Unlocking the secrets to protein-protein interface drug targets using structural mass spectrometry techniques

Protein-protein interactions (PPIs) drive all biologic systems at the subcellular and extracellular level. Changes in the specificity and affinity of these interactions can lead to cellular malfunctions and disease. Consequently, the binding interfaces between interacting protein partners are important drug targets for the next generation of therapies that block such interactions. Unfortunately, protein-protein contact points have proven to be very difficult pharmacological targets because they are hidden within complex 3D interfaces. For the vast majority of characterized binary PPIs, the specific amino acid sequence of their close contact regions remains unknown. There has been an important need for an experimental technology that can rapidly reveal the functionally important contact points of native protein complexes in solution. In this review, experimental techniques employing mass spectrometry to explore protein interaction binding sites are discussed. Hydrogen-deuterium exchange, hydroxyl radical footprinting, crosslinking and the newest technology protein painting are compared and contrasted.

A cross-sectional nationwide survey on esophageal atresia and tracheoesophageal fistula

BACKGROUND

Our study aims at disclosing epidemiology and most relevant clinical features of esophageal atresia (EA) pointing to a model of multicentre collaboration.

METHODS

A detailed questionnaire was sent to all Italian Units of pediatric surgery in order to collect data of patients born with EA between January and December 2012. The results were crosschecked by matching date and place of birth of the patients with those of diagnosis-related group provided by the Italian Ministry of Health (MOH).

RESULTS

A total of 146 questionnaires were returned plus a further 32 patients reported in the MOH database. Basing on a total of 178 patients with EA born in Italy in 2012, the incidence of EA was calculated in 3.33 per 10,000 live births. Antenatal diagnosis was suspected in 29.5% patients. 55.5% showed associated anomalies. The most common type of EA was Gross type C (89%). Postoperative complications occurred in 37% of type C EA and 100% of type A EA. A 9.5% mortality rate was reported.

CONCLUSIONS

This is the first Italian cross-sectional nationwide survey on EA. We can now develop shared guidelines and provide more reliable prognostic expectations for our patients.

Abstract 3064: MicroRNA-21 enhances the effect of ionizing radiation via alteration of the DNA damage response

Micro-RNA 21 (miR-21) is a well-known onco-miR found to be up-regulated in over 18 major cancer types and is linked to radiation and chemotherapy resistance. It is hypothesized that dysregulation of miR-21 may contribute to treatment resistance through multiple DNA damage response pathways by enhancing DNA repair and increasing DNA damage tolerance. Given its involvement in multiple resistance pathways, miR-21 appears to be an attractive target for overcoming resistance with radiation therapy.

In vitro, we demonstrated that knockdown of miR-21 revealed an increase in tumor cell death via clonogenic cell survival curves following exposure to ionizing radiation in multiple cancer cell lines including triple negative breast cancer cells, GBM, and lung cancer. A miR-21 knockout (KO) mouse model was then generated based on deletion of a miR-21 upstream promoter element. To determine if mir-21 KO would lead to radiation sensitivity, miR-21 deficient mice were exposed to 6.5Gy total body irradiation (TBI) and compared to control wild type (WT) mice. miR-21 KO mice died at an average of 12 days after TBI vs. over 100 days survival in wild-type mice. Tissue analysis revealed an increase in double strand breaks measured by elevated γ-H2AX in miR-21 deficient mice. An associated decrease in DNA repair genes such as MSH2 and STAG2 was also seen.

Therefore, we hypothesize deletion or silencing of miR-21 results in a radiation sensitive phenotype due to a decreased DNA repair capacity, particularly in the repair of double-strand breaks. In silico analysis predicted miR-21 targets involved in the DNA repair response including rad21 and stag2, which are both members of the cohesin complex. The cohesion complex is a ring-shaped protein complex involved in homologous repair and the DNA damage-response. When exposed to ionizing radiation, rad21 and stag2 expression appears inversely correlated with miR-21 levels in vivo and in vitro. Similarly, in the setting of miR-21 knockdown, rad21 and stag2 expression are increased, suggesting dysregulation in the function of the cohesin complex may contribute to genomic instability and a DNA damage-permissive phenotype.

In the current study, we propose a novel mechanism for increasing radiation sensitivity through miRNA-mediated pathways controlling cellular DNA-repair. Future studies investigating miR-21 expression in patients may identify subgroups of patients who are at risk for resistance to standard cytotoxic therapies and may open avenues for targeted therapies involving mir-21 mediated DNA repair pathways.

