Abstract 3302: The molecular landscape of oncogenic signaling pathways in The Cancer Genome Atlas

Over the past decade, The Cancer Genome Atlas (TCGA) has profiled more than 11,000 tumors spanning 33 distinct cancer types. The TCGA PanCanAtlas is a collaborative project by the TCGA Research Network that aims to address relevant overarching questions in oncology based on a cross-cancer analysis of the full, uniformly reprocessed TCGA data set. Here, we present results from our analysis of genetic alterations in mitogenic signaling pathways across cancer.

Genetic alterations in signaling pathways that control cell cycle progression, apoptosis, and cell growth are common hallmarks of cancer, but the extent, mechanisms, and co-occurrence of alterations in these pathways differ between individual tumors and tumor types. Using mutations and copy-number changes in 9,125 tumor samples profiled by TCGA, we analyzed the mechanisms and patterns of alterations in 10 canonical pathways: cell cycle, Hippo, Myc, Notch, beta-catenin / WNT, PI-3-Kinase / Akt, receptor-tyrosine kinase / RAS / MAP-kinase signaling, TP53, and TGF-beta signaling, as well as oxidative stress response. For each of these pathways, we propose an expert-curated description (or “template”) that includes the relevant (altered) genes and the connections between them, as well as a detailed catalogue of the driver mutations and copy number changes with known oncogenic relevance. We provide a high-level map of pathway alteration frequencies across tissues and relevant cancer subtypes as well as detailed frequencies of alteration at the gene level for each individual pathway. We also investigate relationships of co-occurrence and mutual exclusivity across pathways and evaluate therapeutic implications, including drug combinations. Forty-nine percent of tumors had at least one potentially targetable alteration in the evaluated pathways, and 31% of tumors had multiple targetable alterations, making them candidates for combination therapy.

Our work delineates the full landscape of oncogenic alterations in mitogenic signaling pathways across cancer, and the pathway templates as well as the richly annotated data set that we provide will constitute an invaluable public resource for future use by the cancer genomics and precision oncology communities.

Citation Format: Francisco Sanchez-Vega, Marco Mina, Joshua Armenia, Walid K. Chatila, Augustin Luna, Konnor La, Sofia Dimitriadoy, David L. Liu, Havish S. Kantheti, Zachary Heins, Angelica Ochoa, Benjamin Gross, Jianjiong Gao, Hongxin Zhang, Ritika Kundra, Cyriac Kandoth, Istemi Bahceci, Leonard Dervishi, Ugur Dogrusoz, Wanding Zhou, Hui Shen, Peter W. Laird, Alice H. Berger, Trever G. Bivona, Alexander J. Lazar, Gary Hammer, Thomas Giordano, Lawrence Kwong, Grant McArthur, Chenfei Huang, Mitchell J. Frederick, Frank McCormick, Matthew Meyerson, The Cancer Genome Atlas Research Network, Eliezer Van Allen, Andrew D. Cherniack, Giovanni Ciriello, Chris Sander, Nikolaus Schultz. The molecular landscape of oncogenic signaling pathways in The Cancer Genome Atlas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3302.

Abstract 5520: Oncogenic RTK signaling inhibits Spred1/NF1 to sustain constitutive Ras/MAPK signaling

Spred proteins negatively regulate Ras/MAPK signaling following growth factor stimulation. Inhibition of Ras primary occurs through Spreds ability to bind and localize NF1, a RasGAP and major tumor suppressor, to the plasma membrane. Spred1 and NF1 loss-of-function mutations occur across multiple cancer types including non-small cell lung carcinoma, glioblastoma, melanoma, stomach carcinoma, and uterine carcinosarcoma. Here we demonstrate that oncogenic RTK signaling leads to phosphorylation of Spred1(S105) in the EVH domain, which disrupts Spred1-NF1 binding and function. Phosphomimetic Spred1 is unable to suppress Ras-GTP following growth factor stimulation and cancer cell proliferation. The Spred1(S105) kinase is likely to be a CDK based on in vitro kinase and in vivo cell line assays. Our findings provide one potential mechanism by which oncogenic RTK signaling disrupts negative feedback to sustain constitutive Ras signaling. Furthermore, this work may elucidate a novel therapeutic target for restoring NF1-mediated inhibition of Ras.

Citation Format: Evan Markegard, Ellen L. Mercado, Pau Castel, Jillian Silva, Jacqueline Galeas, Kathy Li, Anatoly Urisman, Frank McCormick. Oncogenic RTK signaling inhibits Spred1/NF1 to sustain constitutive Ras/MAPK signaling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5520.

Abstract 3104: Establishment of an oral tongue squamous cell carcinoma cell line from a never-smoking patient

