Paul Aiyetan

• Johns Hopkins University

Background: There is a need for diagnostic tests for screening, triaging and staging of epithelial ovarian cancer (EOC). Glycoproteomics of blood samples has shown promise for biomarker discovery. Methods: We applied glycoproteomics to serum of people with EOC or benign pelvic masses and healthy controls. A total of 653 analytes were quantified...

Background Immune checkpoint inhibitors (ICIs) have revolutionized melanoma treatment, necessitating predictive biomarkers to identify patients likely to benefit. To that end, this study leverages a novel platform that combines liquid chromatography/mass spectrometry with a proprietary artificial-intelligence-based data processing engine, allowing...

The clinical success of immune-checkpoint inhibitors (ICI) in both resected and metastatic melanoma has confirmed the validity of therapeutic strategies that boost the immune system to counteract cancer. However, half of patients with metastatic disease treated with even the most aggressive regimen do not derive durable clinical benefit. Thus, ther...

Background: Neuroblastoma (NB) is the 3rd most common childhood cancer and accounts for 15% of all pediatric cancer deaths. Recently, immunotherapy using monoclonal antibodies targeting GD2 have improved survival rates for some patients with NB. Unfortunately, this response is not uniform, suggesting an incomplete understanding of the underlying im...

Minimally invasive technologies for early diagnosis of epithelial ovarian cancer (EOC) remain an unmet clinical need. CA-125, a tumor marker secreted into the circulation, is utilized to monitor treatment response and disease relapse in EOC, but has limited utility in accurately triaging patients with pelvic masses of unknown histology. To address...

Background: Neuroblastoma (NB) is the 3rd most common childhood cancer and accounts for 15% of all pediatric cancer deaths. Recently, immunotherapy using monoclonal antibodies targeting GD2 have improved survival rates for some patients with NB. Unfortunately, this response is not uniform across patients, which suggests an incomplete understanding...

e17604 Background: Ovarian cancer (OC) is the fifth- leading cause of cancer-related deaths among women, and the most lethal gynecological cancer. Currently available biomarkers, including CA-125 and HE4, show suboptimal diagnostic performance for differentiating among benign and malignant pelvic tumors, and the early recognition of OC. Differentia...

With an overall lifetime risk of about 4.3% and 4.0%, in men and women respectively, colorectal cancer remains the third leading cause of cancer-related deaths in the United States. In persons aged 55 and below, its rate increased at 1% per year in the years 2008 to 2017 despite the steady decline associated with improved screening, early diagnosis...

Elucidating mechanistic relationships between and among intracellular macromolecules is fundamental to understanding the molecular basis of normal and diseased processes. Here, we introduce jFuzzyMachine – a fuzzy logic-based regulatory network inference engine for high-throughput biological data. We describe its design and implementation. We demon...

Motivation Although it circumvents hyperparameter estimation of ordinary differential equation (ODE) based models and the complexities of many other models, the computational time complexity of a fuzzy logic regulatory model inference problem, particularly at higher order of interactions, quickly approaches those of computationally intractable prob...

A FAIR Principle Data Model for Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) and the Frederick National Laboratory Data Coordinating Center - Volume 25 Supplement - Paul Aiyetan, Kedar Narayan, David Mott, Rajani Kuchipudi, Corinne Zeitler, Debra Hope, Uma Mudunuri, Andrew Quong

The Frederick National Laboratory for Cancer Research hosts a Data Coordinating Center and Toolset (the Metadata Designer plus Validator) hereafter referred to as the DCC that embodies a scalable, next-generation biological and cancer research data repository that is flexible, intuitive, and adaptive. The DCC provides integrated management of datas...

The Frederick National Laboratory for Cancer Research hosts a Data Coordinating Center and Toolset (the Metadata Designer plus Validator) hereafter referred to as the DCC that embodies a scalable, next-generation biological and cancer research data repository that is flexible, intuitive, and adaptive. The DCC provides integrated management of datas...

Rapid development and wide adoption of mass spectrometry-based proteomics technologies have empowered scientists to study proteins and their modifications in complex samples on a large scale. This progress has also created unprecedented challenges for individual labs to store, manage and analyze proteomics data, both in the cost for proprietary sof...

