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  • 1
    In: The Lancet, Elsevier BV, ( 2023-12)
    Type of Medium: Online Resource
    ISSN: 0140-6736
    RVK:
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2023
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  • 2
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    American Association for Cancer Research (AACR) ; 2020
    In:  Clinical Cancer Research Vol. 26, No. 11_Supplement ( 2020-06-01), p. PR07-PR07
    In: Clinical Cancer Research, American Association for Cancer Research (AACR), Vol. 26, No. 11_Supplement ( 2020-06-01), p. PR07-PR07
    Abstract: Lynch syndrome (LS), an inherited predisposition syndrome associated with an increased risk of colorectal, endometrial, and other cancers, is characterized by germline mutations in mismatch repair pathway genes, which typically lead to microsatellite instability (MSI) in the resulting tumors. The FDA approval of pembrolizumab for all advanced MSI-H solid tumors has led to increasing MSI assessment. The presence of MSI in LS-associated tumors provides a unique and transformative opportunity for early detection and disease monitoring in these patients. Here we describe an approach to detect MSI from plasma cfDNA using MSK-ACCESS, a custom capture “liquid biopsy” approved for clinical use by the NY State Department of Health. In addition to frequently mutated exons of 129 genes, MSK-ACCESS also includes 165 highly informative microsatellite loci, selected from over 1,000 microsatellite regions based on & gt;25,000 tumors sequenced using MSK-IMPACT, an FDA-authorized tumor sequencing panel. A key challenge in detecting MSI from cfDNA is the lack of ground truth in these samples, as cfDNA obtained from patients with MSI-high tumors may not always exhibit sufficient tumor-derived DNA fragments. To address this, we developed a machine learning approach for cfDNA analysis trained on orthogonally validated tumors sequenced via MSK-IMPACT. We present Allelic Distance-based Microsatellite Instability Estimator (ADMIE), an approach to translate deviation in tumor/cfDNA from normal/buffy coat DNA at individual microsatellite loci to a binary MSI call. ADMIE achieved a cross-validation precision of 1.00 +/- 0.02 and recall of 0.99 +/- 0.07. We ran this on 44 plasma samples collected from over 30 patients with MSI tumors including colorectal, prostate, and gastric cancers across multiple time points. We also evaluated plasma from 70 patients with known MSS tumors and 46 healthy controls. None of the cfDNA from healthy controls or patients with MSS tumors were found to be MSI positive, indicating high specificity. To establish our limit of detection, we performed in silico dilution experiments leveraging patient samples and MSI signal of biologic origin to simulate different tumor fractions, establishing our limit of detection at 1%. Among patients with MSI-high tumors, we found the presence and magnitude of MSI in the cfDNA to be correlated with measurable response to treatment with immunotherapy. In these patients, we detected MSI in the cfDNA of 6/8 samples where at least one mutation was detectable in plasma above 0.2% at baseline. Among the 4/6 patients for whom we had additional time points post treatment, we did not detect any mutations or evidence of MSI. In one patient, MSK-ACCESS indicated the presence of a second primary tumor based on the detection of MSI and mutations in cfDNA completely independent from those identified in the previously sequenced tumor. Our results suggest that MSI can be reliably detected in cfDNA using MSK-ACCESS and the MSI signature can represent a marker of occult metastatic disease in LS. This abstract is also being presented as Poster A54. Citation Format: Preethi Srinivasan, Alicia Latham, Zalak Patel, John Ziegler, Maysun Hasan, Juber A. Patel, Ian Johnson, Ronak Shah, Fanli Meng, Xiaohong Jing, Grittney Tam, Rose Brannon, Andrea Cercek, Ahmet Zehir, Brian Houck-Loomis, Dana Tsui, Zsofia Stadler, Michael F. Berger. MSI detection in plasma cfDNA: MSI as a marker of disease burden [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr PR07.
