Stefanie Prast-Nielsen

Stefanie Prast-Nielsen

Senior Research Specialist | Docent
Visiting address: Solnavägen 9, Biomedicum A8, 17165 Solna
Postal address: C1 Mikrobiologi, tumör- och cellbiologi, C1 CTMR Engstrand Bioinformatics, 171 77 Stockholm
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About me

  • Senior Research Specialist in Multiomics, Machine Learning and Data
    Integration at the Centre for Translational Microbiome Research
    PhD in Medical Biochemistry
    I am a Senior Research Specialist in Multiomics, Machine Learning and Data
    Integration at the Centre for Translational Microbiome Research (CTMR), MTC,
    Karolinska Institutet.
    I have a PhD in Medical Biochemistry from the Department of Medical
    Biochemistry and Biophysics (MBB), Karolinska Institutet and spent several
    years as a Postdoc in Bioinformatics at both the Department of Cell and
    Molecular Biology (CMB) and Karolinska University Hospital. I joined the
    Centre for Translational Microbiome Research in 2017 where my main research
    activities focus on the gut microbiota in various diseases with emphasis on
    dietary interventions and the microbiota-gut-brain axis.
    I have several years of work experience in next generation sequencing and
    bioinformatics analysis using LINUX/UNIX, R, Python, Biostatistics, Machine
    Learning and Multiomics Data Integration. I also have experience as Principal
    Investigator and Team Lead.
    *2005-2009 Ph.D.: Medical Biochemistry*
    /Karolinska Institutet, Stockholm, Sweden
  • Department of Medical Biochemistry
    and Biophysics, Division of Biochemistry/
    Dissertation: "Exploring Thioredoxin Reductase as [1]an Anticancer Drug
    Target [2]"
    *1998-2004 Diploma/Master of Science: Human Biology*
    /Ernst Moritz Arndt University, Greifswald, Germany/
    Graduated summa cum laude
    Majored in Pharmacology/Toxicology
    Minored in Biochemistry/Molecular Biology &
  • Microbiology/Virology
    [1] https://pdfs.semanticscholar.org/6ae0/4664de6c4bee1d53f52b0fcb1c6b09ec7412.pdf
    [2] https://pdfs.semanticscholar.org/6ae0/4664de6c4bee1d53f52b0fcb1c6b09ec7412.pdf

