Personal health data clouds to give early warning for cancer, other diseases

Source: Horizon Magazine

Data is everywhere, it affects the things we buy, the way we vote and the news we read. But in healthcare, it is changing how we approach wellness and diseases, allowing us to work out what illnesses we’re at risk of getting, and giving us the chance to take action before they strike.

‘Genomics is moving from the research lab into the healthcare system,’ said Niklas Blomberg, the director of ELIXIR, an ambitious project supported by the EU to create a Europe-wide infrastructure to give researchers access to biological data and research. ‘DNA sequencing allows doctors to predict the likelihood of their patient inheriting a mutation of these genes, and suggest preventive treatments.’

The explosion of biological data has been driven by a meteoric fall in the cost of getting your DNA sequenced. It took thousands of people ten years to sequence the first human genome, whereas now it can be done in a few hours for less than EUR 1 000.

The issue is particularly relevant to Dr Jim Dowling, a senior researcher at the EU-funded BiobankCloud project, as both he and his wife are carriers of the mutation for cystic fibrosis, meaning that each of his children had a one-in-four chance of getting the disease.

If genetic sequencing had been widely available at the time, they would have been able to take measures to reduce the risk. In fact, both of his children have gone on to develop the disease. ‘That’s the kind of thing you could prevent with IVF (in vitro fertilisation),’ he said.

Traffic light dating

He believes that in 10 years genetic information will become so widespread that people will access their genetic data using their smartphone. It could be used, for example, to tell potential partners if their children would be at risk of disease.

‘The cliché is a traffic light dating system,’ he said. ‘Before you talk to someone you’d check, what does the traffic light say.’

Already around 228 000 people had their genomes sequenced in 2014, according to Illumina, a US-based gene sequencing company, which including backups could represent around 66 petabytes of data, or around a million Blu-ray disks.

Dr Dowling explained that the BiobankCloud project has been developing a way to store and read this data quickly, using the same technique that services such as Google use during a search query, and it plans to release the software this spring.

It works by dividing the data between hundreds of machines and then analysing all of them at the same moment.

‘If you read my genome from a single disk it’ll take a thousand seconds, but what big data is about is taking my genome and splitting it up over a thousand machines,’ he said. ‘When you send a computation you send it to all thousand machines.’

Monitored self

These developments come as people also collect health data using gadgets such as the Fitbit monitoring wristband, while smartphones record how far we walk and where we go, giving researchers a more complete view of what happens to our bodies when we are healthy and when we get sick.

‘What we see in terms of the not very far future is that the body will be a digital object,’ said Dr Jesper Tegnér, director and strategic professor of computational medicine at the Karolinska Institutet in Sweden. ‘Every individual will be a data cloud.’

Researchers like him have coined the phrase ‘systems medicine’ to describe the way that all of these kinds of data can be combined to give doctors a better understanding of how diseases affect different systems in the human body.

As well as DNA, systems medicine includes other types of data such as the actions of gene messenger molecules known as RNA, proteins, and information on how our genes react to the environment.

‘You need to look at not just a static blueprint in terms of DNA but you need to look at how it is used in different cells,’ he said. ‘What we see is the convergence of a rich amount of molecular data of different kinds, and interestingly, sensor data from smart devices which together defines your degree of wellness and propensity for disease.’

Dr Tegnér is a leading researcher on the EU-funded CASyM project, which is looking at how this explosion of data will affect the future of medicine. The project has produced a roadmap document to outline what’s needed to implement systems medicine in Europe.

‘The early adopters are already trying this, but on a mass scale (it will be available) maybe in 10 years’ time, not more than that,’ he said.

It could be used, for example, to tap the body’s immune system for an early warning when we are developing cancer or to help lessen the risk of Alzheimer’s disease.

‘The immune system generally attacks and tries to prevent us from having tumours, attacks the different cancer cells, so you will see changes in the immune cell early on when you have some kind of illness so that’s an interesting area within cancer,’ he said.

