Jobs

Call for applicants

Jobs

PhD positions in the EU Horizon 2020 Marie Skłodowska-Curie Project PRECODE:

International training network which sets a joint research programme to train a new generation of leading scientists in model systems and methods for the development of new therapies for pancreatic cancer (PaCa)

The main PRECODE R&D objectives are:

  1. To establish an European resource of pancreatic cancer organoid and integratomic analysis of those organoids.
  2. Identify drug resistance and sensitivity in those organoids to develop new treatment and diagnostic strategies.
  3. To improve organoid culture and establish a model system containing all parts of a pancreatic cancer tissue for growing in vitro.
  4. To identify new genes essential for pancreatic cancer progression and metastasis.

Career stage

Early Stage Researcher (ESR) or 0-4 yrs (Post Graduate)

Benefits

The successful candidates will receive an attractive salary in accordance with the MSCA regulations for Early Stage Researchers. The exact (net) salary will be confirmed upon appointment and is dependent on local tax regulations and on the country correction factor (to allow for the difference in cost of living in different EU Member States). The salary includes a living allowance, a mobility allowance and a family allowance (if married). The guaranteed PhD funding is for 36 months (i.e. EC funding, additional funding is possible, depending on the local Supervisor, and in accordance with the regular PhD time in the country of origin). In addition to their individual scientific projects, all fellows will benefit from further continuing education, which includes internships and secondments, a variety of training modules as well as transferable skills courses and active participation in workshops and conferences.

Eligibility criteria

Applicants need to fully respect three eligibility criteria (to be demonstrated in the Europass CV format):

Early-stage researchers (ESR) are those who are, at the time of recruitment by the host, in the first four years (full-time equivalent) of their research careers. This is measured from the date when they obtained the degree which formally entitles them to embark on a doctorate, either in the country in which the degree was obtained or in the country in which the research training is provided, irrespective of whether or not a doctorate was envisaged.

Conditions of international mobility of researchers:

Researchers are required to undertake trans-national mobility (i.e. move from one country to another) when taking up the appointment. At the time of selection by the host organisation, researchers must not have resided or carried out their main activity (work, studies, etc.) in the country of their host organisation for more than 12 months in the 3 years immediately prior to their recruitment. Short stays, such as holidays, are not taken into account.

English language: Network fellows (ESRs) must demonstrate that their ability to understand and express themselves in both written and spoken English is sufficiently high for them to derive the full benefit from the network training.

Selection process

Deadline for applications is 06.03.2020. To attract the right students, the required profiles are clearly listed for each ESR position.

The candidates apply for a maximum of three specific ESR positions and list their order of preference. The Supervisors provide the names of their preferred candidates to the Supervisory Bord (SB), which in its turn produces a short list. After a thorough evaluation, the candidates are ranked and a collective decision is made. In this way a complementary team of ESRs can be assembled, as positively experienced from previous ETN recruitment events.

The SB is kept informed at all times when new eligible candidates appear. The SB makes an official complaint in case the Code of Conduct for the Recruitment of Researchers is breached. The involved supervisor is then expected to find another candidate.

All chosen candidates are expected to start their contract by the end of March 2020.

All details concerning the recruitment-procedure principles are communicated on the on-line application portal, so that potential ESRs know exactly what to expect and are stimulated to apply. All recruitment (pre and final selection) is in line with the European Charter for Researchers, providing the overarching framework for the roles, responsibilities of both researchers and employers. The Code of Conduct for the Recruitment of Researchers functions ensures that the selection procedures are transparent and fair.

Additional comments

The recruitment strategy of PRECODE fully complies with the Code of Conduct definition of merit. For example, merit is not just measured by a researcher’s grades, but on a range of evaluation criteria, such as teamwork, interdisciplinary knowledge, soft skills and awareness of the policy impact of science.

The SB has members of each gender and considers the promotion of equal opportunities and gender balance as part of the recruitment strategy. Also, in view of the RRI principles, special efforts are made to attract women and ESRs from new EU Member States.

PRECODE aims at a participation of 50% female ESRs in the network. Researchers are employed on fixed-term contracts and are registered as staff candidates for PhD degrees. Therefore, they are entitled to pension contributions, paid holidays, and other benefits as governed by the universities and industrial companies.

