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Tabari E, Lovejoy AF, Lin H, Bolen CR, Lor Saelee S, Lefkowitz JP, Kurtz DM, Bottos A, Nielsen TG, Parreira JM, Luong KT. NGS-determined molecular markers and disease burden metrics from ctDNA correlate with PFS in previously untreated DLBCL. Leuk Lymphoma 2024:1-11. [PMID: 38337191 DOI: 10.1080/10428194.2024.2301924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 01/02/2024] [Indexed: 02/12/2024]
Abstract
Personalized risk stratification and treatment may help improve outcomes among patients with diffuse large B-cell lymphoma (DLBCL). We developed a next-generation sequencing (NGS)-based method to assess a range of potential prognostic indicators, and evaluated it using pretreatment plasma samples from 310 patients with previously untreated DLBCL from the GOYA trial (NCT01287741). Variant calls and DLBCL subtyping with the plasma-based method were concordant with corresponding tissue-based methods. Patients with a tumor burden greater than the median (p = .003) and non-germinal center B-cell-like (non-GCB) DLBCL (p = .049) had worse progression-free survival than patients with a tumor burden less than the median or GCB DLBCL. Multi-factor assessment combining orthogonal features from a single pretreatment plasma sample has promise as a prognostic indicator in this setting (p = .085). This minimally invasive plasma-based NGS assay could enable comprehensive prognostic assessment of patients in a clinical setting, with greater accessibility than current methods.
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Affiliation(s)
| | | | - Hai Lin
- Roche Sequencing Solutions, Pleasanton, CA, USA
| | | | | | | | - David M Kurtz
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
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2
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Saelee SL, Lovejoy AF, Hinzmann B, Mayol K, Huynh S, Harrell A, Lefkowitz J, Deodhar N, Garcia-Montoya G, Yaung SJ, Klass DM. Quantitative PCR-Based Method to Assess Cell-Free DNA Quality, Adjust Input Mass, and Improve Next-Generation Sequencing Assay Performance. J Mol Diagn 2022; 24:566-575. [PMID: 35364322 DOI: 10.1016/j.jmoldx.2022.02.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/19/2021] [Accepted: 02/16/2022] [Indexed: 12/13/2022] Open
Abstract
Cell-free (cf)DNA-based testing has undergone increasingly wide adoption, including assays for the detection of circulating tumor DNA. Due to nucleosome protection, cfDNA has a distinctive fragment size of 160 to 180 bp. However, cfDNA can be contaminated with high molecular weight genomic DNA from blood cells released in plasma during sample collection. Such contamination can lead to decreased sensitivity or inconsistent results in cfDNA next-generation sequencing assays. This article describes a technical advancement in which a quantitative PCR method is used for high molecular weight contamination assessment and input mass adjustment, and has been demonstrated to improve consistency of performance in a circulating tumor DNA next-generation sequencing workflow.
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Affiliation(s)
| | | | | | - Katrina Mayol
- Roche Sequencing Solutions, Inc., Pleasanton, California
| | - Samantha Huynh
- Roche Sequencing Solutions, Inc., Pleasanton, California
| | - Amy Harrell
- Roche Sequencing Solutions, Inc., Pleasanton, California
| | - Josh Lefkowitz
- Roche Sequencing Solutions, Inc., Pleasanton, California
| | | | | | | | - Daniel M Klass
- Roche Sequencing Solutions, Inc., Pleasanton, California.
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3
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Schuurbiers M, Huang Z, Saelee S, Javey M, de Visser L, van den Broek D, Heuvel MVD, Lovejoy AF, Monkhorst K, Klass D. Biological and technical factors in the assessment of blood-based tumor mutational burden (bTMB) in patients with NSCLC. J Immunother Cancer 2022; 10:e004064. [PMID: 35217576 PMCID: PMC8883268 DOI: 10.1136/jitc-2021-004064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2022] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Patients treated with immunotherapy are at risk of considerable adverse events, and the ongoing struggle is to accurately identify the subset of patients who will benefit. Tumor mutational burden (TMB) has emerged as a promising predictive biomarker but requires tumor tissue which is not always available. Blood-based TMB (bTMB) may provide a minimally invasive assessment of mutational load. However, because of the required sequencing depth, bTMB analysis is costly and prone to false negative results. This study attempted to design a minimally sized bTMB panel, examined a counting-based method for bTMB in patients with stage I to IV non-small cell lung cancer (NSCLC) and evaluated both technical factors such as bTMB and tissue-based TMB (tTMB) cut-off, as well as sample-related factors such as cell-free DNA input mass which influence the correlation between bTMB and tTMB. METHODS Tissue, plasma, and whole blood samples collected as part of the LEMA trial (NCT02894853) were used in this study. Samples of 185 treatment naïve patients with stage I to IV NSCLC were sequenced at the Roche Sequencing Solutions with a custom panel designed for TMB, using reagents and workflows derived from the AVENIO Tumor Tissue and circulating tumor DNA Analysis Kits. RESULTS A TMB panel of 1.1 Mb demonstrated highly accurate TMB high calls with a positive predictive value of 95% when using a tTMB cut-off of 16 mut/Mb, corresponding with 42 mut/Mb for bTMB. The positive per cent agreement (PPA) of bTMB was relatively low at 32%. In stage IV samples with at least 20 ng of cfDNA input, PPA of bTMB improved to 63% and minimizing the panel to a subset of 577 kb was possible while maintaining 63% PPA. CONCLUSION Plasma samples with high bTMB values are highly correspondent with tTMB, whereas bTMB low results may also be the result of low tumor burden at earlier stages of disease as well as poorly shedding tumors. For advanced stages of disease, PPA (sensitivity) of bTMB is satisfactory in comparison to tTMB, even when using a panel of less than 600 kb, warranting consideration of bTMB as a predictive biomarker for patients with NSCLC eligible for immunotherapy in the future.
