1
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Liu Y, Jeraldo P, Herbert W, McDonough S, Eckloff B, Schulze-Makuch D, de Vera JP, Cockell C, Leya T, Baqué M, Jen J, Walther-Antonio M. Whole genome sequencing of cyanobacterium Nostoc sp. CCCryo 231-06 using microfluidic single cell technology. iScience 2022; 25:104291. [PMID: 35573199 PMCID: PMC9095746 DOI: 10.1016/j.isci.2022.104291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 03/16/2022] [Accepted: 04/20/2022] [Indexed: 11/26/2022] Open
Abstract
The Nostoc sp. strain CCCryo 231-06 is a cyanobacterial strain capable of surviving under extreme conditions and thus is of great interest for the astrobiology community. The knowledge of its complete genome sequence would serve as a guide for further studies. However, a major concern has been placed on the effects of contamination on the quality of sequencing data without a reference genome. Here, we report the use of microfluidic technology combined with single cell sequencing and de novo assembly to minimize the contamination and recover the complete genome of the Nostoc strain CCCryo 231-06 with high quality. 100% of the whole genome was recovered with all contaminants removed and a strongly supported phylogenetic tree. The data reported can be useful for comparative genomics for phylogenetic and taxonomic studies. The method used in this work can be applied to studies that require high-quality assemblies of genomes of unknown microorganisms. This work uses a microfluidic platform for Nostoc single cell sequencing This technology provides minimal contamination in single cell sequencing Complete genome of the Nostoc strain CCCryo 231-06 was recovered with high quality
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2
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Yu L, Lopez G, Rassa J, Wang Y, Basavanhally T, Browne A, Huang CP, Dorsey L, Jen J, Hersey S. Direct comparison of circulating tumor DNA sequencing assays with targeted large gene panels. PLoS One 2022; 17:e0266889. [PMID: 35482763 PMCID: PMC9049497 DOI: 10.1371/journal.pone.0266889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/29/2022] [Indexed: 11/24/2022] Open
Abstract
Next generation sequencing (NGS) assays with large targeted gene panels can comprehensively profile cancer somatic mutations in a tumor sample. Given the rapid adoption of such assays for circulating tumor DNA (ctDNA) analysis in clinical oncology, it is essential for the community to understand their analytical performance in liquid biopsy settings. Here, we directly compared five ctDNA NGS assays, most of which having a panel of 400 or more genes, with simulated samples harboring mutations relevant to solid tumors or myeloid malignancy. Our results indicate that the detection sensitivity and reproducibility of all five assays was 90% or higher when the mutations were at 0.5% or 1.0% allele frequency, and with optimal DNA input of 30 ng or 50 ng per vendor’s protocol. The performances decreased and varied dramatically, when mutations were at a 0.1% allele frequency and/or when a lower genomic input of 10 ng DNA was used. Interestingly, one of the assays repeatedly showed higher rate of false positivity than the others across two different sample sets. Multiple intrinsic technical factors pertaining to the NGS assays were further investigated. Notable differences among the assays were seen for depth of coverage and background noise, which profoundly impacted assay performance. The results derived from this study are highly informative and provide a framework to assess and select suitable assays for specific application in cancer monitoring and potential clinical use.
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Affiliation(s)
- Lizhi Yu
- Translational Sciences and Diagnostics, Translation Medicine, Bristol Myers Squibb, Summit, New Jersey, United States of America
- * E-mail:
| | - Gonzalo Lopez
- Translational Bioinformatics, Informatics and Predictive Sciences, Bristol Myers Squibb, Summit, New Jersey, United States of America
| | - John Rassa
- Translational Sciences and Diagnostics, Translation Medicine, Bristol Myers Squibb, Summit, New Jersey, United States of America
| | - Yixin Wang
- Translational Sciences and Diagnostics, Translation Medicine, Bristol Myers Squibb, Summit, New Jersey, United States of America
| | - Tara Basavanhally
- Translational Bioinformatics, Informatics and Predictive Sciences, Bristol Myers Squibb, Summit, New Jersey, United States of America
| | - Andrew Browne
- Translational Bioinformatics, Informatics and Predictive Sciences, Bristol Myers Squibb, Summit, New Jersey, United States of America
| | - Chang-Pin Huang
- Translational Research, Immuno-Oncology and Cell Therapy, Bristol Myers Squibb, Seattle, Washington, United States of America
| | - Lauren Dorsey
- Translational Bioinformatics, Informatics and Predictive Sciences, Bristol Myers Squibb, Summit, New Jersey, United States of America
| | - Jin Jen
- Translational Bioinformatics, Informatics and Predictive Sciences, Bristol Myers Squibb, Summit, New Jersey, United States of America
| | - Sarah Hersey
- Translational Sciences and Diagnostics, Translation Medicine, Bristol Myers Squibb, Summit, New Jersey, United States of America
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3
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Rangan A, Hein MS, Jenkinson WG, Koganti T, Aleff RA, Hilker CA, Blommel JH, Porter TR, Swanson KC, Lundquist P, Nguyen PL, Shi M, He R, Viswanatha DS, Jen J, Klee EW, Kipp BR, Hoyer JD, Wieben ED, Oliveira JL. Improved Characterization of Complex β-Globin Gene Cluster Structural Variants Using Long-Read Sequencing. J Mol Diagn 2021; 23:1732-1740. [PMID: 34839893 DOI: 10.1016/j.jmoldx.2021.08.013] [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] [Received: 02/13/2021] [Revised: 07/30/2021] [Accepted: 08/18/2021] [Indexed: 10/19/2022] Open
Abstract
Complex insertion-deletion (indel) events in the globin genes manifest in widely variable clinical phenotypes. Many are incompletely characterized because of a historic lack of efficient methods. A more complete assessment enables improved prediction of clinical impact, which guides emerging therapeutic choices. Current methods have limited capacity for breakpoint assignment and accurate assessment of mutation extent, especially in cases containing duplications or multiple deletions and insertions. Technology, such as long-read sequencing, holds promise for significant impact in the characterization of indel events because of read lengths that span large regions, resulting in improved resolution. Four known complex β-globin gene cluster indel types were assessed using single-molecule, real-time sequencing technology and showed high correlation with previous reports, including the Caribbean locus control deletion (g.5,305,478_5,310,336del), a large β-gene duplication containing the Hb S mutation (g.4,640,335_5,290,171dup with g.5,248,232T>A, c.20A>T; variant allele fraction, 64%), and two nested variants (double deletions with intervening inversion): the Indian Gγ(Aγδβ)0-thalassemia (g.5,246,804-5,254,275del, g.5,254,276_5,269,600inv, and g.5,269,601_5,270,442del) and the Turkish/Macedonian (δβ)0 thalassemia (g.5,235,064_5,236,652del, g.5,236,653_5,244,280inv, and g.5,244,281_5,255,766del). Our data confirm long-read sequencing as an efficient and accurate method to identify these clinically significant complex events. Limitations include high-complexity sample preparation requirements, which hinder routine use in clinical laboratories. Continued improvements in sample and data workflow processes are needed to accommodate volumes in a tertiary clinical laboratory.
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Affiliation(s)
- Aruna Rangan
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.
| | - Molly S Hein
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | - Tejaswi Koganti
- Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Ross A Aleff
- Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | | | - Joseph H Blommel
- Advanced Diagnostics Laboratory, Mayo Clinic, Rochester, Minnesota
| | - Tavanna R Porter
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Kenneth C Swanson
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Patrick Lundquist
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Phuong L Nguyen
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Min Shi
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Rong He
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - David S Viswanatha
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Jin Jen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Eric W Klee
- Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Benjamin R Kipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - James D Hoyer
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Eric D Wieben
- Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Jennifer L Oliveira
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.
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4
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Foox J, Tighe SW, Nicolet CM, Zook JM, Byrska-Bishop M, Clarke WE, Khayat MM, Mahmoud M, Laaguiby PK, Herbert ZT, Warner D, Grills GS, Jen J, Levy S, Xiang J, Alonso A, Zhao X, Zhang W, Teng F, Zhao Y, Lu H, Schroth GP, Narzisi G, Farmerie W, Sedlazeck FJ, Baldwin DA, Mason CE. Author Correction: Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study. Nat Biotechnol 2021; 39:1466. [PMID: 34635840 DOI: 10.1038/s41587-021-01122-z] [Citation(s) in RCA: 1] [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: 11/09/2022]
Affiliation(s)
- Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Scott W Tighe
- University of Vermont Cancer Center, Vermont Integrative Genomics Resource, University of Vermont, Burlington, VT, USA
| | - Charles M Nicolet
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Justin M Zook
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | | | | | - Michael M Khayat
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Phoebe K Laaguiby
- University of Vermont Cancer Center, Vermont Integrative Genomics Resource, University of Vermont, Burlington, VT, USA
| | - Zachary T Herbert
- Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Derek Warner
- DNA Sequencing Core, University of Utah, Salt Lake City, UT, USA
| | - George S Grills
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Jin Jen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jenny Xiang
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Alicia Alonso
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Xia Zhao
- BGI-Shenzhen, Shenzhen, China.,MGI, BGI-Shenzhen, Shenzhen, China
| | | | | | - Yonggang Zhao
- BGI-Shenzhen, Shenzhen, China.,Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Haorong Lu
- BGI-Shenzhen, Shenzhen, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China
| | | | | | - William Farmerie
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Don A Baldwin
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA, USA.
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA. .,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA. .,The Feil Family Brain and Mind Research Institute, New York, NY, USA. .,The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
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5
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Li S, Tang K, Khodadadi-Jamayran A, Jen J, Han H, Guidry K, Chen T, Hao Y, Fedele C, Zebala J, Maeda D, Christensen J, Olson P, Athanas A, Wong K, Neel B. OA12.03 Combined Inhibition of SHP2 and CXCR1/2 Promotes Anti-Tumor T Cell Response in NSCLC. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.08.074] [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: 10/20/2022]
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6
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Zhu C, Zhang M, Wang Q, Jen J, Liu B, Guo M. Intratumor Epigenetic Heterogeneity-A Panel Gene Methylation Study in Thyroid Cancer. Front Genet 2021; 12:714071. [PMID: 34539742 PMCID: PMC8446600 DOI: 10.3389/fgene.2021.714071] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 05/24/2021] [Accepted: 08/16/2021] [Indexed: 11/18/2022] Open
Abstract
Background Thyroid cancer (TC) is the most common endocrine malignancy, and the incidence is increasing very fast. Surgical resection and radioactive iodine ablation are major therapeutic methods, however, around 10% of differentiated thyroid cancer and all anaplastic thyroid carcinoma (ATC) are failed. Comprehensive understanding the molecular mechanisms may provide new therapeutic strategies for thyroid cancer. Even though genetic heterogeneity is rigorously studied in various cancers, epigenetic heterogeneity in human cancer remains unclear. Methods A total of 405 surgical resected thyroid cancer samples were employed (three spatially isolated specimens were obtained from different regions of the same tumor). Twenty-four genes were selected for methylation screening, and frequently methylated genes in thyroid cancer were used for further validation. Methylation specific PCR (MSP) approach was employed to detect the gene promoter region methylation. Results Five genes (AP2, CDH1, DACT2, HIN1, and RASSF1A) are found frequently methylated (>30%) in thyroid cancer. The five genes panel is used for further epigenetic heterogeneity analysis. AP2 methylation is associated with gender (P < 0.05), DACT2 methylation is associated with age, gender and tumor size (all P < 0.05), HIN1 methylation is associated to tumor size (P < 0.05) and extra-thyroidal extension (P < 0.01). RASSF1A methylation is associated with lymph node metastasis (P < 0.01). For heterogeneity analysis, AP2 methylation heterogeneity is associated with tumor size (P < 0.01), CDH1 methylation heterogeneity is associated with lymph node metastasis (P < 0.05), DACT2 methylation heterogeneity is associated with tumor size (P < 0.01), HIN1 methylation heterogeneity is associated with tumor size and extra-thyroidal extension (all P < 0.01). The multivariable analysis suggested that the risk of lymph node metastasis is 2.5 times in CDH1 heterogeneous methylation group (OR = 2.512, 95% CI 1.135, 5.557, P = 0.023). The risk of extra-thyroidal extension is almost 3 times in HIN1 heterogeneous methylation group (OR = 2.607, 95% CI 1.138, 5.971, P = 0.023). Conclusion Five of twenty-four genes were found frequently methylated in human thyroid cancer. Based on 5 genes panel analysis, epigenetic heterogeneity is an universal event. Epigenetic heterogeneity is associated with cancer development and progression.
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Affiliation(s)
- Chaofan Zhu
- Department of Head and Neck Surgery, Peking University Cancer Hospital and Institute, Beijing, China.,Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, Beijing, China
| | - Meiying Zhang
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, Beijing, China
| | - Qian Wang
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, Beijing, China
| | - Jin Jen
- Genome Analysis Core, Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States
| | - Baoguo Liu
- Department of Head and Neck Surgery, Peking University Cancer Hospital and Institute, Beijing, China
| | - Mingzhou Guo
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, Beijing, China.,State Key Laboratory of Kidney Diseases, Chinese PLA General Hospital, Beijing, China
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7
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Foox J, Tighe SW, Nicolet CM, Zook JM, Byrska-Bishop M, Clarke WE, Khayat MM, Mahmoud M, Laaguiby PK, Herbert ZT, Warner D, Grills GS, Jen J, Levy S, Xiang J, Alonso A, Zhao X, Zhang W, Teng F, Zhao Y, Lu H, Schroth GP, Narzisi G, Farmerie W, Sedlazeck FJ, Baldwin DA, Mason CE. Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study. Nat Biotechnol 2021; 39:1129-1140. [PMID: 34504351 PMCID: PMC8985210 DOI: 10.1038/s41587-021-01049-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 08/05/2021] [Indexed: 02/08/2023]
Abstract
Assessing the reproducibility, accuracy and utility of massively parallel DNA sequencing platforms remains an ongoing challenge. Here the Association of Biomolecular Resource Facilities (ABRF) Next-Generation Sequencing Study benchmarks the performance of a set of sequencing instruments (HiSeq/NovaSeq/paired-end 2 × 250-bp chemistry, Ion S5/Proton, PacBio circular consensus sequencing (CCS), Oxford Nanopore Technologies PromethION/MinION, BGISEQ-500/MGISEQ-2000 and GS111) on human and bacterial reference DNA samples. Among short-read instruments, HiSeq 4000 and X10 provided the most consistent, highest genome coverage, while BGI/MGISEQ provided the lowest sequencing error rates. The long-read instrument PacBio CCS had the highest reference-based mapping rate and lowest non-mapping rate. The two long-read platforms PacBio CCS and PromethION/MinION showed the best sequence mapping in repeat-rich areas and across homopolymers. NovaSeq 6000 using 2 × 250-bp read chemistry was the most robust instrument for capturing known insertion/deletion events. This study serves as a benchmark for current genomics technologies, as well as a resource to inform experimental design and next-generation sequencing variant calling.
