Enhancing peptide ligand binding to vascular endothelial growth factor by covalent bond formation.

Formation of a stable covalent bond between a synthetic probe molecule and a specific site on a target protein has many potential applications in biomedical science. For example, the properties of probes used as receptor-imaging ligands may be improved by increasing their residence time on the targeted receptor. Among the more interesting cases are peptide ligands, the strongest of which typically bind to receptors with micromolar dissociation constants, and which may depend on processes other than simple binding to provide images. The side chains of cysteine, histidine, or lysine are attractive for chemical attachment to improve binding to a receptor protein, and a system based on acryloyl probes attaching to engineered cysteine provides excellent positron emission tomographic images in animal models (Wei et al. (2008) J. Nucl. Med. 49, 1828-1835). In nature, lysine is a more common but less reactive residue than cysteine, making it an interesting challenge to modify. To seek practically useful cross-linking yields with naturally occurring lysine side chains, we have explored not only acryloyl but also other reactive linkers with different chemical properties. We employed a peptide-VEGF model system to discover that a 19mer peptide ligand, which carried a lysine-tagged dinitrofluorobenzene group, became attached stably and with good yield to a unique lysine residue on human vascular endothelial growth factor (VEGF), even in the presence of 70% fetal bovine serum. The same peptide carrying acryloyl and related Michael acceptors gave low yields of attachment to VEGF, as did the chloroacetyl peptide.

EarlyCDT®-Lung test: improved clinical utility through additional autoantibody assays.

Tumor-associated autoantibodies (AAbs) have been described in patients with lung cancer, and the EarlyCDT®-Lung test that measures such AAbs is available as an aid for the early detection of lung cancer in high-risk populations. Improvements in specificity would improve its cost-effectiveness, as well as reduce anxiety associated with false positive tests. Samples from 235 patients with newly diagnosed lung cancer and matched controls were measured for the presence of AAbs to a panel of six (p53, NY-ESO-1, CAGE, GBU4-5, Annexin I, and SOX2) or seven (p53, NY-ESO-1, CAGE, GBU4-5, SOX2, HuD, and MAGE A4) antigens. Data were assessed in relation to cancer type and stage. The sensitivity and specificity of these two panels were also compared in two prospective consecutive series of 776 and 836 individuals at an increased risk of developing lung cancer. The six-AAb panel gave a sensitivity of 39% with a specificity of 89 %, while the seven-AAb panel gave a sensitivity of 41 % with a specificity of 91 % which, once adjusted for occult cancers in the population, resulted in a specificity of 93 %. Analysis of these AAb assays in the at-risk population confirmed that the seven-AAb panel resulted in a significant increase in the specificity of the test from 82 to 90 %, with no significant change in sensitivity. The change from a six- to a seven-AAb assay can improve the specificity of the test and would result in a PPV of 1 in 8 and an overall accuracy of 92 %.

Measurement of protein sulfhydryls in response to cellular oxidative stress using gel electrophoresis and multiplexed fluorescent imaging analysis.

The significance of free radicals in biology has been established by numerous investigations spanning a period of over 40 years. Whereas there are many intracellular targets for these radical species, the importance of cysteine thiol posttranslational modification has received considerable attention. The current studies present a highly sensitive method for measurement of the posttranslational modification of protein thiols. This method is based on labeling of proteins with monofunctional maleimide dyes followed by 2D gel electrophoresis to separate proteins and multiplexed fluorescent imaging analysis. The method correctly interrogates the thiol/disulfide ratio present in commercially available proteins. Exposure of pulmonary airway epithelial cells to high concentrations of menadione or t-butyl hydroperoxide resulted in the modification of cysteines in more than 141 proteins of which 60 were subsequently identified by MALDI-TOF/TOF MS. Although some proteins were modified similarly by these two oxidants, several showed detectably different maleimide ratios in response to these two agents. Proteins that were modified by one or both oxidants include those involved in transcription, protein synthesis and folding, and cell death/growth. In conclusion, these studies provide a novel procedure for measuring the redox status of cysteine thiols on individual proteins with a clearly demonstrated applicability to interactions of chemicals with pulmonary epithelial cells.

