-linked immunosorbent assays (ELISA). Samples were selected for the panel when there was agreement on seropositivity by laboratories at National Cancer Institute's Frederick National Laboratory for Cancer Research (NCI-FNLCR) and Centers for Disease Control and Prevention (CDC). The sensitivity and specificity of each assay were assessed to determine Emergency Use Authorization (EUA) suitability. As of January 8, 2021, results from 91 evaluations were made publicly available (https://open.fda.gov/apis/device/covid19serology/, and https://www.cdc.gov/coronavirus/2019-ncov/covid-data/serology-surveillance/serology-test-evaluation.html). Sensitivity ranged from 27% to 100% for IgG (n = 81), from 10% to 100% for IgM (n = 74), and from 73% to 100% for total or pan-immunoglobulins (n = 5). The combined specificity ranged from 58% to 100% (n = 91). Approximately one-third (n = 27) of the assays evaluated are now authorized by FDA for emergency use. This collaboration established a framework for assay performance evaluation that could be used for future outbreaks and could serve as a model for other technologies. IMPORTANCE The SARS-CoV-2 pandemic created a crucial need for accurate serology assays to evaluate seroprevalence and antiviral immune responses. The initial flood of serology assays entering the market with inadequate performance emphasized the need for independent evaluation of commercial SARS-CoV-2 antibody assays using performance evaluation panels to determine suitability for use under EUA. Through a government-wide collaborative network, 91 commercial SARS-CoV-2 serology assay evaluations were performed. Three evaluation panels with similar overall antibody titer distributions were assembled to evaluate performance. Nearly one-third of the assays evaluated met acceptable performance recommendations, and two assays had EUAs revoked and were removed from the U.S. market based on inadequate performance. Data for all serology assays evaluated are available at the FDA and CDC websites (https://open.fda.gov/apis/device/covid19serology/, and https://www.cdc.gov/coronavirus/2019-ncov/covid-data/serology-surveillance/serology-test-evaluation.html).

Therapy-Induced Senescence: Opportunities to Improve Anticancer Therapy

Cellular senescence is an essential tumor suppressive mechanism that prevents the propagation of oncogenically activated, genetically unstable, and/or damaged cells. Induction of tumor cell senescence is also one of the underlying mechanisms by which cancer therapies exert antitumor activity. However, an increasing body of evidence from preclinical studies demonstrates that radiation and chemotherapy cause accumulation of senescent cells (SnCs) both in tumor and normal tissue. SnCs in tumors can, paradoxically, promote tumor relapse, metastasis, and resistance to therapy, in part, through expression of the senescence-associated secretory phenotype. In addition, SnCs in normal tissue can contribute to certain radiation- and chemotherapy-induced side effects. Because of its multiple roles, cellular senescence could serve as an important target in the fight against cancer. This commentary provides a summary of the discussion at the National Cancer Institute Workshop on Radiation, Senescence, and Cancer (August 10-11, 2020, National Cancer Institute, Bethesda, MD) regarding the current status of senescence research, heterogeneity of therapy-induced senescence, current status of senotherapeutics and molecular biomarkers, a concept of "one-two punch" cancer therapy (consisting of therapeutics to induce tumor cell senescence followed by selective clearance of SnCs), and its integration with personalized adaptive tumor therapy. It also identifies key knowledge gaps and outlines future directions in this emerging field to improve treatment outcomes for cancer patients.

Cancer Informatics for Cancer Centers: Scientific Drivers for Informatics, Data Science, and Care in Pediatric, Adolescent, and Young Adult Cancer

Cancer Informatics for Cancer Centers (CI4CC) is a grassroots, nonprofit 501c3 organization intended to provide a focused national forum for engagement of senior cancer informatics leaders, primarily aimed at academic cancer centers anywhere in the world but with a special emphasis on the 70 National Cancer Institute-funded cancer centers. This consortium has regularly held topic-focused biannual face-to-face symposiums. These meetings are a place to review cancer informatics and data science priorities and initiatives, providing a forum for discussion of the strategic and pragmatic issues that we faced at our respective institutions and cancer centers. Here, we provide meeting highlights from the latest CI4CC Symposium, which was delayed from its original April 2020 schedule because of the COVID-19 pandemic and held virtually over three days (September 24, October 1, and October 8) in the fall of 2020. In addition to the content presented, we found that holding this event virtually once a week for 6 hours was a great way to keep the kind of deep engagement that a face-to-face meeting engenders. This is the second such publication of CI4CC Symposium highlights, the first covering the meeting that took place in Napa, California, from October 14-16, 2019. We conclude with some thoughts about using data science to learn from every child with cancer, focusing on emerging activities of the National Cancer Institute's Childhood Cancer Data Initiative.

Antibodies to SARS-CoV-2 in All of Us Research Program Participants, January 2-March 18, 2020

Background

With limited severe acute respiratory syndrome coronavirus (SARS-CoV-2) testing capacity in the United States at the start of the epidemic (January–March 2020), testing was focused on symptomatic patients with a travel history throughout February, obscuring the picture of SARS-CoV-2 seeding and community transmission. We sought to identify individuals with SARS-CoV-2 antibodies in the early weeks of the US epidemic.

Methods

All of Us study participants in all 50 US states provided blood specimens during study visits from 2 January to 18 March 2020. Participants were considered seropositive if they tested positive for SARS-CoV-2 immunoglobulin G (IgG) antibodies with the Abbott Architect SARS-CoV-2 IgG enzyme-linked immunosorbent assay (ELISA) and the EUROIMMUN SARS-CoV-2 ELISA in a sequential testing algorithm. The sensitivity and specificity of these ELISAs and the net sensitivity and specificity of the sequential testing algorithm were estimated, along with 95% confidence intervals (CIs).

Results

The estimated sensitivities of the Abbott and EUROIMMUN assays were 100% (107 of 107 [95% CI: 96.6%–100%]) and 90.7% (97 of 107 [83.5%–95.4%]), respectively, and the estimated specificities were 99.5% (995 of 1000 [98.8%–99.8%]) and 99.7% (997 of 1000 [99.1%–99.9%]), respectively. The net sensitivity and specificity of our sequential testing algorithm were 90.7% (97 of 107 [95% CI: 83.5%–95.4%]) and 100.0% (1000 of 1000 [99.6%–100%]), respectively. Of the 24 079 study participants with blood specimens from 2 January to 18 March 2020, 9 were seropositive, 7 before the first confirmed case in the states of Illinois, Massachusetts, Wisconsin, Pennsylvania, and Mississippi.

Conclusions

Our findings identified SARS-CoV-2 infections weeks before the first recognized cases in 5 US states.

Association of SARS-CoV-2 Seropositive Antibody Test With Risk of Future Infection

IMPORTANCE

Understanding the effect of serum antibodies to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on susceptibility to infection is important for identifying at-risk populations and could have implications for vaccine deployment.

OBJECTIVE

The study purpose was to evaluate evidence of SARS-CoV-2 infection based on diagnostic nucleic acid amplification test (NAAT) among patients with positive vs negative test results for antibodies in an observational descriptive cohort study of clinical laboratory and linked claims data.

DESIGN, SETTING, AND PARTICIPANTS

The study created cohorts from a deidentified data set composed of commercial laboratory tests, medical and pharmacy claims, electronic health records, and hospital chargemaster data. Patients were categorized as antibody-positive or antibody-negative according to their first SARS-CoV-2 antibody test in the database.

MAIN OUTCOMES AND MEASURES

Primary end points were post-index diagnostic NAAT results, with infection defined as a positive diagnostic test post-index, measured in 30-day intervals (0-30, 31-60, 61-90, >90 days). Additional measures included demographic, geographic, and clinical characteristics at the time of the index antibody test, including recorded signs and symptoms or prior evidence of coronavirus 2019 (COVID) diagnoses or positive NAAT results and recorded comorbidities.

RESULTS

The cohort included 3 257 478 unique patients with an index antibody test; 56% were female with a median (SD) age of 48 (20) years. Of these, 2 876 773 (88.3%) had a negative index antibody result, and 378 606 (11.6%) had a positive index antibody result. Patients with a negative antibody test result were older than those with a positive result (mean age 48 vs 44 years). Of index-positive patients, 18.4% converted to seronegative over the follow-up period. During the follow-up periods, the ratio (95% CI) of positive NAAT results among individuals who had a positive antibody test at index vs those with a negative antibody test at index was 2.85 (95% CI, 2.73-2.97) at 0 to 30 days, 0.67 (95% CI, 0.6-0.74) at 31 to 60 days, 0.29 (95% CI, 0.24-0.35) at 61 to 90 days, and 0.10 (95% CI, 0.05-0.19) at more than 90 days.

CONCLUSIONS AND RELEVANCE

In this cohort study, patients with positive antibody test results were initially more likely to have positive NAAT results, consistent with prolonged RNA shedding, but became markedly less likely to have positive NAAT results over time, suggesting that seropositivity is associated with protection from infection. The duration of protection is unknown, and protection may wane over time.

