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Zhang L, Deeb G, Deeb KK, Vale C, Peker Barclift D, Papadantonakis N. Measurable (Minimal) Residual Disease in Myelodysplastic Neoplasms (MDS): Current State and Perspectives. Cancers (Basel) 2024; 16:1503. [PMID: 38672585 PMCID: PMC11048433 DOI: 10.3390/cancers16081503] [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: 02/17/2024] [Revised: 04/08/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Myelodysplastic Neoplasms (MDS) have been traditionally studied through the assessment of blood counts, cytogenetics, and morphology. In recent years, the introduction of molecular assays has improved our ability to diagnose MDS. The role of Measurable (minimal) Residual Disease (MRD) in MDS is evolving, and molecular and flow cytometry techniques have been used in several studies. In this review, we will highlight the evolving concept of MRD in MDS, outline the various techniques utilized, and provide an overview of the studies reporting MRD and the correlation with outcomes.
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Affiliation(s)
- Linsheng Zhang
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - George Deeb
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kristin K. Deeb
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Colin Vale
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Deniz Peker Barclift
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nikolaos Papadantonakis
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
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Kim D, Kim S, Song H, Gwak D, Min S, Byun JM, Koh Y, Hong J, Yoon S, Yun H, Shin D. Pursuing dynamics of minimal residual leukemic subclones in relapsed and refractory acute myeloid leukemia during conventional therapy. Cancer Med 2024; 13:e7182. [PMID: 38591109 PMCID: PMC11002636 DOI: 10.1002/cam4.7182] [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: 12/08/2023] [Revised: 02/23/2024] [Accepted: 03/29/2024] [Indexed: 04/10/2024] Open
Abstract
BACKGROUND Acute myeloid leukemia (AML) is characterized by clonal heterogeneity, leading to frequent relapses and drug resistance despite intensive clinical therapy. Although AML's clonal architecture has been addressed in many studies, practical monitoring of dynamic changes in those subclones during relapse and treatment is still understudied. METHOD Fifteen longitudinal bone marrow (BM) samples were collected from three relapsed and refractory (R/R) AML patients. Using droplet digital polymerase chain reaction (ddPCR), the frequencies of patient's leukemic variants were assessed in seven cell populations that were isolated from each BM sample based on cellular phenotypes. By quantifying mutant clones at the diagnosis, remission, and relapse stages, the distribution of AML subclones was sequentially monitored. RESULTS Minimal residual (MR) leukemic subclones exhibit heterogeneous distribution among BM cell populations, including mature leukocyte populations. During AML progression, these subclones undergo active phenotypic transitions and repopulate into distinct cell population regardless of normal hematopoiesis hierarchic order. Of these, MR subclones in progenitor populations of patient BM predominantly carry MR leukemic properties, leading to more robust expansion and stubborn persistence than those in mature populations. Moreover, a minor subset of MR leukemic subclones could be sustained at an extremely low frequency without clonal expansion during relapse. CONCLUSIONS In this study, we observed treatment persistent MR leukemic subclones and their phenotypic changes during the treatment process of R/R AML patients. This underscores the importance of preemptive inhibition of clonal promiscuity in R/R AML, proposing a practical method for monitoring AML MR subclones.
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Affiliation(s)
- Dongchan Kim
- Cancer Research InstituteSeoul National University College of MedicineSeoulRepublic of Korea
- Center for Medical InnovationSeoul National University HospitalSeoulRepublic of Korea
| | - Sheehyun Kim
- Center for Medical InnovationSeoul National University HospitalSeoulRepublic of Korea
- Center for Precision MedicineSeoul National University HospitalSeoulRepublic of Korea
| | - Hyojin Song
- Center for Medical InnovationSeoul National University HospitalSeoulRepublic of Korea
- Center for Precision MedicineSeoul National University HospitalSeoulRepublic of Korea
| | - Daehyeon Gwak
- Cancer Research InstituteSeoul National University College of MedicineSeoulRepublic of Korea
- Center for Medical InnovationSeoul National University HospitalSeoulRepublic of Korea
| | - Suji Min
- Cancer Research InstituteSeoul National University College of MedicineSeoulRepublic of Korea
- Center for Medical InnovationSeoul National University HospitalSeoulRepublic of Korea
| | - Ja Min Byun
- Cancer Research InstituteSeoul National University College of MedicineSeoulRepublic of Korea
- Center for Medical InnovationSeoul National University HospitalSeoulRepublic of Korea
- Department of Internal MedicineSeoul National University HospitalSeoulRepublic of Korea
| | - Youngil Koh
- Cancer Research InstituteSeoul National University College of MedicineSeoulRepublic of Korea
- Center for Medical InnovationSeoul National University HospitalSeoulRepublic of Korea
- Department of Internal MedicineSeoul National University HospitalSeoulRepublic of Korea
| | - Junshik Hong
- Cancer Research InstituteSeoul National University College of MedicineSeoulRepublic of Korea
- Center for Medical InnovationSeoul National University HospitalSeoulRepublic of Korea
- Department of Internal MedicineSeoul National University HospitalSeoulRepublic of Korea
| | - Sung‐Soo Yoon
- Cancer Research InstituteSeoul National University College of MedicineSeoulRepublic of Korea
- Center for Medical InnovationSeoul National University HospitalSeoulRepublic of Korea
- Department of Internal MedicineSeoul National University HospitalSeoulRepublic of Korea
| | - Hongseok Yun
- Center for Medical InnovationSeoul National University HospitalSeoulRepublic of Korea
- Center for Precision MedicineSeoul National University HospitalSeoulRepublic of Korea
| | - Dong‐Yeop Shin
- Cancer Research InstituteSeoul National University College of MedicineSeoulRepublic of Korea
- Center for Medical InnovationSeoul National University HospitalSeoulRepublic of Korea
- Department of Internal MedicineSeoul National University HospitalSeoulRepublic of Korea
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Schwede M, Jahn K, Kuipers J, Miles LA, Bowman RL, Robinson T, Furudate K, Uryu H, Tanaka T, Sasaki Y, Ediriwickrema A, Benard B, Gentles AJ, Levine R, Beerenwinkel N, Takahashi K, Majeti R. Mutation order in acute myeloid leukemia identifies uncommon patterns of evolution and illuminates phenotypic heterogeneity. Leukemia 2024:10.1038/s41375-024-02211-z. [PMID: 38467769 DOI: 10.1038/s41375-024-02211-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 03/13/2024]
Abstract
Acute myeloid leukemia (AML) has a poor prognosis and a heterogeneous mutation landscape. Although common mutations are well-studied, little research has characterized how the sequence of mutations relates to clinical features. Using published, single-cell DNA sequencing data from three institutions, we compared clonal evolution patterns in AML to patient characteristics, disease phenotype, and outcomes. Mutation trees, which represent the order of select mutations, were created for 207 patients from targeted panel sequencing data using 1 639 162 cells, 823 mutations, and 275 samples. In 224 distinct orderings of mutated genes, mutations related to DNA methylation typically preceded those related to cell signaling, but signaling-first cases did occur, and had higher peripheral cell counts, increased signaling mutation homozygosity, and younger patient age. Serial sample analysis suggested that NPM1 and DNA methylation mutations provide an advantage to signaling mutations in AML. Interestingly, WT1 mutation evolution shared features with signaling mutations, such as WT1-early being proliferative and occurring in younger individuals, trends that remained in multivariable regression. Some mutation orderings had a worse prognosis, but this was mediated by unfavorable mutations, not mutation order. These findings add a dimension to the mutation landscape of AML, identifying uncommon patterns of leukemogenesis and shedding light on heterogeneous phenotypes.
