Group Saavalainen

Immunomics

We focus on finding novel genetic, transcriptomic microbiomic and cellular biomarkers for diseases such as celiac disease and inflammatory bowel disease, and on characterizing their function and role in disease pathogenesis, and applying eventually the results in development of novel diagnostic and therapeutic methods.

Chronic intestinal inflammations such as celiac disease (CD) and inflammatory bowel disease (IBD) show abnormal immunological autoreactivity triggered by harmless environmental antigens: dietary gluten and gut normal flora, respectively. We focus on finding novel genetic, transcriptomic microbiomic and cellular biomarkers for these diseases, on characterizing their function and role in disease pathogenesis, and applying eventually the results in development of novel diagnostic and therapeutic methods.

With our extensive case-control and family based DNA collections we have performed genome wide genotyping, exome and regulome sequencing studies on these diseases. By utilizing the bulk and single cell RNA-seq and T cell receptor sequencing methods on cells collected from gluten challenged CD patients and controls we study the T cell receptor repertoires, antigen specificities and T-cell phenotype plasticity in CD. In IBD we profile the transcriptomes and genomic markers for better prediction of drug response to anti-TNFalpha therapies. With systematic micro- and mycobiota sequencing we have also found bacterial and fungal species predicting the treatment response. Also in various collaborative projects on other autoimmunities such as Type 1 diabetes and narcolepsy, as well as ovarian cancer, we apply our expertize on single cell, immunorepertoire, HLA and KIR sequencing.

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Senior Scientists

Heli Pessa, PhD

Katarzyna Leskinen, PhD

Graduate Students

Tiira Johansson, MSc

Pinja Elomaa, MSc

Rebecka Ventin-Holmberg, MSc

Samineh Barmaki, MSc

Enhanced influenza A H1N1 T cell epitope recognition and cross-reactivity to protein-O-mannosyltransferase 1 in Pandemrix-associated narcolepsy type 1.
Vuorela A, Freitag TL, Leskinen K, Pessa H, Härkönen T, Stracenski I, Kirjavainen T, Olsen P, Saarenpää-Heikkilä O, Ilonen J, Knip M, Vaheri A, Partinen M, Saavalainen P, Meri S, Vaarala O. Nature Communications. 2021. 

Clustering based approach for population level identification of condition-associated T-cell receptor β-chain CDR3 sequences. 
Yohannes DA, Kaukinen K, Kurppa K, Saavalainen P, Greco D. BMC Bioinformatics. 2021. 

Targeted RNA-Based Oxford Nanopore Sequencing for Typing 12 Classical HLA Genes. 
Johansson T, Koskela S, Yohannes DA, Partanen J, Saavalainen P. Frontiers in Genetics. 2021.

HLA RNA Sequencing With Unique Molecular Identifiers Reveals High Allele-Specific Variability in mRNA Expression.
Johansson T, Yohannes DA, Koskela S, Partanen J, Saavalainen P.  Frontiers in Immunology. 2021. 

Effects of In Vivo Gluten Challenge on PBMC Gene Expression Profiles in Diet Treated Celiac Disease.
Yohannes DA, de Kauwe A, Kaukinen K, Kurppa K, Mäki M, Anderson RP, Linnarsson S, Greco D, Saavalainen P.  Frontiers in Immunology. 2020.

Bacterial and Fungal Profiles as Markers of Infliximab Drug Response in Inflammatory Bowel Disease. 
Ventin-Holmberg R, Eberl A, Saqib S, Korpela K, Virtanen S, Sipponen T, Salonen A, Saavalainen P, Nissilä E. J Crohns Colitis. 2021.

The psoriasis risk allele HLA-Cw*06:02 shows evidence of association with chronic or recurrent streptococcal tonsillitis.
Haapasalo K, Koskinen LLE, Suvilehto J, Jousilahti P, Wolin A, Suomela S, Trembath R, Barker J, Vuopio J, Kere J, Jokiranta S, Saavalainen P. Infection and Immunity. 2018. 

