Proteomics Analysis of Pregnancy in Ewes under Heat Stress Conditions and Melatonin Administration

Melatonin is an indoleamine with broad spectrum properties that acts as a regulator of antioxidant and immune response in organisms. In our previous studies, melatonin improved redox status and inflammatory response in pregnant ewes under heat stress conditions. In the present study, using proteomics, the proteins regulated by melatonin during different stages of pregnancy and lambing were assessed. Twenty-two ewes equally divided into two groups, the melatonin (M) (n = 11) and control (C) group (n = 11), participated in the study and were exposed to heat stress during the first months of pregnancy. In the M group, melatonin implants were administered throughout pregnancy, every 40 days, until parturition (a total of four implants per ewe). Blood samples were collected at the beginning of the study simultaneously with the administration of the first melatonin implant (blood samples M1, C1), mating (M2, C2), second implant (M3, C3), fourth implant (M4, C4) and parturition (M5, C5), and MALDI-TOF analysis was performed. The results revealed the existence of 42 extra proteins in samples M2, M3 and M4 and 53 in M5 (sample at parturition) that are linked to melatonin. The biological processes of these proteins refer to boosted immune response, the alleviation of oxidative and endoplasmic reticulum stress, energy metabolism, the protection of the maternal organism and embryo development. This proteomics analysis indicates that melatonin regulates protective mechanisms and controls cell proliferation under exogenous or endogenous stressful stimuli during pregnancy and parturition.

The Role of Early Warning Scoring Systems NEWS and MEWS in the Acute Exacerbation of COPD

Acute exacerbations of chronic obstructive pulmonary disease (AECOPD) are the most devastating events in the course of the disease. Our aim was to investigate the value of early warning scoring systems: National Early Warning Score (NEWS) and Modified Early Warning Score (MEWS) in AECOPD. This is a prospective observational study of patients with AECOPD who were admitted at hospital. The NEWS and MEWS scores were registered at admission (NEWS-d1, MEWS-d1) and on the second day (NEWS-d2, MEWS-d2). A nasopharyngeal and sputum sample was taken for culture. Follow-up was done at 3 and 6 months after hospitalization. Any possible correlations between NEWS and MEWS and other parameters of COPD were explored. A cohort of 64 patients were included. In-hospital mortality was 4.7% while total mortality at 6 months was 26%. We did not find any significant correlation between in-hospital mortality and any of the scores but we could show a higher mortality and more frequent AECOPD at 6 months of follow-up for those with higher NEWS-d2. NEWS-d2 was associated with higher pCO₂ at presentation and a more frequent use of NIV. Higher NEWS-d1 and NEWS-d2 were predictive of a longer hospital stay. The presence of pathogens in the nasopharyngeal sample was related with a higher reduction of both scores on the second day. We therefore support the superiority of NEWS in the evaluation of hospitalized patients with AECOPD. A remaining high NEWS at the second day of hospital stay signals a high risk of hypercapnia and need of NIV but also higher mortality and more frequent exacerbations at 6 months after AECOPD.

Digital Technology in Diagnostic Breast Pathology and Immunohistochemistry

Digital technology has been used in the field of diagnostic breast pathology and immunohistochemistry (IHC) for decades. Examples include automated tissue processing and staining, digital data processing, storing and management, voice recognition systems, and digital technology-based production of antibodies and other IHC reagents. However, the recent application of whole slide imaging technology and artificial intelligence (AI)-based tools has attracted a lot of attention. The use of AI tools in breast pathology is discussed briefly as it is covered in other reviews. Here, we present the main application of digital technology in IHC. This includes automation of IHC staining, using image analysis systems and computer vision technology to interpret IHC staining, and the use of AI-based tools to predict marker expression from haematoxylin and eosin-stained digitalized images.

Discovery and Pharmacological Evaluation of STEAP4 as a Novel Target for HER2 Overexpressing Breast Cancer

Breast cancer (BC) is a highly heterogeneous disease encompassing multiple subtypes with different molecular and histopathological features, disease prognosis, and therapeutic responses. Among these, the Triple Negative BC form (TNBC) is an aggressive subtype with poor prognosis and therapeutic outcome. With respect to HER2 overexpressing BC, although advanced targeted therapies have improved the survival of patients, disease relapse and metastasis remains a challenge for therapeutic efficacy. In this study the aim was to identify key membrane-associated proteins which are overexpressed in these aggressive BC subtypes and can serve as potential biomarkers or drug targets. We leveraged on the development of a membrane enrichment protocol in combination with the global profiling GeLC-MS/MS technique, and compared the proteomic profiles of a HER2 overexpressing (HCC-1954) and a TNBC (MDA-MB-231) cell line with that of a benign control breast cell line (MCF-10A). An average of 2300 proteins were identified from each cell line, of which approximately 600 were membrane-associated proteins. Our global proteomic methodology in tandem with invigoration by Western blot and Immunofluorescence analysis, readily detected several previously-established BC receptors like HER2 and EPHA2, but importantly STEAP4 and CD97 emerged as novel potential candidate markers. This is the first time that the mitochondrial iron reductase STEAP4 protein up-regulation is linked to BC (HER2+ subtype), while for CD97, its role in BC has been previously described, but never before by a global proteomic technology in TNBC. STEAP4 was selected for further detailed evaluation by the employment of Immunohistochemical analysis of BC xenografts and clinical tissue microarray studies. Results showed that STEAP4 expression was evident only in malignant breast tissues whereas all the benign breast cases had no detectable levels. A functional role of STEAP4 intervention was established in HER2 overexpressing BC by pharmacological studies, where blockage of the STEAP4 pathway with an iron chelator (Deferiprone) in combination with the HER2 inhibitor Lapatinib led to a significant reduction in cell growth in vitro. Furthermore, siRNA mediated knockdown of STEAP4 also suppressed cell proliferation and enhanced the inhibition of Lapatinib in HER2 overexpressing BC, confirming its potential oncogenic role in BC. In conclusion, STEAP4 may represent a novel BC related biomarker and a potential pharmacological target for the treatment of HER2 overexpressing BC.