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Affiliation(s)
- Matthew Schwede
- Department of Medicine, Division of Hematology, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, School of Medicine, Stanford, CA, USA
| | - Katharina Jahn
- Biomedical Data Science, Institute for Computer Science, Free University of Berlin, Berlin, Germany
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jack Kuipers
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Linde A Miles
- Division of Experimental Hematology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - Robert L Bowman
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Troy Robinson
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ken Furudate
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hidetaka Uryu
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tomoyuki Tanaka
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yuya Sasaki
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Asiri Ediriwickrema
- Department of Medicine, Division of Hematology, Stanford University, Stanford, CA, USA
- Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Brooks Benard
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Andrew J Gentles
- Department of Biomedical Data Science, Stanford University, School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Medicine, Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA, USA
| | - Ross Levine
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Koichi Takahashi
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Ravindra Majeti
- Department of Medicine, Division of Hematology, Stanford University, Stanford, CA, USA.
- Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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Campillo-Marcos I, Casado-Pelaez M, Davalos V, Ferrer G, Mata C, Mereu E, Roué G, Valcárcel D, Molero A, Zamora L, Xicoy B, Palomo L, Acha P, Manzanares A, Tobiasson M, Hellström-Lindberg E, Solé F, Esteller M. Single-cell Multiomics Analysis of Myelodysplastic Syndromes and Clinical Response to Hypomethylating Therapy. CANCER RESEARCH COMMUNICATIONS 2024; 4:365-377. [PMID: 38300528 PMCID: PMC10860538 DOI: 10.1158/2767-9764.crc-23-0389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/18/2023] [Accepted: 01/26/2024] [Indexed: 02/02/2024]
Abstract
Alterations in epigenetic marks, such as DNA methylation, represent a hallmark of cancer that has been successfully exploited for therapy in myeloid malignancies. Hypomethylating agents (HMA), such as azacitidine, have become standard-of-care therapy to treat myelodysplastic syndromes (MDS), myeloid neoplasms that can evolve into acute myeloid leukemia. However, our capacity to identify who will respond to HMAs, and the duration of response, remains limited. To shed light on this question, we have leveraged the unprecedented analytic power of single-cell technologies to simultaneously map the genome and immunoproteome of MDS samples throughout clinical evolution. We were able to chart the architecture and evolution of molecular clones in precious paired bone marrow MDS samples at diagnosis and posttreatment to show that a combined imbalance of specific cell lineages with diverse mutational profiles is associated with the clinical response of patients with MDS to hypomethylating therapy. SIGNIFICANCE MDS are myeloid clonal hemopathies with a low 5-year survival rate, and approximately half of the cases do not respond to standard HMA therapy. Our innovative single-cell multiomics approach offers valuable biological insights and potential biomarkers associated with the demethylating agent efficacy. It also identifies vulnerabilities that can be targeted using personalized combinations of small drugs and antibodies.
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Affiliation(s)
- Ignacio Campillo-Marcos
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
| | - Marta Casado-Pelaez
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
| | - Veronica Davalos
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
| | - Gerardo Ferrer
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
| | - Caterina Mata
- Single Cell Unit, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Elisabetta Mereu
- Cellular Systems Genomics Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Gael Roué
- Lymphoma Translational Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
| | - David Valcárcel
- Department of Hematology, Experimental Hematology Group, Vall d'Hebron Institute of Oncology (VHIO), University Hospital Vall d'Hebron, Barcelona, Catalonia, Spain
| | - Antonieta Molero
- Department of Hematology, Experimental Hematology Group, Vall d'Hebron Institute of Oncology (VHIO), University Hospital Vall d'Hebron, Barcelona, Catalonia, Spain
| | - Lurdes Zamora
- Department of Hematology, ICO-IJC-Hospital Germans Trias i Pujol, UAB, Badalona, Spain
- Myelodysplastic Syndromes Research Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
| | - Blanca Xicoy
- Department of Hematology, ICO-IJC-Hospital Germans Trias i Pujol, UAB, Badalona, Spain
- Myelodysplastic Syndromes Research Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
| | - Laura Palomo
- Department of Hematology, Experimental Hematology Group, Vall d'Hebron Institute of Oncology (VHIO), University Hospital Vall d'Hebron, Barcelona, Catalonia, Spain
- Myelodysplastic Syndromes Research Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
| | - Pamela Acha
- Myelodysplastic Syndromes Research Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
| | - Ana Manzanares
- Myelodysplastic Syndromes Research Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
| | - Magnus Tobiasson
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden; Medical Unit Hematology, Karolinska University Hospital, Stockholm, Sweden
| | - Eva Hellström-Lindberg
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden; Medical Unit Hematology, Karolinska University Hospital, Stockholm, Sweden
| | - Francesc Solé
- Myelodysplastic Syndromes Research Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
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Ve K, R R, Cac P, A K, E T, Cc S, Ab O. Single Nucleotide Polymorphism (SNP) and Antibody-based Cell Sorting (SNACS): A tool for demultiplexing single-cell DNA sequencing data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.07.579345. [PMID: 38370638 PMCID: PMC10871358 DOI: 10.1101/2024.02.07.579345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Motivation Recently, single-cell DNA sequencing (scDNA-seq) and multi-modal profiling with the addition of cell-surface antibodies (scDAb-seq) have provided key insights into cancer heterogeneity. Scaling these technologies across large patient cohorts, however, is cost and time prohibitive. Multiplexing, in which cells from unique patients are pooled into a single experiment, offers a possible solution. While multiplexing methods exist for scRNAseq, accurate demultiplexing in scDNAseq remains an unmet need. Results Here, we introduce SNACS: Single-Nucleotide Polymorphism (SNP) and Antibody-based Cell Sorting. SNACS relies on a combination of patient-level cell-surface identifiers and natural variation in genetic polymorphisms to demultiplex scDNAseq data. We demonstrated the performance of SNACS on a dataset consisting of multi-sample experiments from patients with leukemia where we knew truth from single-sample experiments from the same patients. Using SNACS, accuracy ranged from 0.948 - 0.991 vs 0.552 - 0.934 using demultiplexing methods from the single-cell literature.
