The kinetics of clonal dominance in myeloproliferative disorders

Stochastic fate decisions of HSCs after transplantation: early contribution, symmetric expansion, and pool formation

Hematopoietic stem cells (HSCs) are assumed to be rare, infrequently dividing, long-lived cells not involved in immediate recovery after transplantation. Here, we performed unprecedented high-density clonal tracking in nonhuman primates and found long-term persisting HSC clones to actively contribute during early neutrophil recovery, and to be the main source of blood production as early as 50 days after transplantation. Most surprisingly, we observed a rapid decline in the number of unique HSC clones, while persisting HSCs expanded, undergoing symmetric divisions to create identical siblings and formed clonal pools ex vivo as well as in vivo. In contrast to the currently assumed model of hematopoietic reconstitution, we provide evidence for contribution of HSCs in short-term recovery as well as symmetric expansion of individual clones into pools. These findings provide novel insights into HSC biology, informing the design of HSC transplantation and gene therapy studies.

A mixed-effects stochastic model reveals clonal dominance in gene therapy safety studies

BACKGROUND

Mathematical models of haematopoiesis can provide insights on abnormal cell expansions (clonal dominance), and in turn can guide safety monitoring in gene therapy clinical applications. Clonal tracking is a recent high-throughput technology that can be used to quantify cells arising from a single haematopoietic stem cell ancestor after a gene therapy treatment. Thus, clonal tracking data can be used to calibrate the stochastic differential equations describing clonal population dynamics and hierarchical relationships in vivo.

RESULTS

In this work we propose a random-effects stochastic framework that allows to investigate the presence of events of clonal dominance from high-dimensional clonal tracking data. Our framework is based on the combination between stochastic reaction networks and mixed-effects generalized linear models. Starting from the Kramers-Moyal approximated Master equation, the dynamics of cells duplication, death and differentiation at clonal level, can be described by a local linear approximation. The parameters of this formulation, which are inferred using a maximum likelihood approach, are assumed to be shared across the clones and are not sufficient to describe situation in which clones exhibit heterogeneity in their fitness that can lead to clonal dominance. In order to overcome this limitation, we extend the base model by introducing random-effects for the clonal parameters. This extended formulation is calibrated to the clonal data using a tailor-made expectation-maximization algorithm. We also provide the companion  package RestoreNet, publicly available for download at https://cran.r-project.org/package=RestoreNet .

CONCLUSIONS

Simulation studies show that our proposed method outperforms the state-of-the-art. The application of our method in two in-vivo studies unveils the dynamics of clonal dominance. Our tool can provide statistical support to biologists in gene therapy safety analyses.

Clonal hematopoiesis: mechanisms driving dominance of stem cell clones

The discovery of clonal hematopoiesis (CH) in older individuals has changed the way hematologists and stem cell biologists view aging. Somatic mutations accumulate in stem cells over time. While most mutations have no impact, some result in subtle functional differences that ultimately manifest in distinct stem cell behaviors. With a large pool of stem cells and many decades to compete, some of these differences confer advantages under specific contexts. Approximately 20 genes are recurrently found as mutated in CH, indicating they confer some advantage. The impact of these mutations has begun to be analyzed at a molecular level by modeling in cell lines and in mice. Mutations in epigenetic regulators such as DNMT3A and TET2 confer an advantage by enhancing self-renewal of stem and progenitor cells and inhibiting their differentiation. Mutations in other genes involved in the DNA damage response may simply enhance cell survival. Here, we review proposed mechanisms that lead to CH, specifically in the context of stem cell biology, based on our current understanding of the function of some of the CH-associated genes.

Visualizing hematopoiesis as a stochastic process

Stochastic simulation has played an important role in understanding hematopoiesis, but implementing and interpreting mathematical models requires a strong statistical background, often preventing their use by many clinical and translational researchers. Here, we introduce a user-friendly graphical interface with capabilities for visualizing hematopoiesis as a stochastic process, applicable to a variety of mammal systems and experimental designs. We describe the visualization tool and underlying mathematical model, and then use this to simulate serial transplantations in mice, human cord blood cell expansion, and clonal hematopoiesis of indeterminate potential. The outcomes of these virtual experiments challenge previous assumptions and provide examples of the flexible range of hypotheses easily testable via the visualization tool.