(Objective) The rising incidence of oral tongue squamous cell carcinoma (OTSCC) in patients who have never smoked and the paucity of knowledge of its biological behavior prompted us to develop a new cell line originating from a never-smoker. (Materials and methods) Fresh tumor tissue of keratinizing OTSCC was collected from a 44-year-old woman who had never smoked. Serum-free media with a low calcium concentration were used in cell culture, and a multifaceted approach was taken to verify and characterize the cell line, designated UCSF-OT-1109.(Results) UCSF-OT-1109 was authenticated by STR DNA fingerprint analysis, presence of an epithelial marker EpCAM, absence of human papilloma virus (HPV) DNA, and SCC-specific microscopic appearance. Sphere-forming assays and mouse xenografts supported its tumorigenic potential. Spectral karyotype (SKY) analysis revealed numerical and structural chromosomal abnormalities. Whole-exome sequencing (WES) identified 46 non-synonymous and 13 synonymous somatic single-nucleotide polymorphisms (SNPs) and one frameshift deletion in the coding regions. Specifically, mutations of CDKN2A, TP53, SPTBN5, NOTCH2, and FAM136A were found in the databases. Copy number aberration (CNA) analysis revealed that the cell line loses chromosome 3p and 9p, but lacks amplification of 3q and 11q (as does HPV-negative, smoking-unrelated OTSCC). It also exhibits four distinctive focal amplifications in chromosome 19p, containing 131 genes without SNPs. Particularly, 52 genes showed >3- to 4-fold amplification and could be potential oncogenic drivers.(Conclusion) We have successfully established a novel OTSCC cell line from a never-smoking patient. UCSF-OT-1109 is potentially a robust experimental model of OTSCC in never-smokers.

Citation Format: Steven J. Wang, Saurabh Asthana, Annemieke van Zante, Adam B. Olshen, Frank McCormick, Osamu Tetsu. Establishment of an oral tongue squamous cell carcinoma cell line from a never-smoking patient [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3104.

Abstract 798: Pathway-directed high-throughput drug screen identifies PI3K inhibitors that synergistically potentiate antitumor activity of HDAC inhibitors in cutaneous T-cell lymphoma

Background: Cutaneous T-cell lymphoma (CTCL) represents a type of malignancy in the skin that is incurable. Recent studies demonstrated dysregulation of several signaling pathways in CTCL, including PI3K/AKT, JAK/STAT, and NFκB pathways. We performed a high-throughput drug screen to determine the potential of novel agents targeting these pathways for the treatment of CTCL.

Methods: We compiled a library of 94 compounds targeting pathways known to be relevant in cancer biology, such as kinases involved in growth factor receptor signaling, HDACs, proteasome, DNA repair and regulators of apoptosis. The compounds were screened for antiproliferative activity against four CTCL cell lines in high-throughput proliferation assays. PI3K inhibitors were selected from the “hits” of the screen and were further studied in xenograft models of CTCL and in primary T-cell lymphomas cells from patients. To examine which PI3K isoform mediates antitumor effect in CTCL, isoform-specific siRNAs were used to knock down each isoforms as well as the combination of doublet isoforms. Based on this experiment, we tested antitumor activity of isoform-specific inhibitors. Promising candidates were also tested in combination assays using a matrix block method designed to detect synergistic activities.

Results: From the high-throughput screen, we identified 14 compounds with antiproliferative activity in CTCL, including multiple inhibitors of the PI3K pathway. Validation assays confirmed the class effect of PI3K inhibitors in growth inhibition. From this class, a pan-PI3K inhibitor BKM120 was selected for in vivo studies. In a xenograft model of CTCL, BKM120 exhibited striking antitumor activity measured by a marked suppression of tumor growth and prolonged survival of tumor-bearing mice compared with vehicle control. To investigate which isoform of the PI3K mediates the antitumor effect in CTCL, we performed isoform-specific siRNA assays and demonstrated that knocking down isoform ð exhibited the most potent growth inhibition. Copanlisib targets α and δ isoforms of PI3K and is newly approved by the FDA for low-grade B-cell lymphoma. We demonstrated that copanlisib exhibits potent antiproliferation activity in CTCL cell lines. Furthermore, combination of copanlisib and LBH, a HDAC inhibitor, display synergistic antiproliferative effects across a broad dose gradient for each agent.

Conclusion: A pan-PI3k inhibitor, BKM120, is highly active in CTCL cell lines and exnograft models. Inhibition of Isoform δ exhibits the most potent growth inhibition. Furthermore, an isoform-specific inhibitor, copanlisib, synergistically potentiates the effect of HDAC inhibitors against CTCL. These are highly promising approaches for the treatment of CTCL and warrant clinical investigation.

Citation Format: Chi-Heng Wu, Chen-Yen Yang, Taha Rakhshandhroo, Laura Pincus, Sourav Bandyopadhyay, Frank McCormick, Weiyun Ai. Pathway-directed high-throughput drug screen identifies PI3K inhibitors that synergistically potentiate antitumor activity of HDAC inhibitors in cutaneous T-cell lymphoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 798.

Direct molecular dissection of tumor parenchyma from tumor stroma in tumor xenograft using mass spectrometry-based glycoproteomics

The most widely used cancer animal model is the human-murine tumor xenograft. Unbiased molecular dissection of tumor parenchyma versus stroma in human-murine xenografts is critical for elucidating dysregulated protein networks/pathways and developing therapeutics that may target these two functionally codependent compartments. Although antibody-reliant technologies (e.g., immunohistochemistry, imaging mass cytometry) are capable of distinguishing tumor-proper versus stromal proteins, the breadth or extent of targets is limited. Here, we report an antibody-free targeted cross-species glycoproteomic (TCSG) approach that enables direct dissection of human tumor parenchyma from murine tumor stroma at the molecular/protein level in tumor xenografts at a selectivity rate presently unattainable by other means. This approach was used to segment/dissect and obtain the protein complement phenotype of the tumor stroma and parenchyma of the metastatic human lung adenocarcinoma A549 xenograft, with no need for tissue microdissection prior to mass-spectrometry analysis. An extensive molecular map of the tumor proper and the associated microenvironment was generated along with the top functional N-glycosylated protein networks enriched in each compartment. Importantly, immunohistochemistry-based cross-validation of selected parenchymal and stromal targets applied on human tissue samples of lung adenocarcinoma and normal adjacent tissue is indicative of a noteworthy translational capacity for this unique approach that may facilitate identifications of novel targets for next generation antibody therapies and development of real time preclinical tumor models.

