Projects / Programmes
Molecular genetic biomarkers and mechanisms of unresponsiveness to biological therapy
anti-TNF in patients with chronic immune diseases
| Code |
Science |
Field |
Subfield |
| 3.01.00 |
Medical sciences |
Microbiology and immunology |
|
| Code |
Science |
Field |
| B220 |
Biomedical sciences |
Genetics, cytogenetics |
| Code |
Science |
Field |
| 3.01 |
Medical and Health Sciences |
Basic medicine |
genetics, phramacogenomics, chronic immune diseases, biological drugs, complex diseases
Researchers (33)
Organisations (5)
Abstract
The proinflammatory cytokine tumour necrosis factor-α (TNF) plays a dominant role in pathogenesis of chronic immune diseases, including rheumatoid arthritis (RA) and inflammatory bowel disease (IBD), which includes Crohn's disease (CD) and ulcerative colitis (UC). Biological drugs capable of blocking it, i.e. etanercept (ETN), infliximab (IFX) and adalimumab (ADA), became leading treatment of several autoimmune conditions including RA and CD in most severe cases. However, from 30%-50% (long-term response) of severe CD and RA cases do not respond to anti-TNF therapy. The causes of this non-response are poorly understood. Clinical predictors and serological biomarkers were associated with anti-TNF response but are not accurate enough for use in clinical practise. Recently, pharmacogenetics and pharmacogenomic studies proved that single nucleotide polymorphisms (SNPs) and gene expression profiles measured before treatment could predict anti-TNF treatment response. Our group discovered that genes in the autophagy pathway, including ATG16L1 and ATG5, are associated with ADA response in CD patients. For efficient pharmacogenomic studies in anti-TNF therapy, a good insight into the genetic architecture of chronic immune diseases is essential. Together with our partners at the International Inflammatory Bowel Disease Genetics Consortium (IIBDGC) we recently performed a Genome Wide Association Study (GWAs) using specialized custom designed genotyping microarray Immunochip (iCHIP) in 75,000 IBD patients and controls. We discovered 163 IBD associated loci, providing the best description of genetic architecture of IBD and related chronic immune diseases so far (Nature, 2012;491(7422):119-24) and discover most important disease causing genes (Nature, 2017; 547(7662):173-178))
The aim of our proposed study is to describe the molecular mechanisms contributing to the anti-TNF therapy nonresponse in patients with CD and RA, and to identify molecular genetic markers that could predict anti-TNF response. These could be used for personalized/precision medicine. Integration of genetic (NGS, genotyping), gene expression (RNAseq), proteomic, epigenetic (DNA modifications) and gene regulation (noncoding RNA profiling, splice variants) data with bioinformatic tools (gene ontology- GO) will ensure identification and description of biological pathways important in anti-TNF treatment response.
Our study is fully feasible, as we have already developed a comprehensive biobank that includes one of the world's largest collections of combined DNA/RNA/protein samples for chronic immune diseases (600 IBD, 300 RA). Part of our biobank represent RNA samples from the subgroup of CD patients that are refractory to standard treatment, collected before and during ADA treatment (weeks 4, 12, 20, 30). Our biobank is unique worldwide and thus holds excellent promise for providing new discoveries. In addition, we also have accurate clinical data of the treatment response, as measured by the IBDQ index and CRP for IBD patients and DAS28 index for RA patients. Our biobank will enable gene expression profiling in patients with the severe form of disease receiving biological therapy and monitoring of the changes in these profiles during anti-TNF therapy in non-responders.
Together, our studies will give a deep insight into molecular biological pathways important for disease progression, recovery and developing resistance to anti-TNF therapy. Interesting new findings are expected from the comparison between gene expression profiles obtained from patients on anti-TNF therapy representing TNF inhibition in vivo and RNA samples obtained from treated cell cultures and cell lines, representing inhibition in vitro. According to our and other preliminary studies, autophagy and Toll-like receptors (TLRs) signalling, seem to be the best candidate molecular pathways associated with anti-TNF treatment response and will be initially the focus of our molecular pathway functional studies.
Significance for science
Original scientific contribution is ensured:
As the first complete transcriptome analysis using NGS (RNA-seq) before and during anti-TNF treatment, this study will provide new expression profiles that will efficiently predict treatment outcomes in CD and RA as part of personalized therapy. Expression profiles, combined with genetic biomarker analyses, proteomics, epigenetic studies and non-coding regulatory RNA profiling will be used to identify potential new biomarkers of response to anti-TNF drugs. Patients could suffer from less adverse side effects if therapy is personalized based on molecular and genetic biomarkers.
