PhD Program

Project Title: Genetic and epigenetic changes in hematopoietic stem cells during chronic inflammation
Supervisor: Meritxell Alberich Jordà

Project Description:
This project will determine the molecular changes in enhancers and promoters that chronic inflammation induces in hematopoietic stem cells. Next, we will investigate how these changes contribute to the development of leukemia, an hematological disorder characterized by the accumulation of malignant cells in bone marrow and blood. Together, the results of this project will uncover the mechanisms regulating hematopoietic stem cell maintenance and fate in the context of chronic inflammation, and lay the path to identify new therapeutic strategies in leukemia.

Candidate Profile:
The laboratory of hemato-oncology is searching for a highly motivated, enthusiastic and hard-working Ph.D student. The candidate should hold a master degree in genetics, molecular biology, cell biology, or in a related field. The candidate should be willing to work with murine models. Excellent English is required. The candidate should be a team-player and willing to work with other lab members and international collaborators.
We offer a friendly and supporting environment in a state-of-the-art institution.

Suggested reading:

• Liss A, Ooi CH, et al. The gene signature in CCAAT-enhancer-binding protein α dysfunctional acute myeloid leukemia predicts responsiveness to histone deacetylase inhibitors. Haematologica. 2014 Apr;99(4):697-705.
• Zjablovskaja P, Kardosova M, et al. EVI2B is a C/EBPa target gene required for granulocytic differentiation and functionality of hematopoietic progenitors. Cell Death Differ. 2017 Apr;24(4):705-716.
• Wurm AA, Zjablovskaja P, et al. Disruption of the C/EBPα-miR-182 balance impairs granulocytic differentiation. Nat Commun. 2017 Jun 29;8(1):46.
• Kardosova M, Zjablovskaja P, et al. C/EBPg is dispensable for steady-state and emergency granulopoiesis. Haematologica. 2018 Aug;103(8):e331-e335.

Project Title: Mechanisms of cell reprogramming
Supervisor: Petr Bartůněk

Project Description:
The project will focus on mechanisms of epigenetic control of hematopoietic cell reprogramming using unique model of zebrafish erythroid progenitor cell line that can be reprogrammed into myeloid lineage using cytokine switch only. The candidate will employ already established methods like ATAC-seq, ChIP-seq, RNAseq and further develop single-cell-based technologies.

Candidate Profile:
MSc or equivalent with strong background in biochemistry and molecular/cell biology.

Suggested reading:

• Graf T (2011) Historical origins of transdifferentiation and reprogramming. Cell Stem Cell. 9(6):504-16.
• Svoboda O, Stachura DL, Machonova O, Pajer P, Brynda J, Zon LI, Traver D, Bartunek P.* Dissection of vertebrate hematopoiesis using zebrafish thrombopoietin. Blood. 2014; 124(2):220-8.
• Svoboda O, Stachura DL, Machonova O, Zon LI, Traver D, Bartunek P.* Ex vivo tools for the clonal analysis of zebrafish hematopoiesis, Nat Protocols. 2016; 11(5):1007-20.

Project Title: The role of mutations in adaptor protein PSTPIP2 in autoinflammatory disease
Supervisor: Tomáš Brdička

Project Description:
The project will focus on explaining the mechanisms contributing to the development of autoinflammatory disease in animals carrying mutations in adaptor protein PSTPIP2. The candidate will explore the molecular mechanisms of how PSTPIP2 suppresses inflammatory signalling in neutrophils and other leukocytes of myeloid lineage and how the disease develops when this protein is mutated or absent. The project will include analysis of leukocyte development, migration, immune response and signalling pathways using genetically modified mouse models and cell lines. The disease closely resembles several human autoinflammatory bone disorders and the relevance of the results obtained within this project for human autoinflammatory disease will also be studied. In addition, the candidate will be involved in projects exploring function of other adaptor proteins involved in the regulation of leukocyte signalling and inflammation.

Candidate Profile:
The candidate must hold a Master degree (or be close to its completion) in immunology, molecular/cell biology, biochemistry or in related field of life sciences. The applicant must have a strong interest in immunology and related biomedical sciences. Ability to communicate in English is required.

Suggested reading:

• Drobek A, Kralova J, Skopcova T, et al. PSTPIP2, a Protein Associated with Autoinflammatory Disease, Interacts with Inhibitory Enzymes SHIP1 and Csk. J Immunol. 2015;195(7):3416-3426.
• Ferguson PJ, Laxer RM. New discoveries in CRMO: IL-1beta, the neutrophil, and the microbiome implicated in disease pathogenesis in Pstpip2-deficient mice. Semin Immunopathol. 2015;37(4):407-412.

Project Title: Adaptor protein OPAL1 in hematopoiesis, bone marrow transplantation and leukemia  
Supervisor: Tomas Brdicka

Project Description:
Until now OPAL1 has only been known at mRNA level as childhood leukemia marker, expression of which correlated with ETV6-RUNX1 translocation and favorable treatment outcome. Our unpublished work shows the involvement of OPAL1 protein in chemokine receptor signalling and in other pathways relevant for leukemia prognosis and development. Using OPAL1 deficient mice and cell lines, the candidate will study the mechanisms of how OPAL1 regulates hematopoiesis, various leukocyte functions and leukemic cell biology. Biochemical analysis of OPAL1 interactome and signalling pathways regulated by OPAL1 will also be included in the project. In addition, the candidate will be involved in exploring other adaptor proteins involved in the regulation of leukocyte signalling and development.

