scholarly journals Genetic diversity within leukemia-associated immunophenotype-defined subclones in AML

2022 ◽  
Author(s):  
F. Tiso ◽  
T. N. Koorenhof-Scheele ◽  
E. Huys ◽  
J. H. A. Martens ◽  
A. O. de Graaf ◽  
...  
Keyword(s):  
Myeloid Leukemia ◽  
Clonal Evolution ◽  
Leukemic Cells ◽  
Genetic Mutations ◽  
Complementary Information ◽  
Isolated Populations ◽  
Driver Genes ◽  
Expansion Pattern ◽  
Incomplete Picture

AbstractAcute myeloid leukemia (AML) is a highly heterogeneous disease showing dynamic clonal evolution patterns over time. Various subclones may be present simultaneously and subclones may show a different expansion pattern and respond differently to applied therapies. It is already clear that immunophenotyping and genetic analyses may yield overlapping, but also complementary information. Detailed information on the genetic make-up of immunophenotypically defined subclones is however scarce. We performed error-corrected sequencing for 27 myeloid leukemia driver genes in 86, FACS-sorted immunophenotypically characterized normal and aberrant subfractions in 10 AML patients. We identified three main scenarios. In the first group of patients, the two techniques were equally well characterizing the malignancy. In the second group, most of the isolated populations did not express aberrant immunophenotypes but still harbored several genetic aberrancies, indicating that the information obtained only by immunophenotyping would be incomplete. Vice versa, one patient was identified in which genetic mutations were found only in a small fraction of the immunophenotypically defined malignant populations, indicating that the genetic analysis gave an incomplete picture of the disease. We conclude that currently, characterization of leukemic cells in AML by molecular and immunophenotypic techniques is complementary, and infer that both techniques should be used in parallel in order to obtain the most complete view on the disease.

scholarly journals Clinical Implications of Inflammation in Acute Myeloid Leukemia

2021 ◽  
Vol 11 ◽  
Author(s):  
Christian Récher
Keyword(s):  
Acute Myeloid Leukemia ◽  
Disease Progression ◽  
Myeloid Leukemia ◽  
Kinase Inhibitors ◽  
Lymphoblastic Leukemia ◽  
Clonal Evolution ◽  
Leukemic Cells ◽  
Prognostic Impact ◽  
Acute Myeloid

Recent advances in the description of the tumor microenvironment of acute myeloid leukemia, including the comprehensive analysis of the leukemic stem cell niche and clonal evolution, indicate that inflammation may play a major role in many aspects of acute myeloid leukemia (AML) such as disease progression, chemoresistance, and myelosuppression. Studies on the mechanisms of resistance to chemotherapy or tyrosine kinase inhibitors along with high-throughput drug screening have underpinned the potential role of glucocorticoids in this disease classically described as steroid-resistant in contrast to acute lymphoblastic leukemia. Moreover, some mutated oncogenes such as RUNX1, NPM1, or SRSF2 transcriptionally modulate cell state in a manner that primes leukemic cells for glucocorticoid sensitivity. In clinical practice, inflammatory markers such as serum ferritin or IL-6 have a strong prognostic impact and may directly affect disease progression, whereas interesting preliminary data suggested that dexamethasone may improve the outcome for AML patients with a high white blood cell count, which paves the way to develop prospective clinical trials that evaluate the role of glucocorticoids in AML.

scholarly journals MutaSeq reveals the transcriptomic consequences of clonal evolution in acute myeloid leukemia

2018 ◽  
Author(s):  
Lars Velten ◽  
Benjamin A. Story ◽  
Pablo Hernandez-Malmierca ◽  
Jennifer Milbank ◽  
Malte Paulsen ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Single Cell ◽  
Myeloid Leukemia ◽  
Clonal Evolution ◽  
Depth Profiling ◽  
Therapy Resistance ◽  
Leukemic Cells ◽  
Cancer Evolution ◽  
Transcriptomic Changes ◽  
Acute Myeloid