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Affiliation(s)
- Milou Schuurbiers
- Department of Pulmonology, Radboud university medical center - Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | | | | | - Manana Javey
- Roche Sequencing Solutions, Pleasanton, California, USA
| | | | - Daan van den Broek
- Department of Laboratory Medicine, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Michel van den Heuvel
- Department of Pulmonology, Radboud university medical center - Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | | | - Kim Monkhorst
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daniel Klass
- Roche Sequencing Solutions, Pleasanton, California, USA
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4
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Jiang J, Adams HP, Yao L, Yaung S, Lal P, Balasubramanyam A, Fuhlbrück F, Tikoo N, Lovejoy AF, Froehler S, Fang LT, Achenbach HJ, Floegel R, Krügel R, Palma JF. Concordance of Genomic Alterations by Next-Generation Sequencing in Tumor Tissue versus Cell-Free DNA in Stage I-IV Non-Small Cell Lung Cancer. J Mol Diagn 2019; 22:228-235. [PMID: 31837429 DOI: 10.1016/j.jmoldx.2019.10.013] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 09/17/2019] [Accepted: 10/17/2019] [Indexed: 02/07/2023] Open
Abstract
Molecular biomarkers hold promise for personalization of cancer treatment. However, a typical tumor biopsy may be difficult to acquire and may not capture genetic variations within or across tumors. Given these limitations, tumor genotyping using next-generation sequencing of plasma-derived circulating tumor (ct)-DNA has the potential to transform non-small cell lung cancer (NSCLC) management. Importantly, mutations detected in biopsied tissue must also be detected in plasma-derived ctDNA at different disease stages. Using the AVENIO ctDNA Surveillance kit (research use only), mutations in ctDNA from NSCLC subjects were compared with those identified in matched tumor tissue samples, retrospectively. Plasma and tissue samples were collected from 141 treatment-naïve NSCLC subjects (stage I, n = 48; stage II, n = 37; stage III, n = 33; stage IV, n = 23). In plasma samples, the median numbers of variants per subject were 4, 6, 8, and 9 in those with stage I, II, III, and IV disease, respectively. The corresponding values in tissue samples were 5, 5, 6, and 4. The overall tissue-plasma concordance of stage II through IV was 62.2% by AVENIO software call. On multivariate analysis, concordance was positively and significantly associated with tumor size and cancer stage. Next-generation sequencing-based analyses with the AVENIO ctDNA Surveillance kit could be an alternative approach to detecting genetic variations in plasma-derived ctDNA isolated from NSCLC subjects.
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Affiliation(s)
- John Jiang
- Roche Sequencing Solutions, Pleasanton, California
| | | | - Lijing Yao
- Roche Sequencing Solutions, Pleasanton, California
| | | | - Preeti Lal
- Roche Sequencing Solutions, Pleasanton, California
| | | | | | - Nalin Tikoo
- Roche Molecular Systems, Pleasanton, California
| | | | | | - Li Tai Fang
- Roche Sequencing Solutions, Pleasanton, California
| | | | - Ralph Floegel
- Department of Thoracic Surgery, Lungenklinik Lostau, Lostau, Germany
| | - Rainer Krügel
- Department of Pneumology/Thoracic Surgery, Johanniter Krankenhaus im Fläming Treuenbrietzen, Treuenbrietzen, Germany
| | - John F Palma
- Roche Sequencing Solutions, Pleasanton, California.
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5
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Butler M, Konigshofer Y, Clement O, Liu L, Zhao C, Arcila ME, Zehir A, Kohle R, Magliocco AM, Gligorich K, Gloeckner C, Lovejoy AF, Hantash F, Sougnez C, Lennon N, Anekella B, Garlick R. Tumor mutational burden reference materials for assay standardization. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.e14746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e14746 Background: Next Generation Sequencing based assays are designed to detect genomic aberrations in a limited number of target regions. However, there is a need for accurate measurement of tumor mutational burden (TMB) as low as 4 to as high as 50. As TMB assessment is added to various targeted panels, consistent results between panels are required to advance the broad use of this biomarker. Properly designed reference materials aid measurement standardization and are required to demonstrate assay concordance. We developed reference materials that vary in TMB score, tumor content 5-50% and are prepared in FFPE format. Methods: Seven lung and two breast tumor cell lines as well as matched “normal” lymphoblastoid cell lines were expanded in cell culture. Genomic DNA (gDNA) from each cell line was extracted. Tumor/normal mixes were made by mixing DNA and by embedding cells in FFPE blocks. Whole exome sequencing (WES) results were obtained using Agilent SureSelectXT for library construction and an Illumina Novaseq for sequencing. The Friends of Cancer Research TMB consensus method for analyzing WES data was used to filter variants and calculate TMB scores. Results: The cell lines were grown at large scale to produce extractable gDNA. 100% gDNA tumor, 30% gDNA tumor mixes and 30% FFPE cell line mixes were prepared. Preliminary results show that a clinically-relevant range of TMB values ranging from 4 to 35 mutations per million bases. The several thousand mutations that were observed across the lines were found in a variety of genes, which may explain why TMB in targeted panels is influenced by the specific target regions. Also, the initial results show that 30% cell line mixes showed similar TMB results to 100% gDNA. Conclusions: Our approach with wide ranging TMB values as tumor normal mixes is flexible and can be used to test different tumors and assays. For this study we established WES as the ground truth measurement for comparison to other assay formats and obtained comparison data from other panels. This approach also allows laboratories to test additional variables including formalin fixation, sample extraction, gene panel size, target regions, sequencing depth, filtering and limits of detection.
