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Proteomics 2015, 15, 179–182
Editorial Signal Transduction
Cells respond to various signals that govern their basic and specific cellular processes. A thorough understanding of the molecular mechanisms involved in cellular signaling is essential as aberrant signaling pathways are implicated in a number of diseases. Studying signaling in disease states forms the basis to developing novel therapeutic strategies. To understand signaling mechanisms in detail, systematic approaches have been developed to comprehensively characterize post-translational modifications (PTMs) such as phosphorylation under various conditions. Recent advances in mass spectrometry-based and array-based approaches have made it possible for the global characterization of signaling pathways. This Special Issue of PROTEOMICS brings together a collection of proteomics studies on signaling carried out by experts in the field of proteomics. This issue comprises a total of 36 contributions from various experts in the field of proteomics and signaling research. The compiled articles cover various topics relevant to the current progress in PTM analysis and delineating signaling mechanisms in health and disease. The first part of this special issue consists of 10 review articles covering diverse areas of research on cell signaling and disease. To date, several approaches have been developed to characterize signaling pathways. In the past decade, mass spectrometry has been used extensively in biological research and has aided effectively in addressing important biological questions. Three groups independently review the current progress in the understanding signaling networks using proteomics-based approaches. The review by Li et al., focuses on recent advances in affinity purification-MS to study protein-protein interactions. Vivelo et al., review in detail the strategies employed for efficient enrichment of ADP-ribosylated proteins and their associated proteins by mass spectrometry, their advantages, limitations and pitfalls. Gahoi et al., review the advantages, disadvantages and applications of various array-based techniques to study the interactions and modifications of biomolecules, their association with signaling pathways and their correlation with disease pathobiology. SRC, a non-receptor tyrosine kinase is a critical regulator of signal transduction plays an essential role in controlling cell growth and migration. Deregulation in SRC signaling is frequently observed in human cancer and is thought to play important roles during tumourigenesis. Sirvent et al., review the current phosphoproteomic strategies that have provided new insights into SRC signaling in normal and cancer cells. Batkulwar and colleagues review the signaling pathways activated by receptor for advanced glycation end products (RAGE) activated kinases. The article also provides insight on the plausible role of RAGE activated phosphoproteome in several diseases. Two reviews in the issue focus on the emerging role of extracellular vesicles as mediators of signaling by means of protein and RNA transfer through paracrine and autocrine manner. The article by Gangoda et al., provides a comprehensive review on extracellular vesicles (EVs) as mediators of signal transduction in cancer as well as neurodegenerative diseases. The authors also emphasize the need for additional studies to obtain a clear understanding of the complex role that extracellular vesicles play in physiological and pathological conditions. Havrylov et al., review the current progresses and challenges in proteomic strategies employed to characterize proteins and PPIs in these invasive cell structures. The other reviews focus on the current progress in elucidation of signaling mechanisms. Yuan and colleagues review the recent advances in the proteomics approaches developed to understand the altered functions of redox sensors and its role in cancer. Angiogenesis is a vital physiological process and plays an important role in numerous pathological conditions. Rahimi and Costello review the significance of post-translational modifications on vascular endothelial growth factor receptor-2 (VEGFR-2) in signaling, angiogenesis and potential therapeutic C 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
Akhilesh Pandey
Michael F. Moran
www.proteomics-journal.com
180
Proteomics 2015, 15, 179–182
