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Vermeulen Lab (spring 2019)

Current lab members

Louis Vermeulen, MD, PhD

Prof Louis Vermeulen is a group leader/principal investigator within the Center for Experimental Molecular Medicine (CEMM), Laboratory for Experimental Oncology and Radiobiology (LEXOR) at the Academic Medical Center (AMC), Amsterdam. Louis Vermeulen studied medicine and obtained his PhD at the AMC, and afterwards worked as a research fellow at the University of Cambridge, UK. His group uses quantitative approaches in combination with state of the art in vitro and in vivo models to study the biology of intestinal cancers in order to improve tumor classification and therapies. Louis Vermeulen is supported by several personal grants, including an ERC starting grant, a VIDI grant from the Dutch Science Organization (NWO/ZonMw), and a career development grant of the Dutch Digestive Foundation (MLDS). He is a EMBO Young investigator and in 2017, he was awarded a Young Investigator New York Stem Cell Foundation (NYSCF) grant.

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Laura Schwarzmuller, MSc

Laura, originally from Germany, did her Bachelor’s and Master’s in Molecular Biotechnology in Heidelberg. She performed her Master thesis in Hanno Glimm’s lab (NCT, Heidelberg) where she worked on IGF2-dependency in colorectal cancer. In November 2017, she joined the Vermeulen lab as PhD student. Her project is focused on the role of long non-coding RNAs in colorectal cancer. Together with Nicolas Leveille she is interested in identifying Wnt-regulated lncRNAs that are involved in transcriptional regulation and other processes in colorectal cancer (stem) cells. By screening a panel of colorectal cancer cell lines they aim to identify transcripts that play a crucial role in the signalling pathway and are biologically relevant for cancer cells.

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Oscar Bril

Oscar did his Bachelor’s in Molecular Life Sciences and Master’s in Drug Innovation at Utrecht University. His two internships were with dr. Frank Redegeld (Pharmacology, Utrecht University) on the development of a high-throughput confocal microscopy method for detecting the effects of nutrition and mast cells on colorectal cancer, and prof. dr. Gunnar Nilsson (Immunology & Allergy, Karolinska Institutet, Stockholm) on alternative cytokines and growth factors for the culturing of mast cell progenitors. He joined the Vermeulen lab in may 2020 as a PhD student. Together with Nicolas Leveille, he will perform genome-wide functional screens to unravel oncogenic lncRNAs in colorectal cancer.

Ronja Adam, MD, MSc

Ronja S. Adam is a medical doctor, who chose to specialize in clinical genetics. Aiming to understand genetic data analysis better, she additionally obtained a master degree in life science informatics in 2016. Afterwards she paused her medical specialization training to fully concentrate on improving her bioinformatics and scientific skills and joined the Vermeulen lab in August 2016 for a PhD position. Ronja aims to unravel how colorectal cancer grows and develops in the background of phenotypic and genotypic diversity. Based on known major influencing factors like wnt-signaling and colorectal cancer subtypes she studies differential transcription, especially of non-coding RNAs. Furthermore she helps to establish a lineage tracing method using a neutral genetic labeling technique. Overall she works with sequencing data from different collaborative projects, which might help optimizing cancer patient care on the long term. Personal travel grants from the German Academic Exchange Service (DAAD) and the Cancer Center Amsterdam (CCA) allowed Ronja to receive co-supervision from Florian Markowetz at the CRUK Cambridge institute.

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Nicolas Leveille, PhD

Nicolas completed his postdoctoral studies in 2015 at the Netherlands Cancer Institute (NKI). During these years he developed an interest to understand how complex noncoding RNA regulatory networks shape gene expression and biological processes. He then joined the Vermeulen lab to apply his expertise on noncoding RNAs to colorectal cancer. In addition, Nicolas recently obtained a KWF grant to develop lineage tracing tools, which will help to uncover how cell population dynamics drive tumor growth, response to therapy and tumor progression.