Oncogenic Signaling Pathways in The Cancer Genome Atlas

Genetic alterations in signaling pathways that control cell-cycle progression, apoptosis, and cell growth are common hallmarks of cancer, but the extent, mechanisms, and co-occurrence of alterations in these pathways differ between individual tumors and tumor types. Using mutations, copy-number changes, mRNA expression, gene fusions and DNA methylation in 9,125 tumors profiled by The Cancer Genome Atlas (TCGA), we analyzed the mechanisms and patterns of somatic alterations in ten canonical pathways: cell cycle, Hippo, Myc, Notch, Nrf2, PI-3-Kinase/Akt, RTK-RAS, TGFβ signaling, p53 and β-catenin/Wnt. We charted the detailed landscape of pathway alterations in 33 cancer types, stratified into 64 subtypes, and identified patterns of co-occurrence and mutual exclusivity. Eighty-nine percent of tumors had at least one driver alteration in these pathways, and 57% percent of tumors had at least one alteration potentially targetable by currently available drugs. Thirty percent of tumors had multiple targetable alterations, indicating opportunities for combination therapy.

c-Raf in KRas Mutant Cancers: A Moving Target

Therapies for KRas cancers remain a major clinical need. In the current issue of Cancer Cell, Sanclemente and coworkers in Mariano Barbacid's group validate c-Raf as a prime target for these cancers. c-Raf ablation caused regression of advanced KRas^G12V/Trp53 tumors, without obvious systemic toxicity and without affecting MAPK signaling.

A concise evidence-based physical examination for diagnosis of acromioclavicular joint pathology: a systematic review

OBJECTIVES

The clinical examination of the shoulder joint is an undervalued diagnostic tool for evaluating acromioclavicular (AC) joint pathology. Applying evidence-based clinical tests enables providers to make an accurate diagnosis and minimize costly imaging procedures and potential delays in care. The purpose of this study was to create a decision tree analysis enabling simple and accurate diagnosis of AC joint pathology.

METHODS

A systematic review of the Medline, Ovid and Cochrane Review databases was performed to identify level one and two diagnostic studies evaluating clinical tests for AC joint pathology. Individual test characteristics were combined in series and in parallel to improve sensitivities and specificities. A secondary analysis utilized subjective pre-test probabilities to create a clinical decision tree algorithm with post-test probabilities.

RESULTS

The optimal special test combination to screen and confirm AC joint pathology combined Paxinos sign and O'Brien's Test, with a specificity of 95.8% when performed in series; whereas, Paxinos sign and Hawkins-Kennedy Test demonstrated a sensitivity of 93.7% when performed in parallel. Paxinos sign and O'Brien's Test demonstrated the greatest positive likelihood ratio (2.71); whereas, Paxinos sign and Hawkins-Kennedy Test reported the lowest negative likelihood ratio (0.35).

CONCLUSION

No combination of special tests performed in series or in parallel creates more than a small impact on post-test probabilities to screen or confirm AC joint pathology. Paxinos sign and O'Brien's Test is the only special test combination that has a small and sometimes important impact when used both in series and in parallel. Physical examination testing is not beneficial for diagnosis of AC joint pathology when pretest probability is unequivocal. In these instances, it is of benefit to proceed with procedural tests to evaluate AC joint pathology. Ultrasound-guided corticosteroid injections are diagnostic and therapeutic. An ultrasound-guided AC joint corticosteroid injection may be an appropriate new standard for treatment and surgical decision-making.

LEVEL OF EVIDENCE

II - Systematic Review.

Dual gene activation and knockout screen reveals directional dependencies in genetic networks

Understanding the direction of information flow is essential for characterizing how genetic networks affect phenotypes. However, methods to find genetic interactions largely fail to reveal directional dependencies. We combine two orthogonal Cas9 proteins from Streptococcus pyogenes and Staphylococcus aureus to carry out a dual screen in which one gene is activated while a second gene is deleted in the same cell. We analyse the quantitative effects of activation and knockout to calculate genetic interaction and directionality scores for each gene pair. Based on the results from over 100,000 perturbed gene pairs, we reconstruct a directional dependency network for human K562 leukemia cells and demonstrate how our approach allows the determination of directionality in activating genetic interactions. Our interaction network connects previously uncharacterised genes to well-studied pathways and identifies targets relevant for therapeutic intervention.