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Affiliation(s)
- Kennedy Ve
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA, 94143
| | - Roy R
- Hellen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA, 94143
| | - Peretz Cac
- Hellen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA, 94143
- Division of Hematology and Oncology, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA, 94143
| | - Koh A
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA, 94143
| | - Tran E
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA, 94143
| | - Smith Cc
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA, 94143
- Hellen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA, 94143
| | - Olshen Ab
- Hellen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA, 94143
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA, 94143
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Bae SG, Kim HJ, Kim MY, Kim DDH, Shin SI, Ahn JS, Park J. Identification of Cell Type-Specific Effects of DNMT3A Mutations on Relapse in Acute Myeloid Leukemia. Mol Cells 2023; 46:611-626. [PMID: 37853686 PMCID: PMC10590706 DOI: 10.14348/molcells.2023.0093] [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: 05/30/2023] [Revised: 07/27/2023] [Accepted: 08/01/2023] [Indexed: 10/20/2023] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease caused by distinctive mutations in individual patients; therefore, each patient may display different cell-type compositions. Although most patients with AML achieve complete remission (CR) through intensive chemotherapy, the likelihood of relapse remains high. Several studies have attempted to characterize the genetic and cellular heterogeneity of AML; however, our understanding of the cellular heterogeneity of AML remains limited. In this study, we performed single-cell RNA sequencing (scRNAseq) of bone marrow-derived mononuclear cells obtained from same patients at different AML stages (diagnosis, CR, and relapse). We found that hematopoietic stem cells (HSCs) at diagnosis were abnormal compared to normal HSCs. By improving the detection of the DNMT3A R882 mutation with targeted scRNAseq, we identified that DNMT3A-mutant cells that mainly remained were granulocyte-monocyte progenitors (GMPs) or lymphoid-primed multipotential progenitors (LMPPs) from CR to relapse and that DNMT3A-mutant cells have gene signatures related to AML and leukemic cells. Copy number variation analysis at the single-cell level indicated that the cell type that possesses DNMT3A mutations is an important factor in AML relapse and that GMP and LMPP cells can affect relapse in patients with AML. This study advances our understanding of the role of DNMT3A in AML relapse and our approach can be applied to predict treatment outcomes.
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Affiliation(s)
- Seo-Gyeong Bae
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
| | - Hyeoung-Joon Kim
- Department of Internal Medicine, Chonnam National University Hwasun Hospital, Chonnam National University, Hwasun 58128, Korea
- Genomic Research Center for Hematopoietic Diseases, Chonnam National University Hwasun Hospital, Hwasun 58128, Korea
| | - Mi Yeon Kim
- Department of Internal Medicine, Chonnam National University Hwasun Hospital, Chonnam National University, Hwasun 58128, Korea
| | - Dennis Dong Hwan Kim
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - So-I Shin
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
| | - Jae-Sook Ahn
- Department of Internal Medicine, Chonnam National University Hwasun Hospital, Chonnam National University, Hwasun 58128, Korea
- Genomic Research Center for Hematopoietic Diseases, Chonnam National University Hwasun Hospital, Hwasun 58128, Korea
| | - Jihwan Park
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
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7
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Peroni E, Randi ML, Rosato A, Cagnin S. Acute myeloid leukemia: from NGS, through scRNA-seq, to CAR-T. dissect cancer heterogeneity and tailor the treatment. J Exp Clin Cancer Res 2023; 42:259. [PMID: 37803464 PMCID: PMC10557350 DOI: 10.1186/s13046-023-02841-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 09/25/2023] [Indexed: 10/08/2023] Open
Abstract
Acute myeloid leukemia (AML) is a malignant blood cancer with marked cellular heterogeneity due to altered maturation and differentiation of myeloid blasts, the possible causes of which are transcriptional or epigenetic alterations, impaired apoptosis, and excessive cell proliferation. This neoplasm has a high rate of resistance to anticancer therapies and thus a high risk of relapse and mortality because of both the biological diversity of the patient and intratumoral heterogeneity due to the acquisition of new somatic changes. For more than 40 years, the old gold standard "one size fits all" treatment approach included intensive chemotherapy treatment with anthracyclines and cytarabine.The manuscript first traces the evolution of the understanding of the pathology from the 1970s to the present. The enormous strides made in its categorization prove to be crucial for risk stratification, enabling an increasingly personalized diagnosis and treatment approach.Subsequently, we highlight how, over the past 15 years, technological advances enabling single cell RNA sequencing and T-cell modification based on the genomic tools are affecting the classification and treatment of AML. At the dawn of the new millennium, the advent of high-throughput next-generation sequencing technologies has enabled the profiling of patients evidencing different facets of the same disease, stratifying risk, and identifying new possible therapeutic targets that have subsequently been validated. Currently, the possibility of investigating tumor heterogeneity at the single cell level, profiling the tumor at the time of diagnosis or after treatments exist. This would allow the identification of underrepresented cellular subclones or clones resistant to therapeutic approaches and thus responsible for post-treatment relapse that would otherwise be difficult to detect with bulk investigations on the tumor biopsy. Single-cell investigation will then allow even greater personalization of therapy to the genetic and transcriptional profile of the tumor, saving valuable time and dangerous side effects. The era of personalized medicine will take a huge step forward through the disclosure of each individual piece of the complex puzzle that is cancer pathology, to implement a "tailored" therapeutic approach based also on engineered CAR-T cells.
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Affiliation(s)
- Edoardo Peroni
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, Padova, 35128, Italy.
| | - Maria Luigia Randi
- First Medical Clinic, Department of Medicine-DIMED, University of Padua, Padua, Italy
| | - Antonio Rosato
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, Padova, 35128, Italy
- Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy
| | - Stefano Cagnin
- Department of Biology, University of Padova, Padova, 35131, Italy
- CIR-Myo Myology Center, University of Padova, Padova, 35131, Italy
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8
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Robinson TM, Bowman RL, Persaud S, Liu Y, Neigenfind R, Gao Q, Zhang J, Sun X, Miles LA, Cai SF, Sciambi A, Llanso A, Famulare C, Goldberg A, Dogan A, Roshal M, Levine RL, Xiao W. Single-cell genotypic and phenotypic analysis of measurable residual disease in acute myeloid leukemia. SCIENCE ADVANCES 2023; 9:eadg0488. [PMID: 37729414 PMCID: PMC10881057 DOI: 10.1126/sciadv.adg0488] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 07/21/2023] [Indexed: 09/22/2023]
Abstract
Measurable residual disease (MRD), defined as the population of cancer cells that persist following therapy, serves as the critical reservoir for disease relapse in acute myeloid leukemia and other malignancies. Understanding the biology enabling MRD clones to resist therapy is necessary to guide the development of more effective curative treatments. Discriminating between residual leukemic clones, preleukemic clones, and normal precursors remains a challenge with current MRD tools. Here, we developed a single-cell MRD (scMRD) assay by combining flow cytometric enrichment of the targeted precursor/blast population with integrated single-cell DNA sequencing and immunophenotyping. Our scMRD assay shows high sensitivity of approximately 0.01%, deconvolutes clonal architecture, and provides clone-specific immunophenotypic data. In summary, our scMRD assay enhances MRD detection and simultaneously illuminates the clonal architecture of clonal hematopoiesis/preleukemic and leukemic cells surviving acute myeloid leukemia therapy.