Research

  • At CTMR I am involved in projects dissecting the taxonomic and functional
    changes in the intestinal microbiota in various cohorts. My current projects
    *combine metagenomics with other -omics data such as metabolomics and
    proteomics.* I use *machine learning *algorithms to detect health or disease
    associated signals in big data. My main focus is a cohort of children with
    severe, drug-resistant *epilepsy* that are treated with the ketogenic diet.
    Epilepsy is the most common chronic neurological disorder characterized by
    recurrent, unprovoked seizures. Here, we analyze how the intestinal
    microbiota composition and function changes after three months of treatment
    using whole metagenomic sequencing. Combining this data with inflammation
    proteomics, we have here identified specific signatures of gut microbes and
    the immune system. Our findings may guide novel microbiota-targeted
    treatment strategies for epilepsy.
    In addition, I have been involved in studies of the gut microbiota in
    *pediatric and adult IBD, autism, heart disease* and *antibiotic eradication
    of Helicobacter pylori infections*, as well as studies involving the *upper
    respiratory tract *and* skin microbiota*.
    /Funding/
    Swedish Brain Foundation, Margarethahemmet Society, Sunnerdahls
    Handikappfond, Jerringfonden, Linnea &
  • Josef Carlssons Foundation,
    Karolinska Institutets Research Funds
    */List of publications/*
    *Peer-reviewed articles*
    Nyström N, *Prast-Nielsen S*, Correia M, Globisch D, Engstrand L, Schuppe
    Koistinen I, Halfvarson J. Mucosal and plasma metabolomes in new-onset
    paediatric inflammatory bowel disease: correlations with disease
    characteristics and plasma inflammation protein markers, /Journal of Crohn's
    and Colitis/, 2022
  • , jjac149, https://doi.org/10.1093/ecco-jcc/jjac149 [1],
    PMID: 36219554 [2]
    Nannapaneni P, Sundh J, * Prast-Nielsen S*, Rhedin S, Örtqvist Å, Naucler P,
    Henriques-Normark B. Metatranscriptomics of nasopharyngeal microbiota and
    host distinguish between pneumonia and health. /Am J Respir Crit Care Med/.
    PMID: 35947760 [3], doi: 10.1164/rccm.202203-0463LE (2022)
    Dahlin M, Singleton SS, David JA, Basuchoudhary A, Wickström R, Mazumder R,
    *Prast-Nielsen S*. Higher levels of Bifidobacteria and tumour necrosis factor
    in children with drug-resistant epilepsy are associated with anti-seizure
    response to the ketogenic diet. /EBioMedicine/ 80:104061 PMID: 35598439 [4]
    (2022)
    Oláh P, Szlávicz E, Kuchner M, Nemmer J, Zeeuwen P, Lefèvre-Utile
    A, Fyhrquist N, *Prast-Nielsen S*, Skoog T, Serra A, Rodríguez E, Raap
    U, Meller S, Gyulai R, Hupé P, Kere J, Levi-Schaffer F, Tsoka
    S, Alexander H, Nestle FO, Schröder JM, Weidinger S, van den Bogaard
    E, Soumelis V, Greco D, Barker J, Lauerma A, Ranki A, Andersson
    B, Alenius H, Homey B. Influence of FLG loss-of-function mutations in
    host-microbe interactions during atopic skin inflammation. /J Dermatol Sci/.
    DOI: 10.1016/j.jdermsci.2022.04.007, PMID: 35537882 [5] (2022)
    Lefèvre-Utile A, Saichi M, Oláh P, Delord M, Homey B, Soumelis V
  • MAARS
    consortium (including *Prast-Nielsen S*). Transcriptome‐based
    identification of novel endotypes in adult atopic dermatitis. /Allergy/
    DOI: 10.1111/all.15150 [6] (2021)
    Shi W, Hu Y, Zhu N, Xia F, Wu M, Hu Y, *Prast-Nielsen S*, Xu B. Alterations
    of gut microbiota in patients with active pulmonary tuberculosis in China: A
    pilot study. /International Journal of Infectious Diseases
    /https://doi.org/10.1016/j.ijid.2021.08.064 [7] (2021)
    Hopson LM, Singleton SS, David JA, Basuchoudhary A, *Prast-Nielsen S*, Klein
    P, Senac S, Mazumder R. Chapter Five - Bioinformatics and machine learning in
    gastrointestinal microbiome research and clinical application. /Progress in
    Molecular Biology and Translational Science/ (2020) [8]