Abstract B098: GPX4 is a broadly shared gene vulnerability among residual tumors

The heterogeneity of tumor cells underlies acquired drug resistance to a variety of therapeutic approaches. The advent of next-generation sequencing has facilitated a wave of studies identifying genetic mutations, which may be preexisting or acquired during treatment, that drive drug resistance and tumor relapse. However, it has recently become clear that non-mutational mechanisms of drug resistance, such as cell state switching from an epithelial to mesenchymal state, can also play an important role in the process of acquired drug resistance. Non-mutational drug resistance is relatively poorly understood and represents fertile ground for the discovery of novel therapeutic targets. Drug-tolerant “persister” cells are an experimental model of non-mutational cancer drug resistance in which small fractions (<5%) of cells within cancer cell lines survive cytotoxic drug exposure despite lacking resistance-conferring mutations. These residual surviving persister cells occupy a reversible quiescent state with a unique chromatin landscape. Persister cells regrow and become resensitized to drug, reminiscent of clinical observations of secondary responses from retreatment after a drug holiday. Persister cells also eventually obtain genetic mutations and reenter the cell cycle after weeks or months of continuous drug exposure, modeling the process of acquisition of resistance-conferring genetic mutations in patients during treatment. Here, we report on our efforts to identify a widely shared gene vulnerability in persister cells that transcends tissue lineage, genetic mutation background, and drug treatment regimens. Through a functional genomics approach entailing RNA-seq, pathway analysis, and a focused chemical inhibitor screen, we have identified a gene, glutathione peroxidase 4 (GPX4), that is specifically essential to persister cells. When GPX4 is chemically inhibited or genetically ablated, persister cells across a wide range of tissue lineages undergo ferroptosis–a recently discovered mechanism of non-apoptotic caspase-independent cell death. Ferroptosis occurs when lipid peroxides accumulate in cells, and as the only human enzyme capable of scavenging lipid peroxides, GPX4 plays a key role in preventing ferroptosis. Compared to drug-naïve parental cells or nontransformed normal cells, persister cells are strongly differentially sensitive to GPX4 inhibition and ferroptosis. This sensitivity is the result of a disabled antioxidant program in persister cells marked by a global downregulation of antioxidant genes including Nrf2 targets, and decreased levels of reducing cofactors glutathione and NADPH. As a first step toward raising GPX4 as a promising preclinical drug target in vivo, we also show that targeting GPX4 in residual melanoma xenograft tumors prevents tumor relapse. Therefore, GPX4 is an extremely promising drug target that may be exploited to prevent tumor relapse across a wide spectrum of tumor types and drug treatments.

Citation Format: Matthew J. Hangauer, Vasanthi S. Viswanathan, Matthew J. Ryan, Dhruv Bole, John K. Eaton, Alexandre Matov, Jacqueline Galeas, Harshil D. Dhruv, Michael E. Berens, Stuart L. Schreiber, Frank McCormick, Michael T. McManus. GPX4 is a broadly shared gene vulnerability among residual tumors [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr B098.

Abstract IA17: New ways of targeting Ras

Activating K-Ras mutations occur frequently in many cancers, and account for about one million cancer deaths per year worldwide. Currently, no therapies exist that target K-Ras directly, and K-Ras cancers are very difficult to treat. Indeed, they are excluded from treatment with targeted agents such as tarceva and vemurafenib. The K-Ras protein is a member of a large family of related proteins, of which H-Ras and N-Ras are the closest relatives. Ablation of all three Ras genes is likely to be toxic, as these proteins are essential in most signaling transduction pathways. We therefore need to target the mutant oncoprotein itself, or target K-Ras, without affecting H-Ras or N-Ras. The striking similarity of these proteins makes this task challenging, together with the fact that the K-Ras gene expresses two splice variants, K-Ras 4A and K-Ras 4B, each of which can contribute to cancer. Nevertheless, differences do exist between these proteins, and ways in which these can be exploited will be discussed. One approach takes advantage of unique properties of K-Ras 4B, the other targets an amino acid that is shared between K-Ras isoforms, but is not present in H-Ras or N-Ras, or other members of the Ras family. K-Ras processing can be prevented by compounds that block the CAAX box cysteine. We have identified compounds that interact covalently with this cysteine and block prenylation by farnesyl transferase or geranylgeranyl transferase. These compounds reduce expression of K-Ras in cells and have specificity for K-Ras relative to H-Ras and N-Ras and represent another approach to targeting K-Ras specifically. We have also used new biophysical methods to target K-Ras, including second harmonic generation. This method detects small allosteric changes in proteins, and thus allows identification of small molecules that bind to K-Ras at novel allosteric sites. Drug resistance is likely to be a problem with Ras inhibitors, as it is for all types of cancer therapies. We have identified an approach to killing drug resistant cells that appears effective against a wide range of resistance mechanisms. This was achieved by targeting persister cells that survive targeted agents, but have unique properties that make them vulnerable to attack. The implications of this new strategy will be discussed.

Citation Format: Frank McCormick. New ways of targeting Ras [abstract]. In: Proceedings of the AACR International Conference: New Frontiers in Cancer Research; 2017 Jan 18-22; Cape Town, South Africa. Philadelphia (PA): AACR; Cancer Res 2017;77(22 Suppl):Abstract nr IA17.

Drug-tolerant persister cancer cells are vulnerable to GPX4 inhibition

Acquired drug resistance prevents cancer therapies from achieving stable and complete responses. Emerging evidence implicates a key role for non-mutational drug resistance mechanisms underlying the survival of residual cancer 'persister' cells. The persister cell pool constitutes a reservoir from which drug-resistant tumours may emerge. Targeting persister cells therefore presents a therapeutic opportunity to impede tumour relapse. We previously found that cancer cells in a high mesenchymal therapy-resistant cell state are dependent on the lipid hydroperoxidase GPX4 for survival. Here we show that a similar therapy-resistant cell state underlies the behaviour of persister cells derived from a wide range of cancers and drug treatments. Consequently, we demonstrate that persister cells acquire a dependency on GPX4. Loss of GPX4 function results in selective persister cell ferroptotic death in vitro and prevents tumour relapse in mice. These findings suggest that targeting of GPX4 may represent a therapeutic strategy to prevent acquired drug resistance.