Expression profiling meta-analysis of ACE2 and TMPRSS2, the putative anti-inflammatory receptor and priming protease of SARS-CoV-2 in human cells, and identification of putative modulators

Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and has resulted in hundreds of thousands of deaths worldwide. While the majority of people with COVID-19 won't require hospitalization, those who do may experience severe life-threatening complications, including acute respiratory distress syndrome. SARS-CoV-2 infects human cells by binding to the cellular surface protein angiotensin-converting enzyme 2 (ACE2); in addition, the cellular transmembrane serine protease 2 (TMPRSS2) is needed for priming of the spike (S) protein of the virus. Virus entry may also depend on the activity of the endosomal/lysosomal cysteine proteases cathepsin B, L (CTSB, CTSL) although their activity is likely dispensable. Given that the uncertainty of how COVID-19 kills, hampers doctors' ability to choose treatments the need for a deep understanding of COVID-19 biology is urgent. Herein, we performed an expression profiling meta-analysis of ACE2, TMPRSS2 and CTSB/L genes (and proteins) in public repository databases and found that all are widely expressed in human tissues; also, the ACE2 and TMPRSS2 genes tend to be co-regulated. The ACE2 and TMPRSS genes expression is (among others) suppressed by TNF, and is induced by pro-inflammatory conditions including obesity, Barrett's esophagus, stomach infection by helicobacter pylori, diabetes, autoimmune diseases and oxidized LDL; by exercise, as well as by growth factors, viruses' infections, cigarette smoke, interferons and androgens. Regarding currently investigated therapies interferon-beta induced ACE2 gene expression in bronchial epithelial cells, while chloroquine tends to upregulate CTSB/L genes. Finally, we analyzed KEGG pathways modulated by ACE2, TMPRSS2 and CTSB/L and probed DrugBank for drugs that target modules of the affected pathways. Our data indicate possible novel high-risk groups for COVID-19; provide a rich resource for future investigations of its pathogenesis and highlight the therapeutic challenges we face.

Deep learning: shaping the medicine of tomorrow

Predicting response to therapy is a major challenge in medicine. Machine learning algorithms are promising tools for assisting this aim. Amongst them, Deep Neural Networks are emerging as the most capable of interrogating across multiple data types. Their further development will lead to sophisticated knowledge extraction, shaping the medicine of tomorrow.

A Deep Learning Framework for Predicting Response to Therapy in Cancer

A major challenge in cancer treatment is predicting clinical response to anti-cancer drugs on a personalized basis. Using a pharmacogenomics database of 1,001 cancer cell lines, we trained deep neural networks for prediction of drug response and assessed their performance on multiple clinical cohorts. We demonstrate that deep neural networks outperform the current state in machine learning frameworks. We provide a proof of concept for the use of deep neural network-based frameworks to aid precision oncology strategies.

Cellular Senescence: Defining a Path Forward

Cellular senescence is a cell state implicated in various physiological processes and a wide spectrum of age-related diseases. Recently, interest in therapeutically targeting senescence to improve healthy aging and age-related disease, otherwise known as senotherapy, has been growing rapidly. Thus, the accurate detection of senescent cells, especially in vivo, is essential. Here, we present a consensus from the International Cell Senescence Association (ICSA), defining and discussing key cellular and molecular features of senescence and offering recommendations on how to use them as biomarkers. We also present a resource tool to facilitate the identification of genes linked with senescence, SeneQuest (available at http://Senequest.net). Lastly, we propose an algorithm to accurately assess and quantify senescence, both in cultured cells and in vivo.

High resolution analysis of the intracellular proteome of cervical cancer cell lines unveils novel regulators of cervical carcinogenesis

Cervical cancer remains the fourth most common and most lethal type of cancer in women, despite the applied regular screening and prevention strategies, while the available treatment schemes still pose a threat to fertility. Substantial understanding of the underlying mechanisms and development of novel diagnostic, prognostic and therapeutic approaches are critical steps for improving cervical cancer management. Towards this goal, a comparative proteomic analysis was conducted between three cervical cancer cell lines (HeLa: HPV18+, SiHa: HPV16+, C33A: HPV‑) and normal cervical keratinocytes (HCK1T). The total cell extract of each cell line was analyzed by liquid chromatography coupled to tandem mass spectrometry (LC‑MS/MS). Differential expression analysis revealed 919, 826 and 1,370 deregulated proteins in the comparisons of HeLa, SiHa and C33A with HCK1T cell lines, respectively. Pathway enrichment analysis of the differentially expressed proteins highlighted common cancer characteristics such as high metabolic demands and increased cell turnover, confirming the validity of the proteomic results. Extensive literature mining of the consistently differentially expressed proteins that resulted from the three comparisons was performed leading to a shortlist of 21 proteins that are potentially involved in cervical malignancy. The criteria for this shortlisting were the association of the proteins with various types of cancer, while there is no study as yet associating their expression to cervical cancer. Moreover, the expression trend of two of the shortlisted proteins was validated using western blot analysis. The proteomic datasets generated in this study can be utilized to enrich the current knowledge on cervical cancer pathology and unveil key molecular mechanisms of carcinogenesis. In conclusion, the shortlist of consistently deregulated proteins between cervical cancer cell lines and normal cervical keratinocytes can be used for validation in clinical samples and in functional investigation experiments that could ultimately lead to the discovery of novel disease biomarkers and drug targets.