Citation Format: Tu Dan, Ajay Palagani, Tiziana DeAngelis, Sunny Han, Lance Liotta, Richard Pestell, Nicole Simone. MicroRNA-21 enhances the effect of ionizing radiation via alteration of the DNA damage response. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3064. doi:10.1158/1538-7445.AM2015-3064

Abstract B55: Molecular characterization of epithelial and stromal crosstalk associated with TRIM28 expression levels in colorectal cancer

Background: TRIM28 is a universal transcriptional co-repressor with pleotropic effects in both normal and tumor cells. We have previously shown that varying TRIM28 levels in epithelial cells and stromal fibroblasts have a prognostic value in colorectal cancer patients. The pathophysiological role of TRIM28 in carcinogenesis may therefore be associated with TRIM28 expression levels and cell type of expression within the tumor microenvironment. In this study we aim to dissect the molecular pathways associated with TRIM28 expression ratios within the tumor microenvironment by isolating individual populations of neoplastic epithelial and stromal cells and investigating their protein signaling networks. Methods: TRIM28 expression was analyzed by immunohistochemistry on FFPE tissue from 19 colorectal cancer patients. TRIM28 staining was evaluated in both epithelial and stromal compartments. IHC scoring of at least 2 units of difference in staining intensity between stromal fibroblasts and epithelial cells was defined as a high TRIM28 expression ratio and a low TRIM28 expression ratio was defined as 1 or 0 units of difference in staining intensity. Reverse-phase protein microarrays (RPMA) were constructed from laser capture micro-dissection (LCM) enriched tumor epithelium and stroma isolated from fresh-frozen tissue of the same patient cohort. The protein signaling networks were measured for 32 downstream signaling endpoints. Spearman rank analysis was used to assess the correlations between individual protein pairs. Correlation coefficient ρ ≥ 0.75 with P ≤ 0.01 was considered significant. Results: Immunohistochemical analysis of the FFPE tissue sections identified 10 TRIM28 high ratio cases and 9 TRIM28 low ratio cases. Proteomic networks were assessed in TRIM28 high and low ratio cases in fresh-frozen tissue using RPMA. Spearman ρ rank correlation analyses for the 32 signaling proteins revealed that 184 highly correlated protein pairs exclusive to the TRIM28 high ratio group, whereas 157 protein pairs were found exclusively in the TRIM28 low ratio group. In addition 191 protein pairs were shared across both TRIM28 high and low ratio groups. The caspases 3 and 7, as well as the cell surface receptor RAGE, were prominent in the high TRIM28 ratio group proteomic network, whereas the Metalloprotease MMP9 and the GTPase Ras-GRF1 were exclusive to the low TRIM28 ratio group. Furthermore we found Survivin and JNK to be prominent in the stromal compartment of the high TRIM28 cases. Conclusions: We characterized molecular pathways associated with TRIM28 expression ratios within the tumor microenvironment. Proteomic analysis revealed distinct protein signaling networks associated with varying TRIM28 expression levels in epithelial and stromal compartments. The study presents a novel way of deciphering molecular crosstalk between the epithelial and stromal compartments within the microenvironment.

Citation Format: Seán Fitzgerald, Virginia Espina, Katherine M. Sheehan, Robert Cummins, Anthony O'Grady, Dermot Kenny, Richard O'Kennedy, Lance Liotta, Elaine W. Kay, Gregor Kijanka. Molecular characterization of epithelial and stromal crosstalk associated with TRIM28 expression levels in colorectal cancer. [abstract]. In: Abstracts: AACR Special Conference on Cellular Heterogeneity in the Tumor Microenvironment; 2014 Feb 26-Mar 1; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(1 Suppl):Abstract nr B55. doi:10.1158/1538-7445.CHTME14-B55

High CerS5 expression levels associate with reduced patient survival and transition from apoptotic to autophagy signalling pathways in colorectal cancer