potential. Mauvoisin and colleagues review the current progress, challenges and opportunities in obtaining a detailed understanding of circadian biology using proteomic approaches. Oncogene-driven signaling networks are highly dynamic. In-depth analysis of these signaling networks and the mechanisms of therapeutic adaptation will enable the development of novel therapeutic regimes, and uncover proteome-based biomarkers to guide in their application. In the study by Blair et al., the signaling changes observed upon PIK3CA mutation was investigated by employing a SILAC-based quantitative phosphoproteomics approach. This study is an excellent example of using this high throughput strategy to study changes in the dynamics of phosphorylation induced by oncogenic mutations in isogenic knock-in cell lines thus unraveling new signaling pathways with potential therapeutic value. In another study, Fedorenko et al., present the first systems level view of adaptive and basal phosphotyrosine signaling in BRAF- and NRAS-mutant in melanoma. Although poorly characterized at a systems level, these adaptations play a key role in therapeutic escape. The study by Zhang et al. highlights the utility of phosphoproteomic studies in the identification of altered signaling pathways in response to inherent mutations in epidermal growth factor receptor (EGFR) in lung adenocarcinoma cells. This is the first report examining erlotinib treatment-induced global phosphorylation changes and provides novel insights into signaling downstream of mutant EGFRs in lung adenocarcinoma. The article by Lemeer and colleagues compares the differential proteomic and kinome profiles between myoma and healthy myometrium samples and identifies molecular signatures as potential biomarkers or drug targets. Since current treatment modalities for myomas include surgical resection of the lesion or hysterectomy, this study could lead to potential benefits to clinicians in providing an alternative to invasive surgery. The relationship between the current histological-based characterization of epithelial ovarian carcinoma and activated signaling networks is “Studying signaling in dispoorly characterized. Sereni et al., in their study employed drug targetease states forms the basis to based protein signaling activation mapping to evaluate the characterization developing novel therapeutic of epithelial ovarian carcinoma subtypes based on activated protein signaling network architecture rather than histology. Their analysis revealed five strategies . . . Recent advances pathway-driven clusters indicating that epithelial ovarian carcinomas are in mass spectrometry-based extremely heterogeneous and classic histopathological categorization alone and array-based approaches is inadequate to classify cancer subtypes. To identify activated signaling pathways in esophageal squamous cell carhave made it possible for the cinoma, Syed et al., carried out phosphotyrosine profiling of ESCC cell lines global characterization of sigand observed hyperphosphorylation of EPHA2 and several proteins associnaling pathways.” ated with EPHA2 signaling in ESCC cell lines. Their study suggests EPHA2 as a promising therapeutic target in ESCC that warrants further evaluation. In another study by the same group, in vitro quantitative approach was employed to identify biomarkers in a panel of head and neck cancer cell lines. They observed an increased expression of high mobility group box 2 (HMGB2) in the cancer cell lines. siRNA-mediated silencing of HMGB2 increased the sensitivity of the HNSCC cell lines to cisplatin and 5-fluorouracil suggesting a combinatorial therapy would increase the efficacy of current treatment regimen. Sharma et al., employed an iTRAQ-based comparative proteomic approach to decipher differentially expressed proteins with potential implications in meningiomas. This study provides new opportunities for early detection of meningiomas. The findings of this study will provide new insights into the association of diverse signaling pathways including integrins, Wnt and FGR signaling with meningioma pathogenesis. Annexin-1, a calcium/phospholipid-binding protein plays an important role in several cancers. To understand its role in tumorogenesis, Swa and colleagues employed reductive dimethyl labeling strategy to identify the proteome differentially expressed in annexin-1 heterozygous positive and null mice. The findings of this study suggest a vital role of Annexin-1 in invasionmetastasis in breast cancer initiation. The trafficking of nascent and endocytosed proteins is a critical feature of signaling pathways involved in many diseases including cancer. Endocytosis of activated receptor tyrosine kinases (RTKs) is a key mechanism of downregulation, which is governed by various PTMs including phosphorylation. St-Germain et al., report that the activity of FGFR3, an RTK frequently activated in multiple myeloma and other malignancies, is modulated by two protein-tyrosine
C 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.proteomics-journal.com
Proteomics 2015, 15, 179–182
181
