PhD Program

Supervisor

Tomáš Brdička

Project description

The project will focus on explaining the mechanisms contributing to the development of autoinflammatory disease chronic recurrent multifocal osteomyelitis (CRMO). It is a chronic disorder characterized by the spontaneous development of inflammatory lesions in the bones. The molecular basis of the disease is unknown. The candidate will explore alterations of pro-inflammatory signaling pathways in white blood cells from patients with CRMO and from a mouse model of the disease and analyze the mechanisms of CRMO pathogenesis. The project will also involve developing and testing potential treatment strategies in the mouse model. In addition, the candidate will contribute to projects investigating the function of other adaptor proteins involved in the regulation of leukocyte signaling 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

• Zhao Y, Ferguson PJ. Chronic non-bacterial osteomyelitis and autoinflammatory bone diseases. Clin Immunol 2020; 216: 108458. [pubmed] [doi]
• Pavliuchenko N, Duric I, Kralova J, Fabisik M, Spoutil F, Prochazka J, Kasparek P, Pokorna J, Skopcova T, Sedlacek R, Brdicka T. Molecular interactions of adaptor protein PSTPIP2 control neutrophil-mediated responses leading to autoinflammation. Frontiers in Immunology 2022; 13. [doi]
• Kralova J, Pavliuchenko N, Fabisik M, Ilievova K, Spoutil F, Prochazka J, Pokorna J, Sedlacek R, Brdicka T. The receptor-type protein tyrosine phosphatase CD45 promotes onset and severity of IL-1β-mediated autoinflammatory osteomyelitis. J Biol Chem. 2021 297(4): 101131. [pubmed] [doi]
• Kralova J, Drobek A, Prochazka J, Spoutil F, Fabisik M, Glatzova D, Borna S, Pokorna J, Skopcova T, Angelisova P, Gregor M, Kovarik P, Sedlacek R, Brdicka T. Dysregulated NADPH Oxidase Promotes Bone Damage in Murine Model of Autoinflammatory Osteomyelitis. J Immunol 2020 204(6): 1607-1620. [pubmed] [doi]

Supervisor

Zbyněk Kozmik

Project description

Vertebrates have greatly elaborated the basic chordate body plan and evolved highly distinctive genomes that have been sculpted by two whole-genome duplications. The genome of invertebrate chordate amphioxus has not undergone whole-genome duplication and serves as a proxy to ancestral chordates. 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. Over the past few years amphioxus has become an established laboratory model and its cultures can be maintained throughout the year at the Institute of Molecular Genetics. This allows for an implementation of plethora of molecular and genetics approaches common to classical vertebrate models such as mouse, chick or fish. Moreover, recent publication on Amphioxus functional genomics and the origins of vertebrate gene regulation (Marletaz et al., Nature 564(7734):64-70) provides a huge genomic resource for future studies focused on gene regulatory mechanisms underlying evolution of vertebrate body plan.

Project will focus on evolution of cell types, ancestral chordate features and vertebrate-specific innovations, using comparative analysis between amphioxus and vertebrates. The methods used will include basic bioinformatics, gene expression studies (single cell RNA-seq, whole-mount in situ hybridization, and immunohistochemistry), analysis of gene knockouts established in the lab using CRISPR/Cas9 system, and reporter gene transgenesis.

Candidate profile

We are searching for a highly motivated and hard-working PhD student with a strong interest in animal evolution and evolution of development (evo-devo). The candidate should hold a master degree in zoology, genetics, molecular biology, cell biology, or in a related field.

Suggested reading

• Kozmikova I, Kozmik Z: Wnt/β-catenin signaling is an evolutionarily conserved determinant of chordate dorsal organizer. Elife 2020 9. [pubmed] [doi]
• Pergner J, Vavrova A, Kozmikova I, Kozmik Z: Molecular Fingerprint of Amphioxus Frontal Eye Illuminates the Evolution of Homologous Cell Types in the Chordate Retina. Front Cell Dev Biol 2020 8: 705. [pubmed] [doi]
• Prummel KD, Hess C, Nieuwenhuize S, Parker HJ, Rogers KW, Kozmikova I, Racioppi C, Brombacher EC, Czarkwiani A, Knapp D, Burger S, Chiavacci E, Shah G, Burger A, Huisken J, Yun MH, Christiaen L, Kozmik Z, Müller P, Bronner M, Krumlauf R, Mosimann C: A conserved regulatory program initiates lateral plate mesoderm emergence across chordates. Nat Commun 2019 10(1): 3857. [pubmed] [doi]
• Marlétaz F, Firbas PN, Maeso I, Tena JJ, Bogdanovic O, Perry M, Wyatt CDR, de la Calle-Mustienes E, Bertrand S, Burguera D, Acemel RD, van Heeringen SJ, Naranjo S, Herrera-Ubeda C, Skvortsova K, Jimenez-Gancedo S, Aldea D, Marquez Y, Buono L, Kozmikova I, Permanyer J, Louis A, Albuixech-Crespo B, Le Petillon Y, Leon A, Subirana L, Balwierz PJ, Duckett PE, Farahani E, Aury JM, Mangenot S, Wincker P, Albalat R, Benito-Gutiérrez È, Cañestro C, Castro F, D’Aniello S, Ferrier DEK, Huang S, Laudet V, Marais GAB, Pontarotti P, Schubert M, Seitz H, Somorjai I, Takahashi T, Mirabeau O, Xu A, Yu JK, Carninci P, Martinez-Morales JR, Crollius HR, Kozmik Z, Weirauch MT, Garcia-Fernàndez J, Lister R, Lenhard B, Holland PWH, Escriva H, Gómez-Skarmeta JL, Irimia M: Amphioxus functional genomics and the origins of vertebrate gene regulation. Nature 2018 564(7734): 64-70. [pubmed] [doi]

