Juan J. Garcia Vallejo


Juan J. Garcia Vallejo is Associate Professor and Principal Investigator at the Department of Molecular Cell Biology & Immunology. Juan has always been interested in combining his medical background with a keen interest in technology-driven biomedical research. He leads the Immune System CytOMICs research group, where he applies cutting-edge cytometry and computational methods for the characterization of the interplay between different components of the immune system and the identification of immune-based biomarkers in different disease models, including brain cancer, COVID-19, and exposure to microplastics. Juan completed an MBA in 2017 with a thesis on the management of core facilities in an academic research environment. Since 2016, he acts as Scientific Director of the Microscopy and Cytometry Core Facility of the Amsterdam UMC – Location VUmc. Juan is an active member of the International Society for the Advancement of Cytometry (ISAC) and the Core Technologies for Life Sciences (CTLS) Society.

Research Line

Characterization of the human immune system cytome (theme Tumor Immunology)

Two of the most relevant characteristics of the immune system are its highly complex heterogeneity in terms of cell types and functional states, and, the interconnectedness of all these cell subsets. Both properties are critical for the functioning of the immune system in  protecting us from infections while maintaining homeostasis; but, at the same time, make this organ extremely difficult to characterize in detail. With the advent of highly multiplexed single-cell technologies we are getting closer to characterize the immune system cytome (the collection of all different cell subsets and cell states within an organ, including their interrelations) which will be critical for the identification of correlates of disease or immunological interventions as well as for elucidating the underlying mechanisms of immunity.

Two major technical advances in the field of cytometry in recent years have made possible the simultaneous characterization of more than 40 markers at a single cell level. Both mass cytometry (cytometry by time-of-flight or CyTOF) and spectral flow cytometry are allowing the routine implementation of comprehensive immunophenotyping panels in research and clinical environments. Despite of the advances, the currently available chemistries present a number of limitations. In CyTOF, the loading of metal isotopes cannot be controlled and only a few elements can be successfully loaded. In spectral flow cytometry, new fluorochromes are needed to fully exploit the configuration of current instruments. In this project, we are exploring the development of new polymer chemistries and computational methods to extend mass and spectral flow cytometry beyond the current limits of the technology and bring it to the level of targeted proteomics at the single cell level.

A functional immune atlas of glioblastoma (theme Tumor Immunology)

Glioblastomas are the most aggressive brain malignancies, for which immunotherapy has so far failed to prolong survival. Glioblastoma-associated immune infiltrates are dominated by tumor-associated macrophages and microglia, which are key mediators of immune suppression and resistance to immunotherapy. We have recently demonstrated that tumor-intrinsic mechanisms, such as altered glycosylation, have an impact in the distribution and phenotype of tumor-infiltrating myeloid cells. Interestingly, altered tumor glycosylation also had a distinct impact on the peripheral immune compartment, even though it is well known that glioblastomas do not metastasize. Our goal is to understand the heterogeneity of the immune infiltrate in glioblastoma with the ultimate aim to identify potential therapeutic targets. In addition, we also focus in the study of the peripheral immune system to explore the presence of signatures that can predict immune composition in the tumor and/or can have predictive/prognostic value.

Figure legend: (H) Three subclusters (F5, F7, and F16) with statistically significant differences in frequency between MGL-Ligand High and WT tumors. (I) Networks of subclusters from WT (Left) and MGL-Ligand High (Right) tumors with nodes visualizing all of the level-two cell subclusters in the experiment and edges representing correlation coefficients for relationships between subclusters. The size of the nodes represents the size of the population, the color intensity of the nodes represents the number of connections to other nodes, and the color intensity of the edges represents the correlation coefficient. The orange nodes highlight population F16, and the red nodes highlight the nearest neighbors of population F16 in both MGL-Ligand High- and WT tumors.

