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Gutierrez-Rodrigues F, Beerman I, Groarke EM, Patel BA, Spitofsky N, Dillon LW, Raffo DQ, Hourigan CS, Kajigaya S, Ferrucci L, Young NS. Utility of plasma cell-free DNA for de novo detection and quantification of clonal hematopoiesis. Haematologica 2022; 107:1815-1826. [PMID: 34587721 PMCID: PMC9335099 DOI: 10.3324/haematol.2021.279230] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/23/2021] [Indexed: 12/03/2022] Open
Abstract
Although cell-free DNA (cfDNA) tests have emerged as a potential non-invasive alternative to bone marrow biopsies for monitoring clonal hematopoiesis in hematologic diseases, whether commercial cfDNA assays can be implemented for the detection and quantification of de novo clonal hematopoiesis in place of blood cells is uncertain. In this study, peripheral plasma cfDNA samples available from patients with aplastic anemia (n=25) or myelodysplastic syndromes (n=27) and a healthy cohort (n=107) were screened for somatic variants in genes related to hematologic malignancies using a Clinical Laboratory Improvement Amendments-certified panel. Results were further compared to DNA sequencing of matched blood cells. In reported results, 85% of healthy subjects, 36% of patients with aplastic anemia and 74% of patients with myelodysplastic syndromes were found to have somatic cfDNA variants, most frequently in DNMT3A, TET2, ASXL1 and SF3B1. However, concordance between cfDNA and blood cell findings was poor for the detection of clonal hematopoiesis when the allele frequency of the variants was <10%, which was mostly observed in the healthy and aplastic anemia cohorts but not in patients with myelodysplastic syndromes. After filtering data for potential artifacts due to low variant allele frequency and sequencing depth, the frequency of clonal hematopoiesis in cfDNA from healthy individuals and patients with aplastic anemia decreased to 52% and 20%, respectively. cfDNA and matched blood cells were not interchangeable for tracking changes in allele burdens as their agreement by Bland-Altman analysis was poor. A commercial cfDNA assay had good performance for de novo detection of clonal hematopoiesis in myelodysplastic syndromes, but showed no advantage over blood cells in diseases with low allele burdens or in healthy individuals.
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Affiliation(s)
| | - Isabel Beerman
- Translational Gerontology Branch, National Institute on Aging, NIH, BRC, Baltimore, Maryland
| | - Emma M Groarke
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland 20892-1202
| | - Bhavisha A Patel
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland 20892-1202
| | - Nina Spitofsky
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland 20892-1202
| | - Laura W Dillon
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland 20892-1202
| | - Diego Quinones Raffo
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland 20892-1202
| | - Christopher S Hourigan
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland 20892-1202
| | - Sachiko Kajigaya
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland 20892-1202
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, NIH, BRC, Baltimore, Maryland
| | - Neal S Young
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland 20892-1202
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Ip A, Della Pia A, Kim GY(G, Lofters J, Behrmann J, Patel D, Kats S, Estella JJ, De Dios I, Ma W, Pecora AL, Goy AH, Koprivnikar J, McCloskey JK, Albitar M. Reliability of Cell-Free DNA and Targeted NGS in Predicting Chromosomal Abnormalities of Patients With Myeloid Neoplasms. Front Oncol 2022; 12:923809. [PMID: 35774119 PMCID: PMC9238409 DOI: 10.3389/fonc.2022.923809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/11/2022] [Indexed: 11/17/2022] Open
Abstract
Introduction Cytogenetic analysis is important for stratifying patients with various neoplasms. We explored the use of targeted next generation sequencing (NGS) in detecting chromosomal structural abnormalities or copy number variations (CNVs) in patients with myeloid neoplasms. Methods Plasma cell-free DNA (cfDNA) from 2821 myeloid or lymphoid neoplasm patients were collected. cfDNA was sequenced using a 275 gene panel. CNVkit software was used for analyzing and visualizing CNVs. Cytogenetic data from corresponding bone marrow (BM) samples was available on 89 myeloid samples. Results Of the 2821 samples, 1539 (54.5%) showed evidence of mutations consistent with the presence of neoplastic clones in circulation. Of these 1539 samples, 906 (59%) showed abnormalities associated with myeloid neoplasms and 633 (41%) with lymphoid neoplasms. Chromosomal structural abnormalities in cfDNA were detected in 146 (16%) myeloid samples and 76 (12%) lymphoid samples. Upon comparison of the myeloid samples with 89 BM patients, NGS testing was able to reliably detect chromosomal gain or loss, except for fusion abnormalities. When cytogenetic abnormalities were classified according to prognostic classes, there was a complete (100%) concordance between cfDNA NGS data and cytogenetic data. Conclusions This data shows that liquid biopsy using targeted NGS is reliable in detecting chromosomal structural abnormalities in myeloid neoplasms. In specific circumstances, targeted NGS may be reliable and efficient to provide adequate information without the need for BM biopsy considering broad mutation profiling can be obtained through adequate sequencing within the same test. Overall, this study supports the use of liquid biopsy for early diagnosis and monitoring of patients with myeloid neoplasms.
