Publications

Lamichhane S, Sen P, Dickens AM, Kråkström M, Ilonen J, Lempainen J, Hyöty H, Lahesmaa R, Veijola R, Toppari J, Hyötyläinen T, Knip M, Orešič M. Circulating metabolic signatures of rapid and slow progression to type 1 diabetes in islet autoantibody-positive children. Front Endocrinol (Lausanne). 2023 Sep 6;14:1211015. doi: 10.3389/fendo.2023.1211015. PMID: 37745723; PMCID: PMC10516565.

Sen P, Orešič M. Integrating Omics Data in Genome-Scale Metabolic Modeling: A Methodological Perspective for Precision Medicine. Metabolites. 2023 Jul 18;13(7):855. doi: 10.3390/metabo13070855. PMID: 37512562; PMCID: PMC10383060.

Salihovic S, Lamichane S, Hyötyläinen T, Orešič M. Recent advances towards mass spectrometry-based clinical lipidomics. Curr Opin Chem Biol. 2023 Oct;76:102370. doi: 10.1016/j.cbpa.2023.102370. Epub 2023 Jul 18. PMID: 37473482.

Lamichhane S, Härkönen T, Vatanen T, Hyötyläinen T, Knip M, Orešič M. Impact of exposure to per- and polyfluoroalkyl substances on fecal microbiota composition in mother-infant dyads. Environ Int. 2023 Jun;176:107965. doi: 10.1016/j.envint.2023.107965. Epub 2023 May 11. PMID: 37210808.

Andreu-Sánchez S, Bourgonje AR, Vogl T, Kurilshikov A, Leviatan S, Ruiz-Moreno AJ, Hu S, Sinha T, Vich Vila A, Klompus S, Kalka IN, de Leeuw K, Arends S, Jonkers I, Withoff S; Lifelines Cohort Study; Brouwer E, Weinberger A, Wijmenga C, Segal E, Weersma RK, Fu J, Zhernakova A. Phage display sequencing reveals that genetic, environmental, and intrinsic factors influence variation of human antibody epitope repertoire. Immunity. 2023 Jun 13;56(6):1376-1392.e8. doi: 10.1016/j.immuni.2023.04.003. Epub 2023 May 9. PMID: 37164013.

Bourgonje AR, Andreu-Sánchez S, Vogl T, Hu S, Vich Vila A, Gacesa R, Leviatan S, Kurilshikov A, Klompus S, Kalka IN, van Dullemen HM, Weinberger A, Visschedijk MC, Festen EAM, Faber KN, Wijmenga C, Dijkstra G, Segal E, Fu J, Zhernakova A, Weersma RK. Phage-display immunoprecipitation sequencing of the antibody epitope repertoire in inflammatory bowel disease reveals distinct antibody signatures. Immunity. 2023 Jun 13;56(6):1393-1409.e6. doi: 10.1016/j.immuni.2023.04.017. Epub 2023 May 9. PMID: 37164015.

Koren O, Konnikova L, Brodin P, Mysorekar IU, Collado MC. The maternal gut microbiome in pregnancy: implications for the developing immune system. Nat Rev Gastroenterol Hepatol. 2023 Dec 14. doi: 10.1038/s41575-023-00864-2. Epub ahead of print. PMID: 38097774.

Zhernakova DV, Wang D, Liu L, Andreu-Sánchez S, Zhang Y, Ruiz-Moreno AJ, Peng H, Plomp N, Del Castillo-Izquierdo Á, Gacesa R, Lopera-Maya EA, Temba GS, Kullaya VI, van Leeuwen SS; Lifelines Cohort Study; Xavier RJ, de Mast Q, Joosten LAB, Riksen NP, Rutten JHW, Netea MG, Sanna S, Wijmenga C, Weersma RK, Zhernakova A, Harmsen HJM, Fu J. Host genetic regulation of human gut microbial structural variation. Nature. 2024 Jan 3. doi: 10.1038/s41586-023-06893-w. Epub ahead of print. PMID: 38172637.

Hyötyläinen T, McGlinchey A, Salihovic S, Schubert A, Douglas A, Hay DC, O’Shaughnessy PJ, Iredale JP, Shaw S, Fowler PA, Orešič M. In utero exposures to perfluoroalkyl substances and the human fetal liver metabolome in Scotland: a cross-sectional study. Lancet Planet Health. 2024 Jan;8(1):e5-e17. doi: 10.1016/S2542-5196(23)00257-7. PMID: 38199723.

Bruzzaniti S, Piemonte E, Bruzzese D, Lepore MT, Strollo R, Izzo L, Di Candia F, Franzese A, Bifulco M, Mozzillo E, Ludvigsson J, Matarese G, Galgani M. Progression of type 1 diabetes is associated with high levels of soluble PD-1 in islet autoantibody-positive children. Diabetologia. 2024 Jan 12. doi: 10.1007/s00125-023-06075-3. Epub ahead of print. PMID: 38214712.

