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Supplementary figure 1 shows visualization of colonic stem cells using stem cell markers ASCL-2 and BMI-1 with negative controls in pigs. Supplementary figure 2 shows colonic stem cells using stem cell markers ASCL-2 and BMI-1 with negative controls in humans. Supplementary figure 3 shows a sketch illustrating the calculation of stem cell zone. Supplementary figure 4 shows separation of proteomic profiles of pigs by hierarchical clustering. Supplementary table 2 shows levels of individual vitamins and minerals in vitamin mix used for the diets. Supplementary table 3 shows levels of inflammatory markers in the colon. Supplementary table 4 shows levels of short chain fatty acids.

Supplementary table 1 shows body weight, daily weight gain and feed intake data.

Studies have shown a causal link between high-calorie diet (HCD) and colon cancer. However, molecular mechanisms are not fully elucidated. To understand etiology of HCD-induced colon carcinogenesis, we screened 10 pathways linked to elevated colonic cell proliferation and chronic inflammation in an HCD-consuming human-relevant pig model. We observed elevated colonic mucosal interleukin-6 (IL-6) expression in HCD-consuming pigs compared to standard diet controls (SD, P=.04), and IL-6 strongly correlated with Ki-67 proliferative index and zone, early biomarkers of colon cancer risk (r=0.604 and 0.743 and P=.017 and .002, respectively). Liquid chromatography-tandem mass spectrometry-based proteomic analysis and Ingenuity Pathway Analysis showed that HCD consumption altered IL-6 signaling pathway proteins (PI3KR4, IL-1α, Mapk10, Akt3, PIK3CG, PIK3R5, Map2k2). Furthermore, these proteins also correlated with Ki-67 proliferative index/zone. Anti-IL-6 therapeutics are available for treating colon cancer; however, they are expensive and induce negative side effects. Thus, whole foods could be a better way to combat low-grade chronic colonic inflammation and colon cancer. Whole plant foods have been shown to decrease chronic diseases due to the potential of anti-inflammatory dietary compounds acting synergistically. We observed that supplementation of HCD with anthocyanin-containing purple-fleshed potatoes (10% w/w), even after baking, suppressed HCD-induced IL-6 expression (P=.03) and the IL-6-related proteins IL-1α and Map2k1 (P≤.1). Our results highlight the importance of IL-6 signaling in diet-linked induction/prevention of colonic inflammation/cancer and demonstrate the potential of a food-based approach to target IL-6 signaling.

Protein S-nitrosation (SNO-protein), the nitric oxide-mediated posttranslational modification of cysteine thiols, is an important regulatory mechanism of protein function in both physiological and pathological pathways. A key first step toward elucidating the mechanism by which S-nitrosation modulates a protein's function is identification of the targeted cysteine residues. Here, we present a strategy for the simultaneous identification of SNO-cysteine sites and their cognate proteins to profile the brain of the CK-p25-inducible mouse model of Alzheimer's disease-like neurodegeneration. The approach-SNOTRAP (SNO trapping by triaryl phosphine)-is a direct tagging strategy that uses phosphine-based chemical probes, allowing enrichment of SNO-peptides and their identification by liquid chromatography tandem mass spectrometry. SNOTRAP identified 313 endogenous SNO-sites in 251 proteins in the mouse brain, of which 135 SNO-proteins were detected only during neurodegeneration. S-nitrosation in the brain shows regional differences and becomes elevated during early stages of neurodegeneration in the CK-p25 mouse. The SNO-proteome during early neurodegeneration identified increased S-nitrosation of proteins important for synapse function, metabolism, and Alzheimer's disease pathology. In the latter case, proteins related to amyloid precursor protein processing and secretion are S-nitrosated, correlating with increased amyloid formation. Sequence analysis of SNO-cysteine sites identified potential linear motifs that are altered under pathological conditions. Collectively, SNOTRAP is a direct tagging tool for global elucidation of the SNO-proteome, providing functional insights of endogenous SNO proteins in the brain and its dysregulation during neurodegeneration.

Mutation in the SHANK3 human gene leads to different neuropsychiatric diseases including Autism Spectrum Disorder (ASD), intellectual disabilities and Phelan-McDermid syndrome. Shank3 disruption in mice leads to dysfunction of synaptic transmission, behavior, and development. Protein S-nitrosylation, the nitric oxide (NO•)-mediated posttranslational modification (PTM) of cysteine thiols (SNO), modulates the activity of proteins that regulate key signaling pathways. We tested the hypothesis that Shank3 mutation would generate downstream effects on PTM of critical proteins that lead to modification of synaptic functions. SNO-proteins in two ASD-related brain regions, cortex and striatum of young and adult InsG3680(+/+) mice (a human mutation-based Shank3 mouse model), were identified by an innovative mass spectrometric method, SNOTRAP. We found changes of the SNO-proteome in the mutant compared to WT in both ages. Pathway analysis showed enrichment of processes affected in ASD. SNO-Calcineurin in mutant led to a significant increase of phosphorylated Synapsin1 and CREB, which affect synaptic vesicle mobilization and gene transcription, respectively. A significant increase of 3-nitrotyrosine was found in the cortical regions of the adult mutant, signaling both oxidative and nitrosative stress. Neuronal NO• Synthase (nNOS) was examined for levels and localization in neurons and no significant difference was found in WT vs. mutant. S-nitrosoglutathione concentrations were higher in mutant mice compared to WT. This is the first study on NO•-related molecular changes and SNO-signaling in the brain of an ASD mouse model that allows the characterization and identification of key proteins, cellular pathways, and neurobiological mechanisms that might be affected in ASD., Army Research Office Institute for Collaborative Biotechnologies (Grant W911NF-09-0001)

