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1.  SELDI-TOF MS Whole Serum Proteomic Profiling with IMAC Surface Does Not Reliably Detect Prostate Cancer 
Clinical chemistry  2007;54(1):53-60.
BACKGROUND
The analysis of bodily fluids using SELDI-TOF MS has been reported to identify signatures of spectral peaks that can be used to differentiate patients with a specific disease from normal or control patients. This report is the 2nd of 2 companion articles describing a validation study of a SELDI-TOF MS approach with IMAC surface sample processing to identify prostatic adenocarcinoma.
METHODS
We sought to derive a decision algorithm for classification of prostate cancer from SELDI-TOF MS spectral data from a new retrospective sample cohort of 400 specimens. This new cohort was selected to minimize possible confounders identified in the previous study described in the companion paper.
RESULTS
The resulting new classifier failed to separate patients with prostate cancer from biopsy-negative controls; nor did it separate patients with prostate cancer with Gleason scores <7 from those with Gleason scores ≥7.
CONCLUSIONS
In this, the 2nd stage of our planned validation process, the SELDI-TOF MS– based protein expression profiling approach did not perform well enough to advance to the 3rd (prospective study) stage. We conclude that the results from our previous studies—in which differentiation between prostate cancer and noncancer was demonstrated—are not generalizable. Earlier study samples likely had biases in sample selection that upon removal, as in the present study, resulted in inability of the technique to discriminate cancer from non-cancer cases.
doi:10.1373/clinchem.2007.091496
PMCID: PMC4332515  PMID: 18024530
2.  A highly sensitive targeted mass spectrometric assay for quantification of AGR2 protein in human urine and serum 
Journal of proteome research  2013;13(2):875-882.
Anterior gradient 2 (AGR2) is a secreted, cancer-associated protein in many types of epithelial cancer cells. We developed a highly sensitive targeted mass spectrometric assay for quantification of AGR2 in urine and serum. Digested peptides from clinical samples were processed by PRISM (high pressure and high resolution separations coupled with intelligent selection and multiplexing), which incorporates high pH reversed-phase LC separations to fractionate and select target fractions for follow-on LC-SRM analyses. The PRISM-SRM assay for AGR2 showed a reproducibility of <10% CV and LOQ values of ~130 pg/mL in serum and ~10 pg per 100 μg total protein mass in urine, respectively. A good correlation (R2 = 0.91) was observed for the measurable AGR2 concentrations in urine between SRM and ELISA. Based on an initial cohort of 37 subjects, urinary AGR2/PSA concentration ratios showed a significant difference (P = 0.026) between non-cancer and cancer. Large clinical cohort studies are needed for the validation of AGR2 as a useful diagnostic biomarker for prostate cancer. Our work validated the approach of identifying candidate secreted protein biomarkers through genomics and measurement by targeted proteomics, especially for proteins where no immunoassays are available.
doi:10.1021/pr400912c
PMCID: PMC3975687  PMID: 24251762
AGR2; PSA; prostate cancer; PRISM-SRM; human urine; human serum
3.  Hepatitis B Management in Vulnerable Populations: Gaps in Disease Monitoring and Opportunities for Improved Care 
Background
Hepatitis B (HBV) is prevalent in certain US populations and regular HBV disease monitoring is critical to reducing associated morbidity and mortality. Adherence to established HBV monitoring guidelines among primary care providers is unknown.
Aims
To evaluate HBV disease monitoring patterns and factors associated with adherence to HBV management guidelines in the primary care setting.
Methods
Primary providers within the San Francisco safety net healthcare system were surveyed for HBV management practices, knowledge, attitudes, and barriers to HBV care. Medical records from 1,727 HBV-infected patients were also reviewed retrospectively.