Supervisor

Libor Macůrek

Project description

Genome instability is one of the main drivers of cancer. Integrity of the genome is protected by a temporal arrest of the cell cycle in the presence of DNA damage and by efficient DNA repair. Tumor suppressor p53 and its downstream target p21 are efficient inducers of the cell cycle checkpoint. Inversely, protein phosphatase PPM1D is a negative regulator of p53/p21 pathway and allows renewal of the proliferation after DNA repair. Defects in p53 pathway or overexpression of PPM1D promote tumorigenesis by silencing the cell cycle checkpoint. This project aims to elucidate new molecular mechanisms of PPM1D function besides its established role in checkpoint recovery. We have recently identified that a fraction of PPM1D localizes at human telomeres and controls phosphorylation of the shelterin complex.

We will investigate how PPM1D activity affects DNA replication and DNA repair at telomeres. To this end we will use CRISPR/Cas9 technique to induce damage of the telomeric DNA and recruitment of DNA repair factors will be followed by quantitative microscopy. Molecular biology and biochemistry will be used to map the regions involved in PPM1D function at telomeres and for control of its protein stability. Overall, the project will contribute to understanding of PPM1D function in control of genome integrity.

Candidate profile

The laboratory of Cancer Cell Biology seeks for a motivated a curious PhD student with deep interest in basic mechanisms of cell function. The candidate should hold degree in cell/molecular biology or biochemistry. The candidate should be able to efficiently work in the team and communicate in English. Previous hands-on experience with cell biology, telomere biology or DNA repair techniques is considered advantage but is not required.

Suggested reading

• Storchova R, Palek M, Palkova N, Veverka P, Brom T, Hofr C, Macurek L. Phosphorylation of TRF2 promotes its interaction with TIN2 and regulates DNA damage response at telomeres. Nucleic Acids Research (in press)
• Burocziova M, Burdova K, Martinikova AS, Kasparek P, Kleiblova P, Danielsen SA, Borecka M, Jenikova G, Janečková L, Pavel J, Zemankova P, Schneiderova M, Schwarzova L, Ticha I, Sun XF, Jiraskova K, Liska V, Vodickova L, Vodicka P, Sedlacek R, Kleibl Z, Lothe RA, Korinek V, Macurek L. Truncated PPM1D impairs stem cell response to genotoxic stress and promotes growth of APC-deficient tumors in the mouse colon. Cell Death Dis. 2019; 10:818. [pubmed] [doi]
• Jaiswal H, Benada J, Müllers E, Akopyan K, Burdova K, Koolmeister T, Helleday T, Medema RH, Macurek L, Lindqvist A. ATM/Wip1 activities at chromatin control Plk1 re-activation to determine G2 checkpoint duration. EMBO J. 2017; 36:2161-2176. [pubmed] [doi]
• Kleiblova P, Shaltiel IA, Benada J, Ševčík J, Pecháčková S, Pohlreich P, Voest EE, Dundr P, Bartek J, Kleibl Z, Medema RH, Macurek L. Gain-of-function mutations of PPM1D/Wip1 impair the p53-dependent G1 checkpoint. J Cell Biol. 2013; 201:511-21. [pubmed] [doi]

Supervisor

Jana Dobrovolná
https://people.img.cas.cz/jana-dobrovolna/

Project description

DNA replication is an essential and one of the most complex processes in the cell. Not only exogenous DNA damage but also intrinsic DNA structures including G-quadruplexes (G4) and R-loops, their stabilization or unscheduled formation represent serious obstacles for replication progression, and have possible detrimental effects on genome integrity. Not surprisingly, those processes are pharmacologically targeted in anticancer therapy, despite the fact that only little is known about the underlying molecular mechanisms. It becomes apparent that maintenance of processive DNA replication requires sophisticated protein networks beyond the core replisome. Whether there is a direct crosstalk between G4 and R-loops, what proteins are involved in their homeostasis and what are the factors diversifying between their beneficial and pathological roles is not well understood.