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Affiliation(s)
| | | | | | | | | | | | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
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6
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Lovejoy AF, Lin H, Tabari E, Saelee SL, Kurtz DM, Vitazka P, Morschhauser F, Chu YW, Szafer-Glusman E, Venstrom JM, Luong K, Klass DM. Changes in circulating tumor DNA levels are associated with treatment response and progression-free survival in relapse/refractory DLBCL subjects. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.7546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
7546 Background: Detection of an initial molecular response to therapy in DLBCL could help differentiate patients who will relapse (30-40% of frontline subjects) from those who will not. Recent studies in DLBCL showed ability to detect residual disease and molecular response to therapy from analysis of circulating tumor DNA (ctDNA). Here we performed targeted next generation sequencing (NGS) of baseline ctDNA vs. tumor tissue, and on-treatment ctDNA samples in 32 relapse/refractory DLBCL subjects from the ROMULUS study to assess correlation of outcome with molecular response. Methods: We sequenced plasma, plasma depleted whole blood (PDWB), and tumor DNA from 32 subjects (range 2-6 samples / subject). Library preparation and NGS were performed using hybrid capture-based workflows, with a panel of ~300 kb targeting regions relevant for disease detection in DLBCL. Variants were called from tissue and plasma data, and PDWB data were used to filter out non-tumor specific variants. Results: 83% of variants detected in tissue (1441/1745) were found in the corresponding plasma samples, and 78% of variants detected in plasma (1441/1846) were found in corresponding tissue samples, in line with previous reports. To follow ctDNA changes with treatment, tumor-specific variants were determined from tissue or cycle 1 day 1 (C1D1) plasma samples. These variants were then monitored in C1D1 and later timepoints, with similar ctDNA levels based on variants determined from C1D1 plasma or tissue (R2=0.99). Change in ctDNA levels from C1D1 to C2D1 separated subjects that responded from subjects that progressed (Wilcoxon p-value: 9.39×10-4). Subjects that showed a 10-fold or higher drop in ctDNA levels between C1D1 and C2D1 had significantly longer PFS than those with a smaller ctDNA fold change (HR: 8.06; p=0.0008). Conclusions: This study showed that tumor-specific variants can be identified in baseline plasma with similar performance as from tumor tissue, and that monitoring molecular response as an early change in ctDNA levels after one cycle of treatment correlated with outcomes in this DLBCL study. Clinical trial information: NCT01691898.
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Affiliation(s)
| | - Hai Lin
- Roche Sequencing Solutions, Pleasanton, CA
| | | | | | | | | | | | | | | | | | - Khai Luong
- Roche Sequencing Solutions, Pleasanton, CA
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7
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Ma XM, Xi L, Yaung S, Tikoo N, Balasubramanyam A, Ju C, Klass D, Lovejoy AF, Pati A, Solberg O, Jiang Y, Adams HP, Wehnl B, Thomas M, Lasitschka F, Meister M, Schneider M, Herth F, Palma JF, Muley T. Early assessment of treatment effect in advanced lung adenocarcinoma via longitudinal ctDNA analysis. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.12088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | - Liu Xi
- Roche Sequencing Solutions, Pleasanton, CA
| | | | | | | | - Christine Ju
- Roche Sequencing Solutions, Inc, Pleasanton, CA, US
| | | | | | | | | | | | | | | | - Michael Thomas
- Thoraxklinik, University of Heidelberg, Heidelberg, Germany
| | - Felix Lasitschka
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Michael Meister
- Thoraxklinik at Heidelberg University Hospital, Null, Germany
| | - Marc Schneider
- Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
| | - Felix Herth
- Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
| | | | - Thomas Muley
- Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
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8
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Yaung S, Xi L, Woestmann C, McNamara S, Hinzmann B, Fröhler S, Tikoo N, Ju C, Balasubramanyam A, Vitazka P, Pati A, Lovejoy AF, Klass DM, Adams HP, Thomas M, Herth F, Muley T, Wehnl B, Palma JF, Ma XM. Mutation count, a potential surrogate for tumor mutation load, of circulating tumor DNA (ctDNA) using targeted panel sequencing correlates with clinical outcomes in late stage lung adenocarcinoma and small cell lung cancer. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.12045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | - Liu Xi
- Roche Sequencing Solutions, Pleasanton, CA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Michael Thomas
- Thoraxklinik, University of Heidelberg, Heidelberg, Germany
| | - Felix Herth
- Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
| | - Thomas Muley
- Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
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9
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Ma XM, Tikoo N, Ju C, Balasubramanyam A, Xi L, Yaung S, Klass D, Lovejoy AF, Pati A, Solberg O, Jiang Y, Adams HP, Thomas M, Lasitschka F, Meister M, Schneider M, Herth F, Muley T, Wehnl B, Palma JF. Longitudinal ctDNA analysis to enable early assessment of prognosis in lung adenocarcinoma in the absence of matched tissue biopsy. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.12077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | - Christine Ju
- Roche Sequencing Solutions, Inc, Pleasanton, CA, US
| | | | - Liu Xi
- Roche Sequencing Solutions, Pleasanton, CA
| | | | | | | | | | | | | | | | - Michael Thomas
- Thoraxklinik, University of Heidelberg, Heidelberg, Germany
| | - Felix Lasitschka
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Michael Meister
- Thoraxklinik at Heidelberg University Hospital, Null, Germany
| | - Marc Schneider
- Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
| | - Felix Herth
- Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
| | - Thomas Muley
- Thoraxklinik at Heidelberg University Hospital, Heidelberg, Germany
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10
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Nakamoto MA, Lovejoy AF, Cygan AM, Boothroyd JC. mRNA pseudouridylation affects RNA metabolism in the parasite Toxoplasma gondii. RNA 2017; 23:1834-1849. [PMID: 28851751 PMCID: PMC5689004 DOI: 10.1261/rna.062794.117] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 08/18/2017] [Indexed: 05/09/2023]
Abstract
RNA contains over 100 modified nucleotides that are created post-transcriptionally, among which pseudouridine (Ψ) is one of the most abundant. Although it was one of the first modifications discovered, the biological role of this modification is still not fully understood. Recently, we reported that a pseudouridine synthase (TgPUS1) is necessary for differentiation of the single-celled eukaryotic parasite Toxoplasma gondii from active to chronic infection. To better understand the biological role of pseudouridylation, we report here gel-based and deep-sequencing methods to identify TgPUS1-dependent Ψ's in Toxoplasma RNA, and the use of TgPUS1 mutants to examine the effect of this modification on mRNAs. In addition to identifying conserved sites of pseudouridylation in Toxoplasma rRNA, tRNA, and snRNA, we also report extensive pseudouridylation of Toxoplasma mRNAs, with the Ψ's being relatively depleted in the 3'-UTR but enriched at position 1 of codons. We show that many Ψ's in tRNA and mRNA are dependent on the action of TgPUS1 and that TgPUS1-dependent mRNA Ψ's are enriched in developmentally regulated transcripts. RNA-seq data obtained from wild-type and TgPUS1-mutant parasites shows that genes containing a TgPUS1-dependent Ψ are relatively more abundant in mutant parasites, while pulse/chase labeling of RNA with 4-thiouracil shows that mRNAs containing TgPUS1-dependent Ψ have a modest but statistically significant increase in half-life in the mutant parasites. These data are some of the first evidence suggesting that mRNA Ψ's play an important biological role.