Emerging research lines in the group

COVID-19 immune monitoring: The pandemic Coronavirus-disease 19 (COVID-19), caused by infection with the SARS-CoV-2 virus is characterized by a heterogeneous clinical course. While the majority of patients experience only mild symptoms, a substantial proportion develops severe disease with increasing hypoxia up to acute respiratory distress syndrome (ARDS), a disease manifestation that seems to be strongly linked to a Cytokine Release Syndrome (CRS). Importantly, severe course of COVID-19 cannot be explained only by patients’ age and concurrent diseases, because young and otherwise healthy subjects can develop lethal complications of COVID-19, suggesting that unknown susceptibility factors are involved. There is an urgent need to develop better diagnostic/prognostic tools for CRS in COVID-19 as early treatment is expected to either prevent or alleviate the severity of the ARDS. This is of special relevance while there is no readily available vaccine and, yet, more cases of COVID-19 patients are expected in successive pandemic waves of SARS-CoV-2 or, potentially, other corona viruses. In collaboration with Dr. F. van Wijk (UMCU) and Prof. S. Nezhentsev (Amsterdam UMC), we propose to use genetics and broad immunophenotyping by spectral flow cytometry to (a) characterize the immune response of COVID-19 patients at risk of developing CRS and (b) identify susceptibility factors for the development of CRS in the context of SARS-CoV-2 infection.

Microplastics and health: Our health is intrinsically related to the quality of the environment. Humans are exposed to unknown quantities of plastic particulate debris on a daily basis via air water and food. That’s why it is important to determine what adverse health outcomes may arise out of plastic particle pollution. One of the important mechanisms we think is involved in the toxicity of these particles is an interference with homeostatic immune function. This study seeks to answer the question if human blood actually contains PET used in textiles and packaging or Teflon powders extensively used in lubricants, inks and thermoplastics. And if so, what kind of hazardous immune system effects can we expect? In Collaboration with Dr. H. Leslie (VU), we are using cutting edge analytical method for the determination of microplastics in blood and, using a human blood in vitro exposure model, we seek to understand the immunological signals that show us how small plastic particles may be interfering with homeostatic immune function.


Key publications

  1. Crommentuijn MHW, Schetters STT, Dusoswa SA, Kruijssen LJW, Garcia-Vallejo JJ, van Kooyk Y. Immune involvement of the contralateral hemisphere in a glioblastoma mouse model. J Immunother Cancer. 2020; 8 (1): e000323.
  2. Dusoswa SA, Verhoeff J, (…), Garcia-Vallejo JJ. Glioblastomas exploit truncated O-linked glycans for local and distant immune modulation via the macrophage galactose-type lectin. Proc Natl Acad Sci U S A. 2020; 117 (7): 3693-3703.
  3. Dusoswa SA, (…), Garcia-Vallejo JJ. Glycan modification of glioblastoma-derived extracellular vesicles enhances receptor-mediated targeting of dendritic cells. J Extracell Vesicles. 2019; 8 (1): 1648995.
  4. Dusoswa SA, Verhoeff J, Garcia-Vallejo JJ. OMIP-054: Broad Immune Phenotyping of Innate and Adaptive Leukocytes in the Brain, Spleen, and Bone Marrow of an Orthotopic Murine Glioblastoma Model by Mass Cytometry. Cytometry A. 2019; 95 (4): 422-426.
  5. Duinkerken S, van Kooyk Y, Garcia-Vallejo JJ. Human cytomegalovirus-based immunotherapy to treat glioblastoma: Into the future. Oncoimmunology. 2016; 5 (9): e1214791. 

Group members

Maartje Rietdijk

Maartje Rietdijk, MSc

PhD student
My project is focused on understanding the exposure and immunotoxicity of micro- and nanoplastic (MNP) contaminants in humans by using in vitro models.


Xiangming Cai, MSc

PhD student
My work focuses on the immune monitoring of glioblastomas.

Other PI's

Marjolein van Egmond


Marjolein van Egmond is professor in Oncology and Inflammation. She is PI at the Department of Molecular Cell Biology & Immunology and staff member at the Department of Surgery. Throughout her career she has been fascinated by the role of antibodies in immunity and the activation of immune cells via antibody receptors (Fc receptors). Initially her research focused on the role of the Fc receptor for IgA (FcαRI) in protective mucosal immunity. Subsequently, her lab discovered that aberrant IgA initiates perpetual neutrophil activation, leading to severe tissue damage in multiple auto-immune diseases and chronic inflammation. Additionally it is now clear that antibodies can be used as therapeutic drugs to engage the immune system to fight cancer. Due to her dual appointment at a research- and clinical department, she is in an excellent position to translate experimental findings into clinical applications. Marjolein van Egmond was awarded a VENI, VIDI and VICI from the Innovational Research Incentives Scheme (Netherlands Organization for Scientific Research, NWO).

