Our research focus is on two common intestinal inflammatory diseases: celiac disease (CD) and inflammatory bowel disease (IBD) which both show abnormal immunological autoreactivity triggered by harmless environmental antigens: dietary gluten and gut normal flora, respectively. We focus on finding novel genetic, transcriptomic and cellular biomarkers for these diseases; on characterizing their function and role in disease (immuno)pathogenesis; and applying eventually the results in development of novel diagnostic and therapeutical methods. Our lab at University of Helsinki works actively with clinicians at University Hospitals of Helsinki and Tampere, and we are also affiliated members of the Celiac Disease Research Center at University of Tampere.

With our extensive DNA materials we have performed genome wide genotyping, exome and regulome sequencing studies on these diseases. In addition to further work on the recently found common risk gene variants in these genomic studies, another future goal of us is on finding novel rare but high-penetrance variants in dozens of multiply affected large pedigrees showing nearly Mendelian inheritance.

By utilizing the RNA-seq and T cell receptor deep sequencing methods on cells collected from gluten challenged CD patients and controls we also aim to characterize the T cell receptor repertoires, antigen specificities and T-cell phenotype plasticity in CD, as well as the poorly known gluten tolerance mechanisms of healthy individuals carrying the CD-associated HLA risk alleles. In IBD we profile the transcriptomes and genomic markers for better prediction of drug response to anti-TNFalpha therapies.

We use the powerful single cell RNAseq techniques such as Drop-seq to profile the transcriptomes of thousands of cells individually, and develop further the lymphocyte clonality analyses and microfluidics platforms for cell capturing. Single cell RNAseq services we offer together with Functional Genomics Unit (FuGU).

We also develop both Illumina and Oxford Nanopore based methods for HLA and KIR typing and allele specific expression level studies. These tools will be applied in autoimmunity, transplantation and histocompatibility research, in joint projects with our collaborators at Finnish Red Cross Blood Service.