Results
Of 148 (45%) responding providers, 79% reported ALT and 44% reported HBV viral load testing every 6–12 months. Most providers were knowledgeable about HBV but 43% were unfamiliar with HBV management guidelines. Patient characteristics included: mean age 51 years; 54% male; 67% Asian. Within the past year, 75% had ALT; 24% viral load; 21% HBeAg tested, and 40% of at-risk patients had abdominal imaging for HCC. Provider familiarity with guidelines (OR 1.02, 95%CI 1.00–1.03), Asian patient race (OR 4.18, 95%CI 2.40–7.27), and patient age were associated with recommended HBV monitoring. Provider HBV knowledge and attitudes were positively associated, while provider age and perceived barriers were negatively associated with HCC surveillance.
Conclusions
Comprehensive HBV disease monitoring including HCC screening with imaging were suboptimal. While familiarity with AASLD guidelines and patient factors were associated with HBV monitoring, only provider and practice factors were associated with HCC surveillance. These findings highlight the importance of targeted provider education to improve HBV care.
doi:10.1007/s10620-013-2870-z
PMCID: PMC3947196  PMID: 24052195
Hepatitis B; Hepatocellular carcinoma; Primary care; Provider education; Practice guidelines; Health disparities
4.  Serum Fucosylated Prostate-specific Antigen (PSA) Improves the Differentiation of Aggressive from Non-aggressive Prostate Cancers 
Theranostics  2015;5(3):267-276.
Background: Clinically, it is still challenging to differentiate aggressive from non-aggressive prostate cancers (Pca) by non-invasive approaches. Our recent studies showed that overexpression of alpha (1-6) fucosyltransferase played an important role in Pca cells. In this study, we have investigated levels of glycoproteins and their fucosylated glycoforms in sera of Pca patients, as well as the potential utility of fucosylated glycoproteins in the identification of aggressive Pca.
Material and Methods: Serum samples from histomorphology-proven Pca cases were included. Prostate-specific antigen (PSA), tissue inhibitor of metallopeptidase 1 (TIMP1) and tissue plasminogen activator (tPA), and their fucosylated glycoforms were captured by Aleuria Aurantia Lectin (AAL), followed by the multiplex magnetic bead-based immunoassay. The level of fucosylated glycoproteins was correlated with patients' Gleason score of the tumor.
Result: Among three fucosylated glycoproteins, the fucosylated PSA was significantly increased and correlated with the tumor Gleason score (p<0.05). The ratio of fucosylated PSA showed a marked increase in aggressive tumors in comparison to non-aggressive tumors. ROC analysis also showed an improved predictive power of fucosylated PSA in the identification of aggressive Pca.
Conclusions: Our data demonstrated that fucosylated PSA has a better predictive power to differentiate aggressive tumors from non-aggressive tumors, than that of native PSA and two other glycoproteins. The fucosylated PSA has the potential to be used as a surrogate biomarker.
doi:10.7150/thno.10349
PMCID: PMC4279190  PMID: 25553114
prostate cancer; multiplex immunoassay; fucosylated glycoprotein; prostate-specific antigen; TIMP1.
5.  Prospective, Multi-Center Evaluation of the Beckman Coulter Prostate Health Index Using WHO Calibration 
The Journal of urology  2012;189(5):1702-1706.
Purpose
Reported prostate-specific antigen (PSA) values may differ substantially between assays with the Hybritech and World Health Organization (WHO) standardization. [-2]proPSA (p2PSA) and the Beckman Coulter prostate health index (phi) are newly approved serum markers, which are associated with prostate cancer risk and aggressiveness. Our objective was to study the influence of assay standardization on these markers.
Materials and Methods
PSA, % free PSA (%fPSA), and p2PSA were measured using the Hybritech calibration in 892 men undergoing prostate biopsy from a prospective multicenter study. Phi was calculated as: [p2PSA/ fPSA) × (square root of PSA)]. Performance characteristics of phi for prostate cancer detection were then determined using re-calculated WHO calibration PSA values.
Results
The median phi was significantly higher in men with prostate cancer compared to those with negative biopsies using the WHO values (47.4 vs 39.8, p<0.001). Phi offered improved discrimination of prostate cancer detection on biopsy (AUC 0.704) compared to %fPSA or total PSA using the WHO calibration.
