"An important achievement of this work is to improve our understanding of how the individual variation in the cross talk between the host and the virus contribute to the disease susceptibility and disease severity", says professor Aarno Palotie, a member of the research team.

Sama influenssavirus vie toisen sairaalaan ja on toiselle vain lievä riesa – miksi?

Tutkijat ovat löytäneet ihmisen ja hiiren perimästä geenimuutoksen, joka vaikuttaa influenssaviruksen lisääntymiskykyyn ja siten siihen, miten vakavaksi ja pitkäaikaiseksi tauti eri yksilöillä muodostuu.

Wellcome Trust Sanger Instituutin, Massachusets General Hospitalin ja Suomen molekyylilääketieteen FIMMin tutkijat ovat osoittaneet, että tietyn IFITM3-geenimuodon kantajilla on muita suurempi riski joutua influenssa vuoksi sairaalahoitoon.

Tutkijat havaitsivat, että niillä hiirillä, joilta on poistettu IFTIM3- geeni, influenssavirustartunta johtaa vaikeampaan tautiin kuin villityypin hiirillä. Influenssavirus lisääntyi tehokkaammin ja pitempään poistogeenisten hiirten hengityselimistössä, ja niillä havaittiin myös virusinfektion seurauksena hengityselinten solukuolemaa huomattavasti enemmän kuin villityypin hiirillä.

Kun tutkijat selvittivät millaisia muutoksia IFTM3-geenissä esiintyy ihmisväestössä, he havaitsivat, että noin seitsemän prosenttia väestöstä kantaa sellaista IFTM3-geenimuotoa, jonka tuottama proteiini toimii puutteellisesti. Noin 0,3 prosenttia väestöstä kantaa tätä geenimuotoa molemmissa kromosomeissaan, eli on perinyt sen sekä äidiltään että isältään. Tämä johtaa siihen, että elimistö ei lainkaan tuota normaalia IFTM3-proteiinia, joka suojaisi influenssaviruksen holtittomalta lisääntymiseltä.

Kävi ilmi, että tätä melko harvinaista IFTM3-geenimuotoa esiintyi enemmän siinä joukossa, jotka olivat joutuneet influenssa vuoksi sairaalahoitoon. Erityisen paljon sairaalahoidossa olleiden influenssapotilaiden joukossa oli niitä, jotka olivat perineet tämän geenimuodon kummaltakin vanhemmaltaan.

Tutkijoiden mukaan ihmisten yksilölliset erot infektioalttiudessa sekä siinä, miten vakaviksi tartuntataudit heillä muodostuvat, ovat varsin suuria ja niillä voi olla paljonkin merkitystä. Uusien geenitutkimusmenetelmien avulla voidaan selvittää, mitkä perintötekijät altistavat tietyille infektiosairauksille. Mikrobien perimä kuitenkin muuttuu jatkuvasti, joten ihmisperimän vaihtelut saattavat suojata vain tietyn virus- tai bakteerikannan infektioilta.

Nature-lehdessä julkaistun tutkimuksen geneettisen osuuden suunnittelivat ja analysoivat Suomen molekyylilääketieteen instituutin FIMMin tutkijat, LK (väit.) Verneri Anttila ja professori Aarno Palotie.

– Opimme askel askeleelta ymmärtämään miten oman perimämme ja virusten välinen vuoropuhelu vaikuttaa sairaustumisriskiin ja taudin vakavuuteen, professori Palotie sanoo.

Teksti: Päivi Lehtinen

In a study to the genetic variance of human metabolism, researchers have identified thirty one regions of the genome that were associated with levels of circulating metabolites, i.e., small molecules that take part in various chemical reactions of human body. Many of the studied metabolites are biomarkers for cardiovascular disease or related disorders, thus the loci uncovered may provide valuable insight into the biological processes leading to common diseases.

Laboratory tests used in the clinic typically monitor one or few circulating metabolites. The researchers at the Institute for Molecular Medicine Finland (FIMM) used a high throughput method called nuclear magnetic resonance (NMR) that can measure more than hundred different metabolites in one assay. This provides a much more in-depth picture of circulating metabolic compounds.

“Using this extensive analysis in thousands of people, we could identify a large number of genetic loci regulating the level of compounds circulating in the blood stream”, says Dr. Samuli Ripatti, the leader of the study.

The team assayed 117 detailed metabolic markers, including lipoprotein subclasses, amino acids and lipids, and conducted the largest genome-wide association analysis of this type, in terms of study sample size of 8330 individuals from six Finnish population-based cohorts and 7.7 million genomic markers studied. They revealed, in total, 31 genetic regions associated with the blood levels of the metabolites.
Eleven of the loci had not been previously shown to be associated with any metabolic measures.

Among the findings were two new loci affecting serum cholesterol subclass measures, well-established risk markers for cardiovascular disease, and five new loci affecting levels of amino acids recently discovered to be potential biomarkers for type 2 diabetes. The discovered variants have significant effects on the metabolite levels, the effect sizes being in general considerably larger than the known common variants for complex disease have.

Also, using Finnish twin pair samples, the researchers indicated that the metabolite levels show a high degree of heritability. “This result suggests that the studied metabolites are describing better the underlying biology than the routinely used laboratory tests. Therefore, the study provides further support for the use of detailed data on multitude of metabolites in genetic studies to provide novel biological insights and to help in elucidating the processes leading to common diseases”, Dr. Ripatti says.