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Sanne van Neerven, MSc

Sanne van Neerven performed her Bachelors in Biomedical Sciences at the University of Amsterdam, and her Master Oncology at the VU Medical Center. After her Masters, she was awarded an NWO-OOA full PhD scholarship and landed in the lab of Louis Vermeulen. Her interests comprise all stages of colorectal cancer development, but her work mostly focuses on the initiating steps leading to the development of pre-malignant adenomatous polyps. More specifically, she studies the competition of healthy and mutant stem cells within the colonic crypt by implementing both in vitro organoid cultures and in vivo mouse models. Insights in this competition aid the development of chemopreventive strategies that could specifically benefit patients with heritable colorectal cancer predisposition syndromes such as familial adenomatous polyposis and Lynch Syndrome.

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Leandro Ferreira Moreno, PhD

After completing his graduation in Biology, Leandro received his Master degree in Molecular Biology/ Biochemistry at the Federal University of Paraná - Brazil. During this time, he was working on the development of a pipeline for in-silico prediction of non-coding RNAs in bacteria using RNA-seq data. In 2013, Leandro moved to the Netherlands to do his PhD at the Westerdijk Fungal Biodiversity Institute - Utrecht. In November of 2018, Leandro defended his PhD thesis entitled "The Biology of Black Yeast genomes". In October of 2018, Leandro joined the Vermeulen group as a bioinformatician, where he is studying the presence of long non-coding RNAs in different cell lines of colorectal cancer by applying GRO-seq technology.

Tom van den Bosch, MSc

Tom did a bachelor in Mathematics and Physics at the University of Amsterdam, and a Master in Mathematics at VU University with a focus on Stochastics and Biomedical Mathematics. In November 2017 he started his PhD under the supervision of Dr Daniel Miedema. In his PhD he focuses on mathematical modelling of intra-tumour heterogeneity in colorectal cancer. He also has running projects on Big Data analysis using statistical models and gets asked to help his colleagues with all their programming problems every now and then.

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Sanne ten Hoorn, MD, MSc

Sanne ten Hoorn is a medical doctor. For her PhD she works on using the consensus molecular subtypes to predict the anti-EGFR response in metastatic colorectal cancer and on the implementation of the consensus molecular subtypes in the clinic.

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Maartje van der Heijden, MD, MSc

Maartje van der Heijden studied Medicine at the Academic Medical Center (AMC) in Amsterdam. From early-on she was interested in oncology and during her studies she worked as a research assistant at the Laboratory for Oncology and Radiobiology (LEXOR) in the AMC and in the Tabar group at the Memorial Sloan-Kettering Cancer Center based in New York. After obtaining her Medical degree, she continued her scientific career as a PhD candidate under the supervision of Louis Vermeulen. Here, in close collaboration with other group members, she studies factors that influence the malignant transformation and outgrowth of intestinal (stem) cells, both in a qualitative and quantitative fashion. In addition, she studies the clonal growth dynamics of colorectal cancer in homeostasis and under drug pressure. Furthermore, she aims to unravel different therapy resistance mechanisms to commonly used chemo- and targeted therapies for CRC.

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Sophie Lodestijn, MD, MSc

Sophie Lodestijn was born in Nijmegen. In 2007, she moved to Amsterdam to study Psychobiology at the University of Amsterdam and later Medicine at the Amsterdam Medical Center (AMC). She finished Medical school in 2015 and started her PhD project at the Center for Experimental and Molecular Medicine at the Amsterdam UMC under supervision of Louis Vermeulen and Maarten Bijlsma. The main focus of her project is to understand the stem cell dynamics in established colorectal cancer and pancreatic ductal adenocarcinoma. She uses a marker-free lineage tracing system in combination with a mathematical model for tumor growth to define the clonal dynamics during unperturbed tumor growth. This way different cancer types can be compared. In another project Sophie tries to unravel the stem cell dynamics during development and homeostasis in the heathy tissues.

