Building a molecular glyco-phenotype ontology to decipher undiagnosed diseases

Abstract-Hundreds of rare diseases are due to mutation on genes related to glycans synthesis, degradation or recognition. These glycan-related defects are well described in the literature but largely absent in ontologies and databases of chemical entities and phenotypes, limiting the application of computational methods and ontology-driven tools for characterization and discovery of glycan related diseases. We are curating articles and textbooks in glycobiology related to genetic diseases to inform the content and the structure of an ontology of Molecular GlycoPhenotypes (MGPO). MGPO will be applied toward use cases including disease diagnosis and disease gene candidate prioritization, using semantic similarity and pattern matching at the glycan level with glycomics data from patient of the Undiagnosed Diseases Network

Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery.

While abnormalities related to carbohydrates (glycans) are frequent for patients with rare and undiagnosed diseases as well as in many common diseases, these glycan-related phenotypes (glycophenotypes) are not well represented in knowledge bases (KBs). If glycan-related diseases were more robustly represented and curated with glycophenotypes, these could be used for molecular phenotyping to help to realize the goals of precision medicine. Diagnosis of rare diseases by computational cross-species comparison of genotype-phenotype data has been facilitated by leveraging ontological representations of clinical phenotypes, using Human Phenotype Ontology (HPO), and model organism ontologies such as Mammalian Phenotype Ontology (MP) in the context of the Monarch Initiative. In this article, we discuss the importance and complexity of glycobiology and review the structure of glycan-related content from existing KBs and biological ontologies. We show how semantically structuring knowledge about the annotation of glycophenotypes could enhance disease diagnosis, and propose a solution to integrate glycophenotypes and related diseases into the Unified Phenotype Ontology (uPheno), HPO, Monarch and other KBs. We encourage the community to practice good identifier hygiene for glycans in support of semantic analysis, and clinicians to add glycomics to their diagnostic analyses of rare diseases

Abstracts from the 50th European Society of Human Genetics Conference: Posters

International audienc

The European Hematology Association Roadmap for European Hematology Research: a consensus document

The European Hematology Association (EHA) Roadmap for European Hematology Research highlights major achievements in diagnosis and treatment of blood disorders and identifies the greatest unmet clinical and scientific needs in those areas to enable better funded, more focused European hematology research. Initiated by the EHA, around 300 experts contributed to the consensus document, which will help European policy makers, research funders, research organizations, researchers, and patient groups make better informed decisions on hematology research. It also aims to raise public awareness of the burden of blood disorders on European society, which purely in economic terms is estimated at €23 billion per year, a level of cost that is not matched in current European hematology research funding. In recent decades, hematology research has improved our fundamental understanding of the biology of blood disorders, and has improved diagnostics and treatments, sometimes in revolutionary ways. This progress highlights the potential of focused basic research programs such as this EHA Roadmap. The EHA Roadmap identifies nine ‘sections’ in hematology: normal hematopoiesis, malignant lymphoid and myeloid diseases, anemias and related diseases, platelet disorders, blood coagulation and hemostatic disorders, transfusion medicine, infections in hematology, and hematopoietic stem cell transplantation. These sections span 60 smaller groups of diseases or disorders. The EHA Roadmap identifies priorities and needs across the field of hematology, including those to develop targeted therapies based on genomic profiling and chemical biology, to eradicate minimal residual malignant disease, and to develop cellular immunotherapies, combination treatments, gene therapies, hematopoietic stem cell treatments, and treatments that are better tolerated by elderly patients

The European Hematology Association Roadmap for European Hematology Research. A Consensus Document

Abstract The European Hematology Association (EHA) Roadmap for European Hematology Research highlights major achievements in diagnosis and treatment of blood disorders and identifies the greatest unmet clinical and scientific needs in those areas to enable better funded, more focused European hematology research. Initiated by the EHA, around 300 experts contributed to the consensus document, which will help European policy makers, research funders, research organizations, researchers, and patient groups make better informed decisions on hematology research. It also aims to raise public awareness of the burden of blood disorders on European society, which purely in economic terms is estimated at Euro 23 billion per year, a level of cost that is not matched in current European hematology research funding. In recent decades, hematology research has improved our fundamental understanding of the biology of blood disorders, and has improved diagnostics and treatments, sometimes in revolutionary ways. This progress highlights the potential of focused basic research programs such as this EHA Roadmap. The EHA Roadmap identifies nine sections in hematology: normal hematopoiesis, malignant lymphoid and myeloid diseases, anemias and related diseases, platelet disorders, blood coagulation and hemostatic disorders, transfusion medicine, infections in hematology, and hematopoietic stem cell transplantation. These sections span 60 smaller groups of diseases or disorders. The EHA Roadmap identifies priorities and needs across the field of hematology, including those to develop targeted therapies based on genomic profiling and chemical biology, to eradicate minimal residual malignant disease, and to develop cellular immunotherapies, combination treatments, gene therapies, hematopoietic stem cell treatments, and treatments that are better tolerated by elderly patients. Received December 15, 2015. Accepted January 27, 2016. Copyright © 2016, Ferrata Storti Foundatio

