Power of proteomics and progress in precision medicine - 13th central and eastern European proteomic conference (CEEPC), Ustron, Poland.

INTRODUCTION: Central and Eastern European Proteomic Conference (CEEPC) provides a platform for researchers to discuss multi-disciplinary integrated approaches to address a range of challenges from present day viral pandemic to on-going progress in Precision Medicine. CEEPC brings together various multi-omics entwined with novel enabling technologies, thus facilitating conceptual advances from cell to society for the benefit of mankind. AREAS COVERED: Proteomic methodologies, databases and software has revolutionized our ability to assess protein interactions and cellular changes, allowing the establishment of biological connections and identification of important cellular regulatory proteins and pathways previously unknown or not fully understood. Additionally, Mass spectrometry (MS) remains a major driving force in the field of 'multi-omics' and a powerful technology for the structural characterization of biomolecules and for analysis of proteins and small molecules such as lipids, sugars and metabolites. Combination of measurements from proteomics, genomics, epigenomics, transcriptomics and metabolomics, present a powerful decision-making format allowing deeper interpretation of a disease scenario in Precision medicine. EXPERT COMMENTARY: Precision Medicine offers novel and promising ways to identify and treat a wide range of diseases. The future success of these therapies will be underpinned by novel proteo-genomic approaches linked to sophisticated databases to evaluate and predict drug-patient interactions.

Driving Precision Medicine through Proteomics and Metabolomics - 12th Central and Eastern European Proteomic Conference (CEEPC), Bucharest, Romania.

As Romanians prepared to celebrate 100 years of the ''Great Unification of 1918'' which united all provinces into one Romania, the 12th Central and Eastern European Proteomic Conference (CEEPC) jointly with the 39th Anniversary of the Institute of Cellular Biology and Pathology ''N. Simionescu'' (ICBP-NS), held their inaugural meeting at the Romanian Academy in Bucharest - a national forum of highest scientific recognition. With an exciting theme entitled, 'Advances in Proteomics and Progress in Precision Medicine', delegates gathered to debate Precision medicine's revolution in diagnosis and treatment, which now accounts for predictive, preventative, and targeted treatment strategies with informed decisions according to individual's unique clinical, molecular and genetic profile. Proteomics has a pivotal role to play in furthering precision health and medicine for the benefit of mankind. To this end, CEEPC continues to drive advances in proteomics, metabolomics, and diseases as well as raising awareness of pressing global humanitarian and health-care issues including mental health diseases, aging, chronic diseases, global epidemics and environmental issues. Today, CEEPC is a well-recognized major annual conference with a focused vision and a highly valued ideology as it continues to propagate scientific, medical and proteomic collaborations whilst expanding as more Eastern European countries prepare to join.

A decade of proteomics accomplished! Central and Eastern European Proteomic Conference (CEEPC) celebrates its 10th Anniversary in Budapest, Hungary.

The Central and Eastern European Proteomic Conference (CEEPC) proudly celebrated its 10th Anniversary with an exciting scientific program inclusive of proteome, proteomics and systems biology in Budapest, Hungary. Since 2007, CEEPC has represented 'state-of the-art' proteomics in and around Central and Eastern Europe and these series of conferences have become a well-recognized event in the proteomic calendar. Fresher challenges and global healthcare issues such as ageing and chronic diseases are driving clinical and scientific research towards regenerative, reparative and personalized medicine. To this end, proteomics may enable diverse intertwining research fields to reach their end goals. CEEPC will endeavor to facilitate these goals.

A decade of Central and Eastern European Proteomic Conference (CEEPC): Credibility, cohesion and vision for the next decade.

The Central and Eastern European Proteomic Conference (CEEPC), has reached a special milestone as it celebrates its 10th anniversary. Today, an expansive network of proteomics in Central and Eastern Europe stands established to facilitate scientific interactions and collaborations in and around Central and Eastern Europe, as well as with international research institutions worldwide. Currently, when many conferences are struggling to attract participants, CEEPC is thriving in its status and stature as well as expanding by attracting newer member countries. CEEPC's success is driven by mutual respect between scientists sharing interest in proteomics and its applications in multidisciplinary research areas related to biological systems. This effort when interwoven with exciting ambience steeped with culture, and tradition is also a reason why participants enjoy it. CEEPC's careful balance between excellence and cohesion holds the key to its success. It is evident that CEEPC is ready for the next decade of excitement and expectations of multifaceted proteomics in Central and Eastern Europe. Additionally, in the era of emerging personalized medicine where treatment selection for each patient is becoming individualized, CEEPC and proteomics is expected to play a significant role moving forward for the benefit of mankind.