The step-wise acquisition of genetic abnormalities in cancer is thought to represent a major driver of disease initiation, relapse and therapy resistance. Acute myeloid leukemia (AML) represents a prime example of an aggressive cancer that develops in a multi-step manner from multipotent hematopoietic progenitors via pre-leukemic intermediates to leukemic cells. While bulk and single-cell genomics provide powerful tools to study the phylogenetics of cancer evolution, the specific transcriptomic changes induced by the accumulation of mutations remain largely unexplored. Here, we introduce MutaSeq, a combined single-cell genetic and transcriptomics platform for the identification of molecular consequences of cancer evolution. Through in-depth profiling of an AML patient, we demonstrate that MutaSeq is capable of: (1) fine-mapping clonal and developmental hierarchies (2) quantifying the ability of leukemic and pre-leukemic clones to give rise to mature lineages and (3) identifying surface markers and mRNA transcripts specific to pre-leukemic, leukemic, and residual healthy cells. The experimental and analytical approach presented here is broadly applicable to other types of cancer, and can help identify targets for eradicating both pre-cancerous and cancerous reservoirs of relapse.

scholarly journals Computational reconstruction of clonal hierarchies from bulk sequencing data of acute myeloid leukemia samples

2021 ◽  
Author(s):  
Thomas Stiehl ◽  
Anna Marciniak-Czochra
Keyword(s):  
Acute Myeloid Leukemia ◽  
Single Cell ◽  
Myeloid Leukemia ◽  
Clonal Evolution ◽  
Malignant Cell ◽  
Leukemic Cells ◽  
Sequencing Data ◽  
Single Cell Sequencing ◽  
Computational Reconstruction ◽  
Acute Myeloid

AbstractAcute myeloid leukemia is an aggressive cancer of the blood forming system. The malignant cell population is composed of multiple clones that evolve over time. Clonal data reflect the mechanisms governing treatment response and relapse. Single cell sequencing provides most direct insights into the clonal composition of the leukemic cells, however it is still not routinely available in clinical practice. In this work we develop a computational algorithm that allows identifying all clonal hierarchies that are compatible with bulk variant allele frequencies measured in a patient sample. The clonal hierarchies represent descendance relations between the different clones and reveal the order in which mutations have been acquired. The proposed computational approach is tested using single cell sequencing data that allow comparing the outcome of the algorithm with the true structure of the clonal hierarchy. We investigate which problems occur during reconstruction of clonal hierarchies from bulk sequencing data. Our results suggest that in many cases only a small number of possible hierarchies fits the bulk data. This implies that bulk sequencing data can be used to obtain insights in clonal evolution.

Expression of Core-Binding Factor (CBF) Fusion Genes in Clonal Evolution of Chronic Myeloid Leukemia (CML).

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 4697-4697
Author(s):  
Farhad Ravandi-Kashani ◽  
Hagop Kantarjian ◽  
Stefan Faderl ◽  
Susan O’Brien ◽  
Mary B. Rios ◽  
...  
Keyword(s):  
Disease Progression ◽  
Myeloid Leukemia ◽  
Clonal Evolution ◽  
Chronic Phase ◽  
Survival Advantage ◽  
Leukemic Cells ◽  
Fusion Genes ◽  
Core Binding Factor ◽  
Blast Phase ◽  
Binding Factor