Grading invasive ductal carcinoma of the breast: advantages of using automated proliferation index instead of mitotic count.

Breast carcinomas are graded according to the "Nottingham modification of the Bloom-Richardson system" (SBR). The system is hindered, however, by lack of precision in assessing all three parameters including nuclear grade, mitosis, and tubular formation, leading to an element of subjectivity. Our objective was to evaluate a new grading system [the nuclear grade plus proliferation (N+P) system] for subjectivity, ease, and better representation of tumor biology. Its components are nuclear grade and automated proliferation index. Invasive ductal carcinomas, consisting of 137 SBR grade I, 247 grade II, and 266 grade III, were re-evaluated by the N+P system. The two systems were compared with each other and correlated with patients' overall survival, tumor size, angiolymphatic invasion, lymph node status, and biomarker status including estrogen receptor, progesterone receptor, p53, epidermal growth factor receptor, BCL-2, and Her-2. Although there was an agreement between the two systems with histologic and prognostic parameters studied, there was 37% disagreement when grading individual tumors. Fifty-three percent of SBR grade II tumors were "down-graded" to N+P grade I, and 7% were "up-graded" to N+P grade III. Distinction among the different histologic grades for overall survival curves was better indicated by the N+P than the SBR system.

IFITM1 suppression blocks proliferation and invasion of aromatase inhibitor-resistant breast cancer in vivo by JAK/STAT-mediated induction of p21.

Interferon induced transmembrane protein 1 (IFITM1) belongs to a family of interferon stimulated genes (ISGs) that is associated with tumor progression and DNA damage resistance; however, its role in endocrine resistance is not known. Here, we correlate IFITM1 expression with clinical stage and poor response to endocrine therapy in a tissue microarray consisting of 94 estrogen receptor (ER)-positive breast tumors. IFITM1 overexpression is confirmed in the AI-resistant MCF-7:5C cell line and not found in AI-sensitive MCF-7 cells. In this study, the orthotopic (mammary fat pad) and mouse mammary intraductal (MIND) models of breast cancer are used to assess tumor growth and invasion in vivo. Lentivirus-mediated shRNA knockdown of IFITM1 in AI-resistant MCF-7:5C cells diminished tumor growth and invasion and induced cell death, whereas overexpression of IFITM1 in wild-type MCF-7 cells promoted estrogen-independent growth and enhanced their aggressive phenotype. Mechanistic studies indicated that loss of IFITM1 in MCF-7:5C cells markedly increased p21 transcription, expression and nuclear localization which was mediated by JAK/STAT activation. These findings suggest IFITM1 overexpression contributes to breast cancer progression and that targeting IFITM1 may be therapeutically beneficial to patients with endocrine-resistant disease.

Characterization of cytosolic glutathione S-transferases in juvenile Chinook salmon (Oncorhynchus tshawytscha).

Four cytosolic glutathione S-transferase (GST) classes were isolated and characterized from juvenile winter run Chinook salmon (Oncorhynchus tshawytscha) liver. Two techniques were used: (1) gel electrophoresis/immunoblotting against a polyclonal striped bass GST antibody and (2) high-pressure liquid chromatography (HPLC). Nanospray liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to elucidate peptide sequences and the proteins were identified as pi, theta, mu and alpha, by searching against the NCBI non-redundant database (nrDB). Catalytic activity of the cytosolic GSTs towards 1-chloro-2,4-dinitrobenzene (CDNB) and ethacrynic acid (ETHA) were determined to be 0.3+/-0.05 U/mg cytosolic protein and 0.06+/-0.02 U/mg cytosolic protein, respectively.

Characterization of glutathione S-transferases in juvenile white sturgeon.