Research Line

Monoclonal antibody therapy of cancer (theme Tumorimmunology)

Because neutrophils and macrophages and have potent cytotoxic abilities we are examining whether it is possible to enlist this potential for tumour cell killing. Both myeloid cell types express Fc receptors and are, as such, able to recognize and kill tumour cells in the presence of specific monoclonal antibodies (mAbs) that opsonize tumour cells. We have demonstrated that macrophages are extremely efficient in phagocytosing and digesting circulating cancer cells in the presence of specific IgG mAbs. By contrast, neutrophils induce tumour cell death especially in the presence of monoclonal antibodies of the IgA subclass. We are currently investigating the mechanisms of neutrophil- and macrophage mediated tumour cell killing in more detail, as we anticipate that this knowledge will help us to develop novel (pre-operative) adjuvant anti-cancer therapies.

The role of neutrophil IgA Fc receptor (Fc-alfa-RI) in health and disease. (theme Mucosal Immunology)

IgA is the principal antibody in mucosal areas and plays a key role in mucosal defence. Neutrophils become highly activated when their IgA Fc receptor (FcaRI) is targeted. Since neutrophils are the first cells to arrive at inflammatory (mucosal) sites upon invasion by pathogens, we postulate that activation of neutrophil FcaRI by IgA-coated microorganisms will trigger an essential immune response that will help to clear the infection. However, aberrant IgA deposits are found in several diseases (e.g. IgA-induced blistering diseases and rheumatoid arthritis). We showed that a perpetuating inflammatory loop is initiated when excessive IgA complexes are present, which leads to sever tissue damage. We therefore aim to unravel the role of IgA- induced neutrophil activation in protective and harmful immune responses in more detail.

Figure adapted from: Aleyd E, et al. Journal of Immunoly 2016;197:4552-4559. Binding of IgA rheumatoid factor (green) to neutrophils. Neutrophils were incubated with plasma of healthy controls (upper panels) or of patients with rheumatoid arthritis (lower panels), and stained for the presence of FcRI (red) and IgA (green). Blue = nucleus.

Key publications

  1. Breedveld A, van Egmond M. IgA and FcαRI: Pathological Roles and Therapeutic Opportunities. Front Immunol. 2019; 10:553.
  2. Abis GSA, Stockmann HBAC, Bonjer HJ, van Veenendaal N, van Doorn-Schepens MLM, Budding AE, Wilschut JA, van Egmond M, Oosterling SJ; SELECT trial study group. Randomized clinical trial of selective decontamination of the digestive tract in elective colorectal cancer surgery (SELECT trial). Br J Surg. 2019;106:355-363.
  3. Grewal S, Korthouwer R, Bögels M, Braster R, Heemskerk N, Budding AE, Pouw SM, van Horssen J, Ankersmit M, Meijerink J, van den Tol P, Oosterling S, Bonjer J, Gül N, van Egmond M. Spillage of bacterial products during colon surgery increases the risk of liver metastases development in a rat colon carcinoma model. Oncoimmunology. 2018;7:e1461302.
  4. Heineke MH, Ballering AV, Jamin A, Ben Mkaddem S, Monteiro RC, Van Egmond M. New insights in the pathogenesis of immunoglobulin A vasculitis (Henoch-Schönlein purpura). Autoimmun Rev. 2017;16:1246-1253.
  5. Gül N, Babes L, Siegmund K, Korthouwer R, Bögels M, Braster R, Vidarsson G, ten Hagen TL, Kubes P, van Egmond M. Macrophages eliminate circulating tumor cells after monoclonal antibody therapy. J Clin Invest. 2014;124:812-23.

Group members

Carolien Zeelen

Carolien Zeelen, MSc

Research technician
One of the projects I work on is the optimization of circulating tumor cell detection in blood of patients using flow cytometry. The goal of this project is to see if CTCs can be targeted with antibody therapy and therefore prevent metastases. Next to that, I work on the visualization of interaction between immune cells and blood vessels in mouse tumors using fluorescent immunohistochemistry.