Candidate Profile:
The candidate must hold a Master degree (or be close to its completion) in immunology, molecular/cell biology, biochemistry or in related field of life sciences. The applicant must have a strong interest in immunology, haematology and related biomedical sciences. Ability to communicate in English is required.

Suggested reading:

• Mosquera-Caro M, Helman P, Veroff R, et al. Identification, validation and cloning of a novel gene (OPAL1) and associated genes highly predictive of outcome in pediatric acute lymphoblastic leukemia using gene expression profiling [abstract]. Blood. 2003;102(4a.
• Holleman A, den Boer ML, Cheok MH, et al. Expression of the outcome predictor in acute leukemia 1 (OPAL1) gene is not an independent prognostic factor in patients treated according to COALL or St Jude protocols. Blood. 2006;108(6):1984-1990.
• Pei J, Grishin NV. Unexpected diversity in Shisa-like proteins suggests the importance of their roles as transmembrane adaptors. Cell Signal. 2012;24(3):758-769.

Project Title: Defective DNA Damage Responses in Neurodegeneration
Supervisor: Hana Hanzlíková

Project Description:
DNA single-strand breaks (SSBs) are the most frequent DNA lesions arising in cells and are a major threat to cell survival and genetic integrity, as indicated by the elevated genetic deletion, embryonic lethality, and neurological disease observed if single-strand break repair (SSBR) is attenuated. Mice harbouring a brain-specific deletion of the critical SSBR protein XRCC1 recapitulate most of the phenotypes observed in patients with SSBR defects including cerebellar atrophy, ataxia and seizures. In this project we will focus on the generation and characterisation of new SSBR-defective mouse models, including a patient XRCC1 knock-in mutation. We will employ these model to address how unrepaired SSBs trigger neurodegeneration, highlighting new potential therapeutic approaches that might alleviate or prevent hereditary and/or sporadic neurodegenerative disease.

Candidate Profile:
The Institute of Molecular Genetics is an internationally renowned research institute that provides a stimulating and supportive environment spanning a range of experimental model systems and is located in a cutting edge research facility with state-of-art infrastructure and equipment. The project will also provide opportunity for periods of research in the Caldecott laboratory at the Genome Damage and Stability Center in Brighton, UK.

The successful applicant will be highly motivated and will have experience of working within a multidisciplinary team. Applicants must have a relevant master degree and preferably expertise in DNA damage responses and/or mice handling or at least must be enthusiastic and willing to work with murine model.

Suggested reading:

• Hoch N & Hanzlikova H et al. XRCC1 Mutation is Associated with PARP1 Hyperactivation and Cerebellar Ataxia. Nature. 2017. 541:87-91.
• Hanzlikova H et al. The Importance of Poly(ADP-Ribose) Polymerase as a Sensor of Unligated Okazaki Fragments during DNA Replication. Mol Cell. 2018. 71(2): 319-331.e3
• Kalasova I & Hanzlikova H et al. Novel PNKP mutations causing defective DNA strand break repair and PARP1 hyperactivity in MCSZ. Neurol Genet. 2019. 5(2): e320.
• Komulainen E et al. Poly(ADP-ribose) Polymerase-1 Hyperactivity at DNA Single-Strand Breaks Triggers Seizures and Shortened Lifespan. BioRxiv preprint. 2018. doi: http://dx.doi.org/10.110

Project Title: The role of PRDM9-mediated synapsis of meiotic chromosomes in hybrid sterility
Supervisors: Jiří Forejt

Project Description:
By using laboratory strains of mice as a model we identified Prdm9 as the first hybrid sterility gene in vertebrates. Although this model of hybrid sterility has proved robust and reproducible, its molecular mechanism remains largely unknown. Thus, in this project we will ascertain the role of Prdm9 in meiotic recombination and chromosome pairing in sterile if mouse hybrids.

Candidate Profile:
The laboratory of Mouse Molecular Genetics is opening the position for a highly motivated Ph.D student. The candidate should hold a master degree in genetics or molecular biology. The bioinformatics skills and previous research experience in cell biology and biochemistry of meiosis is welcome but not necessary. Excellent English is required. We provide a friendly and supportive environment for continuous scientific growth.

Suggested reading:

• Davies, B., E. Hatton, N. Altemose, J. G. Hussin, F. Pratto et al., 2016 Re-engineering the zinc fingers of PRDM9 reverses hybrid sterility in mice. Nature 530: 171–176.
• Forejt J. Genetics: Asymmetric breaks in DNA cause sterility. Nature 530:167-8.2016.
• Gregorova, S., Gergelits, V. Chvatalova, I., Bhattacharyya, T., Valiskova B., Fotopulosova V., Jansa, P., Wiatrowska, D., Forejt, J, 2018 Modulation of Prdm9-controlled meiotic chromosome asynapsis overrides hybrid sterility in mice. Elife pii: e34282

Project Title: The role of extracellular matrix stiffness and composition in development of liver
Supervisors: Martin Gregor

Project Description:
Liver fibrosis is excessive scarring process resulting from chronic insults of heterogenous etiology. The major hallmark of liver fibrosis is deposition of fibrous extracellular matrix (ECM) synthetized mainly by hepatic stellate cells (HSCs). The major goal of this project is analysis of interplay between HSCs and altering ECM niche, using newly developed mouse model harboring HSCs with compromized ECM-receptor signaling. This phenomena will be then studied in vitro, using human HSC line and mouse primary HSCs to better understand the processes regulating deposition and composition of ECM in liver fibrosis.