Glutathione S-transferases (GSTs) are a family of detoxification enzymes that catalyze the conjugation of glutathione (GSH) to electrophiles, thus preventing toxicity. This study characterized the cytosolic GST classes of juvenile white sturgeon (Acipenser transmontanus) liver, using two methods of isolation. The first, which employed affinity chromatography, electrophoresis and immunoblotting against a polyclonal striped bass GST antibody, yielded two cytosolic GSTs. The GSTs were identified by nanospray liquid chromatography-tandem mass spectrometry (LC-MS/MS), peptide mass mapping and MS/MS sequencing, as well as de novo MS/MS sequencing as GST classes pi and mu using the Mascot search engine and the NCBI non-redundant database (nrDB) for both methods. The molecular masses were determined to be 23,548 +/- 23 and 26,027 +/- 23 Da, respectively, using linear matrix assisted laser desorption ionization time of flight (MALDI-TOF) mass spectrometry. The second method of isolation, which used affinity chromatography and high-pressure liquid chromatography (HPLC), yielded pi, mu, and possibly two alpha isoforms by MALDI-TOF-TOF, again searching against the NCBI nrDB. The alpha isoforms were determined to have molecular masses of 25,528 +/- 23 and 25,348 +/- 23 Da by electrospray ionization source (ESI)-MS. Overall, it appears that the HPLC method is more sensitive than immunoblotting with the current antibody. Activity of the cytosolic GSTs was evaluated using the substrate 1-chloro-2,4-dinitrobenzene (CDNB) and found to be 2.4 +/- 0.6 U/mg cytosolic protein, and 0.41 +/- 0.05 U/mg cytosolic protein using ethacrynic acid (ETHA).

Dietary catechin delays tumor onset in a transgenic mouse model.

BACKGROUND: Evidence exists that red wine, which contains a large array of polyphenols, is protective against cardiovascular disease and possibly cancer. OBJECTIVE: We tested the hypothesis that catechin, the major monomeric polyphenol in red wine, can delay tumor onset in transgenic mice that spontaneously develop tumors. DESIGN: Mice were fed a nutritionally complete amino acid-based diet supplemented with (+)-catechin (0-8 mmol/kg diet) or alcohol-free solids from red wine. Mice were examined daily; the age at which a first tumor appeared was recorded as the age at tumor onset. Plasma catechin and metabolite concentrations were quantified at the end of the study. RESULTS: Dietary catechin significantly delayed tumor onset; a positive, linear relation was observed between the age at tumor onset and either the amount of dietary catechin (r(2) = 0.761, P < 0.001) or plasma catechin and metabolite concentrations (r(2) = 0.408, P = 0.003). No significant effects on tumor onset were observed when mice consumed a diet supplemented with wine solids containing <0.22 mmol catechin/kg diet, whereas a previous study showed that wine solids with a similar total polyphenol concentration but containing approximately 4 times more catechin significantly delayed tumor onset by approximately 30 d compared with a control diet. The catechin composition of the wines is directly related to processing conditions during vinification. CONCLUSIONS: Physiologic intakes of specific dietary polyphenols, such as catechin, may play an important role in cancer chemoprevention. Wines have different polyphenol concentrations and compositions; therefore, the overall health benefits of individual wines differ.

Complex karyotype in a low grade phyllodes tumor of the breast.

Cytogenetic analysis of a phyllodes tumor of low grade malignancy disclosed the karyotype 52-55,XX, -1,+5,+7,+9,+10,+11,-15,+18,-19,+20,der(21)t(1;21)(p13;q22),+mar1x 2-4,+mar2[cp18]/46,XX. This study shows that a complex chromosome karyotype can be found in low-grade phyllodes tumors and is not necessarily a sign of extreme malignancy of these neoplasms.

A comparison of prognostic tumor markers obtained on image-guided breast biopsies and final surgical specimens.

