Direct cancer tissue proteomics: a method to identify candidate cancer biomarkers from formalin-fixed paraffin-embedded archival tissues

Successful treatment of multiple cancer types requires early detection and identification of reliable biomarkers present in specific cancer tissues. To test the feasibility of identifying proteins from archival cancer tissues, we have developed a methodology, termed direct tissue proteomics (DTP), which can be used to identify proteins directly from formalin-fixed paraffin-embedded prostate cancer tissue samples. Using minute prostate biopsy sections, we demonstrate the identification of 428 prostate-expressed proteins using the shotgun method. Because the DTP method is not quantitative, we employed the absolute quantification method and demonstrate picogram level quantification of prostate-specific antigen. In depth bioinformatics analysis of these expressed proteins affords the categorization of metabolic pathways that may be important for distinct stages of prostate carcinogenesis. Furthermore, we validate Wnt-3 as an upregulated protein in cancerous prostate cells by immunohistochemistry. We propose that this general strategy provides a roadmap for successful identification of critical molecular targets of multiple cancer types.

Lymphatic mapping and parametrial lymph nodes identification in patients with early stage cervical cancer

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Background: The purpose of this study was to determine the presence, distribution, and metastasis incidence of parametrial lymph nodes (PLN) of patients with cervical cancer, and to investigate the role of lymphatic mapping and topographic section in PLN identification. Methods: Sixty patients with early stage (Ib∼IIa) cervical cancer undergoing radical hysterectomy and pelvic lymphadenectomy were included in the study. Before surgery 4 ml methylene was injected into the cervix around the tumor. The blue-dyed lymph nodes were identified as sentinel lymph nodes (SLN) during operation. An immediate topographic section on uterine specimen was performed to separate the PLNs from parametria for pathologic examination. Results: Ninety five PLNs were presented in 38 (63.3%) of 60 specimens, with a mean size in diameter as (0.67±0.24)cm, and 57 (60.0%) of PLNs were located parallel to the uterine artery through the entire broad ligament. After lymphatic mapping, 69 (72.6%) of PLNs was dyed and found out as SLNs. Parametrial metastasis was found in 12 (20.0%) patients, and parametrium was the only site containing positive nodes in 2 patients with parametrial metastasis. On routine pathologic evaluation, 17 PLNs were found to be positive. Among the remaining 78 PLNs, multilevel sectioning in conjunction with immunohistochemical analysis was carried out and identified 3 other PLNs containing micrometastases. Conclusions: The study showed that PLNs were often found in the parametria, and these nodes often contained metastatic diseases, which were often overlooked. Lymphatic mapping followed by meticulous topographic section is feasible in PLN identification in patients with cervical cancer.

No significant financial relationships to disclose.

An investigation of job satisfaction, organizational commitment and role conflict and ambiguity in a sample of Chinese undergraduate nursing students

This study aimed to explore the relationships between job satisfaction and organizational commitment, role conflict and ambiguity, and demographic variables associated with retention of nurses within the Chinese healthcare workforce. A hypothetical model derived from a review of research studies investigating relationships between these variables was tested in a cross-sectional questionnaire survey of all the final year nursing students in a medical university in China. Seventy-one out of the total sample of 75 final year nursing students completed the questionnaire, producing a response rate of 95%. Descriptive and inferential statistical analysis of the data revealed a positive relationship between job satisfaction and organizational commitment, and a negative relationship between job satisfaction and role conflict and ambiguity. These results largely support the hypothesised associations between variables found in research studies derived mainly from samples of Western qualified nurses. However, contrary to previous studies, the findings suggest that aspirations to work in a clinical post are associated with high job satisfaction, and degree level student nurses have relatively high job satisfaction. The main implications for nursing education and practice are that educators and clinical mentors should work collaboratively to reduce the gap between theory and practice, specifically to improve the quality of student nurses' clinical experience in China and elsewhere. Positive clinical placement experience is related to high job satisfaction, and so, potentially, to improved retention. Future studies are needed which investigate changes in job satisfaction and other related variables over time, which have student nurse samples that are sufficient to enable the predictive value of these variables on retention in the healthcare workforce to be investigated.

