The Innovative Training Network (ITN) “INTERCEPT-MDS - Exploring cell-to-cell heterogeneity and exploiting epigenetic regulation for the interception of myeloid disease cells" is recruiting 12 highly motivated PhD candidates within the emerging field of disease interception. The offered positions are available with a duration of 36 months. The fellowships are funded as part of theMarie Skłodowska-Curie Actions (MSCA) Innovative Training Networks under the European Commission’s Horizon 2020 programme.
Under the supervision of a principal investigator from one of our 10 expert European host institutions, each candidate will carry out a specific research project to study how to intercept early leukaemia cells exploring single cell genomics and epigenetics.
The highly complementary composition of the INTERCEPT-MDS network will provide all the key expertise and infrastructure to support the scientific excellence of our PhD candidates. Experts from two sectors (academia and industry) and two research environments (clinical and basic) across Europe will offer a unique multidisciplinary and multisectoral training opportunity in the novel field of disease interception.
Successful applicants will be enrolled in a PhD programme and will receive a structured training programme consisting of soft skill courses, targeted workshops, conferences, retreats, social events and networking. In addition, our PhD candidates will carry out secondments in other European institutions within the network to provide the needed interactions to achieve research and training excellence, and improve their future career perspectives in academia and the private sector.
PhD Positions
PhD Positions
PhD Project 1: Impact of clonal haematopoiesis with indeterminate potential (CHIP) mutations on transcription in single-cells. The PhD candidate will elucidate how early mutations in CHIP provide a growth advantage and contribute to the emergence of myelodysplastic syndromes. We will take a primarily computational approach but also perform own single-cell sequencing experiments. The ideal candidate will have previous knowledge in R and/or other scripting languages (such as Python), experience in working with Linux environment, bash scripting and knowledge of the main molecular biology techniques.
Host: Josep Carreras Leukaemia Research Institute, Spain.
PhD Project 2: Dissect haematopoietic stem cell/progenitor-bone marrow niche (HSCP-BM) interaction on a single cell level in low risk myelodysplastic syndromes (MDS). The PhD candidate will study the open question in MDS of how HSPCs can gain a clonal advantage in the bone marrow.
Host: Erasmus Medical Center, The Netherlands.
PhD Project 3: Cross-talk between single haematopoietic stem cell/progenitors (HSCP) and bone marrow (BM) niche in myelodysplastic syndromes (MDS) and secondary-type acute myeloid leukaemia (sAML). The PhD candidate will study how aging and disease influences communication between stem and stroma cells. The candidate will be able to distinguish intrinsic and extrinsic alterations and identify pathways and factors that can be further evaluated for as drug targets.
Host: Klinikum rechts der Isar der TU München, Germany.
PhD Project 4: Phenotypic heterogeneity of myelodysplastic cells and influence of epigenetic therapies. The PhD candidate will report, for the first time at the single cell level, the evolution of the transcriptome of leukaemic and nonleukaemic cells upon treatment with hypomethylating agents and IDH inhibitors. This will allow them to compare for the first time the channelling of genetic and phenotypic heterogeneity driven by different epigenetic therapies.
Host: Institut national de la sante et de la recherche medicale (INSERM), France.
PhD Project 5: Understanding and reverting the epigenetic reprogramming of bone marrow (BM) stroma cells in myelodysplastic syndromes. The PhD candidate will study the support capacity of bone marrow stroma cells towards healthy and disease haematopoietic stem cell/progenitors (HSPCs). The fellow will identify candidate chromatin regulators and pinpoint ways for therapeutic intervention. The ideal candidate should have a strong background in immunology and solid wet-lab skills.
Host: Josep Carreras Leukaemia Research Institute, Spain.
PhD Project 6: Targeted inhibition of the NUP98-NSD1 fusion oncogene in myelodysplastic syndromes (MDS) and acute myeloid leukaemia (AML) models by NSD1 inhibitors. The PhD candidate will analyse the efficiency of epigenetic drugs as a mechanism to decrease aberrant histone methylation activity in MDS and sAML driven by the fusion protein of NUP98 and the histone methylase NSD1.
Host: Josep Carreras Leukaemia Research Institute, Spain.
PhD Project 7: Functional identification of effectors of fusion proteins that drive secondary-type acute myeloid leukaemia (sAML). The PhD candidate will identify critical factors that control the initiation and maintenance of fusion protein-driven MDS/AML. Detailed studies will address the mechanistic basis of high-confidence candidates.
Host: Veterinärmedizinische Universität Wien, Austria.
PhD Project 8: DNA methylation as determinant of myelodysplastic syndromes (MDS) treatment with hypomethylating agents. The PhD candidate will study determinants of hypomethylating agent response that could be further exploited for the development of combinatorial drug targets. In addition, the candidate will identify and exploit differentially methylated regions for the development of a predictive biomarker for response and further assess if single-cell resolution would increase diagnostic power.