Ceramide synthase 5 is involved in the de novo synthesis of ceramide, a sphingolipid involved in cell death and proliferation. In this study, we investigated the role of ceramide synthase 5 in colorectal cancer by examining ceramide synthase 5 expression, clinico-pathological parameters and association with survival/death signalling pathways in cancer. Immunohistochemical analysis of CerS5 was performed on 102 colorectal cancer samples using tissue microarrays constructed from formalin-fixed and paraffin-embedded tissues. We found strong membranous ceramide synthase 5 staining in 57 of 102 (56%) colorectal cancers. A multivariate Cox regression analysis of ceramide synthase 5 expression adjusted for disease stage, differentiation and lymphovascular invasion revealed reduced 5-year overall survival (p = 0.001) and 5-year recurrence-free survival (p = 0.002), with hazard ratios of 4.712 and 4.322, respectively. The effect of ceramide synthase 5 expression on tumourigenic processes was further characterised by reverse phase protein array analysis. Reverse phase protein arrays were generated from laser capture microdissection-enriched carcinoma cells from 19 fresh-frozen colorectal cancer tissues. Measurements of phosphorylation and total levels of signalling proteins involved in apoptosis, autophagy and other cancer-related pathways revealed two distinct signalling networks; weak membranous ceramide synthase 5 intensity was associated with a proteomic network dominated by signalling proteins linked to apoptosis, whereas strong ceramide synthase 5 intensity was associated with a proteomic sub-network mostly composed of proteins linked to autophagy. In conclusion, high ceramide synthase 5 expression was found in colorectal cancer tissue and was associated with poorer patient outcomes. Our findings suggest that this may be mediated by a transition from apoptotic to autophagy signalling pathways in ceramide synthase 5 High expressing tumours, thus implicating ceramide synthase 5 in the progression of colorectal cancer.

Use of a novel chagas urine nanoparticle test (chunap) for diagnosis of congenital chagas disease

Background

Detection of congenital T. cruzi transmission is considered one of the pillars of control programs of Chagas disease. Congenital transmission accounts for 25% of new infections with an estimated 15,000 infected infants per year. Current programs to detect congenital Chagas disease in Latin America utilize microscopy early in life and serology after 6 months. These programs suffer from low sensitivity by microscopy and high loss to follow-up later in infancy. We developed a Chagas urine nanoparticle test (Chunap) to concentrate, preserve and detect T. cruzi antigens in urine for early, non-invasive diagnosis of congenital Chagas disease.

Methodology/Principal Findings

This is a proof-of-concept study of Chunap for the early diagnosis of congenital Chagas disease. Poly N-isopropylacrylamide nano-particles functionalized with trypan blue were synthesized by precipitation polymerization and characterized with photon correlation spectroscopy. We evaluated the ability of the nanoparticles to capture, concentrate and preserve T. cruzi antigens. Urine samples from congenitally infected and uninfected infants were then concentrated using these nanoparticles. The antigens were eluted and detected by Western Blot using a monoclonal antibody against T. cruzi lipophosphoglycan. The nanoparticles concentrate T. cruzi antigens by 100 fold (western blot detection limit decreased from 50 ng/ml to 0.5 ng/ml). The sensitivity of Chunap in a single specimen at one month of age was 91.3% (21/23, 95% CI: 71.92%–98.68%), comparable to PCR in two specimens at 0 and 1 month (91.3%) and significantly higher than microscopy in two specimens (34.8%, 95% CI: 16.42%–57.26%). Chunap specificity was 96.5% (71/74 endemic, 12/12 non-endemic specimens). Particle-sequestered T. cruzi antigens were protected from trypsin digestion.

Conclusion/Significance

Chunap has the potential to be developed into a simple and sensitive test for the early diagnosis of congenital Chagas disease.

Congenital Chagas disease is one of the main pillars for the control of Chagas disease because 25% of new infections occur by this route. Conventional diagnosis of congenital Chagas disease is based on microscopy at birth and serology at 9 months. However microscopy misses many infections and many at-risk infants fail to complete serology at six to nine months. We have developed a Chagas urine nanoparticle test (Chunap) for concentration and detection of T. cruzi antigens. Chunap was evaluated in urine samples of 1-month old children. At this age children have the highest levels of parasitemia and therefore also excrete the highest levels of antigen. Parents prefer a urine test to having their baby's blood drawn. Chunap diagnosed congenital infection in a single urine sample as well as PCR in two blood samples. This study also shows that hydrogel/trypan blue particles used in our test efficiently capture, concentrate and protect urinary T. cruzi antigens from enzymatic degradation. Chunap allows for the early diagnosis of congenital Chagas disease, and with appropriate adaptation, may allow early point-of-care intervention.