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Affiliation(s)
- Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Scott W. Tighe
- University of Vermont Cancer Center, Vermont Integrative Genomics Resource, University of Vermont, Burlington, VT, USA
| | - Charles M. Nicolet
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Justin M. Zook
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | | | | | - Michael M. Khayat
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Phoebe K. Laaguiby
- University of Vermont Cancer Center, Vermont Integrative Genomics Resource, University of Vermont, Burlington, VT, USA
| | - Zachary T. Herbert
- Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Derek Warner
- DNA Sequencing Core, University of Utah, Salt Lake City, UT, USA
| | - George S. Grills
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Jin Jen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jenny Xiang
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Alicia Alonso
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Xia Zhao
- BGI-Shenzhen, Shenzhen, China.,MGI, BGI-Shenzhen, Shenzhen, China
| | | | | | - Yonggang Zhao
- BGI-Shenzhen, Shenzhen, China.,Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Haorong Lu
- BGI-Shenzhen, Shenzhen, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China
| | | | | | - William Farmerie
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Correspondence and requests for materials should be addressed to Fritz J. Sedlazeck, Don A. Baldwin or Christopher E. Mason. ; ;
| | - Don A. Baldwin
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA, USA.,Correspondence and requests for materials should be addressed to Fritz J. Sedlazeck, Don A. Baldwin or Christopher E. Mason. ; ;
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.,The Feil Family Brain and Mind Research Institute, New York, NY, USA.,The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.,Correspondence and requests for materials should be addressed to Fritz J. Sedlazeck, Don A. Baldwin or Christopher E. Mason. ; ;
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8
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DiGuardo MA, Davila JI, Jackson RA, Nair AA, Fadra N, Minn KT, Atiq MA, Zarei S, Blommel JH, Knight SM, Jen J, Eckloff BW, Voss JS, Rumilla KM, Kerr SE, Lam-Himlin DM, Bellizzi AM, Graham RP, Kipp BR, Jenkins RB, Halling KC. RNA-Seq Reveals Differences in Expressed Tumor Mutation Burden in Colorectal and Endometrial Cancers with and without Defective DNA-Mismatch Repair. J Mol Diagn 2021; 23:555-564. [PMID: 33549857 DOI: 10.1016/j.jmoldx.2021.01.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/13/2020] [Accepted: 01/12/2021] [Indexed: 12/18/2022] Open
Abstract
Tumor mutation burden (TMB) is an emerging biomarker of immunotherapy response. RNA sequencing in FFPE tissue samples was used for determining TMB in microsatellite-stable (MSS) and microsatellite instability-high (MSI-H) tumors in patients with colorectal or endometrial cancer. Tissue from tumors and paired normal tissue from 46 MSI-H and 12 MSS cases were included. Of the MSI-H tumors, 29 had defective DNA mismatch-repair mutations, and 17 had MLH1 promoter hypermethylation. TMB was measured using the expressed somatic nucleotide variants (eTMB). A method of accurate measurement of eTMB was developed that removes FFPE-derived artifacts by leveraging mutation signatures. There was a significant difference in the median eTMB values observed between MSI-H and MSS cases: 27.3 versus 6.7 mutations/megabase (mut/Mb) (P = 3.5 × 10-9). Among tumors with defective DNA-mismatch repair, those with mismatch-repair mutations had a significantly higher median eTMB than those with hypermethylation: 28.1 versus 17.5 mut/Mb (P = 0.037). Multivariate analysis showed that MSI status, tumor type (endometrial or colorectal), and age were significantly associated with eTMB. Additionally, using whole-exome sequencing in a subset of these patients, it was determined that DNA TMB correlated well with eTMB (Spearman correlation coefficient, 0.83). These results demonstrate that RNA sequencing can be used for measuring eTMB in FFPE tumor specimens.
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Affiliation(s)
- Margaret A DiGuardo
- Division of Laboratory Genetics and Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Jaime I Davila
- Division of Laboratory Genetics and Experimental Pathology, Department of Laboratory Medicine and Pathology, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota; Department of Mathematics, Statistics, and Computer Science, St. Olaf College, Northfield, Minnesota
| | - Rory A Jackson
- Division of Laboratory Genetics and Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Asha A Nair
- Division of Laboratory Genetics and Experimental Pathology, Department of Laboratory Medicine and Pathology, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Numrah Fadra
- Division of Laboratory Genetics and Experimental Pathology, Department of Laboratory Medicine and Pathology, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Kay T Minn
- Division of Laboratory Genetics and Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Mazen A Atiq
- Division of Laboratory Genetics and Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Shabnam Zarei
- Robert J Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Joseph H Blommel
- Division of Laboratory Genetics and Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Shannon M Knight
- Division of Laboratory Genetics and Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Jin Jen
- Division of Laboratory Genetics and Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Bruce W Eckloff
- Division of Laboratory Genetics and Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Jesse S Voss
- Division of Laboratory Genetics and Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Kandelaria M Rumilla
- Division of Laboratory Genetics and Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Sarah E Kerr
- Hospital Pathology Associates, Minneapolis, Minnesota
| | - Dora M Lam-Himlin
- Department of Laboratory Medicine and Pathology, Divisions of Laboratory Genetics and Experimental Pathology, and Health Sciences Research, Mayo Clinic, Phoenix, Arizona
| | - Andrew M Bellizzi
- Holden Comprehensive Cancer Center, Department of Pathology, University of Iowa, Iowa City, Iowa
| | - Rondell P Graham
- Division of Laboratory Genetics and Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Benjamin R Kipp
- Division of Laboratory Genetics and Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Robert B Jenkins
- Division of Laboratory Genetics and Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Kevin C Halling
- Division of Laboratory Genetics and Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.
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9
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Chatzopoulos K, O'Brien DR, Sotiriou S, Khazaie K, Jen J, Kocher JPA, Markovic SN, Flotte TJ. Aberrant immunohistochemical expression of CD4 as a rare finding in metastatic melanoma. J Cutan Pathol 2020; 47:1223-1226. [PMID: 32594533 DOI: 10.1111/cup.13792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/22/2020] [Accepted: 06/24/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Kyriakos Chatzopoulos
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Daniel R O'Brien
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
| | - Sotiris Sotiriou
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Jin Jen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Jean-Pierre A Kocher
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Thomas J Flotte
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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10
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Chabon JJ, Hamilton EG, Kurtz DM, Esfahani MS, Moding EJ, Stehr H, Schroers-Martin J, Nabet BY, Chen B, Chaudhuri AA, Liu CL, Hui AB, Jin MC, Azad TD, Almanza D, Jeon YJ, Nesselbush MC, Co Ting Keh L, Bonilla RF, Yoo CH, Ko RB, Chen EL, Merriott DJ, Massion PP, Mansfield AS, Jen J, Ren HZ, Lin SH, Costantino CL, Burr R, Tibshirani R, Gambhir SS, Berry GJ, Jensen KC, West RB, Neal JW, Wakelee HA, Loo BW, Kunder CA, Leung AN, Lui NS, Berry MF, Shrager JB, Nair VS, Haber DA, Sequist LV, Alizadeh AA, Diehn M. Integrating genomic features for non-invasive early lung cancer detection. Nature 2020; 580:245-251. [PMID: 32269342 PMCID: PMC8230734 DOI: 10.1038/s41586-020-2140-0] [Citation(s) in RCA: 317] [Impact Index Per Article: 79.3] [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: 07/30/2019] [Accepted: 02/13/2020] [Indexed: 11/08/2022]
Abstract
Radiologic screening of high-risk adults reduces lung-cancer-related mortality1,2; however, a small minority of eligible individuals undergo such screening in the United States3,4. The availability of blood-based tests could increase screening uptake. Here we introduce improvements to cancer personalized profiling by deep sequencing (CAPP-Seq)5, a method for the analysis of circulating tumour DNA (ctDNA), to better facilitate screening applications. We show that, although levels are very low in early-stage lung cancers, ctDNA is present prior to treatment in most patients and its presence is strongly prognostic. We also find that the majority of somatic mutations in the cell-free DNA (cfDNA) of patients with lung cancer and of risk-matched controls reflect clonal haematopoiesis and are non-recurrent. Compared with tumour-derived mutations, clonal haematopoiesis mutations occur on longer cfDNA fragments and lack mutational signatures that are associated with tobacco smoking. Integrating these findings with other molecular features, we develop and prospectively validate a machine-learning method termed 'lung cancer likelihood in plasma' (Lung-CLiP), which can robustly discriminate early-stage lung cancer patients from risk-matched controls. This approach achieves performance similar to that of tumour-informed ctDNA detection and enables tuning of assay specificity in order to facilitate distinct clinical applications. Our findings establish the potential of cfDNA for lung cancer screening and highlight the importance of risk-matching cases and controls in cfDNA-based screening studies.
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Affiliation(s)
- Jacob J Chabon
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Emily G Hamilton
- Program in Cancer Biology, Stanford University, Stanford, CA, USA
| | - David M Kurtz
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Mohammad S Esfahani
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Everett J Moding
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Henning Stehr
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Joseph Schroers-Martin
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Barzin Y Nabet
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Binbin Chen
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Aadel A Chaudhuri
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Chih Long Liu
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Angela B Hui
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Michael C Jin
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Tej D Azad
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Diego Almanza
- Program in Cancer Biology, Stanford University, Stanford, CA, USA
| | - Young-Jun Jeon
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | | | | | - Rene F Bonilla
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Christopher H Yoo
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Ryan B Ko
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Emily L Chen
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - David J Merriott
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Pierre P Massion
- Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Aaron S Mansfield
- Department of Oncology, Division of Medical Oncology, Mayo Clinic, Rochester, MN, USA
| | - Jin Jen
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Hong Z Ren
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Steven H Lin
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christina L Costantino
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Risa Burr
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Robert Tibshirani
- Department of Statistics, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Sanjiv S Gambhir
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - Gerald J Berry
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Kristin C Jensen
- Department of Pathology, Stanford University, Stanford, CA, USA
- VA Palo Alto Healthcare System, Palo Alto, Stanford, CA, USA
| | - Robert B West
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Joel W Neal
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Heather A Wakelee
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Billy W Loo
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | | | - Ann N Leung
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - Natalie S Lui
- Division of Thoracic Surgery, Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Mark F Berry
- Division of Thoracic Surgery, Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Joseph B Shrager
- VA Palo Alto Healthcare System, Palo Alto, Stanford, CA, USA
- Division of Thoracic Surgery, Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Viswam S Nair
- Department of Radiology, Stanford University, Stanford, CA, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA, USA
| | - Daniel A Haber
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Lecia V Sequist
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ash A Alizadeh
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA.
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA, USA.
| | - Maximilian Diehn
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA.
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11
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Jen J, Jang J, Zhang J, Tang A, Pierson K, Schrandt A, Xie H, Yang P, Mandreka S, Mansfield A. P1.01-45 A NGS-Based ctDNA Test to Monitor Disease Progression and Treatment Response in Advanced Stage Non-Small Cell Lung Cancer. J Thorac Oncol 2019. [DOI: 10.1016/j.jtho.2019.08.760] [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: 10/25/2022]
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12
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Kurokawa C, Iankov ID, Anderson SK, Aderca I, Leontovich AA, Maurer MJ, Oberg AL, Schroeder MA, Giannini C, Greiner SM, Becker MA, Thompson EA, Haluska P, Jentoft ME, Parney IF, Weroha SJ, Jen J, Sarkaria JN, Galanis E. Constitutive Interferon Pathway Activation in Tumors as an Efficacy Determinant Following Oncolytic Virotherapy. J Natl Cancer Inst 2019; 110:1123-1132. [PMID: 29788332 DOI: 10.1093/jnci/djy033] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 02/08/2018] [Indexed: 12/30/2022] Open
Abstract
Background Attenuated measles virus (MV) strains are promising agents currently being tested against solid tumors or hematologic malignancies in ongoing phase I and II clinical trials; factors determining oncolytic virotherapy success remain poorly understood, however. Methods We performed RNA sequencing and gene set enrichment analysis to identify pathways differentially activated in MV-resistant (n = 3) and -permissive (n = 2) tumors derived from resected human glioblastoma (GBM) specimens and propagated as xenografts (PDX). Using a unique gene signature we identified, we generated a diagonal linear discriminant analysis (DLDA) classification algorithm to predict MV responders and nonresponders, which was validated in additional randomly selected GBM and ovarian cancer PDX and 10 GBM patients treated with MV in a phase I trial. GBM PDX lines were also treated with the US Food and Drug Administration-approved JAK inhibitor, ruxolitinib, for 48 hours prior to MV infection and virus production, STAT1/3 signaling and interferon stimulated gene expression was assessed. All statistical tests were two-sided. Results Constitutive interferon pathway activation, as reflected in the DLDA algorithm, was identified as the key determinant for MV replication, independent of virus receptor expression, in MV-permissive and -resistant GBM PDXs. Using these lines as the training data for the DLDA algorithm, we confirmed the accuracy of our algorithm in predicting MV response in randomly selected GBM PDX ovarian cancer PDXs. Using the DLDA prediction algorithm, we demonstrate that virus replication in patient tumors is inversely correlated with expression of this resistance gene signature (ρ = -0.717, P = .03). In vitro inhibition of the interferon response pathway with the JAK inhibitor ruxolitinib was able to overcome resistance and increase virus production (1000-fold, P = .03) in GBM PDX lines. Conclusions These findings document a key mechanism of tumor resistance to oncolytic MV therapy and describe for the first time the development of a prediction algorithm to preselect for oncolytic treatment or combinatorial strategies.
