1.

May 9, 2021 - Recruitment announcement published
May 24, 2021 - Start of the recruitment
June 6, 2021 - Deadline for documents submission

Research projects for admissions 2021/2022-4:

Poly(A) tails - central hubs of mRNA stability control, Professor Andrzej Dziembowski
The role of mTOR-Brg1 interaction in normal and aberrant neuronal activity (NCN/MAESTRO), Professor Jacek Jaworski
Signaling of AXL receptor in cancer cells, Professor Marta Miączyńska, Daria Zdżalik-Bielecka, PhD
RNA-Protein Interactions in Human Health and Disease (NCN/DIOSUCRI), Gracjan Michlewski, PhD, Professor
Identifying unique adaptive responses of red pulp macrophages to iron deficiency (NCN/SONATA), Wojciech Pokrzywa, PhD DSc, PI: Katarzyna Mleczko-Sanecka, PhD

Poly(A) tails - central hubs of mRNA stability control

Supervisor: Professor Andrzej Dziembowski

Institute: International Institute of Molecular and Cell Biology in Warsaw

Laboratory: Laboratory of RNA Biology

Project description:

Gene expression is regulated at multiple levels. Our lab is interested in the regulation of mRNA stability, especially through the modifications of poly(A) tails. Recently, we have shown that the addition of untemplated uridines to the 3’ end of LINE1 retrotransposons precludes their propagation (Warkocki et al. Cell 2018). Moreover, we have identified a family of poly(A) polymerases TENT5, which reside in the cytoplasm and enhance the expression of mRNAs encoding secreted proteins (Moczek et al. Nature com. 2017; Bilska et al. Nature com. 2020; Gewartowska et al. Cell reports 2021). Those enzymes are differentially expressed in tissues and organs, affecting several aspects of animal physiology. TENT5C is an onco-suppressor in multiple myeloma and control immunoglobulin expression in B cells. TENT5A is essential for collagen secretion, and its mutations lead to congenital bone disease

In the future, we will continue to study the role and mechanism of action of TENT5 poly(A) polymerases, analyze global control of poly(A) tail lengths and develop bioinformatics tools for Direct RNA sequencing. Finally, we are planning to translate our knowledge out poly(A) tails for the design of mRNAs, which are more stable and better translated, which will be very valuable for mRNA-based therapeutics such as mRNA vaccines.

Aim:

The exact nature of the project will depend on the skills, predispositions, and interests of the selected PhD student. It may focus on:

functional analysis of the TENT5A poly(A) polymerases in transgenic mouse models generated in-house using CRISPR/Cas9 methodology
mastering of the DRS methodology in either the experimental part or bioinformatic analysis
analysis of principles of mRNA stability control and design of more efficient mRNA based therapeutics

Requirements:

Master's degree in biology, biochemistry or related field
Eligibility for PhD studies in Poland
Highly talented individuals who are passionate about research and are full of scientific curiosity
Experience in either: molecular biology/transcriptomics, animal models, bioinformatic analysis of transcriptomic data, will be a clear benefit
Written and spoken fluency in English
Willingness to learn and take new challenges, ability to work independently, analytical thinking
Good interpersonal skills and a collaborative attitude.

Number of positions available: 2

Contact: Andrzej Dziembowski

The role of mTOR-Brg1 interaction in normal and aberrant neuronal activity (NCN/MAESTRO)

Supervisor: Professor Jacek Jaworski

Institute: International Institute of Molecular and Cell Biology in Warsaw

Laboratory: Laboratory of Molecular and Cellular Neurobiology

Project description:

Gene expression is key for brain development and function and is regulated by a complex protein apparatus, which, among other things, is responsible for changes in the spatial packing of DNA in the cellular nucleus. mTOR kinase is one of the basic regulators of metabolism Mutations in the mTOR regulating genes, i.e. TSC1 or TSC2 lead to multi-organ diseases with serious neurological and neuropsychological symptoms. One of such diseases is tuberous sclerosis complex characterized by the occurrence of epilepsy, mental retardation and autism spectrum disorders. mTOR acts on many proteins changing their function, but occurs mainly in cytoplasm. However, the results of our previous research and the preliminary data which form the basis of this research proposal indicate that neuronal activity causes mTOR to move to the nucleus of the cell, where it interacts with Brg1. Using advanced molecular, cellular biology and microscopy methods we plan to study how mTOR-Brg1 interaction affects neuronal activity, epileptogenesis and social interactions. The research will use in vitro cultured neurons (rat and human) and Danio rerio. The results will contribute to a better understanding of the role of mTOR in physiology and brain diseases.