Gene Expression Profiles in Hepatitis C Virus (HCV) and HIV Coinfection: Class Prediction Analyses before Treatment Predict the Outcome of Anti‐HCV Therapy among HIV‐Coinfected Persons

Therapy for hepatitis C virus (HCV) infection in human immunodeficiency virus (HIV)-infected patients results in modest cure rates. Gene expression patterns in peripheral blood mononuclear cells from 29 patients coinfected with HIV and HCV were used to predict virological response to therapy for HCV infection. Prediction analysis using pretherapy samples identified 79 genes that correctly classified all 10 patients who did not respond to therapy, 8 of 10 patients with a response at the end of treatment, and 7 of 9 patients with sustained virological response (86% overall). Analysis of 17 posttreatment samples identified 105 genes that correctly classified all 9 patients with response at the end of treatment and 7 of 8 patients with sustained virological response (94% overall). Failure of anti-HCV therapy was associated with elevated expression of interferon-stimulated genes. Gene expression patterns may provide a tool to predict anti-HCV therapeutic response.

Structure Determination and Relative Properties of Novel Noncentrosymmetric Borates MM‘4(BO3)3(M = Na, M‘ = Ca and M = K, M‘ = Ca, Sr)

A series of novel noncentrosymmetric borates, MM'4(BO3)3 (M = Na, M' = Ca; M = K, M' = Ca, Sr), have been successfully synthesized via a standard solid-state reaction. The crystal structures have been determined by the SDPD (structure determination from powder diffraction) method. They crystallize in the noncentrosymmetric space group Ama2 with the following lattice parameters: a = 10.68004(11) A, b = 11.28574(11) A, c = 6.48521(6) A for NaCa4(BO3)3; a = 10.63455(10) A, b = 11.51705(11) A, c = 6.51942(6) A for KCa4(BO3)3; and a = 11.03843(8) A, b = 11.98974(9) A, c = 6.88446(5) A for KSr4(BO3)3. The fundamental building units are isolated BO3 anionic groups. Their second harmonic generation (SHG) coefficients were one-half (NaCa4(BO3)3), one-third (KCa4(BO3)3), and two-thirds (KSr4(BO3)3) as large as that of KH2PO4 (KDP). The infrared and UV-vis spectra of the three compounds are discussed. Moreover, a comparison of the structures of these novel compounds and three other novel cubic compounds with the same formula, MM'4(BO3)3 (M = Li, M' = Sr; M = Na, M' = Sr, Ba), is presented here.

Structural analysis of a set of proteins resulting from a bacterial genomics project

The targets of the Structural GenomiX (SGX) bacterial genomics project were proteins conserved in multiple prokaryotic organisms with no obvious sequence homolog in the Protein Data Bank of known structures. The outcome of this work was 80 structures, covering 60 unique sequences and 49 different genes. Experimental phase determination from proteins incorporating Se-Met was carried out for 45 structures with most of the remainder solved by molecular replacement using members of the experimentally phased set as search models. An automated tool was developed to deposit these structures in the Protein Data Bank, along with the associated X-ray diffraction data (including refined experimental phases) and experimentally confirmed sequences. BLAST comparisons of the SGX structures with structures that had appeared in the Protein Data Bank over the intervening 3.5 years since the SGX target list had been compiled identified homologs for 49 of the 60 unique sequences represented by the SGX structures. This result indicates that, for bacterial structures that are relatively easy to express, purify, and crystallize, the structural coverage of gene space is proceeding rapidly. More distant sequence-structure relationships between the SGX and PDB structures were investigated using PDB-BLAST and Combinatorial Extension (CE). Only one structure, SufD, has a truly unique topology compared to all folds in the PDB.

Roles of the Bloom's syndrome helicase in the maintenance of genome stability

The RecQ family of DNA helicases is highly conserved in evolution from bacteria to humans. Of the five known human RecQ family members, three (BLM, WRN and RECQ4, which cause Bloom's syndrome, Werner's syndrome and Rothmund-Thomson syndrome respectively) are mutated in distinct clinical disorders associated with cancer predisposition and/or premature aging. BLM forms part of a multienzyme complex including topoisomerase IIIalpha, replication protein A and a newly identified factor called BLAP75. Together, these proteins play a role in the resolution of DNA structures that arise during the process of homologous recombination repair. In the absence of BLM, cells show genomic instability and a high incidence of sister-chromatid exchanges. In addition to a DNA structure-specific helicase activity, BLM also catalyses Holliday-junction branch migration and the annealing of complementary single-stranded DNA molecules.