Open data

Researchers say the biggest hurdle for the use of big data in medicine is in the regulations, because if access to gene data ends up being controlled in the same way that medical records are in many countries, the data won’t be able to be passed on for research purposes.

It’s now, in the early stages of big data medicine, that the legal groundwork has to be laid to open up access to people’s medical data to researchers who can use it to look across the population and identify which signs can give us an early warning of disease.

‘The European Commission could have an important role to play here so really pushing for this open system where individuals have the right to their own data,’ said Dr Tegnér. ‘We see this as a very important issue.’

ELIXIR

ELIXIR is an inter-governmental organisation that helps Europe’s life science organisations manage and safeguard public research data, which is generated every day in massive quantities.

It is designed to help life science researchers capitalise on this ever-expanding store of biological data and facilitates research in areas such as medicine, biotechnology, food, agriculture and biodiversity.

ELIXIR consists of a central hub in Cambridge, UK, and a number of centres of excellence across Europe. It has been selected for EU support by the European Strategy Forum for Research Infrastructures.

You can find the original article here:

http://horizon-magazine.eu/article/personal-health-data-clouds-give-early-warning-cancer-other-diseases_en.html

Endurance training changes muscle DNA methylation

A recent publication from our group (finally online) in collaboration with scientist at the Physiology department, show that endurance training alter the DNA methylation profile in skeletal muscle.

We have adopted an integrative approach to investigate the impact of an environmental lifestyle intervention on the epigenome and transcriptome of human skeletal muscle. This is highly important, since regular endurance training induces extensive beneficial effects on skeletal muscle and it contributes to the prevention and treatment of a multitude of some of the most common diseases, e.g. cardiovascular disease, type II diabetes and several forms of cancer. The relationship between specific differential skeletal muscle DNA methylation and gene expression after long-term endurance training is not completely clarified. This human study provides novel insights about the mechanisms underlying the massive functional and health benefits of regular, long-term exercise, supporting the contribution of the epigenome to training response as a mediator between genes and environment.

We have combined a highly controlled prospective study design with a comprehensive bioinformatics analysis integrating transcriptional and epigenomic data at a global level and with single-base resolution. We show that a physiological stimulus can induce small but highly consistent modifications in DNA methylation that are associated to gene expression changes concordant with the observed phenotypic adaptation. This association provides a putative mechanism for the variability in transcriptional and adaptive response to physical activity, given the coordinated modulation that we observe in the proper in vivo context. Distinct ontologies from the sites changing in methylation strongly suggest a non-random effect across the genome. We also applied network-based approach to visualize and analyze the transcriptional changes and connect the associated methylation changes.

About 20% of the differentially expressed genes were affected by methylation changes. The modifications mainly occurred in regulatory enhancer regions, and less in promoters, a novel finding in the context of tissue adaptation to a physiological stimulus in humans. We also identified known binding domains for important transcription factors in close proximity to the differentially methylated sites, indicating that training induces methylation changes relevant for regulation of transcription.

Our study provides a valuable resource in the fields of human exercise physiology and environmental epigenomics because we are able to establish a link between the physiological adaptation of human skeletal muscle to a health-beneficial intervention, and molecular changes in the epigenome and transcriptome.

Poster

Published on figshare (http://dx.doi.org/10.6084/m9.figshare.1239050)

Article

An integrative analysis reveals coordinated reprogramming of the epigenome and the transcriptome in human skeletal muscle after training.

Published in Epigenetics

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Get to know the team members

You may wonder what happens on a typical day on the ComMed group, what the team members deal with during their days in the lab. Because we are a interesting combination of experimental and computational scientists, our work can be surprisingly manifold here. On a chilly autumnal morning, someone is focusing on grant writing, in the wetlab human immune cells are being isolated and cultured, a sequencing run is in progress in another room, while in the office someone else is busy debugging his code or launching a multicore job on a server.

