1
|
Shen Q, Gong X, Feng Y, Hu Y, Wang T, Yan W, Zhang W, Qi S, Gale RP, Chen J. Measurable residual disease (MRD)-testing in haematological cancers: A giant leap forward or sideways? Blood Rev 2024:101226. [PMID: 39164126 DOI: 10.1016/j.blre.2024.101226] [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: 06/20/2024] [Revised: 08/07/2024] [Accepted: 08/07/2024] [Indexed: 08/22/2024]
Abstract
Measurable residual disease (MRD)-testing is used in many haematological cancers to estimate relapse risk and to direct therapy. Sometimes MRD-test results are used for regulatory approval. However, some people including regulators wrongfully believe results of MRD-testing are highly accurate and of proven efficacy in directing therapy. We review MRD-testing technologies and evaluate the accuracy of MRD-testing for predicting relapse and the strength of evidence supporting efficacy of MRD-guided therapy. We show that at the individual level MRD-test results are often an inaccurate relapse predictor. Also, no convincing data indicate that increasing therapy-intensity based on a positive MRD-test reduces relapse risk or improves survival. We caution against adjusting therapy-intensity based solely on results of MRD-testing.
Collapse
Affiliation(s)
- Qiujin Shen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China; Tianjin Institutes of Health Science, Tianjin, China.
| | - Xiaowen Gong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China; Tianjin Institutes of Health Science, Tianjin, China.
| | - Yahui Feng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China; Tianjin Institutes of Health Science, Tianjin, China.
| | - Yu Hu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China; Tianjin Institutes of Health Science, Tianjin, China.
| | - Tiantian Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China; Tianjin Institutes of Health Science, Tianjin, China.
| | - Wen Yan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China; Tianjin Institutes of Health Science, Tianjin, China.
| | - Wei Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China; Tianjin Institutes of Health Science, Tianjin, China.
| | - Saibing Qi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China; Tianjin Institutes of Health Science, Tianjin, China.
| | - Robert Peter Gale
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College of Science, Technology and Medicine, London, UK.
| | - Junren Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China; Tianjin Institutes of Health Science, Tianjin, China.
| |
Collapse
|
2
|
Luna Santamaría M, Andersson D, Parris TZ, Helou K, Österlund T, Ståhlberg A. Digital RNA sequencing using unique molecular identifiers enables ultrasensitive RNA mutation analysis. Commun Biol 2024; 7:249. [PMID: 38429519 PMCID: PMC10907754 DOI: 10.1038/s42003-024-05955-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 02/22/2024] [Indexed: 03/03/2024] Open
Abstract
Mutation analysis is typically performed at the DNA level since most technical approaches are developed for DNA analysis. However, some applications, like transcriptional mutagenesis, RNA editing and gene expression analysis, require RNA analysis. Here, we combine reverse transcription and digital DNA sequencing to enable low error digital RNA sequencing. We evaluate yield, reproducibility, dynamic range and error correction rate for seven different reverse transcription conditions using multiplexed assays. The yield, reproducibility and error rate vary substantially between the specific conditions, where the yield differs 9.9-fold between the best and worst performing condition. Next, we show that error rates similar to DNA sequencing can be achieved for RNA using appropriate reverse transcription conditions, enabling detection of mutant allele frequencies <0.1% at RNA level. We also detect mutations at both DNA and RNA levels in tumor tissue using a breast cancer panel. Finally, we demonstrate that digital RNA sequencing can be applied to liquid biopsies, analyzing cell-free gene transcripts. In conclusion, we demonstrate that digital RNA sequencing is suitable for ultrasensitive RNA mutation analysis, enabling several basic research and clinical applications.
Collapse
Affiliation(s)
- Manuel Luna Santamaría
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Daniel Andersson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Toshima Z Parris
- Sahlgrenska Center for Cancer Research, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Khalil Helou
- Sahlgrenska Center for Cancer Research, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Tobias Österlund
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Genetics and Genomics, Gothenburg, Sweden
| | - Anders Ståhlberg
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Genetics and Genomics, Gothenburg, Sweden.
| |
Collapse
|
3
|
Marchetti F, Cardoso R, Chen CL, Douglas GR, Elloway J, Escobar PA, Harper T, Heflich RH, Kidd D, Lynch AM, Myers MB, Parsons BL, Salk JJ, Settivari RS, Smith-Roe SL, Witt KL, Yauk CL, Young R, Zhang S, Minocherhomji S. Error-corrected next generation sequencing - Promises and challenges for genotoxicity and cancer risk assessment. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2023; 792:108466. [PMID: 37643677 DOI: 10.1016/j.mrrev.2023.108466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 07/12/2023] [Accepted: 08/23/2023] [Indexed: 08/31/2023]
Abstract
Error-corrected Next Generation Sequencing (ecNGS) is rapidly emerging as a valuable, highly sensitive and accurate method for detecting and characterizing mutations in any cell type, tissue or organism from which DNA can be isolated. Recent mutagenicity and carcinogenicity studies have used ecNGS to quantify drug-/chemical-induced mutations and mutational spectra associated with cancer risk. ecNGS has potential applications in genotoxicity assessment as a new readout for traditional models, for mutagenesis studies in 3D organotypic cultures, and for detecting off-target effects of gene editing tools. Additionally, early data suggest that ecNGS can measure clonal expansion of mutations as a mechanism-agnostic early marker of carcinogenic potential and can evaluate mutational load directly in human biomonitoring studies. In this review, we discuss promising applications, challenges, limitations, and key data initiatives needed to enable regulatory testing and adoption of ecNGS - including for advancing safety assessment, augmenting weight-of-evidence for mutagenicity and carcinogenicity mechanisms, identifying early biomarkers of cancer risk, and managing human health risk from chemical exposures.