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Affiliation(s)
- Troy M. Robinson
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert L. Bowman
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sonali Persaud
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ying Liu
- Department of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rosemary Neigenfind
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Qi Gao
- Department of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jingping Zhang
- Department of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xiaotian Sun
- Department of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Linde A. Miles
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sheng F. Cai
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Christopher Famulare
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aaron Goldberg
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Dogan
- Department of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mikhail Roshal
- Department of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ross L. Levine
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wenbin Xiao
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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9
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Schulz E, Aplan PD, Freeman SD, Pavletic SZ. Moving toward a conceptualization of measurable residual disease in myelodysplastic syndromes. Blood Adv 2023; 7:4381-4394. [PMID: 37267435 PMCID: PMC10432617 DOI: 10.1182/bloodadvances.2023010098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/03/2023] [Accepted: 05/22/2023] [Indexed: 06/04/2023] Open
Abstract
Approximately 90% of patients with myelodysplastic syndromes (MDSs) have somatic mutations that are known or suspected to be oncogenic in the malignant cells. The genetic risk stratification of MDSs has evolved substantially with the introduction of the clinical molecular international prognostic scoring system, which establishes next-generation sequencing at diagnosis as a standard of care. Furthermore, the International Consensus Classification of myeloid neoplasms and acute leukemias has refined the MDS diagnostic criteria with the introduction of a new MDS/acute myeloid leukemia category. Monitoring measurable residual disease (MRD) has historically been used to define remission status, improve relapse prediction, and determine the efficacy of antileukemic drugs in patients with acute and chronic leukemias. However, in contrast to leukemias, assessment of MRD, including tracking of patient-specific mutations, has not yet been formally defined as a biomarker for MDS. This article summarizes current evidence and challenges and provides a conceptual framework for incorporating MRD into the treatment of MDS and future clinical trials.
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Affiliation(s)
- Eduard Schulz
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Myeloid Malignancies Program, National Institutes of Health, Bethesda, MD
| | - Peter D. Aplan
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Myeloid Malignancies Program, National Institutes of Health, Bethesda, MD
| | - Sylvie D. Freeman
- Department of Clinical Immunology, Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Steven Z. Pavletic
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Myeloid Malignancies Program, National Institutes of Health, Bethesda, MD
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10
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Bonnett SA, Rosenbloom AB, Ong GT, Conner M, Rininger AB, Newhouse D, New F, Phan CQ, Ilcisin S, Sato H, Lyssand JS, Geiss G, Beechem JM. Ultra High-plex Spatial Proteogenomic Investigation of Giant Cell Glioblastoma Multiforme Immune Infiltrates Reveals Distinct Protein and RNA Expression Profiles. CANCER RESEARCH COMMUNICATIONS 2023; 3:763-779. [PMID: 37377888 PMCID: PMC10155752 DOI: 10.1158/2767-9764.crc-22-0396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 01/20/2023] [Accepted: 04/04/2023] [Indexed: 06/29/2023]
Abstract
A deeper understanding of complex biological processes, including tumor development and immune response, requires ultra high-plex, spatial interrogation of multiple "omes". Here we present the development and implementation of a novel spatial proteogenomic (SPG) assay on the GeoMx Digital Spatial Profiler platform with next-generation sequencing readout that enables ultra high-plex digital quantitation of proteins (>100-plex) and RNA (whole transcriptome, >18,000-plex) from a single formalin-fixed paraffin-embedded (FFPE) sample. This study highlighted the high concordance, R > 0.85 and <15% change in sensitivity between the SPG assay and the single-analyte assays on various cell lines and tissues from human and mouse. Furthermore, we demonstrate that the SPG assay was reproducible across multiple users. When used in conjunction with advanced cellular neighborhood segmentation, distinct immune or tumor RNA and protein targets were spatially resolved within individual cell subpopulations in human colorectal cancer and non-small cell lung cancer. We used the SPG assay to interrogate 23 different glioblastoma multiforme (GBM) samples across four pathologies. The study revealed distinct clustering of both RNA and protein based on pathology and anatomic location. The in-depth investigation of giant cell glioblastoma multiforme (gcGBM) revealed distinct protein and RNA expression profiles compared with that of the more common GBM. More importantly, the use of spatial proteogenomics allowed simultaneous interrogation of critical protein posttranslational modifications alongside whole transcriptomic profiles within the same distinct cellular neighborhoods. Significance We describe ultra high-plex spatial proteogenomics; profiling whole transcriptome and high-plex proteomics on a single FFPE tissue section with spatial resolution. Investigation of gcGBM versus GBM revealed distinct protein and RNA expression profiles.
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Affiliation(s)
| | | | | | - Mark Conner
- NanoString Technologies, Seattle, Washington
| | | | | | - Felicia New
- NanoString Technologies, Seattle, Washington
| | - Chi Q. Phan
- NanoString Technologies, Seattle, Washington
| | | | - Hiromi Sato
- NanoString Technologies, Seattle, Washington
| | | | - Gary Geiss
- NanoString Technologies, Seattle, Washington
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11
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Ogbue O, Unlu S, Ibodeng GO, Singh A, Durmaz A, Visconte V, Molina JC. Single-Cell Next-Generation Sequencing to Monitor Hematopoietic Stem-Cell Transplantation: Current Applications and Future Perspectives. Cancers (Basel) 2023; 15:cancers15092477. [PMID: 37173944 PMCID: PMC10177286 DOI: 10.3390/cancers15092477] [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: 04/02/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS) are genetically complex and diverse diseases. Such complexity makes challenging the monitoring of response to treatment. Measurable residual disease (MRD) assessment is a powerful tool for monitoring response and guiding therapeutic interventions. This is accomplished through targeted next-generation sequencing (NGS), as well as polymerase chain reaction and multiparameter flow cytometry, to detect genomic aberrations at a previously challenging leukemic cell concentration. A major shortcoming of NGS techniques is the inability to discriminate nonleukemic clonal hematopoiesis. In addition, risk assessment and prognostication become more complicated after hematopoietic stem-cell transplantation (HSCT) due to genotypic drift. To address this, newer sequencing techniques have been developed, leading to more prospective and randomized clinical trials aiming to demonstrate the prognostic utility of single-cell next-generation sequencing in predicting patient outcomes following HSCT. This review discusses the use of single-cell DNA genomics in MRD assessment for AML/MDS, with an emphasis on the HSCT time period, including the challenges with current technologies. We also touch on the potential benefits of single-cell RNA sequencing and analysis of accessible chromatin, which generate high-dimensional data at the cellular resolution for investigational purposes, but not currently used in the clinical setting.