For further information, please contact:
Dr. Samuli Ripatti, PhD
FIMM-EMBL Group Leader, Institute for Molecular Medicine Finland (FIMM)
University of Helsinki, Finland
www.fimm.fi
Tel: +358 20 610 8159
E-mail: samuli.ripatti@fimm.fi

Reference:
Johannes Kettunen, Taru Tukiainen, Antti-Pekka Sarin, Alfredo Ortega-Alonso, Emmi Tikkanen, Leo-Pekka Lyytikäinen, Antti J. Kangas, Pasi Soininen, Peter Würtz, Kaisa Silander, Danielle M. Dick, Richard J. Rose, Markku J. Savolainen, Jorma Viikari, Mika Kähönen, Terho Lehtimäki, Kirsi H. Pietiläinen, Michael Inouye, Mark I. McCarthy, Antti Jula, Johan Eriksson, Olli T. Raitakari, Veikko Salomaa, Jaakko Kaprio, Marjo-Riitta Järvelin, Leena Peltonen, Markus Perola, Nelson B. Freimer, Mika Ala-Korpela, Aarno Palotie and Samuli Ripatti: Genome-wide association study identifies multiple loci influencing human serum metabolite levels. Nature Genetics, 29th January, 2012 (online).

At this conference, nearly 150 participants of the Nordic EMBL Partnership for Molecular Medicine, consisting of the Institute for Molecular Medicine Finland (FIMM), Centre for Molecular Medicine Norway (NCMM), Laboratory for Molecular Infection Medicine Sweden (MIMS), and the EMBL came together for a scientific program including technology-based Meet-the-Experts sessions, group discussions, and tours of FIMM facilities.  Meeting Book available here.

We kindly thank all of the participants as well as the meeting sponsors:  Nordforsk, Aushon Biosystems, Essen Bioscience, Labnet, Eppendorf, Promega, PerkinElmer Finland, Corning, DiscoveRx, and LabCyte.

Photographer: Jouko Siro

The aim of the meeting is to provide an overview of what kind of information the structure of a biological macromolecule can give, and how this can be used to strengthen research in the fields of medicine and biosciences. The roadshow consists of two hours of lectures followed by a hands-on computer session that gives the attendees an opportunity to get acquainted with structures of macromolecules. Local structural biologists will be present at the meeting throughout the day for discussions and assistance. Participants receive a certificate, which they can use for applying for credits at their home institution.

• registration
• more information

During recent years European Union has supported planning of building, maintenance and utilization of common European research infrastructures. Examples of such endeavors include ELIXIR aiming at sustainable storage and maintenance of the biological data, BBMRI aiming at improving access to biobank samples and data, as well as EATRIS which aims at improving the “translation” of discoveries in basic biomedical research into new drugs, therapies and diagnostics.

Institute for Molecular Medicine Finland FIMM has been involved in the preparatory phase of the EATRIS translational research infrastructure funded by European Commission during 2007-2010. Now Finland together with the Netherlands, Denmark, Germany, Italy and Spain has signed an agreement to implement joint translational research infrastructure. More countries are expected to follow in early 2012.

“Whereas biomedical research has leaped forward in recent years, new drugs, therapies and diagnostics have nevertheless been in short supply. EATRIS improves the ‘translation’ of discoveries from basic research into practical applications by opening access to member states’ best expertise and research infrastructures.” says Professor Olli Kallioniemi, director of FIMM.

EATRIS will provide access to and facilitate joint use of member states’ major translational research infrastructures thus enabling optimal utilization of expensive equipment and the best expertise. EATRIS services will facilitate the development of biological as well as small molecule drugs, vaccines, tracers and diagnostic biomarkers.

EATRIS Coordination  & Supports office resides in Amsterdam. It provides a simple one-stop-shop –  a single point of access  – to network’s services.

“This consortium will improve healthcare provision and make Europe’s biopharmaceutical sector more competitive”, says Giovanni Migliaccio, scientific director of EATRIS.

ELIXIR is a pan-European initiative to operate a sustainable infrastructure for managing and safeguarding biological information in Europe. It will secure public access to information about the building blocks of life, including genes, proteins and complex networks. This will support life science research and its translation to medicine and the environment, the bio-industries and society to deliver economic growth. Consistent with the movement towards open access to data and publications, ELIXIR will make important information freely available to researchers across academia and industry.

The MoU was signed by Finland on 8 July by Marja-Liisa Niemi, Counsellor of Education at the Ministry of Education and Culture. Countries signing the Memorandum (including EMBL) will be represented on the Interim Board, which will be the main body for negotiating the final legal and governance structure of ELIXIR.

In Finland, ELIXIR is part of the Biomedinfra consortium – an integrated Finnish effort linking national and EU-level research infrastructures for biobanking (BBMRI), bioinformatics (ELIXIR), and translational research (EATRIS). Biomedinfra partners include the IT Center for Science (CSC), the Institute for Molecular Medicine Finland (FIMM) and the National Institute for Health and Welfare (THL).

In 2010–2011 the Biomedinfra consortium received funding of €5 million from the Ministry of Education and Culture through the Academy of Finland. CSC, FIMM and THL provided an additional €1.85 million in that same period. Denmark, Spain, Sweden and the UK have all allocated funding for the construction of ELIXIR Nodes, which will form the bulk of the ELIXIR infrastructure.

“Building the European research infrastructure ELIXIR supports the Ministry of Education and Culture’s central objectives to internationalise research environments, and improve the quality of research and innovation,” commented Counsellor Niemi.

“Finland seeks to play a major role in the ELIXIR research infrastructure, ensuring tight integration with biomedical data processing,” commented Tommi Nyrönen of CSC. CSC already plays an important role in the ELIXIR community.

“ELIXIR is a pivotal infrastructure project for medical research – and the life sciences generally – in Finland,” added Professor Olli Kallioniemi, Director of FIMM. “One of the biggest challenges in the future will be exploiting the exponential growth of biological data and information. ELIXIR, CSC and the national Biomedinfra consortium aim to develop the compute infrastructure – and the know-how to use it – throughout Europe so that we can gain the most from the research that has already been done.”

