Our research projects centre on the following topics:
Projects focused on leukemias:
Natural history and backtracking of leukaemias
We have a long term interest in natural history of leukaemias, origin and nature of genetic changes leading to overt leukaemia and in dynamics of (pre)leukaemic clone between the initial and final "hits". We are interested in backtracking of secondary leukaemias (in a material archived from diagnosis and monitoring of the primary disease) as well as de-novo leukaemias (in neonatal material - archived dried blood spots and cord bloods - and in pre-diagnostic material in leukaemias with slow onset).
Project leader: Jan Zuna
Leukaemias with BCR-ABL1 fusion gene
Comparing levels of residual disease established by quantification of Ig/TCR rearrangements vs. BCR-ABL1 fusion gene (both at RNA and at DNA levels) we described a novel leukaemia subtype situated at the border between acute lymphoblastic and chronic myeloid leukaemia and we assigned it "CML-like" (Zaliova et al., Leukemia 2009; Hovorkova et al., Blood 2017). Now we analyse biological and clinical differences between subtypes of the BCR-ABL1-positive leukaemias in more detail.
Project leader: Jan Zuna
Genomics of Pediatric ALL
During the past few years, the introduction of „high-throughput“ methods such as high-density SNP arrays and next generation sequencing (especially whole-exome and –transcriptome sequencing) largely impacted ALL classification, significantly enlarged the spectrum of known recurrently occurring genetic lesions and helped to identify novel prognostic factors and therapeutic targets. We use the above mentioned methods to study B-other ALLs (B-ALLs that test negative in routine genetic screening) and to classify them into novel ALL subtypes, to identify druggable genetic lesions in therapy resistant ALLs and to study their clonal development.
Selected novel genetic lesions are further studied in individual research projects.
Project leader: Markéta Žaliová
Pathogenesis of Transient Myeloproliferative Disorder
The transient myeloproliferative disorder is a hematopoietic disease characterized by a clonal proliferation of megakaryoblasts which affects approximately 10% of newborns with Down syndrome. In the majority of cases, TMD resolves spontaneously, however, in some patients it gives rise to acute megakaryocytic leukemia. Trisomy 21 together with mutations in the GATA1 gene encoding a hematopoietic transcription factor were shown to play a key role in the pathogenesis of TMD. However, the exact role of trisomy 21 is unknown. We are studying an alternative mechanism of TMD pathogenesis, which does not require trisomy 21, since its role is probably compensated by a single gene mutation.
Project leader: Markéta Žaliová
Integrative analysis of high-throughput genomics and multiparameter flow cytometry to improved diagnosis and monitoring of childhood acute leukemia
Acute lymphoblastic leukemia (ALL) is the most frequent cancer in children. Its improving outcome depends on accurate diagnosis and minimal residual disease (MRD) monitoring as done by flow cytometry. In our project we will develop automatic tools usable in clinical setting to analyse large numbers of multidimensional flow cytometry datasets. This will allow for clinical relevant categorisation of leukemias based on their immunophenotypes (LAIPs) with respect to outcome and other clinical features. Likewise better description of LAIPs dynamics and changes under treatment will allow for optimisation of MRD detection. Moreover, we will use whole genome data to associate genetic traits to immunophenotypes. Such integrative analysis will provide insights into relevance of genetic aberrations and their propagation into phenotype.
Project leader: Karel Fišer
Role of homoeobox genes in leukaemogenesis
Homoeobox genes play a key role in both embryo- and organo-genesis. They are also supposed to be involved in cancer growth, namely in leukaemogenesis, considering the aberrant expression as it has been described. The aim of the project is to study the mechanisms responsible for the dysregulation of HOX genes. We have decided to study three of such mechanisms: DNA metylation, regulating the transcription of HOX genes during the embryonic development; mutations in the core promoter of HOX genes and alternative signalling caused by mutations of tyrosine kinases.
Project leader: Júlia Starková
International Registry of Ambiguous Lineage Leukemia in Children
International studies aiming at optimalization of therapy for children who are diagnostically somewhat between ALL and AML. More here https://clip.lf2.cuni.cz/alal/
Project leader: Ondřej Hrušák
Lineage switch leukemias
In past years we described a new subtype-behaviour of pediatric BCP ALL. In substantial proportion of patients we observe transdifferentiation towards monocytic lineage. Subtype is largely overlapping with ERG gene deleted and DUX4 rearranged BCP ALLs. We search for markers present on the blasts before blasts start to transdifferentiate and for markers enabling separation of switched monocytoid blasts from helathy monocytes.
Project leader: Ester Mejstříková
Differentiation plasticity of haematopoietic cells
For a long time, haematopoiesis was understood to be a strictly regulated process that, by way of gradual narrowing down the developmental choices of cell lineages, gives finally rise to fully differentiated cells. A number of recent papers, though, has documented the development of myeloid cells from myeloid precursors under certain, molecularly defined, conditions. Often seen in blood cancers is the aberrant expression of various antigens. It is not yet clear whether such promiscuousness stems from the naturally occurring developmental changes. The goal of this project is to clarify the relationship between the promiscuousness of the malignant vis-a-vis the plasticity of the normal haematopoietic cells, and to describe the regulatory pathways leading either to lineage restriction or to release from such restriction.
