Enhancers in Art; Post I

 

At the Copenhagen event, I got the opportunity to meet all involved with ENHPATHY, which was a real pleasure.

Among the scientific discussions and lessons, we also spoke about our Enhancer in Art projects.

A defining characteristic of art (I think) is that a piece of art is supposed to provoke thought, or at the very least kindle the imagination. Science, at its core, is aimed at understanding the world around us (or inside us). It seems to me thus that science and art are two different entities when we consider their ‘purpose’.

However, that is not to say that they have nothing in common. For example, to reach the goal of ‘understanding’ the world around us, what is required is thought, and in many cases creativity. In the way that a piece of art may induce serious thought and reflection in a patron such that they start to view an issue in a different way – in this same way can issues be tacked in science.

I will be lazy here and refer to the very famous ‘double slit’ experiment done by Young in 1801, which, together with many efforts from scientists over the globe and across decades, gave rise to quantum mechanics. The point is that the outcome of the experiment (the pattern in the photo) was the same for light, which was thought to be composed purely of waves, and for electrons, which were thought to be particles. This then lead to a lot of thought, and the ultimate conclusion that matter has properties of both waves and particles.

 

I will provide an update on my Enhancer in art project in the next post!

Pictured below is my poster which was displayed at the Copenhagen event, along with its owner. Thanks to Jean-Mehdi for the photograph!

featured image taken from https://ysjournal.com/double-slit-experiment-using-arduino-and-light-sensors/

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GDR Micro-Nano-Fluidics, Toulouse, France (23-24 September 2021)

The purpose of visiting this conference was to present my poster providing an outlook on my project involving multiwise chromatin interaction analysis using our Elveflow droplet microfluidic platform and gain input on my approach to this project. Further, the idea was to network with the French microfluidics community.

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Enhancer in Art: a exploratory way of science dissemination to public

Popular science plays a very important role in scientific research. Not only attracting people to know what we are doing, but also motivating ourselves to thinking the significance of our research.

Recently, I faced a challenge about how to introduce my project to a 13 years old boy with no biology learning experience. I tried my best to let him know what is enhancer, why we research enhancer and how it can influence human health. The boy didn’t show interesting for my projects, excepting a picture instance I showed about mutation in enhancer influences human finger development.

           

          Visel et al. Nature, 2009.                                        Jeff Koons’ exposition in Mucem

It reminded me science in art format maybe impress people better if we find a good way. But how to link my research and art? And what is art? Occasionally, an exposition visiting experience in the Europe and Mediterranean Civilization Museum of Marseille made me understand art differently. It’s an art exposition of Jeff Koons, who is a very famous modern pop artist in the world. As a zero-level person in art, I was confused when I looking at Jeff Koons’ art works. Because many of his art works look like very common daily life product. A student who study in art explained to me, “Art could be anything. According to visiting an exposition of artist, you can know who is him, what is his story, what do he want to say. Sometimes art attracts people and becoming popular. Sometimes art shocks people and full of controversy. That is art! Always brings new idea and lead people to think”.

It opened my mind to art somehow. I’m still thinking how to coincidence my research with art. But cooperating with artist must be very interesting and exciting. We can provide materials and inspirit for artist. One tube of DNA or one DNA sequence also could be art source for them. And artists create art works attracting more attention from people to science research, even leading us to think the deep and far significance and influence of our research in the future.

As a part of ENHPATHY network program, Enhancer in Art is a novel and challenging work to introduce our work to outside world. I’m looking forward to linking enhancer study with art creating!

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1 PhD position available, join the ENHPATHY Innovative Training Network today!

One position is available for a 2-year PhD program funded by the Marie Sklodowska-Curie Innovative Training Network (ITN) ENHPATHY.

Candidates with bioinformatics, genomics and/or molecular and cellular biology backgrounds are encouraged to apply. The host lab offers opportunities to extend this period for one or two years to complete a full PhD thesis in the Centre for Genomics Regulation and Universitat Pompeu Fabra.

Application deadline: September 30th

Organization: Centre for genomic regulation

More information on this link 

Download the full description

 

 

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Starting my PhD!

 

Hello everyone! Thank you for the warm welcoming from all the members from the amazing ENPATHY consortium!

This is, my very first blog post (ever).