Basal colonic crypt stem cells are long lived and play a role in colon homeostasis. Previous evidence has shown that high-calorie diet (HCD) enhances colonic stem cell numbers and expansion of the proliferative zone, an important biomarker for colon cancer. However, it is not clear how HCD drives dysregulation of colon stem cell/colonocyte proliferative kinetics. We used a human-relevant pig model and developed an immunofluorescence technique to detect and quantify colonic stem cells. Pigs (n = 8/group) were provided either standard diet (SD; 5% fat) or HCD (23% fat) for 13 weeks. HCD- and SD-consuming pigs had similar total calorie intake, serum iron, insulin, and glucose levels. However, HCD elevated both colonic proliferative zone (KI-67) and stem cell zone (ASCL-2 and BMI-1). Proliferative zone correlated with elevated innate colonic inflammatory markers TLR-4, NF-κB, IL6, and lipocalin-2 (r ≥ 0.62, P = 0.02). Elevated gut bacterial phyla proteobacteria and firmicutes in HCD-consuming pigs correlated with proliferative and stem cell zone. Colonic proteome data revealed the upregulation of proteins involved in cell migration and proliferation and correlated with proliferative and stem cell zone expansion. Our study suggests that pig colon, unlike mice, has two distinct stem cells (ASCL-2 and BMI-1) similar to humans, and HCD increases expansion of colonic proliferative and stem cell zone. Thus, pig model can aid in the development of preventive strategies against gut bacterial dysbiosis and inflammation-promoted diseases, such as colon cancer. Cancer Prev Res; 10(8); 442–50. ©2017 AACR.

The expression of specificity protein 1 (Sp1) and survivin was evaluated in clinical specimens of epithelial ovarian cancer (EOC) patients. When compared to normal tissue, EOC samples showed high expression of Sp1 and survivin using qPCR (Sp1: ∼2-fold; survivin: ∼5-fold) and Western blot (Sp1: >2.6-fold; survivin: >100-fold). The Sp1 inhibitor, and anti-cancer small molecule, tolfenamic acid (TA), was tested to enhance the response of Cisplatin (Cis) in EOC cell lines. Cell viability (CellTiter-Glo), combination index (CalcuSyn software), apoptosis (Annexin-V staining), cell cycle analyses (flow cytometry), and reactive oxygen species (flow cytometry) were determined. Cell migration and invasion was assessed using matrigel coated transwell chambers. Agilent Technologies proteomics analysis identified potential signaling pathways involved. The combination of TA (50 μM) and Cis (5 μM) synergistically increased the growth inhibition in ES2 (∼80 %, p

Molecular biomarkers of early stage breast cancer may improve the sensitivity and specificity of diagnosis. Plasma biomarkers have additional value in that they can be monitored with minimal invasiveness. Plasma biomarker discovery by genome-wide proteomic methods is impeded by the wide dynamic range of protein abundance and the heterogeneity of protein expression in healthy and disease populations which requires the analysis of a large number of samples. We addressed these issues through the development of a novel protocol that couples a combinatorial peptide ligand library protein enrichment strategy with isobaric label-based 2D LC-MS/MS for the identification of candidate biomarkers in high throughput. Plasma was collected from patients with stage I breast cancer or benign breast lesions. Low abundance proteins were enriched using a bead-based combinatorial library of hexapeptides. This resulted in the identification of 397 proteins, 22% of which are novel plasma proteins. Twenty-three differentially expressed plasma proteins were identified, demonstrating the effectiveness of the described protocol and defining a set of candidate biomarkers to be validated in independent samples. This work can be used as the basis for the design of properly powered investigations of plasma protein expression for biomarker discovery in larger cohorts of patients with complex disease.

The prevailing paradigm is that cardiac ANG II is synthesized in the extracellular space from components of the circulating and/or local renin-angiotensin system. The recent discovery of intracrine effects of ANG II led us to determine whether ANG II is synthesized intracellularly in neonatal rat ventricular myocytes (NRVM). NRVM, incubated in serum-free medium, were exposed to isoproterenol or high glucose in the absence or presence of candesartan, which was used to prevent angiotensin type 1 (AT1) receptor-mediated internalization of ANG II. ANG II was measured in cell lysates and the culture medium, which represented intra- and extracellularly synthesized ANG II, respectively. Isoproterenol increased ANG II concentration in cell lysates and medium of NRVM in the absence or presence of candesartan. High glucose markedly increased ANG II synthesis only in cell lysates in the absence and presence of candesartan. Western analysis showed increased intracellular levels of angiotensinogen, renin, and chymase in high-glucose-exposed cells. Confocal immunofluorocytometry confirmed the presence of ANG II in the cytoplasm and nucleus of high-glucose-exposed NRVM and along the actin filaments in isoproterenol-exposed cells. ANG II synthesis was dependent on renin and chymase in high-glucose-exposed cells and on renin and angiotensin-converting enzyme in isoproterenol-exposed cells. In summary, the site of ANG II synthesis, intracellular localization, and the synthetic pathway in NRVM are stimulus dependent. Significantly, NRVM synthesized and retained ANG II intracellularly, which redistributed to the nucleus under high-glucose conditions, suggesting a role for an intracrine mechanism in diabetic conditions.

