Clonal hematopoiesis and preleukemia—Genetics,biology, and clinical implications

Myeloid neoplasms including myelodysplastic syndromes and acute myeloid leukemia (AML) originate from hematopoietic stem cells through sequential acquisition of genetic and epigenetic alterations that ultimately cause the disease‐specific phenotype of impaired differentiation and increased proliferation. It has become clear that preleukemic clonal hematopoiesis (CH), characterized by an expansion of stem and progenitor cells that carry somatic mutations but are still capable of normal differentiation, can precede the development of clinically overt myeloid neoplasia by many years. CH commonly develops in the aging hematopoietic system, yet progression to myelodysplasia or AML is rare. The discovery that myeloid neoplasms frequently develop from premalignant precursor conditions that are detectable in many healthy individuals has important consequences for the diagnosis, and potentially for the treatment of these disorders. In this review, we summarize the current knowledge on CH as a precursor of myeloid cancers and the implications of CH‐related gene mutations in the diagnostic workup of patients with suspected myelodysplastic syndrome. We will discuss the risk of progression associated with CH in healthy persons and in patients undergoing chemotherapy for a non‐hematologic cancer, and the significance of CH in autologous and allogeneic stem cell transplantation. Finally, we will review the significance of preleukemic clones in AML and their persistence in patients who achieve a remission after chemotherapeutic treatment.     

Centrosome amplification and aneuploidy in bone marrow failure patients

Patients with bone marrow failure are at risk for development of hematopoietic progenitor clones with abnormal numbers of chromosomes (aneuploidy) and leukemia. Numerical centrosome abnormalities or mutations in genes associated with the mitotic spindle checkpoint (BUB1 and MAD2) are two important mechanisms that can induce abnormal mitosis resulting in aneuploid daughter cells. To assess the role of these mechanisms, we used fluorescence in situ hybridization techniques to determine aneuploidy and centrosome copy number and PCR-SSCP to identify gene mutations of BUB1 and MAD2 in marrow cells of 25 patients. No mutations were found in BUB1 or MAD2 genes. However, we found that cells with more than two centrosomes exhibited aneuploidy for three or more chromosomes. We conclude that centrosome amplification may be associated with the development of a clonal population of potentially preleukemic aneuploid cells.     

Leukemia and preleukemia in Fanconi anemia patients. A review of the literature and report of the International Fanconi Anemia Registry

Fanconi anemia (FA) is an autosomal recessive disorder characterized clinically by a progressive pancytopenia, diverse congenital abnormalities, and increased predisposition to malignancy. Although a variable phenotype makes accurate diagnosis on the basis of clinical manifestations difficult in some patients, the unique sensitivity of FA cells to the clastogenic effect of DNA cross-linking agents such as diepoxybutane (DEB) can be used to facilitate the diagnosis. We review all cases of FA reported to have leukemia, preleukemia, or a bone marrow (BM) clonal chromosomal abnormality and include for the first time an analysis of these conditions observed in patients in the International Fanconi Anemia Registry (IFAR). The incidence of acute myelogenous leukemia (AML) in FA patients is more than 15,000 times that observed in children in the general population. Cytogenetic studies of FA-associated leukemias disclose a high frequency of monosomy 7 and duplications involving 1q. There were no occurrences of t(8;21), t(15;17), or abnormalities of 11q, which are associated with M2, M3, and M5 leukemias, respectively, but not with preleukemia. Development of leukemia in FA patients was associated with an exceedingly poor prognosis, with a mean age of death of 15 years. We suggest that all FA patients may be considered preleukemic and that this disorder presents a model for study of the etiology of AML.     

Point mutations in the AML1/RUNX1 gene associated with myelodysplastic syndrome

Myelodysplastic syndrome (MDS) is a clonal disorder of hematopoietic stem cells characterized by ineffective and inadequate hematopoiesis. Because MDS is a heterogeneous disorder, specific gene abnormalities implicated in the pathogenesis of MDS have been difficult to identify. Cytogenetic abnormalities are seen in half of the MDS patients and generally consist of partial or complete chromosome deletion or addition, whereas balanced translocations are rare. Although point mutations of critical genes had been demonstrated to contribute to the development of MDS, there was no strong correlation between these mutations and clinical features. Recently, we reported the high incidence of somatic mutations in the AML1/RUNX1 gene (which is a critical regulator of definitive hematopoiesis and the most frequent target for translocation of acute myeloid leukemia [AML]) in MDS, especially refractory anemia with excess blasts (RAEB), RAEB in transformation (RAEBt), and AML following MDS (defined here as MDS/AML). The MDS/AML patients with AML1 mutations had a significantly worse prognosis than those without AML1 mutations. Most AML1 mutants lose trans-activation potential, which leads to a loss of AML1 function. These data indicate that AML1 point mutation is one of the major causes of MDS/AML, and "MDS/AML with AML1 mutation" represents a distinct clinicopathologic-genetic entity.     