Real-world data suggest antibody positivity to SARS-CoV-2 is associated with a decreased risk of future infection

Importance There is limited evidence regarding whether the presence of serum antibodies to SARS-CoV-2 is associated with a decreased risk of future infection. Understanding susceptibility to infection and the role of immune memory is important for identifying at-risk populations and could have implications for vaccine deployment. Objective The purpose of this study was to evaluate subsequent evidence of SARS-CoV-2 infection based on diagnostic nucleic acid amplification test (NAAT) among individuals who are antibody-positive compared with those who are antibody-negative, using real-world data. Design This was an observational descriptive cohort study. Participants The study utilized a national sample to create cohorts from a de-identified dataset composed of commercial laboratory test results, open and closed medical and pharmacy claims, electronic health records, hospital billing (chargemaster) data, and payer enrollment files from the United States. Patients were indexed as antibody-positive or antibody-negative according to their first SARS-CoV-2 antibody test recorded in the database. Patients with more than 1 antibody test on the index date where results were discordant were excluded. Main Outcomes/Measures Primary endpoints were index antibody test results and post-index diagnostic NAAT results, with infection defined as a positive diagnostic test post-index, as measured in 30-day intervals (0-30, 31-60, 61-90, >90 days). Additional measures included demographic, geographic, and clinical characteristics at the time of the index antibody test, such as recorded signs and symptoms or prior evidence of COVID-19 (diagnoses or NAAT+) and recorded comorbidities. Results We included 3,257,478 unique patients with an index antibody test. Of these, 2,876,773 (88.3%) had a negative index antibody result, 378,606 (11.6%) had a positive index antibody result, and 2,099 (0.1%) had an inconclusive index antibody result. Patients with a negative antibody test were somewhat older at index than those with a positive result (mean of 48 versus 44 years). A fraction (18.4%) of individuals who were initially seropositive converted to seronegative over the follow up period. During the follow-up periods, the ratio (CI) of positive NAAT results among individuals who had a positive antibody test at index versus those with a negative antibody test at index was 2.85 (2.73 - 2.97) at 0-30 days, 0.67 (0.6 - 0.74) at 31-60 days, 0.29 (0.24 - 0.35) at 61-90 days), and 0.10 (0.05 - 0.19) at >90 days. Conclusions Patients who display positive antibody tests are initially more likely to have a positive NAAT, consistent with prolonged RNA shedding, but over time become markedly less likely to have a positive NAAT. This result suggests seropositivity using commercially available assays is associated with protection from infection. The duration of protection is unknown and may wane over time; this parameter will need to be addressed in a study with extended duration of follow up.

Cancer Grand Challenges: Embarking on a New Era of Discovery

Cancer Grand Challenges is a unique funding platform that dares global, multidisciplinary teams of researchers to come together, think differently, and tackle some of the toughest challenges in cancer research. Here, we discuss the nine intractable challenges currently open for application.

Abstract IA01: How the National Cancer Institute is working to reduce cancer health disparities

Disparities in cancer incidence and mortality among members of racial/ethnic minority groups continue to be a daunting public health challenge. While cancer disparities have been well documented, further efforts are needed to understand the factors that cause these disparities and to develop interventions. The National Cancer Institute (NCI) has had programs dedicated to addressing disparities for more than two decades, which now pursue a multipronged approach. Among the most recent NCI efforts is a stipulation included in all Cancer Moonshot funding opportunities that requires applicants to include information on how they will integrate data on populations affected by disparities or data on these populations into the proposed study. The Cancer Moonshot also includes specific disparities-related components, including those to fund the development of preclinical research models and screening programs that target specific racial/ethnic populations. More longstanding NCI efforts include those supporting a portfolio of studies, from basic to translational, that are unmasking biologic, socioeconomic, and cultural factors that contribute to disparities and identifying ways to directly address those factors through precision medicine and other approaches. Recent examples include the RESPOND study, which is focused on better understanding prostate cancer disparities in African American men. Other NCI programs are aimed at increasing the participation of people who are members of racial/ethnic minority groups in clinical studies, including innovative precision medicine studies. These include the NCI Community Oncology Research Program and the Partnerships to Advance Cancer Health Equity program that supports collaborations among institutions that serve large underserved populations and NCI-designated Cancer Centers. NCI also supports programs intended to improve the participation of under-represented populations in the cancer research and clinical workforce. This is helping to ensure that people from varied backgrounds can contribute their viewpoints and experiences to the cancer research enterprise and further deepen the talent pool from which research institutions can draw. From a clinical perspective, improving the diversity of clinicians/researchers can also improve trust among patients from racial/ethnic minority groups, which in turn can help increase the likelihood that these patients will consider participating in clinical studies. NCI programs that are helping to improve the diversity of the cancer workforce include the Continuing Umbrella of Research Experiences (CURE) that supports extramural research training and educational experiences for underrepresented individuals beginning in middle school and continuing through to first academic appointments through individual (F31 and K awards) and institutional (R25) grants, as well as the iCURE program that provides mentored research experiences within the NCI Intramural Research Program for students and fellows. Additional awards aid early-stage investigators in establishing themselves as independent investigators in the laboratory and clinical settings (R37, K23) and promote workforce diversity in basic cancer research (R21).

Citation Format: Norman E. Sharpless. How the National Cancer Institute is working to reduce cancer health disparities [abstract]. In: Proceedings of the Eleventh AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2018 Nov 2-5; New Orleans, LA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl):Abstract nr IA01.

The Prognostic Significance of Low-Frequency Somatic Mutations in Metastatic Cutaneous Melanoma

Background: Little is known about the prognostic significance of somatically mutated genes in metastatic melanoma (MM). We have employed a combined clinical and bioinformatics approach on tumor samples from cutaneous melanoma (SKCM) as part of The Cancer Genome Atlas project (TCGA) to identify mutated genes with potential clinical relevance. Methods: After limiting our DNA sequencing analysis to MM samples (n = 356) and to the CANCER CENSUS gene list, we filtered out mutations with low functional significance (snpEFF). We performed Cox analysis on 53 genes that were mutated in ≥3% of samples, and had ≥50% difference in incidence of mutations in deceased subjects versus alive subjects. Results: Four genes were potentially prognostic [RAC1, FGFR1, CARD11, CIITA; false discovery rate (FDR) < 0.2]. We identified 18 additional genes (e.g., SPEN, PDGFRB, GNAS, MAP2K1, EGFR, TSC2) that were less likely to have prognostic value (FDR < 0.4). Most somatic mutations in these 22 genes were infrequent (< 10%), associated with high somatic mutation burden, and were evenly distributed across all exons, except for RAC1 and MAP2K1. Mutations in only 9 of these 22 genes were also identified by RNA sequencing in >75% of the samples that exhibited corresponding DNA mutations. The low frequency, UV signature type and RNA expression of the 22 genes in MM samples were confirmed in a separate multi-institution validation cohort (n = 413). An underpowered analysis within a subset of this validation cohort with available patient follow-up (n = 224) showed that somatic mutations in SPEN and RAC1 reached borderline prognostic significance [log-rank favorable (p = 0.09) and adverse (p = 0.07), respectively]. Somatic mutations in SPEN, and to a lesser extent RAC1, were not associated with definite gene copy number or RNA expression alterations. High (>2+) nuclear plus cytoplasmic expression intensity for SPEN was associated with longer melanoma-specific overall survival (OS) compared to lower (≤ 2+) nuclear intensity (p = 0.048). We conclude that expressed somatic mutations in infrequently mutated genes beyond the well-characterized ones (e.g., BRAF, RAS, CDKN2A, PTEN, TP53), such as RAC1 and SPEN, may have prognostic significance in MM.

Expression of p16INK 4a is a biomarker of chondrocyte aging but does not cause osteoarthritis

Cellular senescence drives a functional decline of numerous tissues with aging by limiting regenerative proliferation and/or by producing pro‐inflammatory molecules known as the senescence‐associated secretory phenotype (SASP). The senescence biomarker p16^INK4a is a potent inhibitor of the cell cycle but is not essential for SASP production. Thus, it is unclear whether p16^INK4a identifies senescence in hyporeplicative cells such as articular chondrocytes and whether p16^INK4a contributes to pathologic characteristics of cartilage aging. To address these questions, we examined the role of p16^INK4a in murine and human models of chondrocyte aging. We observed that p16^INK4amRNA expression was significantly upregulated with chronological aging in murine cartilage (~50‐fold from 4 to 18 months of age) and in primary human chondrocytes from 57 cadaveric donors (r² = .27, p < .0001). Human chondrocytes exhibited substantial replicative potential in vitro that depended on the activity of cyclin‐dependent kinases 4 or 6 (CDK4/6), and proliferation was reduced in cells from older donors with increased p16^INK4a expression. Moreover, increased chondrocyte p16^INK4a expression correlated with several SASP transcripts. Despite the relationship between p16^INK4a expression and these features of senescence, somatic inactivation of p16^INK4a in chondrocytes of adult mice did not mitigate SASP expression and did not alter the rate of osteoarthritis (OA) with physiological aging or after destabilization of the medial meniscus. These results establish that p16^INK4a expression is a biomarker of dysfunctional chondrocytes, but that the effects of chondrocyte senescence on OA are more likely driven by production of SASP molecules than by loss of chondrocyte replicative function.