Céline Sewnath, MSc

PhD student
The focus of my work is about overcoming the immunosuppressive milieu in order to induce a potent adaptive immune response. For this, I will use new antibody therapies that will target tumor cells but also activate immune cells. Therefore, I will characterize the immune profile in colorectal cancer patients and investigate if these new antibody therapies are able to induce the adaptive immune response and thereby long term anti-tumour immunity. For this project I will use different in vitro assays on primary human cells such as RNA-sequencing data, ADCCs, ADCPs, flow cytometry, cytokine assays (Luminex, ELISA), co-cultures and in vivo work.


Dennis Gout, MSc

PhD student
My main project focuses on the improvement of a neutrophil-targeting, bi-specific antibody therapy for cancers by the addition of an immuno-active payload to the antibody. I’m using these antibody-cytokine fusion proteins (immunocytokines) as a platform to attack the innate immune exclusion in various pre-clinical tumor models from multiple angles. This project involves the design, cloning and production of these immunocytokines as well as the characterization and functional testing of them both in vitro and a pre-clinical tumor model..


Kees Tuk

research technician
Main focus of my work: development of bispecific antibodies for Immunotherapy. All techniques that are necessary for this are used, mainly in vitro techniques. Mostly cell isolation techniques, Cell culture, in vitro cell function assays, ELISA’s. Also: development of in vitro assays to determine cell function of the effect of antibody complexes on cells.


Jasmin I Ersöz

research technician

foto Leonie

Leonie Behrens, MSc

PhD student
My research focuses on the innate immune checkpoint CD47-SIRPα, which limits tumor cell killing by various myeloid cell types. My aim is to determine how SIRPα signaling prevents neutrophil activation, and how blockade of this checkpoint may improve neutrophil-mediated cytotoxicity towards cancer cells. To do so, I perform various in vitro assays to follow the different steps of tumor killing by neutrophils, e.g. formation of an immunological synapse, trogocytosis and tumor cell death.

Mandy Gruijs

Mandy Gruijs, MSc

PhD student
My research focuses on antibody therapy in cancer treatment. We have developed a bispecific antibody, which targets both a tumor antigen and neutrophils, as well as macrophages and NK cells. Additionally, I am involved in a clinical trial in which we test an already clinically used antibody in a new regimen. We have expertise in several experimental techniques, including tumor cell killing assays, flow cytometry, microscopy and ELISA.

Myrthe van Delft

Myrthe van Delft, PhD

postdoctoral researcher
The focus of my work is studying the role of IgA and FcaR1 in auto-immunity. My aim is to unravel the role of IgA induced (myeloid) cell activation in inflammation and tissue damage in auto-immune diseases (like IgA-induced blistering disease and rheumatoid arthritis). For this I make use of multicolor flow cytometry, cytokine and binding ELISAs, myeloid cell assays and mice models.

Foto Niels

Niels Heemskerk, PhD

Senior postdoctoral researcher
My research is focused on the targeting and regulation of selective immune cell trafficking across tumor blood vessels in order to improve immunotherapy of cancer by increasing the entry of antitumor immune cells in tumors.


Paula Winter, BSc

research technician
My research is focused on the IgA Fc receptor (FcaRI) on neutrophils. We look at the difference between this receptor and the IgG Fc receptor (FcyR). And especially the difference in pathway it follows after activation. For this project we use several experimental techniques, including 2d migration, western blot, flow cytometry, chemotaxis and ELISA


Richard van der Mast, BSc

research technician
The projects I am working on are related to antibody therapy in cancer treatment and to the role of the Fc receptor for IgA in mucosal immunity. These projects mainly focus on the role of neutrophils, macrophages and NK cells in the tumor microenvironment or inflammatory (mucosal) sites. I have experience in several techniques, including (live cell) microscopy, tumor cell killing assays, tissue stainings, flow cytometry and ELISA.

Other PI's

Jan van den Bossche


Jan Van den Bossche completed his study in Bioscience Engineering in 2006 at Vrije Universiteit Brussel (Belgium), specializing in Cell and Gene Biotechnology and Immunology. Throughout his career he has been fascinated by the regulation and plasticity of macrophages. 
He obtained his PhD in 2011 at the Myeloid Cell Immunology lab, headed by Prof. Jo Van Ginderachter at VIB, Brussels, Belgium. During this period, he identified E-cadherin as a new marker for M2 macrophages and described polyamines as crucial regulators of macrophages. 
He joined to the group of Prof. Menno de Winther at the Academic Medical Center (AMC) of Amsterdam in 2012. As a starting post-doctoral researcher, Jan Van den Bossche obtained a junior postdoc grant from Netherlands Heart Foundation (Hartstichting) to study histone acetylation as a regulator of macrophages during atherosclerosis. 
Obtaining a VENI grant from NWO allowed him to start an independent research line, investigating the metabolic regulation of macrophages. 
At the end of 2017, Jan became group leader and PI at the Department of Molecular Cell Biology and Immunology where his group investigates how targeting macrophage metabolism can be applied to improve their function and disease outcome.

