Stefanie Prast-Nielsen
Senior Research Specialist
| Docent
E-mail: stefanie.prast-nielsen@ki.se
Visiting address: Solnavägen 9, Biomedicum A8, 17165 Solna
Postal address: C1 Mikrobiologi, tumör- och cellbiologi, C1 CTMR Engstrand Bioinformatics, 171 77 Stockholm
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
-
Journal article: CELL REPORTS. 2023;42(12):113570
-
Article: JOURNAL OF CROHNS & COLITIS. 2023;17(3):418-432
-
Article: JOURNAL OF DERMATOLOGICAL SCIENCE. 2022;106(3):132-140
-
Article: ALLERGY. 2022;77(5):1486-1498
-
Article: INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES. 2021;111:313-321
-
Article: BMC PULMONARY MEDICINE. 2019;19(1):211
-
Article: NATURE COMMUNICATIONS. 2019;10(1):4703
-
Article: BRITISH JOURNAL OF DERMATOLOGY. 2019;181(3):572-579
-
Article: NPJ BIOFILMS AND MICROBIOMES. 2019;5(1):5
-
Article: FREE RADICAL BIOLOGY AND MEDICINE. 2011;50(9):1114-1123
-
Article: FREE RADICAL BIOLOGY AND MEDICINE. 2010;49(11):1765-1778
-
Article: FREE RADICAL BIOLOGY AND MEDICINE. 2009;47(11):1661-1671
-
Article: JOURNAL OF MEDICINAL CHEMISTRY. 2009;52(20):6474-6483
-
Article: PLOS ONE. 2008;3(4):e1846
-
Article: JOURNAL OF BIOLOGICAL CHEMISTRY. 2006;281(9):5593-5603
-
Article: BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS. 2005;327(3):774-779
All other publications
-
Letter: AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE. 2022;206(12):1564-1567
-
Review: PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY. 2020;176:141-178
-
Review: EBIOMEDICINE. 2019;44:741-746
-
Review: BIOCHIMICA ET BIOPHYSICA ACTA: INTERNATIONAL JOURNAL OF BIOCHEMISTRY AND BIOPHYSICS. 2011;1810(12):1262-1271
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