BACKGROUND: The Cancer Genome Atlas (TCGA) project previously identified genetic changes in the DNA sequence and copy number, DNA methylation, and gene expression of glioblastoma multiforme (GBM) tumors, leading to an enthused effort to compile and characterize changes in the genome, transcriptome, and proteome of human GBM tumors, so that aberrantly functioning molecular pathways and tumor subtypes could be identified. METHODS: Agilent GeneSpring and Mass Profiler Professional (MPP) software was used to perform integrated multi-omics analysis of mRNA expression, miRNA expression, protein expression, and copy number aberration associated with GBM. Additionally, analysis was performed on an independent discovery proteomics study of GBM and control (brain fragments from epilepsy surgery) patients measured using a label-free proteomics approach. RESULTS: Correlation analysis performed between mRNA and miRNA datasets from TCGA identified potential candidate miRNAs regulating the known Proneural signature genes OLIG2, NKX2-2, and SOX11. It also highlighted the molecular events leading to suppression of p53 in Proneural tumor signaling. Sample-sample correlation and PCA analysis on patient specimens resulted in clear separation between control and tumor samples. In addition, the tumor samples were segregated into two to three subgroups, suggesting that different TCGA subtypes may be present. Indeed, combined analysis of mRNA expression data from TCGA study and proteomics data from the label-free study identified a core subset of 54 GBM subtype signatures, clearly differentiating the known subtypes in the larger TCGA cohort. CONCLUSION: Our observation suggests that GBM tumor heterogeneity may be best characterized by both mRNA and protein abundance of the signature genes, opening a possibility for follow-up studies with potential diagnostic and clinical significance.

SummaryTransmitochondrial cybrids and multiple OMICs approaches were used to understand mitochondrial reprogramming and mitochondria-regulated cancer pathways in triple-negative breast cancer (TNBC). Analysis of cybrids and established breast cancer (BC) cell lines showed that metastatic TNBC maintains high levels of ATP through fatty acid β oxidation (FAO) and activates Src oncoprotein through autophosphorylation at Y419. Manipulation of FAO including the knocking down of carnitine palmitoyltransferase-1A (CPT1) and 2 (CPT2), the rate-limiting proteins of FAO, and analysis of patient-derived xenograft models confirmed the role of mitochondrial FAO in Src activation and metastasis. Analysis of TCGA and other independent BC clinical data further reaffirmed the role of mitochondrial FAO and CPT genes in Src regulation and their significance in BC metastasis.

Tyrosine nitration is a well-established protein modification that occurs in disease states associated with oxidative stress and increased nitric oxide synthase activity. Nitration of specific tyrosine residues has been reported to affect protein structure and function, suggesting that 3-nitrotyrosine formation may not only be a disease marker but may also be involved in the pathogenesis of some diseases and in normal regulatory processes. It has been, however, difficult to identify sites of nitration. We describe a method that combines specific isolation of nitrated proteins with mass spectrometric determination of the amino acid sequence and the site of nitration of individual proteins. A complex protein mixture, e.g., serum or cell lysate, was enriched for nitrotyrosine-containing proteins by immunoprecipitation with antinitrotyrosine antibodies. The nitrotyrosines were then reduced to aminotyrosines with a strong reducing agent in parallel in-gel and in-solution procedures. Using nitrated human serum albumin as a model, we reduced the disulfide bonds with dithiothreitol and alkylated the free sulfhydryl groups with iodoacetamide. The nitrotyrosines were next reduced to aminotyrosines with sodium dithionite, and-at pH 5.0-cleavable biotin tags were selectively attached to the aminotyrosines and the albumin was then digested with trypsin. The biotinylated tryptic peptides were purified on a streptavidin affinity column and identified by mass spectrometry. We have also purified nitrated human serum albumin from an enriched sample of SJL mouse plasma and confirmed its identity by peptide mass fingerprinting and MASCOT.

C-Phycocyanin (C-PC) is one of the major biliproteins of Spirulina platensis, a blue green algae, with antioxidant and radical scavenging properties. It is also known to exhibit anti-inflammatory and anti-cancer properties. However, the mechanism of action of C-PC is not clearly understood. Previously, we have shown that C-PC selectively inhibits cyclooxygenase-2 (COX-2), an inducible isoform that is upregulated during inflammation and cancer. In view of the reported induction of apoptosis in cancer cells by cyclooxygenase-2 inhibitors, the present study is undertaken to test the effect of C-PC on LPS stimulated RAW 264.7 mouse macrophage cell line. These studies have shown a dose dependent reduction in the growth and multiplication of macrophage cell line by C-PC. This decrease in cell number appears to be mediated by C-PC induced apoptosis as evidenced by flow cytometric and confocal microscopic studies. Cells treated with 20 micro M C-PC showed typical nuclear condensation and 16.6% of cells in sub-G(o)/G(1) phase. These cells also showed DNA fragmentation in a dose dependent manner. The studies on poly(ADP ribose) polymerase (PARP) cleavage showed typical fragmentation pattern in C-PC treated cells. This C-PC induced apoptosis in RAW 264.7 cells appears to be mediated by the release of cytochrome c from mitochondria and independent of Bcl-2 expression. These effects of C-PC on RAW 264.7 cells may be due to reduced PGE(2) levels as a result of COX-2 inhibition.