phosphatases (PTPN1 and PTPN2) as a function of subcellular localization. Knockdown of either PTP activated the receptor in the absence of ligand, leading to a model wherein the expression levels of cellular PTPs, in addition to several regulatory mechanisms, defines conditions that select for ectopic FGFR3 expression and activation during tumorigenesis. Krieger et al., employed an LC-MS/MS-based approach to elucidate some of the phosphorylation sites of Numb, an adaptor protein known to be involved in intracellular trafficking of receptors and in endocytosis. Their results reveal Numb as a substrate for Cdk5, known to regulate neuronal cell cycle arrest and differentiation, and pave the way for further studies into the complex CDK5/Numb/Rac-Rho downstream signaling cascades. An inability to deliver nascent CFTR protein to the cell surface, most frequently due to deletion of the codon encoding F508 , underlies cystic fibrosis. Pasyk et al. approached this protein trafficking defect as a signaling problem. They mapped and compared the phosphorylation status of protein kinase A sites in the phosphoregulatory R domain of wild type (WT) and F508del-CFTR protein. They demonstrate, for the first time, that the mutant protein F508delCFTR has an altered channel activity on the cell surface due to defective phosphorylation resulting from an allosteric change in its R domain. Multiplexed mass spectrometry-based strategies for the analysis of global proteome and phosphoproteome in biological systems have recently been improvised. Paulo and colleagues employed a tandem mass tag (TMT)-based quantitative proteomic approach to analyze the effect of two MEK signaling inhibitors on the phosphoproteomes of three tissues in murine models. MEK inhibitors decreased phosphorylation of proteins involved in ion transport and fluid balance in kidneys corroborating edema, an adverse event known to be associated with these inhibitors. The same group also characterized the proteome and phosphoproteomes of yeast deletion mutants of 14–3–3 orthologs and analyzed the effects of rapamycin treatment using a TMT-based quantitative proteomic strategy. Nirujogi et al., also employed multiplexed proteomic strategy to elucidate the effect of a nerve agent, VX, on the piriform cortex region of brains in rats. Their data reveal the complex toxicity pathway in this brain region following VX exposure and represents new opportunities for the development of novel or adjuvant countermeasures for VX exposure. Two groups have characterized the phosphoproteome of Alzheimer’s disease using refined strategies. Tan et al., employed a modified phosphoproteome enrichment strategy of TiO2 -based phosphoproteome enrichment by using phosphate ion at a low concentration as a non-phosphopeptide competitor to reduce background and a longer duration LC-MS analysis. In another study, Dammer et al., characterized the phosphoproteome of Alzheimer’s disease using immobilized metal affinity chromatography (IMAC) followed by liquid chromatographytandem mass spectrometry to identify phosphopeptides and identified crosstalk between kinases and small heat shock proteins. Early signaling networks initiated by cytokines are fine-tuned by transient phosphorylation events. This issue contains 3 articles focused on immune/cytokine signaling. The article by Osinalde et al., describes the utility of SILAC-based phosphoproteomic approach to quantitatively compare the complex signaling networks triggered by IL-2 and IL-15. Despite being highly similar, their study reveals non-identical IL-2 and IL-15-mediated signaling networks. Pinto et al., also employed SILAC-based global quantitative phosphoproteomic analysis to delineate the signaling mechanisms mediated by IL-33. This study is the first quantitative analysis of IL-33-regulated phosphoproteome. The findings from this study should significantly expand the understanding of IL-33 mediated signaling events. In order to gain better understanding of the host-pathogen interactions, immune functionality and signaling in Kuppfer cells, Tweedell et al., compared the proteome profile of an immortalized rat Kupffer cell line, RKC1 with primary rat Kupffer cells (PRKC) to characterize their respective responses to lipopolysaccharide (LPS)-mediated immune stimulation. The data provides evidence of differences in the responses of the two cell types to inflammatory stimulus. The study highlights the need for studies focused on KC-pathogen interactions and microbial pathogenesis. Apart from studying the phosphorylation changes, two articles in this issue report strategies to identify and characterize other PTMs that will provide a better understanding of signaling regulation. Zhao and colleagues report an in-depth proteomic analysis of human embryonic stem cells (hESCs) characterizing the proteome, secretome, phosphoproteome and O-GlcNAcmodified proteins in these cells. Yang et al., compared the serum glycoproteome obtained from
C 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.proteomics-journal.com
182
Proteomics 2015, 15, 179–182