The successful candidates will learn and utilize advanced cell-biology, molecular-biology, physiology, imaging techniques and atomic force microscopy, while developing and analyzing various mouse models.

Candidate Profile:
We are seeking outstanding self-motivated candidates with master’s degree in molecular biology, physiology, biochemistry or related fields. We are offering research at a state-of-the-art equipped institute with experienced colleagues, international working environment and international collaborations.

Suggested reading:

• Gregor M. et al. Mechanosensing through focal adhesion-anchored intermediate filaments. FASEB J., 28:715-29, 2014.
• Burgstaller G. et al. Keeping the vimentin network under control: cell–matrix adhesion-associated plectin 1f affects cell shape and polarity of fibroblasts. Mol. Biol. Cell, 21:3362–3375, 2010.
• Jirouskova M. et al. Plectin Controls Biliary Tree Architecture and Stability in Cholestasis. J Hepatol., 68:1006-1017, 2018.
• Duscher D. Mechanotransduction and fibrosis. J Biomech. 47:1997–2005, 2014.

Project Title: The role of plectin in cholestasis-induced adaptive response in liver
Supervisors: Martin Gregor

Project Description:
Cholestatic liver diseases are highly prevalent causes of progressive liver disease with a significant morbidity and mortality. A prominent group of genes that becomes upregulated in
response to a cholestatic insult encodes keratins and plakin cytolinkers. Using liver-specific knock-out mice we have recently shown that deficiency for plectin, a highly versatile cytolinker,
has detrimental effect in cholestatic liver injury.

To elucidate the mechanisms by which plectin governs cholestasis-induced adaptive response we will analyze the role of plectin in:

1. adaptation of hepatobiliary transport systems,
2. activation and expansion of hepatic progenitor cells, and
3. hepatocyte-driven liver regeneration.

To fulfill these aims we will combine analysis of liver injury mouse models with analyses of primary and CRISPR/Cas9-targeted cells grown in 2D and 3D cultures.

Candidate Profile:
We are seeking outstanding self-motivated candidates with master’s degree in molecular biology, physiology, biochemistry or related fields. We are offering research at a state-of-the-art equipped institute with experienced colleagues, international working environment and international collaborations.

Suggested reading:

• Jirouskova M. et al. Plectin Controls Biliary Tree Architecture and Stability in Cholestasis. J Hepatol., 68:1006-1017, 2018.

Project Title: Virus-host cell interactions
Supervisors: Jiří Hejnar

Project Description:
The project will focus on cellular factors involved in the retrovirus (mostly ALV, MLV, HIV, HERV) infection and replication. Particular attention will be paid to factors responsible for retrovirus entry. In chicken-ALV system, genome editing will be performed with the aim to confer resistance to virus infection. Our projects are extended from in silico to in vivo levels.

Candidate Profile:
Curiosity and commitment for basic science are expected. We also appreciate proper background in experimental virology, cell cultures and molecular biology. Previous experience with CRISPR/Cas9 editing would be helpful. The candidate should be prepared for long hours and bad jokes in a big team.

Project Title: Unraveling the molecular mechanism of dual response of cancer cells to IFNγ/TGFβ
Supervisor: Iva Kubíková

Project Description:
New experimental data suggests that many cytotoxic cancer therapies can enhance epithelial-mesenchymal transition, induce stem-like characteristics and increase migratory and invasive properties of malignant cells leading to the metastatic behavior. More than 90% of cancer-related mortality is caused by metastatic disease. TGFβ and IFNγ are cytokines well known for their dual role on cancer cells. They have primarily cytostatic effects or can promote cell senescence. However, cancer cells are frequently characterized by the switch to a growth-promoting response to TGFβ and IFNγ which supports phenotypic transitions of cancer cells essential for metastatic process. In the present project we aim to unravel the molecular mechanism behind the two modes of cancer cell response to TGFβ/IFNγ. We will focus on glioblastoma using 3D cell culture and brain organoid in vitro models.

Candidate Profile:
The laboratory of Genome Integrity is looking for a PhD student with background in molecular biology, biochemistry, physiology or medicine. The candidate should be proficient in English.