Revelation of the IFNα, IL-10, IL-8 and IL-1ß as promising biomarkers reflecting immuno-pathological mechanisms in porcine Huntington's disease model.

Studies on Huntington's disease (HD) demonstrated altered immune response in HD gene carriers. Using multiplexing immunoassay, we simultaneously investigated seven cytokines in secretomes of microglia and blood monocytes, cerebrospinal fluid (CSF) and serum collected from transgenic HD minipigs at pre-symptomatic disease stage. Decline in IFNα and IL-10 was observed in CSF and secretome of microglia whilst elevated IL-8 and IL-1ß levels were secreted by microglia. Additionally, IL-8 was increased in serum. The proportion of mutant huntingtin in microglia may have causative impact on cytokine production. IFNα, IL-10, IL-8 and IL-1ß represent promising biomarkers reflecting immuno-pathological mechanisms in porcine HD model.

Proteomic landscape in Central and Eastern Europe: the 9th Central and Eastern European Proteomic Conference, Poznan, Poland.

Every year since 2007, the Central and Eastern European Proteomic Conference (CEEPC) has excelled in representing state-of-the-art proteomics in and around Central and Eastern Europe, and linking it to international institutions worldwide. Its mission remains to contribute to all approaches of proteomics including traditional and often-revisited methodologies as well as the latest technological achievements in clinical, quantitative and structural proteomics with a view to systems biology of a variety of processes. The 9th CEEPC was held from June 15th to 18th, 2015, at the Institute of Bioorganic Chemistry, Polish Academy of Sciences in Poznan, Poland. The scientific program stimulated exchange of proteomic knowledge whilst the spectacular venue of the conference allowed participants to enjoy the cobblestoned historical city of Poznan.

Surface N-glycoproteome patterns reveal key proteins of neuronal differentiation.

Pluripotent stem cell-derived committed neural precursors are an important source of cells to treat neurodegenerative diseases including spinal cord injury. There remains an urgency to identify markers for monitoring of neural progenitor specificity, estimation of neural fate and follow-up correlation with therapeutic effect in preclinical studies using animal disease models. Cell surface capture technology was used to uncover the cell surface exposed N-glycoproteome of neural precursor cells upon neuronal differentiation as well as post-mitotic mature hNT neurons. The data presented depict an extensive study of surfaceome during neuronal differentiation, confirming glycosylation at a particular predicted site of many of the identified proteins. Quantitative changes detected in cell surface protein levels reveal a set of proteins that highlight the complexity of the neuronal differentiation process. Several of these proteins including the cell adhesion molecules ICAM1, CHL1, and astrotactin1 as well as LAMP1 were validated by SRM. Combination of immunofluorescence staining of ICAM1 and flow cytometry indicated a possible direction for future scrutiny of such proteins as targets for enrichment of the neuronal subpopulation from mixed cultures after differentiation of neural precursor cells. These surface proteins hold an important key for development of safe strategies in cell-replacement therapies of neuronal disorders. BIOLOGICAL SIGNIFICANCE: Neural stem and/or precursor cells have a great potential for cell-replacement therapies of neuronal diseases. Availability of well characterised and expandable neural cell lineage specific populations is critical for addressing such a challenge. In our study we identified and relatively quantified several hundred surface N-glycoproteins in the course of neuronal differentiation. We further confirmed the abundant changes for several cell adhesion proteins by SRM and outlined a strategy for utilisation of such N-glycoproteins in antibody based cell sorting. The comprehensive dataset presented here demonstrates the molecular background of neuronal differentiation highly useful for development of new plasma membrane markers to identify and select neuronal subpopulation from mixed neural cell cultures.

Challenges of Huntington's disease and quest for therapeutic biomarkers.