Donor-to-Donor Heterogeneity in the Clonal Dynamics of Transplanted Human Cord Blood Stem Cells in Murine Xenografts

Umbilical cord blood (UCB) provides an alternative source of hematopoietic stem cells (HSCs) for allogeneic transplantation. Administration of sufficient donor HSCs is critical to restore recipient hematopoiesis and to maintain long-term polyclonal blood formation. However, due to lack of unique markers, the frequency of HSCs among UCB CD34⁺ cells is the subject of ongoing debate, urging for reproducible strategies for their counting. Here, we used cellular barcoding to determine the frequency and clonal dynamics of human UCB HSCs and to determine how data analysis methods affect these parameters. We transplanted lentivirally barcoded CD34⁺ cells from 20 UCB donors into Nod/Scid/IL2Ry^–/– (NSG) mice (n = 30). Twelve recipients (of 8 UCB donors) engrafted with >1% GFP⁺ cells, allowing for clonal analysis by multiplexed barcode deep sequencing. Using multiple definitions of clonal diversity and strategies for data filtering, we demonstrate that differences in data analysis can change clonal counts by several orders of magnitude and propose methods to improve their consistency. Using these methods, we show that the frequency of NSG-repopulating cells was low (median ∼1 HSC/10⁴ CD34⁺ UCB cells) and could vary up to 10-fold between donors. Clonal patterns in blood became increasingly consistent over time, likely reflecting initial output of transient progenitors, followed by long-term HSCs with stable hierarchies. The majority of long-term clones displayed multilineage output, yet clones with lymphoid- or myeloid-biased output were also observed. Altogether, this study uncovers substantial interdonor and analysis-induced variability in the frequency of UCB CD34⁺ clones that contribute to post-transplant hematopoiesis. As clone tracing is increasingly relevant, we urge for universal and transparent methods to count HSC clones during normal aging and upon transplantation.     

Lymphokine-activated killer (LAK) cells and cytokines synergize to kill clonal cells in acute myeloid leukemia (AML) in vitro

We studied the influence of autologous lymphokine-activated-killer (LAK) cells on the survival of clonal and CD34-positive bone marrow (BM) cells from patients with acute myeloid leukemia (AML) in a coculture assay in vitro. (1) LAK cells were grown in the presence of IL-2, in some cases additionally with IL-6. (2) These cytotoxic cells were cocultured with (untreated or cytokine pretreated) AML-BM cells obtained at different stages of the disease. Therefore BM cells were (a) either frozen in liquid nitrogen or (b) precultured for 14 days with cytokines: IL-1beta, IL-3, IL-6, erythropoietin (EPO), stem cell factor (SCF) with ('Cytok1') or without granulocyte macrophage colony stimulating factor (GM-CSF) ('Cytok2') or with no added cytokines ('ISC/FCS') as a control. (3) Southern blot analysis was used to detect clonal BM cells. At diagnosis, 76 of 151 cases (50%) studied showed clonal gene rearrangements in marker genes. (4) Southern blot analysis and flow cytometry were used to compare the amount of clonal and CD34 positive BM cells before and after coculture procedures. Coculture experiments with untreated BM and autologous LAK cells led to a reduction of clonal cells in 2 of 5 cases at diagnosis, in 11 of 17 BM samples in complete remission but not in the one case studied at relapse. Similar results were found if precultured AML cells (with or without cytokines) were cocultivated with LAK cells. However the cytotoxic effect of LAK cells was more pronounced if cytokines (especially GM-CSF and SCF) were comprised. Our data indicate, that (1) clonality in AML can be demonstrated by Southern blot analysis; (2) CD34 positive cells in AML are clonal, gene rearranged cells; (3) clonal cell populations persist in BM during complete remission and relapse in most of the patients; (4) incubation of AML-BM cells with LAK cells lead to a reduction of clonal, rearranged cells in 11 of 17 AML cases in complete remission, but only in 2 of 6 cases at diagnosis or relapse; (5) AML cells can be sensitized to theLAK cell treatment by preincubation of AML-BM cells with cytokines (IL-1beta, IL-3, IL-6, SCF, EPO and GM-CSF) or by adding SCF to the coculture conditions. Southern blot analysis and flow cytometry are appropriate methods to detect and quantify leukemic disease. Cytokines and LAK cells synergize to kill AML blasts in vitro. This is a feasible approach to immunotherapy of AML and merits further investigations.     

