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Pouriafar Y, Rostami S, Alizadghandforoush N, Barati M, Amini A, Safa M. CDC27 gene expression patterns as a potential biomarker in Acute Leukemia. Mol Biol Rep 2024; 51:865. [PMID: 39073611 DOI: 10.1007/s11033-024-09744-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 06/20/2024] [Indexed: 07/30/2024]
Abstract
BACKGROUND Treating Acute Myeloid Leukemia (AML) and Acute Lymphoblastic Leukemia (ALL) is difficult due to high relapse rates and drug resistance. Tumorigenesis is largely dependent on disruption of the cell cycle progression. While the role of Cell Division Cycle 27 (CDC27) in the anaphase-promoting complex/cyclosome is well-known, its significance in the pathophysiology of acute leukemia and its potential as a biomarker are less well understood. METHODS AND RESULTS This case-control study used samples from 100 leukemia patients (50 with ALL and 50 with AML) at Shariati Hospital in Tehran, Iran, along with 50 healthy individuals. The expression of CDC27 was analyzed using quantitative real-time PCR (RQ-PCR). Statistical analysis was done using the nonparametric Mann-Whitney U test. The results showed that AML and ALL patients had significantly higher levels of CDC27 expression compared to the control group. Although a weak correlation between CDC27 expression and hematological parameters was found, there was no significant correlation with sample type, demographics, clinical variables or prognosis. CONCLUSIONS This study highlights the potential of CDC27 as an oncogene, as well as a possible prognostic and diagnostic marker in acute leukemias. It suggests that CDC27 could be a valuable biomarker or therapeutic target in the treatment of AML and ALL.
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Affiliation(s)
- Yasaman Pouriafar
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Shahrbano Rostami
- Research Institute for Oncology, Hematology and Cell Therapy, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Nasrin Alizadghandforoush
- Research Institute for Oncology, Hematology and Cell Therapy, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahmood Barati
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Ali Amini
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Majid Safa
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran.
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2
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Gomez F, Fisk B, McMichael JF, Mosior M, Foltz JA, Skidmore ZL, Duncavage EJ, Miller CA, Abel H, Li YS, Russler-Germain DA, Krysiak K, Watkins MP, Ramirez CA, Schmidt A, Martins Rodrigues F, Trani L, Khanna A, Wagner JA, Fulton RS, Fronick CC, O'Laughlin MD, Schappe T, Cashen AF, Mehta-Shah N, Kahl BS, Walker J, Bartlett NL, Griffith M, Fehniger TA, Griffith OL. Ultra-Deep Sequencing Reveals the Mutational Landscape of Classical Hodgkin Lymphoma. CANCER RESEARCH COMMUNICATIONS 2023; 3:2312-2330. [PMID: 37910143 PMCID: PMC10648575 DOI: 10.1158/2767-9764.crc-23-0140] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/27/2023] [Accepted: 10/24/2023] [Indexed: 11/03/2023]
Abstract
The malignant Hodgkin and Reed Sternberg (HRS) cells of classical Hodgkin lymphoma (cHL) are scarce in affected lymph nodes, creating a challenge to detect driver somatic mutations. As an alternative to cell purification techniques, we hypothesized that ultra-deep exome sequencing would allow genomic study of HRS cells, thereby streamlining analysis and avoiding technical pitfalls. To test this, 31 cHL tumor/normal pairs were exome sequenced to approximately 1,000× median depth of coverage. An orthogonal error-corrected sequencing approach verified >95% of the discovered mutations. We identified mutations in genes novel to cHL including: CDH5 and PCDH7, novel stop gain mutations in IL4R, and a novel pattern of recurrent mutations in pathways regulating Hippo signaling. As a further application of our exome sequencing, we attempted to identify expressed somatic single-nucleotide variants (SNV) in single-nuclei RNA sequencing (snRNA-seq) data generated from a patient in our cohort. Our snRNA analysis identified a clear cluster of cells containing a somatic SNV identified in our deep exome data. This cluster has differentially expressed genes that are consistent with genes known to be dysregulated in HRS cells (e.g., PIM1 and PIM3). The cluster also contains cells with an expanded B-cell clonotype further supporting a malignant phenotype. This study provides proof-of-principle that ultra-deep exome sequencing can be utilized to identify recurrent mutations in HRS cells and demonstrates the feasibility of snRNA-seq in the context of cHL. These studies provide the foundation for the further analysis of genomic variants in large cohorts of patients with cHL. SIGNIFICANCE Our data demonstrate the utility of ultra-deep exome sequencing in uncovering somatic variants in Hodgkin lymphoma, creating new opportunities to define the genes that are recurrently mutated in this disease. We also show for the first time the successful application of snRNA-seq in Hodgkin lymphoma and describe the expression profile of a putative cluster of HRS cells in a single patient.
