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An HJ, An E, Rabizadeh S, Liao WL, Burrows J, Hembrough T, Kang JH, Park CK, Kim TJ. Quantitative Multiplexed Proteomics Could Assist Therapeutic Decision Making in Non-Small Cell Lung Cancer Patients with Ambiguous ALK Test Results. Cancers (Basel) 2021; 13:cancers13102337. [PMID: 34066104 PMCID: PMC8150487 DOI: 10.3390/cancers13102337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/05/2021] [Accepted: 05/05/2021] [Indexed: 11/16/2022] Open
Abstract
Therapeutic guidance in non-small cell lung cancer (NSCLC) tumors that are positive for anaplastic lymphoma kinase (ALK) fluorescent in situ hybridization (FISH), but negative for ALK immunohistochemistry, is still challenging. Parallel routine screening of 4588 NSCLC cases identified 22 discordant cases. We rechecked these samples using ALK antibodies and selected reaction monitoring (SRM) quantitative multiplexed proteomics screening multiple protein targets, including ALK and MET for the ALK tyrosine kinase inhibitor (TKI), and FR-alpha, hENT1, RRM1, TUBB3, ERCC1, and XRCC1 for chemotherapy. The presence of ALK (31.8%), MET (36.4%), FR-alpha (72.7%), hENT1 (18.2%), RRM1 (31.8%), TUBB3 (72.9%), ERCC1 (4.5%), and a low level of XRCC1 (54.4%) correlated with clinical outcomes. SRM was more sensitive than the ALK D5F3 assay. Among the eight cases receiving ALK TKI, four cases with ALK or MET detected by SRM had complete or partial responses, whereas four cases without ALK or MET showed progression. Twenty-seven treatment outcomes from 20 cases were assessed and cases expressing more than half of the specific predictive proteins were sensitive to matching therapeutic agents and showed longer progression-free survival than the other cases (p < 0.001). SRM showed a potential role in therapeutic decision making in NSCLC patients with ambiguous ALK test results.
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Affiliation(s)
- Ho Jung An
- Department of Medical Oncology, St. Vincent’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea;
| | - Eunkyung An
- NantOmics, Culver City, CA 90232, USA; (E.A.); (S.R.); (W.-L.L.)
| | | | - Wei-Li Liao
- NantOmics, Culver City, CA 90232, USA; (E.A.); (S.R.); (W.-L.L.)
| | - Jon Burrows
- OncoPlex Diagnostics, Rockville, MD 20850, USA; (J.B.); (T.H.)
| | - Todd Hembrough
- OncoPlex Diagnostics, Rockville, MD 20850, USA; (J.B.); (T.H.)
| | - Jin Hyung Kang
- Department of Medical Oncology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea;
| | - Chan Kwon Park
- Division of Pulmonology, Department of Internal Medicine, Yeouido St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea;
| | - Tae-Jung Kim
- Department of Hospital Pathology, Yeouido St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Correspondence: ; Tel.: 82-2-3779-2157
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Trombetta D, Parente P, Latiano TP, Fabrizio FP, Muscarella LA. Identification of EML4-ALK fusion in a sporadic case of cholangiocarcinoma. Eur J Intern Med 2020; 71:92-94. [PMID: 31711728 DOI: 10.1016/j.ejim.2019.10.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 10/14/2019] [Accepted: 10/22/2019] [Indexed: 02/07/2023]
Affiliation(s)
- Domenico Trombetta
- Laboratory of Oncology, IRCCS Fondazione Casa Sollevo della Sofferenza, San Giovanni Rotondo, Foggia 71013, Italy..