Fernández-Pato A, Sinha T, Gacesa R, Andreu-Sánchez S, Gois MFB, Gelderloos-Arends J, Jansen DBH, Kruk M, Jaeger M, Joosten LAB, Netea MG, Weersma RK, Wijmenga C, Harmsen HJM, Fu J, Zhernakova A, Kurilshikov A. Choice of DNA extraction method affects stool microbiome recovery and subsequent phenotypic association analyses. Sci Rep. 2024 Feb 16;14(1):3911. doi: 10.1038/s41598-024-54353-w. PMID: 38366085; PMCID: PMC10873414.

Ahrens AP, Hyötyläinen T, Petrone JR, Igelström K, George CD, Garrett TJ, Orešič M, Triplett EW, Ludvigsson J. Infant microbes and metabolites point to childhood neurodevelopmental disorders. Cell. 2024 Apr 11;187(8):1853-1873.e15. doi: 10.1016/j.cell.2024.02.035. Epub 2024 Apr 3. PMID: 38574728.

Bernabeu M, Cabello-Yeves E, Flores E, Samarra A, Kimberley Summers J, Marina A, Collado MC. Role of vertical and horizontal microbial transmission of antimicrobial resistance genes in early life: insights from maternal-infant dyads. Curr Opin Microbiol. 2024 Feb;77:102424. doi: 10.1016/j.mib.2023.102424. Epub 2024 Jan 17. PMID: 38237429.

Garmaeva S, Sinha T, Gulyaeva A, Kuzub N, Spreckels JE, Andreu-Sánchez S, Gacesa R, Vich Vila A, Brushett S, Kruk M; Lifelines NEXT cohort study; Dekens J, Sikkema J, Kuipers F, Shkoporov AN, Hill C, Scherjon S, Wijmenga C, Fu J, Kurilshikov A, Zhernakova A. Transmission and dynamics of mother-infant gut viruses during pregnancy and early life. Nat Commun. 2024 Mar 2;15(1):1945. doi: 10.1038/s41467-024-45257-4. PMID: 38431663; PMCID: PMC10908809.

Vochteloo M, Deelen P, Vink B; BIOS Consortium; Tsai EA, Runz H, Andreu-Sánchez S, Fu J, Zhernakova A, Westra HJ, Franke L. PICALO: principal interaction component analysis for the identification of discrete technical, cell-type, and environmental factors that mediate eQTLs. Genome Biol. 2024 Jan 22;25(1):29. doi: 10.1186/s13059-023-03151-0. PMID: 38254182; PMCID: PMC10802033.

Isokääntä H, Pinto da Silva L, Karu N, Kallonen T, Aatsinki AK, Hankemeier T, Schimmel L, Diaz E, Hyötyläinen T, Dorrestein PC, Knight R, Orešič M, Kaddurah-Daouk R, Dickens AM, Lamichhane S. Comparative Metabolomics and Microbiome Analysis of Ethanol versus OMNImet/gene•GUT Fecal Stabilization. Anal Chem. 2024 Jun 4;96(22):8893-8904. doi: 10.1021/acs.analchem.3c04436. Epub 2024 May 23. PMID: 38782403; PMCID: PMC11154662.

Abbadessa G, Lepore MT, Bruzzaniti S, Piemonte E, Miele G, Signoriello E, Perna F, De Falco C, Lus G, Matarese G, Bonavita S, Galgani M. Ocrelizumab Alters Cytotoxic Lymphocyte Function While Reducing EBV-Specific CD8+ T-Cell Proliferation in Patients With Multiple Sclerosis. Neurol Neuroimmunol Neuroinflamm. 2024 Jul;11(4):e200250. doi: 10.1212/NXI.0000000000200250. Epub 2024 Apr 25. PMID: 38662990; PMCID: PMC11087045.

Mandile R, Lerro F, Carpinelli M, D’Antonio L, Greco L, Troncone R, Auricchio R. Potential Celiac Disease in Children: Health Status on A Long-Term Gluten-Containing Diet. Nutrients. 2024; 16(11):1708. doi: 10.3390/nu16111708

Karthikeyan BS, Hyötyläinen T, Ghaffarzadegan T, Triplett E, Orešič M, Ludvigsson J. Prenatal exposure to environmental contaminants and cord serum metabolite profiles in future immune-mediated diseases. J Expo Sci Environ Epidemiol (2024). doi: 10.1038/s41370-024-00680-z

Cruells A, Cabrera-Rubio R, Bustamante M, Pelegrí D, Cirach M, Jimenez-Arenas P, Samarra A, Martínez-Costa C, Collado MC, Gascon M. The influence of pre- and postnatal exposure to air pollution and green spaces on infant’s gut microbiota: Results from the MAMI birth cohort study. Environ Res. 2024 Jun 1;257:119283. doi: 10.1016/j.envres.2024.119283. Epub ahead of print. PMID: 38830395.