Collapse
Affiliation(s)
| | | | - Connie L Chen
- Health and Environmental Sciences Institute, Washington, DC, USA.
| | | | - Joanne Elloway
- Safety Sciences, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | | | - Tod Harper
- Amgen Research, Amgen Inc, Thousand Oaks, CA, USA
| | - Robert H Heflich
- US Food and Drug Administration/National Center for Toxicological Research, Jefferson, AR, USA
| | - Darren Kidd
- Labcorp Early Development Laboratories Limited, Harrogate, North Yorkshire, UK
| | | | - Meagan B Myers
- US Food and Drug Administration/National Center for Toxicological Research, Jefferson, AR, USA
| | - Barbara L Parsons
- US Food and Drug Administration/National Center for Toxicological Research, Jefferson, AR, USA
| | | | | | | | - Kristine L Witt
- NIEHS, Division of the National Toxicology Program, Research Triangle Park, NC, USA
| | | | - Robert Young
- MilliporeSigma, Rockville, MD, USA; Current: Consultant, Bethesda, MD, USA
| | | | - Sheroy Minocherhomji
- Amgen Research, Amgen Inc, Thousand Oaks, CA, USA; Current: Eli Lilly and Company, Indianapolis, IN, USA
| |
Collapse
|
4
|
Guijarro F, Garrote M, Villamor N, Colomer D, Esteve J, López-Guerra M. Novel Tools for Diagnosis and Monitoring of AML. Curr Oncol 2023; 30:5201-5213. [PMID: 37366878 DOI: 10.3390/curroncol30060395] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/11/2023] [Accepted: 05/18/2023] [Indexed: 06/28/2023] Open
Abstract
In recent years, major advances in the understanding of acute myeloid leukemia (AML) pathogenesis, together with technological progress, have led us into a new era in the diagnosis and follow-up of patients with AML. A combination of immunophenotyping, cytogenetic and molecular studies are required for AML diagnosis, including the use of next-generation sequencing (NGS) gene panels to screen all genetic alterations with diagnostic, prognostic and/or therapeutic value. Regarding AML monitoring, multiparametric flow cytometry and quantitative PCR/RT-PCR are currently the most implemented methodologies for measurable residual disease (MRD) evaluation. Given the limitations of these techniques, there is an urgent need to incorporate new tools for MRD monitoring, such as NGS and digital PCR. This review aims to provide an overview of the different technologies used for AML diagnosis and MRD monitoring and to highlight the limitations and challenges of current versus emerging tools.
Collapse
Affiliation(s)
- Francesca Guijarro
- Hematopathology Section, Pathology Department, Hospital Clinic Barcelona, 08036 Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Marta Garrote
- Hematopathology Section, Pathology Department, Hospital Clinic Barcelona, 08036 Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Neus Villamor
- Hematopathology Section, Pathology Department, Hospital Clinic Barcelona, 08036 Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Dolors Colomer
- Hematopathology Section, Pathology Department, Hospital Clinic Barcelona, 08036 Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), 08036 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Jordi Esteve
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), 08036 Barcelona, Spain
- Hematology Department, Hospital Clinic Barcelona, 08036 Barcelona, Spain
| | - Mónica López-Guerra
- Hematopathology Section, Pathology Department, Hospital Clinic Barcelona, 08036 Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), 08036 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| |
Collapse
|
5
|
Polizio AH, Park E, Walsh K. Clonal Hematopoiesis: Connecting Aging and Inflammation in Atherosclerosis. Curr Atheroscler Rep 2023; 25:105-111. [PMID: 36808603 PMCID: PMC10552081 DOI: 10.1007/s11883-023-01083-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2023] [Indexed: 02/20/2023]
Abstract
PURPOSE OF REVIEW Clonal hematopoiesis (CH) is a prevalent condition that results from the acquisition of somatic mutations in hematopoietic stem cells. When these mutations occur in "driver" genes, they can potentially confer fitness advantages to the cell, leading to a clonal expansion. While most clonal expansions of mutant cells are generally considered to be asymptomatic since they do not impact overall blood cell numbers, CH carriers display long-term risks of all-cause mortality and age-associated diseases including cardiovascular disease (CVD). This review summarizes recent findings in CH related to aging, atherosclerotic CVD, and inflammation, emphasizing epidemiological and mechanistic studies, and potential therapeutic options to treat CVDs that are promoted by CH. RECENT FINDINGS Epidemiological studies have revealed associations between CH and CVDs. Experimental studies with CH models employing the Tet2- and Jak2-mutant mouse lines display inflammasome activation and a chronic inflammatory state that leads to accelerated atherosclerotic lesion growth. A body of evidence suggests that CH represents a new causal risk factor for CVD. Studies also indicate that understanding an individual's CH status could provide guidance for personalized approaches to treat atherosclerosis and other CVDs with anti-inflammatory drugs.