Conclusions
Phi can be calculated using Hybritech or WHO standardized assays, and significantly improved the prediction of biopsy outcome over %fPSA or PSA alone.
doi:10.1016/j.juro.2012.11.149
PMCID: PMC4273580  PMID: 23206426
prostate cancer screening; proPSA; phi; prostate health index; assay
6.  Analysis of N-glycoproteins using Genomic N-glycosite Prediction 
Journal of proteome research  2013;12(12):5609-5615.
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 from cells or tissues using mass spectrometry has the potential to provide biological basis for disease development and identify disease associated glycoproteins. However, the information of low abundance but important peptides is lost due to the lack of MS/MS fragmentation or low quality of MS/MS spectra for low abundant peptides. Here, we show the feasibility of formerly N-glycopeptide identification and quantification at MS1 level using genomic N-glycosite prediction (GenoGlyco) coupled with stable isotopic labeling and accurate mass matching. The GenoGlyco Analyzer software uses accurate precursor masses of detected N-deglycopeptide peaks to match them to N-linked deglycopeptides which are predicted from genes expressed in the cells. This method results in more robust glycopeptide identification compared to MS/MS based identification. Our results showed that over three times the quantity of N-deglycopeptide assignments from the same mass spectrometry data could be produced in ovarian cancer cell lines compared to a MS/MS fragmentation method. Furthermore, the method was also applied to N-deglycopeptide analysis of ovarian tumors using the identified deglycopeptides from the two ovarian cell lines as heavy standards. We show that the described method has a great potential in the analysis of detectable N-glycoproteins from cells and tissues.
doi:10.1021/pr400575f
PMCID: PMC4072220  PMID: 24164404
glycosylation; prediction; genome-wide; SILAC; accurate mass matching; ovarian cancer; mass spectrometry
7.  A Ruthenium(II) Complex Supported by Trithiacyclononane and Aromatic Diimine Ligand as Luminescent Switch-On Probe for Biomolecule Detection and Protein Staining 
Scientific Reports  2014;4:7136.
A new ruthenium(II) complex has been developed for detection of biomolecules. This complex is highly selective for histidine over other amino acids and has been applied to protein staining in an SDS-PAGE gel.
doi:10.1038/srep07136
PMCID: PMC4238014  PMID: 25409703
8.  Glycoproteomic Analysis of Bronchoalveolar Lavage (BAL) Fluid Identifies Tumor-associated Glycoproteins from Lung Adenocarcinoma 
Journal of proteome research  2013;12(8):3689-3696.
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, were analyzed using the solid-phase extraction of N-glycoprotein (SPEG), iTRAQ labeling and liquid chromatography tandem mass spectrometry (LC-MS/MS). Of 80 glycoproteins found in BAL specimens, 32 were identified in both cancer BAL and cancer tissues with levels of 25 glycoproteins showing at least a 2-fold difference between cancer and benign BAL. Among them, 8 glycoproteins showed greater than 2-fold elevations in cancer BAL, including Neutrophil elastase (NE), Integrin alpha-M, Cullin-4B, Napsin A, Lysosome-associaed membrane protein 2 (LAMP2), Cathepsin D, BPI fold-containing family B member 2, and Neutrophil gelatinase-associated lipocalin. The levels of Napsin A in cancer BAL were further verified in an independently collected 39 BAL specimens using an ELISA assay. Our study demonstrates that potential protein biomarkers in BAL fluid can be detected and quantified.
doi:10.1021/pr400274w
PMCID: PMC4238415  PMID: 23802180
glycoproteomics; bronchoalveolar lavage (BAL); glycoproteins; lung adenocarcinoma; non-small cell lung cancer (NSCLC)
9.  A colorimetric chemosensor for Cu2+ ion detection based on an iridium(III) complex 
Scientific Reports  2014;4:6794.