Suggested reading:

• Hubackova S, Kucerova A, et al. IFNγ induces oxidative stress, DNA damage and tumor cell senescence via TGFβ/SMAD signaling-dependent induction of Nox4 and suppression of ANT2. Oncogene. 2015 May: 1–14.
• Gorgoulis V, Adams PD, et al. Cellular Senescence: Defining a Path Forward. Cell. 2019 Oct; 179 (4): 813-827.
• Azari H, Millette S, et al. Isolation and Expansion of Human Glioblastoma Multiforme Tumo rCells Using the Neurosphere Assay. Journal of Visualized Experiments. 2011 Oct; 56 (e

Project Title: Role of cell-to-cell communication in malignant traits of glioblastoma multiforme
Supervisor: Zdeněk Hodný

Project Description:
Astrocytoma grade IV (glioblastoma multiforme; GBM) belongs to most deadliest malignant tumors in humans. The current therapeutic modality of GBM represents surgery combined with fractionated brain irradiation and treatment with alkylating agents, however the outcome of therapy is dissatisfactory. The main goal of the project will be to understand glioblastoma biology utilizing an in vitro model of human brain organoids. We will focus on the identification of signalling molecules mediating communication of glioma cells with cerebral organoid tissue to unravel factors supporting proliferation, invasiveness and therapeutic resistance of malignant cells with perspective to improve current or design novel therapeutic approaches to manage GBM. The project will involve culturing organoids, advanced fluorescence microscopic techniques, transcription profiling, mass spectrometry and molecular biology approaches such as manipulation of gene expression.

Candidate Profile:
We are searching for highly motivated Ph.D. student with enthusiasm and passion for research work. The candidate should hold a master degree in life sciences (biology, genetics, biochemistry), medicine or related field.

Suggested reading:

• Lancaster, M.A., and J.A. Knoblich. 2014. Generation of cerebral organoids from human pluripotent stem cells. Nat Protoc. 9:2329-2340.
• Lancaster, M.A., et al. 2013. Cerebral organoids model human brain development and microcephaly. Nature. 501:373-379.
• Linkous, A., et al. 2019. Modeling Patient-Derived Glioblastoma with Cerebral Organoids. Cell reports. 26:3203-3211.e3205.
• Oliveira, B., A. et al. 2019. Modeling cell-cell interactions in the brain using cerebral organoids. Brain Res. 1724:146458.

Project Title: Exploring mechanisms of DNA replication restart upon collisions between transcription and replication
Supervisors: Jana Dobrovolná, Pavel Janščák

Project Description:
Transcription-replication collisions (TRCs) represent a significant source of genomic instability in cells experiencing DNA replication stress. Although there is a great deal of knowledge about the strategies that cells evolved to avoid TRCs, understanding of how a replication fork restarts DNA synthesis upon a TRC remains elusive. Our recent studies have shown that replication restart upon R-loop-mediated TRCs relies on MUS81 endonuclease, RAD52 single-strand annealing protein and DNA ligase 4 (LIG4). In this project, we aim to use a proteomic approach to identify and functionally characterize new factors involved in this process. To study mechanisms of TCRs resolution after oncogene-induced replication stress we will also use advanced microscopic technics and genome wide sequencing (ChIP-seq).

Candidate Profile:
Applicants should be graduates in Molecular Biology/Cellular Biology/Biochemistry with a strong interest in basic research and experimental work. Good English and independent thinking is required. The projects offer training in a broad range of molecular, cell biological and biochemical techniques. The student will also undergo short-term trainings at the Institute of Molecular Cancer Research of the University of Zurich where he/she will be exposed to front-line research in the field of DNA repair and cancer. Interest in bioinformatics is welcomed and we can open an extra position specifically for bioinformatician.

Suggested reading:

• Chappidi N, Nascakova Z, Boleslavska B, Zellweger R, Isik E, Andrs M, Menon S, Dobrovolna J, Balbo Pogliano C, Matos J, Porro A, Lopes M, Janscak P. (2019) Fork Cleavage-Religation Cycle and Active Transcription Mediate Replication Restart after Fork Stalling at Co-transcriptional R-Loops. Mol Cell. pii: S1097-2765(19)30804-4. doi: 10.1016/j.molcel.2019.10.026 (e-publeshed ahead of print)
• Di Marco S, Hasanova Z, Kanagaraj R, Chappidi N, Altmannova V, Menon S, Sedlackova H, Langhoff J, Surendranath K, Hühn D, Bhowmick R, Marini V, Ferrari S, Hickson ID, Krejci L, Janscak P. (2017) RECQ5 Helicase Cooperates with MUS81 Endonuclease in Processing Stalled Replication Forks at Common Fragile Sites during Mitosis. Mol. Cell 66(5), 658-671
• Urban V, Dobrovolna J, Hühn D, Fryzelkova J, Bartek J, Janscak P. (2016) RECQ5 helicase promotes resolution of conflicts between replication and transcription in human cells. J. Cell Biol. 214(4), 401-15.

Project Title: The role of phosphoinositides in spatiotemporal regulation of nuclear processes.
Supervisor: Pavel Hozák

Project Description:
Phosphoinositides (PIPs) are recognized as regulators of many nuclear processes including chromatin remodeling, splicing, transcription, and DNA repair. These processes are spatially organized in different nuclear compartments. Various nuclear compartments are formed by entropy-driven mechanism – phase separation. The surface of such membrane-less structures spatiotemporally coordinates complex nuclear processes. The integration of PIPs into the surface of nuclear structures might therefore provide an additional step in their functional diversification by controlling the localization of different components, in a similar way as PIPs do in membranous cytoplasmic environment. This project focuses on deciphering the molecular mechanisms of various PIPs in establishing a dynamic nuclear architecture. In this project PhD candidate will characterize the PIPs-containing nuclear structures by combination of lipidomics, proteomics (quantitative MS), molecular biology (e.g. CRISPR/Cas9), biochemical and advanced microscopy (e.g. confocal, SIM, STED, FRAP) methods. The project is supported by funding from the Grant Agency of the Czech Republic.