Huntington's disease (HD) is the most common inherited neurodegenerative disorder among polyglutamine (polyQ) diseases caused by cytosine-adenine-guanine repeat expansion in exon 1 of the huntingtin gene whose translation results in polyQ stretch in the N-terminus of the huntingtin protein (HD protein). This mutation significantly affects huntingtin conformation, proteolysis, PTMs, as well as its ability to bind interacting proteins. As a consequence, a variety of cellular mechanisms such as transcription, mitochondrial energy metabolism, axonal transport, neuronal vulnerability to oxidative stress, neurotransmission, and immune response are altered and involved in the pathogenesis of HD. Promising candidate molecular biomarkers of HD have emerged from proteomic studies. Recent analyses focused on HD protein itself, its PTM, and interacting proteins, which are of great importance for disease course. Furthermore, brain, body fluids, and immune system are intensively studied in order to search for additional proteins with a view to their use as a biomarker(s) or set of biomarkers in clinical trials in HD translational research.

Proteome-wide analysis of neural stem cell differentiation to facilitate transition to cell replacement therapies.

Neurodegenerative diseases are devastating disorders and the demands on their treatment are set to rise in connection with higher disease incidence. Knowledge of the spatiotemporal profile of cellular protein expression during neural differentiation and definition of a set of markers highly specific for targeted neural populations is a key challenge. Intracellular proteins may be utilized as a readout for follow-up transplantation and cell surface proteins may facilitate isolation of the cell subpopulations, while secreted proteins could help unravel intercellular communication and immunomodulation. This review summarizes the potential of proteomics in revealing molecular mechanisms underlying neural differentiation of stem cells and presents novel candidate proteins of neural subpopulations, where understanding of their functionality may accelerate transition to cell replacement therapies.

Tremendous progress in proteomics and metabolomics in Central and Eastern Europe.

The ever expanding Central and Eastern European Proteomic Conference (CEEPC) hosted its 8th annual meeting in Vienna, Austria, in July 2014 with resounding success, highlights of which are shared in this report. Tremendous progress in proteomics over the past decade in Central and Eastern Europe continues to rapidly accelerate due to networking across borders as well as access to sophisticated technologies. As the popularity of targeted proteomics in pathogenesis grows to unravel the complexities, so does the use of advanced analytical instrumentation. In addition, development of more sensitive research methodologies and a massive integration of technologies now give optimism to gain better understanding of the structure, functions and isoforms of various proteins as well as their complex interactions in biological systems. This, together with the confidence to qualitatively and/or quantitatively interrogate proteins of interest has led to promising developments for the identification of potential new drug targets for the treatment of various diseases.

Proteomics without boundaries across Central and Eastern Europe.

The 7th Central and Eastern European Proteomic Conference (CEEPC), considered as the bedrock of proteomics in Central and Eastern Europe, was held on 13­16 October 2013 at the Max Planck Institute for Chemical Ecology in Jena, Germany. Established in 2007, CEEPC now represents a cradle of proteomic interactions in and around Central and Eastern Europe, without limitations of borders and linking it to international institutions worldwide. Its mission remains to contribute to all approaches of proteomics including clinical, quantitative and structural proteomics and with a view to identifying potential targets for therapeutic interventions. The 7th CEEPC excelled at stimulating exchange of proteomic knowledge and imbibing local hospitality offered by Jena with its limestone hills and exotic charm.

Revelation of fibroblast protein commonalities and differences and their possible roles in wound healing and tumourigenesis using co-culture models of cells.