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Affiliation(s)
- Margaret A Nakamoto
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Alexander F Lovejoy
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Alicja M Cygan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - John C Boothroyd
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
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11
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Chaudhuri AA, Chabon JJ, Lovejoy AF, Newman AM, Stehr H, Azad TD, Khodadoust MS, Esfahani MS, Liu CL, Zhou L, Scherer F, Kurtz DM, Say C, Carter JN, Merriott DJ, Dudley JC, Binkley MS, Modlin L, Padda SK, Gensheimer MF, West RB, Shrager JB, Neal JW, Wakelee HA, Loo BW, Alizadeh AA, Diehn M. Early Detection of Molecular Residual Disease in Localized Lung Cancer by Circulating Tumor DNA Profiling. Cancer Discov 2017; 7:1394-1403. [PMID: 28899864 DOI: 10.1158/2159-8290.cd-17-0716] [Citation(s) in RCA: 606] [Impact Index Per Article: 86.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 08/07/2017] [Accepted: 08/31/2017] [Indexed: 12/15/2022]
Abstract
Identifying molecular residual disease (MRD) after treatment of localized lung cancer could facilitate early intervention and personalization of adjuvant therapies. Here, we apply cancer personalized profiling by deep sequencing (CAPP-seq) circulating tumor DNA (ctDNA) analysis to 255 samples from 40 patients treated with curative intent for stage I-III lung cancer and 54 healthy adults. In 94% of evaluable patients experiencing recurrence, ctDNA was detectable in the first posttreatment blood sample, indicating reliable identification of MRD. Posttreatment ctDNA detection preceded radiographic progression in 72% of patients by a median of 5.2 months, and 53% of patients harbored ctDNA mutation profiles associated with favorable responses to tyrosine kinase inhibitors or immune checkpoint blockade. Collectively, these results indicate that ctDNA MRD in patients with lung cancer can be accurately detected using CAPP-seq and may allow personalized adjuvant treatment while disease burden is lowest.Significance: This study shows that ctDNA analysis can robustly identify posttreatment MRD in patients with localized lung cancer, identifying residual/recurrent disease earlier than standard-of-care radiologic imaging, and thus could facilitate personalized adjuvant treatment at early time points when disease burden is lowest. Cancer Discov; 7(12); 1394-403. ©2017 AACR.See related commentary by Comino-Mendez and Turner, p. 1368This article is highlighted in the In This Issue feature, p. 1355.
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Affiliation(s)
- Aadel A Chaudhuri
- Department of Radiation Oncology, Stanford University, Stanford, California.,Stanford Cancer Institute, Stanford University, Stanford, California
| | - Jacob J Chabon
- Stanford Cancer Institute, Stanford University, Stanford, California.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California
| | - Alexander F Lovejoy
- Department of Radiation Oncology, Stanford University, Stanford, California.,Stanford Cancer Institute, Stanford University, Stanford, California
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California.,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California
| | - Henning Stehr
- Stanford Cancer Institute, Stanford University, Stanford, California
| | - Tej D Azad
- Stanford Cancer Institute, Stanford University, Stanford, California
| | - Michael S Khodadoust
- Stanford Cancer Institute, Stanford University, Stanford, California.,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California
| | | | - Chih Long Liu
- Stanford Cancer Institute, Stanford University, Stanford, California.,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California
| | - Li Zhou
- Stanford Cancer Institute, Stanford University, Stanford, California.,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California
| | - Florian Scherer
- Stanford Cancer Institute, Stanford University, Stanford, California.,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California
| | - David M Kurtz
- Stanford Cancer Institute, Stanford University, Stanford, California.,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California.,Department of Bioengineering, Stanford University, Stanford, California
| | - Carmen Say
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - Justin N Carter
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - David J Merriott
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - Jonathan C Dudley
- Stanford Cancer Institute, Stanford University, Stanford, California.,Department of Pathology, Stanford University, Stanford, California
| | - Michael S Binkley
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - Leslie Modlin
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - Sukhmani K Padda
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California
| | | | - Robert B West
- Department of Pathology, Stanford University, Stanford, California
| | - Joseph B Shrager
- Division of Thoracic Surgery, Department of Cardiothoracic Surgery, Stanford School of Medicine, Stanford University, Stanford, California
| | - Joel W Neal
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California
| | - Heather A Wakelee
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California
| | - Billy W Loo
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - Ash A Alizadeh
- Stanford Cancer Institute, Stanford University, Stanford, California. .,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California.,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford University, Stanford, California. .,Stanford Cancer Institute, Stanford University, Stanford, California.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California
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12
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Chaudhuri AA, Chabon JJ, Lovejoy AF, Newman AM, Stehr H, Azad TD, Zhou L, Liu CL, Scherer F, Kurtz DM, Esfahani MS, Say C, Carter JN, Merriott D, Dudley J, Binkley MS, Modlin L, Padda SK, Gensheimer M, West RB, Shrager JB, Neal JW, Wakelee HA, Billy, Loo W, Alizadeh AA, Diehn M. (S012) Circulating Tumor DNA Detects Residual Disease and Anticipates Tumor Progression Earlier Than CT Imaging. Int J Radiat Oncol Biol Phys 2017. [DOI: 10.1016/j.ijrobp.2017.02.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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13
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Lee JJ, Palma JF, Yao L, Lovejoy AF, Yaung S, Zhang D, Wingate-Pearse N, Yau M, Williams C, Pimentel M, Munoz A, Mayol K, Mancao C, Nicholas A, Sommer N, Hurwitz H, Bendell JC, Rohr UP. Correlation of pre- and post-induction plasma mutant allele fraction with progression-free survival (PFS) in STEAM, a prospective, randomized, multicenter study in metastatic colorectal cancer (mCRC). J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.e15118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e15118 Background: STEAM (NCT01765582) evaluated the efficacy and safety of concurrent (c) and sequential (s) FOLFOXIRI-bevacizumab (BEV) versus FOLFOX-BEV for first-line treatment of mCRC. Methods: The AVENIO ctDNA Expanded Kit (Research Use Only) was used to identify somatic mutations in 77 cancer-related genes by next-generation sequencing (NGS) in both pre- and post-induction plasma samples (n = 118 for both groups) from STEAM. Demographics for patient tested were similar to the overall cohort. The mutant allele fraction (mAF) represents the mutation frequency in ctDNA for single nucleotide variants (SNVs) and indels detected per patient. Results: Overall, patients with a pre-induction mAF below the median had longer PFS compared to patients with mAF above the median (13.4 vs 9.5 mo, HR 0.49, p = 0.002). A similar trend was seen for overall survival (OS). Within the below median mAF group, longer PFS was observed in patients treated with cFOLFOXIRI-BEV versus FOLFOX-BEV (25.2 vs 9.5 mo, HR 0.34, p = 0.020). In contrast, no differences in PFS were observed in the treatment arms in the above median mAF group. Patients with a post-induction mAF below the median had longer PFS compared to patients with mAF above the median (15.3 vs 8.1 mo, HR 0.51, p = 0.0064). Correlations of post-induction genomic changes with outcomes, according to treatment groups, will also be presented. Conclusions: The level of pre- and post-induction mAF appears to correlate with PFS in STEAM overall. Furthermore, a lower median pre-induction mAF suggests PFS benefit for cFOLFOXIRI-BEV versus FOLFOX-BEV. Thus, plasma analysis of mAF via the AVENIO ctDNA Expanded Kit may identify patients who benefit from specific treatment in mCRC. These results are hypothesis generating and require further clinical validation. Clinical trial information: NCT01765582.