Research Line

Our research aims to explain how metabolic reprogramming regulates macrophage subsets in different settings, focusing on cancer and cardiovascular disease. By unravelling key questions in macrophage immunometabolism, our overall goal is to demonstrate whether and how targeting macrophage metabolism could be used for future therapy.

Our distinct research lines investigate how metabolic enzymes like ATP Citrate Lyase and (immuno)metabolites like succinate and itaconate control macrophage responses and disease progression.

Metabolic rewiring in macrophage subsets
(source: Van den Bossche, O’Neill & Menon, Trends in Immunology, 2017)

Our distinct research lines investigate how metabolic enzymes like ATP Citrate Lyase and (immuno)metabolites like succinate and itaconate control macrophage responses and disease progression.

Key publications

  1. de Goede KE, Harber KJ, Van den Bossche JLet’s enter the wonderful world of immunometabolites. Trends in endocrinology and metabolism. 2019
  2. Van den Bossche J, van der Windt GJW. Fatty acid oxidation in macrophages and T cells; time for reassessment?Cell Metabolism. 2018
  3. Baardman J, Verberk SGS, Prange KHM, van Weeghel M, van der Velden S, Ryan DG, Wüst RCI, Neele AE, Speijer D, Denis SW, Witte ME, Houtkooper RH, O’neill LA, Knatko EV, Dinkova-Kostova AT, Lutgens E, de Winther MPJ, Van den Bossche JA Defective Pentose Phosphate Pathway Reduces Inflammatory Macrophage Responses during Hypercholesterolemia.Cell Reports. 2018 Nov 20
  4. Van den Bossche, L. A. O’Neill, and D. Menon. Macrophage Immunometabolism; Where Are We (Going)?Trends in Immunology, 2017 Apr 7.
  5. Van den Bossche J, Baardman J, Otto NA, van der Velden S, Neele AE, van den Berg SM, Luque-Martin R, Chen HJ, Boshuizen MC, Ahmed M, Hoeksema MA, de Vos AF, de Winther MP. Mitochondrial Dysfunction Prevents Repolarization of Inflammatory Macrophages. Cell Reports. 2016 Oct 11.  




Translational Macrophage Immunometabolism group “ImmunoMetLab” – Kyra de Goede, Sanne Verberk, Jan Van den Bossche, Elisa Meinster, Karl Harber (left to right, august 2019)

Sanne Verberk’s PhD aims to target immunometabolic circuits in atherosclerotic macrophages to improve their function and disease outcome. This work is funded by a Netherlands Heart Foundation senior researcher grant.

Kyra de Goede is funded by a CCA (Cancer Center Amsterdam) PhD grant and studies macrophage immunometabolism and immunometabolites in the tumor microenvironment.

Karl Harber is appointed on a ACS (Amsterdam Cardiovascular Sciences) PhD grant and investigates immunometabolites in the context of atherosclerosis in collaboration with Prof. Menno de Winther and Michel van Weeghel at AMC.

Elisa Meinster is research technician in our group and supports distinct research lines investigating how metabolic alterations in macrophages drive their function and disease outcome. Elisa is funded by a CCA Proof-of-concept grant and an European ERA-CVD consortium grant.

Other PI's

Other PI's

New publication van Vliet group

Check the latest publication by the van Vliet group showing that FUT9 expression conveys stem cell-like properties to colorectal cancer cells.

Blanas A, Zaal A, van der Haar Àvila I, Kempers M, Kruijssen L, de Kok M, Popovic MA, van der Horst JC, van Vliet SJ.
FUT9-Driven Programming of Colon Cancer Cells towards a Stem Cell-Like State.
Cancers (Basel). 2020 Sep 10;12(9):E2580. doi: 10.3390/cancers12092580.