ELIXIR will distribute the management of life science data across several sites hosted by centres of excellence (the ELIXIR Nodes) throughout Europe. These sites will be connected to a central ELIXIR Hub located at the European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI) in Hinxton, near Cambridge in the UK.

More information: Tommi Nyrönen, CSC, e-mail: tommi.nyronen(at)csc.fi, tel. +358 50 381 9511.

See also: http://www.csc.fi/english/csc/news/news/biomedinfra

http://www.csc.fi/english/csc/news/news/highcapacitydataconnectionforbiomedicine

http://www.csc.fi/english/csc/news/news/biomedinfra_implemented

Scientists have identified 29 new genetic variants linked to multiple sclerosis, providing key insights into the biology of a very debilitating neurological disease. Many of the genes implicated in the study are relevant to the immune system, shedding light onto the immunological pathways that underlie the development of multiple sclerosis.

The research, involving an international team of investigators led by the Universities of Cambridge and Oxford, and funded by the Wellcome Trust, is published today, 11 August, in the journal Nature. This is the largest MS genetics study ever undertaken and includes contributions from Professor Leena Palotie’s and Dr Janna Saarela’s research groups from Institute for Molecular Medicine Finland FIMM, almost 250 researchers making up membership of the International Multiple Sclerosis Genetics Consortium and the Wellcome Trust Case Control Consortium.

Multiple sclerosis is one of the most common neurological conditions among young adults, affecting around 2.5 million individuals worldwide. The disease results from damage to nerve fibres and their protective insulation, the myelin sheath, in the brain and spinal cord. The affected pathways - responsible in health for everyday activities such as seeing, walking, feeling, thinking and controlling the bowel and bladder – are prevented from 'firing' properly and eventually are destroyed. The findings announced today focus attention on the pivotal role of the immune system in causing the damage and help to explain the nature of the immune attack on the brain and spinal cord.

In this multi-population study, researchers studied the DNA from 9,772 individuals with multiple sclerosis and 17,376 unrelated healthy controls. They were able to confirm 23 previously known genetic associations and identified a further 29 new genetic variants (and an additional five that are strongly suspected) conferring susceptibility to the disease.

A large number of the genes implicated by these findings play pivotal roles in the workings of the immune system, specifically in the function of T-cells (one type of white blood cell responsible for mounting an immune response against foreign substances in the body but also involved in autoimmunity) as well as the activation of ‘interleukins’ (chemicals that ensure interactions between different types of immune cell). Interestingly, one third of the genes identified in this research have previously been implicated in playing a role in other autoimmune diseases (such as Crohn’s Disease and Type 1 diabetes) indicating that, perhaps as expected, the same general processes occur in more than one type of autoimmune disease.

Previous research has suggested a link between Vitamin D deficiency and an increased risk of multiple sclerosis. Along with the many genes which play a direct role in the immune system, the researchers identified two involved in the metabolism of Vitamin D, providing additional insight into a possible link between genetic and environmental risk factors.

Alastair Compston from the University of Cambridge who, on behalf of the International Multiple Sclerosis Genetics Consortium, led the study jointly with Peter Donnelly from the Wellcome Trust Centre for Human Genetics, University of Oxford, said: “Identifying the basis for genetic susceptibility to any medical condition Embargoed until Wednesday, 10 August at 1800 London time / 1300 US Eastern time provides reliable insights into the disease mechanisms. Our research settles a longstanding debate on what happens first in the complex sequence of events that leads to disability in multiple sclerosis. It is now clear that multiple sclerosis is primarily an immunological disease. This has important implications for future treatment strategies.”

Peter Donnelly, who leads the Wellcome Trust Case Control Consortium, added: “Our findings highlight the value of large genetic studies in uncovering key biological mechanisms underlying common human diseases. This would simply not have been possible without a large international network of collaborators, and the participation of many thousands of patients suffering from this debilitating disease.”

For additional information please contact:

Janna Saarela, Institute for Molecular Medicine Finland, FIMM

Tel: +358 40 5123 801

Email: janna.saarela@helsinki.fi

Genevieve Maul, Office of Communications, University of Cambridge

Tel: direct, +44 (0) 1223 765542, +44 (0) 1223 332300

Mob: +44 (0) 7774 017464

Email: Genevieve.maul@admin.cam.ac.uk

Jonathan Wood, Press Officer, University of Oxford

Tel: +44 (0)1865 280530

Email: jonathan.wood@admin.ox.ac.uk

Leena Peltonen-Palotie’s legacy is immense: “She was a visionary in the field of science, creating an infrastructure for research needs that weren’t even on the horizon yet,” said Richard Durbin of the Wellcome Trust Sanger Institute in England.

“Right now we’re in a situation where genetics research has progressed faster than the methods it requires. We must find a way to bridge this gap. Leena was the one who said, ‘don’t just rely on one method—use all the tools available’,” remembered David Altshuler of the Broad Institute of MIT and Harvard and Massachusetts General Hospital.

Leena Peltonen-Palotie, who passed away a year ago, built an international research network to which many of the symposium’s 35 speakers belong. They discussed their own research projects and shared memories of Leena: “Exceptionally intelligent, warm, supportive and demanding. She inspired her colleagues to strive for better results and helped fellow scientists see beyond the challenges they faced. She believed that researchers should work together instead of competing with each other.”

Numerous beautiful memories of Leena’s luminous persona that supported and inspired others to achieve their best created a very special atmosphere at the symposium.

A warm thank you to all participants!
The planning committee for A Global View of Disease Genomics

Leena Peltonen-Palotien muistosymposiumi keräsi geneetikkoa yhteen

A Global View of Disease Genomics –symposiumiin Helsinkiin kokoontui 18.-19.5.2011 lähes 500 genetiikan alan tutkijaa ja tiedevaikuttajaa Yhdysvalloista ja eripuolilta Eurooppaa.