Frameshift mutations at the C-terminus of HIST1H1E result in a specific DNA hypomethylation signature

BACKGROUND: We previously associated HIST1H1E mutations causing Rahman syndrome with a specific genome-wide methylation pattern. RESULTS: Methylome analysis from peripheral blood samples of six affected subjects led us to identify a specific hypomethylated profile. This "episignature" was enriched for genes involved in neuronal system development and function. A computational classifier yielded full sensitivity and specificity in detecting subjects with Rahman syndrome. Applying this model to a cohort of undiagnosed probands allowed us to reach diagnosis in one subject. CONCLUSIONS: We demonstrate an epigenetic signature in subjects with Rahman syndrome that can be used to reach molecular diagnosis

Cancer Biomarker Research and Personalized Medicine

Biomarkers are measures of a biological state. The treatment of individual patients based on particular factors, such as biomarkers, distinguishes standard, generalized treatment plans from personalized medicine. Even though personalized medicine is applicable to most branches of medicine, the field of oncology is perhaps where it is most easily employed. Cancer is a heterogeneous disease; although patients may be diagnosed histologically with the same cancer type, their tumors can comprise varying tumor microenvironments and molecular characteristics that can impact treatment response and prognosis. There has been a major drive over the past decade to try and realize personalized cancer medicine through the discovery and use of disease-specific biomarkers. This book, entitled “Cancer Biomarker Research and Personalized Medicine”, encompasses 22 publications from colleagues working on a diverse range of cancers, including prostate, breast, ovarian, head and neck, liver, gastric, bladder, colorectal, and kidney. The biomarkers assessed in these studies include genes, intracellular or secreted proteins, exosomes, DNA, RNA, miRNA, circulating tumor cells, circulating immune cells, in addition to radiomic features