Collapse
Affiliation(s)
- Ariel H Polizio
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Eunbee Park
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Kenneth Walsh
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, USA.
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA.
| |
Collapse
|
6
|
Measurable Residual Disease and Clonal Evolution in Acute Myeloid Leukemia from Diagnosis to Post-Transplant Follow-Up: The Role of Next-Generation Sequencing. Biomedicines 2023; 11:biomedicines11020359. [PMID: 36830896 PMCID: PMC9953407 DOI: 10.3390/biomedicines11020359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/24/2023] [Accepted: 01/24/2023] [Indexed: 01/28/2023] Open
Abstract
It has now been ascertained that acute myeloid leukemias-as in most type of cancers-are mixtures of various subclones, evolving by acquiring additional somatic mutations over the course of the disease. The complexity of leukemia clone architecture and the phenotypic and/or genotypic drifts that can occur during treatment explain why more than 50% of patients-in hematological remission-could relapse. Moreover, the complexity and heterogeneity of clone architecture represent a hindrance for monitoring measurable residual disease, as not all minimal residual disease monitoring methods are able to detect genetic mutations arising during treatment. Unlike with chemotherapy, which imparts a relatively short duration of selective pressure on acute myeloid leukemia clonal architecture, the immunological effect related to allogeneic hematopoietic stem cell transplant is prolonged over time and must be overcome for relapse to occur. This means that not all molecular abnormalities detected after transplant always imply inevitable relapse. Therefore, transplant represents a critical setting where a measurable residual disease-based strategy, performed during post-transplant follow-up by highly sensitive methods such as next-generation sequencing, could optimize and improve treatment outcome. The purpose of our review is to provide an overview of the role of next-generation sequencing in monitoring both measurable residual disease and clonal evolution in acute myeloid leukemia patients during the entire course of the disease, with special focus on the transplant phase.
Collapse
|
7
|
Abstract
PURPOSE OF REVIEW The development of high-throughput techniques like next-generation sequencing (NGS) has unraveled the genetic profile of cancer. In this review, we discuss the role of NGS on the diagnostic, risk stratification, and follow-up of patients with acute myeloid leukemia (AML). RECENT FINDINGS NGS has become an essential tool in clinical practice for AML management. Therefore, efforts are being made to improve its applications, automation, and turnaround time. Other high-throughput techniques, such as whole genome sequencing or RNA-sequencing, can be also used to this end. However, not all institutions may be able to implement these approaches. NGS is being investigated for measurable residual disease (MRD) assessment, especially with the development of error-correction NGS. New data analysis approaches like machine learning are being investigated in order to integrate genomic and clinical data and develop comprehensive classifications and risk scores. SUMMARY NGS has proven to be a useful approach for the analysis of genomic alterations in patients with AML, which aids patient management. Current research is being directed at reducing turnaround time and simplifying processes so that these techniques can be universally integrated into clinical practice.
Collapse
Affiliation(s)
- Marta Llop
- Molecular Biology Unit, Service of Clinical Analysis. Hospital Universitari i Politècnic La Fe
- CIBERONC CB16/12/00284
| | - Claudia Sargas
- Instituto de Investigación Sanitaria La Fe, Valencia, Spain
| | - Eva Barragán
- Molecular Biology Unit, Service of Clinical Analysis. Hospital Universitari i Politècnic La Fe
- CIBERONC CB16/12/00284
| |
Collapse
|
8
|
Guess T, Potts CR, Bhat P, Cartailler JA, Brooks A, Holt C, Yenamandra A, Wheeler FC, Savona MR, Cartailler JP, Ferrell PB. Distinct Patterns of Clonal Evolution Drive Myelodysplastic Syndrome Progression to Secondary Acute Myeloid Leukemia. Blood Cancer Discov 2022; 3:316-329. [PMID: 35522837 PMCID: PMC9610896 DOI: 10.1158/2643-3230.bcd-21-0128] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 02/22/2022] [Accepted: 05/04/2022] [Indexed: 11/16/2022] Open
Abstract
Clonal evolution in myelodysplastic syndrome (MDS) can result in clinical progression and secondary acute myeloid leukemia (sAML). To dissect changes in clonal architecture associated with this progression, we performed single-cell genotyping of paired MDS and sAML samples from 18 patients. Analysis of single-cell genotypes revealed patient-specific clonal evolution and enabled the assessment of single-cell mutational cooccurrence. We discovered that changes in clonal architecture proceed via distinct patterns, classified as static or dynamic, with dynamic clonal architectures having a more proliferative phenotype by blast count fold change. Proteogenomic analysis of a subset of patients confirmed that pathogenic mutations were primarily confined to primitive and mature myeloid cells, though we also identify rare but present mutations in lymphocyte subsets. Single-cell transcriptomic analysis of paired sample sets further identified gene sets and signaling pathways involved in two cases of progression. Together, these data define serial changes in the MDS clonal landscape with clinical and therapeutic implications. SIGNIFICANCE Precise clonal trajectories in MDS progression are made possible by single-cell genomic sequencing. Here we use this technology to uncover the patterns of clonal architecture and clonal evolution that drive the transformation to secondary AML. We further define the phenotypic and transcriptional changes of disease progression at the single-cell level. See related article by Menssen et al., p. 330 (31). See related commentary by Romine and van Galen, p. 270. This article is highlighted in the In This Issue feature, p. 265.