We report herein the synthesis and application of a series of novel cyclometalated iridium(III) complexes 1−3 bearing a rhodamine-linked NˆN ligand for the detection of Cu2+ ions. Under the optimised conditions, the complexes exhibited high sensitivity and selectivity for Cu2+ ions over a panel of other metal ions, and showed consistent performance in a pH value range of 6 to 8. Furthermore, the potential application of this system for the monitoring of Cu2+ ions in tap water or natural river water samples was demonstrated.
doi:10.1038/srep06794
PMCID: PMC4210870  PMID: 25348724
10.  Mechanisms by Which Low Glucose Enhances the Cytotoxicity of Metformin to Cancer Cells Both In Vitro and In Vivo 
PLoS ONE  2014;9(9):e108444.
Different cancer cells exhibit altered sensitivity to metformin treatment. Recent studies suggest these findings may be due in part to the common cell culture practice of utilizing high glucose, and when glucose is lowered, metformin becomes increasingly cytotoxic to cancer cells. In low glucose conditions ranging from 0 to 5 mM, metformin was cytotoxic to breast cancer cell lines MCF7, MDAMB231 and SKBR3, and ovarian cancer cell lines OVCAR3, and PA-1. MDAMB231 and SKBR3 were previously shown to be resistant to metformin in normal high glucose medium. When glucose was increased to 10 mM or above, all of these cell lines become less responsive to metformin treatment. Metformin treatment significantly reduced ATP levels in cells incubated in media with low glucose (2.5 mM), high fructose (25 mM) or galactose (25 mM). Reductions in ATP levels were not observed with high glucose (25 mM). This was compensated by enhanced glycolysis through activation of AMPK when oxidative phosphorylation was inhibited by metformin. However, enhanced glycolysis was either diminished or abolished by replacing 25 mM glucose with 2.5 mM glucose, 25 mM fructose or 25 mM galactose. These findings suggest that lowering glucose potentiates metformin induced cell death by reducing metformin stimulated glycolysis. Additionally, under low glucose conditions metformin significantly decreased phosphorylation of AKT and various targets of mTOR, while phospho-AMPK was not significantly altered. Thus inhibition of mTOR signaling appears to be independent of AMPK activation. Further in vivo studies using the 4T1 breast cancer mouse model confirmed that metformin inhibition of tumor growth was enhanced when serum glucose levels were reduced via low carbohydrate ketogenic diets. The data support a model in which metformin treatment of cancer cells in low glucose medium leads to cell death by decreasing ATP production and inhibition of survival signaling pathways. The enhanced cytotoxicity of metformin against cancer cells was observed both in vitro and in vivo.
doi:10.1371/journal.pone.0108444
PMCID: PMC4177919  PMID: 25254953
11.  Structure-Based Discovery of Natural Product-Like TNF-α Inhibitors 
Two natural product-like inhibitors of TNF-α have been identified using structure-based virtual screening. These compounds represent only the third and fourth examples of direct target of TNF-α by a small molecule and display comparable potency to the strongest TNF-α inhibitor reported to date.
doi:10.1002/anie.200907360
PMCID: PMC4162403  PMID: 20235259
inhibitors; tumor necrosis factor; virtual screening; natural products; drug discovery
13.  Predicting Prostate Cancer Biochemical Recurrence Using a Panel of Serum Proteomic Biomarkers 
The Journal of urology  2009;181(3):1407-1414.
Purpose
The pathological state of the prostate may be reflected by serum proteome in a man. We hypothesized that biomarkers are present in preoperative serum, which may be used to predict the probability of biochemical recurrence following radical prostatectomy.
Materials and Methods
Mass spectrometry analysis was used to compare 52 men who experienced biochemical recurrence with 52 who remained biochemical recurrence-free for approximately 5 years after radical retropubic prostatectomy. A total of 30 matched pairs of recurrent and nonrecurrent serum samples were randomly selected as a training set for biomarker discovery and model development. Selected mass spectrometry peaks were combined with pre-radical retropubic prostatectomy prostate specific antigen in a multivariate algorithm to predict recurrence. The algorithm was evaluated using the remaining 22 recurrent and 22 nonrecurrent subjects as test samples. Protein identities of the selected mass spectrometry peaks were investigated.
