PhD Program

Supervisor

Lukáš Čermák

Project description

This project aims to investigate the pivotal role of the proteasome in the regulation of apoptosis within cancer cells. The proteasome, a cellular complex responsible for protein degradation, is known to play a crucial role in maintaining cellular homeostasis. However, its specific involvement in modulating apoptosis in cancer cells remains understudied. Through a series of experiments utilizing cancer cell lines and proteasome inhibitors, we intend to unravel the intricate mechanisms by which the proteasome influences apoptotic pathways. By identifying key protein targets and understanding the interplay between the proteasome and apoptosis regulators, we hope to shed light on potential therapeutic strategies for manipulating apoptosis in cancer cells. This research not only contributes to our fundamental understanding of cell biology but also holds promise for the development of targeted therapies that exploit the proteasome’s control over apoptosis in the context of cancer treatment.

Candidate profile

We invite enthusiastic and goal-oriented students with a keen interest in molecular biology and basic understanding of biochemical methods to join this research project. A comprehensive understanding of fundamental molecular biology techniques will be highly beneficial in unraveling the intricacies of proteasome-mediated control of apoptosis in cancer cells.

Suggested reading

• Shanshan Duan 1, Lukas Cermak, Julia K Pagan, Mario Rossi, Cinzia Martinengo, Paola Francia di Celle, Bjoern Chapuy, Margaret Shipp, Roberto Chiarle, Michele Pagano: FBXO11 targets BCL6 for degradation and is inactivated in diffuse large B-cell lymphomas. Nature 2012 481(7379): 90–93. [pubmed] [doi]
• Dibus N, Korinek V, Cermak L: FBXO38 Ubiquitin Ligase Controls Centromere Integrity via ZXDA/B Stability. Front Cell Dev Biol 2022 10: 929288. [pubmed] [doi]
• Dibus N, Zobalova E, Monleon MAM, Korinek V, Filipp D, Petrusova J, Sedlacek R, Kasparek P, Cermak L: FBXO38 Ubiquitin Ligase Controls Sertoli Cell Maturation. Front Cell Dev Biol 2022 10: 914053. [pubmed] [doi]

Supervisor

Petr Dráber

Project description

Mast cells are immune cells with multifaceted functions in homeostasis and diseases. They have traditionally been associated with type I allergies, such as rhinitis, asthma, and urticaria, causing a global health burden of approximately 20% of the human population worldwide. They play essential roles in both innate and adaptive immunity. Accumulating evidence suggests that a complex network of inhibitory and activating receptors controls mast cell responsiveness to various stimuli. Recently, we found that mast cells from mice with defects in the ORMDL family proteins, inhibitors of serine palmitoyltransferase, exhibit increased antigen-induced degranulation and cytokine response. Mass spectrometry analysis revealed that ORMDL-deficient cells express increased leukocyte-associated immunoglobulin-like receptor 1 (Lair-1). This was an unexpected finding, given that LAIR-1 is a negative regulator of immunoreceptor signaling in several immune cell types. In this project, we will test the hypothesis that increased expressions of LAIR-1 counterbalance the enhanced response of mast cells from ORMDL-deficient mice. We will also test the hypothesis using human mast cell lines ROSA that LAIR-1 regulates the progress of mastocytosis. In the frame of the project, we will also prepare and test bispecific constructs, aggregating LAIR-1 with IgE receptor or cKIT, for the treatment of mast cell-mediated allergies and other inflammatory diseases and mastocytosis. Various techniques will be used to address the research questions of the project, including cell culture of different cell types, analysis of mast cell activation by antigen, immunoprecipitation of selected molecules followed by mass spectrometry, gene expression studies by whole genome transcriptome analysis, immunoblotting and other immunochemical procedure. Part of the project will also be the production of bispecific recombinant constructs for enhanced crosstalk of LAIR-1 with the high-affinity IgE receptor or c-kit and testing the constructs under in vitro and in vivo conditions. In vivo experiments will require working with laboratory mice.