Global stability analysis and optimal control therapy of blood cell production process (hematopoiesis) in acute myeloid leukemia

In this paper we analyze the global stability of a coupled model for Acute Myeloid Leukemia and propose a therapy approach based on an optimal control strategy. Firstly, based on the positivity of the model, stability of trivial solutions for healthy and cancerous cell subsystems is assessed. To this end we use new Lyapunov functionals and take into account the interconnection between cell populations. Secondly, stability conditions for healthy situation in interconnected model are established by using Nyquist criterion. And thirdly, we design an optimal control based therapy that aims to eradicate cancerous cells and minimize the side effects of the treatment on healthy ones. After showing the existence of an optimal control, this one is determined by using Pontriagyn's principal. We assess the effect of interconnection between healthy and cancerous cells on their dynamics and on the stability conditions for different cases. The behavior of the system in open loop and with application of the optimal control therapy is illustrated by simulation and results are biologically explained and motivated.

Study of cohabitation and interconnection effects on normal and leukaemic stem cells dynamics in acute myeloid leukaemia

On the basis of recent studies, understanding the intimate relationship between normal and leukaemic stem cells is very important in leukaemia treatment. The authors' aim in this work is to clarify and assess the effect of coexistence and interconnection phenomenon on the healthy and cancerous stem cell dynamics. To this end, they perform the analysis of two time-delayed stem cell models in acute myeloid leukaemia. The first model is based on decoupled healthy and cancerous stem cell populations (i.e. there is no interaction between cell dynamics) and the second model includes interconnection between both population's dynamics. By using the positivity of both systems, they build new linear functions that permit to derive global stability conditions for each model. Moreover, knowing that most common types of haematological diseases are characterised by the existence of oscillations, they give conditions for the existence of a limit cycle (oscillations) in a particularly interesting healthy situation based on Poincare-Bendixson theorem. The obtained results are simulated and interpreted to be significant in understanding the effect of interconnection and would lead to an improvement in leukaemia treatment.

Prognosis of Primary Myelofibrosis in the Genomic Era

Currently, prognostication in primary myelofibrosis (PMF) relies on the International Prognostic Scoring System (IPSS), dynamic IPSS (DIPSS), and DIPSS-plus, which incorporate age, blood counts, constitutional symptoms, circulating blasts, red cell transfusion need, and karyotype. Although the JAK2 V617F mutation was discovered a decade ago and MPL mutations shortly thereafter, it was the recent discovery of CALR mutations in the vast majority of JAK2/MPL-unmutated patients and recognition of the powerful impact of CALR mutations and triple-negative (JAK2/MPL/CALR-negative) status on outcome that set the stage for revision of traditional prognostic models to include molecular information. Additionally, the advent of next-generation sequencing has identified a host of previously unrecognized somatic mutations across hematologic malignancies. As in the myelodysplastic syndromes, the majority of common and prognostically informative mutations in PMF affect epigenetic regulation and mRNA splicing. Thus, a need has arisen to incorporate mutational information on genes such as ASXL1 and SRSF2 into risk stratification systems. Mutations in yet other genes appear to be important players in leukemic transformation, and new insights into disease pathogenesis are emerging. Finally, the number of prognostically detrimental mutations may affect both survival and response to ruxolitinib, which has significant implications for clinical decision making. In this review, we briefly summarize the prognostic models in use today and discuss in detail the somatic mutations commonly encountered in patients with PMF, along with their prognostic implications and role in leukemic transformation. Emerging prognostic models that incorporate new molecular information into existing systems or exclude clinical variables are also presented.

Clonal dominance and transplantation dynamics in hematopoietic stem cell compartments

Hematopoietic stem cells in mammals are known to reside mostly in the bone marrow, but also transitively passage in small numbers in the blood. Experimental findings have suggested that they exist in a dynamic equilibrium, continuously migrating between these two compartments. Here we construct an individual-based mathematical model of this process, which is parametrised using existing empirical findings from mice. This approach allows us to quantify the amount of migration between the bone marrow niches and the peripheral blood. We use this model to investigate clonal hematopoiesis, which is a significant risk factor for hematologic cancers. We also analyse the engraftment of donor stem cells into non-conditioned and conditioned hosts, quantifying the impact of different treatment scenarios. The simplicity of the model permits a thorough mathematical analysis, providing deeper insights into the dynamics of both the model and of the real-world system. We predict the time taken for mutant clones to expand within a host, as well as chimerism levels that can be expected following transplantation therapy, and the probability that a preconditioned host is reconstituted by donor cells.