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Affiliation(s)
| | | | - Lijing Yao
- Roche Sequencing Solutions, Pleasanton, CA
| | | | | | | | | | - May Yau
- Roche Sequencing Solutions, Pleasanton, CA
| | | | | | | | | | | | | | | | | | - Johanna C. Bendell
- Sarah Cannon Research Institute and Tennessee Oncology, PLLC, Nashville, TN
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14
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Chaudhuri A, Chabon JJ, Lovejoy AF, Newman AM, Stehr H, Azad TD, Carter JN, Merriott DJ, Liu CL, Kurtz DM, Dudley JC, Padda SK, Shrager JB, Neal JW, Wakelee HA, Loo BW, Alizadeh AA, Diehn M. Analysis of circulating tumor DNA in localized lung cancer for detection of molecular residual disease and personalization of adjuvant strategies. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.8519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
8519 Background: Identifying localized non-small cell lung cancer (NSCLC) patients with residual disease following curative intent therapy is difficult due to normal tissue changes caused by surgery or radiation and an inability to detect microscopic disease. Analysis of circulating tumor DNA (ctDNA) might enable identification of molecular residual disease (MRD) and personalization of adjuvant treatment approaches but has not been explored in lung cancer. Methods: We applied CAPP-Seq, an ultra-sensitive next-generation sequencing based ctDNA quantitation method, to pre- and post-treatment blood samples from a cohort of 41 patients treated with chemoradiation, radiotherapy or surgery for stage I-III primary lung cancer. Detection of ctDNA at a single MRD time-point within 4 months of treatment completion was compared with surveillance by cross-sectional imaging. Furthermore, we developed an approach for identification of tumor mutation burden based on mutations detected in plasma, leveraging whole exome sequencing data from 1,177 NSCLCs sequenced by TCGA. Results: Median follow-up time was 35 months. Pre-treatment ctDNA was detected in 38 (93%) patients and 19 (46%) had detectable post-treatment ctDNA MRD. MRD+ patients displayed significantly inferior 3-year freedom from progression (0% vs. 92%; HR 38; P < 0.0001) and 3-year overall survival (8% vs. 75%; HR 12; P < 0.0001) than MRD- patients. Detection of ctDNA MRD had positive and negative predictive values for disease progression of 100% and 93%, respectively. Furthermore, we non-invasively identified activating EGFR mutations or high mutational burden (≥5 CAPP-Seq non-synonymous mutations, corresponding to > 200 non-synonymous mutations per exome or > 4 single nucleotide variants per megabase of exome) in 47% of patients with detectable ctDNA MRD, suggesting potentially favorable responses to TKIs and immune checkpoint inhibitors, respectively. Conclusions: Our results indicate that ctDNA analysis accurately detects MRD in localized lung cancer patients and could facilitate personalized adjuvant treatment at early time-points when disease burden is minimal.
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15
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Lee JJ, Palma JF, Yao L, Lovejoy AF, Yaung S, Zhang D, Wingate-Pearse N, Yau M, Williams C, Pimentel M, Munoz A, Mayol K, Mancao C, Nicholas A, Sommer N, Bendell JC, Hurwitz H, Rohr UP. Evaluation of clinical outcomes by analysis of mutations in tumor tissue and circulating plasma DNA using next-generation sequencing (NGS) from STEAM, a prospective, randomized, multicenter study in metastatic colorectal cancer (mCRC). J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.11510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
11510 Background: STEAM (NCT01765582) assessed the efficacy and safety of concurrent (c) and sequential (s) FOLFOXIRI-bevacizumab (BEV) vs FOLFOX-BEV for first-line treatment of mCRC. Methods: The AVENIO ctDNA Expanded Kit (Research Use Only) was used to assess somatic mutations in 77 cancer-related genes by NGS in tissue, and both pre- and post-induction plasma samples (n = 182, 150 and 118 respectively) from STEAM. Four mutation classes including single-nucleotide variants (SNVs), indels, copy number amplifications (CNAs) and fusions were identified. SNVs and indels were called in tissue and plasma at allele frequencies of 5% and 0.25% respectively. Results: Overall concordance of mutations in pre-induction plasma with tissue was 83%. Concordance for the seven most mutated genes ranged from 91.5%-100%. In pts with matched samples (n = 118), RAS WT pts showed significantly longer progression-free survival (PFS) in both cFOLFOXIRI-BEV (A) and sFOLFOXIRI-BEV (B) arms versus FOLFOX-BEV (C), using genotyping of either tissue or plasma. This was not seen in RAS MUT pts. In contrast, TP53 WT showed no significant treatment differences while TP53 MUT showed longer PFS for cFOLFOXIRI-BEV versus FOLFOX-BEV. A list of mutation frequencies for all samples, as well as hierarchical clustering analysis of tissue mutations will be presented. Conclusions: The AVENIO ctDNA Expanded Kit identified mutations in 77 cancer-related genes, in both plasma and tissue, with high overall concordance. Compared to FOLFOX-BEV, longer PFS was observed for c- or s- FOLFOXIRI-BEV in RAS WT pts and for cFOLFOXIRI-BEV in TP53 MUT pts, irrespective of sample type. These results are hypothesis generating and require further clinical validation. Clinical trial information: NCT01765582. [Table: see text]
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Affiliation(s)
| | | | - Lijing Yao
- Roche Sequencing Solutions, Pleasanton, CA
| | | | | | | | | | - May Yau
- Roche Sequencing Solutions, Pleasanton, CA
| | | | | | | | | | | | | | | | - Johanna C. Bendell
- Sarah Cannon Research Institute and Tennessee Oncology, PLLC, Nashville, TN
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16
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Diehn M, Alizadeh AA, Adams HP, Lee JJ, Klassen S, Palma JF, Hinzman B, Lovejoy AF, Newman AM, Yao L, Yaung S, Balasubramanyam A, Rohr UP, Rosenthal A, Kube R, Steinmüller T, Marusch F, Mantke R, Heise M, Pross M. Early prediction of clinical outcomes in resected stage II and III colorectal cancer (CRC) through deep sequencing of circulating tumor DNA (ctDNA). J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.3591] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