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Affiliation(s)
- Cheyne Kurokawa
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN
| | - Ianko D Iankov
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN
| | - S Keith Anderson
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Ileana Aderca
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN
| | | | - Matthew J Maurer
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Ann L Oberg
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | | | - Caterina Giannini
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | | | - Marc A Becker
- Division of Medical Oncology, Mayo Clinic, Rochester, MN
| | - E Aubrey Thompson
- Cancer Biology, Mayo Clinic Florida, Jacksonville, FL, Mayo Clinic, Rochester, MN
| | - Paul Haluska
- Division of Medical Oncology, Mayo Clinic, Rochester, MN
| | - Mark E Jentoft
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Ian F Parney
- Department of Neurological Surgery, Mayo Clinic, Rochester, MN
| | - S John Weroha
- Division of Medical Oncology, Mayo Clinic, Rochester, MN
| | - Jin Jen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN.,Genome Analysis Core, Medical Genome Facility, Mayo Clinic, Rochester, MN
| | - Jann N Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN
| | - Evanthia Galanis
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN.,Division of Medical Oncology, Mayo Clinic, Rochester, MN
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13
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Liu Y, Jeraldo P, Jang JS, Eckloff B, Jen J, Walther-Antonio M. Bacterial Single Cell Whole Transcriptome Amplification in Microfluidic Platform Shows Putative Gene Expression Heterogeneity. Anal Chem 2019; 91:8036-8044. [PMID: 31188565 PMCID: PMC8422856 DOI: 10.1021/acs.analchem.8b04773] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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] [Indexed: 01/01/2023]
Abstract
Single cell RNA sequencing is a technology that provides the capability of analyzing the transcriptome of a single cell from a population. So far, single cell RNA sequencing has been focused mostly on human cells due to the larger starting amount of RNA template for subsequent amplification. One of the major challenges of applying single cell RNA sequencing to microbial cells is to amplify the femtograms of the RNA template to obtain sufficient material for downstream sequencing with minimal contamination. To achieve this goal, efforts have been focused on multiround RNA amplification, but would introduce additional contamination and bias. In this work, we for the first time coupled a microfluidic platform with multiple displacement amplification technology to perform single cell whole transcriptome amplification and sequencing of Porphyromonas somerae, a microbe of interest in endometrial cancer, as a proof-of-concept demonstration of using single cell RNA sequencing tool to unveil gene expression heterogeneity in single microbial cells. Our results show that the bacterial single-cell gene expression regulation is distinct across different cells, supporting widespread heterogeneity.
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Affiliation(s)
- Yuguang Liu
- Department of Surgery, Division of Surgical Research, Mayo Clinic, Rochester, Minnesota, United States
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States
| | - Patricio Jeraldo
- Department of Surgery, Division of Surgical Research, Mayo Clinic, Rochester, Minnesota, United States
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States
| | - Jin Sung Jang
- Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States
| | - Bruce Eckloff
- Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States
| | - Jin Jen
- Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States
| | - Marina Walther-Antonio
- Department of Surgery, Division of Surgical Research, Mayo Clinic, Rochester, Minnesota, United States
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Minnesota, United States
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14
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Wang L, Dehm SM, Hillman DW, Sicotte H, Tan W, Gormley M, Bhargava V, Jimenez R, Xie F, Yin P, Qin S, Quevedo F, Costello BA, Pitot HC, Ho T, Bryce AH, Ye Z, Li Y, Eiken P, Vedell PT, Barman P, McMenomy BP, Atwell TD, Carlson RE, Ellingson M, Eckloff BW, Qin R, Ou F, Hart SN, Huang H, Jen J, Wieben ED, Kalari KR, Weinshilboum RM, Wang L, Kohli M. A prospective genome-wide study of prostate cancer metastases reveals association of wnt pathway activation and increased cell cycle proliferation with primary resistance to abiraterone acetate-prednisone. Ann Oncol 2019; 29:352-360. [PMID: 29069303 DOI: 10.1093/annonc/mdx689] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [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] [Indexed: 01/16/2023] Open
Abstract
Background Genomic aberrations have been identified in metastatic castration-resistant prostate cancer (mCRPC), but molecular predictors of resistance to abiraterone acetate/prednisone (AA/P) treatment are not known. Patients and methods In a prospective clinical trial, mCRPC patients underwent whole-exome sequencing (n = 82) and RNA sequencing (n = 75) of metastatic biopsies before initiating AA/P with the objective of identifying genomic alterations associated with resistance to AA/P. Primary resistance was determined at 12 weeks of treatment using criteria for progression that included serum prostate-specific antigen measurement, bone and computerized tomography imaging and symptom assessments. Acquired resistance was determined using the end point of time to treatment change (TTTC), defined as time from enrollment until change in treatment from progressive disease. Associations of genomic and transcriptomic alterations with primary resistance were determined using logistic regression, Fisher's exact test, single and multivariate analyses. Cox regression models were utilized for determining association of genomic and transcriptomic alterations with TTTC. Results At 12 weeks, 32 patients in the cohort had progressed (nonresponders). Median study follow-up was 32.1 months by which time 58 patients had switched treatments due to progression. Median TTTC was 10.1 months (interquartile range: 4.4-24.1). Genes in the Wnt/β-catenin pathway were more frequently mutated and negative regulators of Wnt/β-catenin signaling were more frequently deleted or displayed reduced mRNA expression in nonresponders. Additionally, mRNA expression of cell cycle regulatory genes was increased in nonresponders. In multivariate models, increased cell cycle proliferation scores (≥ 50) were associated with shorter TTTC (hazard ratio = 2.11, 95% confidence interval: 1.17-3.80; P = 0.01). Conclusions Wnt/β-catenin pathway activation and increased cell cycle progression scores can serve as molecular markers for predicting resistance to AA/P therapy.
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Affiliation(s)
- L Wang
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Rochester, USA; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, USA
| | - S M Dehm
- Masonic Cancer Center, University of Minnesota, Minneapolis, USA; Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, USA; Department of Urology, University of Minnesota, Minneapolis, USA
| | - D W Hillman
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Rochester, USA
| | - H Sicotte
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Rochester, USA
| | - W Tan
- Department of Medicine, Mayo Clinic, Jacksonville, USA
| | - M Gormley
- Janssen Research and Development, Spring House, Philadelphia, USA
| | - V Bhargava
- Janssen Research and Development, Spring House, Philadelphia, USA
| | - R Jimenez
- Department of Pathology and Lab Medicine, Mayo Clinic, Rochester, USA
| | - F Xie
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, USA
| | - P Yin
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, USA
| | - S Qin
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, USA
| | - F Quevedo
- Department of Oncology, Mayo Clinic, Rochester, USA
| | - B A Costello
- Department of Oncology, Mayo Clinic, Rochester, USA
| | - H C Pitot
- Department of Oncology, Mayo Clinic, Rochester, USA
| | - T Ho
- Department of Medicine, Mayo Clinic, Scottsdale, USA
| | - A H Bryce
- Department of Medicine, Mayo Clinic, Scottsdale, USA
| | - Z Ye
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, USA
| | - Y Li
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Rochester, USA
| | - P Eiken
- Department of Radiology, Mayo Clinic, Rochester, USA
| | - P T Vedell
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Rochester, USA
| | - P Barman
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Rochester, USA
| | - B P McMenomy
- Department of Radiology, Mayo Clinic, Rochester, USA
| | - T D Atwell
- Department of Radiology, Mayo Clinic, Rochester, USA
| | - R E Carlson
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Rochester, USA
| | - M Ellingson
- Medical Genetics, Mayo Clinic, Rochester, USA
| | - B W Eckloff
- Medical Genome Facility, Mayo Clinic, Rochester, USA
| | - R Qin
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Rochester, USA
| | - F Ou
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Rochester, USA
| | - S N Hart
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Rochester, USA
| | - H Huang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, USA
| | - J Jen
- Medical Genome Facility, Mayo Clinic, Rochester, USA; Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, USA; Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Mayo Clinic, Rochester, USA
| | - E D Wieben
- Medical Genome Facility, Mayo Clinic, Rochester, USA
| | - K R Kalari
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Rochester, USA
| | - R M Weinshilboum
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, USA
| | - L Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, USA.
| | - M Kohli
- Department of Oncology, Mayo Clinic, Rochester, USA.
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15
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Mansfield AS, Jen J. Predicting Treatment Response Based on RNA Expression in Large Datasets. Clin Cancer Res 2019; 25:1443-1445. [PMID: 30446588 DOI: 10.1158/1078-0432.ccr-18-2823] [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] [Received: 09/19/2018] [Revised: 10/07/2018] [Accepted: 11/05/2018] [Indexed: 11/16/2022]
Abstract
PD-L1 expression levels derived from >16,000 samples guided the selection of tumor types likely to benefit from pembrolizuamb monotherapy in clinical trials. Although not fail-proof, FDA approvals for most of the prioritized indications speak to the power of RNA expression profiling and the value of large genomic datasets.See related article by Ayers et al., p. 1564.
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Affiliation(s)
| | - Jin Jen
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.
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16
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Ren H, Hou X, Eiken PW, Zhang J, Pierson KE, Nair AA, Davila JI, Kovarikova H, Jang JS, Johnson SH, Molina JR, Marks RS, Yang P, Yi JE, Mansfield AS, Jen J. Identification and Development of a Lung Adenocarcinoma PDX Model With STRN-ALK Fusion. Clin Lung Cancer 2019; 20:e142-e147. [PMID: 30581091 DOI: 10.1016/j.cllc.2018.11.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/29/2018] [Accepted: 11/12/2018] [Indexed: 02/05/2023]
Affiliation(s)
- Hongzheng Ren
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN; Biomarker Discovery Program, Mayo Clinic, Rochester, MN; Cancer Research Center, Shantou University Medical College, Shantou, China
| | - Xiaonan Hou
- Department of Medical Oncology, Mayo Clinic, Rochester, MN
| | | | - Jin Zhang
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN; Department of Neurology, China-Japan Friendship Hospital, Beijing, China
| | | | - Asha A Nair
- Department of Health Science Research, Mayo Clinic, Rochester, MN
| | - Jaime I Davila
- Department of Health Science Research, Mayo Clinic, Rochester, MN
| | - Helena Kovarikova
- Institute of Clinical Biochemistry and Diagnostics, Charles University, Faculty of Medicine, Hradec Kralove, Czech Republic; Institute of Clinical Biochemistry and Diagnostics, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Jin Sung Jang
- The Genome Analysis Core, Center for Individualized Medicine, Mayo Clinic, Rochester, MN
| | | | | | | | - Ping Yang
- Department of Health Science Research, Mayo Clinic, Rochester, MN
| | - Joanne E Yi
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | | | - Jin Jen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN; Biomarker Discovery Program, Mayo Clinic, Rochester, MN; The Genome Analysis Core, Center for Individualized Medicine, Mayo Clinic, Rochester, MN.
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17
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Jang JS, Li Y, Mitra AK, Bi L, Abyzov A, van Wijnen AJ, Baughn LB, Van Ness B, Rajkumar V, Kumar S, Jen J. Molecular signatures of multiple myeloma progression through single cell RNA-Seq. Blood Cancer J 2019; 9:2. [PMID: 30607001 PMCID: PMC6318319 DOI: 10.1038/s41408-018-0160-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 08/17/2018] [Accepted: 08/31/2018] [Indexed: 12/12/2022] Open
Abstract
We used single cell RNA-Seq to examine molecular heterogeneity in multiple myeloma (MM) in 597 CD138 positive cells from bone marrow aspirates of 15 patients at different stages of disease progression. 790 genes were selected by coefficient of variation (CV) method and organized cells into four groups (L1–L4) using unsupervised clustering. Plasma cells from each patient clustered into at least two groups based on gene expression signature. The L1 group contained cells from all MGUS patients having the lowest expression of genes involved in the oxidative phosphorylation, Myc targets, and mTORC1 signaling pathways (p < 1.2 × 10−14). In contrast, the expression level of these pathway genes increased progressively and were the highest in L4 group containing only cells from MM patients with t(4;14) translocations. A 44 genes signature of consistently overexpressed genes among the four groups was associated with poorer overall survival in MM patients (APEX trial, p < 0.0001; HR, 1.83; 95% CI, 1.33–2.52), particularly those treated with bortezomib (p < 0.0001; HR, 2.00; 95% CI, 1.39–2.89). Our study, using single cell RNA-Seq, identified the most significantly affected molecular pathways during MM progression and provided a novel signature predictive of patient prognosis and treatment stratification.
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Affiliation(s)
- Jin Sung Jang
- Genome Analysis Core, Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ying Li
- Division of Bioinformatics and Biostatistics, Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
| | - Amit Kumar Mitra
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, USA
| | - Lintao Bi
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Alexej Abyzov
- Division of Bioinformatics and Biostatistics, Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
| | | | - Linda B Baughn
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Brian Van Ness
- Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, MN, USA
| | - Vincent Rajkumar
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Shaji Kumar
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA.
| | - Jin Jen
- Genome Analysis Core, Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA. .,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
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18
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Mansfield AS, Peikert T, Smadbeck JB, Udell JBM, Garcia-Rivera E, Elsbernd L, Erskine CL, Van Keulen VP, Kosari F, Murphy SJ, Ren H, Serla VV, Schaefer Klein JL, Karagouga G, Harris FR, Sosa C, Johnson SH, Nevala W, Markovic SN, Bungum AO, Edell ES, Dong H, Cheville JC, Aubry MC, Jen J, Vasmatzis G. Neoantigenic Potential of Complex Chromosomal Rearrangements in Mesothelioma. J Thorac Oncol 2018; 14:276-287. [PMID: 30316012 DOI: 10.1016/j.jtho.2018.10.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [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: 08/24/2018] [Revised: 09/19/2018] [Accepted: 10/02/2018] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Malignant pleural mesothelioma is a disease primarily associated with exposure to the carcinogen asbestos. Whereas other carcinogen-related tumors are associated with a high tumor mutation burden, mesothelioma is not. We sought to resolve this discrepancy. METHODS We used mate-pair (n = 22), RNA (n = 28), and T cell receptor sequencing along with in silico predictions and immunologic assays to understand how structural variants of chromosomes affect the transcriptome. RESULTS We observed that inter- or intrachromosomal rearrangements were present in every specimen and were frequently in a pattern of chromoanagenesis such as chromoplexy or chromothripsis. Transcription of rearrangement-related junctions was predicted to result in many potential neoantigens, some of which were proven to bind patient-specific major histocompatibility complex molecules and to expand intratumoral T cell clones. T cells responsive to these predicted neoantigens were also present in a patient's circulating T cell repertoire. Analysis of genomic array data from the mesothelioma cohort in The Cancer Genome Atlas suggested that multiple chromothriptic-like events negatively impact survival. CONCLUSIONS Our findings represent the discovery of potential neoantigen expression driven by structural chromosomal rearrangements. These results may have implications for the development of novel immunotherapeutic strategies and the selection of patients to receive immunotherapies.