Host: Università degli Studi di Firenze, Italy.
PhD Project 9: Exploiting 3D organotypic niche models to dissect the cellular crosstalk between niche and haematopoietic stem cell/progenitors (HSPCs) in myelodysplastic syndromes (MDS). The PhD candidate will use fully humanized 3D organotypic bone marrow niche models as a complementary approach to patient-derived xenograft (PDX) models to explore niche dependencies in MDS and perform screens that aim to identify druggable modules that promote the fitness and progressive clonal dominance of malignant clones.
Host: Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Germany.
PhD Project 10: Enhancing the informative value of bulk bone marrow (BM) RNA-seq by inferring cell-type contributions. The PhD candidate will develop an artificial intelligence-based method that will allow the inference of the contributions of different cell types to bulk RNA-seq data from complex mixtures. The ideal candidate will have previous knowledge in R and/or other scripting languages (such as Python), experience in working with Linux environment, bash scripting and knowledge of the main molecular biology techniques.
Host: MLL Munich Leukemia Laboratory, Germany.
PhD Project 11: Development of pre-clinical patient-derived xenograft (PDX) models of myelodysplastic syndromes (MDS). The PhD candidate will develop new humanized mouse PDX models and assess their ability to maintain the disease phenotype and cellular complexity. The best PDX models will enable the pre-clinical testing of new innovative drugs. Monitoring treatments at the single cell level will allow the determination of treatment efficacy and possible occurrence of resistance.
Host: University of Bergen, Norway.
PhD Project 12: Development of methods for the functional analysis of single cell RNA-seq data.The PhD candidate will develop a new analysis framework that will make possible a better understanding of the underlying biology of cell subpopulations in heterogenic tissues and comparison across experimental conditions. The ideal candidate would have a background in bioinformatics, programming, and functional genomics.
Host: BioBam Bioinformatics, Spain.
Eligibility Criteria:
We welcome applications from PhD candidates from any country fulfilling the following criteria:
Eligible candidates must not have resided or carried out their main activity (work, studies, etc.) in the country of their host institution for more than 12 months in the 3 years immediately prior to their recruitment by the host institution (i.e. the starting date indicated in the employment contract/equivalent direct contract, which is planned between July and October 2021).
Eligible candidates shall at the date of recruitment by the host institution (i.e. the starting date indicated in the employment contract/equivalent direct contract), be in the first 4 years (full-time equivalent research experience) of their research careers and not have been awarded a doctoral degree.
Eligible candidates must have a master’s degree relevant for the chosen position (including biology, medicine, biochemistry, bioinformatics or a related discipline, depending on the individual PhD Project) or its equivalent that would entitle them to a doctorate by July 2021, or must hold an official university qualification from a country of the European Higher Education Area with a minimum of 300 ECTs of official university studies.
Successful candidates must have a high level of proficiency in written and spoken English, which will be assessed with the motivation letter and the interview, respectively.
Application Process
Applications will be solely accepted through the INTERCEPT-MDS online application form and must be in English.
During the application process, candidates will need to upload the following documents as a single PDF (please merge the multiple files into a single document if necessary):
CV including publications (if any),
motivation letter,
2 reference letters,
copies of Bachelor's and Master's degree certificates. Candidates should include the transcripts in English of academic records for the studies that make them eligible for a doctoral programme. If these studies have been completed by the deadline for applications, the total number of credits for the degree and the credits awarded must also appear.
Applicants will receive a confirmation email the first time they submit the application form. After the submission, applications can still be reviewed and edited through the Candidate login option as many times as needed (please note that no confirmation email will be sent after saving changes). Applicants will be able to submit and modify the information until the deadline (23 February 2021 at midnight, Central European Time). Applications will be considered as they are at the time of the deadline.
Each applicant may apply to a maximum of three individual PhD projects. To do so, it is necessary to complete the application process for each of the projects individually. During the application process the candidate will be asked to rank the projects to which she/he is applying in order of preference (please note that there is no need to apply to more than one PhD project).
Deadline: 23 February 2021
Benefits
3-year full time employment contract (salary depends on the country of the recruitment considering both the local and MSCA regulations for Early Stage Researchers and their family status at the time of the recruitment).
Enrolment in a PhD programme.
Shared research and innovative multidisciplinary and multisectoral training by experts and experienced trainers from two sectors (academia and industry) and two research environments (clinic and basic).
A structured training programme consisting of soft skill courses, targeted workshops, retreats, social events and networking.
Secondments at other institutions within the INTERCEPT-MDS consortium.
Gaining experience abroad.
Opportunities for participation in national and international meetings.
Enlarged professional network and improved future scientific career perspective in academia and the private sector.
If you have any further questions about the application process, the eligibility criteria or any other aspect of the call, please write an email to: intercept-mds@carrerasresearch.org.