Compact and integrated 2-D photonic crystal super-prism filter-device for wavelength demultiplexing applications

A two-dimensional photonic crystal (PhC) super-prism integrated with one-dimensional photonic crystal microcavity filters has been designed using the plane wave expansion (PWE) and 2-D Finite Difference Time Domain (FDTD) methods based on Silicon-on-Insulator (SOI) technology. The super-prism operates as a coarse spatial filter with an average response bandwidth of 60 nm, while the 1-D PhC microcavity filters operate as narrow band-pass transmission filters with an average filter response line-width of 10 nm. This work demonstrates the simultaneous operation of two photonic devices for de-multiplexing applications on a single platform that could be useful in future Photonic Crystal Integrated Circuits (PCICs).

Functional variants of antioxidant genes in smokers with COPD and in those with normal lung function

BACKGROUND

Chronic obstructive pulmonary disease (COPD) is predominantly the consequence of chronic smoking exposure, but its development may be influenced by genetic variants that affect lung remodelling, inflammation, and defence from oxidant stress. A study was undertaken to determine whether genetic variants within genes encoding the antioxidant enzymes superoxide dismutase (SOD) and catalase may be associated with the development of impaired lung function.

METHODS

In a case-control study, the allele and genotype frequencies of functional polymorphisms from SOD1 (CuZnSOD), SOD2 (MnSOD), SOD3 (extracellular SOD), and catalase (CAT) were compared in chronic smokers with normal lung function (resistant smokers) and in those with COPD.

RESULTS

Significantly higher frequencies of the G allele and CG/GG genotype of the 213 SOD3 polymorphism were found in resistant smokers (odds ratios (ORs) 4.3 (95% CI 1.5 to 13.3) and 4.2, 95% CI 1.4 to 13.3), Bonferroni corrected p = 0.02 and p = 0.02, respectively) than in those with COPD. There were no differences between the COPD and resistant smokers for the SOD1, SOD2, or CAT polymorphisms tested.

CONCLUSIONS

The 213Gly variant of the SOD3 gene may, through antioxidant or anti-inflammatory effects, confer a degree of resistance in some smokers to the development of COPD.

Cycloxygenase-2 activity promotes cognitive deficits but not increased amyloid burden in a model of Alzheimer’s disease in a sex-dimorphic pattern

Administration of non-steroidal anti-inflammatory agents reduces the risk of developing Alzheimer's disease in normal aging populations, an effect that may occur from inhibition of the cyclooxygenases, the rate-limiting enzymes in the formation of prostaglandins. In this study, we investigated whether increased activity of cyclooxygenase-2 (COX-2), the inducible isoform of cyclooxygenase, potentiates disease progression in a transgenic mouse model of Alzheimer's disease. To study the functional effects of COX-2 activity, male and female bigenic mice (amyloid precursor protein with Swedish mutation [APPswe]-presenilin-1 protein with deletion of exon 9 [PS1dE9] and trigenic COX-2/APPswe-PS1dE9) were behaviorally tested +/-administration of the selective COX-2 inhibitor celecoxib. Behavioral testing included a three-trial Y maze that measures spatial working and recognition memories and an open field task that tested levels of hyperactivity. Overexpression of COX-2 in APPswe-PS1dE9 mice resulted in specific deficits in spatial working memory in female but not male mice. These sex-specific deficits were abolished by pharmacological inhibition of COX-2 activity. Importantly, COX-2-associated deficits were dependent on co-expression of all three transgenes since COX-2 single transgenic and APPswe-PS1dE9 bigenic mice showed normal memory. Quantification of amyloid plaque load and total Abeta 40 and 42 peptides did not reveal significant differences in trigenic versus bigenic mice treated with either vehicle or celecoxib. Taken together, these data indicate an interaction between the effects of COX-2 and Abeta peptides on cognition that occurs in a sex-specific manner in the absence of significant changes in amyloid burden. These findings suggest that pathological activation of COX-2 may potentiate the toxicity of Abeta peptides, particularly in females, without significantly affecting Abeta accumulation.