Evaluation of the selectivity and sensitivity of isoform- and mutation-specific RAS antibodies

There is intense interest in developing therapeutic strategies for RAS proteins, the most frequently mutated oncoprotein family in cancer. Development of effective anti-RAS therapies will be aided by the greater appreciation of RAS isoform-specific differences in signaling events that support neoplastic cell growth. However, critical issues that require resolution to facilitate the success of these efforts remain. In particular, the use of well-validated anti-RAS antibodies is essential for accurate interpretation of experimental data. We evaluated 22 commercially available anti-RAS antibodies with a set of distinct reagents and cell lines for their specificity and selectivity in recognizing the intended RAS isoforms and mutants. Reliability varied substantially. For example, we found that some pan- or isoform-selective anti-RAS antibodies did not adequately recognize their intended target or showed greater selectivity for another; some were valid for detecting G12D and G12V mutant RAS proteins in Western blotting, but none were valid for immunofluorescence or immunohistochemical analyses; and some antibodies recognized nonspecific bands in lysates from "Rasless" cells expressing the oncoprotein BRAFV600E Using our validated antibodies, we identified RAS isoform-specific siRNAs and shRNAs. Our results may help to ensure the accurate interpretation of future RAS studies.

Trends in sports-related concussion diagnoses in the USA: a population-based analysis using a private-payor database

OBJECTIVE

To describe recent epidemiological trends in concussion diagnosis within the United States (US) population.

METHODS

We conducted a retrospective review of PearlDiver, a private-payor insurance database. Our search included International Classification of Disease, Ninth Revision codes for sports-related concussions spanning 2010 through 2014. Overall study population included patients aged 5 to 39 with subgroup analysis performed on Cohort A (Youth), children and adolescents aged 5 to 19, and Cohort B (Adults), adults aged 20 to 39. Incidence was defined as the number of individuals diagnosed normalized to the number of patients in the database for each demographic.

RESULTS

Our search returned 1,599 patients diagnosed during the study period. The average (±SD) annual rate was 4.14 ± 1.42 per 100,000 patients for the overall population. Youth patients were diagnosed at a mean annual rate of 3.78 ± 1.30 versus 0.36 ± 0.16 per 100,000 in Adults. Concussion normalized incidence significantly increased from 2.47 to 3.87 per 100,000 patients (57%) in the Youth cohort (p = 0.048). In Adults, rate grew from 0.34 to 0.44 per 100,000 patients (29%) but was not statistically significant (p = 0.077). Four-year compound annual growth rates for Youth and Adults were 26.3% and 20.4%, respectively. Youth patients comprised 1,422/1,599 (90.18%) of all concussion diagnoses and were predominantly male (75%). Adults also constituted 138/1,599 (8.63%) of the sample and were also largely male (80%). Midwestern states had highest diagnostic rates (Cohort A:19 per 100,000 and Cohort B:1.8 per 100,000). Both cohorts had the most total diagnoses made in the fourth quarter followed by the second quarter.

CONCLUSION

Sports-related concussion diagnostic rates have grown significantly in the youth population. Quarterly, regional and gender distributions appear consistent with participation in concussion-prone sports. Utilization of individualized and multifaceted approaches are recommended to advance diagnosis, assessment and management of concussions in the U.S.

A practical, evidence-based, comprehensive (PEC) physical examination for diagnosing pathology of the long head of the biceps

BACKGROUND

Clinical examination of the shoulder joint has gained attention as clinicians aim to use an evidence-based examination of the biceps tendon, with the desire for a proper diagnosis while minimizing costly imaging procedures. The purpose of this study is to create a decision tree analysis that enables the development of a clinical algorithm for diagnosing long head of biceps (LHB) pathology.

METHODS

A literature review of Level I and II diagnostic studies was conducted to extract characteristics of clinical tests for LHB pathology through a systematic review of PubMed, Medline, Ovid, and Cochrane Review databases. Tests were combined in series and parallel to determine sensitivities and specificities, and positive and negative likelihood ratios were determined for each combination using a subjective pretest probability. The "gold standard" for diagnosis in all included studies was arthroscopy or arthrotomy.

RESULTS

The optimal testing modality was use of the uppercut test combined with the tenderness to palpation of the biceps tendon test. This combination achieved a sensitivity of 88.4% when performed in parallel and a specificity of 93.8% when performed in series. These tests used in combination optimize post-test probability accuracy greater than any single individual test.

CONCLUSION

Performing the uppercut test and biceps groove tenderness to palpation test together has the highest sensitivity and specificity of known physical examinations maneuvers to aid in the diagnosis of LHB pathology compared with diagnostic arthroscopy (practical, evidence-based, comprehensive examination). A decision tree analysis aides in the practical, evidence-based, comprehensive examination diagnostic accuracy post-testing based on the ordinal scale pretest probability.

Farnesyltransferase-Mediated Delivery of a Covalent Inhibitor Overcomes Alternative Prenylation to Mislocalize K-Ras

Mutationally activated Ras is one of the most common oncogenic drivers found across all malignancies, and its selective inhibition has long been a goal in both pharma and academia. One of the oldest and most validated methods to inhibit overactive Ras signaling is by interfering with its post-translational processing and subsequent cellular localization. Previous attempts to target Ras processing led to the development of farnesyltransferase inhibitors, which can inhibit H-Ras localization but not K-Ras due to its ability to bypass farnesyltransterase inhibition through alternative prenylation by geranylgeranyltransferase. Here, we present the creation of a neo-substrate for farnesyltransferase that prevents the alternative prenlation by geranylgeranyltransferase and mislocalizes oncogenic K-Ras in cells.