    Type of Medium: Online Resource
    ISSN: 1078-0432 , 1557-3265
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2020
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  • 3
    In: Journal of Clinical Oncology, American Society of Clinical Oncology (ASCO), Vol. 34, No. 15_suppl ( 2016-05-20), p. 11500-11500
    Type of Medium: Online Resource
    ISSN: 0732-183X , 1527-7755
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    Language: English
    Publisher: American Society of Clinical Oncology (ASCO)
    Publication Date: 2016
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  • 4
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 83, No. 7_Supplement ( 2023-04-04), p. 4284-4284
    Abstract: Cancer is characterized by the ongoing accumulation of somatic mutations, providing selective advantages that may lead to dysregulated cellular proliferation. While the cancer genome at diagnosis has been extensively studied, many cancer types still lack strong prognostic biomarkers. The continuous acquisition and selection for driver mutations in a population of cancer cells acts as a Darwinian process, resulting in clonal expansions of progressively more aberrant and fit phenotypes. Reconstructing tumor evolution allows us to understand key events that drive cancer progression and patterns of mutation co-occurrence within clones. These evolutionary features guide our understanding of fundamental mechanisms that lead to disease lethality. Inferring tumor evolution from DNA sequencing data is becoming part of routine analysis in cancer research. As sequencing costs drop, sequencing multiple tumor samples from a patient becomes routine. These multiple samples can represent different spatial regions of a tumor, longitudinal samples from a single region or a combination of both. This provides an opportunity to study tumor evolution in much greater detail and accuracy than was previously feasible through single-sample datasets. The most widely used methods to reconstruct the subclonal evolution of a tumor utilize stochastic-search algorithms. These approaches iterate through a parameter space to select phylogenetic solutions that maximize the likelihood of observed sequencing data. They are optimized for low complexity cases, where the size and number or subclones are relatively limited. As tumor subclonal structure increases in complexity, the parameter space grows exponentially, and stochastic-search algorithms become computationally intractable. For instance, recent benchmarking studies have revealed that many methods fail to reconstruct clone trees for data with as few as ten subclones. To circumvent current computational limitations, we developed a deterministic algorithm for subclonal reconstruction that leverages fundamental principles of cancer biology to encode heuristics that reduce the solution space to biologically plausible phylogenies. When applied to samples (4-36 tumors; median 16) from 12 patients with metastatic breast cancer, our method reduced the average runtime ten-fold. We were able to delineate the evolutionary history of up to 57 distinct subclones per patient, which is infeasible with most current methods. Benchmarking using methods developed for the SMCHet DREAM challenge on real and simulated datasets further quantifies the accuracy, resolution, and scalability. We have thus presented a novel method for rapid and optimized reconstruction of tumor evolutionary histories. Citation Format: Helena Winata, Daniel Knight, Juber A. Patel, Nicholas K. Wang, Pier Selenica, Stefan E. Eng, Caroline Kostrzewa, Jaron Arbet, Yingjie Zhu, Ronglai Shen, Jorge Reis-Filho, Pedram Razafi, Paul C. Boutros. Enhancing subclonal reconstruction algorithm for resolving complex tumor phylogenies from multi-sample tumor DNA sequencing. [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 4284.