Our lab, the lab46

You might have read my introduction, where I wrote about how I have been moving around for most of my life. Finally, I have truly found my place, in the group of Hematooncology at the institute of molecular genetics (IMG), in Prague, led by Meritxell Alberich Jorda (Or as we call her, Meri). By the way, the picture featuring this post, is the logo of our group. It was designed by Maria Kuzmina, one of the PhDs in our team.

How would I describe the lab 46? Well, we have the kind of people that, without doubting and as many times as necessary, will help you with anything that you will need. Moreover, I feel that we all really support each other, not only when it comes to experimental questions. This group is comprised the kind of people that will make pancakes when you have to wake up at 5 in the morning for an experiment, or that will bring champagne to thank you for the support through a hard time. That will make sure your birthday is something special even when it falls on a Monday full of work. That will text you to check if you are okay after a hard day at work.

I think, that within us and thanks to Meri, we have created a perfect research microenvironment. And I am looking forward to expand it, thanks to the wonderful opportunities that ENPATHY consortium gives us.

Our project, HSCs under Chronic Inflammation – the CMO mouse model

You might have also read a bit about my project. Maybe even our recent publication by Grusanovic et al. If not, here you have the link! I promise you will like it   (nih.gov)https://pubmed.ncbi.nlm.nih.gov/36341527/

Here we have shown, how chronic inflammation decreases HSC fitness via hyperactivation of the druggable IL-6/Jak/Stat3 signaling pathway, and how the CMO model accurately recapitulates sterile chronic inflammation.

There are two things to highlight about this mouse model. The first one, is that it contains a point mutation in the Pstpip2 gene, causing Chronic Multifocal Osteomyelitis (CMO). The second, that this model resembles a human disease know as chronic recurrent multifocal osteomyelitis (CRMO), a progressive autoinflammatory disorder that leads to sterile chronic inflammation.

Using the CMO murine model we were able to bypass the artificial setup of externally inducing inflammation. This allowed us to assess the interactions of an inflammatory BM niche, immune cells and HSCs.

Effects of chronic inflammation in AML progression

Previously, we have reported that the chronic inflammatory environment expands the HSC compartment and induces functional defects in HSC. There are many similarities between HSCs and leukemic stem cells (LSCs). Therefore, will now characterize the effects of chronic inflammation in Acute Myeloid Leukemia (AML). If you would like to know a bit more about AML, read this: Uncovering drug-adaptive epigenetic response in Acute Myeloid Leukaemia (AML) – ENHPATHY Francesco Leonetti has a wonderful blog post about it!

In my project, we would like to determine how chronic inflammation might influence LSCs, and thus alter Leukemia development. Moreover, we will explore the possible role that chronic inflammation has in the deregulation of enhancers in certain (critical) genes. With this, we will gain more mechanistic insight of the correlation between chronic inflammation and Leukemia development.

The results of this project will contribute to a better understanding of the mechanism driving  chronic inflammation and AML.

I will keep you updated about the process!

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CC BY María Mariner Fauli

All Eyes On Enhancers

My name is Sarah, I obtained my bachelor and master’s degrees in Molecular and Cellular Biology from the University of Rennes 1, France. During my last year of studies, I had the opportunity to work in the laboratory of Alvaro Rada-Iglesias, my actual supervisor. It was a wonderful experience; I had the chance to discover a new country and new people. I also discovered what is like to work in a laboratory and get my hands into more concrete biological questions.

A week in research is never the same.

It can be challenging and frustrating. Hard work, long hours in the cell culture room, fails… All this become worthy whenever I get new progresses in my project. In this blog, I will try to share my advances, new concept, and techniques I will learn during my PhD journey.

A day spend in the laboratory is not only about experiments and work but also about the people we get to meet and exchange with. I have the fantastic chance to share the lab with Spanish and international people. If you walk around in the lab, you will have great chance to hear all about Greek etymology, or me asking for Pastéis de nata to our great Portuguese post-doc in the lab.

I am really proud to be part of the ENHPATHY network, that will raise intriguing and relevant questions about enhancers, their functions, mechanisms and relevance in human diseases.

I want to thank the ENHPATHY consortium for this challenge and to offer me a space where to share my thoughts. My future self will with no doubt be thankful to find a trace of the baby researcher that I am today.