Abstract A “2-hit” model of leukemogenesis has been proposed in which one class of mutations confers a proliferative or survival advantage to the cells and the second class serves primarily to interfere with hematopoietic cell differentiation. In support of this, FLT3 receptor mutations have been frequently reported in patients with t(8;21) and inv(16) acute myeloid leukemia (AML), otherwise known as core-binding factor (CBF) leukemias, whose fusion gene products (AML1-ETO and CBFB-MYH11) contribute to impaired differentiation of leukemic cells. In CML, enhanced kinase activity of BCR-ABL confers a proliferative and survival advantage to the leukemic cells and clonal evolution is a common event at the time of disease acceleration. However, the acquisition of CBF fusion genes has not been commonly reported during the clonal evolution of CML. We report 4 patients with CML who developed CBF type rearrangements [inv(16)(n=2) and t(8;21)(n=2)] at the time of disease progression. Patient #1, a 61 year old female, presented with myeloid blast phase disease with 46,XX,t(9;22)(q34;q11.2),inv(16)(p13q22) and was treated with imatinib achieving a hematological but not cytogenetic response. Patient #2, a 48 year old male, presented with chronic phase disease and received imatinib for 2 years, achieved a complete cytogenetic remission (CG CR) but progressed to blast phase with development of 46,XY,t(9;22)(q34;q11.2),inv(16)(p13q22). Both patients had elevated and abnormal marrow eosinophils at the time of clonal evolution. Patient #3, a 54 year old female, presented in chronic phase, received imatinib and achieved CG CR after 3 months. Blast transformation occurred after one year with 48, XX,+8,t(8;21)(q22;q22),t(9;22;19;10)(q34;q11;p13.1;q22),+der(22)t(9;22;19;10). Patient #4, a 47 year old male, presented with an extramedullary myeloid mass on his arm and features of chronic phase in the marrow examination. He was treated with troxacitabine with resolution of the mass. He was then treated with imatinib. Ten months later he developed a recurrent mass with cytogenetic studies of both the mass and marrow showing 47,XY,+8,t(8;21)(q22;q22),del(9)(q13q32),t(9;22)(q34;q11.2). To our knowledge, eleven other patients with CML with inv(16)(n=10) or with t(8;21)(n=1) have been previously reported in the literature, none treated with imatinib. Patients with inv(16) had features of AML with eosinophilia (FAB M4Eo) demonstrating dysplastic eosinophils in the bone marrow examination. Development of the CBF rearrangement was invariably associated with disease progression into the myeloid blast phase with the exception of one patient, reported to develop lymphoid blast phase, based on surface markers. CBF rearrngements occur rarely at the time of disease progression in CML and may contribute to disease transformation based on the “2-hit” hypothesis for leukemogenesis.

Clonal Evolution of Pre-Leukemic Hematopoietic Stem Cells Precedes Human Acute Myeloid Leukemia

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 4-4
Author(s):  
Max Jan ◽  
Thomas M. Snyder ◽  
M. Ryan Corces-Zimmerman ◽  
Irving L. Weissman ◽  
Stephen R. Quake ◽  
...  
Keyword(s):  
Stem Cells ◽  
Myeloid Leukemia ◽  
De Novo ◽  
Clonal Evolution ◽  
Leukemic Cells ◽  
Founder Mutations ◽  
Hematopoietic Stem ◽  
De Novo Aml ◽  
Clonal Progression ◽  
Acute Myeloid