For triple negative breast cancer (TNBC), the driver pathways are still poorly understood. Advances in cancer metabolism research over the last decade have enhanced and modified our understanding on Warburg effect. It is now known that mitochondria in tumors are not always defective in their ability to carry out oxidative phosphorylation. Instead, in proliferating cells, mitochondrial energy pathways are reprogrammed to meet the challenges of macromolecular synthesis and to escape from apoptosis. Tumor initiating cells (TICs) maintain cancer stem cell properties and are known to play significant role in TNBC metastasis. Mitochondrial retrograde regulation (MRR) is a bidirectional communication between mitochondria and nucleus. MRR is triggered by mitochondrial functional demands and it responds in a continuous manner to change metabolic needs of the cell. Using transmitochondrial cybrid (cybrid) technology, we generated different cybrid models under common nuclear backgrounds of benign breast epithelium or TNBC. Mitochondria from cells with different cancer potential such as benign breast epithelium, moderately metastatic and highly metastatic breast cancer cell lines were studied under the common nuclear background to understand MRR-regulated TIC properties and cancer pathways. Using genomic, metabolomic, and proteomic approaches, we confirmed the significance of mitochondrial character in the regulation of epithelial mesenchymal transition (EMT), TIC and metastatic properties. Altogether, our results suggest that MRR is critical in TNBC TIC character and stemness. Citation Format: Park JH, Jung KH, Sirupangi T, Vithayathil S, Jin F, Putluri V, Piyarathna DWB, Yotnda P, Bhat VB, Sreekumar A, Lewis MT, Coarfa C, Putluri N, Creighton CJ, Wong L-JC, Kaipparettu BA. Mitochondria-nuclear communication regulates epithelial-mesenchymal transition and metastasis in triple negative breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P6-01-07.

New water-soluble analogues of 1,3,7-trimethyluric acid with N-1 methyl replaced by various groups were prepared and evaluated for their ability to scavenge hydroxyl radicals as well as their protective potential against lipid peroxidation in erythrocyte membranes. The deoxyribose degradation method indicates that all the analogues tested effectively scavenge hydroxyl radicals and some of them show better activity than uric acid and methyluric acids. These effects are shown to be concentration dependent and are more potent at low concentrations (10-50 microM). Among the analogues tested, 1-butenyl-, 1-propargyl- and 1-benzyl-3,7-dimethyluric acids show high hydroxyl radical scavenging property with a reaction rate constant (Ks) of 3.2-6.7 x 10(10) M(-1) S(-1), 2.3-3.7 x 10(10) M(-1) S(-1) and 2.4-3.7 x 10(10) M(-1) S(-1), respectively. The effectiveness of these analogues as hydroxyl radical scavengers appears to be better than mannitol (Ks, 1.9-2.5 x 10(9) M(-1) S(-1)). With the exception of 1-pentyl- and 1-(2'-oxopropyl)-3,7-dimethyluric acids, all other analogues tested are effective inhibitors of tert-butylhydroperoxide-induced lipid peroxidation in human erythrocyte membranes. All the analogues tested are susceptible to peroxidation in the presence of hemoprotein and hydrogen peroxide. The present study has pointed out that it is possible to significantly enhance the antioxidant property of 1,3,7-trimethyluric acid by structural modification at N-1 position. Such compounds may be useful as antioxidants in vivo.

We report data from two related assay systems (isolated enzyme assays and whole blood assays) that C-phycocyanin a biliprotein from Spirulina platensis is a selective inhibitor of cyclooxygenase-2 (COX-2) with a very low IC(50) COX-2/IC(50) COX-1 ratio (0.04). The extent of inhibition depends on the period of preincubation of phycocyanin with COX-2, but without any effect on the period of preincubation with COX-1. The IC(50) value obtained for the inhibition of COX-2 by phycocyanin is much lower (180 nM) as compared to those of celecoxib (255 nM) and rofecoxib (401 nM), the well-known selective COX-2 inhibitors. In the human whole blood assay, phycocyanin very efficiently inhibited COX-2 with an IC(50) value of 80 nM. Reduced phycocyanin and phycocyanobilin, the chromophore of phycocyanin are poor inhibitors of COX-2 without COX-2 selectivity. This suggests that apoprotein in phycocyanin plays a key role in the selective inhibition of COX-2. The present study points out that the hepatoprotective, anti-inflammatory, and anti-arthritic properties of phycocyanin reported in the literature may be due, in part, to its selective COX-2 inhibitory property, although its ability to efficiently scavenge free radicals and effectively inhibit lipid peroxidation may also be involved.

C-Phycocyanin (from Spirulina platensis) effectively inhibited CCl(4)-induced lipid peroxidation in rat liver in vivo. Both native and reduced phycocyanin significantly inhibited peroxyl radical-induced lipid peroxidation in rat liver microsomes and the inhibition was concentration dependent with an IC(50) of 11.35 and 12.7 microM, respectively. The radical scavenging property of phycocyanin was established by studying its reactivity with peroxyl and hydroxyl radicals and also by competition kinetics of crocin bleaching. These studies have demonstrated that phycocyanin is a potent peroxyl radical scavenger with an IC(50) of 5.0 microM and the rate constant ratios obtained for phycocyanin and uric acid (a known peroxyl radical scavenger) were 1.54 and 3.5, respectively. These studies clearly suggest that the covalently linked chromophore, phycocyanobilin, is involved in the antioxidant and radical scavenging activity of phycocyanin.