| | - Paola Parente
- Unit of Pathology, Fondazione IRCSS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Tiziana Pia Latiano
- Oncology Department, Fondazione IRCSS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Federico Pio Fabrizio
- Laboratory of Oncology, IRCCS Fondazione Casa Sollevo della Sofferenza, San Giovanni Rotondo, Foggia 71013, Italy
| | - Lucia Anna Muscarella
- Laboratory of Oncology, IRCCS Fondazione Casa Sollevo della Sofferenza, San Giovanni Rotondo, Foggia 71013, Italy
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Park J, Oh HJ, Han D, Wang JI, Park IA, Ryu HS, Kim Y. Parallel Reaction Monitoring-Mass Spectrometry (PRM-MS)-Based Targeted Proteomic Surrogates for Intrinsic Subtypes in Breast Cancer: Comparative Analysis with Immunohistochemical Phenotypes. J Proteome Res 2019; 19:2643-2653. [DOI: 10.1021/acs.jproteome.9b00490] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Joonho Park
- Department of Biomedical Engineering, Seoul National University College of Medicine, 103 Daehak-ro, Seoul 03080, Korea
| | - Hyeon Jeong Oh
- Department of Pathology, Seoul National University Hospital, 101 Daehak-ro, Seoul 03080, Korea
| | - Dohyun Han
- Biomedical Research Institute, Seoul National University Hospital, 101 Daehak-ro, Seoul 03080, Korea
| | - Joseph I. Wang
- Biomedical Research Institute, Seoul National University Hospital, 101 Daehak-ro, Seoul 03080, Korea
| | - In Ae Park
- Department of Pathology, Seoul National University Hospital, 101 Daehak-ro, Seoul 03080, Korea
| | - Han Suk Ryu
- Department of Pathology, Seoul National University Hospital, 101 Daehak-ro, Seoul 03080, Korea
| | - Youngsoo Kim
- Department of Biomedical Engineering, Seoul National University College of Medicine, 103 Daehak-ro, Seoul 03080, Korea
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Kim YJ, Sweet SMM, Egertson JD, Sedgewick AJ, Woo S, Liao WL, Merrihew GE, Searle BC, Vaske C, Heaton R, MacCoss MJ, Hembrough T. Data-Independent Acquisition Mass Spectrometry To Quantify Protein Levels in FFPE Tumor Biopsies for Molecular Diagnostics. J Proteome Res 2018; 18:426-435. [PMID: 30481034 DOI: 10.1021/acs.jproteome.8b00699] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mass spectrometry-based protein quantitation is currently used to measure therapeutically relevant protein biomarkers in CAP/CLIA setting to predict likely responses of known therapies. Selected reaction monitoring (SRM) is the method of choice due to its outstanding analytical performance. However, data-independent acquisition (DIA) is now emerging as a proteome-scale clinical assay. We evaluated the ability of DIA to profile the patient-specific proteomes of sample-limited tumor biopsies and to quantify proteins of interest in a targeted fashion using formalin-fixed, paraffin-embedded (FFPE) tumor biopsies ( n = 12) selected from our clinical laboratory. DIA analysis on the tumor biopsies provided 3713 quantifiable proteins including actionable biomarkers currently in clinical use, successfully separated two gastric cancers from colorectal cancer specimen solely on the basis of global proteomic profiles, and identified subtype-specific proteins with prognostic or diagnostic value. We demonstrate the potential use of DIA-based quantitation to inform therapeutic decision-making using TUBB3, for which clinical cutoff expression levels have been established by SRM. Comparative analysis of DIA-based proteomic profiles and mRNA expression levels found positively and negatively correlated protein-gene pairs, a finding consistent with previously reported results from fresh-frozen tumor tissues.