a canine model of dyssynchronous heart failure (DHF) and cardiac resynchronization therapy (CRT) to normal. The study identifies glycopeptides in DHF which were reverted to normal levels after cardiac resynchronization therapy, suggesting molecular changes underlying therapy reflected in the serum. Kang et al., in their article describe a novel chemical enrichment method involving fluorinated carbon tags to enrich nitrosylated proteins. They used Saccharomyces cerevisiae as a model to investigate the potential roles of protein tyrosine nitration in response to the mating signal. Zhong and colleagues employed SILAC-based quantitative proteomics to compare site-specific phosphorylation in O-GlcNAc transferase (OGT) WT and Null cells. Their data suggest that deletion of OGT has a profound effect on the phosphorylation of cell cycle and DNA damage response proteins. This study provides key insights into O-GlcNAc mediated regulation of cellular processes such as the cell cycle, genomic stability, and lysosomal biogenesis. The article by Wong et al., describes the importance of biological networks in identifying relationships between network topology and protein functions, and suggests that the identification of differences between healthy and diseased tissues should include differences in network structures. They developed a graph-based approach that systematically characterizes network structure differences between any graphs, and as a prototype used differential graphlet communities for detecting deregulated subgraphs between any graphs for identifying lung cancer-specific differences between normal and tumor. Finally, as a Technical Brief contribution, Han et al., present a simple, adaptable, integrated multistep enzyme digestion, enrichment, database search strategy to improve coverage of the phosphoproteome from lower sample amounts without the need for prefractionation. We would like to thank all authors for their valuable contributions and everybody else who helped to realize this special issue. We also wish to thank the Editor-in-Chief Professor Michael J. Dunn and the Managing Editor Dr. Hans-Joachim Kraus for their contribution in making this Special Issue possible. We hope that this issue will be a valuable source of information on the current developments in the rapidly evolving field of signal transduction.
Akhilesh Pandey
Michael F. Moran
C 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.proteomics-journal.com
Proteomics 2015, 15, 179–182
Editorial Signal Transduction
Cells respond to various signals that govern their basic and specific cellular processes. A thorough understanding of the molecular mechanisms involved in cellular signaling is essential as aberrant signaling pathways are implicated in a number of diseases. Studying signaling in disease states forms the basis to developing novel therapeutic strategies. To understand signaling mechanisms in detail, systematic approaches have been developed to comprehensively characterize post-translational modifications (PTMs) such as phosphorylation under various conditions. Recent advances in mass spectrometry-based and array-based approaches have made it possible for the global characterization of signaling pathways. This Special Issue of PROTEOMICS brings together a collection of proteomics studies on signaling carried out by experts in the field of proteomics. This issue comprises a total of 36 contributions from various experts in the field of proteomics and signaling research. The compiled articles cover various topics relevant to the current progress in PTM analysis and delineating signaling mechanisms in health and disease. The first part of this special issue consists of 10 review articles covering diverse areas of research on cell signaling and disease. To date, several approaches have been developed to characterize signaling pathways. In the past decade, mass spectrometry has been used extensively in biological research and has aided effectively in addressing important biological questions. Three groups independently review the current progress in the understanding signaling networks using proteomics-based approaches. The review by Li et al., focuses on recent advances in affinity purification-MS to study protein-protein interactions. Vivelo et al., review in detail the strategies employed for efficient enrichment of ADP-ribosylated proteins and their associated proteins by mass spectrometry, their advantages, limitations and pitfalls. Gahoi et al., review the advantages, disadvantages and applications of various array-based techniques to study the interactions and modifications of biomolecules, their association with signaling pathways and their correlation with disease pathobiology. SRC, a non-receptor tyrosine kinase is a critical regulator of signal transduction plays an essential role in controlling cell growth