    Type of Medium: Online Resource
    ISSN: 1538-7445
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2023
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  • 5
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 82, No. 12_Supplement ( 2022-06-15), p. LB517A-LB517A
    Abstract: Tucatinib (Tuc) was recently approved for metastatic disease and is moving towards the early setting in HER2+ breast cancer (BC). Given the increasing clinical use of Tuc, resistance will likely soon emerge as a challenge. Here, we explore the yet unknown mechanisms of resistance to Tuc and identify treatment strategies to overcome it. Our recently developed models of BT474 (AZ and ATCC) with acquired resistance to Tuc (TucR) and their sensitive parental (P) were used. DNA-seq, RNA-seq, and RPPA/western blot were performed. Knockdown studies were performed using EGFR siRNA. Drug efficacy studies involved cell growth assays by imaging-based or methylene blue assays. We recently reported (SABCS 2021) that our BT474 TucR models acquired EGFR amplification. The TucR cells displayed elevated levels of phosphorylated (p) and total (t) EGFR, pHER2, pHER3, and downstream pAKT and pS6, which were substantially suppressed by the EGFR-specific tyrosine kinase inhibitor (TKI) gefitinib (Gef) or even further when combined with Tuc. Our new results demonstrate that EGFR knockdown selectively inhibits the growth and pHER2 levels in TucR vs P cells, supporting our hypothesis that heterodimerization of amplified EGFR with HER2 leads to higher pHER2 levels in TucR cells. We have recently also shown that TucR models were hypersensitive to Gef and this inhibition was further enhanced with Gef+Tuc, implying their survival dependence on EGFR. Here, we demonstrate that the TucR cells made resistant to 200nM Tuc maintain their resistant growth and elevated EGFR-dependent signaling even when exposed to 500nM, and can begrown as xenografts in the presence of clinically relevant dose of Tuc, emphasizing their true resistance via amplified EGFR. Importantly, both TucR models vs P cells were cross-resistant to trastuzumab but maintain partial sensitivity to TDM1. While the EGFR-specific antibody cetuximab (Cet) was partially effective as a single agent only in the ATCC model, it potently inhibited growth and induced cell killing in combination with Tuc in both models. A significantly greater inhibition in cell growth and survival was also observed when trastuzumab or TDM1 was combined with either Gef or Cet. Taken together, our results suggest that the activation of HER2 and the resistant growth and survival in the TucR models is completely dependent on the amplified EGFR, which we are currently further corroborating by additional mechanistic and xenograft studies. Whilst we have previously reported that resistance to lapatinib and neratinib confer cross-resistance to Tuc, our recent findings show that resistance to Tuc may be overcome using dual/pan-HER TKIs or the combination of potent EGFR and HER2 inhibitors. Overall, our novel findings hold crucial implications in light of the current treatment landscape of HER2+ BC and biomarkers of resistance, and places a particular emphasis on considerations to sequence currently available TKIs. Citation Format: Jamunarani Veeraraghavan, Fu-Tien Liao, Tia Gordon, Pier Selenica, Sarmistha Nanda, Lanfang Qin, Yingjie Zhu, Juber A. Patel, Andrea Gazzo, Fabio Stossi, Michael A. Mancini, Carolina Gutierrez, Britta Weigelt, Jorge S. Reis-Filho, C. Kent Osborne, Mothaffar F. Rimawi, Rachel Schiff. The role of EGFR in resistance to tucatinib and its therapeutic implications [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 LB517A.
    Type of Medium: Online Resource
    ISSN: 1538-7445
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2022
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  • 6
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 83, No. 5_Supplement ( 2023-03-01), p. P1-13-17-P1-13-17