Candidate profile

Techniques of molecular immunology

Suggested reading

• Harvima IT, Levi-Schaffer F, Dráber P, Friedman S, Polakovičová I, Gibbs BF, Blank U, Nilsson G, Maurer M: Molecular targets on mast cells and basophils for novel therapies. J Allergy Clin Immunol 2014 134(3): 530-544. [pubmed] [doi]
• Bugajev V, Paulenda T, Utekal P, Mrkacek M, Halova I, Kuchar L, Kuda O, Vavrova P, Schuster B, Fuentes-Liso S, Potuckova L, Smrz D, Cernohouzova S, Draberova L, Bambouskova M, Draber P: Crosstalk between ORMDL3, serine palmitoyltransferase, and 5-lipoxygenase in the sphingolipid and eicosanoid metabolic pathways. J Lipid Res 2021, 100121. [pubmed] [doi]
• Bugajev V, Halova I, Demkova L, Cernohouzova S, Vavrova P, Mrkacek M, Utekal P, Draberova L, Kuchar L, Schuster B, Draber P: ORMDL2 Deficiency Potentiates the ORMDL3-Dependent Changes in Mast Cell Signaling. Front Immunol 2021 11: 591975. [pubmed] [doi]

Supervisor

Zuzana Sumbalová Koledová

Project description

Epithelial-stromal interactions play a crucial role in mammary gland development and homeostasis. Stromal cells, such as fibroblasts, provide instructions for epithelial morphogenesis through paracrine signaling and extracellular matrix production and remodeling. In mammary epithelial organoid-fibroblast cocultures, we have recently described a new mechanism of fibroblast-induced epithelial morphogenesis mediated by fibroblast mechanical forces. In this project, the PhD candidate will investigate 1) the importance of fibroblasts mechanical forces in mammary epithelial morphogenesis in vivo using genetic mouse models, and 2) regulation of fibroblast mechanical activity using scRNA sequencing analysis and functional in vitro and in vivo experiments.

Candidate profile

• Interest in developmental, cell or cancer biology, biophysics or biochemistry,
• Master’s degree in biological sciences,
• Highly motivated and independent with excellent communication skills, enthusiastic about performing interdisciplinary work and open to learn and apply new techniques,
• Excellent organizational skills and the ability to maintain meticulous records, with ability to plan and prioritize own work in order to meet deadlines,
• Committed to personal development and updating of knowledge and skills,
• Hands-on experience in work with genetic mouse models, organoids, live cell imaging, 3D immunofluorescence will be viewed positively.

Suggested reading

• Sumbal J, Fre S, Sumbalova Koledova Z: Fibroblast-induced mammary epithelial branching depends on fibroblast contractility. bioRxiv 2023.03.24.534061. [doi]
• Sumbal J, Belisova D, Koledova Z: Fibroblasts: The grey eminence of mammary gland development. Sem Cell Dev Biol 2020 S1084-9521(20)30169-5. [doi]
• Sumbal J, Koledova Z: FGF signaling in mammary gland fibroblasts regulates multiple fibroblast functions and mammary epithelial morphogenesis. Development 2019 146(23). pii: dev185306. [doi]

Supervisor

Petr Svoboda

Project description

The lab currently studies evolution of mammalian RNA silencing pathways and focuses on several specific aspects of RNAi and piRNA pathways. A PhD candidate will have an opportunity to choose as a main project either evolution of small RNA biogenesis and effector complex formation or adaptations and functional divergence of the piRNA pathway. The laboratory uses rodents and slugs as main experimental models. Laboratory work will range from biochemistry of ribonucleoprotein complexes to genetic modifications and phenotype analysis (largely involving long and small RNA analyses by RNA sequencing).

Candidate profile

We are looking for a curious and motivated PhD student with some experience with molecular biology, experience with laboratory animals, mammalian cell culture, molecular cloning, protein biochemistry or bioinformatics will be an advantage.