and migration. Deregulation in SRC signaling is frequently observed in human cancer and is thought to play important roles during tumourigenesis. Sirvent et al., review the current phosphoproteomic strategies that have provided new insights into SRC signaling in normal and cancer cells. Batkulwar and colleagues review the signaling pathways activated by receptor for advanced glycation end products (RAGE) activated kinases. The article also provides insight on the plausible role of RAGE activated phosphoproteome in several diseases. Two reviews in the issue focus on the emerging role of extracellular vesicles as mediators of signaling by means of protein and RNA transfer through paracrine and autocrine manner. The article by Gangoda et al., provides a comprehensive review on extracellular vesicles (EVs) as mediators of signal transduction in cancer as well as neurodegenerative diseases. The authors also emphasize the need for additional studies to obtain a clear understanding of the complex role that extracellular vesicles play in physiological and pathological conditions. Havrylov et al., review the current progresses and challenges in proteomic strategies employed to characterize proteins and PPIs in these invasive cell structures. The other reviews focus on the current progress in elucidation of signaling mechanisms. Yuan and colleagues review the recent advances in the proteomics approaches developed to understand the altered functions of redox sensors and its role in cancer. Angiogenesis is a vital physiological process and plays an important role in numerous pathological conditions. Rahimi and Costello review the significance of post-translational modifications on vascular endothelial growth factor receptor-2 (VEGFR-2) in signaling, angiogenesis and potential therapeutic C 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
Akhilesh Pandey
Michael F. Moran
www.proteomics-journal.com
180
Proteomics 2015, 15, 179–182
potential. Mauvoisin and colleagues review the current progress, challenges and opportunities in obtaining a detailed understanding of circadian biology using proteomic approaches. Oncogene-driven signaling networks are highly dynamic. In-depth analysis of these signaling networks and the mechanisms of therapeutic adaptation will enable the development of novel therapeutic regimes, and uncover proteome-based biomarkers to guide in their application. In the study by Blair et al., the signaling changes observed upon PIK3CA mutation was investigated by employing a SILAC-based quantitative phosphoproteomics approach. This study is an excellent example of using this high throughput strategy to study changes in the dynamics of phosphorylation induced by oncogenic mutations in isogenic knock-in cell lines thus unraveling new signaling pathways with potential therapeutic value. In another study, Fedorenko et al., present the first systems level view of adaptive and basal phosphotyrosine signaling in BRAF- and NRAS-mutant in melanoma. Although poorly characterized at a systems level, these adaptations play a key role in therapeutic escape. The study by Zhang et al. highlights the utility of phosphoproteomic studies in the identification of altered signaling pathways in response to inherent mutations in epidermal growth factor receptor (EGFR) in lung adenocarcinoma cells. This is the first report examining erlotinib treatment-induced global phosphorylation changes and provides novel insights into signaling downstream of mutant EGFRs in lung adenocarcinoma. The article by Lemeer and colleagues compares the differential proteomic and kinome profiles between myoma and healthy myometrium samples and identifies molecular signatures as potential biomarkers or drug targets. Since current treatment modalities for myomas include surgical resection of the lesion or hysterectomy, this study could lead to potential benefits to clinicians in providing an alternative to invasive surgery. The relationship between the current histological-based characterization of epithelial ovarian carcinoma and activated signaling networks is “Studying signaling in dispoorly characterized. Sereni et al., in their study employed drug targetease states forms the basis to based protein signaling activation mapping to evaluate the characterization developing novel therapeutic of epithelial ovarian carcinoma subtypes based on activated protein signaling network architecture rather than histology. Their analysis revealed five strategies . . . Recent advances pathway-driven clusters indicating that epithelial ovarian carcinomas are in mass spectrometry-based extremely heterogeneous and classic histopathological categorization alone and array-based approaches is inadequate to classify cancer subtypes. To identify activated signaling pathways in esophageal squamous cell carhave made it possible for the cinoma, Syed