Proteasome dysfunction induces excessive proteome instability and loss of mitostasis that can be mitigated by enhancing mitochondrial fusion or autophagy

The ubiquitin-proteasome pathway (UPP) is central to proteostasis network (PN) functionality and proteome quality control. Yet, the functional implication of the UPP in tissue homeodynamics at the whole organism level and its potential cross-talk with other proteostatic or mitostatic modules are not well understood. We show here that knock down (KD) of proteasome subunits in Drosophila flies, induced, for most subunits, developmental lethality. Ubiquitous or tissue specific proteasome dysfunction triggered systemic proteome instability and activation of PN modules, including macroautophagy/autophagy, molecular chaperones and the antioxidant cncC (the fly ortholog of NFE2L2/Nrf2) pathway. Also, proteasome KD increased genomic instability, altered metabolic pathways and severely disrupted mitochondrial functionality, triggering a cncC-dependent upregulation of mitostatic genes and enhanced rates of mitophagy. Whereas, overexpression of key regulators of antioxidant responses (e.g., cncC or foxo) could not suppress the deleterious effects of proteasome dysfunction; these were alleviated in both larvae and adult flies by modulating mitochondrial dynamics towards increased fusion or by enhancing autophagy. Our findings reveal the extensive functional wiring of genomic, proteostatic and mitostatic modules in higher metazoans. Also, they support the notion that age-related increase of proteotoxic stress due to decreased UPP activity deregulates all aspects of cellular functionality being thus a driving force for most age-related diseases. Abbreviations: ALP: autophagy-lysosome pathway; ARE: antioxidant response element; Atg8a: autophagy-related 8a; ATPsynβ: ATP synthase, β subunit; C-L: caspase-like proteasomal activity; cncC: cap-n-collar isoform-C; CT-L: chymotrypsin-like proteasomal activity; Drp1: dynamin related protein 1; ER: endoplasmic reticulum; foxo: forkhead box, sub-group O; GLU: glucose; GFP: green fluorescent protein; GLY: glycogen; Hsf: heat shock factor; Hsp: Heat shock protein; Keap1: kelch-like ECH-associated protein 1; Marf: mitochondrial assembly regulatory factor; NFE2L2/Nrf2: nuclear factor, erythroid 2 like 2; Opa1: optic atrophy 1; PN: proteostasis network; RNAi: RNA interference; ROS: reactive oxygen species; ref(2)P: refractory to sigma P; SQSTM1: sequestosome 1; SdhA: succinate dehydrogenase, subunit A; T-L: trypsin-like proteasomal activity; TREH: trehalose; UAS: upstream activation sequence; Ub: ubiquitin; UPR: unfolded protein response; UPP: ubiquitin-proteasome pathway.

Hyperactivation of Nrf2 increases stress tolerance at the cost of aging acceleration due to metabolic deregulation

Metazoans viability depends on their ability to regulate metabolic processes and also to respond to harmful challenges by mounting anti‐stress responses; these adaptations were fundamental forces during evolution. Central to anti‐stress responses are a number of short‐lived transcription factors that by functioning as stress sensors mobilize genomic responses aiming to eliminate stressors. We show here that increased expression of nuclear factor erythroid 2‐related factor (Nrf2) in Drosophila activated cytoprotective modules and enhanced stress tolerance. However, while mild Nrf2 activation extended lifespan, high Nrf2 expression levels resulted in developmental lethality or, after inducible activation in adult flies, in altered mitochondrial bioenergetics, the appearance of Diabetes Type 1 hallmarks and aging acceleration. Genetic or dietary suppression of Insulin/IGF‐like signaling (IIS) titrated Nrf2 activity to lower levels, largely normalized metabolic pathways signaling, and extended flies’ lifespan. Thus, prolonged stress signaling by otherwise cytoprotective short‐lived stress sensors perturbs IIS resulting in re‐allocation of resources from growth and longevity to somatic preservation and stress tolerance. These findings provide a reasonable explanation of why most (if not all) cytoprotective stress sensors are short‐lived proteins, and it also explains the build‐in negative feedback loops (shown here for Nrf2); the low basal levels of these proteins, and why their suppressors were favored by evolution.

Saliva Proteomics Analysis Offers Insights on Type 1 Diabetes Pathology in a Pediatric Population

The composition of the salivary proteome is affected by pathological conditions. We analyzed by high resolution mass spectrometry approaches saliva samples collected from children and adolescents with type 1 diabetes and healthy controls. The list of more than 2000 high confidence protein identifications constitutes a comprehensive characterization of the salivary proteome. Patients with good glycemic regulation and healthy individuals have comparable proteomic profiles. In contrast, a significant number of differentially expressed proteins were identified in the saliva of patients with poor glycemic regulation compared to patients with good glycemic control and healthy children. These proteins are involved in biological processes relevant to diabetic pathology such as endothelial damage and inflammation. Moreover, a putative preventive therapeutic approach was identified based on bioinformatic analysis of the deregulated salivary proteins. Thus, thorough characterization of saliva proteins in diabetic pediatric patients established a connection between molecular changes and disease pathology. This proteomic and bioinformatic approach highlights the potential of salivary diagnostics in diabetes pathology and opens the way for preventive treatment of the disease.

Proteomic Analysis of Normal and Cancer Cervical Cell Lines Reveals Deregulation of Cytoskeleton-associated Proteins

BACKGROUND

Both HPV-positive and -negative cervical cancers are primarily associated with features of cell cycle and cytoskeletal disruption; however, the actual biological processes affected remain elusive. To this end, we systematically characterized the intracellular proteomic profiles of four distinct and informative cervical cell lines.

MATERIALS AND METHODS

Cell extracts from a normal cervical (HCK1T) and three cervical cancer cell lines, one HPV-negative (C33A), and two HPV-positive, SiHa (HPV16+) and HeLa (HPV18+), were analyzed by 2-dimensional electrophoresis and differentially expressed proteins were identified by MALDI-TOF mass spectrometry, while differential expression was confirmed by western blot analysis.

RESULTS

In total, 113 proteins were found differentially expressed between the normal and the cervical cancer lines. Bioinformatics analysis revealed the actin cytoskeleton signaling pathway to be significantly affected, while up-regulation of cofilin-1, an actin depolymerizing factor, was documented and further validated by western blotting. Furthermore, two-way comparisons among the four cell lines, revealed a set of 18 informative differentially expressed proteins.

CONCLUSION

These novel identified proteins provide the impetus for further functional studies to dissect the mechanisms operating in the two distinct pathways of cervical carcinogenesis.