BACKGROUND INFORMATION: The in vitro co-culture models of communication between normal fibroblasts and epithelial cells, such as keratinocytes or squamous cell carcinoma cells of FaDu line representing wound healing or cancer development, were established by non-direct contact between the cells and utilised in this study to examine epithelia-induced changes in overall fibroblast proteome patterns. RESULTS: We were able to select the proteins co-regulated in both models in order to evaluate possible molecular commonalities between wound healing and tumour development. Amongst the most pronounced were the proteins implemented in contractile activity and formation of actin cytoskeleton such as caldesmon, calponin-2, myosin regulatory light-chain 12A and cofilin-1, which were expressed independently of the presence of α-smooth muscle actin. Additionally, proteins altered differently highlighted functional and cellular phenotypes during transition of fibroblasts towards myofibroblasts or cancer-associated fibroblasts. Results showed coordinated regulation of cytoskeleton proteins selective for wound healing which were lost in tumourigenesis model. Vimentin bridged this group of proteins with other regulated proteins in human fibroblasts involved in protein or RNA processing and metabolic regulation. CONCLUSIONS: The findings provide strong support for crucial role of stromal microenvironment in wound healing and tumourigenesis. In particular, epithelia-induced protein changes in fibroblasts offer new potential targets which may lead to novel tailored cancer therapeutic strategies.

Signaling proteins in spinal parenchyma and dorsal root ganglion in rat with spinal injury-induced spasticity.

Development of progressive muscle spasticity resulting from spinal traumatic injury can be mediated by loss of local segmental inhibition and/or by an increased sensory afferent drive with resulting exacerbated α-motoneuron activity. To identify potential contributions of neuroactive substances in the development of such spasticity state, we employed a well-defined spinal injury-evoked spasticity rat model. Signaling molecules were analyzed in the spinal parenchyma below the level of spinal injury and in the corresponding dorsal root ganglion cells using Kinex™ antibody microarrays. The results uncovered the involvement of angiogenesis and neurodegeneration pathways together with direct cross-talk mediated by several hub proteins with SH-2 domains. At 2 and 5weeks after transection, up-regulation of several proteins including CaMKIV, RONα and PKCδ as well as MAPK3/ERK1 phosphorylation was observed in the spinal ventral horns. Our results indicate that these signaling molecules and their neuronal effector systems cannot only play an important role in the initiation but also in the maintenance of spasticity states after spinal trauma. The exclusivity of specific protein changes observed in lumbar spinal parenchyma but not in dorsal root ganglia indicates that new treatment strategies should primarily target specific spinal segments to prevent or attenuate spasticity states. BIOLOGICAL SIGNIFICANCE: Development of progressive muscle spasticity and rigidity represents a serious complication associated with spinal ischemic or traumatic injury. Signaling proteins, including their phosphorylation status, were analyzed in the spinal parenchyma below the level of spinal injury and in the corresponding dorsal root ganglion cells in a rat model of spinal injury using Kinex™ antibody microarrays. The results uncovered direct protein interaction mediated cross-talk between angiogenesis and neurodegeneration pathways, which may significantly contribute to the healing process in the damaged region. Importantly, we identified several target proteins exclusively observed in the spinal lumbar ventral horns, where such proteins may not only play an important role in the initiation but also in the maintenance of spasticity states after spinal trauma. Hence, potential new treatment strategies such as gene silencing or drug treatment should primarily target spinal parenchymal sites at and around the injury epicenter and most likely employ intrathecal or targeted spinal segment-specific vector or drug delivery. We believe that this work will stimulate future translational research, ultimately leading to the improvement of quality of life of patients with spinal traumatic injury.

New heights and horizons in fostering proteomics in central and eastern Europe.

The annual Central and Eastern European Proteomic Conference can be considered as the bedrock of proteomics in central and eastern Europe and, since its creation, has seen an incredible growth in proteomics. The term 'Central and Eastern European Proteomic Conference' (CEEPC) was coined by the founder members of this series of conference including Josef Chmelik (1953-2007), Suresh Jivan Gadher and Hana Kovarova, over discussions about the apparent lack of visibility of proteomics in central and eastern Europe, as well as infrequent meetings and almost total lack of international collaborations. With trepidation, the 1st Central and Eastern European Proteomic Conference was organized in Prague in 2007 with resultant huge success. The intervening years saw the CEEPC grow and expand, and it now represents a cradle of proteomics interactions in and around central and eastern Europe, nicely linking it to the whole world. The 6th CEEPC in Budapest was attended by 150 participants and excelled once again at promoting proteomics at the highest level.

Cancer cell resistance to aurora kinase inhibitors: identification of novel targets for cancer therapy.