BACKGROUND: This study was initiated to determine whether tumor markers obtained on image-guided breast biopsy specimens provide accurate prognostic information for women with invasive breast cancer. METHODS: Prognostic tumor markers on preoperative image-guided biopsy and final surgical specimens were compared in 44 patients with invasive breast cancer. RESULTS: Progesterone receptor (PR) discordance was 18%. In 87% of PR discordant cases, the image-guided biopsy was positive and the final specimen was negative (P = 0.03). Tumor grade was discordant in 36% of patients Discordance for estrogen receptor (ER) = 2%; MIB-1 = 18%; Her2/neu = 9%; EGFR = 10%; p53 = 9%; and bcl-2 = 0%. The discordance for these markers was random and did not reach statistical significance. CONCLUSION: Image-guided core needle biopsies provide reliable information for the majority of prognostic tumor makers. A positive progesterone receptor is significantly more likely to be determined by core biopsy rather than the final surgical specimen. Tumor grade should be based upon the final surgical specimen whenever possible.

Malignant melanoma of the lip spreading in a pagetoid manner into the minor salivary glands.

We describe a malignant melanoma of the lower lip that upon recurrence extended in a pagetoid manner into the ducts of the oral minor salivary glands. Immunohistochemistry with antibodies to MART-1 and HMB-45 confirmed that the atypical cells in the ducts of the salivary glands were indeed melanoma cells. Pathologists involved in staging of oral melanoma are urged to look out for this previously unreported mode of spread of labial malignant melanoma.

Audit of the autoantibody test, EarlyCDT®-lung, in 1600 patients: an evaluation of its performance in routine clinical practice.

OBJECTIVES: EarlyCDT(®)-Lung may enhance detection of early stage lung cancer by aiding physicians in assessing high-risk patients through measurement of biological markers (i.e., autoantibodies). The test's performance characteristics in routine clinical practice were evaluated by auditing clinical outcomes of 1613 US patients deemed at high risk for lung cancer by their physician, who ordered the EarlyCDT-Lung test for their patient. METHODS: Clinical outcomes for all 1613 patients who provided HIPAA authorization are reported. Clinical data were collected from each patient's treating physician. Pathology reports when available were reviewed for diagnostic classification. Staging was assessed on histology, otherwise on imaging. RESULTS: Six month follow-up for the positives/negatives was 99%/93%. Sixty-one patients (4%) were identified with lung cancer, 25 of whom tested positive by EarlyCDT-Lung (sensitivity=41%). A positive EarlyCDT-Lung test on the current panel was associated with a 5.4-fold increase in lung cancer incidence versus a negative. Importantly, 57% (8/14) of non-small cell lung cancers detected as positive (where stage was known) were stage I or II. CONCLUSIONS: EarlyCDT-Lung has been extensively tested and validated in case-control settings and has now been shown in this audit to perform in routine clinical practice as predicted. EarlyCDT-Lung may be a complementary tool to CT for detection of early lung cancer.

Characterization of model peptide adducts with reactive metabolites of naphthalene by mass spectrometry.

Naphthalene is a volatile polycyclic aromatic hydrocarbon generated during combustion and is a ubiquitous chemical in the environment. Short term exposures of rodents to air concentrations less than the current OSHA standard yielded necrotic lesions in the airways and nasal epithelium of the mouse, and in the nasal epithelium of the rat. The cytotoxic effects of naphthalene have been correlated with the formation of covalent protein adducts after the generation of reactive metabolites, but there is little information about the specific sites of adduction or on the amino acid targets of these metabolites. To better understand the chemical species produced when naphthalene metabolites react with proteins and peptides, we studied the formation and structure of the resulting adducts from the incubation of model peptides with naphthalene epoxide, naphthalene diol epoxide, 1,2-naphthoquinone, and 1,4-naphthoquinone using high resolution mass spectrometry. Identification of the binding sites, relative rates of depletion of the unadducted peptide, and selectivity of binding to amino acid residues were determined. Adduction occurred on the cysteine, lysine, and histidine residues, and on the N-terminus. Monoadduct formation occurred in 39 of the 48 reactions. In reactions with the naphthoquinones, diadducts were observed, and in one case, a triadduct was detected. The results from this model peptide study will assist in data interpretation from ongoing work to detect peptide adducts in vivo as markers of biologic effect.