Abstract 230: Proteomic approaches in the discovery of novel drug targets or potential biomarkers in breast cancer

The aim of this study is the detection, identification and quantification of known and new candidate cell membrane receptors that are overexpressed in Breast Cancer (BC) cells. In order to achieve this goal we have developed State-of-the-Art Proteomic approaches. These novel membrane target receptors can be used either as biomarkers or for the design of targeted drugs against aggressive disease subtypes with poor prognosis and therapeutic outcomes, such as Triple Negative BC (TNBC) and HER2 overexpressing BC.

For our study, four well characterized BC epithelial cell lines were selected: HCC-1954 and SKBR3 (HER2 overexpressing), MDA-MB-231 (TNBC) and MCF-10A (benign control). We employed a combination of subcellular fractionation and membrane enrichment protocols and combined those with quantitative, tandem Mass-Spectrometry (MS) based Proteomics. The discovery phase of our approach included: the GeLC-MS/MS technique, where protein fractions were first separated by 1D-gel electrophoresis followed by In-Gel enzymatic digestion prior to identification by a high resolution Orbitrap mass analyser. A complementary approach for known proteins associated with BC that cannot be readily detected in the discovery phase, such as GPCR receptors, was based on nano LC-MRM analysis. Proof of Concept experiments, with the use of a Triple Quadrupole (QqQ) instrument, were based on the detection of standard peptides derived from the protein of interest after following an in solution tryptic digestion protocol.

Using GeLC-MS/MS approach we identified the well-known BC involved receptors, EGFR and HER2, as well as other potential protein targets in concordance with the literature (e.g. TFR1, EPHA2, GPCR5A). We further confirmed these results by Western blot analysis. Certain GPCRs expected to be present in the cell lines tested were not detected in the studies used on the GeLC-MS/MS analysis, thus we proceeded to the more sensitive and quantitative nanoLC-MRM approach. As a paradigm target we chose the GnRH receptor, an established target for personalized therapy known to be expressed in BC. The quantitative nanoLC-MRM approach revealed GnRHR significant expression in the MDA-MB-231 BC line and in the WPE-NB26-3 Prostate cancer cell line (used as an overexpressing GNRHR positive control).

Our results indicate that the strategy of combining and applying various Proteomic approaches into selected cell lines for the identification of new protein targets will add more information to the genetic and histological classification of the tumor in order to achieve our goal, which is a holistic view of a patient’s molecular profiling that can ultimately lead to treatment in the most effective way.

Citation Format: Ioanna-Maria Orfanou, Theodoros Karampelas, George Mermelekas, Konstantinos Vougas, Constantin Tamvakopoulos. Proteomic approaches in the discovery of novel drug targets or potential biomarkers in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 230. doi:10.1158/1538-7445.AM2017-230

Chronic p53-independent p21 expression causes genomic instability by deregulating replication licensing

The cyclin-dependent kinase inhibitor p21(WAF1/CIP1) (p21) is a cell-cycle checkpoint effector and inducer of senescence, regulated by p53. Yet, evidence suggests that p21 could also be oncogenic, through a mechanism that has so far remained obscure. We report that a subset of atypical cancerous cells strongly expressing p21 showed proliferation features. This occurred predominantly in p53-mutant human cancers, suggesting p53-independent upregulation of p21 selectively in more aggressive tumour cells. Multifaceted phenotypic and genomic analyses of p21-inducible, p53-null, cancerous and near-normal cellular models showed that after an initial senescence-like phase, a subpopulation of p21-expressing proliferating cells emerged, featuring increased genomic instability, aggressiveness and chemoresistance. Mechanistically, sustained p21 accumulation inhibited mainly the CRL4-CDT2 ubiquitin ligase, leading to deregulated origin licensing and replication stress. Collectively, our data reveal the tumour-promoting ability of p21 through deregulation of DNA replication licensing machinery-an unorthodox role to be considered in cancer treatment, since p21 responds to various stimuli including some chemotherapy drugs.

Systemic mechanisms and effects of ionizing radiation: A new 'old' paradigm of how the bystanders and distant can become the players

Exposure of cells to any form of ionizing radiation (IR) is expected to induce a variety of DNA lesions, including double strand breaks (DSBs), single strand breaks (SSBs) and oxidized bases, as well as loss of bases, i.e., abasic sites. The damaging potential of IR is primarily related to the generation of electrons, which through their interaction with water produce free radicals. In their turn, free radicals attack DNA, proteins and lipids. Damage is induced also through direct deposition of energy. These types of IR interactions with biological materials are collectively called 'targeted effects', since they refer only to the irradiated cells. Earlier and sometimes 'anecdotal' findings were pointing to the possibility of IR actions unrelated to the irradiated cells or area, i.e., a type of systemic response with unknown mechanistic basis. Over the last years, significant experimental evidence has accumulated, showing a variety of radiation effects for 'out-of-field' areas (non-targeted effects-NTE). The NTE involve the release of chemical and biological mediators from the 'in-field' area and thus the communication of the radiation insult via the so called 'danger' signals. The NTE can be separated in two major groups: bystander and distant (systemic). In this review, we have collected a detailed list of proteins implicated in either bystander or systemic effects, including the clinically relevant abscopal phenomenon, using improved text-mining and bioinformatics tools from the literature. We have identified which of these genes belong to the DNA damage response and repair pathway (DDR/R) and made protein-protein interaction (PPi) networks. Our analysis supports that the apoptosis, TLR-like and NOD-like receptor signaling pathways are the main pathways participating in NTE. Based on this analysis, we formulate a biophysical hypothesis for the regulation of NTE, based on DNA damage and apoptosis gradients between the irradiation point and various distances corresponding to bystander (5mm) or distant effects (5cm). Last but not least, in order to provide a more realistic support for our model, we calculate the expected DSB and non-DSB clusters along the central axis of a representative 200.6MeV pencil beam calculated using Monte Carlo DNA damage simulation software (MCDS) based on the actual beam energy-to-depth curves used in therapy.