Compared to other subtypes of tumors, triple negative breast cancers (TN BCa) currently suffer from limited knowledge on its etiology and treatment options. Transmitochondrial cybrids (cybrid) and multiple OMICs approaches were used to understand mitochondrial reprogramming and mitochondria-regulated cancer pathways in TN BCa. Analysis of cybrids and established BCa cell lines showed that metastatic TN BCa maintain high levels of ATP through fatty acid β-oxidation and activate Src oncoprotein by its autophosphorylation. Inhibition and induction of β-oxidation including the shRNA mediated knockdown strategies, and analysis of patient derived xenograft (PDX) models confirmed the role of mitochondrial β-oxidation in Src activation and metastasis. Analysis of BCa clinical data further reaffirmed the role of mitochondrial β-oxidation in Src regulation and their significance in BCa metastasis. This study is innovative in showing the mitochondrial reprogramming mediated regulation of a major cancer pathway by its post-translation modification. Citation Format: Jun H. Park, Sajna Vithayathil, Danli Wu, Vasanta Putluri, Pi-Lin Sung, Efrosini Tsouko, Vadiraja B. Bhat, Cristian Coarfa, Daniel E. Frigo, Michael T. Lewis, Arun Sreekumar, Patricia Yotnda, Chad J. Creighton, Nagireddy Putluri, Lee-Jun C. Wong, Benny A. Kaipparettu. Mitochondrial reprogramming regulated cancer pathway in triple negative breast cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 217.

Neuropeptides play many important roles in cell-cell signaling and are involved in the control of anxiety, depression, pain, reward pathways, and many other processes that are relevant to psychiatric disorders. Mass spectrometry-based peptidomics techniques can identify the precise forms of peptides that are present in a given tissue. Utilizing this technique, peptides can be identified with any post-translational modifications that may be present and the exact sequence of the peptides can be determined. Unlike radioimmunoassays, which are limited by specific antibodies and often cannot discriminate between different lengths of peptides from the same precursor, peptidomics reveals the precise sequence and allows for the identification of both known and novel peptides. The use of isotopic labels allows for quantitative peptidomics, which results in the ability to compare peptide levels between differently treated samples. These tags can be synthesized in five different isotopic forms, permitting multivariate analysis of up to five different groups of tissue extracts in a single liquid chromatography/mass spectrometry run; this is ideal for measuring changes in neuropeptides in animals subjected to drug treatments, or in comparing animal models of psychiatric disorders.

Pancreatic Adenocarcinoma (PDAC), the fourth highest cause of cancer related deaths in the United States, has the most aggressive presentation resulting in a very short median survival time for the affected patients. Early detection of PDAC is confounded by lack of specific markers that has motivated the use of high throughput molecular approaches to delineate potential biomarkers. To pursue identification of a distinct marker, this study profiled the secretory proteome in 16 PDAC, 2 carcinoma in situ (CIS) and 7 benign patients using label-free mass spectrometry coupled to 1D-SDS-PAGE and Strong Cation-Exchange Chromatography (SCX). A total of 431 proteins were detected of which 56 were found to be significantly elevated in PDAC. Included in this differential set were Parkinson disease autosomal recessive, early onset 7 (PARK 7) and Alpha Synuclein (aSyn), both of which are known to be pathognomonic to Parkinson's disease as well as metabolic enzymes like Purine Nucleoside Phosphorylase (NP) which has been exploited as therapeutic target in cancers. Tissue Microarray analysis confirmed higher expression of aSyn and NP in ductal epithelia of pancreatic tumors compared to benign ducts. Furthermore, extent of both aSyn and NP staining positively correlated with tumor stage and perineural invasion while their intensity of staining correlated with the existence of metastatic lesions in the PDAC tissues. From the biomarker perspective, NP protein levels were higher in PDAC sera and furthermore serum levels of its downstream metabolites guanosine and adenosine were able to distinguish PDAC from benign in an unsupervised hierarchical classification model. Overall, this study for the first time describes elevated levels of aSyn in PDAC as well as highlights the potential of evaluating NP protein expression and levels of its downstream metabolites to develop a multiplex panel for non-invasive detection of PDAC.

Multiple, complex molecular events characterize cancer development and progression. Deciphering the molecular networks that distinguish organ-confined disease from metastatic disease may lead to the identification of biomarkers of cancer invasion and disease aggressiveness. Although alterations in gene expression have been extensively quantified during neoplastic progression, complementary analyses of proteomic changes have been limited. Here we interrogate the proteomic alterations in a cohort of 15 prostate-derived tissues that included five each from adjacent benign prostate, clinically localized prostate cancer, and metastatic disease from distant sites. The experimental strategy couples isobaric tags for relative and absolute quantitation with multidimensional liquid phase peptide fractionation followed by tandem mass spectrometry. Over 1000 proteins were quantified across the specimens and delineated into clinically localized and metastatic prostate cancer-specific signatures. Included in these class-specific profiles were both proteins that were known to be dysregulated during prostate cancer progression and new ones defined by this study. Enrichment analysis of the prostate cancer-specific proteomic signature, to gain insight into the functional consequences of these alterations, revealed involvement of miR-128-a/b regulation during prostate cancer progression. This finding was validated using real time PCR analysis for microRNA transcript levels in an independent set of 15 clinical specimens. miR-128 levels were elevated in benign prostate epithelial cell lines compared with invasive prostate cancer cells. Knockdown of miR-128 induced invasion in benign prostate epithelial cells, whereas its overexpression attenuated invasion in prostate cancer cells. Taken together, our profiles of the proteomic alterations of prostate cancer progression revealed miR-128 as a potentially important negative regulator of prostate cancer cell invasion.