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Affiliation(s)
- Yeoun Jin Kim
- NantOmics , 9600 Medical Center Drive , Rockville , Maryland 20850 , United States
| | - Steve M M Sweet
- NantOmics , 9600 Medical Center Drive , Rockville , Maryland 20850 , United States
| | - Jarrett D Egertson
- Department of Genome Sciences , University of Washington , 3720 15th Avenue NE , Seattle , Washington 98195 , United States
| | - Andrew J Sedgewick
- NantOmics , 2919 Mission Street , Santa Cruz , California 95060 , United States
| | - Sunghee Woo
- NantOmics , 9600 Medical Center Drive , Rockville , Maryland 20850 , United States
| | - Wei-Li Liao
- NantOmics , 9600 Medical Center Drive , Rockville , Maryland 20850 , United States
| | - Gennifer E Merrihew
- Department of Genome Sciences , University of Washington , 3720 15th Avenue NE , Seattle , Washington 98195 , United States
| | - Brian C Searle
- Department of Genome Sciences , University of Washington , 3720 15th Avenue NE , Seattle , Washington 98195 , United States
| | - Charlie Vaske
- NantOmics , 2919 Mission Street , Santa Cruz , California 95060 , United States
| | - Robert Heaton
- NantOmics , 9600 Medical Center Drive , Rockville , Maryland 20850 , United States
| | - Michael J MacCoss
- Department of Genome Sciences , University of Washington , 3720 15th Avenue NE , Seattle , Washington 98195 , United States
| | - Todd Hembrough
- NantOmics , 9600 Medical Center Drive , Rockville , Maryland 20850 , United States
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Kim YJ, Chambers AG, Cecchi F, Hembrough T. Targeted data-independent acquisition for mass spectrometric detection of RAS mutations in formalin-fixed, paraffin-embedded tumor biopsies. J Proteomics 2018; 189:91-96. [DOI: 10.1016/j.jprot.2018.04.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/13/2018] [Accepted: 04/14/2018] [Indexed: 01/14/2023]
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Liu J, Zhang W, Gu M, Ji Y, Yang L, Cheng X, Xiao X, Xu J, Gu C, Zhang J, Zhang S, Chen D, Pan S. Serum SP70 is a sensitive predictor of chemotherapy response in patients with advanced nonsmall cell lung cancer. Cancer Med 2018; 7:2925-2933. [PMID: 29767438 PMCID: PMC6051171 DOI: 10.1002/cam4.1555] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 04/09/2018] [Accepted: 04/23/2018] [Indexed: 12/15/2022] Open
Abstract
SP70 is a novel tumor biomarker in patients with nonsmall cell lung cancer (NSCLC). However, its role as a marker for predicting the response to chemotherapy for patients with advanced NSCLC has not been investigated. A total of 152 patients were enrolled. Serum SP70, carcinoembryonic antigen (CEA), cytokeratin 19 fragment (CYFRA21-1), and neuron-specific enolase (NSE) were detected before and after 2 cycles of chemotherapy. The correlation between serum tumor biomarker levels and chemotherapy responses and their association with epidermal growth factor receptor (EGFR) mutation status and progression-free survival (PFS) were analyzed. Serum SP70 levels were significantly decreased after chemotherapy in the partial remission (PR) group (P < .001) and increased in the progressive disease (PD) group (P < .001), but not significantly changed in the stable disease (SD) group (P = .114). Although similar changes were observed on CEA and CYFRA21-1 levels but not NSE, ROC analysis demonstrated that SP70 is superior to the others. Additionally, patients with EGFR mutation had higher serum SP70 levels and tissue SP70 expression than patients without EGFR mutation (P = .014 and P = .002, respectively). The median PFS of patients with decreased SP70 levels after chemotherapy was longer than that of patients with stable or increased serum SP70 level (24 months vs 12 months vs 2 months, P < .001), and the differences of all other 3 tumor markers were not obvious. Serum SP70 is a sensitive and real-time indicator of chemotherapeutic efficacy in patients with advanced NSCLC and related to PFS.