Clonal hematopoiesis—where mature myeloid cells in the blood deriving from a single stem cell are over-represented—is a major risk factor for overt hematologic malignancies. To quantify how likely this phenomena is, we combine existing observations with a novel stochastic model and extensive mathematical analysis. This approach allows us to observe the hidden dynamics of the hematopoietic system. We conclude that for a clone to be detectable within the lifetime of a mouse, it requires a selective advantage. I.e. the clonal expansion cannot be explained by neutral drift alone. Furthermore, we use our model to describe the dynamics of hematopoiesis after stem cell transplantation. In agreement with earlier findings, we observe that niche-space saturation decreases engraftment efficiency. We further discuss the implications of our findings for human hematopoiesis where the quantity and role of stem cells is frequently debated.

Dynamical models of mutated chronic myelogenous leukemia cells for a post-imatinib treatment scenario: Response to dasatinib or nilotinib therapy

Targeted inhibition of the oncogenic BCR-ABL1 fusion protein using the ABL1 tyrosine kinase inhibitor imatinib has become standard therapy for chronic myelogenous leukemia (CML), with most patients reaching total and durable remission. However, a significant fraction of patients develop resistance, commonly due to mutated ABL1 kinase domains. This motivated development of second-generation drugs with broadened or altered protein kinase selectivity profiles, including dasatinib and nilotinib. Imatinib-resistant patients undergoing treatment with second-line drugs typically develop resistance to them, but dynamic and clonal properties of this response differ. Shared, however, is the observation of clonal competition, reflected in patterns of successive dominance of individual clones. We present three deterministic mathematical models to study the origins of clinically observed dynamics. Each model is a system of coupled first-order differential equations, considering populations of three mutated active stem cell strains and three associated pools of differentiated cells; two models allow for activation of quiescent stem cells. Each approach is distinguished by the way proliferation rates of the primary stem cell reservoir are modulated. Previous studies have concentrated on simulating the response of wild-type leukemic cells to imatinib administration; our focus is on modelling the time dependence of imatinib-resistant clones upon subsequent exposure to dasatinib or nilotinib. Performance of the three computational schemes to reproduce selected CML patient profiles is assessed. While some simple cases can be approximated by a basic design that does not invoke quiescence, others are more complex and require involvement of non-cycling stem cells for reproduction. We implement a new feedback mechanism for regulation of coupling between cycling and non-cycling stem cell reservoirs that depends on total cell populations. A bifurcation landscape analysis is also performed for solutions to the basic ansatz. Computational models reproducing patient data illustrate potential dynamic mechanisms that may guide optimization of therapy of drug resistant CML.

The landscape of somatic mutations in protein coding genes in apparently benign human tissues carries signatures of relaxed purifying selection

Mutations acquired during development and aging lead to inter- and intra-tissue genetic variations. Evidence linking such mutations to complex traits and diseases is rising. We detected somatic mutations in protein-coding regions in 140 benign tissue samples representing nine tissue-types (bladder, breast, liver, lung, prostate, stomach, thyroid, head and neck) and paired blood from 70 donors. A total of 80% of the samples had 2–39 mutations detectable at tissue-level resolution. Factors such as age and smoking were associated with increased burden of detectable mutations, and tissues carried signatures of distinct mutagenic processes such as oxidative DNA damage and transcription-coupled repair. Using mutational signatures, we predicted that majority of the mutations in blood originated in hematopoietic stem and early progenitor cells. Missense to silent mutations ratio and the persistence of potentially damaging mutations in expressed genes carried signatures of relaxed purifying selection. Our findings have relevance for etiology, diagnosis and treatment of diseases including cancer.

Etiology and treatment of hematological neoplasms: stochastic mathematical models

Leukemias are driven by stemlike cancer cells (SLCC), whose initiation, growth, response to treatment, and posttreatment behavior are often "stochastic", i.e., differ substantially even among very similar patients for reasons not observable with present techniques. We review the probabilistic mathematical methods used to analyze stochastics and give two specific examples. The first example concerns a treatment protocol, e.g., for acute myeloid leukemia (AML), where intermittent cytotoxic drug dosing (e.g., once each weekday) is used with intent to cure. We argue mathematically that, if independent SLCC are growing stochastically during prolonged treatment, then, other things being equal, front-loading doses are more effective for tumor eradication than back loading. We also argue that the interacting SLCC dynamics during treatment is often best modeled by considering SLCC in microenvironmental niches, with SLCC-SLCC interactions occurring only among SLCC within the same niche, and we present a stochastic dynamics formalism, involving "Poissonization," applicable in such situations. Interactions at a distance due to partial control of total cell numbers are also considered. The second half of this chapter concerns chromosomal aberrations, lesions known to cause some leukemias. A specific example is the induction of a Philadelphia chromosome by ionizing radiation, subsequent development of chronic myeloid leukemia (CML), CML treatment, and treatment outcome. This time evolution involves a coordinated sequence of > 10 steps, each stochastic in its own way, at the subatomic, molecular, macromolecular, cellular, tissue, and population scales, with corresponding time scales ranging from picoseconds to decades. We discuss models of these steps and progress in integrating models across scales.