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Affiliation(s)
- Olisaemeka Ogbue
- Internal Medicine, Cleveland Clinic Fairview Hospital, Cleveland, OH 44111, USA
| | - Serhan Unlu
- Internal Medicine, Cleveland Clinic Fairview Hospital, Cleveland, OH 44111, USA
| | - Gogo-Ogute Ibodeng
- Internal Medicine, Infirmary Health's Thomas Hospital, Fairhope, AL 36607, USA
| | - Abhay Singh
- Department of Hematology Medical Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Arda Durmaz
- Department of Translational Hematology and Oncology Research, Cleveland Clinic Taussig Cancer Center, Cleveland, OH 44106, USA
| | - Valeria Visconte
- Department of Translational Hematology and Oncology Research, Cleveland Clinic Taussig Cancer Center, Cleveland, OH 44106, USA
| | - John C Molina
- Department of Hematology Medical Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH 44106, USA
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12
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Zavras PD, Sinanidis I, Tsakiroglou P, Karantanos T. Understanding the Continuum between High-Risk Myelodysplastic Syndrome and Acute Myeloid Leukemia. Int J Mol Sci 2023; 24:ijms24055018. [PMID: 36902450 PMCID: PMC10002503 DOI: 10.3390/ijms24055018] [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: 01/31/2023] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
Myelodysplastic syndrome (MDS) is a clonal hematopoietic neoplasm characterized by bone marrow dysplasia, failure of hematopoiesis and variable risk of progression to acute myeloid leukemia (AML). Recent large-scale studies have demonstrated that distinct molecular abnormalities detected at earlier stages of MDS alter disease biology and predict progression to AML. Consistently, various studies analyzing these diseases at the single-cell level have identified specific patterns of progression strongly associated with genomic alterations. These pre-clinical results have solidified the conclusion that high-risk MDS and AML arising from MDS or AML with MDS-related changes (AML-MRC) represent a continuum of the same disease. AML-MRC is distinguished from de novo AML by the presence of certain chromosomal abnormalities, such as deletion of 5q, 7/7q, 20q and complex karyotype and somatic mutations, which are also present in MDS and carry crucial prognostic implications. Recent changes in the classification and prognostication of MDS and AML by the International Consensus Classification (ICC) and the World Health Organization (WHO) reflect these advances. Finally, a better understanding of the biology of high-risk MDS and the mechanisms of disease progression have led to the introduction of novel therapeutic approaches, such as the addition of venetoclax to hypomethylating agents and, more recently, triplet therapies and agents targeting specific mutations, including FLT3 and IDH1/2. In this review, we analyze the pre-clinical data supporting that high-risk MDS and AML-MRC share the same genetic abnormalities and represent a continuum, describe the recent changes in the classification of these neoplasms and summarize the advances in the management of patients with these neoplasms.
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13
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VanOudenhove J, Halene S, Mendez L. Is it the time to integrate novel sequencing technologies into clinical practice? Curr Opin Hematol 2023; 30:70-77. [PMID: 36602939 DOI: 10.1097/moh.0000000000000754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
PURPOSE OF REVIEW The aim of this study was to provide insight into how novel next-generation sequencing (NGS) techniques are set to revolutionize clinical practice. RECENT FINDINGS Advances in sequencing technologies have focused on improved capture of mutations and reads and cellular resolution. Both short and long read DNA sequencing technology are being refined and combined in novel ways with other multiomic approaches to gain unprecedented biological insight into disease. Single-cell (sc)DNA-seq and integrated scDNA-seq with immunophenotyping provide granular information on disease composition such as clonal hierarchy, co-mutation status, zygosity, clonal diversity and genotype phenotype correlations. These and other techniques can identify rare cell populations providing the opportunity for increased sensitivity in measurable residual disease monitoring and precise characterization of residual clones permitting distinction of leukemic from pre/nonmalignant clones. SUMMARY Increasing genetics-based mechanistic insights and classification of myeloid diseases along with a decrease in the cost of high-throughput NGS mean novel sequencing technologies are closer to being a reality in standard clinical practice. These technologies are poised to improve diagnostics, our ability to monitor treatment response and minimal residual disease and allow the study of premalignant conditions such as clonal haematopoiesis.
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Affiliation(s)
- Jennifer VanOudenhove
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center and Smilow Cancer Hospital, Yale University School of Medicine, New Haven, Connecticut, USA
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14
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Ediriwickrema A, Gentles AJ, Majeti R. Single-cell genomics in AML: extending the frontiers of AML research. Blood 2023; 141:345-355. [PMID: 35926108 PMCID: PMC10082362 DOI: 10.1182/blood.2021014670] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/06/2022] [Accepted: 07/23/2022] [Indexed: 01/31/2023] Open
Abstract
The era of genomic medicine has allowed acute myeloid leukemia (AML) researchers to improve disease characterization, optimize risk-stratification systems, and develop new treatments. Although there has been significant progress, AML remains a lethal cancer because of its remarkably complex and plastic cellular architecture. This degree of heterogeneity continues to pose a major challenge, because it limits the ability to identify and therefore eradicate the cells responsible for leukemogenesis and treatment failure. In recent years, the field of single-cell genomics has led to unprecedented strides in the ability to characterize cellular heterogeneity, and it holds promise for the study of AML. In this review, we highlight advancements in single-cell technologies, outline important shortcomings in our understanding of AML biology and clinical management, and discuss how single-cell genomics can address these shortcomings as well as provide unique opportunities in basic and translational AML research.