In SJL mice, growth of RcsX lymphoma cells induces an inflammatory response by stimulating V(beta)16+ T cells. During inflammation, various serum protein levels can increase (e.g., acute phase reactants) or decrease (e.g., albumin), and most of these altered proteins are thus potential biomarkers. Although blood plasma is a valuable and promising sample for biomarker discovery for diseases or for novel drug targets, its proteome is complex. To address this, we have focused on a comprehensive comparison of the plasma proteomes from normal and RcsX-tumor-bearing SJL mice using the 1D-Gel-LC-MS/MS method after removing albumin and immunoglobulins. This analysis resulted in the identification of a total of 1079 nonredundant mouse plasma proteins; more than 480 in normal and 790 in RcsX-tumor-bearing SJL mouse plasma. Of these, only 191 proteins were found in common. The molecular weights ranged from 2 to 876 kDa, covering the pI values between 4.22 and 12.09, and included proteins with predicted transmembrane domains. By comparing the plasma proteomic profile of normal and RcsX-tumor-bearing SJL mice, we found significant changes in the levels of many proteins in RcsX-tumor-bearing mouse plasma. Most of the up-regulated proteins were identified as acute-phase proteins (APPs). Also, several unique proteins i.e., haptoglobin, proteosome subunits, fetuin-B, 14-3-3 zeta, MAGE-B4 antigen, etc, were found only in the tumor-bearing mouse plasma; either secreted, shed by membrane vesicles, or externalized due to cell death. These results affirm the effectiveness of this approach for protein identification from small samples, and for comparative proteomics in potential animal models of human disorders.

Analysis of proteins in biological samples opens up the possibility of discovering new markers of toxicity. The liver is one of the primary targets of drug-induced toxicity, and it also secretes many plasma proteins, which can be measured clinically. Most of the plasma proteins produced by the liver are secreted by hepatocytes, but there is little information regarding the protein profile secreted by these cells. The purpose of this study was to analyze the secreted proteome of primary rat hepatocytes in a collagen gel sandwich configuration by a gel-LC-MS/MS procedure. We identified over 600 peptides corresponding to more than 200 proteins. The protein profile included over 50 plasma proteins, suggesting that the cultured hepatocytes secrete many of the proteins that they produce in vivo. Our data also suggests that the hepatocytes are actively remodeling their environment, since we identified several structural extracellular matrix proteins as well as some proteins known to be secreted specifically during liver regeneration. We also identified two proteins, alpha1-antitrypsin and alpha2-macroglobulin, whose secretions appear to be down-regulated in cells exposed to aflatoxin B1. It was noted that a 15 nM dose of aflatoxin B1 led to substantially diminished levels of these proteins and that day 6 of incubation was the ideal time point for medium collection. These data suggest that proteins in the conditioned medium of hepatocyte sandwich culture might lead to the discovery of biomarkers for drug-induced chemical toxicity.

Objectives: Specificity protein 1 (Sp1) is a transcription factor that is over-expressed in several cancers and is inversely associated with survival. Survivin is known to cause resistance to chemo- and radiation therapy. Herein, we evaluated the correlation of Sp1 and survivin expression in epithelial ovarian cancer (EOC) patients and tested a pre-clinical strategy to target these candidates using tolfenamic acid (TA) for enhancing the efficacy of a chemotherapeutic agent, Cisplatin (Cis). Methods: Expression of Sp1 and survivin in clinical specimens was determined by qPCR and Western blot analysis. Anti-proliferative response of EOC cell lines (ES2 and OVCAR-3) was assessed in the presence of Cis, TA or Cis+TA using CellTiter-Glo. Apoptosis was determined by flow cytometry using annexin-V staining, measuring the effector caspases activity using caspase3/7 Glo kit. Cell cycle analysis was carried out using flow cytometry. Matrigel coated ranswell chambers were used to assess cell migration/invasion. Proteomics nalysis was performed at Agilent Technologies, Inc. Results: qPCR showed an increase in the expression of urvivin (∼5-fold) and Sp1 (∼2-fold) in clinical specimens, which was corroborated by Western blot analysis [Sp1 (>2.6-fold) and survivin >100-fold)]. TA and Cis showed a dose- and time-dependent inhibition of cell viability in EOC cell lines [50 µM TA caused 50% (ES2) and 40% (OVCAR-3) cell growth inhibition; Cis (5 µM) caused 60% (ES2) and 40% (OVCAR-3) inhibition at 48 h post-treatment]. Combination of TA (50 µM) and Cis (5 µM) resulted in a synergistic response causing higher growth inhibition (ES2: ∼80%, p Conclusions: Elevated expression of Sp1 and survivin suggests a strong association of these two agents in EOC. Our pre-clinical results confirmed that targeting these candidates with small molecule (TA) potentially sensitizes EOC cells to chemotherapy. Citation Format: Umesh T. Sankpal, Susan B. Ingersoll, Vadiraja B. Bhat, Sarfraz Ahmad, Robert W. Holloway, Riyaz M. Basha. Relevance of Sp1 and survivin expression in epithelial ovarian cancer patients and their usefulness as potential therapeutic targets. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1354. doi:10.1158/1538-7445.AM2014-1354