Transient CDK4/6 inhibition protects hematopoietic stem cells from chemotherapy-induced exhaustion

Conventional cytotoxic chemotherapy is highly effective in certain cancers but causes dose-limiting damage to normal proliferating cells, especially hematopoietic stem and progenitor cells (HSPCs). Serial exposure to cytotoxics causes a long-term hematopoietic compromise ("exhaustion"), which limits the use of chemotherapy and success of cancer therapy. We show that the coadministration of G1T28 (trilaciclib), which is a small-molecule inhibitor of cyclin-dependent kinases 4 and 6 (CDK4/6), contemporaneously with cytotoxic chemotherapy protects murine hematopoietic stem cells (HSCs) from chemotherapy-induced exhaustion in a serial 5-fluorouracil treatment model. Consistent with a cell-intrinsic effect, we show directly preserved HSC function resulting in a more rapid recovery of peripheral blood counts, enhanced serial transplantation capacity, and reduced myeloid skewing. When administered to healthy human volunteers, G1T28 demonstrated excellent in vivo pharmacology and transiently inhibited bone marrow (BM) HSPC proliferation. These findings suggest that the combination of CDK4/6 inhibitors with cytotoxic chemotherapy should provide a means to attenuate therapy-induced BM exhaustion in patients with cancer.

New Mechanisms of Resistance to MEK Inhibitors in Melanoma Revealed by Intravital Imaging

Targeted therapeutics that are initially effective in cancer patients nearly invariably engender resistance at some stage, an inherent challenge in the use of any molecular-targeted drug in cancer settings. In this study, we evaluated resistance mechanisms arising in metastatic melanoma to MAPK pathway kinase inhibitors as a strategy to identify candidate strategies to limit risks of resistance. To investigate longitudinal responses, we developed an intravital serial imaging approach that can directly visualize drug response in an inducible RAF-driven, autochthonous murine model of melanoma incorporating a fluorescent reporter allele (tdTomatoLSL). Using this system, we visualized formation and progression of tumors in situ, starting from the single-cell level longitudinally over time. Reliable reporting of the status of primary murine tumors treated with the selective MEK1/2 inhibitor (MEKi) trametinib illustrated a time-course of initial drug response and persistence, followed by the development of drug resistance. We found that tumor cells adjacent to bundled collagen had a preferential persistence in response to MEKi. Unbiased transcriptional and kinome reprogramming analyses from selected treatment time points suggested increased c-Kit and PI3K/AKT pathway activation in resistant tumors, along with enhanced expression of epithelial genes and epithelial-mesenchymal transition downregulation signatures with development of MEKi resistance. Similar trends were observed following simultaneous treatment with BRAF and MEK inhibitors aligned to standard-of-care combination therapy, suggesting these reprogramming events were not specific to MEKi alone. Overall, our results illuminate the integration of tumor-stroma dynamics with tissue plasticity in melanoma progression and provide new insights into the basis for drug response, persistence, and resistance.Significance: A longitudinal study tracks the course of MEKi treatment in an autochthonous imageable murine model of melanoma from initial response to therapeutic resistance, offering new insights into the basis for drug response, persistence, and resistance. Cancer Res; 78(2); 542-57. ©2017 AACR.

Enhancing Next-Generation Sequencing-Guided Cancer Care Through Cognitive Computing

Next‐generation sequencing (NGS) has emerged as an affordable and reproducible means to query tumors for somatic genetic anomalies. To help interpret somatic NGS data, many institutions have created a molecular tumor board to analyze the results of NGS and make recommendations. This article evaluates the utility of cognitive computing systems to analyze data for clinical decision‐making.

Background.

Using next‐generation sequencing (NGS) to guide cancer therapy has created challenges in analyzing and reporting large volumes of genomic data to patients and caregivers. Specifically, providing current, accurate information on newly approved therapies and open clinical trials requires considerable manual curation performed mainly by human “molecular tumor boards” (MTBs). The purpose of this study was to determine the utility of cognitive computing as performed by Watson for Genomics (WfG) compared with a human MTB.

Materials and Methods.

One thousand eighteen patient cases that previously underwent targeted exon sequencing at the University of North Carolina (UNC) and subsequent analysis by the UNCseq informatics pipeline and the UNC MTB between November 7, 2011, and May 12, 2015, were analyzed with WfG, a cognitive computing technology for genomic analysis.

Results.

Using a WfG‐curated actionable gene list, we identified additional genomic events of potential significance (not discovered by traditional MTB curation) in 323 (32%) patients. The majority of these additional genomic events were considered actionable based upon their ability to qualify patients for biomarker‐selected clinical trials. Indeed, the opening of a relevant clinical trial within 1 month prior to WfG analysis provided the rationale for identification of a new actionable event in nearly a quarter of the 323 patients. This automated analysis took <3 minutes per case.

Conclusion.

These results demonstrate that the interpretation and actionability of somatic NGS results are evolving too rapidly to rely solely on human curation. Molecular tumor boards empowered by cognitive computing could potentially improve patient care by providing a rapid, comprehensive approach for data analysis and consideration of up‐to‐date availability of clinical trials.

Implications for Practice.

The results of this study demonstrate that the interpretation and actionability of somatic next‐generation sequencing results are evolving too rapidly to rely solely on human curation. Molecular tumor boards empowered by cognitive computing can significantly improve patient care by providing a fast, cost‐effective, and comprehensive approach for data analysis in the delivery of precision medicine. Patients and physicians who are considering enrollment in clinical trials may benefit from the support of such tools applied to genomic data.

CDK4/6 Inhibition Augments Antitumor Immunity by Enhancing T-cell Activation

Immune checkpoint blockade, exemplified by antibodies targeting the PD-1 receptor, can induce durable tumor regressions in some patients. To enhance the efficacy of existing immunotherapies, we screened for small molecules capable of increasing the activity of T cells suppressed by PD-1. Here, we show that short-term exposure to small-molecule inhibitors of cyclin-dependent kinases 4 and 6 (CDK4/6) significantly enhances T-cell activation, contributing to antitumor effects in vivo, due in part to the derepression of NFAT family proteins and their target genes, critical regulators of T-cell function. Although CDK4/6 inhibitors decrease T-cell proliferation, they increase tumor infiltration and activation of effector T cells. Moreover, CDK4/6 inhibition augments the response to PD-1 blockade in a novel ex vivo organotypic tumor spheroid culture system and in multiple in vivo murine syngeneic models, thereby providing a rationale for combining CDK4/6 inhibitors and immunotherapies.Significance: Our results define previously unrecognized immunomodulatory functions of CDK4/6 and suggest that combining CDK4/6 inhibitors with immune checkpoint blockade may increase treatment efficacy in patients. Furthermore, our study highlights the critical importance of identifying complementary strategies to improve the efficacy of immunotherapy for patients with cancer. Cancer Discov; 8(2); 216-33. ©2017 AACR.See related commentary by Balko and Sosman, p. 143See related article by Jenkins et al., p. 196This article is highlighted in the In This Issue feature, p. 127.

Exploiting Drug Addiction Mechanisms to Select against MAPKi-Resistant Melanoma

Melanoma resistant to MAPK inhibitors (MAPKi) displays loss of fitness upon experimental MAPKi withdrawal and, clinically, may be resensitized to MAPKi therapy after a drug holiday. Here, we uncovered and therapeutically exploited the mechanisms of MAPKi addiction in MAPKi-resistant BRAF^MUT or NRAS^MUT melanoma. MAPKi-addiction phenotypes evident upon drug withdrawal spanned transient cell-cycle slowdown to cell-death responses, the latter of which required a robust phosphorylated ERK (pERK) rebound. Generally, drug withdrawal-induced pERK rebound upregulated p38-FRA1-JUNB-CDKN1A and downregulated proliferation, but only a robust pERK rebound resulted in DNA damage and parthanatos-related cell death. Importantly, pharmacologically impairing DNA damage repair during MAPKi withdrawal augmented MAPKi addiction across the board by converting a cell-cycle deceleration to a caspase-dependent cell-death response or by furthering parthanatos-related cell death. Specifically in MEKi-resistant NRAS^MUT or atypical BRAF^MUT melanoma, treatment with a type I RAF inhibitor intensified pERK rebound elicited by MEKi withdrawal, thereby promoting a cell death-predominant MAPKi-addiction phenotype. Thus, MAPKi discontinuation upon disease progression should be coupled with specific strategies that augment MAPKi addiction.Significance: Discontinuing targeted therapy may select against drug-resistant tumor clones, but drug-addiction mechanisms are ill-defined. Using melanoma resistant to but withdrawn from MAPKi, we defined a synthetic lethality between supraphysiologic levels of pERK and DNA damage. Actively promoting this synthetic lethality could rationalize sequential/rotational regimens that address evolving vulnerabilities. Cancer Discov; 8(1); 74-93. ©2017 AACR.See related commentary by Stern, p. 20This article is highlighted in the In This Issue feature, p. 1.

Identification of Human Papillomavirus Infection in Cancer Tissue by Targeted Next-generation Sequencing

Human papillomaviruses (HPV) are oncogenic DNA viruses implicated in squamous cell carcinomas of several anatomic sites, as well as endocervical adenocarcinomas. Identification of HPV is an actionable finding in some carcinomas, potentially influencing tumor classification, prognosis, and management. We incorporated capture probes for oncogenic HPV strains 16 and 18 into a broader next-generation sequencing (NGS) panel designed to identify actionable mutations in solid malignancies. A total of 21 head and neck, genitourinary, and gynecologic squamous cell carcinomas and endocervical adenocarcinomas were sequenced as part of the UNCSeq project. Using p16 immunohistochemical results as the gold standard, we set a cutoff for proportion of aligned HPV reads that maximized performance of our NGS assay (92% sensitive, 100% specific for HPV). These results suggest that sequencing of oncogenic pathogens can be incorporated into targeted NGS panels, extending the clinical utility of genomic assays.

