A small proteomics-focused group evolved in 2002 as a part of the Laboratory of Biochemistry
and Molecular Biology of Germ Cells at the Institute of Animal Physiology and Genetics, Academy
of Sciences of the Czech Republic (IAPG AS CR) in Libechov. The initial focus on mammalian oocyte maturation and activation was later complemented by general reproductive biology [1–8]. Additionally, cancer research studies including the effects
and biochemical mechanisms of anti-cancer drugs and drug resistance in collaboration
with the Laboratory
of Experimental Medicine, Palacky Univesity
and University Hospital
in Olomouc
and with the Laboratory
of Molecular Structure Characterization, Institute of Microbiology AS CR
in Prague, facilitated
the establishment
of the Centre for Cancer Proteomics [9–14]. Recently, a collaboration with the group of Prof. Karel Smetana Jr. at the 1st Faculty
of Medicine, Charles University in Prague, has added another cancer research aspect of epithelial-mesenchymal cell communication [15, 16]. In 2006, exciting studies in the field of stem cell biology, namely differentiation of neural stem cells and neural precursor cells, have been initiated in co-operation
with the Laboratory of Prof. Martin Marsala at the Department of Anesthesiology, UCSD [17–21]. Coupled with the therapeutic potential of stem cells and their possible application in neurological
or neurodegenerative disorders [22], comprehensive proteome analyses of such cells now represents
the key interest of the Laboratory of Applied Proteome Analyses at IAPG AS CR. To monitor
the effects of such therapy, we plan to characterise animal models of spinal cord injury [22]
as well as a transgenic minipig model of Huntington’s disease recently established at our institute.

The greatest promise for the detection and treatment of diseases lies in the deep understanding
of molecular basis for disease initiation, progression and efficacious treatment allowing
the discovery of candidate biomarkers. Since proteins encoded by the genes were looked upon as ultimately the functional players that drive both physiology and disease pathophysiology, proteomic research
stands to offer exciting platforms for multidisciplinary research in very many disease areas.

Currently there are two main projects in the Laboratory of Applied Proteome Analyses:

1)Neural stem cell differentiation 

To facilitate transition towards therapeutic use, the aim
is comprehensive characterisation of neural differentiation at the level
of protein changes with focus on:

a) surface membrane proteins to select cells of desired phenotype

b) intracellular proteins as a readout for developmental stage

c) secreted proteins for modulation of stem cells niche

2)Huntington’s disease and neurodegeneration

The aim is uncovering the differences at protein level
which are linked to progressing Huntington’s disease
and neurodegeneration with focus on:

a) plasma and cerebrospinal fluid proteome alterations

b) immune response including complement system and cytokine analysis

The laboratory is equipped with a number of platforms including:

Mass spectrometers Sciex TripleTOF 5600+ and Sciex QTRAP 5500 coupled to Eksigent nanoLC 425

Luminex 200 Bead based instrument for multiplex immunoassays

BD FACS Aria cell sorter

Planar antibody microarrays

2D gel electrophoresis and 2D HPLC for protein fractionation

Leica SP5 confocal microscope

The facility is currently funded by:

• The National Sustainability Programme, project Models of the Serious Human Diseases: Traumatic Spinal Cord Injury, Huntington’s Disease, Melanoma and Infertility (LO1609; Czech Ministry of Education, Youth and Sports)
• Czech-Norwegian Research Programme (CZ09), project Comparative study of Huntington’s disease using biochemical, immunocytochemical and molecular genetic methods on the mouse, minipig and human  tissues and cells 
• GA ČR Mikroprostředí v maligním melanomu jako faktor nádorové agresivity (GACR 16-05534S)

Open Positions

Following positions have opened up in our group.

  Head od Laboratory of Applied Proteome Analysis

  Výběrové řízení na obsazení místa Postgraduálního studenta

  Výběrové řízení na pozici Analytik, operátor

Our lab is a member of the PhD program in biomedicine (Developmental and Cell Biology,http://pdsb.avcr.cz/index.html) and prospective students should contact directly Dr. Hana Kovarova ( ">).

Bachelor / Master projects focusing on biological or technological aspects of our research are available for motivated student at the Faculty of Science, Charles University in Prague.

