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Paul Aiyetan

Bio: Paul Aiyetan is an academic researcher from Johns Hopkins University. The author has contributed to research in topics: Medicine & Glycoprotein. The author has an hindex of 12, co-authored 19 publications receiving 1111 citations. Previous affiliations of Paul Aiyetan include Johns Hopkins University School of Medicine & University College Hospital, Ibadan.

Papers
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Journal ArticleDOI
28 Jul 2016-Cell
TL;DR: A view of how the somatic genome drives the cancer proteome and associations between protein and post-translational modification levels and clinical outcomes in HGSC is provided.

728 citations

Journal ArticleDOI
TL;DR: A chemoenzymatic method called solid phase extraction of N-linked glycans and glycosite-containing peptides (NGAG) is described for the comprehensive characterization of glycoproteins that is able to determine glycan heterogeneity for individual glycosites in addition to providing information about the total N- linked glycan, glycosite -containing peptide and glycoprotein content of complex samples.
Abstract: Comprehensive characterization of protein glycosylation is critical for understanding the structure and function of glycoproteins. However, due to the complexity and heterogeneity of glycoprotein conformations, current glycoprotein analyses focus mainly on either the de-glycosylated glycosylation site (glycosite)-containing peptides or the released glycans. Here, we describe a chemoenzymatic method called solid phase extraction of N-linked glycans and glycosite-containing peptides (NGAG) for the comprehensive characterization of glycoproteins that is able to determine glycan heterogeneity for individual glycosites in addition to providing information about the total N-linked glycan, glycosite-containing peptide and glycoprotein content of complex samples. The NGAG method can also be applied to quantitatively detect glycoprotein alterations in total and site-specific glycan occupancies.

191 citations

01 Jun 2016
TL;DR: In this article, a detailed analysis of the molecular components and underlying mechanisms associated with ovarian cancer was provided, such as how different copy-number alterna-tions in the Proteome, the proteins associated with chromosomal instability, the sets of signalingpathways that diverse genome rearrangements converge on, and the ones associated with short overall survival.
Abstract: To provide a detailed analysis of the molecular com-ponents and underlying mechanisms associatedwith ovarian cancer, we performed a comprehensivemass-spectrometry-based proteomic characteriza-tion of 174 ovarian tumors previously analyzed byThe Cancer Genome Atlas (TCGA), of which 169were high-grade serous carcinomas (HGSCs). Inte-grating our proteomic measurements with thegenomic data yielded a number of insights into dis-ease, such as how different copy-number alterna-tionsinfluencetheproteome,theproteinsassociatedwith chromosomal instability, the sets of signalingpathways that diverse genome rearrangementsconverge on, and the ones most associated withshort overall survival. Specific protein acetylationsassociated with homologous recombination defi-ciency suggest a potential means for stratifying pa-tients for therapy. In addition to providing a valuableresource,thesefindingsprovideaviewofhowtheso-maticgenomedrivesthecancerproteomeandasso-ciations between protein and post-translationalmodification levels and clinical outcomes in HGSC.

160 citations

Journal ArticleDOI
TL;DR: This new quantitative glycoform profiling method with use of MALDI-TOF in positive ion mode was validated by first comparing N-glycans isolated from fetuin and serum and was exploited to analyze the effects of increased metabolic flux through the sialic acid pathway in SW1990 pancreatic cancer cells by using a colabeling strategy with light and heavy toluidine.
Abstract: The analysis of sialylated glycans is critical for understanding the role of sialic acid in normal biological processes as well as in disease. However, the labile nature of sialic acid typically renders routine analysis of this monosaccharide by mass spectrometric methods difficult. To overcome this difficulty we pursued derivatization methodologies, extending established acetohydrazide approaches to aniline-based methods, and finally to optimized p-toluidine derivatization. This new quantitative glycoform profiling method with use of MALDI-TOF in positive ion mode was validated by first comparing N-glycans isolated from fetuin and serum and was then exploited to analyze the effects of increased metabolic flux through the sialic acid pathway in SW1990 pancreatic cancer cells by using a colabeling strategy with light and heavy toluidine. The latter results established that metabolic flux, in a complementary manner to the more well-known impact of sialyltransferase expression, can critically modulate the si...

79 citations

Journal ArticleDOI
TL;DR: A new cell-signaling role for MMP-9 is revealed through CD36 degradation to regulate macrophage phagocytosis and neutrophil apoptosis in post-myocardial infarction left ventricular remodeling.
Abstract: Background —After myocardial infarction (MI), the left ventricle (LV) undergoes a wound healing response that includes the robust infiltration of neutrophils and macrophages to facilitate removal of dead myocytes as well as turnover of the extracellular matrix (ECM). Matrix metalloproteinase (MMP)-9 is a key enzyme that regulates post-MI LV remodeling. Methods and Results —Infarct regions from wild type and MMP-9 null mice (n=8/group) analyzed by glycoproteomics showed that of 541 N -glycosylated proteins quantified, 45 proteins were at least two-fold up- or down-regulated with MMP-9 deletion (all p<0.05). Cartilage intermediate layer protein (CILP) and platelet glycoprotein 4 (CD36) were identified as having the highest fold increase in MMP-9 null mice. By immunoblotting, CD36 but not CILP decreased steadily over the time course post-MI, which identified CD36 as a candidate MMP-9 substrate. MMP-9 was confirmed in vitro and in vivo to proteolytically degrade CD36. In vitro stimulation of day 7 post-MI macrophages with MMP-9 or a CD36 blocking peptide reduced phagocytic capacity. Dual immunofluorescence revealed concomitant accumulation of apoptotic neutrophils in the MMP-9 null group compared to WT. In vitro stimulation of isolated neutrophils with MMP-9 decreased neutrophil apoptosis, indicated by reduced caspase-9 expression. Conclusions —Our data reveals a new cell signaling role for MMP-9 through CD36 degradation to regulate macrophage phagocytosis and neutrophil apoptosis.