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Affiliation(s)
- Felicia Gomez
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri
| | - Bryan Fisk
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Joshua F. McMichael
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Matthew Mosior
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Jennifer A. Foltz
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Zachary L. Skidmore
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Eric J. Duncavage
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri
| | - Christopher A. Miller
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Haley Abel
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Yi-Shan Li
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri
| | - David A. Russler-Germain
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Kilannin Krysiak
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri
| | - Marcus P. Watkins
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Cody A. Ramirez
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Alina Schmidt
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Fernanda Martins Rodrigues
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Lee Trani
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Ajay Khanna
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Julia A. Wagner
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Robert S. Fulton
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Catrina C. Fronick
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Michelle D. O'Laughlin
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Timothy Schappe
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Amanda F. Cashen
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Neha Mehta-Shah
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Brad S. Kahl
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Jason Walker
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Nancy L. Bartlett
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
| | - Malachi Griffith
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri
| | - Todd A. Fehniger
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri
| | - Obi L. Griffith
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri
- McDonnell Genome Institute, Department of Medicine, Washington University School of Medicine, St Louis, Missouri
- Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri
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3
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Park H, Kim I, Kim HJ, Shin DY, Lee SY, Kwon OH, Kim DY, Lee KH, Ahn JS, Park J, Sohn SK, Lee JO, Cheong JW, Kim KH, Kim HG, Kim H, Lee YJ, Nam SH, Do YR, Park SG, Park SK, Bae SH, Song HH, Oh D, Jung CW, Park S. Ultra-deep sequencing mutation analysis of the BCR/ABL1 kinase domain in newly diagnosed chronic myeloid leukemia patients. Leuk Res 2021; 111:106728. [PMID: 34673444 DOI: 10.1016/j.leukres.2021.106728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 11/28/2022]
Abstract
Ultra-deep sequencing detects low-frequency genetic mutations with high sensitivity. We used this approach to prospectively examine mutations in the BCR/ABL1 tyrosine kinase from patients with newly diagnosed, chronic-phase chronic myeloid leukemia (CML) treated with the tyrosine kinase inhibitor nilotinib. Between May 2013 and November 2014, 50 patients from 18 institutions were enrolled in the study. We screened 103 somatic mutations and found that mutations in the P-loop domain were the most frequent (173/454 mutations in the P-loop) and noted the presence of the V299 L mutation (dasatinib-resistant/nilotinib-sensitive) in 98 % of patients (49/50). No patients had Y253H, E255 V, or F359 V/C/I mutations, which would recommend dasatinib rather than nilotinib treatment. The S417Y mutation was associated with lower achievement of a major molecular response (MMR) at 6 months, and the V371A mutation was associated with reduced MMR and MR4.5 durations (MMR for 2 years: 100 % for no mutation vs. 75 % for mutation, P=0.039; MR4.5 for 15 months: 94.1 % vs. 25 %, P=0.002). Patients with known nilotinib-resistant mutations had lower rates of MR4.5 achievement. In conclusion, ultra-deep sequencing is a sensitive method for genetic-based treatment decisions. Based on the results of these mutational analyses, nilotinib treatment is a promising option for Korean patients with CML.
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Affiliation(s)
- Hyunkyung Park
- Department of Internal Medicine, Seoul National University Hospital, Biomedical Research Institute, Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea; Department of Internal Medicine, Seoul Metropolitan Government Seoul National University Boramae Medical Center, Seoul, South Korea
| | - Inho Kim
- Department of Internal Medicine, Seoul National University Hospital, Biomedical Research Institute, Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea.
| | - Hyeong-Joon Kim
- Department of Internal Medicine, Chonnam National University, Hwasun Hospital, Hwasun, South Korea.