Aim:

On the basis of our previous research, we hypothesize that neuronal activity causes mTOR to move to the nucleus, where it regulates the chromatin-modelling complexes and gene expression. At the same time, we hypothesize that this sequence of events is disturbed in tuberous sclerosis complex leading to epilepsy as well as disturbances in social interactions characteristic of autism spectrum diseases. The aim of the project is to verify these hypotheses.

Requirements:

Master's degree in biology, biochemistry or related field
Eligibility for PhD studies in Poland
Good knowledge of basics of molecular and cell biology and/or neurobiology
Basic hands-on experience in one of the fields: molecular & cell biology, genetic engineering, fluorescent microscopy, danio rerio animal model
Basic programing skills (e.g., R)
Written and spoken fluency in English
Willingness to learn and take new challenges, ability to work independently, analytical thinking
Good interpersonal skills and a collaborative attitude

Number of positions available: 1

Contact: Jacek Jaworski

Signaling of AXL receptor in cancer cells

Supervisor: Professor Marta Miączyńska, auxiliary supervisor Daria Zdżalik-Bielecka, PhD

Institute: International Institute of Molecular and Cell Biology in Warsaw

Laboratory: Laboratory of Cell Biology

Project description:

AXL is a tyrosine kinase receptor that upon activation by its GAS6 ligand regulates cell growth, survival, migration and invasion. Overexpression of AXL occurs in a wide variety of cancer types
and is associated with increased invasiveness and metastasis, as well as resistance of cancer cells to anticancer therapies. In our previous studies, we identified the AXL receptor interactome (a set of proteins with which the receptor interacts) and discovered that AXL binds numerous proteins that regulate actin cytoskeleton dynamics. Through such interactions, activation of AXL receptor stimulates the formation of peripheral and circular membrane ruffles that promote macropinocytosis and ultimately lead to cell invasion (see our manuscript at https://bit.ly/2QfEVpF for more details). Macropinocytosis is a form of endocytosis that allows cells to take up large volumes of extracellular fluid and the compounds dissolved within it. The macromolecules taken up through this pathway can be an important source of nutrients that fuel cancer cell growth. It has been recently proposed that macropinocytosis may also contribute to resistance of cancer cells to chemotherapeutics. We found that proteins in the AXL interactome may be involved in nutrient uptake by macropinocytosis. Elucidating their mechanisms of action in AXL receptor signaling will be the goal of the proposed project.

Aim:

The goal of this project is to investigate the molecular mechanisms of AXL receptor signaling that regulates cancer cell growth. Specifically, we will investigate how the AXL receptor and its ligand GAS6 stimulate uptake of nutrients from the extracellular environment via macropinocytosis.

We will also determine whether and how this phenomenon contributes to drug resistance of cancer cells and, consequently, to the growth of tumors despite the applied therapy.

Requirements:

Master's degree in biology, biochemistry or related field
Eligibility for PhD studies in Poland
Solid understanding of the principles of molecular and cell biology
Previous experience in laboratory work and familiarity with basic molecular biology techniques
Written and spoken fluency in English
Good interpersonal skills and a collaborative attitude

Number of positions available: 1

Contact: This email address is being protected from spambots. You need JavaScript enabled to view it., Daria Zdżalik-Bielecka

RNA-Protein Interactions in Human Health and Disease (NCN/DIOSUCRI)

Supervisor: Gracjan Michlewski, PhD, Professor

Institute: International Institute of Molecular and Cell Biology in Warsaw

Laboratory: Laboratory of RNA-Protein Interactions

Project description:

RNA-binding proteins (RBPs) are key molecules that control gene expression through RNA-protein interactions. Consequently, they contribute to cellular homeostasis, normal development and majority of human diseases. Importantly, new RBPs are being discovered by high-throughput proteomics, but we still have a limited understanding of their function.

RNA viruses have caused several epidemics in the 21st century. Taking influenza A virus (IAV) infection as an exemplar, it kills 250,000 to 500,000 people annually and generates a significant global socioeconomic burden. Importantly the emergence of COVID-19 pandemic caused by an RNA virus SARS-CoV-2 continue to have catastrophic consequences on public health and world economy. Thus, a detailed molecular understanding of host-virus interactions is imperative in order to know how best to inactivate these viruses and prevent major disruptions in the future.