Leena Peltonen-Palotien jättämä perintö on valtava: ”Tieteen saralla hän oli kaukonäköinen ja loi infrastruktuurin vielä silloin kauas tulevaisuudessa siintävien tutkimusten tarpeisiin”, totesi Richard Durbin Wellcome Trust Sanger Instituutista.  

”Tällä hetkellä olemme tilanteessa, jossa geenitutkimus on edennyt nopeammin kuin siihen tarvittavat metodit. Tämä välimatka täytyy kuroa kiinni. Leena totesikin, että älä usko yhteen metodiin, vaan käytä kaikkia työkaluja”, David Altshuler Broad Institute of MIT and Harvard and Massachusetts General Hospitalista muisteli.

Vuosi sitten edesmennyt Leena Peltonen-Palotie loi kansainvälisen tutkijaverkoston, johon kuuluvat lähes kaikki symposiumin 35 puhujaa. He kertoivat omasta tutkimustyöstään, ja jakoivat muistojaan Leenasta: ”Poikkeuksellisen älykäs, lämmin, kannustava, vaativa, innosti yhä parempiin saavutuksiin, sai näkemään yli vaikeuksien. Hän opetti, että kilpailemisen sijaan tutkijoiden tulee tehdä yhteistyötä.”

Lukuisat kauniit muistot Leenan valoisasta ja huippusuorituksiin kannustavasta persoonasta loivat symposiumiin ainutlaatuisen tunnelman.

Lämmin kiitoksemme osallistujille!
A Global View of Disease Genomics –symposiumin suunnittelukomitea

The Innovative Medicines Initiative (IMI) is the world’s largest public-private partnership, a two billion euro joint undertaking between the European Commission and the European Federation of Pharmaceutical Industries and Associations (EFPIA). IMI promotes the development of better medicines, with the larger goal of boosting the dynamism and technological development of the European biopharmaceutical sector.

The Institute for Molecular Medicine Finland (FIMM) at the University of Helsinki is coordinating the IMI consortium ‘PREDECT’, which will develop innovative models and technologies for the preclinical evaluation of cancer therapy targets. The consortium is a response to the alarmingly high rate of initially promising drugs now shown to lack efficacy when tested in patients – which may reflect the use of laboratory models of cancer that fail to represent the complexity and heterogeneity of human tumours. Working in teams investigating breast, prostate and lung cancers, PREDECT will comprehensively investigate the generation of better laboratory model systems of cancer for cancer drug development, with the goal of eventually increasing the clinical success of new cancer therapies.

PREDECT is a large consortium joining 9 academic laboratories with 3 small biotech enterprises and 7 major pharmaceutical companies. The fact that the consortium is coordinated by the University of Helsinki, but also involves Orion Pharma, VTT Technical Research Institute of Finland and BMGen Ltd, attests to the strength of Finnish cancer research. The team at the Meilahti campus comprises 6 PI’s: Emmy Verschuren (Academic Project Coordinator), Olli Kallioniemi and Johan Lundin from FIMM, Juha Klefström from the Institute of Biomedicine, Panu Kovanen from the Haartman Institute and Outi Monni from Biomedicum Genomics.

FIMM-EMBL Group Leader Dr Emmy Verschuren, Coordinator and representative of the IMI funding Managing Entity, says: “PREDECT is very timely. It is absolutely essential to comprehensively evaluate our cancer model systems now, but it is also a significant task that requires academia and industry to work together. We are bringing experts in key cancer biology areas together with young group leaders and industry partners as never before.”

Professor Olli Kallioniemi, Director of FIMM, adds: “We would like to have model systems which are faithfully representing many aspects of human cancer and we will make extensive comparisons across the model systems to compare their molecular and cellular properties with human patient specimens. If this is achieved, we should see the success rate of cancer drug development efforts improve in the future “

For further details contact Emmy Verschuren PhD: emmy.verschuren@helsinki.fi

Exome Sequencing Identifies Mitochondrial Alanyl-tRNA Synthetase Mutations in Infantile Mitochondrial Cardiomyopathy (Am J Hum Genet. 5.5.2011)

• Suomalaistutkijat löysivät vastasyntyneiden sydänrappeumaa aiheuttavan geenivirheen

• NextGen sequencing services at FIMM Technology Centre
  

FIMM_Annual_Report_2010_050511.pdf

”Each cancer is unique, and analysing its properties demands precise and effective tools. It is only then that doctors can plan targeted cancer treatment for an individual case,” says Johan Lundin, who has developed several methods and tools for individualized cancer profiling.

Lundin’s goal now is to establish an infrastructure and integrated data system for FIMM, which will enable effective use of all existing tools. Researchers and clinicians will have access to a three-level cancer analysis tool comprised of a digitised tissue bank, tissue sample information as well as data visualisation software.

“We have the opportunity to collect a vast amount of information on the genetic makeup and molecular properties of tumours. When this information is combined with hospitals’ follow-up and patient treatment data, we are able to create a more accurate disease prognosis and can better predict the effects of treatment. FIMM offers concise individual disease profiles for doctors working with cancer patients”, Lundin explains.

This system will be based on the Prognomics application developed by Lundin’s research group. Prognomics combines information from various databases to seek out commonalities in cancer cases based on cancer tissue and patient records from over five million individuals. The pooling of data delivers an accurate cancer prognosis and the means for increasingly personalised treatment. Several research groups have already tested Prognomics.

A webmicroscope, developed by Lundin’s research group and the University of Tampere, is an important tool in pulling all of this information together. The webmicroscope enables the analysis of large sets of digitised microscopic images. Working with the University of Oulu, Lundin is currently developing a remote diagnostics system based on computer vision and new microscope technology.