Analysis of naphthalene adduct binding sites in model proteins by tandem mass spectrometry.

The electrophilic metabolites of the polyaromatic hydrocarbon naphthalene have been shown to bind covalently to proteins and covalent adduct formation correlates with the cytotoxic effects of the chemical in the respiratory system. Although 1,2-naphthalene epoxide, naphthalene diol epoxide, 1,2-naphthoquinone, and 1,4-napthoquinone have been identified as reactive metabolites of interest, the role of each metabolite in total covalent protein adduction and subsequent cytotoxicity remains to be established. To better understand the target residues associated with the reaction of these metabolites with proteins, mass spectrometry was used to identify adducted residues following (1) incubation of metabolites with actin and protein disulfide isomerase (PDI), and (2) activation of naphthalene in microsomal incubations containing supplemental actin or PDI. All four reactive metabolites bound to Cys, Lys or His residues in actin and PDI. Cys17 of actin was the only residue adducted by all metabolites; there was substantial metabolite selectivity for the majority of adducted residues. Modifications of actin and PDI, following microsomal incubations containing ¹4C-naphthalene, were detected readily by 2D gel electrophoresis and phosphor imaging. However, target modifications on tryptic peptides from these isolated proteins could not be readily detected by MALDI/TOF/TOF and only three modified peptides were detected using high resolution-selective ion monitoring (HR-SIM). All the reactive metabolites investigated have the potential to modify several residues in a single protein, but even in tissues with very high rates of naphthalene activation, the extent of modification was too low to allow unambiguous identification of a significant number of modified residues in the isolated proteins.

Utility of frozen-section analysis of sentinel lymph node biopsy specimens for melanoma in surgical decision making.

BACKGROUND: Debate exists whether frozen-section analysis of sentinel lymph nodes (SLNs) for melanoma is an accurate method to detect disease that has metastasized to the lymph nodes. The purpose of this study was to evaluate the utility of intraoperative frozen section for SLNs in melanoma. METHODS: We reviewed 133 patients (271 nodes) who underwent SLN biopsy with frozen section for melanoma between April 2003 and September 2007. Frozen-section diagnosis was compared with final diagnosis to determine concordance between intraoperative and postsurgical diagnosis. RESULTS: A total of 11 nodes (8% of patients) were found to have metastatic disease. All patients underwent lymph node dissections at the time of SLN biopsy. No false-positive SLNs were found on frozen section. The false-negative rate for SLN biopsy frozen section was 8% (1 of 133 patients). CONCLUSIONS: Intraoperative frozen section can be an accurate and reliable tool in the right setting for analysis of sentinel nodes in cutaneous melanoma and deserves further study.

Characterization of cytosolic glutathione S-transferases in striped bass (Morone saxitilis).

Electrophilic compounds are ubiquitous in the environment and aquatic life is inevitably affected. Glutathione S-transferases (GSTs) are a class of enzymes that facilitate the detoxification of these electrophiles in phase II metabolism. In this study, cytosolic GSTs were isolated and characterized from striped bass liver (Morone saxitilis). Nanospray liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to elucidate peptide sequences, and the proteins were found to have homology to rho and alpha by searching against the NCBI non-redundant database (nrDB). Catalytic activities of the cytosolic GSTs towards 1-chloro-2,4-dinitrobenzene (CDNB) were determined to be 141+/-34 and 155+/-65nmol/min/mg for males and females, respectively (both n=3). However, sex differences in classes expressed and activity toward CDNB were not statistically significant (p>0.05).