Senescence in Health and Disease

Many cellular stresses activate senescence, a persistent hyporeplicative state characterized in part by expression of the p16^INK4a cell-cycle inhibitor. Senescent cell production occurs throughout life and plays beneficial roles in a variety of physiological and pathological processes including embryogenesis, wound healing, host immunity, and tumor suppression. Meanwhile, the steady accumulation of senescent cells with age also has adverse consequences. These non-proliferating cells occupy key cellular niches and elaborate pro-inflammatory cytokines, contributing to aging-related diseases and morbidity. This model suggests that the abundance of senescent cells in vivo predicts "molecular," as opposed to chronologic, age and that senescent cell clearance may mitigate aging-associated pathology.

Changes in p16INK4a (p16) expression, a biomarker of aging, in peripheral blood T-cells (PBTC) in patients receiving anthracycline (A) vs non-anthracycline (NoA) chemotherapy (CRx) for early-stage breast cancer (EBC)

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Background: Age-related accumulation of senescent cells plays a causal role in some aspects of mammalian aging. We have shown that the total-body burden of senescent cells can be estimated by measuring the expression of the p16 tumor suppressor, a canonical effector of senescence, in human CD3+ PBTC (Liu et al, Aging Cell, 2009). Expression of p16 increases more than 10-fold over an adult human lifespan, and this rate of accumulation is accelerated by age-promoting exposures such as CRx or stem cell transplant (Sanoff et al, JNCI 2014; Wood et al, EbioMed 2016). Increased molecular age as evidenced by increased expression of p16 prior to CRx predicts a patient’s risk of CRx toxicity independently of chronological age (DeMaria et al, Cancer Discovery, 2017).This study investigates the impact of different types of CRx (A vs NoA) regimens on PBTC p16expression in pts with EBC. Methods: EBC pts who received neoAdj or Adj CRx had blood samples drawn for p16 assay prior to CRx initiation and again between 2 months and 1.5 years after the end of CRx. Expression of p16 mRNA in PBTC was determined using TaqMan real-time quantitative reverse transcription PCR. T-test compared p16change between A and NA groups. Results: 70 pts were evaluable. Pt. characteristics: median age 49 (range 32-76); 52 (74%) White, 14 (20%) black, 4 unknown; 39 (56%) ER or PR+ and HER2 neg, 18 (26%) triple negative, 13 (19%) HER-2 pos (all received trastuzumab). 53 pts (76%) had A (47 AC + taxane, 6 AC no taxane) and 17 (24%) NoA (all TC). Expression of p16 increased 2.0-fold in patients who received A-based CRx compared to 1.2-fold in NoA CRx (p = 0.04). There was no relationship of race, ER, PR or HER-2 status on change in p16expression. Conclusions: This study is ongoing and further results will be presented at the ASCO meeting. In this sample of EBC patients treated with A vs. NoA CRx regimens, A-based CRx is more strongly associated with increased biologic aging of T-cells compared to NoA CRx. These changes are equivalent of increased biologic aging of PBTC of 11 years (A) vs.6 years (NoA) and may have major consequences on the long-term survival of these pts.

Lkb1 deletion in murine B lymphocytes promotes cell death and cancer

LKB1 (also known as STK11) is a potent tumor suppressor in solid tumors, such as melanoma and lung adenocarcinoma, but inactivation in hematopoietic cells causes cell death without signs of tumorigenesis. We noted somatic LKB1 deletion or mutation at low frequency in human B-cell lymphoma. To determine if LKB1 inactivation is a passenger or driver event in lymphoid cancers, we examined the effects of conditional inactivation of Lkb1 in murine lymphocytes. Consistent with prior reports, Lkb1 deletion in either T or B cells resulted in massive, lineage-specific apoptosis. Surprisingly, despite an 80% reduction of peripheral B-cell number, animals harboring somatic B-lineage Lkb1 deletion developed aggressive B-cell lymphoma with high penetrance and moderate latency. Malignant B cells exhibited somatic Lkb1 recombination. In contrast, Lkb1 deletion in T cells did not promote tumorigenesis. Concomitant Ras activation with Lkb1 deletion reduced T-cell apoptosis, but did not enhance tumor formation in T or B cells. These results suggest that although physiologic LKB1 expression exerts a potent pro-survival effect in lymphocytes, LKB1 inactivation nonetheless facilitates transformation of B, but not T, lymphocytes.

Abstract P1-05-20: Comparing the frequency and types of genetic aberrations between older and younger women with metastatic breast cancer at the University of North Carolina at Chapel Hill

Background: Targeted therapies have the potential to revolutionize cancer treatment in older adults as they are often oral, convenient, may be better tolerated than cytotoxic chemotherapy, and can be tailored to an individual's biomarker profile. We explore the frequency and distribution of potentially actionable genomic alterations among older (≥65) and younger (&lt;65) patients (pts) with metastatic breast cancer (MBC).

Method: Next generation genetic sequencing (UNCseq™) of a dynamic panel of target genes was prospectively offered to pts with MBC treated at the University of North Carolina at Chapel Hill (UNC). DNA libraries were prepared separately from a retrieved archival FFPE tumor sample and a matched normal sample from each pt. Relevant targets were enriched by custom Agilent SureSelect hybrid capture baits using standard protocols. Samples were sequenced on Illumina HiSeq 2000/2500 platforms. Mutational findings were reviewed by a molecular tumor board; variants identified to be potentially actionable underwent confirmatory testing in a CLIA approved laboratory. Confirmed findings were inserted into the pt's EMR accessible by both the pt and the treating oncologist. Two-sided Fisher's exact test was used to compare percentages between age-specific groups.

Results: As of 3/31/16, results were available for 140 pts. 19% were 65 years or older. Breast cancer clinical subtypes were: HR+/HER2- 49%, HER2+ (HR any) 17%, TN 34% and metastatic location was: bone only 5%, visceral only 44%, bone & visceral 51%; no significant differences were observed between older and younger age groups. Older pts were more likely to be Caucasian compared to younger patients (92% v 75%, p=0.06). Overall, older patients had a higher total number of mutations compared to younger patients (see Table) (p=0.04). Mutation types were similar between age groups, although a trend for more PIK3CA mutations among older patients was seen (37% v 20%, p=0.07).

Observed Mutations by Age. ≥ 65 years (%) N=27&lt; 65 years (%) N=113pNumber of Mutations   01127.0414849.0423320.04374.04Type of mutation   PIK3CA3720.07CCND179.99NF-1115.37FGFR144.99PTEN49.69EGFR04.99

Conclusion: Genomic alterations may allow therapeutic tailoring in both older and younger patients with breast cancer. In this cohort with metastatic disease, older patients had significantly more mutations, but no clear difference in mutational types was seen by age. The relative small number of older pts in this cohort limits generalization, but supports the need for more extensive characterization of molecular aberrations among older pts with metastatic breast cancer in the new era of targeted therapy.

Research support by the University Cancer Research Fund, NCI Breast Cancer SPORE grant (CA58223), John A. Hartford Foundation and Susan G. Komen Foundation.

Citation Format: Jolly TA, Grilley-Olson JE, Deal AM, Ivanova A, Hayward MC, Benbow JM, Parker JS, Patel NM, Eberhard DA, Weck KE, Mieczkowski P, Dees EC, Muss HD, Reeder-Hayes KE, Earp HS, Sharpless NE, Carey LA, Hayes DN, Anders CK. Comparing the frequency and types of genetic aberrations between older and younger women with metastatic breast cancer at the University of North Carolina at Chapel Hill [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-05-20.

Population Pharmacokinetics Modeling of Unbound Efavirenz, Atazanavir, and Ritonavir in HIV-Infected Subjects With Aging Biomarkers

Unbound drug is the pharmacodynamically relevant concentration. This study aimed to determine if chronologic age or markers of biologic aging, such as the frailty phenotype and p16INK4a gene expression, altered unbound pharmacokinetics (PKs) of efavirenz (EFV) and atazanavir/ritonavir (ATV/RTV). Sixty human immunodeficiency virus (HIV)-infected participants receiving EFV and 31 receiving ATV/RTV provided 1 to 11 samples to quantify total and unbound plasma concentrations. Population PK models with total and unbound concentrations simultaneously described are developed for each drug. The unbound fractions for EFV, ATV, and RTV are 0.65%, 5.67%, and 0.63%, respectively. Covariate analysis suggests RTV unbound PK is sensitive to body size; unbound fraction of RTV is 34% lower with body mass index (BMI) above 30 kg/m2 . No alterations in drug clearance or unbound fraction with age, frailty, or p16INK4a expression were observed. Assessing functional and physiologic aging markers to inform potential PK changes is necessary to determine if drug/dosing changes are warranted in the aging population.