3591 Background: Adjuvant chemotherapy is offered to most pts with Stage III CRC, and to a subset with Stage II disease deemed at high-risk for recurrence. Nevertheless, risk stratification strategies remain suboptimal. Detection of minimal residual disease (MRD) through ctDNA analysis has been shown to identify pts at high recurrence risk in Stage II CRC, but not Stage III disease. Methods: The next-generation sequencing based AVENIO ctDNA Surveillance Kit (Research Use Only) was used to identify single nucleotide variants (SNVs) in tumor tissue within a cohort of 145 Stage II and III CRC pts following R0 surgical resection (n = 86 and 59 respectively; median follow-up = 32.1 mo). The same assay was used to monitor ctDNA with a single post-operative blood sample (mean surgery-to-phlebotomy time: 10 days). Regions from 197 genes recurrently mutated in CRC were interrogated, and pts were classified as ctDNA positive (+) or negative (-) in plasma based on the detection of SNVs previously identified in tumor tissue. Results: Variants were identified in 99% of tumors (n = 144) with a median of 4 SNVs/sample (range 1-24) and all post-operative plasma samples were successfully profiled. Pts with detectable ctDNA (n = 12) displayed a significantly shorter 2-year relapse-free survival (RFS; 17% vs 88%; HR 10.3; 95% CI 2.3-46.9; p < 0.00001), time to recurrence (TTR; HR 20.6; 95% CI 3.1-139.0; p < 0.00001) and overall survival (OS; HR 3.4; 95% CI 0.5-25.8; p = 0.041) than ctDNA- pts (n = 132). 11 (92%) of ctDNA+ pts developed recurrence compared to 9 (7%) of ctDNA- pts. Monitoring multiple variants doubled sensitivity of MRD detection compared to tracking a single driver mutation. TTR was shorter in ctDNA+ vs ctDNA- Stage II (HR 23.1, 95% CI 0.28-1900.4; p < 0.00001) and stage III pts (HR 17.9; 95% CI 2.7-117.3, p < 0.00001). TTR of Stage II and III ctDNA- pts was similar (p = 0.7). Conclusions: Our results indicate that ctDNA analysis can detect MRD within days after complete resection of CRC and accurately identifies pts at high risk of recurrence in both Stage II and III CRC. MRD detection via ctDNA sequencing may allow personalization of adjuvant treatment strategies.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Lijing Yao
- Roche Sequencing Solutions, Pleasanton, CA
| | | | | | | | | | - Rainer Kube
- Carl-Thiem-Klinikum Cottbus, Cottbus, Germany
| | | | | | - Rene Mantke
- Staedtisches Klinikum Brandenburg, Brandenburg, Germany
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17
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Scherer F, Kurtz DM, Newman AM, Stehr H, Craig AFM, Esfahani MS, Lovejoy AF, Chabon JJ, Klass DM, Liu CL, Zhou L, Glover C, Visser BC, Poultsides GA, Advani RH, Maeda LS, Gupta NK, Levy R, Ohgami RS, Kunder CA, Diehn M, Alizadeh AA. Distinct biological subtypes and patterns of genome evolution in lymphoma revealed by circulating tumor DNA. Sci Transl Med 2016; 8:364ra155. [PMID: 27831904 PMCID: PMC5490494 DOI: 10.1126/scitranslmed.aai8545] [Citation(s) in RCA: 318] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 10/19/2016] [Indexed: 12/11/2022]
Abstract
Patients with diffuse large B cell lymphoma (DLBCL) exhibit marked diversity in tumor behavior and outcomes, yet the identification of poor-risk groups remains challenging. In addition, the biology underlying these differences is incompletely understood. We hypothesized that characterization of mutational heterogeneity and genomic evolution using circulating tumor DNA (ctDNA) profiling could reveal molecular determinants of adverse outcomes. To address this hypothesis, we applied cancer personalized profiling by deep sequencing (CAPP-Seq) analysis to tumor biopsies and cell-free DNA samples from 92 lymphoma patients and 24 healthy subjects. At diagnosis, the amount of ctDNA was found to strongly correlate with clinical indices and was independently predictive of patient outcomes. We demonstrate that ctDNA genotyping can classify transcriptionally defined tumor subtypes, including DLBCL cell of origin, directly from plasma. By simultaneously tracking multiple somatic mutations in ctDNA, our approach outperformed immunoglobulin sequencing and radiographic imaging for the detection of minimal residual disease and facilitated noninvasive identification of emergent resistance mutations to targeted therapies. In addition, we identified distinct patterns of clonal evolution distinguishing indolent follicular lymphomas from those that transformed into DLBCL, allowing for potential noninvasive prediction of histological transformation. Collectively, our results demonstrate that ctDNA analysis reveals biological factors that underlie lymphoma clinical outcomes and could facilitate individualized therapy.
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Affiliation(s)
- Florian Scherer
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - David M Kurtz
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Aaron M Newman
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Henning Stehr
- Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Alexander F M Craig
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | | | - Alexander F Lovejoy
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA
| | - Jacob J Chabon
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Daniel M Klass
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Chih Long Liu
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Li Zhou
- Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Cynthia Glover
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Brendan C Visser
- Division of Surgical Oncology, Department of Surgery, Stanford University, Stanford, CA 94305, USA
| | - George A Poultsides
- Division of Surgical Oncology, Department of Surgery, Stanford University, Stanford, CA 94305, USA
| | - Ranjana H Advani
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Lauren S Maeda
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Neel K Gupta
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Ronald Levy
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Robert S Ohgami
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | | | - Maximilian Diehn
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA.
- Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA
| | - Ash A Alizadeh
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA.
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
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18
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Chabon JJ, Simmons AD, Lovejoy AF, Esfahani MS, Newman AM, Haringsma HJ, Kurtz DM, Stehr H, Scherer F, Karlovich CA, Harding TC, Durkin KA, Otterson GA, Purcell WT, Camidge DR, Goldman JW, Sequist LV, Piotrowska Z, Wakelee HA, Neal JW, Alizadeh AA, Diehn M. Circulating tumour DNA profiling reveals heterogeneity of EGFR inhibitor resistance mechanisms in lung cancer patients. Nat Commun 2016; 7:11815. [PMID: 27283993 PMCID: PMC4906406 DOI: 10.1038/ncomms11815] [Citation(s) in RCA: 452] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 05/03/2016] [Indexed: 12/20/2022] Open
Abstract
Circulating tumour DNA (ctDNA) analysis facilitates studies of tumour heterogeneity. Here we employ CAPP-Seq ctDNA analysis to study resistance mechanisms in 43 non-small cell lung cancer (NSCLC) patients treated with the third-generation epidermal growth factor receptor (EGFR) inhibitor rociletinib. We observe multiple resistance mechanisms in 46% of patients after treatment with first-line inhibitors, indicating frequent intra-patient heterogeneity. Rociletinib resistance recurrently involves MET, EGFR, PIK3CA, ERRB2, KRAS and RB1. We describe a novel EGFR L798I mutation and find that EGFR C797S, which arises in ∼33% of patients after osimertinib treatment, occurs in <3% after rociletinib. Increased MET copy number is the most frequent rociletinib resistance mechanism in this cohort and patients with multiple pre-existing mechanisms (T790M and MET) experience inferior responses. Similarly, rociletinib-resistant xenografts develop MET amplification that can be overcome with the MET inhibitor crizotinib. These results underscore the importance of tumour heterogeneity in NSCLC and the utility of ctDNA-based resistance mechanism assessment.
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Affiliation(s)
- Jacob J. Chabon
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, California 94305, USA
| | | | - Alexander F. Lovejoy
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, California 94305, USA
| | - Mohammad S. Esfahani
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, California 94305, USA
| | - Aaron M. Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, California 94305, USA
| | | | - David M. Kurtz
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California 94305, USA
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA
| | - Henning Stehr
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, California 94305, USA
| | - Florian Scherer
- Stanford Cancer Institute, Stanford University, Stanford, California 94305, USA
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California 94305, USA
| | | | | | - Kathleen A. Durkin
- Molecular Graphics and Computation Facility, College of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - W. Thomas Purcell
- Division of Medical Oncology, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - D. Ross Camidge
- Division of Medical Oncology, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Jonathan W. Goldman
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Lecia V. Sequist
- Massachusetts General Hospital & Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Zofia Piotrowska
- Massachusetts General Hospital & Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Heather A. Wakelee
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California 94305, USA
| | - Joel W. Neal
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California 94305, USA
| | - Ash A. Alizadeh
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, California 94305, USA
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California 94305, USA
- Division of Hematology, Department of Medicine, Stanford University, Stanford, California 94305, USA
| | - Maximilian Diehn
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, California 94305, USA
- Department of Radiation Oncology, Stanford University, Stanford, California 94305, USA
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19
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Newman AM, Lovejoy AF, Klass DM, Kurtz DM, Chabon JJ, Scherer F, Stehr H, Liu CL, Bratman SV, Say C, Zhou L, Carter JN, West RB, Sledge GW, Shrager JB, Loo BW, Neal JW, Wakelee HA, Alizadeh AA, Diehn M. Integrated digital error suppression for noninvasive detection of circulating tumor DNA in NSCLC. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.e20500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Aaron M. Newman
- Division of Oncology, Stanford University School of Medicine, Stanford, CA
| | | | | | | | - Jacob J. Chabon
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA
| | - Florian Scherer
- Division of Oncology, Stanford University School of Medicine, Stanford, CA
| | | | - Chih Long Liu
- Division of Oncology, Stanford University School of Medicine, Stanford, CA
| | | | | | - Li Zhou
- Division of Oncology, Stanford University School of Medicine, Stanford, CA
| | | | - Robert B. West
- Department of Pathology, Stanford Cancer Institute/Stanford University School of Medicine, Stanford, CA
| | | | | | | | - Joel W. Neal
- Stanford Cancer Institute/Stanford University School of Medicine, Stanford, CA
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20
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Kurtz DM, Scherer F, Newman AM, Craig AF, Khodadoust MS, Lovejoy AF, Klass DM, Chabon JJ, Glover C, Zhou L, Liu CL, Gupta NK, Maeda LS, Advani RH, Levy R, Diehn M, Alizadeh AA. Prediction of therapeutic outcomes in DLBCL from circulating tumor DNA dynamics. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.7511] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | - Florian Scherer
- Division of Oncology, Stanford University School of Medicine, Stanford, CA
| | - Aaron M. Newman
- Division of Oncology, Stanford University School of Medicine, Stanford, CA
| | | | | | | | | | - Jacob J. Chabon
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA
| | - Cynthia Glover
- Division of Oncology, Stanford University School of Medicine, Stanford, CA
| | - Li Zhou
- Division of Oncology, Stanford University School of Medicine, Stanford, CA
| | - Chih Long Liu
- Division of Oncology, Stanford University School of Medicine, Stanford, CA
| | - Neel K. Gupta
- Division of Oncology, Stanford University School of Medicine, Stanford, CA
| | | | | | - Ronald Levy
- Division of Oncology, Stanford University School of Medicine, Stanford, CA
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21