The crystal structure of C-phycocyanin, a light-harvesting phycobiliprotein from cyanobacteria (blue-green algae) Spirulina platensis has been solved by molecular replacement technique. The crystals belong to space group $P2_1$ with cell parameters a = 107.20, b = 115.40, c = 183.04 \AA; $\beta=90.2^o$. The structure has been refined to a crystallographic R factor of 19.2% $(R_{free}=23.9$%) using the X-ray diffraction data extending up to 2.2 \AA resolution. The asymmetric unit of the crystal cell consists of two $(\alpha \beta)_6$-hexamers, each hexamer being the functional unit in the native antenna rod of cyanobacteria. The molecular structure resembles that of other reported C-phycocyanins. However, the unique form of aggregation of two $(\alpha \beta)_6$-hexamers in the crystal asymmetric unit, suggests additional pathways of energy transfer in lateral direction between the adjacent hexamers involving $\beta 155$ phycocyanobilin chromophores.

Ovarian cancer (OC) is one of the most common female cancers and is the leading cause of death from gynecologic malignancies. Although, cisplatin is the front-line chemotherapeutic option for OC, its success is compromised due to dose-limiting toxicity and acquired resistance by tumor cells. Specificity protein 1 (Sp1) is a transcription factor that is over-expressed in several cancers and is inversely associated with survival. Survivin, a member of IAP family, is known to cause resistance to chemo- and radiation therapy. Studies from our laboratories have shown that the NSAID, tolfenamic acid (TA), targets Sp1 protein and inhibits expression of survivin in various cancer models. Our primary objective was to evaluate the expression of Sp1 and survivin in OC patients’ specimens and target these candidates using TA for enhancing the cisplatin response. Expression of Sp1 and survivin in clinical specimens was determined by qPCR and Western blots. qPCR showed increased expression of survivin (∼5-fold) and Sp1 (∼2-fold) in tumor samples. Western blot also revealed over-expression of both Sp1 (>2.6-fold) and survivin (>100-fold). OC cell lines (ES2, OVCAR-3) were used to determine the anti-proliferative response to cisplatin and TA. TA and cisplatin showed a dose- and time-dependent inhibition of cell viability in OC cell lines [TA (50 ÂμM) caused 50% (ES2) and 40% (OVCAR-3) growth inhibition and cisplatin (5 ÂμM) caused 60% and 40% inhibition at 48 h post-treatment]. Combination treatment using optimized doses of TA (50 ÂμM) and cisplatin (5 ÂμM) resulted in a synergistic response and caused stronger inhibition (ES2: ∼80%, OVCAR-3: >60) compared to single-agent. Increased inhibition of proliferation by the combination of TA and cisplatin was accompanied by cell-cycle arrest, predominantly in the G2/M phase. A significant increase in apoptosis, as determined by Caspase 3/7 activity, annexin-V staining, and PARP cleavage, was also observed in the combination treatment. Cell invasion and migration was assessed using matrigel coated transwell chambers. Compared to TA or cisplatin treatment alone, their combination significantly inhibited ES2 cell invasion. Analysis of ES2 cells by global proteomic profiling indicated that the combination treatment upregulated proteins associated with oxidative phosphorylation, apoptosis, and electron transport chain; and down-regulated cytoplasmic ribosomal proteins, translational factors, and proteins involved in DNA damage response, and cell cycle. In conclusion, elevated expression of Sp1 and survivin confirmed their association in OC and demonstrated the relevance of targeting these candidates, which may render the OC cells more sensitive to chemotherapy and offer therapeutic potential. Further studies to delineate underlying mechanism(s) of action possibly involving signaling pathways and reactive oxygen species are currently underway. Citation Format: Umesh T. Sankpal, Susan B. Ingersoll, Mohammed I. Shukoor, Chris M. Lee, Nicole M. Stavitzski, Vadiraja B. Bhat, Sarfraz Ahmad, Robert W. Holloway, Liz Abraham, Riyaz Basha. Expression of Sp1 and survivin in ovarian cancer specimens: potential novel therapeutic targets in disease treatment. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2159. doi:10.1158/1538-7445.AM2013-2159