Docetaxel-Loaded PLGA Nanoparticles Improve Efficacy in Taxane-Resistant Triple-Negative Breast Cancer

Novel treatment strategies, including nanomedicine, are needed for improving management of triple-negative breast cancer. Patients with triple-negative breast cancer, when considered as a group, have a worse outcome after chemotherapy than patients with breast cancers of other subtypes, a finding that reflects the intrinsically adverse prognosis associated with the disease. The aim of this study was to improve the efficacy of docetaxel by incorporation into a novel nanoparticle platform for the treatment of taxane-resistant triple-negative breast cancer. Rod-shaped nanoparticles encapsulating docetaxel were fabricated using an imprint lithography based technique referred to as Particle Replication in Nonwetting Templates (PRINT). These rod-shaped PLGA-docetaxel nanoparticles were tested in the C3(1)-T-antigen (C3Tag) genetically engineered mouse model (GEMM) of breast cancer that represents the basal-like subtype of triple-negative breast cancer and is resistant to therapeutics from the taxane family. This GEMM recapitulates the genetics of the human disease and is reflective of patient outcome and, therefore, better represents the clinical impact of new therapeutics. Pharmacokinetic analysis showed that delivery of these PLGA-docetaxel nanoparticles increased docetaxel circulation time and provided similar docetaxel exposure to tumor compared to the clinical formulation of docetaxel, Taxotere. These PLGA-docetaxel nanoparticles improved tumor growth inhibition and significantly increased median survival time. This study demonstrates the potential of nanotechnology to improve the therapeutic index of chemotherapies and rescue therapeutic efficacy to treat nonresponsive cancers.

Concentrations of Pro-Inflammatory Cytokines Are Not Associated with Senescence Marker p16INK4a or Predictive of Intracellular Emtricitabine/Tenofovir Metabolite and Endogenous Nucleotide Exposures in Adults with HIV Infection

OBJECTIVES

As the HIV-infected population ages, the role of cellular senescence and inflammation on co-morbid conditions and pharmacotherapy is increasingly of interest. p16INK4a expression, a marker for aging and senescence in T-cells, is associated with lower intracellular concentrations of endogenous nucleotides (EN) and nucleos(t)ide reverse transcriptase inhibitors (NRTIs). This study expands on these findings by determining whether inflammation is contributing to the association of p16INK4a expression with intracellular metabolite (IM) exposure and endogenous nucleotide concentrations.

METHODS

Samples from 73 HIV-infected adults receiving daily tenofovir/emtricitabine (TFV/FTC) with either efavirenz (EFV) or atazanavir/ritonavir (ATV/r) were tested for p16INK4a expression, and plasma cytokine and intracellular drug concentrations. Associations between p16INK4a expression and cytokine concentrations were assessed using maximum likelihood methods, and elastic net regression was applied to assess whether cytokines were predictive of intracellular metabolite/endogenous nucleotide exposures.

RESULTS

Enrolled participants had a median age of 48 years (range 23-73). There were no significant associations between p16INK4a expression and cytokines. Results of the elastic net regression showed weak relationships between IL-1Ra and FTC-triphosphate and deoxyadenosine triphosphate exposures, and MIP-1β, age and TFV-diphosphate exposures.

CONCLUSIONS

In this clinical evaluation, we found no relationships between p16INK4a expression and cytokines, or cytokines and intracellular nucleotide concentrations. While inflammation is known to play a role in this population, it is not a major contributor to the p16INK4a association with decreased IM/EN exposures in these HIV-infected participants.

p16INK4a , a Senescence Marker, Influences Tenofovir/Emtricitabine Metabolite Disposition in HIV-Infected Subjects

The goal of this study was to explore the relationships between tenofovir (TFV) and emtricitabine (FTC) disposition and markers of biologic aging, such as the frailty phenotype and p16^INK4a gene expression. Chronologic age is often explored in population pharmacokinetic (PK) analyses, and can be uninformative in capturing the impact of aging on physiology, particularly in human immunodeficiency virus (HIV)‐infected patients. Ninety‐one HIV‐infected participants provided samples to quantify plasma concentrations of TFV/FTC, as well as peripheral blood mononuclear cell (PBMC) samples for intracellular metabolite concentrations; 12 participants provided 11 samples, and 79 participants provided 4 samples, over a dosing interval. Nonlinear mixed effects modeling of TFV/FTC and their metabolites suggests a relationship between TFV/FTC metabolite clearance (CL) from PBMCs and the expression of p16^INK4a, a marker of cellular senescence. This novel approach to quantifying the influence of aging on PKs provides rationale for further work investigating the relationships between senescence and nucleoside phosphorylation and transport.

Cellular Senescence Promotes Adverse Effects of Chemotherapy and Cancer Relapse

Cellular senescence suppresses cancer by irreversibly arresting cell proliferation. Senescent cells acquire a proinflammatory senescence-associated secretory phenotype. Many genotoxic chemotherapies target proliferating cells nonspecifically, often with adverse reactions. In accord with prior work, we show that several chemotherapeutic drugs induce senescence of primary murine and human cells. Using a transgenic mouse that permits tracking and eliminating senescent cells, we show that therapy-induced senescent (TIS) cells persist and contribute to local and systemic inflammation. Eliminating TIS cells reduced several short- and long-term effects of the drugs, including bone marrow suppression, cardiac dysfunction, cancer recurrence, and physical activity and strength. Consistent with our findings in mice, the risk of chemotherapy-induced fatigue was significantly greater in humans with increased expression of a senescence marker in T cells prior to chemotherapy. These findings suggest that senescent cells can cause certain chemotherapy side effects, providing a new target to reduce the toxicity of anticancer treatments.

SIGNIFICANCE

Many genotoxic chemotherapies have debilitating side effects and also induce cellular senescence in normal tissues. The senescent cells remain chronically present where they can promote local and systemic inflammation that causes or exacerbates many side effects of the chemotherapy. Cancer Discov; 7(2); 165-76. ©2016 AACR.This article is highlighted in the In This Issue feature, p. 115.

Abstract IA11: Transient CDK4/6 inhibition protects hematopoietic progenitors from chemotherapy-induced exhaustion

Conventional cytotoxic chemotherapy is highly effective in certain cancers, but causes dose-limiting damage to normal proliferating cells, especially hematopoietic stem and progenitor cells (HSPCs). Serial exposure to cytotoxics causes a long-term hematopoietic compromise (“exhaustion”), which limits the use of chemotherapy and success of cancer therapy. I will discuss the use of small-molecule inhibitors of cyclin-dependent kinases 4 and 6 (CDK4/6) contemporaneously with DNA damaging stimuli such as cytotoxic chemotherapy to protect HSPC from chemotherapy-induced exhaustion. Specifically, CDK4/6 inhibitors will reduce HSPC proliferation, leading to decreased damage from cytotoxic agents, resulting in preserved HSPC function acutely after bone marrow injury as well as late time points well after hematopoietic recovery. In particular, I will show this approach leads to enhanced long-term HSC function resulting in enhanced serial transplantation and reduced myeloid skewing. I will discuss similarities between chemotherapy-induced HSC dysfunction and HSC aging. Moreover, these finding suggest that the combination of CDK4/6 inhibitors with DNA damaging chemotherapy provides a means to prevent therapy-induced bone marrow exhaustion.

Citation Format: Norman E. Sharpless. Transient CDK4/6 inhibition protects hematopoietic progenitors from chemotherapy-induced exhaustion. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Cancer Cell Cycle - Tumor Progression and Therapeutic Response; Feb 28-Mar 2, 2016; Orlando, FL. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(11_Suppl):Abstract nr IA11.

Subtyping sub-Saharan esophageal squamous cell carcinoma by comprehensive molecular analysis

Esophageal squamous cell carcinoma (ESCC) is endemic in regions of sub-Saharan Africa (SSA), where it is the third most common cancer. Here, we describe whole-exome tumor/normal sequencing and RNA transcriptomic analysis of 59 patients with ESCC in Malawi. We observed similar genetic aberrations as reported in Asian and North American cohorts, including mutations of TP53, CDKN2A, NFE2L2, CHEK2, NOTCH1, FAT1, and FBXW7. Analyses for nonhuman sequences did not reveal evidence for infection with HPV or other occult pathogens. Mutational signature analysis revealed common signatures associated with aging, cytidine deaminase activity (APOBEC), and a third signature of unknown origin, but signatures of inhaled tobacco use, aflatoxin and mismatch repair were notably absent. Based on RNA expression analysis, ESCC could be divided into 3 distinct subtypes, which were distinguished by their expression of cell cycle and neural transcripts. This study demonstrates discrete subtypes of ESCC in SSA, and suggests that the endemic nature of this disease reflects exposure to a carcinogen other than tobacco and oncogenic viruses.