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Affiliation(s)
- Asiri Ediriwickrema
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA
- Cancer Institute, Stanford University School of Medicine, Stanford, CA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA
| | - Andrew J. Gentles
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA
| | - Ravindra Majeti
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA
- Cancer Institute, Stanford University School of Medicine, Stanford, CA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA
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15
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Achieving MRD negativity in AML: how important is this and how do we get there? HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2022; 2022:9-14. [PMID: 36485093 PMCID: PMC9820122 DOI: 10.1182/hematology.2022000323] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Multiple studies have demonstrated that patients with acute myeloid leukemia (AML) who have measurable residual disease (MRD) detected during or after treatment have higher relapse rates and worse survival than similar patients testing negative. Updated response criteria for AML reflect the understanding that achievement of complete remission (CR) with no detectable MRD using high-sensitivity tests represents a superior response over conventional cytomorphological CR alone. Potential use cases for AML MRD testing are diverse and include patient selection for clinical trials and therapeutic assignment, early relapse detection and intervention during sequential monitoring, and drug development, including deep quantification for antileukemia efficacy and as a surrogate endpoint for overall survival in regulatory approvals. Testing for AML MRD has not, however, been harmonized, and many technical and clinical questions remain. The implications of MRD test results for specific therapeutic combinations, molecular subsets, test types, treatment time points, sample types, and patient characteristics remain incompletely defined. No perfect AML MRD test or testing strategy currently exists, and the evidence basis for clinical recommendations in this rare disease is sparse but growing. It is unproven whether conversion of an MRD test result from positive to negative by additional therapeutic intervention improves relapse risk and survival. Several national- and international-level consortia have recently been initiated to advance the generation and collection of evidence to support the use of AML MRD testing in clinical practice, drug development, and regulatory approvals.
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16
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Gasic V, Karan-Djurasevic T, Pavlovic D, Zukic B, Pavlovic S, Tosic N. Diagnostic and Therapeutic Implications of Long Non-Coding RNAs in Leukemia. Life (Basel) 2022; 12:1770. [PMID: 36362925 PMCID: PMC9695865 DOI: 10.3390/life12111770] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/27/2022] [Accepted: 10/29/2022] [Indexed: 08/26/2023] Open
Abstract
Leukemia is a heterogenous group of hematological malignancies categorized in four main types (acute myeloid leukemia (AML), acute lymphoblastic leukemia (ALL), chronic myeloid leukemia (CML) and chronic lymphocytic leukemia (CLL). Several cytogenetic and molecular markers have become a part of routine analysis for leukemia patients. These markers have been used in diagnosis, risk-stratification and targeted therapy application. Recent studies have indicated that numerous regulatory RNAs, such as long non-coding RNAs (lncRNAs), have a role in tumor initiation and progression. When it comes to leukemia, data for lncRNA involvement in its etiology, progression, diagnosis, treatment and prognosis is limited. The aim of this review is to summarize research data on lncRNAs in different types of leukemia, on their expression pattern, their role in leukemic transformation and disease progression. The usefulness of this information in the clinical setting, i.e., for diagnostic and prognostic purposes, will be emphasized. Finally, how particular lncRNAs could be used as potential targets for the application of targeted therapy will be considered.
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Affiliation(s)
- Vladimir Gasic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia
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17
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The Landscape of Nucleic-Acid-Based Aptamers for Treatment of Hematologic Malignancies: Challenges and Future Directions. Bioengineering (Basel) 2022; 9:bioengineering9110635. [PMID: 36354547 PMCID: PMC9687288 DOI: 10.3390/bioengineering9110635] [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: 09/29/2022] [Revised: 10/19/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022] Open
Abstract
Hematologic malignancies, including leukemia, lymphoma, myeloproliferative disorder and plasma cell neoplasia, are genetically heterogeneous and characterized by an uncontrolled proliferation of their corresponding cell lineages in the bone marrow, peripheral blood, tissues or plasma. Although there are many types of therapeutic drugs (e.g., TKIs, chemotherapy drugs) available for treatment of different malignancies, the relapse, drug resistance and severe side effects due to the lack of selectivity seriously limit their clinical application. Currently, although antibody–drug conjugates have been well established as able to target and deliver highly potent chemotherapy agents into cancer cells for the reduction of damage to healthy cells and have achieved success in leukemia treatment, they still also have shortcomings such as high cost, high immunogenicity and low stability. Aptamers are ssDNA or RNA oligonucleotides that can also precisely deliver therapeutic agents into cancer cells through specifically recognizing the membrane protein on cancer cells, which is similar to the capabilities of monoclonal antibodies. Aptamers exhibit higher binding affinity, lower immunogenicity and higher thermal stability than antibodies. Therefore, in this review we comprehensively describe recent advances in the development of aptamer–drug conjugates (ApDCs) with cytotoxic payload through chemical linkers or direct incorporation, as well as further introduce the latest promising aptamers-based therapeutic strategies such as aptamer–T cell therapy and aptamer–PROTAC, clarifying their bright application, development direction and challenges in the treatment of hematologic malignancies.
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18
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Weeda V, Mestrum SGC, Leers MPG. Flow Cytometric Identification of Hematopoietic and Leukemic Blast Cells for Tailored Clinical Follow-Up of Acute Myeloid Leukemia. Int J Mol Sci 2022; 23:ijms231810529. [PMID: 36142442 PMCID: PMC9506284 DOI: 10.3390/ijms231810529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Acute myeloid leukemia (AML) is a myeloid malignancy that is characterized by the accumulation of leukemic blast cells, which originate from hematopoietic stem cells that have undergone leukemic transformation and/or are more mature progenitors that have gained stemness features. Currently, no consensus exists for the flow cytometric identification of normal blast cells and their leukemic counterparts by their antigenic expression profile. Differentiating between the benign cells and the malignant cells is crucial for the further deployment of immunophenotype panels for the clinical follow-up of AML patients. This review provides an overview of immunophenotypic markers that allow the identification of leukemic blast cells in the bone marrow with multiparameter flow cytometry. This technique allows the identification of hematopoietic blast cells at the level of maturing cells by their antigen expression profile. While aberrant antigen expression of a single immunophenotypic marker cell cannot be utilized in order to differentiate leukemic blast cells from normal blast cells, combinations of multiple immunophenotypic markers can enable the distinction of normal and leukemic blast cells. The identification of these markers has provided new perspectives for tailored clinical follow-up, including therapy management, diagnostics, and prognostic purposes. The immunophenotypic marker panels, however, should be developed by carefully considering the variable antigen marker expression profile of individual patients.
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Affiliation(s)
- Vera Weeda
- Department of Clinical Chemistry & Hematology, Zuyderland Medical Centre, 6162BG Sittard-Geleen, The Netherlands
| | - Stefan G. C. Mestrum
- Department of Clinical Chemistry & Hematology, Zuyderland Medical Centre, 6162BG Sittard-Geleen, The Netherlands
- Department of Molecular Cell Biology, GROW-School for Oncology and Reproduction, Maastricht University Medical Centre, 6200MD Maastricht, The Netherlands
- Correspondence: ; Tel.: +31-6-36176124
| | - Math P. G. Leers
- Department of Clinical Chemistry & Hematology, Zuyderland Medical Centre, 6162BG Sittard-Geleen, The Netherlands
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19
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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: 16] [Impact Index Per Article: 8.0] [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.