Introduction: Expression of specificity protein 1 (Sp1) transcription factor is negatively associated with survival in some cancer patients. Survivin, a member of Inhibitor of Apoptosis Protein family, causes resistance to chemo- and radiation therapy. Tolfenamic acid (TA), a NSAID, targets Sp1 and inhibits survivin expression in some cancer models. Our aims were to examine the expression of Sp1 and survivin in ovarian cancer (OC) specimens and compare the in vitro anticancer response of cisplatin and TA alone and in combination. Methods: Tissues from clinical specimens (16 advanced stage tumors, 3 normal) were used to isolate RNA and prepare protein extracts. Sp1 and survivin expression was measured using qPCR and Western blots. OC cell lines (ES-2, SKOV3-AF2) were used for in vitro assays. Anti-proliferative response of cisplatin and TA was measured at 24, 48 and 72 h, post-treatment. Cells were treated with DMSO (vehicle), TA (25/50/100 µM) or cisplatin (5/10/20/50 nM), and cell viability was assayed using CellTiter Glo kit. Subsequently, cells were treated with optimized doses of TA (50 µM) or cisplatin (20 nM) for 48 h. Caspase-3/7 activity was measured using Caspase-3/7 Glo kit and Sp1, survivin, and c-PARP expression was determined by Western blots. Cell viability, Sp1 expression, and caspase-3/7 activity were assessed following individual and combination treatment of TA and cisplatin. Results: qPCR revealed that all tumor samples have increased survivin expression (>5 fold) and the majority showed increased Sp1 expression (2-3 fold). Consistent with the qPCR data, Western blot confirmed that all (survivin) or majority (Sp1) of specimens have high expression levels. TA and cisplatin showed a dose- and time-dependent inhibition of cell viability. TA caused 75% (ES-2) and 25% (SKOV3-AF2) growth inhibition while cisplatin caused ∼20% inhibition in both cell lines. Combination TA and cisplatin treatment resulted in maximum inhibition (ES2: >90%; SKOV3-AF2: 75%), showing a synergistic effect. These data confirmed that both agents up-regulated c-PARP and caspase-3/7 indicating activation of apoptotic pathways. However, only TA caused a significant decrease in Sp1, survivin, and c-Met expression. Increased inhibition of cell growth following combination treatment is consistent with increased caspase-3/7 activity and decreased Sp1 expression. Conclusions: Sp1 and survivin expression in OC specimens confirmed that targeting these molecules/pathways would be therapeutically relevant. TA enhanced the response of cisplatin when used in combination. Sp1 regulates survivin expression and targeting survivin with TA might render the OC cells radiation-sensitive. TA is less toxic than cisplatin but causes greater anticancer activity over cisplatin. Further studies to evaluate the mechanism(s) using proteomic and molecular profiling approach are underway. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4656. doi:1538-7445.AM2012-4656

Background: Protein biomarkers for breast cancer are desired for early diagnosis, disease prognosis and drug response monitoring. Biomarkers in bodily fluids, such as plasma, allow for non-invasive monitoring and thus have additional value compared to tissue-based markers. Plasma-based biomarker discovery faces a challenge in that the wide dynamic range of protein concentrations prevents the detection of lower abundance proteins. Additionally, large sample sizes are needed for sufficient statistical power. In this setting, experimental design and normalization are important considerations. In this study, we have investigated the use of a novel protein enrichment strategy combined with isobaric label-based LC-MS/MS as well as two experimental designs for the identification of biomarkers of early stage breast cancer. Methods: Plasma from 12 patients with benign breast lesions and 12 with stage I breast cancer were processed using ProteoMiner enrichment followed by on-bead digestion. Two types of standards were investigated: a pooled standard, consisting of equal portions of the 24 plasma digests and a universal standard, consisting of 12 independent benign, stage I, stage II, and stage III breast cancer plasma samples. These designs have opposing strengths and weaknesses: pooled standards minimize variation but fix the sample size; universal standards allow for addition of new samples but introduce additional variation. The study required 4 iTRAQ-8plex sets which were subjected to 2-D LC separation followed by HPLC-Chip/Q-TOF analysis. Proteins were identified and quantified using Spectrum Mill software. Algorithms were developed for normalization, missing data imputation, protein grouping and identification of differential expression. Results: Use of ProteoMiner beads resulted in extraction of sufficient protein for at least 10 technical replicates and cut down preparation time by 80%, as compared to MARS-based immunodepletion. A total of 416 plasma proteins were identified, 96% of which are low abundance plasma proteins and 14 of which were differentially expressed. Expression values normalized using the pooled vs. universal standards were significantly correlated; however the use of the universal standard design yields a larger variation in expression values. Conclusion: This study demonstrated use of the ProteoMiner technology for enrichment of low abundance proteins from plasma. Fourteen plasma-based biomarkers of stage I breast cancer were identified with statistical significance. A number of these proteins (e.g. protocadherin FAT2, flightless-1 homolog) have been linked to breast cancer relevant processes, such as cell migration, adhesion, estrogen receptor signaling and proliferation. Data indicates that the universal standard is an adequate replacement for pooled standards with the caveat that higher variance should be expected. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 5116. doi:10.1158/1538-7445.AM2011-5116

Background We and others have previously reported that resveratrol (RSV) suppresses colon cancer cell proliferation and elevates apoptosis in vitro and/or in vivo, however molecular mechanisms are not fully elucidated. Particularly, little information is available on RSV's effects on metabolic pathways and the cell-extra cellular matrix (ECM) communication that are critical for cancer cell growth. To identify important targets of RSV, we analyzed whole protein fractions from HT-29 advanced human colon cancer cell line treated with solvent control, IGF-1 (10 nM) and RSV (150 μM) using LC/MS/MS-Mud PIT (Multidimensional Protein Identification Technology). Results Pentose phosphate pathway (PPP), a vital metabolic pathway for cell cycle progression, was elevated and suppressed by IGF-1 and RSV, respectively in the HT-29 cell line. Enzymatic assays confirmed RSV suppression of glucose-6 phosphate dehydrogenase (rate limiting) and transketolase, key enzymes of the PPP. RSV (150 μM) suppressed, whereas IGF-1 (10 nM) elevated focal adhesion complex (FAC) proteins, talin and pFAK, critical for the cell-ECM communication. Western blotting analyses confirmed the suppression or elevation of these proteins in HT-29 cancer cells treated with RSV or IGF-1, respectively. Conclusions Proteomic analysis enabled us to establish PPP and the talin-pFAK as targets of RSV which suppress cancer cell proliferation and induce apoptosis in the colon cancer cell line HT-29. RSV (150 μM) suppressed these pathways in the presence and absence of IGF-1, suggesting its role as a chemo-preventive agent even in obese condition.