PhD positions in the EU Horizon 2020 Marie Skłodowska-Curie Project PRECODE

Host: Friedrich-Alexander University of Erlangen-Nürnberg

Main supervisor: PD Dr. Marc Stemmler (marc.stemmler@fau.de)

Duration: 36 months

Required profile: Master in Life Sciences, Experience in Molecular Biology

Description: The lab is focused on understanding molecular mechanisms of metastasis formation and we have collected ample evidence that Zeb1-depletion diminishes cell plasticity required for efficient metastasis in a genetic mouse model of pancreatic cancer. Using pancreatic cancer organoid cultures, genetic engineering and screening methods we want to decipher the molecular mechanisms how Zeb1 regulates cell plasticity and metastasis. The applicant will learn how to use specific autochthonous mouse models for isolation, culturing and in vitro manipulation of Zeb1 proficient and deficient organoids. The successful candidate will set-up screening methods to identify candidates mediating drug sensitivity, cell plasticity, motility and metastasis. By CRISPR/Cas9 technology candidate genes will be knocked out and phenotypical changes assessed by analysis in gene expression pattern, migration/invasion potential and transplantation experiments.

Host: Karolinska Institutet

As a university, KI is Sweden’s single largest centre of medical academic research and offers the country’s widest range of medical courses and programmes. Since 1901 the Nobel Assembly at Karolinska Institutet has selected the Nobel laureates in Physiology or Medicine. Karolinska Institutet was founded by King Karl XIII in 1810 as an “academy for the training of skilled army surgeons”. Today, Karolinska Institutet is a modern medical university and one of the foremost in the world. With the close relationship to the clinical milieu, a well established infrastructure and a stable financial situation, Karolinska Institutet has excellent prerequisites for sustaining high quality research and education.

Main supervisor: Prof. Matthias Löhr (Matthias.lohr@ki.se)

Duration: 36 months

Required profile: Master in Life Sciences, Experience in Molecular Biology

Description: Culture of cells in 3D is much closer to in vivo growth than 2D culture of cells for many reasons. In recent years it has been demonstrated that growth and therapeutic response behaviour of cancer cells is greatly dependent of their microenvironment. We grow pancreatic cancer cells (monospheroid) alone or together with pancreatic stellate cells (heterospheroid) in 3D in order to learn more about their mutual dependencies and vulnerabilities. In addition, we use these models for high throughput drug screening. The future student will learn 3D culture methods using cell lines as well as patient material and he/she will analyse these cultures by RNAseq in order to identify points for therapeutical attack. This will be complemented by high throughput/content drug screening approaches.

Host: University of Verona

Main supervisor: Dr Vincenzo Corbo (Vincenzo.corbo@univr.it)

Duration: 36 months

Required profile: Master in Life Sciences, Experience in Cell and Molecular Biology, experience of computational biology is a plus

Description: Patient-Derived Organoids (PDOs) are a new biological platform to understand the biology of pancreatic cancer. PDOs can be successfully derived from majority of pancreatic cancer patients and also enable the cocultivation of neoplastic cells with other cellular components, including cancer-associated fibroblasts (CAFs). The successful applicant will learn how to isolate, cultivate and characterize both PDOs and (CAFs). He or She will establish PDOs representative of the different molecular subtypes of pancreatic cancer and study their interaction with CAFs. He/She will subject both PDOs and coculture of PDOs and CAFs to pharmacological treatment to establish resistance/sensitivity of the culture. To understand mechanisms of resistance to a given compound, and specifically the contribution of cell plasticity to this phenomenon, the candidate will avail of single cell sequencing analysis organoids.