Results
Two serum biomarkers for recurrence, P1 and P2, were combined with preoperative prostate specific antigen to predict biochemical recurrence. The ROC AUC for prostate specific antigen and the predicted outcome was 0.606 and 0.691 in the testing data, respectively. Using a single cutoff the samples were divided into 2 groups that were predictive of biochemical recurrence (p = 0.026). In contrast, preoperative prostate specific antigen did not differ between recurrent and nonrecurrent cases (Wilcoxon matched pairs test p = 0.07). The protein identity of P1 was determined to be a truncated form of C4a (C4a des-Arg). Preliminary data indicated that P2 was an N-terminal fragment of protein C inhibitor.
Conclusions
In the current study population, which was matched on Gleason score and TNM staging, pre-radical retropubic prostatectomy prostate specific antigen retained no independent power to predict recurrence. However, by adding 2 proteomic biomarkers to preoperative prostate specific antigen the combined model demonstrated statistically significant value for predicting prostate cancer recurrence in men who underwent radical retropubic prostatectomy.
doi:10.1016/j.juro.2008.10.142
PMCID: PMC4130150  PMID: 19157448
prostate; prostatic neoplasms; neoplasm recurrence; complement C4a; protein C inhibitor
14.  Integrated Analyses of Proteins and Their Glycans in a Magnetic Bead–Based Multiplex Assay Format 
Clinical chemistry  2012;59(1):315-324.
BACKGROUND
Well-annotated clinical samples are valuable resources for biomarker discovery and validation. Multiplex and integrated methods that simultaneously measure multiple analytes and generate integrated information about these analytes from a single measurement are desirable because these methods help conserve precious samples. We developed a magnetic bead–based system for multiplex and integrated glycoprotein quantification by immunoassays and glycan detection by lectin immunosorbent assays (LISAs).
METHODS
Magnetic beads coupled with antibodies were used for capturing proteins of interest. Biotinylated antibodies in combination with streptavidin-labeled phycoerythrin were used for protein quantification. In the LISAs, biotinylated detection antibodies were replaced by biotinylated lectins for glycan detection.
RESULTS
Using tissue inhibitor of metallopeptidase 1 (TIMP-1), tissue plasminogen activator, membrane metallo-endopeptidase, and dipeptidyl peptidase-IV (DPP-4) as models, we found that the multiplex integrated system was comparable to single immunoassays in protein quantification and LISAs in glycan detection. The merits of this system were demonstrated when applied to well-annotated prostate cancer tissues for validation of biomarkers in aggressive prostate cancer. Because of the system’s multiplex ability, we used only 300 ng of tissue protein for the integrated detection of glycans in these proteins. Fucosylated TIMP-1 and DPP-4 offered improved performance over the proteins in distinguishing aggressive and nonaggressive prostate cancer.
CONCLUSIONS
The multiplex and integrated system conserves samples and is a useful tool for validation of glycoproteins and their glycoforms as biomarkers.
doi:10.1373/clinchem.2012.190983
PMCID: PMC4116607  PMID: 23099556
15.  Biomarkers in prostate cancer: what’s new? 
Current opinion in oncology  2014;26(3):259-264.
Purpose of review
This review is intended to provide an overview of the current state of biomarkers for prostate cancer (PCa), with a focus on biomarkers approved by the US Food and Drug Administration (FDA) as well as biomarkers available from Clinical Laboratory Improvement Amendment (CLIA)-certified clinical laboratories within the last 1–2 years.
Recent findings
During the past 2 years, two biomarkers have been approved by the US FDA. These include proPSA as part of the Prostate Health Index (phi) by Beckman Coulter, Inc and PCA3 as Progensa by Gen Probe, Inc. With the advances in genomic and proteomic technologies, several new CLIA-based laboratory-developed tests have become available. Examples are Oncotype DX from Genomics Health, Inc, and Prolaris from Myriad Genetics, Inc. In most cases, these new tests are based on a combination of multiple genomic or proteomic biomarkers.
