Isabella H. Wulur

Whole genome sequencing identifies recurrent mutations in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is one of the most deadly cancers worldwide and has no effective treatment, yet the molecular basis of hepatocarcinogenesis remains largely unknown. Here we report findings from a whole-genome sequencing (WGS) study of 88 matched HCC tumor/normal pairs, 81 of which are Hepatitis B virus (HBV) positive, seeking to identify genetically altered genes and pathways implicated in HBV-associated HCC. We find beta-catenin to be the most frequently mutated oncogene (15.9%) and TP53 the most frequently mutated tumor suppressor (35.2%). The Wnt/beta-catenin and JAK/STAT pathways, altered in 62.5% and 45.5% of cases, respectively, are likely to act as two major oncogenic drivers in HCC. This study also identifies several prevalent and potentially actionable mutations, including activating mutations of Janus kinase 1 (JAK1), in 9.1% of patients and provides a path toward therapeutic intervention of the disease.

Somatic Mutations in GRM1 in Cancer Alter Metabotropic Glutamate Receptor 1 Intracellular Localization and Signaling

The activity of metabotropic glutamate receptors (mGluRs) is known to be altered as the consequence of neurodegenerative diseases such as Alzheimer, Parkinson, and Huntington disease. However, little attention has been paid to this receptor family’s potential link with cancer. Recent reports indicate altered mGluR signaling in various tumor types, and several somatic mutations in mGluR1a in lung cancer were recently described. Group 1 mGluRs (mGluR1a and mGluR5) are coupled primarily to Gαq, leading to the activation of phospholipase C and to the formation of diacylglycerol and inositol 1,4,5-trisphosphate, leading to the release of Ca2+ from intracellular stores and protein kinase C (PKC) activation. In the present study, we investigated the intracellular localization and G protein–dependent and –independent signaling of eight GRM1 (mGluR1a) somatic mutations. Two mutants found in close proximity to the glutamate binding domain and cysteine-rich region (R375G and G396V) show both decreased cell surface expression and basal inositol phosphate (IP) formation. However, R375G shows increased ERK1/2 activation in response to quisqualate stimulation. A mutant located directly in the glutamate binding site (A168V) shows increased quisqualate-induced IP formation and, similar to R375G, increased ERK1/2 activation. Additionally, a mutation in the G protein-coupled receptor kinase 2/PKC regulatory region (R696W) shows decreased ERK1/2 activation, whereas a mutation within the Homer binding region in the carboxyl-terminal tail (P1148L) does not alter the intracellular localization of the receptor, but it induces changes in cellular morphology and exhibits reduced ERK1/2 activation. Taken together, these results suggest that mGluR1a signaling in cancer is disrupted by somatic mutations with multiple downstream consequences.

Somatic mutations in CCK2R alter receptor activity that promote oncogenic phenotypes

The roles of cholecystokinin 2 receptor (CCK2R) in numerous physiologic processes in the gastrointestinal tract and central nervous system are well documented. There has been some evidence that CCK2R alterations play a role in cancers, but the functional significance of these alterations for tumorigenesis is unknown. We have identified six mutations in CCK2R among a panel of 140 colorectal cancers and 44 gastric cancers. We show that these mutations increase receptor activity, activate multiple downstream signaling pathways, increase cell migration, and promote angiogenesis. Our findings suggest that somatic mutations in CCK2R may promote tumorigenesis through deregulated receptor activity and highlight the importance of evaluating CCK2R inhibitors to block both the normal and mutant forms of the receptor. Mol Cancer Res; 10(6); 739–49. ©2012 AACR.

Merestinib (LY2801653) inhibits neurotrophic receptor kinase (NTRK) and suppresses growth of NTRK fusion bearing tumors