    Lindefeldt M, Eng A, Darban H, Bjerkner A, Zetterström C, Allander T,
    Andersson B, Borenstein E, Dahlin M, *Prast-Nielsen S*. The ketogenic diet
    influences taxonomic and functional composition of the gut microbiota in
    children with severe epilepsy. /Nature Biofilms and Microbiomes/ [9].
    Jan
  • 5(1):5 (2019)
    Dahlin M and *Prast-Nielsen S*. The Gut Microbiome and Epilepsy.
    /EBioMedicine/ [10] 2019 Jun
  • 44:741-746. doi: 10.1016/j.ebiom.2019.05.024.
    Epub May 31 (2019).
    Fyhrquist N*, Muirhead G*, *Prast-Nielsen S**, Jeanmougin M, Skoog T,
    Jules-Clement G, Feld M, Barrientos-Somarribas M, Pennino D, Suomela S,
    Tessas I, Lybeck E, Baran AM, Darban H, Singh Gangwar R, Gerstel U, Jahn K,
    Karisola P, Yan L, Hansmann B, Katayama S, Meller S, Bylesjö M, Hupé P,
    Levi-Schaffer F, Greco D, Ranki A, Schröder JM, Barker J, Kere J, Tsoka S,
    Lauerma A, Soumelis V, Nestle FO, Homey B, Andersson B, Alenius H.
    Microbe-host interplay in atopic dermatitis and psoriasis. /Nature
    communications/ [11], 10(1), 4703 (2019).**shared first authorship*
    *Prast-Nielsen S*, Tobin AM, Adamzik K, Powles A, Hugerth LW, Sweeney CM,
    Kirby B, Engstrand L, Fry L. Investigation of the Skin Microbiome: Swabs vs
    Biopsies. /Br J Dermatology/ [12]. DOI: 10.1111/bjd.17691, PMID: 30693476
    (Jan 2019)
    *Prast-Nielsen S**, McNicholl AG*, O’Morain C, Megraud F, J Machado JC,
    Alarcon T, Leja M, Gasbarrini A, Andersen LP, Engstrand L† and Gisbert
    JP†. On behalf of the European Helicobacter and Microbiota Study Group
    (EHMSG
  • www.helicobacter.org). Comparison of the impact of Helicobacter
    pylori eradication treatment with bismuth and non-bismuth quadruple regimens
    on the gut microbiota. /Microb Health Dis/ [13]/ /(2019)
  • 1: e145 **Both
    authors equally contributed as first authors*, †Both authors equally
    contributed as senior authors
    Shi W, Hu Y, Zheng X, Ning Z, Wu M, Xia F, *Prast-Nielsen S*, Hu Y, Xu B.
    Longitudinal profiling of gut microbiome among tuberculosis patients under
    anti-tuberculosis treatment in China: protocol of a prospective cohort study.
    /BMC Pulm Med/ [14] 19, 211 (2019) doi:10.1186/s12890-019-0981-9
    *Prast-Nielsen S*, Huang HH, Williams DL. Thioredoxin glutathione reductase:
    Its role in redox biology and potential as a target for drugs against
    neglected diseases. [15] Biochim Biophys Acta. [16] Dec
  • 1810(12):1262-71
    (2011)
    *Prast-Nielsen S*, Dexheimer T, Schultz L, Stafford WC, Cheng Q, Xu J, Jadhav
    A, Arnér ESJ, Simeonov A. Inhibition of Thioredoxin Reductase by
    Porphyrins and Other Small Molecules Identified by a High Throughput
    Screening Assay./ /Free Radic Biol Med. [17] May 1
  • 50(9):1114-23 (2011)
    *Prast-Nielsen S, * Cebula M, Pader I, Arnér ES. Noble metal targeting of
    thioredoxin reductase - covalent complexes with thioredoxin and
    thioredoxin-related protein of 14 kDa triggered by cisplatin. [18] Free Radic
    Biol Med. 49(11) [19]:1765-78 (2010)
    Eriksson SE, *Prast-Nielsen S*, Flaberg E, Szekely L, Arnér ESJ. High levels
    of thioredoxin reductase 1 modulate drug-specific cytotoxic efficacy. Free
    Radic Biol Med. 47(11) [20]:1661-71 (2009)
    Rai G, Sayed AA, Lea W, Luecke H, Chakrapani H, * Prast-Nielsen S*, Jadhav A,
    Leister W, Shen M, Inglese J, Austin CP, Keefer L, Arnér ESJ, Simeonov A,
    Maloney DJ, Williams DL, Thomas CJ. Structure-Mechanism Insights and the Role
    of Nitric Oxide Donation Guide the Development of Oxadiazole-2-Oxides as
    Therapeutic Agents against Schistosomiasis. J Med Chem. 52(20) [21]:6474-83
    (2009)
    Anestål K, *Prast-Nielsen S*, Cenas N, Arnér ES. Cell Death by SecTRAPs:
    Thioredoxin Reductase as a Prooxidant Killer of Cells. PLoS ONE. 3(4)
    [22]:e1846 (2008)
    Cenas N1, *Prast S1*, Nivinskas H, Sarlauskas J, Arner ES. Interactions of
    nitroaromatic compounds with the mammalian selenoprotein thioredoxin