Abstract 1874: Investigation of the cerebrospinal fluid proteome from central nervous system pediatric tumors using bait loaded hydrogel nanoparticles and mass spectrometry

Central nervous system (CNS) tumors are the second common pediatric malignancies, accounting for approximately 25% of all childhood neoplasms. Cerebrospinal fluid (CSF) is a very valuable source of biomarkers for brain tumors and represents a potential indicator of pathological processes that happen in the CNS. CSF biomarker discovery poses some physiological and technical challenges: low protein levels (total protein concentration 0.3 to 0.7 mg/mL), dynamic range (up to approximately 12 order of magnitude), and the presence of highly abundant proteins masking the less abundant ones. In order to overcome these challenges, we used core-shell capturing hydrogel nanoparticles that can capture, preserve and concentrate candidate low molecular weight, low abundance proteins in solution in one step improving the effective sensitivity of mass-spectrometry by several orders of magnitude. CSF samples from pediatric brain cancer patients (14 medulloblastoma, 4 high-grade glioma, 6 ependimoma, 4 PNET, 2 atypical teratoid rhabdoid tumor) either at initial diagnosis (n=27) or at tumor recurrence (n=3) and 21 non-brain pediatric oncology controls (extra-CNS non Hodgkin lymphoma) were processed with core-shell hydrogel nanoparticles and then analyzed with reverse-phase liquid chromatography/electrospray tandem mass spectrometry (MS/MS). We identified 559 non redundant proteins, 147 (26%) of those not present in the public comprehensive CSF proteome database (www.biosino.org). Functional classification analysis performed with IPA Ingenuity System showed that CSF contained proteins normally involved in neurological diseases, developmental disorders, cellular movement, cellular growth and proliferation. Several candidate proteins that show a statistical difference (p-value <0.05, Fisher test) between brain tumor and non-brain oncology controls, were involved in the process of extracellular matrix (ECM) remodeling which has a key role in the transition to invasive cancer and is often an indicator of worse prognosis. Two examples were a) the ECM protein collagen XVIII, which was previously identified in meningioma tissue with a fast progression, and b) procollagen C-endopeptidase enhancer, an extracellular matrix glycoprotein related to tumor growth and angiogenesis. Statistical analysis between non-metastatic and metastatic patient samples also highlighted potentially relevant proteins such as GDNF family receptor α-2 (GFRα2); two other family members GFRα1 and GFRα3 were reported to have a role in tumor growth and invasiveness. In conclusion, combining a unique dataset of CSF from pediatric cancer patients with a novel enabling nanotechnology allowed us to identify important insights for diagnosis, prognosis and molecular stratification of CNS pediatric tumors.

Citation Format: Ruben Magni, Paolo Verderio, Lance Liotta, Filippo Spreafico, Maura Massimino, Alessandra Luchini, Italia Bongarzone. Investigation of the cerebrospinal fluid proteome from central nervous system pediatric tumors using bait loaded hydrogel nanoparticles and mass spectrometry. [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 1874. doi:10.1158/1538-7445.AM2014-1874

Pilot phase I/II personalized therapy trial for metastatic colorectal cancer: evaluating the feasibility of protein pathway activation mapping for stratifying patients to therapy with imatinib and panitumumab

This nonrandomized phase I/II trial assessed the efficacy/tolerability of imatinib plus panitumumab in patients affected by metastatic colorectal cancer (mCRC) after stratification to treatment by selection of activated imatinib drug targets using reverse-phase protein array (RPPA). mCRC patients presenting with a biopsiable liver metastasis were enrolled. Allocation to the experimental and control arms was established using functional pathway activation mapping of c-Kit, PDGFR, and c-Abl phosphorylation by RPPA. The experimental arm received run-in escalation therapy with imatinib followed by panitumumab. The control arm received panitumumab alone. Seven patients were enrolled in the study. For three of the seven patients, sequential pre- and post-treatment biopsies were used to evaluate the effect of the therapeutic compounds on the drug targets and substrates. A decrease in the activation level of the drug targets and downstream substrates was observed in two of three patients. Combination therapy increased the activation of the AKT-mTOR pathway and several receptor tyrosine kinases. This study proposes a novel methodology for stratifying patients to personalized treatment based on the activation level of the drug targets. This workflow provides the ability to monitor changes in the signaling pathways after the administration of targeted therapies and to identify compensatory mechanisms.