Although XPO5 has been characterized to have tumor-suppressor features in the miRNA biogenesis pathway, the impact of altered expression of XPO5 in cancers is unexplored. Here we report a novel "oncogenic" role of XPO5 in advanced prostate cancer. Using prostate cancer models, we found that excess levels of XPO5 override the inhibitory effect of th...

Global proteomics LC-MS/MS iTRAQ data in LAPC4 cells.

Supplementary Material iTRAQ LC-MS/MS proteoimcs Data for LAPC4 cells.

Fold mRNA in XPO5 shRNA and Control DU145 cells.

Purpose: To identify changes in the outer retina in areas without atrophy or flecks of Stargardt disease (STGD) using spectral-domain optical coherence tomography. Methods: Twenty-three STGD patients and 26 control subjects were assessed for outer retina (from the outer border of Bruch membrane [BrM] to the inner border of the inner segment elli...

Selected and multiple reaction monitoring involves monitoring a multiplexed assay of proteotypic peptides and associated transitions in mass spectrometry runs. To describe peptide and associated transitions as stable, quantifiable, and reproducible representatives of proteins of interest, experimental and analytical validation is required. However,...

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 remod...

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...

Protein glycosylation is one of the most common protein modifications, and the quantitative analysis of glycoproteins has the potential to reveal biological functions and their association with disease. However, the high throughput accurate quantification of glycoproteins is technically challenging due to the scarcity of robust assays to detect and...

MALDI-TOF profiling of low molecular weight (LMW) peptides (peptidome) usage is limited due to the lack of reproducibility from the confounding inferences of sample preparation, data acquisition and processing. We applied MALDI-TOF analysis to profile urine peptidome with the aims to: 1) compare centrifugal ultrafiltration and dialysis pre-treatmen...

Mass spectrometry based glycoproteomics has become a major means of identifying and characterizing previously N-linked glycan attached loci (glycosites). In the bottom-up approach, several factors which include but not limited to sample preparation, mass spectrometry analyses, and protein sequence database searches result in previously N-linked pep...

Purpose: Extracellular proteins are easily accessible, which presents a subproteome of molecular targets that have high diagnostic and therapeutic potential. Efforts have been made to catalog the cardiac extracellular matridome and analyze the topology of identified proteins for the design of therapeutic targets. Although many bioinformatics tools...

Mass spectrometry based glycoproteomics has become a major means of identifying and characterizing previously N-linked glycan attached loci (glycosites). In the bottomup approach, several factors which include but not limited to sample preparation, mass spectrometry analyses, and protein sequence database searches result in previously N-linked pept...

Proteome Discoverer is one of many tools used for protein database search and peptide to spectrum assignment in mass spectrometry-based proteomics. However, the inadequacy of conversion tools makes it challenging to compare and integrate its results to those of other analytical tools. Here we present M2Lite, an open-source, light-weight, easily plu...

Glycoproteins secreted into plasma from T cells infected with human immunodeficiency virus (HIV) latent infection may provide insight into understanding the host response to HIV infection in vivo. Glycoproteomics, which evaluates the level of the glycoproteome, remains a novel approach to study this host response to HIV. In order to identify human...

Protein glycosylation has long been recognized as one of the most common post-translational modifications. Most membrane proteins and extracellular proteins are N-linked glycosylated and they account for the majority of current clinical diagnostic markers or therapeutic targets. Quantitative proteomic analysis of detectable N-linked glycoproteins f...

Histone deacetylases (HDACs) have emerged as important targets for cancer treatment. HDAC-inhibitors (HDACis) are well tolerated in patients and have been approved for the treatment of patients with cutaneous T-cell lymphoma (CTCL). To improve the clinical benefit of HDACis in solid tumors, combination strategies with HDACis could be employed. In t...

Cytological examination of cells from bronchoalveolar lavage (BAL) is commonly used for the diagnosis of lung cancer. Proteins released from lung cancer cells into BAL may serve as biomarkers for cancer detection. In this study, N-glycoproteins in 8 cases of BAL fluid, as well as 8 lung adenocarcinoma tissues and 8 tumor-matched normal lung tissues...

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 has been difficult. To overcome this difficulty we pursued derivatization met...

This study was carried out to determine the prevalence of HIV-positive orphans and to compare their socio-demographic and clinical characteristics with HIV-positive non-orphans. A survey was conducted among patients attending the infectious disease clinic of the Department of Paediatrics, University College Hospital, Ibadan, Nigeria between July 20...