Abstract 4018: Identifying allosteric modulators of KRas using second harmonic generation

The Ras protein family consists of small GTPases that are critical signaling transducers regulating cellular processes including proliferation, differentiation, and survival. As monomeric GTPases, Ras proteins cycle between an inactive GDP-bound state and an active GTP-bound state. Oncogenic mutations in one of the Ras isoforms, H-, N-, and K-Ras, impair GTP hydrolysis, thus de-regulating Ras signaling. Ras mutations are found in one-third of human cancers, and tumors bearing these mutations are notoriously difficult to treat. Conventional approaches to inhibit Ras with small molecules have been largely unsuccessful leading many to characterize the Ras family as an “undruggable” target. However, there is renewed enthusiasm towards Ras drug discovery in response to a recent surge of reports revealing structural complexities to Ras proteins that provide opportunity for innovative drug discovery efforts.

In light of findings suggesting KRas contains transient and dynamic binding pockets, many of which are undetectable with traditional structural techniques, we used a second harmonic generation (SHG) platform to screen a ~2700 chemically diverse fragment collection for allosteric modulators of KRas. This high throughput SHG platform enables real-time measurement of protein conformational change under physiological conditions. We selected ~50 fragments for validation by SPR, and positive binders will be selected for structural and biochemical characterization. Another advantage of the SHG platform is that we can monitor the conformational dynamics of fully processed, farnesylated KRas bound to a phosphatidylserine-enriched membrane that mimics KRas’ physiological interaction with the plasma membrane. No other biophysical method is suitable to monitor the real-time interactions of small molecules or proteins with membrane-bound KRas. This analysis may reveal surface contacts unavailable in solution-based assays. We have successfully implemented SHG as a drug discovery platform against KRas, and we aim to utilize selected KRas conformational modulators towards the identification of novel binding pockets and towards the development of targeted KRas therapies.

Citation Format: Elizabeth Donohue Vo, Gabriel Besserer Mercado, Patrick Alexander, Ben Moree, Que Van, Andrew G. Stephen, Joshua Salafsky, Frank McCormick. Identifying allosteric modulators of KRas using second harmonic generation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4018. doi:10.1158/1538-7445.AM2017-4018

Abstract 1006: Drug-tolerant persister cancer cells are vulnerable to GPX4 inhibition

Acquired drug resistance prevents chemotherapy and targeted therapy from achieving stable and complete responses. Emerging evidence implicates a key role for nonmutational mechanisms during early stages of acquired drug resistance. Drug-tolerant “persister” cells are a model of nonmutational cancer drug resistance in which small fractions (<5%) of cells within cancer cell lines survive cytotoxic drug exposure despite lacking resistance-conferring mutations. These residual surviving cells are quiescent, occupy a unique chromatin state, and exhibit reversible drug resistance: removal of drug allows regrowth of cells which become resensitized to drug treatment. Importantly, this phenomenon has been observed across a wide range of cancer lineages with both chemotherapy and targeted therapy. Persister cells remain quiescent for weeks to months during constant drug exposure, however some persister cells eventually regrow and acquire irreversible drug resistance-conferring mutations that did not preexist. This model mirrors the common clinical scenario in which tumor response is followed by relapse with acquired resistance-conferring mutations. Targeting nonmutational resistance may therefore present a therapeutic opportunity to eliminate residual surviving tumor cells to prevent relapse. We have performed an unbiased functional genomics analysis of HER2+ breast cancer persister cells which survive HER2 targeted therapy. Utilizing RNAseq, pathway analysis, RNAi screens and chemical inhibitor screens, we discovered that persister cells undergo a switch to mesenchymal gene expression and are uniquely susceptible to inhibition of the phospholipid hydroperoxidase GPX4. This finding is not restricted to breast cancer, rather we have observed that all persister cells tested including those derived from melanoma, lung, ovarian and pancreatic cancer, from either targeted therapies or chemotherapies, are each specifically sensitive to loss of GPX4 function. Parental, drug naive cancer cells and normal human cells are insensitive to GPX4 inhibition. Mechanistically, we found that GPX4 dependency in persister cells is due to a disabled antioxidant program characterized by global downregulation of antioxidant genes, decreased levels of reducing cofactors glutathione and NADPH, and immediate ROS increase upon GPX4 inhibition. These findings point toward a GPX4 inhibition strategy to prevent tumor relapse by inducing ferroptosis in the residual pool of surviving persister cells.