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Affiliation(s)
- Andrew Ip
- Hackensack University Medical Center, Oncology, Hackensack, NJ, United States
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, United States
- Hackensack Meridian School of Medicine, Oncology, Nutley, NJ, United States
| | - Alexandra Della Pia
- Hackensack University Medical Center, Oncology, Hackensack, NJ, United States
- Ernest Mario School of Pharmacy at Rutgers University, Department of Pharmacy Practice and Administration, Piscataway, NJ, United States
| | - Gee Youn (Geeny) Kim
- Hackensack University Medical Center, Oncology, Hackensack, NJ, United States
- Ernest Mario School of Pharmacy at Rutgers University, Department of Pharmacy Practice and Administration, Piscataway, NJ, United States
| | - Jason Lofters
- Englewood Health Internal Medicine Residency Program, Englewood, NJ, United States
| | - James Behrmann
- Hackensack Meridian School of Medicine, Oncology, Nutley, NJ, United States
| | - Dylon Patel
- Hackensack Meridian School of Medicine, Oncology, Nutley, NJ, United States
| | - Simone Kats
- Ernest Mario School of Pharmacy at Rutgers University, Department of Pharmacy Practice and Administration, Piscataway, NJ, United States
| | | | - Ivan De Dios
- Genomic Testing Cooperative, Hematology, Irvine, CA, United States
| | - Wanlong Ma
- Genomic Testing Cooperative, Hematology, Irvine, CA, United States
| | - Andrew L. Pecora
- Hackensack University Medical Center, Oncology, Hackensack, NJ, United States
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, United States
- Hackensack Meridian School of Medicine, Oncology, Nutley, NJ, United States
| | - Andre H. Goy
- Hackensack University Medical Center, Oncology, Hackensack, NJ, United States
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, United States
- Hackensack Meridian School of Medicine, Oncology, Nutley, NJ, United States
| | - Jamie Koprivnikar
- Hackensack University Medical Center, Oncology, Hackensack, NJ, United States
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, United States
| | - James K. McCloskey
- Hackensack University Medical Center, Oncology, Hackensack, NJ, United States
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, United States
| | - Maher Albitar
- Genomic Testing Cooperative, Hematology, Irvine, CA, United States
- *Correspondence: Maher Albitar,
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Abnormal Proteomics Profile of Plasma Reveals the Immunological Pathogenesis of Severe Aplastic Anemia. DISEASE MARKERS 2022; 2022:3700691. [PMID: 35571618 PMCID: PMC9106528 DOI: 10.1155/2022/3700691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 04/13/2022] [Indexed: 11/18/2022]
Abstract
Severe aplastic anemia (SAA) is an immune-mediated bone marrow failure characterized by pancytopenia. This study was aimed at uncovering proteins of plasma that were differentially expressed in SAA patients. 8 SAA patients and 8 health controls were enrolled and detected by data independent acquisition (DIA) technology. 154 differential expression proteins (DEPs) in plasma of SAA patients were identified. GO and KEGG analyses indicated DEPs were mainly involved in the immune system process. Specifically, C-C motif chemokine 18 (CCL18), matrix metalloproteinase-3 (MMP3), histidine-rich glycoprotein (HRG), and lactotransferrin (lactoferrin (Lf)) may play an important role in the immune pathogenesis of SAA. CCL18, MMP3, HRG, and Lf might be potential biomarkers for SAA.