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Sanne Bootsma, MD, MSc

Sanne graduated medical school in 2017, after which she worked for one year as a resident-not-in-training at the internal medicine department of the Slotervaart hospital in Amsterdam. In 2018 she joined the Vermeulen lab to start a PhD. The focus of her project is on finding common vulnerabilities of molecular subtypes across gastrointestinal cancers. Furthermore she will work on orthotopic mouse models for gastrointestinal cancers, to test novel subtype specific therapeutics.

Kristiaan Lenos, PhD

Kristiaan studied Life Science and Technology in TU Delft and University of Leiden, followed by a PhD in Molecular Cell Biology at the Leiden University Medical Center, where he studied the regulation of the key tumor suppressor p53. After a 2 year postdoc at the VUMC, he joined the Vermeulen lab in 2014, to work on colorectal cancer stem cell dynamics. This work revealed an important role of the tumor microenvironment on cancer cell clonogenicity, therefore the cross-talk between cancer cells and surrounding cells is now one of his main research topics. Blocking these signals might be a promising new therapeutic approach to treat cancer patients. Another part of his research focusses on the formation of peritoneal metastasis in colorectal cancer patients. Studying the molecular pathways involved in this process could provide new strategies to prevent or treat this condition.

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Lisanne Nijman, BSc

Lisanne Nijman studied Biology and Medical Laboratory Research at the Saxion University in Deventer from 2010 to 2014. After graduation she started in 2015 working as a research technician in the Vermeulen lab as her first job. As a technician she assist multiple projects from other group members with a wide range of research techniques and invivo work. Also, she is responsible for maintenance of the stock and ordering supplies for an optimal workflow in the lab.

Tim de Back, MD, MSc

Tim studied Medicine at the Academic Medical Center (AMC) in Amsterdam and graduated in 2018. During his studies, he was already interested in oncology and hematology and, therefore, attended oncology master classes and performed research into chronic lymphocytic leukemia at the hematology department of the AMC. After obtaining his medical degree, he worked as a resident internal medicine (not in training) at the Flevoziekenhuis in Almere. In 2019 he joined the Vermeulen lab as a PhD candidate. His research focuses on refining the consensus molecular subtypes (CMS) classification for colorectal cancer (CRC) and studying molecular characteristics of small bowel adenocarcinomas (SBA). Furthermore, he aims to unravel prognostic and predictive molecular markers of both CRC and SBA and, ultimately, implement molecular classification systems for intestinal cancer in the clinic.

Daniël Miedema, PhD

Daniël studied physics in Leiden and started his career at Deltares in Delft. At Deltares, he worked on a technique based on acoustic emission to measure the mechanical properties of the soil. Daniël moved to the University of Amsterdam to start a PhD in the group of Prof. Peter Schall, where he studied a wide range of topics in the complexity program of NWO. The topics ranged from shear-banding of colloidal glasses and traffic jam formation on highways, to interactions of kinesin motors that navigate along the cytoskeleton of cells. The work done during his PhD resulted in the thesis “Transport in Complex Driven Systems”. In October 2015, he joined the Vermeulen group at the Amsterdam UMC. He is specialized in data-analysis and mathematical modelling and works together with wet-lab experimentalist in the Vermeulen group to decipher the fundamental growth dynamics of (colorectal) cancers from lineage tracing experiments. Daniël further has an interest in the process of cancer initiation and the aneuploidy of cancers.

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Selami Baglamis, MSc

He has finished his bachelor and master degree in Biochemistry at Ege University (Izmir / Turkey). He has worked on nanoparticles, nanomaterials, controlled release systems, molecularly imprinted polymers and affinity interaction systems. He started Ph.D under Prof. Dr. Louis Vermeulen supervision, on 4th October, 2018. He is working on tracing colorectal cancer cells via nuclear-localization lentiviral gene ontology markers (LeGO) that encode red, green or blue fluorescent proteins.

Khalid El Makrini, BSc

Khalid El Makrini is a research technician who studied Life Sciences at the Hogeschool of Utrecht. He started at the AMC in the lab of Louis Vermeulen shortly after his graduation in September 2017, to work and support in different projects like ‘the role of the tumor microenvironment in colorectal cancer’. Besides, together with a team of technicians, he takes care of organizing and managing the different labs.

