Proteomics in pathology, research and practice

Using more reliable and sophisticated protein biochemical techniques, it is possible to perform large scale, partly high-throughput characterization of the human proteome. Two-dimensional electrophoresis (2-DE) and mass spectrometry largely contribute to the identification of proteins and peptides. 2-DE has been used to study differential expression of peptides and proteins in various disease entities, searching for new diagnostic and therapeutic targets. However, 2-DE usually requires large amounts of starting material, is time-consuming, and reveals only a fraction of the proteins present in a given sample. More recently, the ProteinChip technology coupled with bioinformatics has gained considerable attention. This technique uses surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI TOF/MS) to screen any protein source for putative disease biomarkers in a spectrum from 2 to 20 kDa. Between 15,500 (low resolution SELDI TOF) and > 400,000 peptides and proteins (high-resolution SELDI-TOF) can be resolved from a small sample volume (microl-range). Several studies have provided evidence that ProteinChip technology is capable of detecting early stage cancer by its unique cancer-specific proteomic finger prints, with sensitivities and specificities reaching far beyond well established serum-based tumor markers. In this review, we summarize the recent developments of proteomics in research and pathology, and critically discuss putative limitations and future applications of disease-specific biomarkers. Special emphasis is put on the former Human Protein Index project.     

Depressive symptoms, neurocognitive impairment, and adherence to highly active antiretroviral therapy among HIV-infected persons

The association of depressive symptoms, neurocognitive impairment, and adherence to highly active antiretroviral therapy (HAART) was evaluated in 135 HIV-infected persons. Thirty percent reported nonadherence to HAART. Depressive symptoms (assessed with the Montgomery-Asberg Depression Rating Scale) and neurocognitive impairment (assessed with a neuropsychological test battery) were documented in 24% and 12%, respectively, of the study participants. Nonadherence to HAART was independently associated with worse depression rating scale scores (odds ratio=1.05, 95% confidence interval [CI]=1.00-1.10), acquisition of HIV through injection of drugs (odds ratio=2.59, 95% CI=1.05-6.39), and complaints about impairment of sexual activity (odds ratio=6.62, 95% CI=1.16-37.6). The presence of depressive symptoms, but not neurocognitive impairment, was associated with nonadherence.     

The effect of hormone replacement therapy on bone mass in patients with ovarian failure due to bone marrow transplantation

Long permanent remissions in malignant hematopoietic disorders can often be achieved by autologous bone marrow transplantation (ABMT) or by allogenic bone marrow transplantation (BMT). Previous studies have shown that such therapies may induce osteoporosis due to iatrogenic ovarian failure. The administration of hormone replacement therapy (HRT) in these women could prevent the adverse effects of long-term ovarian failure without remarkable side effects. The aim of this study was to evaluate how the bone mass is affected by HRT in patients undergoing ABMT or BMT adjusting the results for age, weight, and height. Subjects and methods: Thirteen women with previous ABMT/BMT were treated with a standard dose (0.625 mg/day) of conjugated equine estrogen (CEE) or with 50 μg/day of 17-β-estradiol in transdermal therapeutic systems (TTS) plus 5 mg/day of medroxyprogesterone acetate sequentially added to the last 12 days of estrogen therapy. Bone mass was measured prior to and 12 months following HRT. Blood samples were collected before therapy and during the 6th and 12th treatment months. Results: The mean time elapsed between bone transplantation and HRT initiation was 13.0 months (range 3–26 months). Before treatment nine patients were osteopenic and after HRT bone mass increased in all cases. Following ABMT/BMT, hepatic hyperenzymemia was detected in three patients. After 6 and 12 months of treatment no significant changes were observed in hepatic enzymes. Conclusion: Although hepatic hyperenzymemia is commonly considered as a contraindication for HRT, our results suggest that HRT is safe for these patients and that such therapy should be initiated after transplantation in women to prevent adverse effects of long-term ovarian failure.     