Merestinib is an oral multi-kinase inhibitor targeting a limited number of oncokinases including MET, AXL, RON and MKNK1/2. Here, we report that merestinib inhibits neurotrophic receptor tyrosine kinases NTRK1/2/3 which are oncogenic drivers in tumors bearing NTRK fusion resulting from chromosomal rearrangements. Merestinib is shown to be a type II NTRK1 kinase inhibitor as determined by x-ray crystallography. In KM-12 cells harboring TPM3-NTRK1 fusion, merestinib exhibits potent p-NTRK1 inhibition in vitro by western blot and elicits an anti-proliferative response in two- and three-dimensional growth. Merestinib treatment demonstrated profound tumor growth inhibition in in vivo cancer models harboring either a TPM3-NTRK1 or an ETV6-NTRK3 gene fusion. To recapitulate resistance observed from type I NTRK kinase inhibitors entrectinib and larotrectinib, we generated NIH-3T3 cells exogenously expressing TPM3-NTRK1 wild-type, or acquired mutations G595R and G667C in vitro and in vivo. Merestinib blocks tumor growth of both wild-type and mutant G667C TPM3-NTRK1 expressing NIH-3T3 cell-derived tumors. These preclinical data support the clinical evaluation of merestinib, a type II NTRK kinase inhibitor (NCT02920996), both in treatment naïve patients and in patients progressed on type I NTRK kinase inhibitors with acquired secondary G667C mutation in NTRK fusion bearing tumors.

Abstract 519: Antitumor activity of MET antibody emibetuzumab (LY2875358) in combination with EGFR inhibitors in erlotinib resistant (ER) xenograft mouse models

Background: MET amplification (amp) is a resistance mechanism to EGFR TKI treatment. Emibetuzumab, a bivalent MET antibody (Ab) blocks HGF binding to MET and internalizes the receptor. Combination of emibetuzumab with EGFR TKIs (erlotinib, AZD9291, CO1686) or EGFR Ab (necitumumab, cetuximab) was evaluated in 3 ER xenograft models. Methods: Model 1: ER cell line HCC827ERL with high focal MET amp, high pMET, EGFR ex19 del (no T790M) was created from parental HCC827 NSCLC (EGFR ex19 del, EGFR amp, no MET amp) by increasing concentration of erlotinib in vitro over 7 months. Model 2: ER cell line HCC827-A8 was derived from HCC827 parental xenograft tumor serially passed in vivo with long term treatment of gefitinib and erlotinib. HCC827-A8 cells express high focal MET amp, high pMET/AXL (Western blot) while retaining EGFR ex19 del (no T790M). Model 3: LU0858 was an ER patient-derived NSCLC xenograft tumor, with focal MET amp, EGFR L858R (no T790M). MET amp and EGFRmt was determined by FISH and LNA-PCR sequencing respectively. Compound dosing: emibetuzumab 20 mg/kg qw; necitumumab 4 mg/kg or 20 mg/kg biw; cetuximab 4 mg/kg biw; erlotinib 25 mg/kg qd; 5 mg/kg AZD9291 qd; 30 mg/kg CO1686 bid. Results: EGFR inhibitors, but not emibetuzumab showed significant single agent anti-tumor effect in xenograft tumors derived from non-MET amp HCC827 parental cells. In MET amp ER models, single agent emibetuzumab resulted in tumor growth inhibition in Model 1 (T/C= 51.7%-61.0%, p Conclusion: The three erlotinib resistant models with MET amp and retaining sensitizing EGFRmt (ex19 del or L858R), and no acquired T790M were found resistant to other EGFR inhibitors (Abs and TKIs). Emibetuzumab in combination with either EGFR TKI or Ab showed anti-tumor activity in MET amp ER xenograft models including tumor regression in 2 out of 3 models. The combination of emibetuzumab with erlotinib is being evaluated in NSCLC patients with EGFR activating mutation (NCT01897480). Citation Format: Suzane L. Um, Victoria L. Peek, Jennifer R. Stephens, Jessica A. Baker, Holly K. Cannon, Joel D. Cook, Isabella H. Wulur, Roger Agyei, Sudhakar Chintharlapalli, Robert J. Evans, William J. Feaver, Lysiane Huber, Linda N. Lee, Ling Liu, Liandong Ma, Ruslan Novosiadly, Volker Wacheck, Sau-Chi Betty Yan. Antitumor activity of MET antibody emibetuzumab (LY2875358) in combination with EGFR inhibitors in erlotinib resistant (ER) xenograft mouse models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 519. doi:10.1158/1538-7445.AM2017-519

Abstract 4104: Intrinsic and acquired resistance to cetuximab in colorectal cancer patients