Felipe A Vieira Braga, PhD

Felipe is a Post-Doc in the Vermeulen. During his PhD he worked in transcriptional regulation of human CD8 T cells at Sanquin Bloodbank (Amsterdam). He then joined the lab of Sarah Teichmann at the Sanger Institute (Cambridge-UK), where he used single cell transcriptomics to interrogate diverse disease processes such as kidney cancer and asthma. He then joined the group of Louis Vermeulen in November 2018 where he is working on single cell transcriptomics and immune-oncology in colorectal cancer, with the aim to identify novel immune-therapy targets in specific patient cohorts.

Maria Lecca, MSc

Maria studied Experimental Biology at the University of Cagliari (Sardinia, Italy). After completing her degree she moved to the UK where she obtained a Masters in Stem Cells and Regenerative Medicine at the University of Sheffield. There she investigated the signaling network that leads to osteoblast differentiation from mesenchymal precursors using the Zebrafish in vivo model. Following her experience in the UK and her growing interest for developmental biology Maria joined the group of Rogier Versteeg as a PhD student (University of Amsterdam) where she studied the role of BMP signaling in Neuroblastoma, a pediatric tumor of the sympathoadrenal lineage. Currently she works as a research technician in the Vermeulen lab where she is responsible for coordinating the in vivo models of colorectal and pancreatic cancers.

Clara Elbers, PhD

Clara is a scientist with a passion for knowledge valorization. After a PhD in human genetics from Utrecht University, she obtained a scholarship to do a post-doc in population genetics at the University of Pennsylvania (UPENN). Back in the Netherlands, she decided to move into life science consulting and work on research innovation projects. At the company Catalyze, she worked first as a consultant and later as quality manager. In 2018, Clara joined Cancer Center Amsterdam as a research manager.

Rana Ramadan, MSc

Rana graduated with a master in Regenerative Medicine and Technology from the Utrecht University in 2017. Soon after that, she joined the Vermeulen group as a research intern in order to expand her knowledge in the colorectal cancer field. She has recently started her PhD in the lab working 3D in vitro remodelling of stem cell dynamics in the crypt and lineage tracing of early carcinogenesis. Rana has always been fascinated by the combination of biomedical sciences and technology in order to advance research. She wrote her master thesis on the use of organ-on-chip platforms for studying cancer metastasis, where she gained interest in both oncology and microfluidic systems. She hopes that with all the innovation in biotechnology, researchers will have access to better experimental models for studying mechanisms, testing newly developed drugs but also to advance personalised medicine.

Nina de Groot, MSc

Nina de Groot is a research technician in the Vermeulen group since September 2017. Originally from Twente, she completed her Bachelor at the Saxion Hogeschool Enschede and finished her Master Cardiovascular Research at the VU Medical Center. After running a PhD trajectory at the Experimental Cardiology department at the AMC she decided to work in the lab as a technician and switched to the Vermeulen lab. In the lab Nina is working closely with Sanne van Neerven on the competition of healthy and mutant stem cells. Together with the other technicians she maintains and keeps the lab running smoothly.

Vivek Sheraton M

Sheraton, a chemical engineer by training, received his master’s degree from Indian Institute of Technology-Kanpur (IITK). During his masters, he developed lattice Boltzmann method-based models to understand depinning behaviour of droplets on inclined surfaces. His interdisciplinary doctoral studies involved combining chemical engineering, biology and computational science to model solute-cell dynamics in biological systems. During his doctoral studies, he developed two computational frameworks to address healthcare problems. He has a PhD from Nanyang Technological University (NTU) (Cancer Simulations) and a PhD (Science) from University of Amsterdam (UvA). His current research (with Vermeulen group, Institute for Advanced Study and Dutch Burn Centre) concerns with the complexities associated with interactions between immune system and other biological systems in human body.