Candidate Profile:
M.Sc. (Mgr.) degree or equivalent in molecular biology, biochemistry of biophysics. The candidate should be fluent in English, independent, with passion to science, willing to learn and develop new techniques.

Suggested reading:

• Sobol, M., A. Krausova, S. Yildirim, I. Kalasova, V. Faberova, V. Vrkoslav, V. Philimonenko, P. Marasek, L. Pastorek, M. Capek, Z. Lubovska, L. Ulicna, T. Tsuji, M. Lisa, J. Cvacka, T. Fujimoto, and P. Hozak. 2018. Nuclear phosphatidylinositol 4,5-bisphosphate islets contribute to efficient RNA polymerase II-dependent transcription. J Cell Sci. 131.
• Sztacho, M., M. Sobol, C. Balaban, S.E. Escudeiro Lopes, and P. Hozak. 2018. Nuclear phosphoinositides and phase separation: Important players in nuclear compartmentalization. Adv Biol Regul.
• and references therein.

Project Title: Exploring the role of vinculin/DEB-1 in eukaryotic meiosis
Supervisor: Pavel Hozák / Petr Flachs

Project Description:
Our department focuses on the vinculin/DEB-1 protein, and we originally confirmed it in the nucleus of meiotic cells in Mus musculus and C. elegans. Our goal is to study his role in the gametogenesis of this two eukaryotic model organisms. We study vinculin in mouse spermatogenesis and oogenesis using model strains of vinculin conditional knock-out that we developed in our laboratory. Specifically, we proved that vinculin is important for homologous chromosome pairing and formation of the synaptonemal complex, possibly through the vicnulin involvement in the ubiquitine-proteasome system. In C. elegans we showed the interaction of the DEB-1 (ortholog of mammalian vinculin) with the SUN/KASH module at the nuclear periphery. DEB-1 depletion caused a defect in the stabilization of the chromosomal pairing centers and subsequent aneuploidy. The PhD project will implement molecular biology and biochemistry methods as well as the state-of-the-art imaging techniques including fluorescence, confocal and super-resolution (SIM, STED) microscopy (SIM figure in the heading, such a detailed picture of synaptonemal complex would not be possible few years ago). The project is supported by funding from the Grant Agency of the Czech Republic.

Candidate Profile:
Candidates should possess M.Sc. (Mgr.) degree or equivalent in molecular/cellular biology or biochemistry, good English, independent thinking, strong interest in basic research and experimental work, dedication to learn and develop new techniques.

Suggested reading:
All articles are open access (free)!

• Bisig et al, 2012; Synaptonemal Complex Components Persist at Centromeres and Are Required for Homologous Centromere Pairing in Mouse Spermatocytes; PLOS genetics
• Shakes et al, 2009; Spermatogenesis-Specific Features of the Meiotic Program in Caenorhabditis elegans; PLOS genetics
• Shibuya et al, 2014; The Dissection of Meiotic Chromosome Movement in Mice Using an In Vivo Electroporation Technique; PLOS genetics

Project Title: Molecular mechanisms causing intestinal cancer – analyses at the single-cell level
Supervisor: 

Project Description:
Intestinal carcinoma is one of the most frequent types of cancer in Western countries. Intestinal tumors evolve throughout a series of mutational events that produce considerable tumor cell heterogeneity. It is presumed that tumors in the initiation stages of the tumorigenic process – so-called microadenomas – are composed of highly proliferative cells displaying similar molecular and cell biology features. However, our recent results indicate that even early neoplastic lesions formed in the colon of experimental mice are composed of highly heterogeneous cell populations reminding of cell types present in the healthy colon epithelium. We aim to reveal the molecular mechanisms related to the observed tumor cell phenotypic heterogeneity. The research includes work with mouse transgenic models, analysis of gene expression at the single-cell level, and evaluation of the tumor cell epigenetic status. A part of the study will be performed using intestinal organoids derived from healthy or tumor tissue.

Candidate Profile:
Our laboratory is looking for a new, highly motivated team member with interest in biomedical research. The candidates should hold a Master degree in cellular and molecular biology, genetics or related fields. We expect that the prospective candidate is willing to learn advanced research techniques that include work with mouse tissues and human patient samples. We offer a friendly environment well-adjusted to the proposed research topic and decent financial conditions.