The goals of our research are to identify proteins associated with G4 and R-loop structures and understand their roles in G4/R-loop formation and resolution as well as relationship to replication fork progression and associated repair. We are currently working on mass spectrometry-based proteomics approaches, including APEX-based proximity labeling and chromatin affinity precipitation methods, coupled with functional siRNA screens to identify new factors involved in metabolism of R-loops and G4s in conjunction with ongoing replication. The PhD student will use the well-established methods in the laboratory to validate hits and for selected protein to explore its role in replication stress and genomic instability.

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 can also undergo short-term trainings at the Institute of Molecular Cancer Research of the University of Zurich and/or at Masaryk university/CEITEC in Brno, where he/she will be exposed to front-line research in the field of DNA repair and cancer.

Suggested reading

• Boleslavska B, Oravetzova A, Shukla K, Nascakova Z, Ibini ON, Hasanova Z, Andrs M, Kanagaraj R, Dobrovolna J, Janscak P : DDX17 helicase promotes resolution of R-loop-mediated transcription-replication conflicts in human cells. Nucleic Acids Res. 2022 Dec 1:gkac1116. doi: 10.1093/nar/gkac1116. Online ahead of print.
• Bauer M, Nascakova Z, Mihai AI, Cheng PF, Levesque MP, Lampart S, Hurwitz R, Pfannkuch L, Dobrovolna J, Jacobs M, Bartfeld S, Dohlman A, Shen X, Gall AA, Salama NR, Töpfer A, Weber A, Meyer TF, Janscak P, Müller A. The ALPK1/TIFA/NF-κB axis links a bacterial carcinogen to R-loop-induced replication stress. Nat Commun. 2020 Oct 9;11(1):5117. [pubmed] [doi]
• 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.: Fork Cleavage-Religation Cycle and Active Transcription Mediate Replication Restart after Fork Stalling at Co-transcriptional R-Loops. Mol Cell 2020, 77(3):528-541.e8. [pubmed] [doi]

Supervisor

Teije Middelkoop
http://middelkooplab.com/

Project description

An enormous diversity of body shapes can be found in the animal kingdom. Animals acquire their final shape in a step-wise fashion during embryonic development in a process referred to as ‘morphogenesis’. The forces that drive these shape changes are generated by the actomyosin cytoskeleton within embryonic cells. Although much has been learned about the force-generating mechanisms that drive morphogenesis, how these physical mechanisms evolve, such that different body shapes arise, remains elusive. In this project the candidate will study morphogenesis from an evolutionary perspective. Actomyosin-driven early embryo morphogenesis will be studied in related nematode species using time-lapse imaging, followed by quantitative image analysis. Moreover, the candidate will perform mechanical perturbations (laser ablations, micro-rheology) to quantify force-generation in developing embryos. This will result in a highly quantitative biophysical characterization of embryo morphogenesis in species covering more than 100 million years of evolutionary distance. Building on previous work (suggested reading), this quantitative framework will reveal which physical processes are under selective pressure. Together with the evolutionary relationships, this approach will reveal how the physical mechanisms underlying morphogenesis have evolved in response to evolutionary forces, like natural selection and drift.

Candidate profile

The developmental mechanobiology lab is looking for a highly motivated and enthusiastic PhD student with a masters degree in biology (genetics, cell biology, developmental biology, evolutionary biology or biochemistry) or physics (biophysics) having experience in practical lab work. Experience with any of the relevant topics or methodology (C. elegans biology & genetics, biophysics, time-lapse imaging, quantitative image analysis using fiji/matlab/python) will be considered positively but is not an absolute requirement. The willingness to learn new techniques and methodology, and operate outside of the comfort zone is however essential. You will be working with genetically modified nematodes and image them using high-end fluorescence microscopy.

Suggested reading

• Middelkoop TC, Garcia-Baucells J, Quintero-Cadena P, Pimpale L, Yazdi S, Sternberg P, Gross P, Grill SW: CYK-1/Formin activation in cortical RhoA signaling centers promotes organismal left-right symmetry breaking. PNAS 2021, 118(20):e2021814118. [pubmed] [doi]
• Pimpale LG, Middelkoop TC, Mietke A, Grill SW: Cell lineage-dependent chiral actomyosin flows drive cellular rearrangements in early Caenorhabditis elegans development. Elife 2020, 9:e54930. [pubmed] [doi]
• Naganathan SR, Middelkoop TC, Fürthauer S, Grill SW: Actomyosin-driven left-right asymmetry: from molecular torques to chiral self organization. Curr Opin Cell Biol 2016, 38:24-30. [pubmed] [doi]