Comparative Analysis of Label-Free and 8-Plex iTRAQ Approach for Quantitative Tissue Proteomic Analysis

High resolution proteomics approaches have been successfully utilized for the comprehensive characterization of the cell proteome. However, in the case of quantitative proteomics an open question still remains, which quantification strategy is best suited for identification of biologically relevant changes, especially in clinical specimens. In this study, a thorough comparison of a label-free approach (intensity-based) and 8-plex iTRAQ was conducted as applied to the analysis of tumor tissue samples from non-muscle invasive and muscle-invasive bladder cancer. For the latter, two acquisition strategies were tested including analysis of unfractionated and fractioned iTRAQ-labeled peptides. To reduce variability, aliquots of the same protein extract were used as starting material, whereas to obtain representative results per method further sample processing and MS analysis were conducted according to routinely applied protocols. Considering only multiple-peptide identifications, LC-MS/MS analysis resulted in the identification of 910, 1092 and 332 proteins by label-free, fractionated and unfractionated iTRAQ, respectively. The label-free strategy provided higher protein sequence coverage compared to both iTRAQ experiments. Even though pre-fraction of the iTRAQ labeled peptides allowed for a higher number of identifications, this was not accompanied by a respective increase in the number of differentially expressed changes detected. Validity of the proteomics output related to protein identification and differential expression was determined by comparison to existing data in the field (Protein Atlas and published data on the disease). All methods predicted changes which to a large extent agreed with published data, with label-free providing a higher number of significant changes than iTRAQ. Conclusively, both label-free and iTRAQ (when combined to peptide fractionation) provide high proteome coverage and apparently valid predictions in terms of differential expression, nevertheless label-free provides higher sequence coverage and ultimately detects a higher number of differentially expressed proteins. The risk for receiving false associations still exists, particularly when analyzing highly heterogeneous biological samples, raising the need for the analysis of higher sample numbers and/or application of adjustment for multiple testing.

Comparison of Depletion Strategies for the Enrichment of Low-Abundance Proteins in Urine

Proteome analysis of complex biological samples for biomarker identification remains challenging, among others due to the extended range of protein concentrations. High-abundance proteins like albumin or IgG of plasma and urine, may interfere with the detection of potential disease biomarkers. Currently, several options are available for the depletion of abundant proteins in plasma. However, the applicability of these methods in urine has not been thoroughly investigated. In this study, we compared different, commercially available immunodepletion and ion-exchange based approaches on urine samples from both healthy subjects and CKD patients, for their reproducibility and efficiency in protein depletion. A starting urine volume of 500 μL was used to simulate conditions of a multi-institutional biomarker discovery study. All depletion approaches showed satisfactory reproducibility (n=5) in protein identification as well as protein abundance. Comparison of the depletion efficiency between the unfractionated and fractionated samples and the different depletion strategies, showed efficient depletion in all cases, with the exception of the ion-exchange kit. The depletion efficiency was found slightly higher in normal than in CKD samples and normal samples yielded more protein identifications than CKD samples when using both initial as well as corresponding depleted fractions. Along these lines, decrease in the amount of albumin and other targets as applicable, following depletion, was observed. Nevertheless, these depletion strategies did not yield a higher number of identifications in neither the urine from normal nor CKD patients. Collectively, when analyzing urine in the context of CKD biomarker identification, no added value of depletion strategies can be observed and analysis of unfractionated starting urine appears to be preferable.

Heart rate recovery post 6-minute walking test in obstructive sleep apnea: cycle ergometry versus 6-minute walking test in OSA patients

PURPOSE

To examine the clinical usefulness of heart rate recovery (HRR) post 6-minute walking test (6MWT) as a simple marker of cardiovascular risk in obstructive sleep apnea (OSA) patients in comparison to HRR post cycle ergometry, the validated and more sophisticated protocol.

METHODS

Seventy-four participants underwent full overnight polysomnography, cycle ergometry and 6MWT. The HRR at 1, 2 and 3 min (HRR-1, HRR-2 and HRR-3) 6MWT was compared to HRR at 1, 2, and 3 min post cycle ergometry in normal subjects and in moderate and severe OSA patients before and after 6-month CPAP treatment.

RESULTS

The HRR-1, HRR-2 and HRR-3 in 6MWT were significantly different between normal, moderate and severe OSA patients with higher rates achieved in normal. The higher the severity of OSA the lower the HRR was. There were also no differences found between work rate and distance walked during cycle ergometry or 6MWT, respectively, concerning normal, moderate and severe OSA patients. Heart rate recovery was further associated with minimum saturation of oxygen during sleep independently of the duration of apnea episodes of BMI and ESS. The treatment with CPAP had a beneficial effect on HRR both post-6MWT and post cycle ergometry.

CONCLUSIONS

Autonomic nervous system dysfunction in OSA can be found even with submaximal exertion. Heart rate recovery post-6MWT, such as HRR post cycle ergometry, was significantly impaired in OSA patients in comparison to normals and was favorably influenced from CPAP treatment. Furthermore, it was found to be more sensitive compared with distance walked in 6MWT in discriminating severity of OSA. The HRR post-6MWT was found to be an easily measured and reliable marker of OSA severity both before and after CPAP treatment.

Protein biomarkers distinguish between high- and low-risk pediatric acute lymphoblastic leukemia in a tissue specific manner

The current study evaluated the differential expression detected in the proteomic profiles of low risk- and high risk- ALL pediatric patients to characterize candidate biomarkers related to diagnosis, prognosis and patient targeted therapy. Bone marrow and peripheral blood plasma and cell lysates samples were obtained from pediatric patients with low- (LR) and high-risk (HR) ALL at diagnosis. As controls, non-leukemic pediatric patients were studied. Cytogenetic analysis was carried out by G- banding and interphase fluorescent in situ hybridization. Differential proteomic analysis was performed using two-dimensional gel electrophoresis and protein identification by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The differential expression of certain proteins was confirmed by Western blot analysis. The obtained data revealed that CLUS, CERU, APOE, APOA4, APOA1, GELS, S10A9, AMBP, ACTB, CATA and AFAM proteins play a significant role in leukemia prognosis, potentially serving as distinctive biomarkers for leukemia aggressiveness, or as suppressor proteins in HR-ALL cases. In addition, vitronectin and plasminogen probably contributed to leukemogenesis, whilst bicaudal D-related protein 1 could afford a significant biomarker for pediatric ALL therapeutics.