    Abstract: Background: The HER2-specific tyrosine kinase inhibitor (TKI) tucatinib (Tuca) recently approved for advanced HER2+ breast cancer is making a move towards the early setting. Given its growing use, resistance is inevitable, as observed in the HER2CLIMB study, where only one patient with brain metastasis remained progression free after 2 years on Tuca. Driven by the prevailing lack of knowledge about the mechanisms of resistance, in this study, we sought to define these mechanisms and identify treatment strategies to overcome them. We previously reported (SABCS 2021) that our BT474 TucaR models acquired EGFR amplification and showed elevated levels of phosphorylated (p) and total (t) EGFR, pHER2, pHER3, and downstream pAKT and pS6. Since the HER pathway is activated by ligands, here we aim to assess if hyperactivation of EGFR via high levels of its ligands is an alternative mechanism of Tuca resistance. Materials and Methods: Our recently developed HER2+ BT474 (ATCC and AZ) cell models with acquired resistance to Tuca (TucaR) developed through long-term exposure to gradually increasing doses of Tuca and their naïve parental (P) were used. Genomic (DNA-seq), transcriptomic (RNA-seq), and proteomic (western blot) characterization were performed. Changes in cell growth and migration were assessed by methylene blue and Incucyte wound healing assays, respectively. Results: RNA-seq analysis demonstrated that the levels of TGFα was significantly higher in our BT474 TucaR models compared to P cells. Our results now demonstrate that exogenous supplementation of EGF to BT474-P cells rescues the Tuca-mediated inhibition of pEGFR, pHER2, and the downstream pAKT, pERK, and pS6 levels. Exogenous EGF was also found to reduce the levels of apoptosis, as assessed by cleaved PARP, mitigating the Tuca-induced cell death. Exogenous EGF or TGFα rendered naïve BT474 and SKBR3 cells resistant to Tuca while neratinib, a pan-HER TKI, effectively inhibited this ligand-driven cell growth. We previously showed that the HER signaling reactivation observed in our EGFR-amplified TucaR cells was inhibited by the EGFR-specific TKI gefitinib (Gef) (SABCS 2021) and that the TucaR cells displayed enhanced migratory capabilities (AACR 2022). Here, we demonstrate that in addition to curbing the growth of TucaR cells, Gef, either alone or together with Tuca, also markedly reverts the migration of the TucaR cells. Knockdown (KD) of EGFR but not HER2 selectively and substantially inhibited the migration of the TucaR cells. KD of EGFR also had a marked cell killing effect on only the TucaR cells, whereas HER2 KD inhibited the growth of P but not TucaR cells. Our findings are consistent with the notion that while the P cells are functionally dependent on HER2, in TucaR cells the survival dependence could be rewired to rely primarily on the hyperactive EGFR signaling. Genomic analysis further revealed that in addition to EGFR amplification, the AZ TucaR cells also acquired a gain of YES1, a src family receptor tyrosine kinase implicated in cancer cell growth, invasion, and metastasis. Functional studies using 2 siRNAs, however, showed that YES1 KD had no effect on the growth of TucaR cells, and the migration of both TucaR and P cells was equally affected by YES1 KD, precluding the potential role of YES1 in driving the resistant and enhanced migratory phenotypes. Conclusions: Hyperactivation of the EGFR pathway via amplification of EGFR or increased expression of its ligands confers resistance to Tuca, which may be overcome using dual/pan-HER TKIs or the combination of potent EGFR and HER2 inhibitors. Given the rapidly evolving treatment landscape of HER2+ breast cancer and biomarkers of resistance, our novel findings have potentially crucial therapeutic implications and suggest that rationally sequencing the currently available TKIs may be clinically important. Citation Format: Fu-Tien Liao, Tia Gordon, Chia Chia Liu, Pier Selenica, Yingjie Zhu, Juber Patel, Sarmistha Nanda, Lanfang Qin, Xiaoyong Fu, Andrea Gazzo, Antonio Marra, Juan Blanco-Heredia, Britta Weigelt, Jorge Reis-Filho, C. Kent Osborne, Mothaffar Rimawi, Rachel Schiff, Jamunarani Veeraraghavan. Hyperactivation of the EGFR pathway is associated with resistance to tucatinib in HER2-positive breast cancer models [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 P1-13-17.