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Affiliation(s)
| | - Tobias Peikert
- Division of Pulmonary Medicine and Critical Care, Mayo Clinic, Rochester, Minnesota
| | - James B Smadbeck
- Center for Individualized Medicine, Biomarker Discovery Group, Mayo Clinic, Rochester, Minnesota
| | - Julia B M Udell
- Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota
| | | | - Laura Elsbernd
- Department of Immunology, Mayo Clinic, Rochester, Minnesota
| | | | | | - Farhad Kosari
- Center for Individualized Medicine, Biomarker Discovery Group, Mayo Clinic, Rochester, Minnesota
| | - Stephen J Murphy
- Center for Individualized Medicine, Biomarker Discovery Group, Mayo Clinic, Rochester, Minnesota
| | - Hongzheng Ren
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Vishnu V Serla
- Center for Individualized Medicine, Biomarker Discovery Group, Mayo Clinic, Rochester, Minnesota
| | - Janet L Schaefer Klein
- Center for Individualized Medicine, Biomarker Discovery Group, Mayo Clinic, Rochester, Minnesota
| | - Giannoula Karagouga
- Center for Individualized Medicine, Biomarker Discovery Group, Mayo Clinic, Rochester, Minnesota
| | - Faye R Harris
- Center for Individualized Medicine, Biomarker Discovery Group, Mayo Clinic, Rochester, Minnesota
| | - Carlos Sosa
- Center for Individualized Medicine, Biomarker Discovery Group, Mayo Clinic, Rochester, Minnesota
| | - Sarah H Johnson
- Center for Individualized Medicine, Biomarker Discovery Group, Mayo Clinic, Rochester, Minnesota
| | - Wendy Nevala
- Department of Immunology, Mayo Clinic, Rochester, Minnesota
| | | | - Aaron O Bungum
- Division of Pulmonary Medicine and Critical Care, Mayo Clinic, Rochester, Minnesota
| | - Eric S Edell
- Division of Pulmonary Medicine and Critical Care, Mayo Clinic, Rochester, Minnesota
| | - Haidong Dong
- Department of Immunology, Mayo Clinic, Rochester, Minnesota; Department of Urology, Mayo Clinic, Rochester, Minnesota
| | - John C Cheville
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | - Jin Jen
- Medical Genome Facility, Mayo Clinic, Rochester, Minnesota
| | - George Vasmatzis
- Center for Individualized Medicine, Biomarker Discovery Group, Mayo Clinic, Rochester, Minnesota.
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19
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Res H, Hou X, Pierson KE, Eiken P, Nair A, Yang P, Yi JE, Mansfield AS, Jen J. Abstract A17: Establishment of a unique patient-derived tumor model positive for STRN-ALK fusion from a patient with stage IV lung adenocarcinoma. Clin Cancer Res 2018. [DOI: 10.1158/1557-3265.aacriaslc18-a17] [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: 11/16/2022]
Abstract
Abstract
In lung adenocarcinoma, gene fusion involving the anaplastic lymphoma kinase (ALK) gene leads to overexpression of its tyrosine kinase domain, which serves as the oncogenic driver in lung tumors carrying such a molecular alteration. Similar fusions involving ROS1, RET and NTRK are also found in lung cancer and tumors with oncogenic fusions often respond well to targeted therapy. However, these tumors do develop resistance to the targeting drug and patients eventually relapse while on treatment. Although newer drugs have been developed, it remains a challenge to effectively control cancer recurrence after targeted therapy. In vivo tumor models carrying these fusions, particularly those that have progressed while on targeted treatment, will help to facilitate further drug evaluations prior to their administration to the patient as well as offer an opportunity to better understand the molecular mechanisms driving disease onset, progression, and drug resistance in tumors carrying the fusion of interest.
Here, we describe the first patient-derived tumor xenograft (PDX) carrying an STRN-ALK fusion. The patient was diagnosed with stage IV lung adenocarcinoma in 2011. She was initially treated with crizotinib and remained stable until 2015. At the time of disease progression, a biopsy was taken with patient consent under CT guidance from a chest wall mass using an 18-gauge needle and then implanted into two SCID-beige mice subcutaneously and into the fat pad of the kidney. Palpable tumor was observed in both mice at about 28 weeks post implantation and passaged at 36 weeks. They have been passaged two successive times and viably frozen. Pathologic analysis of the PDX showed that both tumors have the same mucinous morphology as observed in the original biopsy sample. RNA-seq and matepair analysis revealed that the tumors carry a rare fusion involving the first three exons of STRN and exon 20 to 3’ end of the ALK gene. The patient has been on ceritinib since January 2016 and remains stable as of last follow up.
Several unique features contributed to the success of this study. 1) The metastatic chest wall lesion used for the PDX developed was easily accessible on the chest wall using a relative large 18-gauge needle for CT-guided biopsies. 2) The slow growth of the tumor biopsy mirrors the clinical course of the disease observed in the patient. 3) The patient remains clinically stable and continues to respond to TKi. The availability of a viable PDX tumor model for this rare STRN-ALK fusion offers a unique opportunity to identify the most appropriate drug for the patient at the time of disease progression as well as the opportunity to examine the unique molecular features associated with this rare ALK fusion.
This work was supported in part by the National Foundation for Cancer Research Hillsberg Lung Cancer Translational Research Grant and by the Biomarker Discovery Program at the Mayo Clinic Center for Individualized Medicine.
Citation Format: HongZheng Res, XiaoNan Hou, Karlyn E. Pierson, Patric Eiken, Asha Nair, PingYang Yang, Joanne Eunhee Yi, Aaron S. Mansfield, Jin Jen. Establishment of a unique patient-derived tumor model positive for STRN-ALK fusion from a patient with stage IV lung adenocarcinoma [abstract]. In: Proceedings of the Fifth AACR-IASLC International Joint Conference: Lung Cancer Translational Science from the Bench to the Clinic; Jan 8-11, 2018; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(17_Suppl):Abstract nr A17.
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20
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Mansfield AS, Peikert T, Smadbeck JB, Udell JB, Kosari F, Murphy SJ, Ren H, Serla VV, Klein JLS, Karagouga G, Harris FR, Sosa C, Johnson SH, Nevala W, Markovic SN, Bungum AO, Edell ES, Dong H, Cheville JC, Aubry MC, Jen J, Vasmatzis G. Abstract 5726: Rearrangement-related peptides with neoantigenic potential in malignant pleural mesothelioma. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-5726] [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: 11/16/2022]
Abstract
Abstract
Malignant pleural mesothelioma is a disease primarily associated with exposure to the carcinogen asbestos. Consistent with this carcinogenic exposure, cytogenetic analyses have identified multiple recurrent structural chromosomal abnormalities in this malignancy, but more recent high-throughput sequencing evaluations of point mutations suggest that there is a low mutational burden in mesothelioma. Since tumor mutational burden has been correlated with responses to treatment with immune checkpoint inhibitors such as nivolumab, it was not consistent that patients with mesothelioma and low mutation burdens would have similar response rates in clinical trials with immune checkpoint inhibitors as patients with non-small cell lung cancer which is associated with a high mutation burden. In order to reconcile these differences, and given the potential for an improved understanding of the molecular pathogenesis of mesothelioma to improve therapeutic options, we used mate-pair sequencing (MPseq) and RNA sequencing (RNAseq) to understand how structural variants affect the transcriptome. MPseq differs from standard next generation sequencing approaches by tiling the whole genome with larger fragments (2-5kb) to reliably detect structural variants such as insertions, deletions and rearrangements. Amongst 22 mesothelioma specimens there were 1535 chromosomal rearrangements (median 41, range 3-298 per specimen), that resulted in junctions or novel fusions of non-coding DNA or genes. Six-hundred thirty-seven of these rearrangements (median 22, range 5-103 range per specimen) resulted in novel fusions of genes. Many of these inter- or intra-chromosomal rearrangements were consistent with a pattern of chromoanagesis such as chromoplexy or chromothripsis. Chromosomal rearrangements detected by MPseq were used to guide analysis of RNAseq data and revealed that these chromosomal junctions resulted in the expression of 179 novel amino acid sequences (median 5, 0-51 range per specimen). To determine whether transcription of chromosomal rearrangement-related junctions have neoantigenic potential, we used in silico tools to determine whether any of the expressed junctions contained peptides that could be presented by patient-specific HLA molecules. The top candidate rearrangement-related peptides with neoantigenic potential bound patient-specific HLA molecules nearly as well or as well as a positive control in competitive binding assays. Our findings represent the discovery of potential neoantigen expression driven by structural chromosomal rearrangements. These results may have implications for the development of novel therapeutic strategies, the selection of patients to receive immunotherapy, and blood-based treatment monitoring strategies.
Citation Format: Aaron S. Mansfield, Tobias Peikert, James B. Smadbeck, Julia B. Udell, Farhad Kosari, Stephen J. Murphy, Hongzheng Ren, Vishnu V. Serla, Janet L. Schaefer Klein, Giannoula Karagouga, Faye R. Harris, Carlos Sosa, Sarah H. Johnson, Wendy Nevala, Svetomir N. Markovic, Aaron O. Bungum, Eric S. Edell, Haidong Dong, John C. Cheville, Marie Christine Aubry, Jin Jen, George Vasmatzis. Rearrangement-related peptides with neoantigenic potential in malignant pleural mesothelioma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5726.
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Affiliation(s)
| | | | | | - Julia B. Udell
- 2Center for International Blood and Marrow Transplant Research, Minneapolis, MN
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21
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Winters JL, Davila JI, McDonald AM, Nair AA, Fadra N, Wehrs RN, Thomas BC, Balcom JR, Jin L, Wu X, Voss JS, Klee EW, Oliver GR, Graham RP, Neff JL, Rumilla KM, Aypar U, Kipp BR, Jenkins RB, Jen J, Halling KC. Development and Verification of an RNA Sequencing (RNA-Seq) Assay for the Detection of Gene Fusions in Tumors. J Mol Diagn 2018; 20:495-511. [DOI: 10.1016/j.jmoldx.2018.03.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 02/15/2018] [Accepted: 03/19/2018] [Indexed: 02/07/2023] Open
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22
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Wu CW, Evans JM, Huang S, Mahoney DW, Dukek BA, Taylor WR, Yab TC, Smyrk TC, Jen J, Kisiel JB, Ahlquist DA. A Comprehensive Approach to Sequence-oriented IsomiR annotation (CASMIR): demonstration with IsomiR profiling in colorectal neoplasia. BMC Genomics 2018; 19:401. [PMID: 29801434 PMCID: PMC5970459 DOI: 10.1186/s12864-018-4794-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [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: 12/06/2017] [Accepted: 05/14/2018] [Indexed: 01/14/2023] Open
Abstract
Background MicroRNA (miRNA) profiling is an important step in studying biological associations and identifying marker candidates. miRNA exists in isoforms, called isomiRs, which may exhibit distinct properties. With conventional profiling methods, limitations in assay and analysis platforms may compromise isomiR interrogation. Results We introduce a comprehensive approach to sequence-oriented isomiR annotation (CASMIR) to allow unbiased identification of global isomiRs from small RNA sequencing data. In this approach, small RNA reads are maintained as independent sequences instead of being summarized under miRNA names. IsomiR features are identified through step-wise local alignment against canonical forms and precursor sequences. Through customizing the reference database, CASMIR is applicable to isomiR annotation across species. To demonstrate its application, we investigated isomiR profiles in normal and neoplastic human colorectal epithelia. We also ran miRDeep2, a popular miRNA analysis algorithm to validate isomiRs annotated by CASMIR. With CASMIR, specific and biologically relevant isomiR patterns could be identified. We note that specific isomiRs are often more abundant than their canonical forms. We identify isomiRs that are commonly up-regulated in both colorectal cancer and advanced adenoma, and illustrate advantages in targeting isomiRs as potential biomarkers over canonical forms. Conclusions Studying miRNAs at the isomiR level could reveal new insight into miRNA biology and inform assay design for specific isomiRs. CASMIR facilitates comprehensive annotation of isomiR features in small RNA sequencing data for isomiR profiling and differential expression analysis. Electronic supplementary material The online version of this article (10.1186/s12864-018-4794-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chung Wah Wu
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Jared M Evans
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Shengbing Huang
- Division of Bioinformatics and Computational Biology, University of Minnesota Rochester, Rochester, MN, USA
| | - Douglas W Mahoney
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Brian A Dukek
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - William R Taylor
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Tracy C Yab
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Thomas C Smyrk
- Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - Jin Jen
- Genome Analysis Core, Medical Genome Facility, Mayo Clinic, Rochester, MN, USA.,Division of Experimental Pathology, Mayo Clinic, Rochester, MN, USA
| | - John B Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - David A Ahlquist
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
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23
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Sharma A, Oishi N, Boddicker RL, Hu G, Benson HK, Ketterling RP, Greipp PT, Knutson DL, Kloft-Nelson SM, He R, Eckloff BW, Jen J, Nair AA, Davila JI, Dasari S, Lazaridis KN, Bennani NN, Wu TT, Nowakowski GS, Murray JA, Feldman AL. Recurrent STAT3-JAK2 fusions in indolent T-cell lymphoproliferative disorder of the gastrointestinal tract. Blood 2018; 131:2262-2266. [PMID: 29592893 PMCID: PMC5958657 DOI: 10.1182/blood-2018-01-830968] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
| | - Naoki Oishi
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
- Department of Pathology, University of Yamanashi, Chuo, Yamanashi, Japan; and
| | | | - Guangzhen Hu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Hailey K Benson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Rhett P Ketterling
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Patricia T Greipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Darlene L Knutson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | | | - Rong He
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | | | - Jin Jen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | | | | | | | | | | | - Tsung-Teh Wu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Grzegorz S Nowakowski
- Center for Individualized Medicine, and
- Division of Hematology, Mayo Clinic, Rochester, MN
| | | | - Andrew L Feldman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
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24
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Yan Y, Cao S, Liu X, Harrington SM, Bindeman WE, Adjei AA, Jang JS, Jen J, Li Y, Chanana P, Mansfield AS, Park SS, Markovic SN, Dronca RS, Dong H. CX3CR1 identifies PD-1 therapy-responsive CD8+ T cells that withstand chemotherapy during cancer chemoimmunotherapy. JCI Insight 2018; 3:97828. [PMID: 29669928 DOI: 10.1172/jci.insight.97828] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 03/20/2018] [Indexed: 12/31/2022] Open
Abstract
Although immune checkpoint inhibitors have resulted in durable clinical benefits in a subset of patients with advanced cancer, some patients who did not respond to initial anti-PD-1 therapy have been found to benefit from the addition of salvage chemotherapy. However, the mechanism responsible for the successful chemoimmunotherapy is not completely understood. Here we show that a subset of circulating CD8+ T cells expressing the chemokine receptor CX3CR1 are able to withstand the toxicity of chemotherapy and are increased in patients with metastatic melanoma who responded to chemoimmunotherapy (paclitaxel and carboplatin plus PD-1 blockade). These CX3CR1+CD8+ T cells have effector memory phenotypes and the ability to efflux chemotherapy drugs via the ABCB1 transporter. In line with clinical observation, our preclinical models identified an optimal sequencing of chemoimmunotherapy that resulted in an increase of CX3CR1+CD8+ T cells. Taken together, we found a subset of PD-1 therapy-responsive CD8+ T cells that were capable of withstanding chemotherapy and executing tumor rejection with their unique abilities of drug efflux (ABCB1), cytolytic activity (granzyme B and perforin), and migration to and retention (CX3CR1 and CD11a) at tumor sites. Future strategies to monitor and increase the frequency of CX3CR1+CD8+ T cells may help to design effective chemoimmunotherapy to overcome cancer resistance to immune checkpoint blockade therapy.