Depression, physical activity, energy consumption, and quality of life in OSA patients before and after CPAP treatment

BACKGROUND

A variety of studies have demonstrated improvement in quality of life and depressive symptoms in obstructive sleep apnea (OSA) patients after continuous positive airway pressure (CPAP) treatment. However, very little is known about the effect of OSA treatment on physical activity and energy consumption.

OBJECTIVES

The aim of this study was to evaluate the changes in depression, physical activity, energy expenditure, and quality of life (QoL) in OSA patients before and after CPAP therapy.

METHODS

Forty-one patients with OSA as revealed by polysomnography, were included to the study. They responded to the generic World Health Organization Quality of Life (WHOQoL) questionnaire, to the specific-disease Quebec Sleep Questionnaire, and to Center for Epidemiologic Studies Depression Scale (CES-D) in order to evaluate QoL and the incidence of depression. In addition, all patients wore an accelerometer which measured physical activity and energy expenditure during a week. At least 6 months after initiation of CPAP treatment (mean time, 9 months) we re-examined 24 patients who met the compliance with the treatment criteria.

RESULTS

Patients after CPAP therapy had significantly higher scores in all domains of the Quebec Sleep Questionnaire and in the domains of physical health/level of independence and psychological health/spirituality of the WHOQoL. Depression scores were also better in CES-D after treatment. However, despite the improvement in QoL and psychological status, CPAP therapy had no impact on physical activity and energy expenditure.

CONCLUSIONS

CPAP therapy improves QoL and lessens depressive symptoms in our group of well-treated OSA patients. However, physical activity and energy expenditure did not present statistically significant improvement in the same group of OSA patients.

Cdc6: a multi-functional molecular switch with critical role in carcinogenesis

Research in the last decade revealed an additional role for the Replication Licensing Factor Cdc6 in transcriptional regulation. This novel function has been linked to human cancer development. Here, we summarize all the findings arguing over a role of Cdc6 as a transcriptional repressor and shed light toward new research directions for this field.

Effects of an early experience of reward through maternal contact or its denial on laterality of protein expression in the developing rat hippocampus

Laterality is a basic characteristic of the brain which is detectable early in life. Although early experiences affect laterality of the mature brain, there are no reports on their immediate neurochemical effects during neonatal life, which could provide evidence as to the mechanisms leading to the lateralized brain. In order to address this issue, we determined the differential protein expression profile of the left and right hippocampus of 13-day-old rat control (CTR) pups, as well as following exposure to an early experience involving either receipt (RER) or denial (DER) of the expected reward of maternal contact. Proteomic analysis was performed by 2-dimensional polyacrylamide gel electrophoresis (PAGE) followed by mass spectroscopy. The majority of proteins found to be differentially expressed either between the three experimental groups (DER, RER, CTR) or between the left and right hemisphere were cytoskeletal (34%), enzymes of energy metabolism (32%), and heat shock proteins (17%). In all three groups more proteins were up-regulated in the left compared to the right hippocampus. Tubulins were found to be most often up-regulated, always in the left hippocampus. The differential expression of β-tubulin, β-actin, dihydropyrimidinase like protein 1, glial fibrillary acidic protein (GFAP) and Heat Shock protein 70 revealed by the proteomic analysis was in general confirmed by Western blots. Exposure to the early experience affected brain asymmetry: In the RER pups the ratio of proteins up-regulated in the left hippocampus to those in the right was 1.8, while the respective ratio was 3.6 in the CTR and 3.4 in the DER. Our results could contribute to the elucidation of the cellular mechanisms mediating the effects of early experiences on the vulnerability for psychopathology, since proteins shown in our study to be differentially expressed (e.g. tubulins, dihydropyrimidinase like proteins, 14-3-3 protein, GFAP, ATP synthase, α-internexin) have also been identified in proteomic analyses of post-mortem brains from psychiatric patients.

A two-dimensional proteomic profile of Tetrahymena thermophila whole cell lysate

Tetrahymena thermophila is a unicellular eukaryotic model organism used for a variety of biochemical, molecular and biological studies. According to its macronucleus genome sequence, it is expected to contain more than 27,000 protein-coding genes, although only a small proportion of them have information published specifically about them. Here, we present a reference map for whole cell lysate of T. thermophila obtained using two-dimensional gel electrophoresis (2-DE) combined with mass spectrometry. Although (2-DE) is one of the most efficient techniques for resolving complex protein mixtures and revealing the relative high-abundance proteins, it has not yet been applied generally to ciliates. In order to obtain qualitative protein samples for analysis, an appropriate homogenization method is required. Optimization of the homogenization method led to the analysis of nearly 4500 protein spots, the final identification of 375 different proteins using Mascot software and an additional 258 gene products using a newly developed web service, called Peptide Finder, resulting in a total of 631 different gene products that are considered to constitute the proteomic profile of the whole cell lysate of T. thermophila.