Suggested reading:

• Krausova M, Korinek V. Wnt signaling in adult intestinal stem cells and cancer. Cell Signal. 2014 Mar;26(3):570-9. doi: 10.1016/j.cellsig.2013.11.032
• Hrckulak D, Janeckova L et al. Wnt Effector TCF4 Is Dispensable for Wnt Signaling in Human Cancer Cells. Genes (Basel). 2018 Sep 1;9(9). pii: E439. doi: 10.3390/genes9090439
• Horazna M, Janeckova L et al. Msx1 loss suppresses formation of the ectopic crypts developed in the Apc-deficient small intestinal epithelium. Sci Rep. 2019 Feb 7;9(1):1629. doi: 10.1038/s41598-018-38310-y
• Merenda A, Fenderico N et al. Wnt Signaling in 3D: Recent Advances in the Applications of Intestinal Organoids. Trends Cell Biol. 2019 Nov 9. pii:S0962-8924(19)30166-7. doi: 10.1016/j.tcb.2019.10.003

Project Title: Molecular pathophysiology of myeloproliferative blood neoplasms
Supervisor: Lucie Láníková

Project Description:
The aim of this project is the identification of the new genetic predispositions to myeloproliferative neoplasms (MPN) and their in vitro/vivo characterization, especially congenital weakly activating mutations in the JAK/STAT pathway. We propose to create a mouse model of prevalent germ-line Jak2 mutation and its cross-breeding with relevant MPN-like models. Reliable characterization of predisposing genetic variants based on analysis of the mouse model is the key step for improving the clinical diagnosis and prevention of hematologic malignancies. We will also identify and characterize new somatic mutations which cooperate or synergistically coexist with predisposing genetic variations in MPN.

Candidate Profile:
Our laboratory is looking for a new, highly motivated team member with interest in biomedical research. The candidates should hold a Master degree in cellular and molecular biology, genetics or related fields or have appropriate medical degree. We expect that the prospective candidate is willing to learn advanced research techniques that include work with mouse tissues and human patient samples. We would appreciate if the candidate is open-minded, with passion for science and eager to work in the lab. We offer a friendly environment well-adjusted to the proposed research topic and decent financial conditions.

Suggested reading:

• Lanikova L. et al. Experimental Modeling of Myeloproliferative Neoplasms.Genes (Basel). 2019;10(10).
• Stetka J. et al. Addiction to DUSP1 protects JAK2V617F-driven polycythemia vera progenitors against inflammatory stress and DNA damage, allowing chronic proliferation. Oncogene. 2019;38(28):5627-5642.
• Mambet C. et al. Cooccurring JAK2 V617F and R1063H mutations increase JAK2 signaling and neutrophilia in myeloproliferative neoplasms. Blood. 2018;132(25):2695-2699.
• Lanikova L. et al. Coexistence of gain-of-function JAK2 germ line mutations with JAK2V617F in polycythemia vera. Blood. 2016;128(18):2266-2270.

Project Title: Evolution of eyes: insight from photoreceptors of invertebrate chordate amphioxus
Supervisor: Zbyněk Kozmik

Project Description:
Position is available in the area of evolutionary developmental biology (evo-devo). Project aims to provide new insight into evolution of animal eyes using invertebrate chordate amphioxus as a laboratory model. Project will specifically focus on amphioxus photoreceptors that are not associated with pigment cells: Joseph cells, bearing similarity to intrinsically photosensitive retinal ganglion cells of vertebrates, and lamellar body that is likely homologous to vertebrate pineal organ. The methods used will include basic bioinformatics analysis, gene isolation, gene expression studies by transcriptomics, whole-mount in situ hybridization and immunohistochemistry, biochemical characterization of photosensitive proteins (opsins) in vitro, characterization of selected gene knockouts produced in the lab by CRISPR/Cas9 system, and behavior visual tests (in collaboration with laboratory in Vienna).

Candidate Profile:
The laboratory of Trancriptional Regulation with a long-term experience in Developmental and Evolutionary Biology is searching for an enthusiastic and hard-working Ph.D student. We prefer self-motivated candidates with a strong commitment to experimental work. The candidate should hold a master degree in genetics, molecular biology, developmental biology, evolutionary biology or zoology. We offer a friendly and supporting environment in a state-of-the-art institution.

Suggested reading:

Although amphioxus lacks the specializations and innovations of vertebrates, it shares with them a basic body plan and has multiple organs and structures homologous to those of vertebrates. For these reasons, amphioxus has widely been used as a reference outgroup to infer ancestral versus novel features during vertebrate evolution. Amphioxus visual system is especially interesting because four types of receptors are involved in light detection – dorsal ocelli and Joseph cells (both rhabdomeric photoreceptors) and the frontal eye and lamellar body (both ciliary photoreceptors).

More here:
Amphioxus photoreceptors – insights into the evolution of vertebrate opsins, vision and circadian rhythmicity. Pergner J, Kozmik Z. Int J Dev Biol. 2017;61(10-11-12):665-681.

Project Title: Impact of PPM1D/Wip1 phosphatase on chromatin organization in human cells
Supervisor: Libor Macurek

Project Description:
Genome instability caused by defects in DNA repair can contribute to various pathologies including cancer. Genome integrity is protected by coordinated action of molecular pathways that control the cell cycle and DNA repair. In addition to the signaling at the DNA break, DNA damage also affects organization of the chromatin at pan-nuclear level. This project aims to study changes in the chromatin organization caused by genotoxic stress.

