Case Studies

Below are the MELGEN stories from three of our ESRs who have completed their studies and moved on to the next phase of their career

Joanna Pozniak (ESR05)

Everyone has their own bigger or smaller dreams. When I was an undergraduate student I had an aspiration to become a researcher hence to pursue doctoral studies in cancer field after my master studies. When the time has come to apply for PhD positions and to think what I really would like to do, I realized that bioinformatics/computational cancer biology was what got my attention the most. However, becoming a PhD student in this field seemed to me more like an unachievable dream since I graduated from molecular biology with background in laboratory techniques and at that time I was convinced that this ground is reserved for males. Nevertheless, I decided to move against my feelings and convictions and started to train myself in bioinformatics and apply for PhD positions related to it. I was successful in an application for a perfectly suited bioinformatic position for my dreamed PhD in cancer immunology at the University of Leeds, UK, funded by Marie Sklodowksa-Curie Association (MSCA) within MELGEN (MELanoma GENetics) European Training Network (ITN). At this time, I was a mother of a toddler and this was another reason why this position was perfect for me, because PhD students within this MSCA framework get family allowances. During my PhD apart from hard, stressful, and at the same time joyful work I had several opportunities to meet a lot of world-leading scientists, I traveled to many conferences and collaborated with researchers from the MELGEN network as well as many others from various research institutions and countries. Especially, one conference organized by MELGEN network member (University of Essen, Germany) was particularly important to me. This meeting opened a door for my future postdoctoral position, by meeting my current boss, Prof. Marine, the head of the Laboratory for Molecular Cancer Biology at VIB, in Leuven, Belgium. I had a chance to talk to him personally, present my skills and just simply ask for a position. This is how I ended up to continue doing what I have dreamed of several years ago, meaning being a researcher in cancer biology using bioinformatic and computational tools.

Obviously, all of this would not happen if not huge amount of work of Prof. Julia Newton Bishop as a coordinator of the MELGEN network and lot of care as my supervisor, as well as effort of Juliette Randerson-Moor as a great MELGEN manager. I am very grateful to them for making MELGEN happen, the whole MELGEN network for great scientific and personal training and the MSCA for funding.

Joanna Poźniak, PhD
Postdoctoral Fellow
VIB Center for Cancer Biology
Laboratory for Molecular Cancer Biology
KU Leuven Oncology Dpt

Rohit Thakur (ESR12)

I am a postdoctoral fellow at Jennifer Wargo’s lab, the University of Texas MD Anderson Cancer Center, Texas, US. My research focuses on understanding how tumor microenvironment regulates response to cancer immunotherapy. I completed my undergraduate degree in Bioinformatics at Vellore Institute of Technology in India, subsequent to which I was awarded the prestigious Marie-Sklodowska Curie fellowship funded by the MELGEN European Commission Horizon 2020 program to pursue my PhD at University of Leeds, UK. During my PhD, I received training in statistics and melanoma tumor genetics under the supervision of Drs. Jenny Barrett, Julia Newton-Bishop and Jeremie Nsengimana. During my PhD, I developed prognostic gene signatures using genomic datasets from one of the largest primary melanoma cohorts to date. Using unsupervised classification approach, I devised a transcriptome-based molecular signature which predicts prognosis, particularly in stage I one tumors. This is an important contribution to the field as majority of the melanomas are diagnosed early and this signature could be useful in identifying patients who may benefit from receiving early adjuvant therapies. Furthermore, the molecular signature described above has demonstrated predictive value to identify patients with metastatic melanoma treated with immunotherapy who are not likely to respond to treatment and this work has now been published in Clinical Cancer Research.

During my PhD, I also received training in machine learning and developed classification models that predict high- and low-risk of melanoma relapse after initial diagnosis. The MELGEN program has been instrumental in defining my career path for me by providing numerous training opportunities to improve my technical and communication skills as well as scientific interactions with world leaders in melanoma research. As part of the MELGEN program, I conducted short research visits to Dr. Goran Jonsson’s group at University of Lund, Sweden, Dr. Will Spooner at Eagle Genomics, Cambridge, UK and Dr. Manolis Kellis’ group at Massachusetts Institute of Technology, USA where I received training in differential gene expression analysis and machine learning using genomic datasets. I also received several opportunities to present my work as oral-talk and poster presentations at national and international meetings like Annual GenoMEL Meeting, American Society of Human Genetics annual meeting, Biology of Genomes, and Society of Melanoma research annual meeting etc which has trained in effectively communicating my research. Overall, MELGEN truly has been a shoulder of a giant for me and it has significantly improved my scientific horizons.

Rohit Thakur, PhD
Postdoctoral Fellow
MD Anderson · Department of Surgical Oncology
University of Texas MD Anderson Cancer Center

Sonia Leonardelli (ESR14)

Sonia Leonardelli is one of the lucky early-career cancer researchers to be awarded with the MELGEN training programme funded by the Marie Skłodowska-Curie grant No 641458.

Sonia grew up in a small village called Mezzolombardo in the north of Italy, closed to the Dolomites. She studied Cellular and Molecular Biotechnology at the University of Trento in Italy, one of the best universities of middle size in Italy and in the top 400 in the world. During her master studies, she won an Erasmus+ scholarship to spend one semester in Ludwig-Maximilians-Universität in Munich (Germany), before graduating in 2015. Both her Master studies and thesis focused on cancer research, and to pursue this line of research she moved to Essen, in Germany, in January 2016, to start her PhD in the Group Molecular Tumor Immunology of Prof. Annette Paschen as part of the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 641458. This grant funded her salary and research expenses on the project focused on understanding resistance mechanisms to immunotherapy of melanoma cells. She also spent a few months at the prestigious Wellcome Trust Sanger Institute in Cambridge under supervision of Dr. David Adams, who helped her with the bioinformatic analysis need for the project. In order to cover the travel expenses of this secondment, she applied and won the EACR Travel Fellowship.

During her four-year long PhD, she managed to publish as a co-first author the paper on “Tumor CDKN2A-Associated JAK2 Loss and Susceptibility to Immunotherapy Resistance” in the renowned peer-reviewed journal JNCI. She was also involved in three other peer-reviewed papers as a co-author.

The outstanding training obtained from the MELGEN Marie Skłodowska-Curie programme and from Prof. Paschen allowed her to defend with honor her PhD in December 2019. Also, she recently won the Mildred Scheel School of Oncology Cologne-Bonn (MSSO Cologne-Bonn) Postdoctoral Fellowship to work under supervision of Prof. Michael Hölzel at the University Hospital in Bonn. There Sonia will investigate the role of human endogenous retroviruses in renal cell carcinoma. This fellowship is awarded to further the careers of translational cancer researchers and further provides a training program in translational oncology. Surely, it will also support Sonia to pursue a career working on cancer and fighting it.

Sonia Leonardelli, PhD
Postdoctoral Fellow
Institute of Experimental Oncology
University of Bonn