Anti-EGFR antibodies, such as cetuximab, are effective therapies for many late-stage colorectal cancer (CRC) patients; unfortunately, many tumors are initially unresponsive while others show initial efficacy but eventually develop acquired resistance. Genomic studies of patient tumors, cell lines, and xenograft models have identified putative anti-EGFR resistance markers, including mutations in KRAS, NRAS, BRAF, PIK3CA, and the EGFR extracellular domain, as well as amplifications in ERBB2 and MET. In order to further confirm and identify new resistance mechanisms to anti-EGFR treatment in CRC, we performed retrospective genomic profiling of 25 CRC patients treated at Samsung Medical Center from 2006-2015. Patients received cetuximab containing chemo regimens with varying duration of responses, including acquired resistance cases. Our analysis identifies mutations in receptor tyrosine kinases, such as EGFR, NTRK1, and PDGFRA, as well as RAS/MAPK pathway genes that affect cetuximab response. We also uncover genomic alterations in ERBB2 and c-KIT as potential novel mechanisms regulating sensitivity to anti-EGFR antibodies. Additional genomic analyses of acquired resistance tumors and in vitro studies of a patient-derived cell line provide added insights into clonal selection and signaling pathways that bypass the EGFR blockade. Overall, our study elucidates important new facets in the landscape of anti-EGFR resistance mechanisms. Note: This abstract was not presented at the meeting. Citation Format: Steven M. Bray, Jeeyun Lee, Seung Tae Kim, Philip J. Ebert, John N. Calley, Isabella H. Wulur, Thejaswini Gopalappa, Swee Seong Wong, Hui-Rong Qian, Jason C. Ting, Jiangang Liu, Melinda D. Willard, Amit Aggarwal, Ruslan D. Novosiadly, Hee-Cheol Kim, Christoph Reinhard. Intrinsic and acquired resistance to cetuximab in colorectal cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4104. doi:10.1158/1538-7445.AM2017-4104

Abstract 29: Concordance of somatic mutations found in primary tumors and plasma circulating-free DNA from early and late-stage colorectal cancer patients

Circulating-free DNA (cfDNA) holds great potential for non-invasive somatic mutation detection in cancer patients as a so-called “liquid biopsy”. A liquid biopsy is especially valuable when tumor tissue is not available and for longitudinal monitoring of tumor burden or emerging resistance. In such cases, tumor-specific mutations are not known a priori and in order to detect tumor-derived somatic mutations it is best to interrogate a broad panel of cancer genes. The primary obstacle to sequencing cfDNA with broad mutation panels is achieving the necessary limit of detection to identify small amounts of tumor-derived cfDNA relative to the predominant wild-type cfDNA in the plasma of cancer patients. Tumor-derived cfDNA levels correlate with tumor stage, also making it an important consideration when investigating the sensitivity of this approach. We demonstrate the detection of somatic variants in several cancer genes in the plasma of early and late-stage colorectal cancer (CRC) patients by deep sequencing (> 8,000X) the cfDNA and matched normal DNA of N=33 CRC patients using the AmpliSeq cancer panel. The AmpliSeq panel requires less than 10ng of input DNA and amplifies hotspot loci of 50 known cancer genes for next-generation sequencing (NGS). We observe at least one somatic mutation with greater than 0.1% variant allele frequency in the cfDNA of all 33 CRC patients. We also show the sensitivity of detecting tumor-derived somatic mutations in cfDNA by exome sequencing of the primary tumor tissue. We find higher sensitivity for tumor mutations in cfDNA of late-stage patients compared to early-stage patients. Overall, we demonstrate the feasibility of using NGS on a small sized cancer panel for identifying somatic mutations, including those with low variant allele frequency, in cfDNA of early and late-stage CRC patients. Although a cfDNA approach holds promise as a tool to aid in pre-clinical and clinical research, more work is needed to understand its performance under different assay and disease conditions. Citation Format: Steven M. Bray, Philip J. Ebert, John N. Calley, Richard E. Higgs, Isabella H. Wulur, Swee Seong Wong, Candice L. Horn, Ricardo Martinez, Christoph Reinhard. Concordance of somatic mutations found in primary tumors and plasma circulating-free DNA from early and late-stage colorectal cancer patients. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Integrating Clinical Genomics and Cancer Therapy; Jun 13-16, 2015; Salt Lake City, UT. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(1_Suppl):Abstract nr 29.