Somatic mutations found in the healthy blood compartment of a 115-yr-old woman demonstrate oligoclonal hematopoiesis

The somatic mutation burden in healthy white blood cells (WBCs) is not well known. Based on deep whole-genome sequencing, we estimate that approximately 450 somatic mutations accumulated in the nonrepetitive genome within the healthy blood compartment of a 115-yr-old woman. The detected mutations appear to have been harmless passenger mutations: They were enriched in noncoding, AT-rich regions that are not evolutionarily conserved, and they were depleted for genomic elements where mutations might have favorable or adverse effects on cellular fitness, such as regions with actively transcribed genes. The distribution of variant allele frequencies of these mutations suggests that the majority of the peripheral white blood cells were offspring of two related hematopoietic stem cell (HSC) clones. Moreover, telomere lengths of the WBCs were significantly shorter than telomere lengths from other tissues. Together, this suggests that the finite lifespan of HSCs, rather than somatic mutation effects, may lead to hematopoietic clonal evolution at extreme ages.Mutations are called somatic if they were acquired in a tissue cell during organismal development or later in life, rather than being inherited from a germ cell. As such, somatic mutations lead to genotypic and possibly phenotypic heterogeneity within and between tissues, and they may compromise growth or lead to a growth advantage (Frank 2010). Because somatic mutations often occur during cell division, frequently dividing cell types are more prone to acquire somatic mutations than tissues that rarely divide (Youssoufian and Pyeritz 2002). Consequently, frequently dividing cell types, i.e., epithelial cells, hematopoietic cells, and male germ cells are vulnerable to somatic mutations that may lead to tumor development or other diseases and disorders. Therefore, most studies regarding somatic mutations have been attempts to discover mechanisms leading to cancer and disease (Youssoufian and Pyeritz 2002; Erickson 2010; Hanahan and Weinberg 2011).It has been estimated that the adult human blood compartment is populated by the offspring of approximately 10,000–20,000 hematopoietic stem cells (HSCs) (Abkowitz et al. 2002). HSCs self-renew about once every 25–50 wk to create two daughter cells equivalent to their parent, and they differentiate to create offspring clones with multipotent progenitor cells that generate the much larger number of diverse blood cells via hematopoiesis (Catlin et al. 2011). Over time, somatic mutations will gradually accumulate within the HSCs, and the genotypes of the HSCs along with their offspring clones will diverge and lead to new clones of varying sizes.Recent publications show that the genomes of patients with acute myeloid leukemia (AML) contain hundreds of somatic mutations that accumulate with age (Ley et al. 2008; Mardis et al. 2009; Ding et al. 2012), and that most of these mutations occur as random events in HSCs before one of them acquires a specific pathogenic mutation leading to AML (Welch et al. 2012). Similar patterns of clonal evolution have also been shown for the development of chronic lymphocytic leukemia (CLL) (Landau et al. 2013). However, it is currently unknown to what extent healthy HSCs acquire somatic mutations and which types of mutations can be tolerated in the genome during a lifetime without causing disease.We set out to determine the prevalence and types of single nucleotide and small insertion/deletion mutations that are somatic within the healthy blood genome. Since the occurrence of somatic copy number changes has been shown to increase with age in several tissues in mice (Dolle and Vijg 2002) and also in peripheral blood in cancer-free humans (Forsberg et al. 2012; Jacobs et al. 2012; Laurie et al. 2012), we assumed that single nucleotide somatic mutations might also increase with age. Therefore, we chose a healthy person of extreme age as our subject, anticipating that during a long lifetime, mutations leading to the fittest HSCs might lead to clonal selection and thus the detectability of somatic mutations (Naylor et al. 2005; Gibson et al. 2009). Together, the large number of cellular divisions during a long lifetime and the expected age-dependent clonality could provide better statistical representation of the mutation rate and spectrum. To detect somatic mutations in peripheral blood, we compared its DNA sequence with that from the brain tissue from the same individual. Since cells in occipital brain tissue rarely divide after birth (Spalding et al. 2005), it is expected that these cells do not acquire many somatic mutations, so that DNA isolated from occipital brain tissue may serve as a candid representation of the germline control genome.Such an analysis of somatic mutations in the healthy white blood cell (WBC) population allowed us to determine the number of (detectable) mutations acquired during a lifetime and to what extent the healthy blood compartment is subject to clonal evolution. Furthermore, we investigated where such somatic mutations occurred in the genome and to what extent the spectrum of somatic mutations compares with the spectrum of germline mutations sustained in offspring populations and with the spectrum of mutations implicated in heritable disease.     

