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.

Mesenchymal stem cell-derived extracellular vesicles can promote cartilage regeneration

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Osteoarthritis (OA) is a rheumatic disease leading to chronic pain and disability with no effective treatment available. Recently, allogeneic human mesenchymal stem cells (MSC) entered clinical trials as a novel therapy for OA. Increasing evidence suggests that therapeutic efficacy of MSC depends on paracrine signaling. Here we investigated the role of extracellular vesicles (EVs) secreted by human bone marrow-derived MSC (BMMSC) in human OA cartilage repair. We show that BMMSC-EVs inhibit the adverse effects of inflammatory mediators on cartilage homeostasis. BMMSC-EVs also promoted cartilage regeneration in vitro. Addition of BMMSC-EVs to cultures of chondrocytes isolated from OA patients stimulated production of proteoglycans and type II collagen by these cells. These data demonstrate that BMMSC-EVs can be important mediators of cartilage repair and hold great promise as a novel therapeutic for cartilage regeneration and osteoarthritis.

This work by Magdalena Lorenowicz is part of a combined research program with the Saris-Vonk Lab and has been accepted for publication in Thernostics.

Foxp1 regulates neurogenesis by modulating the Notch pathway


Mutations in Foxp1 have been linked to neurodevelopmental disorders including intellectual disability and autism, however, the underlying molecular mechanisms remain ill-defined. Here work from Luca Braciolli demonstrates utilizing RNA- and chromatin immunoprecipitation (ChIP)-sequencing that Foxp1 directly regulates genes controlling neurogenesis. We show that Foxp1 is expressed in embryonic neural stem cells (NSCs) and modulation of Foxp1 expression impacts both neuron and astrocyte differentiation. Using a murine model of cortical development, Foxp1-knockdown in utero was found to reduce NSC differentiation and migration during corticogenesis. Furthermore, transplantation of Foxp1-knockdown NSCs in neonatal mice after hypoxia-ischemia (HI) challenge demonstrated that Foxp1 is also required for neuronal differentiation and functionality in vivo. Foxp1 was found to repress the expression of Notch pathway genes including the Notch-ligand Jagged1, resulting in inhibition of Notch signaling.  Finally, blockade of Jagged1 in Foxp1-knockdown NSCs rescued neuronal differentiation in vitro. Together these data support a novel role for Foxp1 in regulating embryonic NSC differentiation by modulating Notch signaling.

This work is part of a collaboration with the Nijboer and Pasterkamp Labs and the full publication in Stem Cell Reports can be read here.


Congratulations Dr Ana Rita Lourenço: PhD survivor !

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Transcriptional mechanisms regulating oncogenic TGF-β signaling in breast cancer

A complex program of epithelial-to-mesenchymal transition (EMT) plays a pivotal role during both embryogenesis and tissue homeostasis. However abnormal activation of this process can lead to tumor progression and metastasis. TGF-β signalling has been demonstrated to induce and support EMT by regulating a complex network of transcription factors. During this process, transcription factors responsible for maintaining the epithelial phenotype are supressed, whereas transcription factors involved in the acquisition of mesenchymal traits are rapidly induced. Such transcription factors are so called EMT-inducers (or EMT master regulators) and include family members of Zeb, Snail and Twis1t transcription factors.

Work in this thesis investigates the role of the transcription factor SOX4 as a crucial regulator of TGF-β-mediated induction of mesenchymal markers, and supports a tole for SOX4 as an EMT ‘master regulator’. Furthermore, the C/EBPα transcription factor was identified as a novel epithelial ‘gate-keeper’, inhibiting EMT. These two transcription factors can therefore control the balance between epithelial and mesenchymal transition in both organogenesis and development of disease, such as cancer metastasis.

Taken together our results provide novel insights into the transcriptional regulation of EMT and how this can be deregulated in disease. This identifies novel molecular pathways that could be therapeutically targeted to control epithelial-mesenchymal cell differentiation as well as tumor metastasis.

SOX4: Joining the Master Regulators of Epithelial-to-Mesenchymal Transition?


The epithelial-to-mesenchymal transition (EMT) is an important developmental program exploited by cancer cells to gain mesenchymal features. Transcription factors globally regulating processes during EMT are often referred as 'master regulators' of EMT, and include members of the Snail and ZEB transcription factor families. The SRY-related HMG box (SOX)4 transcription factor can promote tumorigenesis by endowing cells with migratory and invasive properties, stemness, and resistance to apoptosis, thereby regulating key aspects of the EMT program. In this review recently published in Trends in Cancer, we argue that SOX4 should also be considered as a master regulator of EMT, and review the molecular mechanisms underlying its function.

Congratulations Dr Luca Braccioli - PhD Survivor !

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Transcriptional regulation and cellular strategies in neuroregeneration

Neurogenesis and gliogenesis are processes that occur during development of the CNS as well as after insult of the nervous system. These tightly regulated processes take place in specialized niches during embryogenesis and adulthood to generate functional cells, starting from defined progenitor cells such as neural stem cells (NSCs). During his PhD, Luca took a multifaceted experimental approach to better understand NSC biology both in vitro and in vivo. Transcriptional regulation is essential since the expression of specific genes is the key to control timing and fate of the differentiation process.

How do NSC work? In Luca Braccioli's thesis two NSC transcriptional regulators, Foxp1 and Sox4 are shown to be crucial for control of neurogenesis and gliogenesis respectively. Mutations in the Foxp1 gene have been associated with speech defects, autism and other intellectual disabilities, as well as being defined as necessary for neurogenesis. In the work presented in this thesis, Luca sought to define the molecular mechanisms mediated by Foxp1 that regulate NSC differentiation. Sox4 has been described as inhibitor of gliogenesis and myelination in oligodendrocyte precursor cells. In this context we investigated the role and molecular mechanisms underlying Sox4-mediated regulation of oligodendrogenesis.

Repairing brain damage. The use of cellular strategies to repair CNS insults has been widely investigated in recent years. During his PhD Luca further evaluated the therapeutic potential of NSCs and MSCs to treat perinatal hypoxic-ischemic brain damage (HI). Moreover, he examined the hypothesis of the use of exosomes as a cell-free alternative as a therapeutic option upon brain insults and HI.