| | - Dong-Yeop Shin
- Department of Internal Medicine, Seoul National University Hospital, Biomedical Research Institute, Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | | | | | - Dae-Young Kim
- Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Kyoo-Hyung Lee
- Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Jae-Sook Ahn
- Department of Internal Medicine, Chonnam National University, Hwasun Hospital, Hwasun, South Korea
| | - Jinny Park
- Department of Internal Medicine, Gachon University Gil Medical Center, Incheon, South Korea
| | - Sang-Kyun Sohn
- Department of Internal Medicine, Kyungpook National University Hospital, Daegu, South Korea
| | - Jeong-Ok Lee
- Department of Internal Medicine, Seoul National University, Bundang Hospital, Seongnam, South Korea
| | - June-Won Cheong
- Department of Internal Medicine, Yonsei University, Severance Hospital, Seoul, South Korea
| | - Kyoung Ha Kim
- Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Seoul, South Korea
| | - Hoon-Gu Kim
- Department of Internal Medicine, Gyeongsang Institute of Health Sciences, Gyeongsang National University College of Medicine and Gyeongsang National University Changwon Hospital, Changwon, South Korea
| | - Hawk Kim
- Department of Internal Medicine, Ulsan University Hospital, Ulsan, South Korea
| | - Yoo Jin Lee
- Department of Internal Medicine, Ulsan University Hospital, Ulsan, South Korea
| | - Seung-Hyun Nam
- Department of Internal Medicine, VHS Medical Center, Seoul, South Korea
| | - Young Rok Do
- Department of Internal Medicine, Keimyung University Dongsan Medical Center, Daegu, South Korea
| | - Sang-Gon Park
- Department of Internal Medicine, Chosun University Hospital, Gwangju, South Korea
| | - Seong Kyu Park
- Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, South Korea
| | - Sung Hwa Bae
- Department of Internal Medicine, Daegu Catholic University Medical Center, Daegu, South Korea
| | - Hun Ho Song
- Department of Internal Medicine, Kangdong Sacred Heart Hospital, Seoul, South Korea
| | - Doyeun Oh
- Department of Internal Medicine, CHA Bundang Medical Center, Seongnam, South Korea
| | - Chul Won Jung
- Department of Internal Medicine, Samsung Medical Center, Seoul, South Korea
| | - Seonyang Park
- Department of Internal Medicine, Inje University, Haeundae Paik Hospital, Busan, South Korea
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4
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Wölfl B, te Rietmole H, Salvioli M, Kaznatcheev A, Thuijsman F, Brown JS, Burgering B, Staňková K. The Contribution of Evolutionary Game Theory to Understanding and Treating Cancer. DYNAMIC GAMES AND APPLICATIONS 2021; 12:313-342. [PMID: 35601872 PMCID: PMC9117378 DOI: 10.1007/s13235-021-00397-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/05/2021] [Indexed: 05/05/2023]
Abstract
Evolutionary game theory mathematically conceptualizes and analyzes biological interactions where one's fitness not only depends on one's own traits, but also on the traits of others. Typically, the individuals are not overtly rational and do not select, but rather inherit their traits. Cancer can be framed as such an evolutionary game, as it is composed of cells of heterogeneous types undergoing frequency-dependent selection. In this article, we first summarize existing works where evolutionary game theory has been employed in modeling cancer and improving its treatment. Some of these game-theoretic models suggest how one could anticipate and steer cancer's eco-evolutionary dynamics into states more desirable for the patient via evolutionary therapies. Such therapies offer great promise for increasing patient survival and decreasing drug toxicity, as demonstrated by some recent studies and clinical trials. We discuss clinical relevance of the existing game-theoretic models of cancer and its treatment, and opportunities for future applications. Moreover, we discuss the developments in cancer biology that are needed to better utilize the full potential of game-theoretic models. Ultimately, we demonstrate that viewing tumors with evolutionary game theory has medically useful implications that can inform and create a lockstep between empirical findings and mathematical modeling. We suggest that cancer progression is an evolutionary competition between different cell types and therefore needs to be viewed as an evolutionary game.