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Affiliation(s)
| | | | | | | | | | - Alex A Adjei
- Division of Medical Oncology.,Mayo Clinic Cancer Center Early Therapeutic Program
| | | | - Jin Jen
- Mayo Clinic Center of Individualized Medicine
| | - Ying Li
- Department of Biomedical Statistics and Informatics
| | | | | | | | | | | | - Haidong Dong
- Department of Urology.,Department of Immunology, Mayo Clinic, Rochester, Minnesota, USA
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25
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Cohen JD, Li L, Wang Y, Thoburn C, Afsari B, Danilova L, Douville C, Javed AA, Wong F, Mattox A, Hruban RH, Wolfgang CL, Goggins MG, Dal Molin M, Wang TL, Roden R, Klein AP, Ptak J, Dobbyn L, Schaefer J, Silliman N, Popoli M, Vogelstein JT, Browne JD, Schoen RE, Brand RE, Tie J, Gibbs P, Wong HL, Mansfield AS, Jen J, Hanash SM, Falconi M, Allen PJ, Zhou S, Bettegowda C, Diaz LA, Tomasetti C, Kinzler KW, Vogelstein B, Lennon AM, Papadopoulos N. Detection and localization of surgically resectable cancers with a multi-analyte blood test. Science 2018; 359:926-930. [PMID: 29348365 PMCID: PMC6080308 DOI: 10.1126/science.aar3247] [Citation(s) in RCA: 1557] [Impact Index Per Article: 259.5] [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: 10/31/2017] [Accepted: 01/08/2018] [Indexed: 12/11/2022]
Abstract
Earlier detection is key to reducing cancer deaths. Here, we describe a blood test that can detect eight common cancer types through assessment of the levels of circulating proteins and mutations in cell-free DNA. We applied this test, called CancerSEEK, to 1005 patients with nonmetastatic, clinically detected cancers of the ovary, liver, stomach, pancreas, esophagus, colorectum, lung, or breast. CancerSEEK tests were positive in a median of 70% of the eight cancer types. The sensitivities ranged from 69 to 98% for the detection of five cancer types (ovary, liver, stomach, pancreas, and esophagus) for which there are no screening tests available for average-risk individuals. The specificity of CancerSEEK was greater than 99%: only 7 of 812 healthy controls scored positive. In addition, CancerSEEK localized the cancer to a small number of anatomic sites in a median of 83% of the patients.
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Affiliation(s)
- Joshua D Cohen
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lu Li
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Yuxuan Wang
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Christopher Thoburn
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Bahman Afsari
- Division of Biostatistics and Bioinformatics, Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
| | - Ludmila Danilova
- Division of Biostatistics and Bioinformatics, Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
| | - Christopher Douville
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ammar A Javed
- Department of Surgery, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
| | - Fay Wong
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Austin Mattox
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ralph H Hruban
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
| | | | - Michael G Goggins
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
- Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
| | - Marco Dal Molin
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Tian-Li Wang
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
| | - Richard Roden
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
| | - Alison P Klein
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Janine Ptak
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lisa Dobbyn
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Joy Schaefer
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Natalie Silliman
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Maria Popoli
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Joshua T Vogelstein
- Institute for Computational Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - James D Browne
- Department of Computer Science, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA
| | - Robert E Schoen
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Randall E Brand
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Jeanne Tie
- Division of Systems Biology and Personalized Medicine, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3021, Australia
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC 3010, Australia
- Department of Medical Oncology, Western Health, Melbourne, VIC 3021, Australia
- Department of Medical Oncology, Peter MacCallum Cancer Center, Melbourne, VIC 3000, Australia
| | - Peter Gibbs
- Division of Systems Biology and Personalized Medicine, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3021, Australia
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC 3010, Australia
- Department of Medical Oncology, Western Health, Melbourne, VIC 3021, Australia
- Department of Medical Oncology, Peter MacCallum Cancer Center, Melbourne, VIC 3000, Australia
| | - Hui-Li Wong
- Division of Systems Biology and Personalized Medicine, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3021, Australia
| | - Aaron S Mansfield
- Division of Medical Oncology, Department of Oncology, Mayo Clinic, Rochester, MN 55902, USA
| | - Jin Jen
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55902, USA
| | - Samir M Hanash
- Sheikh Ahmed Center for Pancreatic Cancer Research, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Massimo Falconi
- Division of Pancreatic Surgery, Department of Surgery, San Raffaele Scientific Institute Research Hospital, 20132 Milan, Italy
| | - Peter J Allen
- Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Shibin Zhou
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Chetan Bettegowda
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Luis A Diaz
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Cristian Tomasetti
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Division of Biostatistics and Bioinformatics, Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
| | - Kenneth W Kinzler
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Bert Vogelstein
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Anne Marie Lennon
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Surgery, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
- Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
| | - Nickolas Papadopoulos
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Mansfield AS, Ren H, Sutor S, Sarangi V, Nair A, Davila J, Elsbernd LR, Udell JB, Dronca RS, Park S, Markovic SN, Sun Z, Halling KC, Nevala WK, Aubry MC, Dong H, Jen J. Contraction of T cell richness in lung cancer brain metastases. Sci Rep 2018; 8:2171. [PMID: 29391594 PMCID: PMC5794798 DOI: 10.1038/s41598-018-20622-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 01/17/2018] [Indexed: 12/25/2022] Open
Abstract
Very little is known about how the adaptive immune system responds to clonal evolution and tumor heterogeneity in non-small cell lung cancer. We profiled the T-cell receptor β complementarity determining region 3 in 20 patients with fully resected non-small cell lung cancer primary lesions and paired brain metastases. We characterized the richness, abundance and overlap of T cell clones between pairs, in addition to the tumor mutation burden and predicted neoantigens. We found a significant contraction in the number of unique T cell clones in brain metastases compared to paired primary cancers. The vast majority of T cell clones were specific to a single lesion, and there was minimal overlap in T cell clones between paired lesions. Despite the contraction in the number of T cell clones, brain metastases had higher non-synonymous mutation burdens than primary lesions. Our results suggest that there is greater richness of T cell clones in primary lung cancers than their paired metastases despite the higher mutation burden observed in metastatic lesions. These results may have implications for immunotherapy.
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Affiliation(s)
| | - Hongzheng Ren
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Shari Sutor
- Department of Immunology, Mayo Clinic, Rochester, MN, USA
| | | | - Asha Nair
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Jaime Davila
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | | | - Julia B Udell
- Center for International Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | - Roxana S Dronca
- Division of Medical Oncology, Mayo Clinic, Rochester, MN, USA
| | - Sean Park
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN, USA
| | | | - Zhifu Sun
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Kevin C Halling
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Wendy K Nevala
- Department of Immunology, Mayo Clinic, Rochester, MN, USA
| | | | - Haidong Dong
- Department of Immunology, Mayo Clinic, Rochester, MN, USA
| | - Jin Jen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA. .,Genome Analysis Core and the Biomarker Discovery Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.
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27
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Asiedu MK, Thomas CF, Dong J, Schulte SC, Khadka P, Sun Z, Kosari F, Jen J, Molina J, Vasmatzis G, Kuang R, Aubry MC, Yang P, Wigle DA. Pathways Impacted by Genomic Alterations in Pulmonary Carcinoid Tumors. Clin Cancer Res 2018; 24:1691-1704. [DOI: 10.1158/1078-0432.ccr-17-0252] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 08/23/2017] [Accepted: 01/10/2018] [Indexed: 11/16/2022]
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28
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Scheid AD, Van Keulen VP, Felts SJ, Neier SC, Middha S, Nair AA, Techentin RW, Gilbert BK, Jen J, Neuhauser C, Zhang Y, Pease LR. Gene Expression Signatures Characterized by Longitudinal Stability and Interindividual Variability Delineate Baseline Phenotypic Groups with Distinct Responses to Immune Stimulation. J Immunol 2018; 200:1917-1928. [PMID: 29352003 DOI: 10.4049/jimmunol.1701099] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 11/12/2017] [Indexed: 11/19/2022]
Abstract
Human immunity exhibits remarkable heterogeneity among individuals, which engenders variable responses to immune perturbations in human populations. Population studies reveal that, in addition to interindividual heterogeneity, systemic immune signatures display longitudinal stability within individuals, and these signatures may reliably dictate how given individuals respond to immune perturbations. We hypothesize that analyzing relationships among these signatures at the population level may uncover baseline immune phenotypes that correspond with response outcomes to immune stimuli. To test this, we quantified global gene expression in peripheral blood CD4+ cells from healthy individuals at baseline and following CD3/CD28 stimulation at two time points 1 mo apart. Systemic CD4+ cell baseline and poststimulation molecular immune response signatures (MIRS) were defined by identifying genes expressed at levels that were stable between time points within individuals and differential among individuals in each state. Iterative differential gene expression analyses between all possible phenotypic groupings of at least three individuals using the baseline and stimulated MIRS gene sets revealed shared baseline and response phenotypic groupings, indicating the baseline MIRS contained determinants of immune responsiveness. Furthermore, significant numbers of shared phenotype-defining sets of determinants were identified in baseline data across independent healthy cohorts. Combining the cohorts and repeating the analyses resulted in identification of over 6000 baseline immune phenotypic groups, implying that the MIRS concept may be useful in many immune perturbation contexts. These findings demonstrate that patterns in complex gene expression variability can be used to define immune phenotypes and discover determinants of immune responsiveness.