Collapse
Affiliation(s)
- Tiffany Guess
- Department of Medicine, Division of Hematology/Oncology, Vanderbilt University Medical Center (VUMC), Nashville, Tennessee.,Department of Pathology, Microbiology, and Immunology, VUMC, Nashville, Tennessee
| | - Chad R. Potts
- Department of Medicine, Division of Hematology/Oncology, Vanderbilt University Medical Center (VUMC), Nashville, Tennessee
| | - Pawan Bhat
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Justin A. Cartailler
- Department of Medicine, Division of Hematology/Oncology, Vanderbilt University Medical Center (VUMC), Nashville, Tennessee
| | - Austin Brooks
- Department of Medicine, Division of Hematology/Oncology, Vanderbilt University Medical Center (VUMC), Nashville, Tennessee
| | - Clinton Holt
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Ashwini Yenamandra
- Department of Pathology, Microbiology, and Immunology, VUMC, Nashville, Tennessee
| | - Ferrin C. Wheeler
- Department of Pathology, Microbiology, and Immunology, VUMC, Nashville, Tennessee
| | - Michael R. Savona
- Department of Medicine, Division of Hematology/Oncology, Vanderbilt University Medical Center (VUMC), Nashville, Tennessee.,Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee.,Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Jean-Philippe Cartailler
- Creative Data Solutions Shared Resource, Center for Stem Cell Biology, Vanderbilt University, Nashville, Tennessee
| | - P. Brent Ferrell
- Department of Medicine, Division of Hematology/Oncology, Vanderbilt University Medical Center (VUMC), Nashville, Tennessee.,Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee.,Vanderbilt-Ingram Cancer Center, Nashville, Tennessee.,Corresponding Author: P. Brent Ferrell Jr, Vanderbilt University Medical Center, 777 Preston Research Building, 2220 Pierce Avenue, Nashville, TN 37232. Phone: 615-875-8619; E-mail:
| |
Collapse
|
9
|
Hsu YC, Huang SM, Chang LC, Chen YM, Chang YH, Lin JW, Lin CC, Chen CW, Chen HY, Chiu HM, Yu SL. Screening of early-staged colorectal neoplasia by clonal hematopoiesis-based liquid biopsy and machine-learning. Am J Cancer Res 2022; 12:1088-1101. [PMID: 35411222 PMCID: PMC8984904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 02/23/2022] [Indexed: 06/14/2023] Open
Abstract
Liquid biopsy test has a better uptake for colorectal cancer (CRC) screening. However, suboptimal detection of early-staged colorectal neoplasia (CRN) limits its application. Here, we established an early-staged CRN blood test using error-corrected sequencing by comparing clonal hematopoiesis (CH) of 63 CRN patients and that of 32 controls. We identified 1,446 variants and classified the uniqueness in CRN patients. There was no significance difference in the amount of variant between CRNs and controls, but the uniqueness of variants with defective DNA mismatch repair-related mutational signature was addressed from peripheral blood in early-staged CRN patients. By machine learning approach, the early-staged CRNs was discriminated from controls with an AUC of 0.959 and an accuracy of 0.937 (95% CI, 0.863 to 0.968). The CRN predictive model was further validated by additional 20 CRNs and 10 controls and showed the accuracy, sensitivity, specificity, positive prediction value (PPV) and negative prediction value (NPV) of 0.933 (95% CI: 0.779 to 0.992), 0.95, 0.90, 0.95 and 0.90, respectively. In summary, we develop a CH-based liquid biopsy test with machine learning approach, which not only increase screening uptake but also improve the detection rate of early-staged CRN.