Joining the Rada-Iglesias laboratory.

I have the opportunity to work on the interplay between gene expression control and exposure to environmental factors and how it might contribute to human disease. More specifically, my project focuses on unravel potential gene-environmental interactions involved in the etiology of ZIC2-related holoprosencephaly.

Holoprosencephaly (HPE) is a developmental disorder that affects the early development of the brain and is characterized by the failure of the separation of the two hemispheres; ZIC2 is a member of the ZIC family and encodes a zinc finger transcription factor that, when mutated causes HPE in both, mouse and human.

Intriguingly, humans but not mice are haploinsufficient for ZIC2. In addition, patients carrying the ZIC2+/- genotype show different level of severity of the disease and reduced penetrance. How can these differences be explained? Rather than a specie differences, we hypothesize that because mice live and reproduce in the laboratory in well-controlled conditions and humans live in a non-controlled environment, environmental factors could explain, at least partially, the haploinsufficiency observed in patients carrying ZIC2+/- genotype.

To tackle this question, I will implement a work plan combining genetic engineering, culture of mouse and human embryonic stem cells, genomics approaches… I will be happy to share my advances in the next posts!

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All Eyes on NN’hancers : Greeting

 

This is my very first blogging !!!

        Hi from Copenhagen, Denmark! My name is Natsuda Navamajiti, a PhD fellow at University of Copenhagen (also known in Danish as København Universitet), under the supervision of Prof.Robin Andersson. I am a part of ENHPATHY project (Link to the program here) which basically gathers supervisors and PhD fellows in both academia and industry who are interested in specific part of DNA called “ENHANCER.” 

“Stay tune on my blog, 
and also on people-in-the-program’s, 
to know more about what the enhancer is 
and our projects related to the enhancer!”

        My own project will be related to a blood disease called acute myeloid leukemia (AML) in children. Regulatory activities of enhancers and promoters in blood cells will be mainly explored using techniques called CAGE and ATAC-seq. Computational methods will be a key part in investigating how these can be used to understand clinical data such as disease subtypes or prognosis.I will write more about these interesting techniques in the upcoming blog. 

        It has been 6 months since I arrived here, just before the lock-down period due to the corona crisis. Even though it is not so lively as usual, Copenhagen is still charming. Can’t wait to explore the full version of this “City of Hygge” soon. 

        Inspired by Mickey Mouse Lego Art I am ensemble right now, 

“Miska Mouska Mickey Mouse, 
Welcome to My Blog!”

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Uncovering drug-adaptive epigenetic response in Acute Myeloid Leukaemia (AML)

I am very grateful to ENHPATHY consortium for giving me the opportunity to be part of this PhD project.

 

In my view, it is fascinating to understand how further genetic regulation may occur through chemotherapeutic drug stimuli that can increase the activity of specific enhancers.

In my PhD project I will be involved in studying genetic adaptations taking place after exposure to standard-of-care drug and their association to resistance in acute myeloid leukaemia (AML).

 

The AML is the most common acute leukaemia in adults. The disease is characterized by an uncontrolled clonal proliferation of undifferentiated myeloid precursor cells in the bone marrow and usually their presence in peripheral blood.

With a median age of 68, the World Health Organization (WHO) system divides AML into several groups:

  • AML with recurrent abnormalities;
  • AML with myelodysplasia-related changes;
  • therapy-related AML;
  • AML not otherwise specified.

Although the discovery of the most recurrent genetic mutations (i.e. FLT3-ITD, NMP1 and CEBPA) has certainly helped to provide better treatment support, to date the standard of care remains the intensive chemotherapy treatment with anthracyclines and aracytidine but with poor results. Indeed, responses are not durable, and majority of patients relapse with acquired drug resistance and die from the disease afterwards.
AML remains a clinical challenge and both a better understanding of the resistance mechanism and new therapies are urgently needed.

 

Doubtless drug resistance is related to the gravity of genetic mutations underlying AML, but it is also related to the alterations in the epigenetic regulation of proximal promoters and distal enhancers. In this field, a better understanding of the epigenetic regulation underlying resistance to chemotherapy treatment in AML could respond to the need for new therapies.