JAK2V617F expression in mice amplifies early hematopoietic cells and gives them a competitive advantage that is hampered by IFNα

The acquired gain-of-function V617F mutation in the Janus Kinase 2 (JAK2(V617F)) is the main mutation involved in BCR/ABL-negative myeloproliferative neoplasms (MPNs), but its effect on hematopoietic stem cells as a driver of disease emergence has been questioned. Therefore, we reinvestigated the role of endogenous expression of JAK2(V617F) on early steps of hematopoiesis as well as the effect of interferon-α (IFNα), which may target the JAK2(V617F) clone in humans by using knock-in mice with conditional expression of JAK2(V617F) in hematopoietic cells. These mice develop a MPN mimicking polycythemia vera with large amplification of myeloid mature and precursor cells, displaying erythroid endogenous growth and progressing to myelofibrosis. Interestingly, early hematopoietic compartments [Lin-, LSK, and SLAM (LSK/CD48-/CD150+)] increased with the age. Competitive repopulation assays demonstrated disease appearance and progressive overgrowth of myeloid, Lin-, LSK, and SLAM cells, but not lymphocytes, from a low number of engrafted JAK2(V617F) SLAM cells. Finally, IFNα treatment prevented disease development by specifically inhibiting JAK2(V617F) cells at an early stage of differentiation and eradicating disease-initiating cells. This study shows that JAK2(V617F) in mice amplifies not only late but also early hematopoietic cells, giving them a proliferative advantage through high cell cycling and low apoptosis that may sustain MPN emergence but is lost upon IFNα treatment.

Mathematical modeling of therapeutic strategies for myeloid malignancies

The existence of malignant stem cells has been proven for hematopoietic disorder as well as some solid tumors. Although significant improvements in cancer therapy have been made, tumor recurrence is frequent and can partly be due to the absence of therapeutic target which tumor stem cells are regarded as. In this paper we shall explore different therapeutic scenarios for successful tumor treatment by using a predictive mathematical model based on the cell compartment method. In particular, we shall study the effects of the chemotherapeutic target rate and of the interval of G-CSF administration on therapy for myeloid malignancies through simulating chemotherapy with G-CSF (granulocyte colony-stimulating factor) support. The results indicate that if target rate is raised to an enough high value, the efficiency of chemotherapy increases so greatly that the tumor mature cells perish completely and normal mature cells are maintained at a normal level. Furthermore, the administration of G-CSF can increase the amount of the normal mature cells to a normal level. However, too long interval of G-CSF administration is demonstrated not propitious to patients' healing. These results indicate that the simulations may be an effective approach to help designing therapeutic scenarios for successful tumor treatment by chemotherapy.

New mutations and pathogenesis of myeloproliferative neoplasms

Myeloproliferative neoplasms (MPNs) are clonal disorders characterized by excessive production of mature blood cells. In the majority of classic MPN—polycythemia vera, essential thrombocythemia, and primitive myelofibrosis—driver oncogenic mutations affecting Janus kinase 2 (JAK2) or MPL lead to constitutive activation of cytokine-regulated intracellular signaling pathways. LNK, c-CBL, or SOCSs (all negative regulators of signaling pathways), although infrequently targeted, may either drive the disease or synergize with JAK2 and MPL mutations. IZF1 deletions or TP53 mutations are mainly found at transformation phases and are present at greater frequency than in de novo acute myeloid leukemias. Loss-of-function mutations in 3 genes involved in epigenetic regulation, TET2, ASXL1, and EZH2, may be early events preceding JAK2V617F but may also occur late during disease progression. They are more frequently observed in PMF than PV and ET and are also present in other types of malignant myeloid diseases. A likely hypothesis is that they facilitate clonal selection, allowing the dominance of the JAK2V617F subclone during the chronic phase and, together with cooperating mutations, promote blast crisis. Their precise roles in hematopoiesis and in the pathogenesis of MPN, as well as their prognostic impact and potential as a therapeutic target, are currently under investigation.

Minimal residual disease and discontinuation of therapy in chronic myeloid leukemia: can we aim at a cure?