et al., carried out phosphotyrosine profiling of ESCC cell lines global characterization of sigand observed hyperphosphorylation of EPHA2 and several proteins associnaling pathways.” ated with EPHA2 signaling in ESCC cell lines. Their study suggests EPHA2 as a promising therapeutic target in ESCC that warrants further evaluation. In another study by the same group, in vitro quantitative approach was employed to identify biomarkers in a panel of head and neck cancer cell lines. They observed an increased expression of high mobility group box 2 (HMGB2) in the cancer cell lines. siRNA-mediated silencing of HMGB2 increased the sensitivity of the HNSCC cell lines to cisplatin and 5-fluorouracil suggesting a combinatorial therapy would increase the efficacy of current treatment regimen. Sharma et al., employed an iTRAQ-based comparative proteomic approach to decipher differentially expressed proteins with potential implications in meningiomas. This study provides new opportunities for early detection of meningiomas. The findings of this study will provide new insights into the association of diverse signaling pathways including integrins, Wnt and FGR signaling with meningioma pathogenesis. Annexin-1, a calcium/phospholipid-binding protein plays an important role in several cancers. To understand its role in tumorogenesis, Swa and colleagues employed reductive dimethyl labeling strategy to identify the proteome differentially expressed in annexin-1 heterozygous positive and null mice. The findings of this study suggest a vital role of Annexin-1 in invasionmetastasis in breast cancer initiation. The trafficking of nascent and endocytosed proteins is a critical feature of signaling pathways involved in many diseases including cancer. Endocytosis of activated receptor tyrosine kinases (RTKs) is a key mechanism of downregulation, which is governed by various PTMs including phosphorylation. St-Germain et al., report that the activity of FGFR3, an RTK frequently activated in multiple myeloma and other malignancies, is modulated by two protein-tyrosine
C 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.proteomics-journal.com
Proteomics 2015, 15, 179–182
181
phosphatases (PTPN1 and PTPN2) as a function of subcellular localization. Knockdown of either PTP activated the receptor in the absence of ligand, leading to a model wherein the expression levels of cellular PTPs, in addition to several regulatory mechanisms, defines conditions that select for ectopic FGFR3 expression and activation during tumorigenesis. Krieger et al., employed an LC-MS/MS-based approach to elucidate some of the phosphorylation sites of Numb, an adaptor protein known to be involved in intracellular trafficking of receptors and in endocytosis. Their results reveal Numb as a substrate for Cdk5, known to regulate neuronal cell cycle arrest and differentiation, and pave the way for further studies into the complex CDK5/Numb/Rac-Rho downstream signaling cascades. An inability to deliver nascent CFTR protein to the cell surface, most frequently due to deletion of the codon encoding F508 , underlies cystic fibrosis. Pasyk et al. approached this protein trafficking defect as a signaling problem. They mapped and compared the phosphorylation status of protein kinase A sites in the phosphoregulatory R domain of wild type (WT) and F508del-CFTR protein. They demonstrate, for the first time, that the mutant protein F508delCFTR has an altered channel activity on the cell surface due to defective phosphorylation resulting from an allosteric change in its R domain. Multiplexed mass spectrometry-based strategies for the analysis of global proteome and phosphoproteome in biological systems have recently been improvised. Paulo and colleagues employed a tandem mass tag (TMT)-based quantitative proteomic approach to analyze the effect of two MEK signaling inhibitors on the phosphoproteomes of three tissues in murine models. MEK inhibitors decreased phosphorylation of proteins involved in ion transport and fluid balance in kidneys corroborating edema, an adverse event known to be associated with these inhibitors. The same group also characterized the proteome and phosphoproteomes of yeast deletion mutants of 14–3–3 orthologs and analyzed the effects of rapamycin treatment using a TMT-based quantitative proteomic strategy. Nirujogi et al., also employed multiplexed proteomic strategy to elucidate the effect of a nerve agent, VX, on the piriform cortex region of brains in rats. Their data reveal the complex toxicity pathway in this brain region following VX exposure and represents new opportunities for the development of novel or adjuvant countermeasures for VX exposure. Two groups have characterized the phosphoproteome of Alzheimer’s disease using refined strategies. Tan et al., employed a modified phosphoproteome enrichment strategy of TiO2 -based