Loss of TET2 in hematopoietic cells leads to DNA hypermethylation of active enhancers and induction of leukemogenesis

DNA methylation is tightly regulated throughout mammalian development, and altered DNA methylation patterns are a general hallmark of cancer. The methylcytosine dioxygenase TET2 is frequently mutated in hematological disorders, including acute myeloid leukemia (AML), and has been suggested to protect CG dinucleotide (CpG) islands and promoters from aberrant DNA methylation. In this study, we present a novel Tet2-dependent leukemia mouse model that closely recapitulates gene expression profiles and hallmarks of human AML1-ETO-induced AML. Using this model, we show that the primary effect of Tet2 loss in preleukemic hematopoietic cells is progressive and widespread DNA hypermethylation affecting up to 25% of active enhancer elements. In contrast, CpG island and promoter methylation does not change in a Tet2-dependent manner but increases relative to population doublings. We confirmed this specific enhancer hypermethylation phenotype in human AML patients with TET2 mutations. Analysis of immediate gene expression changes reveals rapid deregulation of a large number of genes implicated in tumorigenesis, including many down-regulated tumor suppressor genes. Hence, we propose that TET2 prevents leukemic transformation by protecting enhancers from aberrant DNA methylation and that it is the combined silencing of several tumor suppressor genes in TET2 mutated hematopoietic cells that contributes to increased stem cell proliferation and leukemogenesis.     

The cell of origin and the leukemia stem cell in acute myeloid leukemia

There is experimental and observational evidence that the cells of the leukemic clone in acute myeloid leukemia (AML) have different phenotypes even though they share the same somatic mutations. The organization of the malignant clone in AML has many similarities to normal hematopoiesis, with leukemia stem cells (LSCs) that sustain leukemia and give rise to more differentiated cells. LSCs, similar to normal hematopoietic stem cells (HSCs), are those cells that are able to give rise to a new leukemic clone when transplanted into a recipient. The cell of origin of leukemia (COL) is defined as the normal cell that is able to transform into a leukemia cell. Current evidence suggests that the COL is distinct from the LSC. Here, we will review the current knowledge about LSCs and the COL in AML.     

Multiple myeloma with monosomy 13 developed in trisomy 13 acute myelocytic leukemia: numerical chromosome abnormality during chromosomal segregation process

We report here an acute myelocytic leukemia (AML-M2) patient with trisomy 13 as the sole cytogenetic anomaly, who had relapse of AML with a normal karyotype and developed multiple myeloma. Fluorescence in situ hybridization analysis using the RB gene probe revealed the plasma cells of multiple myeloma (MM) to have monosomy 13 anomaly, whereas relapsed blast cells of AML carried disomy of chromosome 13. To our knowledge, this is the first case showing clonal evolution of trisomy 13 AML and monosomy 13 MM, which might be derived from the leukemic clone at relapse.     

Clonal evolution of acute myeloid leukemia from diagnosis to relapse

Based on the individual genetic profile, acute myeloid leukemia (AML) patients are classified into clinically meaningful molecular subtypes. However, the mutational profile within these groups is highly heterogeneous and multiple AML subclones may exist in a single patient in parallel. Distinct alterations of single cells may be key factors in providing the fitness to survive in this highly competitive environment. Although the majority of AML patients initially respond to induction chemotherapy and achieve a complete remission, most patients will eventually relapse. These points toward an evolutionary process transforming treatment‐sensitive cells into treatment‐resistant cells. As described by Charles Darwin, evolution by natural selection is the selection of individuals that are optimally adapted to their environment, based on the random acquisition of heritable changes. By changing their mutational profile, AML cell populations are able to adapt to the new environment defined by chemotherapy treatment, ultimately leading to cell survival and regrowth. In this review, we will summarize the current knowledge about clonal evolution in AML, describe different models of clonal evolution, and provide the methodological background that allows the detection of clonal evolution in individual AML patients. During the last years, numerous studies have focused on delineating the molecular patterns that are associated with AML relapse, each focusing on a particular genetic subgroup of AML. Finally, we will review the results of these studies in the light of Darwinian evolution and discuss open questions regarding the molecular background of relapse development.     