Project leader: Ondřej Hrušák
Projects focused on bone marrow failure and immunodeficiencies:
Antigen receptor gene rearrangements and their use in biomedicine
In recent years, next-generation sequencing (NGS) has enabled detailed studies of the rearrangements of the immunoglobulin (Ig) and T-cell receptor (TCR) genes, which are used by lymphocytes to respond to antigenic stimulation. In an international collaboration, our group focuses on the development of tools based on Ig/TCR detection by NGS for application in the diagnosis and research of immunopathological conditions. The main application is the measurement of minimal residual disease in leukemias and lymphomas. We also use this method to study changes in the immune repertoire of lymphocytes in diseases with immune dysregulation.
Project leader: Eva Froňková
Immunopathological mechanisms of bone marrow failure
Bone marrow failure syndromes are rare disorders in childhood. They interconnect immunology and hematology. Immune cells are responsible in individual subtypes of bone marrow failure for hematopoiesis failure. Recently we have new tools (namely mass and spectral cytometry) enabling analysis of many molecules on single cell level and evaluation of complex subpopulations.
Project leader: Ester Mejstříková
Genetic causes of immune system disorders
NGS has provided unprecedented insight into the biology and causes of bone marrow failure, immunodeficiency and immune dysregulation. Using whole-exome sequencing, we are unraveling the genetic mechanisms of these diseases and attempting to functionally demonstrate their causality.
Project leader: Eva Froňková
Detection of complex leukocyte changes by mass cytometry
By using a unique technology of mass cytometry, we study changes in surface markers as well as phosphorylated kinases in patients with failure of the hematopoietic system. Also, we study changes induced by specific inhibitors.
Project leader: Tomáš Kalina
Immune system dysregulation: lymphocyte characteristics of patients with primary immunodeficiency and autoimmune manifestations
We develop methods for early detection of genetically based immunopathological conditions using cytometric analyses. We perform functional testing of abnormalities in the function of lymphocytes of patients with primary immunodeficiency.
Project leader: Tomáš Kalina
Projects focused on cancer metabolism:
Studies on altered metabolism of leukemic cells
Altered metabolism which is present also in leukemic cells is an important player in disease progression, and its rewiring is considered one of the main features accompanying the response to therapy and possible initiation of resistance to current treatment. We aim to study the role of metabolism in leukemogenesis driven by genetic aberrations present at diagnosis or relapse. We also focus our interest on characterization of basal metabolic phenotype of leukemic cells and its impact on the therapy response and metabolic reprogramming triggered by cytostatic drugs administration and its consequences on sensitivity and efficacy of treatment.
Project leader: Júlia Starková
Study of the mechanism of action of L-asparaginase
L-asparaginase is a key cytotoxic agent used in the treatment of pediatric acute lymphoblastic leukemia. The cytotoxic effect of L-Asp lies in the ability to deplete extracellular asparagine and glutamine to which leukemic cells are highly sensitive, probably due to reduced activity of the glutamine-dependent enzyme asparagine synthetase. The role of this project is to describe in more detail the mechanism of L-asparaginase activity, which will help to better understand the differences between sensitive and resistant patients and will also suggest better stratification within the treatment protocol.
Project leader: Júlia Starková
Projects focused on solid tumors:
Molecular aberrations and the potential of liquid biopsy in testicular germ cell tumors and other solid malignancies
In the projects, we analyze molecular aberrations occurring at different stages of the disease in testicular germ cell tumor patients, with the aim to identify those responsible for the tumor progression, chemotherapy resistance, and representing eventually druggable targets. We also study the feasibility, limits and clinical impact of the detection of free circulating tumor DNA and circulating tumor cells in testicular germ cell tumors and other solid malignancies.
Project leader: Ludmila Boublíková
Imunologické vyšetření lymfomů v dětském věku
Vývoj diagnostických a prognostických nástrojů pro subtypy lymfomů v dětském věku pomocí průtokové cytometrie. Histopatologické hodnocení tkáně má nezastupitelné místo v diagnostice lymfoproliferací. Nicméně průtoková cytometrie dokáže množstvím hodnocených znaků velmi dobře popsat, jak vlastní nádorovou tkáň, tak i prostředí okolo.
Vedoucí projektu: Ester Mejstříková
Projects focused on gene therapy:
Genome-editing technologies in the treatment of inherited bone marrow failure syndromes
Gene therapy and CRISPR/Cas9 genome editing, in particular, represents a novel and promising strategy for treatment of rare monogenic disorders because it allows us to correct a disease-causing mutation in patient own cells. In rare diseases affecting hematopoiesis, the gene-corrected stem cells may represent an appealing alternative to the traditional blood and marrow transplantation. Our aim is to develop gene-editing tools for correction of causal mutations in patients with inherited bone marrow failure syndromes.
Project leader: Karolina Škvárová Kramarzová
Modeling of hematological disorders with unknown etihology
For verification of newly identified genetic aberrations and development of new therapies, a unique technology of genome editing can now be employed that allows for a precise modeling of a mutation phenotype. Using CRISPR/Cas9 system, we would like to make biological models for evaluation of pathogenicity of novel mutations identified in patients with atypical hematological diseases.
Project leader: Karolina Škvárová Kramarzová