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Affiliation(s)
- Adam D Scheid
- Immunology Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic College of Medicine and Science, Rochester, MN 55905
| | - Virginia P Van Keulen
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905
| | - Sara J Felts
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905
| | - Steven C Neier
- Immunology Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic College of Medicine and Science, Rochester, MN 55905
| | - Sumit Middha
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Mayo Clinic College of Medicine and Science, Rochester, MN 55905
| | - Asha A Nair
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Mayo Clinic College of Medicine and Science, Rochester, MN 55905
| | - Robert W Techentin
- Special Purpose Processor Development Group, Mayo Clinic, Rochester, MN 55901
| | - Barry K Gilbert
- Special Purpose Processor Development Group, Mayo Clinic, Rochester, MN 55901
| | - Jin Jen
- Medical Genome Facility Gene Expression Core and Department of Experimental Pathology and Laboratory Medicine, Mayo Clinic, Rochester, MN 55905; and
| | - Claudia Neuhauser
- Informatics Institute, University of Minnesota, Minneapolis, MN 55455
| | - Yuji Zhang
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Mayo Clinic College of Medicine and Science, Rochester, MN 55905
| | - Larry R Pease
- Immunology Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic College of Medicine and Science, Rochester, MN 55905; .,Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905
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29
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Mansfield A, Ren H, Sutor S, Dronca R, Park S, Markovic S, Nevala W, Jen J, Aubry M, Dong H. OA 13.07 Contraction of T Cell Clonality in Lung Cancer Metastases. J Thorac Oncol 2017. [DOI: 10.1016/j.jtho.2017.09.406] [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: 10/18/2022]
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30
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Chabon J, Chaudhuri A, Azad T, Kurtz D, Stehr H, Liu C, Martin JS, Merriott D, Carter J, Ayers K, Mansfield A, Jen J, Ren H, West R, Nair V, Shrager J, Neal J, Wakelee H, Loo B, Alizadeh A, Diehn M. MA 13.01 Clinical and Pathological Variables Influencing Noninvasive Detection of Early Stage Lung Cancer Using Circulating Tumor DNA. J Thorac Oncol 2017. [DOI: 10.1016/j.jtho.2017.09.560] [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: 10/18/2022]
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31
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Hu G, Dasari S, Asmann YW, Greipp PT, Knudson RA, Benson HK, Li Y, Eckloff BW, Jen J, Link BK, Jiang L, Sidhu JS, Wellik LE, Witzig TE, Bennani NN, Cerhan JR, Boddicker RL, Feldman AL. Targetable fusions of the FRK tyrosine kinase in ALK-negative anaplastic large cell lymphoma. Leukemia 2017; 32:565-569. [PMID: 29026208 PMCID: PMC5803446 DOI: 10.1038/leu.2017.309] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- G Hu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - S Dasari
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Y W Asmann
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
| | - P T Greipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.,Medical Genome Facility, Mayo Clinic, Rochester, MN, USA
| | - R A Knudson
- Medical Genome Facility, Mayo Clinic, Rochester, MN, USA
| | - H K Benson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Y Li
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - B W Eckloff
- Medical Genome Facility, Mayo Clinic, Rochester, MN, USA
| | - J Jen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - B K Link
- Department of Internal Medicine, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - L Jiang
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Jacksonville, FL, USA
| | - J S Sidhu
- Department of Pathology and Laboratory Medicine, United Health Services Hospitals, Johnson City/Binghamton, NY, USA
| | - L E Wellik
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - T E Witzig
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - N N Bennani
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - J R Cerhan
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - R L Boddicker
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - A L Feldman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
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32
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Jen J, Lin LL, Lo FY, Chen HT, Liao SY, Tang YA, Su WC, Salgia R, Hsu CL, Huang HC, Juan HF, Wang YC. Oncoprotein ZNF322A transcriptionally deregulates alpha-adducin, cyclin D1 and p53 to promote tumor growth and metastasis in lung cancer. Oncogene 2017. [PMID: 28628114 PMCID: PMC5596203 DOI: 10.1038/onc.2017.203] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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33
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Wieben ED, Aleff RA, Tang X, Butz ML, Kalari KR, Highsmith EW, Jen J, Vasmatzis G, Patel SV, Maguire LJ, Baratz KH, Fautsch MP. Trinucleotide Repeat Expansion in the Transcription Factor 4 (TCF4) Gene Leads to Widespread mRNA Splicing Changes in Fuchs' Endothelial Corneal Dystrophy. Invest Ophthalmol Vis Sci 2017; 58:343-352. [PMID: 28118661 PMCID: PMC5270622 DOI: 10.1167/iovs.16-20900] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose To identify RNA missplicing events in human corneal endothelial tissue isolated from Fuchs' endothelial corneal dystrophy (FECD). Methods Total RNA was isolated and sequenced from corneal endothelial tissue obtained during keratoplasty from 12 patients with FECD and 4 patients undergoing keratoplasty or enucleation for other indications. The length of the trinucleotide repeat (TNR) CTG in the transcription factor 4 (TCF4) gene was determined using leukocyte-derived DNA analyzed by a combination of Southern blotting and Genescan analysis. Commercial statistical software was used to quantify expression of alternatively spliced genes. Validation of selected alternative splicing events was performed by using RT-PCR. Gene sets identified were analyzed for overrepresentation using Web-based analysis system. Results Corneal endothelial tissue from FECD patients containing a CTG TNR expansion sequence in the TCF4 gene revealed widespread changes in mRNA splicing, including a novel splicing event involving FGFR2. Differential splicing of NUMA1, PPFIBP1, MBNL1, and MBNL2 transcripts were identified in all FECD samples containing a TNR expansion. The differentially spliced genes were enriched for products that localize to the cell cortex and bind cytoskeletal and cell adhesion proteins. Conclusions Corneal endothelium from FECD patients harbors a unique signature of mis-splicing events due to CTG TNR expansion in the TCF4 gene, consistent with the hypothesis that RNA toxicity contributes to the pathogenesis of FECD. Changes to the endothelial barrier function, a known event in the development of FECD, was identified as a key biological process influenced by the missplicing events.
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Affiliation(s)
- Eric D Wieben
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States
| | - Ross A Aleff
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States
| | - Xiaojia Tang
- Division of Biostatistics and Bioinformatics and Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States
| | - Malinda L Butz
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States
| | - Krishna R Kalari
- Division of Biostatistics and Bioinformatics and Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States
| | - Edward W Highsmith
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States
| | - Jin Jen
- Department of Experimental Pathology and Laboratory Medicine, Mayo Clinic, Rochester, Minnesota, United States
| | - George Vasmatzis
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, United States
| | - Sanjay V Patel
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, United States
| | - Leo J Maguire
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, United States
| | - Keith H Baratz
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, United States
| | - Michael P Fautsch
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, United States
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34
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Liao SY, Chiang CW, Hsu CH, Chen YT, Jen J, Juan HF, Lai WW, Wang YC. CK1δ/GSK3β/FBXW7α axis promotes degradation of the ZNF322A oncoprotein to suppress lung cancer progression. Oncogene 2017; 36:5722-5733. [PMID: 28581525 DOI: 10.1038/onc.2017.168] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 03/30/2017] [Accepted: 04/10/2017] [Indexed: 12/11/2022]
Abstract
Overexpression of Cys2His2 zinc-finger 322A (ZNF322A) oncogenic transcription factor is associated with lung tumorigenesis. However, the mechanism of ZNF322A overexpression remains poorly understood. Here, we discover that protein stability of ZNF322A is regulated by coordinated phosphorylation and ubiquitination through the CK1δ/GSK3β/FBXW7α axis. CK1δ and GSK3β kinases sequentially phosphorylate ZNF322A at serine-396 and then serine-391. Moreover, the doubly phosphorylated ZNF322A protein creates a destruction motif for the ubiquitin ligase FBXW7α leading to ZNF322A protein destruction. Overexpression of FBXW7α induces ZNF322A protein degradation, thereby blocks ZNF322A transcription activity and suppresses ZNF322A-induced tumor growth and metastasis in vitro and in vivo. Clinically, overexpression of ZNF322A correlates with low FBXW7α or defective CK1δ/GSK3β-mediated phosphorylation in lung cancer patients. Multivariate Cox regression analysis indicates that patients with ZNF322A high/FBXW7 low expression profile can be used as an independent factor to predict the clinical outcome in lung cancer patients. Our results reveal a new mechanism of ZNF322A oncoprotein destruction regulated by the CK1δ/GSK3β/FBXW7α axis. Deregulation of this signaling axis results in ZNF322A overexpression and promotes cancer progression.
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Affiliation(s)
- S-Y Liao
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - C-W Chiang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - C-H Hsu
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
| | - Y-T Chen
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - J Jen
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - H-F Juan
- Department of Life Science, Institute of Molecular and Cellular Biology, Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - W-W Lai
- Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Y-C Wang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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35
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Boddicker R, Hu G, Dasari S, Asmann Y, Greipp P, Knudson R, Eckloff B, Jen J, Link B, Bennani N, Cerhan J, Feldman A. TARGETABLE FUSIONS OF THE FRK TYROSINE KINASE IN ALK-NEGATIVE ANAPLASTIC LARGE CELL LYMPHOMA. Hematol Oncol 2017. [DOI: 10.1002/hon.2437_45] [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: 11/09/2022]
Affiliation(s)
- R.L. Boddicker
- Laboratory Medicine and Pathology; Mayo Clinic; Rochester Minnesota USA
| | - G. Hu
- Laboratory Medicine and Pathology; Mayo Clinic; Rochester Minnesota USA
| | - S. Dasari
- Division of Biomedical Statistics and Informatics; Mayo Clinic; Rochester Minnesota USA
| | - Y.W. Asmann
- Department of Health Sciences Research; Mayo Clinic; Jacksonville Florida USA
| | - P.T. Greipp
- Laboratory Medicine and Pathology; Mayo Clinic; Rochester Minnesota USA
| | - R.A. Knudson
- Medical Genome Facility; Mayo Clinic; Rochester Minnesota USA
| | - B.W. Eckloff
- Medical Genome Facility; Mayo Clinic; Rochester Minnesota USA
| | - J. Jen
- Laboratory Medicine and Pathology; Mayo Clinic; Rochester Minnesota USA
| | - B.K. Link
- Department of Internal Medicine; University of Iowa; Iowa City Iowa USA
| | - N. Bennani
- Division of Hematology; Mayo Clinic; Rochester Minnesota USA
| | - J.R. Cerhan
- Department of Health Sciences Research; Mayo Clinic; Rochester Minnesota USA
| | - A.L. Feldman
- Laboratory Medicine and Pathology; Mayo Clinic; Rochester Minnesota USA
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36
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Gao D, Herman JG, Cui H, Jen J, Fuks F, Brock MV, Ushijima T, Croce C, Akiyama Y, Guo M. Meeting Report of the Fifth International Cancer Epigenetics Conference in Beijing, China, October 2016. Epigenomics 2017; 9:937-941. [PMID: 28530839 DOI: 10.2217/epi-2017-0030] [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] [Indexed: 11/21/2022] Open
Abstract
Fifth International Cancer Epigenetics Conference, Beijing, China, 21-23 October 2016 This meeting reported many new findings in the field of cancer epigenetics, including basic science, translational and clinical studies. In this report, we summarize some of the main advancements and prospects in cancer epigenetics presented at this meeting.
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Affiliation(s)
- Dan Gao
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, Beijing 100853, China.,School of Medicine, Nankai University, Tianjin 300071, China
| | - James G Herman
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburg, PA 15232, USA
| | - Hengmi Cui
- Institute of Epigenetics & Epigenomics, Yangzhou University, Yangzhou 225000, China
| | - Jin Jen
- Department of Laboratory of Medicine & Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Francois Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels 1070, Belgium
| | - Malcolm V Brock
- Oncology Center, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Carlo Croce
- Department of Cancer Biology & Genetics, College of Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Yoshimitsu Akiyama
- Department of Molecular Oncology, Graduate School of Medical & Dental Sciences, Tokyo Medical & Dental University, Tokyo 113-8519, Japan
| | - Mingzhou Guo
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, Beijing 100853, China
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37
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Kohli M, Ho Y, Hillman DW, Van Etten JL, Henzler C, Yang R, Sperger JM, Li Y, Tseng E, Hon T, Clark T, Tan W, Carlson RE, Wang L, Sicotte H, Thai H, Jimenez R, Huang H, Vedell PT, Eckloff BW, Quevedo JF, Pitot HC, Costello BA, Jen J, Wieben ED, Silverstein KAT, Lang JM, Wang L, Dehm SM. Androgen Receptor Variant AR-V9 Is Coexpressed with AR-V7 in Prostate Cancer Metastases and Predicts Abiraterone Resistance. Clin Cancer Res 2017; 23:4704-4715. [PMID: 28473535 DOI: 10.1158/1078-0432.ccr-17-0017] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 04/13/2017] [Accepted: 04/27/2017] [Indexed: 01/22/2023]
Abstract
Purpose: Androgen receptor (AR) variant AR-V7 is a ligand-independent transcription factor that promotes prostate cancer resistance to AR-targeted therapies. Accordingly, efforts are under way to develop strategies for monitoring and inhibiting AR-V7 in castration-resistant prostate cancer (CRPC). The purpose of this study was to understand whether other AR variants may be coexpressed with AR-V7 and promote resistance to AR-targeted therapies.Experimental Design: We utilized complementary short- and long-read sequencing of intact AR mRNA isoforms to characterize AR expression in CRPC models. Coexpression of AR-V7 and AR-V9 mRNA in CRPC metastases and circulating tumor cells was assessed by RNA-seq and RT-PCR, respectively. Expression of AR-V9 protein in CRPC models was evaluated with polyclonal antisera. Multivariate analysis was performed to test whether AR variant mRNA expression in metastatic tissues was associated with a 12-week progression-free survival endpoint in a prospective clinical trial of 78 CRPC-stage patients initiating therapy with the androgen synthesis inhibitor, abiraterone acetate.Results: AR-V9 was frequently coexpressed with AR-V7. Both AR variant species were found to share a common 3' terminal cryptic exon, which rendered AR-V9 susceptible to experimental manipulations that were previously thought to target AR-V7 uniquely. AR-V9 promoted ligand-independent growth of prostate cancer cells. High AR-V9 mRNA expression in CRPC metastases was predictive of primary resistance to abiraterone acetate (HR = 4.0; 95% confidence interval, 1.31-12.2; P = 0.02).Conclusions: AR-V9 may be an important component of therapeutic resistance in CRPC. Clin Cancer Res; 23(16); 4704-15. ©2017 AACR.
