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Background: Women with breast cancer account for the largest cohort (23%) of over 18 million cancer survivors in the United States. Of the nearly 4 million breast cancer survivors, many, including individuals with metastatic breast cancer, will require lifelong treatment for chronic conditions. As part of a multi-site study including diverse tumor types, breast cancer survivors are being recruited to explore the feasibility and outcomes of a digital health coaching (DHC) program following the completion of primary therapy to support self-management of symptoms and general wellness. Trial design: A randomized-wait list control design will evaluate outcomes related to engagement in a DHC program following completion of primary therapy. Participants will be enrolled in a 6-month DHC program delivering evidence-based content via weekly calls, text, and email, in addition to usual support from their respective healthcare teams. The intervention group will receive coaching upon enrollment. The control group will receive coaching after a 6-month monitoring period. Twelve months of longitudinal clinical, patient-reported outcomes, activity tracking (via Fitbit), and microbiome data will be collected from both groups. Eligibility criteria: The breast cancer cohort will consist of individuals with both localized and metastatic disease within 1 year of completion of primary therapy, defined as treatment of curative intent, first-line or later, from which the individual is advancing to active surveillance or follow-up, with or without maintenance therapy. All study participants must be >18 years old, able to read and speak English, have access to mobile technology, and agree to wear and have data collected from an activity tracker. Specific aims: 1) Assess the feasibility and acceptability of a DHC program and its effect on participant health self-efficacy; 2) characterize associations between participant symptoms, physical/psychosocial well-being, and health self-management and gut microbiota changes; and 3) explore patient-generated health data outcomes among participants (patient reported and wearable biometrics outcomes). Statistical methods: Feasibility and acceptability will be assessed through descriptive statistics. Feasibility for this study is defined as a retention rate ≥70%, and acceptability is defined as ≤20% scoring “not at all helpful.” Secondary aims will be assessed using linear mixed models. Cross-cohort analysis of physical function, measured by the PROMIS Physical Function 10a, will be conducted. Assuming a power of 0.8 and significance level of .05, we will be able to detect a 2.51 difference in PROMIS score means between the control and intervention group (SD 10) with a sample of 500 total participants. Sub-group analysis will be conducted with the anticipated 250 participants in the breast cancer cohort with a focus on feasibility, acceptability, and descriptive and exploratory endpoints for this population as a whole and comparing early stage and metastatic participants. Target and present accruals: 500 individuals with diverse tumor types will be enrolled across 5 collaborating sites, of which 4 ill include individuals with breast cancer. An estimated 250 breast cancer participants (approximately 50% of the total study population), including 150 with de novo or progressive metastatic breast cancer, are planned to be recruited. To date, 1 Midwestern site has enrolled the first 7 breast cancer survivors. Two additional sites plan to enroll in July 2022, with the remaining 2 sites to begin enrollment by the end of 2022. Citation Format: Robin M. Lally, Rachael L. Schmidt, Gisele Tlusty, Elizabeth K. Arthur, Laura K. Flora, Jessica L. Krok-Schoen, Jessica T. Jones, Meagan Whisenant, Abbey Kaler, Debu Tripathy, Leorey Saligan, Marilyn Hammer, Austin Barr, Lindsey Jackson, Jennifer Loftis, Kelly J. Brassil. Breast Cancer Cohort of the Comprehensive Outcomes for After Cancer Health (COACH) Study: Study Protocol [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr OT2-06-01.

We have previously identified that in the absence of MET amplification or mutation, RTK hyperphosphorylation, indicative of its active state, may contribute to resistance to the EGFR-directed therapeutic, cetuximab in colorectal cancer (CRC). In our in vitro 3D cultures and in vivo xenografts, we showed that inhibition of MET (and RON) by crizotinib can overcome cetuximab resistance in CRC lines and xenografts. We now show that MET may get hyperphosphorylated by the autocrine expression and maturation of its ligand, HGF. This non-genetic mode of cetuximab resistance contrasts with the usual genetic modes of CRC cetuximab resistance, with majority of them being RAS/RAF mutations. Exogenous addition as well as autocrine overexpression of HGF led to cetuximab resistance, which could be overcome by MET inhibition by crizotinib. Interestingly, HGF/HGFL are synthesized as inactive precursors and require cleavage by proteases (HGFA, Matriptase, and Hepsin) to be biologically active. A survey of TCGA datasets indicated that HGF/HGFL were overexpressed in several CRC CMS subtypes, while the endogenous inhibitor of HGF proteases, HAI-I, was downregulated across all CRC CMS subtypes. We next expressed human full-length HGF in cetuximab-sensitive CC cells and observed that HGF overexpression imparts cetuximab resistance. Moreover, cetuximab resistance induced by upstream HGF overexpression could be overcome by the downstream MET inhibition. Next, in a subset of KRAS WT CRC patient-derived xenografts (PDXs) we tested and found that at majority of PDXs exhibit elevated pMET/pRON levels. RNA-seq-based principal component analysis showed that the maximal differences in expression among PDXs could be explained by their pMET/pRON phosphorylation status. Next, we generated nude mice xenografts for one PDX with high pMET/pRON levels and showed that cetuximab inhibition alone was not sufficient to inhibit regrowth of tumors after cessation of drug treatment, but a combined cetuximab/crizotinib treatment was, indicating endogenous MET/RON activation contributes to cetuximab resistance. In a parallel tumor stratification strategy, we have optimized conditions to generate [18F]crizotinib and are testing its efficacy as a new non-invasive PET-based imaging probe to identify crizotinib-avid tumors with high MET/RON activity. Together, these studies may provide novel mechanistic insights into RTK cross-talk and provide a positive predictive biomarker for precision therapy in colorectal cancer. Citation Format: Vivian T. Jones, Ramona Graves-Deal, KyuOK Jeon, Adam J. Rosenberg, Zheng Cao, Galina T. Bogatcheva, Sarah J. Harmych, James N. Higginbotham, Kwangho Kim, James W. Janetka, Gary A. Sulikowski, Bhuminder Singh. Role of MET signaling in cetuximab resistance and generation of an imaging biomarker to identify MET-driven cetuximab resistance in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2562.

Background: Diffuse midline gliomas (DMGs) are a universally fatal brain tumor of childhood. While histone mutations are a critical tumor initiating event, they are insufficient to drive gliomagenesis. Histone mutations co-occur with somatic alterations in other pathways including TP53, MAPK, and MYC signaling. However, the mechanisms through which these pathways are activated have not been fully elucidated. Methods: We applied an integrative approach using transcriptomics, epigenetics, proteomics, in vitro cancer models, and in vivo mouse models to systematically evaluate how FOXR2 mediates gliomagenesis. Results: We have recently found that a subset of DMGs aberrantly express FOXR2, a forkhead transcription factor. FOXR2 is both sufficient to enhance tumor formation, and necessary for FOXR2-expressing DMGs. While FOXR2 indeed enhances MYC protein stability, FOXR2 exerts oncogenesis through MYC-independent functions and specifically hijacks E26-transformation specific (ETS) transcriptional circuits and FOXR2 DNA-binding is highly enriched at ETS motifs. We have performed proteomic and phospho-proteomic analysis of FOXR2-expressing human neural stem cells to identify proteins and phospho-sites that are highly enriched in FOXR2-expressing cells. Conclusion: Taken together, this study elucidates how FOXR2 interacts with ETS transcription factors to mediate oncogenesis, and further highlights a role for FOXR2 in activating ETS and MAPK signaling. Citation Format: Jessica W. Tsai, Paloma Cejas, Marissa Coppola, Dayle K. Wang, Smruti Patel, David W. Wu, Phonepasong Arounleut, Xin Wei, Ningxuan Zhou, Sudeepa Syamala, Frank P. Dubois, Kristine Pelton, Jayne Vogelzang, Cecilia Sousa, Audrey Baguette, Xiaolong Chen, Alexandra L. Condurat, Sarah E. Dixon-Clarke, Annarah Charles, Kevin N. Zhou, Sophie D. Lu, Elizabeth M. Gonzalez, Madison S. Chacon, Jeromy J. Digiacomo, Rushil Kumbhani, Dana Novikov, Maria Tsoli, David S. Ziegler, Uta Dirksen, Natalie Jager, Gnana Prakash Balasubramanian, Christof M. Kramm, Michaela Nathrath, Stefan Bielack, Suzanne J. Baker, Jinghui Zhang, James M. McFarland, Gad Getz, Francois Aguet, Nada Jabado, Olaf Witt, Stefan M. Pfister, Keith L. Ligon, Volker Hovestadt, Claudia Kleinman, Henry Long, David T. Jones, Pratiti Bandopadhayay, Timothy N. Phoenix. Dissecting mechanisms underlying FOXR2-mediated gliomagenesis in diffuse midline gliomas. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3562.

Introduction: Genome-wide methylation analyses recently revealed novel epigenetic pineoblastoma (PBL) subtypes, but so far few data are available on recurrent cytogenetic alterations due to the rarity of these neoplasms. Therefore, our aim was to shed further light onto the molecular and genetic characteristics underlying the pathogenesis of pineoblastoma subtypes. Experimental procedures: Cytogenetic alterations of tumor samples of 60 patients with a diagnosis of PBL confirmed by reference neuropathology and methylation array profiling (450K or EPIC BeadChips (Illumina)) were analyzed by high-resolution genome-wide molecular inversion probe analysis. 52 cases could be screened for mutations by next-generation DNA panel sequencing. Survival data of 41 patients were available. All patients had surgery and older patients (≥4y) received RT followed by maintenance chemotherapy (n=37); infants ( Results: Of the recently published epigenetic consensus PBL subtypes (Liu et al., 2021), our cohort consisted of 37 PBL-miRNA1 (1A, 30; 1B, 7), 17 PBL-miRNA2, 2 PBL-MYC/FOXR2, and 4 PBL-RB1 samples. PBL-miRNA subtype tumors had characteristic alterations in microRNA-processing genes; DICER1 mutations (n=14; 4 in Grp1A/1 in Grp1B/9 in Grp2) were most abundant, followed by homozygous deletions of the DROSHA locus (n=11; 8/1/2) and DROSHA mutations (n=9; 3/3/3). Most frequent cytogenetic aberrations in these subtypes were chromosome (chr.) 7 gains (n=25) and chr. 14 losses (n=20, with all but one of miRNA2 cases). DICER1 mutations were significantly associated with chr. 14 losses (p Conclusion: The epigenetically defined PBL subtypes were characterized by distinct cytogenetic and mutational events. Although we could not demonstrate a prognostic impact of these events, this might be due to the small sample size. A possible prognostic role for a superior (e.g. tetraploidy) or inferior outcome (e.g. OTX2 gains) need studies in larger cohorts and ideally in prospective clinical trials. Citation Format: Tobias Goschzik, Mathias Yuan, Martin Mynarek, Elke Pfaff, Evelyn Dörner, David T. Jones, Stefan M. Pfister, Stefan Rutkowski, Torsten Pietsch. Recurrent genetic alterations in epigenetic pineoblastoma subtypes. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3561.