Accordingly, the main aim of this project is to study regulatory elements that are directly targeted by anticancer drugs in order to analyze in depth associated with drug resistance.

 

The human ALDH gene superfamily consists of 19 isoforms from 19 genes in 11 families and four subfamilies. Physiologically, the major function of ALDH enzymes is cellular detoxification via the NAD(P)H-dependent oxidation of toxic aldehydes into carboxylic acids. Aldehydes are produced naturally as by-products of the metabolism of glucose, amino acids and lipids, but also may come from exogenous sources like exposure to chemicals, including chemotherapeutic agents.  Importantly, the oxidation of aldehydes is not the only catalytic function of ALDHs. Some members of the superfamily are known to have esterase or nitrate reductase activity and other various functions notably in cell differentiation and cell signalling.

Consequently, in cancer cells, where metabolic demands are elevated, and/or genetic mutations lead to an aberrant metabolism, the formation of endogenous toxic aldehydes is often exacerbated. In this contest, ALDH may represent a key survival adaptation and a marker of malignancy.

In particular, the ALDH subfamily 1A is associated with tumor progression and refractoriness and are elevated in multiple cancer types. These isoenzymes have been widely associated to poor prognosis, high tumorigenic potential and drug resistance.

In the context of AML, multiple studies suggest that ALDH1A1 is strikingly associated with drug resistance and increased risk of relapse.

 

Recent progress achieved by Advanced BioDesign (ABD) have shown that higher ALDH1 activity is characteristic of leukemic cells in refractory patients and in patients with adverse prognosis. More so, using different AML cells lines, they have found that certain chemotherapeutic drugs can modulate gene expression of at least three closely related isoforms of the ALDH family associated to drug resistance, thus supporting the idea of this project.

Currently, ABD develops specific inhibitors against ALDHs. The anticancer activity of these compounds has been demonstrated in prostate, non-small cell lung cancer and melanoma and more recently in preclinical models of AML.

 

The specific objectives of our project are:

  • To map enhancer or promoter regions that are disturbed in AML and normal hematopoietic cells during anticancer drug exposure (namely, Daunorubicin, DIMATE and Ara-C) and identify their putative target genes.
  • To characterise the role that the identified regulatory regions have in drug resistance.
  • To assess the ability of the most prominent factors to sensitize or re-sensitize AML cells to undergo programmed cell death.

We expect to:

  • identify the drug-responsive regulatory elements directly responsible for the severity of AML and their drug resistance traits;
  • discover rational strategies with improved therapeutic efficacies by targeting enhancers with inhibitors that can modulate the transcription of the genes linked to drug resistance.

 

I hope you enjoy my blog, and I am looking forward to sharing with you my first results.

 

Francesco.

 

 

 

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Enhancers

It has become apparent to me that computational biology as a field is vast. It can prove to be very quantitative, and methods and approaches used are susceptible to increasing levels of abstraction. Much of this is a by-product of the advent of Next-Generation Sequencing methods, which are able to generate large amounts of data.

The regulation of gene expression is a complex process involving many factors. It can be seen as the product of the interaction between the DNA sequence itself with proteins, protein networks, RNA, and the so-called regulatory elements – which are segments of the DNA sequence that are functional, in that they interact with, or recruit other factors which facilitate the next steps in the process. I think it is easy to appreciate the elegance of the process as we know it, as well as the fine balance of factors and the internal environment that surely must be maintained for the optimal functioning of such machinery.

I have learnt, thanks to the ENHPATHY consortium, that enhancers are one such regulatory element that are more important than previously thought, having been implicated in many regulatory networks, and therefore in many diseases. I find myself keen to uncover more about their influence over the gene regulation and, in this way, the body itself. I am fortunate to be a part of a motivated group of peers and senior researchers alike, whose research and progress I plan to follow with interest. I hope to share more with you soon!

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Science and art: the fusion of two universes

The picture linked to this article has not been chosen by chance. The “Vitruvian Man“ by Leonardo da Vinci perhaps represents one of the first encounters between science and art.
In this drawing, the great artist-scientist represents how the union between science and art is possible by placing the figure of a man symmetrically within geometric spaces defined as the circle and the square, respectively, Heaven and Earth.

Although the science-art partnership has its roots centuries ago, nowadays science does not enjoy the same understanding as art and it is seen by most as something mysterious.