Novel Concepts of Mycobacterial Evasion Mechanisms

Mycobacterium tuberculosis -bakteerin aiheuttama tuberkuloosi on tällä hetkellä maailman tappavin infektiotauti. Nykyinen tuberkuloosin antibioottihoito on useamman lääkkeen yhdistelmä ja se kestää useita kuukausia, mutta ei siitäkään huolimatta takaa onnistunutta mykobakteerin häätämistä. Tehottomien antibioottien käyttö sekä pitkät hoitoajat keskeytyksineen edesauttavat antibioottiresistenttien kantojen syntyä. Lisäksi turvallisen ja tehokkaan rokotteen puute tekee tuberkuloosin ehkäisemisestä hankalaa. Yksi syy näihin haasteisiin tuberkuloosin ehkäisemisessä ja hoidoissa on mykobakteerin kyky kehittää krooninen infektio ja suojella itseään ympäristöhaitoilta kuten aktiiviselta immuunivasteelta sekä antimikrobiaalisilta lääkkeiltä. Tämän tutkimuksen tavoitteena on tutkia mykobakteerin mekanismeja, joiden avulla se pystyy estämään antibioottien ja immuunivasteiden tehokkaan toiminnan, sekä etsiä uusia strategioita näihin mekanismeihin puuttumiseen. Mycobacterium marinum -bakteeria ja seeprakalaa käytettiin tutkimaan isännän ja patogeenin välistä vuorovaikutusta. Mykobakteeri kykenee aktiivisesti vaimentamaan immuunivasteita ja myöhästyttämään hankittujen immuunivasteiden alkamista. Tutkimuksessa testattiin immunomodulaation tehoa näiden mykobakteerin ominaisuuksien estämisessä. Ilman hoitoja noin 10 % aikuisista seeprakaloista pystyy luonnollisesti pitämään mykobakteerimäärän alle qPCR:n detektiorajan. Tätä osuutta voitiin kuitenkin nostaa 25 %:iin aktivoimalla immuunivaste lämpötapetulla Listeria monocytogenes -bakteerilla ennen mykobakteeri-infektiota. Aikaansaatu suojaava immuunivaste vähensi merkitsevästi mykobakteerimääriä mitattuna neljä viikkoa infektion jälkeen ja jopa steriloi mykobakteerin osasta populaatiota sekä villityypin kalassa että rag1-/- -mutanttikaloissa, mikä viittaa synnynnäisten immuunivasteiden tärkeään rooliin mykobakteerin steriloivassa vasteessa. Suojaavassa vasteessa mpeg1, tnf ja nos2b -geenien ilmentyminen oli merkitsevästi lisääntynyt, kun taas sod2 oli vähentynyt verrattuna kontrolliryhmään. Nämä tulokset viittaavat mykobakteerin häätämiseen infektion varhaisessa vaiheessa lisääntyneen tulehdusvasteen ja tehokkaamman mykobakteerin tuhoamisen avulla. Huomattavaa on, että immunolodulaatio lämpötapettua L. monocytogenes -bakteeria hyödyntäen ei saanut aikaan suojaavaa vastetta, jos infektio oli jo olemassa. Vastaavaa immuuniterapiaa voitaisiin kuitenkin käyttää ennaltaehkäisevänä menetelmänä korkean tuberkuloosi- ilmaantuvuuden alueilla. Toinen tutkittu mykobakteerin suojautumiskeino on biofilmin muodostaminen. Immuunivasteiden heikentämisen ja infektion aikaansaamisen jälkeen mykobakteeri muodostaa bakteeriyhteisöjä granuloomissa ja tuottaa solunulkoista matriksia, joka antaa bakteeripopulaatiolle tukea ja suojaa. Nopeakasvuista bioluminoivaa M. marinum -bakteeria käytettiin biofilmin kypsymisen ja koostumuksen tutkimuksessa in vitro. Tulokset osoittivat, että biofilmin kypsyminen ei muuttanut rifampisiinin MIC-arvoa (minimum inhibitory concentration), mutta nosti MBC-arvoa (minimum bactericidal concentration) 63-kertaisesti verrattuna planktoniseen yksisoluisena kasvavaan mykobakteeriin kahden päivän biofilmin kasvattamisen jälkeen. Toistuvilla antibioottialtistuksilla pystyttiin varmistamaan, että biofilmin lisääntynyt antibioottitoleranssi ei johtunut geneettisestä resistenssistä. Elävien mykobakteerien lukumäärää biofilmissä pystyttiin vähentämään hajottamalla solunulkoisen matriksin tärkeimpiä polymeerejä yhdessä rifampisiini-hoidon kanssa, mikä osoitti biofilmin matriksin tärkeyden antibioottitoleranssissa. Nopea bioluminesenssimittaukseen perustuva tappokäyräanalyysi validoitiin mittaamaan erityisesti persistoivien mykobakteerien alapopulaatiota. Analyysissa seurataan bakteeripopulaation tappokinetiikkaa korkealla antibioottikonsentraatiolla, ja voidaan mitata persisteribakteerien alapopulaatiota, joka kykenee sietämään antibioottia keskimääräistä pidemmän ajan. Tappokinetiikka oli merkitsevästi hitaampi yhden viikon ikäisellä M. marinum biofilmillä verrattuna planktoniseen yksisoluiseen kasvatukseen. Lisäksi rifampisiinin konsentraatio saturoitui 400 μg/ml:ssa, jonka jälkeen antibioottikonsentraation nostaminen ei nopeuttanut bakteerien tappoa. Tätä menetelmää on mahdollista käyttää seulomaan hoitoja, jotka vaikuttavat erityisesti persistoiviin soluihin. Lopuksi tutkittiin mykobakteerin biofilmin solunulkoisen matriksin proteiineihin, GroEL1 ja GroEL2, kohdentuvia sybodeja in vitro M. marinum ja M. tuberculosis biofilmeissä sekä ex vivo seeprakalan granuloomissa. Sybodit ovat synteettisiä vasta- aineen sitoutumisosaa matkivia molekyylejä, jonka sitoutumista voidaan helposti muokata ja seuloa halutun kohteen mukaan olemassa olevista sybody-kirjastoista. Seulonnasta saatujen potentiaalisten sybodien sitoutumista mykobakteerin biofilmiin arvioitiin konfokaalimikroskopian avulla. Fluoresenssileimatut anti-GroEL-sybodit tunnistivat GroEL-proteiineja biofilmin päältä sekä in vitro että ex vivo tehden sybodista houkuttelevan vaihtoehdon erilaisten molekyylien kohdentamisessa mykobakteerin biofilmeihin. Nykyisiä antibioottihoitoja voidaan mahdollisesti tehostaa ja hoitojen pituutta