Orthologous proteins of experimental de- and remyelination are differentially regulated in the CSF proteome of multiple sclerosis subtypes

Nellie A Martin; Arkadiusz Nawrocki; Viktor Molnar; Maria L Elkjaer; Eva K Thygesen; Miklos Palkovits; Peter Acs; Tobias Sejbaek; Helle H Nielsen; Zoltan Hegedus; Finn Sellebjerg; Tihamer Molnar; Eudes G V Barbosa; Nicolas Alcaraz; Ferenc Gallyas Jr; Asa F Svenningsen; Jan Baumbach; Hans Lassmann; Martin R Larsen; Zsolt Illes

doi:10.1371/journal.pone.0202530

Orthologous proteins of experimental de- and remyelination are differentially regulated in the CSF proteome of multiple sclerosis subtypes

PLoS One. 2018 Aug 16;13(8):e0202530. doi: 10.1371/journal.pone.0202530. eCollection 2018.

Authors

Nellie A Martin¹, Arkadiusz Nawrocki^{1

2}, Viktor Molnar³, Maria L Elkjaer¹, Eva K Thygesen¹, Miklos Palkovits⁴, Peter Acs⁵, Tobias Sejbaek¹, Helle H Nielsen¹, Zoltan Hegedus⁶, Finn Sellebjerg⁷, Tihamer Molnar⁸, Eudes G V Barbosa⁹, Nicolas Alcaraz^{9

10}, Ferenc Gallyas Jr^{11

12

13}, Asa F Svenningsen¹⁴, Jan Baumbach⁹, Hans Lassmann¹⁵, Martin R Larsen², Zsolt Illes^{1

5

16}

Affiliations

¹ Department of Neurology, Odense University Hospital, Odense, Denmark.
² Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
³ Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary.
⁴ Laboratory of Neuromorphology and Human Brain Tissue Bank/Microdissection Laboratory, Semmelweis University, Budapest, Hungary.
⁵ Department of Neurology, University of Pecs, Pecs, Hungary.
⁶ Laboratory of Bioinformatics, Biological Research Centre, Szeged, Hungary.
⁷ Danish Multiple Sclerosis Center, Department of Neurology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.
⁸ Department of Anaesthesiology and Intensive Therapy, University of Pecs, Pecs, Hungary.
⁹ Computational Biology Group, Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark.
¹⁰ The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
¹¹ Department of Biochemistry and Medical Chemistry, University of Pecs, Pecs, Hungary.
¹² Szentagothai Research Centre, University of Pécs, Pécs, Hungary.
¹³ Nuclear-Mitochondrial Interactions Research Group, Hungarian Academy of Sciences, Budapest, Hungary.
¹⁴ Department of Neurobiology Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark.
¹⁵ Center for Brain Research, Medical University of Vienna, Vienna, Austria.
¹⁶ Department of Clinical Research, BRIDGE, University of Southern Denmark, Odense, Denmark.

Abstract

Objective: Here, we applied a multi-omics approach (i) to examine molecular pathways related to de- and remyelination in multiple sclerosis (MS) lesions; and (ii) to translate these findings to the CSF proteome in order to identify molecules that are differentially expressed among MS subtypes.

Methods: To relate differentially expressed genes in MS lesions to de- and remyelination, we compared transcriptome of MS lesions to transcriptome of cuprizone (CPZ)-induced de- and remyelination. Protein products of the overlapping orthologous genes were measured within the CSF by quantitative proteomics, parallel reaction monitoring (PRM). Differentially regulated proteins were correlated with molecular markers of inflammation by using MesoScale multiplex immunoassay. Expression kinetics of differentially regulated orthologous genes and proteins were examined in the CPZ model.

Results: In the demyelinated and remyelinated corpus callosum, we detected 1239 differentially expressed genes; 91 orthologues were also differentially expressed in MS lesions. Pathway analysis of these orthologues suggested that the TYROBP (DAP12)-TREM2 pathway, TNF-receptor 1, CYBA and the proteasome subunit PSMB9 were related to de- and remyelination. We designed 129 peptides representing 51 orthologous proteins, measured them by PRM in 97 individual CSF, and compared their levels between relapsing (n = 40) and progressive MS (n = 57). Four proteins were differentially regulated among relapsing and progressive MS: tyrosine protein kinase receptor UFO (UFO), TIMP-1, apolipoprotein C-II (APOC2), and beta-2-microglobulin (B2M). The orthologous genes/proteins in the mouse brain peaked during acute remyelination. UFO, TIMP-1 and B2M levels correlated inversely with inflammation in the CSF (IL-6, MCP-1/CCL2, TARC/CCL17). APOC2 showed positive correlation with IL-2, IL-16 and eotaxin-3/CCL26.

Conclusions: Pathology-based multi-omics identified four CSF markers that were differentially expressed in MS subtypes. Upregulated TIMP-1, UFO and B2M orthologues in relapsing MS were associated with reduced inflammation and reflected reparatory processes, in contrast to the upregulated orthologue APOC2 in progressive MS that reflected changes in lipid metabolism associated with increased inflammation.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Axl Receptor Tyrosine Kinase
Axons / metabolism
Cerebrospinal Fluid Proteins / genetics*
Corpus Callosum / metabolism
Corpus Callosum / pathology
Cuprizone / toxicity
Demyelinating Diseases / genetics
Disease Models, Animal
Gene Expression Regulation
Humans
Mice
Multiple Sclerosis / cerebrospinal fluid
Multiple Sclerosis / chemically induced
Multiple Sclerosis / genetics*
Myelin Sheath / genetics
Myelin Sheath / pathology
Proteome / genetics*
Proto-Oncogene Proteins / cerebrospinal fluid
Proto-Oncogene Proteins / genetics
Receptor Protein-Tyrosine Kinases / cerebrospinal fluid
Receptor Protein-Tyrosine Kinases / genetics
Remyelination / genetics*
Tissue Inhibitor of Metalloproteinase-1 / cerebrospinal fluid
Tissue Inhibitor of Metalloproteinase-1 / genetics

Substances

Cerebrospinal Fluid Proteins
Proteome
Proto-Oncogene Proteins
Tissue Inhibitor of Metalloproteinase-1
Cuprizone
Receptor Protein-Tyrosine Kinases
Axl Receptor Tyrosine Kinase

Grants and funding

The work was supported by Lundbeckfonden R118-A11472, OTKA-K77892, Scleroseforeningen R431-A29926-B15690 and R399-A28099-B15690, Region of Southern Denmark 14/24200, Jascha Fonden 5589, Direktør Ejnar Jonasson kaldet Johnsen og hustrus mindelegat 5609, Odense University Hospital (OUH) A474 (to ZI), OTKA-NN109841, GINOP 2.3.2-15-2016-00049, and GINOP 2.3.3-15-2016-00025 (to FG Jr), Fonden for Lægevidenskabensfremme 13-267 (to NAM). JB is grateful for financial support from JB's VILLUM Young Investigator grant nr. 13154. NA received funding from JB's SDU2020 grant. MP was supported by grant from KTIA_NAP_13-1-2013-0001. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.