Drug resistance is the major obstacle to successful cancer therapy. Our study focuses on resistance to Aurora kinase inhibitors tested as anti-cancer drugs in clinical trials. We have used 2D electrophoresis in the pH ranges of 4-7 and 6-11 followed by protein identification using MALDI-TOF/TOF to compare the protein composition of HCT116 colon cancer cells either sensitive to CYC116 and ZM447439 inhibitors or resistant toward these drugs. The analysis also included p53(+/+) and p53(-/-) phenotypes of HCT116 cells. Our findings demonstrate that platelet-activating factor acetylhydrolase and GTP-binding nuclear protein Ran contribute to the development of resistance to ZM447439 only where resistance is related to p53. On the other hand, serine hydroxymethyltransferase was found to promote the tumor growth in cells resistant to CYC116 without the influence of p53. Computer modeling of interaction networks highlighted a direct link of the p53-independent mechanism of resistance to CYC116 with autophagy. Importantly, serine hydroxymethyltransferase, serpin B5, and calretinin represent the target proteins that may help overcome resistance in combination therapies. In addition, serpin B5 and calretinin appear to be candidate biomarkers that may be accessible in patients for monitoring of cancer therapy with ease.

Advances and expansion of Central and Eastern European proteomics.

Prague, also known as the 'City of a Hundred Spires', which is situated on the bank of River Vltava and is a historical Bohemian capital rich in history and beauty, set the stage for an exciting meeting that brought together high-caliber experts to share their knowledge as well as propagate the central theme and focus on 'Proteomes, Proteomics and Biological Systems'. More than 120 delegates from all over the world attended in pursuit of excellence and enjoyed not only excellent science but also took back home fairy-tale memories of Prague and its offerings. The 5th Central and Eastern European Proteomic Conference was organized in Prague, Czech Republic, on 19-22 September 2011, with resounding success.

Development of ovarian hyperstimulation syndrome: interrogation of key proteins and biological processes in human follicular fluid of women undergoing in vitro fertilization.

Ovarian hyperstimulation syndrome (OHSS) is an iatrogenic complication and potentially life-threatening condition resulting from excessive ovarian stimulation during assisted reproductive technologies. Our aim was to identify candidate proteins in follicular fluid (FF) using various proteomic approaches which may help to identify patients at risk of OHSS. We analysed the proteome alterations in FF from patients suffering from severe forms of OHSS (OHSS+) compared with a control group of women without or with only mild signs of OHSS (OHSS-). The 12 abundant proteins of FF were removed using an immunoaffinity system. Pools of remaining depleted proteins were applied to the two-dimensional (2D) electrophoresis and 2D liquid chromatography and proteins in differentially expressed protein spots/fractions were identified by mass spectrometry. Among a total of 19 candidate proteins differentially expressed (P< 0.05) between OHSS+ and OHSS- FF samples, three proteins, namely ceruloplasmin, complement C3 and kininogen-1, were found using both 2D techniques. Computer modelling highlighted the important role of kininogen-1 as an anchor for mediated interactions with other identified proteins including ferritin light chain and ceruloplasmin, hepatocyte growth factor-like protein, as well as complement C3 and gelsolin, thus linking various biological processes including inflammation and angiogenesis, iron transport and storage, blood coagulation, innate immunity, cell adhesion and actin filament polymerization. The delineation of such processes may allow the development of informed corrective therapeutic intervention in patients at risk of OHSS and a set of key proteins of the FF may be helpful as potential biomarkers for monitoring IVF therapy.

Mapping of the secretome of primary isolates of mammalian cells, stem cells and derived cell lines.

Within a mammalian organism, the interaction among cells both at short and long distances is mediated by soluble factors released by cells into the extracellular environment. The secreted proteins may involve extracellular matrix proteins, proteinases, growth factors, protein hormones, immunoregulatory cytokines, chemokines or other bioactive molecules that have a direct impact on target cell phenotype. Stem cells of mesenchymal, adipose, neural and embryonic origin, fibroblast feeder cells as well as primary isolates of astrocytes, endothelial and muscle cells have recently become targets of intensive secretome profiling with the search for proteins regulating cell survival, proliferation, differentiation or inflammatory response. Recent advances and challenges of the stem cell and primary cell secretome analysis together with the most relevant results are discussed in this review.