We have recently discovered and started characterising novel RNA binding protein – E3 ubiquitin ligase TRIM25 (Choudhury et al. 2014; Choudhury et al. 2017). TRIM25 belongs to a large family of tripartite motif-containing proteins (more than 80), most of which have E3 ubiquitin ligase activity. Many of TIRIMs are positive or negative regulators of innate immune response pathways. Importantly, TRIM25 is emerging as a key factor in the innate immune response to RNA viruses (including IAV, CoV, dengue virus and many others). Despite the essential involvement of TRIM25 in viral RNA-induced innate immunity, its RNA-binding functions are still poorly understood.

Aim:

With this project, we aim to take advantage of an assembled multi-disciplinary team to uncover the roles of the novel RNA-protein interactions in the antiviral response to selected RNA virus infections. We hypothesise that TRIM25 binds directly to viral RNAs to restrict virus propagation. We also hypothesise that other members from TRIM family bind RNA. Finally, we hypothesise that specific host RBPs bind to virus derived RNAs and inhibit or augment innate immune response. In summary, this project has the potential to make crucial contributions to understanding the innate immune response to RNA viruses and provide a platform for the development of novel, RNA-based antiviral therapeutics.

Requirements:

Master's degree in biology, biochemistry or related field
Solid knowledge of the principles of cell and molecular biology, virology or biochemistry
Hands-on experience in laboratory work and is familiar with basic cell and molecular biology techniques
Prior experience in virus handling and analysis, cell culture, mass spectrometry or bioinformatics will be an advantage
Proficiency in written and spoken English
Excellent interpersonal skills, initiative and ability to work independently and in a high-performance team

Number of positions available: 1

Contact: Gracjan Michlewski

Identifying unique adaptive responses of red pulp macrophages to iron deficiency (NCN/SONATA)

Supervisor: Wojciech Pokrzywa, PhD DSc, auxiliary supervisor, PI: Katarzyna Mleczko-Sanecka, PhD

Institute: International Institute of Molecular and Cell Biology in Warsaw

Laboratory: Laboratory of Iron Homeostasis

Project description:

Iron deficiency is a global health burden with profound socio-medical impacts, but little is known about how functions of specialized cells are affected by low systemic iron levels. Red pulp macrophages (RPMs) residing in the spleen are responsible for removing aged erythrocytes from the bloodstream. Following erythrocyte lysis, RPMs release iron to the circulation to replenish the pool of serum iron necessary for sustaining erythropoiesis. RPMs are thus critical for maintaining blood and iron homeostasis in the body. Interestingly, it was largely unknown if and how key cellular functions of RPMs are affected by low body iron status. Using a mouse model of nutritional iron deficiency, we uncovered that iron deficiency triggers specific but still elusive signaling mechanisms that modulate RPMs’ phagocytic and metabolic functions. We expect that these newly identified responses likely contribute to the adaptation of the whole organism to limited iron supplies. Within our project, we apply both in vivo and in vitro approaches to decipher the molecular mechanism responsible for the adaptive functional ‘rewiring’ of RPMs in iron deficiency and determine their physiological role for the whole organism. The new knowledge generated by this research is expected to significantly advance our understanding of an organism’s adaptation to iron deficiency.

Aim:

We aim to comprehensively characterize the functional adaptation of RPMs to iron deficiency and identify its molecular triggers. We also plan to determine how this ‘rewiring’ affects RPMs’ inflammatory status. We will explore how the abrogation of this ‘adaptation program’ affects the organism, including iron and blood homeostasis. To this end, we will create and characterize new conditional knock-out mice characterized by specific suppression of the RPMs’ adaptation to low iron conditions.

Requirements:

Master's degree in biology, biochemistry or related field
Eligibility for PhD studies in Poland
Interests in molecular aspects of physiology, motivation for experimental work, passion for science, hands-on experience in laboratory work
Experience in mouse/rat-based studies or willingness to work with animals
Written and spoken fluency in English
Willingness to learn and take new challenges, ability to work independently, analytical thinking
Good interpersonal skills and a collaborative attitude.
Research achievements (eg, publications or manuscripts in preparation) and experience abroad will be of advantage

Number of positions available: 2

Contact: This email address is being protected from spambots. You need JavaScript enabled to view it.

2.