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Affiliation(s)
- Benjamin Wölfl
- Department of Mathematics, University of Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Hedy te Rietmole
- Department of Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Monica Salvioli
- Department of Mathematics, University of Trento, Trento, Italy
- Department of Data Science and Knowledge Engineering, Maastricht University, Maastricht, The Netherlands
| | - Artem Kaznatcheev
- Department of Biology, University of Pennsylvania, Philadelphia, USA
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Frank Thuijsman
- Department of Data Science and Knowledge Engineering, Maastricht University, Maastricht, The Netherlands
| | - Joel S. Brown
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL USA
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL USA
| | - Boudewijn Burgering
- Department of Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands
- The Oncode Institute, Utrecht, The Netherlands
| | - Kateřina Staňková
- Department of Data Science and Knowledge Engineering, Maastricht University, Maastricht, The Netherlands
- Department of Engineering Systems and Services, Faculty of Technology, Policy and Management, Delft University of Technology, Delft, The Netherlands
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5
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Loh JW, Khiabanian H. Leukemia’s Clonal Evolution in Development, Progression, and Relapse. CURRENT STEM CELL REPORTS 2019. [DOI: 10.1007/s40778-019-00157-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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6
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Pogrebniak KL, Curtis C. Harnessing Tumor Evolution to Circumvent Resistance. Trends Genet 2018; 34:639-651. [PMID: 29903534 DOI: 10.1016/j.tig.2018.05.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/16/2018] [Accepted: 05/21/2018] [Indexed: 02/08/2023]
Abstract
High-throughput sequencing can be used to measure changes in tumor composition across space and time. Specifically, comparisons of pre- and post-treatment samples can reveal the underlying clonal dynamics and resistance mechanisms. Here, we discuss evidence for distinct modes of tumor evolution and their implications for therapeutic strategies. In addition, we consider the utility of spatial tissue sampling schemes, single-cell analysis, and circulating tumor DNA to track tumor evolution and the emergence of resistance, as well as approaches that seek to forestall resistance by targeting tumor evolution. Ultimately, characterization of the (epi)genomic, transcriptomic, and phenotypic changes that occur during tumor progression coupled with computational and mathematical modeling of tumor evolutionary dynamics may inform personalized treatment strategies.
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Affiliation(s)
- Katherine L Pogrebniak
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; http://med.stanford.edu/curtislab.html
| | - Christina Curtis
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; http://med.stanford.edu/curtislab.html.
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7
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Ojamies PN, Kontro M, Edgren H, Ellonen P, Heckman C, Porkka K, Wolf M, Kallioniemi O. Case studies investigating genetic heterogeneity between anatomically distinct bone marrow compartments in acute myeloid leukemia. Leuk Lymphoma 2018; 59:3002-3005. [PMID: 29616861 DOI: 10.1080/10428194.2018.1453067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Poojitha N Ojamies
- a Institute for Molecular Medicine Finland, FIMM, University of Helsinki , Helsinki , Finland
| | - Mika Kontro
- b Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center , Helsinki , Finland
| | | | - Pekka Ellonen
- a Institute for Molecular Medicine Finland, FIMM, University of Helsinki , Helsinki , Finland
| | - Caroline Heckman
- a Institute for Molecular Medicine Finland, FIMM, University of Helsinki , Helsinki , Finland
| | - Kimmo Porkka
- b Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center , Helsinki , Finland
| | - Maija Wolf
- a Institute for Molecular Medicine Finland, FIMM, University of Helsinki , Helsinki , Finland
| | - Olli Kallioniemi
- a Institute for Molecular Medicine Finland, FIMM, University of Helsinki , Helsinki , Finland.,d Science for Life Laboratory, Department of Oncology and Pathology , Karolinska Institutet , Solna , Sweden
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8
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Hirsch B, Endris V, Lassmann S, Weichert W, Pfarr N, Schirmacher P, Kovaleva V, Werner M, Bonzheim I, Fend F, Sperveslage J, Kaulich K, Zacher A, Reifenberger G, Köhrer K, Stepanow S, Lerke S, Mayr T, Aust DE, Baretton G, Weidner S, Jung A, Kirchner T, Hansmann ML, Burbat L, von der Wall E, Dietel M, Hummel M. Multicenter validation of cancer gene panel-based next-generation sequencing for translational research and molecular diagnostics. Virchows Arch 2018; 472:557-565. [PMID: 29374318 PMCID: PMC5924673 DOI: 10.1007/s00428-017-2288-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 12/05/2017] [Accepted: 12/19/2017] [Indexed: 12/12/2022]
Abstract
The simultaneous detection of multiple somatic mutations in the context of molecular diagnostics of cancer is frequently performed by means of amplicon-based targeted next-generation sequencing (NGS). However, only few studies are available comparing multicenter testing of different NGS platforms and gene panels. Therefore, seven partner sites of the German Cancer Consortium (DKTK) performed a multicenter interlaboratory trial for targeted NGS using the same formalin-fixed, paraffin-embedded (FFPE) specimen of molecularly pre-characterized tumors (n = 15; each n = 5 cases of Breast, Lung, and Colon carcinoma) and a colorectal cancer cell line DNA dilution series. Detailed information regarding pre-characterized mutations was not disclosed to the partners. Commercially available and custom-designed cancer gene panels were used for library preparation and subsequent sequencing on several devices of two NGS different platforms. For every case, centrally extracted DNA and FFPE tissue sections for local processing were delivered to each partner site to be sequenced with the commercial gene panel and local bioinformatics. For cancer-specific panel-based sequencing, only centrally extracted DNA was analyzed at seven sequencing sites. Subsequently, local data were compiled and bioinformatics was performed centrally. We were able to demonstrate that all pre-characterized mutations were re-identified correctly, irrespective of NGS platform or gene panel used. However, locally processed FFPE tissue sections disclosed that the DNA extraction method can affect the detection of mutations with a trend in favor of magnetic bead-based DNA extraction methods. In conclusion, targeted NGS is a very robust method for simultaneous detection of various mutations in FFPE tissue specimens if certain pre-analytical conditions are carefully considered.