GATA1 mutations in acute leukemia in children with Down syndrome

It has been reported that somatic mutations in the X-linked GATA1 gene are present in hematological clonal disorders in children with Down syndrome (DS). We analyzed retrospective samples of DS children with acute myeloid leukemia, transient leukemia (TL), and myelodysplastic syndrome (MDS) to test whether the specificity of GATA1 mutations can be helpful in distinguishing these hematopoietic disorders. A total of 49 samples were subjected to GATA1 mutation screening by direct sequencing and denaturing polyacrylamide gel electrophoresis (PAGE). Mutations in exon 2 of GATA1 were detected in six of eight DS-AML M7 samples and in four of six DS-TL; no mutation was detected in 13 children with acute lymphoblastic leukemia (DS-ALL), 6 with DS-AML (M0, M2, and M5), 6 with DS-MDS and in 8 DS infants without hematological disorders and 2 children with AML M7 without DS. Blast cells proportion in the sample represented a critical aspect on the sensitivity of mutation detection in GATA1, and a combination of sequence analysis and PAGE is necessary to detect mutations when blast percentage is low. The absence of detected mutations in any of the DS-MDS cases raises the question whether MDS in DS children is an intermediate stage between TL and AML M7, as previously suggested.     

Differentiation in human myeloblastic leukemia studied in cell culture.

Normal adult hemopoiesis orginates in pluripotent stem cells; among the early differentiated descendents of such cells are progenitors committed to the erythropoietic, granulopoietic, or megakaryocytic pathways of myeloid differentiation. These may be detected in cell culture by developmental techniques, in which progenitors form colonies in viscid or semisolid media in response to appropriate stimulation. Certain diseases of hemopoiesis also originate in pluripotent stem cells; these include chronic myeloblastic leukemia, acute myeloblastic leukemia, polycythemia vera, and idiopathic myelofibrosis—the clonal hemopathies. The hypothesis is advanced that the distribution of cell classes among patients with clonal hemopathies is determined both by the differentiation potential of each pluripotent stem cell maintaining an abnormal clone and by random events occurring during clonal expansion. The latter process may account for the large variations observed between patients when committed progenitors are assayed in cultures of marrow from patients with acute myeloblastic leukemia (AML). This variation may also be used to estimate lineage relationships in the clonal hemopathies. When applied to myelopoiesis in AML, obvious differences from the normal are not detected. The analysis is consistent with the view that the blast cell population in AML is distinct from the leukemic myelopoiesis occurring within an abnormal clone. A new assay procedure is described for progenitor cells related to blast cell proliferation. Finally, these concepts are used to develop a model for the pathogenesis and cellular characteristics of AML.     

Age-dependent accumulation of mtDNA mutations in murine hematopoietic stem cells is modulated by the nuclear genetic background

Alterations in mitochondrial DNA (mtDNA) and consequent loss of mitochondrial function underlie the mitochondrial theory of aging. In this study, we systematically analyzed the mtDNA control region somatic mutation pattern in 2864 single hematopoietic stem cells (HSCs) and progenitors, isolated by flow cytometry sorting on Lin(-)Kit(+)CD34(-) parameters from young and old C57BL/6 (B6) and BALB/cBy (BALB) mice, to test the hypothesis that the accumulated mtDNA mutations in HSCs were strain-correlated and associated with HSC functional senescence during aging. An increased level of mtDNA mutations in single HSCs was observed in old B6 when compared with young B6 mice (P=0.003); in contrast, no significant age-dependent accumulation of mutations was observed in BALB mice (old versus young, P=0.202) and the level of mutations in both young and old BALB mice was close to that of old B6 mice (P>0.280). Cellular reactive oxygen species (ROS) in mouse HSCs could not be correlated with the level of mtDNA mutations in these cells, although B6 mice had a higher proportion of ROS(-) cells when compared with the BALB mice. Propagation assays of single HSCs showed B6 cells form larger colonies compared with cells from BALB mice, irrespective of age and mtDNA mutation load. We infer from our data that age-related mtDNA somatic mutation accumulation in mouse HSCs is influenced by the nuclear genetic background and that these mutations may not obviously correlate to either cellular ROS content or HSC senescence.