lyhentää ottamalla huomioon granuloomien sisällä biofilmeissä olevat mykobakteeripersisterit. Ymmärtämällä paremmin mykobakteerin menetelmiä, joilla se suojelee itseään ympäristön haittavaikutuksilta, tulevaisuuden hoitoja voidaan kohdentaa tehokkaammin Mycobacterium tuberculosis -bakteeria vastaan.Tuberculosis is caused by bacterium Mycobacterium tuberculosis, and it is currently the deadliest infectious disease worldwide. The standard antimicrobial regimen is a cocktail of antimicrobials taken for several months, which still does not guarantee a successful eradication of the bacteria. Treatment dropouts and the use of antimicrobials that are inefficient in eradicating the infection have led to emerged drug-resistance. Also, the lack of safe and effective vaccine makes the prevention of tuberculosis difficult. One reason for the challenges in both prevention and treatment of tuberculosis is the ability of mycobacterium to cause chronic infection and protect itself from environmental hazards such as active immune responses and antimicrobials. The aim of this study was to examine mycobacterial evasion mechanisms against antimicrobials and immune responses and propose new intervention strategies. Mycobacterium marinum and zebrafish were used to study the interaction of the host and the pathogen. Mycobacterium can actively suppress immune responses and delay the onset of adaptive responses, and to prevent this immune evasion, an immunomodulation was tested. In the adult zebrafish population, around 10% of the population is able to naturally retain the M. marinum load below the detection limit of qPCR. This proportion could be increased up to 25% by priming with heat- killed Listeria monocytogenes prior the mycobacterial infection. The induced protective immune response significantly reduced mycobacterial loads after four weeks of infection and induced clearance in both wildtype and rag1-/- mutant fish showing the important role of innate immune responses in the sterilizing response. The protective immune response was characterized with an increased expression of mpeg1, tnf and nos2b and decreased expression of sod2. These results indicate early clearance mediated via pro-inflammatory responses and enhanced killing of mycobacteria. Importantly, the immunomodulation was ineffective if the infection was already established. However, a similar approach could be used as a prophylactic treatment in high burden areas. Another mycobacterial evasion strategy is the formation of biofilms. After suppressing immune responses and establishing the infection, mycobacteria form bacterial communities in granulomas and produce extracellular matrix that gives structure and protection for the bacterial population. The fast-growing M. marinum with a bioluminescent cassette was used to study the biofilm maturation and composition in vitro. The results showed that the biofilm maturation did not alter the minimum inhibitory concentration (MIC) but increased minimum bactericidal concentration (MBC) 63 times compared to planktonic cells within two days of biofilm culturing. It was further confirmed with repeated antimicrobial exposures that the increased tolerance of biofilm cultures was not due to genetic resistance. Degrading any of the major extracellular matrix components in combination with rifampicin reduced the number of live bacteria in a biofilm, demonstrating the important role of the biofilm matrix in the antimicrobial tolerance. Time-kill curve analysis with a quick bioluminescence read-out was established to specifically measure the subpopulation of persister mycobacteria. In the analysis, the killing kinetics of a bacterial population was followed after the exposure to high concentration of a bactericidal antimicrobial, here rifampicin, to measure the persister subpopulation that can tolerate the drug for a prolonged time. For maturing M. marinum biofilm, the killing kinetics were significantly different after one week of culturing compared to planktonic cells, and the rifampicin concentration was saturated at 400 μg/ml after which increasing the antimicrobial concentration did not alter the killing kinetics. This method has a potential in screening for treatments that specifically target mycobacterial persisters. Finally, sybodies against biofilm extracellular matrix proteins GroEL1 and GroEL2 were used to specifically target M. marinum and M. tuberculosis biofilms in vitro and in ex vivo zebrafish granulomas. Sybodies are synthetic molecules mimicking the binding domain of antibodies. The binding properties of the sybodies can be easily modified and screened against the wanted target in sybody libraries. The potential sybodies acquired from the screens were assessed by confocal imaging. Fluorescence labelled anti-GroEL sybodies were able to bound GroEL on both in vitro and ex vivo biofilms making sybodies an attractive molecular carrier to target mycobacterial biofilms. A treatment that specifically targets mycobacterial persisters in biofilms inside granulomas could enhance the efficacy of antimicrobial therapy and shorten the current treatment time. By understanding better, the mycobacterial evasion mechanisms, future treatments can more effectively be targeted against Mtb