Realizing the promise of reverse phase protein arrays for clinical, translational, and basic research: a workshop report: the RPPA (Reverse Phase Protein Array) society

Reverse phase protein array (RPPA) technology introduced a miniaturized "antigen-down" or "dot-blot" immunoassay suitable for quantifying the relative, semi-quantitative or quantitative (if a well-accepted reference standard exists) abundance of total protein levels and post-translational modifications across a variety of biological samples including cultured cells, tissues, and body fluids. The recent evolution of RPPA combined with more sophisticated sample handling, optical detection, quality control, and better quality affinity reagents provides exquisite sensitivity and high sample throughput at a reasonable cost per sample. This facilitates large-scale multiplex analysis of multiple post-translational markers across samples from in vitro, preclinical, or clinical samples. The technical power of RPPA is stimulating the application and widespread adoption of RPPA methods within academic, clinical, and industrial research laboratories. Advances in RPPA technology now offer scientists the opportunity to quantify protein analytes with high precision, sensitivity, throughput, and robustness. As a result, adopters of RPPA technology have recognized critical success factors for useful and maximum exploitation of RPPA technologies, including the following: preservation and optimization of pre-analytical sample quality, application of validated high-affinity and specific antibody (or other protein affinity) detection reagents, dedicated informatics solutions to ensure accurate and robust quantification of protein analytes, and quality-assured procedures and data analysis workflows compatible with application within regulated clinical environments. In 2011, 2012, and 2013, the first three Global RPPA workshops were held in the United States, Europe, and Japan, respectively. These workshops provided an opportunity for RPPA laboratories, vendors, and users to share and discuss results, the latest technology platforms, best practices, and future challenges and opportunities. The outcomes of the workshops included a number of key opportunities to advance the RPPA field and provide added benefit to existing and future participants in the RPPA research community. The purpose of this report is to share and disseminate, as a community, current knowledge and future directions of the RPPA technology.

Uso dell'analisi d'immagine per la caratterizzazione fenotipica della popolazione asinina Calabrese

Lo studio ha riguardato la caratterizzazione fenotipica di 56 soggetti (tra 2 e 30 anni di età) riconducibili alla popolazione asinina Calabrese, allevati in 23 aziende. Su ciascun soggetto sono stati eseguiti i più significativi rilievi morfometrici mediante l’impiego di un sistema di analisi d’immagine computerizzato. Tali dati sono stati successi-vamente utilizzati per il calcolo dei più significativi indici biometrici. Inoltre sono stati presi in considerazione il colore e le eventuali particolarità del mantello. Gli indici biometrici ricavati ci hanno permesso di inquadrare questa popolazione asinina nel tipo dolicomorfo, come evidenziato dai valori dell’Indice di conformazione laterale del corpo (97,78), dell’Indice toracico di profilo (44,85), dell’Indice di Compattezza (90,80), dell’Indice lunghezza torace (100,79) e dell’Indice di ossatura (12,82). Il colore del mantello è risultato essere principalmente morello (75 %) anche se si è osser-vata la presenza di soggetti baio scuro (20 %) e grigio (5 %). Il colore dell’addome costantemente bianco come anche il muso e le occhiaie. Il colore dell’ano, vulva e mammella è costantemente nero.

The use of Nanotrap particles for biodefense and emerging infectious disease diagnostics

Detection of early infectious disease may be challenging due to the low copy number of organisms present. To overcome this limitation and rapidly measure low concentrations of the pathogen, we developed a novel technology: Nanotrap particles, which are designed to capture, concentrate, and protect biomarkers from complex biofluids. Nanotrap particles are thermoresponsive hydrogels that are capable of antigen capture through the coupling of affinity baits to the particles. Here, we describe recent findings demonstrating that Nanotrap particles are able to capture live infectious virus, viral RNA, and viral proteins. Capture is possible even in complex mixtures such as serum and allows the concentration and protection of these analytes, providing increased performance of downstream assays. The Nanotrap particles are a versatile sample preparation technology that has far reaching implications for biomarker discovery and diagnostic assays.

Stratification of clear cell renal cell carcinoma by signaling pathway analysis

Investigation of cell signaling pathways in 16 clear cell renal cell carcinomas to identify groups based on commonly shared phosphorylation-driven signaling networks. Using laser capture microdissection and reverse-phase protein arrays, we profiled 75 key nodes spanning signaling pathways important in tumorigenesis. Analysis revealed significantly different (P < 0.05) signaling levels for 27 nodes between two groups of samples, designated A (4 samples; high EGFR, RET, and RASGFR1 levels, converging to activate AKT/mTOR) and B (12 samples; high ERK1/2 and STAT phosphorylation). Group B was further partitioned into groups C (7 samples; elevated expression of LC3B) and D (5 samples; activation of Src and STAT). Network analysis indicated that group A was characterized by signaling pathways related to cell cycle and proliferation, and group B by pathways related to cell death and survival. Homogeneous clear cell renal cell carcinomas could be stratified into at least two major functional groups.