    Type of Medium: Online Resource
    ISSN: 1538-7445
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2023
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  • 7
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 78, No. 13_Supplement ( 2018-07-01), p. 5598-5598
    Abstract: The accessibility of tumor-derived cell-free DNA (cfDNA) in blood plasma provides a means to non-invasively profile somatic mutations in solid tumor patients. Clinical applications include longitudinal monitoring of disease burden and acquired drug resistance, identification of clinically relevant alterations and mutation signatures, and detection of minimal residual disease. However, the low fraction of tumor-derived cfDNA in plasma in many patients requires assays and bioinformatics methods that are much more sensitive than have been used for traditional tissue-based analysis. The design of our cfDNA NGS panel is based on prospectively-collected clinical sequencing data obtained from more than 20,000 patients at Memorial Sloan Kettering Cancer Center using MSK-IMPACT, a custom 468-gene sequencing test authorized by the FDA for somatic mutation profiling. Exons harboring hotspot mutations, clinically actionable mutations, and elevated somatic mutation rates were selected for inclusion in the cfDNA panel. Additional non-coding content was included to enable optimal detection of selected copy number alterations, regions of loss of heterozygosity, rearrangement breakpoints, and microsatellite instability. Altogether the panel contains 208 kilobases of sequence from 129 cancer genes. Ultra-deep sequencing and unique molecular indexing enable PCR-generated replicate sequences to be collapsed into error-free consensus sequences, thereby facilitating the high-confidence detection of mutations present at low allele fractions. We developed an open source bioinformatics tool, Marianas, for collapsing PCR replicates into consensus sequences and computing associated quality and performance metrics. Marianas incorporates many empirically derived features that lead to significant noise reduction. It efficiently processes a bam file with 20,000X coverage in 20 minutes on a single processor. We benchmarked the performance of Marianas against other available tools for collapsing and consensus base calling. The relative contributions of sources of error such as barcode contamination and sample cross-talk during PCR and sequencing were also quantified. We found that using unique dual sample indexes in multiplexed sequencing runs was essential to suppress these sources of noise. Applying these aggregated methods to analyze plasma cfDNA samples obtained from patients across a range of solid tumor types and disease stages, we were able to reliably detect clinically relevant mutations with variant allele fractions below 0.003, including subclonal mutations associated with acquired drug resistance. This approach, when applied prospectively on clinical specimens, has the potential to facilitate diagnosis, prognosis, and treatment selection in an era of precision oncology. Citation Format: Juber Patel, Maysun Hasan, Fanli Meng, Xiaohong Jing, Dilmi Perera, Jonathan Reichel, Erika Gedvilaite, Julie Yang, Maha Shady, Sandeep Raj, Preethi Srinivasan, Ian Johnson, Jiashi Wang, Mirna Jarosz, Aliaksandra Samoila, Agnes Viale, Bob Li, Pedram Razavi, Dana Tsui, Michael Berger. Development and optimization of a comprehensive high-sensitivity NGS cancer assay and bioinformatics pipeline for plasma cfDNA profiling [abstract]. In: Proceedings of the American Associatio n for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5598.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2018
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  • 8
    In: Genome Medicine, Springer Science and Business Media LLC, Vol. 13, No. 1 ( 2021-12)
    Abstract: Cell-free DNA (cfDNA) profiling is increasingly used to guide cancer care, yet mutations are not always identified. The ability to detect somatic mutations in plasma depends on both assay sensitivity and the fraction of circulating DNA in plasma that is tumor-derived (i.e., cfDNA tumor fraction). We hypothesized that cfDNA tumor fraction could inform the interpretation of negative cfDNA results and guide the choice of subsequent assays of greater genomic breadth or depth. Methods Plasma samples collected from 118 metastatic cancer patients were analyzed with cf-IMPACT, a modified version of the FDA-authorized MSK-IMPACT tumor test that can detect genomic alterations in 410 cancer-associated genes. Shallow whole genome sequencing (sWGS) was also performed in the same samples to estimate cfDNA tumor fraction based on genome-wide copy number alterations using z -score statistics. Plasma samples with no somatic alterations detected by cf-IMPACT were triaged based on sWGS-estimated tumor fraction for analysis with either a less comprehensive but more sensitive assay (MSK-ACCESS) or broader whole exome sequencing (WES). Results cfDNA profiling using cf-IMPACT identified somatic mutations in 55/76 (72%) patients for whom MSK-IMPACT tumor profiling data were available. A significantly higher concordance of mutational profiles and tumor mutational burden (TMB) was observed between plasma and tumor profiling for plasma samples with a high tumor fraction ( z -score≥5). In the 42 patients from whom tumor data was not available, cf-IMPACT identified mutations in 16/42 (38%). In total, cf-IMPACT analysis of plasma revealed mutations in 71/118 (60%) patients, with clinically actionable alterations identified in 30 (25%), including therapeutic targets of FDA-approved drugs. Of the 47 samples without alterations detected and low tumor fraction ( z -score 〈 5), 29 had sufficient material to be re-analyzed using a less comprehensive but more sensitive assay, MSK-ACCESS, which revealed somatic mutations in 14/29 (48%). Conversely, 5 patients without alterations detected by cf-IMPACT and with high tumor fraction ( z -score≥5) were analyzed by WES, which identified mutational signatures and alterations in potential oncogenic drivers not covered by the cf-IMPACT panel. Overall, we identified mutations in 90/118 (76%) patients in the entire cohort using the three complementary plasma profiling approaches. Conclusions cfDNA tumor fraction can inform the interpretation of negative cfDNA results and guide the selection of subsequent sequencing platforms that are most likely to identify clinically-relevant genomic alterations.