Lundin (b. 1964) is an experienced cancer biomarker researcher with expertise in microscopic imaging, biobanks, biostatistics and biomedical informatics. He graduated with a Licentiate of Medicine (MD) degree from the University of Helsinki in 1990, earning his doctorate in 1996. Lundin is a Senior Lecturer (Docent) in Biomedical Informatics at the University of Helsinki. Lundin has served as a Senior Researcher at FIMM since 2009, also holding positions at Karolinska Institutet and the Hospital District of Helsinki and Uusimaa (HUS).

The Institute for Molecular Medicine Finland (FIMM) is an international research institution located on the Meilahti Campus in Helsinki. FIMM combines research, new technologies and biobanking to facilitate prevention, diagnosis and treatment of common diseases as well as adaptation of personalised medicine in the clinic.

For further information, images and CV, please contact:
Research Director Johan Lundin, +358 50 415 5459, johan.lundin@fimm.fi 

Director Olli Kallioniemi, +358 50 415 0363, olli.kallioniemi@fimm.fi            

www.fimm.fi www.webmicroscope.net

Johan Lundin Suomen molekyylilääketieteen instituutin (FIMM) tutkimusjohtajaksi
 
Dosentti, LT Johan Lundin on valittu FIMMin tutkimusjohtajaksi. Lundin vastaa 1. toukokuuta lähtien diagnostisten menetelmien kehittämisestä.  Tavoitteina ovat mm. potilaan syöpätaudin tarkka määrittäminen ja siten  tehokkaat välineet henkilökohtaiseen, yksilölliseen syövän hoitoon.
 
"Jokainen syöpä on ainutlaatuinen, ja sen ominaisuuksien analysointiin on oltava tarkat ja tehokkaat välineet. Vain siten syöpää hoitavat lääkärit voivat suunnitella kuhunkin syöpään täsmällisen hoidon", sanoo Johan Lundin, joka on uransa aikana kehittänyt useita menetelmiä ja välineitä henkilökohtaisessa lääketieteessä hyödynnettäväksi.
 
Nyt Johan Lundinin tavoitteena on rakentaa FIMM:iin infrastruktuuri ja tietojärjestelmä, jolloin kaikkia käytössä olleita työkaluja voidaan hyödyntää. Tutkijoiden ja hoitavien lääkärien käyttöön tuleva kolmivaiheinen syövän analysointityökalu sisältää digitaalisen kudosarkiston, kudosnäytetiedot sekä tiedon visualisointiin tarkoitetun ohjelmiston.
 
"Meillä on mahdollisuus saada valtava määrä tietoa kunkin kasvaimen geeneistä ja molekyylien ominaisuuksista. Kun nämä tiedot yhdistetään sairaalan seuranta- ja hoitotietoihin, saadaan tarkempi taudin ennuste ja arvio hoidon vaikutuksista. FIMM tuo yksilöllisen tautiprofiilin jäsenneltynä ja tiivistettynä syöpää hoitavien lääkäreiden käyttöön", Lundin täsmentää.
 
Järjestelmä perustuu Lundinin tutkimusryhmän kehittämään Prognomics -sovellukseen, joka yhdistää kerättyjen tietokantojen tiedot. Prognomics hakee syöpäkudokseltaan ja potilastiedoiltaan samankaltaiset syöpätapaukset yli 5 miljoonan yksilön tietokannasta. Näin potilaan syövästä saadaan tarkka ennuste ja välineet yksilölliselle hoidolle. Useat
tutkimusryhmät ovat jo testanneet uutta menetelmää.
 
Kokonaisuuteen kuuluva tärkeä väline on Lundinin tutkimusryhmän yhdessä Tampereen yliopiston kanssa kehittämä webmikroskooppi (www.webmicroscope.net), joka mahdollistaa laajojen näytesarjojen analysoinnin digitaalimikroskooppikuvista. Monipuolinen Lundin kehittää
parhaillaan yhdessä Oulun yliopiston kanssa konenäköön ja uuteen mikroskooppiteknologiaan perustuvaa etädiagnostiikkajärjestelmää.
 
Lundin (s. 1964) on syöpämerkkiaineiden tutkija ja perehtynyt mikroskooppiseen kuvantamiseen, biopankkeihin, biostatistiikkaan ja bioinformatiikkaan. Lundin valmistui lääketieteen lisensiaatiksi Helsingin yliopistossa 1990 ja väitteli tohtoriksi 1996. Lundin on Helsingin yliopiston bioinformatiikan dosentti. Hän on työskennellyt FIMMissä vanhempana tutkijana vuodesta 2009 lähtien ja sen ohella myös Tukholman Karoliinisessa Instituutissa ja HUSissa.

Meilahden kampuksella, yliopistosairaalan läheisyydessä, toimiva Suomen molekyylilääketieteen instituutti (FIMM) kehittää sovelluksia yleisten sairauksien ehkäisyyn, diagnostisointiin ja hoitoon sekä edistää henkilökohtaisen lääketieteen hyödyntämistä potilastyössä.

Lisätietoja, valokuva ja CV:

Tutkimusjohtaja Johan Lundin, 050 415 5459, johan.lundin@fimm.fi

Johtaja Olli Kallioniemi, 050 415 0363, olli.kallioniemi@fimm.fi
www.fimm.fi

http://www.webmicroscope.net

The multitouch microscope is an innovation developed by researchers at the Institute for Molecular Medicine Finland (FIMM) in collaboration with MultiTouch, a Finnish company. The innovation is based on two technologies created in Finland: virtual microscopy and a giant-size multitouch display.

– Traditional microscopes can only be used to examine a small part of a sample, says Johan Lundin. A virtual microscope can be used to create a comprehensive montage of the sample. The montage can consist of as many as 50,000 images.

The smallest multitouch microscope displays have 46-inch screens, which make iPads seem like postage stamps. Several people can examine the same sample from a display that has been placed on a desk, for example.