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Affiliation(s)
- B Hirsch
- Campus Mitte, Institute of Pathology, Charité-University Medicine Berlin, Virchowweg 15, 10117, Berlin, Germany. .,German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.
| | - V Endris
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, University Medicine Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - S Lassmann
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute for Surgical Pathology, Medical Center, Faculty of Medicine, University of Freiburg, Breisacherstraße 115A, 79106, Freiburg, Germany
| | - W Weichert
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, Technical University Munich (TUM), Munich, Germany
| | - N Pfarr
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, Technical University Munich (TUM), Munich, Germany
| | - P Schirmacher
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, University Medicine Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - V Kovaleva
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute for Surgical Pathology, Medical Center, Faculty of Medicine, University of Freiburg, Breisacherstraße 115A, 79106, Freiburg, Germany
| | - M Werner
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute for Surgical Pathology, Medical Center, Faculty of Medicine, University of Freiburg, Breisacherstraße 115A, 79106, Freiburg, Germany
| | - I Bonzheim
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology and Neuropathology, University Hospital Tuebingen, Eberhard-Karls-University, Liebermeisterstraße 8, 72076, Tuebingen, Germany
| | - F Fend
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology and Neuropathology, University Hospital Tuebingen, Eberhard-Karls-University, Liebermeisterstraße 8, 72076, Tuebingen, Germany
| | - J Sperveslage
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology and Neuropathology, University Hospital Tuebingen, Eberhard-Karls-University, Liebermeisterstraße 8, 72076, Tuebingen, Germany
| | - K Kaulich
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Department of Neuropathology, Heinrich Heine University Duesseldorf and Biological and Medical Research Center (BMFZ), Genomics and Transcriptomics Laboratory, Heinrich Heine University Duesseldorf, 40225, Duesseldorf, Germany
| | - A Zacher
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Department of Neuropathology, Heinrich Heine University Duesseldorf and Biological and Medical Research Center (BMFZ), Genomics and Transcriptomics Laboratory, Heinrich Heine University Duesseldorf, 40225, Duesseldorf, Germany
| | - G Reifenberger
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Department of Neuropathology, Heinrich Heine University Duesseldorf and Biological and Medical Research Center (BMFZ), Genomics and Transcriptomics Laboratory, Heinrich Heine University Duesseldorf, 40225, Duesseldorf, Germany
| | - K Köhrer
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Department of Neuropathology, Heinrich Heine University Duesseldorf and Biological and Medical Research Center (BMFZ), Genomics and Transcriptomics Laboratory, Heinrich Heine University Duesseldorf, 40225, Duesseldorf, Germany
| | - S Stepanow
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Department of Neuropathology, Heinrich Heine University Duesseldorf and Biological and Medical Research Center (BMFZ), Genomics and Transcriptomics Laboratory, Heinrich Heine University Duesseldorf, 40225, Duesseldorf, Germany
| | - S Lerke
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, University Hospital Carl Gustav Carus, Fetscherstraße 74, 01307, Dresden, Germany
| | - T Mayr
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, University Hospital Carl Gustav Carus, Fetscherstraße 74, 01307, Dresden, Germany
| | - D E Aust
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, University Hospital Carl Gustav Carus, Fetscherstraße 74, 01307, Dresden, Germany
| | - G Baretton
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, University Hospital Carl Gustav Carus, Fetscherstraße 74, 01307, Dresden, Germany
| | - S Weidner
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, Ludwig-Maximilians University Munich, Thalkirchner Straße 36, 80337, Munich, Germany
| | - A Jung
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, Ludwig-Maximilians University Munich, Thalkirchner Straße 36, 80337, Munich, Germany
| | - T Kirchner
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, Ludwig-Maximilians University Munich, Thalkirchner Straße 36, 80337, Munich, Germany
| | - M L Hansmann