Collapse
Affiliation(s)
- Yin-Chen Hsu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan UniversityTaipei, Taiwan
| | - Sin-Ming Huang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan UniversityTaipei, Taiwan
| | - Li-Chun Chang
- Department of Internal Medicine, National Taiwan University HospitalTaipei, Taiwan
- Health Management Center, National Taiwan University HospitalTaipei, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan UniversityTaipei, Taiwan
| | - Yan-Ming Chen
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan UniversityTaipei, Taiwan
| | - Ya-Hsuan Chang
- Institute of Statistical Science, Academia SinicaTaipei, Taiwan
| | - Jing-Wei Lin
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan UniversityTaipei, Taiwan
| | - Chien-Chia Lin
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan UniversityTaipei, Taiwan
| | - Ching-Wen Chen
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan UniversityTaipei, Taiwan
| | - Hsuan-Yu Chen
- Institute of Statistical Science, Academia SinicaTaipei, Taiwan
| | - Han-Mo Chiu
- Department of Internal Medicine, National Taiwan University HospitalTaipei, Taiwan
- Health Management Center, National Taiwan University HospitalTaipei, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan UniversityTaipei, Taiwan
| | - Sung-Liang Yu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan UniversityTaipei, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan UniversityTaipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University HospitalTaipei, Taiwan
- Graduate Institute of Pathology, College of Medicine, National Taiwan UniversityTaipei, Taiwan
- Institute of Medical Device and Imaging, College of Medicine, National Taiwan UniversityTaipei, Taiwan
| |
Collapse
|
10
|
Abstract
Sickle cell disease (SCD) is associated with an increased risk of vascular-occlusive events and of leukemia. Clonal hematopoiesis (CH) may increase both risks. In turn, physiologic abnormalities in SCD may modify the incidence and/or distribution of genetic alterations in CH. In a recent issue of the JCI, Liggett et al. found no difference in CH rate between individuals with versus without SCD. Here we contextualize this report and discuss the complex interplay between CH and SCD with particular attention to consequences for emerging gene therapies. We further consider the limitations in our current understanding of these topics that must be addressed in order to optimize therapeutic strategies for SCD.
Collapse
Affiliation(s)
- Aaron J Stonestrom
- Human Oncology and Pathogenesis Program.,Department of Medicine, Leukemia Service
| | - Ross L Levine
- Human Oncology and Pathogenesis Program.,Department of Medicine, Leukemia Service.,Center for Epigenetics Research.,Center for Hematologic Malignancies, and.,Molecular Cancer Medicine Service, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| |
Collapse
|
11
|
Huang YH, Chen CW, Sundaramurthy V, Słabicki M, Hao D, Watson CJ, Tovy A, Reyes JM, Dakhova O, Crovetti BR, Galonska C, Lee M, Brunetti L, Zhou Y, Tatton-Brown K, Huang Y, Cheng X, Meissner A, Valk PJM, Van Maldergem L, Sanders MA, Blundell JR, Li W, Ebert BL, Goodell MA. Systematic Profiling of DNMT3A Variants Reveals Protein Instability Mediated by the DCAF8 E3 Ubiquitin Ligase Adaptor. Cancer Discov 2022; 12:220-235. [PMID: 34429321 PMCID: PMC8758508 DOI: 10.1158/2159-8290.cd-21-0560] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/12/2021] [Accepted: 08/19/2021] [Indexed: 01/09/2023]
Abstract
Clonal hematopoiesis is a prevalent age-related condition associated with a greatly increased risk of hematologic disease; mutations in DNA methyltransferase 3A (DNMT3A) are the most common driver of this state. DNMT3A variants occur across the gene with some particularly associated with malignancy, but the functional relevance and mechanisms of pathogenesis of the majority of mutations are unknown. Here, we systematically investigated the methyltransferase activity and protein stability of 253 disease-associated DNMT3A mutations, and found that 74% were loss-of-function mutations. Half of these variants exhibited reduced protein stability and, as a class, correlated with greater clonal expansion and acute myeloid leukemia development. We investigated the mechanisms underlying the instability using a CRISPR screen and uncovered regulated destruction of DNMT3A mediated by the DCAF8 E3 ubiquitin ligase adaptor. We establish a new paradigm to classify novel variants that has prognostic and potential therapeutic significance for patients with hematologic disease. SIGNIFICANCE: DNMT3A has emerged as the most important epigenetic regulator and tumor suppressor in the hematopoietic system. Our study represents a systematic and high-throughput method to characterize the molecular impact of DNMT3A missense mutations and the discovery of a regulated destruction mechanism of DNMT3A offering new prognostic and future therapeutic avenues.See related commentary by Ma and Will, p. 23.This article is highlighted in the In This Issue feature, p. 1.