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Somatic mutations in lymphocytes in patients with immune-mediated aplastic anemia. Leukemia 2021; 35:1365-1379. [PMID: 33785863 PMCID: PMC8102188 DOI: 10.1038/s41375-021-01231-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 02/04/2021] [Accepted: 03/12/2021] [Indexed: 12/31/2022]
Abstract
The prevalence and functional impact of somatic mutations in nonleukemic T cells is not well characterized, although clonal T-cell expansions are common. In immune-mediated aplastic anemia (AA), cytotoxic T-cell expansions are shown to participate in disease pathogenesis. We investigated the mutation profiles of T cells in AA by a custom panel of 2533 genes. We sequenced CD4+ and CD8+ T cells of 24 AA patients and compared the results to 20 healthy controls and whole-exome sequencing of 37 patients with AA. Somatic variants were common both in patients and healthy controls but enriched to AA patients’ CD8+ T cells, which accumulated most mutations on JAK-STAT and MAPK pathways. Mutation burden was associated with CD8+ T-cell clonality, assessed by T-cell receptor beta sequencing. To understand the effect of mutations, we performed single-cell sequencing of AA patients carrying STAT3 or other mutations in CD8+ T cells. STAT3 mutated clone was cytotoxic, clearly distinguishable from other CD8+ T cells, and attenuated by successful immunosuppressive treatment. Our results suggest that somatic mutations in T cells are common, associate with clonality, and can alter T-cell phenotype, warranting further investigation of their role in the pathogenesis of AA.
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Vicente A, Patel BA, Gutierrez-Rodrigues F, Groarke E, Giudice V, Lotter J, Feng X, Kajigaya S, Weinstein B, Barranta E, Olnes MJ, Parikh AR, Albitar M, Wu CO, Shalhoub R, Calvo KR, Townsley DM, Scheinberg P, Dunbar CE, Young NS, Winkler T. Eltrombopag monotherapy can improve hematopoiesis in patients with low to intermediate risk-1 myelodysplastic syndrome. Haematologica 2020; 105:2785-2794. [PMID: 33256377 PMCID: PMC7716353 DOI: 10.3324/haematol.2020.249995] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Myelodysplastic syndromes (MDS) are a group of clonal myeloid disorders characterized by low blood counts and a propensity to develop acute myeloid leukemia. The management of lowerrisk (LR) MDS with persistent cytopenias remains suboptimal. Eltrombopag, a thrombopoietin-receptor agonist, can improve platelet counts in LR-MDS and trilineage hematopoiesis in aplastic anemia. We conducted a phase II dose modification study to investigate the safety and efficacy of eltrombopag in LR-MDS. The eltrombopag dose was escalated from 50 mg/day to a maximum of 150 mg/day over a period of 16 weeks. The primary efficacy endpoint was hematologic response at 16-20 weeks. Eleven of 25 (44%) patients responded; five and six patients had uni- or bi-lineage hematologic responses, respectively. The predictors of response were presence of a paroxysmal nocturnal hemoglobinuria clone, marrow hypocellularity, thrombocytopenia, and elevated plasma thrombopoietin levels at study entry. The safety profile was consistent with that found in previous eltrombopag studies in aplastic anemia; no patients discontinued the drug due to adverse events. Three patients developed reversible grade 3 liver toxicity and one patient had increased reticulin fibrosis. Ten patients discontinued eltrombopag after achieving a robust response (median time 16 months); four of them reinitiated eltrombopag because of declining blood counts, and all attained a second robust response. Six patients had disease progression not associated with expansion of mutated clones and no patient progressed to develop acute myeloid leukemia on study. In conclusion, eltrombopag was well-tolerated and effective in restoring hematopoiesis in some patients with low or intermediate-1 risk MDS. This study was registered at clinicaltrials.gov as #NCT00932156.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Colin O Wu
- Office of Biostatistics Research, National Institutes of Health
| | - Ruba Shalhoub
- Office of Biostatistics Research, National Institutes of Health
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Cescon DW, Bratman SV, Chan SM, Siu LL. Circulating tumor DNA and liquid biopsy in oncology. ACTA ACUST UNITED AC 2020; 1:276-290. [DOI: 10.1038/s43018-020-0043-5] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/18/2020] [Indexed: 02/07/2023]
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Bingham N, Spencer A. The role of cell free DNA and liquid biopsies in haematological conditions. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2020; 3:521-531. [PMID: 35582436 PMCID: PMC8992501 DOI: 10.20517/cdr.2019.93] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cell free nucleic acids (CFNAs) are nucleic acids released from cells that circulate within bodily fluids. Recent advances in molecular techniques have led the ability to interrogate CFNAs in a clinically meaningful way, for example the identification and assessment of foetal CFNAs in maternal blood, allowing minimally invasive testing for foetal genetic abnormalities. The majority of CFNAs arise from haemopoietic cells, making it a particularly rich source of genetic information in haematological conditions. Furthermore, the innate genetic heterogeneity of haematological malignancies, as epitomised by multiple myeloma, lend itself well to “liquid biopsies”. This approach promises to provide a more wholistic assessment of whole disease genetics, especially when contrasted against the current gold-standard of single site tissue biopsies. This review briefly summarises the definitions and physiology of CFNAs, both cell free DNA (cfDNA) and extracellular RNA (exRNA), before exploring the literature surrounding the current and future roles of cfDNA in the haematological malignancies and patient care.