Summary
Several new tests, as discussed in this review, have become available during the last 2 years. Although the intended use of most of these tests is to distinguish PCa from benign prostatic conditions with better sensitivity and specificity than prostate-specific antigen, studies have shown that some of them may also be useful in the differentiation of aggressive from nonaggressive forms of PCa.
doi:10.1097/CCO.0000000000000065
PMCID: PMC4110681  PMID: 24626128
aggressiveness; biomarkers; genomics; prostate cancer; proteomics
16.  Enzymes and Related Proteins as Cancer Biomarkers: a Proteomic Approach 
Background
The discovery of cancer biomarkers has become a major focus of cancer research, which holds promising future for early detection, diagnosis, monitoring disease recurrence and therapeutic treatment efficacy to improve long-term survival of cancer patients. Most of the functional information of the cancer-associated genes resides in the proteome. Since cancer is a complex disease, it might require a panel of multiple biomarkers in order to achieve sufficient clinical efficacy.
Methods
Serum/plasma is the most accessible biological specimen collected from patients. Therefore, serum proteomic diagnostics would be the most promising new test for cancer. With the advent of new and improved proteomic technologies, such as protein chips and mass spectrometry coupled with advanced bioinformatic tools, it is possible to develop potential cancer biomarkers. However, specimen collection, handling, study design and data analysis are essential components for successful biomarker discovery and validation. Multi-center case control study should be conducted with extensive clinical validation to minimize the impact of possible confounding variables (non-biological).
Conclusions
Enzymes and related proteins, such as inhibitors, are promising candidates for cancer diagnostics.
doi:10.1016/j.cca.2007.02.017
PMCID: PMC4104743  PMID: 17382922
clinical proteomics; cancer biomarkers; mass spectrometry; prostate specific antigen
17.  Validation of a multiplex immunoassay for serum angiogenic factors as biomarkers for aggressive prostate cancer 
Background
Assays used for discovery of biomarkers should be robust and high-throughput, capable of analyzing a sufficiently large number of samples over a sufficiently long period of time with good precision.
Methods
We evaluated the analytical performance of the Bio-Plex Pro™ Human Cancer Biomarker Panel 1, a 16-plex multiplex immunoassay, in serum for composite profiling of angiogenic factors. Because prostate cancer progression and metastasis are pathological events closely linked to angiogenesis, serum angiogenic factors are ideal candidates as prognostic biomarkers.
Results
Our 5-day evaluation indicated that all 16 assays in the panel had good reproducibility (total precisions over 5 independent plates in 5 days of <20%), adequate sensitivity (LOQs of majority of the assays less than 100 pg/ml), and wide dynamic ranges (linearity of majority of the assays spanning across 3 logs in concentrations).
Conclusions
Applying the panel to sera from prostate cancer patients with Gleason scores of 6, 7, 8–10, tumor stages that correlated with clinical outcome, we identified that the levels of sTIE-2, a soluble form of the transmembrane tyrosine kinase receptor for angiopoietins, were increased in patients with Gleason score of 8–10. Future studies are necessary to determine whether sTIE-2 could be used as a prognostic biomarker for identifying aggressive prostate cancer.
doi:10.1016/j.cca.2012.06.017
PMCID: PMC4086634  PMID: 22722017
Multiplex; Immunoassay; Serum angiogenic factors; Aggressive prostate cancer
18.  Proteomic cancer biomarkers from discovery to approval: it’s worth the effort 
Expert review of proteomics  2014;11(2):135-136.
The current landscape of cancer biomarkers is changing rapidly, with new and exciting developments. With the advances of proteomic technologies, many potential cancer biomarkers have been discovered. However, the number of new cancer biomarkers cleared or approved by the US FDA is rather limited. Although technological advances are important, clearly defining intended use, good study design and appropriate patient specimens are critical for the success of FDA approval. While obtaining FDA clearance/approval for newly developed and clinically useful cancer biomarkers has been slow, the reward for patient care could be enormous.
doi:10.1586/14789450.2014.897614
PMCID: PMC4079106  PMID: 24646122
biomarker; cancer; IVDMIA; OVA1; proteomics
19.  A Colorimetric and Luminescent Dual-Modal Assay for Cu(II) Ion Detection Using an Iridium(III) Complex 
PLoS ONE  2014;9(6):e99930.