Gender-related differences in advanced glycation endproducts, oxidative stress markers and nitric oxide synthases in rats

An age- and blood pressure-associated increase in methylglyoxal (MG) and MG-induced advanced glycation endproducts (AGEs), including N(epsilon)-carboxyethyl-lysine (CEL) and N(epsilon)-carboxymethyl-lysine (CML), in the kidney of spontaneously hypertensive rats (SHR) has been shown. In the present study, gender-related changes in AGEs and nitric oxide synthase were investigated in Sprague-Dawley (SD) and stroke-prone SHR (SHRsp) rats. Immunohistochemical analyses were conducted on kidneys from 24-week-old male and female SD rats as well as SHRsp. The systolic blood pressure of SHRsp was significantly higher than that of SD rats. Male SD rats had more intense kidney staining for CEL than female SD rats. Both male and female SHRsp had more marked CEL and CML staining localized to kidney tubules, as opposed to SD rats. Female rats showed more staining in glomerular vessels than male rats in both SD and SHRsp. Nuclei containing nuclear factor-kappaB (NF-kappaB) p65 and activated macrophages were seen in the kidney from SHRsp, not so much in SD rats, localized to renal tubules in male and glomerular vessels in female SHRsp. A higher protein level of NF-kappaB p65 was found in SHRsp than in SD rats. SD rats had more intense kidney neuronal nitric oxide synthase staining than SHRsp. The intensity of inducible nitric oxide synthase staining was significantly higher in SHRsp than in SD rats, with no gender differences in either strain. SHRsp and male rats exhibited higher AGEs and oxidative stress than SD and female rats, respectively. These differences might partly account for the development of hypertension in SHRsp and the higher vulnerability of male animals to renal pathology.

Increased HO-1 Expression and Decreased iNOS Expression in the Hippocampus From Adult Spontaneously Hypertensive Rats

Brain expression of heme oxygenase (HO) and nitric oxide synthase (NOS) in hypertension may participate in the pathogenesis of hypertension-related neuronal disorders, such as vascular dementia. In the present study, expression levels of HO and NOS in spontaneously hypertensive rats (SHR) were investigated using Western immunoblotting assay. Expression level of inducible HO-1 in hippocampus of 4-wk prehypertensive SHR was about twofold of that in age-matched Sprague-Dawley (SD) rats (p < 0.01). In 23-wk SHR with fully developed hypertension, hippocampal HO-1 level was significantly greater than that of age-matched SD rats (p < 0.05), but not different from 4-wk SHR. There was no difference in expression levels of hippocampal HO-2 between SHR and SD rats at different ages. Total enzymatic activity of hippocampal HO was significantly greater in 23-wk SHR than in age-matched SD rats or 4-wk SD/SHR (p < 0.01). Although hippocampal expression of nNOS protein was relatively unchanged, iNOS expression in 23-wk SHR was about fourfold lower than that in age-matched SD rats and 4-wk SD/SHR (p < 0.01). Total enzymatic activity of hippocampal NOS was significantly lower in 23-wk SHR than in age-matched SD rats or 4-wk SD/SHR (p < 0.01). Significantly suppressed Morris water maze performance was found in 23-wk SHR in comparison with age-matched SD rats. Because SHR has been used as a model of vascular dementia and hippocampus is essential for spatial learning and memory, understanding of altered HO/CO and NOS/NO systems in the hippocampus of adult SHR may shed light on the pathogenic development of memory deficits associated with vascular dementia.