August 4, 2021 - Start of the recruitment
August 18, 2021 - Deadline for documents submission

Research projects for admissions 2021/2022-5:

Genomics and Epigenomics of acute myelogenous leukemia (AML)

Supervisor: Professor Matthias Bochtler

Institute: International Institute of Molecular and Cell Biology in Warsaw

Laboratory: Laboratory of Structural Biology

Project description

Epigenomic changes play a prominent role in acute myelogenous leukemia (AML). Mutations in the methyltransferase DNMT3A and the dioxygenase TET2 are among the most frequent alterations in this type of malignancy. It has been proposed that defects in epigenomics entail DNA repair defects, which in turn lead to karyotype degradation. This contrasts with information from the Cancer Genome Atlas and the COSMIC database, which both identify AML as a typical M-type malignancy, i.e. a malignancy that is driven by mutations, rather than by copy-number variation. However, clinical observation suggests that a considerable fraction of AML patients have karyotype aberrations. In some cases, the chromosomal changes can be drastic and resemble the chromothripsis seen in other malignancies. Highly karyotype aberrant AMLs are poorly characterized. It is not clear whether the spectrum of exome mutations is similar in these leukemias and in M-type leukemias and what drives the karyotype degradation. It is also unclear whether changes in the epigenomic machinery and their possible effects on DNA signaling play a role in this process. We hope to clarify these issues, primarily by sequencing approaches, in collaboration with clinicians in Heidelberg and Dresden (Germany).

Aim

The aim of the project is to obtain deep sequencing data for AML patients (bulk and single cell). We plan to compare the spectrum of mutations and copy number variation in highly aberrant and normal karyotype AMLs. We plan to test if the spectrum of mutations in the coding genome and tumor clonal histories are similar in the two types of AML. We want to learn if mutations in the epigenomic enzymes cause DNA repair phenotypes, which could ultimately lead to karyotype degradation.

Requirements:

Master's degree in biology, biochemistry or a related field
Eligibility for PhD studies in Poland
Theoretical knowledge of genetics and epigenetics.
Practical experience with cellular fractionation by FACS.
Experience with preparation of libraries for DNA sequencing using Nanopore and Illumina technologies.
Experience with genotyping (high resolution melting analysis).
Experience with or at least interest in bioinformatic analysis of deep sequencing data.
Written and spoken fluency in English
Willingness to learn and take new challenges, ability to work independently, analytical thinking
Good interpersonal skills and a collaborative attitude

Number of positions available: 1

Contact: This email address is being protected from spambots. You need JavaScript enabled to view it., This email address is being protected from spambots. You need JavaScript enabled to view it.

Poly(A) tails - central hubs of mRNA stability control

Supervisor: Professor Andrzej Dziembowski

Institute: International Institute of Molecular and Cell Biology in Warsaw

Laboratory: Laboratory of RNA Biology

Project description:

Gene expression is regulated at multiple levels. Our lab is interested in the regulation of mRNA stability, especially through the modifications of poly(A) tails.
Recently, we have shown that the addition of untemplated uridines to the 3’ end of LINE1 retrotransposons precludes their propagation (Warkocki et al. Cell 2018). Moreover, we have identified a family of poly(A) polymerases TENT5, which reside in the cytoplasm and enhance the expression of mRNAs encoding secreted proteins (Moczek et al. Nature com. 2017; Bilska et al. Nature com. 2020; Gewartowska et al. Cell reports 2021). Those enzymes are differentially expressed in tissues and organs, affecting several aspects of animal physiology. TENT5C is an onco-suppressor in multiple myeloma and control immunoglobulin expression in B cells. TENT5A is essential for collagen secretion, and its mutations lead to congenital bone disease.

To study the dynamics of poly(A) tails genome-wide, we have implemented a Direct RNA sequencing Nanopore methodology. It is now widely used in our projects, and we also collaborate with other laboratories interested in post-transcriptional gene expression regulation (for instance, Scheer et al. Nature com. 2021). Moreover, we use Direct RNA sequencing to look globally at the regulation of poly(A) tails (Tudek et al. Nature com., under revision).
In the future, we will continue to study the role and mechanism of action of TENT5 poly(A) polymerases, analyze global control of poly(A) tail lengths and develop bioinformatics tools for Direct

RNA sequencing. Finally, we are planning to translate our knowledge out poly(A) tails for the design of mRNAs, which are more stable and better translated, which will be very valuable for mRNA-based therapeutics such as mRNA vaccines.