    Type of Medium: Online Resource
    ISSN: 1756-994X
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
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  • 9
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 77, No. 13_Supplement ( 2017-07-01), p. CT001-CT001
    Abstract: Background: Somatic HER2 (ERBB2) and HER3 (ERBB3) mutations can lead to constitutive HER2 activation in the absence of gene amplification. They occur in a variety of solid tumors with a prevalence that does not exceed 5-10% in any tumor type. Activating HER2 mutations occur in the HER2 receptor extracellular and transmembrane domains, and at multiple hotspots in the kinase domain, with no single mutation predominating. Neratinib, an irreversible pan-HER tyrosine kinase inhibitor, inhibits growth of HER2- and HER3-mutant tumors in preclinical models. We explored the clinical activity of neratinib in pts with HER2/HER3 mutant cancers in SUMMIT, a global (9 countries), multicenter, multi-histology, phase II ‘basket’ trial. Methods: Pts with advanced solid tumors and locally documented HER2/HER3 mutations received neratinib 240 mg daily with high-dose loperamide prophylaxis during cycle 1. Primary endpoint: objective response rate at week 8 (ORR8) per RECIST 1.1; pts without RECIST-measurable disease were assessed separately using FDG-PET. Retrospective confirmation of HER2/HER3 mutations, as well as a broader cancer gene profiling, was performed using both tumor and plasma-derived cfDNA. For each tumor type, using Simon’s optimal 2-stage design, a true ORR8 ≤10% was considered unacceptable (null hypothesis) whereas a true ORR8 ≥30% (alternative hypothesis) merited further study. Interim data cut: 16-Dec-2016. Clinicaltrials.gov: NCT01953926. Results: 141 (125 HER2, 16 HER3) pts have received neratinib including 125 efficacy-evaluable pts (110 HER2, 15 HER3). 21 unique cancer types were enrolled (most common: breast, lung, bladder, colorectal cancer). 30 HER2 and 12 HER3 mutations were observed, the most frequent HER2 variants involving S310, L755, A755_G776insYVMA and V777. In the HER2-mutant cohort, clinical responses were observed in tumors with S310, L755, V777, P780_Y781insGSP, and A775_G776insYVMA. When stratified by tumor type, responses were observed in pts with breast, cervical, biliary, salivary and non-small-cell lung cancers, which led to indication-specific cohort expansions. No activity was observed in the HER3-mutant cohort. Tumor and/or cfDNA from 116 pts has been sequenced centrally. Of these, the locally reported HER2/3 mutation was confirmed in 108 (93%), a discordant HER2/3 mutation detected in 5 (4%), and not detected in 3 (3%). Co-mutation patterns in different tumor types and their association with neratinib sensitivity/resistance are under review. Conclusions: SUMMIT provides the largest body of clinical data to date on the use of a pan-HER inhibitor in pts with solid tumors with somatic HER2/HER3 mutations. Responses in HER2 mutants varied by type of tumor and the specific HER2 mutation, suggesting: 1) mutant HER2 is a driver oncogene in some cancers; and 2) not all mutations generate the same level of HER2 hyperactivity and/or oncogene dependence. Citation Format: David M. Hyman, Sarina A. Piha-Paul, Jordi Rodon, Cristina Saura, Geoffrey I. Shapiro, David I. Quinn, Victor Moreno, Ingrid A. Mayer, Carlos Arteaga, Valentina Boni, Emiliano Calvo, Sherene Loi, Albert C. Lockhart, Lillian M. Smyth, Joseph Erinjeri, Maurizio Scaltriti, Gary Ulaner, Jean Torrisi, Juber Patel, Jiabin Tang, Fanli Meng, Duygu Selcuklu, Helen Won, Nancy Bouvier, Michael F. Berger, Richard E. Cutler, Feng Xu, Anna Butturini, Lisa D. Eli, Grace Mann, Alshad S. Lalani, Richard P. Bryce, Funda Meric-Bernstam, José Baselga, David B. Solit. Neratinib in HER2 or HER3 mutant solid tumors: SUMMIT, a global, multi-histology, open-label, phase 2 "basket" study [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 CT001. doi:10.1158/1538-7445.AM2017-CT001