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Dr. Senckenberg Institute of Pathology, University Hospital, Goethe-University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - L Burbat
- Campus Mitte, Institute of Pathology, Charité-University Medicine Berlin, Virchowweg 15, 10117, Berlin, Germany.,German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - E von der Wall
- Campus Mitte, Institute of Pathology, Charité-University Medicine Berlin, Virchowweg 15, 10117, Berlin, Germany.,German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - M Dietel
- Campus Mitte, Institute of Pathology, Charité-University Medicine Berlin, Virchowweg 15, 10117, Berlin, Germany.,German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - M Hummel
- Campus Mitte, Institute of Pathology, Charité-University Medicine Berlin, Virchowweg 15, 10117, Berlin, Germany.,German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
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9
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Landau DA, Sun C, Rosebrock D, Herman SEM, Fein J, Sivina M, Underbayev C, Liu D, Hoellenriegel J, Ravichandran S, Farooqui MZH, Zhang W, Cibulskis C, Zviran A, Neuberg DS, Livitz D, Bozic I, Leshchiner I, Getz G, Burger JA, Wiestner A, Wu CJ. The evolutionary landscape of chronic lymphocytic leukemia treated with ibrutinib targeted therapy. Nat Commun 2017; 8:2185. [PMID: 29259203 PMCID: PMC5736707 DOI: 10.1038/s41467-017-02329-y] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 11/20/2017] [Indexed: 01/09/2023] Open
Abstract
Treatment of chronic lymphocytic leukemia (CLL) has shifted from chemo-immunotherapy to targeted agents. To define the evolutionary dynamics induced by targeted therapy in CLL, we perform serial exome and transcriptome sequencing for 61 ibrutinib-treated CLLs. Here, we report clonal shifts (change >0.1 in clonal cancer cell fraction, Q < 0.1) in 31% of patients during the first year of therapy, associated with adverse outcome. We also observe transcriptional downregulation of pathways mediating energy metabolism, cell cycle, and B cell receptor signaling. Known and previously undescribed mutations in BTK and PLCG2, or uncommonly, other candidate alterations are present in seventeen subjects at the time of progression. Thus, the frequently observed clonal shifts during the early treatment period and its potential association with adverse outcome may reflect greater evolutionary capacity, heralding the emergence of drug-resistant clones. In a subset of patients with chronic lymphocytic leukemia (CLL) treated with targeted agents, such as ibrutinib, drug resistant subclones emerge. Here, the authors report on transcriptional changes in CLL patients treated with ibrutinib and identify early clonal shifts associated with evolution of resistant clones.
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Affiliation(s)
- Dan A Landau
- New York Genome Center, New York, NY, 10013, USA.,Broad Institute, Cambridge, MA, 02142, USA.,Meyer Cancer Center & Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Clare Sun
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | - Sarah E M Herman
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Joshua Fein
- New York Genome Center, New York, NY, 10013, USA.,Meyer Cancer Center & Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA.,Sackler Medical School, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Mariela Sivina
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Chingiz Underbayev
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Delong Liu
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Julia Hoellenriegel
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Sarangan Ravichandran
- Advanced Biomedical Computing Center, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD, 21701, USA
| | - Mohammed Z H Farooqui
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Wandi Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | | | - Asaf Zviran
- New York Genome Center, New York, NY, 10013, USA.,Meyer Cancer Center & Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Donna S Neuberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | | | - Ivana Bozic
- Department of Applied Mathematics, University of Washington, Seattle, WA, 98195, USA
| | | | - Gad Getz
- Broad Institute, Cambridge, MA, 02142, USA
| | - Jan A Burger
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Adrian Wiestner
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Catherine J Wu
- Broad Institute, Cambridge, MA, 02142, USA. .,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. .,Harvard Medical School, Boston, MA, 02215, USA.
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