A candidate anti-HIV reservoir compound, auranofin, exerts a selective 'anti-memory' effect by exploiting the baseline oxidative status of lymphocytes

Central memory (T_CM) and transitional memory (T_TM) CD4⁺ T cells are known to be the major cellular reservoirs for HIV, as these cells can harbor a transcriptionally silent form of viral DNA that is not targeted by either the immune system or current antiretroviral drug regimens. In the present study, we explored the molecular bases of the anti-HIV reservoir effects of auranofin (AF), a pro-oxidant gold-based drug and a candidate compound for a cure of AIDS. We here show that T_CM and T_TM lymphocytes have lower baseline antioxidant defenses as compared with their naive counterpart. These differences are mirrored by the effects exerted by AF on T-lymphocytes: AF was able to exert a pro-differentiating and pro-apoptotic effect, which was more pronounced in the memory subsets. AF induced an early activation of the p38 mitogen-activated protein kinase (p38 MAPK) followed by mitochondrial depolarization and a final burst in intracellular peroxides. The pro-differentiating effect was characterized by a downregulation of the CD27 marker expression. Interestingly, AF-induced apoptosis was inhibited by pyruvate, a well-known peroxide scavenger, but pyruvate did not inhibit the pro-differentiating effect of AF, indicating that the pro-apoptotic and pro-differentiating effects involve different pathways. In conclusion, our results demonstrate that AF selectively targets the T_CM/T_TM lymphocyte subsets, which encompass the HIV reservoir, by affecting redox-sensitive cell death pathways.

Ultrasound measurement of reproductive organs in juvenile European sea bass Dicentrarchus labrax

In this study, ultrasonographic examination was performed thrice, 15 days apart, on juvenile European sea bass Dicentrarchus labrax, from 330 to 360 days of age, to assess the size and the morphology of male and female. Results have proved this method as a suitable and non-invasive procedure to assess sexual differentiation.

Analysis of urinary human growth hormone (hGH) using hydrogel nanoparticles and isoform differential immunoassays after short recombinant hGH treatment: preliminary results

Successful application clinical-grade human growth hormone (hGH) immunoassays to the discovery of illegal doping cases has been rare. Indeed, the preferred biological matrix in doping control is urine, where the estimated baseline concentration of hGH falls well below the linear range and sensitivity threshold of all commercially available immunoassays, including hGH isoform differential immunoassays which can discriminate pituitary endogenous hGH from recombinant hGH. We employed hydrogel nanoparticles as a pre-processing step that concentrate urinary hGH into the linear range of isoform differential immunoassays. We explored the characteristics of immunoassays in urine spiked with both phGH or rhGH, after pre-treatment with the nanoparticles. Subsequently, pre-treatment was applied to urine obtained from 3 healthy volunteers administered during three days with daily subcutaneous injections of 0.026 mg/kg/day rhGH, Genotonorm(®). Linearity between both rhGH and phGH concentrations in urine measured by a chemoluminescent assay (Immulite) and in the particle eluate was evident for differential immunoassays (R square higher than 0.999). In case of treated individuals the recombinant/pituitary concentration ratios remained above the established World Anti-Doping Agency (WADA) criterion for hGH misuse up to 24h after the last administration dose, using both assays for volunteer 1 and 2 while in case of volunteer 3 results were inconclusive. The use of nanoparticles appears to open the possibility of assessing rhGH misuse in urine.

Individualized therapy for metastatic colorectal cancer

Systemic therapeutic efficacy is central to determining the outcome of patients with metastatic colorectal cancer (CRC). In these patients, there is a critical need for predictive biomarkers to optimize efficacy whilst minimizing toxicity. The integration of a new generation of molecularly targeted drugs into the treatment of CRC, coupled with the development of sophisticated technologies for individual tumours as well as patient molecular profiling, underlines the potential for personalized medicine. In this review, we focus on the latest progress made within the genomic and proteomic fields, concerning predictive biomarkers for individualized therapy in metastatic CRC.