Host: University of Navarre in Pamplona, Spain (Clinica Universidad de Navarra and Center for Applied Medical Research -CIMA-)

Main supervisor:  Dr. Mariano Ponz-Sarvise (e-mail: mponz@unav.es)

Duration: 36 months

Required profile: The applicants should preferably hold an MSc degree in Biological Sciences or a related discipline

Description: The successful PhD candidate will work in the laboratory of Oncogenes and Effector Targets (OnTarget) under the guidance of Dr. Ponz-Sarvise. The group is part of the Solid Tumors Program and is located at the Center for Applied Medical Research, CIMA, in the campus of the University of Navarre. The OnTarget group focuses on KRAS-driven tumors and studies are based on a multimodal approach, which includes functional genomic techniques, mouse genetics, in vitro and xenograft models, analysis of human cancer samples, and clinical parameters. The laboratory also works with organoids from primary human and murine cells. This model makes it possible to carry out in vitro and in vivo studies of gene modulation, pharmacological treatments and cell co-cultures. The overarching goal of the group is to identify molecular targets and/or combinatorial therapeutic approaches that will provide effective treatments for patients harbouring KRAS mutations. The main research lines of the OnTarget group are: 1) to unveil key nodes of gene expression regulation (transcription factors and miRNAs) and tissue-dependent KRAS synthetic lethal interactions that will yield new molecular targets, and 2) to dissect the efficacy of targeted therapy- and immunotherapy-based strategies for the treatment of mutant KRAS cancers. In the last years the group has developed new computational analyses and mouse models that provide the methodological ground for ongoing work. This methodology has provided the seed results to engage international (Systems Biology Ireland, BRIC of Copenhaguen, UCSF, Stanford University) and national (CNIO, VHIO, Biodonostia) groups in active collaborations.

The successful ESR will develop a PhD project focused on an organoid co-culture platform for the development of rational combinations in the field of immune-oncology. The objectives of the project would be: 1) Development of a platform for co-cultivation of pancreatic organoids with cancer-associated fibroblasts and immune cells obtained from patients affected of pancreatic cancer. 2) Drug effects in the different cell types that form the tumour (including stroma). 3) Identification of rational combinations and preclinical studies to test the effect of the combinations. The co-culture platform will be used to analyse both at the cellular and molecular level the effect of the drugs in the different cell types that form the tumour (including the stroma). This analysis will enable to define combination strategies of cytotoxic drugs or targeted therapies with immune-modulatory drugs.

The project should be developed in 3 years. During this period the successful ERS will perform two additional training sessions (secondments) of three months each in:

  • UNIVERSITA DEGLI STUDI DI VERONA, Italy, under the supervision of: Vincenzo Corbo to learn to establish and expand organoid cultures

MIMETAS BV, Netherlands, under the supervision of Remko van Vught about the development and optimisation of assay techniques for co-cultures

Host: Institute of Cancer Sciences (ICS), University of Glasgow, United Kingdom

Main Supervisor: Dr Peter Bailey (peter.bailey.2@glasgow.ac.uk)

Duration: 36 months

Required Profile: Master’s degree in Bioinformatics, Life Sciences, Biomedical Science or related discipline. Although not essential bioinformatic experience is preferable. Applicants can have any nationality, but the MSCA-ITN mobility clause applies (more than 24 months of the past 3 years were spent outside of the United Kingdom).

Description: Large scale sequencing analyses have transformed our understanding of Pancreatic Cancer (PC) and have defined several molecular taxonomies that now guide pre-clinical and clinical therapeutic development. The identification of molecularly defined subgroups of patients with distinct biological underpinnings and potential therapeutic vulnerabilities promises a step change in clinical practice. Patient-derived organoids (PDOs) provide a tractable and biologically relevant model system for understanding the molecular mechanisms underpinning disease progression and drug resistance. The PRECODE consortium aims to perform a deep characterisation of ~200 PDOs using cutting edge techniques to uncover new biology and provide a basis for clinical decision making.

The successful PhD applicant will play a central role in the molecular characterisation of ~200 PDOs using RNAseq and Whole Exome Sequencing (WES). The applicant will implement best practice pipelines for NGS analysis and develop systems biology approaches to identify therapeutically actionable pathways for clinical development. The applicant will work closely with other groups within the consortium to facilitate the deep interrogation of high throughput drug and metabolomic screening data and to develop signatures of drug response and resistance. It is expected that the applicant will develop core competencies in bioinformatics including software development (working knowledge or R and python), database development and management, data visualisation, statistical analysis and systems biology approaches for data analysis.