Turning an tumor suppressor into an oncogene

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SOX4 is an important component in the tumor-promoting transcriptional response induced by TGF-beta in breast cancer. Here, Stephin Vervoort and Ana Rita Lourenco performed an unbiased transcription factor interaction screen and identified SMAD3 as a novel interaction partner of SOX4. SOX4 was found to specifically control a pro-oncogenic subset of SOX4/SMAD3 co-bound TGFbeta-target genes, associated with poor-disease outcome. Our findings thus highlight a novel role of SOX4 in the TGFbeta-pathway by cooperatively regulating target genes with SMAD3 in a context-dependent manner, thereby skewing TGFbeta-responses. This work has been published in Nucleic Acid Research

Regenerative Medicine Utrecht looking for 29 new international PhD students


With an aging population and rising healthcare costs, the need for organs, tissues and personalized strategies in medicine has never been greater. Recent developments in medical technologies such as 3D-bioprinting, stem cell therapy and gene editing hold the promise to provide tissues for transplantation, tailor-made medical solutions and opportunities to help the body repair and regenerate itself. However, our understanding of the fundamentals of cell, tissue and organ regeneration and their potential application for therapeutic purposes are still in its infancy. For Regenerative Medicine to fully capture its potential, a synergistic and multidisciplinary effort remains necessary to achieve essential scientific breakthroughs.

Together the University Medical Center Utrecht (coordinator) and the Utrecht University offer a unique international PhD programme, named RESCUE, for excellent PhD candidates (early stage researchers, ESRs) with 29 high level fellowships for a joint doctorate programme within the Regenerative Medicine Centre Utrecht. The RESCUE programme aims to enhance the potential and future career perspectives of researchers by providing a global training network including over 50 excellent academic and industrial partner organisations, creating a new generation of research experts, empowering them to take leading positions in the field of Regenerative Medicine world-wide.

PhD positions are for Master's students who have not worked in The Netherlands for more than 12 months in the last 3 years. Positions are available in the fields of: stem cells & organoids, cardiovascular regeneration and musculoskeletal regeneration. The Coffer Lab also has a joint position available. 

More information and the application procedure can be found here www.rescue-cofund.eu.

Targeting autophagy in T helper cells may represent a novel therapeutic approach to induce tolerance and treat autoimmune disease

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Activation of CD4+ T cells induces autophagy, a catabolic process through which cell components are sequestered into autophagosomes that fuse with lysosomes to degrade cargo. The functional role of activation-induced autophagy has not been determined yet. In this collaborative work together with Fernando Macian's group (Albert Einstein College of Medicine), we identify autophagy as a key tolerance avoidance mechanism. Data from Enric Mocholi, who has worked in both labs, has revealed that inhibition of autophagy during T cell activation induces a long-lasting state of hypo-responsiveness in effector T helper cells, accompanied by the expression of an anergic gene signature. Cells unable to induce autophagy after TCR engagement show inefficient mitochondrial respiration, and reduced TCR-mediated signaling. In vivo, inhibition of autophagy during antigen priming induces CD4+ T cell anergy and decreases the severity of disease in an experimental autoimmune encephalomyelitis model. Interestingly, CD4+ T cells isolated from the synovial fluid of juvenile idiopathic arthritis (JIA) patients, while resistant to suboptimal stimulation-induced anergy, can be tolerized with autophagy inhibitors. Autophagy constitutes, thus, a tolerance avoidance mechanism which determines CD4+ T cell fate. Targeting autophagy in T helper cells may represent a novel therapeutic approach to induce tolerance and treat autoimmune disease. This work has been published in Cell Reports

Megakaryocyte lineage development is controlled by modulation of protein acetylation

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Treatment with lysine deacetylase inhibitors (KDACi) for haematological malignancies, is accompanied by haematological side effects including thrombocytopenia, suggesting that modulation of protein acetylation affects normal myeloid development, and specifically megakaryocyte development. However, the effects of KDACi inhibitors on human hematopoiesis have not been systematically investigated.  In this study by Marije Bartels and Anita Govers, utilising ex-vivo differentiation of human haematopoietic progenitor cells, we investigated the effects of two functionally distinct KDACi, valproic acid (VPA), and nicotinamide (NAM), on megakaryocyte differentiation, and lineage choice decisions. While both being KDACi, VPA and NAM can differentially regulate cell fate decisions during megakaryocyte, and erythroid (ME) development through specific effects on promoter-acetylation of genes regulating ME-lineage development. Here, we compared the effects of VPA treatment with NAM treatment on human ME-lineage development, and further progression into the megakaryocytic lineage. Our data demonstrate for the first time that KDAC and SIRT inhibition differentially modulates the expansion and differentiation of ME-progenitors (MEP). Utilising a histone 3 lysine 27 acetylation (H3K27ac) chromatin immunoprecipitation- (ChIP) sequencing approach, we identified key regulatory genes implicated in myeloid progenitor function, and ME-lineage differentiation, directly regulated by VPA and NAM treatment. These findings increase our understanding of the effects of KDACi on normal haematopoiesis which should be considered when using KDACi in a clinical context. This work has recently been accepted for publication in PLoS ONE