67 citations


Cited by
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Journal ArticleDOI
TL;DR: The identification of molecules that modulate the release of NETs has helped to refine the view of the role of neutrophils in immune protection, inflammatory and autoimmune diseases and cancer.
Abstract: Neutrophils are innate immune phagocytes that have a central role in immune defence. Our understanding of the role of neutrophils in pathogen clearance, immune regulation and disease pathology has advanced dramatically in recent years. Web-like chromatin structures known as neutrophil extracellular traps (NETs) have been at the forefront of this renewed interest in neutrophil biology. The identification of molecules that modulate the release of NETs has helped to refine our view of the role of NETs in immune protection, inflammatory and autoimmune diseases and cancer. Here, I discuss the key findings and concepts that have thus far shaped the field of NET biology.

1,564 citations

Journal ArticleDOI
TL;DR: It is demonstrated that LinkedOmics provides a unique platform for biologists and clinicians to access, analyze and compare cancer multi-omics data within and across tumor types.
Abstract: The LinkedOmics database contains multi-omics data and clinical data for 32 cancer types and a total of 11 158 patients from The Cancer Genome Atlas (TCGA) project. It is also the first multi-omics database that integrates mass spectrometry (MS)-based global proteomics data generated by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) on selected TCGA tumor samples. In total, LinkedOmics has more than a billion data points. To allow comprehensive analysis of these data, we developed three analysis modules in the LinkedOmics web application. The LinkFinder module allows flexible exploration of associations between a molecular or clinical attribute of interest and all other attributes, providing the opportunity to analyze and visualize associations between billions of attribute pairs for each cancer cohort. The LinkCompare module enables easy comparison of the associations identified by LinkFinder, which is particularly useful in multi-omics and pan-cancer analyses. The LinkInterpreter module transforms identified associations into biological understanding through pathway and network analysis. Using five case studies, we demonstrate that LinkedOmics provides a unique platform for biologists and clinicians to access, analyze and compare cancer multi-omics data within and across tumor types. LinkedOmics is freely available at http://www.linkedomics.org.

1,256 citations

Journal ArticleDOI
TL;DR: Different classes of HDAC inhibitors, mechanisms of their actions and novel results of preclinical and clinical studies are summarized, including the combination with other therapeutic modalities are discussed.
Abstract: Carcinogenesis cannot be explained only by genetic alterations, but also involves epigenetic processes. Modification of histones by acetylation plays a key role in epigenetic regulation of gene expression and is controlled by the balance between histone deacetylases (HDAC) and histone acetyltransferases (HAT). HDAC inhibitors induce cancer cell cycle arrest, differentiation and cell death, reduce angiogenesis and modulate immune response. Mechanisms of anticancer effects of HDAC inhibitors are not uniform; they may be different and depend on the cancer type, HDAC inhibitors, doses, etc. HDAC inhibitors seem to be promising anti-cancer drugs particularly in the combination with other anti-cancer drugs and/or radiotherapy. HDAC inhibitors vorinostat, romidepsin and belinostat have been approved for some T-cell lymphoma and panobinostat for multiple myeloma. Other HDAC inhibitors are in clinical trials for the treatment of hematological and solid malignancies. The results of such studies are promising but further larger studies are needed. Because of the reversibility of epigenetic changes during cancer development, the potency of epigenetic therapies seems to be of great importance. Here, we summarize the data on different classes of HDAC inhibitors, mechanisms of their actions and discuss novel results of preclinical and clinical studies, including the combination with other therapeutic modalities.

815 citations

Journal ArticleDOI
TL;DR: The potential for combining diverse types of data and the utility of this approach in human health and disease is discussed and examples of data integration to understand, diagnose and inform treatment of diseases, including rare and common diseases as well as cancer and transplant biology.
Abstract: Advances in omics technologies - such as genomics, transcriptomics, proteomics and metabolomics - have begun to enable personalized medicine at an extraordinarily detailed molecular level. Individually, these technologies have contributed medical advances that have begun to enter clinical practice. However, each technology individually cannot capture the entire biological complexity of most human diseases. Integration of multiple technologies has emerged as an approach to provide a more comprehensive view of biology and disease. In this Review, we discuss the potential for combining diverse types of data and the utility of this approach in human health and disease. We provide examples of data integration to understand, diagnose and inform treatment of diseases, including rare and common diseases as well as cancer and transplant biology. Finally, we discuss technical and other challenges to clinical implementation of integrative omics.

589 citations

Journal ArticleDOI
TL;DR: This review collected the tools and methods that adopt integrative approach to analyze multiple omics data and summarized their ability to address applications such as disease subtyping, biomarker prediction, and deriving insights into the data.
Abstract: To study complex biological processes holistically, it is imperative to take an integrative approach that combines multi-omics data to highlight the interrelationships of the involved biomolecules and their functions. With the advent of high-throughput techniques and availability of multi-omics data generated from a large set of samples, several promising tools and methods have been developed for data integration and interpretation. In this review, we collected the tools and methods that adopt integrative approach to analyze multiple omics data and summarized their ability to address applications such as disease subtyping, biomarker prediction, and deriving insights into the data. We provide the methodology, use-cases, and limitations of these tools; brief account of multi-omics data repositories and visualization portals; and challenges associated with multi-omics data integration.

542 citations