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Affiliation(s)
- Nicholas Bingham
- Australian Centre for Blood Diseases, Monash University, Victoria 3181, Australia
| | - Andrew Spencer
- Australian Centre for Blood Diseases, Monash University, Victoria 3181, Australia
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Aguilera-Diaz A, Vazquez I, Ariceta B, Mañú A, Blasco-Iturri Z, Palomino-Echeverría S, Larrayoz MJ, García-Sanz R, Prieto-Conde MI, del Carmen Chillón M, Alfonso-Pierola A, Prosper F, Fernandez-Mercado M, Calasanz MJ. Assessment of the clinical utility of four NGS panels in myeloid malignancies. Suggestions for NGS panel choice or design. PLoS One 2020; 15:e0227986. [PMID: 31978184 PMCID: PMC6980571 DOI: 10.1371/journal.pone.0227986] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 01/04/2020] [Indexed: 12/17/2022] Open
Abstract
The diagnosis of myeloid neoplasms (MN) has significantly evolved through the last few decades. Next Generation Sequencing (NGS) is gradually becoming an essential tool to help clinicians with disease management. To this end, most specialized genetic laboratories have implemented NGS panels targeting a number of different genes relevant to MN. The aim of the present study is to evaluate the performance of four different targeted NGS gene panels based on their technical features and clinical utility. A total of 32 patient bone marrow samples were accrued and sequenced with 3 commercially available panels and 1 custom panel. Variants were classified by two geneticists based on their clinical relevance in MN. There was a difference in panel’s depth of coverage. We found 11 discordant clinically relevant variants between panels, with a trend to miss long insertions. Our data show that there is a high risk of finding different mutations depending on the panel of choice, due both to the panel design and the data analysis method. Of note, CEBPA, CALR and FLT3 genes, remains challenging the use of NGS for diagnosis of MN in compliance with current guidelines. Therefore, conventional molecular testing might need to be kept in place for the correct diagnosis of MN for now.
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Affiliation(s)
- Almudena Aguilera-Diaz
- Advanced Genomics Laboratory, Hemato-Oncology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
| | - Iria Vazquez
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
- Hematological Diseases Laboratory, CIMA LAB Diagnostics, University of Navarra, Pamplona, Spain
| | - Beñat Ariceta
- Hematological Diseases Laboratory, CIMA LAB Diagnostics, University of Navarra, Pamplona, Spain
| | - Amagoia Mañú
- Hematological Diseases Laboratory, CIMA LAB Diagnostics, University of Navarra, Pamplona, Spain
| | - Zuriñe Blasco-Iturri
- Hematological Diseases Laboratory, CIMA LAB Diagnostics, University of Navarra, Pamplona, Spain
| | | | - María José Larrayoz
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
- Hematological Diseases Laboratory, CIMA LAB Diagnostics, University of Navarra, Pamplona, Spain
| | - Ramón García-Sanz
- Hematology Department, University Hospital of Salamanca, IBSAL and CIBERONC, Salamanca, Spain
| | | | | | - Ana Alfonso-Pierola
- Hematology Department, Clinica Universidad de Navarra (CUN), Pamplona, Spain
| | - Felipe Prosper
- Advanced Genomics Laboratory, Hemato-Oncology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
- Hematology Department, Clinica Universidad de Navarra (CUN), Pamplona, Spain
| | - Marta Fernandez-Mercado
- Advanced Genomics Laboratory, Hemato-Oncology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
- Hematological Diseases Laboratory, CIMA LAB Diagnostics, University of Navarra, Pamplona, Spain
- Biomedical Engineering Department, School of Engineering, University of Navarra, San Sebastian, Spain
- * E-mail: ,
| | - María José Calasanz
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
- Hematological Diseases Laboratory, CIMA LAB Diagnostics, University of Navarra, Pamplona, Spain
- Scientific Co-Director of CIMA LAB Diagnostics, CIMA LAB Diagnostics, University of Navarra, Pamplona, Spain
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