PDGFRA has been shown to be commonly altered in high-grade gliomas (HGGs), including histone 3 lysine 27-mutated diffuse midline gliomas (H3K27M DMG), a disease with almost no long-term survivors. Here, we performed comprehensive genomic and transcriptomic analysis of 260 high-grade glioma cases, which revealed PDGFRA genomic alterations (mutations and/or amplifications) in 13% of patients. H3K27M DMGs had significantly higher PDGFRA expression compared to H3 wild-type tumors, and PDGFRA gene amplification resulted in even higher expression levels in H3K27M DMGs as well as H3 wild-type HGGs. We tested a panel of patient- derived pHGG/H3K27M DMG models against a range of PDGFRA inhibitors, including avapritinib, a potent small molecule inhibitor with relatively selective activity against both wild-type and mutant PDGFRA. Avapritinib showed supra-micromolar blood-brain barrier penetration in our pre-clinical models and demonstrated significant survival impact in an aggressive patient-derived H3K27M DMG mouse xenograft model. Finally, building on this preclinical activity, we report here the first clinical experience using avapritinib in eight pediatric and young adult patients with high-grade glioma (H3K27M DMG and/or PDGFRA altered). Avapritinib has thus far been well tolerated with no significant acute toxicities. Most importantly, our preliminary data reveal radiographic response evaluated by RAPNO criteria in 50% of patients, a striking outcome rarely seen in this patient population. In summary, we report that avapritinib is a selective, CNS-penetrant small molecule inhibitor of PDGFRA that shows potent activity in preclinical models and produces promising clinical responses with good tolerability in patients with high-grade glioma. This suggests a promising role for avapritinib therapy in this population with previously dismal outcomes. Citation Format: Lisa Mayr, Maria Trissal, Kallen Schwark, Jenna Labelle, Andrew Groves, Julia Furtner-Srajer, Jeffrey Supko, Liesa Weiler-Wichtl, Olivia Hack, Jacob Rozowsky, Joana G. Marques, Eshini Pandatharatna, Ulrike Leiss, Verena Rosenmayr, Frank Dubois, Noah F. Greenwald, Sibylle Madlener, Armin S. Guntner, Hana Pálová, Natalia Stepien, Daniela Lötsch-Gojo, Christian Dorfer, Karin Dieckmann, Andreas Peyrl, Amedeo A. Azizi, Alicia Baumgartner, Ondřej Slabý, Petra Pokorná, Pratiti Bandopadhayay, Rameen Beroukhim, Keith Ligon, Christof Kramm, Annika Bronsema, Simon Bailey, Ana Guerreiro Stücklin, Sabine Mueller, David T. Jones, Natalie Jäger, Jaroslav Štěrba, Leonhard Müllauer, Christine Haberler, Chandan Kumar-Sinha, Arul Chinnaiyan, Rajen Mody, Mary Skrypek, Nina Martinez, Daniel C. Bowers, Carl Koschmann, Johannes Gojo, Mariella Filbin. Clinical response to the PDGFRα inhibitor avapritinib in high-grade glioma patients. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5719.

We have previously identified that activation of receptor tyrosine kinases (RTKs), MET and RON contributed to resistance to the EGF receptor (EGFR)-directed therapeutic antibody, cetuximab. These findings originated from our in vitro 3D type I collagen cultures of human colorectal cancer (CRC) cell line HCA-7 derivatives CC, SC, and CC-CR. CC are sensitive to cetuximab, while SC and CC-CR are resistant. Both de novo and acquired modes of cetuximab resistance in SC and CC-CR, respectively, could be overcome by crizotinib, a multi-RTK inhibitor that also targets MET and RON. Conversely, exogenous administration of MET ligand, HGF could transiently induce cetuximab resistance which could be further overcome by crizotinib addition. HGF/HGFL are synthesized as inactive precursors and require cleavage by proteases (HGFA, Matriptase, and Hepsin) to be biologically active. To inhibit HGF/HGFL cleavage in cetuximab-resistant cells, we employed inhibitors of HGF/HGFL proteases (ZFH7116 and VD2173) and were able to overcome both de novo and acquired cetuximab resistance. A survey of TCGA datasets indicated that HGF/HGFL were overexpressed in several CRC CMS subtypes. We next expressed human HGF in cetuximab-sensitive CC cells and observed that HGF overexpression imparts cetuximab resistance. Moreover, cetuximab resistance induced by HGF overexpression could be overcome by the downstream MET inhibition (with crizotinib), and we are now testing if the upstream inhibition of HGF proteases (with ZFH7116/VD2173) also overcomes cetuximab resistance. Combined these results indicate that inhibition of HGF cleavage and maturation may be a novel way to overcome resistance to EGFR-targeted therapies in CRC. Citation Format: Ramona Graves-Deal, Vivian T. Jones, Galina T. Bogatcheva, Zheng Cao, Sarah J. Harmych, Vishnu Damalanka, Lidija Klampfer, Robert J. Coffey, James W. Janetka, Bhuminder Singh. Inhibition of HGF maturation overcomes cetuximab resistance in colorectal cancer [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer; 2022 Oct 1-4; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_1):Abstract nr PR010.

Ulixertinib (BVD-523) is a well-tolerated, orally delivered, catalytic ERK1/2 inhibitor, which has shown promising responses in adult patients with mitogen-activated protein kinase (MAPK)-driven solid tumors. Pediatric low grade gliomas (pLGGs) are the most common pediatric brain tumors, with the most frequent driving alterations (KIAA:BRAF fusion, BRAF V600E mutation) occurring in the MAPK pathway. To investigate the anti-tumoral activity of ulixertinib in pLGG, cell lines recapitulating both main MAPK alterations were used: DKFZ-BT66 (pilocytic astrocytoma; KIAA:BRAF fusion) and BT40 (pleomorphic xanthoastrocytoma; BRAF V600E mutation and CDKN2A/B deletion). The potential synergism of combinations with MEK inhibitors, senolytics, and chemotherapy was investigated in vitro using metabolic activity and MAPK activity assays. The most promising combinations were validated in vitro by analysis of viable, dead, and apoptotic cells through high-content microscopy. The most clinically relevant combinations were further validated in vivo: 1) in two zebrafish embryo models (respectively, BT40 and DKFZ-BT66 yolk sac injection) and 2) in NSG mice (BT40 orthotopic PDX) including in vivo pharmacokinetic and -dynamic analyses. Our data demonstrate ulixertinib’s ability to inhibit MAPK pathway activity in all used models. Ulixertinib treatment reduced cell viability in the BRAF V600E mutated cell line at a remarkably low concentration of 62.7 nM (compared to other cell lines’ IC50 from the Genomics of Drug Sensitivity in Cancer database). In vivo pharmacokinetic and -dynamic analyses showed good penetrance of the drug into mouse brain tissue, with concentrations above the in vitro IC50 and reduction of MAPK activity as assessed by Western blot. Furthermore, ulixertinib treatment slowed tumor growth and significantly increased survival in NSG mice with orthotopic BT40 xenografts. Ulixertinib showed indications for anti-proliferative synergy in vitro, according to the Loewe and Bliss independence models, in combination with MEK inhibitors (trametinib, binimetinib) or senolytics (navitoclax, A1331852). Combinations with chemotherapy (carboplatin, vinblastine) were at most additive. Indications for synergy with binimetinib and navitoclax were confirmed in the zebrafish embryo xenograft models for both MAPK-altered backgrounds. The combination of ulixertinib with navitoclax was further investigated in the BT40 PDX mouse model, where tumor growth and survival were comparable to ulixertinib monotherapy. In conclusion, our data indicate a strong potential for ulixertinib as a clinically relevant therapeutic option for the treatment of pLGG to be further investigated in upcoming clinical trials. Potential synergism with MEK inhibitors and senolytics was noted and warrants further investigation. Citation Format: Romain Sigaud, Lisa Rösch, Charlotte Gatzweiler, Julia Benzel, Laura von Soosten, Heike Peterziel, Sara Najafi, Simay Ayhan, Nina Hofmann, Kathrin I. Förster, Jürgen Burhenne, Rémi Longuespée, Cornelis M. van Tilburg, David T. Jones, Stefan M. Pfister, Deborah Knoerzer, Brent Kreider, Max Sauter, Kristian W. Pajtler, Marc Zuckermann, Ina Oehme, Olaf Witt, Till Milde. The first-in-class ERK inhibitor ulixertinib (BVD-523) shows activity in MAPK-driven pediatric low-grade glioma models as single agent and in combination with MEK inhibitors or senolytics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5221.

Background: Understanding how aberrant transcription factors (TFs) hijack normal development to induce oncogenesis is a critical question in oncology. Forkhead box (FOX) proteins are a superfamily of transcriptional regulators characterized by a forkhead DNA-binding domain. Within this family, Forkhead Box R2 (FOXR2) expression has been associated with a subset of cancers including CNS and peripheral neuroblastoma. While FOXR2 has been shown to stabilize MYC isoforms, the mechanistic details through which it enhances tumor formation and the true extent of its role as an oncogene across all cancers have not been systematically evaluated. Methods: We applied an integrative approach using transcriptomics, epigenetics, in vitro cancer models, and in vivo mouse models to systematically evaluate the mechanisms by which FOXR2 is activated across human cancers. Results: We performed a pan-cancer analysis of FOXR2 activation across over 10,000 adult and pediatric cancer samples, and found FOXR2 to be aberrantly upregulated in 70% of all cancer types, and 8% of all individual tumors. We identified genetic and epigenetic mechanisms that induce its expression, including hypomethylation of a novel promoter in the vast majority (78%) of FOXR2-expressing cases. We demonstrate that FOXR2 expression is both sufficient and necessary for transformation across multiple lineages, using both in vitro and in vivo models. Conclusion: Taken together, this study demonstrates the role of FOXR2 as a potent oncogene across human cancers, and highlights a novel mechanism by which its expression is activated. Citation Format: Jessica W. Tsai, Paloma Cejas, Dayle K. Wang, Smruti Patel, David W. Wu, Phonepasong Arounleut, Xin Wei, Ningxuan Zhou, Sudeepa Syamala, Frank P. Dubois, Kristine Pelton, Jayne Vogelzang, Cecilia Sousa, Audrey Baguette, Xiaolong Chen, Alexandra L. Condurat, Sarah E. Dixon-Clarke, Kevin N. Zhou, Sophie D. Lu, Elizabeth M. Gonzalez, Madison S. Chacon, Jeromy J. Digiacomo, Rushil Kumbhani, Dana Novikov, J'Ya Hunter, Maria Tsoli, David S. Ziegler, Uta Dirksen, Natalie Jager, Gnana Prakash Balasubramanian, Christof M. Kramm, Michaela Nathrath, Stefan Bielack, Suzanne J. Baker, Jinghui Zhang, James M. McFarland, Gad Getz, Francois Aguet, Nada Jabado, Olaf Witt, Stefan M. Pfister, Keith L. Ligon, Claudia Kleinman, Henry Long, David T. Jones, Pratiti Bandopadhayay, Timothy N. Phoenix. FOXR2 is an oncogenic driver across adult and pediatric cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5730.

