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
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. Enhanced influenza A H1N1 T cell epitope recognition and cross-reactivity to protein-O-mannosyltransferase 1 in Pandemrix-associated narcolepsy type 1. Nat Commun. 2021 Apr 16;12(1):2283. doi: 10.1038/s41467-021-22637-8. PMID: 33863907; PMCID: PMC8052463.
Yohannes DA, Kaukinen K, Kurppa K, Saavalainen P, Greco D. Clustering based approach for population level identification of condition-associated T-cell receptor β-chain CDR3 sequences. BMC Bioinformatics. 2021 Mar 25;22(1):159. doi: 10.1186/s12859-021-04087-7. PMID: 33765908; PMCID: PMC7993519.
Johansson T, Koskela S, Yohannes DA, Partanen J, Saavalainen P. Targeted RNA-Based Oxford Nanopore Sequencing for Typing 12 Classical HLA Genes. Front Genet. 2021 Mar 4;12:635601. doi: 10.3389/fgene.2021.635601. PMID: 33763116; PMCID: PMC7982845.
Johansson T, Yohannes DA, Koskela S, Partanen J, Saavalainen P. HLA RNA Sequencing With Unique Molecular Identifiers Reveals High Allele-Specific Variability in mRNA Expression. Front Immunol. 2021 Feb 25;12:629059. doi: 10.3389/fimmu.2021.629059. PMID: 33717155; PMCID: PMC7949471.
Yohannes DA, de Kauwe A, Kaukinen K, Kurppa K, Mäki M, Anderson RP, Linnarsson S, Greco D, Saavalainen P. Effects of In Vivo Gluten Challenge on PBMC Gene Expression Profiles in Diet Treated Celiac Disease. Front Immunol. 2020 Dec 11;11:594243. doi: 10.3389/fimmu.2020.594243. PMID: 33362776; PMCID: PMC7759501.
Ventin-Holmberg R, Eberl A, Saqib S, Korpela K, Virtanen S, Sipponen T, Salonen A, Saavalainen P, Nissilä E. Bacterial and Fungal Profiles as Markers of Infliximab Drug Response in Inflammatory Bowel Disease. J Crohns Colitis. 2021 Jun 22;15(6):1019-1031. doi: 10.1093/ecco-jcc/jjaa252. PMID: 33300552.
Haapasalo K, Koskinen LLE, Suvilehto J, Jousilahti P, Wolin A, Suomela S, Trembath R, Barker J, Vuopio J, Kere J, Jokiranta S and Saavalainen P. The psoriasis risk allele HLA-Cw*06:02 shows evidence of association with chronic or recurrent streptococcal tonsillitis. Infect Immun. 2018 Sep 21;86(10)
Yohannes DA, Freitag TL, de Kauwe A, Kaukinen K, Kurppa K, Wacklin P, Mäki M, Arstila TP, Anderson RP, Greco D, Saavalainen P. Deep sequencing of blood and gut T-cell receptor β-chains reveals gluten-induced immune signatures in celiac disease. Sci Rep. 2017 Dec 21;7(1):17977
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. A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis. Nat Commun 7:12342, 2016
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. Multiple common variants for celiac disease influencing immune gene expression. Nat Genet 42:295-302, 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
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Päivi Saavalainen
PhD, Docent, Group leader
Tel:
+358-50-4487487-
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