Abstract 2647: Merestinib (LY2801653), targeting several oncokinases including NTRK1/2/3, shows potent anti-tumor effect in colorectal cell line- and patient-derived xenograft (PDX) model bearing TPM3-NTRK1 fusion

In cancer, the formation of chimeric gene fusions by genomic rearrangement causes aberrant receptor tyrosine kinase activation resulting in sustained oncogenic signaling driving tumorigenesis. Neurotrophic tyrosine receptor kinase 1 (NTRK1), the cognate receptor for nerve growth factor (NGF), has been reported in 7 tumor types as a NTRK1 kinase domain fused with several reported partners including the 5’ coiled-coil domain of the tropomysin TPM3 gene. The resultant NTRK1 fusion protein is present in about 1.5% of colorectal cancer (CRC), 3% of lung and 12% of papillary thyroid cancers. In addition, gene fusions involving NTRK2 and NTRK3 are present in about 19 different tumor types. Thus pharmacologically targeting NTRK kinase in cancers bearing NTRK fusions may provide treatment options to patients who otherwise might be resistant to standard oncolytic regimens. Merestinib (LY2801653) is an orally bioavailable small molecule inhibitor of several oncokinases, including MET, AXL, ROS1 and MKNK1/2. Merestinib and its two primary metabolites, M1 (LSN2800870) and M2 (LSN2887652) were shown in scanMaxSM kinase binding assays to inhibit all three NTRKs with an IC50 ranging from 15-320 nM, and in the cell-based PathHunter® NTRK1 assay with an IC50 ranging from 12-92 nM. Merestinib, M1 and M2 were evaluated in vitro in TPM3-NTRK1 fusion bearing CRC cells (KM-12). Merestinib, M1 and M2 reduced p-NTRK1 levels, cell proliferation (IC50 of 11 nM, 18 nM and 100 nM respectively) and anchorage independent growth (IC50 of 45 nM, 79 nM and 206 nM respectively). Crizotinib previously reported (Nat Med. 2013;19:1469-72) to have moderate activity against NTRK1, was used to treat a patient with NTRK1 fusion resulted with transient response. Crizotinib was shown here to also reduce p-NTRK1 levels, cell proliferation (IC50 = 88nM) and anchorage independent growth (IC50 = 276nM) in vitro in KM-12 cells. Merestinib treatment at 24 mg/kg once daily arrested tumor growth (T/C = 4%) in KM-12 xenograft tumor bearing mice. Crizotinib administered at 25 mg/kg twice daily in this same model did not result in tumor growth arrest (T/C = 39.5%). Merestinib treatment at 24 mg/kg once daily led to tumor regression in a CRC PDX xenograft model (EL1989) bearing the TPM3-NTRK1 fusion. Crizotinib treatment at 25 mg/kg twice daily in this model did not show tumor regression. Further pre-clinical studies of Merestinib inhibition of NTRK2 and NTRK3 gene fusion are ongoing. These data support the clinical evaluation of Merestinib in patients with tumors harboring NTRK fusion. Merestinib is currently being studied clinically in advanced cancers (NCT01285037). Citation Format: Bruce W. Konicek, Steve M. Bray, Andrew R. Capen, John N. Calley, Kelly M. Credille, Philip J. Ebert, Gary Heady, Bharvin K. Patel, Victoria L. Peek, Jennifer R. Stephens, Suzane L. Um, Melinda D. Willard, Isabella H. Wulur, Yi Zeng, Richard A. Walgren, Sau-Chi Betty Yan. Merestinib (LY2801653), targeting several oncokinases including NTRK1/2/3, shows potent anti-tumor effect in colorectal cell line- and patient-derived xenograft (PDX) model bearing TPM3-NTRK1 fusion. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2647.

Abstract LB-048: Copy number and loss of heterozygosity (LOH) analysis in 52 breast cancer FFPE samples using molecular Inversion probe array: detailed analysis of reproducibility and performance compared to NGS platforms

