scholarly journals Joint profiling of DNA and proteins in single cells to dissect genotype-phenotype associations in leukemia

2020 ◽  
Author(s):  
Benjamin Demaree ◽  
Cyrille L. Delley ◽  
Harish N. Vasudevan ◽  
Cheryl A.C. Peretz ◽  
David Ruff ◽  
...  
Keyword(s):  
Myeloid Leukemia ◽  
Tumor Heterogeneity ◽  
Single Cells ◽  
Disease Process ◽  
Blast Cell ◽  
Multiple Treatment ◽  
Novel Technology ◽  
Clinical Scenarios ◽  
Dna Variants ◽  
Acute Myeloid

AbstractStudies of acute myeloid leukemia rely on DNA sequencing and immunophenotyping by flow cytometry as primary tools for disease characterization. However, leukemia tumor heterogeneity complicates integration of DNA variants and immunophenotypes from separate measurements. Here we introduce DAb-seq, a novel technology for simultaneous capture of DNA genotype and cell surface phenotype from single cells at high throughput, enabling direct profiling of proteogenomic states in tens of thousands of cells. To demonstrate the approach, we analyze the disease of three patients with leukemia over multiple treatment timepoints and disease recurrences. We observe complex genotype-phenotype dynamics that illustrate the subtlety of the disease process and the degree of incongruity between blast cell genotype and phenotype in different clinical scenarios. Our results highlight the importance of combined single-cell DNA and protein measurements to fully characterize the heterogeneity of leukemia.

scholarly journals Joint profiling of DNA and proteins in single cells to dissect genotype-phenotype associations in leukemia

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Benjamin Demaree ◽  
Cyrille L. Delley ◽  
Harish N. Vasudevan ◽  
Cheryl A. C. Peretz ◽  
David Ruff ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Myeloid Leukemia ◽  
Tumor Heterogeneity ◽  
Single Cells ◽  
Disease Process ◽  
Blast Cell ◽  
Multiple Treatment ◽  
Clinical Scenarios ◽  
Dna Variants ◽  
Acute Myeloid

AbstractStudies of acute myeloid leukemia rely on DNA sequencing and immunophenotyping by flow cytometry as primary tools for disease characterization. However, leukemia tumor heterogeneity complicates integration of DNA variants and immunophenotypes from separate measurements. Here we introduce DAb-seq, a technology for simultaneous capture of DNA genotype and cell surface phenotype from single cells at high throughput, enabling direct profiling of proteogenomic states in tens of thousands of cells. To demonstrate the approach, we analyze the disease of three patients with leukemia over multiple treatment timepoints and disease recurrences. We observe complex genotype-phenotype dynamics that illustrate the subtlety of the disease process and the degree of incongruity between blast cell genotype and phenotype in different clinical scenarios. Our results highlight the importance of combined single-cell DNA and protein measurements to fully characterize the heterogeneity of leukemia.

Early peripheral blast cell clearance predicts minimal residual disease status and refines disease prognosis in acute myeloid leukemia

2020 ◽  
Vol 95 (11) ◽  
pp. 1304-1313
Author(s):  
Francesco Mannelli ◽  
Giacomo Gianfaldoni ◽  
Sara Bencini ◽  
Matteo Piccini ◽  
Ilaria Cutini ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Minimal Residual Disease ◽  
Myeloid Leukemia ◽  
Residual Disease ◽  
Disease Status ◽  
Blast Cell ◽  
Disease Prognosis ◽  
Cell Clearance ◽  
Minimal Residual ◽  
Acute Myeloid

scholarly journals PGK1, a promising biomarker and therapeutic target for patients with acute myeloid leukemia who are susceptible to disease relapse

2020 ◽  
Author(s):  
Junyan Gao ◽  
Xinran Chu ◽  
Shan He ◽  
Li Gao ◽  
Hui Hou ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Cell Lines ◽  
Therapeutic Target ◽  
Myeloid Leukemia ◽  
Blast Cell ◽  
High Expression ◽  
Leukemic Blast ◽  
Leukemic Blast Cell ◽  
Healthy Control ◽  
Acute Myeloid

Abstract Background: Glycolysis, a multi-step enzymatic reaction, is considered to be the root of cancer development and progression. The aim of this study is to figure out the glycolytic enzyme, phosphoglycerate kinase 1 (PGK1) whether participate in the progression of acute myeloid leukemia (AML) and its possible mechanisms. Methods: Four datasets (GSE106096, GSE75086, GSE107968 and GSE106748) containing 30 leukemic blast cell samples of AML at diagnosis, 17 leukemic blast cell samples of AML relapse and 3 bone marrow CD34+ cell samples of healthy donors were downloaded from Gene Expression Omnibus (GEO) database and PGK1 was screened out as a potential survival biomarker in AML. Then we did a series of clinical sample verifications and gene set enrichment analysis (GSEA) focusing on PGK1. We further knocked down expression of PGK1 in myelogenous leukemia cell lines and explored its potential effects. Results: PGK1 expression was up-regulated among AML at diagnosis versus healthy control, AML relapse versus AML at diagnosis and AML relapse versus healthy control datasets. Through a serial of bioinformatic analyses (differentially expressed genes [DEGs] selection, function and pathway enrichments and protein-protein interaction [PPI] network establishment), PGK1 was identified as the most meaningful gene in AML progression. Furthermore, the generally high expression of PGK1 was confirmed in AML samples comparing with healthy controls in our single center and the high-expression PGK1 was associated with a comparatively low complete remission (CR) rate, a significantly high 5-year cumulative incidence of relapse (CIR), a poor 5-year event-free survival (EFS) rate, and a poor 5-year overall survival (OS) rate. The GSEA revealed that high-expression PGK1 in AML was associated with many pathways including cytosolic DNA sensing, pentose phosphate, base excision repair and DNA replication. In vitro, the transfected U937 and K562 cells with PGK1 knock-down showed decreased cell viability and increased apoptotic rate. PGK1 inhibition could greatly decrease the half maximal inhibitory concentrations (IC50) of cytarabine (Ara-C) and daunorubicin (DNR) in U937 and K562 cell lines.Conclusions: High-expression PGK1 was associated with poor prognosis in AML. PGK1 may serve to predict the AML progression and provide a novel therapeutic target for AML.