Deep sequencing of blood and gut T-cell receptor β-chains reveals gluten-induced immune signatures in celiac disease. 
Yohannes DA, Freitag TL, de Kauwe A, Kaukinen K, Kurppa K, Wacklin P, Mäki M, Arstila TP, Anderson RP, Greco D, Saavalainen P. Scientific Reports. 2017. 

A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis. 
Rivas MA, Graham D, Sulem P, Stevens C, Desch AN, Goyette P, Gudbjartsson D, Jonsdottir I, Thorsteinsdottir U, Degenhardt F, Mucha S, Kurki MI, Li D, D'Amato M, Annese V, Vermeire S, Weersma RK, Halfvarson J, Paavola-Sakki P, Lappalainen M, Lek M, Cummings B, Tukiainen T, Haritunians T, Halme L, Koskinen LL, Ananthakrishnan AN, Luo Y, Heap GA, Visschedijk MC; UK IBD Genetics Consortium; NIDDK IBD Genetics Consortium, MacArthur DG, Neale BM, Ahmad T, Anderson CA, Brant SR, Duerr RH, Silverberg MS, Cho JH, Palotie A, Saavalainen P, Kontula K, Färkkilä M, McGovern DP, Franke A, Stefansson K, Rioux JD, Xavier RJ, Daly MJ, Barrett J, de Lane K, Edwards C, Hart A, Hawkey C, Jostins L, Kennedy N, Lamb C, Lee J, Lees C, Mansfield J, Mathew C, Mowatt C, Newman B, Nimmo E, Parkes M, Pollard M, Prescott N, Randall J, Rice D, Satsangi J, Simmons A, Tremelling M, Uhlig H, Wilson D, Abraham C, Achkar JP, Bitton A, Boucher G, Croitoru K, Fleshner P, Glas J, Kugathasan S, Limbergen JV, Milgrom R, Proctor D, Regueiro M, Schumm PL, Sharma Y, Stempak JM, Targan SR, Wang MH. Nature Communications. 2016.

Multiple common variants for celiac disease influencing immune gene expression.
Dubois P,  Trynka G, Franke L, Hunt K, Romanos J, Curtotti A, Zhernakova A, Heap G, Adany R, Aromaa A, Bardella M, van den Berg, L, Bockett N, de la Concha E, Dema B, Fehrmann R, Fernandez-Arquero M, Fiatal S, Grandone E, Green P, Groen H, Gwilliam R, Houwen R, Hunt S, Kaukinen K, Kelleher D, Korponay-Szabo I, Kurppa K, MacMathuna P, Mäki M, Mazzilli M, McCann P, Mearin M, Mein C, Mirza M, Mistry V, Mora B, Morley K, Mulder C, Murray J, Nunez C, Oosterom E, Ophoff R, Polanco I, Peltonen L, Platteel M, Rybak A, Salomaa V, Schweizer J, Sperandeo M, Tack G, Turner G, Veldink J, Verbeek W, Weersma R, Wolters V, Urcelay E, Cukrowska B, Greco L, Neuhausen S, McManus R, Barisani D, Deloukas P, Barrett J,  Saavalainen P, Wijmenga C, van Heel D.  Nature Genetics. 2010.

Celiac Disease Research Center, University of Tampere: Katri Kaukinen, Katri Lindfors, Kalle Kurppa, Teea Salmi, Markku Mäki

Inflammatory Bowel Disease Research Group, University of Helsinki and HUS: Taina Sipponen, Anja Eberl, Martti Färkkilä

Ovarian cancer research: Seppo Meri, Sampsa Hautaniemi, University of Helsinki

Folkhälsan Research Foundation

Academy of Finland

Business Finland

Sigrid Jusélius Foundation

Contact

    • Päivi Saavalainen

      PhD, Docent, Group leader

    • Tel:
      +358-50-4487487

    • Contact