    reductase and the relation to induction of apoptosis in human cancer cells. J
    Biol Chem. 281 [23], 5593-603 (2006) */1/**/shared first authorship/*
    Enoksson M, Fernandes A, *Prast S*, Lillig C.H, Holmgren A, Orrenius S.
    Overexpression of glutaredoxin 2 attenuates apoptosis by preventing
    cytochrome /c/ release. Biochem Biophys Res Commun. 327 [24], 774-9 (2005)
    *List of general articles and book chapters*
    Hopson LM, Singleton SS, David JA, Basuchoudhary A, *Prast-Nielsen S*, Klein
    P, Senac S, Mazumder R. Chapter Five - Bioinformatics and machine learning in
    gastrointestinal microbiome research and clinical application. /Progress in
    Molecular Biology and Translational Science/ [25] (2020)
    *Prast-Nielsen S* and Cryan JF. The Microbiota-Gut-Brain Axis in Epilepsy.
    Book chapter in section 3 on Neurobiology of Epilepsies of the third edition
    of /Epilepsy: A Comprehensive Textbook/, Wolters Kluwer (in Press)
    *Review articles (Peer-reviewed)*
    Dahlin M and *Prast-Nielsen S*. The gut microbiome and epilepsy,
    /EBioMedicine/ [26], https://doi.org/10.1016/j.ebiom.2019.05.024 (2019)
    *Prast-Nielsen S*, Huang HH, Williams DL. Thioredoxin glutathione reductase:
    Its role in redox biology and potential as a target for drugs against
    neglected diseases. [27] /Biochim Biophys Acta/. [28] Dec
  • 1810(12):1262-71
    (2011)
    [1] https://doi.org/10.1093/ecco-jcc/jjac149
    [2] https://pubmed.ncbi.nlm.nih.gov/36219554/
    [3] https://pubmed.ncbi.nlm.nih.gov/35947760/
    [4] https://pubmed.ncbi.nlm.nih.gov/35598439/
    [5] https://pubmed.ncbi.nlm.nih.gov/35537882/
    [6] https://onlinelibrary.wiley.com/doi/10.1111/all.15150
    [7] https://doi.org/10.1016/j.ijid.2021.08.064
    [8] https://doi.org/10.1016/bs.pmbts.2020.08.011
    [9] https://www.nature.com/articles/s41522-018-0073-2
    [10] https://www.ebiomedicine.com/article/S2352-3964(19)30325-1/fulltext
    [11] https://www.nature.com/articles/s41467-019-12253-y
    [12] https://onlinelibrary.wiley.com/doi/abs/10.1111/bjd.17691
    [13] https://www.microbiotajournal.com/2019/11/12/comparison-of-the-impact-of-helicobacter-pylori-eradication-treatment-with-bismuth-and-non-bismuth-quadruple-regimens-on-the-gut-microbiota/
    [14] https://bmcpulmmed.biomedcentral.com/articles/10.1186/s12890-019-0981-9
    [15] http://www.ncbi.nlm.nih.gov/pubmed/21782895
    [16] http://www.ncbi.nlm.nih.gov/pubmed/21782895
    [17] http://www.ncbi.nlm.nih.gov/pubmed/21262347
    [18] http://www.ncbi.nlm.nih.gov/pubmed/20851179
    [19] http://www.ncbi.nlm.nih.gov/pubmed/20851179
    [20] http://www.ncbi.nlm.nih.gov/pubmed/19766715
    [21] http://www.ncbi.nlm.nih.gov/pubmed/19761212
    [22] http://www.ncbi.nlm.nih.gov/pubmed/18382651
    [23] http://www.ncbi.nlm.nih.gov/pubmed/16354662
    [24] http://www.ncbi.nlm.nih.gov/pubmed/15649413
    [25] https://doi.org/10.1016/bs.pmbts.2020.08.011
    [26] https://www.ebiomedicine.com/article/S2352-3964(19)30325-1/fulltext
    [27] http://www.ncbi.nlm.nih.gov/pubmed/21782895
    [28] http://www.ncbi.nlm.nih.gov/pubmed/21782895

Teaching

  • I am co-organizer of the PhD course “Biomedical Ecology - The microbiota
    in health and disease (course 2861)”
    I have previously taught seminars in Biochemistry for the Medical and
    Biomedical Program at KI (2005-2010) and I currently lecture in the following
    courses:
    “Biomedical Ecology - The microbiota in health and disease” (PhD level)
    "DSM2 (Den sjuka människan 2/Disease and Illness 2)" (Medical Program)
    “Cellular and Molecular Infection” (Bachelor Program)
    “Infection and immunity” (Bachelor Program)

Articles

All other publications

Employments

  • Senior Research Specialist, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 2023-

Degrees and Education

  • Docent, Karolinska Institutet, 2023
  • Degree Of Doctor Of Philosophy, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 2009

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