Intra-Tumor Heterogeneity (ITH) in Acute Myeloid Leukemia (AML)

2019 ◽  
Vol 19 ◽  
pp. S237
Author(s):  
Marco Cerrano ◽  
Marie Passet ◽  
Loic Vasseur ◽  
Florence Rabian ◽  
Rhamy Rhamé ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Tumor Heterogeneity ◽  
Acute Myeloid

scholarly journals How I treat acute myeloid leukemia presenting with preexisting comorbidities

Blood ◽  
2016 ◽  
Vol 128 (4) ◽  
pp. 488-496 ◽  
Author(s):  
Yishai Ofran ◽  
Martin S. Tallman ◽  
Jacob M. Rowe
Keyword(s):  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Pulmonary Insufficiency ◽  
Curative Intent ◽  
Term Outcome ◽  
Long Term Outcome ◽  
Clinical Scenarios ◽  
Definitive Therapy ◽  
Acute Myeloid

Abstract Acute myeloid leukemia (AML) is a devastating disease with an incidence that progressively increases with advancing age. Currently, only ∼40% of younger and 10% of older adults are long-term survivors. If untreated, the overall prognosis of AML remains dismal. Initiation of therapy at diagnosis is usually urgent. Barriers to successful therapy for AML are the attendant toxicities directly related to chemotherapy or those associated with inevitable aplasia. Organ dysfunction often further complicates such toxicities and may even be prohibitive. There are few guidelines to manage such patients and the fear of crossing the medico-legal abyss may dominate. Such clinical scenarios provide particular challenges and require experience for optimal management. Herein, we discuss select examples of common pretreatment comorbidities, including cardiomyopathy, ischemic heart disease; chronic renal failure, with and without dialysis; hepatitis and cirrhosis; chronic pulmonary insufficiency; and cerebral vascular disease. These comorbidities usually render patients ineligible for clinical trials and enormous uncertainty regarding management reigns, often to the point of withholding definitive therapy. The scenarios described herein emphasize that with appropriate subspecialty support, many AML patients with comorbidities can undergo therapy with curative intent and achieve successful long-term outcome.

scholarly journals Single Cell Whole Exome Sequencing in NPM1/Flt3 Positive Pediatric Acute Myeloid Leukemia

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 1043-1043
Author(s):  
Christiane Walter ◽  
Winfried Hofmann ◽  
Katarina Reinhardt ◽  
Dirk Reinhardt ◽  
Nils von Neuhoff
Keyword(s):  
Acute Myeloid Leukemia ◽  
Single Cell ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Myeloid Leukemia ◽  
Single Cells ◽  
Clonal Evolution ◽  
Npm1 Mutation ◽  
Whole Exome ◽  
Acute Myeloid

Abstract Introduction: Acute myeloid leukemia (AML) is one of the most frequent forms of leukemia in children younger than 15 years. The detection of several mutations in a blast population of pediatric AML (pAML) is supposed to be caused by a clonal evolution from a leukemic stem cell (LSC) to leukemic blasts. LSC are believed to be more resistant to chemotherapy, to be able to survive during treatment and to be responsible for the emergence of a relapse due to the persistence in the bone marrow (BM) niche. Since LSC and potential leukemic subclones are only present in small subpopulations, it has been a major technical challenge to particular analyse only the specific population. To acquire a better understanding of the underlying mechanisms of mutagenesis, clonal evolution and leukemogenesis, the aim of this study was to establish methods that allow the analysis and detection of mutations in single cells of a subpopulation known to contain HSC as well as LSC (CD34+CD38-). We especially focused on a pAML subgroup with mutations in Nucleophosmin (NPM1) and/or fms related tyrosine kinase 3 (Flt3). Methods and Results: We established methods to perform single cell sorting, whole genome amplification (WGA) using multiple displacement amplification (MDA) technology (Qiagen) and subsequent whole exome sequencing. The sorting efficiency was checked as Hoechst stained cells were sorted onto glas slides with 48 defined spots and the presence of single cells was checked under an inverse fluorescent microscope. Subsequently, single CD34+CD38- patient derived cells were sorted into 0,5ml low binding tubes containing 4µl PBS followed by WGA and whole exome sequencing. The mutational status of the sorted single cells from three patients suffering from pAML was analysed and compared to mutations detected at initial diagnosis in DNA from a bulk of BM cells. WGA from single CD34+CD38-PI- cells resulted in an amount of 29 to 31.7µg DNA from each of five single cells. The quality of the amplified DNA was sufficient for whole exome sequencing. A 4bp insertion in exon 12 of NPM1 reflecting a common NPM1 mutation (MutA) initially detected from a bulk of cells was identified in amplified DNA from single cells using whole exome sequencing in 2/3 patients. Internal tandem duplications in Flt3 indicated by mismatches in the alignment could be detected in amplified DNA from single cells of two patients. The detected ITD resemble those initially detected in DNA from a bulk of BM cells. Discussion and Conclusion: Single cell sequencing provides a useful tool to amend the detection of genetic aberrations from a bulk of cells and to confirm the presence of specific mutations in single cells from small subpopulations. It therefore helps to get further insights into the clonal evolution in pAML. Disclosures No relevant conflicts of interest to declare.

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