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Affiliation(s)
- Manish Kohli
- Division of Medical Oncology, Department of Oncology, Mayo Clinic, Rochester, Minnesota.
| | - Yeung Ho
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - David W Hillman
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Rochester, Minnesota
| | - Jamie L Van Etten
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Christine Henzler
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota
| | - Rendong Yang
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota
| | - Jamie M Sperger
- Department of Medicine, Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin
| | - Yingming Li
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | | | - Ting Hon
- Pacific Biosciences, Menlo Park, California
| | | | - Winston Tan
- Department of Medicine, Mayo Clinic, Jacksonville, Florida
| | - Rachel E Carlson
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Rochester, Minnesota
| | - Liguo Wang
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Rochester, Minnesota.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Hugues Sicotte
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Rochester, Minnesota
| | - Ho Thai
- Department of Medicine, Mayo Clinic, Scottsdale, Arizona
| | - Rafael Jimenez
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Haojie Huang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Peter T Vedell
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Rochester, Minnesota
| | | | - Jorge F Quevedo
- Division of Medical Oncology, Department of Oncology, Mayo Clinic, Rochester, Minnesota
| | - Henry C Pitot
- Division of Medical Oncology, Department of Oncology, Mayo Clinic, Rochester, Minnesota
| | - Brian A Costello
- Division of Medical Oncology, Department of Oncology, Mayo Clinic, Rochester, Minnesota
| | - Jin Jen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.,Medical Genome Facility, Mayo Clinic, Rochester, Minnesota.,Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Eric D Wieben
- Medical Genome Facility, Mayo Clinic, Rochester, Minnesota
| | | | - Joshua M Lang
- Department of Medicine, Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Scott M Dehm
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota. .,Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota.,Department of Urology, University of Minnesota, Minneapolis, Minnesota
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Tseng HY, Chen YA, Jen J, Shen PC, Chen LM, Lin TD, Wang YC, Hsu HL. Oncogenic MCT-1 activation promotes YY1-EGFR-MnSOD signaling and tumor progression. Oncogenesis 2017; 6:e313. [PMID: 28394354 PMCID: PMC5520490 DOI: 10.1038/oncsis.2017.13] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 01/10/2017] [Accepted: 02/10/2017] [Indexed: 12/20/2022] Open
Abstract
Tumor cells often produce high levels of reactive oxygen species (ROS) and display an increased ROS scavenging system. However, the molecular mechanism that balances antioxidative and oxidative stress in cancer cells is unclear. Here, we determined that oncogenic multiple copies in T-cell malignancy 1 (MCT-1) activity promotes the generation of intracellular ROS and mitochondrial superoxide. Overexpression of MCT-1 suppresses p53 accumulation but elevates the manganese-dependent superoxide dismutase (MnSOD) level via the YY1-EGFR signaling cascade, which protects cells against oxidative damage. Conversely, restricting ROS generation and/or targeting YY1 in lung cancer cells effectively inhibits the EGFR-MnSOD signaling pathway and cell invasiveness induced by MCT-1. Significantly, MCT-1 overexpression in lung cancer cells promotes tumor progression, necrosis and angiogenesis, and increases the number of tumor-promoting M2 macrophages and cancer-associated fibroblasts in the microenvironment. Clinical evidence further confirms that high expression of MCT-1 is associated with an increase in YY1, EGFR and MnSOD expression, accompanied by tumor recurrence, poor overall survival and EGFR mutation status in patients with lung cancers. Together, these data indicate that the MCT-1 oncogenic pathway is implicated in oxidative metabolism and lung carcinogenesis.
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Affiliation(s)
- H-Y Tseng
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
| | - Y-A Chen
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
| | - J Jen
- Department of Pharmacology, National Cheng Kung University, Tainan, Taiwan
| | - P-C Shen
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
| | - L-M Chen
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
| | - T-D Lin
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
| | - Y-C Wang
- Department of Pharmacology, National Cheng Kung University, Tainan, Taiwan
| | - H-L Hsu
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
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Jen J, Lin LL, Lo FY, Chen HT, Liao SY, Tang YA, Su WC, Salgia R, Hsu CL, Huang HC, Juan HF, Wang YC. Oncoprotein ZNF322A transcriptionally deregulates alpha-adducin, cyclin D1 and p53 to promote tumor growth and metastasis in lung cancer. Oncogene 2017; 36:4526. [PMID: 28368404 PMCID: PMC5543253 DOI: 10.1038/onc.2017.77] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This corrects the article DOI: 10.1038/onc.2015.296.
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40
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Jang JS, Wang X, Vedell PT, Wen J, Zhang J, Ellison DW, Evans JM, Johnson SH, Yang P, Sukov WR, Oliveira AM, Vasmatzis G, Sun Z, Jen J, Yi ES. Custom Gene Capture and Next-Generation Sequencing to Resolve Discordant ALK Status by FISH and IHC in Lung Adenocarcinoma. J Thorac Oncol 2016; 11:1891-1900. [PMID: 27343444 PMCID: PMC5731243 DOI: 10.1016/j.jtho.2016.06.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 06/05/2016] [Accepted: 06/11/2016] [Indexed: 10/21/2022]
Abstract
INTRODUCTION We performed a genomic study in lung adenocarcinoma cases with discordant anaplastic lymphoma receptor tyrosine kinase gene (ALK) status by fluorescent in situ hybridization (FISH) and immunohistochemical (IHC) analysis. METHODS DNA from formalin-fixed paraffin-embedded tissues of 16 discordant (four FISH-positive/IHC-negative and 12 FISH-negative/IHC-positive) cases by Vysis ALK Break Apart FISH and ALK IHC testing (ALK1 clone) were subjected to whole gene capture and next-generation sequencing (NGS) of nine genes, including ALK, echinoderm microtubule associated protein like 4 gene (EML4), kinesin family member 5B gene (KIF5B), staphylococcal nuclease and tudor domain containing 1 gene (SND1), BRAF, ret proto-oncogene (RET), ezrin gene (EZR), ROS1, and telomerase reverse transcriptase (TERT). All discordant cases (except one FISH-negative/IHC-positive case without sufficient tissue) were analyzed by IHC with D5F3 antibody. In one case with fresh frozen tissue, whole transcriptome sequencing was also performed. Twenty-six concordant (16 FISH-positive/IHC-positive and 10 FISH-negative/IHC-negative) cases were included as controls. RESULTS In four ALK FISH-positive/IHC-negative cases, no EML4-ALK fusion gene was observed by NGS, but in one case using fresh frozen tissue, we identified EML4-baculoviral AIP repeat containing 6 gene (BIRC6) and AP2 associated kinase 1 gene (AAK1)-ALK fusion genes. Whole transcriptome sequencing revealed a highly expressed EML4-BIRC6 fusion transcript and a minimally expressed AAK1 transcript. Among the 12 FISH-negative/IHC-positive cases, no evidence of ALK gene rearrangement was detected by NGS. Eleven of 12 FISH-negative/IHC-positive cases detected by ALK1 clone were concordant by repeat ALK IHC with D5F3 antibody (i.e., FISH-negative/IHC-negative by D5F3 clone). Among the 16 ALK FISH-positive/IHC-positive positive controls, whole gene capture identified ALK gene fusion in 15 cases, including in one case with Huntington interacting protein 1 gene (HIP1)-ALK. No ALK fusion gene was observed in any of the 10 FISH-negative/IHC-negative cases. Other fusion genes involving ROS1, EZR, BRAF, and SND1 were also found. CONCLUSIONS ALK FISH results appeared to be false-positive in three of four FISH-positive/IHC-negative cases, whereas no false-negative ALK FISH case was identified among 12 ALK FISH-negative/IHC-positive cases by ALK1 clone, which was in keeping with the concordant FISH-negative/IHC-negative status by D5F3 clone. Our targeted whole gene capture approach using formalin-fixed paraffin embedded samples was effective for detecting rearrangements involving ALK and other actionable oncogenes.
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Affiliation(s)
- Jin Sung Jang
- Genome Analysis Core, Medical Genome Facility, Mayo Clinic, Rochester, Minnesota; Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Xiaoke Wang
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Peter T Vedell
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Ji Wen
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - David W Ellison
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jared M Evans
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Sarah H Johnson
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Ping Yang
- Division of Epidemiology, Mayo Clinic, Rochester, Minnesota
| | - William R Sukov
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Andre M Oliveira
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - George Vasmatzis
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Zhifu Sun
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Jin Jen
- Genome Analysis Core, Medical Genome Facility, Mayo Clinic, Rochester, Minnesota; Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Eunhee S Yi
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.
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Davila JI, Fadra NM, Wang X, McDonald AM, Nair AA, Crusan BR, Wu X, Blommel JH, Jen J, Rumilla KM, Jenkins RB, Aypar U, Klee EW, Kipp BR, Halling KC. Impact of RNA degradation on fusion detection by RNA-seq. BMC Genomics 2016; 17:814. [PMID: 27765019 PMCID: PMC5072325 DOI: 10.1186/s12864-016-3161-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [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: 06/02/2016] [Accepted: 10/12/2016] [Indexed: 12/22/2022] Open
Abstract
Background RNA-seq is a well-established method for studying the transcriptome. Popular methods for library preparation in RNA-seq such as Illumina TruSeq® RNA v2 kit use a poly-A pulldown strategy. Such methods can cause loss of coverage at the 5′ end of genes, impacting the ability to detect fusions when used on degraded samples. The goal of this study was to quantify the effects RNA degradation has on fusion detection when using poly-A selected mRNA and to identify the variables involved in this process. Results Using both artificially and naturally degraded samples, we found that there is a reduced ability to detect fusions as the distance of the breakpoint from the 3′ end of the gene increases. The median transcript coverage decreases exponentially as a function of the distance from the 3′ end and there is a linear relationship between the coverage decay rate and the RNA integrity number (RIN). Based on these findings we developed plots that show the probability of detecting a gene fusion (“sensitivity”) as a function of the distance of the fusion breakpoint from the 3′ end. Conclusions This study developed a strategy to assess the impact that RNA degradation has on the ability to detect gene fusions by RNA-seq. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3161-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jaime I Davila
- Department of Health Science Research, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Numrah M Fadra
- Department of Health Science Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - Xiaoke Wang
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Amber M McDonald
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Asha A Nair
- Department of Health Science Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - Barbara R Crusan
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Xianglin Wu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Joseph H Blommel
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jin Jen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA.,Genome Analysis Core, Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Kandelaria M Rumilla
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Umut Aypar
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Eric W Klee
- Department of Health Science Research, Mayo Clinic, Rochester, MN, 55905, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Benjamin R Kipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Kevin C Halling
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
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Mansfield AS, Murphy SJ, Harris FR, Robinson SI, Marks RS, Johnson SH, Smadbeck JB, Halling GC, Yi ES, Wigle D, Vasmatzis G, Jen J. Chromoplectic TPM3-ALK rearrangement in a patient with inflammatory myofibroblastic tumor who responded to ceritinib after progression on crizotinib. Ann Oncol 2016; 27:2111-2117. [PMID: 27742657 PMCID: PMC5091324 DOI: 10.1093/annonc/mdw405] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [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: 05/13/2016] [Accepted: 08/11/2016] [Indexed: 01/17/2023] Open
Abstract
Ceritinib resulted in a significant, durable response of a metastatic inflammatory myofibroblastic tumor (IMT) after failure of crizotinib. A chromoplectic TPM3–ALK rearrangement involving many known oncogenes was found in the residual IMT. Ceritinib may be useful for patients with IMT after failure of crizotinib, and chromoplexy may have a role in the oncogenesis or treatment resistance of IMTs. Background Inflammatory myofibroblastic tumors (IMTs) are rare sarcomas that can occur at any age. Surgical resection is the primary treatment for patients with localized disease; however, these tumors frequently recur. Less commonly, patients with IMTs develop or present with metastatic disease. There is no standard of care for these patients and traditional cytotoxic therapy is largely ineffective. Most IMTs are associated with oncogenic ALK, ROS1 or PDGFRβ fusions and may benefit from targeted therapy. Patient and methods We sought to understand the genomic abnormalities of a patient who presented for management of metastatic IMT after progression of disease on crizotinib and a significant and durable partial response to the more potent ALK inhibitor ceritinib. Results The residual IMT was resected based on the recommendations of a multidisciplinary tumor sarcoma tumor board and analyzed by whole-genome mate pair sequencing. Analysis of the residual, resected tumor identified a chromoplectic TPM3–ALK rearrangement that involved many other known oncogenes and was confirmed by rtPCR. Conclusions In our analysis of the treatment-resistant, residual IMT, we identified a complex pattern of genetic rearrangements consistent with chromoplexy. Although it is difficult to know for certain if these chromoplectic rearrangements preceded treatment, their presence suggests that chromoplexy has a role in the oncogenesis of IMTs. Furthermore, this patient's remarkable response suggests that ceritinib should be considered as an option after progression on crizotinib for patients with metastatic or unresectable IMT and ALK mutations.
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Affiliation(s)
- A S Mansfield
- Division of Medical Oncology, Department of Oncology
| | - S J Murphy
- Biomarker Discovery Program, Center of Individualized Medicine, Department of Molecular Medicine
| | - F R Harris
- Biomarker Discovery Program, Center of Individualized Medicine, Department of Molecular Medicine
| | - S I Robinson
- Division of Medical Oncology, Department of Oncology
| | - R S Marks
- Division of Medical Oncology, Department of Oncology
| | - S H Johnson
- Biomarker Discovery Program, Center of Individualized Medicine, Department of Molecular Medicine
| | - J B Smadbeck
- Biomarker Discovery Program, Center of Individualized Medicine, Department of Molecular Medicine
| | - G C Halling
- Biomarker Discovery Program, Center of Individualized Medicine, Department of Molecular Medicine
| | - E S Yi
- Department of Laboratory Medicine and Pathology
| | | | - G Vasmatzis
- Biomarker Discovery Program, Center of Individualized Medicine, Department of Molecular Medicine
| | - J Jen
- Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology.,Medical Genome Facility.,Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Mayo Clinic, Rochester, USA
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Abstract
High-throughput sequencing of cancer genomes is increasingly becoming an essential tool of clinical oncology that facilitates target identification and targeted therapy within the context of precision medicine. The cumulative profiles of somatic mutations in cancer yielded by comprehensive molecular studies also constitute a fingerprint of historical exposures to exogenous and endogenous mutagens, providing insight into cancer evolution and etiology. Mutational signatures that were first established by inspection of the TP53 gene somatic landscape have now been confirmed and expanded by comprehensive sequencing studies. Further, the degree of granularity achieved by deep sequencing allows detection of low-abundance mutations with clinical relevance. In tumors, they represent the emergence of small aggressive clones; in normal tissues, they signal a mutagenic exposure related to cancer risk; and, in blood, they may soon become effective surveillance tools for diagnostic purposes and for monitoring of cancer prognosis and recurrence.
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Affiliation(s)
- Ana I Robles
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Jin Jen
- Department of Laboratory Medicine and Pathology, Division of Experimental Pathology, and Department of Medicine, Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota 55905
| | - Curtis C Harris
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
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Jen J, Mansfield A, Eiken PW, Stoddard S, Pierson K, Hou X, Ren HZ, Molina J, Yi J, Yang P. Abstract B34: Integrated Approaches to Treating Lung Adenocarcinoma Resistant to Targeted Therapy. Clin Cancer Res 2016. [DOI: 10.1158/1557-3265.pdx16-b34] [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: 11/16/2022]
Abstract
Abstract
Mutations in the EGFR gene or transcript fusion involving EML4-ALK result in oncogenic activation of these oncogenes driving lung adenocarcinoma growth in tumors carrying such an alteration. For lung adenocarcinoma with these genetic changes, small-molecule tyrosine kinase inhibitors have been highly effective at reducing tumor burden and improve the outcome of the patients. Unfortunately, drug resistance eventually develops in these tumors and challenges remain in controlling lung cancer recurrence after targeted therapy.