Sustained p16INK4a expression is required to prevent IR-induced tumorigenesis in mice

Exposure of murine and human tissues to ionizing radiation (IR) induces the expression of p16^INK4a, a tumor suppressor gene and senescence/aging biomarker. Increased p16^INK4a expression is often delayed several weeks post exposure to IR. In this context, it remains unclear if it occurs to suppress aberrant cellular growth of potentially transformed cells or is simply a result of IR-induced loss of tissue homeostasis. To address this question, we used a conditional p16^INK4a null mouse model and determined the impact of p16^INK4a inactivation long-term post exposure to IR. We found that, in vitro, bone marrow stromal cells exposed to IR enter DNA replication following p16^INK4a inactivation. However, these cells did not resume growth; instead, they mostly underwent cell cycle arrest in G2. Similarly, delayed inactivation of p16^INK4a in mice several weeks post exposure to IR resulted in increased BrdU incorporation and cancer incidence. In fact, we found that the onset of tumorigenesis was similar whether p16^INK4a was inactivated before or after exposure to IR. Overall, our results suggest that IR-induced p16^INK4a dependent growth arrest is reversible in mice and that sustained p16^INK4a expression is necessary to protect against tumorigenesis.

Chemotherapy and Stem Cell Transplantation Increase p16INK4a Expression, a Biomarker of T-cell Aging

The expression of markers of cellular senescence increases exponentially in multiple tissues with aging. Age-related physiological changes may contribute to adverse outcomes in cancer survivors. To investigate the impact of high dose chemotherapy and stem cell transplantation on senescence markers in vivo, we collected blood and clinical data from a cohort of 63 patients undergoing hematopoietic cell transplantation. The expression of p16^INK4a, a well-established senescence marker, was determined in T-cells before and 6 months after transplant. RNA sequencing was performed on paired samples from 8 patients pre- and post-cancer therapy. In patients undergoing allogeneic transplant, higher pre-transplant p16^INK4a expression was associated with a greater number of prior cycles of chemotherapy received (p = 0.003), prior autologous transplantation (p = 0.01) and prior exposure to alkylating agents (p = 0.01). Transplantation was associated with a marked increase in p16^INK4a expression 6 months following transplantation. Patients receiving autologous transplant experienced a larger increase in p16^INK4a expression (3.1-fold increase, p = 0.002) than allogeneic transplant recipients (1.9-fold increase, p = 0.0004). RNA sequencing of T-cells pre- and post- autologous transplant or cytotoxic chemotherapy demonstrated increased expression of transcripts associated with cellular senescence and physiological aging. Cytotoxic chemotherapy, especially alkylating agents, and stem cell transplantation strongly accelerate expression of a biomarker of molecular aging in T-cells.

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Peripheral blood T-cell senescence, as measured by the marker p16^INK4a, increases following autologous or allogeneic HSCT.

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RNAseq of T-cells post- auto HSCT or chemotherapy show increased expression of transcripts associated with senescence.

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Autologous HCT in particular induces a stronger effect on Tcell p16^INK4a expression than any other environmental stimulus tested to date.

Human chronological aging is associated with increased expression of markers of cellular aging (senescence). Cancer chemotherapy can produce frailty syndromes – recipients of cancer treatment may experience physiological changes ordinarily seen in individuals of more advanced chronological age. In our study, we found that a well-known marker of cellular senescence, p16^INK4a, increased in patients following autologous or allogeneic hematopoietic cell transplantation. Expression of p16^INK4a was higher in patients exposed to greater amounts of chemotherapy before transplant and those exposed to specific types of chemotherapy. These findings may ultimately influence clinical decision-making for patients with diseases that are commonly treated with transplantation.

Abstract 4382: Intravital imaging of endogenous BRAFV600E melanoma reveals plasticity of tumor response and resistance to trametinib over time

Although the number of therapies entering clinical trials continues to increase, the success rate for targeted therapy studies is quite low due, in part, to a lack of relevant preclinical models. The use of targeted therapy has become a popular method for cancer treatment against mutant BRAF melanoma, as studies show that clinical use of selective inhibitors against MEK and BRAF extend life expectancy. However, melanoma becomes refractory to treatment. Since the tumor and stromal factors that contribute to drug resistance remain poorly understood, our ability to treat patients with advanced disease remains limited. Current genetically engineered murine (GEM) models in melanoma research have enhanced our understanding of tumor biology and therapeutic response, but fail to mimic tumor progression in clinical settings as most lack spatial and temporal control of endogenous tumor initiation. To better mimic human disease, we have developed a novel tamoxifen application method that reproducibly induces local tumor formation on the mouse ear, and we have incorporated a tdTomato fluorescent reporter allele (tdTomatoLSL) into an existing tamoxifen-inducible GEM model of BRAFV600E/PTEN-null melanoma. The tdTomato allele serves as a visual marker of Cre recombination in endogenous melanocytes and allows disease progression to be followed through macroscopic and multiphoton intravital imaging.

To investigate therapeutic effects at the cell level, we have performed imaging studies of primary tumors before and after treatment with a selective MEK1/2 inhibitor (MEKi), Trametinib, which is a FDA approved therapy for malignant melanoma. Our melanoma induction method enables longitudinal studies of drug response that ultimately give rise to fully resistant tumors (up to 90 days on MEKi). Our studies show that this treatment causes a striking morphological change of the tumor cells as early as 3 days post-treatment. After several weeks of continuous treatment, the remaining tumor cells are highly spatially correlated with bundled collagen structures detected by second harmonic signal, suggesting that cellular milieu strongly influences drug response. Interestingly, our current studies with MEKi suggest that association of tumor cells with collagen fibrils initially provides a protective effect against this drug, however once true resistance emerges, this dependency on extracellular matrix in the tumor stroma diminishes. Furthermore, in parallel with our imaging studies, we have performed molecular analysis of tumor response using Mib/MS and mRNA-seq. By coupling our imaging studies with transcriptome and kinome reprogramming analysis, we hope to identify properties that promote resistance. Using these novel approaches, we have developed a model that enables direct observation of endogenous tumor development, plasticity, and resistance to targeted therapy at the cell level in situ for the first time.

Citation Format: Hailey E. Brighton, Steven Angus, Tao Bo, David Darr, Norman E. Sharpless, Gary L. Johnson, James E. Bear. Intravital imaging of endogenous BRAFV600E melanoma reveals plasticity of tumor response and resistance to trametinib over time. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4382.

Abstract 4499: Integration of targeted RNA sequencing to targeted DNA sequencing for the characterization of clinically relevant variants in a population of thousands of patients treated on clinical trial

Background: Targeted sequencing has become common in the care of some patients with cancer, both for the detection of standard of care clinical mutations as well as in the care of patients with advanced disease who are looking for clinical trials or other non-standard therapies. Many patients have mutations detected, although many variants are of unknown significance, and many patients have no mutations at all. We added RNA targeted sequencing along with DNA targeted sequencing to add utility of targeted sequencing strategy in cancer genomics and assessed the performances of RNA sequencing analysis.

Methods: Genomic sequencing of investigative biomarkers was prospectively offered to selected patients. DNA and RNA libraries were prepared separately from a retrieved archival FFPE tumor sample or a fresh frozen tumor sample from each patient. Relevant targets were enriched by custom designed Agilent SureSelect hybrid capture baits using standard protocols. Samples were sequenced on Illumina HiSeq 2000/2500 platforms. We compared somatic variants detected by DNA alone to those detected by DNA plus RNA using the UNCeqR algorithm and software.

Results: From a population of 2200 patients consented as part of LCCC1108 (NCT01457196), a subset of 300 patients was selected at random for RNA profiling. Selected patients were 7 to 83 years old (median, 54) and the cases included more than 20 cancer types including uterus, breast, ovary, and thyroid etc. And stages of cancers were as follows; I, 34.6%, II, 16.8%, III, 25.2%, and IV, 23.4% respectively. Sequencing of RNA was successful in 90% of specimens using 2.5 ug of RNA. RNA sequencing could detect 97.5% of sequence variants called by DNA sequencing and detect 20% more variants than DNA sequencing. Also 97.9% of variants showed higher mutant allele fraction (MAF) in RNA sequencing than DNA sequencing. We further interrogated the impact of certain classes of mutations on transcript structure and abundance. Specifically, we observed that splice site mutations and indels were associated with detectable alterations in the full length transcripts of their respective genes as well as overall gene abundance, with nonsense and frameshift mutations associated with decreased relative expression of the transcript relative to controls. We also observed that gene amplification of EGFR and ERBB2 was reflected in the RNA sequencing as increased gene expression with statistical significance by Fishers’ exact test (P &lt; 0.05), which suggests that RNA can be used as a surrogate for known protein and nucleic quantitative assays.

Conclusion: Using clinical samples, including relatively small quantities, we were able to confirm that nucleotide variants detected at DNA level leads to significant alteration at the transcription level and to have additional information potentially helpful for better management of cancer patients.

Citation Format: Woochang Lee, Heejoon Jo, Xiaoying Yin, David A. Eberhard, Nirali M. Patel, Michele C. Hayward, Ashley H. Salazar, Joel S. Parker, William Y. Kim, Henry S. Earp, Norman E. Sharpless, David N. Hayes. Integration of targeted RNA sequencing to targeted DNA sequencing for the characterization of clinically relevant variants in a population of thousands of patients treated on clinical trial. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4499.