Aim:

The exact nature of the project will depend on the skills, predispositions, and interests of the selected PhD student. It may focus on:

functional analysis of the TENT5A poly(A) polymerases in transgenic mouse models generated in-house using CRISPR/Cas9 methodology.
mastering of the DRS methodology in either the experimental part or bioinformatic analysis.
analysis of principles of mRNA stability control and design of more efficient mRNA based therapeutics

Requirements:

Master's degree in biology, biochemistry or related field
Eligibility for PhD studies in Poland
Highly talented individuals who are passionate about research and are full of scientific curiosity
Experience in either: molecular biology/transcriptomics, animal models, bioinformatic analysis of transcriptomic data, will be a clear benefit
Written and spoken fluency in English
Willingness to learn and take new challenges, ability to work independently, analytical thinking
Good interpersonal skills and a collaborative attitude

Number of positions available: 2

Contact: This email address is being protected from spambots. You need JavaScript enabled to view it.

Experimental analysis of molecular determinants involved in epilepsy (NCN/OPUS)

Supervisor: Professor Jacek Kuźnicki, auxiliary supervisor/PI: Vladimir Korzh, PhD

Institute: International Institute of Molecular and Cell Biology in Warsaw

Laboratory: Laboratory of Neurodegeneration

Project description:

The effects of KCNB1 mutations that cause epileptic encephalopathy were analyzed mechanistically mainly using electrophysiology in heterologous cells in vitro. The developmental analysis was limited by the availability of single mutants in mice and zebrafish and did not explore the whole range of effects caused by KCNB1 mutations (Shen et al., 2016). The KCNB1 loss of function (LOF) or gain of function (GOF) cause specific morphological changes in the brain ventricles (Shen et al., 2016) and inner ear (Jedrychowska et al., 2020) in developing zebrafish embryos and larvae. The zebrafish transgenics express fluorescent markers in specific manner. The high-resolution microscopy of transgenic embryos and larvae in vivo provides information about developmental mechanisms as well as changes in activity of specific signaling pathways. These tools satisfy conditions necessary to study the developmental effect of different KCNB1 mutations in real time. This rationale was confirmed in preliminary experiments when analyzing the effect of overexpression of human mutated KCNB1 mRNA. Kcnb1 GOF causes cell delamination in brain ventricles and their expansion (hydrocephalus), and enlargement of the inner ear and otoliths. These features recapitulate the phenotype of the kcnb1 GOF zebrafish mutant and constitute the rationale for the "brain and ear" in vivo test to be used when defining an effect of human mutations.

Aim:

Using the site-specific CRISPR-Cas9 mutagenesis in zebrafish, the representative Kcnb1 mutations that mimic the known human mutations of KCNB1 will be generated and analyzed by a combination of bioimaging, single-cell transcriptomics, electrophysiology and behavioral analysis. This will provide rationale for subfunctionalization of human KCNB1 mutations.

Requirements:

Master's degree in biology, biochemistry or related field
Eligibility for PhD studies in Poland
Prior experience in molecular developmental biology and zebrafish studies is a bonus during selection of candidates, but necessary training will be provided
Written and spoken fluency in English
Willingness to learn and take new challenges, ability to work independently, analytical thinking
Good interpersonal skills and a collaborative attitude

Number of positions available: 2

Contact: Vladimir Korzh

Identifying unique adaptive responses of red pulp macrophages to iron deficiency (NCN/SONATA)

Supervisor: Wojciech Pokrzywa, PhD DSc, auxiliary supervisor, PI: Katarzyna Mleczko-Sanecka, PhD

Institute: International Institute of Molecular and Cell Biology in Warsaw

Laboratory: Laboratory of Iron Homeostasis

Project description:

Aim:

We aim to comprehensively characterize the functional adaptation of RPMs to iron deficiency and identify its molecular triggers. We will explore how the abrogation of this ‘adaptation program’ affects the organism, including iron and blood homeostasis. To this end, we will create and characterize new conditional knock-out mice characterized by specific suppression of the RPMs’ adaptation to low iron conditions.

Requirements:

Master's degree in biology, biochemistry or related field
Eligibility for PhD studies in Poland
Interests in molecular aspects of physiology, motivation for experimental work, passion for science, hands-on experience in laboratory work
Experience in mouse/rat-based studies or willingness to work with animals
Written and spoken fluency in English
Willingness to learn and take new challenges, ability to work independently, analytical thinking
Good interpersonal skills and a collaborative attitude.
Research achievements (eg, publications or manuscripts in preparation) and experience abroad will be of advantage