Characterization of cytosolic glutathione S-transferases in California Halibut (Paralichthys californicus).

Two cytosolic glutathione S-transferase (GST) classes were isolated and characterized from California halibut (Paralichthys californicus) liver. Nanospray liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to elucidate peptide sequences and the proteins were identified as theta and alpha by searching against the NCBI non-redundant database (nrDB). Catalytic activity of the cytosolic GSTs towards 1-chloro-2,4-dinitrobenzene (CDNB) was determined to be 0.23+/-0.003 U/mg cytosolic protein.

Measurement of un-ionized ammonia in complex mixtures.

The toxicity of un-ionized ammonia, NH3 (aq), in anaerobic digestion of high-nitrogen wastes has been researched extensively. Previous estimates of NH3 (aq) concentration have relied on a simple speciation approach, based only on the acid dissociation constant and the sample pH and total ammonia concentration. The distinction between concentration and chemical activity has generally not been made, despite the potential for resulting errors in the calculation of NH3 (aq) concentration, and the greater applicability of activity to toxicity work. The currently accepted approach for estimating NH3 (aq) concentration is based on assumptions that are not valid in digested animal manure or other concentrated wastes. This work presents an approach for directly measuring NH3 (aq) activity in complex mixtures using gaseous/aqueous equilibrium across microporous tubing. Application of this approach to anaerobic digester samples confirms that the currently accepted approach is not accurate; it overestimated NH3 (aq) activity in unaltered samples by 45-200%. Previous work on the toxicity of ammonia to methanogenesis has probably overestimated the tolerance of consortia to NH3 (aq), due to overestimation of concentrations. The method introduced here is expected to be useful in a range of research on ammonia toxicity and volatilization.

Bilateral oncocytic malignant melanoma in axillary lymph nodes without evidence of an extranodal primary.

A malignant melanoma was diagnosed in an axillary lymph node of a 49-year-old man. The tumor was examined by electron microscopy and was found to be composed of large oncocytic cells, filled with abundant mitochondria. No primary tumor could be identified on the skin or within internal organs. Approximately 2 years after the initial diagnosis, the patient presented with malignant melanoma in an axillary lymph node on the contralateral side. The second tumor also expressed the same oncocytic phenotype, favoring the common origin of both tumors. These data illustrate that oncocytic melanomas may retain their oncocytic phenotype during metastatic dissemination.

Characterization of a structurally intact in situ lung model and comparison of naphthalene protein adducts generated in this model vs lung microsomes.

Airway epithelial cells are a susceptible site for injury by ambient air toxicants such as naphthalene that undergo P450-dependent metabolic activation. The metabolism of naphthalene in Clara cells to reactive intermediates that bind covalently to proteins correlates with cell toxicity. Although several proteins adducted by reactive naphthalene metabolites were identified in microsomal incubations, new methods that maintain the structural integrity of the lung are needed to examine protein targets. Therefore, we developed a method that involves inflation of the lungs via the trachea with medium containing (14)C-naphthalene followed by incubation in situ. The viability of this preparation is supported by maintenance of glutathione levels, rates of naphthalene metabolism, and exclusion of ethidium homodimer-1 from airway epithelium. Following in situ incubation, the levels of adduct per milligram of protein were measured in proteins obtained from bronchoalveolar lavage, epithelial cells, and remaining lung. The levels of adducted proteins obtained in lavage and epithelial cells were similar and were 20-fold higher than those in residual lung tissue. (14)C-Labeled adducted proteins were identified by matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) mass spectrometry (MS) and quadrupole-TOF MS/MS. Major adducted proteins include cytoskeletal proteins, proteins involved in folding and translocation, ATP synthase, extracellular proteins, redox proteins, and selenium binding proteins. We conclude that in situ incubation maintains structural integrity of the lung while allowing examination of reactive intermediate activation and interaction with target cell proteins of the lung. The proteins adducted and identified from in situ incubations were not the same proteins identified from microsomal incubations.