An oncogenic Ezh2 mutation induces tumors through global redistribution of histone 3 lysine 27 trimethylation

B cell lymphoma and melanoma harbor recurrent mutations in the gene encoding the EZH2 histone methyltransferase (EZH2), but the carcinogenic role of these mutations is unclear. Here we describe a mouse model in which the most common somatic Ezh2 gain-of-function mutation (EZH2(Y646F) in human; Ezh2(Y641F) in mouse) is conditionally expressed. Expression of Ezh2(Y641F) in mouse B cells or melanocytes caused high-penetrance lymphoma or melanoma, respectively. Overexpression of the anti-apoptotic protein Bcl2, but not the oncoprotein Myc, or loss of the tumor suppressor protein p53 (encoded by Trp53 in mice) further accelerated lymphoma progression. Expression of the mutant Braf but not the mutant Nras oncoprotein further accelerated melanoma progression. Although expression of Ezh2(Y641F) globally increased the abundance of trimethylated Lys27 of histone H3 (H3K27me3), it also caused a widespread redistribution of this repressive mark, including a loss of H3K27me3 that was associated with increased transcription at many loci. These results suggest that Ezh2(Y641F) induces lymphoma and melanoma through a vast reorganization of chromatin structure, inducing both repression and activation of polycomb-regulated loci.

Lamellipodia are crucial for haptotactic sensing and response

Haptotaxis is the process by which cells respond to gradients of substrate-bound cues, such as extracellular matrix proteins (ECM); however, the cellular mechanism of this response remains poorly understood and has mainly been studied by comparing cell behavior on uniform ECMs with different concentrations of components. To study haptotaxis in response to gradients, we utilized microfluidic chambers to generate gradients of the ECM protein fibronectin, and imaged the cell migration response. Lamellipodia are fan-shaped protrusions that are common in migrating cells. Here, we define a new function for lamellipodia and the cellular mechanism required for haptotaxis - differential actin and lamellipodial protrusion dynamics lead to biased cell migration. Modest differences in lamellipodial dynamics occurring over time periods of seconds to minutes are summed over hours to produce differential whole cell movement towards higher concentrations of fibronectin. We identify a specific subset of lamellipodia regulators as being crucial for haptotaxis. Numerous studies have linked components of this pathway to cancer metastasis and, consistent with this, we find that expression of the oncogenic Rac1 P29S mutation abrogates haptotaxis. Finally, we show that haptotaxis also operates through this pathway in 3D environments.

Germline Analysis from Tumor-Germline Sequencing Dyads to Identify Clinically Actionable Secondary Findings

PURPOSE

To evaluate germline variants in hereditary cancer susceptibility genes among unselected cancer patients undergoing tumor-germline sequencing.

EXPERIMENTAL DESIGN

Germline sequence data from 439 individuals undergoing tumor-germline dyad sequencing through the LCCC1108/UNCseq™ (NCT01457196) study were analyzed for genetic variants in 36 hereditary cancer susceptibility genes. These variants were analyzed as an exploratory research study to determine whether pathogenic variants exist within the germline of patients undergoing tumor-germline sequencing. Patients were unselected with respect to indicators of hereditary cancer predisposition.

RESULTS

Variants indicative of hereditary cancer predisposition were identified in 19 (4.3%) patients. For about half (10/19), these findings represent new diagnostic information with potentially important implications for the patient and their family. The others were previously identified through clinical genetic evaluation secondary to suspicion of a hereditary cancer predisposition. Genes with pathogenic variants included ATM, BRCA1, BRCA2, CDKN2A, and CHEK2 In contrast, a substantial proportion of patients (178, 40.5%) had Variants of Uncertain Significance (VUS), 24 of which had VUS in genes pertinent to the presenting cancer. Another 143 had VUS in other hereditary cancer genes, and 11 had VUS in both pertinent and nonpertinent genes.

CONCLUSIONS

Germline analysis in tumor-germline sequencing dyads will occasionally reveal significant germline findings that were clinically occult, which could be beneficial for patients and their families. However, given the low yield for unexpected germline variation and the large proportion of patients with VUS results, analysis and return of germline results should adhere to guidelines for secondary findings rather than diagnostic hereditary cancer testing. Clin Cancer Res; 22(16); 4087-94. ©2016 AACRSee related commentary by Mandelker, p. 3987.

IL2 Inducible T-cell Kinase, a Novel Therapeutic Target in Melanoma

PURPOSE

IL2 inducible T-cell kinase (ITK) promoter CpG sites are hypomethylated in melanomas compared with nevi. The expression of ITK in melanomas, however, has not been established and requires elucidation.

EXPERIMENTAL DESIGN

An ITK-specific monoclonal antibody was used to probe sections from deidentified, formalin-fixed paraffin-embedded tumor blocks or cell line arrays and ITK was visualized by IHC. Levels of ITK protein differed among melanoma cell lines and representative lines were transduced with four different lentiviral constructs that each contained an shRNA designed to knockdown ITK mRNA levels. The effects of the selective ITK inhibitor BI 10N on cell lines and mouse models were also determined.

RESULTS

ITK protein expression increased with nevus to metastatic melanoma progression. In melanoma cell lines, genetic or pharmacologic inhibition of ITK decreased proliferation and migration and increased the percentage of cells in the G0-G1 phase. Treatment of melanoma-bearing mice with BI 10N reduced growth of ITK-expressing xenografts or established autochthonous (Tyr-Cre/Pten(null)/Braf(V600E)) melanomas.

CONCLUSIONS

We conclude that ITK, formerly considered an immune cell-specific protein, is aberrantly expressed in melanoma and promotes tumor development and progression. Our finding that ITK is aberrantly expressed in most metastatic melanomas suggests that inhibitors of ITK may be efficacious for melanoma treatment. The efficacy of a small-molecule ITK inhibitor in the Tyr-Cre/Pten(null)/Braf(V600E) mouse melanoma model supports this possibility.

Tenofovir/emtricitabine metabolites and endogenous nucleotide exposures are associated with p16(INK4a) expression in subjects on combination therapy

BACKGROUND

HIV may amplify immunological, physiological and functional changes of ageing. We determined associations of frailty phenotype, a T-cell senescence marker (p16(INK4a) expression), age and demographics with exposures of the intracellular metabolites (IM) and endogenous nucleotides (EN) of tenofovir/emtricitabine (TFV/FTC), efavirenz (EFV), atazanavir (ATV) and ritonavir (RTV).

METHODS

Plasma and peripheral blood mononuclear cell samples for drug, IM and EN concentrations were collected at four time points in HIV+ adults receiving TFV/FTC with EFV or ATV/RTV. Subjects underwent frailty phenotyping and p16(INK4a) expression analysis. Non-compartmental analysis generated an area under the curve (AUC) for each analyte. Spearman rank correlation and Kruskal-Wallis tests were used to assess associations between AUC, demographics and ageing markers, adjusting for multiple comparisons with the Holm procedure.

RESULTS

Subjects (n=79) ranged in age from 22-73 years (median 48 years); 48 were African-American, 24 were female, 54 received EFV. Three subjects (range 51-60 years) demonstrated frailty, with 17 subjects (range 26-60 years) demonstrating pre-frailty. Negative associations were observed between p16(INK4a) expression and each of FTC-triphosphate (r=-0.45), deoxyadenosine triphosphate (dATP; r=-0.47) and deoxycytidine triphosphate (dCTP; r=-0.57) AUCs (P-values <0.02). TFV and FTC AUCs were larger among subjects with lower renal function or higher chronological age (P-values ≤0.05). No associations were observed for EFV, ATV or RTV AUCs.

CONCLUSIONS

Associations of IM/EN exposure and p16(INK4a) expression observed here suggest that senescence may alter drug phosphorylation, metabolism or transport. This finding warrants further mechanistic study to ensure optimal treatment in the ageing HIV+ population. Clinicaltrials.gov NCT01180075.

Abstract B39: Multitarget approach against PI3K, Aurora kinase, and BRD4 leads to improved antitumor activity in Myc-overexpressing lymphoma cells

Background: Myc has proven extremely difficult to target therapeutically. Therefore, we hypothesized that optimal inhibition of several key targetable pathways involved in Myc signaling could overcome this long-standing problem. We identified phosphoinositide 3-kinase (PI3K), aurora kinase (Aurk), and bromodomain protein (BRD)4 as the primary therapeutic targets to counteract Myc deregulation based on strong evidence that these pathways are essential for tumor maintenance in Myc-driven malignancies.

Methods: Cytotoxicity assays using MTS and trypan blue were used to compare levels of drug sensitivity in lymphoma cell lines with high and low Myc mRNA expression. Apoptosis and cell cycle assays were performed using Annexin V and Propidium Iodide staining. Murine xenograft models were used to assess the efficacy and tolerability of single vs. combined inhibition.