Seen this, I wondered why.

It is a fact that science is a hard subject to understand, especially for the large number of concepts not owned by common people which cannot be found among the general knowledges of a country.

Well, actually I think that the “Enhancer in Art” (EIA) project within the ENHPATHY program can be a way to bring people closer to science, taking off that mystery dress it wears for common people. Making science more “popular” in its understanding could also increase people’s interest in it.

Plus, the EIA project will be a way to test us as young researchers.

Not by chance, the first difficult purpose will be to make our project and our research understandable to the artist who will follow us, using a language that is not as much scientific as direct. That is why, we would try to address him as friends, turning scientific language into a friendly conversation.

One of the articles I have recently read about science-art partnership published in Nature states that the collaboration between scientists and artists is the most valuable when these “have a shared stake in a project” which can help the scientist so much in stimulating new research work as much as the artist in creating something unique also leading to new career opportunities as desired by Virginia Gewin.

So, what do I expect from this project? My greatest goal is to try to get people feel what we, young researchers, feel about science and scientific research. The feeling, the emotion, the pride that we feel in contributing to the knowledge of a specific topic, hoping that it will be useful to the community.

And in this sense, I feel lucky to be able to tackle the EIA project in Marseille, a city with a deep sense of art, as it was the European capital of culture in 2013, which boasts a multitude of young local artists.

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Millefiori by Fabian OefnerFabian Oefner

Art vs Mystery of Science

We live in the era of technological advancement where scientific contribution is the primary driving force of progress. Despite a rapid decrease in the distance between the achievements of science and their implementation in our daily life, it is still a widespread opinion that research is separated from reality and that scientists live in their own universe. To overcome this prejudice and fear of science, and to increase the general public’s willingness to trust and accept inventions, we have to find ways of efficient communication between scientists and society.

During my undergraduate studies, I was learning some abstract concepts in pure mathematics, so later on, when I started studying computational biology, I thought, “Wow! Now I am finally engaged in solving applied problems!”. The application of mathematics in the interdisciplinary field of Life Sciences fascinates me. And perhaps results of my future research could be used to either improve our understanding of diseases, or facilitate the creation of a new drug, or invent a new therapy. Who knows, right?

And while science is fascinating to us researchers, in a non-academic environment, the word “science” is often surrounded by mystery. It is associated with something distant and incomprehensible. This “fear” of science has a negative impact on society as it weakens the general credibility of scientific discoveries. This, of course, slows down the progress because new technologies’ success depends a lot on the public’s willingness to accept them. We, researchers, can help to reduce the general level of anxiety towards science by making it more inclusive and sharing our knowledge in an understandable form.

Lately, the concept of Open Science has started attracting significant attention from the scientific community, especially in applied fields. This movement aims not only to make research reproducible and accessible but also understandable to everyone, regardless of a person’s educational background. The more I dive into various scientific activities, the more I understand why it is crucial to efficiently communicate and disseminate science. News from the scientific world have to sound less like magic spells but more like intriguing stories*. How can we bridge this gap?

Art, being the universal language of emotions and senses, can serve as a mean of communication between scientists and the rest of the world. Perhaps, the ideas coming from science are easier to understand not logically but through emotions? At first glance, it may seem that science and art are absolutely incompatible. However, if you think about it, these two worlds — both abstract and creative — have a lot in common! They aim at exploring new horizons, providing another perspective on already existing things, and communicating this position to others. Moreover, scientists are often artists as well! A number of great inventors and scientists of the past — such as Leonardo da Vinci, Mikhail Lomonosov, Lewis Carroll, and many others — are known for their works of both scientific and cultural value.

From our side, we can contribute to the creation of things emerging on the edge of the two so different but at the same time so similar worlds. Within the ENHPATHY consortium, there is a program called Enhancer in Art that aims at communicating science (in particular genomics) to the general audience with the help of artists. I will soon contact an artist and tell her about my research. I expect it to be challenging mainly because of the need to “translate” some of the terms and concepts we use in our work to tell a fascinating and understandable story. My research focuses on studying the impact of gene regulatory variation on disease utilizing the concept of Variable Chromatin Modules (VCMs). I hope that in the final artwork, we could show the dynamic nature of the VCMs and the complexity of our genome organization.