A non-conservative, coding single-nucleotide polymorphism in the N-terminal region of lactoferrin is associated with aggressive periodontitis in an African-American, but not a Caucasian population

Lactoferrin is an antimicrobial protein which plays an important role in regulating bacteria that are associated with aggressive periodontitis. Lactoferrin kills directly (via its strongly cationic N-terminal region) and indirectly, through sequestering the iron that bacteria require for growth. As aggressive periodontitis has a strong heritable component, we hypothesized that genetic variation within the lactoferrin gene may play a role in susceptibility to this condition. We have identified and examined a novel, functional, single-point A/G nucleotide mutation causing a threonine/alanine substitution at position 11 (T11A) of the secreted lactoferrin protein. In a pilot case-controlled study of aggressive periodontitis, analysis of 46 African-American patients and 78 controls showed that patients were twice as likely to express the G nucleotide (alanine) allele over controls (60.3 vs 30.4%; P=0.0007, odds ratio=2.564, 95% CI=1.475-4.459). A Caucasian population of 77 patients and 131 controls showed no such association (P=0.5201, odds ratio=0.862, 95% CI=0.548-1.356). The data presented provide a new insight into the genetic susceptibility to aggressive periodontitis.

Global transcriptome analysis of Shewanella oneidensis MR-1 exposed to different terminal electron acceptors

To gain insight into the complex structure of the energy-generating networks in the dissimilatory metal reducer Shewanella oneidensis MR-1, global mRNA patterns were examined in cells exposed to a wide range of metal and non-metal electron acceptors. Gene expression patterns were similar irrespective of which metal ion was used as electron acceptor, with 60% of the differentially expressed genes showing similar induction or repression relative to fumarate-respiring conditions. Several groups of genes exhibited elevated expression levels in the presence of metals, including those encoding putative multidrug efflux transporters, detoxification proteins, extracytoplasmic sigma factors and PAS-domain regulators. Only one of the 42 predicted c-type cytochromes in MR-1, SO3300, displayed significantly elevated transcript levels across all metal-reducing conditions. Genes encoding decaheme cytochromes MtrC and MtrA that were previously linked to the reduction of different forms of Fe(III) and Mn(IV), exhibited only slight decreases in relative mRNA abundances under metal-reducing conditions. In contrast, specific transcriptome responses were displayed to individual non-metal electron acceptors resulting in the identification of unique groups of nitrate-, thiosulfate- and TMAO-induced genes including previously uncharacterized multi-cytochrome gene clusters. Collectively, the gene expression results reflect the fundamental differences between metal and non-metal respiratory pathways of S. oneidensis MR-1, where the coordinate induction of detoxification and stress response genes play a key role in adaptation of this organism under metal-reducing conditions. Moreover, the relative paucity and/or the constitutive nature of genes involved in electron transfer to metals is likely due to the low-specificity and the opportunistic nature of the metal-reducing electron transport pathways.

Inhaled corticosteroids and mortality in chronic obstructive pulmonary disease

BACKGROUND

Clinical studies suggest that inhaled corticosteroids reduce exacerbations and improve health status in chronic obstructive pulmonary disease (COPD). However, their effect on mortality is unknown.

METHODS

A pooled analysis, based on intention to treat, of individual patient data from seven randomised trials (involving 5085 patients) was performed in which the effects of inhaled corticosteroids and placebo were compared over at least 12 months in patients with stable COPD. The end point was all-cause mortality.

RESULTS

Overall, 4% of the participants died during a mean follow up period of 26 months. Inhaled corticosteroids reduced all-cause mortality by about 25% relative to placebo. Stratification by individual trials and adjustments for age, sex, baseline post-bronchodilator percentage predicted forced expiratory volume in 1 second, smoking status, and body mass index did not materially change the results (adjusted hazard ratio (HR) 0.73; 95% confidence interval (CI) 0.55 to 0.96). Although there was considerable overlap between subgroups in terms of effect sizes, the beneficial effect was especially noticeable in women (adjusted HR 0.46; 95% CI 0.24 to 0.91) and former smokers (adjusted HR 0.60; 95% CI 0.39 to 0.93).

CONCLUSIONS

Inhaled corticosteroids reduce all-cause mortality in COPD. Further studies are required to determine whether the survival benefits persist beyond 2-3 years.