Protein phosphatase PPM1D/Wip1 is localized at chromatin and inactivates cellular response to DNA damage. Here we will address the impact PPM1D/Wip1 phosphatase on chromatin organization in human cells. In particular we will compare distribution of the heterochromatin in control cells, cells where PPM1D/Wip1 was inactivated by CRISPR/Cas9 technology and in cells treated with a small molecule inhibitor of PPM1D/Wip1. Chromatin organization will be studied in normal conditions and after induction of DNA damage using various molecular and cell biology techniques. We expect that this project will contribute to better understanding of cellular responses to DNA damage.

Candidate Profile:
We seek a motivated PhD student to join our young international team located in Prague, Czech Republic. We are especially interested in candidates with strong background in molecular/cell biology or biochemistry and with enthusiasm for basic science and experimental work.

Suggested reading:

• Jaiswal et al., ATM/Wip1 activities at chromatin control Plk1 re-activation to determine G2 checkpoint duration. EMBO J. 2017; 36:2161-2176.
• Kleiblova et al., Gain-of-function mutations of PPM1D/Wip1 impair the p53-dependent G1 checkpoint. J Cell Biol. 2013; 201:511-21.
• Macůrek et al., Wip1 phosphatase is associated with chromatin and dephosphorylates gammaH2AX to promote checkpoint inhibition. Oncogene. 2010; 29:2281-91.

Project Title: Unraveling oncogenic signaling that imparts tumors with tolerance to nutrient starvation  
Supervisor: Mohamed Elgendy

Project Description:
Tumors require dramatically high levels of energy to fuel their rapid growth. Solid tumors often grow in metabolically-challenging microenvironments far from blood and nutrient supply. How tumor cells adapt their metabolism to meet these metabolic challenges, have always fascinated scientists. Almost a century ago, Otto Warburg suggested that tumor cells specifically uptake high levels of glucose, which they metabolize through the process of glycolysis to generate the energy and biomass they need. Indeed, tracing radio-labeled glucose administrated to cancer patients is routinely used in the clinic to visualize tumors and detect metastasis. Surprisingly however, specific inhibitors developed to inhibit glycolysis failed to eliminate tumors when tested clinically. So it seems that while some tumors may upregulate glycolysis, they are able to tolerate the inhibition of glycolysis through shuffling to other metabolic pathways. This project aims to dissect oncogenic signaling that mediates metabolic adaptations of tumors. The work aims to unravel how activation of certain oncogenes influences the ability of tumors to tolerate specific metabolic challenges.

Candidate Profile:

• Motivated
• Motivated again!
• High learning capabilities
• Prior experience in cellular and molecular biology is advantageous
• Master’s degree in medicine, biology or relevant fields

Suggested reading:

• Fundamentals of cancer metabolism.
• Beclin 1 restrains tumorigenesis through Mcl-1 destabilization in an autophagy-independent reciprocal manner.

Project Title: STAT3 signalling in tumour growth and immune suppression.
Supervisor: Milan Reiniš

Project Description:
STAT3 signalling pathway provides an attractive target for therapeutic approaches in cancer. We can assume that inhibition of the STAT3 pathway can be a powerful tool for elimination of the detrimental effects of chemotherapy or to increase its effectiveness. The objective of this project is to evaluate the antitumour efficacy of existing and novel STAT3 inhibitors, including their additive/synergic effects in combination with chemotherapy or immunotherapy, as well as their effects on immune responses. We will also focus on the role of the STAT3 pathway in immunosuppressive cells of myeloid origin.

Candidate Profile:
We are looking for a motivated hard-working Ph.D. student, proficient in English, who will be able to closely collaborate with other lab members. The candidate should hold a master degree in molecular biology, cell biology, biochemistry or in a related field. Animal work using murine tumour models will be required. We offer a friendly and collaborative environment in a state-of-the-art institution.

Suggested reading:

• Yu H, Lee H, Herrmann A, Buettner R, Jove R. Revisiting STAT3 signalling in cancer: new and unexpected biological functions. Nat Rev Cancer. 2014 14:736-46.
• Mikyšková R, Indrová M, Polláková et al. Cyclophosphamide-induced myeloid-derived suppressor cell population is immunosuppressive but not identical to myeloid-derived suppressor cells induced by growing TC-1 tumors. J Immunother. 2012 35:374-84.
• Mikyskova R, Indrova M, Stepanek I et al. Dendritic cells pulsed with tumor cells killed by high hydrostatic pressure inhibit prostate tumor growth in TRAMP mice. Oncoimmunology. 2017 24;6:e1362528.

Project Title: The role of new candidate genes in glucose homeostasis and insulin sensitivity
Supervisors: Jan Rozman

Project Description:
Among several other genes, C4orf22 and CNBD1 were recently found to show a link to dysfunctional glucose homeostasis and impaired insulin sensitivity both in knockout mutant mice as well as in genome wide association studies in humans (Rozman et al. 2018). The exact physiological roles of these genes and their involvement in the development of metabolic disorders on the genetic and molecular level are unknown so far. The project will focus on the in-depth characterization of one or two candidate genes both on the physiological and the molecular level. The candidate will make use of different mouse models with the aim to characterize new targets for the diagnosis and possibly treatment of diabetes.