Circulating tumor cells (CTCs), CTC heterogeneity and distinct morphological CTC subtypes predict worse survival in metastatic breast cancer (MBC)BackgroundThe presence of CTCs has been shown to be a poor prognostic factor in patients with MBC. Studies in prostate cancer have shown patients with distinct morphological subtypes of CTCs have worse outcomes than high CTC burden alone and could have treatment implications. In this study, we report a comprehensive analysis of CTC phenotypes in MBC and their impact on survival.MethodsA total of 148 blood samples from 90 patients with MBC whose disease was progressing on therapy were enrolled for CTC analysis. Blood was sent overnight to Epic Sciences, processed onto glass slides and biobanked. Replicate slides were stained with antibodies targeting the androgen receptor (AR), estrogen receptor (ER), and human epidermal growth factor receptor 2 (HER2) in addition to cytokeratin, CD45, and DAPI. Total CTCs were quantified per sample from approximately 3 mL of blood. A threshold defining positive AR, ER, and HER2 protein expression was set using cultured cancer cell lines expressing the individual proteins. CTC morphology subtypes (heterogeneity [Scher et al Cancer Res 2017], small cell/neuroendocrine-like [SC/NE; Brown et al CCR 2021] and chromosomal instability [CIN+; Schonhoft et al Cancer Res 2020]) were quantified as previously described. High heterogeneity samples (Het+) were defined as having a Shannon Index (SI; a measure of morphologic diversity) of ≥1. CIN positivity was defined as having ≥0.7 CIN+ CTC/mL. Association with these CTC subtypes and survival were evaluated with a univariate COX proportional hazard model. ResultsOver 90% of samples and patients had CTCs (Table 1). The percentage of patients with the CTC subtypes evaluated are below. Table 1. Percentage of blood samples with CTCs and CTC subtypes in MBC patients, by MBC subtype The presence of CTCs was associated with worse survival, with a median survival of 15.3 months (mos) vs 24.0 mos with no CTCs (p=0.028). The presence of AR+ or HER2+ CTCs was not associated with survival. Analysis of ER is ongoing and will be presented. High morphologic heterogeneity or the presence of the SC/NE or CIN+ CTC subtypes, predicted for a worse survival outcome (Table 2). Table 2. Overall survival of patients with and without distinct CTC subtypes CTC morphological subtypes did not correlate with each other, except CTC heterogeneity by SI which correlated weakly with SC/NE and CIN+. HER2+ CTCs strongly correlated with a higher SI while AR+ CTCs did not. AR and HER2 expression did not associate with the CIN+ or SC/NE subtypes. ConclusionsDigital pathology analysis of CTCs identifies distinct CTC morphological subtypes that predict for worse prognosis in MBC patients. To our knowledge, this is the first report of SC/NE CTCs in MBC patients and that MBC patients with SC/NE and CIN+ CTCs have worse outcomes. Longitudinal characterization of CTC subtypes across the MBC continuum could potentially identify effective therapies against these more lethal cancers. Citation Format: Joyce A O'Shaughnessy, Maren K Levin, Esther San Roman Rodriguez, James Lu, Joshua T Jones, Amanda KL Anderson, Alisa Tubbs, Joseph D Schonhoft, Rick Wenstrup. Circulating tumor cells (CTCs), CTC heterogeneity and distinct morphological CTC subtypes predict worse survival in metastatic breast cancer (MBC) [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P2-02-03.

Gemcitabine and cisplatin (GC) combination neoadjuvant chemotherapy (NAC) is standard of care for patients with muscle-invasive bladder cancer (MIBC). This combination is preferred due to its favorable toxicity profile. Approximately 25% of NAC treated patients will experience complete pathological response (pT0) at time of radical cystectomy (RC). NAC-treated patients with residual disease at RC have poorer prognosis compared to those who achieved pT0. Here we systematically defined the in vitro functional determinants of resistance to gemcitabine and cisplatin in bladder cancer. To accomplish this, we performed molecular profiling and functional genomic screening on a panel of bladder cancer cell lines (KU-19-19, T24, TCCSUP, 253J and 5637), each having the parental cell line with matched gemcitabine-, cisplatin-, and dual GC-resistant derivatives. We performed whole exome sequencing, RNA sequencing, and phospho-proteomic profiling on these 20 cell lines. To identify chemogenetic interactions that govern sensitivity or resistance to these agents, we performed whole genome CRISPR knockout screening in the GC-resistant cells both in the presence and absence of GC. We identified several novel genes that when inactivated are capable of sensitizing GC resistant cell lines to the two agents. The majority of shared chemosensitizing genes fall into several DNA damage response pathways. This is consistent with the established mechanism of action of GC chemotherapy and observations that have been made from clinical cohorts, where loss-of-function mutations in these pathways correlate with response to platinum-based chemotherapy. Notably, our work has identified several druggable candidates that could serve as potential targets for enhancing responses rates to GC. Interestingly, comparing these candidate genes and pathways with those differentially expressed in the RNA sequencing and proteomic profiling showed limited overlap. This work provides a comprehensive view of the functional determinants of GC sensitivity in bladder cancer. In support of and expanding on previous studies, we identified additional DNA damage response genes that when lost enhance sensitivity to GC. These genes should be further explored for their utility as predictive biomarkers of response to GC-based therapy in clinical cohorts. Importantly, a number of these could be targeted in combination with GC-based NAC to potentially improve response. Citation Format: Robert T. Jones, Tahlita C. Zuiverloon, Hedvig Vekony, Andrew Goodspeed, Teemu D. Laajala, Molishree Joshi, Colin Sempeck, Annie Jean, Megan Tu, Julia D. Wulfkuhle, Emanuel F. Petricoin, James C. Costello, Dan Theodorescu. Functional genomic screening in gemcitabine and cisplatin resistant bladder cancer cell lines identifies DNA repair pathways as mediators of chemosensitivity [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4091.

Single-cell RNA sequencing (scRNAseq) has been performed across a range of intermediate to high-grade gliomas that each harbor multiple driver mutations. Pilocytic astrocytoma (PA), the most common childhood brain tumor, is a low-grade glioma. PAs frequently harbor oncogenic KIAA1549-BRAF fusions, and exhibit low rates of other driver mutations. While PAs exhibit a favorable prognosis compared to the higher-grade gliomas, treatment morbidity and tumor recurrence can represent major challenges for some PA patients. We performed scRNAseq of both tumor and non-tumor cells in newly-diagnosed PAs that contained KIAA1549-BRAF rearrangements. To confidently distinguish tumor cells from nontumor cells, we sorted cells by glial progenitor marker A2B5 status and profiled KIAA1549-BRAF fusion status of cells using a sensitive quantitative PCR-based assay. Results were validated using RNA in situ hybridization. When compared to higher-grade gliomas, a higher proportion of the PA tumor cells exhibited a differentiated, astrocyte-like phenotype. A smaller proportion of cells exhibited a progenitor-like phenotype with evidence of proliferation. These progenitor-like tumor cells expressed a mitogen-activated protein kinase (MAPK) program that was absent from higher-grade gliomas. Similar patterns of expression of genes associated with the astrocyte-like and MAPK gene programs were also seen in formalin fixed, paraffin embedded PA tissues using RNA in situ hybridization. Immune cells, especially microglia, comprised almost half of all cells in the PAs and accounted for differences in bulk expression profiles between tumor locations and subtypes. These single cell transcriptional data reveal a transcriptional developmental hierarchy in a pediatric low grade glioma that is skewed towards more mature brain cells compared to higher-grade gliomas. The results indicate that future analyses of bulk PA tissues should attempt to account for considerable infiltration by nontumor cells. Finally, the finding that a MAPK gene program is not uniformly expressed in PA tumor cells has implications for ongoing clinical investigations of therapies directed at the MAPK pathway for the treatment of PA. Citation Format: Zachary J. Reitman, Brenton Paolella, Guillaume Bergthold, Kristine Pelton, Robert Jones, Sarah Becker, Claire E. Sinai, Haley Malkin, Ying Huang, Leslie Grimmett, Zachary T. Herbert, Yu Sun, Jessica Weatherbee, John Alberta, John Daley, Orit Rozenblatt-Rosen, Rosalind Segal, Daphne Haas-Kogan, Mariella G. Filbin, Mario L. Suva, Aviv Regev, Charles Stiles, Mark W. Kieran, Liliana Goumnerova, Keith L. Ligon, Alex K. Shalek, Pratiti Bandopadhayay, Rameen Beroukhim. Single cell RNA sequencing reveals mitogenic and progenitor gene programs inBRAF-rearranged pilocytic astrocytomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3647.

Introduction: Immune repertoire is a highly diverse pool of B and T cell receptors (B/TCR) that determine boundaries of immune surveillance. Pre-existing immune clones within Tumor MicroEnvironment (TME) suggest existence of a functional antigen presenting machinery and recognizing T cells, which fail to eliminate tumor, likely due to immunosuppressive environment. Shifts in composition of immune repertoire upon immune checkpoint blockade have been reported in adult cancers and shown to be associated with clinical response. As immunotherapy is being introduced to pediatric oncology, there is a need to better understand immunogenomic aspects of TME in childhood cancers. Objective: We hypothesize that characteristics of TCRs in conjunction with gene expression profile of immune cells are key determinants of immune response in pediatric patients. Methods: We compiled a pan-pediatric cohort and associated RNAseq datasets through multiple research initiatives. Participating programs include NCI TARGET (n ~ 270), International Cancer Genome Consortium (ICGC, n ~ 250) and Children’s Brain Tumor Tissue Consortium (CBTTC, n ~ 790). As comparator, we analyzed 7 adult cancer types as well as data from constitutive mismatch repair deficiency (CMMRD) consortium. We devised a simple and reliable index to estimate immune diversity. We used CIBERSORT tool to infer immune fraction of TME and investigated immune-related gene expression. In partnership with Gabriela Miller’s Kids First Data Resource Centre, analyses were performed on CAVATICA computational platform. Results: While median number of RNAseq reads were comparable across TARGET, CBTTC and TCGA datasets (~ 67-90 million reads), ICGC dataset contained a median of ~ 208 million reads. However, number of reads mapped to immune loci were comparable across all datasets and appeared to be confounded by infiltration extent rather than technical discordance. Our preliminary results indicate Neuroblastoma harbored the highest median of inferred diversity across pediatric cancers (TRβ=59.38). Inferred immune content indicated a range of infiltration from 0.59 in Teratoma/Germinoma to 0.15 in Medulloblastoma. Immune checkpoint gene expression across pediatric cancers show overall downward trend compared to adult counterparts. Conclusions: Our comprehensive study will serve as a common ground for researchers to delineate immune component of pediatric tumor microenvironment. Covered in this study are common solid tumors as well as rare malignancies, characterization of which will aid rational design of immunotherapy-related clinical trials of pediatric cancers. Note: This abstract was not presented at the meeting. Citation Format: Arash Nabbi, Natalie Jäger, Sumedha Sudhaman, Pengbo Sun, S. Y. Cindy Yang, Kelsey Zhu, Marcel Kool, Komal Rathi, Karthik Kalletla, Pichai Raman, Yuankun Zhu, Joseph N. Paulson, David T. Jones, Uri Tabori, Adam C. Resnick, Stefan M. Pfister, Trevor J. Pugh. Landscape of infiltrating immune repertoire in pediatric solid tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2891.