Collaboration:

Prof. Martin Marsala, Department of Anesthesiology, University of California San Diego, CA, USA

Prof. Karel Smetana Jr., Institute of Anatomy, 1st Faculty of Medicine, Charles University, Prague

Prof. Paola Picotti, Institute of Biochemistry, ETH Zurich, Switzerland

Prof. Vladimir Havlicek, Laboratory of Molecular Structure Characterization,
Institute of Microbiology AS CR, Prague

           Prof. Jennifer Van Eyk, JHU-Bayview Proteomics Cente, Baltimore, MA, USA

[1]          Ellederova Z, Halada P, Man P, Kubelka M, Motlik J, Kovarova H. Protein patterns of pig oocytes during in vitro maturation. Biol Reprod 2004;71:1533–9.

[2]          Susor A, Ellederova Z, Jelinkova L, Halada P, Kavan D, Kubelka M, et al. Proteomic analysis of porcine oocytes during in vitro maturation reveals essential role for the ubiquitin C-terminal hydrolase-L1. Reprod Camb Engl 2007;134:559–68.

[3]          Ellederova Z, Kovarova H, Melo-Sterza F, Livingstone M, Tomek W, Kubelka M. Suppression of translation during in vitro maturation of pig oocytes despite enhanced formation of cap-binding protein complex eIF4F and 4E-BP1 hyperphosphorylation. Mol Reprod Dev 2006;73:68–76.

[4]          Ellederová Z, Cais O, Susor A, Uhlírová K, Kovárová H, Jelínková L, et al. ERK1/2 map kinase metabolic pathway is responsible for phosphorylation of translation initiation factor eIF4E during in vitro maturation of pig oocytes. Mol Reprod Dev 2008;75:309–17.

[5]          Pelech S, Jelinkova L, Susor A, Zhang H, Shi X, Pavlok A, et al. Antibody microarray analyses of signal transduction protein expression and phosphorylation during porcine oocyte maturation. J Proteome Res 2008;7:2860–71.

[6]          Jarkovska K, Martinkova J, Liskova L, Halada P, Moos J, Rezabek K, et al. Proteome mining of human follicular fluid reveals a crucial role of complement cascade and key biological pathways in women undergoing in vitro fertilization. J Proteome Res 2010;9:1289–301.

[7]          Jarkovska K, Kupcova Skalnikova H, Halada P, Hrabakova R, Moos J, Rezabek K, et al. Development of ovarian hyperstimulation syndrome: interrogation of key proteins and biological processes in human follicular fluid of women undergoing in vitro fertilization. Mol Hum Reprod 2011;17:679–92.

[8]          Gadher SJ, Jarkovska K, Kovarova H. Reproductive therapies and a need for potential biomarkers for prognostic and diagnostic screening of women desperate to conceive. Expert Rev Proteomics 2009;6:591–3.

[9]          Skalnikova H, Halada P, Dzubak P, Hajduch M, Kovarova H. Protein fingerprints of anti-cancer effects of cyclin-dependent kinase inhibition: identification of candidate biomarkers using 2-D liquid phase separation coupled to mass spectrometry. Technol Cancer Res Treat 2005;4:447–54.

 [10]       Kovarova H, Halada P, Man P, Dzubak P, Hajduch M. Application of proteomics in the search for novel proteins associated with the anti-cancer effect of the synthetic cyclin-dependent kinases inhibitor, bohemine. Technol Cancer Res Treat 2002;1:247–56.

[11]        Tyleckova J, Hrabakova R, Mairychova K, Halada P, Radova L, Dzubak P, et al. Cancer cell response to anthracyclines effects: mysteries of the hidden proteins associated with these drugs. Int J Mol Sci 2012;13:15536–64.

[12]        Martinkova J, Gadher SJ, Hajduch M, Kovarova H. Challenges in cancer research and multifaceted approaches for cancer biomarker quest. FEBS Lett 2009;583:1772–84.

[13]        Hrabakova R, Kollareddy M, Tyleckova J, Halada P, Hajduch M, Gadher SJ, et al. Cancer cell resistance to aurora kinase inhibitors: identification of novel targets for cancer therapy. J Proteome Res 2013;12:455–69.