By touching the screen, the image can be enlarged and reduced in the same manner as in smartphones.

– There is one difference, though, says Lundin. Smartphones can be controlled with fingertips, but both palms are needed when zooming an image on the giant-size display of a multitouch microscope.

The multitouch microscope is suitable for many scientific fields, including pathology, microbiology and cell biology.

– It can be used in all fields in which microscopy is needed, Lundin sums up. The multitouch microscope is particularly useful in teaching.

It is much easier to learn than a traditional microscope, which only allows one person at a time to examine a sample. The multitouch microscope adds a new, interactive dimension to teaching.

The multitouch microscope was presented to the media last week at the ChemBio Finland event at the Helsinki Exhibition & Convention Centre.

An introductory video is available on YouTube.

Text: Nadine Aschan
Photo: Visa Noronen
Translation: AAC Global
28.3.2011

Olli Kallioniemi 

Tero Aittokallio received his PhD in Applied Mathematics from the University of Turku in 2001. In his PhD work, he used mathematical modeling to study the behavior of cardio-respiratory control system; such as sleep-disordered breathing in cardiovascular and metabolic diseases. He then went to a post-doctoral training (2006-2007) in the Systems Biology Lab at the Institut Pasteur, with Dr. Benno Schwikowski. During this time he focused on network biology applications using high-throughput experimental assays and software tools such as Cytoscape. One of the research directions, which is still under active development, involves genetic interaction mapping in yeast.  

Dr. Aittokallio then launched his independent career as a principal investigator at the Turku Biomathematics Research Group in 2007 and received a five-year appointment as an Academy Research Fellow. Tero Aittokallio continued the development of systems biology modeling approaches to reveal molecular mechanisms behind systems behavior and to predict responses to various environmental and genetic perturbations. His Data Mining and Modeling Group, which is part of the Turku Systems Biology Research Program, has implemented efficient computational tools for analyzing, integrating and visualizing high-dimensional data generated by a wide range of molecular profiling technologies in several collaborative projects combining expertise from both computational sciences as well as from biology, medicine, and bio-technologies. At the moment, Tero Aittokallio is again a visiting researcher at the Institut Pasteur until the end of March 2011. His work in Paris involves designing and testing of an experimental-computational algorithm for network-based drug discovery.

At FIMM, the Aittokallio group will apply the network-centric systems biology approaches to concrete medical problems in close collaboration with his national and international collaborators. In-depth analysis of the large-scale datasets produced at FIMM and its partner institutes using such modeling approaches has the potential to improve our understanding of medical conditions such as cardiovascular diseases. His group will attempt to identify genetic and environmental risk factors and their dynamic relationships responsible for multi-factorial behavior in complex human disease networks. Another specific area of interest concerns synthetic lethal genetic interactions in cancer. The long-term goal is to provide systematic strategies to the identification of novel molecular markers and putative drug targets for pharmaceutical and diagnostic developments.

Selected publications:

T. Aittokallio and B. Schwikowski: Graph-based methods for analyzing networks in cell biology, Invited review in the Special issue on Annual Progress in Bioinformatics, Briefings in Bioinformatics 7 (2006) 243-255.

O. Garcia, C. Saveanu, M. Cline, M. Fromont-Racine, A. Jacquier, B. Schwikowski and T. Aittokallio: GOlorize – a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring, Bioinformatics 23 (2007) 394-396.

L. L. Elo, J. Hiissa, J. Tuimala, A. Kallio, E. Korpelainen and T. Aittokallio: Optimized detection of differential expression in global profiling experiments: case studies in clinical transcriptomic and quantitative proteomic datasets, Briefings in Bioinformatics 10 (2009) 547-55.

L. L. Elo, H. Järvenpää, S. Tuomela, S. Raghav, H. Ahlfors, K. Laurila, B. Gupta, R. J. Lund, J. Tahvanainen, R. D. Hawkins, M. Orešič, H. Lähdesmäki, O. Rasool, K. V. S. Rao, T. Aittokallio and R. Lahesmaa: Genome-wide profiling of interleukin-4 and STAT6 transcription factor regulation of human Th2 cell programming, Immunity 32 (2010) 852-862.

S. Okser, T. Lehtimäki, L. L. Elo, N. Mononen, N. Peltonen, M. Kähönen, M. Juonala, Y. M. Fan, J. A. Hernesniemi, T. Laitinen, L. P. Lyytikäinen, R. Rontu, C. Eklund, N. Hutri-Kähönen, L. Taittonen, M. Hurme, J. S. A. Viikari, O. T. Raitakari and T. Aittokallio: Genetic variants and their interactions in the prediction of increased pre-clinical carotid atherosclerosis – The Cardiovascular Risk in Young Finns Study, PLoS Genetics 6 (2010) e1001146.

http://www.chembiofinland.fi

People from northern and southern Sweden differ from each other genetically, according to the largest genetic study of the Swedish population yet. Swedes also have genetically more in common with Germans and British than with Finns.

"A knowledge of the population's genetic structure is important for understanding where we come from and for identifying genes that underlie diseases," says one of the leaders of the study, professor Per Hall from the Department of Medical Epidemiology and Biostatistics at Karolinska Institutet.

The study showed that people from Northern and Southern Sweden are genetically different from each other. However, the genetic change from south to north is gradual, and no strong genetic borders exist within Sweden. The study, performed jointly at Karolinska Institutet and University of Helsinki, has been published in PLoS ONE.

In the study, the researchers used more than 350,000 genetic markers called single nucleotide polymorphisms (SNPs) that are distributed across the human genome. More than 1500 people of Swedish origin from different parts of the country were analysed, and also compared to many neighboring populations.

"Despite close contacts within the Nordic region, the Swedes appeared genetically closer to Germans and British than to Finns", says professor Juha Kere from the Department of Biosciences and Nutrition at Karolinska Institutet.