To overcome recurrence, we initiated a prove-of-principle study to evaluate the feasibility of an integrated strategy utilizing genomic profiles of the tumor and patient-specific tumor xenografts derived (PDX) from biopsies for ex vivo evaluation of antitumor drugs to help guide personalized treatment of lung cancer in patients who have developed resistance to targeted therapy drugs. Our study has three main objectives. 1) Use tumor biopsies obtained at the time of recurrence for oncogene mutation and RNAseq analyses to identify molecular changes in oncogenes and gene pathways that can be potentially targeted. 2) Evaluate drug efficacy and optimize personalized therapy for each patient using PDX models. 3) Assess clinical feasibility and our experience using integrated approaches for lung cancer patients who failed targeted therapy.
This study was approved by the Mayo Clinic Institutional Review Board (IRB) and utilizes both clinical and research biopsies. A dedicated nurse study coordinator reviews clinical patient list and history on weekly basis and informs the study team of each potential candidate patient. A total of 30 patients having ALK positive lung cancers have been identified and followed up from nearly 500 potentially ALK positive cases between April 2014 to Sept. 2015. Most patients were never smokers but six were former smokers and two were current smokers. Age at diagnoses ranged from 27-78 years (median = 61). Seven patients (23%) were 45 years or younger at the time of diagnosis. A total of 22 patients are currently being treated with crizotinib while eight are on ceritinib or alectinib. For each biopsy, tumor tissues are obtained using a 20 gauge needle, transferred on ice in preserving media and implanted within one hour into 6-8 week old NOD/SCID mice. Many patients have been on treatment for 2-3 years with stable disease so they do not require biopsy. Using a similar strategy, we also obtained biopsies from patients with EGFR gene mutations in their tumors and have progressed while on targeted therapy.
A total of seven cases have been implanted. We will report our experiences in patient selection, clinical follow up, patient consent, PDX development, time from biopsy to tumor establishment, and the results of molecular analyses. Our study enabled us to gain new insights regarding the molecular changes associated with recurring tumors after they have failed targeted therapy as well as clinical experiences on how to utilize state-of-the art approaches and comprehensive genomic information to further improve cancer patient care upon disease progression.
Acknowledgements: This work is supported in part by the Hillsberg Award from the National Foundation for Cancer Research and by the Biomarker Discovery Program at the Mayo Clinic Center for Individualized Medicine.
Citation Format: Jin Jen, Aaron Mansfield, Patrick W. Eiken, Shawn Stoddard, Karlyn Pierson, Xiaonan Hou, Hong Zheng Ren, Julian Molina, Joanne Yi, Ping Yang. Integrated Approaches to Treating Lung Adenocarcinoma Resistant to Targeted Therapy. [abstract]. In: Proceedings of the AACR Special Conference: Patient-Derived Cancer Models: Present and Future Applications from Basic Science to the Clinic; Feb 11-14, 2016; New Orleans, LA. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(16_Suppl):Abstract nr B34.
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Abstract
We present genetically identical twin patients who experienced late-onset migraine with visual and somatosensory auras and later developed hemiplegic migraines associated with severe cortical oedema and enhancement. Both positron emission tomography and electroencephalography showed an increase in activity contralateral to the hemiplegic side. Brain biopsy during the attack showed reactive astrogliosis and microgliosis. Mutations in CACNA1A, ATP1A2, SLC1A3 and NOTCH3 were ruled out by sequencing. This report shows the clinical and genetic evaluation of a severe form of familial hemiplegic migraine as well as the evolution of the imaging changes.
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Affiliation(s)
- Y-H Cha
- Department of Neurology, University of California-Los Angeles, 710 Westwood Plaza, Los Angeles, CA 90095, USA.
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Wang L, Nie J, Sicotte H, Li Y, Eckel-Passow JE, Dasari S, Vedell PT, Barman P, Wang L, Weinshiboum R, Jen J, Huang H, Kohli M, Kocher JPA. Measure transcript integrity using RNA-seq data. BMC Bioinformatics 2016; 17:58. [PMID: 26842848 PMCID: PMC4739097 DOI: 10.1186/s12859-016-0922-z] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 01/29/2016] [Indexed: 11/21/2022] Open
Abstract
Background Stored biological samples with pathology information and medical records are invaluable resources for translational medical research. However, RNAs extracted from the archived clinical tissues are often substantially degraded. RNA degradation distorts the RNA-seq read coverage in a gene-specific manner, and has profound influences on whole-genome gene expression profiling. Result We developed the transcript integrity number (TIN) to measure RNA degradation. When applied to 3 independent RNA-seq datasets, we demonstrated TIN is a reliable and sensitive measure of the RNA degradation at both transcript and sample level. Through comparing 10 prostate cancer clinical samples with lower RNA integrity to 10 samples with higher RNA quality, we demonstrated that calibrating gene expression counts with TIN scores could effectively neutralize RNA degradation effects by reducing false positives and recovering biologically meaningful pathways. When further evaluating the performance of TIN correction using spike-in transcripts in RNA-seq data generated from the Sequencing Quality Control consortium, we found TIN adjustment had better control of false positives and false negatives (sensitivity = 0.89, specificity = 0.91, accuracy = 0.90), as compared to gene expression analysis results without TIN correction (sensitivity = 0.98, specificity = 0.50, accuracy = 0.86). Conclusion TIN is a reliable measurement of RNA integrity and a valuable approach used to neutralize in vitro RNA degradation effect and improve differential gene expression analysis. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-0922-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Liguo Wang
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Jinfu Nie
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Hugues Sicotte
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Ying Li
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, 55905, USA.
| | | | - Surendra Dasari
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Peter T Vedell
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Poulami Barman
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Richard Weinshiboum
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Jin Jen
- Department of laboratory medicine and pathology, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Haojie Huang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Manish Kohli
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Jean-Pierre A Kocher
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, 55905, USA.
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Yang JD, Campion MB, Liu MC, Chaiteerakij R, Giama NH, Mohammed HA, Zhang X, Hu C, Campion VL, Jen J, Venkatesh SK, Halling KC, Kipp BR, Roberts LR. Circulating tumor cells are associated with poor overall survival in patients with cholangiocarcinoma. Hepatology 2016; 63:148-58. [PMID: 26096702 PMCID: PMC4684812 DOI: 10.1002/hep.27944] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 05/11/2015] [Accepted: 06/17/2015] [Indexed: 12/13/2022]
Abstract
UNLABELLED Circulating tumor cells (CTCs) in blood are associated with poor survival of patients with breast, prostate, or colon cancer. We hypothesized that CTCs are associated with poor survival of patients with cholangiocarcinoma (CCA). Eighty-eight patients with CCA were prospectively enrolled at Mayo Clinic Rochester between June 2010 and September 2014. The CellSearch system by Veridex was used for detection of CTCs in peripheral blood. Associations between CTC, patient and tumor characteristics, and survival were examined using the Cox's proportional hazards model. Fifteen patients (17%) were positive for CTC ≥2 and 8 patients (9%) for CTC ≥5. CTCs were associated with tumor extent. CTC ≥2 (hazard ratio [HR]: 2.5; 95% confidence interval [CI]: 1.1-5.4; P = 0.02) and CTC ≥5 (HR, 4.1; 95% CI: 1.4-10.8; P = 0.01) were both independent predictors of survival. In subgroup analyses, CTC ≥2 (HR, 8.2; 95% CI: 1.8-57.5; P < 0.01) and CTC ≥5 (HR, 7.7; 95% CI: 1.4-42.9; P = 0.02) were both associated with shorter survival among patients with metastasis. There was a trend toward association of CTC ≥5 with shorter survival in patients with nonmetastatic CCA (HR, 4.3; 95% CI: 1.0-13.8; P = 0.06). CTC ≥2 (HR, 10.5; 95% CI: 2.2-40.1; P < 0.01) and CTC ≥5 (HR, 10.2; 95% CI: 1.5-42.3; P = 0.02) were both associated with shorter survival among patients with perihilar/distal CCA. CTC ≥5 was associated with shorter survival of patients with intrahepatic CCA (HR, 4.2; 95% CI: 1.1-14.1; P = 0.04). CONCLUSION CTCs were associated with more-aggressive tumor characteristics and independently associated with survival in patients with CCA. Assessment of CTCs may be useful for identifying CCA patients at risk of early mortality.
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Affiliation(s)
- Ju Dong Yang
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Michael B. Campion
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Minetta C. Liu
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA,Division of Medical Oncology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Roongruedee Chaiteerakij
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine, Rochester, MN, USA,Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Nasra H. Giama
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Hager Ahmed Mohammed
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Xiaodan Zhang
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Chunling Hu
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Victoria L. Campion
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Jin Jen
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | | | - Kevin C. Halling
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Benjamin R. Kipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Lewis R. Roberts
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine, Rochester, MN, USA
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48
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Mitra AK, Mukherjee UK, Harding T, Jang JS, Stessman H, Li Y, Abyzov A, Jen J, Kumar S, Rajkumar V, Van Ness B. Single-cell analysis of targeted transcriptome predicts drug sensitivity of single cells within human myeloma tumors. Leukemia 2015; 30:1094-102. [DOI: 10.1038/leu.2015.361] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 11/30/2015] [Accepted: 12/15/2015] [Indexed: 12/14/2022]
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49
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Lee SB, Kim JJ, Nam HJ, Gao B, Yin P, Qin B, Yi SY, Ham H, Evans D, Kim SH, Zhang J, Deng M, Liu T, Zhang H, Billadeau DD, Wang L, Giaime E, Shen J, Pang YP, Jen J, van Deursen JM, Lou Z. Parkin Regulates Mitosis and Genomic Stability through Cdc20/Cdh1. Mol Cell 2015; 60:21-34. [PMID: 26387737 PMCID: PMC4592523 DOI: 10.1016/j.molcel.2015.08.011] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [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: 02/19/2015] [Revised: 06/04/2015] [Accepted: 08/12/2015] [Indexed: 01/04/2023]
Abstract
Mutations in the E3 ubiquitin ligase Parkin have been linked to familial Parkinson's disease. Parkin has also been implicated in mitosis through mechanisms that are unclear. Here we show that Parkin interacts with anaphase promoting complex/cyclosome (APC/C) coactivators Cdc20 and Cdh1 to mediate the degradation of several key mitotic regulators independent of APC/C. We demonstrate that ordered progression through mitosis is orchestrated by two distinct E3 ligases through the shared use of Cdc20 and Cdh1. Furthermore, Parkin is phosphorylated and activated by polo-like kinase 1 (Plk1) during mitosis. Parkin deficiency results in overexpression of its substrates, mitotic defects, genomic instability, and tumorigenesis. These results suggest that the Parkin-Cdc20/Cdh1 complex is an important regulator of mitosis.
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Affiliation(s)
- Seung Baek Lee
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Jung Jin Kim
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Hyun-Ja Nam
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Bowen Gao
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Ping Yin
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Bo Qin
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Sang-Yeop Yi
- Department of Pathology, International St. Mary's Hospital, College of Medicine, Catholic Kwandong University, Incheon 404 834, Republic of Korea
| | - Hyoungjun Ham
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
- Mayo Graduate School, Mayo Clinic, Rochester, MN 55905, USA
| | - Debra Evans
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
- Mayo Graduate School, Mayo Clinic, Rochester, MN 55905, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Sun-Hyun Kim
- Department of Family Medicine, International St. Mary's Hospital, College of Medicine, Catholic Kwandong University, Incheon 404 834, Republic of Korea
| | - Jun Zhang
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Min Deng
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Tongzheng Liu
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Haoxing Zhang
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Daniel D. Billadeau
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
- Division of Oncology Research and Schulze Center for Novel Therapeutics, College of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Emilie Giaime
- Center for Neurologic Diseases, Department of Neurology, Brigham & Women's Hospital, Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA
| | - Jie Shen
- Center for Neurologic Diseases, Department of Neurology, Brigham & Women's Hospital, Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA
| | - Yuan-Ping Pang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Jin Jen
- Division of Pulmonary and Critical Care Medicine, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA, Mayo Clinic, Rochester, MN 55905, USA
| | - Jan M. van Deursen
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhenkun Lou
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
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50
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Salmaninejad A, Estiar MA, Gill RK, Shih JH, Hewitt S, Jeon HS, Fukuoka J, Shilo K, Shakoori A, Jen J. Expression Analysis of p16, c-Myc, and mSin3A in Non-small Cell Lung Cancer by Computer Aided Scoring and Analysis (CASA). Clin Lab 2015; 61:549-59. [PMID: 26118188 DOI: 10.7754/clin.lab.2014.141125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Immunohistochemical analysis (IHC) of tissue microarray (TMA) slides enables large sets of tissue samples to be analyzed simultaneously on a single slide. However, manual evaluation of small cores on a TMA slide is time consuming and error prone. METHODS We describe a computer aided scoring and analysis (CASA) method to allow facile and reliable scoring of IHC staining using TMA containing 300 non-small cell lung cancer (NSCLC) cases. In the two previous published papers utilizing our TMA slides of lung cancer we examined 18 proteins involved in the chromatin machinery. We developed our study using more proteins of the chromatin complex and several transcription factors that facilitate the chromatin machinery. Then, a total of 78 antibodies were evaluated by CASA to derive a normalized intensity value that correlated with the overall staining status of the targeting protein. The intensity values for TMA cores were then examined for association to clinical variables and predictive significance individually and with other factors. RESULTs: Using our TMA, the intensity of several protein pairs were significantly correlated with an increased risk of death in NSCLC. These included c-Myc with p16, mSin3A with p16 and c-Myc with mSinA. Predictive values of these pairs remained significant when evaluated based on standard IHC scores. CONCLUSIONS Our results demonstrate the usefulness of CASA as a valuable tool for systematic assessment of TMA slides to identify potential predictive biomarkers using a large set of primary human tissues.
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