Candidate Profile:
We are seeking a PhD student to join our new research team at the Czech Center for Phenogenomics in Prague, Czech Republic. Candidates with a strong background both in physiology, molecular biology and animal models in the field of energy metabolism and diabetes are strongly encouraged to apply for the new position.

Suggested reading:
Rozman, J., Rathkolb, B., Oestereicher, M.A., Schütt, C., Ravindranath, A.C., Leuchtenberger, S., Sharma, S., Kistler, M., Willershäuser, M., Brommage, R., et al. (2018). Identification of genetic elements in metabolism by high-throughput mouse phenotyping. Nature communications 9, 288.

Project Title: Mutations in splicing factors linked with retina degeneration – molecular mechanism
Supervisors: David Staněk

Project Description:
Retinitis pigmentosa (RP) is a human hereditary disorder caused by a progressive loss of photoreceptors. Surprisingly, mutations in six key splicing proteins have been associated with autosomal dominant form of RP. The mutated splicing factors are essential for every cell in a human body and thus it is enigmatic why their mutations have such a cell specific phenotype. In our laboratory, we have developed several model systems including mice and eye organoids to study how the RP-linked mutations in splicing factors affect target cell metabolism. The aim of the proposed PhD project is to characterize at molecular level, how RP-linked mutations change behavior of mutated proteins. Specifically, we plan to study how the mutations affect protein and RNA interactome of splicing factors in targeted cells and to identofy small molecules that could revert the observed phenotype.

Candidate Profile:
We seek an enthusiastic colleague with strong interest in RNA biology. Previous experience with molecular biology, cell culture or animal models is welcomed.

Requirements:

• MSc, MRes, Diploma or an equivalent degree in Biology, Biomedicine, Chemistry or related sciences, to be obtained latest by the start of the fall term in September 2020
• Practical experience in the lab working on scientific projects
• Excellent English language skills and the desire to work in a dynamic international team

Suggested reading:

• Krausova and Stanek (2017) snRNP proteins in health and disease. Semin Cell Dev Biol. DOI: 10.1016/j.semcdb.2017.10.011
• Ruzickova and Stanek (2017) Mutations in spliceosomal proteins and retina degeneration. RNA Biology. DOI: 10.1080/15476286.2016.1191735

Project Title: Reviving canonical RNAi in mammals
Supervisors: Petr Svoboda

Project Description:
The aim of the project is to examine different strategies for enhancing mammalian RNA interference in vivo.

Candidate Profile:
Curious,determined, open-minded, English-speaking, willing to work in a hard-working team. MSc. in molecular biology, developmental biology, cell biology or related areas. Experience with mice, micromanipulation, protein biochemistry or virology would be an advantage.

Suggested reading:

• Liu Z, Wang J, Cheng H, Ke X, Sun L, Zhang QC, Wang HW. Cryo-EM Structure of Human Dicer and Its Complexes with a Pre-miRNA Substrate. Cell. 2018 May 17;173(5):1191-1203.e12.
• Svoboda P: Renaissance of mammalian endogenous RNAi. FEBS Lett 2014 588(15): 2550-6.

Project Title: Cell communication in inflammation, autoimmunity and cancer
Supervisors: Peter Dráber

Project Description:
Immune system has evolved to protect the body from invading pathogens and cancer, while preventing development of autoimmune diseases. In order to regulate ongoing inflammation, cells communicate with each other by producing cytokines. Cytokines are small proteins that bind to receptors on target cells and instruct them how to deal with ongoing infection. Defects in sensing cytokines can have grave implications for organism, ranging from immunodeficiency to autoimmunity. For example, cytokine TNF is critical to fight infection, but in pathological situations is responsible for the progression of rheumatoid arthritis or inflammatory bowel disease. Similarly, cytokine IL-17 can organize the immune system to protect from candidiasis, but is also highly involved in the progression of psoriasis. This project aims to uncover new molecular mechanisms how these and other crucial pro-inflammatory cytokines signal upon binding to their receptors and develop new approaches to modulate immune responses: either inhibit them in autoimmune diseases or enhance them in cancer.

Candidate Profile:
The present research will allow the candidate to learn a number of different experimental approaches, ranging from the study of protein complexes by mass-spectrometry, preparation of knockout cell lines via CRISPR/Cas9, analysis of signaling using methods of molecular biology and study of experimental mouse models. As such, the candidate should be deeply interested in science, proficient in English, willing to collaborate and share experience with colleagues, and willing to handle mouse work. The candidate should hold a master degree in immunology, cell biology, biochemistry, or a related field. Prior laboratory experience is advantageous.

The project will be carried at BIOCEV research campus. Candidates interested in this research should also contact Peter Draber directly at email: peter.draber@img.cas.cz.

Suggested reading:

• Lafont et al. TBK1 and IKKε prevent TNF-induced cell death by RIPK1 phosphorylation. Nat Cell Biol. 2018 Dec;20(12):1389-1399.
• Draber et al. LUBAC-Recruited CYLD and A20 Regulate Gene Activation and Cell Death by Exerting Opposing Effects on Linear Ubiquitin in Signaling Complexes. Cell Rep. 2015 Dec 15;13(10):2258-72.