The results also show that local genetic differences are small in Southern Sweden but larger in the north. These differences are a result of population history: in the north, the population has been smaller, which has led to pronounced local differences.

The study can be downloaded free of charge from www.plosone.org.

Publication:

Elina Salmela, Tuuli Lappalainen, Jianjun Liu, Pertti Sistonen, Peter M. Andersen, Stefan Schreiber, Marja-Liisa Savontaus, Kamila Czene, Päivi Lahermo, Per Hall and Juha Kere: Swedish population substructure revealed by genome-wide single nucleotide polymorphism data. PLoS ONE 2011 6(2): e16747.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0016747

For further information, please contact:

Ei ihan samaa perhettä, mutta sukua kuitenkin

Tutkimus valottaa suomalaisen ja ruotsalaisen väestön geneettistä sukulaisuutta

Vastikään julkaistu tutkimus osoittaa, että ruotsalaiset ovat geneettisesti läheisempää sukua saksalaisille kuin suomalaisille. Toisaalta Suomen tapaan myös Ruotsissa maakunnat poikkeavat geneettisesti toisistaan; etelä- ja pohjoisruotsalaisten välillä on huomattavia geneettisiä eroavuuksia.

Ruotsalaiset ovat geneettisesti lähempänä saksalaisia kuin suomalaisia, kertoo tuore tutkimus. Toistaiseksi laajin ruotsalaisen väestön perimää koskeva selvitys on Helsingin yliopiston ja Tukholman Karoliinisen Instituutin yhteishanke, jonka vetäjinä ovat toimineet professori Juha Kere ja dosentti Päivi Lahermo. Tutkimus on julkaistu tiedelehti PLoS ONE:ssa.

Tutkimukseen osallistui yli 1500 ruotsalaista, joilta tutkittiin noin 350 000 perimän kohtaa, ns. snippiä (single nucleotide polymorphism). Erityisesti eteläruotsalaisten havaittiin olevan geneettisesti lähellä keskieurooppalaisia. Ruotsin pohjois- ja eteläosat poikkesivat toisistaan, ja pohjoisessa näkyi myös selviä paikallisia eroja.

Tulosta verrattiin myös suomalaisiin. Mukana olleista suomalaisnäytteistä perimältään eniten ruotsalaisia muistuttivat länsisuomalaiset, erityisesti Pohjanmaan rannikon ruotsinkieliset. "Sen sijaan pohjoispohjalaiset eivät olleet geneettisesti erityisen lähellä pohjoisruotsalaisia naapureitaan", kertoo hankkeen tutkija Elina Salmela Helsingin yliopistosta.

Eroista huolimatta tulokset kertovat myös ruotsalaisten ja suomalaisten läheisestä sukulaissuhteesta. Pohjolan harvan asutuksen vuoksi geneettiset erot ovat kuitenkin korostuneet sekä väestöjen välillä että niiden sisällä. "Väestön perimä kertoo asutushistoriasta, mutta sen tunteminen on tärkeää myös tautigeenien tutkimuksen kannalta", sanoo professori Juha Kere.

Tutkimus on vapaasti luettavissa osoitteessa www.plosone.org.

Viite:

Elina Salmela, Tuuli Lappalainen, Jianjun Liu, Pertti Sistonen, Peter M. Andersen, Stefan Schreiber, Marja-Liisa Savontaus, Kamila Czene, Päivi Lahermo, Per Hall and Juha Kere: Swedish population substructure revealed by genome-wide single nucleotide polymorphism data. PLoS ONE 2011 6(2): e16747.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0016747

Lisätietoja:

The approach that Finland has selected is based on the realisation that biobanking, bioinformatics and translational biomedical research infrastructures support one another and all of them build on existing Finnish strengths. New funding of 4 M€ for 2011 is provided by the Ministry of Education and Culture through the Academy of Finland, with 1 M€ co-financing from the participating institutes; Institute for Molecular Medicine Finland (FIMM) at the University of Helsinki, CSC - IT Center for Science Ltd (CSC) and the National Institute for Health and Welfare (THL).

Specifically Biomedinfra will focus on three related pillars:

1) Improved biobanking infrastructures for epidemiological, biomedical and clinical research
2) High-performance computing infrastructure for facilitating next-generation biomedical data analysis needs
3) Translational infrastructure focusing on the application of biobanks to advance diagnostics and personalised medicine  

Taken together, it is hoped that these infrastructures will eventually improve health care in Finland and in the EU. These infrastructures will be opened to international collaborations and provide research services. They will also help to integrate national Finnish research infrastructures with the European efforts.

Professor Olli Kallioniemi,  Director of FIMM and coordinator of Biomedinfra, says "We are delighted about the opportunity to start building biomedical infrastructures that help Finland to contribute to the European ESFRI infrastructures. Therefore, even though these funds are still modest in the European scale, they represent significant new funding on top of a strong existing scientific base and in some cases decades of national investment. Biomedinfra is therefore a very timely effort, leverages Finnish strengths optimally and builds important links between these key European infrastructures".

Dr. Tommi Nyrönen, who leads the development at CSC, explains that Biomedinfra’s support will enable Finland to make a substantial contribution to the effort. "CSC is developing cloud based high-performance computing and storage services that are tailored to the needs of biomedical researchers," he says. "Importantly, the new funding will also enable us to develop technologies and policies to ensure that distributed biomedical data can be managed and used efficiently and securely. Research institutes should be able to access supercomputing resources easily and securely."

"This new funding is essential to build the Finnish national biobank network, BBMRI.FI", adds Dr. Anu Jalanko, Head of Public Health Genomics Unit, THL . "Biobanking requires close collaboration locally, nationally and internationally. Finland has strong traditions and expertise in biobank-related research and has created several world-class population biobank resources that are often also used in international collaborations. New biobank legistlation is anticipated in Finland in 2012 and common procedures and new centralised biobank services are essential to ensure efficient utilisation of biobanks for public health and translational research."