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Chabon JJ, Simmons A, Newman AM, Lovejoy AF, Esfahani MS, Haringsma H, Kurtz DM, Stehr H, Scherer F, Durkin KA, Otterson GA, Purcell WT, Camidge DR, Goldman JW, Sequist LV, Piotrowska Z, Wakelee HA, Neal JW, Alizadeh AA, Diehn M. Inter- and intra-patient heterogeneity of resistance mechanisms to the mutant EGFR selective inhibitor rociletinib. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.9000] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Jacob J. Chabon
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA
| | | | - Aaron M. Newman
- Division of Oncology, Stanford University School of Medicine, Stanford, CA
| | | | | | | | | | | | - Florian Scherer
- Division of Oncology, Stanford University School of Medicine, Stanford, CA
| | | | | | | | | | | | | | | | | | - Joel W. Neal
- Stanford Cancer Institute/Stanford University School of Medicine, Stanford, CA
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22
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Scherer F, Kurtz DM, Newman AM, Stehr H, Craig AF, Esfahani MS, Lovejoy AF, Chabon JJ, Klass DM, Liu CL, Zhou L, Glover C, Advani RH, Maeda LS, Gupta NK, Levy R, Ohgami RS, Kunder C, Diehn M, Alizadeh AA. Noninvasive molecular subtyping and risk stratification of DLBCL. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.7554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Florian Scherer
- Division of Oncology, Stanford University School of Medicine, Stanford, CA
| | | | - Aaron M. Newman
- Division of Oncology, Stanford University School of Medicine, Stanford, CA
| | | | | | | | | | - Jacob J. Chabon
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA
| | | | - Chih Long Liu
- Division of Oncology, Stanford University School of Medicine, Stanford, CA
| | - Li Zhou
- Division of Oncology, Stanford University School of Medicine, Stanford, CA
| | - Cynthia Glover
- Division of Oncology, Stanford University School of Medicine, Stanford, CA
| | | | | | - Neel K. Gupta
- Division of Oncology, Stanford University School of Medicine, Stanford, CA
| | - Ronald Levy
- Division of Oncology, Stanford University School of Medicine, Stanford, CA
| | - Robert S. Ohgami
- Department of Pathology, Stanford University Medical Center, Stanford, CA
| | - Christian Kunder
- Department of Pathology, Stanford University Medical Center, Stanford, CA
| | | | - Ash A. Alizadeh
- Division of Oncology, Stanford University School of Medicine, Stanford, CA
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23
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Karmakar S, Harcourt EM, Hewings DS, Scherer F, Lovejoy AF, Kurtz DM, Ehrenschwender T, Barandun LJ, Roost C, Alizadeh AA, Kool ET. Corrigendum: Organocatalytic removal of formaldehyde adducts from RNA and DNA bases. Nat Chem 2015; 7:1033. [PMID: 26587722 DOI: 10.1038/nchem.2401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Lovejoy AF, Riordan DP, Brown PO. Transcriptome-wide mapping of pseudouridines: pseudouridine synthases modify specific mRNAs in S. cerevisiae. PLoS One 2014; 9:e110799. [PMID: 25353621 PMCID: PMC4212993 DOI: 10.1371/journal.pone.0110799] [Citation(s) in RCA: 271] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 09/17/2014] [Indexed: 12/23/2022] Open
Abstract
We developed a novel technique, called pseudouridine site identification sequencing (PSI-seq), for the transcriptome-wide mapping of pseudouridylation sites with single-base resolution from cellular RNAs based on the induced termination of reverse transcription specifically at pseudouridines following CMCT treatment. PSI-seq analysis of RNA samples from S. cerevisiae correctly detected all of the 43 known pseudouridines in yeast 18S and 25S ribosomal RNA with high specificity. Moreover, application of PSI-seq to the yeast transcriptome revealed the presence of site-specific pseudouridylation within dozens of mRNAs, including RPL11a, TEF1, and other genes implicated in translation. To identify the mechanisms responsible for mRNA pseudouridylation, we genetically deleted candidate pseudouridine synthase (Pus) enzymes and reconstituted their activities in vitro. These experiments demonstrated that the Pus1 enzyme was necessary and sufficient for pseudouridylation of RPL11a mRNA, whereas Pus4 modified TEF1 mRNA, and Pus6 pseudouridylated KAR2 mRNA. Finally, we determined that modification of RPL11a at Ψ -68 was observed in RNA from the related yeast S. mikitae, and Ψ -239 in TEF1 mRNA was maintained in S. mikitae as well as S. pombe, indicating that these pseudouridylations are ancient, evolutionarily conserved RNA modifications. This work establishes that site-specific pseudouridylation of eukaryotic mRNAs is a genetically programmed RNA modification that naturally occurs in multiple yeast transcripts via distinct mechanisms, suggesting that mRNA pseudouridylation may provide an important novel regulatory function. The approach and strategies that we report here should be generally applicable to the discovery of pseudouridylation, or other RNA modifications, in diverse biological contexts.
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Affiliation(s)
- Alexander F. Lovejoy
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (AFL); (DPR)
| | - Daniel P. Riordan
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (AFL); (DPR)
| | - Patrick O. Brown
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
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Friend K, Lovejoy AF, Steitz JA. U2 snRNP binds intronless histone pre-mRNAs to facilitate U7-snRNP-dependent 3' end formation. Mol Cell 2008; 28:240-52. [PMID: 17964263 PMCID: PMC2149891 DOI: 10.1016/j.molcel.2007.09.026] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Revised: 08/08/2007] [Accepted: 09/14/2007] [Indexed: 11/17/2022]
Abstract
In metazoa, pre-mRNA 3' end formation occurs via two pathways: cleavage/polyadenylation for the majority of RNA polymerase II transcripts and U7-snRNP-dependent cleavage for replication-dependent histone pre-mRNAs. An RNA element derived from a replication-dependent histone gene affects multiple steps of pre-mRNA processing. Here, we demonstrate that a portion of this RNA element, present in the majority of histone mRNAs, stimulates U7-snRNP-dependent cleavage. Surprisingly, this element binds U2 snRNP, although it is derived from an intronless mRNA. Specifically, SF3b, a U2 and U12-snRNP component, contacts the RNA element both in vitro and in vivo in conjunction with hPrp43, a DEAH-box helicase. Tethering either U2 or U12 snRNP to histone pre-mRNA substrates stimulates U7-snRNP-dependent cleavage in vitro and in vivo. Finally, we show that U2 snRNP associates with histone pre-mRNAs in vivo. We conclude that U2 snRNP plays a nonsplicing role in histone mRNA maturation.
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Affiliation(s)
- Kyle Friend
- Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
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