Abstract 1889: Can the moonlighting glycolytic enzyme α-enolase be a therapeutic target in pancreatic cancer

Aberrant metabolism together with invasion and metastasis are hallmarks of cancer. This is particularly true for pancreatic ductal adenocarcinoma (PDAC), characterized by rapid progression, invasiveness and resistance to treatments. We have previously described α-enolase (ENOA) as a PDAC-associated antigen. It is a moonlighting protein that works both as a key metabolic enzyme and as a membrane plasminogen receptor. In order to clarify its multifunctional role in pancreatic tumorigenesis we investigated the effect of ENOA knockdown in PDAC cells. Protein expression alterations following ENOA knockdown in the human PDAC cell line CFPAC-1 were revealed by LC-MS/MS analysis. On the basis of a spectra count label-free quantitation approach a large number of proteins mainly involved in cell adhesion, metabolism and proliferation were found to be differentially expressed in ENOA silenced cells compared to the control. After ENOA silencing, PDAC cells displayed a delay in proliferation and decreased survival and colony formation capabilities, even if the pyruvate production was not affected. The growth inhibition was partially due to an increased concentration of intracellular reactive oxygen species (ROS) mainly generated through the sorbitol and NADPH oxidase pathways. Moreover in ENOA silenced cells, the in vitro plasminogen-driven invasion was abolished and the number of lung tumor masses was significantly reduced in SCID-beige mice injected with ENOA silenced cells compared to mice injected with control cells. These effects are under further confirmation in other PDAC cell lines. All together, these findings propose ENOA as a promising target for developing new therapies in pancreatic cancer management.

Citation Format: Michela Capello, Moitza Principe, Michelle Samuel Chattaragada, Chiara Riganti, Weidong Zhou, Sammy Ferri-Borgogno, Simona Rolla, Lance Liotta, Emanuel Petricoin, Paola Cappello, Francesco Novelli. Can the moonlighting glycolytic enzyme α-enolase be a therapeutic target in pancreatic cancer. [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 1889. doi:10.1158/1538-7445.AM2013-1889

Abstract 2043: Protein pathway activation mapping analysis of metastatic breast cancer reveals potential new targets for personalized therapy

Introduction: It is well known that the development of distant metastasis is the strongest prognostic factor associated with cancer mortality. Recent genomic and proteomic studies have demonstrated that the molecular profile of the metastatic lesions significantly differs from the primary tumor. For this reason, to improve response to therapy the identification of new drug targets needs to be based on the molecular profile of the metastatic lesions rather than the primary tumor. Since most targeted therapies work by modulating hyperactivated protein kinase signaling, the aim of this study was to utilize reverse phase protein arrays (RPPA) to quantitatively measure the drug target signaling architecture to identify new therapeutic options for Stage IV breast cancer patients based on the molecular profile of the metastatic lesion. Methods: Snap frozen material collected from 25 metastatic breast cancer patients enrolled in a prospective phase II trial (“Side Out” 1) were used for this study. Sites of metastasis were: liver (n=12), skin (n=5), lymph nodes (n=5), breast (n=2), and pelvis (n=1). All samples were subjected to Laser Capture Microdissection (LCM) and RPPA whereby the activation/phosphorylation level of 55 drug targets and linked substrates for FDA cleared/experimental therapies were measured. Results: Unsupervised hieratical clustering analysis revealed distinct patient subgroups driven largely by pathway activation more than by site of metastasis. Based on the activation level of the drug targets and the downstream effectors, three major clusters were identified. Each cluster appeared to be driven by a specific subset of drug targets: a) pan-HER family members, b) EGFR/SRC/ERK/mTOR, and c) IGFR/RAF/MEK/PLK1. Conclusion: This is the first study evaluating the activation status of FDA approved/experimental drug targets and downstream effectors in a relatively large number of breast cancer metastatic lesions. This type of approach provides a unique opportunity for identifying new drug targets for this group of patients and provides initial insights on which pathways should be considered in the delivery of targeted therapy to this group of patients.