At the same time, some administrative work has to be done, a revised version of an important document has to be fixed or a presentation must be prepared. Actually, it is not so much different from any other lab working in the “omics” era. Current biology has experienced the need for multidisciplinary research and multiple skills are required to tackle engaging research questions. Therefore, how do we combine or integrate our scientific activity? What is the fil rouge (unifying thread) of our research? I would doubtless say that everyone in the group is familiar with the immune system, either because he/she is an immunologist by training or because in his/her career the immune system has been a close encounter, that has produced a long-term friend.

On a typical day in the lab, it happens also to have have more or less intellectual discussions, geeky conversations or sometimes share funny links (on top of the important brand-new publications, of course…). Recently, some of us took a test to decide what is the immune cell that mostly fits our personality (link here).

A graph with the results is shown below.

A graph with the results is shown below.

And here the description of the cell type personalities:

(Disclaimer: we do not own the images or the text, the original source is linked here)

Stem cell

You’re a jack-of-all-trades, as evidenced by you polling evenly in several categories. You’re good at just about everything, andyou’ve got the potential to do whatever you want in life. Try to focus on what’s truly important so your talent can be put to good use. Like you, a stem cell has the potential to become just about anything the body might need. And, it also divides almost limitlessly, allowing your body to maintain homeostasis.

Marcophage

You’re all about you. Your well-being means the most to you, and that means seeking happiness in whatever form you see fit, whether it be through food or money or love. You can be prone to mood swings as your goals and outlook in life change, but you’re determined to discover who you truly are. Macrophages are efficient phagocytes, taking up antigen from the environment and digesting them for antigen presentation. These cells are capable of differentiating into M1 or M2 macrophages, which deal with pathogen clearance and wound healing respectively.

B cell

You’re the hopeless romantic. Through all the difficulties, you always believe ‘the one’ is out there for you. You also build strong one-on-one relationships with a variety of people, and you can’t survive without that contact. Once you have the support you need, you’re an incredibly productive person. B cells depend on a variety of cells (dendritic cells, T helper cells) to survive and mature. Once they’re developed, they can release antibodies to track down pathogens and activate other immune cells.

Dendritic cell

You’re the social butterfly. You believe it’s your job to interact with as many people in life as possible and make them comfortable. You’re most at-home hosting events or leading a social gathering. You’re also great in providing assistance to others and developing their skill sets. Dendritic cells help to bridge the gap between innate and adaptive immunity. They sample antigens from the environment and display them to T cells for adaptive immune responses. They also aid in B cell development, ensuring only the top ones make it to maturity.

Natural Killer cell

You are the law. There’s a time and a place for everything, and it better not deviate. You believe rules are meant to be upheld. No exceptions. You tend to pick on or notice people’s flaws, but you can be a tireless worker when you’re called upon to help or lend a hand. You are constantly vigilant and see details others may not. As such, you might notice when your friends aren’t feeling their greatest. Natural Killer (NK) cells are intrinsically capable of detecting cells that just don’t look right. If they’re stressed by infection or damage, they may not express markers they usually do. NK cells can then target these cells for destruction.

Treg

You’re the pacifist. In any situation or confrontation, you want things resolved peacefully. You likely also take time to calm your friends or support them when life gets them down. You’re kind at heart and just want everyone to get along. But, sometimes you just gotta’ let ’em duke it out. Like a T regulatory cell, you’re hoping to keep conflict to a minimum. Tregs spend their time making sure inflammation in the body isn’t excessive. Their immunosuppressive ability is important, but can become detrimental when it’s necessary for the body to clear an infection or tumor cells.

Granulocyte

You’re the odd-ball. You like to wear your emotions on your sleeve and sometimes, you can over-share. You believe life is short-lived, and every moment must be celebrated and enjoyed. As such, you’ve got wild stories to tell and are willing to tell them to anyone who will listen. Granulocytes are composed of eosinophils, basophils, and neutrophils and release granules in allergic or anti-parasitic responses. Neutrophils are often the first responders to inflammation or infection. Neutrophils are the most abundant immune cell in your blood, but have a short life-span of a few days.

PS: The author of this post is a NK cells (He’s the law…)