As an essential pillar of today’s cancer treatment, radiation therapy has led to improved survival rates of patients with childhood malignancies including leukemia and central nervous system (CNS) tumors. However, long-term complications such as radiation-induced malignancies occur in a subset of patients following radiation therapy, especially observed in pediatric patients due to their long follow-up period in case of survival. Radiation-induced glioblastomas (RIGs) have been reported in patients after treatment with cranial irradiation for various primary malignancies such as acute lymphoblastic leukemia (ALL) and medulloblastoma (MB). Histopathologically, most RIGs are best described as high-grade gliomas resembling de novo glioblastoma, and histopathological features to distinguish RIGs from their sporadic counterparts are lacking. Recent large-scale genomic and epigenomic analyses have revealed key genetic alterations in various types of CNS tumors. Here, we performed comprehensive (epi-)genomic and gene expression profiling of RIGs following radiation therapy for primary MB (n=24) and ALL (n=8). DNA methylation profiling demonstrates a high similarity of global DNA methylation patterns among RIGs, regardless of the primary malignancy. Known genetic alterations in high-grade gliomas such as PDGFRA amplification (53%, 17/32) and loss of CDKN2A/B (63%, 20/32) occur in RIGs. None of the RIGs harbored somatic hotspot mutations in genes encoding histone variants H3.3 and H3.1/H3.2 or IDH1/2, which are frequently observed in high-grade glioma subtypes of children and young adults. Germline alterations causing cancer predisposition syndromes were not found more frequently in RIG patients than in patients suffering from high-grade gliomas without previous irradiation treatment. The genetic homogeneity of RIGs with the absence of histone 3 and IDH1/2 mutations suggests that RIGs share a common cell of origin, which might be particularly vulnerable to radiation. We performed in vitro drug screens on patient-derived RIG tumor spheres, exhibiting amplified and overexpressed PDGFRA, alongside with non-PDGFRA-amplified GBM cell lines to assess the potential efficacy of RTK inhibitors. The median latency time between cranial irradiation and RIG occurrence was 4.5 years (range: 2.5-15). Patients treated for ALL were diagnosed with RIG at age 9-14 years, exposing a particularly vulnerable but narrow time frame for RIG occurrence in ALL patients, in contrast to RIG patients treated for MB (range: 3-39 years). In summary, our study uncovers diagnostic biomarkers and potential targetable alterations in RIG, which could become relevant for the stratification into future clinical trials with e.g. specific RTK inhibitors, with the objective of improving the outcome of survivors of childhood cancer. Citation Format: Maximilian Y. Deng, Dominik Sturm, Elke Pfaff, Gnana P. Balasubramanian, Jens Schittenhelm, Martin Ebinger, Martin U. Schuhmann, Andrey Korshunov, Andreas von Deimling, Olaf Witt, Stefan M. Pfister, David T. Jones. (Epi-)genomic homogeneity in radiation-induced glioblastoma with recurrent PDGFRA amplification and loss of CDKN2A/B following primary acute lymphatic leukemia and medulloblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3646.

Therapies targeting PD-1 are used in multiple cancer types. While a fraction of patients show durable therapeutic responses, most remain unresponsive, highlighting an urgent need to better understand and improve these therapies. Using an in vivo screening approach with a customized shRNA pooled library, we identified DDR2 as a leading target for the enhancement of response to anti-PD-1 immunotherapy. Using isogenic in vivo murine models across five different tumor histologies, bladder, breast, colon, sarcoma and melanoma, we show that DDR2 depletion increases sensitivity to anti-PD-1 treatment compared to monotherapy. Combination treatment of tumor-bearing mice with anti-PD-1 and dasatinib, a tyrosine kinase inhibitor of DDR2, also led to tumor load reduction and in some cases, complete clearance. RNAseq and CyTOF analysis revealed higher CD8+ T cell populations in tumors with DDR2 depletion and those treated with dasatinib when either was combined with anti-PD-1 treatment. Our work provides strong scientific rationale for targeting DDR2 in combination with PD-1 inhibitors. Citation Format: Megan M. Tu, Francis Y. Lee, Robert T. Jones, Abigail K. Kimball, Elizabeth Saravia, Robert F. Graziano, Brianne Coleman, Krista Menard, Jun Yan, Erin Michaud, Han Chang, Hany A. Abdel-Hafiz, Andrii I. Rozhok, Jason E. Duex, Neeraj Agarwal, Ana Chauca-Diaz, Linda K. Johnson, Terry L. Ng, John C. Cambier, Eric T. Clambey, James C. Costello, Alan J. Korman, Dan Theodorescu. DDR2 inhibition enhances response to anti-PD-1 immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4085.

Gemcitabine and cisplatin (GC) combination neoadjuvant chemotherapy (NAC) followed by radical cystectomy (RC) is the standard of care for treating muscle-invasive bladder cancer (MIBC). Approximately 25% of patients experience complete pathologic response (pT0), while the remaining ~75% have residual disease and poorer prognosis. Therefore, defining mechanisms that enable bladder cancer cells to survive NAC will allow us to I) identify predictive biomarkers of response to NAC and improve MIBC patient stratification for NAC, and II) define novel genetic dependencies in GC-resistant bladder cancers for future drug development. We have performed RNA sequencing on a panel of six genetically diverse urothelial cancer cell lines, each with matched derivatives possessing acquired resistance to single agent gemcitabine, cisplatin, and combination GC. Initial analyses of RNA sequencing data has revealed hundreds of differentially expressed genes and associated pathways as potential drivers of resistance to these agents. Examples of significantly dysregulated pathways seen in gene set enrichment analyses implicate a range of pathways known to be associated with many diverse cellular processes such as: extracellular matrix organization, invasion and migration, interferon signaling, lipid and cholesterol metabolism and cellular differentiation status, among others. Importantly, these candidates include both shared and context-specific resistance phenotypes, which vary based on the genetic and molecular alterations found in the parental cell line. To complement these transcriptomic profiling experiments and to better understand how these changes in gene expression relate to mutation status and pathway activation status on the protein level, we have performed whole-exome sequencing, and are currently conducting phospho-proteomic profiling with reverse-phase protein microarray to enable more integrative analyses. Together the complement of transcriptomic, genomic and proteomic analyses will facilitate a more comprehensive assessment of which molecular patterns are drivers of resistance in our resistant cell lines. Finally, we have taken a more systematic approach to define functional genetic dependencies acquired in these NAC-resistant cells. To accomplish this we have performed whole-genome CRISPR knockout screening on the combined GC-resistant cells to identify vulnerabilities associated with GC-resistance. Taken together, our data provide a deep look into the context-specific and shared molecular mechanisms driving resistance to GC chemotherapy and provide a rational basis for the future development of molecularly guided therapies for NAC resistant bladder cancers. Citation Format: Robert T. Jones, Tahlita C. Zuiverloon, Hedvig Vekony, Andrew Goodspeed, Teemu D. Laajala, Molishree Joshi, Colin Sempeck, Megan Tu, James C. Costello, Dan Theodorescu. Integrative molecular and functional genomic analysis of chemotherapy resistant bladder cancer cell lines identifies novel mediators of therapeutic response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2107.

Introduction: Pediatric high-grade glioma (pHGG) are a group of aggressive and difficult-to-treat childhood brain tumors (1), including grade III and IV anaplastic astrocytoma, and diffuse intrinsic pontine glioma (DIPG); the latter occurs almost exclusively in children. Aggressive, multidisciplinary treatment approaches incorporate surgery (where possible) followed by adjuvant chemo- and radiotherapy. Despite this treatment regimen, clinical prognosis remains poor, characterized by drug resistance and significant toxicity (2). There is an urgent need to identify novel therapeutic approaches that are more effective with reduced side effects. pHGG are increasingly characterized into distinct molecular subgroups, based on gene expression and epigenetic regulation (3). Critical to identifying novel therapeutic agents (and associated targets) for pHGG patients is understanding the complex biology of tumor cells further and elucidating the mechanisms pHGG utilize to proliferate and survive (4). The identification of these critical “survival” genes facilitates the design of pHGG target-specific compounds, potentially improving clinical prognosis. Methods and Results: Using a CRISPR-Cas9 Loss of Function (LOF) genome-wide gene engineering technology, we have silenced 19,050 genes across the human genome in a pHGG in vitro model. Silencing genes that are essential for survival results in cell death and the loss of this gene from the population. This LOF is identified by next-generation sequencing (NGS) of the CRISPR-Cas9 constructs in the Reference (immediately after initial CRISPR-Cas9 edit) and Experiment (following 6 cell doublings) population. We have analyzed these data using a custom-designed bioinformatics pipeline to identify genes absent from the experiment population, and further, to identify signaling pathways based on gene cluster analysis, that are essential for pHGG cell survival. With these results, we will select both novel and repurposed chemotherapeutics that interact with (by activating or repressing target genes, and their associated proteins) for further characterization, analysis, and study in patient-derived cell lines and primary biopsy tissue. Future Work: This work will identify novel pHGG survival genes and substantially contribute to our understanding of pHGG tumor biology, facilitating the identification of novel therapeutics or repurposed agents for progression into the clinic. We hypothesize that targeting multiple genes within key survival pathways with a combined treatment regimen will lead to more complete pathway abrogation, increasing treatment efficacy, circumventing resistance, and reducing adverse toxicity. Key Message: pHGG are highly aggressive and resistant to current therapeutics. There is an urgent need to identify novel therapeutics for progression to the clinic. Using CRISPR-Cas9 technology we have silenced 19,050 pHGG genes to determine which genes are specific to pHGG survival. Identification of these genes will aid the design of novel therapeutics for pHGG. We hypothesize that using a combined drug treatment approach for complete pathway disruption will increase efficacy and minimize adverse side effects. References: 1. Rizzo D et al. Molecular biology in pediatric high-grade glioma: Impact on prognosis and treatment. Biomed Res Int 2015;1:10. 2. Stupp R et al. Effects of radiotherapy with concomitant and adjuvant temozolomide versus radiotherapy alone on survival in glioblastoma in a randomised phase III study: 5-year analysis of the EORTC-NCIC trial. Lancet Oncol 2009;10:459-66. 3. Jones C, Baker SJ. Unique genetic and epigenetic mechanisms driving paediatric diffuse high-grade glioma. Nat Rev Cancer 2014;14. 4. Jones C et al. Pediatric high-grade glioma: Biologically and clinically in need of new thinking. Neuro Oncol 2016;now101. Citation Format: Alison Howarth, Dylan Jones, Daniel Ebner, Anbarasu Lourdusamy, Ruman Rahman, Geoff Pilkington, Richard Hill. Gene editing with CRISPR-Cas9: Investigating novel therapeutic targets for the treatment of pediatric high-grade glioma [abstract]. In: Proceedings of the AACR Special Conference: Pediatric Cancer Research: From Basic Science to the Clinic; 2017 Dec 3-6; Atlanta, Georgia. Philadelphia (PA): AACR; Cancer Res 2018;78(19 Suppl):Abstract nr A34.

Activation of the canonical TGF-β signaling pathway provides growth inhibitory signals in the normal intestinal epithelium. Colorectal cancers (CRCs) frequently harbor somatic mutations in the pathway members TGFBR2 and SMAD4, but to what extent mutations in SMAD2 or SMAD3 contribute to tumorigenesis is unclear. A cohort of 744 primary CRCs and 36 CRC cell lines were sequenced for SMAD4, SMAD2, and SMAD3 and analyzed for allelic loss by single-nucleotide polymorphism (SNP) microarray analysis. Mutation spectra were compared between the genes, the pathogenicity of mutations was assessed, and relationships with clinicopathologic features were examined. The prevalence of SMAD4, SMAD2, and SMAD3 mutations in sporadic CRCs was 8.6% (64 of 744), 3.4% (25 of 744), and 4.3% (32 of 744), respectively. A significant overrepresentation of two genetic hits was detected for SMAD4 and SMAD3, consistent with these genes acting as tumor suppressors. SMAD4 mutations were associated with mucinous histology. The mutation spectra of SMAD2 and SMAD3 were highly similar to that of SMAD4, both in mutation type and location within the encoded proteins. In silico analyses suggested the majority of the mutations were pathogenic, with most missense changes predicted to reduce protein stability or hinder SMAD complex formation. The latter altered interface residues or disrupted the phosphorylation-regulated Ser-Ser-X-Ser motifs within SMAD2 and SMAD3. Functional analyses of selected mutations showed reductions in SMAD3 transcriptional activity and SMAD2–SMAD4 complex formation. Joint biallelic hits in SMAD2 and SMAD3 were overrepresented and mutually exclusive to SMAD4 mutation, underlining the critical roles of these three proteins within the TGF-β signaling pathway. Cancer Res; 73(2); 725–35. ©2012 AACR.