“BBMRI is ready submit to the European Commission its application for an “ERIC” legal structure in the near future. I am very happy that Finland has joined a growing number of European nations that have recognised the fundamental role of high-quality biobanking for the health of aging populations, development of diagnostics, new drugs and treatments.” adds Professor Kurt Zatloukal from Medical University of Graz and coordinator of BBMRI.

Professor Janet Thornton, coordinator of the ELIXIR infrastructure for biological information, continues "These developments in Finland to build a national infrastructure for biomedical sciences are very exciting. They uniquely involve strong coordination between the data e-infrastructure (ELIXIR), the biobanks (BBMRI) and translational research (EATRIS). This good communication, together with cooperation with the pan-European efforts,  will provide a sustainable bedrock to allow data and sample exchange both within and between countries and will accelerate future scientific discoveries."

Business & Finance Director of EATRIS Frank de Man comments "We are delighted about Finland committing to the construction of the European translational research infrastructure. Translational research is highly relevant to the future of European science and urgent investments are needed to keep EU competitive in the light of recent plans in the US. Despite economically challenging times in many European countries, we are looking forward to engagement of other countries".


Contact: Director, Professor Olli Kallioniemi, FIMM
Telephone: 09-191 25731
E-mail: olli.kallioniemi@helsinki.fi

Notes for editors

About FIMM

FIMM is an international research institute established in 2006. It is founded as part of the Nordic Molecular Medicine Partnership with the EMBL. FIMM aims to advance research and training in molecular medicine and the translation of molecular discoveries into practical clinical applications in collaboration with the industry. At the national level, FIMM brings together several strategic national resources and scientific expertise and is operated by the University of Helsinki in collaboration with sector research institutes (National Institute for Health and Welfare, and the VTT Technical Research Centre of Finland) as well as the Hospital District of Helsinki and Uusimaa. FIMM is the Finnish partner in European Advanced Translational Research Infrastructure (EATRIS).

About CSC

CSC - IT Center for Science Ltd. is a non-profit limited company administered by the Ministry of Education, Science and Culture. Having core competences in modeling, computing and information services, CSC provides versatile IT services, support and resources for academia, research institutes, and companies. The Funet communication links provide research workers with Finland's widest selection of scientific software and databases and Finland's most powerful supercomputers. CSC is the Finnish representative in European Life-Science Infrastructure for Biological Information (ELIXIR).

About THL

The National Institute for Health and Welfare (THL) is a research and development institute under the Finnish Ministry of Social Affairs and Health. THL works to promote the well-being and health of the population, prevent diseases and social problems, and develop social and health services. THL is the statutory statistical authority in health and welfare and maintains a strong knowledge base within its own field of operations. THL carries out its responsibilities through a wide range of activities: research, follow-up and evaluation, development, expert influence, official tasks as well as international co-operation. THL is the Finnish partner in Biobanking and Biomolecular Resources Research Infrastructure (BBMRI).

About BBMRI

The Biobanking and BioMolecular Resources Research Infrastructure (BBMRI) addresses the increasing demands of accessing human biological samples and data, and biomolecular resources that are identified as limiting key resources for the advancement of medical research and related industries. BBMRI generates an advanced framework for systematic investigation of biological samples such as blood or tissues from diseased or healthy people as well as the careful analysis of disease outcomes and effects of therapies.
By providing sustainable biological sample collections BBMRI will provide the basis for better understanding of the interaction of genetic, environmental, life style, nutritional and other factors causing variables of individual diseases and provide thereby a foundation for effective treatment and prevention measures. This will require, in addition to the innovative technical solutions as foreseen in BBMRI, a Europe-wide harmonized policy, regulatory and ethical framework for biobanking and related data management and access.

About EATRIS

To improve human health, scientific discoveries at the level of basic biomedical research have to be “translated” into practical, clinical applications. At the same time, novel observations about the nature or progression of a disease made by clinical researchers can be passed back to inspire new approaches in basic research. This two-way process of developing new tools or treatments for use in patients is called “translational research”. The translation of discoveries from the lab to commercially viable clinical applications is a complex and lengthy process. Basic biomedical research in Europe has traditionally been strong. However, Europe lags behind when it comes to bringing clinical innovation into clinical practice. It is against this background that European governments and centres of excellence in translational biomedical research have come together to create EATRIS, the European Advanced Translational Research Infrastructure in Medicine. EATRIS aims to be a European, globally competitive infrastructure for biomedical translational research which provides researchers across Europe broad access to state-of-the-art facilities, training and supporting services to optimise the outputs of both basic and clinical research.

About ELIXIR

The European Strategic Forum for Research Infrastructures published its first roadmap in 2005 (http://cordis.europa.eu/esfri/). The mission of ELIXIR is to construct and operate a sustainable infrastructure for biological information in Europe to support life science research and its translation to medicine and the environment, the bio-industries and society. It has been singled out as one of very few research infrastructures of global significance. ELIXIR is coordinated by the European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI) in the UK. To date, 54 organisations throughout Europe have put themselves forward as potential ELIXIR ‘nodes’ which, with the EMBL-EBI at the hub, will make up this infrastructure.

About the Academy of Finland

The Academy of Finland is the prime funding agency for basic research in Finland. The Academy operates within the administrative sector of the Ministry of Education. The Academy funds research annually with 314 million euros (year 2010), which accounts for 16 per cent of government R&D spending. Each year the Academy receives funding applications worth 1.1 billion euros. The Academy of Finland’s mission is to finance high-quality scientific research, act as a science and science policy expert, and strengthen the position of science and research.