Collapse
Affiliation(s)
- Yung-Hsin Huang
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas
- Stem Cells and Regenerative Medicine Center, and Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas
- Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, Texas
| | - Chun-Wei Chen
- Stem Cells and Regenerative Medicine Center, and Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas
- Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, Texas
- Interdepartmental Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, Texas
| | - Venkatasubramaniam Sundaramurthy
- Stem Cells and Regenerative Medicine Center, and Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas
- Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Mikołaj Słabicki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Division of Hematology, Brigham and Women's Hospital, and Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Dapeng Hao
- Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Caroline J Watson
- Department of Oncology, University of Cambridge, Cambridge; Early Detection Programme, CRUK Cambridge Cancer Centre, University of Cambridge, Cambridge, United Kingdom
| | - Ayala Tovy
- Stem Cells and Regenerative Medicine Center, and Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas
- Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, Texas
| | - Jaime M Reyes
- Stem Cells and Regenerative Medicine Center, and Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas
- Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Olga Dakhova
- Section of Hematology-Oncology, Department of Pediatrics, Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas
| | - Brielle R Crovetti
- Stem Cells and Regenerative Medicine Center, and Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas
- Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, Texas
| | - Christina Galonska
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Minjung Lee
- Center for Translational Cancer Research, Texas A&M University, Institute of Biosciences and Technology, Houston, Texas
| | - Lorenzo Brunetti
- Stem Cells and Regenerative Medicine Center, and Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas
- Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, Texas
| | - Yubin Zhou
- Center for Translational Cancer Research, Texas A&M University, Institute of Biosciences and Technology, Houston, Texas
| | - Katrina Tatton-Brown
- Division of Genetics and Epidemiology, Institute of Cancer Research, South West Thames Regional Genetics Service, St George's University Hospitals NHS Foundation Trust, London, United Kingdom
| | - Yun Huang
- Center for Translational Cancer Research, Texas A&M University, Institute of Biosciences and Technology, Houston, Texas
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Peter J M Valk
- Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Lionel Van Maldergem
- Centre de Génétique Humaine and Integrative and Cognitive Neuroscience Research Unit EA481, University of Franche-Comté, Besançon, France
| | - Mathijs A Sanders
- Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Jamie R Blundell
- Department of Oncology, University of Cambridge, Cambridge; Early Detection Programme, CRUK Cambridge Cancer Centre, University of Cambridge, Cambridge, United Kingdom
| | - Wei Li
- Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Division of Hematology, Brigham and Women's Hospital, and Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Margaret A Goodell
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas.
- Stem Cells and Regenerative Medicine Center, and Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas
- Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, Texas
- Interdepartmental Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| |
Collapse
|
12
|
Pincez T, Santiago R, Bittencourt H, Louis I, Bilodeau M, Rouette A, Jouan L, Landry JR, Couture F, Richer J, Teira P, Duval M, Cellot S. Intensive monitoring of minimal residual disease and chimerism after allogeneic hematopoietic stem cell transplantation for acute leukemia in children. Bone Marrow Transplant 2021; 56:2981-2989. [PMID: 34475524 DOI: 10.1038/s41409-021-01408-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 06/04/2021] [Accepted: 07/01/2021] [Indexed: 02/07/2023]
Abstract
Posttransplant leukemia detection before overt relapse is key to the success of immunotherapeutic interventions, as they are more efficient when leukemia burden is low. However, optimal schedule and monitoring methods are not well defined. We report the intensive bone marrow monitoring of minimal residual disease (MRD) using flow cytometry (FC) and nested reverse transcription polymerase chain reaction (RT-PCR) whenever a fusion transcript allowed it and chimerism by PCR at 11 timepoints in the first 2 years after transplant. Seventy-one transplants were performed in 59 consecutive children, for acute myeloid (n = 38), lymphoid (n = 31), or mixed-phenotype (n = 2) leukemia. MRD was monitored in 62 cases using FC (n = 58) and/or RT-PCR (n = 35). Sixty-seven percent of leukemia recurrences were detected before overt relapse, with a detection rate of 89% by RT-PCR and 40% by FC alone. Increased mixed chimerism was never the first evidence of recurrence. Two patients monitored by RT-PCR relapsed without previous MRD detection, one after missed scheduled evaluation and the other 4.7 years post transplant. Among the 22 cases with MRD detection without overt relapse, 19 received therapeutic interventions. Eight (42%) never relapsed. In conclusion, intensive marrow monitoring by RT-PCR effectively allows for early detection of posttransplant leukemia recurrence.