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Affiliation(s)
- Jingping Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,National Key Clinical Department of Laboratory Medicine, Jiangsu Province Hospital, Nanjing Medical University, Nanjing, China
| | - Wei Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,National Key Clinical Department of Laboratory Medicine, Jiangsu Province Hospital, Nanjing Medical University, Nanjing, China
| | - Min Gu
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,National Key Clinical Department of Laboratory Medicine, Jiangsu Province Hospital, Nanjing Medical University, Nanjing, China
| | - Yazhou Ji
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,National Key Clinical Department of Laboratory Medicine, Jiangsu Province Hospital, Nanjing Medical University, Nanjing, China
| | - Lu Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,National Key Clinical Department of Laboratory Medicine, Jiangsu Province Hospital, Nanjing Medical University, Nanjing, China
| | - Xiangjun Cheng
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,National Key Clinical Department of Laboratory Medicine, Jiangsu Province Hospital, Nanjing Medical University, Nanjing, China
| | - Xuelian Xiao
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,National Key Clinical Department of Laboratory Medicine, Jiangsu Province Hospital, Nanjing Medical University, Nanjing, China
| | - Jian Xu
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,National Key Clinical Department of Laboratory Medicine, Jiangsu Province Hospital, Nanjing Medical University, Nanjing, China
| | - Chunrong Gu
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,National Key Clinical Department of Laboratory Medicine, Jiangsu Province Hospital, Nanjing Medical University, Nanjing, China
| | - Jiexin Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,National Key Clinical Department of Laboratory Medicine, Jiangsu Province Hospital, Nanjing Medical University, Nanjing, China
| | - Shichang Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,National Key Clinical Department of Laboratory Medicine, Jiangsu Province Hospital, Nanjing Medical University, Nanjing, China
| | - Dan Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,National Key Clinical Department of Laboratory Medicine, Jiangsu Province Hospital, Nanjing Medical University, Nanjing, China
| | - Shiyang Pan
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,National Key Clinical Department of Laboratory Medicine, Jiangsu Province Hospital, Nanjing Medical University, Nanjing, China
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Abstract
INTRODUCTION Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers worldwide. However, there remain many unmet clinical needs, from diagnosis to treatment strategies. The inherent complexity of the molecular characteristics of PDAC has made it difficult to meet these challenges, rendering proteomic profiling of PDAC a critical area of research. Area covered: In this review, we present recent advances in mass spectrometry (MS) and its current application in proteomic studies on PDAC. In addition, we discuss future directions for research that can efficiently incorporate current MS-based technologies that address key issues of PDAC proteomics. Expert commentary: Compared with other cancer studies, little progress has been made in PDAC proteomics, perhaps attributed to the difficulty in performing in-depth and large-scale clinical studies on PDAC. However, recent advances in mass spectrometry can advance PDAC proteomics past the fundamental research stage.
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Affiliation(s)
- Hyunsoo Kim
- a Department of Biomedical Sciences , Seoul National University College of Medicine , Yongon-Dong, Seoul 110-799 , Korea.,b Department of Biomedical Engineering , Seoul National University College of Medicine , Yongon-Dong, Seoul 110-799 , Korea.,c Institute of Medical and Biological Engineering, Medical Research Center, Seoul National University College of Medicine , Yongon-Dong, Seoul 110-799 , Korea
| | - Joonho Park
- b Department of Biomedical Engineering , Seoul National University College of Medicine , Yongon-Dong, Seoul 110-799 , Korea
| | - Joseph I Wang
- b Department of Biomedical Engineering , Seoul National University College of Medicine , Yongon-Dong, Seoul 110-799 , Korea
| | - Youngsoo Kim
- a Department of Biomedical Sciences , Seoul National University College of Medicine , Yongon-Dong, Seoul 110-799 , Korea.,b Department of Biomedical Engineering , Seoul National University College of Medicine , Yongon-Dong, Seoul 110-799 , Korea.,c Institute of Medical and Biological Engineering, Medical Research Center, Seoul National University College of Medicine , Yongon-Dong, Seoul 110-799 , Korea
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Abstract
Lung cancer is the most common cause of cancer-related death worldwide, less than 7% of patients survive 10 years following diagnosis across all stages of lung cancer. Late stage of diagnosis and lack of effective and personalized medicine reflect the need for a better understanding of the mechanisms that underlie lung cancer progression. Quantitative proteomics provides the relative different protein abundance in normal and cancer patients which offers the information for molecular interactions, signaling pathways, and biomarker identification. Here we introduce both theoretical and practical applications in the use of quantitative proteomics approaches, with principles of current technologies and methodologies including gel-based, label free, stable isotope labeling as well as targeted proteomics. Predictive markers of drug resistance, candidate biomarkers for diagnosis, and prognostic markers in lung cancer have also been discovered and analyzed by quantitative proteomic analysis. Moreover, construction of protein networks enables to provide an opportunity to interpret disease pathway and improve our understanding in cancer therapeutic strategies, allowing the discovery of molecular markers and new therapeutic targets for lung cancer.