Position dominant sequence elements in experimentally verified human promoters and their putative relation to cancer

Promoter regions of the human genome play a key role in our understanding of the regulatory mechanisms related to the physiological and disease states. The aim of this study was to investigate the sequence positional properties of experimentally verified human promoters. Consequently, we determined short sequence elements ranging from 4 to 9mers presenting position dominance close to, or away from the transcription start site (TSS). For this purpose rigid statistical criteria were used and whether position dominance was in any way related to transcription control was determined. To achieve this goal we designed and implemented a dedicated filtering method to massively detect position-dominant sequence elements embedded in the promoter set. Additionally, via a high throughput procedure, we gathered data on the majority of the publicly available transcription factor-binding sites (TFBSs) and matched them to our findings, aiming to accomplish a large-scale correlation between position-dominant sequence elements and TFBSs. In this analysis, we present unique compositional and conservational perturbations at the TSS and the core promoter region. Using our filtering method, 7,088 short sequences ranging from 4 to 9mers were found to present strong positional dominance close to or away from the TSS, while the aforementioned short sequences were matched to a large number of known TFBSs. Moreover, using probability theory, evidence is presented showing that TFBSs tend to present strong positional preferences. In addition, we demonstrate that the actual TFBS copy number is related to the transcription regulatory process. On the basis of the last argument, it is suggested that all the detected short sequences which did not match any known TFBS, have a high potential for being novel transcription control elements. Furthermore, using a well-described ;high potential cancer biomarker resource', we attempted to identify position dominant sequence elements associated with cancer, as derived by their presence in the respective promoters of cancer related proteins.

UniMaP: finding unique mass and peptide signatures in the human proteome

The uniqueness of a measured molecular mass or peptide sequence plays a very important role in the fields of protein identification and peptide/protein-biomarker investigation. We present a publicly available web application that offers information concerning the uniqueness of one or more molecular masses and one or more peptide sequences in the human proteome. When a sequence is found to be unique in humans, the application is able to search across all species querying whether this sequence is unique, not only in humans but also in other species found in the Swiss-Prot Database. The application is also able to search for unique protein fragments derived computationally from enzymatic digestion driven by certain enzymes. Furthermore, the application can list all the unique masses and peptides of a given protein. Through this application, researchers are able to find unique tags, either on a molecular mass level or on a sequence level. These unique tags are remarkably important in research related to protein identification or biomarker discovery and measurements.

AVAILABILITY

UniMaP web-application is available at http://bioserver-1.bioacademy.gr/Bioserver/UniMaP/

Modulation of the E2F1-driven cancer cell fate by the DNA damage response machinery and potential novel E2F1 targets in osteosarcomas

Osteosarcoma is the most common primary bone cancer. Mutations of the RB gene represent the most frequent molecular defect in this malignancy. A major consequence of this alteration is that the activity of the key cell cycle regulator E2F1 is unleashed from the inhibitory effects of pRb. Studies in animal models and in human cancers have shown that deregulated E2F1 overexpression possesses either "oncogenic" or "oncosuppressor" properties, depending on the cellular context. To address this issue in osteosarcomas, we examined the status of E2F1 relative to cell proliferation and apoptosis in a clinical setting of human primary osteosarcomas and in E2F1-inducible osteosarcoma cell line models that are wild-type and deficient for p53. Collectively, our data demonstrated that high E2F1 levels exerted a growth-suppressing effect that relied on the integrity of the DNA damage response network. Surprisingly, induction of p73, an established E2F1 target, was also DNA damage response-dependent. Furthermore, a global proteome analysis associated with bioinformatics revealed novel E2F1-regulated genes and potential E2F1-driven signaling networks that could provide useful targets in challenging this aggressive neoplasm by innovative therapies.

Peptide Finder: mapping measured molecular masses to peptides and proteins

The identification of unknown amino acid sequences of peptides as well as protein identification is of great significance in proteomics. Here, we present a publicly available web application that facilitates a high resolution mapping of measured molecular masses to peptides and proteins, irrespectively of the enzyme/digestion method used. Furthermore, multi-filtering may be applied in terms of measured mass tolerance, molecular mass and isoelectric point range as well as pattern matching to refine the results. This approach serves complementary to the existing solutions for protein identification and gives insights in novel peptides discovery and protein identification at the cases where the identification scores from the other approaches may be below significance threshold. Peptide Finder has been proven useful in proteomics procedures with experimental data from MALDI-TOF.

AVAILABILITY

Peptide Finder web-application is available at http://bioserver-1.bioacademy.gr/Bioserver/PeptideFinder/.

The proteome profile of two cell lines and their xenografts isolated from a patient with clear cell sarcoma (soft tissue melanoma)

We report the establishment of two novel clear cell sarcoma (CCS) cell lines (soft tissue melanoma) from a patient and the production of the corresponding xenografts after xenotransplantation of those cells to NOD/SCID mice. As no comprehensive study on the relevant proteomes of this type of cancer has been reported to date, proteomics technologies were applied in a first attempt to analyze the proteins of the two cell lines and their corresponding primary xenografts. Total protein extracts were separated by two dimensional gel electrophoresis (2-DE) and analysed by MALDI-MS and MALDI-MS-MS following in-gel digestion with trypsin. Protein identification was carried out by peptide mass fingerprint (PMF) and post source decay (PSD), respectively. Comparative analysis revealed that 124 proteins were common between the cell lines and the xenografts; 249 proteins were found to be expressed only in the proteome of the cell lines, while 178 proteins were expressed only in the proteome of xenografts. Our results demonstrated that both cell lines and xenografts were positive for vimentin and S100 reported as markers for CCS. After functional analysis, 27 different protein groups were identified in the analysed proteomes, including apoptosis-related proteins, oncogenes and several proteins closely related to TP-53 and NF-kappa B pathways. Furthermore, the proteins nestin, stem cell growth factor CLC11 and mdr-1, closely related to malignant-melanoma-initiating cells, were found to be expressed in both the cell lines and their corresponding xenografts. Since there are no data concerning protein expression in CCS, this study may contribute to the understanding of the molecular basis of the disease, while the cell lines as well as the developed xenografts may be used as tools for the development of new therapeutic strategies to tackle this rare but fatal malignancy.

Two-dimensional electrophoresis and immunohistochemical study of calreticulin in colorectal adenocarcinoma and mirror biopsies

PURPOSE

The purpose of this study was to analyse the polypeptide patterns of colorectal adenocarcinomas and mirror biopsies and to investigate the expression of calreticulin and the relationship of this chaperon to colon cancer.