Patients with chronic myeloid leukemia (CML) who have achieved a complete molecular response (CMR) defined by no detectable BCR-ABL mRNA on imatinib (IM) treatment often ask whether it is necessary for treatment to continue. We now know that approximately 40% of patients with a stable CMR for at least 2 years are able to stop IM treatment and remain in molecular remission for at least 2 years. This exciting observation has raised hopes that many patients can be cured of CML without the need for transplantation and its attendant risks. One might argue that for many patients maintenance therapy with IM or an alternative kinase inhibitor is so well tolerated that there is no imperative to stop treatment; however, chronic medical therapy may be associated with impaired quality of life and reduced compliance. Inferences about the biology of CML in patients responding to kinase inhibitors can be drawn from clinical experience, molecular monitoring data, and experimental observations. We summarize this information herein, and propose 3 possible pathways to "cure" of CML by kinase inhibitors: stem-cell depletion, stem-cell exhaustion, and immunological control.

Disease burden at the progenitor level is a feature of primary myelofibrosis: a multivariable analysis of 164 JAK2 V617F-positive myeloproliferative neoplasm patients

OBJECTIVE

Suppression of normal hematopoiesis by the neoplastic clone (clonal dominance) is a feature of the myeloproliferative neoplasms, but the determinants that predict clonal dominance are unknown. The objective of this study was to identify clinical and laboratory variables that associate with the JAK2 V617F CD34(+) progenitor allele burden and clonal dominance, which was defined by congruence of the JAK2 V617F CD34(+) progenitor and neutrophil allele burdens.

MATERIALS AND METHODS

A cross-sectional analysis was performed on 164 consecutive JAK2 V617F-positive patients: 30 with essential thrombocytosis (ET), 100 with polycythemia vera (PV), and 34 with myelofibrosis (MF), including 8 post-ET MF and 3 post-PV MF. The JAK2 V617F CD34(+) progenitor and neutrophil allele burdens were measured using an allele-specific, quantitative real-time polymerase chain reaction assay.

RESULTS

After adjusting for genotype, sex, age at diagnosis, and disease duration, disease type was the strongest predictor of clonal dominance, with the odds ratio being nearly 61.9 times higher for MF patients when compared with ET patients (p < 0.001), and 9.7 times higher when compared with PV patients (p = 0.002). Additionally, clonal dominance was associated with a clinical phenotype of an increased spleen size (p = 0.006), increased white blood cell count (p = 0.009), and lower hemoglobin (p < 0.001), even after adjusting for disease type and duration.

CONCLUSIONS

These data indicate that loss of wild-type clones at the progenitor level is a feature of MF (primary MF, post-ET MF, and post-PV MF), presumably due to expansion of the JAK2 V617F clone and that this characteristic is surprisingly independent of JAK2 V617F homozygosity, suggesting that additional genomic lesions may contribute to this unique molecular process that distinguishes MF from ET and PV.

Global dynamics of hematopoietic stem cells and differentiated cells in a chronic myeloid leukemia model

We consider a mathematical model describing evolution of normal and leukemic hematopoietic stem cells (HSC) and differentiated cells in bone marrow. We focus on chronic myeloid leukemia (CML), a cancer of blood cells resulting from a malignant transformation of hematopoietic stem cells. The dynamics are given by a system of ordinary differential equations for normal and leukemic cells. Homeostasis regulates the proliferation of normal HSC and leads the dynamics to an equilibrium. This mechanism is partially efficient for leukemic cells. We define homeostasis by a functional of either hematopoietic stem cells, differentiated cells or both cell lines. We determine the number of hematopoietic stem cells and differentiated cells at equilibrium. Conditions for regeneration of hematopoiesis and persistence of CML are obtained from the global asymptotic stability of equilibrium states. We prove that normal and leukemic cells can not coexist for a long time. Numerical simulations illustrate our analytical results. The study may be helpful in understanding the dynamics of normal and leukemic hematopoietic cells.

Hematopoiesis and its disorders: a systems biology approach

Scientists have traditionally studied complex biologic systems by reducing them to simple building blocks. Genome sequencing, high-throughput screening, and proteomics have, however, generated large datasets, revealing a high level of complexity in components and interactions. Systems biology embraces this complexity with a combination of mathematical, engineering, and computational tools for constructing and validating models of biologic phenomena. The validity of mathematical modeling in hematopoiesis was established early by the pioneering work of Till and McCulloch. In reviewing more recent papers, we highlight deterministic, stochastic, statistical, and network-based models that have been used to better understand a range of topics in hematopoiesis, including blood cell production, the periodicity of cyclical neutropenia, stem cell production in response to cytokine administration, and the emergence of imatinib resistance in chronic myeloid leukemia. Future advances require technologic improvements in computing power, imaging, and proteomics as well as greater collaboration between experimentalists and modelers. Altogether, systems biology will improve our understanding of normal and abnormal hematopoiesis, better define stem cells and their daughter cells, and potentially lead to more effective therapies.