1. A Pilot Study Utilizing Molecular Profiling by IHC, FISH, DNA Microarray, and Reverse Phase Protein Microarray (RPMA) of Patients’ Tumors to Find Potential Targets and Select Treatments for Patients with Metastatic Breast Cancer, sponsored by the Side Out Foundation

Citation Format: Mariaelena Pierobon, Kimberly A. Reeder, Gayle Jameson, Nicholas Robert, Stephen P. Anthony, Jasgit Sachdev, Linda Vocila, Julia Wulfkuhle, Elisa Baldelli, Lance Liotta, Emanuel F. Petricoin. Protein pathway activation mapping analysis of metastatic breast cancer reveals potential new targets for personalized therapy. [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 2043. doi:10.1158/1538-7445.AM2013-2043

Protein pathway activation mapping of colorectal metastatic progression reveals metastasis-specific network alterations

The mechanism by which tissue microecology influences invasion and metastasis is largely unknown. Recent studies have indicated differences in the molecular architecture of the metastatic lesion compared to the primary tumor, however, systemic analysis of the alterations within the activated protein signaling network has not been described. Using laser capture microdissection, protein microarray technology, and a unique specimen collection of 34 matched primary colorectal cancers (CRC) and synchronous hepatic metastasis, the quantitative measurement of the total and activated/phosphorylated levels of 86 key signaling proteins was performed. Activation of the EGFR-PDGFR-cKIT network, in addition to PI3K/AKT pathway, was found uniquely activated in the hepatic metastatic lesions compared to the matched primary tumors. If validated in larger study sets, these findings may have potential clinical relevance since many of these activated signaling proteins are current targets for molecularly targeted therapeutics. Thus, these findings could lead to liver metastasis specific molecular therapies for CRC.

Interlaboratory reproducibility of selective reaction monitoring assays using multiple upfront analyte enrichment strategies

Over the past few years, mass spectrometry has emerged as a technology to complement and potentially replace standard immunoassays in routine clinical core laboratories. Application of mass spectrometry to protein and peptide measurement can provide advantages including high sensitivity, the ability to multiplex analytes, and high specificity at the amino acid sequence level. In our previous study, we demonstrated excellent reproducibility of mass spectrometry-selective reaction monitoring (MS-SRM) assays when applying standardized standard operating procedures (SOPs) to measure synthetic peptides in a complex sample, as lack of reproducibility has been a frequent criticism leveled at the use of mass spectrometers in the clinical laboratory compared to immunoassays. Furthermore, an important caveat of SRM-based assays for proteins is that many low-abundance analytes require some type of enrichment before detection with MS. This adds a level of complexity to the procedure and the potential for irreproducibility increases, especially across different laboratories with different operators. The purpose of this study was to test the interlaboratory reproducibility of SRM assays with various upfront enrichment strategies and different types of clinical samples (representing real-world body fluids commonly encountered in routine clinical laboratories). Three different, previously published enrichment strategies for low-abundance analytes and a no-enrichment strategy for high-abundance analytes were tested across four different laboratories using different liquid chromatography-SRM (LC-SRM) platforms and previously developed SOPs. The results demonstrated that these assays were indeed reproducible with coefficients of variation of less than 30% for the measurement of important clinical proteins across all four laboratories in real world samples.

Multiplexed protein signal pathway mapping identifies patients with rectal cancer that responds to neoadjuvant treatment

BACKGROUND

Currently there is no reliable technique for predicting clinical or pathologic complete tumor response after radiochemotherapy (RCT) in patients with rectal cancer. We applied reverse phase protein microarray (RPMA) technology to find a signal pathway that may predict the response to preoperative treatment.

PATIENTS AND METHODS

Fifteen rectal cancer samples were collected during preoperative RCT. Seven patients had a good response to preoperative therapy (Mandard grade I-II) and 8 patients had a poor response (Mandard grade III-V). Using laser capture microdissection (LCM) and RPMA analysis, we measured the phosphorylation level of nearly 80 end points and analyzed the signaling pathways.

RESULTS

We identified 4 signaling proteins whose phosphorylation levels were significantly different (P < .05) between the good vs. poor responders; CHK2 and β-catenin were more highly phosphorylated in poor responders, whereas PDK1 and glycogen synthase kinase (GSK)-3α/β had lower phosphorylation levels in poor responders. Interestingly GSK-3α/β, β-catenin, and PDK1 are all present in the phosphatidylinositol-3-kinase (PI3K)-AKT signaling pathway.

CONCLUSIONS

Based on our results, we hypothesize that the activating state of the PI3K-AKT pathway can stratify patients who could benefit most from neoadjuvant treatment. Moreover, identification of theranostic targets has the potential to pinpoint new therapeutic strategies for the nonresponsive population.