Non-invasive imaging of a transgenic mouse model using a prostate-specific two-step transcriptional amplification strategy

Non-invasive assessment of transgenic animals using bioluminescence imaging offers a rapid means of evaluating disease progression in animal models of disease. One of the challenges in the field is to develop models with robust expression to image repetitively live intact animals through solid tissues. The prostate-specific antigen (PSA) promoter is an attractive model for studying gene regulation due to its hormonal response and tissue-specificity permitting us to measure signaling events that occur within the native tissues. The use of the GAL4-VP16 activator offers a powerful means to augment gene expression levels driven by a weak promoter. We have used a two-step transcriptional amplification (TSTA) system to develop a transgenic mouse model to investigate the tissue-specificity and developmental regulation of firefly luciferase (fl) gene expression in living mice using bioluminescence imaging. We employed an enhanced prostate-specific promoter to drive the yeast transcriptional activator, GAL4-VP16 (effector). The reporter construct carries five Gal4 binding sites upstream of the fl gene. We generated a transgenic mouse model using a single vector carrying the effector and reporter constructs. The transgenic mice show prostate-specific expression as early as three weeks of age. The bioluminescence signal in the prostate is significantly higher than in other organs. We also demonstrate that blocking androgen availability can downregulate the fl expression in the prostate. The transgenic mice display normal physical characteristics and developmental behavior, indicating that the high level of GAL4 driven expression is well tolerated. These findings suggest that the GAL4-VP16 transactivator can be used to amplify reporter gene expression from a relatively weak promoter in a transgenic mouse model. The transgenic TSTA model in conjunction with other transgenic cancer models should also help to detect and track malignancies. The strategies developed will be useful for transgenic research in general by allowing for amplified tissue specific gene expression.

Prevalence and risk factors of chlamydia and gonorrhea among rural Nepali women

OBJECTIVES

The epidemiology of sexually transmitted infections (STI) in rural, developing world populations is poorly understood. We estimated the prevalence and risk factors of Neisseria gonorrhoeae and Chlamydia trachomatis in a female population in rural Nepal.

METHODS

We conducted a cross sectional study in a sample of 1177 postpartum women participating in a micronutrient supplementation trial in Nepal. Urine samples were collected to test for the two infections using the ligase chain reaction (LCR).

RESULTS

C trachomatis was detected in 1.0% (95% confidence intervals (CI): 0.4 to 1.5) and N gonorrhoeae in 2.3% (95% CI: 1.2 to 3.4) of women. None of the women tested positive for both. Self report of all three symptoms of lower abdominal pain, pain and burning on urination, and vaginal discharge was associated with the presence of gonorrhoea (odds ratio (OR): 12.1, 95% CI: 1.3 to 115.0). Neonatal eye discharge was associated with maternal gonococcal infection (OR = 5.2, 95% CI: 1.1 to 24.9). Incidence of low birth weight was not related to these maternal infections, but very preterm delivery (<32 weeks) was higher among women positive for gonorrhoea (OR = 4.7, 95% CI: 1.0 to 22.0). In a multivariable analysis, low body mass index (<18.5) and cattle ownership were associated with gonorrhoea (p <0.05), whereas woman's literacy was associated with chlamydia (p = 0.06).

CONCLUSION

We found the rates of N gonorrhoeae and C trachomatis to be low among women in this rural population of Nepal.

Structure Determination and Relative Properties of Novel Cubic Borates MM‘4(BO3)3 (M = Li, M‘ = Sr; M = Na, M‘ = Sr, Ba)

A series of novel borates, MM'4(BO3)3 (M = Li, M' = Sr; M = Na, M' = Sr, Ba), have been successfully synthesized by standard solid-state reaction. The crystal structures have been determined from powder X-ray diffraction data. They crystallize in the cubic space group Iad with large lattice parameters: a = 14.95066(5) A for LiSr4(BO3)3, a = 15.14629(6) A for NaSr4(BO3)3, and a = 15.80719(8) A for NaBa4(BO3)3. The structure was built up from 64 small cubic grids, in which the M' atoms took up the corner angle and the BO3 triangles or MO6 cubic octahedra filled in the interspaces. The isolated [BO3]3- anionic groups are perpendicular to each other, distributed along three 100 directions. The anisotropic polarizations were counteracting, forming an isotropic crystal. Sr and Ba atoms were found to be completely soluble in the solid solution NaSr(4-)xBax(BO3)3 (0 < or = x < or = 4). The photoluminescence of samples doped with the ions Eu2+ and Eu3+ was studied, and effective yellow and red emission was detected, respectively. The results are consistent with the crystallographic study. The DTA and TGA curves of them show that they are chemically stable and congruent melting compounds.