[14]        Skalnikova H, Martinkova J, Hrabakova R, Halada P, Dziechciarkova M, Hajduch M, et al. Cancer drug-resistance and a look at specific proteins: Rho GDP-dissociation inhibitor 2, Y-box binding protein 1, and HSP70/90 organizing protein in proteomics clinical application. J Proteome Res 2011;10:404–15.

[15]        Kolar M, Szabo P, Dvorankova B, Lacina L, Gabius H-J, Strnad H, et al. Upregulation of IL-6, IL-8 and CXCL-1 production in dermal fibroblasts by normal/malignant epithelial cells in vitro: Immunohistochemical and transcriptomic analyses. Biol Cell Auspices Eur Cell Biol Organ 2012;104:738–51.

[16]        Jarkovska K, Dvorankova B, Halada P, Kodet O, Szabo P, Gadher SJ, Motlik J,Kovarova H, Smetana K Jr. Revelation of fibroblast protein commonalities and differences and their possible roles in wound healing and tumorigenesis using co-culture models of cells. Biol Cell. 2014 Apr 2. doi: 10.1111/boc.201400014. [Epub ahead of print] PubMed PMID: 24698078.

[17]        Vodicka P, Skalnikova H, Kovarova H. The characterization of stem cell proteomes. Curr Opin Mol Ther 2006;8:232–9.

[18]        Skalnikova H, Halada P, Vodicka P, Motlik J, Rehulka P, Hørning O, et al. A proteomic approach to studying the differentiation of neural stem cells. Proteomics 2007;7:1825–38.

[19]        Skalnikova H, Vodicka P, Pelech S, Motlik J, Gadher SJ, Kovarova H. Protein signaling pathways in differentiation of neural stem cells. Proteomics 2008;8:4547–59.

[20]        Skalnikova H, Vodicka P, Gadher SJ, Kovarova H. Proteomics of neural stem cells. Expert Rev Proteomics 2008;5:175–86.

[21]        Skalnikova H, Motlik J, Gadher SJ, Kovarova H. Mapping of the secretome of primary isolates of mammalian cells, stem cells and derived cell lines. Proteomics 2011;11:691–708.

[22]        Kupcova Skalnikova H, Navarro R, Marsala S, Hrabakova R, Vodicka P, Gadher SJ, et al. Signaling proteins in spinal parenchyma and dorsal root ganglion in rat with spinal injury-induced spasticity. J Proteomics 2013;91:41–57.

[23]        Tyleckova J, Valekova I, Zizkova M, Rakocyova M, Marsala S, Marsala M, Gadher SJ, Kovarova H. Surface N-glycoproteome patterns reveal key proteins of neuronal differentiation. J Proteomics 2016; 132:13-20.

[24]        Zizkova M, Sucha R, Tyleckova J, Jarkovska K, Mairychova K, Kotrcova E, Marsala M, Gadher SJ, Kovarova H. Proteome-wide analysis of neural stem cell differentiation to facilitate transition to cell replacement therapies. Expert Rev Proteomics 2015; 12(1):83-95.

[25]        Kotrcova E, Jarkovska K, Valekova I, Zizkova M, Motlik J, Gadher SJ,Kovarova H. Challenges of Huntington's disease and quest for therapeutic biomarkers. Proteomics Clin Appl 2015; 9(1-2):147-58.

[26]        Soste M, Hrabakova R, Wanka S, Melnik A, Boersema P, Maiolica A et al. A sentinel protein assay for simultaneously quantifying cellular processes. Nat Methods 2014; 11(10):1045-8.

[27]        Valekova I, Kupcova Skalnikova H, Jarkovska K, Motlik J, Kovarova H. Multiplex immunoassays for quantification of cytokines, growth factors, and other proteins in stem cell communication. Methods Mol Biol 2015; 1212:39-63.

[28]        Sheng S, Skalnikova H, Meng A, Tra J, Fu Q, Everett A, Van Eyk J. Intact protein separation by one- and two-dimensional liquid chromatography for the comparative proteomic separation of partitioned serum or plasma. Methods Mol Biol 2011; 728:29-46.

[29]        Kupcova Skalnikova H. Proteomic techniques for characterisation of mesenchymal stem cell secretome. Biochimie 2013; 95(12):2196-211.