Suggested reading

• Ketting RF. The many faces of RNAi. Dev Cell. 2011 Feb 15;20(2):148-61. [pubmed] [doi]
• Loubalova Z, Fulka H, Horvat F, Pasulka J, Malik R, Hirose M, Ogura A, Svoboda P: Formation of spermatogonia and fertile oocytes in golden hamsters requires piRNAs. Nat Cell Biol 2021 23(9): 992-1001. [pubmed] [doi]
• Zapletal D, Taborska E, Pasulka J, Malik R, Kubicek K, Zanova M, Much C, Sebesta M, Buccheri V, Horvat F, Jenickova I, Prochazkova M, Prochazka J, Pinkas M, Novacek J, Joseph DF, Sedlacek R, Bernecky C, O’Carroll D, Stefl R, Svoboda P: Structural and functional basis of mammalian microRNA biogenesis by Dicer. Mol Cell 2022 82(21): 4064-4079.e13. [pubmed] [doi]

Supervisor

Martina Huranová

Project description

Cilia are thin surface structures present in most mammalian cells. Cilia accumulate multiple transmembrane receptors involved in signaling pathways important for the development and tissue homeostasis. For instance, cilia are crucial for the development and migration of neurons, the synaptic plasticity, and satiety management in the brain. Mutations in key ciliary genes in humans lead to cilia dysfunction manifesting as pleiotropic syndromes, collectively called ciliopathies. One of these rare recessive genetic diseases is Bardet-Biedl syndrome (BBS), characterized by diverse clinical symptoms such as obesity, renal dysfunction, retinal degeneration, polydactyly, and neurological disorder. The genetic cause of the BBS are mutations in the genes associated with the formation and function of an octameric ciliary adaptor complex called BBSome. The applicant will investigate the physiological role of primary cilia and the BBSome in the brain and molecular mechanisms associated with the pathophysiology in the BBS. The applicant will employ a multifaceted approach integrating model systems and experimental pipelines of a different scale and complexity. The applicant will work with specific ciliopathy mouse models and cell lines and gain expertise in the modern cell and molecular biology approaches including the in vivo experiments, transcriptome analysis and fluorescence microscopy. Finally, the applicant will utilize clinical data from ciliopathic patients, which will provide insights into ciliopathy pathologies.

Cilia team

We uncover mechanisms how cells employ their “antenna” called cilium to sense and respond to extracellular signals within our bodies. The failure of these mechanisms leads to severe diseases manifesting with obesity, neurodegeneration and dysfunction of multiple organs.    

Candidate profile

We are looking for an ethusiastic and curious student with background in cell biology, molecular biology, biochemistry or a related field who is motivated to work on a project with biological and medicinal relevance. We offer a friendly and supporting environment, and excellent infrastructures at the Institute of Molecular Genetics. We are a young research group, where the students learn to lead a scientific project and accomplish the PhD studies within four to five years. We encourage the candidates to contact the supervisor directly (martina.huranova@img.cas.cz).

Suggested reading

• Niederlova V, Modrak M, Tsyklauri O, Huranova M, Stepanek O: Meta-analysis of genotype-phenotype associations in Bardet-Biedl syndrome uncovers differences among causative genes. Hum Mutat 2019 40(11): 2068-2087. [pubmed] [doi] [dataBBaSe]
• Prasai A, Schmidt Cernohorska M, Ruppova K, Niederlova V, Andelova M, Draber P, Stepanek O, Huranova M: The BBSome assembly is spatially controlled by BBS1 and BBS4 in human cells. J Biol Chem 2020 295(42): 14279-14290. [pubmed] [doi]
• Tsyklauri O, Niederlova V, Forsythe E, Prasai A, Drobek A, Kasparek P, Sparks K, Trachtulec Z, Prochazka J, Sedlacek R, Beales P, Huranova M, Stepanek O: Bardet-Biedl Syndrome ciliopathy is linked to altered hematopoiesis and dysregulated self-tolerance. EMBO Rep 2021, e50785. [pubmed] [doi]
• Avishek Prasai, Olha Ivashchenko, Kristyna Maskova, Marketa Schmidt Cernohorska, Ondrej Stepanek, Martina Huranova: BBSome-deficient cells activate intraciliary CDC42 to trigger actin-dependent ciliary ectocytosis. bioRxiv 2023 [doi]