Polymorphism of the DQA1 promoter region (QAP) and DRB1, QAP, DQA1, DQB1 haplotypes in the Dai minority population in South-Western China

We have investigated the polymorphism of the DQA1 promoter region (QAP) and we have deduced four point (DRB1, QAP, DQA1, DQB1) haplotypes of 60 unrelated healthy Dai minority individuals using the polymerase chain reaction and Dig-ddUTP labeled oligonucleotides. A total of eight QAP alleles (QAP1.1, 1.2, 1.3, 1.4, 3.1, 3.2, 4.1 and 4.2) were detected and two QAP alleles, QAP1.5 and QAP2.1 were absent in this population. The most predominant allele was QAP1.2 with 80% allele frequency. We also found that QAP alleles are in strong linkage disequilibrium with certain alleles of the neighboring loci DQA1 and DQB1. Complete positive association was found for QAP4.1-DQA1^*05, QAP4.2-DQA1^*0601, QAP1.2-DR2 group, QAP3.2-DRB1^*09, QAP4.1-DRB1^*03. A total of 28 different four point (DRB1-QAP-DQA1-DQB1) haplotypes were deduced and the most frequent haplotypes were DRB1^*1602-QAP1.2-DQA1^*0102-DQB1^*0502 (N = 18, H.f. = 15%) and DRB1^*09-QAP3.2-DQA1^*03-DQB1^*03032 (N = 18, H.f. = 15%) followed by the haplotypes DRB1^*1401-QAP1.3-DQA1^*01-DQB1^*0502, DRB1^*1202-QAP4.2-DQA1^*0601-DQB1^*0301 and DRB1^*1502-QAP1.2-DQA1^*0101-DQB1^*0501 with H.f. 9.1%, 6.7% and 5.0% respectively. The other 23 haplotypes were all less than 5% (H.f. 0.8%-5%). The relationship between the QAP alleles and DQA1 in the Dai minority is the same as that in the Chinese and the Caucasoid population.     

Monoclonal antibodies to the enterotoxin of Bacteroides fragilis: production, characterization, and immunodiagnostic application.

A monoclonal antibody, ICT11, specific for the toxin of enterotoxigenic Bacteroides fragilis (ETBF) neutralized the cytotoxic effect of the toxin on human colonic cell line HT-29/C1. In an evaluation using 115 diarrheal stool specimens and culture as the "gold standard," the assay showed a sensitivity of 85% and a specificity of 100%. An ICT11-based sandwich enzyme-linked immunosorbent assay showed a sensitivity of 100% and a specificity of 98% for direct detection of toxin from stool samples compared with those of culture. Thus, ICT11-based assays will be useful for screening for ETBF.     

Comparative study of nasopharyngeal aspirate and nasal swab specimens for diagnosis of acute viral respiratory infection

Paired nasopharyngeal aspirate (NPA) and nasal swab (NS) samples from 475 children hospitalized for acute respiratory infection were studied for the detection of influenza virus, parainfluenza virus, respiratory syncytial virus, and adenovirus by immunofluorescence test, viral culture, and multiplex PCR assay. The overall sensitivity of viral detection with NPA specimens was higher than that obtained with NS specimens.     

In vitro and in vivo toxicity of rinsed and aged nanocellulose-polypyrrole composites

Novel composites of nanocellulose and the conducting polymer polypyrrole (PPy) are herein suggested as potential candidates for active ion-extraction membranes in electrochemically controlled hemodialysis. This study has defined processing parameters to obtain a biocompatible nanocellulose-PPy composite, and for the first time, the effect of the composite aging on cell viability has been studied. The influence of rinsing and extraction process steps, as well as aging under different conditions (i.e. in air, at -20°C and in argon), on the electroactivity and cytotoxicity of a PPy-nanocellulose composite has been investigated. The biocompatibility evaluation was based on indirect toxicity assays with fibroblasts and monocyte cell lines and an acute toxicity test in mice, while the electroactivity was evaluated by cyclic voltammetry experiments. The as-prepared composite did not induce any cytotoxic response in vitro or in vivo. Extensive rinsing and 48 h incubation in biological buffer previous to the preparation of the culture medium extracts were, however, necessary to obtain a noncytotoxic composite. The as-prepared composite was also found to exhibit acceptable electrochemical performance, which was retained upon 4 weeks storage in argon atmosphere. It was shown that aging of the composite had a negative effect on biocompatibility, regardless of the storage condition. Thus, to allow for longtime storage of electroactive nanocellulose-PPy hemodialysis membranes, the degradation of PPy upon storage must be controlled. The present results show that the biocompatibility of PPy composites depends on the rinsing and pretreatment of the composite material as well as the aging of the material.     