Interesting new findings are expected from the comparison between gene expression profiles obtained from patients on anti-TNF therapy representing TNF inhibition in vivo and RNA samples obtained from treated cell cultures and cell lines, representing inhibition in vitro. This comparison will help to distinguish gene expression regulation that is caused primarily by inhibition of TNF (in vitro study) from the regulation that is caused in vivo by other more complex (multiple) downstream patterns. Furthermore, in vitro analyses will enable detailed elucidation of molecular pathways that are implicated in the responsiveness of IBD patients to anti-TNF treatment.
The progress beyond the state-of-the-art and scientific impact is ensured:
Identification of biological and signalling pathways that change during anti-TNF treatment in responders but do not show the same trend in non-responders will provide new molecular targets that will enhance development of novel biological drugs.
Identification of new parameters with clinical importance (e.g. transcript variants, SNPs) will facilitate functional studies and development of biomarkers and predictive models for precision medicine. Personalized therapy represents an optimal approach to treatment: as precisely fitted therapy can be applied from the beginning of treatment, patients could suffer from less adverse side effects and overall treatment costs can be reduced.
Obtained results will expose and outline new research areas. For example, mapping of functional regulatory polymorphisms will help better understand mechanisms of gene expression regulation. Elucidating the genes and proteins affected by SNPs will help understand biological pathways involved in disease pathogenesis and identify molecular targets for new biological drugs.
Results of this project will enhance development of biological drugs. Prof. Potočnik´s group is member of consortium that has already developed project “Isolation procedures in modern production of biological drugs”, and consist of partners from industry, Brinox .d.o.o., Labena d.o.o., EVG. d.o.o., Cleangrad d.o.o. and research institutions Faculty of Medicine, UM, Institute Jožef Stefan and Faculty for Pharmacy, UL. The consortium contract has already been signed, for a total of: 2,1 milion eur; MF UM: 230, 000, 00 eur.
Significance for the country
Original scientific contribution is ensured:
As the first complete transcriptome analysis using NGS (RNA-seq) before and during anti-TNF treatment, this study will provide new expression profiles that will efficiently predict treatment outcomes in CD and RA as part of personalized therapy. Expression profiles, combined with genetic biomarker analyses, proteomics, epigenetic studies and non-coding regulatory RNA profiling will be used to identify potential new biomarkers of response to anti-TNF drugs. Patients could suffer from less adverse side effects if therapy is personalized based on molecular and genetic biomarkers.
Interesting new findings are expected from the comparison between gene expression profiles obtained from patients on anti-TNF therapy representing TNF inhibition in vivo and RNA samples obtained from treated cell cultures and cell lines, representing inhibition in vitro. This comparison will help to distinguish gene expression regulation that is caused primarily by inhibition of TNF (in vitro study) from the regulation that is caused in vivo by other more complex (multiple) downstream patterns. Furthermore, in vitro analyses will enable detailed elucidation of molecular pathways that are implicated in the responsiveness of IBD patients to anti-TNF treatment.
The progress beyond the state-of-the-art and scientific impact is ensured:
Identification of biological and signalling pathways that change during anti-TNF treatment in responders but do not show the same trend in non-responders will provide new molecular targets that will enhance development of novel biological drugs.
Identification of new parameters with clinical importance (e.g. transcript variants, SNPs) will facilitate functional studies and development of biomarkers and predictive models for precision medicine. Personalized therapy represents an optimal approach to treatment: as precisely fitted therapy can be applied from the beginning of treatment, patients could suffer from less adverse side effects and overall treatment costs can be reduced.
Obtained results will expose and outline new research areas. For example, mapping of functional regulatory polymorphisms will help better understand mechanisms of gene expression regulation. Elucidating the genes and proteins affected by SNPs will help understand biological pathways involved in disease pathogenesis and identify molecular targets for new biological drugs.
Results of this project will enhance development of biological drugs. Prof. Potočnik´s group is member of consortium that has already developed project “Isolation procedures in modern production of biological drugs”, and consist of partners from industry, Brinox .d.o.o., Labena d.o.o., EVG. d.o.o., Cleangrad d.o.o. and research institutions Faculty of Medicine, UM, Institute Jožef Stefan and Faculty for Pharmacy, UL. The consortium contract has already been signed, for a total of: 2,1 milion eur; MF UM: 230, 000, 00 eur.
Most important scientific results
Interim report
Most important socioeconomically and culturally relevant results