A novel iridium(III) complex-based chemosensor bearing the 5,6-bis(salicylideneimino)-1,10-phenanthroline ligand receptor was developed, which exhibited a highly sensitive and selective color change from colorless to yellow and a visible turn-off luminescence response upon the addition of Cu(II) ions. The interactions of this iridium(III) complex with Cu2+ ions and thirteen other cations have been investigated by UV-Vis absorption titration, emission titration, and 1H NMR titration.
doi:10.1371/journal.pone.0099930
PMCID: PMC4057321  PMID: 24927177
21.  STAT3 down regulates LC3 to inhibit autophagy and pancreatic cancer cell growth 
Oncotarget  2014;5(9):2529-2541.
The dismal 5-year survival (<5%) for pancreatic cancer (PanCA) underscores the need for developing effective therapeutic options. Recent studies from our laboratory have shown that Nexrutine® (Nx), a bark extract from Phellodendron amurense exhibits excellent anticancer activity in human pancreatic cancer cells through inhibition of inflammatory signaling via STAT3/NFκB/Cox-2. Given the apparent high oxidative stress and autophagic activity in pancreatic tumors, we investigated the potential of Nx to modulate autophagy, reactive oxygen species (ROS), and their crosstalk. Our results show that Nx inhibits autophagy and decreases ROS generation. Pharmacological inhibition of autophagy led to decreased ROS generation and proliferation with no significant effect on apoptosis. Further, using combination index analysis we also found that combination of late-stage autophagy inhibitor with Nx exhibited a moderate synergistic to additive effect. Additionally, genetic or pharmacological inactivation of STAT3 reduced LC3-II levels and expression indicating a possible role for STAT3 in transcriptional regulation of autophagy. Since both inflammatory and oxidative stress signaling activate STAT3, our data implicates that STAT3 plays a vital role in the regulation of autophagy through its contributions to the positive feedback loop between ROS and autophagy. Overall, our findings reveal an important role for STAT3/LC3/ROS in Nx-mediated anti-pancreatic cancer effects.
PMCID: PMC4058024  PMID: 24796733
Pancreatic cancer; Nexrutine®; STAT3; inflammation; autophagy; LC3
22.  Discovery of a Natural Product-Like iNOS Inhibitor by Molecular Docking with Potential Neuroprotective Effects In Vivo 
PLoS ONE  2014;9(4):e92905.
In this study, we applied structure-based virtual screening techniques to identify natural product or natural product-like inhibitors of iNOS. The iNOS inhibitory activity of the hit compounds was characterized using cellular assays and an in vivo zebrafish larvae model. The natural product-like compound 1 inhibited NO production in LPS-stimulated Raw264.7 macrophages, without exerting cytotoxic effects on the cells. Significantly, compound 1 was able to reverse MPTP-induced locomotion deficiency and neurotoxicity in an in vivo zebrafish larval model. Hence, compound 1 could be considered as a scaffold for the further development of iNOS inhibitors for potential anti-inflammatory or anti-neurodegenerative applications.
doi:10.1371/journal.pone.0092905
PMCID: PMC3972188  PMID: 24690920
23.  Neuromedin B receptors regulate EGF receptor tyrosine phosphorylation in lung cancer cells 
European journal of pharmacology  2010;637(0):38-45.