MATERIALS AND METHODS

The investigation was carried out on 21 adenocarcinomas and 21 mirror biopsies using high-resolution two-dimensional (2D) electrophoresis and immunohistochemical PAP method.

RESULTS

2D electrophoresis revealed several polypeptide patterns that were shown to be upregulated in colorectal adenocarcinomas compared to their mirror biopsies. One polypeptide spot being upregulated in colorectal adenocarcinoma, turned out to be calreticulin. The overexpression of calreticulin was confirmed by further examination in immunohistochemical level.

CONCLUSION

Calreticulin was found overexpressed in colon cancer tissues as compared to the corresponding mirror biopsy tissues. The overexpression was particularly intense to high-malignancy tissues and particularly in the poorly differentiated regions of the tissue. Calreticulin showed a direct relationship to the disease stage, a fact strongly indicating that the functional role of calreticulin is directly associated with tumor growth and metastasis.

The proteome profile of the human osteosarcoma U2OS cell line

The human osteosarcoma U2OS cell line is one of the first generated cell lines and is used in various areas of biomedical research. Knowledge of its protein expression is limited and no comprehensive study on the proteome of this cell line has been reported to date. Proteomics technology was used in order to analyse the proteins of the U2OS cell line. Total protein extracts were separated by two-dimensional gel electrophoresis (2-DE) and analysed by matrix-assisted laser desorption ionisation-mass spectrometry (MALDI-MS) and MALDI--MS-MS following in-gel digestion with trypsin and, finally, protein identification was carried out by peptide mass fingerprint (PMF) and post source decay (PSD), respectively. Approximately 3,000 spots were excised from two 2-DE gels and were analysed, resulting in the identification of 237 different gene products. The majority of the identified proteins were enzymes, regulatory proteins and RNA-associated proteins, while leukocyte markers and oncogenes were also present. Our findings include 11 protooncogenes (FKBP4, SRC8, PSD10, FUBP1, PARK7, NPM, PDIA1, OXRP, SET, TCTP and GRP75) related to the cancerous state of the U2OS cell line. The U2OS 2-DE database provides the basis for future protein studies.

Analysis of whole cell lysate from the intercellular bacterium Coxiella burnetii using two gel-based protein separation techniques

Coxiella burnetii, the causative agent of Q fever, is an obligate intracellular gamma-proteobacterium, which replicates within large phagolysosome-like compartments formed in the host cell. The global protein profile of intracellular C. burnetii strain Nine Mile phase II was analyzed by two gel-based approaches coupled to MALDI-TOF MS. Colloidal Coomassie brilliant blue-stained 2-DE gels at the pH range 3-10 resolved over 600 protein spots and 125 spots in doubled-SDS-PAGE gels. Mass spectra obtained for each trypsin-digested protein-spot were compared to the C. burnetii genome database, and a total number of 185 different C. burnetii proteins were identified by both techniques. 2-DE in combination with MALDI-TOF MS, as a high-throughput method, allowed the identification of 172 proteins. On the other hand, the application of doubled-SDS-PAGE allowed the identification of 38 proteins, with some of them being very alkaline and membrane proteins not identified in the 2-DE approach. Most identified proteins were predicted to be involved in metabolism and biosynthesis. Several identified proteins are speculated to have a distinct and vital role in the pathogenesis and survival of C. burnetii within the harsh phagolysosomal environment.

Characterization of the human urine proteome by preparative electrophoresis in combination with 2-DE

The protein components of urine are useful indicators of renal function and human health in general. Urine samples are easily attainable making them ideal substrates for biomarker research. Analysis of the urine proteome however, has been hindered by the great variability of the urine specimens, and the presence of various proteins in low abundance or modified forms. To alleviate some of these problems urine samples from five different individuals were pooled, concentrated and the proteome characterized by a combination of preparative electrophoresis and 2-DE, followed by PMF. A total of 778 protein spots corresponding to 141 different gene products were identified. In comparison, 171 spots corresponding to 44 unique proteins were identified in the unfractionated starting material. Among the proteins identified from the preparative electrophoresis were many of low abundance such as proteins involved in signal transduction. Furthermore, the median molecular mass of the identified proteins from the preparative electrophoresis was significantly lower in comparison to the proteins identified from the unfractionated starting material (39 886 Da versus 71 317 Da, respectively). Concluding, application of this methodology provides a coherent analysis of the urine proteome and contributes to the generation of the urine protein map in health and disease.

Sample sonication after trichloroacetic acid precipitation increases protein recovery from cultured hippocampal neurons, and improves resolution and reproducibility in two-dimensional gel electrophoresis

Protein precipitation with TCA followed by acetone washing is frequently used to clean samples before 2-DE. However, the difficulty in solubilizing TCA-precipitated proteins causes some variability in 2-D gels and makes it difficult to detect some proteins. In this work we show that sonication of the samples, after TCA precipitation followed by elution in sample buffer, increases total protein recovery, and improves reproducibility and matching ratios between gels when analyzed by specialized software.

The Protein Profile of the Human Immature T-cell Line CCRF-CEM

The human immature T-cell line CCRF-CEM is widely used for all kinds of in vitro studies in biochemistry, biology, toxicology and medicine. Knowledge about protein expression is limited and no comprehensive study on the proteome of this cell type has been reported to date. Proteomics technologies were applied in order to analyse the proteins of the CEM cell line. The proteins were separated by two-dimensional (2-D) gel electrophoresis and analysed by MALDI-MS and MALDI-MS-MS following in-gel digestion with trypsin and, finally, protein identification was carried out by peptide mass fingerprint (PMF) and post source decay (PSD), respectively. Approximately 4,500 spots, excised from four 2-D gels, were analysed. The analysis resulted in the identification of about 1,150 proteins, the products of 451 different genes. The majority of the identified proteins were enzymes, regulatory proteins and transporters, while leukocyte markers and oncogenes were also included. The CCRF-CEM cell database today represents one of the largest 2-D databases for eukaryotic proteomes, forming the basis for future expressional studies at the protein level.