Introduction: Rova-T (SC16LD6.5) is an ADC targeting delta-like protein 3 (DLL3), a member of the delta-notch signaling pathway, composed of the monoclonal antibody SC16 conjugated to the DNA-damaging D6.5 pyrrolobenzodiazepine (PBD) dimer toxin. In clinical trials, Rova-T demonstrated anti-tumor activity in patients with small cell lung cancer with high DLL3 protein expression. We have identified DLL3 as highly expressed in NBs, especially the MYCN-amplified subset. Here, we characterize the expression of DLL3 in NB patient derived xenografts (PDX), and define the efficacy of Rova-T in these models ex vivo and in vivo. Methods: To assess DLL3 protein expression, we performed immunohistochemistry (IHC) on 32 PDXs from high-risk human primary tumors in tissue microarrays. We quantified cell surface DLL3 from dissociated PDX tumors using immunoblotting and flow-cytometry with a PE-conjugated DLL3 antibody. The cytotoxic activity of Rova-T against 8 dissociated PDXs placed in short term culture was evaluated using cell viability assays and a testing range of 10 fm to 10 nM. The in vivo activity of Rova-T was tested against 3 NB PDX models (Felix-PDX, COG-N-452x and COG-N-415x) using single intraperitoneal injection on day 0. Treatment groups included: vehicle control, IgGADC6.5 at 0.6 mg/kg, and Rova-T at 0.1 mg/kg, 0.3 mg/kg or 0.6 mg/kg. Events were defined as quadrupling of tumor volume from day 0. Results: DLL3 protein was expressed in 27 of 32 NB PDXs. The median percentage of tumor cells with a ≥ 2+ intensity was 25%-55% in 12/27 samples, 55%-85% in 8/27 samples and 85%-100% in 7/27 samples. The relative IHC scores in the tested samples correlated with levels of cell surface DLL3 and with DLL3 protein and RNA expression levels assessed by immunoblotting and RNAseq. Rova-T showed IC50 values from 0.026-47.25 nM, whereas PBD alone showed IC50 values from 0.003-0.345 nM. Tumors that expressed high DLL3 levels did not necessarily show a higher sensitivity to Rova-T ex vivo. In vivo, Rova-T induced significant differences in EFS distribution compared to control in 3 of 3 PDX models treated with 0.6 mg/kg and in 1 of 2 PDX models dosed at 0.1 and 0.3 mg/kg. All 3 PDX models showed a >2-fold extension in median EFS for treated compared to control animals at 0.6 mg/kg. Two PDXs, COG-N-452x and Felix-PDX, had a minimum relative tumor volume Conclusions: These data suggest that targeting DLL3 using an ADC approach in NB could be an active therapeutic strategy. Studies are ongoing to further explore biomarkers of response as DLL3 expression alone may be insufficient for NB. Citation Format: Renata Sano, Kateryna Krytska, Matthew Tsang, Stephen W. Erickson, Beverly A. Teicher, Laura Saunders, Ryan T. Jones, Malcom A. Smith, John M. Maris, Yael P. Mosse. Pediatric Preclinical Testing Consortium evaluation of a DLL3-targeted antibody drug conjugate rovalpituzumab tesirine, in neuroblastoma [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 LB-136.

Cell cycle checkpoints play critical roles in the maintenance of genomic integrity. The inactivation of checkpoint genes by genetic and epigenetic mechanisms is frequent in all cancer types, as a less-efficient cell cycle control can lead to genetic instability and tumorigenesis. In an on-going case-control study consisting of 216 patients with non–small cell lung cancer, 226 population-based controls, and 114 hospital-based controls, we investigated the relationship of γ-radiation-induced G2-M arrest and lung cancer risk. Peripheral blood lymphocytes were cultured for 90 hours, exposed to 1.0 Gy γ-radiation, and harvested at 3 hours after γ-radiation treatment. γ-Radiation-induced G2-M arrest was measured as the percentage of mitotic cells in untreated cultures minus the percentage of mitotic cells in γ-radiation-treated cultures from the same subject. The mean percentage of γ-radiation-induced G2-M arrest was significantly lower in cases than in population controls (1.18 versus 1.44, P < 0.01) and hospital controls (1.18 versus 1.40, P = 0.01). When dichotomized at the 50th percentile value in combined controls (population and hospital controls), a lower level of γ-radiation-induced G2-M arrest was associated with an increased risk of lung cancer among African Americans after adjusting for baseline mitotic index, age, gender, and pack-years of smoking [adjusted odd ratio (OR), 2.25; 95% confidence interval (95% CI), 0.97-5.20]. A significant trend of an increased risk of lung cancer with a decreased level of G2-M arrest was observed (Ptrend = 0.02) among African Americans, with a lowest-versus-highest quartile adjusted OR of 3.74 (95% CI, 0.98-14.3). This trend was most apparent among African American females (Ptrend < 0.01), with a lowest-versus-highest quartile adjusted OR of 11.75 (95% CI, 1.47-94.04). The results suggest that a less-efficient DNA damage–induced G2-M checkpoint is associated with an increased risk of lung cancer among African Americans. Interestingly, we observed a stronger association of DNA damage–induced G2-M arrest and lung cancer among African Americans when compared with Caucasians. If replicated, these results may provide clues to the exceedingly high lung cancer incidence experienced by African Americans.

Background: Brain metastases are associated with a dismal prognosis. There is a limited understanding of the oncogenic alterations harbored by brain metastases and whether these are shared with their primary tumors. Our objectives were to (1) elucidate the evolutionary patterns leading to brain metastases and (2) identify whether brain metastases are genetically distinct from their primary tumors and other distal metastatic sites. Methods: We performed whole-exome sequencing of 104 matched brain metastases, primary tumors and normal tissue, including 7 cases with spatially and temporally separated brain metastasis sites and 8 cases with additional extracranial disease sites, including regional lymph nodes, and distal metastases. We developed novel computational tools to perform an integrative analysis of somatic mutations and copy-number alterations. This analysis allowed us to estimate the clonal architecture of the primary and metastases, and to reconstruct a phylogenetic tree relating the subclones from each patient. Results: In all related cancer samples, we observed branched evolution, where all metastatic and primary sites shared a common ancestor yet continued to evolve independently. In 53% of cases, we found clinically actionable driver alterations in the brain metastases that were not detectable in the matched primary-tumor sample. In contrast, spatially and temporally separated brain metastasis sites were more genetically homogenous and shared nearly all driver alterations detected. Extracranial metastases and regional lymph nodes were highly divergent from brain metastases. Several clinically actionable pathways were enriched in brain metastases. Conclusions: These observations demonstrate that brain metastasis tissue provides an opportunity to identify clinically important driver alterations that may be undetected in single samples of primary tumors, regional lymph nodes, or extracranial metastases. Genetic divergence between primary tumors and brain metastases may underlie some of the difficulties encountered with the combined treatment of systemic disease and brain metastases in patients. When clinically feasible, genomic characterization of brain metastasis tissue should be considered when selecting therapeutic agents for patients with brain metastases. Citation Format: Priscilla K. Brastianos, Scott L. Carter, Sandro Santagata, Daniel Cahill, Amaro Taylor-Weiner, Robert T. Jones, Eliezer Van Allen, Peleg Horowitz, Keith L. Ligon, William T. Curry, Ian F. Dunn, Paul Van Hummelen, Matthew Meyerson, Levi Garraway, Josep Tabernero, Joan Seoane, Stacey Gabriel, Eric S. Lander, Rameen Beroukhim, Tracy T. Batchelor, Jose Baselga, David N. Louis, William C. Hahn, Gad Getz. Genomic characterization of brain metastases reveals branched evolution and metastasis-specific mutations. [abstract]. In: Proceedings of the AACR Special Conference: Advances in Brain Cancer Research; May 27-30, 2015; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2015;75(23 Suppl):Abstract nr PR04.

Background: Brain metastases represent an unmet need in current oncologic care. Approximately 8-10% of cancer patients will develop brain metastases, and more than half of these patients will pass away within a few months of their diagnosis. We have a limited understanding of how brain metastases genetically evolve from their primary tumors. Our objectives were to (1) elucidate the genomic evolutionary patterns leading to brain metastases (2) identify whether brain metastases harbor clinically significant genetic differences compared to their primary tumors and other extracranial metastatic sites, and (3) examine the extent of genetic heterogeneity across regionally separated and anatomically distinct sites of brain metastasis. Methods: We subjected 104 matched primary tumor biopsies, brain metastases, and normal tissue to whole exome sequencing, including 20 cases with regionally and anatomically separated brain metastasis sites, regional lymph nodes, and distal extracranial metastases. We performed an integrative analysis of somatic single nucleotide variants and copy-number alterations to reconstruct phylogenetic trees relating the subclones from each patient. We analyzed evolutionary relationships between related cancer samples and annotated phylogenetic trees with clinically significant genetic alterations. Results: Every brain metastasis displayed branched evolution: the brain metastasis and primary tumor shared a common ancestor yet both the primary tumor and brain metastasis continued to evolve independently. We found novel clinically actionable genetic alterations that were exclusive to brain metastases in 56% of cases. The brain metastases were also enriched for several pathways, some pathways specific to a particular histology. Distal extracranial metastases and regional lymph nodes were highly divergent from brain metastases, and in no cases, did we observe an extracranial site that closely resembled the brain metastasis. In contrast, regionally and anatomically separated brain metastasis sites were genetically homogenous and shared nearly all genetic alterations detected. Conclusions: Brain metastases are genetically divergent from primary tumors. Clinically, these observations demonstrate that biopsies of primary tumors fail to capture the heterogeneity with patients with brain metastases, potentially missing clinically actionable mutations in these life-threatening metastases. Notably, regional lymph nodes and distal extracranial metastases were not reliable genetic surrogates for brain metastases. When clinically feasible, characterization of even a single brain metastasis lesion is superior to that of a primary or lymph node biopsy for selection of a targeted therapeutic agent. Citation Format: Priscilla K. Brastianos, Scott L. Carter, Sandro Santagata, Amaro Taylor-Weiner, Robert T. Jones, Eli Van Allen, Keith L. Ligon, Josep Tabernero, Joan Seoane, Elena Martinez-Saez, Daniel Cahill, William T. Curry, Ian F. Dunn, Sun Ha Paek, Paul Van Hummelen, Aaron R. Thorner, Bruce E. Johnson, Nancy U. Lin, Toni K. Choueiri, Michael S. Rabin, Rameen Beroukhim, Anat Stemmer-Rachamimov, Matthew Meyerson, Levi Garraway, Tracy Batchelor, Jose Baselga, David N. Louis, William C. Hahn, Gad Getz. Genomic characterization of brain metastases reveals divergent evolution and metastasis specific mutations. [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 4727. doi:10.1158/1538-7445.AM2015-4727

Cellular iron is needed for cell survival and hydroxylation of hypoxia-inducible factor-1α (HIF-α) by prolyl hydroxylases (PHD). One mechanism of iron uptake is mediated by the cell surface transferrin receptor (TfR). Because iron is required for cell growth and suppression of HIF-α levels, we tested the effects of the two anti-TfR monoclonal antibodies (mAb) E2.3 and A27.15 on growth of breast cancer cells and induction of HIF-α and hypoxia-regulated genes. Treatment with both mAbs together synergistically inhibited cell proliferation in a dose-responsive manner by up to 80% following 8 days of exposure, up-regulated HIF-1α and HIF transcription targets, down-regulated TfR expression, and down-regulated cellular labile iron pool by 60%. Because combined treatment with anti-TfR mAbs resulted in the up-regulation of the hypoxia pathway, which may increase tumor angiogenesis, we analyzed the effects of ascorbate on cell viability and HIF-1α levels in cells treated with both anti-TfR mAbs together, as ascorbate has been shown to be required by PHD enzymes for full catalytic activity. Ascorbate at physiologic concentrations (25 μmol/L) suppressed HIF-1α protein levels and HIF transcriptional targets in anti-TfR mAb-treated cells but did not suppress the antiproliferative effect of the mAbs. These results indicate that the addition of ascorbate increased the activity of the PHD enzymes in down-regulating HIF but not the proliferation of iron-starved anti-TfR mAb-treated cells. The use of anti-TfR mAbs and ascorbate in inhibiting both cell proliferation and HIF-1α and angiogenesis under normoxic conditions may be of therapeutic use. (Cancer Res 2006; 66(5): 2749-56)