Neuromedin B (NMB), a member of the bombesin family of peptides, is an autocrine growth factor for many lung cancer cells. The present study investigated the ability of NMB to cause transactivation of the epidermal growth factor (EGF) receptor in lung cancer cells. By Western blot, addition of NMB or related peptides to NCI-H1299 human non-small cell lung cancer (NSCLC) cells, caused phosphorylation of Tyr1068 of the EGF receptor. The signal was amplified using NCI-H1299 cells stably transected with NMB receptors. The transactivation of the EGF receptor or the tyrosine phosphorylation of ERK caused by NMB-like peptides was inhibited by AG1478 or gefitinib (tyrosine kinase inhibitors) and NMB receptor antagonist PD168368 but not the GRP receptor antagonist, BW2258U89. The transactivation of the EGF receptor caused by NMB-like peptides was inhibited by GM6001 (matrix metalloprotease inhibitor), PP2 (Src inhibitor), or transforming growth factor (TGF)α antibody. The transactivation of the EGF receptor and the increase in reactive oxygen species caused by NMB-like peptides was inhibited by N-acetylcysteine (NAC) or Tiron. Gefitinib inhibited the proliferation of NCI-H1299 cells and its sensitivity was increased by the addition of PD168368. The results indicate that the NMB receptor regulates EGF receptor transactivation by a mechanism dependent on Src as well as metalloprotease activation and generation of reactive oxygen species.
doi:10.1016/j.ejphar.2010.03.057
PMCID: PMC3921891  PMID: 20388507
lung cancer; neuromedin B; epidermal growth factor receptor; transactivation; reactive oxygen species
24.  Targeted Peptide Measurements in Biology and Medicine: Best Practices for Mass Spectrometry-based Assay Development Using a Fit-for-Purpose Approach* 
Adoption of targeted mass spectrometry (MS) approaches such as multiple reaction monitoring (MRM) to study biological and biomedical questions is well underway in the proteomics community. Successful application depends on the ability to generate reliable assays that uniquely and confidently identify target peptides in a sample. Unfortunately, there is a wide range of criteria being applied to say that an assay has been successfully developed. There is no consensus on what criteria are acceptable and little understanding of the impact of variable criteria on the quality of the results generated. Publications describing targeted MS assays for peptides frequently do not contain sufficient information for readers to establish confidence that the tests work as intended or to be able to apply the tests described in their own labs. Guidance must be developed so that targeted MS assays with established performance can be made widely distributed and applied by many labs worldwide. To begin to address the problems and their solutions, a workshop was held at the National Institutes of Health with representatives from the multiple communities developing and employing targeted MS assays. Participants discussed the analytical goals of their experiments and the experimental evidence needed to establish that the assays they develop work as intended and are achieving the required levels of performance. Using this “fit-for-purpose” approach, the group defined three tiers of assays distinguished by their performance and extent of analytical characterization. Computational and statistical tools useful for the analysis of targeted MS results were described. Participants also detailed the information that authors need to provide in their manuscripts to enable reviewers and readers to clearly understand what procedures were performed and to evaluate the reliability of the peptide or protein quantification measurements reported. This paper presents a summary of the meeting and recommendations.
doi:10.1074/mcp.M113.036095
PMCID: PMC3945918  PMID: 24443746
25.  Tyramide Signal Amplification for Antibody-overlay Lectin Microarray: A Strategy to Improve the Sensitivity of Targeted Glycan Profiling 
Journal of proteome research  2011;10(3):10.1021/pr1010873.
Antibody-overlay lectin microarray (ALM) has been used for targeted glycan profiling to identify disease-related protein glycoforms. In this context, high sensitivity is desired because it allows for the identification of disease-related glycoforms that are often present at low concentration. We describe a new Tyramide Signal Amplification (TSA) for Antibody-overlay Lectin Microarray procedure for sensitive profiling of glycosylation patterns. We demonstrated that TSA increased the sensitivity of the microarray over 100 times for glycan profiling using the model protein Prostate Specific Antigen (PSA). The glycan profile of PSA enriched from LNCAP cells, obtained at a sub-nanogram level with the aid of TSA, was consistent with the previous reports. We also established the glycan profile of Prostate Specific Membrane Antigen (PSMA) using the TSA and ALM. Thus, the Tyramide Signal Amplification for Antibody-overlay Lectin Microarray is a sensitive, rapid, comprehensive, and high-throughput method for targeted glycan profiling and can potentially be used for the identification of disease-related protein glycoforms.
doi:10.1021/pr1010873
PMCID: PMC3831023  PMID: 21133419

Results 1-25 (87)