Citation Format: Matthew J. Hangauer, Vasanthi S. Viswanathan, Matthew J. Ryan, Dhruv Bole, Jake Eaton, Stuart L. Schreiber, Frank McCormick, McManus T. Michael. Drug-tolerant persister cancer cells are vulnerable to GPX4 inhibition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1006. doi:10.1158/1538-7445.AM2017-1006

Abstract 1366: Structural basis of impaired GTP hydrolysis in oncogenic mutants of KRAS

RAS mutations are found in one-third of all human cancers. Among the three RAS isoforms - HRAS, KRAS and NRAS, KRAS is the most commonly mutated gene (in 86% of RAS-driven cancers) and the mutations are often detected in pancreatic, colorectal and lung cancers. RAS proteins function as molecular switches by alternating between inactive GDP-bound and active GTP-bound states. The active or inactive state of RAS proteins is regulated by guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). In the GTP-bound state, RAS proteins interact with a variety of effector proteins, such as Raf, PI3K, and RalGDS, leading to activation of several signaling cascades within the cell. In 98% of the cases, oncogenic RAS mutations are found at amino acid positions G12, G13, and Q61 which impair intrinsic and GAP-mediated GTPase function resulting in accumulation of constitutively GTP-bound RAS in cells. To gain insights into the effect of oncogenic mutations on overall structure and GTP hydrolysis, we solved high-resolution crystal structures of wild type and six oncogenic mutants (G12C, G12D, G12V, G13D, Q61L and Q61R) of KRAS4b in complex with GMPPNP (a non-hydrolysable GTP analog) and magnesium. Comparison of GDP and GMPPNP bound structures of wild type (WT) KRAS4b suggests conformational changes that occur when KRAS4b transitions from inactive to active state. Comparison of mutant and wild-type KRAS structures has shown the appearance of new pockets in some cases that could be exploited for structure-based drug design. Structural superposition of mutants vs. wild type KRAS4b in complex with GMPPNP/Mg2+, and KRAS4b mutants vs. WT-HRAS bound to RASA1-GAP provides a rationale for impaired intrinsic and GAP-mediated GTP hydrolysis in the KRAS mutants.

Citation Format: Timothy Tran, Sathiya Dharmaiah, Oleg Chertov, Timothy Waybright, William Gillette, Dominic Esposito, Dwight Nissley, Frank McCormick, Andrew Stephen, Dhirendra Simanshu. Structural basis of impaired GTP hydrolysis in oncogenic mutants of KRAS [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1366. doi:10.1158/1538-7445.AM2017-1366

Abstract 435: Regulation of macropinocytosis-dependent cell survival in pancreatic cancer cells

Cancer cells utilize multiple scavenging mechanisms to support growth in nutrient-poor, hypoxic environments. Signaling pathways to accommodate these mechanisms may not be required for oncogenesis per se but are crucial for cancer cell survival. These processes, known as non-oncogene addiction, can be conferred by specific oncogenes that reprogram metabolism or by the tumor microenvironment. Understanding how these pathways are regulated can provide novel opportunities for therapeutic intervention.

Studies showed that KRAS-mutant cancer cells, including pancreatic ductal adenocarcinoma (PDAC), upregulate macropinocytosis, a caveolin- and clathrin-independent endocytic process, to import extracellular protein to support growth upon nutrient depletion. Similarly, high levels of macropinocytic uptake are observed in PDAC murine models and also in human PDAC specimens. This process serves as a scavenging mechanism for cancer cells to survive and proliferate in nutrient-deprived tumor microenvironments. Thus, uncovering the key players of this pathway and the mechanisms underlying their regulation will be important to find potential therapeutic targets.

Here, we used the Informer set of small molecules to screen regulators of survival in culture conditions supplemented with either glutamine or extracellular protein. The Informer set drug library consists of small molecules including FDA-approved drugs and clinical candidates that have high selectivity for their targets and regulate many cellular pathways. We find that survival of cells grown in conditions supplemented with glutamine or exogenous protein is differentially regulated by distinct drug subsets. This suggests that different pathways of nutrient uptake, processing, and utilization are used in cells depending on the nutrient source. Further examination to determine the mechanism of pathway inhibition and applicability may unravel potential uses for therapeutics.

Citation Format: Sung Eun Kim, Man-Tzu Wang, Frank McCormick. Regulation of macropinocytosis-dependent cell survival in pancreatic cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 435. doi:10.1158/1538-7445.AM2017-435

Abstract 1370: EGFR-mediated Spred1 phosphorylation inhibits NF1 to sustain constitutive Ras/MAPK signaling

Spred proteins negatively regulate Ras/MAPK signaling following growth factor stimulation. Inhibition of Ras primary occurs through Spreds ability to bind and localize NF1, a RasGAP and major tumor suppressor, to the plasma membrane. Spred1 and NF1 loss-of-function mutations occur across multiple cancer types including non-small cell lung carcinoma, glioblastoma, melanoma, stomach carcinoma, and uterine carcinosarcoma. Here we demonstrate that EGFR signaling disrupts Spred1-NF1 binding. Mass spectrometry was performed on cells overexpressing EGFRL858R to identify potential phosphorylation sites on Spred1 and NF1 that could disrupt Spred1-NF1 binding by steric hindrance. A serine phosphorylation site on Spred1 was identified in which a phosphomimetic and phosphodeficient mutant decreased or increased Spred1-NF1 binding, respectively. Phosphomimetic Spred1 is unable to suppress Ras-GTP following EGF stimulation. Therefore, phosphorylation of Spred1 at this site by a serine kinase downstream of EGFR may disrupt Spred1-NF1 binding. To identify the Spred1 kinase we are performing an in vitro kinase assay and an unbiased CRISPRa screen. Our findings provide one potential mechanism by which EGFR signaling disrupts negative feedback to sustain constitutive Ras signaling. Furthermore, this work may elucidate a novel therapeutic target for restoring NF1-mediated inhibition of Ras.