phosphoproteome enrichment by using phosphate ion at a low concentration as a non-phosphopeptide competitor to reduce background and a longer duration LC-MS analysis. In another study, Dammer et al., characterized the phosphoproteome of Alzheimer’s disease using immobilized metal affinity chromatography (IMAC) followed by liquid chromatographytandem mass spectrometry to identify phosphopeptides and identified crosstalk between kinases and small heat shock proteins. Early signaling networks initiated by cytokines are fine-tuned by transient phosphorylation events. This issue contains 3 articles focused on immune/cytokine signaling. The article by Osinalde et al., describes the utility of SILAC-based phosphoproteomic approach to quantitatively compare the complex signaling networks triggered by IL-2 and IL-15. Despite being highly similar, their study reveals non-identical IL-2 and IL-15-mediated signaling networks. Pinto et al., also employed SILAC-based global quantitative phosphoproteomic analysis to delineate the signaling mechanisms mediated by IL-33. This study is the first quantitative analysis of IL-33-regulated phosphoproteome. The findings from this study should significantly expand the understanding of IL-33 mediated signaling events. In order to gain better understanding of the host-pathogen interactions, immune functionality and signaling in Kuppfer cells, Tweedell et al., compared the proteome profile of an immortalized rat Kupffer cell line, RKC1 with primary rat Kupffer cells (PRKC) to characterize their respective responses to lipopolysaccharide (LPS)-mediated immune stimulation. The data provides evidence of differences in the responses of the two cell types to inflammatory stimulus. The study highlights the need for studies focused on KC-pathogen interactions and microbial pathogenesis. Apart from studying the phosphorylation changes, two articles in this issue report strategies to identify and characterize other PTMs that will provide a better understanding of signaling regulation. Zhao and colleagues report an in-depth proteomic analysis of human embryonic stem cells (hESCs) characterizing the proteome, secretome, phosphoproteome and O-GlcNAcmodified proteins in these cells. Yang et al., compared the serum glycoproteome obtained from
C 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.proteomics-journal.com
182
Proteomics 2015, 15, 179–182
a canine model of dyssynchronous heart failure (DHF) and cardiac resynchronization therapy (CRT) to normal. The study identifies glycopeptides in DHF which were reverted to normal levels after cardiac resynchronization therapy, suggesting molecular changes underlying therapy reflected in the serum. Kang et al., in their article describe a novel chemical enrichment method involving fluorinated carbon tags to enrich nitrosylated proteins. They used Saccharomyces cerevisiae as a model to investigate the potential roles of protein tyrosine nitration in response to the mating signal. Zhong and colleagues employed SILAC-based quantitative proteomics to compare site-specific phosphorylation in O-GlcNAc transferase (OGT) WT and Null cells. Their data suggest that deletion of OGT has a profound effect on the phosphorylation of cell cycle and DNA damage response proteins. This study provides key insights into O-GlcNAc mediated regulation of cellular processes such as the cell cycle, genomic stability, and lysosomal biogenesis. The article by Wong et al., describes the importance of biological networks in identifying relationships between network topology and protein functions, and suggests that the identification of differences between healthy and diseased tissues should include differences in network structures. They developed a graph-based approach that systematically characterizes network structure differences between any graphs, and as a prototype used differential graphlet communities for detecting deregulated subgraphs between any graphs for identifying lung cancer-specific differences between normal and tumor. Finally, as a Technical Brief contribution, Han et al., present a simple, adaptable, integrated multistep enzyme digestion, enrichment, database search strategy to improve coverage of the phosphoproteome from lower sample amounts without the need for prefractionation. We would like to thank all authors for their valuable contributions and everybody else who helped to realize this special issue. We also wish to thank the Editor-in-Chief Professor Michael J. Dunn and the Managing Editor Dr. Hans-Joachim Kraus for their contribution in making this Special Issue possible. We hope that this issue will be a valuable source of information on the current developments in the rapidly evolving field of signal transduction.
Akhilesh Pandey
Michael F. Moran
C 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.proteomics-journal.com