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2017
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  • 10
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    American Association for Cancer Research (AACR) ; 2022
    In:  Cancer Research Vol. 82, No. 12_Supplement ( 2022-06-15), p. 5688-5688
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 82, No. 12_Supplement ( 2022-06-15), p. 5688-5688
    Abstract: Genome instability has long been considered the primary driver of most cancer types. A double strand break (DSB) in DNA can have deleterious consequences for a cell, which if not repaired faithfully, can lead to mutations and chromosomal rearrangements, or even cell death. DSBs can be processed by several DNA repair pathways, of which homologous recombination (HR) is the preferred method due to its error-free nature. HR uses an intact homologous DNA sequence as a template for recovering the information lost at the break site. A significant proportion of all cancers, especially triple-negative breast, ovarian pancreatic and prostate cancers, have loss of function alterations affecting genes involved in HR-mediated DNA repair. Alternate repair pathways operate when HR is defective in tumors, but the pathways operative in this context remain a matter of contention. Previous work in vivo in yeast and in vitro systems has established a new role of RNA in DNA repair. Owing to its abundance in the cell and its sequence similarity to parental DNA, we sought to define whether RNA can act as a template for the repair of DSBs in human cells. We developed a novel high throughput assay to test if DNA breaks can be repaired using RNA as an alternative template in mammalian cells. Human cells were transfected with a guide RNA cloned in a Cas9 expression vector to generate a site-specific DSB at the AAVS1 locus, a safe harbour, in the human genome. Furthermore, a donor template in the form of DNA or RNA (homologous to the DSB locus) containing a unique mutational signature was provided at the time of transfection. The unique mutational signature enables us to determine if the donor has been utilized as a template for DNA repair. Using this assay, we demonstrate that cells can use a spliced RNA transcript as a functional template to repair a DSB. We have identified that Rev3L, a key component of the translesion synthesis polymerase Pol Zeta (ζ), has a novel reverse-transcriptase activity in human cells and can help repair the DSB using RNA as a template. Further characterization of this repair pathway and its associated mutational scar will provide new insights into the mutational signatures seen in HR-defective cancers, enabling a better understanding of the DNA repair pathways upregulated in these tumours. The proposed studies could help prioritize novel therapeutic approaches by exploiting synthetic lethality in HR-deficient cancers as well as HR-proficient cancers when used in combinatorial cancer therapy. Citation Format: Manisha Jalan, Juber Patel, Kyrie S Olsen, Sana Ahmed-Seghir, Daniel S Higginson, Jorge S Reis-Filho, Nadeem Riaz, Simon N Powell. RNA-mediated DNA repair: A novel repair pathway in homologous recombination-deficient 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 5688.
    Type of Medium: Online Resource
    ISSN: 1538-7445
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2022
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