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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:
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20
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Kim T, Lee H, Capo‐Chichi J, Chang MH, Yoo YS, Basi G, Ketela T, Smith AC, Tierens A, Zhang Z, Minden MD, Kim DDH. Single cell proteogenomic sequencing identifies a relapse-fated AML subclone carrying FLT3-ITD with CN-LOH at chr13q. EJHAEM 2022; 3:426-433. [PMID: 35846029 PMCID: PMC9175792 DOI: 10.1002/jha2.390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 01/09/2023]
Abstract
Internal tandem duplication of the Feline McDonough Sarcoma (FMS)-like tyrosine kinase 3 (FLT3-ITD) is one of the most clinically relevant mutations in acute myeloid leukemia (AML), with a high FLT3-ITD allelic ratio (AR) (≥0.5) being strongly associated with poor prognosis. FLT3-ITDs are heterogeneous, varying in size and location, with some patients having multiple FLT3-ITDs. Bulk cell-based approaches are limited in their ability to reveal the clonal structure in such cases. Using single-cell proteogenomic sequencing (ScPGseq), we attempted to identify a relapse-fated subclone in an AML case with mutations in WT1, NPM1, and FLT3 tyrosine kinase domain and two FLT3-ITDs (21 bp and 39 bp) (low AR) at presentation, then relapsed only with WT1 and NPM1 mutations and one FLT3-ITD (high AR). This relapse-fated subclone at presentation (∼2.1% of sequenced cells) was characterized by the presence of a homozygous 21 bp FLT3-ITD resulting from copy neutral loss of heterozygosity (CN-LOH) of chr13q and an aberrant, immature myeloid cell surface signature, contrast to the cell surface phenotype at presentation. In contrast to results from multicolor flow-cytometry, ScPGseq not only enabled the early detection of rare relapse-fated subclone showing immature myeloid signature but also highlighted the presence of homozygous 21 bp FLT3-ITDs in the clone at presentation.
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Affiliation(s)
- TaeHyung Kim
- Division of Medical Oncology and HematologyPrincess Margaret Cancer CentreTorontoOntarioCanada,Department of Computer ScienceUniversity of TorontoTorontoOntarioCanada,The Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoOntarioCanada
| | - Hyewon Lee
- Division of Medical Oncology and HematologyPrincess Margaret Cancer CentreTorontoOntarioCanada,Center for Hematologic MalignanciesNational Cancer CenterGoyangRepublic of Korea
| | - Jose‐Mario Capo‐Chichi
- Department of Clinical Laboratory GeneticsGenome Diagnostics Laboratory Medicine ProgramUniversity of TorontoTorontoOntarioCanada
| | - Myung Hee Chang
- Division of Medical Oncology and HematologyPrincess Margaret Cancer CentreTorontoOntarioCanada,Division of Oncology‐HematologyDepartment of Internal MedicineNational Health Insurance Service Ilsan HospitalGoyangRepublic of Korea
| | - Young Seok Yoo
- Division of Medical Oncology and HematologyPrincess Margaret Cancer CentreTorontoOntarioCanada
| | - Gurbaksh Basi
- Princess Margaret Genomics CentrePrincess Margaret Cancer CentreTorontoOntarioCanada
| | - Troy Ketela
- Princess Margaret Genomics CentrePrincess Margaret Cancer CentreTorontoOntarioCanada
| | - Adam C. Smith
- Laboratory Medicine ProgramUniversity Health NetworkTorontoOntarioCanada,Department of Laboratory Medicine and PathobiologyUniversity of TorontoTorontoOntarioCanada
| | - Anne Tierens
- Laboratory Medicine ProgramUniversity Health NetworkTorontoOntarioCanada,Department of Laboratory Medicine and PathobiologyUniversity of TorontoTorontoOntarioCanada
| | - Zhaolei Zhang
- Department of Computer ScienceUniversity of TorontoTorontoOntarioCanada,The Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoOntarioCanada,Department of Molecular GeneticsUniversity of TorontoTorontoOntarioCanada
| | - Mark D. Minden
- Division of Medical Oncology and HematologyPrincess Margaret Cancer CentreTorontoOntarioCanada
| | - Dennis Dong Hwan Kim
- Division of Medical Oncology and HematologyPrincess Margaret Cancer CentreTorontoOntarioCanada,Hans Messner Allogeneic Blood and Marrow Transplant UnitPrincess Margaret Cancer CentreTorontoOntarioCanada
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21
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Goswami M, Gui G, Dillon LW, Lindblad KE, Thompson J, Valdez J, Kim DY, Ghannam JY, Oetjen KA, Destefano CB, Smith DM, Tekleab H, Li Y, Dagur P, Hughes T, Marté JL, Del Rivero J, Klubo-Gwiezdzinksa J, Gulley JL, Calvo KR, Lai C, Hourigan CS. Pembrolizumab and decitabine for refractory or relapsed acute myeloid leukemia. J Immunother Cancer 2022; 10:jitc-2021-003392. [PMID: 35017151 PMCID: PMC8753450 DOI: 10.1136/jitc-2021-003392] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2021] [Indexed: 12/11/2022] Open
Abstract
Background The powerful ‘graft versus leukemia’ effect thought partly responsible for the therapeutic effect of allogeneic hematopoietic cell transplantation in acute myeloid leukemia (AML) provides rationale for investigation of immune-based therapies in this high-risk blood cancer. There is considerable preclinical evidence for potential synergy between PD-1 immune checkpoint blockade and the hypomethylating agents already commonly used for this disease. Methods We report here the results of 17 H-0026 (PD-AML, NCT02996474), an investigator sponsored, single-institution, single-arm open-label 10-subject pilot study to test the feasibility of the first-in-human combination of pembrolizumab and decitabine in adult patients with refractory or relapsed AML (R-AML). Results In this cohort of previously treated patients, this novel combination of anti-PD-1 and hypomethylating therapy was feasible and associated with a best response of stable disease or better in 6 of 10 patients. Considerable immunological changes were identified using T cell receptor β sequencing as well as single-cell immunophenotypic and RNA expression analyses on sorted CD3+ T cells in patients who developed immune-related adverse events (irAEs) during treatment. Clonal T cell expansions occurred at irAE onset; single-cell sequencing demonstrated that these expanded clones were predominately CD8+ effector memory T cells with high cell surface PD-1 expression and transcriptional profiles indicative of activation and cytotoxicity. In contrast, no such distinctive immune changes were detectable in those experiencing a measurable antileukemic response during treatment. Conclusion Addition of pembrolizumab to 10-day decitabine therapy was clinically feasible in patients with R-AML, with immunological changes from PD-1 blockade observed in patients experiencing irAEs.