Microglial activation in healthy aging

Healthy brain aging is characterized by neuronal loss and decline of cognitive function. Neuronal loss is closely associated with microglial activation and postmortem studies have indeed suggested that activated microglia may be present in the aging brain. Microglial activation can be quantified in vivo using (R)-[(11)C]PK11195 and positron emission tomography. The purpose of this study was to measure specific binding of (R)-[(11)C]PK11195 in healthy subjects over a wide age range. Thirty-five healthy subjects (age range 19-79 years) were included. In all subjects 60-minute dynamic (R)-[(11)C]PK11195 scans were acquired. Specific binding of (R)-[(11)C]PK11195 was calculated using receptor parametric mapping in combination with supervised cluster analysis to extract the reference tissue input function. Increased binding of (R)-[(11)C]PK11195 with aging was found in frontal lobe, anterior and posterior cingulate cortex, medial inferior temporal lobe, insula, hippocampus, entorhinal cortex, thalamus, parietal and occipital lobes, and cerebellum. This indicates that activated microglia appear in several cortical and subcortical areas during healthy aging, suggesting widespread neuronal loss.     

Determinants of cerebellar and cerebral volume in the general elderly population

In a population-based study of 3962 community-dwelling nondemented elderly we investigated the relation of age, sex, cardiovascular risk factors, and the presence of infarcts with cerebellar volume, and its interrelationship with cerebral volumes. Cerebellar and cerebral gray and white matter were segmented using Freesurfer version 4.5 (http://surfer.nmr.mgh.harvard.edu/). We used linear regression analyses to model the relationship between age, sex, cardiovascular risk factors, brain infarcts, white matter lesions (WMLs) and cerebellar and cerebral volume. Smaller cerebellar volumes with increasing age were mainly driven by loss of white matter. Diabetes, higher serum glucose and lower cholesterol levels were related to smaller cerebellar volume. No association was found between hypertension, smoking, apolipoprotein E (ApoE) genotype, and cerebellar volume. Supratentorial lacunar infarcts and WMLs were related to smaller cerebellar volume. Infratentorial infarcts were related to smaller cerebellar white matter volume and total cerebral volume. This study suggests that determinants of cerebellar volume do not entirely overlap with those established for cerebral volume. Furthermore, presence of infarcts or WMLs in the cerebrum can affect cerebellar volume.     

Enabling semantic similarity estimation across multiple ontologies: an evaluation in the biomedical domain

The estimation of the semantic similarity between terms provides a valuable tool to enable the understanding of textual resources. Many semantic similarity computation paradigms have been proposed both as general-purpose solutions or framed in concrete fields such as biomedicine. In particular, ontology-based approaches have been very successful due to their efficiency, scalability, lack of constraints and thanks to the availability of large and consensus ontologies (like WordNet or those in the UMLS). These measures, however, are hampered by the fact that only one ontology is exploited and, hence, their recall depends on the ontological detail and coverage. In recent years, some authors have extended some of the existing methodologies to support multiple ontologies. The problem of integrating heterogeneous knowledge sources is tackled by means of simple terminological matchings between ontological concepts. In this paper, we aim to improve these methods by analysing the similarity between the modelled taxonomical knowledge and the structure of different ontologies. As a result, we are able to better discover the commonalities between different ontologies and hence, improve the accuracy of the similarity estimation. Two methods are proposed to tackle this task. They have been evaluated and compared with related works by means of several widely-used benchmarks of biomedical terms using two standard ontologies (WordNet and MeSH). Results show that our methods correlate better, compared to related works, with the similarity assessments provided by experts in biomedicine.