Recruitment 21/22-5

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), Professor Matthias Bochtler
Poly(A) tails - central hubs of mRNA stability control, Professor Andrzej Dziembowski
Experimental analysis of molecular determinants involved in epilepsy (NCN/OPUS), Professor Jacek Kuźnicki, PI: Vladimir Korzh, PhD
Identifying unique adaptive responses of red pulp macrophages to iron deficiency (NCN/SONATA), Wojciech Pokrzywa, PhD DSc, PI: Katarzyna Mleczko-Sanecka, PhD

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: Ten adres pocztowy jest chroniony przed spamowaniem. Aby go zobaczyć, konieczne jest włączenie w przeglądarce obsługi JavaScript., Ten adres pocztowy jest chroniony przed spamowaniem. Aby go zobaczyć, konieczne jest włączenie w przeglądarce obsługi JavaScript.

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: Ten adres pocztowy jest chroniony przed spamowaniem. Aby go zobaczyć, konieczne jest włączenie w przeglądarce obsługi JavaScript.

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:

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 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: 1

Contact: Katarzyna Mleczko-Sanecka