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Affiliation(s)
- Meghali Goswami
- National Heart Lung and Blood Institute, Bethesda, Maryland, USA.,National Cancer Institute, Bethesda, Maryland, USA
| | - Gege Gui
- National Heart Lung and Blood Institute, Bethesda, Maryland, USA
| | - Laura W Dillon
- National Heart Lung and Blood Institute, Bethesda, Maryland, USA
| | | | - Julie Thompson
- National Heart Lung and Blood Institute, Bethesda, Maryland, USA
| | - Janet Valdez
- National Heart Lung and Blood Institute, Bethesda, Maryland, USA
| | - Dong-Yun Kim
- National Heart Lung and Blood Institute, Bethesda, Maryland, USA
| | - Jack Y Ghannam
- National Heart Lung and Blood Institute, Bethesda, Maryland, USA
| | - Karolyn A Oetjen
- National Heart Lung and Blood Institute, Bethesda, Maryland, USA
| | | | - Dana M Smith
- Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Hanna Tekleab
- National Heart Lung and Blood Institute, Bethesda, Maryland, USA
| | - Yeusheng Li
- National Heart Lung and Blood Institute, Bethesda, Maryland, USA
| | - Pradeep Dagur
- National Heart Lung and Blood Institute, Bethesda, Maryland, USA
| | - Thomas Hughes
- National Institutes of Health Clinical Center, Bethesda, Maryland, USA
| | | | | | | | | | - Katherine R Calvo
- National Institutes of Health Clinical Center, Bethesda, Maryland, USA
| | - Catherine Lai
- National Heart Lung and Blood Institute, Bethesda, Maryland, USA
| | - Christopher S Hourigan
- National Heart Lung and Blood Institute, Bethesda, Maryland, USA .,Trans-NIH Center for Human Immunology, National Institutes of Health, Bethesda, Maryland, USA
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22
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Penter L, Gohil SH, Wu CJ. Natural Barcodes for Longitudinal Single Cell Tracking of Leukemic and Immune Cell Dynamics. Front Immunol 2022; 12:788891. [PMID: 35046946 PMCID: PMC8761982 DOI: 10.3389/fimmu.2021.788891] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 12/08/2021] [Indexed: 11/26/2022] Open
Abstract
Blood malignancies provide unique opportunities for longitudinal tracking of disease evolution following therapeutic bottlenecks and for the monitoring of changes in anti-tumor immunity. The expanding development of multi-modal single-cell sequencing technologies affords newer platforms to elucidate the mechanisms underlying these processes at unprecedented resolution. Furthermore, the identification of molecular events that can serve as in-vivo barcodes now facilitate the tracking of the trajectories of malignant and of immune cell populations over time within primary human samples, as these permit unambiguous identification of the clonal lineage of cell populations within heterogeneous phenotypes. Here, we provide an overview of the potential for chromosomal copy number changes, somatic nuclear and mitochondrial DNA mutations, single nucleotide polymorphisms, and T and B cell receptor sequences to serve as personal natural barcodes and review technical implementations in single-cell analysis workflows. Applications of these methodologies include the study of acquired therapeutic resistance and the dissection of donor- and host cellular interactions in the context of allogeneic hematopoietic stem cell transplantation.
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Affiliation(s)
- Livius Penter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, United States
- Harvard Medical School, Boston, MA, United States
- Department of Hematology, Oncology, and Tumorimmunology, Campus Virchow Klinikum, Berlin, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Satyen H. Gohil
- Department of Academic Haematology, University College London Cancer Institute, London, United Kingdom
- Department of Haematology, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, United States
- Harvard Medical School, Boston, MA, United States
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
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23
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Measurable Residual Disease Assessment as a Surrogate Marker in New Drug Development in Acute Myeloid Leukemia. Cancer J 2022; 28:73-77. [PMID: 35072377 PMCID: PMC8849520 DOI: 10.1097/ppo.0000000000000572] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
ABSTRACT Response criteria for patients treated for acute myeloid leukemia (AML) based on cytomorphology are inadequate. Many patients achieving a complete remission by such criteria will later relapse. Patients with AML in such remissions who test negative using higher sensitivity measures of residual disease burden (measurable residual disease [MRD]) have on average lower relapse rates and better survival than those testing positive. This association has raised the possibility that these technological advances in measurement of tumor burden could be used to optimize the drug development and regulatory approval processes in AML. The heterogeneous genetic etiology, diverse immunophenotypic profiles, related precursor states and polyclonal architecture however combine to make the development of standardized and validated MRD assessments for AML challenging. Current and future methods to measure residual disease in AML, performance characteristics of testing currently in use, and potential uses for optimized AML MRD tests including as a surrogate endpoint are discussed.
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24
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Vonk CM, Al Hinai ASA, Hanekamp D, Valk PJM. Molecular Minimal Residual Disease Detection in Acute Myeloid Leukemia. Cancers (Basel) 2021; 13:5431. [PMID: 34771594 PMCID: PMC8582498 DOI: 10.3390/cancers13215431] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 02/06/2023] Open
Abstract
Initial induction chemotherapy to eradicate the bulk of acute myeloid leukemia (AML) cells results in complete remission (CR) in the majority of patients. However, leukemic cells persisting in the bone marrow below the morphologic threshold remain unaffected and have the potential to proliferate and re-emerge as AML relapse. Detection of minimal/measurable residual disease (MRD) is a promising prognostic marker for AML relapse as it can assess an individual patients' risk profile and evaluate their response to treatment. With the emergence of molecular techniques, such as next generation sequencing (NGS), a more sensitive assessment of molecular MRD markers is available. In recent years, the detection of MRD by molecular assays and its association with AML relapse and survival has been explored and verified in multiple studies. Although most studies show that the presence of MRD leads to a worse clinical outcome, molecular-based methods face several challenges including limited sensitivity/specificity, and a difficult distinction between mutations that are representative of AML rather than clonal hematopoiesis. This review describes the studies that have been performed using molecular-based assays for MRD detection in the context of other MRD detection approaches in AML, and discusses limitations, challenges and opportunities.
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Affiliation(s)
- Christian M Vonk
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 CN Rotterdam, The Netherlands
| | - Adil S A Al Hinai
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 CN Rotterdam, The Netherlands
- National Genetic Center, Ministry of Health, Muscat 111, Oman
| | - Diana Hanekamp
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 CN Rotterdam, The Netherlands
- Department of Hematology, Cancer Center VU University Medical Center, Amsterdam University Medical Centers, 1081 HV Amsterdam, The Netherlands
| | - Peter J M Valk
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3015 CN Rotterdam, The Netherlands
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