Craniopharyngiomas are epithelial tumors that typically arise in the suprasellar region of the brain. Patients experience substantial clinical sequelae both from extension of the tumors and from therapeutic interventions which damage the optic chiasm, the pituitary stalk, and the hypothalamic area. Using whole exome sequencing we identified mutations in beta-catenin (CTNNB1) in nearly all adamantinomatous craniopharyngiomas (11/12; 92%) and recurrent mutations in BRAF (V600E) in all papillary craniopharyngiomas (3/3; 100%). Targeted genotyping revealed BRAF V600E in 95% of papillary craniopharyngiomas (36 of 39 tumors) and CTNNB1 mutation in 96% of adamantinomatous craniopharyngiomas (51 of 53 tumors). The CTNNB1 and BRAF mutations were clonal in each tumor subtype and no other recurrent mutations or genomic aberrations were detected in either subtype. Adamantinomatous and papillary craniopharyngiomas harbor mutations that are mutually exclusive and clonal. These findings have important implications for the diagnosis and treatment of these neoplasms. Citation Format: Amaro N. Taylor-Weiner, Priscilla K. Brastianos, Peter E. Manley, Robert T. Jones, Dora Dias-Sangata, Aaron Thorner, Fausto Rodriguez, Lindsay Bernardo, Laura Schubert, Chip Stewart, Mark Keiran, William C. Hahn, Adam Resnick, David Louis, Sandro Sangata, Gad Getz. Exome sequencing reveals BRAF mutations in papillary craniopharyngiomas. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 935. doi:10.1158/1538-7445.AM2014-935

Background: Brain metastases are the most frequently occurring intracranial tumors in adults. Median survival after the diagnosis of a brain metastasis is in the order of a few months. Despite its large burden of disease and devastating clinical sequelae, we continue to have a limited understanding of how brain metastases evolve from their primary tumor. Our objectives were to (1) elucidate the evolutionary patterns leading the brain metastases and (2) identify whether brain metastases are genetically distinct from their matched primary tumors. Materials and Methods: We subjected 101 trios consisting of primary tumor, brain metastasis, and matched normal tissue to whole exome sequencing (WES). To analyze the data, we developed novel computational tools to perform an integrative analysis of somatic single nucleotide variants (SSNVs) and somatic copy-number alterations (SCNAs). This analysis allowed us to estimate the clonal architecture of the primary and metastatic samples from each patient, and to reconstruct a phylogenetic tree relating all of the subclones.Results: Every metastasis developed from a single clone, consistent with a single cell of origin. We did not detect evidence of self-seeding or a multiclonal origin of metastasis. In all cases, we observed a sibling or a branched evolutionary relationship; the brain metastasis and primary tumor share a common ancestor, but there was continued evolution in the primary tumor reflected by fully clonal mutations in the primary biopsy that were not present in the metastasis. When we average over all the phylogenetic trees, 61% of mutations are present in the common ancestor, 24% are unique to the metastasis and 15% are unique to the primary tumor. Subclonal mutations in the metastasis by definition occurred within the brain; these mutations displayed different mutational signatures than those acquired in the primary tumor. These contrasts were most pronounced in cases of lung cancer or melanoma, with tobacco and UV signatures prominent in these primaries and nearly absent from the mutations acquired after metastasis. In order to understand the molecular drivers of clonal evolution and metastasis in our data, we annotated each subclone with driver mutations identified using large numbers of cancer samples analyzed by the cancer genome atlas (TCGA) consortium. This produced a detailed portrait of each patient's cancer, with nearly node in each phylogenetic tree associated with at least one known driver. We found novel drivers, many of which are known actionable targets, in the clonal and subclonal populations within the brain metastases that were not present in the primary tumor. This suggests ongoing evolution within the brain. Similarly, novel subclonal and clonal drivers were detected in the biopsy of the primary tumor that were not present in the metastasis. The brain metastases were enriched for several pathways when compared to their matched primary tumors, some pathways specific to a particular histologic subtype.Conclusions: In this study, we report the latest results of the largest massively parallel sequencing study to date of matched brain metastases and primary tumors. We used intratumoral heterogeneity estimates to elucidate the evolutionary patterns observed in the process of metastasis. This study shifts our understanding of the metastasis paradigm and sheds light on the evolutionary and molecular mechanisms that are critical for brain metastasis. Our data suggests that single biopsies do not capture the heterogeneity within patients. Assessment of the subclonal phylogenetic architecture of primaries and their metastases should be considered when selecting targeted agents for patients with brain metastases. Citation Format: Priscilla K. Brastianos, Scott L. Carter, Sandro Santagata, Amaro Taylor-Weiner, Robert T. Jones, Peleg M. Horowitz, Keith L. Ligon, Joan Seaone, Elena Martinez-Saez, Josep Tabernero, Daniel P. Cahill, Sun-Ha Paek, Ian F. Dunn, Bruce E. Johnson, Toni K. Choueiri, Michael S. Rabin, Eric P. Winer, Nancy U. Lin, Paul Van Hummelen, Anat Stemmer-Rachamimov, Rameen Beroukhim, David L. Louis, Tracy T. Batchelor, Jose Baselga, Gad Getz, William C. Hahn. Genomic characterization of 101 brain metastases and paired primary tumors reveals patterns of clonal evolution and selection of driver mutations. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr NG03. doi:10.1158/1538-7445.AM2014-NG03

Next-generation sequencing (NGS) is increasingly used in the laboratory and clinic to identify genomic factors contributing to tumorigenesis, such as somatic mutations, DNA insertions and deletions, transcriptome and epigenetic changes, and chromosomal abnormalities. Because tumor specimen tissues are often quite limited or are from rare and precious samples, it is necessary to prepare sequencing libraries from minimal amounts of DNA. Consequently, limited DNA input necessitates amplification during NGS library preparation. Therefore, it is of great importance to amplify the library in an efficient and uniform manner to achieve reproducible amplification of the library fragments and limit GC content bias. Variable GC-bias among libraries is of particular importance for copy number variant (CNV) detection based on sequence coverage. Here, we compare the TruSeq DNA Sample Preparation Kit (Illumina Inc., San Diego, CA) and the KAPA Library Preparation Kit (Kapa Biosystems, Wilmington, MA) to determine which technique achieves optimal library coverage. The major difference between the methods is the DNA polymerase used for library enrichment. The Kapa HiFi polymerase was engineered to have higher fidelity and increased DNA affinity relative to the Herculase II Fusion DNA Polymerase (Agilent Technologies, Inc., Santa Clara, CA) that we used for library enrichment with the TruSeq kit. Thus, the Kapa HiFi polymerase should more efficiently amplify targets across a larger GC content range and improve sequence coverage uniformity. Relative to TruSeq-prepared libraries, the Kapa-prepared libraries had a larger mean insert size, more uniform coverage distribution, and better coverage of GC-rich regions of the genome. This was observed for DNA extracted from blood, cell lines, and formalin-fixed paraffin embedded (FFPE) tumor samples. More experiments are underway to determine the effect of the improved recovery of high-GC content DNA fragments on CNV detection. Citation Format: Aaron R. Thorner, Ashwini Sunkavalli, Ling Lin, Robert T. Jones, Laura Schubert, Matthew D. Ducar, Ravali Adusumilli, Deniz Nesli Dolcen, Liuda Ziaugra, Jack Lepine, Laura E. MacConaill, William C. Hahn, Matthew Meyerson, Paul Van Hummelen. Reducing GC-bias and improving coverage distribution in Illumina sequencing using the Kapa Biosystems library construction method. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3583. doi:10.1158/1538-7445.AM2014-3583

Formalin fixation followed by paraffin embedding (FFPE) is the most widely used method of tissue preservation and often used in the clinical setting for cancer specimens. However, this process of fixation has negative consequences on the quality of extracted DNA, and inevitably adversely affects downstream analyses such as next generation sequencing (NGS). DNA extraction from FFPE samples requires paraffin disassociation, tissue rehydration and de-crosslinking. Low efficiency in any step will yield low quantities of nucleic acids with incomplete reversal of formaldehyde crosslinks, and mixtures of single and double stranded DNA. In addition, low quality nucleic acids will often result in poor sequencing quality due to inefficient library preparation, lower number of reads with high quality, and variable recovery of sequence reads with high GC-content. Here we describe the use of Adaptive Focused Acoustics technology (Covaris Inc. 2013) to remove paraffin and break down tissue, and we compared this method to traditional xylene-based paraffin removal. We found that Covaris had superior performance overall: (1) DNA yields were 6 times higher, and less specimens failed extraction: this is critically important when dealing with small tumor biopsies. (2) DNA was more readily available for PCR amplification. (3) Mean coverage of DNA fragments with high GC content was higher and more reproducible. (4) Library complexity was higher. In addition, the Covaris protocol required less hands-on time in the lab, and eliminated the need for hazardous organic solvents for paraffin removal. In conclusion, the Covaris FFPE DNA extraction method is very efficient, enhances DNA availability, improves reproducibility and provides higher DNA quality for NGS. Citation Format: Ling Lin, Mikenah Vega, Robert T. Jones, Liuda Ziaugra, Deniz N. Dolcen, Ashwini Sunkavalli, Laura Schubert, Jack R. Lepine, Aaron R. Thorner, Matthew D. Ducar, William C. Hahn, Matthew L. Meyerson, Laura E. MacConaill, Paul Van Hummelen. Improved FFPE DNA extraction for next generation sequencing using adaptive focused acoustics technology. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4286. doi:10.1158/1538-7445.AM2014-4286

Recent expression profile analyses revealed that lung adenocarcinomas can be divided into several subgroups with diverse pathological features. Because cellular heterogeneity of tumors can confound these analyses, we used laser capture microdissection and microarray expression analysis to characterize the molecular profiles of lung adenocarcinomas. We found 45 genes delineating smokers and nonsmokers that were located at chromosomal loci frequently altered in non-small cell lung cancers, and 27 genes, which were differentially expressed between survivors and nonsurvivors 5 years after surgery. These results are consistent with the hypothesis that the abnormal expression of genes involved in maintaining the mitotic spindle checkpoint and genomic stability, e.g., hBUB3, hZW10, and APC2, contribute to the molecular pathogenesis and tumor progression of tobacco smoke-induced adenocarcinoma of the lung.