From genes to cells to tissues--modelling the haematopoietic system

Haematopoiesis (or blood formation) in general and haematopoietic stem cells more specifically represent some of the best studied mammalian developmental systems. Sophisticated purification protocols coupled with powerful biological assays permit functional analysis of highly purified cell populations both in vitro and in vivo. However, despite several decades of intensive research, the sheer complexity of the haematopoietic system means that many important questions remain unanswered or even unanswerable with current experimental tools. Scientists have therefore increasingly turned to modelling to tackle complexity at multiple levels ranging from networks of genes to the behaviour of cells and tissues. Early modelling attempts of gene regulatory networks have focused on core regulatory circuits but have more recently been extended to genome-wide datasets such as expression profiling and ChIP-sequencing data. Modelling of haematopoietic cells and tissues has provided insight into the importance of phenotypic heterogeneity for the differentiation of normal progenitor cells as well as a greater understanding of treatment response for particular pathologies such as chronic myeloid leukaemia. Here we will review recent progress in attempts to reconstruct segments of the haematopoietic system. A variety of modelling strategies will be covered from small-scale, protein-DNA or protein-protein interactions to large scale reconstructions. Also discussed will be examples of how stochastic modelling may be applied to multi cell systems such as those seen in normal and malignant haematopoiesis.

New experimental and theoretical investigations of hematopoietic stem cells and chronic myeloid leukemia

We report on a focused workshop of The Leukemia and Lymphoma Society that was held at Goldsmiths, University of London in 2008. During this workshop we discussed new clinical and experimental data in chronic myeloid leukemia (CML) research, particularly focusing on the validity (or otherwise) of corresponding mathematical models and simulations. We were specifically interested in whether the models could shed light on any of the fundamental mechanisms underlying this disease. Moreover, we were aiming to form a new community of clinicians and modelers looking at this disease and to define a common language and theoretical framework within which collaboration could flourish. The workshop showed the role that models can play, not just in trying to fit to existing data or predicting what individual mechanisms or system behaviors might occur, but also in challenging the orthodoxy of the concept of a stem cell and concepts such as "differentiation" and "determination". For years the prevailing view of a stem cell has been an entity (object) with a fixed set of behaviors and with a pre-determined fate. New perspectives in modeling, coupled with the new data that are being accumulated in the genesis of CML and its treatment, questions these assumptions. We propose how we can reach a consensus about a functional view of stem cells in a more continuous and flexible way and how, within this context, we can investigate the significance of modeling results and how they might impact on our interpretation of experimental observations and the development of new clinical strategies. This paper reports on the workshop and the state-of-the-art models and data from experimental and clinical trials, and sets out a roadmap for more interdisciplinary collaboration between modelers, wet-lab experimentalists, and clinicians interested in CML. It is our strong belief that a more integrated and coherent interdisciplinary approach will further advance the treatment of CML in future years.

Does primary myelofibrosis involve a defective stem cell niche? From concept to evidence

Primary myelofibrosis (PMF) is the rarest and the most severe Philadelphia-negative chronic myeloproliferative syndrome. By associating a clonal proliferation and a mobilization of hematopoietic stem cells from bone marrow to spleen with profound alterations of the stroma, PMF is a remarkable model in which deregulation of the stem cell niche is of utmost importance for the disease development. This paper reviews key data suggesting that an imbalance between endosteal and vascular niches participates in the development of clonal stem cell proliferation. Mechanisms by which bone marrow niches are altered with ensuing mobilization and homing of neoplastic hematopoietic stem cells in new or reinitialized niches in the spleen and liver are examined. Differences between signals delivered by both endosteal and vascular niches in the bone marrow and spleen of patients as well as the responsiveness of PMF stem cells to their specific signals are discussed. A proposal for integrating a potential role for the JAK2 mutation in their altered sensitivity is made. A better understanding of the cross talk between stem cells and their niche should imply new therapeutic strategies targeting not only intrinsic defects in stem cell signaling but also regulatory hematopoietic niche-derived signals and, consequently, stem cell proliferation.

