OBJECTIVES/GOALS: Our objective is to establish a proteomic protein labeling method from tumor tissue and blood samples obtained from patients undergoing surgery for pancreatic cancer in Puerto Rico. Our goal is to discover potential biomarkers in the patient tumor/blood samples that are not expressed in normal control samples obtained from potential organ donors. METHODS/STUDY POPULATION: A pilot study with ten patients undergoing surgery for pancreatic cancer will obtain tumor tissue and blood samples. Protein extracts isolated from tissue/cells will be reduced, alkylated, and digested overnight. Samples will be labeled with TMT reagents and mixed before fractionation and cleanup. Labeled samples will be analyzed with a high-resolution Orbitrap LC-MS/MS before data analysis to identify peptides and quantify the reporter ions. The altered proteins will be analyzed by ELISA to confirm their presence. The protein arrangements will be compared with results from proteomic profile banks to assess their prevalence. As controls, parallel protein analyses will be performed on normal tissue/blood samples from organ donors, facilitated by our local organ procurement organization. RESULTS/ANTICIPATED RESULTS: We anticipate finding proteogenomic material defining PC and new proteomic subtypes not previously described in this population. In addition, studying protein overexpression and underexpression can identify relevant genes and potential biomarkers. We hypothesize that PC in the Hispanic population will show slight variations in tumor protein expression than in other populations, which could lead to the discovery of a new Hispanic-specific biomarker. DISCUSSION/SIGNIFICANCE: We expect to provide essential information that will influence the next steps in developing future screening tests. Identifying specific proteins with the potential to become a preventive test should eventually lead to a reduction in morbidity and mortality of PC. The results of this work should lay the foundation that can guide future research.

Hypospadias, which is characterised by the displacement of the urethral meatus from its typical anatomical location in males, shows various degrees of severity. In this systematic review, we surveyed our current understanding of the genetics of isolated hypospadias in humans according to the severity of the condition. We found that sequencing and genotyping approaches were the preferred methods of study and that single nucleotide polymorphisms were the most common finding associated with hypospadias. Most genes fell into four gene-pathway categories related to androgens, oestrogens, growth factors, or transcription factors. Few hypospadias studies classify their findings by severity. Taken together, we argue that it is advantageous to take into consideration the severity of the condition in search of novel candidates in the aetiology of hypospadias.Abbreviations: AR: androgen receptor; ATF3: activating transcription factor 3; BMP4: bone morphogenetic protein 4; BMP7: bone morphogenetic protein 7; CYP17: steroid 17-alpha-hydroxylase/17,20 lyase; CYP1A1: cytochrome P450 1A1; CYP3A4: cytochrome P450 3A4; CNVs: copy number variants; DGKK: diacylglycerol kinase kappa; ESR1: oestrogen receptor 1; ESR2: oestrogen receptor 2; FGF8: fibroblast growth factor 8; FGF10: fibroblast growth factor 10; FGFR2: fibroblast growth factor receptor 2; HOXA4: homeobox protein Hox-A4; HOXB6: homeobox protein Hox-B6; HSD17B3: hydroxysteroid 17-beta dehydrogenase 3; MAMLD1: mastermind-like domain-containing protein 1; SF-1: splicing factor 1; SHH: sonic hedgehog; SNPs: single nucleotide polymorphisms; SOX9: SRY-box 9; SRD5A2: steroid 5 alpha-reductase 2; SRY: sex-determining region Y protein; STAR: steroidogenic acute regulatory protein; STARD3: StAR-related lipid transfer protein 3; STS: steryl-sulfatase; WT1: Wilms tumour protein; ZEB1: zinc finger oestrogen-box binding homeobox 1

Background and Objective: Mild hypospadias is a birth congenital condition characterized by the relocation of the male urethral meatus from its typical anatomical position near the tip of the glans penis, to a lower ventral position up to the brim of the glans corona, which can also be accompanied by foreskin ventral deficiency. For the most part, a limited number of cases have known etiology. We have followed a high-throughput proteomics approach to study the proteome in mild hypospadias patients. Methods: Foreskin samples from patients with mild hypospadias were collected during urethroplasty, while control samples were collected during elective circumcision (n = 5/group). A high-throughput, quantitative proteomics approach based on multiplexed peptide stable isotope labeling (SIL) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis was used to ascertain protein abundance changes in hypospadias patients when compared to control samples. Results: A total of 4,815 proteins were quantitated (2,522 with at least two unique peptides). One hundred and thirty-three proteins from patients with mild hypospadias showed significant abundance changes with respect to control samples, where 38 proteins were increased, and 95 proteins were decreased. Unbiased functional biological analysis revealed that both mitochondrial energy production and apoptotic signaling pathways were enriched in mild hypospadias. Conclusions: This first comprehensive proteomics characterization of mild hypospadias shows molecular changes associated with essential cellular processes related to energy production and apoptosis. Further evaluation of the proteome may expand the search of novel candidates in the etiology of mild hypospadias and could also lead to the identification of biomarkers for this congenital urogenital condition.