Abstract Abstract 4 Acute myeloid leukemia (AML) is an aggressive malignancy of hematopoietic progenitors with poor clinical outcomes. Despite the power of next-generation genome sequencing to describe AML genomes and to identify recurrent mutations, our fundamental understanding of the genomics of leukemogenesis is incomplete. Founding mutations in the majority of AML cases are largely unknown because pre-leukemic cells are clinically silent and are outcompeted by their malignant descendants. Our limited knowledge of founding mutations comes from infrequent cases of AML arising secondary to antecedent clonal bone marrow disorders or rare instances of inherited syndromes, but this does not include the large majority of de novo AML cases. Previously, we showed that non-leukemic hematopoietic stem cells (HSC) contain clonal antecedents of AML in patients in long-term remission post-therapy, and have proposed a model in which serial acquisition of mutations occurs in self-renewing HSC. More recently, we demonstrated the prospective separation of residual HSC from AML cells, based on differential expression of surface markers such as CD47 and TIM3.1,2 Here, we investigated this model and the nature of founder mutations through the genomic analysis of de novo AML and patient-matched residual non-leukemic HSC, speculating that these residual non-leukemic HSC might in fact constitute a reservoir of pre-leukemic HSC harboring founder mutations, but lacking the complete complement of abnormalities required to generate AML. Using exome sequencing, we identified mutations present in multiple individual AML genomes (mean 10 mutations per patient) and screened for them in the residual HSC. In most cases, we identified several mutations present in residual HSC that retained normal multilineage differentiation in vivo. These “early” mutations include NPM1c and novel AML mutations in genes involved in the cell cycle and mRNA biogenesis. Putative “late” mutations absent from residual HSC and only found in leukemic cells include FLT3 ITD and IDH1 R132H. Next, using custom-designed SNP Taqman genotyping assays, we analyzed single residual HSC for the presence of the identified “early” mutations. As hypothesized, we determined that a clonal progression of mutations occurs in non-leukemic HSC, based on the identification of individual cells containing subsets of these “early” mutations. Quantitative genetic analyses of the HSC compartment enabled us to reconstruct the subclonal architecture of normal and pre-leukemic stem cells. In all cases, normal HSC were 6–50 times more numerous than pre-leukemic HSC, and in one case where we identified two sequential populations of pre-leukemic HSC, the less mutated population was 25 times more numerous than its more mutated descendent. This result contrasts with the classical model of a linear succession of increasingly dominant pre-leukemic subclones, suggesting that the relationship between subclone size and clonal progression may be complex. In summary, our results show that pre-leukemic HSC reveal the clonal evolution of AML genomes from founder mutations. Ultimately, these clonal antecedents of leukemia may prove to be clinically important. Indeed, some cases of relapsed pediatric ALL have been shown to arise from a clone ancestral to the presenting leukemia. The same may be true in AML, in which relapsed disease develops from a pre-leukemic HSC clone that acquires additional novel mutations resulting in a genetically divergent leukemic relapse. This possibility suggests that pre-leukemic HSC constitute a cellular reservoir that may need to be targeted for more durable remissions. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Computational Reconstruction of Clonal Hierarchies From Bulk Sequencing Data of Acute Myeloid Leukemia Samples

2021 ◽  
Vol 12 ◽  
Author(s):  
Thomas Stiehl ◽  
Anna Marciniak-Czochra
Keyword(s):  
Acute Myeloid Leukemia ◽  
Single Cell ◽  
Myeloid Leukemia ◽  
Clonal Evolution ◽  
Malignant Cell ◽  
Leukemic Cells ◽  
Sequencing Data ◽  
Single Cell Sequencing ◽  
Computational Reconstruction ◽  
Acute Myeloid

Acute myeloid leukemia is an aggressive cancer of the blood forming system. The malignant cell population is composed of multiple clones that evolve over time. Clonal data reflect the mechanisms governing treatment response and relapse. Single cell sequencing provides most direct insights into the clonal composition of the leukemic cells, however it is still not routinely available in clinical practice. In this work we develop a computational algorithm that allows identifying all clonal hierarchies that are compatible with bulk variant allele frequencies measured in a patient sample. The clonal hierarchies represent descendance relations between the different clones and reveal the order in which mutations have been acquired. The proposed computational approach is tested using single cell sequencing data that allow comparing the outcome of the algorithm with the true structure of the clonal hierarchy. We investigate which problems occur during reconstruction of clonal hierarchies from bulk sequencing data. Our results suggest that in many cases only a small number of possible hierarchies fits the bulk data. This implies that bulk sequencing data can be used to obtain insights in clonal evolution.

scholarly journals Targeting the MTF2-MDM2 Axis Sensitizes Refractory Acute Myeloid Leukemia to Chemotherapy

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 5232-5232
Author(s):  
Hani Jrade ◽  
Harinad B Maganti ◽  
Christopher Cafariello ◽  
Christopher J Porter ◽  
Julien Yockell-Lelièvre ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Risk Groups ◽  
Epigenetic Mechanism ◽  
Leukemic Cells ◽  
Driver Genes ◽  
Advisory Committees ◽  
Hematopoietic Stem ◽  
Acute Myeloid ◽  
Refractory Aml