This study reports on the biodistribution and metabolism of the 11C-labeled novel antitumor agent N-[2-(dimethylamino)ethyl]acridine-4-carboxamide (DACA) (also known as NSC 601316) in rats (plasma and tissues) and humans (plasma). Information on plasma metabolites was uniquely obtained in humans prior to Phase I clinical trial following i.v. injection of [11C]DACA at tracer dose. DACA was labeled in the N-methyl position using no-carrier-added [11C]iodomethane. Rapid high-performance liquid chromatography methods were developed for metabolite analysis of [11C]DACA. The metabolism of [11C]DACA was investigated in patients by plasma sampling. The biodistribution and metabolism of [11C]DACA was investigated in rats by plasma sampling, sacrifice experiments with tissue analyses, and imaging using positron emission tomography scanning. Analysis of human plasma demonstrated rapid and extensive metabolism of [11C]DACA. The levels of [11C]DACA changed from 77 +/- 8% (SD) at 5 min to 25 +/- 5% at 45 min postinjection. Seven radioactive metabolites were observed in human plasma, and one was identified as [11C]DACA-N-oxide. Rapid clearance of 11C radioactivity from rat blood, plasma, and major organs was observed. The half-life of 11C radioactivity clearance in rat blood between 15 and 90 min was calculated to be 3.2 h; the levels of [11C]DACA in rat plasma decreased from 69 +/- 3% (SD) at 2 min to 29 +/- 1.5% at 25 min. The number of radioactive metabolites in rat plasma was the same as in human plasma except that the proportions differed. Again, one metabolite was identified as the [11C]DACA-N-oxide. Analysis of rat tissues showed rapid and extensive metabolism in tissues, particularly liver and kidney; however, [11C]DACA (i.e., the parent compound) was the major radioactive component in the lung, heart, and brain over 40 min. Positron emission tomography scanning using [11C]DACA in the rat showed little retention of 11C radioactivity in major organs with rapid excretion via gut and kidney. The rat data were consistent with animal (mouse and rat) preclinical data obtained with preexisting techniques with longer-lived isotopes. Labeling of potential anticancer drugs with positron-emitting radionuclides and performing in vivo preclinical evaluation at tracer doses in animals and humans prior to Phase I clinical trials provides unique information that could speed up the assessment of the drug and could potentially assist drug development programs. In this example, there was no unexpected interspecies difference in metabolism of DACA that would have alerted us to make a change in the planned Phase I study.

The ability to harness the power of next generation sequencing for characterizing the cancer genome would be extremely valuable to the cancer research community and ultimately improve diagnosis and individualized therapy. We present a targeted approach using massively parallel sequencing to simultaneously detect mutations, translocations and copy-number variations in archived clinical tumor specimen. Targeted sequencing was achieved by designing RNA baits to capture the exons of 504 genes with relevance to cancer. The bait set was augmented with specific intronic sequences to detect translocations often involved in cancer. The overall performance of the hybrid capture was improved by optimizing the tiling strategy of the baits. These improvements significantly shifted fragments with low or no-coverage closer to the overall mean, resulting in a more uniform coverage distribution. To validate the targeted gene panel we sequenced tumor samples harboring mutations, translocations and copy-number alterations that were previously identified by clinically approved assays. All the known alterations were confirmed with additional potentially actionable mutations. The ultimate goal of the targeted panel is to screen cancer patients quickly and economically allowing simultaneous detection of all common genomic alterations in the cancer genome. Citation Format: Paul Van Hummelen, Matthew Ducar, Robert T. Jones, Alina Raza, Ashwini Sunkavalli, Megan Hanna, Adri Mills, Ravali Adusumilli, Prateek Kumar, Laura Schubert, Marc Breneiser, Anna C. Cooley, Elizabeth Garcia, Lynette M. Scholl, Neal I. Lindeman, Nikhil Wagle, Levi Garraway, Kristian Cibulskis, Scott L. Carter, Michael Lawrence, Gad Getz, Matthew L. Meyerson, William C. Hahn, Laura E. MacConaill. Targeted sequencing to detect somatic mutations, translocations and copy-number variation in human tumors simultaneously. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 819. doi:10.1158/1538-7445.AM2013-819

Meningiomas are the most common primary brain tumor in the US. While many Grade I meningiomas are cured by surgery, 20% recur and are minimally responsive to systemic therapy. Meningiomas of higher grades are particularly challenging to treat and are associated with a poor prognosis. Though the tumor suppressor gene NF2 has been linked to meningiomagenesis, the spectrum of genetic changes in meningiomas remains poorly understood, particularly in the large subset of tumors without NF2 alterations. We performed whole-exome or whole-genome sequencing on 17 meningiomas and focused sequencing using a 645 gene-set on an additional 48 tumors. The majority of meningiomas exhibited simple genomes, with fewer copy-number alterations, mutations, and rearrangements compared to other adult tumors. However, several meningiomas harbored more complex patterns of copy-number changes and rearrangements including one tumor with chromothripsis. We confirmed focal NF2 inactivation in 43% of tumors. A subset of NF2-wildtype meningiomas harbored recurrent oncogenic mutations in AKT1 and the Hedgehog pathway regulator SMO. Tumors with these mutations varied histologically from their NF2-mutated counterparts, and exhibited immunohistochemical evidence of pathway activation. These results begin to define the spectrum of genetic alterations in meningiomas. Our findings of known driver oncogenic mutations including AKT1 and SMO have immediate therapeutic potential. Citation Format: Priscilla Brastianos, Peleg M. Horowitz, Sandro Santagata, Robert T. Jones, Aaron McKenna, Gad Getz, Keith Ligon, Paul Van Hummelen, Matt Ducar, Alina Raza, Ashwini Sunkavalli, Laura MacConaill, Anat Stemmer-Rachamimov, David N. Louis, William C. Hahn, Ian Dunn, Rameen Beroukhim. Genomic sequencing of meningiomas reveals oncogenic SMO and AKT1 mutations. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 803. doi:10.1158/1538-7445.AM2013-803

Although advances in technology and the biological understanding of cancer pathogenesis have brought the goal of personalized cancer medicine closer, important challenges remain in several areas. One such challenge is the reliable and sensitive detection of somatic mutations in clinical tumor specimens. Somatic mutation detection in clinical tumor specimens is confounded by biological variables such as the percentage of tumor cells in a specimen, stromal contamination, sequence quality (particularly in DNA derived from formalin-fixed clinical samples), tumor heterogeneity and ploidy considerations. These and other experimental factors can lead to allele signal ratios very different from the 1:0, 1:1 or 0:1 ratio expected for a classically-defined SNP. Germline genotyping using the Sequenom MALDI-TOF mass spectrometry platform has been used to reliably detect single-nucleotide polymorphisms (SNPs) in a wide variety of samples. The automated genotype calling algorithm included with the Sequenom platform falters, however, when the ratio of allele peak signals for a given assay in a specific sample do not approximate the native algorithm's expectations of frequency, confounding accurate genotype calling by the system. We report here a cancer-specific algorithm for sensitive genotype calling of somatic mutations, based on an independent clustering of raw allele peak data for each assay run, and the identification and stratification of outliers from an empirical background (‘wildtype’) cluster of genotypes. Outliers from this cluster are then evaluated using a number of criteria to determine the quality and performance of the overall assay run, as well as the individual call; these factors include the relative signal-to-noise ratio (SNR) of each allele peak, the ratio of variant allele peak height to peak area, the percentage of signal lost in unextended probe (UEP) and relative distance of a putative mutation call from the wildtype cluster In a scatter plot of peak area values. Based on these criteria, a confidence value is assigned to each candidate outlier, allowing for stratification and prioritization of these candidates for validation. We applied the algorithm to samples run against the our OncoMap genotyping panel, comprised of 460 assays interrogating mutations in 33 cancer-associated genes. Candidate mutations produced by this algorithm correlate strongly with those called by users manually, and use of the algorithm increases the sensitivity and reliability of the OncoMap platform to detect somatic mutations in clinical tumor samples, particularly in FFPE-derived material. The algorithm code and documentation will be made publicly available in a form compatible with most Sequenom genotyping platform installations. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3965. doi:1538-7445.AM2012-3965

The Cancer Genome Project (CGP) was set up in 2000 to use systematic mutation screening methods to increase our understanding of human cancer. With the advent of next generation sequencing, and the large volumes of data that it generates, a new suite of software was required to rapidly and accurately screen these data for somatic changes. We have built an analysis pipeline to track and analyse large numbers of tumour samples, using in-house and externally available tools. The analysis pipeline is built around a ∼2,000 node compute farm and Lustre filesystem which outputs into our archive and data storage system, FileTrk. FileTrk holds the raw data files (BAM, CEL etc), the results of the analysis and any versioning information about the software used to generate these results. Sample lanes are aligned back to the genome using Burrows-Wheeler Aligner (BWA) and lane-to-lane comparisons are made to ensure data integrity. Lanes from each sample are merged into a single sample BAM file and once 30 - 40x coverage is reached and the lanes have been quality assessed the sample is locked and ready for analysis. Mutation callers detect point mutations (Caveman, in-house software), small insertions/deletions (Pindel), breakpoints (BRASS, in-house software) and copy number changes (ASCAT & PICNIC, in-house software). The resulting mutations are post-processed to remove false positives, annotated to the RNA and protein level using standard nomenclature (Vagrent, in-house software) and uploaded to a database. Interfaces have been developed to enable the selection of random sets of mutations for validation, the outcome of the validations is recorded so specificity can be calculated for each sample in the system. IT systems are being developed to automatically export lists of somatic changes to COSMIC, the ICGC data portal and raw data to the European Genome-Phenome Archive (EGA). Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3967. doi:1538-7445.AM2012-3967

Background: Genetic intra-tumor heterogeneity (ITH) may foster tumor adaptation by providing selectable phenotypes for Darwinian evolution. Extensive genetic heterogeneity may also hinder personalized medicine strategies that rely on the portrayal of the mutational landscape from single tumor biopsies. Methods: To examine ITH, we have subjected multiple biopsies from primary renal cell carcinomas and associated metastatic sites to exome capture sequencing (n=2), SNP-array based chromosomal aberration and ploidy profiling analysis (n=4). Phylogenetic relationships of tumor regions were reconstructed by clonal ordering of non-synonymous somatic mutations. The phenotypic consequences of genetic ITH were characterised by immunohistochemistry, mutation functional analysis and mRNA expression profiling. Results: Phylogenetic reconstruction revealed branched evolutionary tumor growth with 63-69% of somatic mutations identified from single biopsies not detectable across all sequenced tumor regions. Independent tumor suppressor gene loss of function mutations with distinct regional distributions were detected within individual tumors: SETD2 harbored 5 different mutations in 2 tumors and PTEN and KDM5C two different mutations in one tumor, each. Thus, despite genetic divergence during tumor progression, phenotypic convergent evolution occurred, indicating a high degree of early mutational diversity. ITH was observed for a mutation in the kinase domain of mTOR, correlating with S6 and 4EBP phosphorylation specifically in cancer regions carrying the mutation and constitutive activation of mTOR kinase activity in vitro. Expression of a renal cancer-specific prognostic signature differed between tumor regions. Chromosomal aberration analysis revealed extensive ITH with 26/30 tumor biopsies from four tumors harboring divergent allelic imbalance profiles. Ploidy profiling revealed heterogeneity in two out of four tumors and identified an aneuploid tumor cell population in a metastasis that probably evolved from a tetraploid intermediate detectable in the primary tumor. Conclusions: Genetic ITH was present in all tumors and occurs through spatially separated heterogeneous somatic mutations and chromosomal and ploidy aberrations leading to both, phenotypic intra-tumor diversity (mTOR activating mutation) and convergent loss of function(SETD2, PTEN and KDM5C). ITH can lead to underestimation of the tumor genomic landscape portrayed from single biopsies and may present significant challenges to personalized medicine and biomarker development. ITH, associated with heterogeneous protein function, may foster tumor adaptation and therapeutic failure through Darwinian selection. Targeting mutations commonly located on the trunks, rather than the branches of phylogenetic trees, may improve therapeutic outcomes. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 964. doi:1538-7445.AM2012-964