Csf3r mutations in mice confer a strong clonal HSC advantage via activation of Stat5

A fundamental property of leukemic stem cells is clonal dominance of the bone marrow microenvironment. Truncation mutations of CSF3R, which encodes the G-CSF receptor (G-CSFR), are implicated in leukemic progression in patients with severe congenital neutropenia. Here we show that expression of a truncated mutant Csf3r in mice confers a strong clonal advantage at the HSC level that is dependent upon exogenous G-CSF. G-CSF-induced proliferation, phosphorylation of Stat5, and transcription of Stat5 target genes were increased in HSCs isolated from mice expressing the mutant Csf3r. Conversely, the proliferative advantage conferred by the mutant Csf3r was abrogated in myeloid progenitors lacking both Stat5A and Stat5B, and HSC function was reduced in mice expressing a truncated mutant Csf3r engineered to have impaired Stat5 activation. These data indicate that in mice, inappropriate Stat5 activation plays a key role in establishing clonal dominance by stem cells expressing mutant Csf3r.

Insertional mutagenesis and clonal dominance: biological and statistical considerations

Improvements of (retroviral) gene transfer vectors, stem cell isolation and culture techniques as well as transduction protocols eventually resulted not only in the successful genetic modification of cells capable of reconstituting the haematopoietic system in various animal models, but also human beings. This was a conditio sine qua non for the successful application of gene therapy for inherited diseases as meanwhile achieved for severe combined immune deficiencies (SCID-X1, ADA-SCID) and chronic granulomatous disease (CGD). Unexpectedly, in long-term animal experiments as well as in the follow up of patients from the CGD trial, haematopoietic clones bearing insertions in certain gene loci became dominant, which was most apparent in the myeloid blood compartment. Accumulating data strongly suggest that this clonal dominance was due to some growth and/or survival advantage conferred by gene-activating or -suppressing effects of the integrated retroviral vector (insertional mutagenesis). Importantly, such induced clonal dominance seems not to lead to malignant transformation of affected cell clones inadvertently. The latter finding has become the basis for the concept of 'induced haematopoietic stem cells', a potentially powerful tool to investigate genes involved in the regulation of mechanisms underlying competitive advantages of stem cells, but also in the multi-step nature of malignant transformation. Here we discuss promises and open issues of this concept as well as the important question of common insertion sites statistics and its pitfalls.

JAK2 617V>F–positive polycythemia rubra vera maintained by approximately 18 stochastic stem-cell divisions per year, explaining age of onset by a single rate-limiting mutation

As the rates of most cancers are proportional to the fourth to fifth power of age (“log-log” behavior), it is widely believed that 5 to 6 independent mutations are necessary for malignant transformation. Conversely, the peak incidences of most cancers are similar to stem-cell mutation rates at single loci, implying only one rate-limiting mutation. Here, flow cytometrically measured red blood cells mutated at a selectively neutral locus, glycophorin A, allow observation of individual stem-cell differentiation events in a log-log malignancy, polycythemia rubra vera. Contrary to predictions from multistep models, the clone is driven by infrequent (< annual) and rare (∼ 18 per year) differentiation events. These parameters imply that malignant stem cells have a modest selective advantage. Correspondingly minor, typically less than 20%, increases in stochastic self-renewal ratios are modeled to show that single mutations can result in the observed fourth power relationship with age. The conundrum between log-log behavior and mutation rate is thereby reconcilable, with the age of onset arising not from the requirement for multiple, independent mutations but from infrequent, stochastic stem-cell division rates and single mutations causing initially minor effects, but initiating a clone whose expected number increases successively with age—an “exponential phenotype.”

Acquired hematopoietic stem-cell disorders and mammalian size

Hematopoietic stem cells (HSCs) can both self renew and differentiate into precursors of all types of blood cells. HSCs are divided into an active pool and a quiescent reserve. Cells selected for the active pool contribute to hematopoiesis for many years. Mutations in HSCs can lead to neoplasms such as chronic myeloid leukemia, although the risk of neoplastic HSC disorders varies across mammals. We use allometric scaling relations combined with mutation-selection evolutionary dynamics to determine which mammalian species is most resistant to HSC disorders. We find that the advantage of large mammals at escaping the selective pressure of cancer cells is insufficient to overcome the increased risk of acquiring mutations. Hence, mutation dominates, which favors smaller stem-cell pools and, consequently, smaller mammals, since these minimize the development of mutations in the active stem-cell pool. Consequently, the smaller the active stem-cell pools, the better.