Protein-protein interactions are an important mechanism for the regulation of enzyme function allowing metabolite channeling, crosstalk between pathways or the introduction of post-translational modifications. Therefore, a number of high-throughput studies have been carried out to shed light on the protein networks established under different pathophysiological settings. Surprisingly, this type of information is quite limited for enzymes of intermediary metabolism such as betaine homocysteine S-methyltransferase, despite its high hepatic abundancy and its role in homocysteine metabolism. Here, we have taken advantage of two approaches, affinity purification combined with mass spectrometry and yeast two-hybrid, to further uncover the array of interactions of betaine homocysteine S-methyltransferase in normal liver of Rattus norvegicus. A total of 131 non-redundant putative interaction targets were identified, out of which 20 were selected for further validation by coimmunoprecipitation. Interaction targets validated by two different methods include: S-methylmethionine homocysteine methyltransferase or betaine homocysteine methyltransferase 2, methionine adenosyltransferases α1 and α2, cAMP-dependent protein kinase catalytic subunit alpha, 4-hydroxyphenylpyruvic acid dioxygenase and aldolase b. Network analysis identified 122 nodes and 165 edges, as well as a limited number of KEGG pathways that comprise: the biosynthesis of amino acids, cysteine and methionine metabolism, the spliceosome and metabolic pathways. These results further expand the connections within the hepatic methionine cycle and suggest putative cross-talks with additional metabolic pathways that deserve additional research.

The proper handling of samples to be analyzed by mass spectrometry (MS) can guarantee excellent results and a greater depth of analysis when working in quantitative proteomics. This is critical when trying to assess non-traditional sources such as ear wax, saliva, vitreous humor, aqueous humor, tears, nipple aspirate fluid, breast milk/colostrum, cervical-vaginal fluid, nasal secretions, bronco-alveolar lavage fluid, and stools. We intend to provide the investigator with relevant aspects of quantitative proteomics and to recognize the most recent clinical research work conducted with atypical samples and analyzed by quantitative proteomics. Having as reference the most recent and different approaches used with non-traditional sources allows us to compare new strategies in the development of novel experimental models. On the other hand, these references help us to contribute significantly to the understanding of the proportions of proteins in different proteomes of clinical interest and may lead to potential advances in the emerging field of precision medicine.

Purpose Drug abuse is a major risk factor in the development and progression of HIV‐1. This study defines the alterations in the plasma proteome of HIV‐1‐infected women that use cocaine. Experimental design Plasma samples from 12 HIV‐seropositive Hispanic women under antiretroviral therapy were selected for this study. Six sample pairs were matched between nondrug users and cocaine users. After IgG and albumin depletion, SDS‐PAGE, and in‐gel digestion, peptides from nondrug users and cocaine users were labeled with 16 O and 18 O, respectively, and subjected to LC‐MS/MS and quantitation using Proteome Discover and QuiXoT softwares and validated by ELISA. Results A total of 1015 proteins were identified at 1% false discovery rates (FDR). Statistical analyses revealed 13 proteins with significant changes between the two groups, cocaine and noncocaine users ( p < 0.05). The great majority pertained to protection defense function and the rest pertained to transport, homeostatic, regulation, and binding of ligands. Apolipoprotein CIII was increased in plasma of HIV+ Hispanic women positive for cocaine compared to HIV+ nondrug users ( p ≤ 0.05). Conclusions and clinical relevance Increased human apolipoprotein CIII warrants that these patients be carefully monitored to avoid the increased risk of cardiovascular events associated with HIV, HAART, and cocaine use.

Statistical models for the analysis of protein expression changes by stable isotope labeling are still poorly developed, particularly for data obtained by O-16/O-18 labeling. Besides large scale test experiments to validate the null hypothesis are lacking. Although the study of mechanisms underlying biological actions promoted by vascular endothelial growth factor (VEGF) on endothelial cells is of considerable interest, quantitative proteomics studies on this subject are scarce and have been performed after exposing cells to the factor for long periods of time. In this work we present the largest quantitative proteomics study to date on the short term effects of VEGF on human umbilical vein endothelial cells by O-18/O-16 labeling. Current statistical models based on normality and variance homogeneity were found unsuitable to describe the null hypothesis in a large scale test experiment performed on these cells, producing false expression changes. A random effects model was developed including four different sources of variance at the spectrum-fitting, scan, peptide, and protein levels. With the new model the number of outliers at scan and peptide levels was negligible in three large scale experiments, and only one false protein expression change was observed in the test experiment among more than 1000 proteins. The new model allowed the detection of significant protein expression changes upon VEGF stimulation for 4 and 8 h. The consistency of the changes observed at 4 h was confirmed by a replica at a smaller scale and further validated by Western blot analysis of some proteins. Most of the observed changes have not been described previously and are consistent with a pattern of protein expression that dynamically changes over time following the evolution of the angiogenic response. With this statistical model the O-18 labeling approach emerges as a very promising and robust alternative to perform quantitative proteomics studies at a depth of several thousand proteins. Molecular & Cellular Proteomics 8: 1130-1149, 2009.

Estefania Nunez1, Elena Bonzon1, Horacio Serrano3, Marisol Ruiz2, Elisabet Miro-Casas2, Pedro J. Navarro1, Pablo Martinez-Acedo1, Daniel Perez-Hernandez1, David Garcia-Dorado2, Jesus Vazquez1 1Laboratorio de Quimica de Proteinas y Proteomica, Centro de Biologia Molecular Severo Ochoa, Madrid; 2Servicio de Cardiologia, Hospital Vall d’Hebron, Barcelona, Espana; 3Department of Biology, University of Puerto Rico in Arecibo, Puerto Rico, USA