Citation Format: Evan Markegard, Ellen L. Mercado, Jillian M. Silva, Jacqueline Galeas, Marena I. Trinidad, Anatoly Urisman, Frank McCormick. EGFR-mediated Spred1 phosphorylation inhibits NF1 to sustain constitutive Ras/MAPK signaling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1370. doi:10.1158/1538-7445.AM2017-1370

Abstract 4589: Preclinical investigation of SGN-CD70A antibody-drug conjugate in T cell lymphomas

CD70 is a member of the tumor necrosis factor (TNF) superfamily and aberrantly expressed in several solid tumors and a variety of hematologic malignancies. The CD70 protein is expressed on highly activated lymphocytes (like in T and B cell lymphomas). Since normal lymphocytes do not express much CD70, it is suggested that anti-CD70 antibodies could be a potential treatment for CD70 positive lymphomas. SGN-CD70A is a novel antibody-drug conjugate that combines an anti-CD70 monoclonal antibody with a synthetic DNA cross-linking molecule, pyrrolobenzodiazepine (PBD) dimer. It is currently under phase I clinical trials for renal cell carcinoma, mantle-cell, diffuse large B-cell, and follicular lymphoma. The aim of this study is to investigate the anti-tumor activity of SGN-CD70A in T cell lymphomas. We first examined CD70 expression in 36 cases of mature T or NK cell lymphomas using immunohistochemical (IHC) staining of patient biopsy specimens. The IHC results were reviewed and scored by 2 independent pathologists. We further investigated CD70 expression in Sezary syndrome (SS), mycosis fungoides (MF), and T cell acute lymphoblastic leukemia (T-ALL) cell lines, along with patient-derived T cell lymphoma primary cells and healthy donors’ peripheral blood mononuclear cells (PBMC) by flow cytometry. We next evaluated the anti-tumor activity of SGN-CD70A in cutaneous T cell lymphoma (CTCL) cell lines and patient-derived T cell lymphoma primary cells. Cell lines or primary cells were treated with SGN-CD70A at various concentrations, after which growth inhibition and apoptosis were assessed by CellTiter-Glo Assay, flow cytometry or Caspase-Glo 3/7 Assay, respectively. CD70 negative T-ALL cell lines were treated in parallel as negative controls for CD70 positive CTCL cell lines. Additionally, h00d-1910, an isotype control of the anti-CD70 antibody conjugated to PBD, was used as the negative control for SGN-CD70A. CD70 expression was observed across all subtypes of T cell lymphomas and all CTCL cell lines. In contrast, CD70 is not expressed in PBMC from healthy subjects. We demonstrated that SGN-CD70A potently inhibited cell growth in CD70-positive CTCL lines, but had no significant activity in CD70-negative T-ALL lines. In addition, SGN-CD70A induced more apoptosis and cell death in CTCL cell lines compared with media and h00d-1910 treated controls. Furthermore, we showed that SGN-CD70A inhibited cell proliferation and induced higher caspase 3/7 activity in CD70-expressing patient-derived T cell lymphoma primary cells in a dose-dependent manner, while h00d-1910 treated in parallel had no significant effects. In summary, CD70 is expressed in both nodal and cutaneous T cell lymphomas but not in healthy donors. SGN-CD70A not only shows anti-tumor activity in CTCL cell lines expressing CD70, but also inhibits proliferation and induces apoptosis in patient-derived T cell lymphoma primary cells, indicating it is a promising treatment for T cell lymphomas.

Citation Format: Chen-Yen Yang, Linlin Wang, Laura Pincus, Frank McCormick, Ryan Gill, Wei Ai. Preclinical investigation of SGN-CD70A antibody-drug conjugate in T cell lymphomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4589. doi:10.1158/1538-7445.AM2017-4589

Abstract 3182: Cytoskeletal modulation results in increased tumor survival and drug resistance through attenuation of p53 dependent apoptosis

One of the major challenges to eradicating cancer involves the evolution of drug resistant clones and persistence of residual disease that escapes our current limit of detection but may proliferate upon cessation of therapy. These microscopic foci of residual diseases often exhibit stem-cell like properties and are intrinsically more resistant to drug therapy. A better understanding of the mechanisms underlying the innate drug resistance of these cellular populations may lead to improved treatment strategies, resulting in more durable remissions and ultimately improved patient survival.

We utilize functional genomic platforms to identify mechanisms responsible for the persistence of drug tolerant cells. A genome wide shRNA enrichment screen was performed using the c-Met addicted cell line GTL-16 to identify genes whose knockdown conferred DTP survival. Inhibition of the RhoA-ROCK-myosin pathway promotes drug resistance in a variety of tumor models, including those treated with either targeted therapy or conventional chemotherapy. Furthermore, pharmacological validation using multiple small molecule inhibitors of ROCK1 phenocopied both myosin heavy chain (MYH9) and light chain (MYL12) shRNA knockdown. More recently, utilizing a combination of gene expression and biochemical approaches, we have identified attenuation of p53 induced apoptosis to be a key event in mediating survival of these drug tolerant persisters. Reactivation of p53 using nutlin results in increased cell death.

These findings demonstrate that modulation of cytoskeleton is an important, but underappreciated, mechanism of drug resistance across many tumor types. These downstream effectors may serve as novel therapeutic targets for intervention and also biomarkers to stratify patients and their response to treatment.

Citation Format: Victoria E. Wang, John Doench, David Root, Rene Bernards, Jeffrey Settleman, Frank McCormick. Cytoskeletal modulation results in increased tumor survival and drug resistance through attenuation of p53 dependent apoptosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3182. doi:10.1158/1538-7445.AM2017-3182