 

* One of the examples that I find absolutely adorable is the series of coloring and comic books created by the Cell Press team: “Coloring with Cell” and “Color-In Comics: Neurons at Play”!

 

Photo credit: Millefiori by Fabian Oefner

https://fabianoefner.com

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The Art-Science Kinship

The estrangement of artists and scientists appears to have been a feature of ancient civilisation even before the time of Plato, who deduces that poets are imitators of the world, and therefore far from the truth: “the tragic poet is an imitator, and therefore, like all other imitators, he is thrice removed from the king and the truth.”Even now, the opinion is very widely prevalent that art and science are in some sense mutually antagonistic, where one is considered closer to truth and the other an artefact of one’s imagination. Though there are people who would repudiate such an opinion but, even amongst them, there seems to be very little feeling of any need to establish their essential harmony. In such times, the Enhancer in Art (EIA) initiative by the ENHPATHY program stand unfazed by the criticism and determined to compose an exemplar for the budding scientific art community.

Art and Science

Amongst the most celebrated instances in history of intertwining of art and science, nothing stands closer to that of Marianne North and Charles Darwin in my opinion. Born in Hastings, England, Marianne North was a Victorian plant hunter and prolific botanical painter. She played a key role in botanising, and in the transfer of botanical knowledge, not only as illustrators of the physical characteristics of botanical subjects but also in advancing the ways that scientists (in this case study, those that study plant sciences at Kew) have understood, named, represented, categorised and related to plants. Around the same time, Charles Darwin was studying phenomena like ‘pleasures of pseudocopulation’ in The Power of Movement in Plants, which was believed to be induced by the enticing colours of orchids. Later, she was invited to Australia in 1880, on the recommendation of Darwin to paint their extraordinary flora. Charles Darwin was an avid supporter and considered North’s paintings to be excellent examples of his theory of nature.

Art and ENHPATHY

Continuing the legacy of Marianne North, Charles Darwin and many more, ENHPATHY has created a platform for knowledge dissemination and public engagement in the field of enhancers and associated diseases by the medium of art. In my view, the research community is constricted and often requires a certain level of scientific acumen as a premise to step into. Collaborating with a local artist, I would be able to covert my research of complex biological phenomena to intelligible concepts, bypassing the gatekeepers of the scientific community and reaching out to the general public.

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Functional assay of regulatory elements could aid early detection of Congenital Heart Defects (CHD)

In the world of scientific investigations and innovative research, biomedical research offers a great many opportunities to contribute to improving both longevity and quality of life. An educational background in computer science and numerical computing intertwined with bioinformatics made me more conscious of the importance of the ENHPATHY initiative. ENHPATHY is not only an excellent research endeavour but also a significant step towards the humanitarian cause. During my stay in the UK, I was heavily involved in the COVID research on cancer patients with UK Coronavirus Cancer Monitoring Project (UKCCMP), which further motivated me to work towards health science and genetics-based research.

Congenital heart defects 

Congenital heart defects (CHD) are a varied group of structural and functional disorders that occur in the developing heart of neonates and children. CHD is the leading cause of infant morbidity and is prevalent in about 1-3% of all live newborns. Routine clinical diagnosis of CHD is often performed prenatally to examine the heart structure for defects in the walls, valves, and vessels. Surgical intervention and therapeutic management techniques for CHD have improved significantly over the last few decades and an early diagnosis and subsequent treatment have the potential to drastically improve perinatal outcomes. However, studies have found that a number of these CHD diagnoses are missed in the birthing clinic and thus infants are later diagnosed upon hospital admission for critical symptoms such as cardiac shock.

The advent of next-generation sequencing made prenatal genetic diagnosis possible. However, the underlying genetic architecture suggested that the causal CHD variants were found to be those identified on a family-by-family basis rather than identified statistically at a population level with GWAS (Genome-Wide Association Study). In conclusion, the theory of CHD aetiology became that many common variants, as detected by GWAS, add to the risk of CHD, but these exist alongside rare variants which carry a much higher contribution. Therefore, an unbiased whole-exome sequencing (WES) approach started to be utilized to identify rare causal sequence variants in familial or sporadic CHD cases. Unfortunately, due to poor diagnostic success rates of both CHD gene panels and WES, along with the limited genome-wide coverage of both methods, the focus is now turning to whole-genome sequencing (WGS) to investigate whether non-coding sequence variants can lead to an improved diagnostic yield for CHD.