Pathogenesis, treatment effects, and resistance dynamics in chronic myeloid leukemia--insights from mathematical model analyses

Mathematical models and simulation studies are powerful tools to investigate dynamic properties of complex systems. Specifically, they can be used to test alternative hypotheses on underlying biological mechanisms for their consistency with real data and therefore to effectively guide the design of new experimental strategies or clinical trials. In this study, we present an overview of recently published mathematical approaches applied to the description of chronic myeloid leukemia (CML). We discuss three different fields relevant to clinical issues: the pathogenesis of the malignancy, the treatment effects of the tyrosine kinase inhibitor imatinib, and the process of acquired treatment resistance highlighting both the differences and the consistencies in the proposed hypotheses and the resulting conclusions. The mathematical models presented agree that CML can adequately be described as a clonal competition between normal and leukemic stem cells for a common resource. Furthermore, a certain therapeutic effect of imatinib on leukemic stem cells turned out to be necessary to consistently explain clinical data on the long-term response of CML patients under imatinib treatment. However, the approaches described cannot resolve the question whether or not this effect is sufficient to ultimately eradicate malignant stem cells. A number of different hypotheses have been proposed concerning the initiation and the dynamics of treatment-resistant malignant stem cell clones. The theoretical results clearly indicate that further experimental effort with the particular focus on the quantitative monitoring of resistant clones will be required to definitely distinguish between these hypotheses.

Dynamic modeling of imatinib-treated chronic myeloid leukemia: functional insights and clinical implications

Treatment of chronic myeloid leukemia (CML) with the tyrosine kinase inhibitor imatinib represents a successful application of molecularly targeted cancer therapy. A rapid hematologic and cytogenetic response can be induced in the majority of people, even in advanced disease. However, complete eradication of malignant cells, which are characterized by the expression of the BCR-ABL1 fusion protein, is rare. Reasons for the persistence of the malignant clone are currently not known and provide a substantial challenge for clinicians and biologists. Based on a mathematical modeling approach that quantitatively explains a broad range of phenomena, we show for two independent datasets that clinically observed BCR-ABL1 transcript dynamics during imatinib treatment of CML can consistently be explained by a selective functional effect of imatinib on proliferative leukemia stem cells. Our results suggest the general potential of imatinib to induce a complete elimination of the malignant clone. Moreover, we predict that the therapeutic benefit of imatinib can, under certain circumstances, be accelerated by combination with proliferation-stimulating treatment strategies.

Quantitative stem cell biology: computational studies in the hematopoietic system

PURPOSE OF REVIEW

This review is intended to provide an overview of recently published computational methods, including bioinformatic algorithms, mathematical models and simulation studies, applied to stem cell biology, with particular reference to the hematopoietic system.

RECENT FINDINGS

The analysis of molecular data is making an increased contribution to identify dynamic system responses. Specifically, there are promising computational approaches to characterizing the functional interrelation of network components regulating the process of differentiation and lineage specification of hematopoietic stem cells. Furthermore, evidence is accumulating that stem cell organization should be regarded as a flexible, self-organizing process rather than as a predetermined sequence of events. A number of mathematical models relevant to the hematopoietic (stem cell) system are applied successfully to clinical situations, demonstrating the predictive power of theoretical methods.

SUMMARY

Based on the advances in measurement technology, an increasing amount of cellular and molecular data is being generated within the field of stem cell biology. The complexity of the underlying systems, however, most often limits a direct interpretation of the data and makes computational methods indispensable. Mathematical models and simulation techniques are contributing considerably to the discovery of general regulatory principles of stem cell organization and are providing clinically relevant predictions.

Relation between JAK2 (V617F) mutation status, granulocyte activation, and constitutive mobilization of CD34+ cells into peripheral blood in myeloproliferative disorders

We studied the relationship between granulocyte JAK2 (V617F) mutation status, circulating CD34(+) cells, and granulocyte activation in myeloproliferative disorders. Quantitative allele-specific polymerase chain reaction (PCR) showed significant differences between various disorders with respect to either the proportion of positive patients (53%-100%) or that of mutant alleles, which overall ranged from 1% to 100%. In polycythemia vera, JAK2 (V617F) was detected in 23 of 25 subjects at diagnosis and in 16 of 16 patients whose disease had evolved into myelofibrosis; median percentages of mutant alleles in these subgroups were significantly different (32% versus 95%, P < .001). Circulating CD34(+) cell counts were variably elevated and associated with disease category and JAK2 (V617F) mutation status. Most patients had granulocyte activation patterns similar to those induced by administration of granulocyte colony-stimulating factor. A JAK2 (V617F) gene dosage effect on both CD34(+) cell counts and granulocyte activation was clearly demonstrated in polycythemia vera, where abnormal patterns were mainly found in patients carrying more than 50% mutant alleles. These observations suggest that JAK2 (V617F) may constitutively activate granulocytes and by this means mobilize CD34(+) cells. This exemplifies a novel paradigm in which a somatic gain-of-function mutation is initially responsible for clonal expansion of hematopoietic cells and later for their abnormal trafficking via an activated cell progeny.