Results: Myc-overexpressing Burkitt lymphoma (Raji) cells were treated with various concentrations of small molecule inhibitors against PI3K (BEZ-235), Aurk (MLN-8237), or BRD4 (I-BET-151) for 48 to 72 hours and cell viability was evaluated. BEZ-235, MLN-8237, and I-BET-151 inhibited cell growth individually with IC-50 of 30 nM, 10 nM, and 650 nM, respectively. Dual treatment with BEZ-235/MLN-8237, BEZ-235/I-BET-151, or MLN-8237/I-BET-151 induced more significant cell growth inhibition as compared to treatment with the single agent alone. The combination index (CI) values were less than 1 at various drug concentrations, indicating that different combinations of BEZ-235, MLN-8237, and I-BET-151 were synergistic in terms of inhibitory effect on tumor cell viability. Superior activity of the dual inhibition was also noted in other Myc-overexpressing lymphoma cells, including Ramos and SUDHL4. Combination treatments also increased apoptosis and induced more pronounced cell cycle arrest compared to the single agent treatment alone. We then analyzed protein expression by Western blot in Myc-overexpressing cells treated with various combinations of BEZ-235, MLN-8237, and I-BET-151. Treatment with BEZ-235 in Myc-overexpressing lymphoma cells resulted in reduced phosphorylated levels of the downstream effector RPS6K, which promotes protein translation and proliferation. MLN-8237 reduced the expression of p-HisH3 and p-Aurk while increasing the expression of p-S6K. Treatment with I-BET-151 resulted in significant reduction of Myc expression. Combined treatments had minimal impact on protein expression patterns compared to individual treatments, and the synergistic effect was independent of depletion of cytoplasmic levels of Myc. Lastly, athymic nude mice bearing Ramos lymphoma xenografts were treated with BEZ-235, MLN-8237, I-BET-151, and various dual-combinations of each agent. The mean tumor volumes in mice treated with negative control, BEZ-235, I-BET-151, and MLN-8237 as single agents were 3480, 2364, 2320, and 671 mm3, respectively, at Day 28. Mice treated with BEZ-235/I-BET-151, MLN-8237/I-BET-151, and BEZ-235/MLN-8237 combinations had mean tumor volumes of 1709, 461, and 166 mm3, respectively, at Day 28. The survival rates for mice treated with negative control, BEZ-235, I-BET-151, and MLN-8237 as single agents were 0%, 10%, 10%, and 70%, respectively, at Day 35. The combination of BEZ-235 and MLN-8237 was associated with significant toxicity with 60% of mice dying from weight loss and failure to thrive despite tumor regression. Mice treated with the MLN-8237 and I-BET-151 combination demonstrated the best survival rate of 100% at Day 35.

Conclusion: Our data demonstrated that Myc-overexpressing tumors can be successfully targeted by inhibiting kinases associated with Myc-signaling. Specifically, MLN-8237, a small molecule inhibitor against AURK, induced apoptosis of Myc-overexpressing tumor cells in vitro and showed the most promising anti-tumor activity in mice bearing Myc-overexpressing lymphoma, especially when combined with I-BET-151, a BRD4 inhibitor.

Citation Format: Steven I. Park, Carolina P. Lin, Michael Foote, Trevor Parton, David B. Darr, Daniel Roth, Aadra P. Bhatt, Dirk P. Dittmer, Norman E. Sharpless, Blossom Damania. Multitarget approach against PI3K, Aurora kinase, and BRD4 leads to improved antitumor activity in Myc-overexpressing lymphoma cells. [abstract]. In: Proceedings of the AACR Special Conference on Myc: From Biology to Therapy; Jan 7-10, 2015; La Jolla, CA. Philadelphia (PA): AACR; Mol Cancer Res 2015;13(10 Suppl):Abstract nr B39.

Abstract 941: G1T28-1, a novel CDK4/6 inhibitor, protects murine hematopoietic stem and progenitor cells from cytotoxic chemotherapy

G1T28-1 is a clinical stage, small molecule inhibitor of cyclin dependent kinases 4 and 6 (CDK4/6). Hematopoietic stem and progenitor cells (HSPC) require CDK4/6 for proliferation, allowing the transient arrest of HSPC in the G1 phase of the cell cycle by CDK4/6 inhibition. The CDK4/6 transient arrest may reduce the sensitivity of HSPC to DNA damaging chemotherapies by limiting G1 to S-phase progression in the setting of unrepaired DNA damage. A reduction in chemotherapy-induced HSPC death would in turn reduce chemotherapy-induced myelosuppression (CIM), the major dose-limiting toxicity of most cytotoxic anti-cancer agents. G1T28-1 is highly potent, exhibits exquisite selectivity, and has favorable pharmacology allowing the induction of a predictable and well-defined transient arrest of HSPC with greater uniformity and distinct profile from the arrest induced by less potent and selective CDK4/6 inhibitors.

To characterize HSPC inhibition induced by G1T28-1 treatment, we studied the compound's pharmacodynamic properties in mice. Murine HSPC proliferation was measured in vivo using EdU incorporation. This work showed that G1T28-1 induces a significant, rapid and reversible G1 arrest in all early hematopoietic lineages in a dose-dependent manner. Above a determined threshold dose, higher doses do not augment the percentage of specific HSPC fractions in G1, but instead extend the duration of the block of G1 to S-phase traversal of these populations. The degree of G1 arrest differed for specific HSPC fractions, multipotent progenitors, and early lymphoid progenitors being more sensitive than populations of early myeloid and erythroid progenitors.

To determine the ability of G1T28-1 to ameliorate CIM, we assessed the effect of concomitant G1T28-1 administration in a well-characterized murine model of 5FU-induced myelosuppression. A single dose of G1T28-1 given 30-minutes prior to 5FU provided multilineage protection resulting in a more rapid recovery of complete blood counts (CBCs) compared to animals who received 5FU + vehicle. This effect persisted through multiple cycles of 5FU. After four cycles of 5FU, even at count recovery, the CBC's in animals treated with vehicle + 5FU were significantly worse compared to cycle one, whereas this chronic myelosuppressive effect was completely ameliorated in animals that received G1T28-1 prior to each 5FU dose.

In conclusion, we have demonstrated that G1T 28-1 is a highly potent CDK4/6 inhibitor that causes robust and transient inhibition in a broad range of HSPC. Arrest at the time of 5FU administration significantly lessens CIM; benefitting all hematopoietic lineages and attenuating the acute myelosuppression of each cycle of chemotherapy as well as reducing a chronic reduction in peripheral blood counts caused by repeated, serial chemotherapy dosing.

Citation Format: Jessica A. Sorrentino, Shenghui He, John E. Bisi, Patrick J. Roberts, Jay C. Strum, Norman E. Sharpless. G1T28-1, a novel CDK4/6 inhibitor, protects murine hematopoietic stem and progenitor cells from cytotoxic chemotherapy. [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 941. doi:10.1158/1538-7445.AM2015-941

Abstract CT133: The impact of gene panel sequencing on clinical care in patients with cancer

Introduction: Analysis of tumors for somatic mutations of individual cancer-associated genes has proven valuable in defined clinical scenarios, but the incorporation of multi-gene panels into routine clinical use has proven complex. Here, we describe UNCseq™, a single-institution experience evaluating how care providers use testing of a 247 gene panel in a study of &gt;1400 patients with cancer.

Approach: Somatic and germline DNA was captured and sequenced in the context of an IRB-approved clinical trial, with somatic events (point mutations (PM) and copy number alterations (CNA)) determined using an institution-designed bioinformatic pipeline. Mutations deemed ‘actionable’ by a molecular tumor board (MTB) were confirmed in a CLIA-compliant manner, and reported to the patient's caregiver. The clinical use of sequencing information by caregivers was determined through follow-up questionnaire.

Results: Somatic events were noted in 444 of 718 (62%) patients as of 11/30/2014 (79% PM/21% CNA). Although 247 genes were analyzed, reports were only made regarding a minority (77) of genes. PMs of PIK3CA/PTEN/KRAS/BRAF/PIK3R1 and CNAs of CCDN1/EGFR/ERBB2/FGFR1 were the most commonly reported events. Non-canonical (71%) events were observed more frequently than canonical events (29%, p&lt;0.05). Among 30 tumor types, events were most commonly noted in uterus, (n = 75, 17%) colorectal, (n = 37, 8%) and bladder (n = 31, 7%), and most infrequently noted in kidney (n = 13, 3%) and soft-tissue sarcoma (n = 7, 2%). Healthcare providers reported changes in clinical care based on mutations discovered through UNCseq™ in 15% of patients. Caregivers reported changes primarily in therapy (e.g. trial enrollment, prescription of targeted kinase inhibitors) and prognosis (e.g. HPV status put the patient in a more favorable prognostic category) based on UNCseq™ results. Care was not changed in many patients, despite their tumor harboring an actionable event(s), because of: i) inappropriate clinical stage, ii) patient dying prior to or soon after results, iii) inability to procure indicated therapy because of payment issues or sub-optimal clinical trials design or iv) patient lost to follow up. The cost is comparable to other molecular testing such as fluorescence in-situ hybridization of HER2 done clinically.

Conclusions: An analysis of 247 genes for somatic mutations in patients with advanced cancer is cost-effective and feasible, and can lead to significant changes in clinical care in a minority of patients. Non-canonical events are common, and determination of events for reporting requires pathological review by an MTB. Patients with advanced disease and certain tumor types benefit most from cancer panel sequencing. A majority of patients harbor actionable events, although changes in therapeutic care are less frequent largely because of practical considerations related to care delivery. These data suggest a need to re-structure clinical trials in the era of modern genomic testing.

Citation Format: David Neil Hayes, Juneko E. Grilley-Olson, David A. Eberhard, Nirali M. Patel, Joel S. Parker, Karen E. Weck, William Y. Kim, Michele C. Hayward, H. Shelton Earp, Norman E. Sharpless. The impact of gene panel sequencing on clinical care in patients with cancer. [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 CT133. doi:10.1158/1538-7445.AM2015-CT133