Introducing SuRE and its potential role in new CHD variants identification

However, identification of variants is just the first step, major challenges lie within identifying causal variants amongst them. Due to the intricate spatial-temporal regulation of transcription-factor binding to non-coding cis-regulatory elements, the functional effect of these variants is not predictable just from the sequence. Functional assays are commonly employed alongside WGS to determine whether a variant has a functionally significant effect on gene expression. Survey of Regulatory Elements (SuRE) is a massively parallel reporter assay platform that can identify and assay novel promoters/enhancers at high throughput. Additionally, SuRE can assay CRE activity in any transfectable cell line and previous applications have found differing cell types to have unique regulatory profiles. We hypothesize that using SuRE technology, we would be able to detect some of these causal variants while establishing a database with millions of non-coding sequence variants – all functionally annotated for their effect on enhancer and promoter activity in several disease-relevant cell types. This database of non-coding sequence variants and causal variants would not only be a major accomplishment of the project but also an important resource for strategies aiming to link genotypes to phenotypes like the GWAS and eQTL (Expression Quantitative Trait Loci) studies.

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EMBO workshop, October 6-9, 2021 | Santander Spain

The new  EMBO workshop co-organized by Álvaro Rada-Iglesias, Salvatore Spicuglia and Susanne Mandrup is now open for registration –> register here. 

About the Workshop

Due to the current COVID-19 emergency this workshop might need to be cancelled depending on national and local recommendations. In order to give both organizers and participants more time before making any decision, the registration and payment deadlines have been extended. In case of cancellation, registration fees will be reimbursed. We also recommend all invited speakers and participants to purchase their flight tickets with a cancellation insurance

Mutations within coding genes have traditionally been considered the major genetic cause of human disease. However, it is becoming increasingly clear that the genetic, structural and/or epigenetic disruption of enhancers represent major etiological factors in numerous human diseases (i.e. enhanceropathies), ranging from rare congenital disorders to common diseases associated with ageing and lifestyle (e.g. cancer, diabetes). Although changes in enhancer activity are predicted to have broad pathological and therapeutic implications, we currently have a limited understanding of human enhanceropathies. This reflects, at least partly, our still primitive and partial understanding of the mechanisms whereby enhancers can control gene expression. To overcome these limitations, this workshop will bring together experts in enhancer biology, gene regulation and medical genetics that, during three days, will present their latest work. Our invited speakers and participants will discuss the multidisciplinary approaches required to investigate enhancer function as well as debate about the role of enhancers in fundamental biological processes (e.g. embryonic development, evolution) and in the etiology of human disorders. Ultimately, the goal of this EMBO Workshop will be to provide a complete view of how a deep and systems-level understanding of enhancer function can facilitate elucidating the molecular basis of human enhanceropathies.

 

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Supervisors

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COORDINATION BOARD

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INFOS ESRs

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Publications

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Kickoff meeting …checked! Enhpathy officially launched its program.

ENHPATHY is a multidisciplinary science consortium created in the frame of the Marie Sklodowska-Curie actions (MSCA)-ITN-ETN European Training Networks call and regrouping 12 academic and 3 non-academic European organisations in the continuum of basic, translational and clinical research on enhancers and associated diseases.

ESR applications to ENHPATHY ‘s training program : all applications should be made using the recruitment form to be published from March 15 to April 16, 2020 (https://www.enhpathy.eu/recruitment/).

Candidates with bioinformatics, genomics and/or molecular and cellular biology backgrounds are encouraged to apply.

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The (MSCA)-ITN the Innovative Training Networks program ENHPATHY to be launched on March 01, 2020

We are pleased to announce that the EnhPathy ITN H2020 PhD call will open on March 15th 2020. EnhPathy will be recruiting 15 PhD students to start their training program within the September-December 2020 period.

Please check the Nature careers ad on this link

ENHPATHY is a multidisciplinary science consortium created in the frame of the Marie Sklodowska-Curie actions (MSCA)-ITN-ETN European Training Networks call and regrouping 12 academic and 3 non-academic European organisations in the continuum of basic, translational and clinical research on enhancers and associated diseases.