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Affiliation(s)
| | - Hsueh-Fen Juan
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan. .,Department of Life Science, National Taiwan University, Taipei, Taiwan. .,Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617, Taiwan.
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Kennedy JJ, Whiteaker JR, Schoenherr RM, Yan P, Allison K, Shipley M, Lerch M, Hoofnagle AN, Baird GS, Paulovich AG. Optimized Protocol for Quantitative Multiple Reaction Monitoring-Based Proteomic Analysis of Formalin-Fixed, Paraffin-Embedded Tissues. J Proteome Res 2016; 15:2717-28. [PMID: 27462933 DOI: 10.1021/acs.jproteome.6b00245] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Despite a clinical, economic, and regulatory imperative to develop companion diagnostics, precious few new biomarkers have been successfully translated into clinical use, due in part to inadequate protein assay technologies to support large-scale testing of hundreds of candidate biomarkers in formalin-fixed paraffin-embedded (FFPE) tissues. Although the feasibility of using targeted, multiple reaction monitoring mass spectrometry (MRM-MS) for quantitative analyses of FFPE tissues has been demonstrated, protocols have not been systematically optimized for robust quantification across a large number of analytes, nor has the performance of peptide immuno-MRM been evaluated. To address this gap, we used a test battery approach coupled to MRM-MS with the addition of stable isotope-labeled standard peptides (targeting 512 analytes) to quantitatively evaluate the performance of three extraction protocols in combination with three trypsin digestion protocols (i.e., nine processes). A process based on RapiGest buffer extraction and urea-based digestion was identified to enable similar quantitation results from FFPE and frozen tissues. Using the optimized protocols for MRM-based analysis of FFPE tissues, median precision was 11.4% (across 249 analytes). There was excellent correlation between measurements made on matched FFPE and frozen tissues, both for direct MRM analysis (R(2) = 0.94) and immuno-MRM (R(2) = 0.89). The optimized process enables highly reproducible, multiplex, standardizable, quantitative MRM in archival tissue specimens.
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Affiliation(s)
- Jacob J Kennedy
- Clinical Research Division, Fred Hutchinson Cancer Research Center , Seattle, Washington 98109, United States
| | - Jeffrey R Whiteaker
- Clinical Research Division, Fred Hutchinson Cancer Research Center , Seattle, Washington 98109, United States
| | - Regine M Schoenherr
- Clinical Research Division, Fred Hutchinson Cancer Research Center , Seattle, Washington 98109, United States
| | - Ping Yan
- Clinical Research Division, Fred Hutchinson Cancer Research Center , Seattle, Washington 98109, United States
| | - Kimberly Allison
- Department of Pathology, Stanford University , Stanford, California 94305 United States
| | - Melissa Shipley
- Department of Laboratory Medicine, University of Washington , Seattle, Washington 98195 United States
| | - Melissa Lerch
- Department of Laboratory Medicine, University of Washington , Seattle, Washington 98195 United States
| | - Andrew N Hoofnagle
- Department of Laboratory Medicine, University of Washington , Seattle, Washington 98195 United States
| | - Geoffrey Stuart Baird
- Department of Laboratory Medicine, University of Washington , Seattle, Washington 98195 United States
| | - Amanda G Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center , Seattle, Washington 98109, United States
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