Collapse
Affiliation(s)
- Thomas Pincez
- Service d'Hématologie-Oncologie Pédiatrique, Centre de Cancérologie Charles-Bruneau, CHU Sainte-Justine, Montréal, QC, Canada
| | - Raoul Santiago
- Service d'Hématologie-Oncologie Pédiatrique, Centre de Cancérologie Charles-Bruneau, CHU Sainte-Justine, Montréal, QC, Canada
| | - Henrique Bittencourt
- Service d'Hématologie-Oncologie Pédiatrique, Centre de Cancérologie Charles-Bruneau, CHU Sainte-Justine, Montréal, QC, Canada.,Département de Pédiatrie, Faculté de Médecine, Université de Montréal, Montréal, QC, Canada
| | - Isabelle Louis
- Service d'Hématologie-Oncologie Pédiatrique, Centre de Cancérologie Charles-Bruneau, CHU Sainte-Justine, Montréal, QC, Canada
| | - Mélanie Bilodeau
- Service d'Hématologie-Oncologie Pédiatrique, Centre de Cancérologie Charles-Bruneau, CHU Sainte-Justine, Montréal, QC, Canada
| | - Alexandre Rouette
- Laboratoire de Diagnostic Moléculaire, CHU Sainte-Justine, Montréal, QC, Canada
| | - Loubna Jouan
- Centre Intégré de Génomique Clinique Pédiatrique, CHU Sainte-Justine, Montréal, QC, Canada
| | - Josette-Renée Landry
- Département de Pédiatrie, Faculté de Médecine, Université de Montréal, Montréal, QC, Canada
| | - Françoise Couture
- Laboratoire de Diagnostic Moléculaire, CHU Sainte-Justine, Montréal, QC, Canada
| | - Johanne Richer
- Service d'Hématologie-Oncologie Pédiatrique, Centre de Cancérologie Charles-Bruneau, CHU Sainte-Justine, Montréal, QC, Canada
| | - Pierre Teira
- Service d'Hématologie-Oncologie Pédiatrique, Centre de Cancérologie Charles-Bruneau, CHU Sainte-Justine, Montréal, QC, Canada.,Département de Pédiatrie, Faculté de Médecine, Université de Montréal, Montréal, QC, Canada
| | - Michel Duval
- Service d'Hématologie-Oncologie Pédiatrique, Centre de Cancérologie Charles-Bruneau, CHU Sainte-Justine, Montréal, QC, Canada. .,Département de Pédiatrie, Faculté de Médecine, Université de Montréal, Montréal, QC, Canada.
| | - Sonia Cellot
- Service d'Hématologie-Oncologie Pédiatrique, Centre de Cancérologie Charles-Bruneau, CHU Sainte-Justine, Montréal, QC, Canada.,Département de Pédiatrie, Faculté de Médecine, Université de Montréal, Montréal, QC, Canada
| |
Collapse
|
13
|
Yang RK, Toruner GA, Wang W, Fang H, Issa GC, Wang L, Quesada AE, Thakral B, Patel KP, Peng G, Liu S, Yin CC, Borthakur G, Tang Z, Wang SA, Miranda RN, Khoury JD, Medeiros LJ, Tang G. CBFB Break-Apart FISH Testing: An Analysis of 1629 AML Cases with a Focus on Atypical Findings and Their Implications in Clinical Diagnosis and Management. Cancers (Basel) 2021; 13:5354. [PMID: 34771519 PMCID: PMC8582369 DOI: 10.3390/cancers13215354] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 10/20/2021] [Accepted: 10/23/2021] [Indexed: 02/05/2023] Open
Abstract
Fluorescence in situ hybridization (FISH) is a confirmatory test to establish a diagnosis of inv(16)/t(16;16) AML. However, incidental findings and their clinical diagnostic implication have not been systemically studied. We studied 1629 CBFB FISH cases performed in our institution, 262 (16.1%), 1234 (75.7%), and 133 (8.2%) were reported as positive, normal, and abnormal, respectively. The last included CBFB copy number changes (n = 120) and atypical findings such as 3'CBFB deletion (n = 11), 5'CBFB deletion (n = 1), and 5'CBFB gain (n = 1). Correlating with CBFB-MYH11 RT-PCR results, totally 271 CBFB rearrangement cases were identified, including five with discrepancies between FISH and RT-PCR due to new partner genes (n = 3), insertion (n = 1), or rare CBFB-MYH11 variant (n = 1) and eight with 3'CBFB deletion. All cases with atypical findings and/or discrepancies presented clinical diagnostic challenges. Correlating FISH signal patterns and karyotypes, additional chromosome 16 aberrations (AC16As) show impacts on the re-definition of a complex karyotype and prognostic prediction. The CBFB rearrangement but not all AC16As will be detected by NGS-based methods. Therefore, FISH testing is currently still needed to provide a quick and straightforward confirmatory inv(16)/t(16;16) AML diagnosis and additional information related to clinical management.
Collapse
Affiliation(s)
- Richard K. Yang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.K.Y.); (G.A.T.); (W.W.); (H.F.); (A.E.Q.); (B.T.); (K.P.P.); (C.C.Y.); (S.A.W.); (R.N.M.); (J.D.K.); (L.J.M.); (G.T.)
| | - Gokce A. Toruner
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.K.Y.); (G.A.T.); (W.W.); (H.F.); (A.E.Q.); (B.T.); (K.P.P.); (C.C.Y.); (S.A.W.); (R.N.M.); (J.D.K.); (L.J.M.); (G.T.)
| | - Wei Wang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.K.Y.); (G.A.T.); (W.W.); (H.F.); (A.E.Q.); (B.T.); (K.P.P.); (C.C.Y.); (S.A.W.); (R.N.M.); (J.D.K.); (L.J.M.); (G.T.)
| | - Hong Fang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.K.Y.); (G.A.T.); (W.W.); (H.F.); (A.E.Q.); (B.T.); (K.P.P.); (C.C.Y.); (S.A.W.); (R.N.M.); (J.D.K.); (L.J.M.); (G.T.)