Introduction: Somatic mutations are routinely identified using NGS cancer panels but these panels lack genome-wide coverage for copy number (CN) and LOH analysis. To investigate mutation, CN, and LOH in late-stage breast cancer we tested >50 samples using the Oncoscan molecular inversion probe (MIP) array and evaluated its reproducibility and performance compared to NGS platforms. Methods: 52 breast cancer samples (stage IIIA - IV) were analyzed using MIP array (Oncoscan, Affymetrix). Four samples were tested in technical triplicates to determine assay reproducibility. In addition, 28 samples were sequenced by amplicon-based NGS and five of these samples were also tested using a capture-based NGS platform for mutation, CN, and LOH comparison. Results: MIP array provided highly reproducible results for CN and LOH, with >98% of calls showing CN range in the technical triplicates of 2 copies seen in only two cases, once for ERBB2 (CN range 32 - 35 copies) and once for FLOT2 (CN range 22 - 25 copies). Gene level results were then categorized in five groups: homozygous deletion, single copy loss, diploid, low grade amplification (≤6 copies), or high grade amplification (>6 copies). Using these predetermined cut points, we saw >99% concordance rate among the technical replicates in the MIP array. We found a 93% concordance rate between MIP array and CN/LOH calls by capture-based NGS. Discordant calls between NGS and MIP array were either LOH calls or single copy number change (diploid vs. single copy loss or gain). MIP array mutation analysis of 28 samples showed good sensitivity, correctly detecting the 17 PIK3CA mutations and one TP53 mutation identified by NGS in this cohort. There were seven false positive calls by MIP array, five of them occurring in two genotypes (2x NRAS G12S/C, and 3x EGFR L858R). The other two false positives occurred in PIK3CA , with one false positive (H1047L) occurring in association with a high-grade PIK3CA amplification (7 copies). Increasing CN at the mutation locus was associated with a higher mutation score provided by MIP array (p Conclusions: MIP array platform provides a great alternative for assessing CN and LOH in FFPE samples at lower cost and using less input DNA than NGS (80ng vs. 250ng). There was good correlation between CN and LOH results from MIP array and capture-based NGS, with discordant results limited to small CN differences or LOH calls. Mutation analysis by MIP array showed no false negatives when compared to NGS, while false positives seem to occur either due to probe-specific issues or in association with amplifications at the genotyping locus. Citation Format: Candice L. Horn, Fabio Nunes, John Calley, Steven Bray, Isabella Wulur, Mark Farmen, Robert Gallavan, Iris Halfpenny, Paul Medlow, Keith McGreeghan-Crosby, Gera Jellema. Copy number and loss of heterozygosity (LOH) analysis in 52 breast cancer FFPE samples using molecular Inversion probe array: detailed analysis of reproducibility and performance compared to NGS platforms. [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 LB-048. doi:10.1158/1538-7445.AM2015-LB-048

Abstract LB-229: Whole genome sequencing reveals genetic landscape of hepatocellular carcinoma.

Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC Hepatocellular carcinoma (HCC) is one of the most deadly cancers worldwide and has no effective treatment, yet the molecular basis of hepatocarcinogenesis remains largely unknown. Here we report findings from a whole genome sequencing (WGS) study of 88 matched HCC tumour/normal pairs, 81 of which are HBV positive, seeking to identify genetically altered genes and pathways implicated in HBV-associated HCC. We find β-catenin to be the most frequently mutated oncogene (15.9%) and TP53 the most frequently mutated tumour suppressor (35.2%). The Wnt/β-catenin pathway, altered in 62.5% of cases, is likely to act as the major oncogenic driver in HCC. TP53 alterations appear to cause increased levels of genomic arrangement and chromosomal instability. We identified chromothripsis in 5 HCC genomes (5.7%) recurrently affecting chromosomal arms 1q and 8q. We also identified recurrent HBV integration events at the known and putative cancer-related genes such as TERT, MLL4 and CCNE1, which showed upregulated gene expression in tumour versus normal tissue. The frequently altered genes and pathways in HCC reflect classical cancer hallmarks. This study identified several prevalent and actionable mutations that provide a path towards therapeutic intervention of the disease. Citation Format: Mao Mao, Hancheng Zheng, Zhengyan Kan, Jiangchun Xu, Xiao Liu, Shuyu Li, Thomas Barber, Zhuolin Gong, Huan Gao, Ke Hao, Melinda Willard, Robert Hauptschein, Paul Rejto, Julio Fernandez, Guan Wang, Qinghui Zhang, Bo Wang, Ronghua Chen, Jian Wang, Nikki Lee, Wei Zhou, Zhao Lin, Zhiyu Peng, Kang Yi, Shengpei Chen, Lin Li, Xiaomei Fan, Jie Yang, Rui Ye, Jia Ju, Kai Wang, Heather Estrella, Shibing Deng, Ping Wei, Ming Qiu, Isabella Wulur, Jiangang Liu, Mariam Ehsani, Chunsheng Zhang, Andrey Loboda, Wing Kin Sung, Amit Aggarwal, Ronnie Poon, Sheung Tat Fan, Jun Wang, James Hardwick, Christoph Reinhard, Hongyue Dai, Yingrui Li, John Luk. Whole genome sequencing reveals genetic landscape of hepatocellular carcinoma. [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 LB-229. doi:10.1158/1538-7445.AM2013-LB-229