PKB/AKT in Top 10 of the most popular genes in human genome


A recent study by postdoc Peter Kerpedjiev and highlighted in Nature has reported a list of the ten most studied genes of all time — a sort of ‘top hits’ of the human genome, and several other genomes besides. This sheds light on important trends in biomedical research, revealing how concerns over specific diseases or public-health issues have shifted research priorities towards underlying genes. It also shows how just a few genes, many of which span disciplines and disease areas, have dominated research.

Creeping in at number 10 is Protein Kinase B (AKT) which, together with Brian Hemmings and Philip Tsichlis, we were the first to identify (Coffer & Woodgett, 1992).  Subsequently, together with  Boudewijn Burgering, we were able to demonstrate that PKB/AKT was the missing link downstream of PI3K transducing a plethora of extracellular stimuli to intracellular signaling events (Burgering & Coffer, 1995). 

Great to see how much research has gone into understanding PKB/AKT biology over the last 20 years, with more than 350 clinical trials exploiting these findings.  If you would like to learn more then take a look at the recent excellent review from Brendan Manning and Alex Toker (Manning & Toker, 2017). 

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Congratulations Dr Desiree Haaften-Visser: PhD Survivor !

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Congratulations to Dr. Desiree Haaften-Visser who has successfully defended her PhD thesis entitled: Identification and characterisation of genes associated with congenital intestinal disease. 

A proper function of the intestine is essential for normal growth and function of the human body. Disturbance of this function can lead to severe illness, both due to local disease and malnutrition. Treatment can be challenging, since current therapies are often unable to offer a cure, but at best ameliorate symptoms. To improve the  therapy of diseases of the gastrointestinal tract a better understanding of the pathogenesis of these disorders is essential. During her PhD research, Desiree has focussed on understanding the pathogenesis of a few rare hereditary intestinal diseases through the use of molecular genetic methods, including next-generation sequencing, followed by in vitro functional assays. This approach of ‘functional genomics’ has the ultimate goal to improve the therapy of these diseases.

Here, for the first time, association of mutations in ANKZF1 with infantile-onset IBD has been described. ANKZF1 is an essential protein in the mitochondrial response to cellular stress and ANKZF1 deficiency leads to mitochondrial dysfunction. In a second study, mutations in STX3 leading to disturbed enterocyte polarity, were found to be a novel cause of microvillus inclusion disease. Additionally, a novel mutation in DGAT1 was found as a cause of severe congenital fat intolerance. Finally, a novel whole-exome sequencing (WES) diagnostic approach was developed for congenital intestinal diseases.

Taken together, this work contributes to the unravelling of the pathogenesis of rare congenital intestinal diseases, which is crucial to develop novel treatment options for these patients. This work was a collaboration between the Coffer Lab, Prof. Roderick Houwen and Dr. Sabine Middendorp at the Regenerative Medicine Center and Wilhelmina Children's Hospital, University Medical Center Utrecht.


Reducing animal experiments: 3 R's grant for Guy Roukens


The process of cancer metastasis is a complex one and involves multiple steps. It involves cancer cells leaving the primary tumor and moving into the blood vascular system (intravasation), traveling to a distant site in the body, often the lungs, bone or brain. Here the tumor cells need to move out of the blood vessels  (extravasation) and then settle and grow into a secondary tumor (metastasis). Until now it has been very difficult to study these aspects of cancer biology in the lab, and almost all studies tend to use animal models. However, with recent developments in tumor-organoid culture and vascularization, together with microfluidic technologies, the possibility to develop in vitro systems for studying metastasis is becoming a possibility. 

At Utrecht University, the Animal Welfare Body awards research grants for projects aim at reducing the use of animal experiments. Guy Roukens, senior postdoc in the Coffer Lab, has been awarded such funding to explore the possibility of developing in vitro microfluidic systems that can be used to investigate tumor vascularization, intravasation and extravasation and thereby help understand the process of tumor metastasis.