| | - Ghayas C. Issa
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (G.C.I.); (G.B.)
| | - Lulu Wang
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (L.W.); (G.P.)
| | - Andrés E. Quesada
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.K.Y.); (G.A.T.); (W.W.); (H.F.); (A.E.Q.); (B.T.); (K.P.P.); (C.C.Y.); (S.A.W.); (R.N.M.); (J.D.K.); (L.J.M.); (G.T.)
| | - Beenu Thakral
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.K.Y.); (G.A.T.); (W.W.); (H.F.); (A.E.Q.); (B.T.); (K.P.P.); (C.C.Y.); (S.A.W.); (R.N.M.); (J.D.K.); (L.J.M.); (G.T.)
| | - Keyur P. Patel
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.K.Y.); (G.A.T.); (W.W.); (H.F.); (A.E.Q.); (B.T.); (K.P.P.); (C.C.Y.); (S.A.W.); (R.N.M.); (J.D.K.); (L.J.M.); (G.T.)
| | - Guang Peng
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (L.W.); (G.P.)
| | - Shujuan Liu
- Parkview Regional Medical Center, Allied Hospital Pathologists, Fort Wayne, IN 46845, USA;
| | - C. Cameron Yin
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.K.Y.); (G.A.T.); (W.W.); (H.F.); (A.E.Q.); (B.T.); (K.P.P.); (C.C.Y.); (S.A.W.); (R.N.M.); (J.D.K.); (L.J.M.); (G.T.)
| | - Gautam Borthakur
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (G.C.I.); (G.B.)
| | - Zhenya Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.K.Y.); (G.A.T.); (W.W.); (H.F.); (A.E.Q.); (B.T.); (K.P.P.); (C.C.Y.); (S.A.W.); (R.N.M.); (J.D.K.); (L.J.M.); (G.T.)
| | - Sa A. Wang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.K.Y.); (G.A.T.); (W.W.); (H.F.); (A.E.Q.); (B.T.); (K.P.P.); (C.C.Y.); (S.A.W.); (R.N.M.); (J.D.K.); (L.J.M.); (G.T.)
| | - Roberto N. Miranda
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.K.Y.); (G.A.T.); (W.W.); (H.F.); (A.E.Q.); (B.T.); (K.P.P.); (C.C.Y.); (S.A.W.); (R.N.M.); (J.D.K.); (L.J.M.); (G.T.)
| | - Joseph D. Khoury
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.K.Y.); (G.A.T.); (W.W.); (H.F.); (A.E.Q.); (B.T.); (K.P.P.); (C.C.Y.); (S.A.W.); (R.N.M.); (J.D.K.); (L.J.M.); (G.T.)
| | - L. Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.K.Y.); (G.A.T.); (W.W.); (H.F.); (A.E.Q.); (B.T.); (K.P.P.); (C.C.Y.); (S.A.W.); (R.N.M.); (J.D.K.); (L.J.M.); (G.T.)
| | - Guilin Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.K.Y.); (G.A.T.); (W.W.); (H.F.); (A.E.Q.); (B.T.); (K.P.P.); (C.C.Y.); (S.A.W.); (R.N.M.); (J.D.K.); (L.J.M.); (G.T.)
| |
Collapse
|
14
|
Barwe SP, Gopalakrisnapillai A, Mahajan N, Druley TE, Kolb EA, Crowgey EL. Strong concordance between RNA structural and single nucleotide variants identified via next generation sequencing techniques in primary pediatric leukemia and patient-derived xenograft samples. Genomics Inform 2020; 18:e6. [PMID: 32224839 PMCID: PMC7120351 DOI: 10.5808/gi.2020.18.1.e6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/27/2020] [Accepted: 02/27/2020] [Indexed: 02/07/2023] Open
Abstract
Acute leukemia represents the most common pediatric malignancy comprising diverse subtypes with varying prognosis and treatment outcomes. New and targeted treatment options are warranted for this disease. Patient-derived xenograft (PDX) models are increasingly being used for preclinical testing of novel treatment modalities. A novel approach involving targeted error-corrected RNA sequencing using ArcherDX HemeV2 kit was employed to compare 25 primary pediatric acute leukemia samples and their corresponding PDX samples. A comparison of the primary samples and PDX samples revealed a high concordance between single nucleotide variants and gene fusions whereas other complex structural variants were not as consistent. The presence of gene fusions representing the major driver mutations at similar allelic frequencies in PDX samples compared to primary samples and over multiple passages confirms the utility of PDX models for preclinical drug testing. Characterization and tracking of these novel cryptic fusions and exonal variants in PDX models is critical in assessing response to potential new therapies.
Collapse
Affiliation(s)
- Sonali P. Barwe
- Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA
| | | | - Nitin Mahajan
- Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Todd E. Druley
- Washington University School of Medicine, St. Louis, MO 63110, USA
| | - E. Anders Kolb
- Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA
| | - Erin L. Crowgey
- Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA
| |
Collapse
|