All applications should be made using the recruitment form to be published from March 15 to April 16, 2020 (https://www.enhpathy.eu/recruitment/).

Candidates with bioinformatics, genomics and/or molecular and cellular biology backgrounds are encouraged to apply.

Read full press release

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Blocs Images

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EMBO workshop, May 25-28 2020, Santander Spain (Rescheduled)

The new  EMBO workshop co-organized by Álvaro Rada-Iglesias, Salvatore Spicuglia and Susanne Mandrup is now open for registration –> https://bit.ly/2qoO4yC 

About the workshop : 
Mutations within coding genes have traditionally been considered the major genetic cause of human disease. However, it is becoming increasingly clear that the genetic, structural and/or epigenetic disruption of enhancers represent major etiological factors in numerous human diseases (i.e. enhanceropathies), ranging from rare congenital disorders to common diseases associated with ageing and lifestyle (e.g. cancer, diabetes). Although changes in enhancer activity are predicted to have broad pathological and therapeutic implications, we currently have a limited understanding of human enhanceropathies. This reflects, at least partly, our still primitive and partial understanding of the mechanisms whereby enhancers can control gene expression. To overcome these limitations, this workshop will bring together experts in enhancer biology, gene regulation and medical genetics that, during three days, will present their latest work. Our invited speakers and participants will discuss the multidisciplinary approaches required to investigate enhancer function as well as debate about the role of enhancers in fundamental biological processes (e.g. embryonic development, evolution) and in the etiology of human disorders. Ultimately, the goal of this EMBO Workshop will be to provide a complete view of how a deep and systems-level understanding of enhancer function can facilitate elucidating the molecular basis of human enhanceropathies.

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ENHPATHY 1ST MEETING – NOV 6TH 2018, MARSEILLE FRANCE

Brainstorming meeting gathering Enhpathy members – Marseille.

List of beneficiaries :

Salvatore Spicuglia (Coordinator), Institut Nationale pour la Santé et la Recherche Médicale (INSERM), France

Alvaro Rada-Iglesias (Vice Coordinator), University of Cantabria (UNICAN), Spain

Meritxell Alberich-Jorda, Institute of Molecular Genetics of the AS CR (IMG), Czech Republic

Robin Andersson, University of Copenhagen (UCPH), Denmark

Bart Deplancke, Swiss Federal Institute of Technology Lausanne (EPFL), Switzerland

Jorge Ferrer, Centre for Genomic Regulation (CRG), Spain

Wouter de Laat, Royal Netherlands Academy of Arts and Sciences (KNAW), The Netherlands

Susanne Mandrup, University of Southern Denmark (SDU), Denmark

Gioacchino Natoli,  European Institute of Oncology (IEO), Italy

Dariusz Plewczynski, University of Warsaw (UoW), Poland

Pelin Sahlén, Royal Institute of Technology (KTH), Sweden

Judith Zaugg, European Molecular Biology Laboratory (EMBL), Germany

Joris van Arensbergen, Gen-X B.V. (Gen-X), The Netherlands

Julia Sepulveda Diaz, ELVESYS SAS (Elvesys), France

Mileidys Perez Alea, Advances BioDesign (ABD), France

List of partnering organisations :

Christian Thirion (Sirion), Germany

Gonzalo R. Ordóñez (Dreamgenics), Spain

Remi Terranova (Novartis Pharma AG), Switzerland

James B. Meigs, Alisa Manning (TOPMed), United States of America

Thomas Lemberger (GLWF, EMBO Press), Germany

J.C. Fitzsimons (Leadership Sculptor), Germany

Jean M. Grangeon (KOM Agency), France

Jacques van Helden (Institut Français de Bioinformatique)

Alain Arnaudet (La Friche Belle de Mai), France

Jorge Ferrer (UPF, Universitat Pompeu Fabra), Spain

Meritxel Alberich-Jorda (CUNI, Univerzita Karlova, Charles University), Czech Republic

Wouter de Laat (UU, Universiteit Utrecht), Netherlands

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Marie CurieThis project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 860002. The information contained in this website reflects only the authors’ view. REA and EC are not responsible for any use that may be made of this information.