Tumor angiogenesis is vital for tumor growth and progression. Defining genes that are involved in tumor driven angiogenesis may yield therapeutically important targets for cancer therapy. We have developed and optimized a rapid 25 minute immunohistochemical staining method using CD31 antibody (Pecam1) specific to endothelial cells in vessels on sections from frozen human breast cancer (n=3) and normal breast (n=3), followed by laser capture microdisection (LCM) of vessels. Good quality RNA was extracted amplified, and fluorescently labeled cDNA was synthesized and hybridized onto Affymetrix U-133 Plus 2.0 array. Using this methodology, we were able to elucidate the genetic profile of tumor associated vessels from invasive breast cancer and compare it with vessels in normal breast tissue. This technique has the advantage over other methods in analyzing genetic profile of tissue as it analyses the genetic profile of isolated cell population and eliminates genes expressed by surrounding tissue, allowing for the detection of low expression of genes that were not detected in whole tumor arrays. Using false discovery rate statistical analysis (q Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4848. doi:10.1158/1538-7445.AM2011-4848

The genetics of renal cancer is dominated by inactivation of the VHL tumour suppressor gene in clear cell carcinoma (ccRCC), the commonest histological subtype. A recent large-scale screen of ∼3500 genes by PCR-based exon re-sequencing identified several new cancer genes in ccRCC including UTX (KDM6A), JARID1C (KDM5C) and SETD2. These genes encode enzymes that demethylate (UTX, JARID1C) or methylate (SETD2) key lysine residues of histone H3. Modification of the methylation state of these lysine residues of histone H3 regulates chromatin structure and is implicated in transcriptional control. However, together these mutations are present in fewer than 15% of ccRCC, suggesting the existence of additional, currently unidentified cancer genes. Here, we have sequenced the protein coding exome in a series of primary ccRCC and report the identification of the SWI/SNF chromatin remodeling complex gene PBRM1 as a second major ccRCC cancer gene, with truncating mutations in 41% (92/227) of cases. These data further elucidate the somatic genetic architecture of ccRCC and emphasize the marked contribution of aberrant chromatin biology. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2805. doi:10.1158/1538-7445.AM2011-2805

The Cancer Genome Project at the Wellcome Trust Sanger Institute, UK is using massively parallel sequencing technologies to systematically screen exome and genome sequence for diverse categories of mutations. The rapid developments in new sequencing technologies have allowed many new approaches for the detection and characterisation of a wide range of mutation types. We employ a variety of automated and semi-automated techniques to identify and classify copy number variation, chromosomal rearrangements, small insertion/deletion and substitution mutations in both cell lines and primary tumours. Large scale, genome wide changes are detected by mapping read-pairs to a reference genome. Copy number is assessed by taking correctly mapping read-pairs, applying a circular binary segmentation algorithm and correcting for regional mapping bias throughout the genome. Using the high quality read mappings where the paired reads are an unexpected distance apart, putative rearrangements can be identified and confirmed either by local de novo sequence assembly where high sequencing coverage is available or by capillary sequencing for low coverage data. Smaller scale mutations are detected using local read coverage to provide detailed information on the genotype and allelic content of samples. The detection techniques can be used on both whole genome and exome pull-down sequence data. Substitutions are detected using a novel algorithm based on expectation maximisation (Calculate Variants with Expectation Maximisation using New sequencing technology, or CaVEMaN) written in-house and confirmed using capillary sequencing. Putative mutations of all types are compared to external resources (eg Ensembl, dbSNP) to infer genomic context and possible deleterious consequences. In-house tools have been developed to help automate the curation and annotation of mutations and once confirmed they are submitted to COSMIC as gene associated mutations, small scale intragenic mutations, chromosomal rearrangements or fusion gene products. Reference URL's Wellcome Trust Sanger Institute - http://www.sanger.ac.uk COSMIC - http://www.sanger.ac.uk/genetics/CGP/cosmic CGP - http://www.sanger.ac.uk/genetics/CGP/ Ensembl - http://www.ensembl.org dbSNP - http://www.ncbi.nlm.nih.gov/projects/SNP Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 90.

Six antibody-maytansinoid conjugates (AMCs) consisting of the cytotoxic maytansinoid, DM1 or DM4, linked to a tumor-targeting monoclonal antibody are undergoing clinical evaluation, with the most advanced in Phase III testing. In these AMCs, the maytansinoid is attached through its C3 side chain to the antibody via a thioether or disulfide bond. The antibody moiety of the conjugate binds specifically to a tumor cell after which the conjugate is internalized and processed to release one or more maytansinoid metabolites (MMs) which kill the cell. Some of these MMs are hydrophobic and highly potent against both the forming cell and neighboring dividing cells, while others are charged or polar compounds that are highly toxic to the cell that intracellularly released them, but have a relatively low toxicity to adjacent cells due to poor membrane permeability. Similar MMs are formed from AMCs inside cells of the reticulo-endothelial system (RES), the primary route of elimination of proteinaceous therapeutics such as AMCs. We have previously reported, from studies with radiolabeled MMs in mice, that the primary elimination route of RES-formed MMs is via the liver, and entails biliary excretion of relatively low potency charged or polar maytansinoids. It would be desirable to know if MMs generated from AMCs in the RES systems of patients can be inactivated by the oxidative processes of the human liver. To model this, MMs and other maytansinoids were synthesized and then exposed in vitro to human liver microsomes. The resulting microsomal metabolites were identified by HPLC/MS and their cytotoxicities were determined. In general, the major metabolites formed from microsome exposure occurred via oxidation on the C3 side chain, with only minimal microsome-dependent alterations noted in the macrocycle. Non-charged hydrophobic maytansinoids containing at least one sulfur atom were oxidized on the sulfur atom(s) to yield one or more products which were significantly less cytotoxic than the substrate. For example, the highly cytotoxic tumor cell metabolite, S-methyl DM4, was converted to its sulfoxide and sulfone analogues, which were more than 20-fold less potent than S-methyl DM4. Charged maytansinoids containing an amino acid or a carboxylic acid were poorly metabolized by the human liver microsomes even when these maytansinoids contained one or more sulfur atoms. These data suggest that the highly potent, non-charged MMs formed in the tumor cells or the RES systems of patients would be rendered less toxic through oxidation in the liver prior to biliary elimination. Furthermore, the less potent, charged MMs likely would not be further processed by liver in a way that would increase their systemic toxicity. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2668.

A noninvasive dynamic method for the measurement of blood flow, using 15O-labeled water and positron emission tomography, has been developed and used to study 20 patients with breast carcinoma. The mean tumor flow was 29.8 +/- 17.0 (SE) ml/dl/min of tissue, while normal breast flow was 5.6 +/- 1.4 ml/dl/min of tissue. The exchanging water space of tissue known as the volume of distribution of the tracer (Vd) was also derived. This is defined as the volume of water in tissue that exchanges with a unit volume of water in arterial blood during the period of the study (7 min). The mean tumor Vd was 0.56 +/- 0.15 ml/ml while normal breast Vd was 0.14 +/- 0.05 ml/ml. The low value in normal breast is partly due to the high fat content of the tissue. The mean flow per unit of exchangeable volume was similar in tumor (52.8 +/- 22.0) and normal breast tissue (45.2 +/- 20.0). This suggests that the major discrepancy seen in measured values of flow between breast tumors and normal breast principally reflects the different composition of the two tissues. This method is rapid and suited for studying the reactivity of human tumor vasculature, so extending studies are being performed on animal tumors.

We have previously described the neoplastic transformation of immortalized human bronchial epithelial cells (BEAS-2B) by the combination of the c-raf-1 and c-myc protooncogenes and the concomitant induction of neuron-specific enolase mRNA expression (A. Pfeifer et al., Proc. Natl. Acad. Sci. USA, 86: 10075-10079, 1989). In this paper we describe the morphological, biochemical, and immunohistochemical characteristics of the primary c-raf-1/c-myc tumors, xenografts of these tumors, and tumors that originated from cell lines of the primary neoplasm. The tumors were morphologically characterized by the appearance of desmosomes and tonofilaments, microvilli, and dense core granules representing markers of squamous, glandular, and neuroendocrine differentiation, respectively. A total of 11 of 13 tumors were positive by immunohistochemical techniques for neuron-specific enolase, serotonin (nine of 13), and calcitonin (six of 13). Keratins were expressed in 11 of 13 tumors, and while specific keratins (K5, K7, K16/K17) decreased, there was an increase of vimentin in the tumor cells. Gastrin-releasing peptide immunoreactivity was detectable in a small number of tumors (five of 13). BEAS-2B cells transfected with the c-raf-1 and c-myc protooncogenes and cell lines established from the primary tumors expressed major histocompatibility Class II antigen which has been found on small cell lung carcinoma cells. The tumors induced by the c-raf-1 and c-myc protooncogenes resemble the multidifferentiated phenotype of small cell lung cancer frequently detected in vivo and present a defined model to study the relation between molecular markers, phenotypical appearance, and response to chemotherapeutic agents and radiation.

Four urinary metabolites of the cytostatic drug cyclophosphamide were tested for mutagenicity in the Ames Salmonella assay: nornitrogen mustard (NM), 4-ketocyclophosphamide, 3-(2-chloroethyl)oxazolidone (OZ), and N,N'-bis(2-chloroethyl)piperazine. All four acted as direct base substitution mutagens although 4-ketocyclophosphamide showed an increase in mutagenicity after metabolic activation with S-9 rat liver fraction. Of the four compounds tested, NM was the strongest mutagen while all the others had weak mutagenic activity, with OZ being the weakest. We observed that, under conditions which facilitate the conversion of NM to OZ (presence of HCO-3 at neutral pH), the former lost both mutagenic and alkylating activities. Our findings, taken together with other reports in the literature, indicate that NM could be a major cause of secondary bladder carcinoma since it is a potent mutagen ad seems to be present in high levels in the urine of cyclophosphamide-treated patients. The fact that it can be detoxified to the weak mutagen OZ in the presence of HCO-3 suggests the possibility that, by increasing the concentration of HCO-3 in the urine of patients, that undesirable side effect of cyclophosphamide treatment can be alleviated.

Data are presented indicating marked antineoplastic activity for cis-dichlorodiammineplatinum(II) in MOPC 104E myeloma. One-eighteenth of the dose that produced 100% cures can be combined with noncurative, low doses of cyclophosphamide and 1,3-bis(2-chloroethyl)-1-nitrosourea to produce antineoplastic activity of the same degree as that produced by much higher dose regimens which regularly produce cures. Since, in the past, results of therapeutic trials in plasma cell tumors in humans have paralleled results in this animal model, clinical trials of cis-dichlorodiammineplatinum in multiple myeloma appear warranted.

The in vivo rates of protein synthesis were assessed in tumor tissue, skeletal muscle, and whole body of rats bearing the Walker 256 carcinosarcoma. Estimates of protein synthesis in the nontumorous tissues were compared to tumor-free controls. Changes in size of the whole animal and tumor (i.e., growth) were measured, and fractional rates of growth, synthesis, and breakdown were estimated. Muscle protein synthesis and whole-body growth were significantly reduced in rats bearing larger tumors, and both were negatively correlated with tumor size (r = -0.723 and -0.825, respectively; P less than 0.01). Furthermore, whole-body and muscle protein synthesis were positively correlated with body growth (r = 0.380 and 0.563, respectively; P less than 0.05). Tumor growth followed first-order kinetics between days 7 and 13 following implantation, with a mean rate constant of 34.3%/day for the larger tumors and 27.7%/day for the small tumors. The difference in tumor growth became statistically significant over the final 3 days of tumor volume measurements. Fractional protein synthesis was significantly lower in the larger compared to the smaller tumors (48.6 versus 84.8%/day; P less than 0.05) as measured on day 14. This finding indicates a lower protein breakdown rate for the larger tumors (14.3 versus 59.0%/day; P less than 0.01) and suggests that the process of protein breakdown could play a significant role in determining tumor size, leading support to the theory of tumors acting as nitrogen traps.