Abstract Next generation sequencing of acute myeloid leukemia (AML) patient samples has enabled more granular risk stratification of patients; however, refractory AML patients can be found across all risk groups, suggesting that non-genetic lesions regulate chemoresponsiveness. Consistent with this hypothesis is the finding that many of the mutated AML driver genes are encode epigenetic modifiers. Thus, unraveling the epigenetic dysregulation in AML is critical to better understand disease initiation and progression, as well as develop targeted therapies. Metal Response Element Binding Transcription Factor 2/Polycomblike 2 (MTF2/PCL2) plays a fundamental role in recruiting the Polycomb repressive complex 2 (PRC2) to chromatin and we show that it is commonly silenced in primary AML patient cells at diagnosis. Furthermore, the loss of MTF2 in hematopoietic stem and progenitor cells (HSPCs) leads to an altered epigenetic state that underlies refractory AML. By implementing unbiased systems analyses, we identified the E3 ubiquitin ligase MDM2 that inhibits p53 as a direct target of MTF2-PRC2. MTF2 deficiency leads to over-expression of MDM2 and inhibition of p53-mediated cell cycle regulation and apoptosis, leading to chemoresistance and refractory AML. Targeting this dysregulated signaling pathway by MTF2 overexpression or MDM2 inhibitors sensitized refractory patient leukemic cells to induction chemotherapeutics and prevented relapse in AML patient-derived xenograft (PDX) mice. Therefore, we have uncovered a direct epigenetic mechanism by which MTF2 functions as a tumor suppressor required for AML chemotherapeutic sensitivity and identified a potential therapeutic strategy to treat refractory AML. Disclosures Sabloff: Celgene: Membership on an entity's Board of Directors or advisory committees.

scholarly journals Immunophenotypic characterization of pediatric acute myeloid leukemia with inv(16)(p13.1q22)/t(16;16)(p13.1;q22)/CBFb-MYH11

2021 ◽  
Vol 20 (1) ◽  
pp. 46-53
Author(s):  
E. V. Mikhailova ◽  
S. A. Kashpor ◽  
E. A. Zerkalenkova ◽  
A. A. Semchenkova ◽  
M. E. Dubrovina ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Leukemic Cells ◽  
Pediatric Acute Myeloid Leukemia ◽  
Pediatric Hematology ◽  
National Medical ◽  
Early Markers ◽  
Mature Part ◽  
Acute Myeloid

The aim of this study was to describe the immunophenotype of leukemic cells in acute myeloid leukemia (AML) with inv(16) (p13.1q22)/CBFb-MYH11 and t(16;16)(p13.1;q22)/CBFb-MYH11 in children. This study is supported by the Independent Ethics Committee and approved by the Academic Council of the Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology. We investigated bone marrow samples from 36 pediatric patients with initially diagnosed AML with inv(16)(p13.1q22)/t(16;16)(p13.1;q22)/CBFb-MYH11. Immunophenotypic profile of leukemic cells was very heterogeneous: cells expressed antigens of early stages of differentiation (CD34, CD117, CD123) as well as markers of mature monocytes (CD11c, CD14, CD64) and neutrophils (CD65, CD15). Moreover, in 55.6% of cases lymphoid coexpressions were noticed (CD2 – the most frequent one). Furthermore, in 83.3% of cases we detected the separation of leukemic cells population into two parts: more “immature” – myeloblastic, which expressed early markers of differentiation (CD34, CD117), and more “mature” part, expressing monocytic antigens (CD11b, CD14, CD33). There was no clear separation between these parts of population. Despite the immunophenotypic similarity between monocytic part of leukemic population and normal monocytes, in 87.5% of studied cases there were same lymphoid coexpressions on these cells as on leukemic myeloblasts. Moreover, we showed that levels of CBFb-MYH11 expression in leukemic monocytes and myeloblasts were comparable. Presence of these characteristics in monocytes allows to consider them as part of leukemic cells population and take into consideration during the total immunophenotype reporting. 

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